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I=this.parseIntStr(A[0])+this.iatom0-1,q=this.parseFloatStr(A[1]);Float.isNaN(q)||(x[I].partialCharge=q)}}catch(n){if(y(n,Exception))break;else throw n;}},"~N,~N");c(c$,"addMolAtom",function(a,b,d,e,c,f,j){switch(b){case 0:break;case -1:d="D";break;case -2:d="T";break;default:d=b+d}this.is2D&&0!=j&&(this.is2D=!1);b=new J.adapter.smarter.Atom;b.elementSymbol=d;b.formalCharge=e;this.setAtomCoordXYZ(b,c,f,j);-2147483648==a?this.asc.addAtom(b):(this.haveAtomSerials=!0,b.atomSerial=a,this.asc.addAtomWithMappedSerialNumber(b))},
"~N,~N,~S,~N,~N,~N,~N");c(c$,"fixOrder",function(a,b){switch(a){default:case 0:case -10:return 1;case 1:switch(b){case 1:return 1025;case 3:case 6:return 1041}break;case 2:case 3:break;case 4:return 515;case 5:return 66;case 6:return 513;case 7:return 514;case 8:case 9:return 33}return a},"~N,~N");c(c$,"addMolBond",function(a,b,d,e){d=this.fixOrder(d,e);this.haveAtomSerials?this.asc.addNewBondFromNames(a,b,d):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(a)-1,this.iatom0+this.parseIntStr(b)-
1,d)},"~S,~S,~N,~N")});n("J.adapter.readers.molxyz");w(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.XyzReader",["java.lang.Float","JU.Logger"],function(){c$=B(J.adapter.readers.molxyz,"XyzReader",J.adapter.smarter.AtomSetCollectionReader);h(c$,"checkLine",function(){var a=this.parseIntStr(this.line);if(-2147483648==a)return this.continuing=!1;this.vibrationNumber=++this.modelNumber;if(0>=this.desiredVibrationNumber?this.doGetModel(this.modelNumber,null):this.doGetVibration(this.vibrationNumber)){this.rd();
this.checkCurrentLineForScript();this.asc.newAtomSet();var b=this.line;this.readAtoms(a);this.applySymmetryAndSetTrajectory();this.asc.setAtomSetName(b);if(this.isLastModel(this.modelNumber))return this.continuing=!1}else this.skipAtomSet(a);this.discardLinesUntilNonBlank();return!1});h(c$,"finalizeReader",function(){this.isTrajectory=!1;this.finalizeReaderASCR()});c(c$,"skipAtomSet",function(a){for(this.rd();0<=--a;)this.rd()},"~N");c(c$,"readAtoms",function(a){for(var b=0;b<a;++b){this.rd();var d=
this.getTokens();if(4>d.length)JU.Logger.warn("line cannot be read for XYZ atom data: "+this.line);else{var e=this.addAtomXYZSymName(d,1,null,null);this.setElementAndIsotope(e,d[0]);var c=4;switch(d.length){case 4:continue;case 5:case 6:case 8:case 9:if(0<=d[4].indexOf("."))e.partialCharge=this.parseFloatStr(d[4]);else{var f=this.parseIntStr(d[4]);-2147483648!=f&&(e.formalCharge=f)}switch(d.length){case 5:continue;case 6:e.radius=this.parseFloatStr(d[5]);continue;case 9:e.atomSerial=this.parseIntStr(d[8])}c++;
default:var f=this.parseFloatStr(d[c++]),j=this.parseFloatStr(d[c++]),d=this.parseFloatStr(d[c++]);if(Float.isNaN(f)||Float.isNaN(j)||Float.isNaN(d))continue;this.asc.addVibrationVector(e.index,f,j,d)}}}},"~N")});n("J.adapter.smarter");w(["JU.P3"],"J.adapter.smarter.Atom",["java.lang.Float","JU.AU","$.Lst","$.V3","JU.Vibration"],function(){c$=t(function(){this.index=this.atomSetIndex=0;this.bsSymmetry=null;this.atomSite=0;this.elementSymbol=null;this.elementNumber=-1;this.atomName=null;this.formalCharge=
-2147483648;this.partialCharge=NaN;this.vib=null;this.bfactor=NaN;this.foccupancy=1;this.radius=NaN;this.isHetero=!1;this.atomSerial=-2147483648;this.chainID=0;this.altLoc="\x00";this.group3=null;this.sequenceNumber=-2147483648;this.insertionCode="\x00";this.tensors=this.anisoBorU=null;this.ignoreSymmetry=!1;s(this,arguments)},J.adapter.smarter,"Atom",JU.P3,Cloneable);c(c$,"addTensor",function(a,b,d){if(null==a)return null;if(d||null==this.tensors)this.tensors=new JU.Lst;this.tensors.addLast(a);null!=
b&&a.setType(b);return a},"JU.Tensor,~S,~B");W(c$,function(){this.set(NaN,NaN,NaN)});c(c$,"getClone",function(){var a=this.clone();null!=this.vib&&(a.vib=p(this.vib,JU.Vibration)?this.vib.clone():JU.V3.newV(a.vib));null!=this.anisoBorU&&(a.anisoBorU=JU.AU.arrayCopyF(this.anisoBorU,-1));if(null!=this.tensors){a.tensors=new JU.Lst;for(var b=this.tensors.size();0<=--b;)a.tensors.addLast(this.tensors.get(b).copyTensor())}return a});c(c$,"getElementSymbol",function(){if(null==this.elementSymbol&&null!=
this.atomName){for(var a=this.atomName.length,b=0,d=String.fromCharCode(0);b<a&&!J.adapter.smarter.Atom.isValidFirstSymbolChar(d=this.atomName.charAt(b));)++b;switch(a-b){case 0:break;default:if(a=this.atomName.charAt(b+1),J.adapter.smarter.Atom.isValidElementSymbolNoCaseSecondChar2(d,a)){this.elementSymbol=""+d+a;break}case 1:J.adapter.smarter.Atom.isValidElementSymbol(d)&&(this.elementSymbol=""+d)}}return this.elementSymbol});c$.isValidElementSymbol=c(c$,"isValidElementSymbol",function(a){return"A"<=
a&&"Z">=a&&0>J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");c$.isValidElementSymbol2=c(c$,"isValidElementSymbol2",function(a,b){return"A"<=a&&"Z">=a&&"a"<=b&&"z">=b&&0!=(J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]>>b.charCodeAt(0)-97&1)},"~S,~S");c$.isValidElementSymbolNoCaseSecondChar2=c(c$,"isValidElementSymbolNoCaseSecondChar2",function(a,b){"A"<=b&&"Z">=b&&(b=String.fromCharCode(b.charCodeAt(0)+32));return"A">a||"Z"<a||"a">b||"z"<b?!1:0!=(J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-
65]>>b.charCodeAt(0)-97&1)},"~S,~S");c$.isValidFirstSymbolChar=c(c$,"isValidFirstSymbolChar",function(a){return"A"<=a&&"Z">=a&&0!=J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");c$.isValidElementSymbolNoCaseSecondChar=c(c$,"isValidElementSymbolNoCaseSecondChar",function(a){if(null==a)return!1;var b=a.length;if(0==b)return!1;var d=a.charAt(0);if(1==b)return J.adapter.smarter.Atom.isValidElementSymbol(d);if(2<b)return!1;a=a.charAt(1);return J.adapter.smarter.Atom.isValidElementSymbolNoCaseSecondChar2(d,
a)},"~S");c(c$,"scaleVector",function(a){null==this.vib||Float.isNaN(this.vib.z)||this.vib.scale(a)},"~N");C(c$,"elementCharMasks",[1972292,-2147351151,-2146019271,-2130706430,1441792,-2147348464,25,-2147205008,-2147344384,0,-2147352576,1179905,548936,-2147434213,-2147221504,-2145759221,0,1056947,-2147339946,-2147477097,-2147483648,-2147483648,-2147483648,8388624,-2147483646,139264])});n("J.adapter.smarter");w(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["java.lang.Float","J.api.JmolAdapter"],
function(){c$=t(function(){this.iatom=0;this.atom=null;this.ac=0;this.bsAtoms=this.atoms=null;s(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);u(c$,function(a){this.ac=a.ac;this.atoms=a.atoms;this.bsAtoms=a.bsAtoms;this.iatom=0},"J.adapter.smarter.AtomSetCollection");h(c$,"hasNext",function(){if(this.iatom==this.ac)return!1;for(;null==(this.atom=this.atoms[this.iatom++])||null!=this.bsAtoms&&!this.bsAtoms.get(this.atom.index);)if(this.iatom==this.ac)return!1;
this.atoms[this.iatom-1]=null;return!0});h(c$,"getAtomSetIndex",function(){return this.atom.atomSetIndex});h(c$,"getSymmetry",function(){return this.atom.bsSymmetry});h(c$,"getAtomSite",function(){return this.atom.atomSite+1});h(c$,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});h(c$,"getElementNumber",function(){return 0<this.atom.elementNumber?this.atom.elementNumber:J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});h(c$,"getAtomName",function(){return this.atom.atomName});
h(c$,"getFormalCharge",function(){return this.atom.formalCharge});h(c$,"getPartialCharge",function(){return this.atom.partialCharge});h(c$,"getTensors",function(){return this.atom.tensors});h(c$,"getRadius",function(){return this.atom.radius});h(c$,"getVib",function(){return null==this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});h(c$,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1095761940!=this.atom.vib.z?0:z(this.atom.vib.x)});h(c$,"getBfactor",
function(){return this.atom.bfactor});h(c$,"getOccupancy",function(){return 100*this.atom.foccupancy});h(c$,"getIsHetero",function(){return this.atom.isHetero});h(c$,"getSerial",function(){return this.atom.atomSerial});h(c$,"getChainID",function(){return this.atom.chainID});h(c$,"getAltLoc",function(){return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc)});h(c$,"getGroup3",function(){return this.atom.group3});h(c$,"getSequenceNumber",function(){return this.atom.sequenceNumber});h(c$,
"getInsertionCode",function(){return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode)});h(c$,"getXYZ",function(){return this.atom})});n("J.adapter.smarter");w(["java.util.Hashtable"],"J.adapter.smarter.AtomSetCollection","java.lang.Boolean $.Float java.util.Collections $.Properties JU.AU $.BS $.Lst $.P3 $.V3 J.adapter.smarter.Atom $.Bond $.SmarterJmolAdapter J.api.Interface JU.Logger".split(" "),function(){c$=t(function(){this.atoms=this.ascAuxiliaryInfo=this.collectionName=this.fileTypeName=
this.bsAtoms=this.reader=null;this.ac=0;this.bonds=null;this.bondCount=0;this.structures=null;this.atomSetCount=this.structureCount=0;this.iSet=-1;this.errorMessage=this.atomSetAuxiliaryInfo=this.atomSetBondCounts=this.atomSetAtomCounts=this.atomSetAtomIndexes=this.atomSetNumbers=null;this.isTrajectory=this.coordinatesAreFractional=!1;this.trajectoryStepCount=0;this.trajectoryNames=this.vibrationSteps=this.trajectorySteps=null;this.allowMultiple=this.doFixPeriodic=!1;this.bsStructuredModels=this.readerList=
null;this.haveAnisou=!1;this.baseSymmetryAtomCount=0;this.checkLatticeOnly=!1;this.xtalSymmetry=null;this.bondIndex0=0;this.checkSpecial=!0;this.atomSymbolicMap=null;this.haveUnitCell=!1;this.vibScale=0;s(this,arguments)},J.adapter.smarter,"AtomSetCollection");K(c$,function(){this.ascAuxiliaryInfo=new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=D(16,0);this.atomSetAtomIndexes=D(16,0);this.atomSetAtomCounts=D(16,0);this.atomSetBondCounts=
D(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSymbolicMap=new java.util.Hashtable});c(c$,"setCollectionName",function(a){if(!(null==a||0==(a=a.trim()).length))this.collectionName=a},"~S");c(c$,"clearGlobalBoolean",function(a){this.ascAuxiliaryInfo.remove(J.adapter.smarter.AtomSetCollection.globalBooleans[a])},"~N");c(c$,"setGlobalBoolean",function(a){this.setInfo(J.adapter.smarter.AtomSetCollection.globalBooleans[a],Boolean.TRUE)},"~N");c(c$,"getGlobalBoolean",function(a){return this.getAtomSetCollectionAuxiliaryInfo(J.adapter.smarter.AtomSetCollection.globalBooleans[a])===
Boolean.TRUE},"~N");u(c$,function(a,b,d,e){this.fileTypeName=a;this.reader=b;this.allowMultiple=null==b||0>b.desiredVibrationNumber;a=new java.util.Properties;a.put("PATH_KEY",".PATH");a.put("PATH_SEPARATOR",J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR);this.setInfo("properties",a);if(null!=d){e=0;this.readerList=new JU.Lst;for(a=0;a<d.length;a++)(0<d[a].ac||null!=d[a].reader&&d[a].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(e++,d[a]);1<e&&this.setInfo("isMultiFile",Boolean.TRUE)}else null!=
e&&(this.setInfo("isMultiFile",Boolean.TRUE),this.appendAtomSetCollectionList(e))},"~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.Lst");c(c$,"appendAtomSetCollectionList",function(a){var b=a.size();if(0==b)this.errorMessage="No file found!";else for(var d=0;d<b;d++){var e=a.get(d);p(e,JU.Lst)?this.appendAtomSetCollectionList(e):this.appendAtomSetCollection(d,e)}},"JU.Lst");c(c$,"setTrajectory",function(){this.isTrajectory||(this.trajectorySteps=new JU.Lst);this.isTrajectory=!0;var a=null==this.bsAtoms?
this.ac:this.bsAtoms.cardinality();if(0!=a){for(var b=Array(a),d=0<a&&null!=this.atoms[0].vib&&!Float.isNaN(this.atoms[0].vib.z),a=d?Array(a):null,e=0==this.trajectoryStepCount?null:this.trajectorySteps.get(this.trajectoryStepCount-1),c=0,f=0;c<this.ac;c++)if(null==this.bsAtoms||this.bsAtoms.get(c)){var j=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=e&&(j=J.adapter.smarter.AtomSetCollection.fixPeriodic(j,e[c]));b[f]=j;d&&(a[f]=this.atoms[c].vib);f++}if(d){if(null==this.vibrationSteps){this.vibrationSteps=
new JU.Lst;for(c=0;c<this.trajectoryStepCount;c++)this.vibrationSteps.addLast(null)}this.vibrationSteps.addLast(a)}this.trajectorySteps.addLast(b);this.trajectoryStepCount++}});c(c$,"appendAtomSetCollection",function(a,b){null!=b.reader&&b.reader.mustFinalizeModelSet&&this.readerList.addLast(b.reader);var d=this.ac;this.setInfo("loadState",b.getAtomSetCollectionAuxiliaryInfo("loadState"));if(null!=b.bsAtoms){null==this.bsAtoms&&(this.bsAtoms=new JU.BS);for(var e=b.bsAtoms.nextSetBit(0);0<=e;e=b.bsAtoms.nextSetBit(e+
1))this.bsAtoms.set(d+e)}for(var e=0,c=this.atomSetCount,f=0;f<b.atomSetCount;f++){this.newAtomSet();var j=(this.atomSetAuxiliaryInfo[this.iSet]=b.atomSetAuxiliaryInfo[f]).get("PDB_CONECT_firstAtom_count_max");null!=j&&(j[0]+=d);this.setAtomSetAuxiliaryInfo("title",b.collectionName);this.setAtomSetName(b.getAtomSetName(f));for(j=0;j<b.atomSetAtomCounts[f];j++){try{null!=this.bsAtoms&&this.bsAtoms.set(this.ac),this.newCloneAtom(b.atoms[e])}catch(k){if(y(k,Exception))this.errorMessage="appendAtomCollection error: "+
k;else throw k;}e++}this.atomSetNumbers[this.iSet]=0>a?this.iSet+1:1E6*(a+1)+b.atomSetNumbers[f]}for(e=0;e<b.bondCount;e++)f=b.bonds[e],this.addNewBondWithOrder(f.atomIndex1+d,f.atomIndex2+d,f.order);for(e=J.adapter.smarter.AtomSetCollection.globalBooleans.length;0<=--e;)b.getGlobalBoolean(e)&&this.setGlobalBoolean(e);for(e=0;e<b.structureCount;e++)d=b.structures[e],this.addStructure(d),d.modelStartEnd[0]+=c,d.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(c$,"setNoAutoBond",function(){this.setInfo("noAutoBond",
Boolean.TRUE)});c(c$,"freeze",function(a){1==this.atomSetCount&&null==this.collectionName&&(this.collectionName=this.getAtomSetAuxiliaryInfoValue(0,"name"));a&&this.reverseAtomSets();1<this.trajectoryStepCount&&this.finalizeTrajectory();this.getList(!0);this.getList(!1);for(a=0;a<this.atomSetCount;a++)this.setAtomSetAuxiliaryInfoForSet("initialAtomCount",Integer.$valueOf(this.atomSetAtomCounts[a]),a),this.setAtomSetAuxiliaryInfoForSet("initialBondCount",Integer.$valueOf(this.atomSetBondCounts[a]),
a)},"~B");c(c$,"reverseAtomSets",function(){this.reverseArray(this.atomSetAtomIndexes);this.reverseArray(this.atomSetNumbers);this.reverseArray(this.atomSetAtomCounts);this.reverseArray(this.atomSetBondCounts);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectorySteps);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectoryNames);J.adapter.smarter.AtomSetCollection.reverseList(this.vibrationSteps);this.reverseObject(this.atomSetAuxiliaryInfo);for(var a=0;a<this.ac;a++)this.atoms[a].atomSetIndex=
this.atomSetCount-1-this.atoms[a].atomSetIndex;for(a=0;a<this.structureCount;a++){var b=this.structures[a].modelStartEnd[0];0<=b&&(this.structures[a].modelStartEnd[0]=this.atomSetCount-1-this.structures[a].modelStartEnd[1],this.structures[a].modelStartEnd[1]=this.atomSetCount-1-b)}for(a=0;a<this.bondCount;a++)this.bonds[a].atomSetIndex=this.atomSetCount-1-this.atoms[this.bonds[a].atomIndex1].atomSetIndex;this.reverseSets(this.bonds,this.bondCount);for(var d=JU.AU.createArrayOfArrayList(this.atomSetCount),
a=0;a<this.atomSetCount;a++)d[a]=new JU.Lst;for(a=0;a<this.ac;a++)d[this.atoms[a].atomSetIndex].addLast(this.atoms[a]);for(var b=D(this.ac,0),e=this.ac,a=this.atomSetCount;0<=--a;)for(var c=d[a].size();0<=--c;){var f=this.atoms[--e]=d[a].get(c);b[f.index]=e;f.index=e}for(a=0;a<this.bondCount;a++)this.bonds[a].atomIndex1=b[this.bonds[a].atomIndex1],this.bonds[a].atomIndex2=b[this.bonds[a].atomIndex2];for(a=0;a<this.atomSetCount;a++)d=this.getAtomSetAuxiliaryInfoValue(a,"PDB_CONECT_firstAtom_count_max"),
null!=d&&(d[0]=b[d[0]],d[1]=this.atomSetAtomCounts[a])});c(c$,"reverseSets",function(a,b){for(var d=JU.AU.createArrayOfArrayList(this.atomSetCount),e=0;e<this.atomSetCount;e++)d[e]=new JU.Lst;for(e=0;e<b;e++){if(0>a[e].atomSetIndex)return;d[a[e].atomSetIndex].addLast(a[e])}for(e=this.atomSetCount;0<=--e;)for(var c=d[e].size();0<=--c;)a[--b]=d[e].get(c)},"~A,~N");c(c$,"reverseObject",function(a){for(var b=this.atomSetCount,d=q(b/2);0<=--d;)JU.AU.swap(a,d,b-1-d)},"~A");c$.reverseList=c(c$,"reverseList",
function(a){null!=a&&java.util.Collections.reverse(a)},"JU.Lst");c(c$,"reverseArray",function(a){for(var b=this.atomSetCount,d=q(b/2);0<=--d;)JU.AU.swapInt(a,d,b-1-d)},"~A");c(c$,"getList",function(a){var b;for(b=this.ac;0<=--b&&!(null!=this.atoms[b]&&"\x00"!=(a?this.atoms[b].altLoc:this.atoms[b].insertionCode)););if(!(0>b)){var d=Array(this.atomSetCount);for(b=0;b<this.atomSetCount;b++)d[b]="";var e;for(b=0;b<this.ac;b++)if(null!=this.atoms[b]){var c=a?this.atoms[b].altLoc:this.atoms[b].insertionCode;
if("\x00"!=c&&0>d[e=this.atoms[b].atomSetIndex].indexOf(c))d[e]+=c}a=a?"altLocs":"insertionCodes";for(b=0;b<this.atomSetCount;b++)0<d[b].length&&this.setAtomSetAuxiliaryInfoForSet(a,d[b],b)}},"~B");c(c$,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=D(16,0);this.atomSetAuxiliaryInfo=Array(16);this.ascAuxiliaryInfo=new java.util.Hashtable;
this.atomSetCount=0;this.atomSetNumbers=D(16,0);this.atomSymbolicMap=new java.util.Hashtable;this.bonds=null;this.iSet=-1;this.xtalSymmetry=this.readerList=null;this.structures=Array(16);this.structureCount=0;this.vibrationSteps=this.trajectorySteps=null});c(c$,"discardPreviousAtoms",function(){for(var a=this.ac;0<=--a;)this.atoms[a]=null;this.ac=0;this.clearSymbolicMap();this.atomSetCount=0;this.iSet=-1;for(a=this.atomSetAuxiliaryInfo.length;0<=--a;)this.atomSetAtomCounts[a]=0,this.atomSetBondCounts[a]=
0,this.atomSetAuxiliaryInfo[a]=null});c(c$,"removeAtomSet",function(a){null==this.bsAtoms&&(this.bsAtoms=new JU.BS,this.bsAtoms.setBits(0,this.ac));var b=this.atomSetAtomIndexes[a],d=b+this.atomSetAtomCounts[a];this.bsAtoms.clearBits(b,d);for(b=d;b<this.ac;b++)this.atoms[b].atomSetIndex--;for(b=a+1;b<this.atomSetCount;b++)this.atomSetAuxiliaryInfo[b-1]=this.atomSetAuxiliaryInfo[b],this.atomSetAtomIndexes[b-1]=this.atomSetAtomIndexes[b],this.atomSetBondCounts[b-1]=this.atomSetBondCounts[b],this.atomSetAtomCounts[b-
1]=this.atomSetAtomCounts[b],this.atomSetNumbers[b-1]=this.atomSetNumbers[b];for(b=d=0;b<this.structureCount;b++){var e=this.structures[b];e.modelStartEnd[0]==a&&e.modelStartEnd[1]==a&&(this.structures[b]=null,d++)}if(0<d){a=Array(this.structureCount-d);for(d=b=0;b<this.structureCount;b++)null!=this.structures[b]&&(a[d++]=this.structures[b]);this.structures=a}for(b=0;b<this.bondCount;b++)this.bonds[b].atomSetIndex=this.atoms[this.bonds[b].atomIndex1].atomSetIndex;this.atomSetAuxiliaryInfo[--this.atomSetCount]=
null},"~N");c(c$,"removeCurrentAtomSet",function(){0>this.iSet||(this.iSet--,this.atomSetCount--)});c(c$,"getHydrogenAtomCount",function(){for(var a=0,b=0;b<this.ac;b++)(1==this.atoms[b].elementNumber||this.atoms[b].elementSymbol.equals("H"))&&a++;return a});c(c$,"newCloneAtom",function(a){a=a.getClone();this.addAtom(a);return a},"J.adapter.smarter.Atom");c(c$,"cloneFirstAtomSet",function(a){if(!this.allowMultiple)return 0;this.newAtomSet();0==a&&(a=this.atomSetAtomCounts[0]);for(var b=0;b<a;++b)this.newCloneAtom(this.atoms[b]);
return this.ac},"~N");c(c$,"cloneAtomSetWithBonds",function(a){var b=this.atomSetBondCounts[a?this.iSet:0];a=a?this.cloneLastAtomSet():this.cloneFirstAtomSet(0);if(0<a)for(var d=0;d<b;d++){var e=this.bonds[this.bondCount-b];this.addNewBondWithOrder(e.atomIndex1+a,e.atomIndex2+a,e.order)}},"~B");c(c$,"cloneLastAtomSet",function(){return this.cloneLastAtomSetFromPoints(0,null)});c(c$,"cloneLastAtomSetFromPoints",function(a,b){if(!this.allowMultiple)return 0;var d=0<a?a:this.getLastAtomSetAtomCount(),
e=this.getLastAtomSetAtomIndex();this.newAtomSet();for(var c=0;c<d;++c){var f=this.newCloneAtom(this.atoms[e++]);null!=b&&f.setT(b[c])}return d},"~N,~A");c(c$,"getFirstAtomSetAtomCount",function(){return this.atomSetAtomCounts[0]});c(c$,"getLastAtomSetAtomCount",function(){return this.atomSetAtomCounts[this.iSet]});c(c$,"getLastAtomSetAtomIndex",function(){return this.ac-this.atomSetAtomCounts[this.iSet]});c(c$,"addNewAtom",function(){return this.addAtom(new J.adapter.smarter.Atom)});c(c$,"addAtom",
function(a){this.ac==this.atoms.length&&(this.atoms=2E5<this.ac?JU.AU.ensureLength(this.atoms,this.ac+5E4):JU.AU.doubleLength(this.atoms));0==this.atomSetCount&&this.newAtomSet();a.index=this.ac;this.atoms[this.ac++]=a;a.atomSetIndex=this.iSet;a.atomSite=this.atomSetAtomCounts[this.iSet]++;return a},"J.adapter.smarter.Atom");c(c$,"addAtomWithMappedName",function(a){var b=this.addAtom(a).atomName;null!=b&&this.atomSymbolicMap.put(b,a)},"J.adapter.smarter.Atom");c(c$,"addAtomWithMappedSerialNumber",
function(a){var b=this.addAtom(a).atomSerial;-2147483648!=b&&this.atomSymbolicMap.put(""+b,a)},"J.adapter.smarter.Atom");c(c$,"getAtomFromName",function(a){return this.atomSymbolicMap.get(a)},"~S");c(c$,"getAtomIndex",function(a){a=this.atomSymbolicMap.get(a);return null==a?-1:a.index},"~S");c(c$,"addNewBondWithOrder",function(a,b,d){if(0>a||a>=this.ac||0>b||b>=this.ac)return null;a=new J.adapter.smarter.Bond(a,b,d);this.addBond(a);return a},"~N,~N,~N");c(c$,"addNewBondFromNames",function(a,b,d){return this.addNewBondWithOrderA(this.getAtomFromName(a),
this.getAtomFromName(b),d)},"~S,~S,~N");c(c$,"addNewBondWithOrderA",function(a,b,d){return null==a||null==b?null:this.addNewBondWithOrder(a.index,b.index,d)},"J.adapter.smarter.Atom,J.adapter.smarter.Atom,~N");c(c$,"addBond",function(a){0<this.trajectoryStepCount||(0>a.atomIndex1||0>a.atomIndex2||0>a.order||this.atoms[a.atomIndex1].atomSetIndex!=this.atoms[a.atomIndex2].atomSetIndex?JU.Logger.debugging&&JU.Logger.debug(">>>>>>BAD BOND:"+a.atomIndex1+"-"+a.atomIndex2+" order="+a.order):(this.bondCount==
this.bonds.length&&(this.bonds=JU.AU.arrayCopyObject(this.bonds,this.bondCount+1024)),this.bonds[this.bondCount++]=a,this.atomSetBondCounts[this.iSet]++))},"J.adapter.smarter.Bond");c(c$,"finalizeStructures",function(){if(0!=this.structureCount){this.bsStructuredModels=new JU.BS;for(var a=new java.util.Hashtable,b=0;b<this.structureCount;b++){var d=this.structures[b];-1==d.modelStartEnd[0]&&(d.modelStartEnd[0]=0,d.modelStartEnd[1]=this.atomSetCount-1);this.bsStructuredModels.setBits(d.modelStartEnd[0],
d.modelStartEnd[1]+1);if(0!=d.strandCount){var d=d.structureID+" "+d.modelStartEnd[0],e=a.get(d),e=(null==e?0:e.intValue())+1;a.put(d,Integer.$valueOf(e))}}for(b=0;b<this.structureCount;b++)d=this.structures[b],1==d.strandCount&&(d.strandCount=a.get(d.structureID+" "+d.modelStartEnd[0]).intValue())}});c(c$,"addStructure",function(a){this.structureCount==this.structures.length&&(this.structures=JU.AU.arrayCopyObject(this.structures,this.structureCount+32));this.structures[this.structureCount++]=a},
"J.adapter.smarter.Structure");c(c$,"addVibrationVectorWithSymmetry",function(a,b,d,e,c){if(c){c=this.atoms[a].atomSite;for(var f=this.atoms[a].atomSetIndex;a<this.ac&&this.atoms[a].atomSetIndex==f;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,b,d,e)}else this.addVibrationVector(a,b,d,e)},"~N,~N,~N,~N,~B");c(c$,"addVibrationVector",function(a,b,d,e){this.allowMultiple||(a%=this.ac);return this.atoms[a].vib=JU.V3.new3(b,d,e)},"~N,~N,~N,~N");c(c$,"setAtomSetSpaceGroupName",function(a){this.setAtomSetAuxiliaryInfo("spaceGroup",
a+"")},"~S");c(c$,"setCoordinatesAreFractional",function(a){this.coordinatesAreFractional=a;this.setAtomSetAuxiliaryInfo("coordinatesAreFractional",Boolean.$valueOf(a));a&&this.setGlobalBoolean(0)},"~B");c(c$,"setAnisoBorU",function(a,b,d){this.haveAnisou=!0;a.anisoBorU=b;b[6]=d},"J.adapter.smarter.Atom,~A,~N");c(c$,"setU",function(a,b,d){var e=a.anisoBorU;null==e&&this.setAnisoBorU(a,e=L(8,0),8);e[b]=d},"J.adapter.smarter.Atom,~N,~N");c(c$,"getXSymmetry",function(){null==this.xtalSymmetry&&(this.xtalSymmetry=
J.api.Interface.getOption("adapter.smarter.XtalSymmetry").set(this));return this.xtalSymmetry});c(c$,"getSymmetry",function(){return this.getXSymmetry().getSymmetry()});c(c$,"setSymmetry",function(a){return null==a?null:this.getXSymmetry().setSymmetry(a)},"J.api.SymmetryInterface");c(c$,"setTensors",function(){this.haveAnisou&&this.getXSymmetry().setTensors()});c(c$,"setCheckSpecial",function(a){this.checkSpecial=a},"~B");c(c$,"clearSymbolicMap",function(){this.atomSymbolicMap.clear()});c(c$,"setInfo",
function(a,b){null==b?this.ascAuxiliaryInfo.remove(a):this.ascAuxiliaryInfo.put(a,b)},"~S,~O");c(c$,"setAtomSetCollectionPartialCharges",function(a){if(!this.ascAuxiliaryInfo.containsKey(a))return!1;for(var b=this.ascAuxiliaryInfo.get(a),d=b.size();0<=--d;)this.atoms[d].partialCharge=b.get(d).floatValue();JU.Logger.info("Setting partial charges type "+a);return!0},"~S");c(c$,"mapPartialCharge",function(a,b){this.getAtomFromName(a).partialCharge=b},"~S,~N");c(c$,"getAtomSetCollectionAuxiliaryInfo",
function(a){return this.ascAuxiliaryInfo.get(a)},"~S");c$.fixPeriodic=c(c$,"fixPeriodic",function(a,b){a.x=J.adapter.smarter.AtomSetCollection.fixPoint(a.x,b.x);a.y=J.adapter.smarter.AtomSetCollection.fixPoint(a.y,b.y);a.z=J.adapter.smarter.AtomSetCollection.fixPoint(a.z,b.z);return a},"JU.P3,JU.P3");c$.fixPoint=c(c$,"fixPoint",function(a,b){for(;0.9<a-b;)a-=1;for(;-0.9>a-b;)a+=1;return a},"~N,~N");c(c$,"finalizeTrajectoryAs",function(a,b){this.trajectorySteps=a;this.vibrationSteps=b;this.trajectoryStepCount=
a.size();this.finalizeTrajectory()},"JU.Lst,JU.Lst");c(c$,"finalizeTrajectory",function(){if(0!=this.trajectoryStepCount){var a=this.trajectorySteps.get(0),b=null==this.vibrationSteps?null:this.vibrationSteps.get(0),d=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(null!=this.vibrationSteps&&null!=b&&b.length<d||a.length<d)this.errorMessage="File cannot be loaded as a trajectory";else{for(var d=new JU.V3,e=0,c=0;e<this.ac;e++)if(null==this.bsAtoms||this.bsAtoms.get(e))null!=this.vibrationSteps&&
(this.atoms[e].vib=null==b?d:b[c]),null!=a[c]&&this.atoms[e].setT(a[c]),c++;this.setInfo("trajectorySteps",this.trajectorySteps);null!=this.vibrationSteps&&this.setInfo("vibrationSteps",this.vibrationSteps)}}});c(c$,"newAtomSet",function(){this.newAtomSetClear(!0)});c(c$,"newAtomSetClear",function(a){!this.allowMultiple&&0<=this.iSet&&this.discardPreviousAtoms();this.bondIndex0=this.bondCount;this.isTrajectory&&this.discardPreviousAtoms();this.iSet=this.atomSetCount++;this.atomSetCount>this.atomSetNumbers.length&&
(this.atomSetAtomIndexes=JU.AU.doubleLengthI(this.atomSetAtomIndexes),this.atomSetAtomCounts=JU.AU.doubleLengthI(this.atomSetAtomCounts),this.atomSetBondCounts=JU.AU.doubleLengthI(this.atomSetBondCounts),this.atomSetAuxiliaryInfo=JU.AU.doubleLength(this.atomSetAuxiliaryInfo));this.atomSetAtomIndexes[this.iSet]=this.ac;this.atomSetCount+this.trajectoryStepCount>this.atomSetNumbers.length&&(this.atomSetNumbers=JU.AU.doubleLengthI(this.atomSetNumbers));this.isTrajectory?this.atomSetNumbers[this.iSet+
this.trajectoryStepCount]=this.atomSetCount+this.trajectoryStepCount:this.atomSetNumbers[this.iSet]=this.atomSetCount;a&&this.atomSymbolicMap.clear();this.setAtomSetAuxiliaryInfo("title",this.collectionName)},"~B");c(c$,"getAtomSetAtomIndex",function(a){return this.atomSetAtomIndexes[a]},"~N");c(c$,"getAtomSetAtomCount",function(a){return this.atomSetAtomCounts[a]},"~N");c(c$,"getAtomSetBondCount",function(a){return this.atomSetBondCounts[a]},"~N");c(c$,"setAtomSetName",function(a){this.isTrajectory?
this.setTrajectoryName(a):(this.setAtomSetAuxiliaryInfoForSet("name",a,this.iSet),this.allowMultiple||this.setCollectionName(a))},"~S");c(c$,"setTrajectoryName",function(a){if(0!=this.trajectoryStepCount){null==this.trajectoryNames&&(this.trajectoryNames=new JU.Lst);for(var b=this.trajectoryNames.size();b<this.trajectoryStepCount;b++)this.trajectoryNames.addLast(null);this.trajectoryNames.set(this.trajectoryStepCount-1,a)}},"~S");c(c$,"setAtomSetNames",function(a,b,d){for(var e=this.iSet;0<=--b&&
0<=e;--e)(null==d||!d.get(e))&&this.setAtomSetAuxiliaryInfoForSet("name",a,e)},"~S,~N,JU.BS");c(c$,"setCurrentAtomSetNumber",function(a){this.setAtomSetNumber(this.iSet+(this.isTrajectory?this.trajectoryStepCount:0),a)},"~N");c(c$,"setAtomSetNumber",function(a,b){this.atomSetNumbers[a]=b},"~N,~N");c(c$,"setAtomSetModelProperty",function(a,b){this.setAtomSetModelPropertyForSet(a,b,this.iSet)},"~S,~S");c(c$,"setAtomSetModelPropertyForSet",function(a,b,d){var e=this.getAtomSetAuxiliaryInfoValue(d,"modelProperties");
null==e&&this.setAtomSetAuxiliaryInfoForSet("modelProperties",e=new java.util.Properties,d);e.put(a,b);a.startsWith(".")&&e.put(a.substring(1),b)},"~S,~S,~N");c(c$,"setAtomProperties",function(a,b,d){p(b,String)&&!b.endsWith("\n")&&(b+="\n");0>d&&(d=this.iSet);var e=this.getAtomSetAuxiliaryInfoValue(d,"atomProperties");null==e&&this.setAtomSetAuxiliaryInfoForSet("atomProperties",e=new java.util.Hashtable,d);e.put(a,b)},"~S,~O,~N,~B");c(c$,"setAtomSetPartialCharges",function(a){if(!this.atomSetAuxiliaryInfo[this.iSet].containsKey(a))return!1;
a=this.getAtomSetAuxiliaryInfoValue(this.iSet,a);for(var b=a.size();0<=--b;)this.atoms[b].partialCharge=a.get(b).floatValue();return!0},"~S");c(c$,"getAtomSetAuxiliaryInfoValue",function(a,b){return this.atomSetAuxiliaryInfo[0<=a?a:this.iSet].get(b)},"~N,~S");c(c$,"setAtomSetAuxiliaryInfo",function(a,b){this.setAtomSetAuxiliaryInfoForSet(a,b,this.iSet)},"~S,~O");c(c$,"setAtomSetAuxiliaryInfoForSet",function(a,b,d){0>d||(null==this.atomSetAuxiliaryInfo[d]&&(this.atomSetAuxiliaryInfo[d]=new java.util.Hashtable),
null==b?this.atomSetAuxiliaryInfo[d].remove(a):this.atomSetAuxiliaryInfo[d].put(a,b))},"~S,~O,~N");c(c$,"setAtomSetPropertyForSets",function(a,b,d){for(var e=this.iSet;0<=--d&&0<=e;--e)this.setAtomSetModelPropertyForSet(a,b,e)},"~S,~S,~N");c(c$,"cloneLastAtomSetProperties",function(){this.cloneAtomSetProperties(this.iSet-1)});c(c$,"cloneAtomSetProperties",function(a){a=this.getAtomSetAuxiliaryInfoValue(a,"modelProperties");null!=a&&this.setAtomSetAuxiliaryInfoForSet("modelProperties",a.clone(),this.iSet)},
"~N");c(c$,"getAtomSetNumber",function(a){return this.atomSetNumbers[a>=this.atomSetCount?0:a]},"~N");c(c$,"getAtomSetName",function(a){if(null!=this.trajectoryNames&&a<this.trajectoryNames.size())return this.trajectoryNames.get(a);a>=this.atomSetCount&&(a=this.atomSetCount-1);return this.getAtomSetAuxiliaryInfoValue(a,"name")},"~N");c(c$,"getAtomSetAuxiliaryInfo",function(a){a=a>=this.atomSetCount?this.atomSetCount-1:a;return 0>a?null:this.atomSetAuxiliaryInfo[a]},"~N");c(c$,"setAtomNames",function(a){if(null==
a)return null;for(var b,d=0;d<this.ac;d++)if(null!=(b=a.getProperty(this.atoms[d].atomName)))this.atoms[d].atomName=b;return null},"java.util.Properties");c(c$,"setAtomSetEnergy",function(a,b){0>this.iSet||(JU.Logger.info("Energy for model "+(this.iSet+1)+" = "+a),this.setAtomSetAuxiliaryInfo("EnergyString",a),this.setAtomSetAuxiliaryInfo("Energy",Float.$valueOf(b)),this.setAtomSetModelProperty("Energy",""+b))},"~S,~N");c(c$,"setAtomSetFrequency",function(a,b,d,e){this.setAtomSetModelProperty("FreqValue",
d);d+=" "+(null==e?"cm^-1":e);e=(null==b?"":b+" ")+d;this.setAtomSetName(e);this.setAtomSetModelProperty("Frequency",d);null!=b&&this.setAtomSetModelProperty("FrequencyLabel",b);this.setAtomSetModelProperty(".PATH",(null==a?"":a+J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR+"Frequencies")+"Frequencies");return e},"~S,~S,~S,~S");c(c$,"toCartesian",function(a){for(var b=this.getLastAtomSetAtomIndex();b<this.ac;b++)a.toCartesian(this.atoms[b],!0)},"J.api.SymmetryInterface");c(c$,"getBondList",
function(){for(var a=Array(this.bondCount),b=0;b<this.bondCount;b++)a[b]=[this.atoms[this.bonds[b].atomIndex1].atomName,this.atoms[this.bonds[b].atomIndex2].atomName,""+this.bonds[b].order];return a});c(c$,"centralize",function(){for(var a=new JU.P3,b=0;b<this.atomSetCount;b++){var d=this.atomSetAtomCounts[b],e=this.atomSetAtomIndexes[b];a.set(0,0,0);for(var c=e+d;--c>=e;)a.add(this.atoms[c]);a.scale(1/d);for(c=e+d;--c>=e;)this.atoms[c].sub(a)}});c(c$,"mergeTrajectories",function(a){if(this.isTrajectory&&
a.isTrajectory&&null==this.vibrationSteps){for(var b=0;b<a.trajectoryStepCount;b++)this.trajectorySteps.add(this.trajectoryStepCount++,a.trajectorySteps.get(b));this.setInfo("trajectorySteps",this.trajectorySteps)}},"J.adapter.smarter.AtomSetCollection");C(c$,"globalBooleans","someModelsHaveFractionalCoordinates someModelsHaveSymmetry someModelsHaveUnitcells someModelsHaveCONECT isPDB someModelsHaveDomains someModelsHaveValidations".split(" "),"GLOBAL_FRACTCOORD",0,"GLOBAL_SYMMETRY",1,"GLOBAL_UNITCELLS",
2,"GLOBAL_CONECT",3,"GLOBAL_ISPDB",4,"GLOBAL_DOMAINS",5,"GLOBAL_VALIDATIONS",6)});n("J.adapter.smarter");w(["javajs.api.GenericLineReader","JU.SB"],"J.adapter.smarter.AtomSetCollectionReader","java.io.BufferedReader java.lang.Boolean $.Character $.Float javajs.api.GenericBinaryDocument JU.BS $.Lst $.M3 $.P3 $.PT $.Quat $.V3 J.adapter.smarter.Atom $.AtomSetCollection J.api.Interface $.JmolAdapter JU.BSUtil $.Logger $.Parser".split(" "),function(){c$=t(function(){this.isBinary=!1;this.next=this.prevline=
this.line=this.validation=this.domains=this.trajectorySteps=this.htParams=this.readerName=this.binaryDoc=this.reader=this.asc=null;this.ptLine=0;this.latticeCells=null;this.iHaveSymmetryOperators=this.iHaveUnitCell=this.doProcessLines=!1;this.continuing=!0;this.vwr=null;this.isSequential=this.getHeader=this.doCheckUnitCell=this.applySymmetryToBonds=this.isTrajectory=this.ignoreFileSymmetryOperators=this.doApplySymmetry=!1;this.vibrationNumber=this.modelNumber=this.templateAtomCount=0;this.desiredVibrationNumber=
-2147483648;this.bsModels=null;this.havePartialChargeFilter=!1;this.calculationType="?";this.sgName=null;this.ignoreFileSpaceGroupName=this.ignoreFileUnitCell=!1;this.notionalUnitCell=null;this.desiredModelNumber=-2147483648;this.out=this.symmetry=null;this.doPackUnitCell=this.iHaveFractionalCoordinates=!1;this.ptSupercell=this.strSupercell=null;this.forcePacked=this.mustFinalizeModelSet=!1;this.packingError=0.02;this.loadNote=null;this.merging=this.fileCoordinatesAreFractional=this.doConvertToFractional=
!1;this.symmetryRange=0;this.firstLastStep=null;this.lastModelNumber=2147483647;this.desiredSpaceGroupIndex=-1;this.unitCellOffset=this.fileOffsetFractional=this.fileOffset=this.fileScaling=null;this.unitCellOffsetFractional=!1;this.fileName=this.filePath=this.moreUnitCellInfo=null;this.stateScriptVersionInt=2147483647;this.baseAtomIndex=0;this.haveModel=!1;this.previousUnitCell=this.previousSpaceGroup=null;this.nMatrixElements=0;this.filter=this.bsFilter=this.matUnitCellOrientation=null;this.filterAtomType=
this.filterAtomName=this.filterChain=this.filterGroup3=this.filterAltLoc=this.haveAtomFilter=!1;this.filterAtomTypeStr=null;this.filterAtomNameTerminator=";";this.filterEveryNth=this.filterHetero=this.filterElement=!1;this.filterSymop=null;this.nFiltered=this.filterN=0;this.reverseModels=this.doReadMolecularOrbitals=this.allowPDBFilter=this.useAltNames=this.addVibrations=this.doCentralize=this.doSetOrientation=!1;this.nameRequired=null;this.centroidPacked=this.doCentroidUnitCell=!1;this.ms=this.matRot=
this.filter2=this.filter1=this.altCell=null;this.vibsFractional=!1;this.siteScript=this.previousScript=null;s(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);K(c$,function(){this.next=D(1,0);this.loadNote=new JU.SB});c(c$,"setup",function(a,b,d){this.setupASCR(a,b,d)},"~S,java.util.Map,~O");c(c$,"setupASCR",function(a,b,d){null!=a&&(this.htParams=b,this.filePath=a.$replace("\\","/"),a=this.filePath.lastIndexOf("/"),this.fileName=this.filePath.substring(a+
1),p(d,java.io.BufferedReader)?this.reader=d:p(d,javajs.api.GenericBinaryDocument)&&(this.binaryDoc=d))},"~S,java.util.Map,~O");c(c$,"readData",function(){this.initialize();this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);try{this.initializeReader();if(null==this.binaryDoc)for(null==this.line&&this.continuing&&this.rd();null!=this.line&&this.continuing;)this.checkLine()&&this.rd();else this.binaryDoc.setOutputChannel(this.out),this.processBinaryDocument();this.finalizeReader()}catch(a){JU.Logger.info("Reader error: "+
a),this.vwr.isJS||a.printStackTrace(),this.setError(a)}null!=this.reader&&this.reader.close();null!=this.binaryDoc&&this.binaryDoc.close();return this.finish()});c(c$,"fixBaseIndices",function(){try{var a=this.htParams.get("baseModelIndex").intValue();this.baseAtomIndex+=this.asc.ac;a+=this.asc.atomSetCount;this.htParams.put("baseAtomIndex",Integer.$valueOf(this.baseAtomIndex));this.htParams.put("baseModelIndex",Integer.$valueOf(a))}catch(b){if(!y(b,Exception))throw b;}});c(c$,"readDataObject",function(a){this.initialize();
this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);this.initializeReader();this.processDOM(a);return this.finish()},"~O");c(c$,"processDOM",function(){},"~O");c(c$,"processBinaryDocument",function(){});c(c$,"initializeReader",function(){});c(c$,"checkLine",function(){return!0});c(c$,"checkLastModel",function(){if(this.isLastModel(this.modelNumber)&&this.doProcessLines)return this.continuing=this.doProcessLines=!1;this.doProcessLines=!1;return!0});c(c$,"isLastModel",function(a){return 0<
this.desiredModelNumber||a>=this.lastModelNumber},"~N");c(c$,"appendLoadNote",function(a){null==a?this.loadNote=new JU.SB:(this.loadNote.append(a).append("\n"),JU.Logger.info(a))},"~S");c(c$,"initializeTrajectoryFile",function(){this.asc.addAtom(new J.adapter.smarter.Atom);this.trajectorySteps=this.htParams.get("trajectorySteps");null==this.trajectorySteps&&this.htParams.put("trajectorySteps",this.trajectorySteps=new JU.Lst)});c(c$,"finalizeReader",function(){this.finalizeReaderASCR()});c(c$,"finalizeReaderASCR",
function(){this.applySymmetryAndSetTrajectory();this.asc.finalizeStructures();this.doCentralize&&this.asc.centralize();var a=this.asc.getAtomSetAuxiliaryInfo(0);if(null!=this.domains&&null!=a){this.asc.setGlobalBoolean(5);var b=this.domains.getMapKeys(2,!0),d=b.indexOf("{ ",2);0<=d&&(b=b.substring(d+2));d=b.indexOf("_metadata");0>d&&(d=b.indexOf("metadata"));0<=d&&(b=b.substring(0,d));b=JU.PT.rep(JU.PT.replaceAllCharacters(b,"{}","").trim(),"\n","\n  ")+"\n\nUse SHOW DOMAINS for details.";this.appendLoadNote("\nDomains loaded:\n   "+
b);for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("domains",this.domains)}if(null!=this.validation&&null!=a)for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("validation",this.validation);this.setLoadNote()});c(c$,"setLoadNote",function(){var a=this.loadNote.toString();0<this.loadNote.length()&&this.asc.setInfo("modelLoadNote",a);return a});c(c$,"setIsPDB",function(){this.asc.setGlobalBoolean(4);null!=this.htParams.get("pdbNoHydrogens")&&
this.asc.setInfo("pdbNoHydrogens",this.htParams.get("pdbNoHydrogens"));this.checkFilterKey("ADDHYDROGENS")&&this.asc.setInfo("pdbAddHydrogens",Boolean.TRUE)});c(c$,"setModelPDB",function(a){this.asc.setAtomSetAuxiliaryInfo("isPDB",a?Boolean.TRUE:null)},"~B");c(c$,"finish",function(){var a=this.htParams.get("loadState");this.asc.setInfo("loadState",null==a?"":a);a=this.htParams.get("smilesString");null!=a&&this.asc.setInfo("smilesString",a);this.htParams.containsKey("templateAtomCount")||this.htParams.put("templateAtomCount",
Integer.$valueOf(this.asc.ac));this.htParams.containsKey("bsFilter")&&this.htParams.put("filteredAtomCount",Integer.$valueOf(JU.BSUtil.cardinalityOf(this.htParams.get("bsFilter"))));this.calculationType.equals("?")||this.asc.setInfo("calculationType",this.calculationType);var b=a=this.asc.fileTypeName;0<=b.indexOf("(")&&(b=b.substring(0,b.indexOf("(")));for(var d=this.asc.atomSetCount;0<=--d;)this.asc.setAtomSetAuxiliaryInfoForSet("fileName",this.filePath,d),this.asc.setAtomSetAuxiliaryInfoForSet("fileType",
b,d);this.asc.freeze(this.reverseModels);if(null!=this.asc.errorMessage)return this.asc.errorMessage+"\nfor file "+this.filePath+"\ntype "+a;if(0==(null==this.asc.bsAtoms?this.asc.ac:this.asc.bsAtoms.cardinality())&&0>b.indexOf("DataOnly")&&null==this.asc.getAtomSetCollectionAuxiliaryInfo("dataOnly"))return"No atoms found\nfor file "+this.filePath+"\ntype "+a;this.fixBaseIndices();return this.asc});c(c$,"setError",function(a){var b;b=a.getMessage?a.getMessage():a.toString();this.asc.errorMessage=
null==this.line?"Error reading file at end of file \n"+b:"Error reading file at line "+this.ptLine+":\n"+this.line+"\n"+b;this.vwr.isJS||a.printStackTrace()},"Throwable");c(c$,"initialize",function(){this.baseAtomIndex=this.htParams.get("baseAtomIndex").intValue();var a=this.htParams.get("supercell");p(a,String)?this.strSupercell=a:this.ptSupercell=a;if(null!=(a=this.htParams.get("packingError")))this.packingError=a.floatValue();this.initializeSymmetry();this.vwr=this.htParams.remove("vwr");this.htParams.containsKey("stateScriptVersionInt")&&
(this.stateScriptVersionInt=this.htParams.get("stateScriptVersionInt").intValue());this.merging=this.htParams.containsKey("merging");this.getHeader=this.htParams.containsKey("getHeader");this.isSequential=this.htParams.containsKey("isSequential");this.readerName=this.htParams.get("readerName");this.htParams.containsKey("outputChannel")&&(this.out=this.htParams.get("outputChannel"));this.htParams.containsKey("vibrationNumber")?this.desiredVibrationNumber=this.htParams.get("vibrationNumber").intValue():
this.htParams.containsKey("modelNumber")&&(this.desiredModelNumber=this.htParams.get("modelNumber").intValue());this.applySymmetryToBonds=this.htParams.containsKey("applySymmetryToBonds");this.bsFilter=this.htParams.get("bsFilter");this.setFilter(null);null!=this.altCell&&!this.checkFilterKey("NOPACK")&&(this.forcePacked=!0);a=this.htParams.containsKey("ptFile")?this.htParams.get("ptFile").intValue():-1;this.isTrajectory=this.htParams.containsKey("isTrajectory");0<a&&this.htParams.containsKey("firstLastSteps")?
(a=this.htParams.get("firstLastSteps").get(a-1),p(a,JU.BS)?this.bsModels=a:this.firstLastStep=a):this.htParams.containsKey("firstLastStep")?this.firstLastStep=this.htParams.get("firstLastStep"):this.htParams.containsKey("bsModels")&&(this.bsModels=this.htParams.get("bsModels"));this.htParams.containsKey("templateAtomCount")&&(this.templateAtomCount=this.htParams.get("templateAtomCount").intValue());if(null!=this.bsModels||null!=this.firstLastStep)this.desiredModelNumber=-2147483648;if(null==this.bsModels&&
null!=this.firstLastStep){0>this.firstLastStep[0]&&(this.firstLastStep[0]=0);if(0==this.firstLastStep[2]||this.firstLastStep[1]<this.firstLastStep[0])this.firstLastStep[1]=-1;1>this.firstLastStep[2]&&(this.firstLastStep[2]=1);this.bsModels=JU.BSUtil.newAndSetBit(this.firstLastStep[0]);if(this.firstLastStep[1]>this.firstLastStep[0])for(a=this.firstLastStep[0];a<=this.firstLastStep[1];a+=this.firstLastStep[2])this.bsModels.set(a)}if(null!=this.bsModels&&(null==this.firstLastStep||-1!=this.firstLastStep[1]))this.lastModelNumber=
this.bsModels.length();this.symmetryRange=this.htParams.containsKey("symmetryRange")?this.htParams.get("symmetryRange").floatValue():0;this.initializeSymmetryOptions();this.htParams.containsKey("spaceGroupIndex")&&(this.desiredSpaceGroupIndex=this.htParams.get("spaceGroupIndex").intValue(),-2==this.desiredSpaceGroupIndex&&(this.sgName=this.htParams.get("spaceGroupName")),this.ignoreFileSpaceGroupName=-2==this.desiredSpaceGroupIndex||0<=this.desiredSpaceGroupIndex,this.ignoreFileSymmetryOperators=
-1!=this.desiredSpaceGroupIndex);this.htParams.containsKey("unitCellOffset")&&(this.fileScaling=JU.P3.new3(1,1,1),this.fileOffset=this.htParams.get("unitCellOffset"),this.fileOffsetFractional=JU.P3.newP(this.fileOffset),this.unitCellOffsetFractional=this.htParams.containsKey("unitCellOffsetFractional"));this.htParams.containsKey("unitcell")&&(a=this.htParams.get("unitcell"),this.merging&&this.setFractionalCoordinates(!0),9==a.length?(this.addPrimitiveLatticeVector(0,a,0),this.addPrimitiveLatticeVector(1,
a,3),this.addPrimitiveLatticeVector(2,a,6)):this.setUnitCell(a[0],a[1],a[2],a[3],a[4],a[5]),this.ignoreFileUnitCell=this.iHaveUnitCell,this.merging&&!this.iHaveUnitCell&&this.setFractionalCoordinates(!1));this.domains=this.htParams.get("domains");this.validation=this.htParams.get("validation")});c(c$,"initializeSymmetryOptions",function(){this.latticeCells=D(3,0);this.doApplySymmetry=!1;var a=this.htParams.get("lattice");if(null==a||0==a.length()){if(!this.forcePacked)return;a=JU.P3.new3(1,1,1)}this.latticeCells[0]=
z(a.x);this.latticeCells[1]=z(a.y);this.latticeCells[2]=z(a.z);if((this.doCentroidUnitCell=this.htParams.containsKey("centroid"))&&(-1==this.latticeCells[2]||0==this.latticeCells[2]))this.latticeCells[2]=1;a=this.forcePacked||this.htParams.containsKey("packed");this.centroidPacked=this.doCentroidUnitCell&&a;this.doPackUnitCell=!this.doCentroidUnitCell&&(a||0>this.latticeCells[2]);this.doApplySymmetry=0<this.latticeCells[0]&&0<this.latticeCells[1];this.doApplySymmetry||(this.latticeCells=D(3,0))});
c(c$,"doGetModel",function(a,b){if(null!=b&&null!=this.nameRequired&&0<this.nameRequired.length&&0>b.toUpperCase().indexOf(this.nameRequired))return!1;var d=null==this.bsModels?1>this.desiredModelNumber||a==this.desiredModelNumber:a>this.lastModelNumber?!1:0<a&&this.bsModels.get(a-1)||this.haveModel&&null!=this.firstLastStep&&0>this.firstLastStep[1]&&(2>this.firstLastStep[2]||0==(a-1-this.firstLastStep[0])%this.firstLastStep[2]);d&&0==this.desiredModelNumber&&this.asc.discardPreviousAtoms();this.haveModel=
(new Boolean(this.haveModel|d)).valueOf();d&&(this.doProcessLines=!0);return d},"~N,~S");c(c$,"initializeSymmetry",function(){this.previousSpaceGroup=this.sgName;this.previousUnitCell=this.notionalUnitCell;this.iHaveUnitCell=this.ignoreFileUnitCell;if(!this.ignoreFileUnitCell){this.notionalUnitCell=L(25,0);for(var a=25;0<=--a;)this.notionalUnitCell[a]=NaN;null!=this.ptSupercell&&(this.notionalUnitCell[22]=Math.max(1,z(this.ptSupercell.x)),this.notionalUnitCell[23]=Math.max(1,z(this.ptSupercell.y)),
this.notionalUnitCell[24]=Math.max(1,z(this.ptSupercell.z)));this.symmetry=null}this.ignoreFileSpaceGroupName||(this.sgName="unspecified!");this.doCheckUnitCell=!1});c(c$,"newAtomSet",function(a){0<=this.asc.iSet?(this.asc.newAtomSet(),this.asc.setCollectionName("<collection of "+(this.asc.iSet+1)+" models>")):this.asc.setCollectionName(a);this.asc.setAtomSetAuxiliaryInfoForSet("name",a,Math.max(0,this.asc.iSet))},"~S");c(c$,"cloneLastAtomSet",function(a,b){var d=this.asc.getLastAtomSetAtomCount();
this.asc.cloneLastAtomSetFromPoints(a,b);this.asc.haveUnitCell&&(this.doCheckUnitCell=this.iHaveUnitCell=!0,this.sgName=this.previousSpaceGroup,this.notionalUnitCell=this.previousUnitCell);return d},"~N,~A");c(c$,"setSpaceGroupName",function(a){this.ignoreFileSpaceGroupName||(this.sgName=a.trim(),JU.Logger.info("Setting space group name to "+this.sgName))},"~S");c(c$,"setSymmetryOperator",function(a){if(this.ignoreFileSymmetryOperators)return-1;var b=this.asc.getXSymmetry().addSpaceGroupOperation(this,
a);0>b&&JU.Logger.warn("Skippings symmetry operation "+a);this.iHaveSymmetryOperators=!0;return b},"~S");c(c$,"initializeCartesianToFractional",function(){for(var a=0;16>a;a++)if(!Float.isNaN(this.notionalUnitCell[6+a]))return;for(a=0;16>a;a++)this.notionalUnitCell[6+a]=0==a%5?1:0;this.nMatrixElements=0});c(c$,"clearUnitCell",function(){if(!this.ignoreFileUnitCell){for(var a=6;22>a;a++)this.notionalUnitCell[a]=NaN;this.checkUnitCell(6)}});c(c$,"setUnitCellItem",function(a,b){if(!this.ignoreFileUnitCell&&
!(0==a&&1==b||3==a&&0==b))!Float.isNaN(b)&&(6<=a&&Float.isNaN(this.notionalUnitCell[6]))&&this.initializeCartesianToFractional(),this.notionalUnitCell[a]=b,JU.Logger.debugging&&JU.Logger.debug("setunitcellitem "+a+" "+b),6>a||Float.isNaN(b)?this.iHaveUnitCell=this.checkUnitCell(6):12==++this.nMatrixElements&&this.checkUnitCell(22)},"~N,~N");c(c$,"setUnitCell",function(a,b,d,e,c,f){this.ignoreFileUnitCell||(this.clearUnitCell(),this.notionalUnitCell[0]=a,this.notionalUnitCell[1]=b,this.notionalUnitCell[2]=
d,0!=e&&(this.notionalUnitCell[3]=e),0!=c&&(this.notionalUnitCell[4]=c),0!=f&&(this.notionalUnitCell[5]=f),this.iHaveUnitCell=this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");c(c$,"addPrimitiveLatticeVector",function(a,b,d){if(!this.ignoreFileUnitCell){if(0==a)for(var e=0;6>e;e++)this.notionalUnitCell[e]=0;a=6+3*a;this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a]=b[d];if(Float.isNaN(this.notionalUnitCell[0]))for(a=0;6>a;a++)this.notionalUnitCell[a]=-1;this.iHaveUnitCell=
this.checkUnitCell(15)}},"~N,~A,~N");c(c$,"checkUnitCell",function(a){for(var b=0;b<a;b++)if(Float.isNaN(this.notionalUnitCell[b]))return!1;this.doApplySymmetry&&(this.getSymmetry(),this.doConvertToFractional=!this.fileCoordinatesAreFractional);return!0},"~N");c(c$,"getSymmetry",function(){if(!this.iHaveUnitCell)return null;null==this.symmetry&&(this.getNewSymmetry().setUnitCell(this.notionalUnitCell,!1),this.checkUnitCellOffset());return this.symmetry});c(c$,"checkUnitCellOffset",function(){null==
this.fileOffsetFractional||null==this.symmetry||(this.fileOffset.setT(this.fileOffsetFractional),this.unitCellOffsetFractional!=this.fileCoordinatesAreFractional&&(this.unitCellOffsetFractional?this.symmetry.toCartesian(this.fileOffset,!1):this.symmetry.toFractional(this.fileOffset,!1)))});c(c$,"getNewSymmetry",function(){return this.symmetry=J.api.Interface.getSymmetry()});c(c$,"setFractionalCoordinates",function(a){this.iHaveFractionalCoordinates=this.fileCoordinatesAreFractional=a;this.checkUnitCellOffset()},
"~B");c(c$,"setFilterAtomTypeStr",function(a){this.filterAtomTypeStr=a;this.filterAtomNameTerminator="\x00"},"~S");c(c$,"setFilter",function(a){null==a?a=this.htParams.get("filter"):this.bsFilter=null;null!=a&&(a=a.toUpperCase());this.filter=a;this.doSetOrientation=!this.checkFilterKey("NOORIENT");this.doCentralize=!this.checkFilterKey("NOCENTER")&&this.checkFilterKey("CENTER");this.addVibrations=!this.checkFilterKey("NOVIB");this.doReadMolecularOrbitals=!this.checkFilterKey("NOMO");this.useAltNames=
this.checkFilterKey("ALTNAME");this.reverseModels=this.checkFilterKey("REVERSEMODELS");if(null!=this.filter&&(this.checkFilterKey("HETATM")&&(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"HETATM","HETATM-Y")),this.checkFilterKey("ATOM")&&(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"ATOM","HETATM-N")),this.checkFilterKey("CELL=")&&(this.altCell=this.filter.substring(this.filter.indexOf("CELL=")+5).toLowerCase()),this.nameRequired=JU.PT.getQuotedAttribute(this.filter,"NAME"),null!=
this.nameRequired&&(this.nameRequired.startsWith("'")?this.nameRequired=JU.PT.split(this.nameRequired,"'")[1]:this.nameRequired.startsWith('"')&&(this.nameRequired=JU.PT.split(this.nameRequired,'"')[1]),this.filter=JU.PT.rep(this.filter,this.nameRequired,""),this.filter=JU.PT.rep(this.filter,"NAME=","")),this.filterAtomName=this.checkFilterKey("*.")||this.checkFilterKey("!."),this.filterElement=this.checkFilterKey("_"),this.filterGroup3=this.checkFilterKey("["),this.filterChain=this.checkFilterKey(":"),
this.filterAltLoc=this.checkFilterKey("%"),(this.filterEveryNth=this.checkFilterKey("/="))?this.filterN=this.parseIntStr(this.filter.substring(this.filter.indexOf("/=")+2)):this.filterAtomType=this.checkFilterKey("="),-2147483648==this.filterN&&(this.filterEveryNth=!1),this.haveAtomFilter=this.filterAtomName||this.filterAtomType||this.filterElement||this.filterGroup3||this.filterChain||this.filterAltLoc||this.filterHetero||this.filterEveryNth||this.checkFilterKey("/="),null==this.bsFilter&&(this.bsFilter=
new JU.BS,this.htParams.put("bsFilter",this.bsFilter),this.filter=(";"+this.filter+";").$replace(",",";"),a=this.getFilter("SYMOP="),null!=a&&(this.filterSymop=" "+a+" "),JU.Logger.info("filtering with "+this.filter),this.haveAtomFilter&&(this.filter1=this.filter,0<=(a=this.filter.indexOf("|"))))))this.filter1=this.filter.substring(0,a).trim()+";",this.filter2=";"+this.filter.substring(a).trim()},"~S");c(c$,"getFilter",function(a){var b=null==this.filter?-1:this.filter.indexOf(a);return 0>b?null:
this.filter.substring(b+a.length,this.filter.indexOf(";",b))},"~S");c(c$,"checkFilterKey",function(a){return null!=this.filter&&0<=this.filter.indexOf(a)},"~S");c(c$,"filterAtom",function(a,b){if(!this.haveAtomFilter)return!0;var d=this.checkFilter(a,this.filter1);null!=this.filter2&&(d=(new Boolean(d|this.checkFilter(a,this.filter2))).valueOf());d&&this.filterEveryNth&&(d=0==this.nFiltered++%this.filterN);this.bsFilter.setBitTo(0<=b?b:this.asc.ac,d);return d},"J.adapter.smarter.Atom,~N");c(c$,"checkFilter",
function(a,b){return(!this.filterGroup3||null==a.group3||!this.filterReject(b,"[",a.group3.toUpperCase()+"]"))&&(!this.filterAtomName||this.allowAtomName(a.atomName,b))&&(null==this.filterAtomTypeStr||null==a.atomName||0<=a.atomName.toUpperCase().indexOf("\x00"+this.filterAtomTypeStr))&&(!this.filterElement||null==a.elementSymbol||!this.filterReject(b,"_",a.elementSymbol.toUpperCase()+";"))&&(!this.filterChain||0==a.chainID||!this.filterReject(b,":",""+this.vwr.getChainIDStr(a.chainID)))&&(!this.filterAltLoc||
"\x00"==a.altLoc||!this.filterReject(b,"%",""+a.altLoc))&&(!this.filterHetero||!this.allowPDBFilter||!this.filterReject(b,"HETATM",a.isHetero?"-Y":"-N"))},"J.adapter.smarter.Atom,~S");c(c$,"rejectAtomName",function(a){return this.filterAtomName&&!this.allowAtomName(a,this.filter)},"~S");c(c$,"allowAtomName",function(a,b){return null==a||!this.filterReject(b,".",a.toUpperCase()+this.filterAtomNameTerminator)},"~S,~S");c(c$,"filterReject",function(a,b,d){return 0<=a.indexOf(b)&&0<=a.indexOf("!"+b)==
0<=a.indexOf(b+d)},"~S,~S,~S");c(c$,"set2D",function(){this.asc.setInfo("is2D",Boolean.TRUE);this.checkFilterKey("NOMIN")||this.asc.setInfo("doMinimize",Boolean.TRUE)});c(c$,"doGetVibration",function(a){return this.addVibrations&&(0>=this.desiredVibrationNumber||a==this.desiredVibrationNumber)},"~N");c(c$,"setTransform",function(a,b,d,e,c,f,j,k,l){null==this.matRot&&this.doSetOrientation&&(this.matRot=new JU.M3,a=JU.V3.new3(a,b,d),a.normalize(),this.matRot.setColumnV(0,a),a.set(e,c,f),a.normalize(),
this.matRot.setColumnV(1,a),a.set(j,k,l),a.normalize(),this.matRot.setColumnV(2,a),this.asc.setInfo("defaultOrientationMatrix",JU.M3.newM3(this.matRot)),e=JU.Quat.newM(this.matRot),this.asc.setInfo("defaultOrientationQuaternion",e),JU.Logger.info("defaultOrientationMatrix = "+this.matRot))},"~N,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"setAtomCoordXYZ",function(a,b,d,e){a.set(b,d,e);this.setAtomCoord(a)},"J.adapter.smarter.Atom,~N,~N,~N");c(c$,"setAtomCoordScaled",function(a,b,d,e){null==a&&(a=this.asc.addNewAtom());
this.setAtomCoordXYZ(a,this.parseFloatStr(b[d])*e,this.parseFloatStr(b[d+1])*e,this.parseFloatStr(b[d+2])*e);return a},"J.adapter.smarter.Atom,~A,~N,~N");c(c$,"setAtomCoordTokens",function(a,b,d){this.setAtomCoordXYZ(a,this.parseFloatStr(b[d]),this.parseFloatStr(b[d+1]),this.parseFloatStr(b[d+2]))},"J.adapter.smarter.Atom,~A,~N");c(c$,"addAtomXYZSymName",function(a,b,d,e){var c=this.asc.addNewAtom();null!=d&&(c.elementSymbol=d);null!=e&&(c.atomName=e);this.setAtomCoordTokens(c,a,b);return c},"~A,~N,~S,~S");
c(c$,"setAtomCoord",function(a){null!=this.fileScaling&&(a.x=a.x*this.fileScaling.x+this.fileOffset.x,a.y=a.y*this.fileScaling.y+this.fileOffset.y,a.z=a.z*this.fileScaling.z+this.fileOffset.z);this.doConvertToFractional&&(!this.fileCoordinatesAreFractional&&null!=this.getSymmetry())&&(this.symmetry.haveUnitCell()||this.symmetry.setUnitCell(this.notionalUnitCell,!1),this.symmetry.toFractional(a,!1),this.iHaveFractionalCoordinates=!0);this.doCheckUnitCell=!0},"J.adapter.smarter.Atom");c(c$,"addSites",
function(a){this.asc.setAtomSetAuxiliaryInfo("pdbSites",a);var b="",d;for(a=a.entrySet().iterator();a.hasNext()&&((d=a.next())||1);){for(var e=d.getKey(),c=d.getValue(),f,j=e.length;0<=--j;)if(!Character.isLetterOrDigit(f=e.charAt(j))&&"'"!=f)e=e.substring(0,j)+"_"+e.substring(j+1);c=c.get("groups");0!=c.length&&(this.addSiteScript("@site_"+e+" "+c),this.addSiteScript("site_"+e+' = ["'+JU.PT.rep(c,",",'","')+'"]'),b+=',"site_'+e+'"')}0<b.length&&this.addSiteScript("site_list = ["+b.substring(1)+"]")},
"java.util.Map");c(c$,"applySymmetryAndSetTrajectory",function(){this.applySymTrajASCR()});c(c$,"applySymTrajASCR",function(){this.forcePacked&&this.initializeSymmetryOptions();var a=this.iHaveUnitCell&&this.doCheckUnitCell?this.asc.getXSymmetry().applySymmetryFromReader(this,this.getSymmetry()):null;null==a&&this.asc.setTensors();this.isTrajectory&&this.asc.setTrajectory();null!=this.moreUnitCellInfo&&(this.asc.setAtomSetAuxiliaryInfo("moreUnitCellInfo",this.moreUnitCellInfo),this.moreUnitCellInfo=
null);this.initializeSymmetry();return a});c(c$,"doPreSymmetry",function(){});c(c$,"finalizeMOData",function(a){this.asc.setAtomSetAuxiliaryInfo("moData",a);null!=a&&(a=a.get("mos"),null!=a&&JU.Logger.info(a.size()+" molecular orbitals read in model "+this.asc.atomSetCount))},"java.util.Map");c$.getElementSymbol=c(c$,"getElementSymbol",function(a){return J.api.JmolAdapter.getElementSymbol(a)},"~N");c(c$,"fillDataBlockFixed",function(a,b,d,e){if(0==d)this.fillDataBlock(a,e);else{e=a.length;for(var c=
0;c<e;c++){this.discardLinesUntilNonBlank();var f=q((this.line.length-b+1)/d);a[c]=Array(f);for(var j=0,k=b;j<f;j++,k+=d)a[c][j]=this.line.substring(k,Math.min(this.line.length,k+d))}}},"~A,~N,~N,~N");c(c$,"fillDataBlock",function(a,b){for(var d=a.length,e=0;e<d;e++)a[e]=J.adapter.smarter.AtomSetCollectionReader.getTokensStr(this.discardLinesUntilNonBlank()),a[e].length<b&&--e},"~A,~N");c(c$,"fillFloatArray",function(a,b,d){for(var e=[],c=0,f=0;f<d.length;f++){for(;null!=e&&c>=e.length;){null==a&&
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this.dzB,this.clipped),this.drawBackside&&this.line3d.plotLineDelta(this.shadesA[f],d,this.shadesB[f],e,this.xA-j,this.yA-k,this.zA+l,this.dxB,this.dyB,this.dzB,this.clipped);this.g3d.setZMargin(0);3==c&&this.renderSphericalEndcaps()}}},"~N,~N,~B,~B,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"renderBits",function(a,b,d,e,c,f,j,k,l,h,r,x){if(!(f>3*this.g3d.getRenderHeight())){var A=q(f/2)+1,I=Math.round(j),n=Math.round(k),p=Math.round(l),s=Math.round(h),u=Math.round(r),t=Math.round(x),v=this.g3d.clipCode3(I-A,
n-A,p-A),I=this.g3d.clipCode3(I+A,n+A,p+A),n=this.g3d.clipCode3(s-A,u-A,t-A),A=this.g3d.clipCode3(s+A,u+A,t+A);this.clipped=0!=(v|I|n|A);if(0==(v&A&I&n))if(this.dxBf=h-j,this.dyBf=r-k,this.dzBf=x-l,0==f||1==f)this.line3d.plotLineDelta(this.g3d.getColorArgbOrGray(a),d,this.g3d.getColorArgbOrGray(b),e,z(j),z(k),z(l),z(this.dxBf),z(this.dyBf),z(this.dzBf),this.clipped);else{0<f&&(this.diameter=f,this.xAf=j,this.yAf=k,this.zAf=l);this.drawBackside=!d&&!e&&(this.clipped||2==c||0==c);this.xA=z(this.xAf);
this.yA=z(this.yAf);this.zA=z(this.zAf);this.dxB=z(this.dxBf);this.dyB=z(this.dyBf);this.dzB=z(this.dzBf);this.shadesA=this.g3d.getShades(this.colixA=a);this.shadesB=this.g3d.getShades(this.colixB=b);this.endcaps=c;this.calcArgbEndcap(!0,!0);0<f&&this.generateBaseEllipsePrecisely(!1);2==c&&this.renderFlatEndcapPrecisely(!0);this.line3d.setLineBits(this.dxBf,this.dyBf);this.g3d.setZMargin(5);for(a=this.rasterCount;0<=--a;)b=this.fp8ShadeIndexUp[a]>>8,f=b>>1,j=this.xRaster[a],k=this.yRaster[a],l=this.zRaster[a],
this.tEndcapOpen&&0!=this.argbEndcap&&(this.clipped?(this.g3d.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+j,this.yEndcap+k,this.zEndcap-l-1),this.g3d.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-j,this.yEndcap-k,this.zEndcap+l-1)):(this.g3d.plotPixelUnclippedArgb(this.argbEndcap,this.xEndcap+j,this.yEndcap+k,this.zEndcap-l-1),this.g3d.plotPixelUnclippedArgb(this.argbEndcap,this.xEndcap-j,this.yEndcap-k,this.zEndcap+l-1))),this.line3d.plotLineDeltaBits(this.shadesA,d,this.shadesB,e,b,this.xA+
j,this.yA+k,this.zA-l,this.dxB,this.dyB,this.dzB,this.clipped),this.drawBackside&&this.line3d.plotLineDelta(this.shadesA[f],d,this.shadesB[f],e,this.xA-j,this.yA-k,this.zA+l,this.dxB,this.dyB,this.dzB,this.clipped);this.g3d.setZMargin(0);3==c&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;this.zAf+=this.dzBf}}},"~N,~N,~B,~B,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"renderCone",function(a,b,d,e,c,f,j,k,l,h,r,x){if(!(e>3*this.g3d.getRenderHeight()))if(this.dxBf=k-(this.xAf=c),this.dyBf=
l-(this.yAf=f),this.dzBf=h-(this.zAf=j),this.xA=q(Math.floor(this.xAf)),this.yA=q(Math.floor(this.yAf)),this.zA=q(Math.floor(this.zAf)),this.dxB=q(Math.floor(this.dxBf)),this.dyB=q(Math.floor(this.dyBf)),this.dzB=q(Math.floor(this.dzBf)),this.xTip=k,this.yTip=l,this.zTip=h,this.colixA=a,this.shadesA=this.g3d.getShades(a),a=this.shader.getShadeIndex(this.dxB,this.dyB,-this.dzB),this.g3d.plotPixelClippedScreened(this.shadesA[a],b,z(k),z(l),z(h)),this.diameter=e,1>=e)1==e&&this.line3d.plotLineDelta(this.colixA,
b,this.colixA,b,this.xA,this.yA,this.zA,this.dxB,this.dyB,this.dzB,this.clipped);else{this.endcaps=d;this.calcArgbEndcap(!1,!0);this.generateBaseEllipsePrecisely(x);!x&&2==this.endcaps&&this.renderFlatEndcapPrecisely(!1);this.g3d.setZMargin(5);for(d=this.rasterCount;0<=--d;)h=this.txRaster[d],a=this.tyRaster[d],c=this.tzRaster[d],e=this.xAf+h,k=this.yAf+a,l=this.zAf-c,h=this.xAf-h,a=this.yAf-a,c=this.zAf+c,f=this.shadesA[0],this.tEndcapOpen&&0!=this.argbEndcap&&(this.g3d.plotPixelClippedScreened(this.argbEndcap,
b,z(e),z(k),z(l)),this.g3d.plotPixelClippedScreened(this.argbEndcap,b,z(h),z(a),z(c))),j=this.fp8ShadeIndexUp[d]>>8,0!=f&&(this.line3d.plotLineDeltaA(this.shadesA,b,this.shadesA,b,j,z(e),z(k),z(l),q(Math.ceil(this.xTip-e)),q(Math.ceil(this.yTip-k)),q(Math.ceil(this.zTip-l)),!0),r&&(this.line3d.plotLineDeltaA(this.shadesA,b,this.shadesA,b,j,z(e),z(k)+1,z(l),q(Math.ceil(this.xTip-e)),q(Math.ceil(this.yTip-k))+1,q(Math.ceil(this.zTip-l)),!0),this.line3d.plotLineDeltaA(this.shadesA,b,this.shadesA,b,j,
z(e)+1,z(k),z(l),q(Math.ceil(this.xTip-e))+1,q(Math.ceil(this.yTip-k)),q(Math.ceil(this.zTip-l)),!0)),!x&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDelta(f,b,f,b,z(h),z(a),z(c),q(Math.ceil(this.xTip-h)),q(Math.ceil(this.yTip-a)),q(Math.ceil(this.zTip-c)),!0));this.g3d.setZMargin(0)}},"~N,~B,~N,~N,~N,~N,~N,~N,~N,~N,~B,~B");c(c$,"generateBaseEllipse",function(){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;var a=this.dxB*this.dxB+
this.dyB*this.dyB;if(0==a)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var b=Math.sqrt(a),a=Math.sqrt(a+this.dzB*this.dzB);this.cosTheta=this.dzB/a;this.cosPhi=this.dxB/b;this.sinPhi=this.dyB/b}this.calcRotatedPoint(0,0,!1);this.calcRotatedPoint(0.5,1,!1);this.calcRotatedPoint(1,2,!1);this.rasterCount=3;this.interpolate(0,1);this.interpolate(1,2)});c(c$,"generateBaseEllipsePrecisely",function(a){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;
var b=this.dxBf*this.dxBf+this.dyBf*this.dyBf;if(0==b)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var d=Math.sqrt(b),b=Math.sqrt(b+this.dzBf*this.dzBf);this.cosTheta=this.dzBf/b;this.cosPhi=this.dxBf/d;this.sinPhi=this.dyBf/d}a?(this.calcRotatedPoint(0,0,!0),this.calcRotatedPoint(0.5,1,!0),this.rasterCount=2,this.interpolatePrecisely(0,1)):(this.calcRotatedPoint(0,0,!0),this.calcRotatedPoint(0.5,1,!0),this.calcRotatedPoint(1,2,!0),this.rasterCount=3,this.interpolatePrecisely(0,1),this.interpolatePrecisely(1,
2));for(a=0;a<this.rasterCount;a++)this.xRaster[a]=q(Math.floor(this.txRaster[a])),this.yRaster[a]=q(Math.floor(this.tyRaster[a])),this.zRaster[a]=q(Math.floor(this.tzRaster[a]))},"~B");c(c$,"calcRotatedPoint",function(a,b,d){this.tRaster[b]=a;a*=3.141592653589793;var e=Math.sin(a)*this.cosTheta,c=Math.cos(a);a=this.radius*(e*this.cosPhi-c*this.sinPhi);e=this.radius*(e*this.sinPhi+c*this.cosPhi);c=this.radius2-(a*a+e*e);c=0<c?Math.sqrt(c):0;d?(this.txRaster[b]=a,this.tyRaster[b]=e,this.tzRaster[b]=
c):(this.tEvenDiameter?(this.xRaster[b]=q(a-0.5),this.yRaster[b]=q(e-0.5)):(this.xRaster[b]=q(a),this.yRaster[b]=q(e)),this.zRaster[b]=q(c+0.5));this.fp8ShadeIndexUp[b]=this.shader.getShadeFp8(a,e,c)},"~N,~N,~B");c(c$,"interpolate",function(a,b){var d=this.xRaster[b]-this.xRaster[a];0>d&&(d=-d);var e=this.yRaster[b]-this.yRaster[a];0>e&&(e=-e);if(!(1>=d+e)){for(var d=this.tRaster[a],e=this.tRaster[b],c=this.allocRaster(!1),f=4;0<=--f;){var j=(d+e)/2;this.calcRotatedPoint(j,c,!1);if(this.xRaster[c]==
this.xRaster[a]&&this.yRaster[c]==this.yRaster[a])this.fp8ShadeIndexUp[a]=this.fp8ShadeIndexUp[a]+this.fp8ShadeIndexUp[c]>>>1,d=j;else if(this.xRaster[c]==this.xRaster[b]&&this.yRaster[c]==this.yRaster[b])this.fp8ShadeIndexUp[b]=this.fp8ShadeIndexUp[b]+this.fp8ShadeIndexUp[c]>>>1,e=j;else{this.interpolate(a,c);this.interpolate(c,b);return}}this.xRaster[c]=this.xRaster[a];this.yRaster[c]=this.yRaster[b]}},"~N,~N");c(c$,"interpolatePrecisely",function(a,b){var d=q(Math.floor(this.txRaster[b]))-q(Math.floor(this.txRaster[a]));
0>d&&(d=-d);var e=q(Math.floor(this.tyRaster[b]))-q(Math.floor(this.tyRaster[a]));0>e&&(e=-e);if(!(1>=d+e)){for(var d=this.tRaster[a],e=this.tRaster[b],c=this.allocRaster(!0),f=4;0<=--f;){var j=(d+e)/2;this.calcRotatedPoint(j,c,!0);if(q(Math.floor(this.txRaster[c]))==q(Math.floor(this.txRaster[a]))&&q(Math.floor(this.tyRaster[c]))==q(Math.floor(this.tyRaster[a])))this.fp8ShadeIndexUp[a]=this.fp8ShadeIndexUp[a]+this.fp8ShadeIndexUp[c]>>>1,d=j;else if(q(Math.floor(this.txRaster[c]))==q(Math.floor(this.txRaster[b]))&&
q(Math.floor(this.tyRaster[c]))==q(Math.floor(this.tyRaster[b])))this.fp8ShadeIndexUp[b]=this.fp8ShadeIndexUp[b]+this.fp8ShadeIndexUp[c]>>>1,e=j;else{this.interpolatePrecisely(a,c);this.interpolatePrecisely(c,b);return}}this.txRaster[c]=this.txRaster[a];this.tyRaster[c]=this.tyRaster[b]}},"~N,~N");c(c$,"allocRaster",function(a){for(;this.rasterCount>=this.xRaster.length;)this.xRaster=JU.AU.doubleLengthI(this.xRaster),this.yRaster=JU.AU.doubleLengthI(this.yRaster),this.zRaster=JU.AU.doubleLengthI(this.zRaster),
this.tRaster=JU.AU.doubleLengthF(this.tRaster);for(;this.rasterCount>=this.fp8ShadeIndexUp.length;)this.fp8ShadeIndexUp=JU.AU.doubleLengthI(this.fp8ShadeIndexUp);if(a)for(;this.rasterCount>=this.txRaster.length;)this.txRaster=JU.AU.doubleLengthF(this.txRaster),this.tyRaster=JU.AU.doubleLengthF(this.tyRaster),this.tzRaster=JU.AU.doubleLengthF(this.tzRaster);return this.rasterCount++},"~B");c(c$,"findMinMaxY",function(){this.yMin=this.yMax=this.yRaster[0];for(var a=this.rasterCount;0<--a;){var b=this.yRaster[a];
b<this.yMin?this.yMin=b:b>this.yMax?this.yMax=b:(b=-b,b<this.yMin?this.yMin=b:b>this.yMax&&(this.yMax=b))}});c(c$,"findMinMaxX",function(a){this.xMin=2147483647;this.xMax=-2147483648;for(var b=this.rasterCount;0<=--b;){if(this.yRaster[b]==a){var d=this.xRaster[b];d<this.xMin&&(this.xMin=d,this.zXMin=this.zRaster[b]);d>this.xMax&&(this.xMax=d,this.zXMax=this.zRaster[b])}this.yRaster[b]==-a&&(d=-this.xRaster[b],d<this.xMin&&(this.xMin=d,this.zXMin=-this.zRaster[b]),d>this.xMax&&(this.xMax=d,this.zXMax=
-this.zRaster[b]))}},"~N");c(c$,"renderFlatEndcap",function(a){if(0!=this.dzB&&this.g3d.setC(this.colixEndcap)){var b=this.xA,d=this.yA,e=this.zA;if(a&&0>this.dzB){if(4==this.endcaps)return;b+=this.dxB;d+=this.dyB;e+=this.dzB}this.findMinMaxY();for(a=this.yMin;a<=this.yMax;++a){this.findMinMaxX(a);var c=this.xMax-this.xMin+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(c,b+this.xMin,d+a,e-this.zXMin-1,e-this.zXMax-1,null,null)}}},"~B");c(c$,"renderFlatEndcapPrecisely",
function(a){if(0!=this.dzBf&&this.g3d.setC(this.colixEndcap)){var b=this.xAf,d=this.yAf,e=this.zAf;a&&0>this.dzBf&&(b+=this.dxBf,d+=this.dyBf,e+=this.dzBf);a=z(b);d=z(d);e=z(e);this.findMinMaxY();for(b=this.yMin;b<=this.yMax;++b){this.findMinMaxX(b);var c=this.xMax-this.xMin+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(c,a+this.xMin,d+b,e-this.zXMin-1,e-this.zXMax-1,null,null)}}},"~B");c(c$,"renderSphericalEndcaps",function(){0!=this.colixA&&this.g3d.setC(this.colixA)&&
this.g3d.fillSphereXYZ(this.diameter,this.xA,this.yA,this.zA+1);0!=this.colixB&&this.g3d.setC(this.colixB)&&this.g3d.fillSphereXYZ(this.diameter,this.xA+this.dxB,this.yA+this.dyB,this.zA+this.dzB+1)});c(c$,"calcArgbEndcap",function(a,b){this.tEndcapOpen=!1;var d=b?this.dzBf:this.dzB;if(!(3==this.endcaps||0==d)){this.xEndcap=this.xA;this.yEndcap=this.yA;this.zEndcap=this.zA;var e=b?this.dxBf:this.dxB,c=b?this.dyBf:this.dyB;0<=d||!a?(this.endcapShadeIndex=this.shader.getShadeIndex(-e,-c,d),this.colixEndcap=
this.colixA,d=this.shadesA):(this.endcapShadeIndex=this.shader.getShadeIndex(e,c,-d),this.colixEndcap=this.colixB,d=this.shadesB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB);56<this.endcapShadeIndex&&(this.endcapShadeIndex=56);this.argbEndcap=d[this.endcapShadeIndex];this.tEndcapOpen=1==this.endcaps}},"~B,~B")});n("J.g3d");H(J.g3d,"G3DRenderer");n("J.g3d");w(["J.api.JmolRendererInterface","JU.GData","JU.V3","JU.Normix"],"J.g3d.Graphics3D","java.lang.NullPointerException java.util.Arrays javajs.awt.Font JU.AU J.api.Interface J.c.STER J.g3d.CylinderRenderer $.ImageRenderer $.LineRenderer $.Pixelator $.PixelatorShaded $.Platform3D $.SphereRenderer $.TextRenderer $.TextSorter $.TextString JU.C".split(" "),
function(){c$=t(function(){this.hermite3d=this.circle3d=this.triangle3d=this.cylinder3d=this.sphere3d=this.line3d=this.platform=null;this.antialias2=this.isFullSceneAntialiasingEnabled=!1;this.strings=null;this.stringCount=0;this.anaglyphChannelBytes=null;this.$haveTranslucentObjects=this.aap=this.twoPass=!1;this.zbufT=this.zbuf=this.pbufT=this.pbuf=null;this.translucencyMask=0;this.renderLow=!1;this.shadesCurrent=null;this.anaglyphLength=0;this.isScreened=!1;this.argbNoisyDn=this.argbNoisyUp=0;this.pixel=
this.currentFont=null;this.zMargin=0;this.aobuf=null;this.saveDiffuse=this.saveAmbient=this.translucencyLog=this.lastRawColor=this.currentShadeIndex=0;this.$currentlyRendering=!1;this.shadeIndexes2Sided=this.shadeIndexes=this.transformedVectors=this.vectorNormal=this.vectorAC=this.vectorAB=null;s(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);K(c$,function(){this.vectorAB=new JU.V3;this.vectorAC=new JU.V3;this.vectorNormal=new JU.V3;this.transformedVectors=Array(J.g3d.Graphics3D.normixCount);
for(var a=J.g3d.Graphics3D.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3;this.shadeIndexes=O(J.g3d.Graphics3D.normixCount,0);this.shadeIndexes2Sided=O(J.g3d.Graphics3D.normixCount,0)});h(c$,"clear",function(){this.stringCount=0;this.strings=null;J.g3d.TextRenderer.clearFontCache()});h(c$,"destroy",function(){this.releaseBuffers();this.graphicsForMetrics=this.platform=null});h(c$,"getGData",function(){return this});c(c$,"setZMargin",function(a){this.zMargin=a},"~N");u(c$,function(){E(this,
J.g3d.Graphics3D,[])});h(c$,"initialize",function(a){this.apiPlatform=a;this.platform=new J.g3d.Platform3D(a);this.graphicsForMetrics=this.platform.getGraphicsForMetrics();this.line3d=new J.g3d.LineRenderer(this);this.sphere3d=new J.g3d.SphereRenderer(this);this.cylinder3d=new J.g3d.CylinderRenderer(this)},"javajs.api.GenericPlatform");h(c$,"addRenderer",function(a){switch(a){case 1073741880:null==this.circle3d&&(this.circle3d=this.getRenderer("Circle"));break;case 553648147:null==this.hermite3d&&
(this.hermite3d=this.getRenderer("Hermite"));case 1073742182:null==this.triangle3d&&(this.triangle3d=this.getRenderer("Triangle"))}},"~N");c(c$,"getRenderer",function(a){return J.api.Interface.getOption("g3d."+a+"Renderer").set(this)},"~S");h(c$,"currentlyRendering",function(){return this.$currentlyRendering});h(c$,"setWindowParameters",function(a,b,d){this.setWinParams(a,b,d);this.$currentlyRendering&&this.endRendering()},"~N,~N,~B");h(c$,"checkTranslucent",function(a){a&&(this.$haveTranslucentObjects=
!0);return!this.twoPass||this.twoPass&&this.$isPass2==a},"~B");h(c$,"beginRendering",function(a,b,d,e){this.$currentlyRendering&&this.endRendering();this.renderLow=e;if(this.windowWidth!=this.newWindowWidth||this.windowHeight!=this.newWindowHeight||this.newAntialiasing!=this.isFullSceneAntialiasingEnabled)this.windowWidth=this.newWindowWidth,this.windowHeight=this.newWindowHeight,this.isFullSceneAntialiasingEnabled=this.newAntialiasing,this.releaseBuffers();this.setRotationMatrix(a);this.antialiasEnabled=
this.antialiasThisFrame=this.newAntialiasing;this.$currentlyRendering=!0;if(null!=this.strings)for(a=Math.min(this.strings.length,this.stringCount);0<=--a;)this.strings[a]=null;this.stringCount=0;this.twoPass=!0;this.$isPass2=!1;this.colixCurrent=0;this.$haveTranslucentObjects=!1;this.translucentCoverOnly=!b;this.aap=!0;null==this.pbuf&&(this.platform.allocateBuffers(this.windowWidth,this.windowHeight,this.antialiasThisFrame,d),this.pbuf=this.platform.pBuffer,this.zbuf=this.platform.zBuffer,this.aobuf=
null);this.setWidthHeight(this.antialiasThisFrame);this.platform.clearBuffer();null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,null,0,0,0)},"JU.M3,~B,~B,~B");h(c$,"setBackgroundTransparent",function(a){null!=this.platform&&this.platform.setBackgroundTransparent(a)},"~B");c(c$,"releaseBuffers",function(){this.aobuf=this.zbufT=this.pbufT=this.zbuf=this.pbuf=null;this.platform.releaseBuffers();this.line3d.clearLineCache()});h(c$,"setPass2",function(a){if(!this.$haveTranslucentObjects||
!this.$currentlyRendering)return!1;this.$isPass2=!0;this.colixCurrent=0;this.aap=!0;if(null==this.pbufT||this.antialias2!=a)this.platform.allocateTBuffers(a),this.pbufT=this.platform.pBufferT,this.zbufT=this.platform.zBufferT;this.antialias2=a;this.antialiasThisFrame&&!this.antialias2&&this.downsampleFullSceneAntialiasing(!0);this.platform.clearTBuffer();return!0},"~B");h(c$,"endRendering",function(){if(this.$currentlyRendering){if(null!=this.pbuf){if(this.$isPass2&&null!=this.pbufT)for(var a=this.pbufT.length;0<=
--a;)J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,this.pbufT[a],this.bgcolor);if(0!=this.ambientOcclusion){if(null==this.aobuf)this.aobuf=D(this.pbuf.length,0);else for(a=this.pbuf.length;0<=--a;)this.aobuf[a]=0;this.shader.occludePixels(this.pbuf,this.zbuf,this.aobuf,this.width,this.height,this.ambientOcclusion)}this.antialiasThisFrame&&this.downsampleFullSceneAntialiasing(!1)}this.platform.setBackgroundColor(this.bgcolor);this.platform.notifyEndOfRendering();this.$currentlyRendering=!1}});c$.mergeBufferPixel=
c(c$,"mergeBufferPixel",function(a,b,d,e){if(0!=d){var c=a[b];if(c!=d){0==c&&(c=e);e=c&16711935;var c=c&65280,f=d&16711935,j=d&65280;switch(d>>24&15){case 0:e=f;c=j;break;case 1:e=(f<<2)+(f<<1)+f+e>>3&16711935;c=(j<<2)+ +(j<<1)+j+c>>3&65280;break;case 2:e=(f<<1)+f+e>>2&16711935;c=(j<<1)+j+c>>2&65280;break;case 3:e=(f<<2)+f+(e<<1)+e>>3&16711935;c=(j<<2)+j+(c<<1)+c>>3&65280;break;case 4:e=e+f>>1&16711935;c=c+j>>1&65280;break;case 5:e=(f<<1)+f+(e<<2)+e>>3&16711935;c=(j<<1)+j+(c<<2)+c>>3&65280;break;
case 6:e=(e<<1)+e+f>>2&16711935;c=(c<<1)+c+j>>2&65280;break;case 7:e=(e<<2)+(e<<1)+e+f>>3&16711935,c=(c<<2)+(c<<1)+c+j>>3&65280}a[b]=4278190080|e|c}}},"~A,~N,~N,~N");h(c$,"getScreenImage",function(a){var b=this.platform.bufferedImage;a&&this.releaseBuffers();return b},"~B");h(c$,"applyAnaglygh",function(a,b){switch(a){case J.c.STER.REDCYAN:this.applyCyanAnaglyph();break;case J.c.STER.CUSTOM:this.applyCustomAnaglyph(b);break;case J.c.STER.REDBLUE:this.applyBlueAnaglyph();break;case J.c.STER.REDGREEN:this.applyGreenAnaglyph()}},
"J.c.STER,~A");h(c$,"snapshotAnaglyphChannelBytes",function(){if(this.$currentlyRendering)throw new NullPointerException;this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=O(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});c(c$,"applyCustomAnaglyph",function(a){var b=a[0];a=a[1]&16777215;for(var d=this.anaglyphLength;0<=--d;){var e=
this.anaglyphChannelBytes[d]&255,e=(e|(e|e<<8)<<8)&a;this.pbuf[d]=this.pbuf[d]&b|e}},"~A");c(c$,"applyGreenAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;)this.pbuf[a]=this.pbuf[a]&4294901760|(this.anaglyphChannelBytes[a]&255)<<8});c(c$,"applyBlueAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;)this.pbuf[a]=this.pbuf[a]&4294901760|this.anaglyphChannelBytes[a]&255});c(c$,"applyCyanAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;){var b=this.anaglyphChannelBytes[a]&255;
this.pbuf[a]=this.pbuf[a]&4294901760|b<<8|b}});h(c$,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});h(c$,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});c(c$,"setTempZSlab",function(a){this.zSlab=a},"~N");h(c$,"setZShade",function(a,b,d,e){a?(this.setZShade2(b,d,e),this.pixel=new J.g3d.PixelatorShaded(this)):this.pixel=new J.g3d.Pixelator(this)},"~B,~N,~N,~N");c(c$,"downsampleFullSceneAntialiasing",function(a){var b=this.width,d=0,e=0,c=this.bgcolor;
a&&(c+=255==(c&255)?-1:1);for(var f=this.pbuf.length;0<=--f;)0==this.pbuf[f]&&(this.pbuf[f]=c);c&=16777215;for(f=this.windowHeight;0<=--f;e+=b)for(var j=this.windowWidth;0<=--j;++d){var k=(this.pbuf[e]>>2&1061109567)+(this.pbuf[e++ +b]>>2&1061109567)+(this.pbuf[e]>>2&1061109567)+(this.pbuf[e++ +b]>>2&1061109567),k=k+((k&3233857728)>>6);this.pbuf[d]=k&16777215|4278190080}if(a){d=e=0;for(f=this.windowHeight;0<=--f;e+=b)for(j=this.windowWidth;0<=--j;++d,++e)a=Math.min(this.zbuf[e],this.zbuf[e+b]),a=
Math.min(a,this.zbuf[++e]),a=Math.min(a,this.zbuf[e+b]),2147483647!=a&&(a>>=1),this.zbuf[d]=this.pbuf[d]==c?2147483647:a;this.antialiasThisFrame=!1;this.setWidthHeight(!1)}},"~B");c(c$,"hasContent",function(){return this.platform.hasContent()});h(c$,"setColor",function(a){this.argbCurrent=this.argbNoisyUp=this.argbNoisyDn=a},"~N");h(c$,"setC",function(a){var b=JU.C.isColixLastAvailable(a);if(!b&&a==this.colixCurrent&&-1==this.currentShadeIndex)return!0;var d=a&30720;if(16384==d)return!1;this.renderLow&&
(d=0);var e=0!=d;this.isScreened=e&&30720==d;if(!this.checkTranslucent(e&&!this.isScreened))return!1;this.aap=this.$isPass2||!e;this.$isPass2?(this.translucencyMask=d<<13|16777215,this.translucencyLog=d>>11):this.translucencyLog=0;this.colixCurrent=a;b&&this.argbCurrent!=this.lastRawColor&&(0==this.argbCurrent&&(this.argbCurrent=4294967295),this.lastRawColor=this.argbCurrent,this.shader.setLastColix(this.argbCurrent,this.inGreyscaleMode));this.shadesCurrent=this.getShades(a);this.currentShadeIndex=
-1;this.setColor(this.getColorArgbOrGray(a));return!0},"~N");c(c$,"addPixel",function(a,b,d){this.pixel.addPixel(a,b,d)},"~N,~N,~N");c(c$,"clearPixel",function(a,b){this.pixel.clearPixel(a,b)},"~N,~N");h(c$,"drawFilledCircle",function(a,b,d,e,c,f){if(!this.isClippedZ(f)){var j=q((d+1)/2),j=e<j||e+j>=this.width||c<j||c+j>=this.height;if(!j||!this.isClippedXY(d,e,c))0!=a&&this.setC(a)&&(j?this.circle3d.plotCircleCenteredClipped(e,c,f,d):this.circle3d.plotCircleCenteredUnclipped(e,c,f,d)),0!=b&&this.setC(b)&&
(j?this.circle3d.plotFilledCircleCenteredClipped(e,c,f,d):this.circle3d.plotFilledCircleCenteredUnclipped(e,c,f,d))}},"~N,~N,~N,~N,~N,~N");h(c$,"volumeRender4",function(a,b,d,e){if(1==a)this.plotPixelClippedXYZ(b,d,e);else if(!this.isClippedZ(e)){var c=q((a+1)/2),c=b<c||b+c>=this.width||d<c||d+c>=this.height;if(!c||!this.isClippedXY(a,b,d))c?this.circle3d.plotFilledCircleCenteredClipped(b,d,e,a):this.circle3d.plotFilledCircleCenteredUnclipped(b,d,e,a)}},"~N,~N,~N,~N");h(c$,"fillSphereXYZ",function(a,
b,d,e){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,b,d,e);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,!this.aap,a,b,d,e,null,null,null,-1,null,this.aap)},"~N,~N,~N,~N");h(c$,"volumeRender",function(a){a?(this.saveAmbient=this.shader.ambientPercent,this.saveDiffuse=this.shader.diffusePercent,this.setAmbientPercent(100),this.setDiffusePercent(0),this.addRenderer(1073741880)):(this.setAmbientPercent(this.saveAmbient),this.setDiffusePercent(this.saveDiffuse))},
"~B");h(c$,"fillSphereI",function(a,b){this.fillSphereXYZ(a,b.x,b.y,b.z)},"~N,JU.P3i");h(c$,"fillSphere",function(a,b){this.fillSphereXYZ(a,Math.round(b.x),Math.round(b.y),Math.round(b.z))},"~N,JU.P3");h(c$,"fillEllipsoid",function(a,b,d,e,c,f,j,k,l,h,r){switch(f){case 1:this.plotPixelClippedArgb(this.argbCurrent,d,e,c);return;case 0:return}f<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,!this.aap,f,d,e,c,j,k,l,h,r,this.aap)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");
h(c$,"drawRect",function(a,b,d,e,c,f){if(!(0!=e&&this.isClippedZ(e))){e=c-1;f-=1;c=a+e;var j=b+f;0<=b&&b<this.height&&this.drawHLine(a,b,d,e);0<=j&&j<this.height&&this.drawHLine(a,j,d,e);0<=a&&a<this.width&&this.drawVLine(a,b,d,f);0<=c&&c<this.width&&this.drawVLine(c,b,d,f)}},"~N,~N,~N,~N,~N,~N");c(c$,"drawHLine",function(a,b,d,e){0>e&&(a+=e,e=-e);0>a&&(e+=a,a=0);a+e>=this.width&&(e=this.width-1-a);var c=a+this.width*b;if(this.aap)for(a=0;a<=e;a++)d<this.zbuf[c]&&this.addPixel(c,d,this.argbCurrent),
c++;else{b=0!=((a^b)&1);for(a=0;a<=e;a++)(b=!b)&&d<this.zbuf[c]&&this.addPixel(c,d,this.argbCurrent),c++}},"~N,~N,~N,~N");c(c$,"drawVLine",function(a,b,d,e){0>e&&(b+=e,e=-e);0>b&&(e+=b,b=0);b+e>=this.height&&(e=this.height-1-b);var c=a+this.width*b;if(this.aap)for(a=0;a<=e;a++)d<this.zbuf[c]&&this.addPixel(c,d,this.argbCurrent),c+=this.width;else{b=0!=((a^b)&1);for(a=0;a<=e;a++)(b=!b)&&d<this.zbuf[c]&&this.addPixel(c,d,this.argbCurrent),c+=this.width}},"~N,~N,~N,~N");h(c$,"fillRect",function(a,b,
d,e,c,f){if(!this.isClippedZ(e)){if(0>a){c+=a;if(0>=c)return;a=0}if(a+c>this.width&&(c=this.width-a,0>=c))return;if(0>b){f+=b;if(0>=f)return;b=0}for(b+f>this.height&&(f=this.height-b);0<=--f;)this.plotPixelsUnclippedCount(c,a,b++,d)}},"~N,~N,~N,~N,~N,~N");h(c$,"drawString",function(a,b,d,e,c,f,j){this.currentShadeIndex=0;null!=a&&(this.isClippedZ(f)||this.drawStringNoSlab(a,b,d,e,c,j))},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");h(c$,"drawStringNoSlab",function(a,b,d,e,c,f){if(null!=a){null==this.strings&&
(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));var j=new J.g3d.TextString;j.setText(a,null==b?this.currentFont:this.currentFont=b,this.argbCurrent,JU.C.isColixTranslucent(f)?this.getColorArgbOrGray(f)&16777215|(f&30720)<<13:0,d,e,c);this.strings[this.stringCount++]=j}},"~S,javajs.awt.Font,~N,~N,~N,~N");h(c$,"renderAllStrings",function(a){if(null!=this.strings){2<=this.stringCount&&(null==J.g3d.Graphics3D.sort&&(J.g3d.Graphics3D.sort=
new J.g3d.TextSorter),java.util.Arrays.sort(this.strings,J.g3d.Graphics3D.sort));for(var b=0;b<this.stringCount;b++){var d=this.strings[b];this.plotText(d.x,d.y,d.z,d.argb,d.bgargb,d.text,d.font,a)}this.strings=null;this.stringCount=0}},"~O");h(c$,"plotText",function(a,b,d,e,c,f,j,k){J.g3d.TextRenderer.plot(a,b,d,e,c,f,j,this,k,this.antialiasThisFrame)},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.api.JmolRendererInterface");h(c$,"drawImage",function(a,b,d,e,c,f,j,k){null==a||(0==j||0==k||this.isClippedZ(c))||
this.plotImage(b,d,e,a,null,f,j,k)},"~O,~N,~N,~N,~N,~N,~N,~N");h(c$,"plotImage",function(a,b,d,e,c,f,j,k){this.setC(f);this.$isPass2||(this.translucencyMask=-1);0==f&&(this.argbCurrent=0);J.g3d.ImageRenderer.plotImage(a,b,d,e,this,c,this.antialiasThisFrame,this.argbCurrent,j,k)},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");h(c$,"setFontFid",function(a){this.currentFont=javajs.awt.Font.getFont3D(a)},"~N");h(c$,"setFont",function(a){this.currentFont=a},"javajs.awt.Font");h(c$,"getFont3DCurrent",
function(){return this.currentFont});h(c$,"drawPixel",function(a,b,d){this.plotPixelClippedXYZ(a,b,d)},"~N,~N,~N");h(c$,"drawPoints",function(a,b,d){if(1<d)for(var e=0.8*d*d,c=-d;c<d;c++)for(var f=-d;f<d;f++)c*c+f*f>e||(this.plotPoints(a,b,c,f),this.plotPoints(a,b,c,f));else this.plotPoints(a,b,0,0)},"~N,~A,~N");h(c$,"drawDashedLine",function(a,b,d,e){this.line3d.plotDashedLine(this.argbCurrent,!this.aap,a,b,d.x,d.y,d.z,e.x,e.y,e.z,!0)},"~N,~N,JU.P3i,JU.P3i");h(c$,"drawDottedLine",function(a,b){this.line3d.plotDashedLine(this.argbCurrent,
!this.aap,2,1,a.x,a.y,a.z,b.x,b.y,b.z,!0)},"JU.P3i,JU.P3i");h(c$,"drawLineXYZ",function(a,b,d,e,c,f){this.line3d.plotLine(this.argbCurrent,!this.aap,this.argbCurrent,!this.aap,a,b,d,e,c,f,!0)},"~N,~N,~N,~N,~N,~N");h(c$,"drawLine",function(a,b,d,e,c,f,j,k){this.setC(a)||(a=0);var l=!this.aap,h=this.argbCurrent;this.setC(b)||(b=0);0==a&&0==b||this.line3d.plotLine(h,l,this.argbCurrent,!this.aap,d,e,c,f,j,k,!0)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"drawLineAB",function(a,b){this.line3d.plotLine(this.argbCurrent,
!this.aap,this.argbCurrent,!this.aap,a.x,a.y,a.z,b.x,b.y,b.z,!0)},"JU.P3i,JU.P3i");h(c$,"fillCylinderXYZ",function(a,b,d,e,c,f,j,k,l,h){this.setC(a)||(a=0);var r=!this.aap;this.setC(b)||(b=0);0==a&&0==b||this.cylinder3d.render(a,b,r,!this.aap,d,e,c,f,j,k,l,h)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen",function(a,b,d,e,c,f,j,k){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d,e,c,f,j,k)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen3I",function(a,
b,d,e){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d.x,d.y,d.z,e.x,e.y,e.z)},"~N,~N,JU.P3i,JU.P3i,JU.P3,JU.P3,~N");h(c$,"fillCylinder",function(a,b,d,e){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d.x,d.y,d.z,e.x,e.y,e.z)},"~N,~N,JU.P3i,JU.P3i");h(c$,"fillCylinderBits",function(a,b,d,e){this.cylinder3d.renderBits(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d.x,d.y,d.z,e.x,e.y,e.z)},"~N,~N,JU.P3,JU.P3");h(c$,
"fillConeScreen",function(a,b,d,e,c){this.cylinder3d.renderCone(this.colixCurrent,!this.aap,a,b,d.x,d.y,d.z,e.x,e.y,e.z,!1,c)},"~N,~N,JU.P3i,JU.P3i,~B");h(c$,"fillConeSceen3f",function(a,b,d,e){this.cylinder3d.renderCone(this.colixCurrent,!this.aap,a,b,d.x,d.y,d.z,e.x,e.y,e.z,!0,!1)},"~N,~N,JU.P3,JU.P3");h(c$,"drawHermite4",function(a,b,d,e,c){this.hermite3d.renderHermiteRope(!1,a,0,0,0,b,d,e,c)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawHermite7",function(a,b,d,e,c,f,j,k,l,h,r,x,A){if(0==A)this.hermite3d.renderHermiteRibbon(a,
b,d,e,c,f,j,k,l,h,r,x,0);else{this.hermite3d.renderHermiteRibbon(a,b,d,e,c,f,j,k,l,h,r,x,1);var I=this.colixCurrent;this.setC(A);this.hermite3d.renderHermiteRibbon(a,b,d,e,c,f,j,k,l,h,r,x,-1);this.setC(I)}},"~B,~B,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,~N,~N");h(c$,"fillHermite",function(a,b,d,e,c,f,j,k){this.hermite3d.renderHermiteRope(!0,a,b,d,e,c,f,j,k)},"~N,~N,~N,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawTriangle3C",function(a,b,d,e,c,f,j){1==(j&1)&&this.drawLine(b,e,a.x,
a.y,a.z,d.x,d.y,d.z);2==(j&2)&&this.drawLine(e,f,d.x,d.y,d.z,c.x,c.y,c.z);4==(j&4)&&this.drawLine(b,f,a.x,a.y,a.z,c.x,c.y,c.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");h(c$,"drawTriangle3I",function(a,b,d,e){1==(e&1)&&this.line3d.plotLine(this.argbCurrent,!this.aap,this.argbCurrent,!this.aap,a.x,a.y,a.z,b.x,b.y,b.z,!0);2==(e&2)&&this.line3d.plotLine(this.argbCurrent,!this.aap,this.argbCurrent,!this.aap,b.x,b.y,b.z,d.x,d.y,d.z,!0);4==(e&4)&&this.line3d.plotLine(this.argbCurrent,!this.aap,this.argbCurrent,
!this.aap,a.x,a.y,a.z,d.x,d.y,d.z,!0)},"JU.P3i,JU.P3i,JU.P3i,~N");h(c$,"fillTriangleTwoSided",function(a,b,d,e,c,f,j,k,l,h){this.setColorNoisy(this.getShadeIndex(a));this.triangle3d.fillTriangleXYZ(b,d,e,c,f,j,k,l,h,!1)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillTriangle3f",function(a,b,d,e){var c=this.getShadeIndexP3(a,b,d);e?this.setColorNoisy(c):this.setColor(this.shadesCurrent[c]);this.triangle3d.fillTriangleP3f(a,b,d,!1)},"JU.P3,JU.P3,JU.P3,~B");h(c$,"fillTriangle3i",function(a,b,d){this.triangle3d.fillTriangleP3i(a,
b,d,!1)},"JU.P3i,JU.P3i,JU.P3i,JU.P3,JU.P3,JU.P3");h(c$,"fillTriangle",function(a,b,d,e,c,f,j,k,l,h){if(!this.$isPass2&&d==f&&d==l&&b==c&&b==k)this.setTriangleColixAndShadeIndex(b,this.getShadeIndex(d)),b=!1;else{if(!this.setTriangleTranslucency(b,c,k))return;this.triangle3d.setGouraud(this.getShades(b)[this.getShadeIndex(d)],this.getShades(c)[this.getShadeIndex(f)],this.getShades(k)[this.getShadeIndex(l)]);b=!0}this.triangle3d.fillTriangleP3if(a,e,j,h,b)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N,~N");
h(c$,"fillTriangle3CN",function(a,b,d,e,c,f,j,k,l){if(!this.$isPass2&&d==f&&d==l&&b==c&&b==k)this.setTriangleColixAndShadeIndex(b,this.getShadeIndex(d)),b=!1;else{if(!this.setTriangleTranslucency(b,c,k))return;this.triangle3d.setGouraud(this.getShades(b)[this.getShadeIndex(d)],this.getShades(c)[this.getShadeIndex(f)],this.getShades(k)[this.getShadeIndex(l)]);b=!0}this.triangle3d.fillTriangleP3i(a,e,j,b)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");c(c$,"setTriangleColixAndShadeIndex",function(a,b){a==
this.colixCurrent&&this.currentShadeIndex==b||(this.currentShadeIndex=-1,this.setC(a),this.setColorNoisy(b))},"~N,~N");c(c$,"setTriangleTranslucency",function(a,b,d){if(!this.$isPass2)return!0;a&=14336;b&=14336;d&=14336;this.translucencyMask=(JU.GData.roundInt(q((a+b+d)/3))&30720)<<13|16777215;return!0},"~N,~N,~N");h(c$,"drawQuadrilateral",function(a,b,d,e,c){this.setC(a);this.drawLineAB(b,d);this.drawLineAB(d,e);this.drawLineAB(e,c);this.drawLineAB(c,b)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"fillQuadrilateral",
function(a,b,d,e){this.setColorNoisy(this.getShadeIndexP3(a,b,d));this.triangle3d.fillTriangleP3f(a,b,d,!1);this.triangle3d.fillTriangleP3f(a,d,e,!1)},"JU.P3,JU.P3,JU.P3,JU.P3");h(c$,"fillQuadrilateral3i",function(a,b,d,e,c,f,j,k,l,h,r,x){this.fillTriangle3CN(a,b,d,e,c,f,j,k,l);this.fillTriangle3CN(a,b,d,j,k,l,h,r,x)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");h(c$,"drawSurface",function(){},"JU.MeshSurface,~N");c(c$,"plotPixelClippedXYZ",function(a,b,d){this.isClipped3(a,b,d)||(a=b*this.width+
a,d<this.zbuf[a]&&this.addPixel(a,d,this.argbCurrent))},"~N,~N,~N");h(c$,"plotPixelClippedP3i",function(a){this.plotPixelClippedXYZ(a.x,a.y,a.z)},"JU.P3i");c(c$,"plotPixelClippedArgb",function(a,b,d,e){this.isClipped3(b,d,e)||(b=d*this.width+b,e<this.zbuf[b]&&this.addPixel(b,e,a))},"~N,~N,~N,~N");h(c$,"plotImagePixel",function(a,b,d,e,c,f){this.isClipped(b,d)||(b=d*this.width+b,e<this.zbuf[b]&&this.shadeTextPixel(b,e,a,f,c))},"~N,~N,~N,~N,~N,~N");c(c$,"plotPixelClippedScreened",function(a,b,d,e,c){!this.isClipped3(d,
e,c)&&!(b&&0!=((d^e)&1))&&(b=e*this.width+d,c<this.zbuf[b]&&this.addPixel(b,c,a))},"~N,~B,~N,~N,~N");c(c$,"plotPixelUnclipped",function(a,b,d){a=b*this.width+a;d<this.zbuf[a]&&this.addPixel(a,d,this.argbCurrent)},"~N,~N,~N");c(c$,"plotPixelUnclippedArgb",function(a,b,d,e){b=d*this.width+b;e<this.zbuf[b]&&this.addPixel(b,e,a)},"~N,~N,~N,~N");c(c$,"plotPixelsClipped",function(a,b,d,e){if(!(0>d||d>=this.height||b>=this.width))if(0>b&&(a+=b,b=0),a+b>this.width&&(a=this.width-b),!(0>=a)){var c=d*this.width+
b;a=c+a;var f=1;this.aap||(f=2,0!=((b^d)&1)&&++c);for(;c<a;)e<this.zbuf[c]&&this.addPixel(c,e,this.argbCurrent),c+=f}},"~N,~N,~N,~N");c(c$,"plotPixelsClippedRaster",function(a,b,d,e,c,f,j){if(!(0>=a||0>d||d>=this.height||b>=this.width||e<this.slab&&c<this.slab||e>this.depth&&c>this.depth)){var k=(b<<16)+(d<<1)^858993459,l=(e<<10)+512;e=c-e;c=q(a/2);e=JU.GData.roundInt(q(((e<<10)+(0<=e?c:-c))/a));if(0>b){b=-b;l+=e*b;a-=b;if(0>=a)return;b=0}a+b>this.width&&(a=this.width-b);c=0!=((b^d)&1);b=d*this.width+
b;if(null==f)for(;0<=--a;){if(this.aap||!0==(c=!c))j=l>>10,j>=this.slab&&(j<=this.depth&&j<this.zbuf[b])&&(k=(k<<16)+(k<<1)+k&2147483647,f=k>>16&7,this.addPixel(b,j,0==f?this.argbNoisyDn:1==f?this.argbNoisyUp:this.argbCurrent));++b;l+=e}else{k=f.r<<8;d=q((j.r-f.r<<8)/a);var h=f.g,r=q((j.g-h)/a);f=f.b;for(var x=q((j.b-f)/a);0<=--a;){if(this.aap||(c=!c))j=l>>10,j>=this.slab&&(j<=this.depth&&j<this.zbuf[b])&&this.addPixel(b,j,4278190080|k&16711680|h&65280|f>>8&255);++b;l+=e;k+=d;h+=r;f+=x}}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");
c(c$,"plotPixelsUnclippedRaster",function(a,b,d,e,c,f,j){if(!(0>=a)){var k=((b<<16)+(d<<1)^858993459)&2147483647,l=0!=((b^d)&1),h=(e<<10)+512;e=c-e;c=q(a/2);e=JU.GData.roundInt(q(((e<<10)+(0<=e?c:-c))/a));b=d*this.width+b;if(null==f)for(;0<=--a;){if(this.aap||(l=!l))j=h>>10,j<this.zbuf[b]&&(k=(k<<16)+(k<<1)+k&2147483647,f=k>>16&7,this.addPixel(b,j,0==f?this.argbNoisyDn:1==f?this.argbNoisyUp:this.argbCurrent));++b;h+=e}else{k=f.r<<8;d=JU.GData.roundInt(q((j.r-f.r<<8)/a));c=f.g;var r=JU.GData.roundInt(q((j.g-
c)/a));f=f.b;for(var x=JU.GData.roundInt(q((j.b-f)/a));0<=--a;){if(this.aap||(l=!l))j=h>>10,j<this.zbuf[b]&&this.addPixel(b,j,4278190080|k&16711680|c&65280|f>>8&255);++b;h+=e;k+=d;c+=r;f+=x}}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsUnclippedCount",function(a,b,d,e){var c=d*this.width+b;if(this.aap)for(;0<=--a;)e<this.zbuf[c]&&this.addPixel(c,e,this.argbCurrent),++c;else if(a=c+a,!(0!=((b^d)&1)&&++c==a)){do e<this.zbuf[c]&&this.addPixel(c,e,this.argbCurrent),c+=2;while(c<a)}},"~N,~N,~N,~N");
c(c$,"plotPoints",function(a,b,d,e){for(a*=3;0<a;){var c=b[--a],f=b[--a]+e,j=b[--a]+d;if(!this.isClipped3(j,f,c)){var k=f*this.width+j++;c<this.zbuf[k]&&this.addPixel(k,c,this.argbCurrent);this.antialiasThisFrame&&(k=f*this.width+j,!this.isClipped3(j,f,c)&&c<this.zbuf[k]&&this.addPixel(k,c,this.argbCurrent),k=++f*this.width+j,!this.isClipped3(j,f,c)&&c<this.zbuf[k]&&this.addPixel(k,c,this.argbCurrent),k=f*this.width+--j,!this.isClipped3(j,f,c)&&c<this.zbuf[k]&&this.addPixel(k,c,this.argbCurrent))}}},
"~N,~A,~N,~N");c(c$,"setColorNoisy",function(a){this.currentShadeIndex=a;this.argbCurrent=this.shadesCurrent[a];this.argbNoisyUp=this.shadesCurrent[63>a?a+1:63];this.argbNoisyDn=this.shadesCurrent[0<a?a-1:0]},"~N");h(c$,"setNoisySurfaceShade",function(a,b,d){this.vectorAB.set(b.x-a.x,b.y-a.y,b.z-a.z);null==d?a=this.shader.getShadeIndex(-this.vectorAB.x,-this.vectorAB.y,this.vectorAB.z):(this.vectorAC.set(d.x-a.x,d.y-a.y,d.z-a.z),this.vectorAB.cross(this.vectorAB,this.vectorAC),a=0<=this.vectorAB.z?
this.shader.getShadeIndex(-this.vectorAB.x,-this.vectorAB.y,this.vectorAB.z):this.shader.getShadeIndex(this.vectorAB.x,this.vectorAB.y,-this.vectorAB.z));56<a&&(a=56);this.setColorNoisy(a)},"JU.P3i,JU.P3i,JU.P3i");c(c$,"getShadeIndexP3",function(a,b,d){this.vectorAB.sub2(b,a);this.vectorAC.sub2(d,a);this.vectorNormal.cross(this.vectorAB,this.vectorAC);return 0<=this.vectorNormal.z?this.shader.getShadeIndex(-this.vectorNormal.x,-this.vectorNormal.y,this.vectorNormal.z):this.shader.getShadeIndex(this.vectorNormal.x,
this.vectorNormal.y,-this.vectorNormal.z)},"JU.P3,JU.P3,JU.P3");h(c$,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");h(c$,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,a.sY,a.sZ)},"JM.Atom");h(c$,"getExportType",function(){return 0});h(c$,"getExportName",function(){return null});c(c$,"canDoTriangles",function(){return!0});c(c$,"isCartesianExport",function(){return!1});h(c$,"initializeExporter",
function(){return null},"JV.Viewer,~N,JU.GData,java.util.Map");h(c$,"finalizeOutput",function(){return null});h(c$,"drawBond",function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");h(c$,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(c$,"getPrivateKey",function(){return 0});h(c$,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});h(c$,"getTransformedVertexVectors",function(){return this.transformedVectors});h(c$,"isDirectedTowardsCamera",function(a){return 0>a||0<this.transformedVectors[a].z},
"~N");c(c$,"setRotationMatrix",function(a){for(var b=JU.Normix.getVertexVectors(),d=J.g3d.Graphics3D.normixCount;0<=--d;){var e=this.transformedVectors[d];a.rotate2(b[d],e);this.shadeIndexes[d]=this.shader.getShadeB(e.x,-e.y,e.z);this.shadeIndexes2Sided[d]=0<=e.z?this.shadeIndexes[d]:this.shader.getShadeB(-e.x,e.y,-e.z)}},"JU.M3");c(c$,"getShadeIndex",function(a){return-1E4==a||9999==a?J.g3d.Graphics3D.nullShadeIndex:0>a?this.shadeIndexes2Sided[~a]:this.shadeIndexes[a]},"~N");h(c$,"renderCrossHairs",
function(a,b,d,e,c){b=this.isAntialiased();this.setC(0>c?10:100<c?11:23);c=Math.max(Math.min(this.width,Math.round(e.x)),0);d=Math.max(Math.min(this.height,Math.round(e.y)),0);var f=Math.round(e.z)+1,j=b?8:4,k=b?20:10;b=b?2:1;this.drawRect(c-j,d,f,0,k,b);this.drawRect(c,d-j,f,0,b,k);this.drawRect(c-j,d-j,f,0,k,k);j=k;k>>=1;this.setC(a[1]<e.x?21:11);this.drawRect(c-j,d,f,0,k,b);this.setC(a[0]>e.x?21:11);this.drawRect(c+k,d,f,0,k,b);this.setC(a[3]<e.y?21:11);this.drawRect(c,d-j,f,0,b,k);this.setC(a[2]>
e.y?21:11);this.drawRect(c,d+k,f,0,b,k)},"~A,~N,~N,JU.P3,~N");h(c$,"initializeOutput",function(){return!1},"JV.Viewer,~N,JU.GData,java.util.Map");c(c$,"shadeTextPixel",function(a,b,d,e,c){switch(c){case 8:this.addPixel(a,b,d);return}0!=e&&J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,e,this.bgcolor);c+=this.translucencyLog;7<c||(J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,d&16777215|c<<24,this.bgcolor),this.zbuf[a]=b)},"~N,~N,~N,~N,~N");C(c$,"sort",null);c$.normixCount=c$.prototype.normixCount=
JU.Normix.getNormixCount();C(c$,"nullShadeIndex",50)});n("J.g3d");c$=B(J.g3d,"ImageRenderer");c$.plotImage=c(c$,"plotImage",function(a,b,d,e,c,f,j,k,l,h){k=(j=-2147483648==a)?c.bgcolor:k;j&&(a=0,d=2147483646,l=c.width,h=c.height);0>=a+l||(a>=c.width||0>=b+h||b>=c.height)||(e=c.apiPlatform.drawImageToBuffer(null,c.platform.offscreenImage,e,l,h,j?k:0),null!=e&&(null!=f||0>a||a+l>c.width||0>b||b+h>c.height?J.g3d.ImageRenderer.plotImageClipped(a,b,d,c,f,l,h,e,k):J.g3d.ImageRenderer.plotImageUnClipped(a,
b,d,c,l,h,e,k)))},"~N,~N,~N,~O,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B,~N,~N,~N");c$.plotImageClipped=c(c$,"plotImageClipped",function(a,b,d,e,c,f,j,k,l){null==c&&(c=e);for(var h=e=0;e<j;e++)for(var r=0;r<f;r++){var x=k[h++];c.plotImagePixel(x,a+r,b+e,d,8,l)}},"~N,~N,~N,J.g3d.Graphics3D,J.api.JmolRendererInterface,~N,~N,~A,~N");c$.plotImageUnClipped=c(c$,"plotImageUnClipped",function(a,b,d,e,c,f,j){var k=e.zbuf,l=e.width;a=b*l+a;for(var h=b=0,r=0;b<f;){for(;h<c;)d<k[a]&&e.addPixel(a,d,j[r]),
++r,++h,++a;++b;h-=c;a+=l-c}},"~N,~N,~N,J.g3d.Graphics3D,~N,~N,~A,~N");n("J.g3d");w(["java.util.Hashtable"],"J.g3d.LineRenderer",["java.lang.Float","JU.BS","JU.Logger"],function(){c$=t(function(){this.lineBits=this.shader=this.g3d=null;this.slope=0;this.lineTypeX=!1;this.nFound=this.nCached=this.nBits=0;this.slopeKey=this.lineCache=null;this.cc2=this.cc1=this.z2t=this.y2t=this.x2t=this.z1t=this.y1t=this.x1t=0;s(this,arguments)},J.g3d,"LineRenderer");K(c$,function(){this.lineCache=new java.util.Hashtable});
u(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"setLineBits",function(a,b){this.slope=0!=a?b/a:0<=b?3.4028235E38:-3.4028235E38;this.nBits=(this.lineTypeX=1>=this.slope&&-1<=this.slope)?this.g3d.getRenderWidth():this.g3d.getRenderHeight();if(!this.getCachedLine()){this.lineBits=JU.BS.newN(this.nBits);b=Math.abs(b);a=Math.abs(a);if(b>a){var d=a;a=b;b=d}for(var d=0,e=a+a,c=b+b,f=0;f<this.nBits;f++)d+=c,d>a&&(this.lineBits.set(f),d-=e);this.lineCache.put(this.slopeKey,this.lineBits);
this.nCached++}},"~N,~N");c(c$,"clearLineCache",function(){this.lineCache.clear();this.nCached=0});c(c$,"plotLine",function(a,b,d,e,c,f,j,k,l,h,r){this.x1t=c;this.x2t=k;this.y1t=f;this.y2t=l;this.z1t=j;this.z2t=h;if(r)switch(this.getTrimmedLine()){case 0:r=!1;break;case 2:return}this.plotLineClipped(a,b,d,e,c,f,j,k-c,l-f,h-j,r,0,0)},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDelta",function(a,b,d,e,c,f,j,k,l,h,r){this.x1t=c;this.x2t=c+k;this.y1t=f;this.y2t=f+l;this.z1t=j;this.z2t=j+h;if(r)switch(this.getTrimmedLine()){case 2:return;
case 0:r=!1}this.plotLineClipped(a,b,d,e,c,f,j,k,l,h,r,0,0)},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaA",function(a,b,d,e,c,f,j,k,l,h,r,x){this.x1t=f;this.x2t=f+l;this.y1t=j;this.y2t=j+h;this.z1t=k;this.z2t=k+r;if(x)switch(this.getTrimmedLine()){case 2:return;case 0:x=!1}this.plotLineClippedA(a,b,d,e,c,f,j,k,l,h,r,x,0,0)},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaBits",function(a,b,d,e,c,f,j,k,l,h,r,x){this.x1t=f;this.x2t=f+l;this.y1t=j;this.y2t=j+h;this.z1t=k;this.z2t=
k+r;x&&2==this.getTrimmedLine()||this.plotLineClippedBits(a,b,d,e,c,f,j,k,l,h,r,0,0)},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotDashedLine",function(a,b,d,e,c,f,j,k,l,h,r){this.x1t=c;this.x2t=k;this.y1t=f;this.y2t=l;this.z1t=j;this.z2t=h;if(r)switch(this.getTrimmedLine()){case 2:return;case 0:r=!1}this.plotLineClipped(a,b,a,b,c,f,j,k-c,l-f,h-j,r,d,e)},"~N,~B,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"getCachedLine",function(){this.slopeKey=Float.$valueOf(this.slope);if(!this.lineCache.containsKey(this.slopeKey))return!1;
this.lineBits=this.lineCache.get(this.slopeKey);JU.Logger.debugging&&(this.nFound++,1E6==this.nFound&&JU.Logger.debug("nCached/nFound lines: "+this.nCached+" "+this.nFound));return!0});c(c$,"getTrimmedLine",function(){this.cc1=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t);this.cc2=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t);if(0==(this.cc1|this.cc2))return 0;var a=this.g3d.xLast,b=this.g3d.yLast,d=this.g3d.slab,e=this.g3d.depth;do{if(0!=(this.cc1&this.cc2))return 2;var c=this.x2t-this.x1t,f=this.y2t-
this.y1t,j=this.z2t-this.z1t;0!=this.cc1?(0!=(this.cc1&8)?(this.y1t+=z(-this.x1t*f/c),this.z1t+=z(-this.x1t*j/c),this.x1t=0):0!=(this.cc1&4)?(this.y1t+=z((a-this.x1t)*f/c),this.z1t+=z((a-this.x1t)*j/c),this.x1t=a):0!=(this.cc1&2)?(this.x1t+=z(-this.y1t*c/f),this.z1t+=z(-this.y1t*j/f),this.y1t=0):0!=(this.cc1&1)?(this.x1t+=z((b-this.y1t)*c/f),this.z1t+=z((b-this.y1t)*j/f),this.y1t=b):0!=(this.cc1&32)?(this.x1t+=z((d-this.z1t)*c/j),this.y1t+=z((d-this.z1t)*f/j),this.z1t=d):(this.x1t+=z((e-this.z1t)*
c/j),this.y1t+=z((e-this.z1t)*f/j),this.z1t=e),this.cc1=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(this.cc2&8)?(this.y2t+=z(-this.x2t*f/c),this.z2t+=z(-this.x2t*j/c),this.x2t=0):0!=(this.cc2&4)?(this.y2t+=z((a-this.x2t)*f/c),this.z2t+=z((a-this.x2t)*j/c),this.x2t=a):0!=(this.cc2&2)?(this.x2t+=z(-this.y2t*c/f),this.z2t+=z(-this.y2t*j/f),this.y2t=0):0!=(this.cc2&1)?(this.x2t+=z((b-this.y2t)*c/f),this.z2t+=z((b-this.y2t)*j/f),this.y2t=b):0!=(this.cc2&32)?(this.x2t+=z((d-this.z2t)*c/j),this.y2t+=
z((d-this.z2t)*f/j),this.z2t=d):(this.x2t+=z((e-this.z2t)*c/j),this.y2t+=z((e-this.z2t)*f/j),this.z2t=e),this.cc2=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(this.cc1|this.cc2));return 1});c(c$,"plotLineClipped",function(a,b,d,e,c,f,j,k,l,h,r,x,A){var I=this.g3d.zbuf,n=this.g3d.getRenderWidth(),p=0;0==x&&(A=2147483647,x=1);var s=f*n+c,u=this.g3d.bufferSize,t=0!=((c^f)&1);0!=a&&(!r&&0<=s&&s<u&&j<I[s]&&(!b||(t=!t)))&&this.g3d.addPixel(s,j,a);if(!(0==k&&0==l)){r=1;var v=n;c+=k;var w=f+
l;0>k&&(k=-k,r=-1);0>l&&(l=-l,v=-n);n=k+k;f=l+l;j<<=10;if(l<=k){var y=k-1;0>h&&(y=-y);h=q(((h<<10)+y)/k);l=0;y=Math.abs(c-this.x2t)-1;c=Math.abs(c-this.x1t)-1;for(var w=k-1,B=q(w/2);--w>=y&&!(w==B&&(b=e,a=d,0==a));){s+=r;j+=h;l+=f;l>k&&(s+=v,l-=n,t=!t);if(0!=a&&w<c&&0<=s&&s<u&&p<A&&(!b||(t=!t))){var z=j>>10;z<I[s]&&this.g3d.addPixel(s,z,a)}p=(p+1)%x}}else{y=l-1;0>h&&(y=-y);h=q(((h<<10)+y)/l);k=0;y=Math.abs(w-this.y2t)-1;c=Math.abs(w-this.y1t)-1;w=l-1;for(B=q(w/2);--w>=y&&!(w==B&&(b=e,a=d,0==a));){s+=
v;j+=h;k+=n;k>l&&(s+=r,k-=f,t=!t);if(0!=a&&w<c&&0<=s&&s<u&&p<A&&(!b||(t=!t)))z=j>>10,z<I[s]&&this.g3d.addPixel(s,z,a);p=(p+1)%x}}}},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedA",function(a,b,d,e,c,f,j,k,l,h,r,x,A,I){var n=this.g3d.zbuf,s=this.g3d.getRenderWidth(),p=0;0==A&&(I=2147483647,A=1);var t=j*s+f,u=this.g3d.bufferSize,v=63>c?c+1:c,w=0<c?c-1:c,y=a[v],z=a[w],B=d[c],v=d[v];d=d[w];a=a[c];c=b;var C=0!=((f^j)&1);0!=a&&(!x&&0<=t&&t<u&&k<n[t]&&(!c||(C=!C)))&&this.g3d.addPixel(t,
k,a);if(!(0==l&&0==h)){x=1;var w=s,D=f+l,E=j+h;0>l&&(l=-l,x=-1);0>h&&(h=-h,w=-s);j=l+l;f=h+h;k<<=10;if(h<=l){var F=l-1;0>r&&(F=-F);r=q(((r<<10)+F)/l);h=0;for(var F=Math.abs(D-this.x2t)-1,D=Math.abs(D-this.x1t)-1,E=l-1,G=q(E/2);--E>=F;){if(E==G){a=B;if(0==a)break;y=v;z=d;if((c=e)&&!b)var C=q(t/s),H=t%s,C=0==((H^C)&1)}t+=x;k+=r;h+=f;h>l&&(t+=w,h-=j,C=!C);if(0!=a&&E<D&&0<=t&&t<u&&p<I&&(!c||(C=!C)))if(H=k>>10,H<n[t]){var K=this.shader.nextRandom8Bit();this.g3d.addPixel(t,H,85>K?z:170<K?y:a)}p=(p+1)%A}}else{F=
h-1;0>r&&(F=-F);r=q(((r<<10)+F)/h);l=0;F=Math.abs(E-this.y2t)-1;D=Math.abs(E-this.y1t)-1;E=h-1;for(G=q(E/2);--E>=F;){if(E==G){a=B;if(0==a)break;y=v;z=d;if((c=e)&&!b)C=q(t/s),H=t%s,C=0==((H^C)&1)}t+=w;k+=r;l+=j;l>h&&(t+=x,l-=f,C=!C);if(0!=a&&E<D&&0<=t&&t<u&&p<I&&(!c||(C=!C)))H=k>>10,H<n[t]&&(K=this.g3d.shader.nextRandom8Bit(),this.g3d.addPixel(t,H,85>K?z:170<K?y:a));p=(p+1)%A}}}},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedBits",function(a,b,d,e,c,f,j,k,l,h,r,x,A){var I=this.g3d.zbuf,
n=this.g3d.width,s=0;0==x&&(A=2147483647,x=1);var t=63>c?c+1:c,p=0<c?c-1:c,u=a[c],v=a[t],w=a[p];c=d[c];t=d[t];d=d[p];var p=b,y=0!=((f^j)&1);a=j*n+f;var B=this.g3d.bufferSize,C,D,E,F,G;this.lineTypeX?(C=f,D=this.x1t,E=this.x2t,f+=q(l/2),F=j=0<=l?1:-1,G=0<=h?n:-n,l=r/Math.abs(l)):(C=j,D=this.y1t,E=this.y2t,f=j+q(h/2),j=0<=h?1:-1,F=0<=h?n:-n,G=0<=l?1:-1,l=r/Math.abs(h));h=!1;for(r=C;;r+=j,C+=j){r==D&&(h=!0);if(r==f){u=c;if(0==u)break;v=t;w=d;if((p=e)&&!b)y=q(a/n),y=0==((a%n^y)&1)}if(0!=u&&(h&&0<=a&&
a<B&&s<A&&(!p||(y=!y)))&&k<I[a]){var H=this.shader.nextRandom8Bit();this.g3d.addPixel(a,z(k),85>H?w:170<H?v:u)}if(r==E)break;s=(s+1)%x;for(a+=F;0>C;)C+=this.nBits;this.lineBits.get(C%this.nBits)&&(a+=G);k+=l}},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~N,~N");C(c$,"VISIBILITY_UNCLIPPED",0,"VISIBILITY_CLIPPED",1,"VISIBILITY_OFFSCREEN",2)});n("J.g3d");w(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){c$=t(function(){this.g=null;s(this,arguments)},J.g3d,"Pixelator");u(c$,function(a){this.g=a},"J.g3d.Graphics3D");
c(c$,"clearPixel",function(a,b){!this.g.$isPass2&&this.g.zbuf[a]>b&&(this.g.zbuf[a]=2147483647)},"~N,~N");c(c$,"addPixel",function(a,b,d){this.addPixel1(a,b,d)},"~N,~N,~N");c(c$,"addPixel1",function(a,b,d){if(this.g.$isPass2){var c=this.g.zbufT[a];if(b<c){var g=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=g&&c-b>this.g.zMargin)&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,g,this.g.bgcolor);this.g.zbufT[a]=b;this.g.pbufT[a]=d&this.g.translucencyMask}else b!=c&&!this.g.translucentCoverOnly&&
b-c>this.g.zMargin&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,d&this.g.translucencyMask,this.g.bgcolor)}else this.g.zbuf[a]=b,this.g.pbuf[a]=d},"~N,~N,~N")});n("J.g3d");w(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){c$=B(J.g3d,"PixelatorShaded",J.g3d.Pixelator);h(c$,"addPixel",function(a,b,d){if(!(b>this.g.zDepth)){if(b<=this.g.zDepth&&b>=this.g.zSlab){var c=(d&65280)>>8,g=(d&16711680)>>16,f=d&4278190080,j=(this.g.zDepth-b)/(this.g.zDepth-this.g.zSlab);if(1<this.g.zShadePower)for(var k=
0;k<this.g.zShadePower;k++)j*=j;d=this.g.zShadeR+z(j*((d&255)-this.g.zShadeR));c=this.g.zShadeG+z(j*(c-this.g.zShadeG));g=this.g.zShadeB+z(j*(g-this.g.zShadeB));d=g<<16|c<<8|d|f}this.addPixel1(a,b,d)}},"~N,~N,~N")});n("J.g3d");c$=t(function(){this.bufferSizeT=this.bufferSize=this.bufferHeight=this.bufferWidth=this.windowSize=this.windowHeight=this.windowWidth=0;this.zBufferT=this.zBuffer=this.pBufferT=this.pBuffer=this.bufferedImage=null;this.heightOffscreen=this.widthOffscreen=0;this.apiPlatform=
this.graphicsForTextOrImage=this.offscreenImage=null;s(this,arguments)},J.g3d,"Platform3D");u(c$,function(a){this.apiPlatform=a},"javajs.api.GenericPlatform");c(c$,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))});c(c$,"allocateTBuffers",function(a){this.bufferSizeT=a?this.bufferSize:this.windowSize;this.zBufferT=D(this.bufferSizeT,0);this.pBufferT=D(this.bufferSizeT,0)},"~B");c(c$,"allocateBuffers",function(a,b,d,c){this.windowWidth=a;this.windowHeight=
b;this.windowSize=a*b;d&&(a*=2,b*=2);this.bufferWidth=a;this.bufferHeight=b;this.bufferSize=this.bufferWidth*this.bufferHeight;this.zBuffer=D(this.bufferSize,0);this.pBuffer=D(this.bufferSize,0);this.bufferedImage=this.apiPlatform.allocateRgbImage(this.windowWidth,this.windowHeight,this.pBuffer,this.windowSize,J.g3d.Platform3D.backgroundTransparent,c)},"~N,~N,~B,~B");c(c$,"releaseBuffers",function(){this.windowWidth=this.windowHeight=this.bufferWidth=this.bufferHeight=this.bufferSize=-1;null!=this.bufferedImage&&
(this.apiPlatform.flushImage(this.bufferedImage),this.bufferedImage=null);this.zBufferT=this.pBufferT=this.zBuffer=this.pBuffer=null});c(c$,"hasContent",function(){for(var a=this.bufferSize;0<=--a;)if(2147483647!=this.zBuffer[a])return!0;return!1});c(c$,"clearScreenBuffer",function(){for(var a=this.bufferSize;0<=--a;)this.zBuffer[a]=2147483647,this.pBuffer[a]=0});c(c$,"setBackgroundColor",function(a){if(null!=this.pBuffer)for(var b=this.bufferSize;0<=--b;)0==this.pBuffer[b]&&(this.pBuffer[b]=a)},
"~N");c(c$,"clearTBuffer",function(){for(var a=this.bufferSizeT;0<=--a;)this.zBufferT[a]=2147483647,this.pBufferT[a]=0});c(c$,"clearBuffer",function(){this.clearScreenBuffer()});c(c$,"clearScreenBufferThreaded",function(){});c(c$,"notifyEndOfRendering",function(){this.apiPlatform.notifyEndOfRendering()});c(c$,"getGraphicsForTextOrImage",function(a,b){if(a>this.widthOffscreen||b>this.heightOffscreen)null!=this.offscreenImage&&(this.apiPlatform.disposeGraphics(this.graphicsForTextOrImage),this.apiPlatform.flushImage(this.offscreenImage)),
a>this.widthOffscreen&&(this.widthOffscreen=a),b>this.heightOffscreen&&(this.heightOffscreen=b),this.offscreenImage=this.allocateOffscreenImage(this.widthOffscreen,this.heightOffscreen),this.graphicsForTextOrImage=this.apiPlatform.getStaticGraphics(this.offscreenImage,J.g3d.Platform3D.backgroundTransparent);return this.graphicsForTextOrImage},"~N,~N");c(c$,"allocateOffscreenImage",function(a,b){return this.apiPlatform.newOffScreenImage(a,b)},"~N,~N");c(c$,"setBackgroundTransparent",function(a){J.g3d.Platform3D.backgroundTransparent=
a},"~B");C(c$,"backgroundTransparent",!1);n("J.g3d");w(["JU.P3"],"J.g3d.SphereRenderer",["JU.GData"],function(){c$=t(function(){this.shader=this.g3d=null;this.diameter=this.z=this.y=this.x=this.maxZ=this.minZ=this.maxY=this.minY=this.maxX=this.minX=0;this.tScreened=!1;this.mDeriv=this.coef=this.mat=this.zroot=this.shades=null;this.selectedOctant=0;this.octantPoints=null;this.planeShade=0;this.zbuf=null;this.offsetPbufBeginLine=this.slab=this.depth=this.height=this.width=0;this.addAllPixels=!1;this.dxyz=
this.planeShades=this.ptTemp=null;this.z0=0;s(this,arguments)},J.g3d,"SphereRenderer");K(c$,function(){this.zroot=X(2,0);this.ptTemp=new JU.P3;this.planeShades=D(3,0);this.dxyz=L(3,3,0)});u(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"render",function(a,b,d,c,g,f,j,k,l,h,r,x){if(1!=f&&(this.width=this.g3d.width,this.height=this.g3d.height,49<d&&(d&=-2),!this.g3d.isClippedXY(d,c,g))){var A=d+1>>1;this.minX=c-A;this.maxX=c+A;this.minY=g-A;this.maxY=g+A;this.slab=this.g3d.slab;
this.depth=this.g3d.depth;this.minZ=f-A;this.maxZ=f+A;this.maxZ<this.slab||this.minZ>this.depth||(this.shader.nOut=this.shader.nIn=0,this.zbuf=this.g3d.zbuf,this.addAllPixels=x,this.offsetPbufBeginLine=this.width*g+c,this.x=c,this.y=g,this.z=f,this.diameter=d,this.tScreened=b,this.shades=a,this.mat=j,null!=j&&(this.coef=k,this.mDeriv=l,this.selectedOctant=h,this.octantPoints=r),null!=j||128<d?(this.renderLarge(),null!=j&&(this.octantPoints=this.mDeriv=this.coef=this.mat=null)):(a=this.shader.sphereShapeCache[d-
1],null==a&&(a=this.createSphereShape(d)),0>this.minX||this.maxX>=this.width||0>this.minY||this.maxY>=this.height||this.minZ<this.slab||f>this.depth?this.renderShapeClipped(a,c,g,f,d):this.renderShapeUnclipped(a,c,g,f,d)),this.zbuf=this.shades=null)}},"~A,~B,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A,~B");c(c$,"createSphereShape",function(a){for(var b=this.shader,d=0,c=0!=(a&1),g=a/2,f=g*g,j=q((a+1)/2),k=c?0:0.5,l=0;l<j;++l,++k)for(var h=k*k,r=c?0:0.5,x=0;x<j;++x,++r){var A=r*r,A=f-h-A;0<=A&&++d}for(var d=
D(d,0),I=0,k=c?0:0.5,l=0;l<j;++l,++k){h=k*k;r=c?0:0.5;for(x=0;x<j;++x,++r)if(A=r*r,A=f-h-A,0<=A){var n=Math.sqrt(A),A=z(n),s=b.getShadeN(r,k,n,g),t=b.getShadeN(-r,k,n,g),p=b.getShadeN(r,-k,n,g),n=b.getShadeN(-r,-k,n,g),A=A|s<<7|t<<13|p<<19|n<<25;d[I++]=A}d[I-1]|=2147483648}return b.sphereShapeCache[a-1]=d},"~N");c(c$,"renderShapeUnclipped",function(a,b,d,c,g){var f=0,j=1-(g&1),k=this.offsetPbufBeginLine,h=k-j*this.width;g=q((g+1)/2);var m=this.shades,r=this.g3d,x=this.zbuf,A=this.width;if(this.tScreened){b=
(b^d)&1;d=b^j;b=b|(b^j)<<1|d<<2|(d^j)<<3;do{I=k;n=k-j;s=h;t=h-j;d=b=~b;do p=a[f++],u=c-(p&127),0!=(d&1)&&u<x[I]&&r.addPixel(I,u,m[p>>7&63]),0!=(d&2)&&u<x[n]&&r.addPixel(n,u,m[p>>13&63]),0!=(d&4)&&u<x[s]&&r.addPixel(s,u,m[p>>19&63]),0!=(d&8)&&u<x[t]&&r.addPixel(t,u,m[p>>25&63]),++I,--n,++s,--t,d=~d;while(0<=p);k+=A;h-=A}while(0<--g)}else{do{var I=k,n=k-j,s=h,t=h-j,p;do{p=a[f++];var u=c-(p&127);u<x[I]&&r.addPixel(I,u,m[p>>7&63]);u<x[n]&&r.addPixel(n,u,m[p>>13&63]);u<x[s]&&r.addPixel(s,u,m[p>>19&63]);
u<x[t]&&r.addPixel(t,u,m[p>>25&63]);++I;--n;++s;--t}while(0<=p);k+=A;h-=A}while(0<--g)}},"~A,~N,~N,~N,~N");c(c$,"renderShapeClipped",function(a,b,d,c,g){var f=0,j=1-(g&1),k=this.offsetPbufBeginLine,h=k-j*this.width;g=q((g+1)/2);var m=d,r=d-j,x=(b<<16)+(d<<1)^858993459;d=(b^d)&1;var A=d^j;d=d|(d^j)<<1|A<<2|(A^j)<<3;var A=this.shades,I=this.g3d,n=this.zbuf;do{var s=0<=m&&m<this.height,t=0<=r&&r<this.height,p=k,u=k-j,v=h,w=h-j,y,z=d=~d,B=b,C=b-j;do{var D=0<=C&&C<this.width,E=0<=B&&B<this.width;y=a[f++];
var F;F=y&127;var G;c<this.slab?(G=c+F,F=G>=this.slab):(G=c-F,F=G<this.slab);F&&(G=this.slab);if(G>=this.slab&&G<=this.depth){if(s){if(E&&(this.addAllPixels||0!=(z&1))&&G<n[p]){var H=F?44+(x>>7&7):y>>7&63;I.addPixel(p,G,A[H])}if(D&&(this.addAllPixels||0!=(z&2))&&G<n[u])H=F?44+(x>>13&7):y>>13&63,I.addPixel(u,G,A[H])}if(t){if(E&&(!this.tScreened||0!=(z&4))&&G<n[v])H=F?44+(x>>19&7):y>>19&63,I.addPixel(v,G,A[H]);if(D&&(!this.tScreened||0!=(z&8))&&G<n[w])H=F?44+(x>>25&7):y>>25&63,I.addPixel(w,G,A[H])}}++p;
--u;++v;--w;++B;--C;z=~z;F&&(x=(x<<16)+(x<<1)+x&2147483647)}while(0<=y);k+=this.width;h-=this.width;++m;--r}while(0<--g)},"~A,~N,~N,~N,~N");c(c$,"renderLarge",function(){null!=this.mat&&(null==this.shader.ellipsoidShades&&this.shader.createEllipsoidShades(),null!=this.octantPoints&&this.setPlaneDerivatives());this.renderQuadrant(-1,-1);this.renderQuadrant(-1,1);this.renderQuadrant(1,-1);this.renderQuadrant(1,1)});c(c$,"renderQuadrant",function(a,b){var d=q(this.diameter/2),c=this.x+d*a,g=(0>this.x?
-1:this.x<this.width?0:1)+(0>c?-2:c<this.width?0:2);-3==g||3==g||(c=this.y+d*b,c=(0>this.y?-1:this.y<this.height?0:1)+(0>c?-2:c<this.height?0:2),-3==c||3==c||(null==this.mat&&0==g&&0==c&&this.z-d>=this.slab&&this.z<=this.depth?this.renderQuadrantUnclipped(d,a,b):this.renderQuadrantClipped(d,a,b)))},"~N,~N");c(c$,"renderQuadrantUnclipped",function(a,b,d){for(var c=a*a,g=2*a+1,f=0==((this.x^this.y)&1),j=0>d?-this.width:this.width,k=this.offsetPbufBeginLine,h=0,m=0;m<=c;m+=h+ ++h,k+=j)for(var r=k,x=
f=!f,A=c-m,I=this.z-a,n=q((h*d+a<<8)/g),p=0,s=0;s<=A;s+=p+ ++p,r+=b)if((this.addAllPixels||(x=!x))&&!(this.zbuf[r]<=I))if(I=q(Math.sqrt(A-s)),I=this.z-I,!(this.zbuf[r]<=I)){var t=q((p*b+a<<8)/g);this.g3d.addPixel(r,I,this.shades[this.shader.sphereShadeIndexes[(n<<8)+t]])}},"~N,~N,~N");c(c$,"renderQuadrantClipped",function(a,b,d){for(var c=null!=this.mat,g=0<=this.selectedOctant,f=a*a,j=2*a+1,k=0>d?-this.width:this.width,h=this.offsetPbufBeginLine,m=(this.x<<16)+(this.y<<1)^858993459,r=this.y,x=0,
A=0,I=0,n=0;n<=f;n+=I+ ++I,h+=k,r+=d)if(0>r){if(0>d)break}else if(r>=this.height){if(0<d)break}else{var s=f-(c?0:n),p=this.x;c||(x=q((I*d+a<<8)/j));for(var m=(m<<16)+(m<<1)+m&2147483647,t=-1,u=1,v=h,w=0,y=0;y<=s;y+=w+ ++w,v+=b,p+=b)if(0>p){if(0>b)break}else if(p>=this.width){if(0<b)break}else if(!(this.tScreened&&0!=((p^r)&1))){var z;if(c){if(!J.g3d.SphereRenderer.getQuardricZ(p,r,this.coef,this.zroot)){if(0<=t)break;continue}t=this.z<this.slab?1:0;z=q(this.zroot[t]);0==z&&(z=this.z);u=2;this.z0=
z;if(g){this.ptTemp.set(p-this.x,r-this.y,z-this.z);this.mat.rotate(this.ptTemp);JU.GData.getScreenOctant(this.ptTemp)==this.selectedOctant&&(A=this.getPlaneShade(p,r,this.zroot),z=q(this.zroot[0]),u=3);var B=this.z<this.slab?z>=this.slab:z<this.slab;B&&(this.z0=z=this.slab,u=0)}if(z<this.slab||z>this.depth||this.zbuf[v]<=this.z0)continue}else{z=q(Math.sqrt(s-y));z=this.z+(this.z<this.slab?z:-z);if(B=this.z<this.slab?z>=this.slab:z<this.slab)z=this.slab,u=0;if(z<this.slab||z>this.depth||this.zbuf[v]<=
z)continue}switch(u){case 0:A=44+(m>>8&7);m=(m<<16)+(m<<1)+m&2147483647;u=1;break;case 2:A=this.shader.getEllipsoidShade(p,r,this.zroot[t],a,this.mDeriv);break;case 3:this.g3d.clearPixel(v,this.z0);break;default:A=q((w*b+a<<8)/j),A=this.shader.sphereShadeIndexes[(x<<8)+A]}this.g3d.addPixel(v,z,this.shades[A])}m=(m+p+r|1)&2147483647}},"~N,~N,~N");c$.getQuardricZ=c(c$,"getQuardricZ",function(a,b,d,c){var g=(d[4]*a+d[5]*b+d[8])/d[2]/2;a=g*g-(d[0]*a*a+d[1]*b*b+d[3]*a*b+d[6]*a+d[7]*b-1)/d[2];if(0>a)return!1;
a=Math.sqrt(a);c[0]=-g-a;c[1]=-g+a;return!0},"~N,~N,~A,~A");c(c$,"setPlaneDerivatives",function(){this.planeShade=-1;for(var a=0;3>a;a++){var b=this.dxyz[a][0]=this.octantPoints[a].x-this.x,d=this.dxyz[a][1]=this.octantPoints[a].y-this.y,c=this.dxyz[a][2]=this.octantPoints[a].z-this.z;this.planeShades[a]=this.shader.getShadeIndex(b,d,-c);if(0==b&&0==d){this.planeShade=this.planeShades[a];break}}});c(c$,"getPlaneShade",function(a,b,d){if(0<=this.planeShade)return this.planeShade;for(var c=3,g,f=3.4028235E38,
j=0;3>j;j++)if(0!=(g=this.dxyz[j][2]))g=this.z+(-this.dxyz[j][0]*(a-this.x)-this.dxyz[j][1]*(b-this.y))/g,g<f&&(f=g,c=j);3==c&&(c=0,f=this.z);d[0]=f;return this.planeShades[c]},"~N,~N,~A");C(c$,"maxOddSizeSphere",49,"maxSphereDiameter",1E3,"maxSphereDiameter2",2E3,"SHADE_SLAB_CLIPPED",47)});n("J.g3d");w(["java.util.Hashtable"],"J.g3d.TextRenderer",["JU.CU"],function(){c$=t(function(){this.size=this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=null;this.isInvalid=!1;s(this,arguments)},J.g3d,
"TextRenderer");c$.clearFontCache=c(c$,"clearFontCache",function(){J.g3d.TextRenderer.working||(J.g3d.TextRenderer.htFont3d.clear(),J.g3d.TextRenderer.htFont3dAntialias.clear())});c$.plot=c(c$,"plot",function(a,b,d,c,g,f,j,k,h,m){if(0==f.length)return 0;if(0<=f.indexOf("<su")||0<=f.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,b,d,c,g,f,j,k,h,m);var r=j.getAscent();b-=r;f=J.g3d.TextRenderer.getPlotText3D(a,b,k,f,j,m);if(f.isInvalid)return f.width;m&&0==(c&12632256)&&(c|=263172);null!=
h||0>a||a+f.width>k.width||0>b||b+f.height>k.height?J.g3d.TextRenderer.plotClipped(a,b,d,c,g,k,h,f.mapWidth,f.height,f.tmap):J.g3d.TextRenderer.plotUnclipped(a,b,d,c,g,k,f.mapWidth,f.height,f.tmap);return f.width},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");c$.plotByCharacter=c(c$,"plotByCharacter",function(a,b,d,c,g,f,j,k,h,m){for(var r=0,x=f.length,A=Math.round(0.25*j.getHeight()),I=-Math.round(0.3*j.getHeight()),n=0,q=0;q<x;q++){if("<"==f.charAt(q)){if(q+
5<x&&f.substring(q,q+6).equals("<color")){var n=c,p=f.indexOf(">",q);if(0>p)continue;c=JU.CU.getArgbFromString(f.substring(q+7,p).trim());q=p;continue}if(q+7<x&&f.substring(q,q+8).equals("</color>")){q+=7;c=n;continue}if(q+4<x&&f.substring(q,q+5).equals("<sub>")){q+=4;b+=A;continue}if(q+4<x&&f.substring(q,q+5).equals("<sup>")){q+=4;b+=I;continue}if(q+5<x&&f.substring(q,q+6).equals("</sub>")){q+=5;b-=A;continue}if(q+5<x&&f.substring(q,q+6).equals("</sup>")){q+=5;b-=I;continue}}p=J.g3d.TextRenderer.plot(a+
r,b,d,c,g,f.substring(q,q+1),j,k,h,m);r+=p}return r},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");c$.plotUnclipped=c(c$,"plotUnclipped",function(a,b,d,c,g,f,j,k,h){var m=0,r=f.zbuf,x=f.width;a=b*x+a;for(b=0;b<k;b++){for(var A=0;A<j;A++){var I=h[m++];0!=I&&d<r[a]&&f.shadeTextPixel(a,d,c,g,I);a++}a+=x-j}},"~N,~N,~N,~N,~N,J.g3d.Graphics3D,~N,~N,~A");c$.plotClipped=c(c$,"plotClipped",function(a,b,d,c,g,f,j,k,h,m){null==j&&(j=f);for(var r=f=0;r<h;r++)for(var x=0;x<
k;x++){var A=m[f++];0!=A&&j.plotImagePixel(c,a+x,b+r,d,A,g)}},"~N,~N,~N,~N,~N,J.g3d.Graphics3D,J.api.JmolRendererInterface,~N,~N,~A");u(c$,function(a,b){this.ascent=b.getAscent();this.height=b.getHeight();this.width=b.stringWidth(a);0!=this.width&&(this.mapWidth=this.width,this.size=this.mapWidth*this.height)},"~S,javajs.awt.Font");c$.getPlotText3D=c(c$,"getPlotText3D",function(a,b,d,c,g,f){J.g3d.TextRenderer.working=!0;f=f?J.g3d.TextRenderer.htFont3dAntialias:J.g3d.TextRenderer.htFont3d;var j=f.get(g),
k=null,h=!1,m=!1;null!=j?k=j.get(c):(j=new java.util.Hashtable,h=!0);null==k&&(k=new J.g3d.TextRenderer(c,g),m=!0);k.isInvalid=0==k.width||0>=a+k.width||a>=d.width||0>=b+k.height||b>=d.height;if(k.isInvalid)return k;h&&f.put(g,j);m&&(k.setTranslucency(c,g,d),j.put(c,k));J.g3d.TextRenderer.working=!1;return k},"~N,~N,J.g3d.Graphics3D,~S,javajs.awt.Font,~B");c(c$,"setTranslucency",function(a,b,d){a=d.apiPlatform.getTextPixels(a,b,d.platform.getGraphicsForTextOrImage(this.mapWidth,this.height),d.platform.offscreenImage,
this.mapWidth,this.height,this.ascent);if(null!=a){this.tmap=O(this.size,0);for(b=a.length;0<=--b;)d=a[b]&255,0!=d&&(this.tmap[b]=J.g3d.TextRenderer.translucency[d>>5])}},"~S,javajs.awt.Font,J.g3d.Graphics3D");C(c$,"translucency",[7,6,5,4,3,2,1,8],"working",!1);c$.htFont3d=c$.prototype.htFont3d=new java.util.Hashtable;c$.htFont3dAntialias=c$.prototype.htFont3dAntialias=new java.util.Hashtable});n("J.g3d");c$=B(J.g3d,"TextSorter",null,java.util.Comparator);h(c$,"compare",function(a,b){return null==
a||null==b?0:a.z>b.z?-1:a.z<b.z?1:0},"J.g3d.TextString,J.g3d.TextString");n("J.g3d");w(["JU.P3i"],"J.g3d.TextString",null,function(){c$=t(function(){this.font=this.text=null;this.bgargb=this.argb=0;s(this,arguments)},J.g3d,"TextString",JU.P3i);c(c$,"setText",function(a,b,d,c,g,f,j){this.text=a;this.font=b;this.argb=d;this.bgargb=c;this.x=g;this.y=f;this.z=j},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");c(c$,"toString",function(){return R(this,J.g3d.TextString,"toString",[])+" "+this.text})});n("J.g3d");w(["J.g3d.G3DRenderer",
"JU.Rgb16"],"J.g3d.TriangleRenderer",["JU.GData"],function(){c$=t(function(){this.rgb16t2=this.rgb16t1=this.rgb16sGouraud=this.rgb16sE=this.rgb16sW=this.azE=this.axE=this.azW=this.axW=this.az=this.ay=this.ax=this.g3d=null;s(this,arguments)},J.g3d,"TriangleRenderer",null,J.g3d.G3DRenderer);K(c$,function(){this.ax=D(3,0);this.ay=D(3,0);this.az=D(3,0);this.axW=D(64,0);this.azW=D(64,0);this.axE=D(64,0);this.azE=D(64,0);this.rgb16t1=new JU.Rgb16;this.rgb16t2=new JU.Rgb16});u(c$,function(){});h(c$,"set",
function(a){try{this.rgb16sW=Array(64);this.rgb16sE=Array(64);for(var b=64;0<=--b;)this.rgb16sW[b]=new JU.Rgb16,this.rgb16sE[b]=new JU.Rgb16;this.g3d=a;this.rgb16sGouraud=Array(3);for(b=3;0<=--b;)this.rgb16sGouraud[b]=new JU.Rgb16}catch(d){if(!y(d,Exception))throw d;}return this},"J.api.JmolRendererInterface");c(c$,"reallocRgb16s",function(a,b){var d=Array(b);System.arraycopy(a,0,d,0,a.length);for(var c=a.length;c<b;++c)d[c]=new JU.Rgb16;return d},"~A,~N");c(c$,"setGouraud",function(a,b,d){this.rgb16sGouraud[0].setInt(a);
this.rgb16sGouraud[1].setInt(b);this.rgb16sGouraud[2].setInt(d)},"~N,~N,~N");c(c$,"drawfillTriangle",function(a,b,d,c,g,f,j,k,h,m){this.ax[0]=a;this.ax[1]=c;this.ax[2]=j;this.ay[0]=b;this.ay[1]=g;this.ay[2]=k;this.az[0]=d;this.az[1]=f;this.az[2]=h;this.fillTriangleB(m)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"fillTriangleXYZ",function(a,b,d,c,g,f,j,k,h,m){this.ax[0]=a;this.ax[1]=c;this.ax[2]=j;this.ay[0]=b;this.ay[1]=g;this.ay[2]=k;this.az[0]=d;this.az[1]=f;this.az[2]=h;this.fillTriangleB(m)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B");
c(c$,"fillTriangleP3i",function(a,b,d,c){this.ax[0]=a.x;this.ax[1]=b.x;this.ax[2]=d.x;this.ay[0]=a.y;this.ay[1]=b.y;this.ay[2]=d.y;this.az[0]=a.z;this.az[1]=b.z;this.az[2]=d.z;this.fillTriangleB(c)},"JU.P3i,JU.P3i,JU.P3i,~B");c(c$,"fillTriangleP3f",function(a,b,d,c){this.ax[0]=Math.round(a.x);this.ax[1]=Math.round(b.x);this.ax[2]=Math.round(d.x);this.ay[0]=Math.round(a.y);this.ay[1]=Math.round(b.y);this.ay[2]=Math.round(d.y);this.az[0]=Math.round(a.z);this.az[1]=Math.round(b.z);this.az[2]=Math.round(d.z);
this.fillTriangleB(c)},"JU.P3,JU.P3,JU.P3,~B");c(c$,"fillTriangleP3if",function(a,b,d,c,g){this.ax[0]=a.x;this.ax[1]=b.x;this.ax[2]=d.x;this.ay[0]=a.y;this.ay[1]=b.y;this.ay[2]=d.y;this.az[0]=a.z;this.az[1]=b.z;this.az[2]=d.z;J.g3d.TriangleRenderer.adjustVertex(this.ax,c);J.g3d.TriangleRenderer.adjustVertex(this.ay,c);J.g3d.TriangleRenderer.adjustVertex(this.az,c);this.fillTriangleB(g)},"JU.P3i,JU.P3i,JU.P3i,~N,~B");c$.adjustVertex=c(c$,"adjustVertex",function(a,b){for(var d=(a[0]+a[1]+a[2])/3,c=
0;3>c;c++)a[c]+=b*(d-a[c])},"~A,~N");c(c$,"fillTriangleB",function(a){if(!(1>=this.az[0]||1>=this.az[1]||1>=this.az[2])){var b=this.g3d.clipCode3(this.ax[0],this.ay[0],this.az[0]),d=this.g3d.clipCode3(this.ax[1],this.ay[1],this.az[1]),c=this.g3d.clipCode3(this.ax[2],this.ay[2],this.az[2]),g=0!=(b|d|c);if(!(g&&0!=(b&d&c))){b=0;this.ay[1]<this.ay[b]&&(b=1);this.ay[2]<this.ay[b]&&(b=2);d=(b+1)%3;c=(b+2)%3;if(this.ay[d]>this.ay[c])var f=d,d=c,c=f;var j=this.ay[b],k=this.ay[d],h=this.ay[c],m=h-j+1;if(!(m>
3*this.g3d.height)){m>this.axW.length&&this.reallocRasterArrays(m);var r,x;a?(r=this.rgb16sW,x=this.rgb16sE):r=x=null;f=k-j;0==f?(this.ax[d]<this.ax[b]&&(f=d,d=b,b=f),this.generateRaster(m,b,c,this.axW,this.azW,0,r),this.generateRaster(m,d,c,this.axE,this.azE,0,x)):k==h?(this.ax[c]<this.ax[d]&&(f=d,d=c,c=f),this.generateRaster(m,b,d,this.axW,this.azW,0,r),this.generateRaster(m,b,c,this.axE,this.azE,0,x)):(k=this.ax[c]-this.ax[b],h=JU.GData.roundInt(q(m/2)),0>k&&(h=-h),this.ax[b]+q((k*f+h)/m)<this.ax[d]?
(this.generateRaster(m,b,c,this.axW,this.azW,0,r),this.generateRaster(f+1,b,d,this.axE,this.azE,0,x),this.generateRaster(m-f,d,c,this.axE,this.azE,f,x)):(this.generateRaster(f+1,b,d,this.axW,this.azW,0,r),this.generateRaster(m-f,d,c,this.axW,this.azW,f,r),this.generateRaster(m,b,c,this.axE,this.azE,0,x)));this.g3d.setZMargin(5);a?this.fillRasterG(j,m,g,this.g3d.$isPass2?1:0):this.fillRaster(j,m,g,this.g3d.$isPass2?1:0);this.g3d.setZMargin(0)}}}},"~B");c(c$,"reallocRasterArrays",function(a){a=a+31&
-32;this.axW=D(a,0);this.azW=D(a,0);this.axE=D(a,0);this.azE=D(a,0);this.rgb16sW=this.reallocRgb16s(this.rgb16sW,a);this.rgb16sE=this.reallocRgb16s(this.rgb16sE,a)},"~N");c(c$,"generateRaster",function(a,b,d,c,g,f,j){var k=this.ax[b],h=this.az[b],m=this.ax[d]-k,r=this.az[d]-h,x,A,I;0<=m?(x=1,A=m,I=0):(x=-1,A=-m,I=1-a);var h=(h<<10)+512,n=JU.GData.roundInt(q(a/2));0>r&&(n=-n);r=q(((r<<10)+n)/a);A<=a?n=0:(n=JU.GData.roundInt(q(m/a)),A%=a);for(var p=0,m=f;p<a;h+=r,++m,++p)c[m]=k,g[m]=h>>10,k+=n,I+=A,
0<I&&(k+=x,I-=a);if(null!=j){c=this.rgb16t1;c.setRgb(this.rgb16sGouraud[b]);b=this.rgb16t2;b.diffDiv(this.rgb16sGouraud[d],c,a);m=f;for(a=f+a;m<a;++m)j[m].setAndIncrement(c,b)}},"~N,~N,~N,~A,~A,~N,~A");c(c$,"fillRaster",function(a,b,d,c){var g=0;0>a&&(b+=a,g-=a,a=0);a+b>this.g3d.height&&(b=this.g3d.height-a);if(d)for(;--b>=c;++a,++g){d=this.axW[g];var f=this.axE[g]-d+1-c;0<f&&this.g3d.plotPixelsClippedRaster(f,d,a,this.azW[g],this.azE[g],null,null)}else for(;--b>=c;++a,++g)f=this.axE[g]-(d=this.axW[g])+
1-c,1==c&&0>f&&(f=1,d--),0<f&&this.g3d.plotPixelsUnclippedRaster(f,d,a,this.azW[g],this.azE[g],null,null)},"~N,~N,~B,~N");c(c$,"fillRasterG",function(a,b,d,c){var g=0;0>a&&(b+=a,g-=a,a=0);a+b>this.g3d.height&&(b=this.g3d.height-a);if(d)for(;--b>=c;++a,++g){d=this.axW[g];var f=this.axE[g]-d+1-c;0<f&&this.g3d.plotPixelsClippedRaster(f,d,a,this.azW[g],this.azE[g],this.rgb16sW[g],this.rgb16sE[g])}else for(;--b>=c;++a,++g)f=this.axE[g]-(d=this.axW[g])+1-c,1==c&&0>f&&(f=1,d--),0<f&&this.g3d.plotPixelsUnclippedRaster(f,
d,a,this.azW[g],this.azE[g],this.rgb16sW[g],this.rgb16sE[g])},"~N,~N,~B,~N");C(c$,"DEFAULT",64)});n("J.i18n");w(["J.api.Translator","java.util.Hashtable","J.i18n.Language","$.Resource"],"J.i18n.GT",["java.text.MessageFormat","JU.Logger"],function(){c$=t(function(){this.resources=null;this.resourceCount=0;this.doTranslate=!0;this.language=null;s(this,arguments)},J.i18n,"GT",null,J.api.Translator);u(c$,function(){});h(c$,"translate",function(a){return J.i18n.GT._(a)},"~S");u(c$,function(a,b){J.i18n.GT.vwr=
a;this.resources=null;this.resourceCount=0;J.i18n.GT.$getTextWrapper=this;null!=b&&0==b.length&&(b="none");null!=b&&(this.language=b);"none".equals(this.language)&&(this.language=null);null==this.language&&(this.language=J.i18n.Resource.getLanguage());null==this.language&&(this.language="en");var d=this.language,c=null,g=null,f=this.language.indexOf("_");if(0<=f&&(d=d.substring(0,f),c=this.language,0<=(f=c.indexOf("_",++f))))c=c.substring(0,f),g=this.language;if(null==(this.language=this.getSupported(g))&&
null==(this.language=this.getSupported(c))&&null==(this.language=this.getSupported(d)))this.language="en",System.out.println(this.language+" not supported -- using en");else{c=g=null;switch(this.language.length){default:g=this.language;c=this.language.substring(0,5);d=this.language.substring(0,2);break;case 5:c=this.language;d=this.language.substring(0,2);break;case 2:d=this.language}c=this.getSupported(c);d=this.getSupported(d);if(d===c||"en_US".equals(d))d=null;c===g&&(c=null);"en_US".equals(c)||
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this.atomB,d,!0))},"JU.P3,JU.P3,~N,JU.P3i,JU.P3i,~B");c(c$,"drawTicks",function(a,b,d,c){Float.isNaN(this.tickInfo.first)&&(this.tickInfo.first=0);this.drawTicks2(a,b,this.tickInfo.ticks.x,8,d,!c?null:null==this.tickInfo.tickLabelFormats?["%0.2f"]:this.tickInfo.tickLabelFormats);this.drawTicks2(a,b,this.tickInfo.ticks.y,4,d,null);this.drawTicks2(a,b,this.tickInfo.ticks.z,2,d,null)},"JU.Point3fi,JU.Point3fi,~N,~B");c(c$,"drawTicks2",function(a,b,d,c,g,f){if(0!=d&&(this.g3d.isAntialiased()&&(c*=2),
this.vectorT2.set(b.sX,b.sY,0),this.vectorT.set(a.sX,a.sY,0),this.vectorT2.sub(this.vectorT),!(50>this.vectorT2.length()))){var j=this.tickInfo.signFactor;this.vectorT.sub2(b,a);var k=this.vectorT.length();if(null!=this.tickInfo.scale)if(Float.isNaN(this.tickInfo.scale.x)){var h=this.vwr.getUnitCellInfo(0);Float.isNaN(h)||this.vectorT.set(this.vectorT.x/h,this.vectorT.y/this.vwr.getUnitCellInfo(1),this.vectorT.z/this.vwr.getUnitCellInfo(2))}else this.vectorT.set(this.vectorT.x*this.tickInfo.scale.x,
this.vectorT.y*this.tickInfo.scale.y,this.vectorT.z*this.tickInfo.scale.z);h=this.vectorT.length()+1E-4*d;if(!(h<d)){this.vectorT.scale(d/h*k/h);b=(b.sZ-a.sZ)/(h/d);h+=this.tickInfo.first;k=q(Math.floor(this.tickInfo.first/d))*d-this.tickInfo.first;this.pointT.scaleAdd2(k/d,this.vectorT,a);k+=this.tickInfo.first;a=a.sZ;0>g&&(g=1);this.vectorT2.set(-this.vectorT2.y,this.vectorT2.x,0);this.vectorT2.scale(c/this.vectorT2.length());c=this.tickInfo.reference;null==c?(this.pointT3.setT(this.vwr.getBoundBoxCenter()),
this.vwr.g.axesMode===J.c.AXES.BOUNDBOX&&this.pointT3.add3(1,1,1)):this.pointT3.setT(c);this.tm.transformPtScr(this.pointT3,this.pt2i);c=0.2>Math.abs(this.vectorT2.x/this.vectorT2.y);for(var m=!c,r=!c&&0>this.vectorT2.x,x=null!=f&&0<f.length,A,I,n=Array(1),p=this.draw000?0:-1;k<h;){if(k>=this.tickInfo.first&&(this.pointT2.setT(this.pointT),this.tm.transformPt3f(this.pointT2,this.pointT2),this.drawLine(q(Math.floor(this.pointT2.x)),q(Math.floor(this.pointT2.y)),z(a),A=q(Math.floor(this.pointT2.x+this.vectorT2.x)),
I=q(Math.floor(this.pointT2.y+this.vectorT2.y)),z(a),g),x&&(this.draw000||0!=k))){n[0]=Float.$valueOf(0==k?0:k*j);var s=JU.Txt.sprintf(f[p%f.length],"f",n);this.drawString(A,I,z(a),4,r,c,m,q(Math.floor(this.pointT2.y)),s)}this.pointT.add(this.vectorT);k+=d;a+=b;p++}}}},"JU.Point3fi,JU.Point3fi,~N,~N,~N,~A");c(c$,"drawLine",function(a,b,d,c,g,f,j){return this.drawLine2(a,b,d,c,g,f,j)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawLine2",function(a,b,d,c,g,f,j){this.pt0i.set(a,b,d);this.pt1i.set(c,g,f);if(this.dotsOrDashes)null!=
this.dashDots&&this.drawDashed(a,b,d,c,g,f,this.dashDots);else{if(0>j)return this.g3d.drawDashedLine(4,2,this.pt0i,this.pt1i),1;this.g3d.fillCylinder(2,j,this.pt0i,this.pt1i)}return q((j+1)/2)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawString",function(a,b,d,c,g,f,j,k,h){if(null!=h){var m=this.font3d.stringWidth(h),r=this.font3d.getAscent();a=g?a-(q(c/2)+2+m):f?a-(q(c/2)+2+q(m/2)):a+(q(c/2)+2);g=b;g=j?g+q(r/2):0==k||k<b?g+r:g-q(c/2);b=d-c-2;1>b&&(b=1);this.g3d.drawString(h,this.font3d,a,g,b,b,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");
c(c$,"drawDashed",function(a,b,d,c,g,f,j){if(!(null==j||0>this.width)){var k=j[0];c-=a;g-=b;f-=d;var h=0,m=j===J.render.FontLineShapeRenderer.ndots,r=m||j===J.render.FontLineShapeRenderer.sixdots;if(r){var x=(c*c+g*g)/(this.width*this.width);m?(k=Math.sqrt(x)/1.5,h=z(k)+3):8>x?j=J.render.FontLineShapeRenderer.twodots:32>x&&(j=J.render.FontLineShapeRenderer.fourdots)}var x=j[1],A=j[2],I=this.colixA,n=0==A?this.colixB:this.colixA;0==h&&(h=j.length);for(var p=0,s=3;s<h;s++){var p=m?p+1:j[s],t=q(Math.floor(a+
c*p/k)),u=q(Math.floor(b+g*p/k)),v=q(Math.floor(d+f*p/k));if(r)this.s1.set(t,u,v),s==x?this.g3d.setC(this.colixA):s==A&&this.g3d.setC(this.colixB),this.g3d.fillSphereI(this.width,this.s1);else{s==x&&(I=this.colixB);p=j[++s];s==A&&(n=this.colixB);var w=q(Math.floor(a+c*p/k)),y=q(Math.floor(b+g*p/k)),B=q(Math.floor(d+f*p/k));this.fillCylinder(I,n,2,this.width,t,u,v,w,y,B)}}}},"~N,~N,~N,~N,~N,~N,~A");c(c$,"fillCylinder",function(a,b,d,c,g,f,j,k,h,m){this.asLineOnly?this.g3d.drawLine(a,b,g,f,j,k,h,m):
this.g3d.fillCylinderXYZ(a,b,d,!this.isExport||1==this.mad?c:this.mad,g,f,j,k,h,m)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");C(c$,"dashes",[12,0,0,2,5,7,10],"hDashes",[10,7,6,1,3,4,6,7,9],"ndots",[0,3,1E3],"sixdots",[12,3,6,1,3,5,7,9,11],"fourdots",[13,3,5,2,5,8,11],"twodots",[12,3,4,3,9])});n("J.render");w(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["JU.C"],function(){c$=B(J.render,"FrankRenderer",J.render.ShapeRenderer);h(c$,"render",function(){var a=this.shape,b=this.vwr.getBooleanProperty("allowKeyStrokes"),
d=this.vwr.getBoolean(603979883);this.colix=d?20:this.vwr.isSignedApplet()?b||this.vwr.isJS&&!this.vwr.isWebGL?5:10:b?7:12;if(this.isExport||!this.vwr.getShowFrank())return!1;if(!this.g3d.setC(JU.C.getColixTranslucent3(this.colix,this.g3d.haveTranslucentObjects(),0.5)))return!0;b=this.vwr.getImageFontScaling();a.getFont(b);var b=z(a.frankWidth+4*b),c=a.frankDescent;this.g3d.drawStringNoSlab(a.frankString,a.font3d,this.g3d.getRenderWidth()-b,this.g3d.getRenderHeight()-c,0,0);d&&this.g3d.fillRect(0,
0,0,0,2*c,q(3*b/2));return!1})});n("J.render");w(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["J.api.Interface","JU.Logger","JV.JC"],function(){c$=t(function(){this.bsTranslucent=this.renderers=this.shapeManager=this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;s(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);K(c$,function(){this.bsTranslucent=JU.BS.newN(36)});u(c$,function(){});h(c$,"set",function(a,b){this.vwr=a;this.shapeManager=b},"JV.Viewer,JV.ShapeManager");
h(c$,"isRepaintPending",function(){return this.repaintPending});h(c$,"pushHoldRepaint",function(){++this.holdRepaint},"~S");h(c$,"popHoldRepaint",function(a,b){--this.holdRepaint;0>=this.holdRepaint&&(this.holdRepaint=0,a&&(this.repaintPending=!0,this.repaintNow(b)))},"~B,~S");h(c$,"requestRepaintAndWait",function(){"undefined"!=typeof Jmol&&Jmol._repaint&&Jmol._repaint(this.vwr.html5Applet,!1);this.repaintDone()},"~S");h(c$,"repaintIfReady",function(a){if(this.repaintPending)return!1;this.repaintPending=
!0;0==this.holdRepaint&&this.repaintNow(a);return!0},"~S");c(c$,"repaintNow",function(){this.vwr.haveDisplay&&this.vwr.apiPlatform.repaint(this.vwr.getDisplay())},"~S");h(c$,"repaintDone",function(){this.repaintPending=!1});h(c$,"clear",function(a){if(null!=this.renderers)if(0<=a)this.renderers[a]=null;else for(a=0;36>a;++a)this.renderers[a]=null},"~N");c(c$,"getRenderer",function(a){if(null!=this.renderers[a])return this.renderers[a];var b=JV.JC.getShapeClassName(a,!0)+"Renderer";if(null==(b=J.api.Interface.getInterface(b)))return null;
b.setViewerG3dShapeID(this.vwr,a);return this.renderers[a]=b},"~N");h(c$,"render",function(a,b,d,c){var g=this.vwr.getBoolean(603979934);try{a.renderBackground(null);if(d){this.bsTranslucent.clearAll();null!=c&&a.renderCrossHairs(c,this.vwr.getScreenWidth(),this.vwr.getScreenHeight(),this.vwr.tm.getNavigationOffset(),this.vwr.tm.getNavigationDepthPercent());var f=this.vwr.getRubberBandSelection();null!=f&&a.setC(this.vwr.cm.colixRubberband)&&a.drawRect(f.x,f.y,0,0,f.width,f.height)}null==this.renderers&&
(this.renderers=Array(36));c=null;for(f=0;36>f&&a.currentlyRendering();++f){var j=this.shapeManager.getShape(f);null!=j&&(g&&(c="rendering "+JV.JC.getShapeClassName(f,!1),JU.Logger.startTimer(c)),(d||this.bsTranslucent.get(f))&&this.getRenderer(f).renderShape(a,b,j)&&this.bsTranslucent.set(f),g&&JU.Logger.checkTimer(c,!1))}a.renderAllStrings(null)}catch(k){if(y(k,Exception))this.vwr.isJS||k.printStackTrace(),JU.Logger.error("rendering error? "+k);else throw k;}},"JU.GData,JM.ModelSet,~B,~A");h(c$,
"renderExport",function(a,b,d){a=this.vwr.getBoolean(603979934);this.vwr.finalizeTransformParameters();this.shapeManager.finalizeAtoms(null,null);var c=this.vwr.initializeExporter(d);if(null==c)return JU.Logger.error("Cannot export "+d.get("type")),null;c.renderBackground(c);null==this.renderers&&(this.renderers=Array(36));d=null;for(var g=0;36>g;++g){var f=this.shapeManager.getShape(g);null!=f&&(a&&(d="rendering "+JV.JC.getShapeClassName(g,!1),JU.Logger.startTimer(d)),this.getRenderer(g).renderShape(c,
b,f),a&&JU.Logger.checkTimer(d,!1))}c.renderAllStrings(c);return c.finalizeOutput()},"JU.GData,JM.ModelSet,java.util.Map")});n("J.render");w(null,"J.render.ShapeRenderer",["JV.JC"],function(){c$=t(function(){this.shape=this.ms=this.g3d=this.tm=this.vwr=null;this.exportType=this.madEnd=this.madMid=this.madBeg=this.mad=this.colix=this.shapeID=this.myVisibilityFlag=0;this.isExport=!1;s(this,arguments)},J.render,"ShapeRenderer");c(c$,"initRenderer",function(){});c(c$,"setViewerG3dShapeID",function(a,
b){this.vwr=a;this.tm=a.tm;this.shapeID=b;this.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(b);this.initRenderer()},"JV.Viewer,~N");c(c$,"renderShape",function(a,b,d){this.g3d=a;this.ms=b;this.shape=d;this.exportType=a.getExportType();this.isExport=0!=this.exportType;a=this.render();this.exportType=0;this.isExport=!1;return a},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");c(c$,"isVisibleForMe",function(a){return a.isVisible(this.myVisibilityFlag|9)},"JM.Atom")});n("J.render");w(["J.render.FontLineShapeRenderer",
"JU.BS","$.P3","$.V3"],"J.render.SticksRenderer",["java.lang.Float","J.c.PAL","JM.Bond","JU.C","$.Edge"],function(){c$=t(function(){this.showMultipleBonds=!1;this.modeMultipleBond=this.multipleBondRadiusFactor=this.multipleBondSpacing=0;this.isCartesianExport=!1;this.endcaps=0;this.hbondsSolid=this.bondsBackbone=this.hbondsBackbone=this.ssbondsBackbone=!1;this.bond=this.b=this.a=null;this.bondOrder=this.mag2d=this.dy=this.dx=this.zB=this.yB=this.xB=this.zA=this.yA=this.xA=0;this.slabByAtom=this.slabbing=
this.isAntialiased=this.wireframeOnly=!1;this.bsForPass2=this.p2=this.p1=this.z=this.y=this.x=null;this.isPass2=!1;this.dyStep=this.dxStep=this.yAxis2=this.xAxis2=this.yAxis1=this.xAxis1=0;s(this,arguments)},J.render,"SticksRenderer",J.render.FontLineShapeRenderer);K(c$,function(){this.x=new JU.V3;this.y=new JU.V3;this.z=new JU.V3;this.p1=new JU.P3;this.p2=new JU.P3;this.bsForPass2=JU.BS.newN(64)});h(c$,"render",function(){var a=this.ms.bo;if(null==a)return!1;(this.isPass2=this.g3d.isPass2())||this.bsForPass2.clearAll();
this.slabbing=this.tm.slabEnabled;this.slabByAtom=this.vwr.getBoolean(603979939);this.endcaps=3;this.dashDots=this.vwr.getBoolean(603979889)?J.render.FontLineShapeRenderer.sixdots:J.render.FontLineShapeRenderer.dashes;this.isCartesianExport=1==this.exportType;this.getMultipleBondSettings(!1);this.wireframeOnly=!this.vwr.checkMotionRendering(1678770178);this.ssbondsBackbone=this.vwr.getBoolean(603979952);this.hbondsBackbone=this.vwr.getBoolean(603979852);this.bondsBackbone=(new Boolean(this.hbondsBackbone|
this.ssbondsBackbone)).valueOf();this.hbondsSolid=this.vwr.getBoolean(603979854);this.isAntialiased=this.g3d.isAntialiased();var b=!1;if(!this.isExport&&this.isPass2)for(var d=this.bsForPass2.nextSetBit(0);0<=d;d=this.bsForPass2.nextSetBit(d+1))this.bond=a[d],this.renderBond();else for(d=this.ms.bondCount;0<=--d;)this.bond=a[d],0!=(this.bond.getShapeVisibilityFlags()&this.myVisibilityFlag)&&this.renderBond()&&(b=!0,this.bsForPass2.set(d));return b});c(c$,"getMultipleBondSettings",function(a){this.multipleBondSpacing=
a?0.15:this.vwr.getFloat(570425370);this.multipleBondRadiusFactor=a?0.4:this.vwr.getFloat(570425369);0==this.multipleBondSpacing&&this.isCartesianExport&&(this.multipleBondSpacing=0.2);this.modeMultipleBond=this.vwr.g.modeMultipleBond;this.showMultipleBonds=0!=this.multipleBondSpacing&&0!=this.modeMultipleBond&&this.vwr.getBoolean(603979928)},"~B");c(c$,"renderBond",function(){var a,b;this.a=a=this.bond.getAtom1();this.b=b=this.bond.getAtom2();var d=this.bond.order&-131073;this.bondsBackbone&&(this.ssbondsBackbone&&
0!=(d&256)?(this.a=this.a.getGroup().getLeadAtomOr(this.a),this.b=this.b.getGroup().getLeadAtomOr(this.b)):this.hbondsBackbone&&JM.Bond.isOrderH(d)&&(this.a=this.a.getGroup().getLeadAtomOr(this.a),this.b=this.b.getGroup().getLeadAtomOr(this.b)));if(!this.isPass2&&(!this.a.isVisible(9)||!this.b.isVisible(9)||!this.g3d.isInDisplayRange(this.a.sX,this.a.sY)||!this.g3d.isInDisplayRange(this.b.sX,this.b.sY))||this.slabbing&&(this.g3d.isClippedZ(this.a.sZ)&&this.g3d.isClippedZ(this.b.sZ)||this.slabByAtom&&
(this.g3d.isClippedZ(this.a.sZ)||this.g3d.isClippedZ(this.b.sZ))))return!1;this.zA=this.a.sZ;this.zB=this.b.sZ;if(1==this.zA||1==this.zB)return!1;this.colixA=a.getColix();this.colixB=b.getColix();2==((this.colix=this.bond.colix)&-30721)?(this.colix&=30720,this.colixA=JU.C.getColixInherited(this.colix|this.vwr.getColixAtomPalette(a,J.c.PAL.CPK.id),this.colixA),this.colixB=JU.C.getColixInherited(this.colix|this.vwr.getColixAtomPalette(b,J.c.PAL.CPK.id),this.colixB)):(this.colixA=JU.C.getColixInherited(this.colix,
this.colixA),this.colixB=JU.C.getColixInherited(this.colix,this.colixB));a=!1;if(!this.isExport&&!this.isPass2){b=!JU.C.isColixTranslucent(this.colixA);var c=!JU.C.isColixTranslucent(this.colixB);if(!b||!c){if(!b&&!c&&!a)return this.g3d.setC(!b?this.colixA:this.colixB),!0;a=!0}}this.bondOrder=d&-131073;if(0==(this.bondOrder&224)&&(0!=(this.bondOrder&256)&&(this.bondOrder&=-257),0!=(this.bondOrder&1023)&&(!this.showMultipleBonds||2==this.modeMultipleBond&&500<this.mad||65536==(this.bondOrder&98304))))this.bondOrder=
1;b=0;switch(this.bondOrder){case 1:case 2:case 3:case 4:break;case 17:case 513:this.bondOrder=1;b=513==d?0:1;break;case 515:case 514:this.bondOrder=2;b=515==d?this.getAromaticDottedBondMask():0;break;default:0!=(this.bondOrder&224)?(this.bondOrder=JU.Edge.getPartialBondOrder(d),b=JU.Edge.getPartialBondDotted(d)):JM.Bond.isOrderH(this.bondOrder)?(this.bondOrder=1,this.hbondsSolid||(b=-1)):32768==this.bondOrder?this.bondOrder=1:98304==(this.bondOrder&98304)&&(this.getMultipleBondSettings(!0),this.bondOrder&=
3,b=-2)}this.xA=this.a.sX;this.yA=this.a.sY;this.xB=this.b.sX;this.yB=this.b.sY;this.mad=this.bond.mad;0<this.multipleBondRadiusFactor&&1<this.bondOrder&&(this.mad*=this.multipleBondRadiusFactor);this.dx=this.xB-this.xA;this.dy=this.yB-this.yA;this.width=z(this.vwr.tm.scaleToScreen(q((this.zA+this.zB)/2),this.mad));this.wireframeOnly&&0<this.width&&(this.width=1);if(!this.isCartesianExport&&(this.asLineOnly=1>=this.width)&&this.isAntialiased)this.width=3,this.asLineOnly=!1;switch(b){case -2:this.drawBond(0);
this.getMultipleBondSettings(!1);break;case -1:this.drawDashed(this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,J.render.FontLineShapeRenderer.hDashes);break;default:this.drawBond(b)}return a});c(c$,"drawBond",function(a){if(this.isCartesianExport&&1==this.bondOrder)this.g3d.drawBond(this.a,this.b,this.colixA,this.colixB,this.endcaps,this.mad,-1);else{var b=0==this.dx&&0==this.dy;if(!b||!this.asLineOnly){var d=1<this.bondOrder&&0<this.multipleBondSpacing,c=d&&(null!=this.vwr.getHybridizationAndAxes(this.a.i,
this.z,this.x,"pz")||null!=this.vwr.getHybridizationAndAxes(this.b.i,this.z,this.x,"pz"))&&!Float.isNaN(this.x.x);if(b&&!d){a=q(this.width/8)+3;a=this.width+a;d=this.yA-q((this.bondOrder-1)*a/2);do this.fillCylinder(this.colixA,this.colixA,this.endcaps,this.width,this.xA,d,this.zA,this.xA,d,this.zA),d+=a;while(0<--this.bondOrder)}else if(b=0!=(a&1),1==this.bondOrder)b?this.drawDashed(this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,this.dashDots):this.fillCylinder(this.colixA,this.colixB,this.endcaps,
this.width,this.xA,this.yA,this.zA,this.xB,this.yB,this.zB);else if(d){c||this.z.set(3.141592653589793,2.718281828459045,8.539734222673566);this.x.sub2(this.b,this.a);this.y.cross(this.x,this.z);this.y.normalize();Float.isNaN(this.y.x)&&(this.z.set(3.141592653589793,2.718281828459045,8.539734222673566),this.y.cross(this.x,this.z),this.y.cross(this.y,this.x),this.y.normalize());this.y.scale(this.multipleBondSpacing);this.x.setT(this.y);this.x.scale((this.bondOrder-1)/2);this.p1.sub2(this.a,this.x);
for(this.p2.sub2(this.b,this.x);;){this.isCartesianExport&&!b?this.g3d.drawBond(this.p1,this.p2,this.colixA,this.colixB,this.endcaps,this.mad,-2):(this.tm.transformPtScr(this.p1,this.s1),this.tm.transformPtScr(this.p2,this.s2),b?this.drawDashed(this.s1.x,this.s1.y,this.s1.z,this.s2.x,this.s2.y,this.s2.z,this.dashDots):this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.s1.x,this.s1.y,this.s1.z,this.s2.x,this.s2.y,this.s2.z),a>>=1,b=0!=(a&1));if(0>=--this.bondOrder)break;this.p1.add(this.y);
this.p2.add(this.y);this.stepAxisCoordinates()}}else{this.mag2d=Math.round(Math.sqrt(this.dx*this.dx+this.dy*this.dy));for(this.resetAxisCoordinates();;){0!=(a&1)?this.drawDashed(this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,this.dashDots):this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB);a>>=1;if(0>=--this.bondOrder)break;this.stepAxisCoordinates()}}}}},"~N");c(c$,"resetAxisCoordinates",function(){var a=
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(this.bsColixSet=new JU.BS);null==this.bsSizeSet&&(this.bsSizeSet=new JU.BS);b=d.nextSetBit(0);null==this.mads&&0<=b&&(this.mads=T(this.ac,0));for(var k=0;0<=b;b=d.nextSetBit(b+1),k++){c=null==a?0:a[k];0==c&&(c=0);var h=null==g?0:g[k];0.01<h&&(c=JU.C.getColixTranslucent3(c,!0,h));this.setColixAndPalette(c,J.c.PAL.UNKNOWN.id,b);null!=f&&(c=0<(j.value=f[k]),this.setSizeRD2(b,j,c))}}else if("translucency"===a){this.isActive=!0;a=b.equals("translucent");null==this.bsColixSet&&(this.bsColixSet=new JU.BS);
for(b=d.nextSetBit(0);0<=b;b=d.nextSetBit(b+1))null==this.colixes&&(this.colixes=T(this.ac,0),this.paletteIDs=O(this.ac,0)),this.colixes[b]=JU.C.getColixTranslucent3(this.colixes[b],a,this.translucentLevel),a&&this.bsColixSet.set(b)}else"deleteModelAtoms"===a?(this.atoms=b[1],a=b[2],this.ac=this.ms.getAtomCount(),b=a[1],a=a[2],this.mads=JU.AU.deleteElements(this.mads,b,a),this.colixes=JU.AU.deleteElements(this.colixes,b,a),this.paletteIDs=JU.AU.deleteElements(this.paletteIDs,b,a),JU.BSUtil.deleteBits(this.bsSizeSet,
d),JU.BSUtil.deleteBits(this.bsColixSet,d)):this.setPropS(a,b,d)},"~S,~O,JU.BS");c(c$,"setColixAndPalette",function(a,b,d){if(null==this.colixes||d>=this.colixes.length){if(0==a)return;this.colixes=JU.AU.ensureLengthShort(this.colixes,d+1);this.paletteIDs=JU.AU.ensureLengthByte(this.paletteIDs,d+1)}null==this.bsColixSet&&(this.bsColixSet=JU.BS.newN(this.ac));this.colixes[d]=a=this.getColixI(a,b,d);this.bsColixSet.setBitTo(d,0!=a);this.paletteIDs[d]=b},"~N,~N,~N");h(c$,"setModelClickability",function(){if(this.isActive)for(var a=
this.ac;0<=--a;){var b=this.atoms[a];0==(b.shapeVisibilityFlags&this.vf)||this.ms.isAtomHidden(a)||b.setClickable(this.vf)}});h(c$,"getShapeState",function(){return this.isActive?this.vwr.getAtomShapeState(this):""});c(c$,"getInfoAsString",function(){return null},"~N")});n("J.shape");w(["J.shape.AtomShape"],"J.shape.Balls",["JU.BS","J.c.PAL","JU.C"],function(){c$=B(J.shape,"Balls",J.shape.AtomShape);h(c$,"setSize",function(a,b){2147483647==a?(this.isActive=!0,null==this.bsSizeSet&&(this.bsSizeSet=
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for(a=d.nextSetBit(0);0<=a;a=d.nextSetBit(a+1)){var f=this.atoms[a];f.setColixAtom(this.getColixA(c,g,f));this.bsColixSet.setBitTo(a,2!=c||g!=J.c.PAL.NONE.id);f.setPaletteID(g)}}else if("colorValues"===a){if(0!=b.length){null==this.bsColixSet&&(this.bsColixSet=new JU.BS);var j=0,g=null;for(a=d.nextSetBit(0);0<=a&&!(j>=b.length);a=d.nextSetBit(a+1))g=Integer.$valueOf(b[j++]),c=JU.C.getColixO(g),0==c&&(c=2),g=J.c.PAL.pidOf(g),f=this.atoms[a],f.setColixAtom(this.getColixA(c,g,f)),this.bsColixSet.setBitTo(a,
2!=c||g!=J.c.PAL.NONE.id),f.setPaletteID(g)}}else if("colors"===a){b=b[0];null==this.bsColixSet&&(this.bsColixSet=new JU.BS);for(a=d.nextSetBit(0);0<=a;a=d.nextSetBit(a+1))a>=b.length||(this.atoms[a].setColixAtom(b[a]),this.atoms[a].setPaletteID(J.c.PAL.UNKNOWN.id),this.bsColixSet.set(a))}else if("translucency"===a){b=b.equals("translucent");null==this.bsColixSet&&(this.bsColixSet=new JU.BS);for(a=d.nextSetBit(0);0<=a;a=d.nextSetBit(a+1))this.atoms[a].setTranslucent(b,this.translucentLevel),b&&this.bsColixSet.set(a)}else a.startsWith("ball")&&
(a=a.substring(4).intern()),this.setPropAS(a,b,d)},"~S,~O,JU.BS");h(c$,"setModelClickability",function(){for(var a=this.vwr.getDeletedAtoms(),b=this.ac;0<=--b;){var d=this.atoms[b];d.setClickable(0);null!=a&&a.get(b)||(0==(d.shapeVisibilityFlags&this.vf)||this.ms.isAtomHidden(b))||d.setClickable(this.vf)}});h(c$,"getShapeState",function(){return this.vwr.getShapeState(this)})});n("J.shape");w(["J.shape.FontShape"],"J.shape.FontLineShape",null,function(){c$=t(function(){this.tickInfos=null;this.mad=
0;s(this,arguments)},J.shape,"FontLineShape",J.shape.FontShape);K(c$,function(){this.tickInfos=Array(4)});c(c$,"setPropFLS",function(a,b){"tickInfo"===a?null==b.ticks?b.type.equals(" ")?this.tickInfos[0]=this.tickInfos[1]=this.tickInfos[2]=this.tickInfos[3]=null:this.tickInfos["xyz".indexOf(b.type)+1]=null:this.tickInfos["xyz".indexOf(b.type)+1]=b:this.setPropFS(a,b)},"~S,~O");h(c$,"getShapeState",function(){var a=this.vwr.getFontState(this.myType,this.font3d);return null==this.tickInfos?a:this.vwr.getFontLineShapeState(a,
this.myType,this.tickInfos)})});n("J.shape");w(["J.shape.Shape"],"J.shape.FontShape",null,function(){c$=t(function(){this.font3d=this.myType=null;s(this,arguments)},J.shape,"FontShape",J.shape.Shape);h(c$,"initShape",function(){this.translucentAllowed=!1});c(c$,"setPropFS",function(a,b){"font"===a&&(this.font3d=b)},"~S,~O")});n("J.shape");w(["J.shape.FontShape"],"J.shape.Frank",["J.i18n.GT"],function(){c$=t(function(){this.frankString="Jmol";this.baseFont3d=this.currentMetricsFont3d=null;this.dy=
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4&&b>c-this.frankAscent-4},"~N,~N");h(c$,"checkObjectHovered",function(a,b){if(!this.vwr.getShowFrank()||!this.wasClicked(a,b)||!this.vwr.menuEnabled())return!1;this.gdata.isDisplayAntialiased()&&!this.vwr.isSingleThreaded&&(a<<=1,b<<=1);this.vwr.hoverOnPt(a,b,J.i18n.GT._("Click for menu..."),null,null);return!0},"~N,~N,JU.BS");c(c$,"calcMetrics",function(){this.vwr.isJS?this.frankString="JSmol":this.vwr.isSignedApplet()&&(this.frankString="Jmol_S");this.font3d!==this.currentMetricsFont3d&&(this.currentMetricsFont3d=
this.font3d,this.frankWidth=this.font3d.stringWidth(this.frankString),this.frankDescent=this.font3d.getDescent(),this.frankAscent=this.font3d.getAscent())});c(c$,"getFont",function(a){this.font3d=this.gdata.getFont3DScaled(this.baseFont3d,a);this.calcMetrics()},"~N");h(c$,"getShapeState",function(){return this.vwr.getFontState(this.myType,this.font3d)});C(c$,"defaultFontName","SansSerif","defaultFontStyle","Plain","defaultFontSize",16,"frankMargin",4)});n("J.shape");w(null,"J.shape.Shape",["J.c.PAL",
"JU.C","$.Logger","JV.JC"],function(){c$=t(function(){this.gdata=this.ms=this.vwr=null;this.translucentLevel=this.vf=this.shapeID=0;this.translucentAllowed=!0;this.isBioShape=!1;this.bsColixSet=this.bsSizeSet=null;s(this,arguments)},J.shape,"Shape");c(c$,"getViewer",function(){return this.vwr});c(c$,"initializeShape",function(a,b,d,c){this.vwr=a;this.gdata=b;this.shapeID=c;this.vf=JV.JC.getShapeVisibilityFlag(c);this.setModelSet(d);this.initShape()},"JV.Viewer,JU.GData,JM.ModelSet,~N");c(c$,"setVisibilityFlags",
function(){},"JU.BS");c(c$,"getSize",function(){return 0},"~N");c(c$,"getSizeG",function(){return 0},"JM.Group");c(c$,"setModelSet",function(a){this.ms=a;this.initModelSet()},"JM.ModelSet");c(c$,"initModelSet",function(){});c(c$,"setShapeVisibility",function(a,b){a.setShapeVisibility(this.vf,b)},"JM.Atom,~B");c(c$,"initShape",function(){});c(c$,"merge",function(){},"J.shape.Shape");c(c$,"setShapeSizeRD",function(a,b,d){null==b?this.setSize(a,d):this.setSizeRD(b,d)},"~N,J.atomdata.RadiusData,JU.BS");
c(c$,"setSize",function(){},"~N,JU.BS");c(c$,"setSizeRD",function(){},"J.atomdata.RadiusData,JU.BS");c(c$,"getPropertyData",function(){return!1},"~S,~A");c(c$,"setPropS",function(a,b,d){if("setProperties"===a)for(null==d&&(d=this.vwr.bsA());0<b.size();)a=b.remove(0),this.setProperty(a[0].intern(),a[1],d);else"translucentLevel"===a?this.translucentLevel=b.floatValue():"refreshTrajectories"!==a&&JU.Logger.warn("unassigned "+JV.JC.shapeClassBases[this.shapeID]+" + shape setProperty:"+a+":"+b)},"~S,~O,JU.BS");
c(c$,"getProperty",function(){return null},"~S,~N");c(c$,"getIndexFromName",function(){return-1},"~S");c(c$,"wasClicked",function(){return!1},"~N,~N");c(c$,"findNearestAtomIndex",function(){},"~N,~N,~A,JU.BS");c(c$,"checkBoundsMinMax",function(){},"JU.P3,JU.P3");c(c$,"setModelClickability",function(){});c(c$,"checkObjectClicked",function(){return null},"~N,~N,~N,JU.BS,~B");c(c$,"checkObjectHovered",function(){return!1},"~N,~N,JU.BS");c(c$,"checkObjectDragged",function(){return!1},"~N,~N,~N,~N,~N,JU.BS");
c(c$,"coordinateInRange",function(a,b,d,c,g){this.vwr.tm.transformPtScr(d,g);a=(a-g.x)*(a-g.x)+(b-g.y)*(b-g.y);return a<c?a:-1},"~N,~N,JU.T3,~N,JU.P3i");c(c$,"getColixI",function(a,b,d){return this.getColixA(a,b,this.ms.at[d])},"~N,~N,~N");c(c$,"getColixA",function(a,b,d){return 2==a?this.vwr.getColixAtomPalette(d,b):a},"~N,~N,JM.Atom");c(c$,"getColixB",function(a,b,d){return 2==a?this.vwr.getColixBondPalette(d,b):a},"~N,~N,JM.Bond");c(c$,"getShapeDetail",function(){return null});c$.getColix=c(c$,
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0==d?"":(c?J.shape.Shape.getTranslucentLabel(d)+" ":"")+(b!=J.c.PAL.UNKNOWN.id&&!J.c.PAL.isPaletteVariable(b)?J.c.PAL.getPaletteName(b):J.shape.Shape.encodeColor(d));return"color "+a+" "+b},"~S,~N,~N,~B");c$.encodeColor=c(c$,"encodeColor",function(a){return JU.C.isColixColorInherited(a)?"none":JU.C.getHexCode(a)},"~N");c$.getTranslucentLabel=c(c$,"getTranslucentLabel",function(a){return JU.C.isColixTranslucent(a)?"translucent "+JU.C.getColixTranslucencyFractional(a):"opaque"},"~N");c$.appendCmd=c(c$,
"appendCmd",function(a,b){0!=b.length&&a.append("  ").append(b).append(";\n")},"JU.SB,~S");C(c$,"RADIUS_MAX",4)});n("J.shape");w(["J.shape.Shape","JU.P3i"],"J.shape.Sticks","java.util.Hashtable JU.BS $.P3 J.c.PAL JU.BSUtil $.C $.Edge $.Escape".split(" "),function(){c$=t(function(){this.myMask=0;this.reportAll=!1;this.ptXY=this.selectedBonds=this.bsOrderSet=null;s(this,arguments)},J.shape,"Sticks",J.shape.Shape);K(c$,function(){this.ptXY=new JU.P3i});c(c$,"initShape",function(){R(this,J.shape.Sticks,
"initShape",[]);this.myMask=1023;this.reportAll=!1});h(c$,"setSize",function(a,b){if(2147483647==a)this.selectedBonds=JU.BSUtil.copy(b);else if(-2147483648==a)null==this.bsOrderSet&&(this.bsOrderSet=new JU.BS),this.bsOrderSet.or(b);else{null==this.bsSizeSet&&(this.bsSizeSet=new JU.BS);for(var d=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,b);d.hasNext();)this.bsSizeSet.set(d.nextIndex()),d.next().setMad(a)}},"~N,JU.BS");h(c$,"setProperty",
function(a,b,d){if("type"===a)this.myMask=b.intValue();else if("reportAll"===a)this.reportAll=!0;else if("reset"===a)this.selectedBonds=this.bsColixSet=this.bsSizeSet=this.bsOrderSet=null;else if("bondOrder"===a){null==this.bsOrderSet&&(this.bsOrderSet=new JU.BS);a=b.shortValue();for(d=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(65535,d);d.hasNext();)this.bsOrderSet.set(d.nextIndex()),d.next().setOrder(a)}else if("color"===a)if(null==this.bsColixSet&&
(this.bsColixSet=new JU.BS),a=JU.C.getColixO(b),b=p(b,J.c.PAL)?b:null,b===J.c.PAL.TYPE||b===J.c.PAL.ENERGY){var c=b===J.c.PAL.ENERGY;for(d=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,d);d.hasNext();){this.bsColixSet.set(d.nextIndex());var g=d.next();c?(g.setColix(this.getColixB(a,b.id,g)),g.setPaletteID(b.id)):g.setColix(JU.C.getColix(JU.Edge.getArgbHbondType(g.order)))}}else{if(!(2==a&&b!==J.c.PAL.CPK))for(d=null!=this.selectedBonds?
this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,d);d.hasNext();)b=d.nextIndex(),g=d.next(),g.setColix(a),this.bsColixSet.setBitTo(b,0!=a&&2!=a)}else if("translucency"===a){null==this.bsColixSet&&(this.bsColixSet=new JU.BS);a=b.equals("translucent");for(d=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,d);d.hasNext();)this.bsColixSet.set(d.nextIndex()),d.next().setTranslucent(a,this.translucentLevel)}else"deleteModelAtoms"!==
a&&this.setPropS(a,b,d)},"~S,~O,JU.BS");h(c$,"getProperty",function(a){return a.equals("selectionState")?null!=this.selectedBonds?"select BONDS "+JU.Escape.eBS(this.selectedBonds)+"\n":"":a.equals("sets")?[this.bsOrderSet,this.bsSizeSet,this.bsColixSet]:null},"~S,~N");h(c$,"setModelClickability",function(){for(var a=this.ms.bo,b=this.ms.bondCount;0<=--b;){var d=a[b];0==(d.getShapeVisibilityFlags()&this.vf)||(this.ms.isAtomHidden(d.getAtomIndex1())||this.ms.isAtomHidden(d.getAtomIndex2()))||(d.getAtom1().setClickable(this.vf),
d.getAtom2().setClickable(this.vf))}});h(c$,"getShapeState",function(){return this.vwr.getBondState(this,this.bsOrderSet,this.reportAll)});h(c$,"checkObjectHovered",function(a,b,d){var c=new JU.P3;a=this.findPickedBond(a,b,d,c);if(null==a)return!1;this.vwr.highlightBond(a.index,!0);return!0},"~N,~N,JU.BS");h(c$,"checkObjectClicked",function(a,b,d,c){d=new JU.P3;a=this.findPickedBond(a,b,c,d);if(null==a)return null;b=a.getAtom1().mi;c=a.getIdentity();var g=new java.util.Hashtable;g.put("pt",d);g.put("index",
Integer.$valueOf(a.index));g.put("modelIndex",Integer.$valueOf(b));g.put("model",this.vwr.getModelNumberDotted(b));g.put("type","bond");g.put("info",c);this.vwr.setStatusAtomPicked(-3,'["bond","'+a.getIdentity()+'",'+d.x+","+d.y+","+d.z+"]",g);return g},"~N,~N,~N,JU.BS,~B");c(c$,"findPickedBond",function(a,b,d,c){d=100;this.gdata.isAntialiased()&&(a<<=1,b<<=1,d<<=1);for(var g=null,f=new JU.P3,j=this.ms.bo,k=this.ms.bondCount;0<=--k;){var h=j[k];if(0!=h.getShapeVisibilityFlags()){var m=h.getAtom1(),
r=h.getAtom2();if(m.checkVisible()&&r.checkVisible()){f.ave(m,r);var x=this.coordinateInRange(a,b,f,d,this.ptXY);0<=x&&(m=1*(this.ptXY.x-m.sX)/(r.sX-m.sX),0.4>m||0.6<m||(d=x,g=h,c.setT(f)))}}}return g},"~N,~N,JU.BS,JU.P3");C(c$,"MAX_BOND_CLICK_DISTANCE_SQUARED",100)});n("J.thread");w(["J.thread.JmolThread"],"J.thread.HoverWatcherThread",["java.lang.Thread"],function(){c$=t(function(){this.moved=this.current=this.actionManager=null;this.hoverDelay=0;s(this,arguments)},J.thread,"HoverWatcherThread",
J.thread.JmolThread);u(c$,function(a,b,d,c){E(this,J.thread.HoverWatcherThread);this.setViewer(c,"HoverWatcher");this.actionManager=a;this.current=b;this.moved=d;this.start()},"JV.ActionManager,JV.MouseState,JV.MouseState,JV.Viewer");h(c$,"run1",function(a){for(;;)switch(a){case -1:this.isJS||Thread.currentThread().setPriority(1);a=0;break;case 0:this.hoverDelay=this.vwr.getHoverDelay();if(this.stopped||0>=this.hoverDelay||!this.runSleep(this.hoverDelay,1))return;a=1;break;case 1:this.moved.is(this.current)&&
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c(c$,"getIdentityXYZ",function(a,b){b=this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!1,b):this;return this.getIdentity(a)+" "+b.x+" "+b.y+" "+b.z},"~B,JU.P3");c(c$,"getIdentity",function(a){var b=new JU.SB,d=this.getGroup3(!0);if(null!=d&&0<d.length){b.append("[");b.append(d);b.append("]");d=this.getSeqcodeString();null!=d&&b.append(d);d=this.getChainID();if(0!=d&&32!=d){b.append(":");var c=this.getChainIDStr();256<=d&&(c=JU.PT.esc(c));b.append(c)}if(!a)return b.toString();b.append(".")}b.append(this.getAtomName());
0==b.length()&&(b.append(this.getElementSymbolIso(!1)),b.append(" "),b.appendI(this.getAtomNumber()));0!=this.altloc.charCodeAt(0)&&(b.append("%"),b.appendC(this.altloc));1<this.group.chain.model.ms.mc&&(b.append("/"),b.append(this.getModelNumberForLabel()));b.append(" #");b.appendI(this.getAtomNumber());return b.toString()},"~B");h(c$,"getGroup3",function(a){var b=this.group.getGroup3();return a||null!=b&&0<b.length?b:"UNK"},"~B");h(c$,"getGroup1",function(a){var b=this.group.getGroup1();return"\x00"!=
b?""+b:"\x00"!=a?""+a:""},"~S");h(c$,"isProtein",function(){return this.group.isProtein()});c(c$,"isCarbohydrate",function(){return this.group.isCarbohydrate()});h(c$,"isNucleic",function(){return this.group.isNucleic()});h(c$,"isDna",function(){return this.group.isDna()});h(c$,"isRna",function(){return this.group.isRna()});h(c$,"isPurine",function(){return this.group.isPurine()});h(c$,"isPyrimidine",function(){return this.group.isPyrimidine()});c(c$,"getSeqcode",function(){return this.group.seqcode});
h(c$,"getResno",function(){return this.group.getResno()});c(c$,"isClickable",function(){return this.checkVisible()&&0!=this.clickabilityFlags&&0!=((this.shapeVisibilityFlags|this.group.shapeVisibilityFlags)&this.clickabilityFlags)});c(c$,"setClickable",function(a){0==a?this.clickabilityFlags=0:(this.clickabilityFlags|=a,this.shapeVisibilityFlags|=a)},"~N");c(c$,"checkVisible",function(){if(this.isVisible(2))return this.isVisible(4);var a=this.isVisible(9);if(a){a=this.shapeVisibilityFlags;if(0!=this.group.shapeVisibilityFlags&&
(8192!=this.group.shapeVisibilityFlags||this.isLeadAtom()))a|=this.group.shapeVisibilityFlags;a&=-10;32==a&&0==this.clickabilityFlags&&(a=0);if(a=0!=a)this.shapeVisibilityFlags|=4}this.shapeVisibilityFlags|=2;return a});h(c$,"isLeadAtom",function(){return this.group.isLeadAtom(this.i)});c(c$,"getGroupParameter",function(a){return this.group.getGroupParameter(a)},"~N");h(c$,"getChainID",function(){return this.group.chain.chainID});h(c$,"getChainIDStr",function(){return this.group.chain.getIDStr()});
c(c$,"getSurfaceDistance100",function(){return this.group.chain.model.ms.getSurfaceDistance100(this.i)});c(c$,"getVibrationVector",function(){return this.group.chain.model.ms.getVibration(this.i,!1)});c(c$,"getVibrationCoord",function(a){return this.group.chain.model.ms.getVibrationCoord(this.i,a)},"~S");c(c$,"getPolymerLength",function(){return this.group.getBioPolymerLength()});c(c$,"getPolymerIndexInModel",function(){return this.group.getBioPolymerIndexInModel()});c(c$,"getMonomerIndex",function(){return this.group.getMonomerIndex()});
c(c$,"getSelectedGroupCountWithinChain",function(){return this.group.chain.selectedGroupCount});c(c$,"getSelectedGroupIndexWithinChain",function(){return this.group.getSelectedGroupIndex()});c(c$,"getSelectedMonomerCountWithinPolymer",function(){return this.group.getSelectedMonomerCount()});c(c$,"getSelectedMonomerIndexWithinPolymer",function(){return this.group.getSelectedMonomerIndex()});c(c$,"getChain",function(){return this.group.chain});c(c$,"getModelNumberForLabel",function(){return this.group.chain.model.ms.getModelNumberForAtomLabel(this.mi)});
c(c$,"getModelNumber",function(){return this.group.chain.model.ms.getModelNumber(this.mi)%1E6});c(c$,"getModelFileIndex",function(){return this.group.chain.model.fileIndex});c(c$,"getModelFileNumber",function(){return this.group.chain.model.ms.getModelFileNumber(this.mi)});h(c$,"getBioStructureTypeName",function(){return this.getProteinStructureType().getBioStructureTypeName(!0)});c(c$,"getProteinStructureType",function(){return this.group.getProteinStructureType()});c(c$,"getProteinStructureSubType",
function(){return this.group.getProteinStructureSubType()});c(c$,"getStrucNo",function(){return this.group.getStrucNo()});c(c$,"getStructureId",function(){return this.group.getStructureId()});c(c$,"getProteinStructureTag",function(){return this.group.getProteinStructureTag()});c(c$,"getGroupID",function(){return this.group.groupID});c(c$,"getSeqcodeString",function(){return this.group.getSeqcodeString()});c(c$,"getInsertionCode",function(){return this.group.getInsertionCode()});h(c$,"equals",function(a){return this===
a},"~O");h(c$,"hashCode",function(){return this.i});c(c$,"findAromaticNeighbor",function(a){if(null==this.bonds)return null;for(var b=this.bonds.length;0<=--b;){var d=this.bonds[b],c=d.getOtherAtom(this);if(d.isAromatic()&&c.i!=a)return c}return null},"~N");c$.atomPropertyInt=c(c$,"atomPropertyInt",function(a,b){switch(b){case 1095763969:return a.getAtomNumber();case 1095761940:return a.getSeqID();case 1095761922:return a.atomID;case 1095761923:return a.i;case 1095761924:return a.getCovalentBondCount();
case 1095761927:return a.group.chain.index+1;case 1766856708:return a.group.chain.model.ms.vwr.getColorArgbOrGray(a.getColix());case 1087375365:case 1095763978:return a.getElementNumber();case 1095761929:return a.atomicAndIsotopeNumber;case 1229984263:return a.getModelFileIndex()+1;case 1632634891:return a.getFormalCharge();case 1095761932:return a.getGroupID();case 1095761933:return a.group.getGroupIndex();case 1095766030:return a.getModelNumber();case -1095766030:return a.getModelFileNumber();case 1095761935:return a.mi;
case 1095761936:return a.getMoleculeNumber(!0);case 1129318401:return a.getOccupancy100();case 1095761937:return a.getGroup().getBioPolymerIndexInModel()+1;case 1095761938:return a.getPolymerLength();case 1666189314:return a.getRasMolRadius();case 1095761939:return a.getResno();case 1095761941:return a.getAtomSite();case 1641025539:return a.getProteinStructureType().getId();case 1238369286:return a.getProteinStructureSubType().getId();case 1095761942:return a.getStrucNo();case 1297090050:return a.getSymOp();
case 1095763991:return a.getValence()}return 0},"JM.Atom,~N");c(c$,"getSymOp",function(){return null==this.atomSymmetry?0:this.atomSymmetry.nextSetBit(0)+1});c$.atomPropertyFloat=c(c$,"atomPropertyFloat",function(a,b,d,c){switch(d){case 1112539137:return b.getADPMinMax(!0);case 1112539138:return b.getADPMinMax(!1);case 1112541185:case 1112541205:return b.x;case 1112541186:case 1112541206:return b.y;case 1112541187:case 1112541207:return b.z;case 1115297793:case 1113200642:case 1113198595:case 1113198596:case 1113198597:case 1113200646:case 1113200647:case 1113200649:case 1113200650:case 1113200652:case 1650071565:case 1113200654:return a.shm.getAtomShapeValue(d,
b.group,b.i);case 1112541195:return b.getBondingRadius();case 1112539139:return a.getNMRCalculation().getChemicalShift(b);case 1112539140:return JU.Elements.getCovalentRadius(b.atomicAndIsotopeNumber);case 1112539141:case 1112539152:case 1112539150:return b.getGroupParameter(d);case 1112541188:return b.getFractionalCoord("X",!0,c);case 1112541189:return b.getFractionalCoord("Y",!0,c);case 1112541190:return b.getFractionalCoord("Z",!0,c);case 1112541191:return b.getFractionalCoord("X",!1,c);case 1112541192:return b.getFractionalCoord("Y",
!1,c);case 1112541193:return b.getFractionalCoord("Z",!1,c);case 1114638362:return b.getHydrophobicity();case 1112539142:return a.getNMRCalculation().getMagneticShielding(b);case 1112539143:return b.getMass();case 1129318401:return b.getOccupancy100()/100;case 1112541196:return b.getPartialCharge();case 1112539145:case 1112539146:case 1112539144:if(b.group.chain.model.isJmolDataFrame&&b.group.chain.model.jmolFrameType.startsWith("plot ramachandran"))switch(d){case 1112539145:return b.getFractionalCoord("X",
!1,c);case 1112539146:return b.getFractionalCoord("Y",!1,c);case 1112539144:if(b.group.chain.model.isJmolDataFrame&&b.group.chain.model.jmolFrameType.equals("plot ramachandran"))return a=b.getFractionalCoord("Z",!1,c)-180,-180>a?360+a:a}return b.getGroupParameter(d);case 1666189314:case 1113200651:return b.getRadius();case 1112539147:return b.sX;case 1112539148:return b.group.chain.model.ms.vwr.getScreenHeight()-b.sY;case 1112539149:return b.sZ;case 1114638363:return a.isAtomSelected(b.i)?1:0;case 1112539151:return b.group.chain.model.ms.getSurfaceDistanceMax(),
b.getSurfaceDistance100()/100;case 1112541199:return b.getBfactor100()/100;case 1112539153:return b.getFractionalUnitCoord("X",c);case 1112539154:return b.getFractionalUnitCoord("Y",c);case 1112539155:return b.getFractionalUnitCoord("Z",c);case 1649412120:return b.getVanderwaalsRadiusFloat(a,J.c.VDW.AUTO);case 1649410049:return b=b.getVibrationVector(),null==b?0:b.length()*a.getFloat(1649410049);case 1112541202:return b.getVibrationCoord("X");case 1112541203:return b.getVibrationCoord("Y");case 1112541204:return b.getVibrationCoord("Z");
case 1313866249:return b.getVolume(a,J.c.VDW.AUTO);case 1146095627:case 1146095629:case 1146093582:case 1146095628:case 1146095631:case 1146095626:return JM.Atom.atomPropertyTuple(b,d,c).length()}return JM.Atom.atomPropertyInt(b,d)},"JV.Viewer,JM.Atom,~N,JU.P3");c(c$,"getMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getAtomicMass(this.getElementNumber())});c$.atomPropertyString=c(c$,"atomPropertyString",function(a,b,d){switch(d){case 1087373315:return a=b.altloc,"\x00"==
a?"":""+a;case 1087375362:return b.getAtomName();case 1087375361:return b.getAtomType();case 1087373316:return b.getChainIDStr();case 1087373320:return b.getGroup1("?");case 1087373319:return b.getGroup1("\x00");case 1087373318:return b.getGroup3(!1);case 1087375365:return b.getElementSymbolIso(!0);case 1087373321:return b.getIdentity(!0);case 1087373322:return a=b.getInsertionCode(),"\x00"==a?"":""+a;case 1826248716:case 1288701959:return a=a.shm.getShapePropertyIndex(5,"label",b.i),null==a&&(a=
""),a;case 1641025539:return b.getProteinStructureType().getBioStructureTypeName(!1);case 1238369286:return b.getProteinStructureSubType().getBioStructureTypeName(!1);case 1087373324:return b.getStructureId();case 1087373323:return a.getHybridizationAndAxes(b.i,null,null,"d");case 1087375373:return b.getElementSymbolIso(!1);case 1089470478:return b.getSymmetryOperatorList()}return""},"JV.Viewer,JM.Atom,~N");c$.atomPropertyTuple=c(c$,"atomPropertyTuple",function(a,b,d){switch(b){case 1146095627:return a.getFractionalCoordPt(!a.group.chain.model.isJmolDataFrame,
d);case 1146095629:return a.getFractionalCoordPt(!1,d);case 1146093582:return a.group.chain.model.isJmolDataFrame?a.getFractionalCoordPt(!1,d):a.getFractionalUnitCoordPt(!1,d);case 1146095628:return JU.P3.new3(a.sX,a.group.chain.model.ms.vwr.getScreenHeight()-a.sY,a.sZ);case 1146095631:return a=a.getVibrationVector(),null==a&&(a=new JU.V3),a;case 1146095626:return a;case 1766856708:return JU.CU.colorPtFromInt(a.group.chain.model.ms.vwr.getColorArgbOrGray(a.getColix()),d)}return null},"JM.Atom,~N,JU.P3");
c(c$,"isWithinStructure",function(a){return this.group.isWithinStructure(a)},"J.c.STR");h(c$,"getOffsetResidueAtom",function(a,b){return this.group.getAtomIndex(a,b)},"~S,~N");h(c$,"isCrossLinked",function(a){return this.group.isCrossLinked(a.getGroup())},"JU.BNode");h(c$,"getCrossLinkLeadAtomIndexes",function(a){return this.group.getCrossLinkLead(a)},"JU.Lst");h(c$,"toString",function(){return this.getInfo()});c(c$,"isWithinFourBonds",function(a){if(this.mi!=a.mi)return!1;if(this.isCovalentlyBonded(a))return!0;
for(var b=a.bonds,d=0;d<b.length;d++){var c=b[d].getOtherAtom(a);if(this.isCovalentlyBonded(c))return!0;for(var g=0;g<this.bonds.length;g++)if(this.bonds[g].getOtherAtom(this).isCovalentlyBonded(c))return!0}return!1},"JM.Atom");h(c$,"findAtomsLike",function(a){return this.group.chain.model.ms.vwr.getAtomBitSet(a)},"~S");C(c$,"VIBRATION_VECTOR_FLAG",1,"IS_HETERO_FLAG",2,"FLAG_MASK",3,"RADIUS_MAX",16,"RADIUS_GLOBAL",16.1,"MAD_GLOBAL",32200)});n("JM");w(["java.lang.Float","JU.BS","$.V3"],"JM.AtomCollection",
"java.lang.Character java.util.Arrays $.Hashtable JU.A4 $.AU $.Lst $.M3 $.Measure $.P3 $.PT J.api.Interface J.atomdata.RadiusData J.c.PAL $.STR $.VDW JM.Group JS.T JU.BSUtil $.Elements $.Escape $.Logger $.Parser $.Txt $.Vibration JV.JC".split(" "),function(){c$=t(function(){this.at=this.g3d=this.vwr=null;this.ac=0;this.surfaceDistance100s=this.atomTensors=this.atomTensorList=this.hydrophobicities=this.bondingRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.atomSeqIDs=
this.atomSerials=this.atomTypes=this.atomNames=null;this.haveStraightness=!1;this.labeler=this.bsHidden=null;this.maxVanderwaalsRadius=this.maxBondingRadius=1.4E-45;this.hasBfactorRange=!1;this.surfaceDistanceMax=this.bfactor100Hi=this.bfactor100Lo=0;this.bsSurface=null;this.nSurfaceAtoms=0;this.bspf=this.averageAtomPoint=null;this.preserveState=!0;this.tainted=null;this.canSkipLoad=!0;this.aaRet=this.bsFoundRectangle=this.bsEmpty=null;N("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();
this.bsClickable=this.bsVisible=null;this.haveBSClickable=this.haveBSVisible=!1;this.bsModulated=null;s(this,arguments)},JM,"AtomCollection");K(c$,function(){this.bsHidden=new JU.BS;this.bsEmpty=new JU.BS;this.bsFoundRectangle=new JU.BS;this.bsVisible=new JU.BS;this.bsClickable=new JU.BS});c(c$,"releaseModelSet",function(){this.releaseModelSetAC()});c(c$,"releaseModelSetAC",function(){this.atomTensors=this.bondingRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.atomSeqIDs=
this.atomSerials=this.atomTypes=this.atomNames=this.tainted=this.bsSurface=this.surfaceDistance100s=this.bspf=this.g3d=this.vwr=this.at=null});c(c$,"mergeAtomArrays",function(a){this.tainted=a.tainted;this.atomNames=a.atomNames;this.atomTypes=a.atomTypes;this.atomSerials=a.atomSerials;this.atomSeqIDs=a.atomSeqIDs;this.vibrations=a.vibrations;this.occupancies=a.occupancies;this.bfactor100s=a.bfactor100s;this.bondingRadii=a.bondingRadii;this.partialCharges=a.partialCharges;this.atomTensors=a.atomTensors;
this.atomTensorList=a.atomTensorList;this.bsModulated=a.bsModulated;this.setHaveStraightness(!1);this.surfaceDistance100s=null},"JM.AtomCollection");c(c$,"setHaveStraightness",function(a){this.haveStraightness=a},"~B");c(c$,"getHaveStraightness",function(){return this.haveStraightness});c(c$,"getAtomPointVector",function(a){var b=new JU.Lst;if(null!=a)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))b.addLast(this.at[d]);return b},"JU.BS");c(c$,"getAtomCount",function(){return this.ac});c(c$,"modelSetHasVibrationVectors",
function(){return null!=this.vibrations});c(c$,"getAtomTypes",function(){return this.atomTypes});c(c$,"getPartialCharges",function(){return this.partialCharges});c(c$,"getBondingRadii",function(){return this.bondingRadii});c(c$,"getBFactors",function(){return this.bfactor100s});c(c$,"getHydrophobicity",function(){return this.hydrophobicities});c(c$,"setBsHidden",function(a){this.bsHidden=a},"JU.BS");c(c$,"isAtomHidden",function(a){return this.bsHidden.get(a)},"~N");c(c$,"getLabeler",function(){return null==
this.labeler?this.labeler=J.api.Interface.getInterface("JM.LabelToken"):this.labeler});c(c$,"getAtomInfo",function(a,b,d){return null==b?this.at[a].getInfo():this.getLabeler().formatLabel(this.vwr,this.at[a],b,d)},"~N,~S,JU.P3");c(c$,"getAtomInfoXYZ",function(a,b,d){return this.at[a].getInfoXYZ(b,d)},"~N,~B,JU.P3");c(c$,"getElementSymbol",function(a){return this.at[a].getElementSymbol()},"~N");c(c$,"getElementNumber",function(a){return this.at[a].getElementNumber()},"~N");c(c$,"getElementName",function(a){return JU.Elements.elementNameFromNumber(this.at[a].getAtomicAndIsotopeNumber())},
"~N");c(c$,"getAtomName",function(a){return this.at[a].getAtomName()},"~N");c(c$,"getAtomNumber",function(a){return this.at[a].getAtomNumber()},"~N");c(c$,"getAtomPoint3f",function(a){return this.at[a]},"~N");c(c$,"getAtomRadius",function(a){return this.at[a].getRadius()},"~N");c(c$,"getAtomVdwRadius",function(a,b){return this.at[a].getVanderwaalsRadiusFloat(this.vwr,b)},"~N,J.c.VDW");c(c$,"getAtomColix",function(a){return this.at[a].getColix()},"~N");c(c$,"getAtomChain",function(a){return this.at[a].getChainIDStr()},
"~N");c(c$,"getQuaternion",function(a,b){return 0>a?null:this.at[a].group.getQuaternion(b)},"~N,~S");c(c$,"getAtomIndexFromAtomNumber",function(a,b){for(var d=0;d<this.ac;d++){var c=this.at[d];if(c.getAtomNumber()==a&&b.get(c.mi))return d}return-1},"~N,JU.BS");c(c$,"setFormalCharges",function(a,b){if(null!=a)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.at[d].setFormalCharge(b),this.taintAtom(d,4)},"JU.BS,~N");c(c$,"getAtomicCharges",function(){for(var a=L(this.ac,0),b=this.ac;0<=--b;)a[b]=
this.at[b].getElementNumber();return a});c(c$,"getRadiusVdwJmol",function(a){return JU.Elements.getVanderwaalsMar(a.getElementNumber(),J.c.VDW.JMOL)/1E3},"JM.Atom");c(c$,"getMaxVanderwaalsRadius",function(){1.4E-45==this.maxVanderwaalsRadius&&this.findMaxRadii();return this.maxVanderwaalsRadius});c(c$,"findMaxRadii",function(){for(var a,b=this.ac;0<=--b;){var d=this.at[b];if((a=d.getBondingRadius())>this.maxBondingRadius)this.maxBondingRadius=a;if((a=d.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO))>
this.maxVanderwaalsRadius)this.maxVanderwaalsRadius=a}});c(c$,"clearBfactorRange",function(){this.hasBfactorRange=!1});c(c$,"calcBfactorRange",function(a){if(!this.hasBfactorRange){this.bfactor100Lo=2147483647;this.bfactor100Hi=-2147483648;if(null==a)for(var b=0;b<this.ac;b++)this.setBf(b);else for(b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.setBf(b);this.hasBfactorRange=!0}},"JU.BS");c(c$,"setBf",function(a){a=this.at[a].getBfactor100();a<this.bfactor100Lo?this.bfactor100Lo=a:a>this.bfactor100Hi&&
(this.bfactor100Hi=a)},"~N");c(c$,"getBfactor100Lo",function(){this.hasBfactorRange||(this.vwr.g.rangeSelected?this.calcBfactorRange(this.vwr.bsA()):this.calcBfactorRange(null));return this.bfactor100Lo});c(c$,"getBfactor100Hi",function(){this.getBfactor100Lo();return this.bfactor100Hi});c(c$,"getSurfaceDistanceMax",function(){null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistanceMax});c(c$,"calculateVolume",function(a,b){var d=0;if(null!=a)for(var c=a.nextSetBit(0);0<=
c;c=a.nextSetBit(c+1))d+=this.at[c].getVolume(this.vwr,b);return d},"JU.BS,J.c.VDW");c(c$,"getSurfaceDistance100",function(a){if(0==this.nSurfaceAtoms)return-1;null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistance100s[a]},"~N");c(c$,"calcSurfaceDistances",function(){this.calculateSurface(null,-1)});c(c$,"calculateSurface",function(a,b){0>b&&(b=3);var d=J.api.Interface.getOption("geodesic.EnvelopeCalculation").set(this.vwr,this.ac,null);d.calculate(new J.atomdata.RadiusData(null,
b,J.atomdata.RadiusData.EnumType.ABSOLUTE,null),3.4028235E38,a,JU.BSUtil.copyInvert(a,this.ac),!1,!1,!1,!0);var c=d.getPoints();this.surfaceDistanceMax=0;this.bsSurface=d.getBsSurfaceClone();this.surfaceDistance100s=D(this.ac,0);this.nSurfaceAtoms=JU.BSUtil.cardinalityOf(this.bsSurface);if(0==this.nSurfaceAtoms||null==c||0==c.length)return c;for(var d=3.4028235E38==b?0:b,g=0;g<this.ac;g++)if(this.bsSurface.get(g))this.surfaceDistance100s[g]=0;else{for(var f=3.4028235E38,j=this.at[g],k=c.length;0<=
--k;){var h=Math.abs(c[k].distance(j)-d);0>h&&JU.Logger.debugging&&JU.Logger.debug("draw d"+k+" "+JU.Escape.eP(c[k])+' "'+h+" ? "+j.getInfo()+'"');f=Math.min(h,f)}h=this.surfaceDistance100s[g]=q(Math.floor(100*f));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,h)}return c},"JU.BS,~N");c(c$,"setAtomCoord2",function(a,b,d){var c=null,g=null,f=null,j=0,k=1;if(p(d,JU.P3))c=d;else if(p(d,JU.Lst)){f=d;if(0==(k=f.size()))return;j=1}else if(JU.PT.isAP(d)){g=d;if(0==(k=g.length))return;j=2}else return;
d=0;if(null!=a)for(var h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){switch(j){case 1:if(d>=k)return;c=f.get(d++);break;case 2:if(d>=k)return;c=g[d++]}switch(b){case 1146095626:this.setAtomCoord(h,c.x,c.y,c.z);break;case 1146095627:this.at[h].setFractionalCoordTo(c,!0);this.taintAtom(h,2);break;case 1146095629:this.at[h].setFractionalCoordTo(c,!1);this.taintAtom(h,2);break;case 1146095631:this.setAtomVibrationVector(h,c)}}},"JU.BS,~N,~O");c(c$,"setAtomVibrationVector",function(a,b){this.setVibrationVector(a,
b);this.taintAtom(a,12)},"~N,JU.T3");c(c$,"setAtomCoord",function(a,b,d,c){if(!(0>a||a>=this.ac)){var g=this.at[a];g.set(b,d,c);this.fixTrajectory(g);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"fixTrajectory",function(a){var b=a.mi;if(this.isTrajectory(b)){var d=null!=this.unitCells&&this.unitCells[b].getCoordinatesAreFractional(),c=this.trajectorySteps.get(b)[a.i-this.am[b].firstAtomIndex];c.set(a.x,a.y,a.z);d&&this.unitCells[b].toFractional(c,!0)}},"JM.Atom");c(c$,"setAtomCoordRelative",function(a,
b,d,c){if(!(0>a||a>=this.ac)){var g=this.at[a];g.add3(b,d,c);this.fixTrajectory(g);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"setAtomsCoordRelative",function(a,b,d,c){if(null!=a)for(var g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))this.setAtomCoordRelative(g,b,d,c)},"JU.BS,~N,~N,~N");c(c$,"setAPa",function(a,b,d,c,g,f,j){var k=0;if(!(null!=f&&0==f.length||null==a)){for(var h=null!=f&&f.length==this.ac||null!=j&&j.length==this.ac,m=a.nextSetBit(0);0<=m;m=a.nextSetBit(m+1)){h&&(k=m);if(null!=f){if(k>=
f.length)return;c=f[k++];d=z(c)}else if(null!=j){if(k>=j.length)return;g=j[k++]}var r=this.at[m];switch(b){case 1087375362:this.taintAtom(m,0);this.setAtomName(m,g);break;case 1095763969:this.taintAtom(m,13);this.setAtomNumber(m,d);break;case 1095761940:this.taintAtom(m,14);this.setAtomSeqID(m,d);break;case 1087375361:this.taintAtom(m,1);this.setAtomType(m,g);break;case 1112541185:case 1112541205:this.setAtomCoord(m,c,r.y,r.z);break;case 1112541186:case 1112541206:this.setAtomCoord(m,r.x,c,r.z);break;
case 1112541187:case 1112541207:this.setAtomCoord(m,r.x,r.y,c);break;case 1112541202:case 1112541203:case 1112541204:this.setVibrationVector2(m,b,c);break;case 1112541188:case 1112541189:case 1112541190:r.setFractionalCoord(b,c,!0);this.taintAtom(m,2);break;case 1112541191:case 1112541192:case 1112541193:r.setFractionalCoord(b,c,!1);this.taintAtom(m,2);break;case 1095763978:case 1087375365:this.setElement(r,d);break;case 1632634891:r.setFormalCharge(d);this.taintAtom(m,4);break;case 1114638362:this.setHydrophobicity(m,
c)&&this.taintAtom(m,5);break;case 1826248716:case 1288701959:this.vwr.shm.setAtomLabel(g,m);break;case 1129318401:2>c&&0.01<c&&(c*=100);this.setOccupancy(m,c)&&this.taintAtom(m,7);break;case 1112541196:this.setPartialCharge(m,c)&&this.taintAtom(m,8);break;case 1112541195:this.setBondingRadius(m,c)&&this.taintAtom(m,6);break;case 1666189314:case 1113200651:0>c?c=0:16<c&&(c=16.1);r.madAtom=Y(2E3*c);break;case 1114638363:this.vwr.slm.setSelectedAtom(r.i,0!=c);break;case 1112541199:this.setBFactor(m,
c)&&this.taintAtom(m,9);break;case 1095763991:r.setValence(d);this.taintAtom(m,10);break;case 1649412120:r.setRadius(c)?this.taintAtom(m,11):this.untaint(m,11);break;default:JU.Logger.error("unsettable atom property: "+JS.T.nameOf(b))}}switch(b){case 1114638363:this.vwr.slm.setSelectedAtom(-1,!1);break;case 1666189314:case 1113200651:this.vwr.setShapeSize(0,2147483647,a)}}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"setElement",function(a,b){this.taintAtom(a.i,3);a.setAtomicAndIsotopeNumber(b);a.setPaletteID(J.c.PAL.CPK.id);
a.setColixAtom(this.vwr.getColixAtomPalette(a,J.c.PAL.CPK.id))},"JM.Atom,~N");c(c$,"getVibrationCoord",function(a,b){var d;if(null==this.vibrations||null==(d=this.vibrations[a]))return 0;switch(b){case "X":return d.x;case "Y":return d.y;default:return d.z}},"~N,~S");c(c$,"getVibration",function(a,b){var d=null==this.vibrations?null:this.vibrations[a];return null==d&&b?new JU.Vibration:d},"~N,~B");c(c$,"setVibrationVector",function(a,b){if(!Float.isNaN(b.x)&&!Float.isNaN(b.y)&&!Float.isNaN(b.z)){if(null==
this.vibrations||this.vibrations.length<a)this.vibrations=Array(this.at.length);p(b,JU.Vibration)?this.vibrations[a]=b:(null==this.vibrations[a]&&(this.vibrations[a]=new JU.Vibration),this.vibrations[a].setT(b));this.at[a].setVibrationVector()}},"~N,JU.T3");c(c$,"setVibrationVector2",function(a,b,d){var c=this.getVibration(a,!0);switch(b){case 1112541202:c.x=d;break;case 1112541203:c.y=d;break;case 1112541204:c.z=d}this.setAtomVibrationVector(a,c)},"~N,~N,~N");c(c$,"setAtomName",function(a,b){var d=
JV.JC.lookupSpecialAtomID(b);this.at[a].atomID=d;0<d&&this.am[this.at[a].mi].isBioModel||(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[a]=b)},"~N,~S");c(c$,"setAtomType",function(a,b){null==this.atomTypes&&(this.atomTypes=Array(this.at.length));this.atomTypes[a]=b},"~N,~S");c(c$,"setAtomNumber",function(a,b){null==this.atomSerials&&(this.atomSerials=D(this.at.length,0));this.atomSerials[a]=b;return!0},"~N,~N");c(c$,"setAtomSeqID",function(a,b){null==this.atomSeqIDs&&
(this.atomSeqIDs=D(this.at.length,0));this.atomSeqIDs[a]=b;return!0},"~N,~N");c(c$,"setOccupancy",function(a,b){if(null==this.occupancies){if(100==b)return!1;this.occupancies=L(this.at.length,0);for(var d=this.at.length;0<=--d;)this.occupancies[d]=100}this.occupancies[a]=b;return!0},"~N,~N");c(c$,"setPartialCharge",function(a,b){if(Float.isNaN(b))return!1;if(null==this.partialCharges){if(0==b&&!Float.$valueOf(b).equals(JM.AtomCollection.MINUSZERO))return!1;this.partialCharges=L(this.at.length,0)}this.partialCharges[a]=
b;return!0},"~N,~N");c(c$,"setBondingRadius",function(a,b){if(Float.isNaN(b))return!1;null==this.bondingRadii&&(this.bondingRadii=L(this.at.length,0));this.bondingRadii[a]=b;return!0},"~N,~N");c(c$,"setBFactor",function(a,b){if(Float.isNaN(b))return!1;if(null==this.bfactor100s){if(0==b&&null==this.bfactor100s)return!1;this.bfactor100s=T(this.at.length,0)}this.bfactor100s[a]=ka(100*(-327.68>b?-327.68:327.67<b?327.67:b)+(0>b?-0.5:0.5));return!0},"~N,~N");c(c$,"setHydrophobicity",function(a,b){if(Float.isNaN(b))return!1;
if(null==this.hydrophobicities){this.hydrophobicities=L(this.at.length,0);for(var d=0;d<this.at.length;d++)this.hydrophobicities[d]=JU.Elements.getHydrophobicity(this.at[d].getGroupID())}this.hydrophobicities[a]=b;return!0},"~N,~N");c(c$,"setAtomData",function(a,b,d,c){var g=null,f=null;switch(a){case 2:this.loadCoordinates(d,!1,!c);return;case 12:this.loadCoordinates(d,!0,!0);return;case 15:g=L(this.ac,0),f=JU.BS.newN(this.ac)}c=JU.Parser.markLines(d,";");var j=0;try{for(var k=JU.PT.parseInt(d.substring(0,
c[0]-1)),h=1;h<=k;h++){var m=JU.PT.getTokens(JU.PT.parseTrimmed(d.substring(c[h],c[h+1]-1))),r=JU.PT.parseInt(m[0])-1;if(!(0>r||r>=this.ac)){var x=this.at[r];j++;var A=m.length-1,I=JU.PT.parseFloat(m[A]);switch(a){case 15:g[r]=I;f.set(r);continue;case 13:this.setAtomNumber(r,z(I));break;case 14:this.setAtomSeqID(r,z(I));break;case 0:this.setAtomName(r,m[A]);break;case 1:this.setAtomType(r,m[A]);break;case 3:x.setAtomicAndIsotopeNumber(z(I));x.setPaletteID(J.c.PAL.CPK.id);x.setColixAtom(this.vwr.getColixAtomPalette(x,
J.c.PAL.CPK.id));break;case 4:x.setFormalCharge(z(I));break;case 5:this.setHydrophobicity(r,I);break;case 6:this.setBondingRadius(r,I);break;case 8:this.setPartialCharge(r,I);break;case 9:this.setBFactor(r,I);break;case 10:x.setValence(z(I));break;case 11:x.setRadius(I)}this.taintAtom(r,a)}}15==a&&0<j&&this.vwr.setData(b,[b,g,f,Integer.$valueOf(1)],0,0,0,0,0)}catch(n){if(y(n,Exception))JU.Logger.error("AtomCollection.loadData error: "+n);else throw n;}},"~N,~S,~S,~B");c(c$,"loadCoordinates",function(a,
b,d){var c=JU.Parser.markLines(a,";"),g=b?new JU.V3:null;try{for(var f=JU.PT.parseInt(a.substring(0,c[0]-1)),j=1;j<=f;j++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[j],c[j+1]))),h=JU.PT.parseInt(k[0])-1,m=JU.PT.parseFloat(k[3]),r=JU.PT.parseFloat(k[4]),x=JU.PT.parseFloat(k[5]);b?(g.set(m,r,x),this.setAtomVibrationVector(h,g)):(this.setAtomCoord(h,m,r,x),d||this.untaint(h,2))}}catch(A){if(y(A,Exception))JU.Logger.error("Frame.loadCoordinate error: "+A);else throw A;}},"~S,~B,~B");c(c$,
"validateBspf",function(a){null!=this.bspf&&this.bspf.validate(a);this.averageAtomPoint=null},"~B");c(c$,"validateBspfForModel",function(a,b){null!=this.bspf&&this.bspf.validateModel(a,b)},"~N,~B");c(c$,"setPreserveState",function(a){this.preserveState=a},"~B");c$.getUserSettableType=c(c$,"getUserSettableType",function(a){var b=0==a.indexOf("property_");a=b?a.substring(9):a;for(var d=0;15>d;d++)if(JM.AtomCollection.userSettableValues[d].equalsIgnoreCase(a))return d;return b?15:-1},"~S");c(c$,"getTaintedAtoms",
function(a){return null==this.tainted?null:this.tainted[a]},"~N");c(c$,"taintAtoms",function(a,b){this.canSkipLoad=!1;if(this.preserveState)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.taintAtom(d,b)},"JU.BS,~N");c(c$,"taintAtom",function(a,b){this.preserveState&&(null==this.tainted&&(this.tainted=Array(15)),null==this.tainted[b]&&(this.tainted[b]=JU.BS.newN(this.ac)),this.tainted[b].set(a),2==b&&this.validateBspfForModel(this.am[this.at[a].mi].trajectoryBaseIndex,!1))},"~N,~N");c(c$,"untaint",
function(a,b){this.preserveState&&(null==this.tainted||null==this.tainted[b]||this.tainted[b].clear(a))},"~N,~N");c(c$,"setTaintedAtoms",function(a,b){this.preserveState&&(null==a?null!=this.tainted&&(this.tainted[b]=null):(null==this.tainted&&(this.tainted=Array(15)),null==this.tainted[b]&&(this.tainted[b]=JU.BS.newN(this.ac)),JU.BSUtil.copy2(a,this.tainted[b])))},"JU.BS,~N");c(c$,"unTaintAtoms",function(a,b){if(!(null==this.tainted||null==this.tainted[b])){for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+
1))this.tainted[b].clear(d);0>this.tainted[b].nextSetBit(0)&&(this.tainted[b]=null)}},"JU.BS,~N");c(c$,"findNearest2",function(a,b,d,c,g){for(var f=null,j=this.ac;0<=--j;)if(!(null!=c&&c.get(j))){var k=this.at[j];k.isClickable()&&this.isCursorOnTopOf(k,a,b,g,f)&&(f=k)}d[0]=f},"~N,~N,~A,JU.BS,~N");c(c$,"isCursorOnTopOf",function(a,b,d,c,g){return 1<a.sZ&&!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(b,d,c,g)},"JM.Atom,~N,~N,~N,JM.Atom");c(c$,"findAtomsInRectangle",
function(a){var b=this.vwr.getVisibleFramesBitSet();this.bsFoundRectangle.and(this.bsEmpty);for(var d=this.ac;0<=--d;){var c=this.at[d];b.get(c.mi)&&(c.checkVisible()&&a.contains(c.sX,c.sY))&&this.bsFoundRectangle.set(d)}return this.bsFoundRectangle},"JU.Rectangle");c(c$,"fillADa",function(a,b){a.atomXyz=this.at;a.ac=this.ac;a.atomicNumber=D(this.ac,0);var d=0!=(b&2);d&&(a.atomRadius=L(this.ac,0));for(var c=0!=(b&16),g=0;g<this.ac;g++){var f=this.at[g];f.isDeleted()||!c&&0<=a.modelIndex&&f.mi!=a.firstModelIndex?
(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(g)):(a.atomicNumber[g]=f.getElementNumber(),a.lastModelIndex=f.mi,d&&(a.atomRadius[g]=this.getWorkingRadius(f,a)))}},"J.atomdata.AtomData,~N");c(c$,"getWorkingRadius",function(a,b){var d=0,c=b.radiusData;switch(c.factorType){case J.atomdata.RadiusData.EnumType.ABSOLUTE:d=c.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:case J.atomdata.RadiusData.EnumType.OFFSET:switch(c.vdwType){case J.c.VDW.BONDING:d=a.getBondingRadius();break;case J.c.VDW.ADPMAX:d=
a.getADPMinMax(!0);break;case J.c.VDW.ADPMIN:d=a.getADPMinMax(!1);break;default:d=a.getVanderwaalsRadiusFloat(this.vwr,b.radiusData.vdwType)}d=c.factorType===J.atomdata.RadiusData.EnumType.FACTOR?d*c.value:d+c.value}return d+c.valueExtended},"JM.Atom,J.atomdata.AtomData");c(c$,"calculateHydrogens",function(a,b,d,c,g){var f=new JU.V3,j=new JU.V3,k=Array(this.ac),h=this.vwr.getDeletedAtoms(),m,r=0;if(null!=a)for(var x=a.nextSetBit(0);0<=x;x=a.nextSetBit(x+1))if(!(null!=h&&h.get(x))){var A=this.at[x],
I=A.getElementNumber();if(!(c&&6!=I)){var n=6>=I?1.1:10>=I?1:1.3;switch(I){case 7:case 8:n=1}if(!(d&&0<A.getCovalentHydrogenCount())&&(m=this.getImplicitHydrogenCount(A,!1),0!=m)){var q=this.aaRet[0],p=this.aaRet[2],s=this.aaRet[3];k[x]=Array(m);var t=0;if(0==s)switch(m){case 4:f.set(0.635,0.635,0.635),m=JU.P3.newP(f),m.add(A),k[x][t++]=m,null!=g&&g.addLast(A);case 3:f.set(-0.635,-0.635,0.635),m=JU.P3.newP(f),m.add(A),k[x][t++]=m,null!=g&&g.addLast(A);case 2:f.set(-0.635,0.635,-0.635),m=JU.P3.newP(f),
m.add(A),k[x][t++]=m,null!=g&&g.addLast(A);case 1:f.set(0.635,-0.635,-0.635),m=JU.P3.newP(f),m.add(A),k[x][t++]=m,null!=g&&g.addLast(A)}else switch(m){case 3:this.getHybridizationAndAxes(x,I,f,j,"sp3b",!1,!0);m=new JU.P3;m.scaleAdd2(n,f,A);k[x][t++]=m;null!=g&&g.addLast(A);this.getHybridizationAndAxes(x,I,f,j,"sp3c",!1,!0);m=new JU.P3;m.scaleAdd2(n,f,A);k[x][t++]=m;null!=g&&g.addLast(A);this.getHybridizationAndAxes(x,I,f,j,"sp3d",!1,!0);m=new JU.P3;m.scaleAdd2(n,f,A);k[x][t++]=m;null!=g&&g.addLast(A);
break;case 2:p=2==p||5==I||1==s&&4==q||7==I&&this.isAdjacentSp2(A);this.getHybridizationAndAxes(x,I,f,j,p?"sp2b":3==q?"sp3c":"lpa",!1,!0);m=JU.P3.newP(f);m.scaleAdd2(n,f,A);k[x][t++]=m;null!=g&&g.addLast(A);this.getHybridizationAndAxes(x,I,f,j,p?"sp2c":3==q?"sp3d":"lpb",!1,!0);m=JU.P3.newP(f);m.scaleAdd2(n,f,A);k[x][t++]=m;null!=g&&g.addLast(A);break;case 1:switch(q-s){case 1:if(8==I&&A===A.getGroup().getCarbonylOxygenAtom()){k[x]=null;continue}null!=this.getHybridizationAndAxes(x,I,f,j,2==p||5==
I||7==I&&this.isAdjacentSp2(A)?"sp2c":"sp3d",!0,!1)?(m=JU.P3.newP(f),m.scaleAdd2(n,f,A),k[x][t++]=m,null!=g&&g.addLast(A)):k[x]=[];break;case 2:this.getHybridizationAndAxes(x,I,f,j,4==q?"sp2c":"sp2b",!1,!1);m=JU.P3.newP(f);m.scaleAdd2(n,f,A);k[x][t++]=m;null!=g&&g.addLast(A);break;case 3:this.getHybridizationAndAxes(x,I,f,j,"spb",!1,!0),m=JU.P3.newP(f),m.scaleAdd2(n,f,A),k[x][t++]=m,null!=g&&g.addLast(A)}}r+=t}}}b[0]=r;return k},"JU.BS,~A,~B,~B,JU.Lst");c(c$,"isAdjacentSp2",function(a){for(var b=
a.bonds,d=0;d<b.length;d++)for(var c=b[d].getOtherAtom(a).bonds,g=0;g<c.length;g++)switch(c[g].order){case 515:case 514:case 2:case 3:return!0}return!1},"JM.Atom");c(c$,"getImplicitHydrogenCount",function(a,b){var d=a.getTargetValence();if(0>d)return 0;var c=a.getFormalCharge();null==this.aaRet&&(this.aaRet=D(4,0));this.aaRet[0]=d;this.aaRet[1]=c;this.aaRet[2]=0;this.aaRet[3]=a.getCovalentBondCount();var g=this.am[a.mi],g=g.isBioModel&&!g.isPdbWithMultipleBonds?a.group.getGroup3():null;null!=g&&0==
c&&JV.JC.getAminoAcidValenceAndCharge(g,a.getAtomName(),this.aaRet)&&(d=this.aaRet[0],c=this.aaRet[1]);0!=c&&(d+=4==d?-Math.abs(c):c,this.aaRet[0]=d);d-=a.getValence();return 0>d&&!b?0:d},"JM.Atom,~B");c(c$,"fixFormalCharges",function(a){for(var b=0,d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1)){var c=this.at[d],g=this.getImplicitHydrogenCount(c,!0);if(0!=g){var f=c.getFormalCharge(),g=f-g;c.setFormalCharge(g);this.taintAtom(d,4);JU.Logger.debugging&&JU.Logger.debug("atom "+c+" formal charge "+f+" -> "+
g);b++}}return b},"JU.BS");c(c$,"getHybridizationAndAxes",function(a,b,d,c,g,f,j){var k=0<g.length&&"-"==g.charAt(0)?g.substring(1):g;if(0<=g.indexOf("d")&&!g.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,d,c,k);g=this.at[a];0==b&&(b=g.getElementNumber());var h=this.getAttached(g,4,f),m=h.length,r=k.charCodeAt(k.length-1)-97;if(0>r||6<r)r=0;d.set(0,0,0);c.set(0,0,0);for(var x=Array(4),A=0;A<m;A++)x[A]=JU.V3.newVsub(g,h[A]),x[A].normalize(),d.add(x[A]);0<m&&c.setT(x[0]);A=!1;a=new JU.V3;
if(3<=m){2.984513>c.angle(x[1])?a.cross(c,x[1]):a.cross(c,x[2]);a.normalize();var n=new JU.V3;2.984513>x[1].angle(x[2])?n.cross(x[1],x[2]):n.cross(c,x[2]);n.normalize();A=0.95<=Math.abs(n.dot(a))}var q=0==k.indexOf("sp3"),p=!q&&0==k.indexOf("sp2"),s=!q&&!p&&0==k.indexOf("sp"),t=0==k.indexOf("p"),u=0==k.indexOf("lp"),n=null;if(f){if(0==m)return null;if(q){if(3<r||4<m)return null}else if(p){if(2<r||3<m)return null}else if(s&&(1<r||2<m))return null;switch(m){case 1:if(1==b&&!q)return null;if(q){n="sp3";
break}switch(h[0].getCovalentBondCount()){case 1:if(2!=h[0].getValence()){n="sp";break}case 2:n=s?"sp":"sp2";break;case 3:if(!p&&!t)return null;n="sp2"}break;case 2:if(0.1>d.length()){if(0<=k.indexOf("2")||0<=k.indexOf("3"))return null;n="sp";break}n=q?"sp3":"sp2";if(0==k.indexOf("sp"))break;if(u){n="lp";break}n=k;break;default:if(A)n="sp2";else{if(u&&3==m){n="lp";break}n="sp3"}}if(null==n)return null;if(0==k.indexOf("p")){if("sp3"===n)return null}else if(0>k.indexOf(n))return null}if(r<m&&!k.startsWith("p")&&
!k.startsWith("l"))return d.sub2(h[r],g),d.normalize(),n;switch(m){case 0:k.equals("sp3c")||k.equals("sp2d")||k.equals("lpa")?d.set(-0.5,-0.7,1):k.equals("sp3b")||k.equals("lpb")?d.set(0.5,-0.7,-1):k.equals("sp3a")?d.set(0,1,0):d.set(0,0,1);c.set(1,0,0);break;case 1:a.setT(JM.AtomCollection.vRef);c.cross(a,d);if(q){for(A=0;A<h[0].bonds.length;A++)if(h[0].bonds[A].isCovalent()&&h[0].getBondedAtomIndex(A)!=g.i&&(c.sub2(h[0],h[0].bonds[A].getOtherAtom(h[0])),c.cross(d,c),0!=c.length())){c.cross(c,d);
break}c.normalize();Float.isNaN(c.x)&&(c.setT(JM.AtomCollection.vRef),c.cross(c,d));a.cross(d,c);a.normalize();d.normalize();c.scaleAdd2(2.828,c,d);3!=r&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(d.x,d.y,d.z,2.09439507*(2==r?1:-1))).rotate(c));d.setT(c);c.cross(a,d);break}a.cross(c,d);switch(h[0].getCovalentBondCount()){case 1:if(2!=h[0].getValence())break;case 2:j=h[0];c.setT(d);for(a.setT(JM.AtomCollection.vRef);null!=j&&2==j.getCovalentBondCount();){k=j.bonds;b=null;for(A=0;A<k.length;A++)if(k[A].isCovalent()&&
(b=k[A].getOtherAtom(j),b!==g)){a.sub2(b,j);break}a.cross(a,c);if(0.1<a.length()||2!=b.getCovalentBondCount())break;g=j;j=b}0.1<a.length()?(d.cross(a,c),d.normalize(),1==r&&d.scale(-1),d.scale(JM.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,c,d),t&&(a.cross(d,c),d.setT(a),a.setT(c)),c.cross(a,d)):(d.setT(c),c.cross(JM.AtomCollection.vRef,c));break;case 3:this.getHybridizationAndAxes(h[0].i,0,c,a,"pz",!1,j),a.setT(c),p?(c.cross(c,d),1==r&&c.scale(-1),c.scale(JM.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,d,
c)):(a.setT(d),d.setT(c)),c.cross(a,d)}break;case 2:if(0.1>d.length()){if(!k.equals("pz")){b=h[0];(g=3==b.getCovalentBondCount())||(g=3==(b=h[1]).getCovalentBondCount());if(g){this.getHybridizationAndAxes(b.i,0,c,d,"pz",!1,j);k.equals("px")&&c.scale(-1);d.setT(x[0]);break}a.setT(JM.AtomCollection.vRef);d.cross(a,c);a.cross(d,c)}d.setT(c);c.cross(a,d);break}a.cross(d,c);if(p){c.cross(d,a);break}if(q||u){a.normalize();d.normalize();k.equals("lp")||(0==r||2==r?d.scaleAdd2(-1.2,a,d):d.scaleAdd2(1.2,a,
d));c.cross(d,a);break}c.cross(d,a);d.setT(a);0>d.z&&(d.scale(-1),c.scale(-1));break;default:if(q)break;if(!A){c.cross(d,c);break}d.setT(a);0>d.z&&j&&(d.scale(-1),c.scale(-1))}c.normalize();d.normalize();return n},"~N,~N,JU.V3,JU.V3,~S,~B,~B");c(c$,"getHybridizationAndAxesD",function(a,b,d,c){c.startsWith("sp3d2")&&(c="d2sp3"+(5==c.length?"a":c.substring(5)));c.startsWith("sp3d")&&(c="dsp3"+(4==c.length?"a":c.substring(4)));if(c.equals("d2sp3")||c.equals("dsp3"))c+="a";var g=c.startsWith("dsp3"),
f=c.charCodeAt(c.length-1)-97;if(null!=b&&(!g&&(5<f||!c.startsWith("d2sp3"))||g&&4<f))return null;a=this.at[a];c=this.getAttached(a,6,!0);if(null==c)return null==b?null:"?";var j=c.length;if(3>j&&null!=b)return null;for(var k=f>=j,h=q(j*(j-1)/2),m=JU.AU.newInt2(h),r=D(3,0),h=D(3,h,0),x=0,A=0,n=0;n<j-1;n++)for(var p=n+1;p<j;p++){var s=JU.Measure.computeAngleABC(c[n],a,c[p],!0),s=105>s?0:150<=s?2:1;h[s][r[s]]=x;r[s]++;m[x++]=[n,p];0==n&&1==s&&A++}x=100*r[0]+10*r[1]+r[2];if(null==b)switch(x){default:return"";
case 0:return"";case 1:return"linear";case 100:case 10:return"bent";case 111:case 201:return"T-shaped";case 30:case 120:case 210:case 300:return 162<Math.abs(JU.Measure.computeTorsion(c[0],a,c[1],c[2],!0))?"trigonal planar":"trigonal pyramidal";case 330:return 1==A%2?"tetrahedral":"uncapped trigonal pyramid";case 60:case 150:case 240:return"tetrahedral";case 402:return"square planar";case 411:case 501:return"see-saw";case 631:return"trigonal bipyramidal";case 802:return"uncapped square pyramid";case 1203:return"octahedral"}switch(x){default:return null;
case 201:break;case 210:case 330:case 411:case 631:if(!g)return null;break;case 300:case 402:case 501:case 802:case 1203:if(g)return null}if(k)if(g)switch(r[1]){case 0:b.sub2(c[m[h[0][0]][0]],a);d.sub2(c[m[h[0][0]][1]],a);b.cross(b,d);b.normalize();4==f&&b.scale(-1);r=this.findNotAttached(j,m,h[2],r[2]);n=r.nextSetBit(0);d.sub2(c[n],a);d.normalize();d.scale(0.5);b.scaleAdd2(JM.AtomCollection.sqrt3_2,b,d);f=-1;break;case 1:4==f?(d=m[h[1][0]],b.add2(c[d[0]],c[d[1]]),b.scaleAdd2(-2,a,b),f=-1):(r=this.findNotAttached(j,
m,h[1],r[1]),f=r.nextSetBit(0));break;default:r=this.findNotAttached(j,m,h[1],r[1]),f=r.nextSetBit(0)}else{x=!1;if(4==j)switch(r[2]){case 1:r=this.findNotAttached(j,m,h[2],r[2]);n=r.nextSetBit(0);f=4==f?n:r.nextSetBit(n+1);break;default:x=!0}else{r=this.findNotAttached(j,m,h[2],r[2]);n=r.nextSetBit(0);for(p=j;p<f&&0<=n;p++)n=r.nextSetBit(n+1);-1==n?x=!0:f=n}x&&(b.sub2(c[m[h[0][0]][0]],a),d.sub2(c[m[h[0][0]][1]],a),b.cross(b,d),4==f&&b.scale(-1),f=-1)}0<=f&&b.sub2(c[f],a);k&&b.scale(-1);b.normalize();
return g?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(c$,"getAttached",function(a,b,d){var c=a.getCovalentBondCount();if(c>b)return null;b=Array(c);if(0<c){for(var c=a.bonds,g=0,f=0;f<c.length;f++)c[f].isCovalent()&&(b[g++]=c[f].getOtherAtom(a));d&&java.util.Arrays.sort(b,M(JM.AtomCollection.AtomSorter,this,null))}return b},"JM.Atom,~N,~B");c(c$,"findNotAttached",function(a,b,d,c){var g=JU.BS.newN(a);g.setBits(0,a);for(var f=0;f<a;f++)for(var j=0;j<c;j++){var k=b[d[j]];(k[0]==f||k[1]==f)&&g.clear(f)}return g},
"~N,~A,~A,~N");c(c$,"getAtomBitsMDa",function(a,b){var d=new JU.BS,c,g;c=p(b,Integer)?b.intValue():0;var f=0;switch(a){case 1613758488:return this.getWaterAtoms(d);case 1095761939:for(f=this.ac;0<=--f;)this.at[f].getResno()==c&&d.set(f);break;case 1297090050:for(f=this.ac;0<=--f;)this.at[f].getSymOp()==c&&d.set(f);break;case 1095763969:for(f=this.ac;0<=--f;)this.at[f].getAtomNumber()==c&&d.set(f);break;case 1087375362:c=","+b+",";for(f=this.ac;0<=--f;)g=this.at[f].getAtomName(),0<=c.indexOf(g)&&0<=
c.indexOf(","+g+",")&&d.set(f);break;case 1087375361:c=","+b+",";for(f=this.ac;0<=--f;)g=this.at[f].getAtomType(),0<=c.indexOf(g)&&0<=c.indexOf(","+g+",")&&d.set(f);break;case 1048613:for(f=this.ac;0<=--f;)this.at[f].getGroupID()==c&&d.set(f);break;case 1048609:return JU.BSUtil.copy(this.getChainBits(c));case 1048614:return JU.BSUtil.copy(this.getSeqcodeBits(c,!0));case 1613758470:for(f=this.ac;0<=--f;)this.at[f].isHetero()&&d.set(f);break;case 1613758476:for(f=this.ac;0<=--f;)1==this.at[f].getElementNumber()&&
d.set(f);break;case 3145741:for(f=this.ac;0<=--f;)this.at[f].isLeadAtom()&&d.set(f);break;case 3145744:for(f=this.ac;0<=--f;)this.at[f].isProtein()&&d.set(f);break;case 3145764:for(f=this.ac;0<=--f;)this.at[f].isCarbohydrate()&&d.set(f);break;case 137363467:case 3145760:g=137363467==a?J.c.STR.HELIX:J.c.STR.SHEET;for(f=this.ac;0<=--f;)this.at[f].isWithinStructure(g)&&d.set(f);break;case 3145742:for(f=this.ac;0<=--f;)this.at[f].isNucleic()&&d.set(f);break;case 3145732:for(f=this.ac;0<=--f;)this.at[f].isDna()&&
d.set(f);break;case 3145750:for(f=this.ac;0<=--f;)this.at[f].isRna()&&d.set(f);break;case 3145746:for(f=this.ac;0<=--f;)this.at[f].isPurine()&&d.set(f);break;case 3145748:for(f=this.ac;0<=--f;)this.at[f].isPyrimidine()&&d.set(f);break;case 1087375365:c=b;g=new JU.BS;for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))g.set(this.getElementNumber(f));for(f=this.ac;0<=--f;)g.get(this.getElementNumber(f))&&d.set(f);break;case 1095761941:c=b;g=new JU.BS;for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))g.set(this.at[f].atomSite);
for(f=this.ac;0<=--f;)g.get(this.at[f].atomSite)&&d.set(f);break;case 1073741824:return this.getIdentifierOrNull(b);case 1048608:c=b.toUpperCase();0<=c.indexOf("\\?")&&(c=JU.PT.rep(c,"\\?","\u0001"));(g=c.startsWith("?*"))&&(c=c.substring(1));for(f=this.ac;0<=--f;)this.isAtomNameMatch(this.at[f],c,g,g)&&d.set(f);break;case 1048607:for(f=this.ac;0<=--f;)this.at[f].isAltLoc(b)&&d.set(f);break;case 1048612:return this.getSpecName(b)}if(0>f)return d;c=b;var j;g=c.nextSetBit(0);if(0>g)return d;f=0;switch(a){case 1087373318:for(f=
g;0<=f;f=c.nextSetBit(f+1))g=this.at[f].getGroup().selectAtoms(d),g>f&&(f=g);break;case 1095766030:for(f=g;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.at[f].mi;d.set(f);for(g=f;0<=--g;)if(this.at[g].mi==j)d.set(g);else break;for(;++f<this.ac;)if(this.at[f].mi==j)d.set(f);else break}break;case 1087373316:c=JU.BSUtil.copy(b);for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))this.at[f].getChain().setAtomBitSet(d),c.andNot(d);break;case 1095761937:for(f=g;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.at[f].getPolymerIndexInModel();
d.set(f);for(g=f;0<=--g;)if(this.at[g].getPolymerIndexInModel()==j)d.set(g);else break;for(;++f<this.ac;)if(this.at[f].getPolymerIndexInModel()==j)d.set(f);else break}break;case 1641025539:for(f=g;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.at[f].getGroup().getStructure();d.set(f);for(g=f;0<=--g;)if(this.at[g].getGroup().getStructure()===j)d.set(g);else break;for(;++f<this.ac;)if(this.at[f].getGroup().getStructure()===j)d.set(f);else break}}0==f&&JU.Logger.error("MISSING getAtomBits entry for "+
JS.T.nameOf(a));return d},"~N,~O");c(c$,"getWaterAtoms",function(a){for(var b=D(2,0),d,c=this.ac;0<=--c;){var g=this.at[c].getGroupID();if(42<=g&&45>g)a.set(c);else if(8==(d=this.at[c]).getElementNumber()&&2==d.getCovalentBondCount()){for(var g=d.getBonds(),f=0,j,k=g.length;0<=--k&&3>f;)if(g[k].isCovalent()&&1==(j=g[k].getOtherAtom(d)).getElementNumber())b[f++%2]=j.i;2==f&&(a.set(b[1]),a.set(b[0]),a.set(c))}}return a},"JU.BS");c(c$,"getIdentifierOrNull",function(a){var b=this.getSpecNameOrNull(a,
!1);0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));if(null!=b||0<a.indexOf("?"))return b;if(0<a.indexOf("*"))return this.getSpecNameOrNull(a,!0);for(var d=a.length,c=0;c<d&&Character.isLetter(a.charAt(c));)++c;b=this.getSpecNameOrNull(a.substring(0,c),!1);if(c==d)return b;null==b&&(b=new JU.BS);for(var g=c;c<d&&Character.isDigit(a.charAt(c));)++c;var f=0;try{f=Integer.parseInt(a.substring(g,c))}catch(j){if(y(j,NumberFormatException))return null;throw j;}g=" ";c<d&&"^"==a.charAt(c)&&++c<d&&(g=
a.charAt(c));f=JM.Group.getSeqcodeFor(f,g);f=this.getSeqcodeBits(f,!1);if(null==f){" "!=g&&(f=this.getSeqcodeBits(Character.toUpperCase(a.charAt(c)).charCodeAt(0),!1));if(null==f)return null;c++}b.and(f);if(c>=d)return b;if(c!=d-1)return null;b.and(this.getChainBits(a.charCodeAt(c)));return b},"~S");c(c$,"getSpecName",function(a){var b=this.getSpecNameOrNull(a,!1);if(null!=b)return b;0<a.indexOf("*")&&(b=this.getSpecNameOrNull(a,!0));return null==b?new JU.BS:b},"~S");c(c$,"getSpecNameOrNull",function(a,
b){var d=null;a=a.toUpperCase();0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));var c=a.startsWith("?*");c&&(a=a.substring(1));for(var g=this.ac;0<=--g;){var f=this.at[g].getGroup3(!0);if(null!=f&&0<f.length){if(JU.Txt.isMatch(f,a,b,!0)){null==d&&(d=JU.BS.newN(g+1));for(d.set(g);0<=--g&&this.at[g].getGroup3(!0).equals(f);)d.set(g);g++}}else this.isAtomNameMatch(this.at[g],a,b,c)&&(null==d&&(d=JU.BS.newN(g+1)),d.set(g))}return d},"~S,~B");c(c$,"isAtomNameMatch",function(a,b,d,c){return JU.Txt.isMatch(a.getAtomName().toUpperCase(),
b,d,c)},"JM.Atom,~S,~B,~B");c(c$,"getSeqcodeBits",function(a,b){var d=new JU.BS,c=JM.Group.getSeqNumberFor(a),g=2147483647!=c,f=!0,j=JM.Group.getInsertionCodeChar(a);switch(j){case "?":for(var k=this.ac;0<=--k;){var h=this.at[k].getSeqcode();if(!g||c==JM.Group.getSeqNumberFor(h)&&0!=JM.Group.getInsertionCodeFor(h))d.set(k),f=!1}break;default:for(k=this.ac;0<=--k;)if(h=this.at[k].getSeqcode(),a==h||!g&&a==JM.Group.getInsertionCodeFor(h)||"*"==j&&c==JM.Group.getSeqNumberFor(h))d.set(k),f=!1}return!f||
b?d:null},"~N,~B");c(c$,"getChainBits",function(a){var b=256>a&&this.vwr.getBoolean(603979823);b||(a=JM.AtomCollection.chainToUpper(a));for(var d=new JU.BS,c=JU.BS.newN(this.ac),g,f=c.nextClearBit(0);f<this.ac;f=c.nextClearBit(f+1)){var j=this.at[f].getChain();a==(g=j.chainID)||!b&&a==JM.AtomCollection.chainToUpper(g)?(j.setAtomBitSet(d),c.or(d)):j.setAtomBitSet(c)}return d},"~N");c$.chainToUpper=c(c$,"chainToUpper",function(a){return String.fromCharCode(a).toUpperCase().charCodeAt(0)},"~N");c(c$,
"getAtomIndices",function(a){for(var b=0,d=D(this.ac,0),c=a.nextSetBit(0);0<=c&&c<this.ac;c=a.nextSetBit(c+1))d[c]=++b;return d},"JU.BS");c(c$,"getAtomsNearPlane",function(a,b){for(var d=new JU.BS,c=this.ac;0<=--c;){var g=this.at[c],f=JU.Measure.distanceToPlane(b,g);(0<a&&-0.1<=f&&f<=a||0>a&&0.1>=f&&f>=a||0==a&&0.01>Math.abs(f))&&d.set(g.i)}return d},"~N,JU.P4");c(c$,"getAtomsNearPts",function(a,b,d){var c=new JU.BS;if(0==b.length||null!=d&&0==d.cardinality())return c;null==d&&(d=JU.BSUtil.setAll(b.length));
for(var g=this.ac;0<=--g;)for(var f=this.at[g],j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))if(f.distance(b[j])<a){c.set(g);break}return c},"~N,~A,JU.BS");c(c$,"getRenderable",function(a){a.clearAll();this.haveBSClickable=this.haveBSVisible=!1;for(var b=this.ac;0<=--b;)this.at[b].isVisible(1)&&a.set(b)},"JU.BS");c(c$,"getVisibleSet",function(){if(this.haveBSVisible)return this.bsVisible;this.bsVisible.clearAll();for(var a=this.ac;0<=--a;)this.at[a].checkVisible()&&this.bsVisible.set(a);this.haveBSVisible=
!0;return this.bsVisible});c(c$,"getClickableSet",function(){if(this.haveBSClickable)return this.bsClickable;this.bsClickable.clearAll();for(var a=this.ac;0<=--a;)this.at[a].isClickable()&&this.bsClickable.set(a);this.haveBSClickable=!0;return this.bsClickable});c(c$,"isModulated",function(a){return null!=this.bsModulated&&this.bsModulated.get(a)},"~N");c(c$,"deleteModelAtoms",function(a,b,d){this.at=JU.AU.deleteElements(this.at,a,b);this.ac=this.at.length;for(var c=a;c<this.ac;c++)this.at[c].i=c,
this.at[c].mi--;null!=this.bsModulated&&JU.BSUtil.deleteBits(this.bsModulated,d);this.deleteAtomTensors(d);this.atomNames=JU.AU.deleteElements(this.atomNames,a,b);this.atomTypes=JU.AU.deleteElements(this.atomTypes,a,b);this.atomSerials=JU.AU.deleteElements(this.atomSerials,a,b);this.atomSeqIDs=JU.AU.deleteElements(this.atomSeqIDs,a,b);this.bfactor100s=JU.AU.deleteElements(this.bfactor100s,a,b);this.hasBfactorRange=!1;this.occupancies=JU.AU.deleteElements(this.occupancies,a,b);this.partialCharges=
JU.AU.deleteElements(this.partialCharges,a,b);this.atomTensorList=JU.AU.deleteElements(this.atomTensorList,a,b);this.vibrations=JU.AU.deleteElements(this.vibrations,a,b);this.nSurfaceAtoms=0;this.surfaceDistance100s=this.bsSurface=null;if(null!=this.tainted)for(a=0;15>a;a++)JU.BSUtil.deleteBits(this.tainted[a],d)},"~N,~N,JU.BS");c(c$,"getAtomIdentityInfo",function(a,b,d){b.put("_ipt",Integer.$valueOf(a));b.put("atomIndex",Integer.$valueOf(a));b.put("atomno",Integer.$valueOf(this.getAtomNumber(a)));
b.put("info",this.getAtomInfo(a,null,d));b.put("sym",this.getElementSymbol(a))},"~N,java.util.Map,JU.P3");c(c$,"getAtomTensorList",function(a){return 0>a||null==this.atomTensorList||a>=this.atomTensorList.length?null:this.atomTensorList[a]},"~N");c(c$,"deleteAtomTensors",function(a){if(null!=this.atomTensors){for(var b=new JU.Lst,d,c=this.atomTensors.keySet().iterator();c.hasNext()&&((d=c.next())||1);){for(var g=this.atomTensors.get(d),f=g.size();0<=--f;){var j=g.get(f);(a.get(j.atomIndex1)||0<=j.atomIndex2&&
a.get(j.atomIndex2))&&g.remove(f)}0==g.size()&&b.addLast(d)}for(f=b.size();0<=--f;)this.atomTensors.remove(b.get(f))}},"JU.BS");c(c$,"setAtomTensors",function(a,b){if(!(null==b||0==b.size())){null==this.atomTensors&&(this.atomTensors=new java.util.Hashtable);null==this.atomTensorList&&(this.atomTensorList=Array(this.at.length));this.atomTensorList=JU.AU.ensureLength(this.atomTensorList,this.at.length);this.atomTensorList[a]=JM.AtomCollection.getTensorList(b);for(var d=b.size();0<=--d;){var c=b.get(d);
c.atomIndex1=a;c.atomIndex2=-1;c.modelIndex=this.at[a].mi;this.addTensor(c,c.type);null!=c.altType&&this.addTensor(c,c.altType)}}},"~N,JU.Lst");c$.getTensorList=c(c$,"getTensorList",function(a){for(var b=-1,d=!1,c=a.size(),g=c;0<=--g;){var f=a.get(g);f.forThermalEllipsoid?b=g:2==f.iType&&(d=!0)}var j=Array((0<=b||!d?0:1)+c);if(0<=b&&(j[0]=a.get(b),1==a.size()))return j;if(d){b=0;for(g=c;0<=--g;)f=a.get(g),f.forThermalEllipsoid||(j[++b]=f)}else for(g=0;g<c;g++)j[g]=a.get(g);return j},"JU.Lst");c(c$,
"getAtomTensor",function(a,b){var d=this.getAtomTensorList(a);if(null!=d&&null!=b){b=b.toLowerCase();for(var c=0;c<d.length;c++){var g=d[c];if(null!=g&&(b.equals(g.type)||b.equals(g.altType)))return g}}return null},"~N,~S");c(c$,"addTensor",function(a,b){b=b.toLowerCase();var d=this.atomTensors.get(b);null==d&&this.atomTensors.put(b,d=new JU.Lst);d.addLast(a)},"JU.Tensor,~S");c(c$,"getAllAtomTensors",function(a){if(null==this.atomTensors)return null;if(null!=a)return this.atomTensors.get(a.toLowerCase());
a=new JU.Lst;for(var b,d=this.atomTensors.entrySet().iterator();d.hasNext()&&((b=d.next())||1);)a.addAll(b.getValue());return a},"~S");c$.$AtomCollection$AtomSorter$=function(){G(self.c$);c$=t(function(){Q(this,arguments);s(this,arguments)},JM.AtomCollection,"AtomSorter",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.i>b.i?1:a.i<b.i?-1:0},"JM.Atom,JM.Atom");c$=F()};c$.MINUSZERO=c$.prototype.MINUSZERO=Float.$valueOf(-0);C(c$,"TAINT_ATOMNAME",0,"TAINT_ATOMTYPE",1,"TAINT_COORD",2,"TAINT_ELEMENT",
3,"TAINT_FORMALCHARGE",4,"TAINT_HYDROPHOBICITY",5,"TAINT_BONDINGRADIUS",6,"TAINT_OCCUPANCY",7,"TAINT_PARTIALCHARGE",8,"TAINT_TEMPERATURE",9,"TAINT_VALENCE",10,"TAINT_VANDERWAALS",11,"TAINT_VIBRATION",12,"TAINT_ATOMNO",13,"TAINT_SEQID",14,"TAINT_MAX",15,"userSettableValues",null);JM.AtomCollection.userSettableValues="atomName atomType coord element formalCharge hydrophobicity ionic occupany partialCharge temperature valence vanderWaals vibrationVector atomNo seqID".$plit(" ");c$.sqrt3_2=c$.prototype.sqrt3_2=
Math.sqrt(3)/2;c$.vRef=c$.prototype.vRef=JU.V3.new3(3.14159,2.71828,1.41421);C(c$,"almost180",2.984513)});n("JM");w(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){c$=t(function(){this.bspf=this.cubeIterator=null;this.isZeroBased=this.hemisphereOnly=this.threadSafe=!1;this.modelIndex=2147483647;this.atomIndex=-1;this.distanceSquared=this.zeroBase=0;this.bsSelected=null;this.checkGreater=this.isGreaterOnly=!1;this.radiusData=null;this.vdw1=0;this.isVdw=
!1;this.vwr=this.atoms=null;this.iNext=0;s(this,arguments)},JM,"AtomIteratorWithinModel",null,J.api.AtomIndexIterator);u(c$,function(){});c(c$,"initialize",function(a,b,d,c,g,f){this.bspf=a;this.bsSelected=b;this.isGreaterOnly=d;this.isZeroBased=c;this.hemisphereOnly=g;this.threadSafe=f;this.cubeIterator=null},"J.bspt.Bspf,JU.BS,~B,~B,~B,~B");h(c$,"setModel",function(a,b,d,c,g,f,j){this.threadSafe&&(b=-1-b);if(b!=this.modelIndex||null==this.cubeIterator)this.cubeIterator=this.bspf.getCubeIterator(b),
this.modelIndex=b;this.zeroBase=this.isZeroBased?d:0;if(-2147483648!=f){this.atomIndex=0>f?-1:c;if(this.isVdw=null!=j)this.radiusData=j,this.atoms=a.at,this.vwr=a.vwr,f=j.factorType===J.atomdata.RadiusData.EnumType.OFFSET?5+j.value:5*j.value,this.vdw1=this.atoms[c].getVanderwaalsRadiusFloat(this.vwr,j.vdwType);this.checkGreater=this.isGreaterOnly&&2147483647!=c;this.setCenter(g,f)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");h(c$,"setCenter",function(a,b){this.setCenter2(a,b)},"JU.T3,~N");
c(c$,"setCenter2",function(a,b){null!=this.cubeIterator&&(this.cubeIterator.initialize(a,b,this.hemisphereOnly),this.distanceSquared=b*b)},"JU.T3,~N");h(c$,"hasNext",function(){return this.hasNext2()});c(c$,"hasNext2",function(){if(0<=this.atomIndex)for(;this.cubeIterator.hasMoreElements();){var a=this.cubeIterator.nextElement();if((this.iNext=a.i)!=this.atomIndex&&(!this.checkGreater||this.iNext>this.atomIndex)&&(null==this.bsSelected||this.bsSelected.get(this.iNext)))return!0}else if(this.cubeIterator.hasMoreElements())return a=
this.cubeIterator.nextElement(),this.iNext=a.i,!0;this.iNext=-1;return!1});h(c$,"next",function(){return this.iNext-this.zeroBase});h(c$,"foundDistance2",function(){return null==this.cubeIterator?-1:this.cubeIterator.foundDistance2()});h(c$,"addAtoms",function(a){for(var b;this.hasNext();)if(0<=(b=this.next())){var d;if(this.isVdw){d=this.atoms[b].getVanderwaalsRadiusFloat(this.vwr,this.radiusData.vdwType)+this.vdw1;switch(this.radiusData.factorType){case J.atomdata.RadiusData.EnumType.OFFSET:d+=
2*this.radiusData.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:d*=this.radiusData.value}d*=d}else d=this.distanceSquared;this.foundDistance2()<=d&&a.set(b)}},"JU.BS");h(c$,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)})});n("JM");w(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){c$=t(function(){this.center=this.bsModels=null;this.distance=0;s(this,arguments)},JM,"AtomIteratorWithinModelSet",JM.AtomIteratorWithinModel);
u(c$,function(a){E(this,JM.AtomIteratorWithinModelSet,[]);this.bsModels=a},"JU.BS");h(c$,"setCenter",function(a,b){this.center=a;this.distance=b;this.set(0)},"JU.T3,~N");c(c$,"set",function(a){if(0>(this.modelIndex=this.bsModels.nextSetBit(a))||null==(this.cubeIterator=this.bspf.getCubeIterator(this.modelIndex)))return!1;this.setCenter2(this.center,this.distance);return!0},"~N");h(c$,"hasNext",function(){return this.hasNext2()?!0:!this.set(this.modelIndex+1)?!1:this.hasNext()})});n("JM");w(["JU.Edge",
"JV.JC"],"JM.Bond",["JU.C"],function(){c$=t(function(){this.atom2=this.atom1=null;this.shapeVisibilityFlags=this.colix=this.mad=0;s(this,arguments)},JM,"Bond",JU.Edge);u(c$,function(a,b,d,c,g){E(this,JM.Bond,[]);this.atom1=a;this.atom2=b;this.colix=g;this.setOrder(d);this.setMad(c)},"JM.Atom,JM.Atom,~N,~N,~N");c(c$,"setMad",function(a){this.mad=a;this.setShapeVisibility(0!=a)},"~N");c(c$,"setShapeVisibilityFlags",function(a){this.shapeVisibilityFlags=a},"~N");c(c$,"getShapeVisibilityFlags",function(){return this.shapeVisibilityFlags});
c(c$,"setShapeVisibility",function(a){0!=(this.shapeVisibilityFlags&JM.Bond.myVisibilityFlag)!=a&&(this.atom1.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.atom2.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.shapeVisibilityFlags=a?this.shapeVisibilityFlags|JM.Bond.myVisibilityFlag:this.shapeVisibilityFlags&~JM.Bond.myVisibilityFlag)},"~B");c(c$,"getIdentity",function(){return this.index+1+" "+this.getOrderNumberAsString()+" "+this.atom1.getInfo()+" -- "+this.atom2.getInfo()+" "+this.atom1.distance(this.atom2)});
h(c$,"isCovalent",function(){return 0!=(this.order&1023)});h(c$,"isHydrogen",function(){return JM.Bond.isOrderH(this.order)});c$.isOrderH=c(c$,"isOrderH",function(a){return 0!=(a&30720)},"~N");c(c$,"isStereo",function(){return 0!=(this.order&1024)});c(c$,"isPartial",function(){return 0!=(this.order&224)});c(c$,"isAromatic",function(){return 0!=(this.order&512)});c(c$,"isPymolStyle",function(){return 98304==(this.order&98304)});c(c$,"setPaletteID",function(){},"~N");c(c$,"getEnergy",function(){return 0});
c(c$,"getValence",function(){return!this.isCovalent()?0:this.isPartial()||this.is(515)?1:this.order&7});c(c$,"deleteAtomReferences",function(){null!=this.atom1&&this.atom1.deleteBond(this);null!=this.atom2&&this.atom2.deleteBond(this);this.atom1=this.atom2=null});c(c$,"setColix",function(a){this.colix=a},"~N");c(c$,"setTranslucent",function(a,b){this.colix=JU.C.getColixTranslucent3(this.colix,a,b)},"~B,~N");c(c$,"setOrder",function(a){16==this.atom1.getElementNumber()&&16==this.atom2.getElementNumber()&&
(a|=256);512==a&&(a=515);this.order=a|this.order&131072},"~N");c(c$,"getAtom1",function(){return this.atom1});c(c$,"getAtom2",function(){return this.atom2});h(c$,"getAtomIndex1",function(){return this.atom1.i});h(c$,"getAtomIndex2",function(){return this.atom2.i});c(c$,"getRadius",function(){return this.mad/2E3});h(c$,"getCovalentOrder",function(){return JU.Edge.getCovalentBondOrder(this.order)});c(c$,"getOrderName",function(){return JU.Edge.getBondOrderNameFromOrder(this.order)});c(c$,"getOrderNumberAsString",
function(){return JU.Edge.getBondOrderNumberFromOrder(this.order)});c(c$,"getColix1",function(){return JU.C.getColixInherited(this.colix,this.atom1.colixAtom)});c(c$,"getColix2",function(){return JU.C.getColixInherited(this.colix,this.atom2.colixAtom)});c(c$,"getOtherAtom",function(a){return this.atom1===a?this.atom2:this.atom2===a?this.atom1:null},"JM.Atom");c(c$,"setIndex",function(a){this.index=a},"~N");c(c$,"is",function(a){return(this.order&-131073)==a},"~N");h(c$,"getOtherAtomNode",function(a){return this.atom1===
a?this.atom2:this.atom2===a?this.atom1:null},"JU.Node");h(c$,"toString",function(){return this.atom1+" - "+this.atom2});c$.myVisibilityFlag=c$.prototype.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(1)});n("JM");w(["JM.AtomCollection","JU.BS"],"JM.BondCollection","JU.AU JM.Bond $.BondIteratorSelected $.HBond JU.BSUtil $.Edge $.Logger".split(" "),function(){c$=t(function(){this.molecules=null;this.moleculeCount=0;this.bo=null;this.bondCount=0;this.freeBonds=this.numCached=null;this.haveWarned=!1;this.defaultCovalentMad=
0;this.bsAromatic=this.bsAromaticDouble=this.bsAromaticSingle=null;this.haveHiddenBonds=!1;s(this,arguments)},JM,"BondCollection",JM.AtomCollection);K(c$,function(){this.numCached=D(5,0);this.freeBonds=Array(5);for(var a=5;0<--a;)this.freeBonds[a]=Array(200);this.bsAromatic=new JU.BS});h(c$,"releaseModelSet",function(){this.releaseModelSetBC()});c(c$,"releaseModelSetBC",function(){this.freeBonds=this.bo=null;this.releaseModelSetAC()});c(c$,"resetMolecules",function(){this.molecules=null;this.moleculeCount=
0});c(c$,"getBondAt",function(a){return this.bo[a]},"~N");c(c$,"getBondIteratorForType",function(a,b){return new JM.BondIteratorSelected(this.bo,this.bondCount,a,b,this.vwr.getBoolean(603979812))},"~N,JU.BS");c(c$,"getBondIterator",function(a){return new JM.BondIteratorSelected(this.bo,this.bondCount,131071,a,!1)},"JU.BS");c(c$,"getBondAtom1",function(a){return this.bo[a].atom1},"~N");c(c$,"getBondAtom2",function(a){return this.bo[a].atom2},"~N");c(c$,"getBondRadius",function(a){return this.bo[a].getRadius()},
"~N");c(c$,"getBondOrder",function(a){return this.bo[a].order},"~N");c(c$,"getBondColix1",function(a){return this.bo[a].getColix1()},"~N");c(c$,"getBondColix2",function(a){return this.bo[a].getColix2()},"~N");c(c$,"getBondModelIndex",function(a){return this.bo[a].atom1.mi},"~N");c(c$,"getBondCountInModel",function(a){for(var b=0,d=this.bondCount;0<=--d;)this.bo[d].atom1.mi==a&&b++;return b},"~N");c(c$,"getBondsForSelectedAtoms",function(a,b){for(var d=new JU.BS,c=0;c<this.bondCount;++c){var g=this.bo[c],
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p(this.bo[a],JM.HBond)&&(this.bo[a].energy=f))):(this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+250)),a=this.setBond(this.bondCount++,this.bondMutually(a,b,d,c,f)).index);null!=g&&g.set(a);return this.bo[a]},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B");c(c$,"setBond",function(a,b){return this.bo[b.index=a]=b},"~N,JM.Bond");c(c$,"bondMutually",function(a,b,d,c,g){d=JM.Bond.isOrderH(d)?new JM.HBond(a,b,d,c,0,g):new JM.Bond(a,b,d,c,0);this.addBondToAtom(a,d);this.addBondToAtom(b,
d);return d},"JM.Atom,JM.Atom,~N,~N,~N");c(c$,"addBondToAtom",function(a,b){null==a.bonds?(a.bonds=Array(1),a.bonds[0]=b):a.bonds=this.addToBonds(b,a.bonds)},"JM.Atom,JM.Bond");c(c$,"addToBonds",function(a,b){var d;if(null==b)d=0<this.numCached[1]?this.freeBonds[1][--this.numCached[1]]:Array(1),d[0]=a;else{var c=b.length;d=c+1;d=5>d&&0<this.numCached[d]?this.freeBonds[d][--this.numCached[d]]:Array(d);d[c]=a;for(var g=c;0<=--g;)d[g]=b[g];5>c&&200>this.numCached[c]&&(this.freeBonds[c][this.numCached[c]++]=
b)}return d},"JM.Bond,~A");c(c$,"addHBond",function(a,b,d,c){this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+250));return this.setBond(this.bondCount++,this.bondMutually(a,b,d,1,c)).index},"JM.Atom,JM.Atom,~N,~N");c$.getBondOrderFull=c(c$,"getBondOrderFull",function(a,b,d,c,g){if(0==a||0==b||d<c)return 0;a=a+b+g;return d>a*a?0:1},"~N,~N,~N,~N,~N");c(c$,"checkValencesAndBond",function(a,b,d,c,g){if(20<a.getCurrentBondCount()||20<b.getCurrentBondCount())return this.haveWarned||
JU.Logger.warn("maximum auto bond count reached"),this.haveWarned=!0,!1;var f=a.getFormalCharge();if(0!=f){var j=b.getFormalCharge();if(0>f&&0>j||0<f&&0<j)return!1}if(a.altloc!=b.altloc&&"\x00"!=a.altloc&&"\x00"!=b.altloc&&null==this.getVibration(a.i,!1))return!1;this.getOrAddBond(a,b,d,c,g,0,!1);return!0},"JM.Atom,JM.Atom,~N,~N,JU.BS");c(c$,"deleteAllBonds2",function(){this.vwr.setShapeProperty(1,"reset",null);for(var a=this.bondCount;0<=--a;)this.bo[a].deleteAtomReferences(),this.bo[a]=null;this.bondCount=
0});c(c$,"getDefaultMadFromOrder",function(a){return JM.Bond.isOrderH(a)?1:32768==a?q(Math.floor(2E3*this.vwr.getFloat(570425406))):this.defaultCovalentMad},"~N");c(c$,"deleteConnections",function(a,b,d,c,g,f,j){var k=0>a,h=0>b,m=k||h;a=this.fixD(a,k);b=this.fixD(b,h);var r=new JU.BS,x=0,A=d|=131072;!j&&JM.Bond.isOrderH(d)&&(d=30720);if(f)f=c;else{f=new JU.BS;for(var n=c.nextSetBit(0);0<=n;n=c.nextSetBit(n+1)){var q=this.at[n];if(null!=q.bonds)for(var p=q.bonds.length;0<=--p;)g.get(q.getBondedAtomIndex(p))&&
f.set(q.bonds[p].index)}}for(n=f.nextSetBit(0);n<this.bondCount&&0<=n;n=f.nextSetBit(n+1))if(c=this.bo[n],this.isInRange(c.atom1,c.atom2,a,b,k,h,m)&&(j||A==(c.order&-257|131072)||0!=(d&c.order&30720)))r.set(n),x++;0<x&&this.dBm(r,!1);return[0,x]},"~N,~N,~N,JU.BS,JU.BS,~B,~B");c(c$,"fixD",function(a,b){return b?-a:a*a},"~N,~B");c(c$,"isInRange",function(a,b,d,c,g,f,j){var k=a.distanceSquared(b);return j?(j=Math.sqrt(k),a=a.getBondingRadius()+b.getBondingRadius(),(g?j>=a*d:k>=d)&&(f?j<=a*c:k<=c)):k>=
d&&k<=c},"JM.Atom,JM.Atom,~N,~N,~B,~B,~B");c(c$,"dBm",function(a,b){this.deleteBonds(a,b)},"JU.BS,~B");c(c$,"dBb",function(a,b){var d=a.nextSetBit(0);if(!(0>d)){this.resetMolecules();for(var c=-1,g=a.cardinality(),f=d;f<this.bondCount;++f){var j=this.bo[f];if(0<g&&a.get(f)){g--;if(!b){var k=j.atom1.mi;k!=c&&this.am[c=k].resetBoundCount()}j.deleteAtomReferences()}else this.setBond(d++,j)}for(c=this.bondCount;--c>=d;)this.bo[c]=null;this.bondCount=d;d=this.vwr.getShapeProperty(1,"sets");if(null!=d)for(c=
0;c<d.length;c++)JU.BSUtil.deleteBits(d[c],a);JU.BSUtil.deleteBits(this.bsAromatic,a)}},"JU.BS,~B");c(c$,"resetAromatic",function(){for(var a=this.bondCount;0<=--a;){var b=this.bo[a];b.isAromatic()&&b.setOrder(515)}});c(c$,"assignAromaticBonds",function(){this.assignAromaticBondsBs(!0,null)});c(c$,"assignAromaticBondsBs",function(a,b){a||(this.bsAromatic=new JU.BS);this.bsAromaticSingle=new JU.BS;this.bsAromaticDouble=new JU.BS;for(var d=null==b,c=d?this.bondCount-1:b.nextSetBit(0),g=c;0<=g;g=d?g-
1:b.nextSetBit(g+1)){var f=this.bo[g];this.bsAromatic.get(g)&&f.setOrder(515);switch(f.order&-131073){case 515:this.bsAromatic.set(g);break;case 513:this.bsAromaticSingle.set(g);break;case 514:this.bsAromaticDouble.set(g)}}for(g=c=(d=null==b)?this.bondCount-1:b.nextSetBit(0);0<=g;g=d?g-1:b.nextSetBit(g+1))f=this.bo[g],f.is(515)&&(!this.bsAromaticDouble.get(g)&&!this.bsAromaticSingle.get(g))&&(this.assignAromaticDouble(f)||this.assignAromaticSingle(f));for(g=c;0<=g;g=d?g-1:b.nextSetBit(g+1))if(f=this.bo[g],
this.bsAromaticDouble.get(g))f.is(514)||(this.bsAromatic.set(g),f.setOrder(514));else if((this.bsAromaticSingle.get(g)||f.isAromatic())&&!f.is(513))this.bsAromatic.set(g),f.setOrder(513);this.assignAromaticNandO(b);this.bsAromaticDouble=this.bsAromaticSingle=null},"~B,JU.BS");c(c$,"assignAromaticDouble",function(a){var b=a.index;if(this.bsAromaticSingle.get(b))return!1;if(this.bsAromaticDouble.get(b))return!0;this.bsAromaticDouble.set(b);return!this.assignAromaticSingleForAtom(a.atom1,b)||!this.assignAromaticSingleForAtom(a.atom2,
b)?(this.bsAromaticDouble.clear(b),!1):!0},"JM.Bond");c(c$,"assignAromaticSingle",function(a){var b=a.index;if(this.bsAromaticDouble.get(b))return!1;if(this.bsAromaticSingle.get(b))return!0;this.bsAromaticSingle.set(b);return!this.assignAromaticDoubleForAtom(a.atom1)||!this.assignAromaticDoubleForAtom(a.atom2)?(this.bsAromaticSingle.clear(b),!1):!0},"JM.Bond");c(c$,"assignAromaticSingleForAtom",function(a,b){var d=a.bonds;if(null==d||this.assignAromaticSingleHetero(a))return!1;for(var c=d.length;0<=
--c;){var g=d[c],f=g.index;if(!(f==b||!g.isAromatic()||this.bsAromaticSingle.get(f)))if(this.bsAromaticDouble.get(f)||!this.assignAromaticSingle(g))return!1}return!0},"JM.Atom,~N");c(c$,"assignAromaticDoubleForAtom",function(a){var b=a.bonds;if(null==b)return!1;a=this.assignAromaticSingleHetero(a);for(var d=-1,c=b.length;0<=--c;)this.bsAromaticDouble.get(b[c].index)&&(a=!0),b[c].isAromatic()&&(d=c);for(c=b.length;0<=--c;){var g=b[c],f=g.index;if(g.isAromatic()&&!this.bsAromaticDouble.get(f)&&!this.bsAromaticSingle.get(f))if(!a&&
this.assignAromaticDouble(g))a=!0;else if((a||c<d)&&!this.assignAromaticSingle(g))return!1}return a},"JM.Atom");c(c$,"assignAromaticSingleHetero",function(a){var b=a.getElementNumber();switch(b){case 6:case 7:case 8:case 16:break;default:return!0}var d=a.getValence();switch(b){case 6:return 4==d;case 7:case 8:return d==10-b&&1>a.getFormalCharge();case 16:return d==18-b&&1>a.getFormalCharge()}return!1},"JM.Atom");c(c$,"assignAromaticNandO",function(a){for(var b,d=null==a,c=d?this.bondCount-1:a.nextSetBit(0);0<=
c;c=d?c-1:a.nextSetBit(c+1))if(b=this.bo[c],b.is(513)){var g,f=b.atom2,j,k=f.getElementNumber();7==k||8==k?(j=k,g=f,f=b.atom1,k=f.getElementNumber()):(g=b.atom1,j=g.getElementNumber());if(!(7!=j&&8!=j)){var h=g.getValence();if(!(0>h)){var m=g.getCovalentBondCount();g=g.getFormalCharge();switch(j){case 7:3==h&&(3==m&&1>g&&6==k&&3==f.getValence())&&b.setOrder(514);break;case 8:1==h&&(0==g&&(14==k||16==k))&&b.setOrder(514)}}}}},"JU.BS");c(c$,"getAtomBitsMDb",function(a,b){var d;switch(a){default:return this.getAtomBitsMDa(a,
b);case 1678770178:d=new JU.BS;for(var c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))d.set(this.bo[c].atom1.i),d.set(this.bo[c].atom2.i);return d;case 1048585:d=new JU.BS;for(c=this.bondCount;0<=--c;)this.bo[c].isAromatic()&&(d.set(this.bo[c].atom1.i),d.set(this.bo[c].atom2.i));return d}},"~N,~O");c(c$,"setBondOrder",function(a,b){var d=b.charCodeAt(0)-48,c=this.bo[a];switch(b){case "0":case "1":case "2":case "3":break;case "p":case "m":d=JU.Edge.getBondOrderNumberFromOrder(c.getCovalentOrder()).charCodeAt(0)-
48+("p"==b?1:-1);3<d?d=1:0>d&&(d=3);break;default:return null}var g=new JU.BS;try{if(0==d){var f=new JU.BS;f.set(c.index);g.set(c.getAtomIndex1());g.set(c.getAtomIndex2());this.dBm(f,!1);return g}c.setOrder(d|131072);this.removeUnnecessaryBonds(c.atom1,!1);this.removeUnnecessaryBonds(c.atom2,!1);g.set(c.getAtomIndex1());g.set(c.getAtomIndex2())}catch(j){if(y(j,Exception))JU.Logger.error("Exception in seBondOrder: "+j.toString());else throw j;}return g},"~N,~S");c(c$,"removeUnnecessaryBonds",function(a,
b){var d=new JU.BS,c=new JU.BS,g=a.bonds;if(null!=g){for(var f=0;f<g.length;f++)g[f].isCovalent()?1==g[f].getOtherAtom(a).getElementNumber()&&d.set(g[f].getOtherAtom(a).i):c.set(g[f].index);0<=c.nextSetBit(0)&&this.dBm(c,!1);b&&d.set(a.i);0<=d.nextSetBit(0)&&this.vwr.deleteAtoms(d,!1)}},"JM.Atom,~B");c(c$,"displayBonds",function(a,b){b||(this.haveHiddenBonds=!0);for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))d<this.bondCount&&0!=this.bo[d].mad&&this.bo[d].setShapeVisibility(b)},"JM.BondSet,~B");
C(c$,"BOND_GROWTH_INCREMENT",250,"MAX_BONDS_LENGTH_TO_CACHE",5,"MAX_NUM_TO_CACHE",200)});n("JM");H(JM,"BondIterator");n("JM");w(["JM.BondIterator"],"JM.BondIteratorSelected",null,function(){c$=t(function(){this.bonds=null;this.iBond=this.bondType=this.bondCount=0;this.bsSelected=null;this.bondSelectionModeOr=!1;s(this,arguments)},JM,"BondIteratorSelected",null,JM.BondIterator);u(c$,function(a,b,d,c,g){this.bonds=a;this.bondCount=b;this.bondType=d;this.bsSelected=c;this.bondSelectionModeOr=g},"~A,~N,~N,JU.BS,~B");
h(c$,"hasNext",function(){if(131071==this.bondType)return this.iBond=this.bsSelected.nextSetBit(this.iBond),0<=this.iBond&&this.iBond<this.bondCount;for(;this.iBond<this.bondCount;++this.iBond){var a=this.bonds[this.iBond];if(!(65535!=this.bondType&&0==(a.order&this.bondType))&&!(65535==this.bondType&&32768!=a.order)){var b=this.bsSelected.get(a.atom1.i),a=this.bsSelected.get(a.atom2.i);if(!this.bondSelectionModeOr&&b&&a||this.bondSelectionModeOr&&(b||a))return!0}}return!1});h(c$,"nextIndex",function(){return this.iBond});
h(c$,"next",function(){return this.bonds[this.iBond++]})});n("JM");w(["JU.BS"],"JM.BondSet",["JU.BSUtil"],function(){c$=t(function(){this.associatedAtoms=null;s(this,arguments)},JM,"BondSet",JU.BS);u(c$,function(){E(this,JM.BondSet,[])});c(c$,"getAssociatedAtoms",function(){return this.associatedAtoms});u(c$,function(a){E(this,JM.BondSet,[]);JU.BSUtil.copy2(a,this)},"JU.BS");u(c$,function(a,b){this.construct(a);this.associatedAtoms=b},"JU.BS,~A")});n("JM");c$=t(function(){this.model=null;this.index=
this.chainID=0;this.isRna=this.isDna=!1;this.groupCount=0;this.groups=null;this.selectedGroupCount=0;s(this,arguments)},JM,"Chain");K(c$,function(){this.groups=Array(16)});c(c$,"getAtom",function(a){return this.model.ms.at[a]},"~N");u(c$,function(a,b,d){this.model=a;this.chainID=b;this.index=d},"JM.Model,~N,~N");c(c$,"getGroup",function(a){return this.groups[a]},"~N");c(c$,"getGroupCount",function(){return this.groupCount});c(c$,"calcSelectedGroupsCount",function(a){for(var b=this.selectedGroupCount=
0;b<this.groupCount;b++)this.groups[b].selectedIndex=this.groups[b].isSelected(a)?this.selectedGroupCount++:-1},"JU.BS");c(c$,"selectSeqcodeRange",function(a,b,d,c){var g,f,j,k=!1;for(f=a;f<this.groupCount&&this.groups[f].seqcode!=b;f++);if(f==this.groupCount){if(0<a)return-1;k=!0;j=2147483647;for(var h=this.groupCount;0<=--h;)if((g=this.groups[h].seqcode)>b&&g-b<j)f=h,j=g-b;if(2147483647==j)return-1}if(2147483647==d)b=this.groupCount-1,k=!0;else{for(b=f;b<this.groupCount&&this.groups[b].seqcode!=
d;b++);if(b==this.groupCount){if(0<a)return-1;k=!0;j=2147483647;for(h=f;h<this.groupCount;h++)if((g=this.groups[h].seqcode)<d&&d-g<j)b=h,j=d-g;if(2147483647==j)return-1}}for(h=f;h<=b;++h)this.groups[h].selectAtoms(c);return k?-1:b+1},"~N,~N,~N,JU.BS");c(c$,"fixIndices",function(a,b){for(var d=0;d<this.groupCount;d++)this.groups[d].fixIndices(a,b)},"~N,JU.BS");c(c$,"setAtomBitSet",function(a){for(var b=0;b<this.groupCount;b++)this.groups[b].selectAtoms(a)},"JU.BS");c(c$,"getIDStr",function(){return 0==
this.chainID?"":256>this.chainID?""+String.fromCharCode(this.chainID):this.model.ms.vwr.chainMap.get(Integer.$valueOf(this.chainID))});n("JM");w(["java.lang.Short","JV.JC"],"JM.Group","java.util.Hashtable JU.BS $.Quat J.c.STR JU.BSUtil $.Escape $.Logger".split(" "),function(){c$=t(function(){this.groupIndex=0;this.group1="\x00";this.chain=null;this.leadAtomIndex=this.firstAtomIndex=-1;this.groupID=this.seqcode=this.lastAtomIndex=0;this.$isProtein=!1;this.shapeVisibilityFlags=this.selectedIndex=0;
this.bsAdded=null;s(this,arguments)},JM,"Group");c(c$,"getGroupIndex",function(){return this.groupIndex});c(c$,"setGroupIndex",function(a){this.groupIndex=a},"~N");u(c$,function(){});c(c$,"setGroup",function(a,b,d,c,g){this.chain=a;this.seqcode=d;null==b&&(b="");this.groupID=JV.JC.getGroupIdFor(b);this.$isProtein=1<=this.groupID&&24>this.groupID;this.firstAtomIndex=c;this.lastAtomIndex=g;return this},"JM.Chain,~S,~N,~N,~N");c(c$,"setModelSet",function(a){this.chain.model.ms=a},"JM.ModelSet");c(c$,
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function(){return this.$isProtein});c(c$,"isNucleic",function(){return 24<=this.groupID&&42>this.groupID});c(c$,"isDna",function(){return!1});c(c$,"isRna",function(){return!1});c(c$,"isPurine",function(){return!1});c(c$,"isPyrimidine",function(){return!1});c(c$,"isCarbohydrate",function(){return!1});c(c$,"getResno",function(){return-2147483648==this.seqcode?0:this.seqcode>>8});c$.getSeqNumberFor=c(c$,"getSeqNumberFor",function(a){return JM.Group.haveSequenceNumber(a)?a>>8:2147483647},"~N");c$.haveSequenceNumber=
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this.bsAdded&&(this.bsAdded=new JU.BS);this.bsAdded.set(a)},"~N");c(c$,"selectAtoms",function(a){a.setBits(this.firstAtomIndex,this.lastAtomIndex+1);null!=this.bsAdded&&a.or(this.bsAdded);return this.lastAtomIndex},"JU.BS");c(c$,"isSelected",function(a){var b=a.nextSetBit(this.firstAtomIndex);return 0<=b&&b<=this.lastAtomIndex||null!=this.bsAdded&&this.bsAdded.intersects(a)},"JU.BS");c(c$,"isHetero",function(){return this.chain.getAtom(this.firstAtomIndex).isHetero()});h(c$,"toString",function(){return"["+
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a[++b],a[++b])},"~A");c(c$,"setStrucNo",function(){},"~N");c(c$,"getHelixData",function(a){return JU.Escape.escapeHelical(null,a,null,null,null)},"~N,~S,~N");c(c$,"isWithinStructure",function(){return!1},"J.c.STR");c(c$,"getProteinStructureTag",function(){return null});c(c$,"getStructureId",function(){return""});c(c$,"getBioPolymerIndexInModel",function(){return-1});c(c$,"isCrossLinked",function(){return!1},"JM.Group");c(c$,"getCrossLinkLead",function(){return!1},"JU.Lst");c(c$,"isConnectedPrevious",
function(){return!1});c(c$,"getNitrogenAtom",function(){return null});c(c$,"getCarbonylOxygenAtom",function(){return null});c(c$,"fixIndices",function(a,b){this.firstAtomIndex-=a;this.leadAtomIndex-=a;this.lastAtomIndex-=a;null!=this.bsAdded&&JU.BSUtil.deleteBits(this.bsAdded,b)},"~N,JU.BS");c(c$,"getGroupInfo",function(a,b){var d=new java.util.Hashtable;d.put("groupIndex",Integer.$valueOf(a));d.put("groupID",Short.$valueOf(this.groupID));var c=this.getSeqcodeString();null!=c&&d.put("seqCode",c);
d.put("_apt1",Integer.$valueOf(this.firstAtomIndex));d.put("_apt2",Integer.$valueOf(this.lastAtomIndex));null!=this.bsAdded&&d.put("addedAtoms",this.bsAdded);d.put("atomInfo1",this.chain.model.ms.getAtomInfo(this.firstAtomIndex,null,b));d.put("atomInfo2",this.chain.model.ms.getAtomInfo(this.lastAtomIndex,null,b));d.put("visibilityFlags",Integer.$valueOf(this.shapeVisibilityFlags));return d},"~N,JU.P3");c(c$,"getMinZ",function(a,b){b[0]=2147483647;for(var d=this.firstAtomIndex;d<=this.lastAtomIndex;d++)this.checkMinZ(a[d],
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["JU.Logger"],function(){c$=t(function(){this.paletteID=this.energy=0;s(this,arguments)},JM,"HBond",JM.Bond);u(c$,function(a,b,d,c,g,f){E(this,JM.HBond,[a,b,d,c,g]);this.energy=f;JU.Logger.debugging&&JU.Logger.debug("HBond energy = "+f+" #"+this.getIdentity())},"JM.Atom,JM.Atom,~N,~N,~N,~N");c(c$,"getEnergy",function(){return this.energy});c(c$,"getPaletteId",function(){return this.paletteID});h(c$,"setPaletteID",function(a){this.paletteID=a},"~N");c$.getEnergy=c(c$,"getEnergy",function(a,b,d,c){return Math.round(-27888/
a- -27888/c+-27888/d- -27888/b)},"~N,~N,~N,~N");C(c$,"QConst",-27888)});n("JM");w(null,"JM.LabelToken","java.lang.Character $.Float java.util.Hashtable JU.PT $.SB JM.Atom JS.T".split(" "),function(){c$=t(function(){this.data=this.key=this.text=null;this.tok=0;this.pt=-1;this.ch1="\x00";this.width=0;this.precision=2147483647;this.intAsFloat=this.zeroPad=this.alignLeft=!1;s(this,arguments)},JM,"LabelToken");u(c$,function(){});c(c$,"set",function(a,b){this.text=a;this.pt=b;return this},"~S,~N");c$.isLabelPropertyTok=
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k),a.autoCalculate(f.tok),f=JM.LabelToken.setToken(a,b,f,j,d.charCodeAt(0),c);f<j&&(g[h++]=(new JM.LabelToken).set(b.substring(f),-1));return g},"JV.Viewer,~S,~S,java.util.Map");c(c$,"formatLabel",function(a,b,d,c){return null==d||0==d.length?null:JM.LabelToken.formatLabelAtomArray(a,b,JM.LabelToken.compile(a,d,"\x00",null),"\x00",null,c)},"JV.Viewer,JM.Atom,~S,JU.P3");c$.formatLabelAtomArray=c(c$,"formatLabelAtomArray",function(a,b,d,c,g,f){if(null==b)return null;var j="0"<c?null:new JU.SB;if(null!=
d)for(var k=0;k<d.length;k++){var h=d[k];if(null==h)break;"0"<c&&h.ch1!=c||(0>=h.tok||null!=h.key?null!=j&&(j.append(h.text),"\x00"!=h.ch1&&j.appendC(h.ch1)):JM.LabelToken.appendAtomTokenValue(a,b,h,j,g,f))}return null==j?null:j.toString().intern()},"JV.Viewer,JM.Atom,~A,~S,~A,JU.P3");c$.getBondLabelValues=c(c$,"getBondLabelValues",function(){var a=new java.util.Hashtable;a.put("#","");a.put("ORDER","");a.put("TYPE","");a.put("LENGTH",Float.$valueOf(0));a.put("ENERGY",Float.$valueOf(0));return a});
c$.formatLabelBond=c(c$,"formatLabelBond",function(a,b,d,c,g,f){c.put("#",""+(b.index+1));c.put("ORDER",""+b.getOrderNumberAsString());c.put("TYPE",b.getOrderName());c.put("LENGTH",Float.$valueOf(b.atom1.distance(b.atom2)));c.put("ENERGY",Float.$valueOf(b.getEnergy()));JM.LabelToken.setValues(d,c);JM.LabelToken.formatLabelAtomArray(a,b.atom1,d,"1",g,f);JM.LabelToken.formatLabelAtomArray(a,b.atom2,d,"2",g,f);return JM.LabelToken.getLabel(d)},"JV.Viewer,JM.Bond,~A,java.util.Map,~A,JU.P3");c$.formatLabelMeasure=
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function(a,b){for(var d=0;d<a.length;d++){var c=a[d];if(null==c)break;if(null!=c.key){var g=b.get(c.key);c.text=p(g,Float)?c.format(g.floatValue(),null,null):c.format(NaN,g,null)}}},"~A,java.util.Map");c$.getLabel=c(c$,"getLabel",function(a){for(var b=new JU.SB,d=0;d<a.length;d++){var c=a[d];if(null==c)break;b.append(c.text)}return b.toString()},"~A");c$.setToken=c(c$,"setToken",function(a,b,d,c,g,f){var j=d.pt+1;if(j>=c)return j;var k;"-"==b.charAt(j)&&(d.alignLeft=!0,++j);j<c&&"0"==b.charAt(j)&&
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c(c$,"format",function(a,b,d){return Float.isNaN(a)?null!=b?JU.PT.formatS(b,this.width,this.precision,this.alignLeft,this.zeroPad):null!=d?(0==this.width&&2147483647==this.precision&&(this.width=6,this.precision=2),JU.PT.formatF(d.x,this.width,this.precision,!1,!1)+JU.PT.formatF(d.y,this.width,this.precision,!1,!1)+JU.PT.formatF(d.z,this.width,this.precision,!1,!1)):this.text:JU.PT.formatF(a,this.width,this.precision,this.alignLeft,this.zeroPad)},"~N,~S,JU.T3");C(c$,"labelTokenParams","AaBbCcDEefGgIiLlMmNnoPpQqRrSsTtUuVvWXxxYyyZzz%%%gqW",
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a[1],c;switch(this.count){case 2:return b.distance(d);case 3:return c=null==a?this.getAtom(3):a[2],JU.Measure.computeAngleABC(b,d,c,!0);case 4:return c=null==a?this.getAtom(3):a[2],a=null==a?this.getAtom(4):a[3],JU.Measure.computeTorsion(b,d,c,a,!0);default:return NaN}},"~A");c(c$,"getLabel",function(a,b,d){var c=this.countPlusIndices[a];return 0>c?(d?"modelIndex "+this.getAtom(a).mi+" ":"")+JU.Escape.eP(this.getAtom(a)):b?"(({"+c+"}))":this.vwr.getAtomInfo(c)},"~N,~B,~B");c(c$,"setModelIndex",function(a){if(null!=
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d=g}}return!0},"~A,~N");c(c$,"getInfoAsString",function(a){var b=this.fixValue(a,!0);a=new JU.SB;a.append(2==this.count?null==this.type?"distance":this.type:3==this.count?"angle":"dihedral");a.append(" \t").appendF(b);a.append(" \t").append(JU.PT.esc(this.strMeasurement));for(b=1;b<=this.count;b++)a.append(" \t").append(this.getLabel(b,!1,!1));null!=this.thisID&&a.append(" \t").append(this.thisID);return a.toString()},"~S");c(c$,"isInRange",function(a,b){if(a.factorType===J.atomdata.RadiusData.EnumType.FACTOR){var d=
this.getAtom(1),c=this.getAtom(2),d=(d.getVanderwaalsRadiusFloat(this.vwr,a.vdwType)+c.getVanderwaalsRadiusFloat(this.vwr,a.vdwType))*a.value;return b<=d}return 3.4028235E38==a.values[0]||b>=a.values[0]&&b<=a.values[1]},"J.atomdata.RadiusData,~N");c(c$,"isIntramolecular",function(a,b){for(var d=-1,c=1;c<=b;c++){var g=this.getAtomIndex(c);if(!(0>g))if(g=a[g].getMoleculeNumber(!1),0>d)d=g;else if(g!=d)return!1}return!0},"~A,~N");c(c$,"isMin",function(a){var b=this.getAtom(1),d=this.getAtom(2),c=z(100*
d.distanceSquared(b)),b=b.getAtomName(),d=d.getAtomName(),d=0>b.compareTo(d)?b+d:d+b;a=a.get(d);return null!=a&&c==a.intValue()},"java.util.Map");C(c$,"NMR_NOT",0,"NMR_DC",1,"NMR_JC",2)});n("JM");w(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["java.lang.Float","JU.BS","$.Lst","JM.Measurement","JU.BSUtil"],function(){c$=t(function(){this.points=this.measurements=this.measurementStrings=this.client=null;this.mustNotBeConnected=this.mustBeConnected=!1;this.tickInfo=null;this.tokAction=1060866;
this.note=this.strFormat=this.radiusData=null;this.isAll=!1;this.colix=0;this.intramolecular=null;this.mad=0;this.vwr=this.ms=this.minArray=this.units=this.atoms=this.text=this.thisID=null;this.iFirstAtom=0;this.justOneModel=!0;this.htMin=null;s(this,arguments)},JM,"MeasurementData",null,J.api.JmolMeasurementClient);u(c$,function(){});c(c$,"init",function(a,b,d){this.vwr=b;this.points=d;this.thisID=a;return this},"~S,JV.Viewer,JU.Lst");c(c$,"setModelSet",function(a){this.ms=a;return this},"JM.ModelSet");
c(c$,"set",function(a,b,d,c,g,f,j,k,h,m,r,x,n){this.ms=this.vwr.ms;this.tokAction=a;2<=this.points.size()&&(p(this.points.get(0),JU.BS)&&p(this.points.get(1),JU.BS))&&(this.justOneModel=JU.BSUtil.haveCommon(this.vwr.ms.getModelBS(this.points.get(0),!1),this.vwr.ms.getModelBS(this.points.get(1),!1)));this.htMin=b;this.radiusData=d;this.strFormat=c;this.units=g;this.tickInfo=f;this.mustBeConnected=j;this.mustNotBeConnected=k;this.intramolecular=h;this.isAll=m;this.mad=r;this.colix=x;this.text=n;return this},
"~N,java.util.Map,J.atomdata.RadiusData,~S,~S,JM.TickInfo,~B,~B,Boolean,~B,~N,~N,JM.Text");c(c$,"processNextMeasure",function(a){var b=a.getMeasurement(null);if(!(null!=this.htMin&&!a.isMin(this.htMin)||null!=this.radiusData&&!a.isInRange(this.radiusData,b)))if(null==this.measurementStrings&&null==this.measurements){var d=this.minArray[this.iFirstAtom];a.value=b;b=a.fixValue(this.units,!1);this.minArray[this.iFirstAtom]=-Infinity==1/d?b:Math.min(d,b)}else null!=this.measurementStrings?this.measurementStrings.addLast(a.getStringUsing(this.vwr,
this.strFormat,this.units)):this.measurements.addLast(Float.$valueOf(a.getMeasurement(null)))},"JM.Measurement");c(c$,"getMeasurements",function(a,b){if(b){this.minArray=L(this.points.get(0).cardinality(),0);for(var d=0;d<this.minArray.length;d++)this.minArray[d]=-0;this.define(null,this.ms);return this.minArray}if(a)return this.measurements=new JU.Lst,this.define(null,this.ms),this.measurements;this.measurementStrings=new JU.Lst;this.define(null,this.ms);return this.measurementStrings},"~B,~B");
c(c$,"define",function(a,b){this.client=null==a?this:a;this.atoms=b.at;var d=this.points.size();if(!(2>d)){var c=-1,g=Array(4),f=D(5,0),j=(new JM.Measurement).setPoints(b,f,g,null);j.setCount(d);for(var k=-1,h=0;h<d;h++){var m=this.points.get(h);if(p(m,JU.BS)){k=m.cardinality();if(0==k)return;1<k&&(c=0);k=h;0==h&&(this.iFirstAtom=0);f[h+1]=m.nextSetBit(0)}else g[h]=m,f[h+1]=-2-h}this.nextMeasure(0,k,j,c)}},"J.api.JmolMeasurementClient,JM.ModelSet");c(c$,"nextMeasure",function(a,b,d,c){if(a>b)d.isValid()&&
((!this.mustBeConnected||d.isConnected(this.atoms,a))&&(!this.mustNotBeConnected||!d.isConnected(this.atoms,a))&&(null==this.intramolecular||d.isIntramolecular(this.atoms,a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(d);else{var g=this.points.get(a),f=d.countPlusIndices,j=0==a?2147483647:f[a];if(0>j)this.nextMeasure(a+1,b,d,c);else{for(var k=!1,h=g.nextSetBit(0),m=0;0<=h;h=g.nextSetBit(h+1),m++)if(h!=j){var r=this.atoms[h].getModelIndex();if(0<=c&&this.justOneModel)if(0==
a)c=r;else if(c!=r)continue;f[a+1]=h;0==a&&(this.iFirstAtom=m);k=!0;this.nextMeasure(a+1,b,d,c)}k||this.nextMeasure(a+1,b,d,c)}}},"~N,~N,JM.Measurement,~N")});n("JM");w(["JM.Measurement"],"JM.MeasurementPending",null,function(){c$=t(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;s(this,arguments)},JM,"MeasurementPending",JM.Measurement);c(c$,"set",function(a){return this.setM(a,null,NaN,0,null,0)},"JM.ModelSet");c(c$,"checkPoint",function(a){for(var b=1;b<=this.numSet;b++)if(this.countPlusIndices[b]==
-1-b&&0.01>this.pts[b-1].distance(a))return!1;return!0},"JU.Point3fi");c(c$,"getIndexOf",function(a){for(var b=1;b<=this.numSet;b++)if(this.countPlusIndices[b]==a)return b;return 0},"~N");h(c$,"setCount",function(a){this.setCountM(a);this.numSet=a},"~N");c(c$,"addPoint",function(a,b,d){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==b){if(0<this.getIndexOf(a))return d&&(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=
this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(b))return d&&(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=!0;this.count=this.numSet+1;this.pts[a]=b;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;d&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);return this.count},"~N,JU.Point3fi,~B")});n("JM");w(["JU.BS","$.SB"],"JM.Model",["java.util.Hashtable",
"JU.AU","JU.BSUtil"],function(){c$=t(function(){this.ms=null;this.hydrogenCount=this.fileIndex=this.modelIndex=0;this.hasRasmolHBonds=this.isPdbWithMultipleBonds=this.isBioModel=!1;this.loadState="";this.loadScript=null;this.isModelKit=!1;this.dataFrames=null;this.dataSourceFrame=-1;this.jmolFrameType=this.jmolData=null;this.ac=this.firstAtomIndex=0;this.bsAtomsDeleted=this.bsAtoms=null;this.trajectoryBaseIndex=0;this.isTrajectory=!1;this.bondCount=this.selectedTrajectory=-1;this.nInsertions=this.nAltLocs=
this.moleculeCount=this.firstMoleculeIndex=0;this.groupCount=-1;this.chainCount=0;this.chains=null;this.biosymmetryCount=0;this.properties=this.auxiliaryInfo=null;this.defaultRotationRadius=0;this.orientation=this.biosymmetry=this.defaultStructure=null;this.isJmolDataFrame=this.structureTainted=!1;this.frameDelay=0;this.dssrCache=this.simpleCage=null;s(this,arguments)},JM,"Model");K(c$,function(){this.loadScript=new JU.SB;this.bsAtoms=new JU.BS;this.bsAtomsDeleted=new JU.BS;this.chains=Array(8)});
c(c$,"getModelSet",function(){return this.ms});c(c$,"isModelkit",function(){return this.isModelKit});c(c$,"getTrueAtomCount",function(){return this.bsAtoms.cardinality()-this.bsAtomsDeleted.cardinality()});c(c$,"setSelectedTrajectory",function(a){this.selectedTrajectory=a},"~N");c(c$,"getSelectedTrajectory",function(){return this.selectedTrajectory});c(c$,"resetBoundCount",function(){this.bondCount=-1});c(c$,"getBondCount",function(){if(0<=this.bondCount)return this.bondCount;var a=this.ms.bo;this.bondCount=
0;for(var b=this.ms.bondCount;0<=--b;)a[b].atom1.mi==this.modelIndex&&this.bondCount++;return this.bondCount});u(c$,function(){});c(c$,"set",function(a,b,d,c,g,f){this.ms=a;this.dataSourceFrame=this.modelIndex=b;this.trajectoryBaseIndex=(this.isTrajectory=0<=d)?d:b;null==f&&(f=new java.util.Hashtable);this.auxiliaryInfo=f;f.containsKey("biosymmetryCount")&&(this.biosymmetryCount=f.get("biosymmetryCount").intValue(),this.biosymmetry=f.get("biosymmetry"));this.properties=g;null==c?this.jmolFrameType=
"modelSet":(this.jmolData=c,this.isJmolDataFrame=!0,f.put("jmolData",c),f.put("title",c),this.jmolFrameType=0<=c.indexOf("ramachandran")?"ramachandran":0<=c.indexOf("quaternion")?"quaternion":"data");return this},"JM.ModelSet,~N,~N,~S,java.util.Properties,java.util.Map");c(c$,"setNAltLocs",function(a){this.nAltLocs=a},"~N");c(c$,"setNInsertions",function(a){this.nInsertions=a},"~N");c(c$,"getModelNumberDotted",function(){return this.ms.getModelNumberDotted(this.modelIndex)});c(c$,"getModelTitle",
function(){return this.ms.getModelTitle(this.modelIndex)});c(c$,"isStructureTainted",function(){return this.structureTainted});c(c$,"getChains",function(){return this.chains});c(c$,"getChainCount",function(a){if(1<this.chainCount&&!a)for(a=0;a<this.chainCount;a++)if(0==this.chains[a].chainID)return this.chainCount-1;return this.chainCount},"~B");c(c$,"getGroupCountHetero",function(a){for(var b=0,d=this.chainCount;0<=--d;)for(var c=this.chains[d].groupCount;0<=--c;)this.chains[d].groups[c].isHetero()==
a&&b++;return b},"~B");c(c$,"calcSelectedGroupsCount",function(a){for(var b=this.chainCount;0<=--b;)this.chains[b].calcSelectedGroupsCount(a)},"JU.BS");c(c$,"getGroupCount",function(){if(0>this.groupCount){this.groupCount=0;for(var a=this.chainCount;0<=--a;)this.groupCount+=this.chains[a].getGroupCount()}return this.groupCount});c(c$,"getChainAt",function(a){return a<this.chainCount?this.chains[a]:null},"~N");c(c$,"getChain",function(a){for(var b=this.chainCount;0<=--b;){var d=this.chains[b];if(d.chainID==
a)return d}return null},"~N");c(c$,"fixIndices",function(a,b,d){this.fixIndicesM(a,b,d)},"~N,~N,JU.BS");c(c$,"fixIndicesM",function(a,b,d){this.dataSourceFrame>a&&this.dataSourceFrame--;this.trajectoryBaseIndex>a&&this.trajectoryBaseIndex--;this.firstAtomIndex-=b;for(a=0;a<this.chainCount;a++)this.chains[a].fixIndices(b,d);JU.BSUtil.deleteBits(this.bsAtoms,d);JU.BSUtil.deleteBits(this.bsAtomsDeleted,d)},"~N,~N,JU.BS");c(c$,"freeze",function(){this.freezeM()});c(c$,"freezeM",function(){this.chains=
JU.AU.arrayCopyObject(this.chains,this.chainCount);this.groupCount=-1;this.getGroupCount();for(var a=0;a<this.chainCount;++a)this.chains[a].groups=JU.AU.arrayCopyObject(this.chains[a].groups,this.chains[a].groupCount)});c(c$,"getPdbData",function(){},"JV.Viewer,~S,~S,~B,JU.BS,JU.OC,~A,JU.SB,JU.BS");c(c$,"getDefaultLargePDBRendering",function(){},"JU.SB,~N");c(c$,"getBioBranches",function(a){return a},"JU.Lst");c(c$,"getGroupsWithin",function(){},"~N,JU.BS,JU.BS");c(c$,"getSequenceBits",function(){},
"~S,JU.BS,JU.BS");c(c$,"getRasmolHydrogenBonds",function(){},"JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS");c(c$,"clearRasmolHydrogenBonds",function(){},"JU.BS");c(c$,"clearBioPolymers",function(){});c(c$,"calcSelectedMonomersCount",function(){},"JU.BS");c(c$,"calculatePolymers",function(){},"~A,~N,~N,JU.BS,~B");c(c$,"getAllPolymerInfo",function(){},"JU.BS,java.util.Map,JU.Lst");c(c$,"getBioPolymerCount",function(){return 0});c(c$,"getPolymerPointsAndVectors",function(){},"JU.BS,JU.Lst,~B,~N");c(c$,"getPolymerLeadMidPoints",
function(){return null},"~N");c(c$,"recalculateLeadMidpointsAndWingVectors",function(){});c(c$,"calculateStructures",function(){return""},"~B,~B,~B,~B,~B");c(c$,"setStructureList",function(){},"java.util.Map");c(c$,"getChimeInfo",function(a,b){this.getChimeInfoM(a,b)},"JU.SB,~N");c(c$,"getChimeInfoM",function(a,b){a.append("\nNumber of Atoms ..... "+(this.ms.ac-b));0<b&&a.append(" ("+b+")");a.append("\nNumber of Bonds ..... "+this.ms.bondCount);a.append("\nNumber of Models ...... "+this.ms.mc)},"JU.SB,~N");
c(c$,"calculateStruts",function(){return 0},"JM.ModelSet,JU.BS,JU.BS");c(c$,"calculateStraightness",function(){},"JV.Viewer,~S,~S,~N");c(c$,"selectSeqcodeRange",function(){},"~N,~N,~N,JU.BS,~B");c(c$,"setConformation",function(){},"JU.BS");c(c$,"getPdbConformation",function(){return!1},"JU.BS,~N");c(c$,"getProteinStructureState",function(){return null},"JU.BS,~B,~B,~N");c(c$,"getFullPDBHeader",function(){return null})});n("JM");w(["java.util.Hashtable","JU.BS","JV.JC"],"JM.ModelLoader","java.lang.Boolean $.Float $.NullPointerException java.util.Arrays JU.AU $.Lst $.P3 $.PT $.SB $.V3 J.api.Interface JM.Chain $.Group $.Model $.ModelSet JU.BSUtil $.Elements $.JmolMolecule $.Logger".split(" "),
function(){c$=t(function(){this.mergeModelSet=this.ms=this.vwr=null;this.appendNew=this.merging=!1;this.specialAtomIndexes=this.group3Counts=this.group3Lists=this.jmolData=null;this.doAddHydrogens=this.doMinimize=this.isPyMOLsession=this.isTrajectory=this.isPDB=this.is2D=this.someModelsAreModulated=this.someModelsHaveUnitcells=!1;this.groups=this.jbr=this.fileHeader=null;this.groupCount=0;this.firstAtomIndexes=this.seqcodes=this.group3Of=this.chainOf=this.htAtomMap=null;this.iModel=0;this.model=null;
this.currentChainID=0;this.isNewChain=!1;this.currentChain=null;this.currentGroupSequenceNumber=0;this.currentGroupInsertionCode="\x00";this.nullGroup=this.currentGroup3=null;this.adapterTrajectoryCount=this.adapterModelCount=this.baseTrajectoryCount=this.baseGroupIndex=this.baseAtomIndex=this.baseModelCount=this.baseModelIndex=0;this.modulationOn=this.noAutoBond=!1;this.$mergeGroups=this.htGroup1=null;this.iChain=0;this.structuresDefinedInFile=this.vStereo=null;s(this,arguments)},JM,"ModelLoader");
K(c$,function(){this.specialAtomIndexes=D(JV.JC.ATOMID_MAX,0);this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});u(c$,function(a,b,d,c,g,f){this.vwr=a;this.ms=new JM.ModelSet(a,b);var j=a.getModelAdapter();this.mergeModelSet=g;(this.merging=null!=this.mergeModelSet&&0<this.mergeModelSet.ac)?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);null==f?(this.initializeInfo(b,null),this.createModelSet(null,
null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||(this.ms.canSkipLoad=!1),a=j.getAtomSetCollectionAuxiliaryInfo(c),a.put("loadScript",d),this.initializeInfo(j.getFileTypeName(c).toLowerCase().intern(),a),this.createModelSet(j,c,f))},"JV.Viewer,~S,JU.SB,~O,JM.ModelSet,JU.BS");c(c$,"initializeInfo",function(a,b){this.ms.g3d=this.vwr.gdata;this.ms.modelSetTypeName=a;this.ms.isXYZ="xyz"===a;this.ms.msInfo=b;this.ms.modelSetProperties=this.ms.getInfoM("properties");if(this.isPDB=
this.ms.isPDB=this.ms.getMSInfoB("isPDB"))this.jbr=J.api.Interface.getInterface("JM.Resolver"),this.jbr.initialize(this);this.jmolData=this.ms.getInfoM("jmolData");this.fileHeader=this.ms.getInfoM("fileHeader");this.ms.trajectorySteps=this.ms.getInfoM("trajectorySteps");this.isTrajectory=null!=this.ms.trajectorySteps;this.isPyMOLsession=this.ms.getMSInfoB("isPyMOL");this.doAddHydrogens=null!=this.jbr&&!this.isTrajectory&&!this.isPyMOLsession&&!this.ms.getMSInfoB("pdbNoHydrogens")&&(this.ms.getMSInfoB("pdbAddHydrogens")||
this.vwr.getBooleanProperty("pdbAddHydrogens"));null!=b&&(b.remove("pdbNoHydrogens"),b.remove("pdbAddHydrogens"),b.remove("trajectorySteps"),this.isTrajectory&&(this.ms.vibrationSteps=b.remove("vibrationSteps")));this.htGroup1=this.ms.getInfoM("htGroup1");this.modulationOn=this.ms.getMSInfoB("modulationOn");this.noAutoBond=this.ms.getMSInfoB("noAutoBond");this.doMinimize=(this.is2D=this.ms.getMSInfoB("is2D"))&&this.ms.getMSInfoB("doMinimize");this.adapterTrajectoryCount=null==this.ms.trajectorySteps?
0:this.ms.trajectorySteps.size();this.ms.someModelsHaveSymmetry=this.ms.getMSInfoB("someModelsHaveSymmetry");this.someModelsHaveUnitcells=this.ms.getMSInfoB("someModelsHaveUnitcells");this.someModelsAreModulated=this.ms.getMSInfoB("someModelsAreModulated");this.ms.someModelsHaveFractionalCoordinates=this.ms.getMSInfoB("someModelsHaveFractionalCoordinates");this.merging&&(this.ms.isPDB=(new Boolean(this.ms.isPDB|this.mergeModelSet.isPDB)).valueOf(),this.ms.someModelsHaveSymmetry=(new Boolean(this.ms.someModelsHaveSymmetry|
this.mergeModelSet.getMSInfoB("someModelsHaveSymmetry"))).valueOf(),this.someModelsHaveUnitcells=(new Boolean(this.someModelsHaveUnitcells|this.mergeModelSet.getMSInfoB("someModelsHaveUnitcells"))).valueOf(),this.ms.someModelsHaveFractionalCoordinates=(new Boolean(this.ms.someModelsHaveFractionalCoordinates|this.mergeModelSet.getMSInfoB("someModelsHaveFractionalCoordinates"))).valueOf(),this.ms.someModelsHaveAromaticBonds=(new Boolean(this.ms.someModelsHaveAromaticBonds|this.mergeModelSet.someModelsHaveAromaticBonds)).valueOf(),
this.ms.msInfo.put("someModelsHaveSymmetry",Boolean.$valueOf(this.ms.someModelsHaveSymmetry)),this.ms.msInfo.put("someModelsHaveUnitcells",Boolean.$valueOf(this.someModelsHaveUnitcells)),this.ms.msInfo.put("someModelsHaveFractionalCoordinates",Boolean.$valueOf(this.ms.someModelsHaveFractionalCoordinates)),this.ms.msInfo.put("someModelsHaveAromaticBonds",Boolean.$valueOf(this.ms.someModelsHaveAromaticBonds)))},"~S,java.util.Map");c(c$,"getGroup3",function(a){return a>=this.group3Of.length?null:this.group3Of[a]},
"~N");c(c$,"getFirstAtomIndex",function(a){return this.firstAtomIndexes[a]},"~N");c(c$,"getAtomCount",function(){return this.ms.ac});c(c$,"createModelSet",function(a,b,d){var c=null==a?0:a.getAtomCount(b);0<c&&JU.Logger.info("reading "+c+" atoms");this.adapterModelCount=null==a?1:a.getAtomSetCount(b);this.appendNew=!this.merging||null==a||1<this.adapterModelCount||this.isTrajectory||this.vwr.getBoolean(603979792);this.htAtomMap.clear();this.chainOf=Array(32);this.group3Of=Array(32);this.seqcodes=
D(32,0);this.firstAtomIndexes=D(32,0);this.currentChainID=2147483647;this.currentChain=null;this.currentGroupInsertionCode="\uffff";this.currentGroup3="xxxxx";this.iModel=-1;this.model=null;if(this.merging&&(this.baseModelCount=this.mergeModelSet.mc,this.baseTrajectoryCount=this.mergeModelSet.mergeTrajectories(this.isTrajectory),0<this.baseTrajectoryCount)){if(this.isTrajectory){if(null==this.mergeModelSet.vibrationSteps){this.mergeModelSet.vibrationSteps=new JU.Lst;for(var g=this.mergeModelSet.trajectorySteps.size();0<=
--g;)this.mergeModelSet.vibrationSteps.addLast(null)}for(g=0;g<this.ms.trajectorySteps.size();g++)this.mergeModelSet.trajectorySteps.addLast(this.ms.trajectorySteps.get(g)),this.mergeModelSet.vibrationSteps.addLast(null==this.ms.vibrationSteps?null:this.ms.vibrationSteps.get(g))}this.ms.trajectorySteps=this.mergeModelSet.trajectorySteps;this.ms.vibrationSteps=this.mergeModelSet.vibrationSteps}this.initializeAtomBondModelCounts(c);null!=d&&(this.doMinimize||this.is2D)&&d.setBits(this.baseAtomIndex,
this.baseAtomIndex+c);null==a?this.setModelNameNumberProperties(0,-1,"",1,null,null,null):(0<this.adapterModelCount&&(JU.Logger.info("ModelSet: haveSymmetry:"+this.ms.someModelsHaveSymmetry+" haveUnitcells:"+this.someModelsHaveUnitcells+" haveFractionalCoord:"+this.ms.someModelsHaveFractionalCoordinates),JU.Logger.info(this.adapterModelCount+" model"+(1==this.ms.mc?"":"s")+' in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.')),g=this.ms.getInfoM("defaultOrientationQuaternion"),
null!=g&&(JU.Logger.info("defaultOrientationQuaternion = "+g),JU.Logger.info('Use "set autoLoadOrientation TRUE" before loading or "restore orientation DEFAULT" after loading to view this orientation.')),this.iterateOverAllNewModels(a,b),this.iterateOverAllNewAtoms(a,b),this.iterateOverAllNewBonds(a,b),this.merging&&!this.appendNew&&(g=a.getAtomSetAuxiliaryInfo(b,0),this.ms.setInfo(this.baseModelIndex,"initialAtomCount",g.get("initialAtomCount")),this.ms.setInfo(this.baseModelIndex,"initialBondCount",
g.get("initialBondCount"))),this.initializeUnitCellAndSymmetry(),this.initializeBonding());this.finalizeGroupBuild();this.is2D&&this.doMinimize&&this.applyStereochemistry();this.doAddHydrogens&&this.jbr.finalizeHydrogens();null!=a&&(this.ms.calculatePolymers(this.groups,this.groupCount,this.baseGroupIndex,null),null!=this.jbr&&this.jbr.iterateOverAllNewStructures(a,b));this.setDefaultRendering(this.vwr.getInt(553648170));var f=this.vwr.rd;d=this.ms.ac;c=this.ms.at;for(g=this.baseAtomIndex;g<d;g++)c[g].setMadAtom(this.vwr,
f);f=this.ms.am;for(g=f[this.baseModelIndex].firstAtomIndex;g<d;g++)f[c[g].mi].bsAtoms.set(g);this.freeze();this.finalizeShapes();this.vwr.setModelSet(this.ms);this.setAtomProperties();null!=a&&a.finish(b);null!=this.mergeModelSet&&this.mergeModelSet.releaseModelSet();this.mergeModelSet=null},"J.api.JmolAdapter,~O,JU.BS");c(c$,"setDefaultRendering",function(a){if(!this.isPyMOLsession){for(var b=new JU.SB,d=this.ms.mc,c=this.ms.am,g=this.baseModelIndex;g<d;g++)c[g].isBioModel&&c[g].getDefaultLargePDBRendering(b,
a);0!=b.length()&&(b.append("select *;"),a=this.ms.getInfoM("jmolscript"),null==a&&(a=""),b.append(a),this.ms.msInfo.put("jmolscript",b.toString()))}},"~N");c(c$,"setAtomProperties",function(){for(var a=this.ms.mc,b=this.baseModelIndex;b<a;b++){var d=this.ms.getInfo(b,"atomProperties"),c=this.ms.getInfo(b,"groupPropertyList");if(null!=d)for(var g,d=d.entrySet().iterator();d.hasNext()&&((g=d.next())||1);){var f=g.getKey(),j=g.getValue(),k=this.ms.getModelAtomBitSetIncludingDeleted(b,!0);if(this.doAddHydrogens)var h=
null!=c&&JU.PT.isOneOf(f,c),j=this.jbr.fixPropertyValue(k,j,h);f="property_"+f.toLowerCase();JU.Logger.info("creating "+f+" for model "+this.ms.getModelName(b));this.vwr.setData(f,[f,j,k,Integer.$valueOf(-1),Boolean.FALSE],this.ms.ac,0,0,2147483647,0)}}});c(c$,"initializeAtomBondModelCounts",function(a){var b=this.adapterTrajectoryCount;this.merging?(this.appendNew?(this.baseModelIndex=this.baseModelCount,this.ms.mc=this.baseModelCount+this.adapterModelCount):(this.baseModelIndex=this.vwr.am.cmi,
0>this.baseModelIndex&&(this.baseModelIndex=this.baseModelCount-1),this.ms.mc=this.baseModelCount),this.ms.ac=this.baseAtomIndex=this.mergeModelSet.ac,this.ms.bondCount=this.mergeModelSet.bondCount,this.$mergeGroups=this.mergeModelSet.getGroups(),this.groupCount=this.baseGroupIndex=this.$mergeGroups.length,this.ms.mergeModelArrays(this.mergeModelSet),this.ms.growAtomArrays(this.ms.ac+a)):(this.ms.mc=this.adapterModelCount,this.ms.ac=0,this.ms.bondCount=0,this.ms.at=Array(a),this.ms.bo=Array(250+a));
this.doAddHydrogens&&this.jbr.initializeHydrogenAddition();1<b&&(this.ms.mc+=b-1);this.ms.am=JU.AU.arrayCopyObject(this.ms.am,this.ms.mc);this.ms.modelFileNumbers=JU.AU.arrayCopyI(this.ms.modelFileNumbers,this.ms.mc);this.ms.modelNumbers=JU.AU.arrayCopyI(this.ms.modelNumbers,this.ms.mc);this.ms.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.ms.modelNumbersForAtomLabel,this.ms.mc);this.ms.modelNames=JU.AU.arrayCopyS(this.ms.modelNames,this.ms.mc);this.ms.frameTitles=JU.AU.arrayCopyS(this.ms.frameTitles,
this.ms.mc);if(this.merging)for(a=0;a<this.mergeModelSet.mc;a++)(this.ms.am[a]=this.mergeModelSet.am[a]).ms=this.ms},"~N");c(c$,"mergeGroups",function(){var a=this.mergeModelSet.getAuxiliaryInfo(null),b=a.get("group3Lists"),a=a.get("group3Counts");if(null!=b){for(var d=0;d<this.baseModelCount;d++)this.group3Lists[d+1]=b[d+1],this.group3Counts[d+1]=a[d+1],this.structuresDefinedInFile.set(d);this.group3Lists[0]=b[0];this.group3Counts[0]=a[0]}!this.appendNew&&this.isPDB&&this.structuresDefinedInFile.clear(this.baseModelIndex)});
c(c$,"iterateOverAllNewModels",function(a,b){this.group3Lists=Array(this.ms.mc+1);this.group3Counts=JU.AU.newInt2(this.ms.mc+1);this.structuresDefinedInFile=new JU.BS;this.merging&&this.mergeGroups();for(var d=this.isTrajectory?this.baseTrajectoryCount:-1,c=this.baseModelIndex,g=0;g<this.adapterModelCount;++g,++c){var f=a.getAtomSetNumber(b,g),j=a.getAtomSetName(b,g),k=a.getAtomSetAuxiliaryInfo(b,g);k.containsKey("modelID")&&k.put("modelID0",k.get("modelID"));var h=k.get("modelProperties");this.vwr.setStringProperty("_fileType",
k.get("fileType"));null==j&&(j=null!=this.jmolData&&2<this.jmolData.indexOf(";")?this.jmolData.substring(this.jmolData.indexOf(":")+2,this.jmolData.indexOf(";")):this.appendNew?""+f%1E6:"");this.setModelNameNumberProperties(c,d,j,f,h,k,this.jmolData)&&(this.group3Lists[c+1]=JV.JC.getGroup3List(),this.group3Counts[c+1]=D(JV.JC.getGroup3Count()+10,0),null==this.group3Lists[0]&&(this.group3Lists[0]=JV.JC.getGroup3List(),this.group3Counts[0]=D(JV.JC.getGroup3Count()+10,0)));null!=this.ms.getInfo(c,"periodicOriginXyz")&&
(this.ms.someModelsHaveSymmetry=!0)}d=this.ms.am[this.baseModelIndex];this.vwr.setSmilesString(this.ms.msInfo.get("smilesString"));g=this.ms.msInfo.remove("loadState");f=this.ms.msInfo.remove("loadScript");if(0>f.indexOf("Viewer.AddHydrogens")||!d.isModelKit){j=JU.PT.split(g,"\n");k=new JU.SB;for(g=0;g<j.length;g++)h=d.loadState.indexOf(j[g]),(0>h||h!=d.loadState.lastIndexOf(j[g]))&&k.append(j[g]).appendC("\n");d.loadState+=d.loadScript.toString()+k.toString();d.loadScript=new JU.SB;d.loadScript.append("  ").appendSB(f).append(";\n")}if(this.isTrajectory){g=
this.ms.mc-c+1;JU.Logger.info(g+" trajectory steps read");this.ms.setInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(g));d=this.adapterModelCount;for(g=c;g<this.ms.mc;g++,d++)this.ms.am[g]=this.ms.am[this.baseModelCount],this.ms.modelNumbers[g]=a.getAtomSetNumber(b,d),this.ms.modelNames[g]=a.getAtomSetName(b,d),this.structuresDefinedInFile.set(g)}this.finalizeModels(this.baseModelCount)},"J.api.JmolAdapter,~O");c(c$,"setModelNameNumberProperties",function(a,b,d,c,g,f,j){var k=null!=
f&&Boolean.TRUE===f.get("isPDB");this.appendNew?(this.ms.am[a]=k?this.jbr.getBioModel(a,b,j,g,f):(new JM.Model).set(this.ms,a,b,j,g,f),this.ms.modelNumbers[a]=c,this.ms.modelNames[a]=d):(b=f.get("PDB_CONECT_firstAtom_count_max"),null!=b&&this.ms.setInfo(a,"PDB_CONECT_firstAtom_count_max",b));b=this.ms.am;c=this.ms.at;b[a].bsAtoms.set(c.length+1);b[a].bsAtoms.clear(c.length+1);c=this.ms.getInfo(a,"altLocs");b[a].setNAltLocs(null==c?0:c.length);null!=c&&(c=c.toCharArray(),java.util.Arrays.sort(c),c=
String.valueOf(c),this.ms.setInfo(a,"altLocs",c));c=this.ms.getInfo(a,"insertionCodes");b[a].setNInsertions(null==c?0:c.length);d=null!=this.ms.modelSetName&&this.ms.modelSetName.startsWith("Jmol Model Kit")||d.startsWith("Jmol Model Kit")||"Jme".equals(this.ms.getInfo(a,"fileType"));b[a].isModelKit=d;return k},"~N,~N,~S,~N,java.util.Properties,java.util.Map,~S");c(c$,"finalizeModels",function(a){var b=this.ms.mc;if(b!=a){var d,c=0,g=-1,f=this.ms.modelNumbers,j=this.ms.modelNames;if(this.isTrajectory)for(var k=
a;++k<this.ms.mc;)f[k]=f[k-1]+1;if(0<a){if(1E6>f[0])for(k=0;k<a;k++)0==j[k].length&&(j[k]=""+f[k]),f[k]+=1E6,this.ms.modelNumbersForAtomLabel[k]="1."+(k+1);var h=f[a-1],h=h-h%1E6;1E6>f[a]&&(h+=1E6);for(k=a;k<b;k++)f[k]+=h}for(var m=this.ms.am,k=a;k<b;++k)if(this.ms.setInfo(k,"fileType",this.ms.modelSetTypeName),null!=this.fileHeader&&this.ms.setInfo(k,"fileHeader",this.fileHeader),h=q(f[k]/1E6),h!=g&&(c=0,g=h),c++,0==h?(d=""+this.ms.getModelNumber(k),h=1):d=h+"."+c,this.ms.modelNumbersForAtomLabel[k]=
d,m[k].fileIndex=h-1,this.ms.modelFileNumbers[k]=1E6*h+c,null==j[k]||0==j[k].length)j[k]=d;if(this.merging)for(k=0;k<a;k++)m[k].ms=this.ms;for(k=0;k<b;k++)this.ms.setInfo(k,"modelName",j[k]),this.ms.setInfo(k,"modelNumber",Integer.$valueOf(f[k]%1E6)),this.ms.setInfo(k,"modelFileNumber",Integer.$valueOf(this.ms.modelFileNumbers[k])),this.ms.setInfo(k,"modelNumberDotted",this.ms.getModelNumberDotted(k)),a=this.ms.getInfo(k,"altLocs"),null!=a&&JU.Logger.info("model "+this.ms.getModelNumberDotted(k)+
" alternative locations: "+a)}},"~N");c(c$,"iterateOverAllNewAtoms",function(a,b){var d=-1,c=!1,g=!1,f=a.getAtomIterator(b),j=0,k=this.ms.am;0<this.ms.mc&&(this.nullGroup=(new JM.Group).setGroup(new JM.Chain(this.ms.am[this.baseModelIndex],32,-1),"",0,-1,-1));for(;f.hasNext();){j++;var h=f.getAtomSetIndex()+this.baseModelIndex;h!=d&&(this.iChain=0,this.iModel=h,this.model=k[h],this.currentChainID=2147483647,this.isNewChain=!0,k[h].bsAtoms.clearAll(),c=k[h].isBioModel,d=h,g=c&&this.doAddHydrogens,
null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var h=f.getGroup3(),m=f.getChainID();this.checkNewGroup(a,m,h,f.getSequenceNumber(),f.getInsertionCode(),g,!1);m=f.getElementNumber();g&&1==JU.Elements.getElementNumber(m)&&this.jbr.setHaveHsAlready(!0);var r=f.getAtomName(),x=g?this.getPdbCharge(h,r):f.getFormalCharge();this.addAtom(c,f.getSymmetry(),f.getAtomSite(),f.getUniqueID(),m,r,x,f.getPartialCharge(),f.getTensors(),f.getOccupancy(),f.getBfactor(),f.getXYZ(),f.getIsHetero(),f.getSerial(),f.getSeqID(),
h,f.getVib(),f.getAltLoc(),f.getRadius())}0<this.groupCount&&g&&this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain?1:0);d=-1;c=null;g=this.ms.at;for(f=0;f<this.ms.ac;f++)g[f].mi!=d&&(d=g[f].mi,k[d].firstAtomIndex=f,h=this.ms.getDefaultVdwType(d),h!==c&&(JU.Logger.info("Default Van der Waals type for model set to "+h.getVdwLabel()),c=h));JU.Logger.info(j+" atoms created")},"J.api.JmolAdapter,~O");c(c$,"getPdbCharge",function(a,b){return a.equals("ARG")&&b.equals("NH1")||a.equals("LYS")&&
b.equals("NZ")||a.equals("HIS")&&b.equals("ND1")?1:0},"~S,~S");c(c$,"addAtom",function(a,b,d,c,g,f,j,k,h,m,r,x,n,q,p,s,t,u,v){var w=0;null!=f&&(a&&0<=f.indexOf("*")&&(f=f.$replace("*","'")),w=JV.JC.lookupSpecialAtomID(f),a&&(2==w&&"CA".equalsIgnoreCase(s))&&(w=0));a=this.ms.addAtom(this.iModel,this.nullGroup,g,f,q,p,d,x,v,t,j,k,m,r,h,n,w,b);a.setAltLoc(u);this.htAtomMap.put(c,a)},"~B,JU.BS,~N,~O,~N,~S,~N,~N,JU.Lst,~N,~N,JU.P3,~B,~N,~N,~S,JU.V3,~S,~N");c(c$,"checkNewGroup",function(a,b,d,c,g,f,j){var k=
null==d?null:d.intern();b!=this.currentChainID&&(this.currentChainID=b,this.currentChain=this.getOrAllocateChain(this.model,b),this.currentGroupInsertionCode="\uffff",this.currentGroupSequenceNumber=-1,this.currentGroup3="xxxx",this.isNewChain=!0);if(c!=this.currentGroupSequenceNumber||g!=this.currentGroupInsertionCode||k!==this.currentGroup3){0<this.groupCount&&f&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!j?1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=
c;this.currentGroupInsertionCode=g;for(this.currentGroup3=k;this.groupCount>=this.group3Of.length;)this.chainOf=JU.AU.doubleLength(this.chainOf),this.group3Of=JU.AU.doubleLengthS(this.group3Of),this.seqcodes=JU.AU.doubleLengthI(this.seqcodes),this.firstAtomIndexes=JU.AU.doubleLengthI(this.firstAtomIndexes);this.firstAtomIndexes[this.groupCount]=this.ms.ac;this.chainOf[this.groupCount]=this.currentChain;this.group3Of[this.groupCount]=d;this.seqcodes[this.groupCount]=JM.Group.getSeqcodeFor(c,g);++this.groupCount}},
"J.api.JmolAdapter,~N,~S,~N,~S,~B,~B");c(c$,"getOrAllocateChain",function(a,b){var d=a.getChain(b);if(null!=d)return d;a.chainCount==a.chains.length&&(a.chains=JU.AU.doubleLength(a.chains));return a.chains[a.chainCount++]=new JM.Chain(a,b,0==b||32==b?-1:this.iChain++)},"JM.Model,~N");c(c$,"iterateOverAllNewBonds",function(a,b){var d=a.getBondIterator(b);if(null!=d){var c=this.vwr.getMadBond();this.ms.defaultCovalentMad=null==this.jmolData?c:0;for(var g=!1;d.hasNext();){var f=d.getEncodedOrder(),j=
f,k=this.bondAtoms(d.getAtomUniqueID1(),d.getAtomUniqueID2(),j);null!=k&&(1<j&&(1025!=j&&1041!=j)&&(g=!0),j=d.getRadius(),0<j&&k.setMad(Y(2E3*j)),j=d.getColix(),0<=j&&k.setColix(j),k.order|=f&98304)}g&&(this.ms.someModelsHaveSymmetry&&!this.vwr.getBoolean(603979794))&&JU.Logger.info('ModelSet: use "set appletSymmetryToBonds TRUE " to apply the file-based multiple bonds to symmetry-generated atoms.');this.ms.defaultCovalentMad=c}},"J.api.JmolAdapter,~O");c(c$,"bondAtoms",function(a,b,d){var c=this.htAtomMap.get(a);
if(null==c)return JU.Logger.error("bondAtoms cannot find atomUid1?:"+a),null;a=this.htAtomMap.get(b);if(null==a)return JU.Logger.error("bondAtoms cannot find atomUid2?:"+b),null;if(c.isBonded(a))return null;1025==d||1041==d?(b=this.ms.bondMutually(c,a,this.is2D?d:1,this.ms.getDefaultMadFromOrder(1),0),null==this.vStereo&&(this.vStereo=new JU.Lst),this.vStereo.addLast(b)):(b=this.ms.bondMutually(c,a,d,this.ms.getDefaultMadFromOrder(d),0),b.isAromatic()&&(this.ms.someModelsHaveAromaticBonds=!0));this.ms.bondCount==
this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount+250));this.ms.setBond(this.ms.bondCount++,b);return b},"~O,~O,~N");c(c$,"initializeUnitCellAndSymmetry",function(){this.someModelsAreModulated&&null==this.ms.bsModulated&&(this.ms.bsModulated=new JU.BS);if(this.someModelsHaveUnitcells){this.ms.unitCells=Array(this.ms.mc);this.ms.haveUnitCells=!0;for(var a=null!=this.mergeModelSet&&null!=this.mergeModelSet.unitCells,b=0,d=0;b<this.ms.mc;b++)if(a&&b<this.baseModelCount)this.ms.unitCells[b]=
this.mergeModelSet.unitCells[b];else{this.ms.unitCells[b]=J.api.Interface.getSymmetry();var c=null;if(this.isTrajectory){var g=this.ms.getInfoM("unitCells");null!=g&&(c=g.get(d++))}this.ms.unitCells[b].setSymmetryInfo(b,this.ms.getModelAuxiliaryInfo(b),c)}}if(this.appendNew&&this.ms.someModelsHaveSymmetry){this.ms.getAtoms(1089470478,null);a=this.ms.at;b=this.baseAtomIndex;d=-1;for(c=0;b<this.ms.ac;b++)a[b].mi!=d&&(d=a[b].mi,c=this.baseAtomIndex+this.ms.getInfoI(d,"presymmetryAtomIndex")+this.ms.getInfoI(d,
"presymmetryAtomCount")),b>=c&&this.ms.bsSymmetry.set(b)}if(this.appendNew&&this.ms.someModelsHaveFractionalCoordinates){a=this.ms.at;c=-1;d=null;for(b=this.baseAtomIndex;b<this.ms.ac;b++)a[b].mi!=c&&(c=a[b].mi,d=this.ms.getUnitCell(c)),null!=d&&d.getCoordinatesAreFractional()&&(d=a[b].getUnitCell(),d.toCartesian(d.toSupercell(a[b]),!1));for(a=this.baseModelIndex;a<this.ms.mc;a++)if(this.ms.isTrajectory(a)&&(d=this.ms.getUnitCell(a),null!=d&&d.getCoordinatesAreFractional()&&d.isSupercell())){c=this.ms.trajectorySteps.get(a);
for(b=c.length;0<=--b;)null!=c[b]&&d.toSupercell(c[b])}}});c(c$,"initializeBonding",function(){var a=null==this.ms.getInfoM("someModelsHaveCONECT")?null:new JU.BS;null!=a&&this.ms.setPdbConectBonding(this.baseAtomIndex,this.baseModelIndex,a);var b=0,d=this.vwr.getBoolean(603979794),c=this.vwr.getBoolean(603979798),g=this.vwr.getBoolean(603979846),f=null,j=!1,k=this.ms.mc,h=this.ms.am;if(!this.noAutoBond)for(var m=this.baseModelIndex;m<k;m++){var b=h[m].bsAtoms.cardinality(),r=this.ms.getInfoI(m,"initialBondCount"),
x=h[m].isBioModel;0>r&&(r=this.ms.bondCount);var n=this.ms.getInfoB(m,"hasSymmetry");if(g||c&&(0==r||x&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||r<q(b/2))||n&&!d&&!this.ms.getInfoB(m,"hasBonds")))if(j=!0,this.merging||1<k)null==f&&(f=JU.BS.newN(this.ms.ac)),(m==this.baseModelIndex||!this.isTrajectory)&&f.or(h[m].bsAtoms)}j?(this.modulationOn&&this.ms.setModulation(null,!0,null,!1),this.ms.autoBondBs4(f,f,a,null,this.ms.defaultCovalentMad,this.vwr.getBoolean(603979874)),JU.Logger.info("ModelSet: autobonding; use  autobond=false  to not generate bonds automatically")):
(this.ms.initializeBspf(),JU.Logger.info("ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation"))});c(c$,"finalizeGroupBuild",function(){this.groups=Array(this.groupCount);if(this.merging)for(var a=0;a<this.$mergeGroups.length;a++)this.groups[a]=this.$mergeGroups[a],this.groups[a].setModelSet(this.ms);for(a=this.baseGroupIndex;a<this.groupCount;++a)this.distinguishAndPropagateGroup(a,this.chainOf[a],this.group3Of[a],this.seqcodes[a],this.firstAtomIndexes[a],a==this.groupCount-
1?this.ms.ac:this.firstAtomIndexes[a+1]);if(null!=this.group3Lists&&null!=this.ms.msInfo){this.ms.msInfo.put("group3Lists",this.group3Lists);this.ms.msInfo.put("group3Counts",this.group3Counts);for(a=0;a<this.group3Counts.length;a++)null==this.group3Counts[a]&&(this.group3Counts[a]=D(0,0))}});c(c$,"distinguishAndPropagateGroup",function(a,b,d,c,g,f){var j=f-1;if(j<g)throw new NullPointerException;var k=this.ms.at[g].mi,h=null==d||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(b,d,c,g,f,
k,this.specialAtomIndexes,this.ms.at);null==h?(h=(new JM.Group).setGroup(b,d,c,g,j),c="o>"):c=h.isProtein()?"p>":h.isNucleic()?"n>":h.isCarbohydrate()?"c>":"o>";null!=d&&(this.countGroup(k,c,d),h.isNucleic()&&(d=null==this.htGroup1?null:this.htGroup1.get(d),null!=d&&(h.group1=d.charAt(0))));this.addGroup(b,h);this.groups[a]=h;h.setGroupIndex(a);for(a=f;--a>=g;)this.ms.at[a].setGroup(h)},"~N,JM.Chain,~S,~N,~N,~N");c(c$,"addGroup",function(a,b){a.groupCount==a.groups.length&&(a.groups=JU.AU.doubleLength(a.groups));
a.groups[a.groupCount++]=b},"JM.Chain,JM.Group");c(c$,"countGroup",function(a,b,d){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var g=(d+"   ").substring(0,3),f=this.group3Lists[c].indexOf(g);0>f&&(this.group3Lists[c]+=",["+g+"]",f=this.group3Lists[c].indexOf(g),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][q(f/6)]++;f=this.group3Lists[c].indexOf(",["+g);0<=f&&(this.group3Lists[c]=this.group3Lists[c].substring(0,
f)+b+this.group3Lists[c].substring(f+2));0<=a&&this.countGroup(-1,b,d)}},"~N,~S,~S");c(c$,"freeze",function(){this.htAtomMap.clear();this.ms.ac<this.ms.at.length&&this.ms.growAtomArrays(this.ms.ac);this.ms.bondCount<this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount));for(var a=5;0<--a;){this.ms.numCached[a]=0;for(var b=this.ms.freeBonds[a],d=b.length;0<=--d;)b[d]=null}this.ms.setAtomNamesAndNumbers(0,this.baseAtomIndex,this.mergeModelSet);this.findElementsPresent();
this.ms.resetMolecules();this.currentChain=this.model=null;!this.isPDB||this.isPyMOLsession?this.ms.freezeModels():(a=this.vwr.getBoolean(603979826),a=this.ms.calculateStructuresAllExcept(this.structuresDefinedInFile,a,!1,!0,!0,a),0<a.length&&JU.Logger.info(a))});c(c$,"findElementsPresent",function(){this.ms.elementsPresent=Array(this.ms.mc);for(var a=0;a<this.ms.mc;a++)this.ms.elementsPresent[a]=JU.BS.newN(64);for(a=this.ms.ac;0<=--a;){var b=this.ms.at[a].getAtomicAndIsotopeNumber();b>=JU.Elements.elementNumberMax&&
(b=JU.Elements.elementNumberMax+JU.Elements.altElementIndexFromNumber(b));this.ms.elementsPresent[this.ms.at[a].mi].set(b)}});c(c$,"applyStereochemistry",function(){this.set2dZ(this.baseAtomIndex,this.ms.ac);if(null!=this.vStereo){var a=new JU.BS;a.setBits(this.baseAtomIndex,this.ms.ac);for(var b=this.vStereo.size();0<=--b;){var d=this.vStereo.get(b),c=1025==d.order?3:-3;d.order=1;d.atom2.z!=d.atom1.z&&0>c==d.atom2.z<d.atom1.z&&(c/=3);var g=JU.JmolMolecule.getBranchBitSet(this.ms.at,d.atom2.i,a,null,
d.atom1.i,!1,!0);g.set(d.atom2.i);for(var f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1))this.ms.at[f].z+=c;d.atom2.x=(d.atom1.x+d.atom2.x)/2;d.atom2.y=(d.atom1.y+d.atom2.y)/2}this.vStereo=null}this.is2D=!1});c(c$,"set2dZ",function(a,b){var d=JU.BS.newN(b),c=new JU.BS,g=new JU.V3,f=JU.V3.new3(0,1,0),j=new JU.V3,k=new JU.BS;k.setBits(a,b);for(var h=a;h<b;h++)!d.get(h)&&!c.get(h)&&(c=this.getBranch2dZ(h,-1,k,c,g,f,j),d.or(c))},"~N,~N");c(c$,"getBranch2dZ",function(a,b,d,c,g,f,j){c=JU.BS.newN(this.ms.ac);
if(0>a)return c;var k=new JU.BS;k.or(d);0<=b&&k.clear(b);JM.ModelLoader.setBranch2dZ(this.ms.at[a],c,k,g,f,j);return c},"~N,~N,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setBranch2dZ=c(c$,"setBranch2dZ",function(a,b,d,c,g,f){var j=a.i;if(d.get(j)&&(d.clear(j),b.set(j),null!=a.bonds))for(j=a.bonds.length;0<=--j;){var k=a.bonds[j];k.isHydrogen()||(k=k.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,k,c,g,f),JM.ModelLoader.setBranch2dZ(k,b,d,c,g,f))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setAtom2dZ=c(c$,
"setAtom2dZ",function(a,b,d,c,g){d.sub2(b,a);d.z=0;d.normalize();g.cross(c,d);d=Math.acos(d.dot(c));b.z=a.z+0.8*Math.sin(4*d)},"JM.Atom,JM.Atom,JU.V3,JU.V3,JU.V3");c(c$,"finalizeShapes",function(){this.ms.sm=this.vwr.shm;this.ms.sm.setModelSet(this.ms);this.ms.setBsHidden(this.vwr.slm.getHiddenSet());this.merging||this.ms.sm.resetShapes();this.ms.sm.loadDefaultShapes(this.ms);this.ms.someModelsHaveAromaticBonds&&this.vwr.getBoolean(603979944)&&this.ms.assignAromaticBondsBs(!1,null);this.merging&&
1==this.baseModelCount&&this.ms.sm.setShapePropertyBs(6,"clearModelIndex",null,null)});c(c$,"undeleteAtom",function(a){this.ms.at[a].valence=0},"~N");c$.createAtomDataSet=c(c$,"createAtomDataSet",function(a,b,d,c,g){if(null==c)return null;var f=a.getModelAdapter(),j=new JU.P3,k=b.at,h=a.getFloat(570425363);if(null!=b.unitCells)for(var m=g.nextSetBit(0);0<=m;m=g.nextSetBit(m+1))if(null!=k[m].getAtomSymmetry()){h=-h;break}for(var m=-1,r=0,x=JU.BSUtil.cardinalityOf(g)==a.getAtomCount(),n=f.getAtomIterator(c);n.hasNext();){var q=
n.getXYZ();if(!Float.isNaN(q.x+q.y+q.z))if(1146095626==d){m=g.nextSetBit(m+1);if(0>m)break;r++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+m+": "+k[m]+" --\x3e ("+q.x+","+q.y+","+q.z);b.setAtomCoord(m,q.x,q.y,q.z)}else{j.setT(q);q=JU.BS.newN(b.ac);b.getAtomsWithin(h,j,q,-1);q.and(g);if(x)if(r=JU.BSUtil.cardinalityOf(q),0==r){JU.Logger.warn("createAtomDataSet: no atom found at position "+j);continue}else 1<r&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+r+" atoms found at position "+
j);switch(d){case 1146095631:var p=n.getVib();if(null==p)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+j+" vib: "+p);b.setAtomCoords(q,1146095631,p);break;case 1129318401:b.setAtomProperty(q,d,0,n.getOccupancy(),null,null,null);break;case 1112541196:b.setAtomProperty(q,d,0,n.getPartialCharge(),null,null,null);break;case 1112541199:b.setAtomProperty(q,d,0,n.getBfactor(),null,null,null)}}}switch(d){case 1146095631:b=f.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+b);a.setStringProperty("_vibrationName",
b);break;case 1146095626:if(JU.Logger.info(r+" atom positions read"),b.recalculateLeadMidpointsAndWingVectors(-1),r==b.ac)return"boundbox {*};reset"}return null},"JV.Viewer,JM.ModelSet,~N,~O,JU.BS");C(c$,"defaultGroupCount",32)});n("JM");w("JM.BondCollection JU.BS $.Lst $.M3 $.M4 $.P3 $.V3 JU.BoxInfo".split(" "),"JM.ModelSet","java.lang.Boolean $.Float java.util.Hashtable JU.A4 $.AU $.Measure $.P4 $.PT $.Quat $.SB J.api.Interface $.JmolModulationSet J.atomdata.RadiusData J.bspt.Bspf J.c.PAL $.VDW JM.Atom $.AtomIteratorWithinModel $.AtomIteratorWithinModelSet $.Bond $.BondSet $.HBond $.Model $.StateScript JS.SV JU.BSUtil $.Elements $.Escape $.JmolMolecule $.Logger $.Txt JV.JC".split(" "),
function(){c$=t(function(){this.echoShapeActive=this.selectionHaloEnabled=!1;this.am=this.modelSetName=this.bsSymmetry=this.pointGroup=this.closest=this.modelSetTypeName=null;this.mc=0;this.unitCells=null;this.haveUnitCells=!1;this.elementsPresent=this.frameTitles=this.modelNames=this.modelNumbersForAtomLabel=this.modelFileNumbers=this.modelNumbers=null;this.isPDB=this.isXYZ=!1;this.msInfo=this.modelSetProperties=null;this.someModelsHaveFractionalCoordinates=this.someModelsHaveAromaticBonds=this.someModelsHaveSymmetry=
!1;this.ptTemp=null;this.isBbcageDefault=!1;this.stateScripts=this.boxInfo=this.bboxAtoms=this.bboxModels=null;this.thisStateModel=0;this.selectedMolecules=this.vibrationSteps=this.trajectorySteps=null;this.showRebondTimes=!0;this.ptTemp2=this.ptTemp1=this.sm=this.bsAll=null;this.proteinStructureTainted=!1;this.vTemp=this.mat4t=this.mat4=this.matInv=this.matTemp=this.triangulator=this.vOrientations=this.htPeaks=this.symTemp=null;s(this,arguments)},JM,"ModelSet",JM.BondCollection);K(c$,function(){this.closest=
Array(1);this.am=Array(1);this.modelNumbers=D(1,0);this.modelFileNumbers=D(1,0);this.modelNumbersForAtomLabel=Array(1);this.modelNames=Array(1);this.frameTitles=Array(1);this.ptTemp=new JU.P3;this.boxInfo=new JU.BoxInfo;this.boxInfo.addBoundBoxPoint(JU.P3.new3(-10,-10,-10));this.boxInfo.addBoundBoxPoint(JU.P3.new3(10,10,10));this.stateScripts=new JU.Lst;this.selectedMolecules=new JU.BS;this.ptTemp1=new JU.P3;this.ptTemp2=new JU.P3;this.matTemp=new JU.M3;this.matInv=new JU.M3;this.mat4=new JU.M4;this.mat4t=
new JU.M4;this.vTemp=new JU.V3});u(c$,function(a,b){E(this,JM.ModelSet,[]);this.vwr=a;this.modelSetName=b},"JV.Viewer,~S");h(c$,"releaseModelSet",function(){this.am=null;this.unitCells=this.bsAll=this.bsSymmetry=this.am=this.closest[0]=null;this.releaseModelSetBC()});c(c$,"setSelectionHaloEnabled",function(a){this.selectionHaloEnabled=a},"~B");c(c$,"getSelectionHaloEnabled",function(){return this.selectionHaloEnabled});c(c$,"getEchoStateActive",function(){return this.echoShapeActive});c(c$,"setEchoStateActive",
function(a){this.echoShapeActive=a},"~B");c(c$,"getModelSetTypeName",function(){return this.modelSetTypeName});c(c$,"getModelNumberIndex",function(a,b,d){if(b){for(b=0;b<this.mc;b++)if(this.modelNumbers[b]==a||1E6>a&&this.modelNumbers[b]==1E6+a)return b;return-1}for(b=0;b<this.mc;b++)if(this.modelFileNumbers[b]==a)return d&&this.isTrajectory(b)&&this.setTrajectory(b),b;return-1},"~N,~B,~B");c(c$,"getBitSetTrajectories",function(){if(null==this.trajectorySteps)return null;for(var a=new JU.BS,b=this.mc;0<=
--b;){var d=this.am[b].getSelectedTrajectory();0<=d&&(a.set(d),b=this.am[b].trajectoryBaseIndex)}return a});c(c$,"setTrajectoryBs",function(a){for(var b=0;b<this.mc;b++)a.get(b)&&this.setTrajectory(b)},"JU.BS");c(c$,"setTrajectory",function(a){if(!(0>a)&&this.isTrajectory(a)&&this.at[this.am[a].firstAtomIndex].mi!=a){var b=this.am[a].trajectoryBaseIndex;this.am[b].setSelectedTrajectory(a);this.setAtomPositions(b,a,this.trajectorySteps.get(a),null,0,null==this.vibrationSteps?null:this.vibrationSteps.get(a),
!0);b=this.vwr.am.cmi;0<=b&&(b!=a&&this.am[b].fileIndex==this.am[a].fileIndex)&&this.vwr.setCurrentModelIndexClear(a,!1)}},"~N");c(c$,"morphTrajectories",function(a,b,d){if(!(0>a||0>b||!this.isTrajectory(a)||!this.isTrajectory(b)))if(0==d)this.setTrajectory(a);else if(1==d)this.setTrajectory(b);else{var c=this.am[a].trajectoryBaseIndex;this.am[c].setSelectedTrajectory(a);this.setAtomPositions(c,a,this.trajectorySteps.get(a),this.trajectorySteps.get(b),d,null==this.vibrationSteps?null:this.vibrationSteps.get(a),
!0);b=this.vwr.am.cmi;0<=b&&(b!=a&&this.am[b].fileIndex==this.am[a].fileIndex)&&this.vwr.setCurrentModelIndexClear(a,!1)}},"~N,~N,~N");c(c$,"setAtomPositions",function(a,b,d,c,g,f,j){var k=new JU.BS,h=new JU.V3,m=this.am[a].firstAtomIndex,r=m+this.getAtomCountInModel(a);if(0==g)for(var x=0;m<r&&x<d.length;m++,x++)this.at[m].mi=b,null!=d[x]&&(j?this.at[m].setFractionalCoordTo(d[x],!0):this.at[m].setT(d[x]),null!=this.vibrationSteps&&(null!=f&&null!=f[x]&&(h=f[x]),this.setVibrationVector(m,h)),k.set(m));
else{f=new JU.P3;h=Math.min(d.length,c.length);for(x=0;m<r&&x<h;m++,x++)this.at[m].mi=b,null==d[x]||null==c[x]||(f.sub2(c[x],d[x]),f.scaleAdd2(g,f,d[x]),j?this.at[m].setFractionalCoordTo(f,!0):this.at[m].setT(f),k.set(m))}this.initializeBspf();this.validateBspfForModel(a,!1);this.recalculateLeadMidpointsAndWingVectors(a);this.sm.refreshShapeTrajectories(a,k,null);this.am[a].hasRasmolHBonds&&(this.am[a].clearRasmolHydrogenBonds(null),this.am[a].getRasmolHydrogenBonds(k,k,null,!1,2147483647,!1,null))},
"~N,~N,~A,~A,~N,~A,~B");c(c$,"getFrameOffsets",function(a){if(null==a)return null;for(var b=Array(this.mc),d=0;d<this.mc;d++)b[d]=new JU.P3;for(var c=0,g=0,f=b[0],j=null!=this.trajectorySteps&&this.trajectorySteps.size()==this.mc,k=j?this.mc:1,h=0;h<k;h++){j&&this.setTrajectory(h);for(d=0;d<=this.ac;d++){if(d==this.ac||this.at[d].mi!=c){0<g&&(f.scale(-1/g),0!=c&&f.sub(b[0]),g=0);if(d==this.ac)break;c=this.at[d].mi;f=b[c]}a.get(d)&&(f.add(this.at[d]),g++)}}b[0].set(0,0,0);return b},"JU.BS");c(c$,"getAtoms",
function(a,b){switch(a){default:return JU.BSUtil.andNot(this.getAtomBitsMaybeDeleted(a,b),this.vwr.getDeletedAtoms());case 1048610:var d=b.intValue(),c=this.getModelNumberIndex(d,!0,!0);return 0>c&&0<d?new JU.BS:this.vwr.getModelUndeletedAtomsBitSet(c)}},"~N,~O");c(c$,"findNearestAtomIndex",function(a,b,d,c){if(0==this.ac)return-1;this.closest[0]=null;this.g3d.isAntialiased()&&(a<<=1,b<<=1);this.findNearest2(a,b,this.closest,d,c);this.sm.findNearestShapeAtomIndex(a,b,this.closest,d);a=null==this.closest[0]?
-1:this.closest[0].i;this.closest[0]=null;return a},"~N,~N,JU.BS,~N");c(c$,"calculateStructures",function(a,b,d,c,g){var f=new JU.BS;a=JU.BSUtil.copyInvert(this.modelsOf(a,f),this.mc);if(!g)return this.calculateStructuresAllExcept(a,b,d,c,!1,!1);for(g=0;g<this.mc;g++)a.get(g)||this.am[g].clearBioPolymers();this.calculatePolymers(null,0,0,a);b=this.calculateStructuresAllExcept(a,b,d,c,!0,!1);this.vwr.shm.resetBioshapes(f);this.setStructureIndexes();return b},"JU.BS,~B,~B,~B,~B");c(c$,"calculatePointGroup",
function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,!1,null,0,0)},"JU.BS");c(c$,"getPointGroupInfo",function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,!0,null,0,0)},"JU.BS");c(c$,"getPointGroupAsString",function(a,b,d,c,g){return this.calculatePointGroupForFirstModel(a,!0,b,!1,d,c,g)},"JU.BS,~B,~S,~N,~N");c(c$,"calculatePointGroupForFirstModel",function(a,b,d,c,g,f,j){var k=this.vwr.am.cmi,h=null==a?-1:a.nextSetBit(0);0>k&&0<=h&&(k=this.at[h].getModelIndex());0>k&&(k=this.vwr.getVisibleFramesBitSet().nextSetBit(0),
a=null);var m=this.vwr.getModelUndeletedAtomsBitSet(k);null!=a&&m.and(a);h=m.nextSetBit(0);0>h&&(m=this.vwr.getModelUndeletedAtomsBitSet(k),h=m.nextSetBit(0));a=this.vwr.shm.getShapePropertyIndex(18,"mad",h);a=null!=a&&0!=a.intValue()||this.vwr.tm.vibrationOn;this.pointGroup=J.api.Interface.getSymmetry().setPointGroup(this.pointGroup,this.at,m,a,this.vwr.getFloat(570425382),this.vwr.getFloat(570425384));if(!b&&!c)return this.pointGroup.getPointGroupName();b=this.pointGroup.getPointGroupInfo(k,d,c,
g,f,j);return c?b:(1<this.mc?"frame "+this.getModelNumberDotted(k)+"; ":"")+b},"JU.BS,~B,~B,~B,~S,~N,~N");c(c$,"modelsOf",function(a,b){for(var d=JU.BS.newN(this.mc),c=null==a,g=c?this.ac-1:a.nextSetBit(0);0<=g;g=c?g-1:a.nextSetBit(g+1)){var f=this.am[this.at[g].mi].trajectoryBaseIndex;this.isJmolDataFrameForModel(f)||(d.set(f),b.set(g))}return d},"JU.BS,JU.BS");c(c$,"getDefaultStructure",function(a,b){for(var d=this.modelsOf(a,b),c=new JU.SB,g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))this.am[g].isBioModel&&
null!=this.am[g].defaultStructure&&c.append(this.am[g].defaultStructure);return c.toString()},"JU.BS,JU.BS");c(c$,"makeConnections",function(a,b,d,c,g,f,j,k,h,m){if(1073741852==c&&2048!=d){var r="connect ";0.1!=a&&(r+=a+" ");1E8!=b&&(r+=b+" ");this.addStateScript(r,k?g:null,k?null:g,k?null:f," auto",!1,!0)}this.moleculeCount=0;return this.makeConnections2(a,b,d,c,g,f,j,k,h,m)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"setPdbConectBonding",function(a,b,d){for(var c=this.vwr.getMadBond();b<this.mc;b++){var g=
this.getInfo(b,"PDB_CONECT_bonds");if(null!=g){var f=g.size();this.setInfo(b,"initialBondCount",Integer.$valueOf(f));for(var j=this.getInfo(b,"PDB_CONECT_firstAtom_count_max"),k=j[0]+a,h=k+j[1],j=j[2],m=D(j+1,0),r=k;r<h;r++)if(0<(k=this.atomSerials[r]))m[k]=r+1;for(h=0;h<f;h++){var r=g.get(h),x=r[0],k=r[1],r=r[2];0>x||(0>k||x>j||k>j)||(x=m[x]-1,k=m[k]-1,0>x||0>k||(null!=d&&(this.at[x].isHetero()&&d.set(x),this.at[k].isHetero()&&d.set(k)),this.checkValencesAndBond(this.at[x],this.at[k],r,2048==r?1:
c,null)))}}}},"~N,~N,JU.BS");c(c$,"deleteAllBonds",function(){this.moleculeCount=0;for(var a=this.stateScripts.size();0<=--a;)this.stateScripts.get(a).isConnect()&&this.stateScripts.remove(a);this.deleteAllBonds2()});c(c$,"includeAllRelatedFrames",function(a){for(var b,d=0;d<this.mc;d++)if(a.get(d)){if(this.isTrajectory(d)&&!a.get(b=this.am[d].trajectoryBaseIndex)){a.set(b);this.includeAllRelatedFrames(a);break}}else(this.isTrajectory(d)&&a.get(this.am[d].trajectoryBaseIndex)||this.isJmolDataFrameForModel(d)&&
a.get(this.am[d].dataSourceFrame))&&a.set(d)},"JU.BS");c(c$,"deleteModels",function(a){this.moleculeCount=0;this.includeAllRelatedFrames(a);var b=JU.BSUtil.cardinalityOf(a);if(0==b)return null;for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.clearDataFrameReference(d);if(b==this.mc)return b=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.vwr.zap(!0,!1,!1),b;this.validateBspf(!1);for(var c=Array(this.mc-b),g=this.am,b=new JU.BS,f=d=0;d<this.mc;d++)a.get(d)?(this.getAtomCountInModel(d),b.or(this.getModelAtomBitSetIncludingDeleted(d,
!1))):(this.am[d].modelIndex=f,c[f++]=this.am[d]);this.am=c;var j=this.mc,k=this.getBondsForSelectedAtoms(b,!0);this.deleteBonds(k,!0);for(f=d=0;d<j;d++)if(a.get(d)){var h=g[d].ac;if(0!=h){var m=g[d].bsAtoms,r=g[d].firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,m);this.deleteModel(f,r,h,m,k);for(var x=j;--x>d;)g[x].fixIndices(f,h,m);this.vwr.shm.deleteShapeAtoms([c,this.at,[f,r,h]],m);this.mc--}}else f++;this.deleteModel(-1,0,0,null,null);return b},"JU.BS");c(c$,"setAtomProperty",function(a,
b,d,c,g,f,j){switch(b){case 1115297793:case 1113200642:case 1113200647:case 1113200649:case 1113200650:case 1650071565:case 1113200654:if(4<c&&(c=4),null!=f){d=L(this.ac,0);try{var k=a.nextSetBit(0);for(g=0;0<=k;k=a.nextSetBit(k+1))d[k]=f[g++]}catch(h){if(y(h,Exception))return;throw h;}f=d}case 1113200646:case 1113200652:k=null;d=0;null==f?(16<c&&(c=16.1),0>c&&(c=0),d=q(Math.floor(2E3*c))):k=new J.atomdata.RadiusData(f,0,null,null);this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(b),d,k,a);return}this.setAPm(a,
b,d,c,g,f,j)},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"getFileData",function(a){if(0>a)return"";var b=this.getInfo(a,"fileData");if(null!=b)return b;if(!this.getInfoB(a,"isCIF"))return this.getPDBHeader(a);b=this.vwr.getCifData(a);this.setInfo(a,"fileData",b);return b},"~N");c(c$,"addHydrogens",function(a,b){var d=this.mc-1,c=new JU.BS;if(this.isTrajectory(d)||1<this.am[d].getGroupCount())return c;this.growAtomArrays(this.ac+b.length);var g=this.vwr.rd,f=this.getDefaultMadFromOrder(1);this.am[d].dssrCache=
null;for(var j=0,k=this.am[d].ac+1;j<a.size();j++,k++){var h=a.get(j),m=this.addAtom(d,h.group,1,"H"+k,k,h.getSeqID(),k,b[j],NaN,null,0,0,100,NaN,null,!1,0,null);m.setMadAtom(this.vwr,g);c.set(m.i);this.bondAtoms(h,m,1,f,null,0,!1,!1)}this.sm.loadDefaultShapes(this);return c},"JU.Lst,~A");c(c$,"mergeModelArrays",function(a){this.at=a.at;this.bo=a.bo;this.stateScripts=a.stateScripts;this.proteinStructureTainted=a.proteinStructureTainted;this.thisStateModel=-1;this.bsSymmetry=a.bsSymmetry;this.modelFileNumbers=
a.modelFileNumbers;this.modelNumbersForAtomLabel=a.modelNumbersForAtomLabel;this.modelNames=a.modelNames;this.modelNumbers=a.modelNumbers;this.frameTitles=a.frameTitles;this.mergeAtomArrays(a)},"JM.ModelSet");c(c$,"getUnitCell",function(a){return!this.haveUnitCells||0>a||a>=this.mc?null:null!=this.am[a].simpleCage?this.am[a].simpleCage:null==this.unitCells||a>=this.unitCells.length||!this.unitCells[a].haveUnitCell()?null:this.unitCells[a]},"~N");c(c$,"setModelCage",function(a,b){0>a||a>=this.mc||
(this.am[a].simpleCage=b,this.haveUnitCells=!0)},"~N,J.api.SymmetryInterface");c(c$,"getPlaneIntersection",function(a,b,d,c,g){var f=null;switch(a){case 1614417948:if(null==g)return null;f=g.getCanonicalCopy(d,!0);break;case 1679429641:f=this.boxInfo.getCanonicalCopy(d)}a=new JU.Lst;a.addLast(f);return this.intersectPlane(b,a,c)},"~N,JU.P4,~N,~N,J.api.SymmetryInterface");c(c$,"getModelName",function(a){return 1>this.mc?"":0<=a?this.modelNames[a]:this.modelNumbersForAtomLabel[-1-a]},"~N");c(c$,"getModelTitle",
function(a){return this.getInfo(a,"title")},"~N");c(c$,"getModelFileName",function(a){return this.getInfo(a,"fileName")},"~N");c(c$,"getModelFileType",function(a){return this.getInfo(a,"fileType")},"~N");c(c$,"setFrameTitle",function(a,b){if(p(b,String))for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.frameTitles[d]=b;else for(var d=a.nextSetBit(0),c=0;0<=d;d=a.nextSetBit(d+1))c<b.length&&(this.frameTitles[d]=b[c++])},"JU.BS,~O");c(c$,"getFrameTitle",function(a){return 0<=a&&a<this.mc?this.frameTitles[a]:
""},"~N");c(c$,"getModelNumberForAtomLabel",function(a){return this.modelNumbersForAtomLabel[a]},"~N");c(c$,"calculatePolymers",function(a,b,d,c){if(this.isPDB)for(var g=!this.vwr.getBoolean(603979892),f=0;f<this.mc;f++)if((null==c||!c.get(f))&&this.am[f].isBioModel){this.am[f].calculatePolymers(a,b,d,c,g);break}},"~A,~N,~N,JU.BS");c(c$,"getGroups",function(){for(var a=0,b=0;b<this.mc;b++)a+=this.am[b].getGroupCount();for(var a=Array(a),d=b=0;b<this.mc;b++)for(var c=0;c<this.am[b].chainCount;c++)for(var g=
0;g<this.am[b].chains[c].groupCount;g++)a[d]=this.am[b].chains[c].groups[g],a[d].groupIndex=d,d++;return a});c(c$,"getNotionalUnitcell",function(){var a=this.getUnitCell(0);return null==a?null:a.getNotionalUnitCell()});c(c$,"setCrystallographicDefaults",function(){return!this.isPDB&&this.someModelsHaveSymmetry&&this.someModelsHaveFractionalCoordinates});c(c$,"getBoundBoxCenter",function(a){return this.isJmolDataFrameForModel(a)?new JU.P3:this.boxInfo.getBoundBoxCenter()},"~N");c(c$,"getBoundBoxCornerVector",
function(){return this.boxInfo.getBoundBoxCornerVector()});c(c$,"getBBoxVertices",function(){return this.boxInfo.getBoundBoxVertices()});c(c$,"getBoundBoxModels",function(){return this.bboxModels});c(c$,"setBoundBox",function(a,b,d,c){this.isBbcageDefault=!1;this.bboxAtoms=this.bboxModels=null;this.boxInfo.setBoundBox(a,b,d,c)},"JU.P3,JU.P3,~B,~N");c(c$,"getBoundBoxCommand",function(a){if(!a&&null!=this.bboxAtoms)return"boundbox "+JU.Escape.eBS(this.bboxAtoms);this.ptTemp.setT(this.boxInfo.getBoundBoxCenter());
var b=this.boxInfo.getBoundBoxCornerVector();a=a?"boundbox "+JU.Escape.eP(this.ptTemp)+" "+JU.Escape.eP(b)+"\n#or\n":"";this.ptTemp.sub(b);a+="boundbox corners "+JU.Escape.eP(this.ptTemp)+" ";this.ptTemp.scaleAdd2(2,b,this.ptTemp);b=Math.abs(8*b.x*b.y*b.z);return a+=JU.Escape.eP(this.ptTemp)+" # volume = "+b},"~B");c(c$,"getDefaultVdwType",function(a){return!this.am[a].isBioModel?J.c.VDW.AUTO_BABEL:0==this.am[a].hydrogenCount?J.c.VDW.AUTO_JMOL:J.c.VDW.AUTO_BABEL},"~N");c(c$,"setRotationRadius",function(a,
b){return this.isJmolDataFrameForModel(a)?(this.am[a].defaultRotationRadius=b,!1):!0},"~N,~N");c(c$,"calcRotationRadius",function(a,b){if(this.isJmolDataFrameForModel(a)){var d=this.am[a].defaultRotationRadius;return 0==d?10:d}for(var d=0,c=this.ac;0<=--c;)if(this.isJmolDataFrameForAtom(this.at[c]))for(a=this.at[c].mi;0<=c&&this.at[c].mi==a;)c--;else{var g=this.at[c],g=b.distance(g)+this.getRadiusVdwJmol(g);g>d&&(d=g)}return 0==d?10:d},"~N,JU.P3");c(c$,"calcBoundBoxDimensions",function(a,b){null!=
a&&0>a.nextSetBit(0)&&(a=null);null==a&&this.isBbcageDefault||0==this.ac||(this.bboxModels=this.getModelBS(this.bboxAtoms=JU.BSUtil.copy(a),!1),this.calcAtomsMinMax(a,this.boxInfo)==this.ac&&(this.isBbcageDefault=!0),null==a&&null!=this.unitCells&&this.calcUnitCellMinMax(),this.boxInfo.setBbcage(b))},"JU.BS,~N");c(c$,"getBoxInfo",function(a,b){if(null==a)return this.boxInfo;var d=new JU.BoxInfo;this.calcAtomsMinMax(a,d);d.setBbcage(b);return d},"JU.BS,~N");c(c$,"calcAtomsMinMax",function(a,b){b.reset();
for(var d=0,c=null==a,g=c?this.ac-1:a.nextSetBit(0);0<=g;g=c?g-1:a.nextSetBit(g+1))d++,this.isJmolDataFrameForAtom(this.at[g])||b.addBoundBoxPoint(this.at[g]);return d},"JU.BS,JU.BoxInfo");c(c$,"calcUnitCellMinMax",function(){for(var a=0;a<this.mc;a++)if(this.unitCells[a].getCoordinatesAreFractional())for(var b=this.unitCells[a].getUnitCellVertices(),d=0;8>d;d++)this.boxInfo.addBoundBoxPoint(b[d])});c(c$,"calcRotationRadiusBs",function(a){for(var b=this.getAtomSetCenter(a),d=0,c=a.nextSetBit(0);0<=
c;c=a.nextSetBit(c+1)){var g=this.at[c],g=b.distance(g)+this.getRadiusVdwJmol(g);g>d&&(d=g)}return 0==d?10:d},"JU.BS");c(c$,"getCenterAndPoints",function(a,b){for(var d,c,g=b?1:0,f=a.size();0<=--f;){var j=a.get(f);d=j[0];p(j[1],JU.BS)?(c=j[1],g+=Math.min(d.cardinality(),c.cardinality())):g+=Math.min(d.cardinality(),j[1].length)}var k=P(2,g,null);b&&(k[0][0]=new JU.P3,k[1][0]=new JU.P3);for(f=a.size();0<=--f;)if(j=a.get(f),d=j[0],p(j[1],JU.BS)){c=j[1];for(var j=d.nextSetBit(0),h=c.nextSetBit(0);0<=
j&&0<=h;j=d.nextSetBit(j+1),h=c.nextSetBit(h+1))k[0][--g]=this.at[j],k[1][g]=this.at[h],b&&(k[0][0].add(this.at[j]),k[1][0].add(this.at[h]))}else{c=j[1];j=d.nextSetBit(0);for(h=0;0<=j&&h<c.length;j=d.nextSetBit(j+1),h++)k[0][--g]=this.at[j],k[1][g]=c[h],b&&(k[0][0].add(this.at[j]),k[1][0].add(c[h]))}b&&(k[0][0].scale(1/(k[0].length-1)),k[1][0].scale(1/(k[1].length-1)));return k},"JU.Lst,~B");c(c$,"getAtomSetCenter",function(a){for(var b=new JU.P3,d=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.isJmolDataFrameForAtom(this.at[c])||
(d++,b.add(this.at[c]));0<d&&b.scale(1/d);return b},"JU.BS");c(c$,"getAverageAtomPoint",function(){null==this.averageAtomPoint&&(this.averageAtomPoint=new JU.P3).setT(this.getAtomSetCenter(this.vwr.getAllAtoms()));return this.averageAtomPoint});c(c$,"setAPm",function(a,b,d,c,g,f,j){this.setAPa(a,b,d,c,g,f,j);switch(b){case 1095763991:case 1632634891:this.vwr.getBoolean(603979944)&&this.assignAromaticBonds()}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"addStateScript",function(a,b,d,c,g,f,j){var k=this.vwr.am.cmi;
f?(this.thisStateModel!=k&&(a="frame "+(0>k?"all #"+k:this.getModelNumberDotted(k))+";\n  "+a),this.thisStateModel=k):this.thisStateModel=-1;a=new JM.StateScript(this.thisStateModel,a,b,d,c,g,j);a.isValid()&&this.stateScripts.addLast(a);return a},"~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");c(c$,"calculateStructuresAllExcept",function(a,b,d,c,g,f){this.freezeModels();var j="";a=JU.BSUtil.copyInvert(a,this.mc);g&&this.setDefaultStructure(a);for(var k=a.nextSetBit(0);0<=k;k=a.nextSetBit(k+1))j+=this.am[k].calculateStructures(b,
d,c,g,f);g&&this.setStructureIndexes();return j},"JU.BS,~B,~B,~B,~B,~B");c(c$,"setDefaultStructure",function(a){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.am[b].isBioModel&&null==this.am[b].defaultStructure&&(this.am[b].defaultStructure=this.getProteinStructureState(this.am[b].bsAtoms,!1,!1,0))},"JU.BS");c(c$,"setProteinType",function(a,b){var d=-1,c=-1,g=this.getModelBS(a,!1);this.setDefaultStructure(g);for(var f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){c!=f-1&&(d=-1);var d=this.at[f].group.setProteinStructureType(b,
d),j=this.at[f].mi;this.proteinStructureTainted=this.am[j].structureTainted=!0;c=f=this.at[f].group.lastAtomIndex}d=D(this.mc,0);for(f=0;f<this.ac;)j=this.at[f].mi,g.get(j)?(c=this.at[f].getStrucNo(),1E3>c&&c>d[j]&&(d[j]=c),f=this.at[f].group.lastAtomIndex+1):f=this.am[j].firstAtomIndex+this.am[j].ac;for(f=0;f<this.ac;)j=this.at[f].mi,g.get(j)?(1E3<this.at[f].getStrucNo()&&this.at[f].group.setStrucNo(++d[j]),f=this.at[f].group.lastAtomIndex+1):f=this.am[j].firstAtomIndex+this.am[j].ac},"JU.BS,J.c.STR");
c(c$,"freezeModels",function(){for(var a=this.mc;0<=--a;)this.am[a].freeze()});c(c$,"getStructureList",function(){return this.vwr.getStructureList()});c(c$,"setStructureList",function(a){for(var b=this.mc;0<=--b;)this.am[b].setStructureList(a)},"java.util.Map");c(c$,"setConformation",function(a){for(var b=this.getModelBS(a,!1),d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.am[d].setConformation(a);return a},"JU.BS");c(c$,"getConformation",function(a,b,d){for(var c=new JU.BS,g=this.mc;0<=--g;)if(g==
a||0>a){var f=this.getAltLocListInModel(g),j=this.getAltLocCountInModel(g);if(!(0<b&&b>=j)){var k=this.vwr.getModelUndeletedAtomsBitSet(g);if(0<=b&&!this.am[g].getPdbConformation(k,b))for(;0<=--j;)j!=b&&k.andNot(this.getAtomBitsMDa(1048607,f.substring(j,j+1)));0<=k.nextSetBit(0)&&(c.or(k),d&&this.am[g].setConformation(k))}}return c},"~N,~N,~B");c(c$,"getHeteroList",function(a){for(var b=new java.util.Hashtable,d=!1,c=this.mc;0<=--c;)if(0>a||c==a){var g=this.getInfo(c,"hetNames");if(null!=g)for(var d=
!0,f,g=g.entrySet().iterator();g.hasNext()&&((f=g.next())||1);){var j=f.getKey();b.put(j,f.getValue())}}return d?b:this.getInfoM("hetNames")},"~N");c(c$,"getMSProperties",function(){return this.modelSetProperties});c(c$,"getMSInfo",function(){return this.msInfo});c(c$,"getInfoM",function(a){return null==this.msInfo?null:this.msInfo.get(a)},"~S");c(c$,"getMSInfoB",function(a){a=this.getInfoM(a);return p(a,Boolean)&&a.booleanValue()},"~S");c(c$,"mergeTrajectories",function(a){if(null==this.trajectorySteps){if(!a)return 0;
this.trajectorySteps=new JU.Lst}for(a=this.trajectorySteps.size();a<this.mc;a++)this.trajectorySteps.addLast(null);return this.mc},"~B");c(c$,"getTrajectoryIndex",function(a){return this.am[a].trajectoryBaseIndex},"~N");c(c$,"isTrajectory",function(a){return this.am[a].isTrajectory},"~N");c(c$,"isTrajectoryMeasurement",function(a){if(null==a)return!1;for(var b=a[0],d,c=1;c<=b;c++)if(0<=(d=a[c])&&this.am[this.at[d].mi].isTrajectory)return!0;return!1},"~A");c(c$,"getModelBS",function(a,b){for(var d=
new JU.BS,c=0,g=null==a,c=g?0:a.nextSetBit(0);0<=c&&c<this.ac;c=g?c+1:a.nextSetBit(c+1)){d.set(c=this.at[c].mi);if(b)for(var f=this.am[c].trajectoryBaseIndex,j=0;j<this.mc;j++)this.am[j].trajectoryBaseIndex==f&&d.set(j);c=this.am[c].firstAtomIndex+this.am[c].ac-1}return d},"JU.BS,~B");c(c$,"getIterativeModels",function(a){for(var b=new JU.BS,d=0;d<this.mc;d++)(a||!this.isJmolDataFrameForModel(d))&&this.am[d].trajectoryBaseIndex==d&&b.set(d);return b},"~B");c(c$,"isTrajectorySubFrame",function(a){return this.am[a].isTrajectory&&
this.am[a].trajectoryBaseIndex!=a},"~N");c(c$,"selectDisplayedTrajectories",function(a){for(var b=0;b<this.mc;b++)this.am[b].isTrajectory&&this.at[this.am[b].firstAtomIndex].mi!=b&&a.clear(b);return a},"JU.BS");c(c$,"fillAtomData",function(a,b){if(0!=(b&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);a.atomMolecule=D(this.ac,0);for(var d,c=0;c<this.molecules.length;c++){d=a.bsMolecules[c]=this.molecules[c].atomList;for(var g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))a.atomMolecule[g]=
c}}0!=(b&8)?(d=D(1,0),a.hAtomRadius=this.vwr.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,d,!1,!0,null),a.hydrogenAtomCount=d[0]):(a.firstAtomIndex=0>a.modelIndex?null==a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.am[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=0==this.ac?0:this.at[a.firstAtomIndex].mi,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,b))},"J.atomdata.AtomData,~N");c(c$,"getModelNumberDotted",function(a){return 1>
this.mc||a>=this.mc||0>a?"":JU.Escape.escapeModelFileNumber(this.modelFileNumbers[a])},"~N");c(c$,"getModelNumber",function(a){2147483647==a&&(a=this.mc-1);return this.modelNumbers[a]},"~N");c(c$,"getModelFileNumber",function(a){return this.modelFileNumbers[a]},"~N");c(c$,"getModelProperties",function(a){return this.am[a].properties},"~N");c(c$,"getModelProperty",function(a,b){var d=this.am[a].properties;return null==d?null:d.getProperty(b)},"~N,~S");c(c$,"getModelAuxiliaryInfo",function(a){return 0>
a?null:this.am[a].auxiliaryInfo},"~N");c(c$,"setInfo",function(a,b,d){this.am[a].auxiliaryInfo.put(b,d)},"~N,~O,~O");c(c$,"getInfo",function(a,b){return 0>a?null:this.am[a].auxiliaryInfo.get(b)},"~N,~S");c(c$,"getInfoB",function(a,b){var d=this.am[a].auxiliaryInfo;return null!=d&&d.containsKey(b)&&d.get(b).booleanValue()},"~N,~S");c(c$,"getInfoI",function(a,b){var d=this.am[a].auxiliaryInfo;return null!=d&&d.containsKey(b)?d.get(b).intValue():-2147483648},"~N,~S");c(c$,"getAtomProp",function(a,b){var d=
this.getInfo(a.mi,b);if(!p(d,Array))return"";var c=a.i-this.am[a.mi].firstAtomIndex;return c<d.length?d[c].toString():""},"JM.Atom,~S");c(c$,"getInsertionCountInModel",function(a){return this.am[a].nInsertions},"~N");c$.modelFileNumberFromFloat=c(c$,"modelFileNumberFromFloat",function(a){var b=q(Math.floor(a));for(a=q(Math.floor(1E4*(a-b+1E-5)));0!=a&&0==a%10;)a/=10;return 1E6*b+a},"~N");c(c$,"getAltLocCountInModel",function(a){return this.am[a].nAltLocs},"~N");c(c$,"getChainCount",function(a){for(var b=
0,d=this.mc;0<=--d;)b+=this.am[d].getChainCount(a);return b},"~B");c(c$,"getBioPolymerCount",function(){for(var a=0,b=this.mc;0<=--b;)this.isTrajectorySubFrame(b)||(a+=this.am[b].getBioPolymerCount());return a});c(c$,"getBioPolymerCountInModel",function(a){return 0>a?this.getBioPolymerCount():this.isTrajectorySubFrame(a)?0:this.am[a].getBioPolymerCount()},"~N");c(c$,"getPolymerPointsAndVectors",function(a,b,d,c){for(var g=0;g<this.mc;++g)this.am[g].getPolymerPointsAndVectors(a,b,d,c)},"JU.BS,JU.Lst,~B,~N");
c(c$,"recalculateLeadMidpointsAndWingVectors",function(a){if(0>a)for(a=0;a<this.mc;a++)this.isTrajectorySubFrame(a)||this.am[a].recalculateLeadMidpointsAndWingVectors();else this.am[a].recalculateLeadMidpointsAndWingVectors()},"~N");c(c$,"getPolymerLeadMidPoints",function(a,b){return this.am[a].getPolymerLeadMidPoints(b)},"~N,~N");c(c$,"getChainCountInModelWater",function(a,b){return 0>a?this.getChainCount(b):this.am[a].getChainCount(b)},"~N,~B");c(c$,"getGroupCount",function(){for(var a=0,b=this.mc;0<=
--b;)a+=this.am[b].getGroupCount();return a});c(c$,"getGroupCountInModel",function(a){return 0>a?this.getGroupCount():this.am[a].getGroupCount()},"~N");c(c$,"calcSelectedGroupsCount",function(){for(var a=this.vwr.bsA(),b=this.mc;0<=--b;)this.am[b].calcSelectedGroupsCount(a)});c(c$,"calcSelectedMonomersCount",function(){for(var a=this.vwr.bsA(),b=this.mc;0<=--b;)this.am[b].calcSelectedMonomersCount(a)});c(c$,"calcRasmolHydrogenBonds",function(a,b,d,c,g,f,j){for(var k=null==b||a.equals(b),h=this.mc;0<=
--h;)this.am[h].isBioModel&&this.am[h].trajectoryBaseIndex==h&&(null==d&&(this.am[h].clearRasmolHydrogenBonds(a),k||this.am[h].clearRasmolHydrogenBonds(b)),this.am[h].getRasmolHydrogenBonds(a,b,d,c,g,f,j))},"JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS");c(c$,"calculateStraightness",function(){if(!this.getHaveStraightness()){for(var a=this.vwr.getQuaternionFrame(),b=this.vwr.getInt(553648146),d=this.mc;0<=--d;)this.am[d].calculateStraightness(this.vwr,"S",a,b);this.setHaveStraightness(!0)}});c(c$,"getAtomGroupQuaternions",
function(a,b,d){for(var c=0,g=new JU.Lst,f=a.nextSetBit(0);0<=f&&c<b;f=a.nextSetBit(f+1)){var j=this.at[f].group,k=j.getQuaternion(d);if(null==k&&(-2147483648==j.seqcode&&(k=j.getQuaternionFrame(this.at)),null==k))continue;c++;g.addLast(k);f=j.lastAtomIndex}return g.toArray(Array(g.size()))},"JU.BS,~N,~S");c(c$,"isJmolDataFrameForModel",function(a){return 0<=a&&a<this.mc&&this.am[a].isJmolDataFrame},"~N");c(c$,"isJmolDataFrameForAtom",function(a){return this.am[a.mi].isJmolDataFrame},"JM.Atom");c(c$,
"setJmolDataFrame",function(a,b,d){var c=this.am[null==a?this.am[d].dataSourceFrame:b];null==a&&(a=this.am[d].jmolFrameType);0<=b&&(null==c.dataFrames&&(c.dataFrames=new java.util.Hashtable),this.am[d].dataSourceFrame=b,this.am[d].jmolFrameType=a,c.dataFrames.put(a,Integer.$valueOf(d)));a.startsWith("quaternion")&&0>a.indexOf("deriv")&&(a=a.substring(0,a.indexOf(" ")),c.dataFrames.put(a,Integer.$valueOf(d)))},"~S,~N,~N");c(c$,"getJmolDataFrameIndex",function(a,b){if(null==this.am[a].dataFrames)return-1;
var d=this.am[a].dataFrames.get(b);return null==d?-1:d.intValue()},"~N,~S");c(c$,"clearDataFrameReference",function(a){for(var b=0;b<this.mc;b++){var d=this.am[b].dataFrames;if(null!=d)for(d=d.values().iterator();d.hasNext();)d.next().intValue()==a&&d.remove()}},"~N");c(c$,"getJmolFrameType",function(a){return 0<=a&&a<this.mc?this.am[a].jmolFrameType:"modelSet"},"~N");c(c$,"getJmolDataSourceFrame",function(a){return 0<=a&&a<this.mc?this.am[a].dataSourceFrame:-1},"~N");c(c$,"saveModelOrientation",
function(a,b){this.am[a].orientation=b},"~N,JM.Orientation");c(c$,"getModelOrientation",function(a){return this.am[a].orientation},"~N");c(c$,"getPDBHeader",function(a){return this.am[a].isBioModel?this.am[a].getFullPDBHeader():this.getFileHeader(a)},"~N");c(c$,"getFileHeader",function(a){if(0>a)return"";if(this.am[a].isBioModel)return this.am[a].getFullPDBHeader();a=this.getInfo(a,"fileHeader");null==a&&(a=this.modelSetName);return null!=a?a:"no header information found"},"~N");c(c$,"getAltLocIndexInModel",
function(a,b){if("\x00"==b)return 0;var d=this.getAltLocListInModel(a);return 0==d.length?0:d.indexOf(b)+1},"~N,~S");c(c$,"getInsertionCodeIndexInModel",function(a,b){if("\x00"==b)return 0;var d=this.getInsertionListInModel(a);return 0==d.length?0:d.indexOf(b)+1},"~N,~S");c(c$,"getAltLocListInModel",function(a){if(0>a)return"";a=this.getInfo(a,"altLocs");return null==a?"":a},"~N");c(c$,"getInsertionListInModel",function(a){a=this.getInfo(a,"insertionCodes");return null==a?"":a},"~N");c(c$,"getModelSymmetryCount",
function(a){return 0<this.am[a].biosymmetryCount?this.am[a].biosymmetryCount:null==this.unitCells||null==this.unitCells[a]?0:this.unitCells[a].getSpaceGroupOperationCount()},"~N");c(c$,"getModelCellRange",function(a){return null==this.unitCells?null:this.unitCells[a].getCellRange()},"~N");c(c$,"getLastVibrationVector",function(a,b){if(null!=this.vibrations)for(var d=this.ac;0<=--d;)if((0>a||this.at[d].mi==a)&&null!=this.vibrations[d]&&0<this.vibrations[d].length()&&(0==b||1276121113==b==p(this.vibrations[d],
J.api.JmolModulationSet)))return d;return-1},"~N,~N");c(c$,"getModulationList",function(a,b,d){var c=new JU.Lst;if(null!=this.vibrations)for(var g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))p(this.vibrations[g],J.api.JmolModulationSet)?c.addLast(this.vibrations[g].getModulation(b,d)):c.addLast(null);return c},"JU.BS,~S,JU.P3");c(c$,"getElementsPresentBitSet",function(a){if(0<=a)return this.elementsPresent[a];a=new JU.BS;for(var b=0;b<this.mc;b++)a.or(this.elementsPresent[b]);return a},"~N");c(c$,"getMoleculeIndex",
function(a,b){0==this.moleculeCount&&this.getMolecules();for(var d=0;d<this.moleculeCount;d++)if(this.molecules[d].atomList.get(a))return b?this.molecules[d].indexInModel:d;return 0},"~N,~B");c(c$,"getMoleculeBitSet",function(a){0==this.moleculeCount&&this.getMolecules();var b=JU.BSUtil.copy(a);a=JU.BSUtil.copy(a);for(var d=0,c=new JU.BS;0<=(d=a.length()-1);)c=this.getMoleculeBitSetForAtom(d),null==c?(a.clear(d),b.clear(d)):(a.andNot(c),b.or(c));return b},"JU.BS");c(c$,"getMoleculeBitSetForAtom",
function(a){0==this.moleculeCount&&this.getMolecules();for(var b=0;b<this.moleculeCount;b++)if(this.molecules[b].atomList.get(a))return this.molecules[b].atomList;return null},"~N");c(c$,"getModelDipole",function(a){if(0>a)return null;var b=this.getInfo(a,"dipole");null==b&&(b=this.getInfo(a,"DIPOLE_VEC"));return b},"~N");c(c$,"calculateMolecularDipole",function(a,b){if(null!=b){var d=b.nextSetBit(0);if(0>d)return null;a=this.at[d].getModelIndex()}if(null==this.partialCharges||0>a)return null;var c=
d=0,g=0,f=0,j=new JU.V3,k=new JU.V3;null==b&&(b=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var h=b.nextSetBit(0);0<=h;h=b.nextSetBit(h+1))if(!(this.at[h].mi!=a||this.at[h].isDeleted())){var m=this.partialCharges[h];0>m?(c++,f+=m,k.scaleAdd2(m,this.at[h],k)):0<m&&(d++,g+=m,j.scaleAdd2(m,this.at[h],j))}if(0.01<Math.abs(g+f))return JU.Logger.info("Dipole calculation requires balanced charges: "+g+" "+f),null;if(0==c||0==d)return null;j.add(k);j.scale(4.8);return j},"~N,JU.BS");c(c$,"getMoleculeCountInModel",
function(a){var b=0;0==this.moleculeCount&&this.getMolecules();if(0>a)return this.moleculeCount;for(var d=0;d<this.mc;d++)a==d&&(b+=this.am[d].moleculeCount);return b},"~N");c(c$,"calcSelectedMoleculesCount",function(){var a=this.vwr.bsA();0==this.moleculeCount&&this.getMolecules();this.selectedMolecules.xor(this.selectedMolecules);for(var b=new JU.BS,d=0;d<this.moleculeCount;d++)JU.BSUtil.copy2(a,b),b.and(this.molecules[d].atomList),0<b.length()&&this.selectedMolecules.set(d)});c(c$,"setCentroid",
function(a,b){var d=this.getNotInCentroid(a,b);null!=d&&0<=d.nextSetBit(0)&&this.vwr.deleteAtoms(d,!1)},"JU.BS,~A");c(c$,"getNotInCentroid",function(a,b){var d=a.nextSetBit(0);if(0>d)return null;d=this.getUnitCell(this.at[d].mi);return null==d?null:d.notInCentroid(this,a,b)},"JU.BS,~A");c(c$,"getMolecules",function(){if(0<this.moleculeCount)return this.molecules;null==this.molecules&&(this.molecules=Array(4));this.moleculeCount=0;for(var a=null,b=Array(this.mc),d=null,c=0;c<this.mc;c++)b[c]=this.vwr.getModelUndeletedAtomsBitSet(c),
a=this.am[c],a.moleculeCount=0,d=a.getBioBranches(d);this.molecules=JU.JmolMolecule.getMolecules(this.at,b,d,null);for(c=this.moleculeCount=this.molecules.length;0<=--c;)a=this.am[this.molecules[c].modelIndex],a.firstMoleculeIndex=c,a.moleculeCount++;return this.molecules});c(c$,"initializeBspf",function(){if(!(null!=this.bspf&&this.bspf.isInitialized())){this.showRebondTimes&&JU.Logger.startTimer("build bspf");var a=new J.bspt.Bspf(3);JU.Logger.debugging&&JU.Logger.debug("sequential bspt order");
for(var b=JU.BS.newN(this.mc),d=this.ac;0<=--d;){var c=this.at[d];!c.isDeleted()&&!this.isTrajectorySubFrame(c.mi)&&(a.addTuple(this.am[c.mi].trajectoryBaseIndex,c),b.set(c.mi))}this.showRebondTimes&&(JU.Logger.checkTimer("build bspf",!1),a.stats());for(d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))a.validateModel(d,!0);a.validate(!0);this.bspf=a}});c(c$,"initializeBspt",function(a){this.initializeBspf();this.bspf.isInitializedIndex(a)||this.bspf.initialize(a,this.at,this.vwr.getModelUndeletedAtomsBitSet(a))},
"~N");c(c$,"setIteratorForPoint",function(a,b,d,c){0>b?a.setCenter(d,c):(this.initializeBspt(b),a.setModel(this,b,this.am[b].firstAtomIndex,2147483647,d,c,null))},"J.api.AtomIndexIterator,~N,JU.T3,~N");c(c$,"setIteratorForAtom",function(a,b,d,c,g){0>b&&(b=this.at[d].mi);b=this.am[b].trajectoryBaseIndex;this.initializeBspt(b);a.setModel(this,b,this.am[b].firstAtomIndex,d,this.at[d],c,g)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");c(c$,"getSelectedAtomIterator",function(a,b,d,c,g){this.initializeBspf();
if(g){g=this.getModelBS(a,!1);for(var f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1))this.initializeBspt(f);g=new JM.AtomIteratorWithinModelSet(g)}else g=new JM.AtomIteratorWithinModel;g.initialize(this.bspf,a,b,d,c,this.vwr.isParallel());return g},"JU.BS,~B,~B,~B,~B");h(c$,"getBondCountInModel",function(a){return 0>a?this.bondCount:this.am[a].getBondCount()},"~N");c(c$,"calculateStruts",function(a,b){this.vwr.setModelVisibility();this.makeConnections2(0,3.4028235E38,32768,12291,a,b,null,!1,!1,0);var d=
a.nextSetBit(0);if(0>d)return 0;d=this.am[this.at[d].mi];return d.isBioModel?d.calculateStruts(this,a,b):0},"JU.BS,JU.BS");c(c$,"getAtomCountInModel",function(a){return 0>a?this.ac:this.am[a].ac},"~N");c(c$,"getModelAtomBitSetIncludingDeletedBs",function(a){var b=new JU.BS;null==a&&null==this.bsAll&&(this.bsAll=JU.BSUtil.setAll(this.ac));if(null==a)b.or(this.bsAll);else for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))b.or(this.getModelAtomBitSetIncludingDeleted(d,!1));return b},"JU.BS");c(c$,"getModelAtomBitSetIncludingDeleted",
function(a,b){var d=0>a?this.bsAll:this.am[a].bsAtoms;null==d&&(d=this.bsAll=JU.BSUtil.setAll(this.ac));return b?JU.BSUtil.copy(d):d},"~N,~B");c(c$,"getAtomBitsMaybeDeleted",function(a,b){var d,c;switch(a){default:return this.getAtomBitsMDa(a,b);case 1073741925:return this.getAnnotationBits("domains",1073741925,b);case 1073742189:return this.getAnnotationBits("validation",1073742189,b);case 1073741916:return this.getAnnotationBits("dssr",1073741916,b);case 1678770178:case 1048585:return this.getAtomBitsMDb(a,
b);case 1073741864:return this.getBasePairBits(b);case 1679429641:var g=this.getBoxInfo(b,1);c=this.getAtomsWithin(g.getBoundBoxCornerVector().length()+1E-4,g.getBoundBoxCenter(),null,-1);for(d=c.nextSetBit(0);0<=d;d=c.nextSetBit(d+1))g.isWithin(this.at[d])||c.clear(d);return c;case 1095761925:c=new JU.BS;d=b;this.ptTemp1.set(d[0]/1E3,d[1]/1E3,d[2]/1E3);for(d=this.ac;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,!1)&&c.set(d);return c;case 1095761926:c=JU.BSUtil.newBitSet2(0,this.ac);d=
b;g=[q(d[0]/1E3)-1,q(d[1]/1E3)-1,q(d[2]/1E3)-1,q(d[0]/1E3),q(d[1]/1E3),q(d[2]/1E3),0];for(d=this.mc;0<=--d;){var f=this.getUnitCell(d);null==f?JU.BSUtil.andNot(c,this.am[d].bsAtoms):c.andNot(f.notInCentroid(this,this.am[d].bsAtoms,g))}return c;case 3145754:c=b.nextSetBit(0);if(0>c)return new JU.BS;if(this.at[c].group.$isProtein)return this.at[c].group.getBSSideChain();case 1095761936:return this.getMoleculeBitSet(b);case 1087373320:return this.getSequenceBits(b,null);case 1048615:d=b;var g=d[0],f=
d[1],j=d[2];c=new JU.BS;var k=this.vwr.getBoolean(603979823);0<=j&&(256>j&&!k)&&(j=JM.AtomCollection.chainToUpper(j));for(d=this.mc;0<=--d;)this.am[d].isBioModel&&this.am[d].selectSeqcodeRange(g,f,j,c,k);return c;case 3145772:c=JU.BS.newN(this.ac);g=-1;f=0;for(d=this.ac;0<=--d;)if(k=this.at[d],j=k.getAtomSymmetry(),null!=j){if(k.mi!=g){g=k.mi;if(null==this.getModelCellRange(g))continue;f=this.getModelSymmetryCount(g)}for(var k=0,h=f;0<=--h;)if(j.get(h)&&1<++k){c.set(d);break}}return c;case 1089470478:return JU.BSUtil.copy(null==
this.bsSymmetry?this.bsSymmetry=JU.BS.newN(this.ac):this.bsSymmetry);case 1614417948:c=new JU.BS;if(null==this.vwr.getCurrentUnitCell())return c;this.ptTemp1.set(1,1,1);for(d=this.ac;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,!1)&&c.set(d);return c}},"~N,~O");c(c$,"getAnnotationBits",function(a,b,d){for(var c=new JU.BS,g=this.vwr.getAnnotationParser(),f,j=this.mc;0<=--j;)null!=(f=this.getInfo(j,a))&&c.or(g.getAtomBits(this.vwr,d,this.getCachedAnnotationMap(j,a+" V ",f),this.am[j].dssrCache,
b,j,this.am[j].bsAtoms));return c},"~S,~N,~S");c(c$,"getCachedAnnotationMap",function(a,b,d){a=null==this.am[a].dssrCache&&null!=d?this.am[a].dssrCache=new java.util.Hashtable:this.am[a].dssrCache;if(null==a)return null;var c=a.get(b);null==c&&null!=d&&(c=p(d,JS.SV)?d:this.vwr.evaluateExpressionAsVariable(d),a.put(b,c));return p(c,JS.SV)?c:null},"~N,~S,~O");c(c$,"isInLatticeCell",function(a,b,d,c){var g=this.getUnitCell(this.at[a].mi);d.setT(this.at[a]);return null!=g&&g.checkUnitCell(g,b,d,c)},"~N,JU.P3,JU.P3,~B");
c(c$,"getAtomsWithinRadius",function(a,b,d,c){var g=new JU.BS,f=this.getIterativeModels(!1);b=JU.BSUtil.andNot(b,this.vwr.getDeletedAtoms());var j=this.getSelectedAtomIterator(null,!1,!1,!1,!1);if(d){d=new JU.P3;for(var k=b.nextSetBit(0);0<=k;k=b.nextSetBit(k+1))for(var h=this.mc;0<=--h;)f.get(h)&&(0>a?this.getAtomsWithin(a,this.at[k].getFractionalUnitCoordPt(!0,d),g,-1):(this.setIteratorForAtom(j,h,k,a,c),j.addAtoms(g)))}else{g.or(b);for(k=b.nextSetBit(0);0<=k;k=b.nextSetBit(k+1))0>a?this.getAtomsWithin(a,
this.at[k],g,this.at[k].mi):(this.setIteratorForAtom(j,-1,k,a,c),j.addAtoms(g))}j.release();return g},"~N,JU.BS,~B,J.atomdata.RadiusData");c(c$,"getGroupsWithin",function(a,b){for(var d=this.getIterativeModels(!1),c=new JU.BS,g=this.mc;0<=--g;)d.get(g)&&this.am[g].isBioModel&&this.am[g].getGroupsWithin(a,b,c);return c},"~N,JU.BS");c(c$,"getAtomsWithin",function(a,b,d,c){null==d&&(d=new JU.BS);if(0>a){a=-a;for(var g=this.ac;0<=--g;){var f=this.at[g];0<=c&&this.at[g].mi!=c||!d.get(g)&&f.getFractionalUnitDistance(b,
this.ptTemp1,this.ptTemp2)<=a&&d.set(f.i)}return d}c=this.getIterativeModels(!0);g=this.getSelectedAtomIterator(null,!1,!1,!1,!1);for(f=this.mc;0<=--f;)c.get(f)&&(this.setIteratorForAtom(g,-1,this.am[f].firstAtomIndex,-1,null),g.setCenter(b,a),g.addAtoms(d));g.release();return d},"~N,JU.P3,JU.BS,~N");c(c$,"getBasePairBits",function(a){var b=new JU.BS;if(0!=a.length%2)return b;var d=null,c=null,b=new JU.Lst;if(0==a.length)d=c=this.vwr.getAllAtoms(),this.calcRasmolHydrogenBonds(d,c,b,!0,1,!1,null);
else for(var g=0;g<a.length;)d=this.getSequenceBits(a.substring(g,++g),null),0!=d.cardinality()&&(c=this.getSequenceBits(a.substring(g,++g),null),0!=c.cardinality()&&this.calcRasmolHydrogenBonds(d,c,b,!0,1,!1,null));a=new JU.BS;for(g=b.size();0<=--g;)d=b.get(g),a.set(d.atom1.i),a.set(d.atom2.i);return this.getAtomBitsMDb(1087373318,a)},"~S");c(c$,"getSequenceBits",function(a,b){null==b&&(b=this.vwr.getAllAtoms());var d=new JU.BS;if(0<a.length)for(var c=0;c<this.mc;++c)this.am[c].isBioModel&&this.am[c].getSequenceBits(a,
b,d);return d},"~S,JU.BS");c(c$,"deleteBonds",function(a,b){if(!b)for(var d=new JU.BS,c=new JU.BS,g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1)){var f=this.bo[g].atom1;this.am[f.mi].isModelKit||(d.clearAll(),c.clearAll(),d.set(f.i),c.set(this.bo[g].getAtomIndex2()),this.addStateScript("connect ",null,d,c,"delete",!1,!0))}this.dBb(a,b)},"JU.BS,~B");c(c$,"makeConnections2",function(a,b,d,c,g,f,j,k,h,m){null==j&&(j=new JU.BS);var r=65535==d,x=131071==d;x&&(d=1);var n=JM.Bond.isOrderH(d),q=!1,p=!1,s=!1,
t=!1;switch(c){case 12291:return this.deleteConnections(a,b,d,g,f,k,x);case 603979874:case 1073741852:if(515!=d)return this.autoBond(g,f,j,k,n,603979874==c);p=t=!0;break;case 1087373321:q=p=!0;break;case 1073742025:p=!0;break;case 1073741904:s=!0}c=!q||r;r=!q&&!r;this.defaultCovalentMad=this.vwr.getMadBond();var x=0>a,u=0>b,v=x||u,w=!k||0.1!=a||1E8!=b;w&&(a=this.fixD(a,x),b=this.fixD(b,u));var z=this.getDefaultMadFromOrder(d),B=0,C=0,D=null,E=null,F=null,G="\x00",H=d|131072;try{for(var K=g.nextSetBit(0);0<=
K;K=g.nextSetBit(K+1)){if(k)D=this.bo[K],E=D.atom1,F=D.atom2;else{E=this.at[K];if(E.isDeleted())continue;G=this.isModulated(K)?"\x00":E.altloc}for(var L=k?0:f.nextSetBit(0);0<=L;L=f.nextSetBit(L+1)){if(k)L=2147483646;else{if(L==K)continue;F=this.at[L];if(E.mi!=F.mi||F.isDeleted())continue;if("\x00"!=G&&G!=F.altloc&&"\x00"!=F.altloc)continue;D=E.getBond(F)}if(!((null==D?p:s)||w&&!this.isInRange(E,F,a,b,x,u,v)))if(null==D)j.set(this.bondAtoms(E,F,d,z,j,m,h,!0).index),B++;else if(r&&(D.setOrder(d),this.bsAromatic.clear(D.index)),
c||d==D.order||H==D.order||n&&D.isHydrogen())j.set(D.index),C++}}}catch(M){if(!y(M,Exception))throw M;}t&&this.assignAromaticBondsBs(!0,j);q||this.sm.setShapeSizeBs(1,-2147483648,null,j);return[B,C]},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"autoBondBs4",function(a,b,d,c,g,f){if(f)return this.autoBond_Pre_11_9_24(a,b,d,c,g);if(0==this.ac)return 0;0==g&&(g=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();f=this.vwr.getFloat(570425348);var j=this.vwr.getFloat(570425364),j=j*j,h=0;this.showRebondTimes&&
JU.Logger.startTimer("autobond");var l=-1,m=null==a,r,x;m?(x=0,r=null):(a.equals(b)?r=a:(r=JU.BSUtil.copy(a),r.or(b)),x=r.nextSetBit(0));for(var n=this.getSelectedAtomIterator(null,!1,!1,!0,!1),q=!1;0<=x&&x<this.ac;x=m?x+1:r.nextSetBit(x+1)){var p=m||a.get(x),s=m||b.get(x),t=this.at[x];if(!t.isDeleted()){var u=t.mi;if(u!=l){l=u;if(this.isJmolDataFrameForModel(u)){x=this.am[u].firstAtomIndex+this.am[u].ac-1;continue}q=this.getInfoB(u,"autoBondUsingOccupation")}u=t.getBondingRadius();if(0!=u){var v=
null!=d&&d.get(x);for(this.setIteratorForAtom(n,-1,x,u+this.maxBondingRadius+f,null);n.hasNext();){var w=this.at[n.next()];if(!w.isDeleted()){var y=w.i,z=m||a.get(y),B=m||b.get(y);!z&&!B||(!(p&&B||s&&z)||v&&d.get(y)||q&&null!=this.occupancies&&50>this.occupancies[x]!=50>this.occupancies[y])||(y=JM.BondCollection.getBondOrderFull(u,w.getBondingRadius(),n.foundDistance2(),j,f),0<y&&this.checkValencesAndBond(t,w,y,g,c)&&h++)}}n.release()}}}this.showRebondTimes&&JU.Logger.checkTimer("autoBond",!1);return h},
"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B");c(c$,"autoBond_Pre_11_9_24",function(a,b,d,c,g){if(0==this.ac)return 0;0==g&&(g=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var f=this.vwr.getFloat(570425348),j=this.vwr.getFloat(570425364),j=j*j,h=0;this.initializeBspf();for(var l=-1,m=this.ac;0<=--m;){var r=null==a||a.get(m),x=null==b||b.get(m);if(r||x){var n=this.at[m];if(!n.isDeleted()){var q=n.mi;if(q!=l&&(l=q,this.isJmolDataFrameForModel(q))){for(;0<=--m&&this.at[m].mi==q;);m++;continue}var p=n.getBondingRadius();
if(0!=p){var s=p+this.maxBondingRadius+f;this.initializeBspt(q);q=this.bspf.getCubeIterator(q);for(q.initialize(n,s,!0);q.hasMoreElements();)if(s=q.nextElement(),!(s===n||s.isDeleted())){var t=s.i,u=null==a||a.get(t),v=null==b||b.get(t);if(!(!u&&!v||null!=d&&d.get(t)&&d.get(m)))if(r&&v||x&&u)t=JM.BondCollection.getBondOrderFull(p,s.getBondingRadius(),q.foundDistance2(),j,f),0<t&&this.checkValencesAndBond(n,s,t,g,c)&&h++}q.release()}}}}return h},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(c$,"autoBond",function(a,
b,d,c,g,f){if(c){c=a;a=new JU.BS;b=new JU.BS;for(var j=c.nextSetBit(0);0<=j;j=c.nextSetBit(j+1))a.set(this.bo[j].atom1.i),b.set(this.bo[j].atom2.i)}return[g?this.autoHbond(a,b,!1):this.autoBondBs4(a,b,null,d,this.vwr.getMadBond(),f),0]},"JU.BS,JU.BS,JU.BS,~B,~B,~B");c(c$,"autoHbond",function(a,b,d){if(d){for(var c=this.getModelBS(a,!1),g=c.nextSetBit(0);0<=g&&d;g=c.nextSetBit(g+1))d=!this.am[g].hasRasmolHBonds;if(d)return 0}d=!1;for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))if(1==this.at[g].getElementNumber()){d=
!0;break}c=new JU.BS;g=this.vwr.getBoolean(603979853);if(null==b||g&&!d)return JU.Logger.info((null==b?"DSSP/DSSR ":"RasMol")+" pseudo-hbond calculation"),this.calcRasmolHydrogenBonds(a,b,null,!1,2147483647,!1,c),-JU.BSUtil.cardinalityOf(c);JU.Logger.info(d?"Standard Hbond calculation":"Jmol pseudo-hbond calculation");var f=null;if(!d){f=new JU.BS;for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))switch(this.at[g].atomID){case 64:case 4:case 14:case 15:case 16:case 17:f.set(g)}}var j=this.vwr.getFloat(570425361),
h=3.141592653589793*this.vwr.getFloat(570425360)/180,l=j*j,m=JM.ModelSet.hbondMin*JM.ModelSet.hbondMin,r=j>JM.ModelSet.hbondMin?m:l,x=j>JM.ModelSet.hbondMin?JM.ModelSet.hbondMin:j,n=0,q=0,p=new JU.V3,s=new JU.V3;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var t=null,u=null;b=this.getSelectedAtomIterator(b,!1,!1,!1,!1);for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1)){var v=this.at[g],w=v.getElementNumber(),y=1==w;if(!(!y&&(d||7!=w&&8!=w)||y&&!d)){var z,B,C;if(y){w=v.bonds;
if(null==w)continue;C=!1;for(z=0;z<w.length&&!C;z++)C=w[z].getOtherAtom(v).getElementNumber(),C=7==C||8==C;if(!C)continue;B=x;w=1;z=r;C=!1}else B=j,w=m,z=l,C=f.get(g);for(this.setIteratorForAtom(b,-1,v.i,B,null);b.hasNext();){B=this.at[b.next()];var D=B.getElementNumber();if(!(B===v||!y&&7!=D&&8!=D||y&&1==D||(q=b.foundDistance2())<w||q>z||C&&f.get(B.i)||v.isBonded(B))){if(0<h){p.sub2(v,B);if(null==(u=JM.ModelSet.checkMinAttachedAngle(v,h,p,s,d)))continue;p.scale(-1);if(null==(t=JM.ModelSet.checkMinAttachedAngle(B,
h,p,s,d)))continue}var D=0,E;y&&!Float.isNaN(t.x)&&!Float.isNaN(u.x)?(E=4096,D=JM.HBond.getEnergy(Math.sqrt(q),t.distance(v),t.distance(u),B.distance(u))/1E3):E=2048;c.set(this.addHBond(v,B,E,D));n++}}}}b.release();this.sm.setShapeSizeBs(1,-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return d?n:-n},"JU.BS,JU.BS,~B");c$.checkMinAttachedAngle=c(c$,"checkMinAttachedAngle",function(a,b,d,c,g){var f=a.bonds;if(null==f||0==f.length)return JU.P3.new3(NaN,0,0);for(var j=null,
h=3.4028235E38,l=f.length;0<=--l;)if(f[l].isCovalent()){var m=f[l].getOtherAtom(a);if(g||1!=m.getElementNumber()){c.sub2(a,m);var r=c.angle(d);if(r<b)return null;r<h&&(j=m,h=r)}}return j},"JM.Atom,~N,JU.V3,JU.V3,~B");c(c$,"setStructureIndexes",function(){for(var a,b=0,d=-1,c=-1,g=-1,f=0;f<this.ac;f++){if((c=this.at[f].mi)!=g)b=0,g=c,d=-1;if((a=this.at[f].getStrucNo())!=d&&0!=a)this.at[f].getGroup().setStrucNo(++b),d=b}});c(c$,"getProteinStructureState",function(a,b,d,c){if(!this.isPDB)return"";for(var g=
0;g<this.mc;g++)if(this.am[g].isBioModel)return this.am[g].getProteinStructureState(a,b,d,c);return""},"JU.BS,~B,~B,~N");c(c$,"getModelInfoAsString",function(){var a=(new JU.SB).append('<models count="');a.appendI(this.mc).append('" modelSetHasVibrationVectors="').append(this.modelSetHasVibrationVectors()+'">\n<properties>');if(null!=this.modelSetProperties){for(var b=this.modelSetProperties.propertyNames();b.hasMoreElements();){var d=b.nextElement();a.append('\n <property name="').append(d).append('" value=').append(JU.PT.esc(this.modelSetProperties.getProperty(d))).append(" />")}a.append("\n</properties>")}for(b=
0;b<this.mc;++b)a.append('\n<model index="').appendI(b).append('" n="').append(this.getModelNumberDotted(b)).append('" id=').append(JU.PT.esc(""+this.getInfo(b,"modelID"))),d=this.vwr.getJDXBaseModelIndex(b),d!=b&&a.append(" baseModelId=").append(JU.PT.esc(this.getInfo(d,"jdxModelID"))),a.append(" name=").append(JU.PT.esc(this.getModelName(b))).append(" title=").append(JU.PT.esc(this.getModelTitle(b))).append(' hasVibrationVectors="').appendB(this.vwr.modelHasVibrationVectors(b)).append('" />');a.append("\n</models>");
return a.toString()});c(c$,"getSymmetryInfoAsString",function(){for(var a=(new JU.SB).append("Symmetry Information:"),b=0;b<this.mc;++b){a.append("\nmodel #").append(this.getModelNumberDotted(b)).append("; name=").append(this.getModelName(b)).append("\n");var d=this.getUnitCell(b);a.append(null==d?"no symmetry information":d.getSymmetryInfoStr())}return a.toString()});c(c$,"getAtomsConnected",function(a,b,d,c){for(var g=p(c,JM.BondSet),f=g?new JM.BondSet:new JU.BS,j=D(this.ac,0),h,l=30720==d,m=65535==
d,r=0;r<this.bondCount;r++){var x=this.bo[r];if(m||x.is(d)||l&&x.isHydrogen())g?f.set(r):(c.get(x.atom1.i)&&(j[h=x.atom2.i]++,f.set(h)),c.get(x.atom2.i)&&(j[h=x.atom1.i]++,f.set(h)))}if(g)return f;d=0==a;for(h=this.ac;0<=--h;)c=j[h],c<a||c>b?f.clear(h):d&&0==c&&f.set(h);return f},"~N,~N,~N,JU.BS");c(c$,"getSymTemp",function(a){return null==this.symTemp||a?this.symTemp=J.api.Interface.getSymmetry():this.symTemp},"~B");c(c$,"createModels",function(a){a=this.mc+a;var b=JU.AU.arrayCopyObject(this.am,
a);this.validateBspf(!1);this.modelNumbers=JU.AU.arrayCopyI(this.modelNumbers,a);this.modelFileNumbers=JU.AU.arrayCopyI(this.modelFileNumbers,a);this.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.modelNumbersForAtomLabel,a);this.modelNames=JU.AU.arrayCopyS(this.modelNames,a);this.frameTitles=JU.AU.arrayCopyS(this.frameTitles,a);for(var d=q(this.getModelFileNumber(this.mc-1)/1E6)+1,c=this.mc,g=0;c<a;c++)this.modelNumbers[c]=c+this.mc,this.modelFileNumbers[c]=1E6*d+ ++g,this.modelNumbersForAtomLabel[c]=
this.modelNames[c]=d+"."+g;this.thisStateModel=-1;d=this.getInfoM("group3Lists");null!=d&&(c=this.getInfoM("group3Counts"),d=JU.AU.arrayCopyS(d,a),c=JU.AU.arrayCopyII(c,a),this.msInfo.put("group3Lists",d),this.msInfo.put("group3Counts",c));this.unitCells=JU.AU.arrayCopyObject(this.unitCells,a);for(c=this.mc;c<a;c++)b[c]=(new JM.Model).set(this,c,-1,null,null,null),b[c].loadState=" model create #"+c+";";this.am=b;this.mc=a},"~N");c(c$,"deleteModel",function(a,b,d,c,g){if(0>a)this.validateBspf(!1),
this.bsAll=null,this.resetMolecules(),this.isBbcageDefault=!1,this.calcBoundBoxDimensions(null,1);else{this.modelNumbers=JU.AU.deleteElements(this.modelNumbers,a,1);this.modelFileNumbers=JU.AU.deleteElements(this.modelFileNumbers,a,1);this.modelNumbersForAtomLabel=JU.AU.deleteElements(this.modelNumbersForAtomLabel,a,1);this.modelNames=JU.AU.deleteElements(this.modelNames,a,1);this.frameTitles=JU.AU.deleteElements(this.frameTitles,a,1);this.thisStateModel=-1;var f=this.getInfoM("group3Lists"),j=this.getInfoM("group3Counts"),
h=a+1;if(null!=f&&null!=f[h])for(var l=q(f[h].length/6);0<=--l;)0<j[h][l]&&(j[0][l]-=j[h][l],0==j[0][l]&&(f[0]=f[0].substring(0,6*l)+",["+f[0].substring(6*l+2)));null!=f&&(this.msInfo.put("group3Lists",JU.AU.deleteElements(f,a,1)),this.msInfo.put("group3Counts",JU.AU.deleteElements(j,a,1)));null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(l=this.stateScripts.size();0<=--l;)this.stateScripts.get(l).deleteAtoms(a,g,c)||this.stateScripts.remove(l);this.deleteModelAtoms(b,
d,c);this.vwr.deleteModelAtoms(a,b,d,c)}},"~N,~N,~N,JU.BS,JU.BS");c(c$,"getMoInfo",function(a){for(var b=new JU.SB,d=0;d<this.mc;d++)if(!(0<=a&&d!=a)){var c=this.vwr.getModelAuxiliaryInfoValue(d,"moData");if(null!=c){var c=c.get("mos"),g=null==c?0:c.size();if(0!=g)for(;0<=--g;){var f=c.get(g),j=f.get("type");null==j&&(j="");var h=f.get("energyUnits");null==h&&(h="");var l=f.get("occupancy");null!=l&&(j="occupancy "+l.floatValue()+" "+j);l=f.get("symmetry");null!=l&&(j+=l);l=""+f.get("energy");Float.isNaN(JU.PT.parseFloat(l))?
b.append(JU.Txt.sprintf("model %-2s;  mo %-2i # %s\n","sis",[this.getModelNumberDotted(d),Integer.$valueOf(g+1),j])):b.append(JU.Txt.sprintf("model %-2s;  mo %-2i # energy %-8.3f %s %s\n","sifss",[this.getModelNumberDotted(d),Integer.$valueOf(g+1),f.get("energy"),h,j]))}}}return b.toString()},"~N");c(c$,"assignAtom",function(a,b,d){null==b&&(b="C");var c=this.at[a],g=new JU.BS,f=1==c.getElementNumber(),g=JU.Elements.elementNumberFromSymbol(b,!0),j=!1;if(0<g)this.setElement(c,g),this.vwr.shm.setShapeSizeBs(0,
0,this.vwr.rd,JU.BSUtil.newAndSetBit(a)),this.setAtomName(a,b+c.getAtomNumber()),this.am[c.mi].isModelKit||this.taintAtom(a,0);else if(b.equals("Pl"))c.setFormalCharge(c.getFormalCharge()+1);else if(b.equals("Mi"))c.setFormalCharge(c.getFormalCharge()-1);else if(b.equals("X"))j=!0;else if(!b.equals("."))return;this.removeUnnecessaryBonds(c,j);b=0;1==c.getCovalentBondCount()&&(f?b=1.5:!f&&1==g&&(b=1));0!=b&&(f=JU.V3.newVsub(c,this.at[c.getBondedAtomIndex(0)]),j=f.length(),f.normalize(),f.scale(b-j),
this.setAtomCoordRelative(a,f.x,f.y,f.z));a=JU.BSUtil.newAndSetBit(a);1!=g&&d&&(this.validateBspf(!1),g=this.getAtomsWithinRadius(1,a,!1,null),g.andNot(a),0<=g.nextSetBit(0)&&this.vwr.deleteAtoms(g,!1),g=this.vwr.getModelUndeletedAtomsBitSet(c.mi),g.andNot(this.getAtomBitsMDa(1613758476,null)),this.makeConnections2(0.1,1.8,1,1073741904,a,g,null,!1,!1,0));this.vwr.addHydrogens(a,!1,!0)},"~N,~S,~B");c(c$,"deleteAtoms",function(a){this.averageAtomPoint=null;if(null!=a){for(var b=new JU.BS,d=a.nextSetBit(0);0<=
d&&d<this.ac;d=a.nextSetBit(d+1))this.at[d].deleteBonds(b);for(d=0;d<this.mc;d++)this.am[d].bsAtomsDeleted.or(a),this.am[d].bsAtomsDeleted.and(this.am[d].bsAtoms),this.am[d].dssrCache=null;this.deleteBonds(b,!1)}},"JU.BS");c(c$,"adjustAtomArrays",function(a,b,d){this.ac=d;for(var c=b;c<d;c++){this.at[c]=this.at[a[c]];this.at[c].i=c;var g=this.am[this.at[c].mi];g.firstAtomIndex==a[c]&&(g.firstAtomIndex=c);g.bsAtoms.set(c)}if(null!=this.vibrations)for(c=b;c<d;c++)this.vibrations[c]=this.vibrations[a[c]];
if(null!=this.occupancies)for(c=b;c<d;c++)this.occupancies[c]=this.occupancies[a[c]];if(null!=this.bfactor100s)for(c=b;c<d;c++)this.bfactor100s[c]=this.bfactor100s[a[c]];if(null!=this.partialCharges)for(c=b;c<d;c++)this.partialCharges[c]=this.partialCharges[a[c]];if(null!=this.atomTensorList)for(c=b;c<d;c++)if(g=this.atomTensorList[c]=this.atomTensorList[a[c]],null!=g)for(var f=g.length;0<=--f;){var j=g[f];null!=j&&(j.atomIndex1=c)}if(null!=this.atomNames)for(c=b;c<d;c++)this.atomNames[c]=this.atomNames[a[c]];
if(null!=this.atomTypes)for(c=b;c<d;c++)this.atomTypes[c]=this.atomTypes[a[c]];if(null!=this.atomSerials)for(c=b;c<d;c++)this.atomSerials[c]=this.atomSerials[a[c]];if(null!=this.atomSeqIDs)for(c=b;c<d;c++)this.atomSeqIDs[c]=this.atomSeqIDs[a[c]]},"~A,~N,~N");c(c$,"growAtomArrays",function(a){this.at=JU.AU.arrayCopyObject(this.at,a);null!=this.vibrations&&(this.vibrations=JU.AU.arrayCopyObject(this.vibrations,a));null!=this.occupancies&&(this.occupancies=JU.AU.arrayCopyF(this.occupancies,a));null!=
this.bfactor100s&&(this.bfactor100s=JU.AU.arrayCopyShort(this.bfactor100s,a));null!=this.partialCharges&&(this.partialCharges=JU.AU.arrayCopyF(this.partialCharges,a));null!=this.atomTensorList&&(this.atomTensorList=JU.AU.arrayCopyObject(this.atomTensorList,a));null!=this.atomNames&&(this.atomNames=JU.AU.arrayCopyS(this.atomNames,a));null!=this.atomTypes&&(this.atomTypes=JU.AU.arrayCopyS(this.atomTypes,a));null!=this.atomSerials&&(this.atomSerials=JU.AU.arrayCopyI(this.atomSerials,a));null!=this.atomSeqIDs&&
(this.atomSeqIDs=JU.AU.arrayCopyI(this.atomSeqIDs,a))},"~N");c(c$,"addAtom",function(a,b,d,c,g,f,j,h,l,m,r,x,n,q,p,s,t,u){j=(new JM.Atom).setAtom(a,this.ac,h,l,u,j,d,r,s);this.am[a].ac++;this.am[a].bsAtoms.set(this.ac);JU.Elements.isElement(d,1)&&this.am[a].hydrogenCount++;this.ac>=this.at.length&&this.growAtomArrays(this.ac+100);this.at[this.ac]=j;this.setBFactor(this.ac,q);this.setOccupancy(this.ac,n);this.setPartialCharge(this.ac,x);null!=p&&this.setAtomTensors(this.ac,p);j.group=b;j.colixAtom=
this.vwr.getColixAtomPalette(j,J.c.PAL.CPK.id);if(null!=c){if(0<=(a=c.indexOf("\x00")))null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[this.ac]=c.substring(a+1),c=c.substring(0,a);j.atomID=t;0==t&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern())}-2147483648!=g&&(null==this.atomSerials&&(this.atomSerials=D(this.at.length,0)),this.atomSerials[this.ac]=g);0!=f&&(null==this.atomSeqIDs&&(this.atomSeqIDs=D(this.at.length,0)),this.atomSeqIDs[this.ac]=
f);null!=m&&this.setVibrationVector(this.ac,m);this.ac++;return j},"~N,JM.Group,~N,~S,~N,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.Lst,~B,~N,JU.BS");c(c$,"getInlineData",function(a){var b=null;if(0<=a)b=this.am[a].loadScript;else for(a=this.mc;0<=--a&&!(0<(b=this.am[a].loadScript).length()););a=b.lastIndexOf('data "');if(0>a)return null;a=b.indexOf2('"',a+7);var d=b.lastIndexOf('end "');return d<a||0>a?null:b.substring2(a+2,d)},"~N");c(c$,"isAtomPDB",function(a){return 0<=a&&this.am[this.at[a].mi].isBioModel},
"~N");c(c$,"isAtomAssignable",function(a){return 0<=a&&this.at[a].mi==this.mc-1},"~N");c(c$,"haveModelKit",function(){for(var a=0;a<this.mc;a++)if(this.am[a].isModelKit)return!0;return!1});c(c$,"getModelKitStateBitset",function(a,b){for(var d=JU.BSUtil.copy(b),c=0;c<this.mc;c++)this.am[c].isModelKit||d.andNot(this.am[c].bsAtoms);return JU.BSUtil.deleteBits(a,d)},"JU.BS,JU.BS");c(c$,"setAtomNamesAndNumbers",function(a,b,d){0>b&&(a=this.am[this.at[a].mi].firstAtomIndex);null==this.atomSerials&&(this.atomSerials=
D(this.ac,0));null==this.atomNames&&(this.atomNames=Array(this.ac));for(var c=this.isXYZ&&this.vwr.getBoolean(603979978),g=2147483647,f=1;a<this.ac;++a){var j=this.at[a];j.mi!=g&&(g=j.mi,f=c?0:1);if(a>=-b){if(0==this.atomSerials[a]||0>b)this.atomSerials[a]=a<b?d.atomSerials[a]:f;if(null==this.atomNames[a]||0>b)this.atomNames[a]=(j.getElementSymbol()+this.atomSerials[a]).intern()}(!this.am[g].isModelKit||0<j.getElementNumber()&&!j.isDeleted())&&f++}},"~N,~N,JM.AtomCollection");c(c$,"setUnitCellOffset",
function(a,b,d){null!=a&&(null==b?a.setOffset(d):a.setOffsetPt(b))},"J.api.SymmetryInterface,JU.T3,~N");c(c$,"connect",function(a){this.resetMolecules();for(var b=new JU.BS,d=0;d<a.length;d++){var c=a[d];if(!(null==c||2>c.length)){var g=z(c[0]),f=0>g;f&&(g=-1-g);var j=z(c[1]);if(!(0>j||g>=this.ac||j>=this.ac)){var h=2<c.length?z(c[2]):1;0>h&&(h&=65535);var l=3<c.length?Y(1E3*a[d][3]):this.getDefaultMadFromOrder(h);0==h||0==l&&32768!=h&&!JM.Bond.isOrderH(h)?(c=this.at[g].getBond(this.at[j]),null!=
c&&b.set(c.index)):this.bondAtoms(this.at[g],this.at[j],h,l,null,4<c.length?c[4]:0,f,!0)}}}0<=b.nextSetBit(0)&&this.deleteBonds(b,!1)},"~A");c(c$,"allowSpecAtom",function(){return 1!=this.mc||this.am[0].isBioModel});c(c$,"setFrameDelayMs",function(a,b){for(var d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.am[this.am[d].trajectoryBaseIndex].frameDelay=a},"~N,JU.BS");c(c$,"getFrameDelayMs",function(a){return a<this.am.length&&0<=a?this.am[this.am[a].trajectoryBaseIndex].frameDelay:0},"~N");c(c$,"getModelIndexFromId",
function(a){var b=0<=a.indexOf("#"),d=a.toLowerCase().endsWith(".basemodel");d&&(a=a.substring(0,a.length-10));for(var c=-1,g=null,f=0;f<this.mc;f++){var j=this.getInfo(f,"modelID"),h=a.startsWith("~")?"~"+this.getModelNumberDotted(f):null;if(!(null==h&&null==j&&null==(j=this.getModelTitle(f)))){b&&(g=this.getModelFileName(f),g.endsWith("#molfile")?j=g:(g+="#",j=g+j));if(a.equalsIgnoreCase(j)||a.equalsIgnoreCase(h))return d?this.vwr.getJDXBaseModelIndex(f):f;null!=g&&a.startsWith(g)&&(c=-2)}}return null==
g&&!b?-2:c},"~S");c(c$,"getAuxiliaryInfo",function(a){var b=this.msInfo;if(null==b)return null;for(var d=new JU.Lst,c=0;c<this.mc;++c)if(null==a||a.get(c)){var g=this.getModelAuxiliaryInfo(c);d.addLast(g)}b.put("models",d);return b},"JU.BS");c(c$,"getDihedralMap",function(a){for(var b=new JU.Lst,d=a.length,c=null,g=null,f=null,j=null,h=d-1;0<=--h;)for(var l=d;--l>h;)if(c=this.at[a[h]],g=this.at[a[l]],c.isBonded(g))for(var m=d;0<=--m;)if(m!=h&&m!=l&&(f=this.at[a[m]]).isBonded(c))for(var r=d;0<=--r;)if(r!=
h&&r!=l&&r!=m&&(j=this.at[a[r]]).isBonded(g)){var x=D(4,0);x[0]=f.i;x[1]=c.i;x[2]=g.i;x[3]=j.i;b.addLast(x)}d=b.size();a=JU.AU.newInt2(d);for(h=d;0<=--h;)a[d-h-1]=b.get(h);return a},"~A");c(c$,"setModulation",function(a,b,d,c){if(null==this.bsModulated)if(b)this.bsModulated=new JU.BS;else if(null==a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var g=this.vwr.getFloat(1276121113),f=!1,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){var h=this.getVibration(j,!1);p(h,J.api.JmolModulationSet)&&
(h.setModTQ(this.at[j],b,d,c,g),null!=this.bsModulated&&this.bsModulated.setBitTo(j,b),f=!0)}f||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(c$,"getBoundBoxOrientation",function(a,b){var d=b.nextSetBit(0);if(0>d)return"{0 0 0 1}";var c=null==this.vOrientations?0:this.vOrientations.length;if(0==c){for(var g=Array(3375),c=0,f=new JU.P4,j=-7;7>=j;j++)for(var h=-7;7>=h;h++)for(var l=0;14>=l;l++,c++)1<(g[c]=JU.V3.new3(j/7,h/7,l/14)).length()&&--c;this.vOrientations=Array(c);for(j=c;0<=--j;)l=Math.sqrt(1-
g[j].lengthSquared()),Float.isNaN(l)&&(l=0),f.set4(g[j].x,g[j].y,g[j].z,l),this.vOrientations[j]=JU.Quat.newP4(f)}for(var g=new JU.P3,f=3.4028235E38,m=null,r=null,j=0;j<c;j++){var l=this.vOrientations[j],x=new JU.BoxInfo;x.setMargin(0);for(h=d;0<=h;h=b.nextSetBit(h+1))x.addBoundBoxPoint(l.transformP2(this.at[h],g));switch(a){default:case 1313866249:case 1073741863:h=(x.bbCorner1.x-x.bbCorner0.x)*(x.bbCorner1.y-x.bbCorner0.y)*(x.bbCorner1.z-x.bbCorner0.z);break;case 1112541205:h=x.bbCorner1.x-x.bbCorner0.x;
break;case 1112541206:h=x.bbCorner1.y-x.bbCorner0.y;break;case 1112541207:h=x.bbCorner1.z-x.bbCorner0.z}h<f&&(m=l,r=x,f=h)}if(1313866249!=a&&1073741863!=a)return m.toString();l=JU.Quat.newQ(m);d=r.bbCorner1.x-r.bbCorner0.x;c=r.bbCorner1.y-r.bbCorner0.y;j=r.bbCorner1.z-r.bbCorner0.z;d<c&&(g.set(0,0,1),l=JU.Quat.newVA(g,90).mulQ(l),h=d,d=c,c=h);c<j&&(j>d&&(g.set(0,1,0),l=JU.Quat.newVA(g,90).mulQ(l),h=d,d=j,j=h),g.set(1,0,0),l=JU.Quat.newVA(g,90).mulQ(l),h=c,c=j,j=h);return 1313866249==a?f+"\t{"+d+" "+
c+" "+j+"}":0==l.getTheta()?"{0 0 0 1}":l.toString()},"~N,JU.BS");c(c$,"intersectPlane",function(a,b,d){return(null==this.triangulator?this.triangulator=J.api.Interface.getUtil("TriangleData"):this.triangulator).intersectPlane(a,b,d)},"JU.P4,JU.Lst,~N");c(c$,"getUnitCellForAtom",function(a){if(0>a||a>this.ac)return null;if(null!=this.bsModulated){var b=this.getVibration(a,!1),b=null==b?null:b.getUnitCell();if(null!=b)return b}return this.getUnitCell(this.at[a].mi)},"~N");c(c$,"clearCache",function(){for(var a=
this.mc;0<=--a;)this.am[a].dssrCache=null});c(c$,"getSymMatrices",function(a){var b=this.getModelSymmetryCount(a);if(0==b)return null;var d=Array(b),c=this.am[a].biosymmetry;null==c&&(c=this.getUnitCell(a));for(a=b;0<=--a;)d[a]=c.getSpaceGroupOperation(a);return d},"~N");c(c$,"getBsBranches",function(a){for(var b=q(a.length/6),d=Array(b),c=new java.util.Hashtable,g=0,f=0;g<b;g++,f+=6)if(!(1>Math.abs(a[f+5]-a[f+4]))){var j=z(a[f+1]),h=z(a[f+2]),l=""+j+"_"+h;if(!c.containsKey(l)){c.put(l,Boolean.TRUE);
for(var l=this.vwr.getBranchBitSet(h,j,!0),m=this.at[j].bonds,j=this.at[j],r=0;r<m.length;r++){var x=m[r];if(x.isCovalent()&&(x=x.getOtherAtom(j).i,x!=h&&l.get(x))){l=null;break}}d[g]=l}}return d},"~A");c(c$,"recalculatePositionDependentQuantities",function(a,b){this.getHaveStraightness()&&this.calculateStraightness();this.recalculateLeadMidpointsAndWingVectors(-1);for(var d=this.getModelBS(a,!1),c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))this.sm.refreshShapeTrajectories(c,a,b);this.averageAtomPoint=
null},"JU.BS,JU.M4");c(c$,"moveAtoms",function(a,b,d,c,g,f,j){if(!j){null==a?this.matTemp.setM3(b):(this.matInv.setM3(b),this.matInv.invert(),this.ptTemp.set(0,0,0),this.matTemp.mul2(a,b),this.matTemp.mul2(this.matInv,this.matTemp));f?(this.vTemp.setT(g),this.mat4.setIdentity(),this.mat4.setTranslation(this.vTemp),this.mat4t.setToM3(this.matTemp),this.mat4.mul(this.mat4t),this.mat4t.setIdentity(),this.vTemp.scale(-1),this.mat4t.setTranslation(this.vTemp),this.mat4.mul(this.mat4t)):this.mat4.setToM3(this.matTemp);
for(a=c.nextSetBit(0);0<=a;a=c.nextSetBit(a+1))f?this.mat4.rotTrans(this.at[a]):(this.ptTemp.add(this.at[a]),this.mat4.rotTrans(this.at[a]),this.ptTemp.sub(this.at[a])),this.taintAtom(a,2);f||(this.ptTemp.scale(1/c.cardinality()),null==d&&(d=new JU.V3),d.add(this.ptTemp))}if(null!=d){for(a=c.nextSetBit(0);0<=a;a=c.nextSetBit(a+1))this.at[a].add(d);j||(this.mat4t.setIdentity(),this.mat4t.setTranslation(d),this.mat4.mul2(this.mat4t,this.mat4))}this.recalculatePositionDependentQuantities(c,this.mat4)},
"JU.M3,JU.M3,JU.V3,JU.BS,JU.P3,~B,~B");c(c$,"setDihedrals",function(a,b,d){var c=q(a.length/6);1<d&&(d=1);for(var g=0,f=0;g<c;g++,f+=6){var j=b[g];if(!(null==j||j.isEmpty())){var h=this.at[z(a[f+1])],l=JU.V3.newVsub(this.at[z(a[f+2])],h),l=JU.A4.newVA(l,-((a[f+5]-a[f+4])*d)/57.29577951308232);this.matTemp.setAA(l);this.ptTemp.setT(h);for(h=j.nextSetBit(0);0<=h;h=j.nextSetBit(h+1))this.at[h].sub(this.ptTemp),this.matTemp.rotate(this.at[h]),this.at[h].add(this.ptTemp),this.taintAtom(h,2)}}},"~A,~A,~N");
c(c$,"setAtomCoordsRelative",function(a,b){this.setAtomsCoordRelative(b,a.x,a.y,a.z);this.mat4.setIdentity();this.vTemp.setT(a);this.mat4.setTranslation(this.vTemp);this.recalculatePositionDependentQuantities(b,this.mat4)},"JU.T3,JU.BS");c(c$,"setAtomCoords",function(a,b,d){this.setAtomCoord2(a,b,d);switch(b){case 1112541202:case 1112541203:case 1112541204:case 1146095631:break;default:this.recalculatePositionDependentQuantities(a,null)}},"JU.BS,~N,~O");c(c$,"invertSelected",function(a,b,d,c,g){if(null!=
a)for(var f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1)){d=2*(a.x-this.at[f].x);c=2*(a.y-this.at[f].y);var j=2*(a.z-this.at[f].z);this.setAtomCoordRelative(f,d,c,j)}else if(null!=b){a=JU.V3.new3(b.x,b.y,b.z);a.normalize();for(var h=Math.sqrt(b.x*b.x+b.y*b.y+b.z*b.z),f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1))j=2*-JU.Measure.distanceToPlaneD(b,h,this.at[f]),d=a.x*j,c=a.y*j,j*=a.z,this.setAtomCoordRelative(f,d,c,j)}else if(0<=d&&(b=this.at[d],a=b.bonds,null!=a)){g=new JU.BS;j=new JU.Lst;h=this.vwr.getModelUndeletedAtomsBitSet(b.mi);
for(f=0;f<a.length;f++){var l=a[f].getOtherAtom(b);c.get(l.i)?g.or(JU.JmolMolecule.getBranchBitSet(this.at,l.i,h,null,d,!0,!0)):j.addLast(l)}0!=j.size()&&(a=JU.Measure.getCenterAndPoints(j)[0],f=JU.V3.newVsub(b,a),f=JU.Quat.newVA(f,180),this.moveAtoms(null,f.getMatrix(),null,g,b,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS,JU.BS");c(c$,"setMSInfo",function(a,b){this.msInfo.put(a,b)},"~S,~O");C(c$,"hbondMin",2.5)});n("JM");w(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){c$=t(function(){this.rotationMatrix=
this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=null;this.cameraY=this.cameraX=this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.vwr=this.pymolView=this.moveToText=null;s(this,arguments)},JM,"Orientation");K(c$,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});u(c$,function(a,b,d){this.vwr=a;null!=d?(this.pymolView=d,this.moveToText="moveTo -1.0 PyMOL "+
JU.Escape.eAF(d)):(a.finalizeTransformParameters(),b?(b=a.ms.getInfoM("defaultOrientationMatrix"),null==b?this.rotationMatrix.setScale(1):this.rotationMatrix.setM3(b)):a.tm.getRotation(this.rotationMatrix),this.xTrans=a.tm.getTranslationXPercent(),this.yTrans=a.tm.getTranslationYPercent(),this.zoom=a.tm.getZoomSetting(),this.center.setT(a.tm.getRotationCenter()),this.windowCenteredFlag=a.tm.isWindowCentered(),this.rotationRadius=a.getFloat(570425388),this.navigationMode=a.getBoolean(603979887),this.moveToText=
a.tm.getMoveToText(-1,!1),this.navigationMode&&(this.xNav=a.tm.getNavigationOffsetPercent("X"),this.yNav=a.tm.getNavigationOffsetPercent("Y"),this.navDepth=a.tm.getNavigationDepthPercent(),this.navCenter=JU.P3.newP(a.tm.getNavigationCenter())),0!=a.tm.camera.z&&(this.cameraDepth=a.tm.getCameraDepth(),this.cameraX=a.tm.camera.x,this.cameraY=a.tm.camera.y))},"JV.Viewer,~B,~A");c(c$,"getMoveToText",function(a){return a?"   "+this.moveToText+"\n  save orientation "+JU.PT.esc(this.saveName.substring(12))+
";\n":this.moveToText},"~B");c(c$,"restore",function(a,b){b?(this.vwr.setBooleanProperty("windowCentered",this.windowCenteredFlag),this.vwr.setBooleanProperty("navigationMode",this.navigationMode),null==this.pymolView?this.vwr.moveTo(this.vwr.eval,a,this.center,null,NaN,this.rotationMatrix,this.zoom,this.xTrans,this.yTrans,this.rotationRadius,this.navCenter,this.xNav,this.yNav,this.navDepth,this.cameraDepth,this.cameraX,this.cameraY):this.vwr.tm.moveToPyMOL(this.vwr.eval,a,this.pymolView)):this.vwr.tm.setRotation(this.rotationMatrix);
return!0},"~N,~B")});n("JM");w(null,"JM.StateScript",["JU.SB","JU.BSUtil","$.Escape"],function(){c$=t(function(){this.modelIndex=0;this.script2=this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;s(this,arguments)},JM,"StateScript");u(c$,function(a,b,d,c,g,f,j){this.modelIndex=a;this.script1=b;this.bsBonds=JU.BSUtil.copy(d);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(g);this.script2=f;this.inDefinedStateBlock=j},"~N,~S,JU.BS,JU.BS,JU.BS,~S,~B");
c(c$,"isValid",function(){return null!=this.script1&&0<this.script1.length&&(null==this.bsBonds||0<=this.bsBonds.nextSetBit(0))&&(null==this.bsAtoms1||0<=this.bsAtoms1.nextSetBit(0))&&(null==this.bsAtoms2||0<=this.bsAtoms2.nextSetBit(0))});h(c$,"toString",function(){if(!this.isValid())return"";var a=JU.SB.newS(this.script1);null!=this.bsBonds&&a.append(" ").append(JU.Escape.eBond(this.bsBonds));null!=this.bsAtoms1&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms1));null!=this.bsAtoms2&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms2));
null!=this.script2&&a.append(" ").append(this.script2);a=a.toString();a.endsWith(";")||(a+=";");return a});c(c$,"isConnect",function(){return 0<=this.script1.indexOf("connect")});c(c$,"deleteAtoms",function(a,b,d){if(a==this.modelIndex)return!1;if(a>this.modelIndex)return!0;JU.BSUtil.deleteBits(this.bsBonds,b);JU.BSUtil.deleteBits(this.bsAtoms1,d);JU.BSUtil.deleteBits(this.bsAtoms2,d);return this.isValid()},"~N,JU.BS,JU.BS");c(c$,"setModelIndex",function(a){this.modelIndex=a},"~N")});n("JM");c$=t(function(){this.id=
"";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=0;this.signFactor=1;this.reference=null;s(this,arguments)},JM,"TickInfo");u(c$,function(a){this.ticks=a},"JU.P3");n("JU");w(["JU.P3","$.P3i","$.V3"],"JU.BoxInfo",["JU.Lst","$.Measure","$.P4","JU.Point3fi"],function(){c$=t(function(){this.bbVertices=this.bbVector=this.bbCenter=this.bbCorner1=this.bbCorner0=null;this.isScaleSet=!1;this.margin=0;s(this,arguments)},JU,"BoxInfo");K(c$,function(){this.bbCorner0=new JU.P3;this.bbCorner1=
new JU.P3;this.bbCenter=new JU.P3;this.bbVector=new JU.V3;this.bbVertices=Array(8);for(var a=8;0<=--a;)this.bbVertices[a]=new JU.Point3fi;for(a=0;8>a;a++)JU.BoxInfo.unitBboxPoints[a]=JU.P3.new3(-1,-1,-1),JU.BoxInfo.unitBboxPoints[a].scaleAdd2(2,JU.BoxInfo.unitCubePoints[a],JU.BoxInfo.unitBboxPoints[a])});u(c$,function(){this.reset()});c(c$,"intersectPlane",function(a,b,d,c){var g=new JU.Lst;g.addLast(this.getCanonicalCopy(d));return a.intersectPlane(b,g,c)},"JM.ModelSet,JU.P4,~N,~N");c(c$,"getCanonicalCopy",
function(a){return JU.BoxInfo.getCanonicalCopy(this.bbVertices,a)},"~N");c$.getCanonicalCopy=c(c$,"getCanonicalCopy",function(a,b){for(var d=Array(8),c=0;8>c;c++)d[JU.BoxInfo.toCanonical[c]]=JU.P3.newP(a[c]);JU.BoxInfo.scaleBox(d,b);return d},"~A,~N");c$.scaleBox=c(c$,"scaleBox",function(a,b){if(!(0==b||1==b)){for(var d=new JU.P3,c=new JU.V3,g=0;8>g;g++)d.add(a[g]);d.scale(0.125);for(g=0;8>g;g++)c.sub2(a[g],d),c.scale(b),a[g].add2(d,c)}},"~A,~N");c$.getFacesFromCriticalPoints=c(c$,"getFacesFromCriticalPoints",
function(a){for(var b=Array(6),d=new JU.V3,c=new JU.V3,g=new JU.V3,f=new JU.P3,j=new JU.P3,h=new JU.P3,l=Array(8),m=0;8>m;m++)l[m]=JU.P3.newP(a[0]),1==(m&1)&&l[m].add(a[1]),2==(m&2)&&l[m].add(a[2]),4==(m&4)&&l[m].add(a[3]);for(m=0;6>m;m++)f.setT(l[JU.BoxInfo.facePoints[m].x]),j.setT(l[JU.BoxInfo.facePoints[m].y]),h.setT(l[JU.BoxInfo.facePoints[m].z]),JU.Measure.getPlaneThroughPoints(f,j,h,d,c,g,b[m]=new JU.P4);return b},"~A");c$.getCriticalPoints=c(c$,"getCriticalPoints",function(a,b){var d=JU.P3.newP(a[0]),
c=JU.P3.newP(a[1]),g=JU.P3.newP(a[2]),f=JU.P3.newP(a[4]);c.sub(d);g.sub(d);f.sub(d);null!=b&&d.add(b);return[d,c,g,f]},"~A,JU.T3");c(c$,"getBoundBoxCenter",function(){this.isScaleSet||this.setBbcage(1);return this.bbCenter});c(c$,"getBoundBoxCornerVector",function(){this.isScaleSet||this.setBbcage(1);return this.bbVector});c(c$,"getBoundBoxPoints",function(a){this.isScaleSet||this.setBbcage(1);return a?[this.bbCenter,JU.P3.newP(this.bbVector),this.bbCorner0,this.bbCorner1]:[this.bbCorner0,this.bbCorner1]},
"~B");c(c$,"getBoundBoxVertices",function(){this.isScaleSet||this.setBbcage(1);return this.bbVertices});c(c$,"setBoundBox",function(a,b,d,c){if(null!=a){if(0==c)return;if(d){if(0==a.distance(b))return;this.bbCorner0.set(Math.min(a.x,b.x),Math.min(a.y,b.y),Math.min(a.z,b.z));this.bbCorner1.set(Math.max(a.x,b.x),Math.max(a.y,b.y),Math.max(a.z,b.z))}else{if(0==b.x||0==b.y&&0==b.z)return;this.bbCorner0.set(a.x-b.x,a.y-b.y,a.z-b.z);this.bbCorner1.set(a.x+b.x,a.y+b.y,a.z+b.z)}}this.setBbcage(c)},"JU.P3,JU.P3,~B,~N");
c(c$,"reset",function(){this.isScaleSet=!1;this.bbCorner0.set(3.4028235E38,3.4028235E38,3.4028235E38);this.bbCorner1.set(-3.4028235E38,-3.4028235E38,-3.4028235E38)});c(c$,"setMargin",function(a){this.margin=a},"~N");c(c$,"addBoundBoxPoint",function(a){this.isScaleSet=!1;JU.BoxInfo.addPoint(a,this.bbCorner0,this.bbCorner1,this.margin)},"JU.T3");c$.addPoint=c(c$,"addPoint",function(a,b,d,c){a.x-c<b.x&&(b.x=a.x-c);a.x+c>d.x&&(d.x=a.x+c);a.y-c<b.y&&(b.y=a.y-c);a.y+c>d.y&&(d.y=a.y+c);a.z-c<b.z&&(b.z=a.z-
c);a.z+c>d.z&&(d.z=a.z+c)},"JU.T3,JU.P3,JU.P3,~N");c$.addPointXYZ=c(c$,"addPointXYZ",function(a,b,d,c,g,f){a-f<c.x&&(c.x=a-f);a+f>g.x&&(g.x=a+f);b-f<c.y&&(c.y=b-f);b+f>g.y&&(g.y=b+f);d-f<c.z&&(c.z=d-f);d+f>g.z&&(g.z=d+f)},"~N,~N,~N,JU.P3,JU.P3,~N");c(c$,"setBbcage",function(a){this.isScaleSet=!0;this.bbCenter.add2(this.bbCorner0,this.bbCorner1);this.bbCenter.scale(0.5);this.bbVector.sub2(this.bbCorner1,this.bbCenter);0<a?this.bbVector.scale(a):(this.bbVector.x-=a/2,this.bbVector.y-=a/2,this.bbVector.z-=
a/2);for(a=8;0<=--a;){var b=this.bbVertices[a];b.setT(JU.BoxInfo.unitBboxPoints[a]);b.x*=this.bbVector.x;b.y*=this.bbVector.y;b.z*=this.bbVector.z;b.add(this.bbCenter)}this.bbCorner0.setT(this.bbVertices[0]);this.bbCorner1.setT(this.bbVertices[7])},"~N");c(c$,"isWithin",function(a){this.isScaleSet||this.setBbcage(1);return a.x>=this.bbCorner0.x&&a.x<=this.bbCorner1.x&&a.y>=this.bbCorner0.y&&a.y<=this.bbCorner1.y&&a.z>=this.bbCorner0.z&&a.z<=this.bbCorner1.z},"JU.P3");C(c$,"bbcageTickEdges","z\x00\x00yx\x00\x00\x00\x00\x00\x00\x00".split(""),
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7,1,2,5,6]);c$.cubeVertexOffsets=c$.prototype.cubeVertexOffsets=[JU.P3i.new3(0,0,0),JU.P3i.new3(1,0,0),JU.P3i.new3(1,0,1),JU.P3i.new3(0,0,1),JU.P3i.new3(0,1,0),JU.P3i.new3(1,1,0),JU.P3i.new3(1,1,1),JU.P3i.new3(0,1,1)];c$.unitBboxPoints=c$.prototype.unitBboxPoints=Array(8)});n("JU");w(["JU.BS"],"JU.BSUtil",null,function(){c$=B(JU,"BSUtil");c$.newAndSetBit=c(c$,"newAndSetBit",function(a){var b=JU.BS.newN(a+1);b.set(a);return b},"~N");c$.areEqual=c(c$,"areEqual",function(a,b){return null==a||null==b?
null==a&&null==b:a.equals(b)},"JU.BS,JU.BS");c$.haveCommon=c(c$,"haveCommon",function(a,b){return null==a||null==b?!1:a.intersects(b)},"JU.BS,JU.BS");c$.cardinalityOf=c(c$,"cardinalityOf",function(a){return null==a?0:a.cardinality()},"JU.BS");c$.newBitSet2=c(c$,"newBitSet2",function(a,b){var d=JU.BS.newN(b);d.setBits(a,b);return d},"~N,~N");c$.setAll=c(c$,"setAll",function(a){var b=JU.BS.newN(a);b.setBits(0,a);return b},"~N");c$.andNot=c(c$,"andNot",function(a,b){null!=b&&null!=a&&a.andNot(b);return a},
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a||null==b)){for(var g=b.length(),f=JU.BS.newN(g),j=!1,h=!1,l=d,m=0,r=0;m<g&&r<c;m++)b.get(m)?(h&&f.set(m),l=d,j=!1):a.get(r++)?(f.set(m),l&&(l=!1,h=j=!0)):l&&!j&&(h=!1);a.clearAll();a.or(f)}},"JU.BS,JU.BS,~B,~N");c$.offset=c(c$,"offset",function(a,b,d){if(null!=a){for(var c=JU.BS.newN(a.length()+d),g=a.nextSetBit(0);g>=b;g=a.nextSetBit(g+1))c.set(g+d);JU.BSUtil.copy2(c,a)}},"JU.BS,~N,~N");c$.setMapBitSet=c(c$,"setMapBitSet",function(a,b,d,c){var g;a.containsKey(c)?g=a.get(c):a.put(c,g=new JU.BS);
g.setBits(b,d+1)},"java.util.Map,~N,~N,~S");c$.emptySet=c$.prototype.emptySet=new JU.BS});n("JU");w(["JU.Int2IntHash"],"JU.C","java.lang.Byte $.Float JU.AU $.CU $.PT $.SB J.c.PAL JU.Escape $.Logger".split(" "),function(){c$=B(JU,"C");u(c$,function(){});c$.getColix=c(c$,"getColix",function(a){if(0==a)return 0;var b=0;-16777216!=(a&4278190080)&&(b=JU.C.getTranslucentFlag(a>>24&255),a|=4278190080);var c=JU.C.colixHash.get(a);3==(c&3)&&(b=0);return(0<c?c:JU.C.allocateColix(a))|b},"~N");c$.allocateColix=
c(c$,"allocateColix",function(a){for(var b=JU.C.colixMax;4<=--b;)if((a&16777215)==(JU.C.argbs[b]&16777215))return b;JU.C.colixMax==JU.C.argbs.length&&(b=2*JU.C.colixMax,2048<b&&(b=2048),JU.C.argbs=JU.AU.arrayCopyI(JU.C.argbs,b),null!=JU.C.argbsGreyscale&&(JU.C.argbsGreyscale=JU.AU.arrayCopyI(JU.C.argbsGreyscale,b)));JU.C.argbs[JU.C.colixMax]=a;null!=JU.C.argbsGreyscale&&(JU.C.argbsGreyscale[JU.C.colixMax]=JU.CU.toFFGGGfromRGB(a));JU.C.colixHash.put(a,JU.C.colixMax);return 2047>JU.C.colixMax?JU.C.colixMax++:
JU.C.colixMax},"~N");c$.setLastGrey=c(c$,"setLastGrey",function(a){JU.C.calcArgbsGreyscale();JU.C.argbsGreyscale[2047]=JU.CU.toFFGGGfromRGB(a)},"~N");c$.calcArgbsGreyscale=c(c$,"calcArgbsGreyscale",function(){if(null==JU.C.argbsGreyscale){for(var a=D(JU.C.argbs.length,0),b=JU.C.argbs.length;4<=--b;)a[b]=JU.CU.toFFGGGfromRGB(JU.C.argbs[b]);JU.C.argbsGreyscale=a}});c$.getArgbGreyscale=c(c$,"getArgbGreyscale",function(a){null==JU.C.argbsGreyscale&&JU.C.calcArgbsGreyscale();return JU.C.argbsGreyscale[a&
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a?256:a))>>5&15)<<11},"~N");c$.isColixLastAvailable=c(c$,"isColixLastAvailable",function(a){return 0<a&&2047==(a&2047)},"~N");c$.getArgb=c(c$,"getArgb",function(a){return JU.C.argbs[a&-30721]},"~N");c$.isColixColorInherited=c(c$,"isColixColorInherited",function(a){switch(a){case 0:case 1:return!0;default:return 1==(a&-30721)}},"~N");c$.getColixInherited=c(c$,"getColixInherited",function(a,b){switch(a){case 0:return b;case 1:return b&-30721;default:return 1==(a&-30721)?b&-30721|a&30720:a}},"~N,~N");
c$.isColixTranslucent=c(c$,"isColixTranslucent",function(a){return 0!=(a&30720)},"~N");c$.getChangeableColixIndex=c(c$,"getChangeableColixIndex",function(a){return 0<=a?-1:a&2047},"~N");c$.getColixTranslucent3=c(c$,"getColixTranslucent3",function(a,b,c){a&=-30721;0==a&&(a=1);return b?a|JU.C.getTranslucentFlag(c):a},"~N,~B,~N");c$.copyColixTranslucency=c(c$,"copyColixTranslucency",function(a,b){return JU.C.getColixTranslucent3(b,JU.C.isColixTranslucent(a),JU.C.getColixTranslucencyLevel(a))},"~N,~N");
c$.getColixTranslucencyFractional=c(c$,"getColixTranslucencyFractional",function(a){a=JU.C.getColixTranslucencyLevel(a);return-1==a?0.5:0==a?0:255==a?1:a/256},"~N");c$.getColixTranslucencyLevel=c(c$,"getColixTranslucencyLevel",function(a){a=a>>11&15;switch(a){case 0:return 0;case 1:case 2:case 3:case 4:case 5:case 6:case 7:return a<<5;case 15:return-1;default:return 255}},"~N");c$.getColixS=c(c$,"getColixS",function(a){var b=JU.CU.getArgbFromString(a);return 0!=b?JU.C.getColix(b):"none".equalsIgnoreCase(a)?
0:"opaque".equalsIgnoreCase(a)?1:2},"~S");c$.getColixArray=c(c$,"getColixArray",function(a){if(null==a||0==a.length)return null;a=JU.PT.getTokens(a);for(var b=T(a.length,0),c=0;c<a.length;c++)if(b[c]=JU.C.getColix(JU.CU.getArgbFromString(a[c])),0==b[c])return null;return b},"~S");c$.getHexCode=c(c$,"getHexCode",function(a){return JU.Escape.escapeColor(JU.C.getArgb(a))},"~N");c$.getHexCodes=c(c$,"getHexCodes",function(a){if(null==a)return null;for(var b=new JU.SB,c=0;c<a.length;c++)b.append(0==c?"":
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new JU.Int2IntHash(256);C(c$,"RAW_RGB_INT",3,"UNMASK_CHANGEABLE_TRANSLUCENT",2047,"CHANGEABLE_MASK",32768,"LAST_AVAILABLE_COLIX",2047,"TRANSLUCENT_SHIFT",11,"ALPHA_SHIFT",13,"TRANSLUCENT_MASK",30720,"TRANSLUCENT_SCREENED",30720,"TRANSPARENT",16384,"OPAQUE_MASK",-30721,"BLACK",4,"ORANGE",5,"PINK",6,"BLUE",7,"WHITE",8,"CYAN",9,"RED",10,"GREEN",11,"GRAY",12,"SILVER",13,"LIME",14,"MAROON",15,"NAVY",16,"OLIVE",17,"PURPLE",18,"TEAL",19,"MAGENTA",20,"YELLOW",21,"HOTPINK",22,"GOLD",23);for(var a=[4278190080,
4294944E3,4294951115,4278190335,4294967295,4278255615,4294901760,4278222848,4286611584,4290822336,4278255360,4286578688,4278190208,4286611456,4286578816,4278222976,4294902015,4294967040,4294928820,4294956800],b=0;b<a.length;++b)JU.C.getColix(a[b])});n("JU");w(null,"JU.ColorEncoder","java.lang.Boolean $.Float java.util.Hashtable JU.AU $.CU $.Lst $.PT J.c.PAL JU.C $.Escape $.Logger JV.JC".split(" "),function(){c$=t(function(){this.argbsAmino=this.argbsShapely=this.argbsRwb=this.argbsRoygb=this.argbsCpk=
this.paletteFriendly=this.paletteWB=this.paletteBW=null;this.ihalf=0;this.schemes=null;this.currentPalette=0;this.currentSegmentCount=1;this.isTranslucent=!1;this.hi=this.lo=0;this.isReversed=!1;this.thisScale=this.userScale=null;this.thisName="scheme";this.isColorIndex=!1;this.ce=null;s(this,arguments)},JU,"ColorEncoder");K(c$,function(){this.userScale=[-8355712];this.thisScale=[-8355712]});u(c$,function(a){null==a?(this.schemes=new java.util.Hashtable,this.argbsCpk=J.c.PAL.argbsCpk,this.argbsRoygb=
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JV.JC.argbsRwbScale;break;case 2:this.argbsCpk=J.c.PAL.argbsCpk;break;case 3:JU.ColorEncoder.getRasmolScale();break;case 5:this.argbsAmino=JV.JC.argbsAmino;break;case 4:this.argbsShapely=JV.JC.argbsShapely}return a}this.schemes.put(a,b);this.setThisScheme(a,b);a=this.createColorScheme(a,!1,d);if(d)switch(a){case 10:this.paletteBW=this.thisScale;break;case 11:this.paletteWB=this.thisScale;break;case 0:case 1:this.argbsRoygb=this.thisScale;this.ihalf=q(this.argbsRoygb.length/3);break;case 6:case 7:this.argbsRwb=
this.thisScale;break;case 2:this.argbsCpk=this.thisScale;break;case 5:this.argbsAmino=this.thisScale;break;case 4:this.argbsShapely=this.thisScale}return-1},"~S,~A,~B");c(c$,"createColorScheme",function(a,b,d){a=a.toLowerCase();if(a.equals("inherit"))return 15;var c=Math.max(a.indexOf("="),a.indexOf("["));if(0<=c){b=JU.PT.replaceAllCharacters(a.substring(0,c)," =","");0<b.length&&(d=!0);var g=0;a.length>c+1&&!a.contains("[")&&(a="["+a.substring(c+1).trim()+"]",a=JU.PT.rep(a.$replace("\n"," "),"  ",
" "),a=JU.PT.rep(a,", ",",").$replace(" ",","),a=JU.PT.rep(a,",","]["));for(c=-1;0<=(c=a.indexOf("[",c+1));)g++;if(0==g)return this.makeColorScheme(b,null,d);for(var f=D(g,0),g=0;0<=(c=a.indexOf("[",c+1));){var j=a.indexOf("]",c);0>j&&(j=a.length-1);var h=JU.CU.getArgbFromString(a.substring(c,j+1));0==h&&(h=JU.CU.getArgbFromString(a.substring(c+1,j).trim()));if(0==h)return JU.Logger.error("error in color value: "+a.substring(c,j+1)),0;f[g++]=h}return b.equals("user")?(this.setUserScale(f),-13):this.makeColorScheme(b,
f,d)}a=JU.ColorEncoder.fixName(a);d=JU.ColorEncoder.getSchemeIndex(a);return this.schemes.containsKey(a)?(this.setThisScheme(a,this.schemes.get(a)),d):-1!=d?d:b?0:2147483647},"~S,~B,~B");c(c$,"setUserScale",function(a){this.ce.userScale=a;this.makeColorScheme("user",a,!1)},"~A");c(c$,"getColorSchemeArray",function(a){switch(a){case -1:return this.thisScale;case 0:return this.ce.argbsRoygb;case 1:return JU.AU.arrayCopyRangeRevI(this.ce.argbsRoygb,0,-1);case 8:return JU.AU.arrayCopyRangeI(this.ce.argbsRoygb,
0,this.ce.ihalf);case 9:var b=JU.AU.arrayCopyRangeI(this.ce.argbsRoygb,this.ce.argbsRoygb.length-2*this.ce.ihalf,-1);a=D(this.ce.ihalf,0);for(var d=a.length,c=b.length;0<=--d&&0<=--c;)a[d]=b[c--];return a;case 12:return this.getPaletteAC();case 10:return this.getPaletteBW();case 11:return this.getPaletteWB();case 6:return this.ce.argbsRwb;case 7:return JU.AU.arrayCopyRangeRevI(this.ce.argbsRwb,0,-1);case 2:return this.ce.argbsCpk;case 3:return JU.ColorEncoder.getRasmolScale();case 4:return this.ce.argbsShapely;
case 5:return this.ce.argbsAmino;case -13:return this.ce.userScale;case -14:return JU.AU.arrayCopyRangeRevI(this.ce.userScale,0,-1);default:return null}},"~N");c(c$,"getColorIndexFromPalette",function(a,b,d,c,g){c=JU.C.getColix(this.getArgbFromPalette(a,b,d,c));g&&(a=(d-a)/(d-b),1<a?a=1:0.125>a&&(a=0.125),c=JU.C.getColixTranslucent3(c,!0,a));return c},"~N,~N,~N,~N,~B");c(c$,"getPaletteColorCount",function(a){switch(a){case -1:return this.thisScale.length;case 10:case 11:return this.getPaletteBW().length;
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0<=JU.Measure.distanceToPlane(f,a);JU.Measure.getPlaneThroughPoints(b,g,d,j,h,l,f);if(r!=0<=JU.Measure.distanceToPlane(f,a))return!1;JU.Measure.getPlaneThroughPoints(d,g,c,j,h,l,f);if(r!=0<=JU.Measure.distanceToPlane(f,a))return!1;JU.Measure.getPlaneThroughPoints(b,d,c,j,h,l,f);a=JU.Measure.distanceToPlane(f,a);if(m)return r==0<=a;g=JU.Measure.distanceToPlane(f,g);return 0>=g*a||Math.abs(g)>Math.abs(a)},"JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P4,JU.V3,JU.V3,JU.V3,~B");c$.getIntersectionPP=c(c$,"getIntersectionPP",
function(a,b){var d=a.x,c=a.y,g=a.z,f=a.w,j=b.x,h=b.y,l=b.z,m=b.w,r=JU.V3.new3(d,c,g),x=JU.V3.new3(j,h,l),n=new JU.V3;n.cross(r,x);var r=Math.abs(n.x),x=Math.abs(n.y),q=Math.abs(n.z);switch(r>x?r>q?1:3:x>q?2:3){case 1:r=0;x=c*l-h*g;if(0.01>Math.abs(x))return null;g=(g*m-l*f)/x;d=(h*f-m*c)/x;break;case 2:x=d*l-j*g;if(0.01>Math.abs(x))return null;r=(g*m-l*f)/x;g=0;d=(j*f-m*d)/x;break;default:x=d*h-j*c;if(0.01>Math.abs(x))return null;r=(c*m-h*f)/x;g=(j*f-m*d)/x;d=0}c=new JU.Lst;c.addLast(JU.P3.new3(r,
g,d));n.normalize();c.addLast(n);return c},"JU.P4,JU.P4");c$.getIntersection=c(c$,"getIntersection",function(a,b,d,c,g,f){JU.Measure.getPlaneProjection(a,d,c,g);g.set(d.x,d.y,d.z);g.normalize();null==b&&(b=JU.V3.newV(g));d=b.dot(g);if(0.01>Math.abs(d))return null;f.sub2(c,a);c.scaleAdd2(f.dot(g)/d,b,a);return c},"JU.P3,JU.V3,JU.P4,JU.P3,JU.V3,JU.V3");c$.calculateQuaternionRotation=c(c$,"calculateQuaternionRotation",function(a,b){b[1]=NaN;var d=new JU.Quat;if(1==a[0].length||a[0].length!=a[1].length)return d;
var c=a[0].length-1;if(2>c)return d;for(var g=0,f=0,j=0,h=0,l=0,m=0,r=0,x=0,n=0,q=new JU.P3,p=new JU.P3,c=c+1;1<=--c;){var s=a[1][c];q.sub2(a[0][c],a[0][0]);p.sub2(s,a[0][1]);g+=q.x*p.x;f+=q.x*p.y;j+=q.x*p.z;h+=q.y*p.x;l+=q.y*p.y;m+=q.y*p.z;r+=q.z*p.x;x+=q.z*p.y;n+=q.z*p.z}b[0]=JU.Measure.getRmsd(a,d);d=X(4,4,0);d[0][0]=g+l+n;d[0][1]=d[1][0]=m-x;d[0][2]=d[2][0]=r-j;d[0][3]=d[3][0]=f-h;d[1][1]=g-l-n;d[1][2]=d[2][1]=f+h;d[1][3]=d[3][1]=r+j;d[2][2]=-g+l-n;d[2][3]=d[3][2]=m+x;d[3][3]=-g-l+n;g=javajs.api.Interface.getInterface("JU.Eigen").setM(d).getEigenvectorsFloatTransposed()[3];
d=JU.Quat.newP4(JU.P4.new4(g[1],g[2],g[3],g[0]));b[1]=JU.Measure.getRmsd(a,d);return d},"~A,~A");c$.getTransformMatrix4=c(c$,"getTransformMatrix4",function(a,b,d,c){a=JU.Measure.getCenterAndPoints(a);var g=JU.Measure.getCenterAndPoints(b);b=L(2,0);var f=JU.Measure.calculateQuaternionRotation([a,g],b),g=JU.V3.newVsub(g[0],a[0]);d.setMV(f.getMatrix(),g);null!=c&&c.setT(a[0]);return b[1]},"JU.Lst,JU.Lst,JU.M4,JU.P3");c$.getCenterAndPoints=c(c$,"getCenterAndPoints",function(a){var b=a.size(),d=Array(b+
1);d[0]=new JU.P3;if(0<b){for(var c=0;c<b;c++)d[0].add(d[c+1]=a.get(c));d[0].scale(1/b)}return d},"JU.Lst");c$.getRmsd=c(c$,"getRmsd",function(a,b){for(var d=0,c=a[0],g=a[1],f=c[0],j=g[0],h=c.length-1,l=new JU.P3,m=h+1;1<=--m;)l.sub2(c[m],f),b.transformP2(l,l).add(j),d+=l.distanceSquared(g[m]);return Math.sqrt(d/h)},"~A,JU.Quat");C(c$,"radiansPerDegree",0.017453292519943295);c$.axisY=c$.prototype.axisY=JU.V3.new3(0,1,0)});n("JU");w(null,"JU.MeshSurface","java.lang.Float java.util.Hashtable JU.AU $.BS $.Lst $.Measure $.P3 $.P4 $.PT $.SB JU.BSUtil $.BoxInfo $.C $.Escape $.Geodesic $.TempArray".split(" "),
function(){c$=t(function(){this.meshType=this.spanningVectors=null;this.vc=0;this.vertexSource=this.vvs=this.vs=null;this.pc=0;this.polygonTranslucencies=this.pis=null;this.haveQuads=this.isTriangleSet=!1;this.colixBack=this.colix=0;this.isColorSolid=!0;this.normalsTemp=this.normals=this.vcs=this.pcs=this.altVertices=this.offset=null;this.normixCount=this.normalCount=0;this.vertexSets=this.surfaceSet=this.mat4=this.bsPolygons=null;this.nSets=0;this.checkCount=2;this.vertexCount0=this.polygonCount0=
this.iC=this.iB=this.iA=this.lastColix=this.lastColor=0;this.bsTransPolygons=this.bsSlabGhost=this.bsSlabDisplay=null;this.slabColix=this.slabMeshType=0;this.slabOptions=this.bsDisplay=null;this.doCap=this.doGhost=this.doClear=!1;this.mergePolygonCount0=this.mergeVertexCount0=this.iE=this.iD=0;this.isMerged=!1;s(this,arguments)},JU,"MeshSurface");u(c$,function(){});c$.newMesh=c(c$,"newMesh",function(a,b,d,c,g,f){var j=new JU.MeshSurface;j.pis=c;a?j.altVertices=b:j.vs=b;j.vc=0==d?b.length:d;j.normals=
g;j.normalCount=0==f&&null!=g?g.length:f;return j},"~B,~A,~N,~A,~A,~N");c$.newSlab=c(c$,"newSlab",function(a,b,d,c,g,f){var j=new JU.MeshSurface;j.vs=a;j.vvs=d;j.vc=b;j.pis=c;j.pc=g;j.checkCount=f;return j},"~A,~N,~A,~A,~N,~N");c(c$,"getVertices",function(){return null==this.altVertices?this.vs:this.altVertices});c(c$,"getFaces",function(){return this.pis});c(c$,"setColix",function(a){this.colix=a},"~N");c(c$,"setColixBack",function(a){this.colixBack=a},"~N");c(c$,"addV",function(a,b){0==this.vc?
this.vs=Array(25):this.vc==this.vs.length&&(this.vs=JU.AU.doubleLength(this.vs));this.vs[this.vc]=b?JU.P3.newP(a):a;return this.vc++},"JU.T3,~B");c(c$,"addTriangle",function(a,b,d){this.addPolygon([a,b,d],null)},"~N,~N,~N");c(c$,"addQuad",function(a,b,d,c){this.haveQuads=!0;this.addPolygon([a,b,d,c],null)},"~N,~N,~N,~N");c(c$,"setPolygonCount",function(a){this.pc=a;if(!(0>a)&&(null==this.pis||a>this.pis.length))this.pis=JU.AU.newInt2(a)},"~N");c(c$,"addVCVal",function(a,b,d){0==this.vc?this.vvs=L(25,
0):this.vc>=this.vvs.length&&(this.vvs=JU.AU.doubleLengthF(this.vvs));this.vvs[this.vc]=b;return this.addV(a,d)},"JU.T3,~N,~B");c(c$,"addTriangleCheck",function(a,b,d,c,g,f){return null==this.vs||null!=this.vvs&&(Float.isNaN(this.vvs[a])||Float.isNaN(this.vvs[b])||Float.isNaN(this.vvs[d]))||Float.isNaN(this.vs[a].x)||Float.isNaN(this.vs[b].x)||Float.isNaN(this.vs[d].x)?-1:this.addPolygonV3(a,b,d,c,g,f,null)},"~N,~N,~N,~N,~N,~N");c(c$,"addPolygonV3",function(a,b,d,c,g,f,j){return 2==this.checkCount?
this.addPolygonC([a,b,d,c,g],f,j):this.addPolygon([a,b,d,c],j)},"~N,~N,~N,~N,~N,~N,JU.BS");c(c$,"addPolygonC",function(a,b,d){if(0!=b){if(null==this.pcs||0==this.pc)this.lastColor=0;b=b==this.lastColor?this.lastColix:this.lastColix=JU.C.getColix(this.lastColor=b);this.setPolygonColix(this.pc,b)}return this.addPolygon(a,d)},"~A,~N,JU.BS");c(c$,"addPolygon",function(a,b){var d=this.pc;0==this.pc?this.pis=JU.AU.newInt2(25):this.pc==this.pis.length&&(this.pis=JU.AU.doubleLength(this.pis));null!=b&&b.set(this.pc);
this.pis[this.pc++]=a;return d},"~A,JU.BS");c(c$,"setPolygonColix",function(a,b){null==this.pcs?this.pcs=T(25,0):a>=this.pcs.length&&(this.pcs=JU.AU.doubleLengthShort(this.pcs));this.pcs[a]=b},"~N,~N");c(c$,"invalidatePolygons",function(){for(var a=this.pc;--a>=this.mergePolygonCount0;)if((null==this.bsSlabDisplay||this.bsSlabDisplay.get(a))&&!this.setABC(a))this.pis[a]=null});c(c$,"setABC",function(a){if(null!=this.bsSlabDisplay&&!this.bsSlabDisplay.get(a)&&(null==this.bsSlabGhost||!this.bsSlabGhost.get(a)))return!1;
a=this.pis[a];if(null==a||3>a.length)return!1;this.iA=a[0];this.iB=a[1];this.iC=a[2];return null==this.vvs||!(Float.isNaN(this.vvs[this.iA])||Float.isNaN(this.vvs[this.iB])||Float.isNaN(this.vvs[this.iC]))},"~N");c(c$,"setTranslucentVertices",function(){},"JU.BS");c(c$,"setSlab",function(a,b,d,c,g){this.bsSlabDisplay=a;this.bsSlabGhost=b;this.slabMeshType=d.equalsIgnoreCase("mesh")?1073742018:1073741938;this.slabColix=JU.C.getColixTranslucent3(JU.C.getColixS(c),!0,g)},"JU.BS,JU.BS,~S,~S,~N");c(c$,
"getSlabColor",function(){return null==this.bsSlabGhost?null:JU.C.getHexCode(this.slabColix)});c(c$,"getSlabTranslucency",function(){return null==this.bsSlabGhost?null:""+JU.C.getColixTranslucencyFractional(this.slabColix)});c(c$,"getSlabType",function(){return null!=this.bsSlabGhost&&1073742018==this.slabMeshType?"mesh":null});c(c$,"resetTransPolygons",function(){for(var a=JU.C.isColixTranslucent(this.colix),b=JU.C.getColixTranslucencyFractional(this.colix),d=0;d<this.pc;d++)this.bsTransPolygons.get(d)&&
this.setABC(d)&&(this.vcs[this.iA]=JU.C.getColixTranslucent3(this.vcs[this.iA],a,b),this.vcs[this.iB]=JU.C.getColixTranslucent3(this.vcs[this.iB],a,b),this.vcs[this.iC]=JU.C.getColixTranslucent3(this.vcs[this.iC],a,b));this.polygonTranslucencies=this.bsTransPolygons=null});c(c$,"resetSlab",function(){this.slabPolygons(JU.TempArray.getSlabObjectType(1048587,null,!1,null),!1)});c$.getCapSlabObject=c(c$,"getCapSlabObject",function(a,b){try{if(0==a.indexOf("array")){var d=JU.PT.split(a.substring(6,a.length-
1),",");return JU.TempArray.getSlabObjectType(1679429641,[JU.Escape.uP(d[0]),JU.Escape.uP(d[1]),JU.Escape.uP(d[2]),JU.Escape.uP(d[3])],b,null)}var c=JU.Escape.uP(a);if(p(c,JU.P4))return JU.TempArray.getSlabObjectType(135266319,c,b,null)}catch(g){if(!y(g,Exception))throw g;}return null},"~S,~B");c(c$,"slabPolygonsList",function(a,b){for(var d=0;d<a.size()&&this.slabPolygons(a.get(d),b);d++);},"JU.Lst,~B");c(c$,"slabPolygons",function(a,b){if(0>this.polygonCount0)return!1;var d=a[0].intValue();if(1048587==
d||1073741872==d){if(null!=this.bsSlabDisplay&&(0!=this.polygonCount0||0!=this.vertexCount0))this.pc=this.polygonCount0,this.vc=this.vertexCount0,this.polygonCount0=this.vertexCount0=0,this.normixCount=this.isTriangleSet?this.pc:this.vc,this.bsSlabDisplay.setBits(0,0==this.pc?this.vc:this.pc),this.slabOptions=(new JU.SB).append(this.meshType+" slab none"),this.bsSlabGhost=null,this.slabMeshType=1048587;if(1048587==d)return!1}var c=a[1],g=a[2].booleanValue()&&1073741872!=d;if(g&&!b)return!1;var f=
a[3],j=null!=f;if(null==this.bsSlabDisplay||0==this.polygonCount0&&0==this.vertexCount0){if(this.polygonCount0=this.pc,this.vertexCount0=this.vc,this.bsSlabDisplay=JU.BSUtil.setAll(0==this.pc?this.vc:this.pc),this.bsSlabGhost=null,0==this.pc&&0==this.vc)return!1}else this.isMerged&&(0==this.pc?this.bsSlabDisplay.setBits(this.mergeVertexCount0,this.vc):this.bsSlabDisplay.setBits(this.mergePolygonCount0,this.pc));j&&(null==this.bsSlabGhost&&(this.bsSlabGhost=new JU.BS),this.slabMeshType=f[0].intValue(),
this.slabColix=f[1].shortValue(),g=!1,this.colix=JU.C.getColixTranslucent3(this.colix,!1,0));f=new JU.SB;f.append(g?" cap ":" slab ");if(j){f.append("translucent ").appendF(JU.C.getColixTranslucencyFractional(this.slabColix)).append(" ");var h=JU.C.getHexCode(this.slabColix);null!=h&&f.append(h).append(" ");1073742018==this.slabMeshType&&f.append("mesh ")}switch(d){case 1073741872:f.append("brillouin");this.slabBrillouin(c);break;case 3:this.getIntersection(0,null,null,null,null,c,null,g,!1,3,j);
break;case 135266319:f.append(JU.Escape.eP4(c));this.getIntersection(0,c,null,null,null,null,null,g,!1,135266319,j);break;case 1614417948:case 1679429641:f.append("within ").append(JU.Escape.eAP(c));c=JU.BoxInfo.getFacesFromCriticalPoints(c);for(h=0;h<c.length;h++)this.getIntersection(0,c[h],null,null,null,null,null,g,!1,135266319,j);break;case 135270408:this.getIntersection(0,null,null,null,c,null,null,!1,!1,32,j);break;case 135266325:case 1073742114:case 1073742018:switch(h=c[0].floatValue(),d){case 135266325:d=
c[1];c=c[2];f.append("within ").appendF(h).append(null==c?JU.Escape.e(d):JU.Escape.e(c));this.getIntersection(h,null,d,null,null,null,null,g,!1,0<h?1276118018:1073742154,j);break;case 1073742114:if(null==this.vvs)return!1;d=c[1].floatValue();f.append("within range ").appendF(h).append(" ").appendF(d);c=d<h?JU.BSUtil.copy(this.bsSlabDisplay):null;this.getIntersection(h,null,null,null,null,null,null,g,!1,32,j);h=null==c?null:JU.BSUtil.copy(this.bsSlabDisplay);JU.BSUtil.copy2(c,this.bsSlabDisplay);this.getIntersection(d,
null,null,null,null,null,null,g,!1,64,j);null!=h&&this.bsSlabDisplay.or(h);break;case 1073742018:this.getIntersection(0,null,null,null,null,null,c[1],g,!1,0>h?32:64,j)}}g=f.toString();null==this.slabOptions&&(this.slabOptions=new JU.SB);0>this.slabOptions.indexOf(g)&&this.slabOptions.append(0<this.slabOptions.length()?"; ":"").append(this.meshType).append(g);return!0},"~A,~B");c(c$,"slabBrillouin",function(){},"~A");c(c$,"addIntersectionVertex",function(a,b,d,c,g,f,j){j=f>j?j+"_"+f:f+"_"+j;if(0<=
f&&(f=g.get(j),null!=f))return f.intValue();null!=this.vertexSource&&(this.vc>=this.vertexSource.length&&(this.vertexSource=JU.AU.doubleLengthI(this.vertexSource)),this.vertexSource[this.vc]=d);null!=this.vertexSets&&(this.vc>=this.vertexSets.length&&(this.vertexSets=JU.AU.doubleLengthI(this.vertexSets)),this.vertexSets[this.vc]=c);a=this.addVCVal(a,b,!0);g.put(j,Integer.$valueOf(a));return a},"JU.T3,~N,~N,~N,java.util.Map,~N,~N");c(c$,"getIntersection",function(a,b,d,c,g,f,j,h,l,m,r){var n=null==
c,q=null;if(null==g)if(3==m&&null!=f){if(null==this.vertexSource)return;g=L(this.vc,0);for(j=0;j<this.vc;j++)-1==(g[j]=this.vertexSource[j])&&System.out.println("meshsurface hmm")}else g=this.vvs;var p=new java.util.Hashtable;if(null!=d||r)h=!1;var s=L(2,0),t=L(2,0),u=Math.abs(a),v,w,y,z,B,C,E=0,F=0,G=0,H=0,K=h?new JU.Lst:null;if(0==this.pc)for(j=this.mergeVertexCount0;j<this.vc;j++)(Float.isNaN(g[j])||0<JU.MeshSurface.checkSlab(m,this.vs[j],g[j],a,b,d,f))&&this.bsSlabDisplay.clear(j);else{var M=
this.pc;for(j=this.mergePolygonCount0;j<M;j++)if(this.setABC(j)){var N=null!=this.bsSlabGhost&&this.bsSlabGhost.get(j)?this.bsSlabGhost:this.bsSlabDisplay,O=this.pis[j][3],P=2==this.checkCount?this.pis[j][4]:0,Q=this.vs[this.iA],R=this.vs[this.iB],S=this.vs[this.iC];z=g[this.iA];B=g[this.iB];C=g[this.iC];null!=this.vertexSource&&(E=this.vertexSource[this.iA],F=this.vertexSource[this.iB],G=this.vertexSource[this.iC]);null!=this.vertexSets&&(H=this.vertexSets[this.iA]);v=JU.MeshSurface.checkSlab(m,
Q,z,null==f?a:E,b,d,f);w=JU.MeshSurface.checkSlab(m,R,B,null==f?a:F,b,d,f);y=JU.MeshSurface.checkSlab(m,S,C,null==f?a:G,b,d,f);var T=(0!=v&&0>v?1:0)+(0!=w&&0>w?2:0)+(0!=y&&0>y?4:0);switch(T){case 1:case 6:q=null==d?[JU.MeshSurface.interpolatePoint(Q,R,-v,w,z,B,s,t,0),JU.MeshSurface.interpolatePoint(Q,S,-v,y,z,C,s,t,1)]:[this.interpolateSphere(Q,R,-v,-w,u,z,B,s,t,0),this.interpolateSphere(Q,S,-v,-y,u,z,C,s,t,1)];break;case 2:case 5:q=null==d?[JU.MeshSurface.interpolatePoint(R,Q,-w,v,B,z,s,t,1),JU.MeshSurface.interpolatePoint(R,
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3>g||0<=a.indexOf(b.substring(1,g-1)):a.endsWith(b.substring(1));if(j)return a.startsWith(b.substring(0,g-1))}for(var h=a.length,l="????",m=4;m<h;)l+=l,m+=4;d&&(f&&(b=l+b.substring(1),g+=m-1),j&&(b=b.substring(0,g-1)+l,g+=m-1));if(g<h)return!1;for(d=0;g>h;){if(c&&"?"==b.charAt(d))++d;else if("?"!=b.charAt(d+g-1))return!1;--g}for(c=h;0<=--c;)if(g=b.charAt(d+c),"?"!=g&&(h=a.charAt(c),g!=h&&("\u0001"!=g||"?"!=h)))return!1;return!0},"~S,~S,~B,~B");c$.replaceQuotedStrings=c(c$,"replaceQuotedStrings",function(a,
b,d){for(var c=b.size(),g=0;g<c;g++){var f=b.get(g),j=d.get(g);j.equals(f)||(a=JU.PT.rep(a,'"'+f+'"','"'+j+'"'))}return a},"~S,java.util.List,java.util.List");c$.replaceStrings=c(c$,"replaceStrings",function(a,b,d){for(var c=b.size(),g=0;g<c;g++){var f=b.get(g),j=d.get(g);j.equals(f)||(a=JU.PT.rep(a,f,j))}return a},"~S,java.util.List,java.util.List");c$.ichMathTerminator=c(c$,"ichMathTerminator",function(a,b,d){for(var c=1,g="\x00",f="\x00";0<c&&++b<d;){var j=a.charAt(b);if("\x00"!=g)"\\"==f?j="\x00":
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-1==this.modDim?"vib":"mod")},"java.util.Map");c(c$,"getUnitCell",function(){return null});h(c$,"clone",function(){var a=new JU.Vibration;a.setT(this);a.modDim=this.modDim;return a});C(c$,"twoPI",6.283185307179586,"TYPE_MODULATION",0,"TYPE_VIBRATION",-1,"TYPE_SPIN",-2,"TYPE_DISPLACEMENT",-3)});n("JV");w(["javajs.api.EventManager","JU.Rectangle","JV.MouseState"],"JV.ActionManager","java.lang.Character $.Float JU.P3 $.PT J.api.Interface J.i18n.GT J.thread.HoverWatcherThread JU.BSUtil $.Escape $.Logger $.Point3fi JV.binding.Binding $.JmolBinding".split(" "),
function(){c$=t(function(){this.vwr=null;this.haveMultiTouchInput=!1;this.predragBinding=this.rasmolBinding=this.dragBinding=this.pfaatBinding=this.jmolBinding=this.b=null;this.LEFT_DRAGGED=this.LEFT_CLICKED=0;this.hoverWatcherThread=null;N("JV.ActionManager.MotionPoint")||JV.ActionManager.$ActionManager$MotionPoint$();this.dragGesture=null;N("JV.ActionManager.Gesture")||JV.ActionManager.$ActionManager$Gesture$();this.apm=1;this.pickingStyleSelect=this.pickingStyle=this.bondPickingMode=0;this.pickingStyleMeasure=
5;this.rootPickingStyle=0;this.pickAtomAssignType="C";this.pickBondAssignType="p";this.isPickAtomAssignCharge=!1;this.xyRange=0;this.mouseDragFactor=this.gestureSwipeFactor=1;this.mouseWheelFactor=1.15;this.dragged=this.pressed=this.clicked=this.moved=this.current=null;this.clickedCount=this.pressedCount=0;this.dragSelectedMode=this.labelMode=this.drawMode=!1;this.measuresEnabled=!0;this.hoverActive=this.haveSelection=!1;this.mp=null;this.dragAtomIndex=-1;this.rubberbandSelectionMode=!1;this.rectRubber=
null;this.isAltKeyReleased=!0;this.isMultiTouchServer=this.isMultiTouchClient=this.keyProcessing=!1;this.clickAction=this.dragAction=this.pressAction=0;this.measurementQueued=null;this.selectionWorking=!1;s(this,arguments)},JV,"ActionManager",null,javajs.api.EventManager);K(c$,function(){this.dragGesture=M(JV.ActionManager.Gesture,this,null,20);this.current=new JV.MouseState("current");this.moved=new JV.MouseState("moved");this.clicked=new JV.MouseState("clicked");this.pressed=new JV.MouseState("pressed");
this.dragged=new JV.MouseState("dragged");this.rectRubber=new JU.Rectangle});c(c$,"setViewer",function(a){this.vwr=a;this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.LEFT_CLICKED=JV.binding.Binding.getMouseAction(1,16,2);this.LEFT_DRAGGED=JV.binding.Binding.getMouseAction(1,16,1)},"JV.Viewer,~S");c(c$,"checkHover",function(){if(!this.vwr.getInMotion(!0)&&!this.vwr.tm.spinOn&&!this.vwr.tm.navOn&&!this.vwr.checkObjectHovered(this.current.x,this.current.y)){var a=this.vwr.findNearestAtomIndex(this.current.x,
this.current.y);if(!(0>a)){var b=2==this.getAtomPickingMode()&&this.bnd(JV.binding.Binding.getMouseAction(this.clickedCount,this.moved.modifiers,1),10);this.vwr.hoverOn(a,b)}}});c(c$,"processMultitouchEvent",function(){},"~N,~N,~N,~N,JU.P3,~N");c(c$,"bnd",function(a,b){return this.b.isBound(a,b)},"~N,~N");c(c$,"bind",function(a,b){var d=JV.ActionManager.getActionFromName(b),c=JV.binding.Binding.getMouseActionStr(a);0!=c&&(0<=d?this.b.bindAction(c,d):this.b.bindName(c,b))},"~S,~S");c(c$,"clearBindings",
function(){this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.rasmolBinding=this.dragBinding=this.pfaatBinding=null});c(c$,"unbindAction",function(a,b){if(null==a&&null==b)this.clearBindings();else{var d=JV.ActionManager.getActionFromName(b),c=JV.binding.Binding.getMouseActionStr(a);0<=d?this.b.unbindAction(c,d):0!=c&&this.b.unbindName(c,b);null==b&&this.b.unbindUserAction(a)}},"~S,~S");c$.newAction=c(c$,"newAction",function(a,b,d){JV.ActionManager.actionInfo[a]=d;JV.ActionManager.actionNames[a]=
b},"~N,~S,~S");c$.getActionName=c(c$,"getActionName",function(a){return a<JV.ActionManager.actionNames.length?JV.ActionManager.actionNames[a]:null},"~N");c$.getActionFromName=c(c$,"getActionFromName",function(a){for(var b=0;b<JV.ActionManager.actionNames.length;b++)if(JV.ActionManager.actionNames[b].equalsIgnoreCase(a))return b;return-1},"~S");c(c$,"getBindingInfo",function(a){return this.b.getBindingInfo(JV.ActionManager.actionInfo,JV.ActionManager.actionNames,a)},"~S");c(c$,"setBinding",function(a){this.b=
a},"JV.binding.Binding");c$.getPickingModeName=c(c$,"getPickingModeName",function(a){return 0>a||a>=JV.ActionManager.pickingModeNames.length?"off":JV.ActionManager.pickingModeNames[a]},"~N");c$.getPickingMode=c(c$,"getPickingMode",function(a){for(var b=JV.ActionManager.pickingModeNames.length;0<=--b;)if(a.equalsIgnoreCase(JV.ActionManager.pickingModeNames[b]))return b;return-1},"~S");c$.getPickingStyleName=c(c$,"getPickingStyleName",function(a){return 0>a||a>=JV.ActionManager.pickingStyleNames.length?
"toggle":JV.ActionManager.pickingStyleNames[a]},"~N");c$.getPickingStyleIndex=c(c$,"getPickingStyleIndex",function(a){for(var b=JV.ActionManager.pickingStyleNames.length;0<=--b;)if(a.equalsIgnoreCase(JV.ActionManager.pickingStyleNames[b]))return b;return-1},"~S");c(c$,"getAtomPickingMode",function(){return this.apm});c(c$,"setPickingMode",function(a){var b=!1;switch(a){case -1:b=!0;this.bondPickingMode=35;a=1;break;case 35:case 34:case 33:this.vwr.setBooleanProperty("bondPicking",!0);this.bondPickingMode=
a;return;case 8:this.bondPickingMode=a;if(this.vwr.getBondPicking())return;b=!0}b=(new Boolean(b|this.apm!=a)).valueOf();this.apm=a;b&&this.resetMeasurement()},"~N");c(c$,"setAtomPickingOption",function(a){switch(this.apm){case 32:this.pickAtomAssignType=a,this.isPickAtomAssignCharge=this.pickAtomAssignType.equals("Pl")||this.pickAtomAssignType.equals("Mi")}},"~S");c(c$,"setBondPickingOption",function(a){switch(this.bondPickingMode){case 33:this.pickBondAssignType=Character.toLowerCase(a.charAt(0))}},
"~S");c(c$,"getPickingState",function(){var a=";set modelkitMode "+this.vwr.getBoolean(603979883)+";set picking "+JV.ActionManager.getPickingModeName(this.apm);32==this.apm&&(a+="_"+this.pickAtomAssignType);a+=";";0!=this.bondPickingMode&&(a+="set picking "+JV.ActionManager.getPickingModeName(this.bondPickingMode));33==this.bondPickingMode&&(a+="_"+this.pickBondAssignType);return a+";"});c(c$,"getPickingStyle",function(){return this.pickingStyle});c(c$,"setPickingStyle",function(a){this.pickingStyle=
a;4<=a?(this.pickingStyleMeasure=a,this.resetMeasurement()):(3>a&&(this.rootPickingStyle=a),this.pickingStyleSelect=a);this.rubberbandSelectionMode=!1;switch(this.pickingStyleSelect){case 2:this.b.name.equals("extendedSelect")||this.setBinding(null==this.pfaatBinding?this.pfaatBinding=JV.binding.Binding.newBinding("Pfaat"):this.pfaatBinding);break;case 3:this.b.name.equals("drag")||this.setBinding(null==this.dragBinding?this.dragBinding=JV.binding.Binding.newBinding("Drag"):this.dragBinding);this.rubberbandSelectionMode=
!0;break;case 1:this.b.name.equals("selectOrToggle")||this.setBinding(null==this.rasmolBinding?this.rasmolBinding=JV.binding.Binding.newBinding("Rasmol"):this.rasmolBinding);break;default:this.b!==this.jmolBinding&&this.setBinding(this.jmolBinding)}this.b.name.equals("drag")||(this.predragBinding=this.b)},"~N");c(c$,"setGestureSwipeFactor",function(a){this.gestureSwipeFactor=a},"~N");c(c$,"setMouseDragFactor",function(a){this.mouseDragFactor=a},"~N");c(c$,"setMouseWheelFactor",function(a){this.mouseWheelFactor=
a},"~N");c(c$,"setCurrent",function(a,b,d,c){this.vwr.hoverOff();this.current.set(a,b,d,c)},"~N,~N,~N,~N");c(c$,"getCurrentX",function(){return this.current.x});c(c$,"getCurrentY",function(){return this.current.y});c(c$,"setMouseMode",function(){this.drawMode=this.labelMode=!1;this.dragSelectedMode=this.vwr.getDragSelected();this.measuresEnabled=!this.dragSelectedMode;if(!this.dragSelectedMode)switch(this.apm){default:return;case 32:this.measuresEnabled=!this.isPickAtomAssignCharge;return;case 4:this.drawMode=
!0;this.measuresEnabled=!1;break;case 2:this.labelMode=!0;this.measuresEnabled=!1;break;case 9:this.measuresEnabled=!1;break;case 19:case 22:case 20:case 21:this.measuresEnabled=!1;return}this.exitMeasurementMode(null)});c(c$,"clearMouseInfo",function(){this.pressedCount=this.clickedCount=0;this.dragGesture.setAction(0,0);this.exitMeasurementMode(null)});c(c$,"isMTClient",function(){return this.isMultiTouchClient});c(c$,"isMTServer",function(){return this.isMultiTouchServer});c(c$,"dispose",function(){this.clear()});
c(c$,"clear",function(){this.startHoverWatcher(!1);null!=this.predragBinding&&(this.b=this.predragBinding);this.vwr.setPickingMode(null,1);this.vwr.setPickingStyle(null,this.rootPickingStyle);this.isAltKeyReleased=!0});c(c$,"startHoverWatcher",function(a){if(!this.vwr.isPreviewOnly())try{a?null==this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread=new J.thread.HoverWatcherThread(this,this.current,this.moved,this.vwr)):null!=this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread.interrupt(),
this.hoverWatcherThread=null)}catch(b){if(!y(b,Exception))throw b;}},"~B");c(c$,"setModeMouse",function(a){-1==a&&this.startHoverWatcher(!1)},"~N");h(c$,"keyPressed",function(a,b){if(this.keyProcessing)return!1;this.vwr.hoverOff();this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&this.isAltKeyReleased&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1);this.isAltKeyReleased=!1;this.moved.modifiers|=8;break;case 16:this.dragged.modifiers|=1;this.moved.modifiers|=
1;break;case 17:this.moved.modifiers|=2;break;case 27:this.exitMeasurementMode("escape")}var d=8464|this.moved.modifiers;!this.labelMode&&!this.b.isUserAction(d)&&this.checkMotionRotateZoom(d,this.current.x,0,0,!1);if(this.vwr.getBoolean(603979887))switch(a){case 38:case 40:case 37:case 39:case 32:case 46:this.vwr.navigate(a,b)}this.keyProcessing=!1;return!0},"~N,~N");h(c$,"keyReleased",function(a){switch(a){case 18:this.dragSelectedMode&&this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,
-2147483648,null,!1,!1);this.isAltKeyReleased=!0;this.moved.modifiers&=-9;break;case 16:this.moved.modifiers&=-2;break;case 17:this.moved.modifiers&=-3}0==this.moved.modifiers&&this.vwr.setCursor(0);if(this.vwr.getBoolean(603979887))switch(a){case 38:case 40:case 37:case 39:this.vwr.navigate(0,0)}},"~N");h(c$,"mouseEnterExit",function(a,b,d,c){this.setCurrent(a,b,d,0);c&&this.exitMeasurementMode("mouseExit")},"~N,~N,~N,~B");c(c$,"setMouseActions",function(a,b,d){this.pressAction=JV.binding.Binding.getMouseAction(a,
b,d?5:4);this.dragAction=JV.binding.Binding.getMouseAction(a,b,1);this.clickAction=JV.binding.Binding.getMouseAction(a,b,2)},"~N,~N,~B");h(c$,"mouseAction",function(a,b,d,c,g,f){if(this.vwr.getMouseEnabled())switch(JU.Logger.debuggingHigh&&0!=a&&this.vwr.showString("mouse action: "+a+" "+f+" "+JV.binding.Binding.getMouseActionName(JV.binding.Binding.getMouseAction(g,f,a),!1),!1),a){case 0:this.setCurrent(b,d,c,f);this.moved.setCurrent(this.current,0);if(null!=this.mp||this.hoverActive){this.clickAction=
JV.binding.Binding.getMouseAction(this.clickedCount,f,0);this.checkClickAction(d,c,b,0);break}if(this.isZoomArea(d)){this.checkMotionRotateZoom(this.LEFT_DRAGGED,0,0,0,!1);break}8==this.vwr.currentCursor&&this.vwr.setCursor(0);break;case 4:this.setMouseMode();this.pressedCount=this.pressed.check(20,d,c,f,b,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.vwr.checkInMotion(1),this.setCurrent(b,d,c,f));this.pressAction=JV.binding.Binding.getMouseAction(this.pressedCount,f,4);this.vwr.setCursor(12);
this.pressed.setCurrent(this.current,1);this.dragged.setCurrent(this.current,1);this.vwr.setFocus();this.dragGesture.setAction(this.dragAction,b);this.checkPressedAction(d,c,b);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,f,!1);a=d-this.dragged.x;g=c-this.dragged.y;this.setCurrent(b,d,c,f);this.dragged.setCurrent(this.current,-1);32!=this.apm&&this.exitMeasurementMode(null);this.dragGesture.add(this.dragAction,d,c,b);this.checkDragWheelAction(this.dragAction,d,c,a,g,b,1);
break;case 5:this.setMouseActions(this.pressedCount,f,!0);this.setCurrent(b,d,c,f);this.vwr.spinXYBy(0,0,0);f=!this.pressed.check(this.xyRange,d,c,f,b,9223372036854775E3);this.checkReleaseAction(d,c,b,f);break;case 3:if(this.vwr.isApplet()&&!this.vwr.hasFocus())break;this.setCurrent(b,this.current.x,this.current.y,f);this.checkDragWheelAction(JV.binding.Binding.getMouseAction(0,f,3),this.current.x,this.current.y,0,c,b,3);break;case 2:this.setMouseMode();this.clickedCount=1<g?g:this.clicked.check(0,
0,0,f,b,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(b,d,c,f);this.setMouseActions(this.clickedCount,f,!1);this.clicked.setCurrent(this.current,this.clickedCount);this.vwr.setFocus();if(9!=this.apm&&this.bnd(JV.binding.Binding.getMouseAction(1,f,4),31))break;this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,f,2);this.checkClickAction(d,c,b,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(c$,"checkPressedAction",function(a,b,d){var c=JV.binding.Binding.getButtonMods(this.pressAction),
g=this.bnd(JV.binding.Binding.getMouseAction(1,c,4),31);if(0!=c){this.pressAction=this.vwr.notifyMouseClicked(a,b,this.pressAction,4);if(0==this.pressAction)return;c=JV.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,c,!1);JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));if(this.drawMode&&(this.bnd(this.dragAction,8)||this.bnd(this.dragAction,9))||this.labelMode&&this.bnd(this.dragAction,10))this.vwr.checkObjectDragged(-2147483648,
0,a,b,this.dragAction);else{this.checkUserAction(this.pressAction,a,b,0,0,d,4);d=!1;switch(this.apm){case 32:d=this.bnd(this.clickAction,0);break;case 28:d=this.bnd(this.dragAction,7)||this.bnd(this.dragAction,14);break;case 26:case 36:case 27:d=this.bnd(this.dragAction,7)||this.bnd(this.dragAction,27)||this.bnd(this.dragAction,14);break;case 29:d=this.bnd(this.dragAction,11)||this.bnd(this.dragAction,14);break;case 30:d=this.bnd(this.dragAction,12)||this.bnd(this.dragAction,27)||this.bnd(this.dragAction,
14)}if(d){if(this.dragAtomIndex=this.vwr.findNearestAtomIndexMovable(a,b,!0),0<=this.dragAtomIndex&&(32==this.apm||31==this.apm)&&this.vwr.isAtomAssignable(this.dragAtomIndex))this.enterMeasurementMode(this.dragAtomIndex),this.mp.addPoint(this.dragAtomIndex,null,!1)}else this.bnd(this.pressAction,23)?(g="j",this.vwr.getBoolean(603979883)&&(g=this.vwr.checkObjectClicked(a,b,this.LEFT_CLICKED),g=null!=g&&"bond".equals(g.get("type"))?"b":0<=this.vwr.findNearestAtomIndex(a,b)?"a":"m"),this.vwr.popupMenu(a,
b,g)):this.dragSelectedMode?(this.haveSelection=!0,g&&(this.haveSelection=0<=this.vwr.findNearestAtomIndexMovable(a,b,!0)),this.haveSelection&&(this.bnd(this.dragAction,13)||this.bnd(this.dragAction,14))&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1)):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(c$,"checkDragWheelAction",function(a,b,d,c,g,f,j){var h=JV.binding.Binding.getButtonMods(a);if(0!=h){h=this.vwr.notifyMouseClicked(b,d,JV.binding.Binding.getMouseAction(this.pressedCount,
h,j),j);if(0==h)return;0<h&&(a=h)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.vwr.refresh(3,"rubberBand selection");else if(!this.checkUserAction(a,b,d,c,g,f,j)){if(0<=this.vwr.getRotateBondIndex()){if(this.bnd(a,26)){this.vwr.moveSelected(c,g,-2147483648,b,d,null,!1,!1);return}this.bnd(a,25)||this.vwr.setRotateBondIndex(-1)}f=null;if(0<=this.dragAtomIndex)switch(this.apm){case 26:this.setMotion(13,!0);this.bnd(a,27)&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(c,
!0),this.getDegrees(g,!1),null):this.vwr.moveSelected(c,g,this.bnd(a,14)?-g:-2147483648,-2147483648,-2147483648,null,!0,!1);return;case 36:case 27:case 30:f=this.vwr.ms.getAtoms(3145754,JU.BSUtil.newAndSetBit(this.dragAtomIndex)),36==this.apm&&f.and(this.vwr.getAtomBitSet("ligand"));case 28:case 29:1==this.dragGesture.getPointCount()&&this.vwr.undoMoveActionClear(this.dragAtomIndex,2,!0);this.setMotion(13,!0);if(this.bnd(a,27))this.vwr.rotateSelected(this.getDegrees(c,!0),this.getDegrees(g,!1),f);
else{switch(this.apm){case 36:case 27:case 30:this.vwr.select(f,!1,0,!0)}this.vwr.moveAtomWithHydrogens(this.dragAtomIndex,c,g,this.bnd(a,14)?-g:-2147483648,f)}return}0<=this.dragAtomIndex&&1==j&&this.bnd(this.clickAction,0)&&32==this.apm?(a=this.vwr.findNearestAtomIndexMovable(b,d,!1),0<=a?(null!=this.mp?this.mp.setCount(1):this.measuresEnabled&&this.enterMeasurementMode(a),this.addToMeasurement(a,null,!0),this.mp.colix=20):null!=this.mp&&(this.mp.setCount(1),this.mp.colix=23),null!=this.mp&&(this.mp.traceX=
b,this.mp.traceY=d,this.vwr.refresh(3,"assignNew"))):!this.drawMode&&!this.labelMode&&this.bnd(a,45)?this.vwr.translateXYBy(c,g):this.dragSelectedMode&&this.haveSelection&&(this.bnd(a,13)||this.bnd(a,27))?(b=this.vwr.bsA().nextSetBit(0),0>b||(1==this.dragGesture.getPointCount()?this.vwr.undoMoveActionClear(b,2,!0):this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1),this.setMotion(13,!0),this.bnd(a,27)&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(c,
!0),this.getDegrees(g,!1),null):this.vwr.moveSelected(c,g,-2147483648,-2147483648,-2147483648,null,!0,!1))):this.drawMode&&(this.bnd(a,8)||this.bnd(a,9))||this.labelMode&&this.bnd(a,10)?(this.setMotion(13,!0),this.vwr.checkObjectDragged(this.dragged.x,this.dragged.y,b,d,a)):this.checkMotionRotateZoom(a,b,c,g,!0)?this.vwr.tm.slabEnabled&&this.checkSlideZoom(a)?this.vwr.slabDepthByPixels(g):this.vwr.zoomBy(g):this.bnd(a,25)?this.vwr.rotateXYBy(this.getDegrees(c,!0),this.getDegrees(g,!1)):this.bnd(a,
29)?0==c&&1<Math.abs(g)?(this.setMotion(8,!0),this.vwr.zoomBy(g+(0<g?-1:1))):0==g&&1<Math.abs(c)&&(this.setMotion(13,!0),this.vwr.rotateZBy(-c+(0<c?1:-1),2147483647,2147483647)):this.bnd(a,46)?this.zoomByFactor(g,2147483647,2147483647):this.bnd(a,28)?(this.setMotion(13,!0),this.vwr.rotateZBy(-c,2147483647,2147483647)):this.vwr.tm.slabEnabled&&(this.bnd(a,6)?this.vwr.depthByPixels(g):this.bnd(a,38)?this.vwr.slabByPixels(g):this.bnd(a,39)&&this.vwr.slabDepthByPixels(g))}},"~N,~N,~N,~N,~N,~N,~N");c(c$,
"checkReleaseAction",function(a,b,d,c){JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));this.vwr.checkInMotion(0);this.vwr.setInMotion(!1);this.vwr.setCursor(0);this.dragGesture.add(this.dragAction,a,b,d);c&&this.vwr.setRotateBondIndex(-2147483648);0<=this.dragAtomIndex&&(29==this.apm||30==this.apm)&&this.minimize(!0);if(32==this.apm&&this.bnd(this.clickAction,0))null==this.mp||0>this.dragAtomIndex||this.assignNew(a,b);else if(this.dragAtomIndex=-1,
this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=this.b.name.equals("drag"),this.rectRubber.x=2147483647,c&&this.vwr.notifyMouseClicked(a,b,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.drawMode&&(this.bnd(this.dragAction,8)||this.bnd(this.dragAction,9))||this.labelMode&&this.bnd(this.dragAction,10))this.vwr.checkObjectDragged(2147483647,0,a,b,this.dragAction);else if(this.dragSelectedMode&&(this.bnd(this.dragAction,13)&&this.haveSelection)&&
this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1),(!c||!this.checkUserAction(this.pressAction,a,b,0,0,d,5))&&this.vwr.getBoolean(603979780)&&this.bnd(this.dragAction,44))a=this.getExitRate(),0<a&&this.vwr.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.vwr.g.logGestures&&this.vwr.log("$NOW$ swipe "+this.dragGesture+" "+a)},"~N,~N,~N,~B");c(c$,"checkClickAction",function(a,b,d,c){if(this.vwr.haveModelSet()){if(0<c){if(this.checkUserAction(this.clickAction,
a,b,0,0,d,32768))return;this.clickAction=this.vwr.notifyMouseClicked(a,b,this.clickAction,32768);if(0==this.clickAction)return}JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.clickAction,!1));if(this.bnd(this.clickAction,2)){if(this.vwr.frankClicked(a,b)){this.vwr.popupMenu(-a,b,"j");return}if(this.vwr.frankClickedModelKit(a,b)){this.vwr.popupMenu(0,0,"m");return}}d=null;var g=!1,f=!1,j=null;this.drawMode||(j=this.vwr.checkObjectClicked(a,b,this.clickAction),null!=
j&&(g="bond".equals(j.get("type")),f="isosurface".equals(j.get("type")),d=this.getPoint(j)));g&&(c=1);if(!(null!=d&&Float.isNaN(d.x))){var h=this.findNearestAtom(a,b,d,0<c);if(0==c&&32!=this.apm)null!=this.mp&&((null!=d||0==this.mp.getIndexOf(h))&&this.mp.addPoint(h,d,!1),this.mp.haveModified&&this.vwr.setPendingMeasurement(this.mp),this.vwr.refresh(3,"measurementPending"));else if(this.setMouseMode(),this.bnd(this.clickAction,43)&&this.vwr.tm.stopMotion(),this.vwr.getBoolean(603979887)&&23==this.apm&&
this.bnd(this.clickAction,21))this.vwr.navTranslatePercent(100*a/this.vwr.getScreenWidth()-50,100*b/this.vwr.getScreenHeight()-50);else{if(g){if(this.bnd(this.clickAction,34==this.bondPickingMode||33==this.bondPickingMode?0:5)){this.bondPicked(j.get("index").intValue());return}}else{if(f)return;if(32!=this.apm&&null!=this.mp&&this.bnd(this.clickAction,20)){this.atomOrPointPicked(h,d);4==this.addToMeasurement(h,d,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,37)){null!=this.mp?
(this.addToMeasurement(h,d,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(h),this.addToMeasurement(h,d,!0));this.atomOrPointPicked(h,d);return}}this.isSelectAction(this.clickAction)?f||this.atomOrPointPicked(h,d):this.bnd(this.clickAction,24)&&0>h&&this.reset()}}}},"~N,~N,~N,~N");c(c$,"checkUserAction",function(a,b,d,c,g,f,j){if(!this.b.isUserAction(a))return!1;for(var h=!1,l,m=this.b.getBindings(),r=a+"\t",
n,q=m.keySet().iterator();q.hasNext()&&((n=q.next())||1);)if(0==n.indexOf(r)&&JU.PT.isAS(l=m.get(n))){var p=l[1],s=null;if(0<=p.indexOf("_ATOM")){var t=this.findNearestAtom(b,d,null,!0),p=JU.PT.rep(p,"_ATOM","({"+(0<=t?""+t:"")+"})");0<=t&&(p=JU.PT.rep(p,"_POINT",JU.Escape.eP(this.vwr.ms.at[t])))}if(!this.drawMode&&(0<=p.indexOf("_POINT")||0<=p.indexOf("_OBJECT")||0<=p.indexOf("_BOND"))){t=this.vwr.checkObjectClicked(b,d,a);if(null!=t&&null!=(s=t.get("pt")))t.get("type").equals("bond")&&(p=JU.PT.rep(p,
"_BOND","[{"+t.get("index")+"}]")),p=JU.PT.rep(p,"_POINT",JU.Escape.eP(s)),p=JU.PT.rep(p,"_OBJECT",JU.Escape.escapeMap(t));p=JU.PT.rep(p,"_BOND","[{}]");p=JU.PT.rep(p,"_OBJECT","{}")}p=JU.PT.rep(p,"_POINT","{}");p=JU.PT.rep(p,"_ACTION",""+a);p=JU.PT.rep(p,"_X",""+b);p=JU.PT.rep(p,"_Y",""+(this.vwr.getScreenHeight()-d));p=JU.PT.rep(p,"_DELTAX",""+c);p=JU.PT.rep(p,"_DELTAY",""+g);p=JU.PT.rep(p,"_TIME",""+f);p=JU.PT.rep(p,"_MODE",""+j);p.startsWith("+:")&&(h=!0,p=p.substring(2));this.vwr.evalStringQuiet(p)}return!h},
"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkMotionRotateZoom",function(a,b,d,c,g){b=this.checkSlideZoom(a);var f=this.bnd(a,25),j=this.bnd(a,29);if(!b&&!f&&!j)return!1;a=(d=j&&(0==d||Math.abs(c)>5*Math.abs(d)))||this.isZoomArea(this.moved.x)||this.bnd(a,46)?8:f||j?13:this.bnd(a,1)?12:0;this.setMotion(a,g);return d||b},"~N,~N,~N,~N,~B");c(c$,"getExitRate",function(){return 10<this.dragGesture.getTimeDifference(2)?0:this.dragGesture.getSpeedPixelsPerMillisecond(4,2)});c(c$,"isRubberBandSelect",function(a){a=
a&-8193|32768;return this.rubberbandSelectionMode&&(this.bnd(a,35)||this.bnd(a,34)||this.bnd(a,32))},"~N");c(c$,"getRubberBand",function(){return this.rubberbandSelectionMode&&2147483647!=this.rectRubber.x?this.rectRubber:null});c(c$,"calcRectRubberBand",function(){var a=this.vwr.antialiased?2:1;this.current.x<this.pressed.x?(this.rectRubber.x=this.current.x*a,this.rectRubber.width=(this.pressed.x-this.current.x)*a):(this.rectRubber.x=this.pressed.x*a,this.rectRubber.width=(this.current.x-this.pressed.x)*
a);this.current.y<this.pressed.y?(this.rectRubber.y=this.current.y*a,this.rectRubber.height=(this.pressed.y-this.current.y)*a):(this.rectRubber.y=this.pressed.y*a,this.rectRubber.height=(this.current.y-this.pressed.y)*a)});c(c$,"getDegrees",function(a,b){return 180*(a/Math.min(500,b?this.vwr.getScreenWidth():this.vwr.getScreenHeight()))*this.mouseDragFactor},"~N,~B");c(c$,"checkSlideZoom",function(a){return this.bnd(a,40)&&this.isZoomArea(this.pressed.x)},"~N");c(c$,"isZoomArea",function(a){return a>
98*this.vwr.getScreenWidth()*(this.vwr.isStereoDouble()?2:1)/100},"~N");c(c$,"getPoint",function(a){var b=new JU.Point3fi;b.setT(a.get("pt"));b.mi=a.get("modelIndex").intValue();return b},"java.util.Map");c(c$,"findNearestAtom",function(a,b,d,c){a=this.drawMode||null!=d?-1:this.vwr.findNearestAtomIndexMovable(a,b,!1);return 0<=a&&(c||null==this.mp)&&!this.vwr.slm.isInSelectionSubset(a)?-1:a},"~N,~N,JU.Point3fi,~B");c(c$,"isSelectAction",function(a){return this.bnd(a,17)||!this.drawMode&&!this.labelMode&&
1==this.apm&&this.bnd(a,1)||this.dragSelectedMode&&(this.bnd(this.dragAction,27)||this.bnd(this.dragAction,13))||this.bnd(a,22)||this.bnd(a,35)||this.bnd(a,32)||this.bnd(a,34)||this.bnd(a,36)||this.bnd(a,30)},"~N");c(c$,"enterMeasurementMode",function(a){this.vwr.setPicked(-1);this.vwr.setPicked(a);this.vwr.setCursor(1);this.vwr.setPendingMeasurement(this.mp=this.getMP());this.measurementQueued=this.mp},"~N");c(c$,"getMP",function(){return J.api.Interface.getInterface("JM.MeasurementPending").set(this.vwr.ms)});
c(c$,"addToMeasurement",function(a,b,d){if(-1==a&&null==b||null==this.mp)return this.exitMeasurementMode(null),0;var c=this.mp.count;-2147483648!=this.mp.traceX&&2==c&&this.mp.setCount(c=1);return 4==c&&!d?c:this.mp.addPoint(a,b,!0)},"~N,JU.Point3fi,~B");c(c$,"resetMeasurement",function(){this.exitMeasurementMode(null);this.measurementQueued=this.getMP()});c(c$,"exitMeasurementMode",function(a){null!=this.mp&&(this.vwr.setPendingMeasurement(this.mp=null),this.vwr.setCursor(0),null!=a&&this.vwr.refresh(3,
a))},"~S");c(c$,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),b=this.measurementQueued.getAtomIndex(2);if(!(0>a||0>b))try{var d=this.vwr.getSmilesOpt(null,a,b,!1,!0,!1,!1,!1);this.vwr.setStatusMeasuring("measureSequence",-2,d,0)}catch(c){if(y(c,Exception))JU.Logger.error(c.toString());else throw c;}});c(c$,"minimize",function(a){this.vwr.stopMinimization();var b=this.dragAtomIndex;a&&(this.dragAtomIndex=-1);a=0==this.vwr.getMotionFixedAtoms().cardinality()?this.vwr.ms.getAtoms(this.vwr.isAtomPDB(b)?
1087373318:1095761936,JU.BSUtil.newAndSetBit(b)):JU.BSUtil.setAll(this.vwr.getAtomCount());this.vwr.minimize(2147483647,0,a,null,0,!1,!1,!1,!1)},"~B");c(c$,"queueAtom",function(a,b){var d=this.measurementQueued.addPoint(a,b,!0);0<=a&&this.vwr.setStatusAtomPicked(a,"Atom #"+d+":"+this.vwr.getAtomInfo(a),null);return d},"~N,JU.Point3fi");c(c$,"setMotion",function(a,b){switch(this.vwr.currentCursor){case 3:break;default:this.vwr.setCursor(a)}b&&this.vwr.setInMotion(!0)},"~N,~B");c(c$,"zoomByFactor",
function(a,b,d){0!=a&&(this.setMotion(8,!0),this.vwr.zoomByFactor(Math.pow(this.mouseWheelFactor,a),b,d),this.vwr.setInMotion(!1))},"~N,~N,~N");c(c$,"runScript",function(a){this.vwr.script(a)},"~S");c(c$,"atomOrPointPicked",function(a,b){if(0>a){this.resetMeasurement();if(this.bnd(this.clickAction,33)){this.runScript("select none");return}if(5!=this.apm&&6!=this.apm)return}var d=2;switch(this.apm){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var c=8==this.apm,d=25==this.apm;if(!this.bnd(this.clickAction,
c?5:3))return;if(null==this.measurementQueued||0==this.measurementQueued.count||2<this.measurementQueued.count)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);if(2!=this.queueAtom(a,b))return;c=c||this.measurementQueued.isConnected(this.vwr.ms.at,2)?" DELETE":d?"STRUTS":"";this.runScript("connect "+this.measurementQueued.getMeasurementScript(" ",!0)+c);this.resetMeasurement();return;case 21:d++;case 20:d++;case 18:case 19:case 22:if(!this.bnd(this.clickAction,20))return;
if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>d)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);this.queueAtom(a,b);c=this.measurementQueued.count;1==c&&(this.vwr.setPicked(-1),this.vwr.setPicked(a));if(c<d)return;22==this.apm?this.getSequence():(this.vwr.setStatusMeasuring("measurePicked",d,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.apm||4==this.pickingStyleMeasure)&&this.runScript("measure "+
this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();return}c=null!=this.mp&&1!=this.apm?1:this.apm;switch(c){case 3:if(!this.bnd(this.clickAction,17))return;null==b?this.zoomTo(a):this.runScript("zoomTo "+JU.Escape.eP(b));return;case 5:case 6:this.bnd(this.clickAction,17)&&this.checkTwoAtomAction(b,a)}if(null==b){switch(c){case 1:!this.drawMode&&!this.labelMode&&this.bnd(this.clickAction,1)?this.zoomTo(a):this.bnd(this.clickAction,17)&&this.vwr.setStatusAtomPicked(a,null,
null);return;case 2:this.bnd(this.clickAction,19)&&(this.runScript("set labeltoggle {atomindex="+a+"}"),this.vwr.setStatusAtomPicked(a,null,null));return;case 31:if(this.bnd(this.clickAction,0)){var d=this.vwr.getAtomBitSet("connected(atomIndex="+a+") and !within(SMARTS,'[r50,R]')"),g=d.cardinality();switch(g){case 0:case 1:return;case 3:case 4:for(var f=D(g,0),j=D(g,0),h=0,c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1),h++)f[h]=this.vwr.getBranchBitSet(c,a,!0).cardinality(),j[h]=c;for(h=0;h<g-2;h++){for(var l=
-2147483648,m=0,c=0;c<g;c++)f[c]>=l&&d.get(j[c])&&(m=j[c],l=f[c]);d.clear(m)}}this.vwr.undoMoveActionClear(a,2,!0);this.vwr.invertSelected(null,null,a,d);this.vwr.setStatusAtomPicked(a,"inverted: "+JU.Escape.eBS(d),null)}return;case 7:this.bnd(this.clickAction,4)&&(d=JU.BSUtil.newAndSetBit(a),this.vwr.deleteAtoms(d,!1),this.vwr.setStatusAtomPicked(a,"deleted: "+JU.Escape.eBS(d),null));return}c="atomindex="+a;switch(this.apm){default:return;case 9:this.selectAtoms(c);break;case 10:this.selectAtoms("within(group, "+
c+")");break;case 11:this.selectAtoms("within(chain, "+c+")");break;case 13:this.selectAtoms("within(polymer, "+c+")");break;case 14:this.selectAtoms("within(structure, "+c+")");break;case 12:this.selectAtoms("within(molecule, "+c+")");break;case 16:this.selectAtoms("within(model, "+c+")");break;case 17:this.selectAtoms("visible and within(element, "+c+")");break;case 15:this.selectAtoms("visible and within(site, "+c+")")}this.vwr.clearClickCount();this.vwr.setStatusAtomPicked(a,null,null)}},"~N,JU.Point3fi");
c(c$,"assignNew",function(a,b){if(2==this.mp.count)this.vwr.undoMoveActionClear(-1,4146,!0),this.runScript("assign connect "+this.mp.getMeasurementScript(" ",!1));else if(this.pickAtomAssignType.equals("Xx"))this.exitMeasurementMode("bond dropped");else if(this.pressed.inRange(this.xyRange,this.dragged.x,this.dragged.y)){var d="assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'"';this.isPickAtomAssignCharge?(d+=";{atomindex="+this.dragAtomIndex+"}.label='%C'; ",this.vwr.undoMoveActionClear(this.dragAtomIndex,
4,!0)):this.vwr.undoMoveActionClear(-1,4146,!0);this.runScript(d)}else this.isPickAtomAssignCharge||(this.vwr.undoMoveActionClear(-1,4146,!0),d=this.vwr.ms.at[this.dragAtomIndex],1==d.getElementNumber()?this.runScript("assign atom ({"+this.dragAtomIndex+'}) "X"'):(d=JU.P3.new3(a,b,d.sZ),this.vwr.tm.unTransformPoint(d,d),this.runScript("assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'" '+JU.Escape.eP(d))));this.exitMeasurementMode(null)},"~N,~N");c(c$,"bondPicked",function(a){33==
this.bondPickingMode&&this.vwr.undoMoveActionClear(-1,4146,!0);switch(this.bondPickingMode){case 33:this.runScript("assign bond [{"+a+'}] "'+this.pickBondAssignType+'"');break;case 34:this.vwr.setRotateBondIndex(a);break;case 8:this.vwr.deleteBonds(JU.BSUtil.newAndSetBit(a))}},"~N");c(c$,"checkTwoAtomAction",function(a,b){var d=5==this.apm;if(this.vwr.tm.spinOn||this.vwr.tm.navOn||null!=this.vwr.getPendingMeasurement())this.resetMeasurement(),this.vwr.tm.spinOn&&this.runScript("spin off");else{2<=
this.measurementQueued.count&&this.resetMeasurement();var c=this.measurementQueued.count;if(1==c)if(null==a){if(this.measurementQueued.getAtomIndex(1)==b)return}else if(0==this.measurementQueued.getAtom(1).distance(a))return;if(0<=b||null!=a)c=this.queueAtom(b,a);2>c?d?this.vwr.scriptStatus(1==c?J.i18n.GT._("pick one more atom in order to spin the model around an axis"):J.i18n.GT._("pick two atoms in order to spin the model around an axis")):this.vwr.scriptStatus(1==c?J.i18n.GT._("pick one more atom in order to display the symmetry relationship"):
J.i18n.GT._("pick two atoms in order to display the symmetry relationship between them")):(c=this.measurementQueued.getMeasurementScript(" ",!1),d?this.runScript("spin"+c+" "+this.vwr.getInt(553648157)):this.runScript("draw symop"+c+";show symop"+c))}},"JU.Point3fi,~N");c(c$,"reset",function(){this.runScript("!reset")});c(c$,"selectAtoms",function(a){if(!(null!=this.mp||this.selectionWorking)){this.selectionWorking=!0;var b=this.rubberbandSelectionMode||this.bnd(this.clickAction,35)?"selected and not ("+
a+") or (not selected) and ":this.bnd(this.clickAction,32)?"selected and not ":this.bnd(this.clickAction,34)?"selected or ":0==this.clickAction||this.bnd(this.clickAction,36)?"selected tog ":this.bnd(this.clickAction,30)?"":null;if(null!=b)try{var d=this.vwr.getAtomBitSetEval(null,b+("("+a+")"));this.vwr.select(d,!1,0,!1);this.vwr.refresh(3,"selections set")}catch(c){if(!y(c,Exception))throw c;}this.selectionWorking=!1}},"~S");c(c$,"selectRb",function(a){var b=this.vwr.ms.findAtomsInRectangle(this.rectRubber);
0<b.length()&&(b=JU.Escape.eBS(b),this.bnd(a,34)?this.runScript("selectionHalos on;select selected or "+b):this.bnd(a,32)?this.runScript("selectionHalos on;select selected and not "+b):this.runScript("selectionHalos on;select selected tog "+b));this.vwr.refresh(3,"mouseReleased")},"~N");c(c$,"toggleMeasurement",function(){if(null!=this.mp){var a=this.mp.count;2<=a&&4>=a&&this.runScript("!measure "+this.mp.getMeasurementScript(" ",!0));this.exitMeasurementMode(null)}});c(c$,"zoomTo",function(a){this.runScript("zoomTo (atomindex="+
a+")");this.vwr.setStatusAtomPicked(a,null,null)},"~N");h(c$,"keyTyped",function(){return!1},"~N,~N");c$.$ActionManager$MotionPoint$=function(){G(self.c$);c$=t(function(){Q(this,arguments);this.time=this.y=this.x=this.index=0;s(this,arguments)},JV.ActionManager,"MotionPoint");c(c$,"set",function(a,b,d,c){this.index=a;this.x=b;this.y=d;this.time=c},"~N,~N,~N,~N");h(c$,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});c$=F()};c$.$ActionManager$Gesture$=function(){G(self.c$);
c$=t(function(){Q(this,arguments);this.action=0;this.nodes=null;this.time0=this.ptNext=0;s(this,arguments)},JV.ActionManager,"Gesture");u(c$,function(a){this.nodes=Array(a);for(var b=0;b<a;b++)this.nodes[b]=M(JV.ActionManager.MotionPoint,this,null)},"~N");c(c$,"setAction",function(a,b){this.action=a;this.ptNext=0;this.time0=b;for(var d=0;d<this.nodes.length;d++)this.nodes[d].index=-1},"~N,~N");c(c$,"add",function(a,b,d,c){this.action=a;this.getNode(this.ptNext).set(this.ptNext,b,d,c-this.time0);this.ptNext++;
return this.ptNext},"~N,~N,~N,~N");c(c$,"getTimeDifference",function(a){a=this.getPointCount2(a,0);if(2>a)return 0;var b=this.getNode(this.ptNext-1);a=this.getNode(this.ptNext-a);return b.time-a.time},"~N");c(c$,"getSpeedPixelsPerMillisecond",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b),g=360*((d.x-c.x)/this.b$["JV.ActionManager"].vwr.getScreenWidth()),f=360*((d.y-c.y)/this.b$["JV.ActionManager"].vwr.getScreenHeight());
return Math.sqrt(g*g+f*f)/(d.time-c.time)},"~N,~N");c(c$,"getDX",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b);return d.x-c.x},"~N,~N");c(c$,"getDY",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b);return d.y-c.y},"~N,~N");c(c$,"getPointCount",function(){return this.ptNext});c(c$,"getPointCount2",function(a,b){a>this.nodes.length-b&&(a=this.nodes.length-
b);for(var d=a+1;0<=--d&&!(0<=this.getNode(this.ptNext-d-b).index););return d},"~N,~N");c(c$,"getNode",function(a){return this.nodes[(a+this.nodes.length+this.nodes.length)%this.nodes.length]},"~N");h(c$,"toString",function(){return 0==this.nodes.length?""+this:JV.binding.Binding.getMouseActionName(this.action,!1)+" nPoints = "+this.ptNext+" "+this.nodes[0]});c$=F()};C(c$);c$.actionInfo=c$.prototype.actionInfo=
Array(47);c$.actionNames=c$.prototype.actionNames=Array(47);JV.ActionManager.newAction(0,"_assignNew",J.i18n.GT.o(J.i18n.GT._("assign/new atom or bond (requires {0})"),"set picking assignAtom_??/assignBond_?"));JV.ActionManager.newAction(1,"_center",J.i18n.GT._("center"));JV.ActionManager.newAction(2,"_clickFrank",J.i18n.GT._("pop up recent context menu (click on Jmol frank)"));JV.ActionManager.newAction(4,"_deleteAtom",J.i18n.GT.o(J.i18n.GT._("delete atom (requires {0})"),"set picking DELETE ATOM"));
JV.ActionManager.newAction(5,"_deleteBond",J.i18n.GT.o(J.i18n.GT._("delete bond (requires {0})"),"set picking DELETE BOND"));JV.ActionManager.newAction(6,"_depth",J.i18n.GT.o(J.i18n.GT._("adjust depth (back plane; requires {0})"),"SLAB ON"));JV.ActionManager.newAction(7,"_dragAtom",J.i18n.GT.o(J.i18n.GT._("move atom (requires {0})"),"set picking DRAGATOM"));JV.ActionManager.newAction(8,"_dragDrawObject",J.i18n.GT.o(J.i18n.GT._("move whole DRAW object (requires {0})"),"set picking DRAW"));JV.ActionManager.newAction(9,
"_dragDrawPoint",J.i18n.GT.o(J.i18n.GT._("move specific DRAW point (requires {0})"),"set picking DRAW"));JV.ActionManager.newAction(10,"_dragLabel",J.i18n.GT.o(J.i18n.GT._("move label (requires {0})"),"set picking LABEL"));JV.ActionManager.newAction(11,"_dragMinimize",J.i18n.GT.o(J.i18n.GT._("move atom and minimize molecule (requires {0})"),"set picking DRAGMINIMIZE"));JV.ActionManager.newAction(12,"_dragMinimizeMolecule",J.i18n.GT.o(J.i18n.GT._("move and minimize molecule (requires {0})"),"set picking DRAGMINIMIZEMOLECULE"));
JV.ActionManager.newAction(13,"_dragSelected",J.i18n.GT.o(J.i18n.GT._("move selected atoms (requires {0})"),"set DRAGSELECTED"));JV.ActionManager.newAction(14,"_dragZ",J.i18n.GT.o(J.i18n.GT._("drag atoms in Z direction (requires {0})"),"set DRAGSELECTED"));JV.ActionManager.newAction(15,"_multiTouchSimulation",J.i18n.GT._("simulate multi-touch using the mouse)"));JV.ActionManager.newAction(16,"_navTranslate",J.i18n.GT.o(J.i18n.GT._("translate navigation point (requires {0} and {1})"),["set NAVIGATIONMODE",
"set picking NAVIGATE"]));JV.ActionManager.newAction(17,"_pickAtom",J.i18n.GT._("pick an atom"));JV.ActionManager.newAction(3,"_pickConnect",J.i18n.GT.o(J.i18n.GT._("connect atoms (requires {0})"),"set picking CONNECT"));JV.ActionManager.newAction(18,"_pickIsosurface",J.i18n.GT.o(J.i18n.GT._("pick an ISOSURFACE point (requires {0}"),"set DRAWPICKING"));JV.ActionManager.newAction(19,"_pickLabel",J.i18n.GT.o(J.i18n.GT._("pick a label to toggle it hidden/displayed (requires {0})"),"set picking LABEL"));
JV.ActionManager.newAction(20,"_pickMeasure",J.i18n.GT.o(J.i18n.GT._("pick an atom to include it in a measurement (after starting a measurement or after {0})"),"set picking DISTANCE/ANGLE/TORSION"));JV.ActionManager.newAction(21,"_pickNavigate",J.i18n.GT.o(J.i18n.GT._("pick a point or atom to navigate to (requires {0})"),"set NAVIGATIONMODE"));JV.ActionManager.newAction(22,"_pickPoint",J.i18n.GT.o(J.i18n.GT._("pick a DRAW point (for measurements) (requires {0}"),"set DRAWPICKING"));JV.ActionManager.newAction(23,
"_popupMenu",J.i18n.GT._("pop up the full context menu"));JV.ActionManager.newAction(24,"_reset",J.i18n.GT._("reset (when clicked off the model)"));JV.ActionManager.newAction(25,"_rotate",J.i18n.GT._("rotate"));JV.ActionManager.newAction(26,"_rotateBranch",J.i18n.GT.o(J.i18n.GT._("rotate branch around bond (requires {0})"),"set picking ROTATEBOND"));JV.ActionManager.newAction(27,"_rotateSelected",J.i18n.GT.o(J.i18n.GT._("rotate selected atoms (requires {0})"),"set DRAGSELECTED"));JV.ActionManager.newAction(28,
"_rotateZ",J.i18n.GT._("rotate Z"));JV.ActionManager.newAction(29,"_rotateZorZoom",J.i18n.GT._("rotate Z (horizontal motion of mouse) or zoom (vertical motion of mouse)"));JV.ActionManager.newAction(30,"_select",J.i18n.GT.o(J.i18n.GT._("select an atom (requires {0})"),"set pickingStyle EXTENDEDSELECT"));JV.ActionManager.newAction(31,"_selectAndDrag",J.i18n.GT.o(J.i18n.GT._("select and drag atoms (requires {0})"),"set DRAGSELECTED"));JV.ActionManager.newAction(32,"_selectAndNot",J.i18n.GT.o(J.i18n.GT._("unselect this group of atoms (requires {0})"),
"set pickingStyle DRAG/EXTENDEDSELECT"));JV.ActionManager.newAction(33,"_selectNone",J.i18n.GT.o(J.i18n.GT._("select NONE (requires {0})"),"set pickingStyle EXTENDEDSELECT"));JV.ActionManager.newAction(34,"_selectOr",J.i18n.GT.o(J.i18n.GT._("add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT"));JV.ActionManager.newAction(35,"_selectToggle",J.i18n.GT.o(J.i18n.GT._("toggle selection (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT/RASMOL"));
JV.ActionManager.newAction(36,"_selectToggleOr",J.i18n.GT.o(J.i18n.GT._("if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG"));JV.ActionManager.newAction(37,"_setMeasure",J.i18n.GT._("pick an atom to initiate or conclude a measurement"));JV.ActionManager.newAction(38,"_slab",J.i18n.GT.o(J.i18n.GT._("adjust slab (front plane; requires {0})"),"SLAB ON"));JV.ActionManager.newAction(39,"_slabAndDepth",J.i18n.GT.o(J.i18n.GT._("move slab/depth window (both planes; requires {0})"),
"SLAB ON"));JV.ActionManager.newAction(40,"_slideZoom",J.i18n.GT._("zoom (along right edge of window)"));JV.ActionManager.newAction(41,"_spinDrawObjectCCW",J.i18n.GT.o(J.i18n.GT._("click on two points to spin around axis counterclockwise (requires {0})"),"set picking SPIN"));JV.ActionManager.newAction(42,"_spinDrawObjectCW",J.i18n.GT.o(J.i18n.GT._("click on two points to spin around axis clockwise (requires {0})"),"set picking SPIN"));JV.ActionManager.newAction(43,"_stopMotion",J.i18n.GT.o(J.i18n.GT._("stop motion (requires {0})"),
"set waitForMoveTo FALSE"));JV.ActionManager.newAction(44,"_swipe",J.i18n.GT._("spin model (swipe and release button and stop motion simultaneously)"));JV.ActionManager.newAction(45,"_translate",J.i18n.GT._("translate"));JV.ActionManager.newAction(46,"_wheelZoom",J.i18n.GT._("zoom"));C(c$);JV.ActionManager.pickingModeNames="off identify label center draw spin symmetry deleteatom deletebond atom group chain molecule polymer structure site model element measure distance angle torsion sequence navigate connect struts dragselected dragmolecule dragatom dragminimize dragminimizemolecule invertstereo assignatom assignbond rotatebond identifybond dragligand".$plit(" ");
C(c$,"pickingStyleNames",null);JV.ActionManager.pickingStyleNames="toggle selectOrToggle extendedSelect drag measure measureoff".$plit(" ");C(c$,"MAX_DOUBLE_CLICK_MILLIS",700,"MININUM_GESTURE_DELAY_MILLISECONDS",10,"SLIDE_ZOOM_X_PERCENT",98,"DEFAULT_MOUSE_DRAG_FACTOR",1,"DEFAULT_MOUSE_WHEEL_FACTOR",1.15,"DEFAULT_GESTURE_SWIPE_FACTOR",1)});n("JV");w(["JU.BS","J.c.ANIM"],"JV.AnimationManager",["J.api.Interface","JU.BSUtil"],function(){c$=t(function(){this.vwr=this.animationThread=null;this.animationOn=
!1;this.lastFrameDelayMs=this.firstFrameDelayMs=this.animationFps=0;this.animationFrames=this.bsDisplay=this.animationReplayMode=this.bsVisibleModels=null;this.animationPaused=this.isMovie=!1;this.morphCount=this.caf=this.cmi=0;this.currentDirection=this.animationDirection=1;this.frameStep=this.lastFrameIndex=this.firstFrameIndex=0;this.backgroundModelIndex=-1;this.firstFrameDelay=this.currentMorphModel=0;this.lastFrameDelay=1;this.intAnimThread=this.lastModelPainted=this.lastFramePainted=0;this.cai=
-1;s(this,arguments)},JV,"AnimationManager");K(c$,function(){this.bsVisibleModels=new JU.BS;this.animationReplayMode=J.c.ANIM.ONCE});u(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"setAnimationOn",function(a){a!=this.animationOn&&(!a||!this.vwr.haveModelSet()||this.vwr.isHeadless()?this.stopThread(!1):(this.vwr.tm.spinOn||this.vwr.refresh(3,"Anim:setAnimationOn"),this.setAnimationRange(-1,-1),this.resumeAnimation()))},"~B");c(c$,"stopThread",function(a){var b=!1;null!=this.animationThread&&(this.animationThread.interrupt(),
this.animationThread=null,b=!0);this.animationPaused=a;b&&!this.vwr.tm.spinOn&&this.vwr.refresh(3,"Viewer:setAnimationOff");this.animation(!1);this.vwr.setStatusFrameChanged(!1,!0)},"~B");c(c$,"setAnimationNext",function(){return this.setAnimationRelative(this.animationDirection)});c(c$,"currentIsLast",function(){return this.isMovie?this.lastFramePainted==this.caf:this.lastModelPainted==this.cmi});c(c$,"currentFrameIs",function(a){var b=this.cmi;return 0==this.morphCount?b==a:0.001>Math.abs(this.currentMorphModel-
a)},"~N");c(c$,"clear",function(){this.setMovie(null);this.initializePointers(0);this.setAnimationOn(!1);this.setModel(0,!0);this.currentDirection=1;this.cai=-1;this.setAnimationDirection(1);this.setAnimationFps(10);this.setAnimationReplayMode(J.c.ANIM.ONCE,0,0);this.initializePointers(0)});c(c$,"getModelSpecial",function(a){switch(a){case -1:a=this.firstFrameIndex;break;case 0:if(0<this.morphCount)return"-"+(1+this.currentMorphModel);a=this.cmi;break;case 1:a=this.lastFrameIndex}return this.vwr.getModelNumberDotted(a)},
"~N");c(c$,"setDisplay",function(a){this.bsDisplay=null==a||0==a.cardinality()?null:JU.BSUtil.copy(a)},"JU.BS");c(c$,"setMorphCount",function(a){this.morphCount=this.isMovie?0:a},"~N");c(c$,"morph",function(a){var b=z(a);0.001>Math.abs(b-a)?a=b:0.999<Math.abs(b-a)&&(a=b+=1);a-=b;b-=1;if(0==a)this.currentMorphModel=b,this.setModel(b,!0);else{var d;this.setModel(b,!0);d=b+1;this.currentMorphModel=b+a;d==b||(0>d||0>b)||this.vwr.ms.morphTrajectories(b,d,a)}},"~N");c(c$,"setModel",function(a,b){0>a&&this.stopThread(!1);
var d=this.cmi,c=this.vwr.ms,g=null==c?0:c.mc;if(1==g)this.cmi=a=0;else if(0>a||a>=g)a=-1;var c=null,f=!1;if(this.cmi!=a){if(0<g){var g=this.vwr.ms,j=g.isJmolDataFrameForModel(a),h=g.isJmolDataFrameForModel(this.cmi);h&&g.setJmolDataFrame(null,-1,this.cmi);-1!=this.cmi&&this.vwr.saveModelOrientation();if(h||j)c=g.getJmolFrameType(a)+" "+a+" <--  "+this.cmi+" "+g.getJmolFrameType(this.cmi),f=g.getJmolDataSourceFrame(a)==g.getJmolDataSourceFrame(this.cmi)}this.cmi=a;null!=c&&(0<=a&&this.vwr.restoreModelOrientation(a),
f&&(0<=c.indexOf("quaternion")||0>c.indexOf("plot")&&0>c.indexOf("ramachandran")&&0>c.indexOf(" property "))&&this.vwr.restoreModelRotation(d))}this.setViewer(b)},"~N,~B");c(c$,"setBackgroundModelIndex",function(a){var b=this.vwr.ms;if(null==b||0>a||a>=b.mc)a=-1;this.backgroundModelIndex=a;0<=a&&this.vwr.ms.setTrajectory(a);this.vwr.setTainted(!0);this.setFrameRangeVisible()},"~N");c(c$,"initializePointers",function(a){this.firstFrameIndex=0;this.lastFrameIndex=(0==a?0:this.getFrameCount())-1;this.frameStep=
a;this.vwr.setFrameVariables()},"~N");c(c$,"setAnimationDirection",function(a){this.animationDirection=a},"~N");c(c$,"setAnimationFps",function(a){1>a&&(a=1);50<a&&(a=50);this.animationFps=a;this.vwr.setFrameVariables()},"~N");c(c$,"setAnimationReplayMode",function(a,b,d){this.firstFrameDelay=0<b?b:0;this.firstFrameDelayMs=z(1E3*this.firstFrameDelay);this.lastFrameDelay=0<d?d:0;this.lastFrameDelayMs=z(1E3*this.lastFrameDelay);this.animationReplayMode=a;this.vwr.setFrameVariables()},"J.c.ANIM,~N,~N");
c(c$,"setAnimationRange",function(a,b){var d=this.getFrameCount();0>a&&(a=0);0>b&&(b=d);a>=d&&(a=d-1);b>=d&&(b=d-1);this.currentMorphModel=this.firstFrameIndex=a;this.lastFrameIndex=b;this.frameStep=b<a?-1:1;this.rewindAnimation()},"~N,~N");c(c$,"pauseAnimation",function(){this.stopThread(!0)});c(c$,"reverseAnimation",function(){this.currentDirection=-this.currentDirection;this.animationOn||this.resumeAnimation()});c(c$,"repaintDone",function(){this.lastModelPainted=this.cmi;this.lastFramePainted=
this.caf});c(c$,"resumeAnimation",function(){0>this.cmi&&this.setAnimationRange(this.firstFrameIndex,this.lastFrameIndex);1>=this.getFrameCount()?this.animation(!1):(this.animation(!0),this.animationPaused=!1,null==this.animationThread&&(this.intAnimThread++,this.animationThread=J.api.Interface.getOption("thread.AnimationThread"),this.animationThread.setManager(this,this.vwr,[this.firstFrameIndex,this.lastFrameIndex,this.intAnimThread]),this.animationThread.start()))});c(c$,"setAnimationLast",function(){this.setFrame(0<
this.animationDirection?this.lastFrameIndex:this.firstFrameIndex)});c(c$,"rewindAnimation",function(){this.setFrame(0<this.animationDirection?this.firstFrameIndex:this.lastFrameIndex);this.currentDirection=1;this.vwr.setFrameVariables()});c(c$,"setAnimationPrevious",function(){return this.setAnimationRelative(-this.animationDirection)});c(c$,"getAnimRunTimeSeconds",function(){var a=this.getFrameCount();if(this.firstFrameIndex==this.lastFrameIndex||0>this.lastFrameIndex||0>this.firstFrameIndex||this.lastFrameIndex>=
a||this.firstFrameIndex>=a)return 0;for(var b=Math.min(this.firstFrameIndex,this.lastFrameIndex),a=Math.max(this.firstFrameIndex,this.lastFrameIndex),d=1*(a-b)/this.animationFps+this.firstFrameDelay+this.lastFrameDelay;b<=a;b++)d+=this.vwr.getFrameDelayMs(this.modelIndexForFrame(b))/1E3;return d});c(c$,"setMovie",function(a){if(this.isMovie=null!=a&&null==a.get("scripts")){this.animationFrames=a.get("frames");if(null==this.animationFrames||0==this.animationFrames.length)this.isMovie=!1;else if(this.caf=
a.get("currentFrame").intValue(),0>this.caf||this.caf>=this.animationFrames.length)this.caf=0;this.setFrame(this.caf)}this.isMovie||(this.animationFrames=null);this.vwr.setBooleanProperty("_ismovie",this.isMovie);this.bsDisplay=null;this.currentMorphModel=this.morphCount=0},"java.util.Map");c(c$,"getAnimationFrames",function(){return this.animationFrames});c(c$,"getCurrentFrameIndex",function(){return this.caf});c(c$,"modelIndexForFrame",function(a){return this.isMovie?this.animationFrames[a]-1:a},
"~N");c(c$,"getFrameCount",function(){return this.isMovie?this.animationFrames.length:this.vwr.getModelCount()});c(c$,"setFrame",function(a){try{if(this.isMovie){var b=this.modelIndexForFrame(a);this.caf=a;a=b}else this.caf=a;this.setModel(a,!0)}catch(d){if(!y(d,Exception))throw d;}},"~N");c(c$,"setViewer",function(a){this.vwr.ms.setTrajectory(this.cmi);this.vwr.tm.setFrameOffset(this.cmi);-1==this.cmi&&a&&this.setBackgroundModelIndex(-1);this.vwr.setTainted(!0);this.setFrameRangeVisible();this.vwr.setStatusFrameChanged(!1,
!0);null!=this.vwr.ms&&!this.vwr.g.selectAllModels&&this.vwr.setSelectionSubset(this.vwr.getModelUndeletedAtomsBitSet(this.cmi))},"~B");c(c$,"setFrameRangeVisible",function(){this.bsVisibleModels.clearAll();0<=this.backgroundModelIndex&&this.bsVisibleModels.set(this.backgroundModelIndex);if(0<=this.cmi)this.bsVisibleModels.set(this.cmi);else if(0!=this.frameStep){for(var a=0,b=0,d=this.firstFrameIndex;d!=this.lastFrameIndex;d+=this.frameStep){var c=this.modelIndexForFrame(d);this.vwr.ms.isJmolDataFrameForModel(c)||
(this.bsVisibleModels.set(c),a++,b=d)}c=this.modelIndexForFrame(this.lastFrameIndex);if(this.firstFrameIndex==this.lastFrameIndex||!this.vwr.ms.isJmolDataFrameForModel(c)||0==a)this.bsVisibleModels.set(c),0==a&&(this.firstFrameIndex=this.lastFrameIndex),a=0;1==a&&0>this.cmi&&this.setFrame(b)}});c(c$,"animation",function(a){this.animationOn=a;this.vwr.setBooleanProperty("_animating",a)},"~B");c(c$,"setAnimationRelative",function(a){a=this.getFrameStep(a);var b=(this.isMovie?this.caf:this.cmi)+a,d=
0,c=0,g;0<this.morphCount?(d=1/(this.morphCount+1),c=this.currentMorphModel+a*d,g=this.isNotInRange(c)):g=this.isNotInRange(b);if(g)switch(this.animationReplayMode){case J.c.ANIM.ONCE:return!1;case J.c.ANIM.LOOP:c=b=this.animationDirection==this.currentDirection?this.firstFrameIndex:this.lastFrameIndex;break;case J.c.ANIM.PALINDROME:this.currentDirection=-this.currentDirection,b-=2*a,c-=2*a*d}if(1>this.morphCount){if(0>b||b>=this.getFrameCount())return!1;this.setFrame(b);return!0}this.morph(c+1);
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b){a=a.$replace("\\","/");var d=a.indexOf("|");0<=d&&(a=a.substring(0,d));d=null;(d=Jmol.Cache.get(a))||(d=this.cache.get(a));return b&&p(d,String)?null:d},"~S,~B");c(c$,"cacheClear",function(){JU.Logger.info("cache cleared");this.cache.clear();this.clearPngjCache(null)});c(c$,"cacheFileByNameAdd",function(a,b){if(null==a||!b&&a.equalsIgnoreCase(""))return this.cacheClear(),-1;var d;if(b){a=this.vwr.resolveDatabaseFormat(a);d=this.getFileAsBytes(a,null,!0);if(p(d,String))return 0;this.cachePut(a,
d)}else{if(a.endsWith("*"))return JU.AU.removeMapKeys(this.cache,a.substring(0,a.length-1));d=this.cache.remove(a.$replace("\\","/"))}return null==d?0:(p(d,String),d.length)},"~S,~B");c(c$,"cacheList",function(){for(var a=new java.util.Hashtable,b,d=this.cache.entrySet().iterator();d.hasNext()&&((b=d.next())||1);)a.put(b.getKey(),Integer.$valueOf(JU.PT.isAB(b.getValue())?b.getValue().length:b.getValue().toString().length));return a});c(c$,"getCanonicalName",function(a){var b=this.getClassifiedName(a,
!0);return null==b?a:b[2]},"~S");h(c$,"postByteArray",function(a,b){var d=this.getBufferedInputStreamOrErrorMessageFromName(a,null,!1,!1,b,!1,!0);if(p(d,String))return d;try{d=JU.Rdr.getStreamAsBytes(d,null)}catch(c){if(y(c,java.io.IOException))try{d.close()}catch(g){if(!y(g,java.io.IOException))throw g;}else throw c;}return null==d?"":JU.Rdr.fixUTF(d)},"~S,~A");C(c$,"SIMULATION_PROTOCOL","http://SIMULATION/","URL_LOCAL",4,"urlPrefixes",["http:","https:","sftp:","ftp:","file:"]);c$.scriptFilePrefixes=
c$.prototype.scriptFilePrefixes=['/*file*/"','FILE0="','FILE1="']});n("JV");w(["java.util.Hashtable","JU.P3","J.c.AXES","$.CBK"],"JV.GlobalSettings","java.lang.Boolean $.Float JU.BS $.DF $.Lst $.PT $.SB J.c.STR JS.SV JU.BSUtil $.Escape $.Logger $.Txt JV.JC $.StateManager $.Viewer".split(" "),function(){c$=t(function(){this.databases=this.htUserVariables=this.htPropertyFlagsRemoved=this.htBooleanParameterFlags=this.htNonbooleanParameterValues=this.vwr=null;this.ambientPercent=45;this.diffusePercent=
84;this.specular=!0;this.specularExponent=6;this.phongExponent=64;this.specularPercent=22;this.specularPower=40;this.zDepth=0;this.zShadePower=3;this.zSlab=50;this.slabByAtom=this.slabByMolecule=!1;this.appendNew=this.allowEmbeddedScripts=!0;this.appletProxy="";this.applySymmetryToBonds=!1;this.atomTypes="";this.autoBond=!0;this.axesOrientationRasmol=!1;this.bondRadiusMilliAngstroms=150;this.bondTolerance=0.45;this.defaultDirectory="";this.defaultStructureDSSP=!0;this.ptDefaultLattice=null;this.defaultLoadFilter=
this.defaultLoadScript="";this.defaultDropScript="zap; load SYNC \"%FILE\";if (%ALLOWCARTOONS && _loadScript == '' && defaultLoadScript == '' && _filetype == 'Pdb') {if ({(protein or nucleic)&*/1.1} && {*/1.1}[1].groupindex != {*/1.1}[0].groupindex){select protein or nucleic;cartoons only;}if ({visible}){color structure}else{wireframe -0.1};if (!{visible}){spacefill 23%};select *}";this.forceAutoBond=!1;this.fractionalRelative=!0;this.inlineNewlineChar="|";this.pubChemFormat=this.nihResolverFormat=
this.smilesUrlFormat=this.nmrPredictFormat=this.nmrUrlFormat=this.loadLigandFormat=this.loadFormat=null;this.edsUrlFormat="http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";this.edsUrlCutoff="http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat";this.edsUrlOptions="within 2.0 {*}";this.minBondDistance=0.4;this.minPixelSelRadius=6;this.pdbSequential=this.pdbGetHeader=this.pdbAddHydrogens=!1;this.percentVdwAtom=23;this.smallMoleculeMaxAtoms=4E4;this.smartAromatic=!0;this.allowMoveAtoms=this.allowRotateSelected=
this.legacyHAddition=this.legacyAutoBonding=this.zeroBasedXyzRasmol=!1;this.defaultPerspectiveDepth=!0;this.visualRange=5;this.solventOn=!1;this.defaultTorsionLabel=this.defaultDistanceLabel=this.defaultAngleLabel="%VALUE %UNITS";this.measureAllModels=this.justifyMeasurements=!1;this.minimizationSteps=100;this.minimizationRefresh=!0;this.minimizationSilent=!1;this.minimizationCriterion=0.001;this.antialiasDisplay=!1;this.displayCellParameters=this.antialiasTranslucent=this.imageState=this.antialiasImages=
!0;this.dotsSelectedOnly=!1;this.dotSurface=!0;this.dotDensity=3;this.meshScale=this.dotScale=1;this.isosurfaceKey=this.greyscaleRendering=!1;this.isosurfacePropertySmoothing=!0;this.isosurfacePropertySmoothingPower=7;this.platformSpeed=10;this.repaintWaitMs=1E3;this.showHiddenSelectionHalos=!1;this.showMeasurements=this.showKeyStrokes=!0;this.showTiming=!1;this.zoomLarge=!0;this.zoomHeight=!1;this.backgroundImageFileName=null;this.hbondsBackbone=this.bondModeOr=this.partialDots=!1;this.hbondsAngleMinimum=
90;this.hbondsDistanceMaximum=3.25;this.hbondsRasmol=!0;this.hbondsSolid=!1;this.modeMultipleBond=2;this.showMultipleBonds=this.showHydrogens=!0;this.ssbondsBackbone=!1;this.multipleBondSpacing=-1;this.multipleBondRadiusFactor=0;this.chainCaseSensitive=this.cartoonRibose=this.cartoonLadders=this.cartoonFancy=this.backboneSteps=this.cartoonRockets=this.cartoonBaseEdges=!1;this.hermiteLevel=0;this.rangeSelected=this.highResolutionFlag=!1;this.rasmolHeteroSetting=this.rasmolHydrogenSetting=!0;this.ribbonAspectRatio=
16;this.rocketBarrels=this.ribbonBorder=!1;this.sheetSmoothing=1;this.translucent=this.traceAlpha=!0;this.allowGestures=this.twistedSheets=!1;this.allowMultiTouch=this.allowModelkit=!0;this.allowKeyStrokes=!1;this.animationFps=10;this.atomPicking=!0;this.autoFps=!1;this.axesMode=null;this.axesScale=2;this.starWidth=0.05;this.bondPicking=!1;this.defaultCameraDepth=3;this.celShading=!1;this.celShadingPower=10;this.dataSeparator="~~~";this.debugScript=!1;this.defaultDrawArrowScale=0.5;this.defaultLabelXYZ=
"%a";this.defaultLabelPDB="%m%r";this.defaultTranslucent=0.5;this.delayMaximumMs=0;this.dipoleScale=1;this.drawFontSize=14;this.drawPicking=this.drawHover=this.dragSelected=this.disablePopupMenu=!1;this.dsspCalcHydrogen=!0;this.energyUnits="kJ";this.exportScale=1;this.helpPath="http://chemapps.stolaf.edu/jmol/docs/index.htm";this.fontScaling=!1;this.fontCaching=!0;this.forceField="MMFF";this.helixStep=1;this.hideNameInPopup=!1;this.hoverDelayMs=500;this.loadAtomDataTolerance=0.01;this.logGestures=
this.logCommands=!1;this.measureDistanceUnits="nanometers";this.measurementLabels=!0;this.monitorEnergy=this.messageStyleChime=!1;this.modulationScale=1;this.multiProcessor=!0;this.particleRadius=20;this.pickingSpinRate=10;this.pickLabel="";this.pointGroupDistanceTolerance=0.2;this.pointGroupLinearTolerance=8;this.preserveState=!0;this.propertyColorScheme="roygb";this.quaternionFrame="p";this.showUnitCellInfo=this.showUnitCellDetails=this.saveProteinStructureState=!0;this.solventProbeRadius=1.2;this.scriptDelay=
0;this.statusReporting=this.selectAllModels=!0;this.strandCountForStrands=5;this.strandCountForMeshRibbon=7;this.strutSpacing=6;this.strutLengthMaximum=7;this.strutDefaultRadius=0.3;this.strutsMultiple=!1;this.waitForMoveTo=this.useScriptQueue=this.useNumberLocalization=this.useMinimizationThread=!0;this.vectorScale=1;this.vectorsCentered=this.vectorSymmetry=!1;this.vibrationScale=this.vibrationPeriod=1;this.navigationPeriodic=this.navigationMode=this.hideNavigationPoint=this.wireframeRotation=!1;
this.navigationSpeed=5;this.showNavigationPointAlways=!1;this.stereoState=null;this.modelKitMode=!1;this.objMad=this.objStateOn=this.objColors=null;this.ellipsoidFill=this.ellipsoidArrows=this.ellipsoidArcs=this.ellipsoidDots=this.ellipsoidAxes=!1;this.ellipsoidBall=!0;this.ellipsoidDotCount=200;this.ellipsoidAxisDiameter=0.02;this.testFlag4=this.testFlag3=this.testFlag2=this.testFlag1=!1;this.structureList=null;this.haveSetStructureList=!1;this.userDatabases=null;this.bondingVersion=0;s(this,arguments)},
JV,"GlobalSettings");K(c$,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.axesMode=J.c.AXES.BOUNDBOX;this.objColors=D(8,0);this.objStateOn=ca(8,!1);this.objMad=D(8,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,[30,90,-15,95]);this.structureList.put(J.c.STR.SHEET,[-180,-10,70,180,-180,-45,-180,-130,140,180,90,180]);this.structureList.put(J.c.STR.HELIX,[-160,0,-100,45])});u(c$,function(a,b,d){this.vwr=a;this.registerAllValues(b,
d)},"JV.Viewer,JV.GlobalSettings,~B");c(c$,"clear",function(){for(var a=this.htUserVariables.keySet().iterator();a.hasNext();){var b=a.next();("@"==b.charAt(0)||b.startsWith("site_"))&&a.remove()}this.setPicked(-1);this.setI("_atomhovered",-1);this.setO("_pickinfo","");this.setB("selectionhalos",!1);this.setB("hidenotselected",!1);this.setB("measurementlabels",this.measurementLabels=!0);this.setB("drawHover",this.drawHover=!1);this.vwr.stm.saveScene("DELETE",null)});c(c$,"registerAllValues",function(a,
b){this.htNonbooleanParameterValues=new java.util.Hashtable;this.htBooleanParameterFlags=new java.util.Hashtable;this.htPropertyFlagsRemoved=new java.util.Hashtable;null!=a&&(b||(this.htUserVariables=a.htUserVariables),this.debugScript=a.debugScript,this.disablePopupMenu=a.disablePopupMenu,this.messageStyleChime=a.messageStyleChime,this.defaultDirectory=a.defaultDirectory,this.allowGestures=a.allowGestures,this.allowModelkit=a.allowModelkit,this.allowMultiTouch=a.allowMultiTouch,this.allowKeyStrokes=
a.allowKeyStrokes,this.legacyAutoBonding=a.legacyAutoBonding,this.legacyHAddition=a.legacyHAddition,this.bondingVersion=a.bondingVersion,this.platformSpeed=a.platformSpeed,this.useScriptQueue=a.useScriptQueue,this.databases=a.databases,this.showTiming=a.showTiming,this.wireframeRotation=a.wireframeRotation,this.testFlag1=a.testFlag1,this.testFlag2=a.testFlag2,this.testFlag3=a.testFlag3,this.testFlag4=a.testFlag4);null==this.databases&&(this.databases=new java.util.Hashtable,this.getDataBaseList(JV.JC.databases),
this.getDataBaseList(this.userDatabases));this.loadFormat=this.databases.get("pdb");this.loadLigandFormat=this.databases.get("ligand");this.nmrUrlFormat=this.databases.get("nmr");this.nmrPredictFormat=this.databases.get("nmrdb");this.smilesUrlFormat=this.databases.get("nci")+"/file?format=sdf&get3d=True";this.nihResolverFormat=this.databases.get("nci");this.pubChemFormat=this.databases.get("pubchem");for(var d,c=0,g=J.c.CBK.values();c<g.length&&((d=g[c])||1);c++)this.resetValue(d.name()+"Callback",
a);this.setI("historyLevel",0);this.setI("depth",0);this.setF("gestureSwipeFactor",1);this.setB("hideNotSelected",!1);this.setO("hoverLabel","");this.setB("isKiosk",this.vwr.isKiosk());this.setO("logFile",this.vwr.getLogFileName());this.setI("logLevel",JU.Logger.getLogLevel());this.setF("mouseWheelFactor",1.15);this.setF("mouseDragFactor",1);this.setI("navFps",10);this.setI("navigationDepth",0);this.setI("navigationSlab",0);this.setI("navX",0);this.setI("navY",0);this.setI("navZ",0);this.setO("pathForAllFiles",
"");this.setI("perspectiveModel",11);this.setO("picking","identify");this.setO("pickingStyle","toggle");this.setB("refreshing",!0);this.setI("rotationRadius",0);this.setI("scaleAngstromsPerInch",0);this.setI("scriptReportingLevel",0);this.setB("selectionHalos",!1);this.setB("showaxes",!1);this.setB("showboundbox",!1);this.setB("showfrank",!1);this.setB("showUnitcell",!1);this.setI("slab",100);this.setB("slabEnabled",!1);this.setF("slabrange",0);this.setI("spinX",0);this.setI("spinY",30);this.setI("spinZ",
0);this.setI("spinFps",30);this.setI("stereoDegrees",-5);this.setI("stateversion",0);this.setB("syncScript",this.vwr.getStatusManager().syncingScripts);this.setB("syncMouse",this.vwr.getStatusManager().syncingMouse);this.setB("syncStereo",this.vwr.getStatusManager().stereoSync);this.setB("windowCentered",!0);this.setB("zoomEnabled",!0);this.setI("zDepth",0);this.setB("zShade",!1);this.setI("zSlab",50);this.setI("_version",JV.JC.versionInt);this.setB("axesWindow",!0);this.setB("axesMolecular",!1);
this.setB("axesPosition",!1);this.setB("axesUnitcell",!1);this.setI("backgroundModel",0);this.setB("colorRasmol",!1);this.setO("currentLocalPath","");this.setO("defaultLattice","{0 0 0}");this.setO("defaultColorScheme","Jmol");this.setO("defaultDirectoryLocal","");this.setO("defaults","Jmol");this.setO("defaultVDW","Jmol");this.setO("exportDrivers","Idtf;Maya;Povray;Vrml;X3d;Tachyon;Obj");this.setI("propertyAtomNumberColumnCount",0);this.setI("propertyAtomNumberField",0);this.setI("propertyDataColumnCount",
0);this.setI("propertyDataField",0);this.setB("undo",!0);this.setB("allowEmbeddedScripts",this.allowEmbeddedScripts);this.setB("allowGestures",this.allowGestures);this.setB("allowKeyStrokes",this.allowKeyStrokes);this.setB("allowModelkit",this.allowModelkit);this.setB("allowMultiTouch",this.allowMultiTouch);this.setB("allowRotateSelected",this.allowRotateSelected);this.setB("allowMoveAtoms",this.allowMoveAtoms);this.setI("ambientPercent",this.ambientPercent);this.setI("animationFps",this.animationFps);
this.setB("antialiasImages",this.antialiasImages);this.setB("antialiasDisplay",this.antialiasDisplay);this.setB("antialiasTranslucent",this.antialiasTranslucent);this.setB("appendNew",this.appendNew);this.setO("appletProxy",this.appletProxy);this.setB("applySymmetryToBonds",this.applySymmetryToBonds);this.setB("atomPicking",this.atomPicking);this.setO("atomTypes",this.atomTypes);this.setB("autoBond",this.autoBond);this.setB("autoFps",this.autoFps);this.setI("axesMode",this.axesMode.getCode());this.setF("axesScale",
this.axesScale);this.setB("axesOrientationRasmol",this.axesOrientationRasmol);this.setB("backboneSteps",this.backboneSteps);this.setB("bondModeOr",this.bondModeOr);this.setB("bondPicking",this.bondPicking);this.setI("bondRadiusMilliAngstroms",this.bondRadiusMilliAngstroms);this.setF("bondTolerance",this.bondTolerance);this.setF("cameraDepth",this.defaultCameraDepth);this.setB("cartoonBaseEdges",this.cartoonBaseEdges);this.setB("cartoonFancy",this.cartoonFancy);this.setB("cartoonLadders",this.cartoonLadders);
this.setB("cartoonLadders",this.cartoonRibose);this.setB("cartoonRockets",this.cartoonRockets);this.setB("chainCaseSensitive",this.chainCaseSensitive);this.setB("celShading",this.celShading);this.setI("celShadingPower",this.celShadingPower);this.setI("bondingVersion",this.bondingVersion);this.setO("dataSeparator",this.dataSeparator);this.setB("debugScript",this.debugScript);this.setO("defaultAngleLabel",this.defaultAngleLabel);this.setF("defaultDrawArrowScale",this.defaultDrawArrowScale);this.setO("defaultDirectory",
this.defaultDirectory);this.setO("defaultDistanceLabel",this.defaultDistanceLabel);this.setO("defaultDropScript",this.defaultDropScript);this.setO("defaultLabelPDB",this.defaultLabelPDB);this.setO("defaultLabelXYZ",this.defaultLabelXYZ);this.setO("defaultLoadFilter",this.defaultLoadFilter);this.setO("defaultLoadScript",this.defaultLoadScript);this.setB("defaultStructureDSSP",this.defaultStructureDSSP);this.setO("defaultTorsionLabel",this.defaultTorsionLabel);this.setF("defaultTranslucent",this.defaultTranslucent);
this.setI("delayMaximumMs",this.delayMaximumMs);this.setI("diffusePercent",this.diffusePercent);this.setF("dipoleScale",this.dipoleScale);this.setB("disablePopupMenu",this.disablePopupMenu);this.setB("displayCellParameters",this.displayCellParameters);this.setI("dotDensity",this.dotDensity);this.setI("dotScale",this.dotScale);this.setB("dotsSelectedOnly",this.dotsSelectedOnly);this.setB("dotSurface",this.dotSurface);this.setB("dragSelected",this.dragSelected);this.setB("drawHover",this.drawHover);
this.setF("drawFontSize",this.drawFontSize);this.setB("drawPicking",this.drawPicking);this.setB("dsspCalculateHydrogenAlways",this.dsspCalcHydrogen);this.setO("edsUrlFormat",this.edsUrlFormat);this.setO("edsUrlCutoff",this.edsUrlCutoff);this.setB("ellipsoidArcs",this.ellipsoidArcs);this.setB("ellipsoidArrows",this.ellipsoidArrows);this.setB("ellipsoidAxes",this.ellipsoidAxes);this.setF("ellipsoidAxisDiameter",this.ellipsoidAxisDiameter);this.setB("ellipsoidBall",this.ellipsoidBall);this.setI("ellipsoidDotCount",
this.ellipsoidDotCount);this.setB("ellipsoidDots",this.ellipsoidDots);this.setB("ellipsoidFill",this.ellipsoidFill);this.setO("energyUnits",this.energyUnits);this.setF("exportScale",this.exportScale);this.setB("fontScaling",this.fontScaling);this.setB("fontCaching",this.fontCaching);this.setB("forceAutoBond",this.forceAutoBond);this.setO("forceField",this.forceField);this.setB("fractionalRelative",this.fractionalRelative);this.setF("particleRadius",this.particleRadius);this.setB("greyscaleRendering",
this.greyscaleRendering);this.setF("hbondsAngleMinimum",this.hbondsAngleMinimum);this.setF("hbondsDistanceMaximum",this.hbondsDistanceMaximum);this.setB("hbondsBackbone",this.hbondsBackbone);this.setB("hbondsRasmol",this.hbondsRasmol);this.setB("hbondsSolid",this.hbondsSolid);this.setI("helixStep",this.helixStep);this.setO("helpPath",this.helpPath);this.setI("hermiteLevel",this.hermiteLevel);this.setB("hideNameInPopup",this.hideNameInPopup);this.setB("hideNavigationPoint",this.hideNavigationPoint);
this.setB("highResolution",this.highResolutionFlag);this.setF("hoverDelay",this.hoverDelayMs/1E3);this.setB("imageState",this.imageState);this.setB("isosurfaceKey",this.isosurfaceKey);this.setB("isosurfacePropertySmoothing",this.isosurfacePropertySmoothing);this.setI("isosurfacePropertySmoothingPower",this.isosurfacePropertySmoothingPower);this.setB("justifyMeasurements",this.justifyMeasurements);this.setB("legacyAutoBonding",this.legacyAutoBonding);this.setB("legacyHAddition",this.legacyHAddition);
this.setF("loadAtomDataTolerance",this.loadAtomDataTolerance);this.setO("loadFormat",this.loadFormat);this.setO("loadLigandFormat",this.loadLigandFormat);this.setB("logCommands",this.logCommands);this.setB("logGestures",this.logGestures);this.setB("measureAllModels",this.measureAllModels);this.setB("measurementLabels",this.measurementLabels);this.setO("measurementUnits",this.measureDistanceUnits);this.setI("meshScale",this.meshScale);this.setB("messageStyleChime",this.messageStyleChime);this.setF("minBondDistance",
this.minBondDistance);this.setI("minPixelSelRadius",this.minPixelSelRadius);this.setI("minimizationSteps",this.minimizationSteps);this.setB("minimizationRefresh",this.minimizationRefresh);this.setB("minimizationSilent",this.minimizationSilent);this.setF("minimizationCriterion",this.minimizationCriterion);this.setB("modelKitMode",this.modelKitMode);this.setF("modulationScale",this.modulationScale);this.setB("monitorEnergy",this.monitorEnergy);this.setF("multipleBondRadiusFactor",this.multipleBondRadiusFactor);
this.setF("multipleBondSpacing",this.multipleBondSpacing);this.setB("multiProcessor",this.multiProcessor&&1<JV.Viewer.nProcessors);this.setB("navigationMode",this.navigationMode);this.setB("navigationPeriodic",this.navigationPeriodic);this.setF("navigationSpeed",this.navigationSpeed);this.setO("nmrPredictFormat",this.nmrPredictFormat);this.setO("nmrUrlFormat",this.nmrUrlFormat);this.setB("partialDots",this.partialDots);this.setB("pdbAddHydrogens",this.pdbAddHydrogens);this.setB("pdbGetHeader",this.pdbGetHeader);
this.setB("pdbSequential",this.pdbSequential);this.setB("perspectiveDepth",this.defaultPerspectiveDepth);this.setI("percentVdwAtom",this.percentVdwAtom);this.setI("phongExponent",this.phongExponent);this.setI("pickingSpinRate",this.pickingSpinRate);this.setO("pickLabel",this.pickLabel);this.setI("platformSpeed",this.platformSpeed);this.setF("pointGroupLinearTolerance",this.pointGroupLinearTolerance);this.setF("pointGroupDistanceTolerance",this.pointGroupDistanceTolerance);this.setB("preserveState",
this.preserveState);this.setO("propertyColorScheme",this.propertyColorScheme);this.setO("quaternionFrame",this.quaternionFrame);this.setB("rangeSelected",this.rangeSelected);this.setI("repaintWaitMs",this.repaintWaitMs);this.setI("ribbonAspectRatio",this.ribbonAspectRatio);this.setB("ribbonBorder",this.ribbonBorder);this.setB("rocketBarrels",this.rocketBarrels);this.setB("saveProteinStructureState",this.saveProteinStructureState);this.setB("scriptqueue",this.useScriptQueue);this.setB("selectAllModels",
this.selectAllModels);this.setB("selectHetero",this.rasmolHeteroSetting);this.setB("selectHydrogen",this.rasmolHydrogenSetting);this.setF("sheetSmoothing",this.sheetSmoothing);this.setB("showHiddenSelectionHalos",this.showHiddenSelectionHalos);this.setB("showHydrogens",this.showHydrogens);this.setB("showKeyStrokes",this.showKeyStrokes);this.setB("showMeasurements",this.showMeasurements);this.setB("showMultipleBonds",this.showMultipleBonds);this.setB("showNavigationPointAlways",this.showNavigationPointAlways);
this.setI("showScript",this.scriptDelay);this.setB("showtiming",this.showTiming);this.setB("slabByMolecule",this.slabByMolecule);this.setB("slabByAtom",this.slabByAtom);this.setB("smartAromatic",this.smartAromatic);this.setI("smallMoleculeMaxAtoms",this.smallMoleculeMaxAtoms);this.setO("smilesUrlFormat",this.smilesUrlFormat);this.setO("nihResolverFormat",this.nihResolverFormat);this.setO("pubChemFormat",this.pubChemFormat);this.setB("showUnitCellDetails",this.showUnitCellDetails);this.setB("showUnitCellInfo",
this.showUnitCellInfo);this.setB("solventProbe",this.solventOn);this.setF("solventProbeRadius",this.solventProbeRadius);this.setB("specular",this.specular);this.setI("specularExponent",this.specularExponent);this.setI("specularPercent",this.specularPercent);this.setI("specularPower",this.specularPower);this.setB("ssbondsBackbone",this.ssbondsBackbone);this.setF("starWidth",this.starWidth);this.setB("statusReporting",this.statusReporting);this.setI("strandCount",this.strandCountForStrands);this.setI("strandCountForStrands",
this.strandCountForStrands);this.setI("strandCountForMeshRibbon",this.strandCountForMeshRibbon);this.setF("strutDefaultRadius",this.strutDefaultRadius);this.setF("strutLengthMaximum",this.strutLengthMaximum);this.setI("strutSpacing",this.strutSpacing);this.setB("strutsMultiple",this.strutsMultiple);this.setB("testFlag1",this.testFlag1);this.setB("testFlag2",this.testFlag2);this.setB("testFlag3",this.testFlag3);this.setB("testFlag4",this.testFlag4);this.setB("traceAlpha",this.traceAlpha);this.setB("translucent",
this.translucent);this.setB("twistedSheets",this.twistedSheets);this.setB("useMinimizationThread",this.useMinimizationThread);this.setB("useNumberLocalization",this.useNumberLocalization);this.setB("vectorsCentered",this.vectorsCentered);this.setF("vectorScale",this.vectorScale);this.setB("vectorSymmetry",this.vectorSymmetry);this.setF("vibrationPeriod",this.vibrationPeriod);this.setF("vibrationScale",this.vibrationScale);this.setF("visualRange",this.visualRange);this.setB("waitForMoveTo",this.waitForMoveTo);
this.setB("wireframeRotation",this.wireframeRotation);this.setI("zDepth",this.zDepth);this.setB("zeroBasedXyzRasmol",this.zeroBasedXyzRasmol);this.setB("zoomHeight",this.zoomHeight);this.setB("zoomLarge",this.zoomLarge);this.setI("zShadePower",this.zShadePower);this.setI("zSlab",this.zSlab)},"JV.GlobalSettings,~B");c(c$,"setUnits",function(a){var b=this.measureDistanceUnits,d=this.energyUnits;a.equalsIgnoreCase("angstroms")?this.measureDistanceUnits="angstroms":a.equalsIgnoreCase("nanometers")||a.equalsIgnoreCase("nm")?
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this.app(b,"set smartAromatic "+this.smartAromatic);this.zeroBasedXyzRasmol&&this.app(b,"set zeroBasedXyzRasmol true");return b.toString()},"java.util.Map");c(c$,"app",function(a,b){0!=b.length&&a.append("  ").append(b).append(";\n")},"JU.SB,~S");c$.unreportedProperties=c$.prototype.unreportedProperties=(";ambientpercent;animationfps;antialiasdisplay;antialiasimages;antialiastranslucent;appendnew;axescolor;axesposition;axesmolecular;axesorientationrasmol;axesunitcell;axeswindow;axis1color;axis2color;axis3color;backgroundcolor;backgroundmodel;bondsymmetryatoms;boundboxcolor;cameradepth;bondingversion;debug;debugscript;defaultlatttice;defaults;defaultdropscript;diffusepercent;;exportdrivers;exportscale;_filecaching;_filecache;fontcaching;fontscaling;forcefield;language;legacyautobonding;legacyhaddition;loglevel;logfile;loggestures;logcommands;measurestylechime;loadformat;loadligandformat;smilesurlformat;pubchemformat;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;;pathforallfiles;perspectivedepth;phongexponent;perspectivemodel;platformspeed;preservestate;refreshing;repaintwaitms;rotationradius;showaxes;showaxis1;showaxis2;showaxis3;showboundbox;showfrank;showtiming;showunitcell;slabenabled;slab;slabrange;depth;zshade;zshadepower;specular;specularexponent;specularpercent;celshading;celshadingpower;specularpower;stateversion;statusreporting;stereo;stereostate;vibrationperiod;unitcellcolor;visualrange;windowcentered;zerobasedxyzrasmol;zoomenabled;mousedragfactor;mousewheelfactor;scriptqueue;scriptreportinglevel;syncscript;syncmouse;syncstereo;;defaultdirectory;currentlocalpath;defaultdirectorylocal;ambient;bonds;colorrasmol;diffuse;fractionalrelative;frank;hetero;hidenotselected;hoverlabel;hydrogen;languagetranslation;measurementunits;navigationdepth;navigationslab;picking;pickingstyle;propertycolorschemeoverload;radius;rgbblue;rgbgreen;rgbred;scaleangstromsperinch;selectionhalos;showscript;showselections;solvent;strandcount;spinx;spiny;spinz;spinfps;navx;navy;navz;navfps;"+
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JV.JC.group3Count=q(a.length()/6);return JV.JC.group3List=a.toString()});c$.isHetero=c(c$,"isHetero",function(a){return 42<=JV.JC.getGroup3Pt(a)},"~S");c$.getGroup3Pt=c(c$,"getGroup3Pt",function(a){JV.JC.getGroup3List();var b=(new JU.SB).append("[");b.append(a);switch(a.length){case 1:b.append("  ");break;case 2:b.append(" ")}a=JV.JC.group3List.indexOf(b.toString());return 0>a?2147483647:q(a/6)+1},"~S");c$.getGroup3Count=c(c$,"getGroup3Count",function(){if(0<JV.JC.group3Count)return JV.JC.group3Count;
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"ALIGN_CENTER",2,"ALIGN_RIGHT",3,"JSV_NOT",-1,"JSV_SEND_JDXMOL",0,"JSV_SETPEAKS",7,"JSV_SELECT",14,"JSV_STRUCTURE",21,"JSV_SEND_H1SIMULATE",28)});n("JV");w(null,"JV.ModelManager",["JM.ModelLoader"],function(){c$=t(function(){this.fileName=this.modelSetPathName=this.modelSet=this.vwr=null;s(this,arguments)},JV,"ModelManager");u(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"zap",function(){this.modelSetPathName=this.fileName=null;new JM.ModelLoader(this.vwr,this.vwr.getZapName(),null,null,null,null)});
c(c$,"getModelSetFileName",function(){return null!=this.fileName?this.fileName:this.vwr.getZapName()});c(c$,"getModelSetPathName",function(){return this.modelSetPathName});c(c$,"createModelSet",function(a,b,d,c,g,f){var j=null;f?(j=this.modelSet.modelSetName,j.equals("zapped")?j=null:0>j.indexOf(" (modified)")&&(j+=" (modified)")):null==c?this.zap():(this.modelSetPathName=a,this.fileName=b);null!=c&&(null==j&&(j=this.vwr.getModelAdapter().getAtomSetCollectionName(c),null!=j&&(j=j.trim(),0==j.length&&
(j=null)),null==j&&(j=JV.ModelManager.reduceFilename(b))),new JM.ModelLoader(this.vwr,j,d,c,f?this.modelSet:null,g));0==this.modelSet.getAtomCount()&&!this.modelSet.getMSInfoB("isPyMOL")&&this.zap()},"~S,~S,JU.SB,~O,JU.BS,~B");c$.reduceFilename=c(c$,"reduceFilename",function(a){if(null==a)return null;var b=a.indexOf(".");0<b&&(a=a.substring(0,b));24<a.length&&(a=a.substring(0,20)+" ...");return a},"~S");c(c$,"createAtomDataSet",function(a,b){return JM.ModelLoader.createAtomDataSet(this.vwr,this.modelSet,
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c(c$,"check",function(a,b,d,c,g,f){return this.modifiers==c&&(2147483647<=f?this.inRange(a,b,d):g-this.time<f&&20<g-this.time)},"~N,~N,~N,~N,~N,~N");c(c$,"is",function(a){return a.x==this.x&&a.y==this.y&&a.time==this.time},"JV.MouseState");C(c$,"MIN_DELAY_MS",20);n("JV");w(["JU.BS"],"JV.SelectionManager",["JU.AU","J.i18n.GT","JU.BSUtil"],function(){c$=t(function(){this.bsDeleted=this.bsSubset=this.bsFixed=this.bsSelection=this.bsHidden=this.listeners=this.vwr=null;this.empty=1;this.hideNotSelected=
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c||this.vwr.reportSelection(J.i18n.GT.i(J.i18n.GT._("{0} atoms hidden"),this.bsHidden.cardinality()))},"JM.ModelSet,JU.BS,~N,~B");c(c$,"hide",function(a,b,d,c){JV.SelectionManager.setBitSet(this.bsHidden,b,d);null!=a&&a.setBsHidden(this.bsHidden);c||this.vwr.reportSelection(J.i18n.GT.i(J.i18n.GT._("{0} atoms hidden"),this.bsHidden.cardinality()))},"JM.ModelSet,JU.BS,~N,~B");c(c$,"setSelectionSet",function(a,b){JV.SelectionManager.setBitSet(this.bsSelection,a,b);this.empty=-1;this.selectionChanged(!1)},
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b))},"JU.BS,~N,~B");c(c$,"selectAll",function(a){var b=this.vwr.getAtomCount();for(this.empty=0==b?1:0;0<=--b;)this.bsSelection.set(b);JU.BSUtil.andNot(this.bsSelection,this.bsDeleted);this.selectionChanged(a)},"~B");c(c$,"clearSelection",function(a){this.setHideNotSelected(!1);this.bsSelection.clearAll();this.empty=1;this.selectionChanged(a)},"~B");c(c$,"isAtomSelected",function(a){return((null==this.bsSubset||this.bsSubset.get(a))&&null==this.bsDeleted||!this.bsDeleted.get(a))&&this.bsSelection.get(a)},
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return a});c(c$,"getSelectedAtomsNoSubset",function(){return JU.BSUtil.copy(this.bsSelection)});c(c$,"getSelectionSubset",function(){return this.bsSubset});c(c$,"excludeAtoms",function(a,b){null!=this.bsDeleted&&a.andNot(this.bsDeleted);!b&&null!=this.bsSubset&&a.and(this.bsSubset)},"JU.BS,~B");c(c$,"setMotionFixedAtoms",function(a){this.bsFixed.clearAll();null!=a&&this.bsFixed.or(a)},"JU.BS");c(c$,"getMotionFixedAtoms",function(){return this.bsFixed});C(c$,"TRUE",1,"FALSE",0,"UNKNOWN",-1)});n("JV");
w(["JU.BS"],"JV.ShapeManager","java.lang.Boolean JU.P3 J.api.Interface J.c.PAL $.VDW JM.Atom JU.BSUtil JV.JC".split(" "),function(){c$=t(function(){this.navigationCrossHairMinMax=this.bsRenderableAtoms=this.vwr=this.shapes=this.ms=this.gdata=null;s(this,arguments)},JV,"ShapeManager");K(c$,function(){this.bsRenderableAtoms=new JU.BS;this.navigationCrossHairMinMax=D(4,0)});u(c$,function(a){this.vwr=a;this.gdata=a.gdata},"JV.Viewer");c(c$,"findNearestShapeAtomIndex",function(a,b,d,c){if(null!=this.shapes)for(var g=
0;g<this.shapes.length&&null==d[0];++g)null!=this.shapes[g]&&this.shapes[g].findNearestAtomIndex(a,b,d,c)},"~N,~N,~A,JU.BS");c(c$,"getShapes",function(){return this.shapes});c(c$,"getShapePropertyIndex",function(a,b,d){if(null==this.shapes||null==this.shapes[a])return null;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getProperty(b,d);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~N");c(c$,"getShapePropertyData",function(a,b,d){if(null==this.shapes||null==this.shapes[a])return!1;
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for(var g=0;36>g;g++)null!=this.shapes[g]&&this.setShapePropertyBs(g,"refreshTrajectories",[c,b,d],a)},"~N,JU.BS,JU.M4");c(c$,"releaseShape",function(a){null!=this.shapes&&(this.shapes[a]=null)},"~N");c(c$,"resetShapes",function(){this.vwr.noGraphicsAllowed()||(this.shapes=Array(36))});c(c$,"setShapeSizeBs",function(a,b,d,c){if(null!=this.shapes){if(null==c&&(1!=a||2147483647!=b))c=this.vwr.bsA();null!=d&&(0!=d.value&&d.vdwType===J.c.VDW.TEMP)&&this.ms.getBfactor100Lo();this.vwr.setShapeErrorState(a,
"set size");(null==d?0!=b:0!=d.value)&&this.loadShape(a);null!=this.shapes[a]&&this.shapes[a].setShapeSizeRD(b,d,c);this.vwr.setShapeErrorState(-1,null)}},"~N,~N,J.atomdata.RadiusData,JU.BS");c(c$,"setLabel",function(a,b){if(null==a){if(null==this.shapes[5])return}else this.loadShape(5),this.setShapeSizeBs(5,0,null,b);this.setShapePropertyBs(5,"label",a,b)},"~O,JU.BS");c(c$,"setShapePropertyBs",function(a,b,d,c){null==this.shapes||null==this.shapes[a]||(null==c&&(c=this.vwr.bsA()),this.vwr.setShapeErrorState(a,
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b,d,c,g)))return j;return null},"~N,~N,~N,JU.BS,~B");c(c$,"checkObjectDragged",function(a,b,d,c,g,f,j){for(var h=!1,l=0<j?j+1:36;!h&&j<l;++j)null!=this.shapes[j]&&(h=this.shapes[j].checkObjectDragged(a,b,d,c,g,f));return h},"~N,~N,~N,~N,~N,JU.BS,~N");c(c$,"checkObjectHovered",function(a,b,d,c){var g=this.shapes[1];if(c&&null!=g&&g.checkObjectHovered(a,b,d))return!0;for(c=0;c<JV.ShapeManager.hoverable.length;c++)if(g=this.shapes[JV.ShapeManager.hoverable[c]],null!=g&&g.checkObjectHovered(a,b,d))return!0;
return!1},"~N,~N,JU.BS,~B");c(c$,"deleteShapeAtoms",function(a,b){if(null!=this.shapes)for(var d=0;36>d;d++)null!=this.shapes[d]&&this.setShapePropertyBs(d,"deleteModelAtoms",a,b)},"~A,JU.BS");c(c$,"deleteVdwDependentShapes",function(a){null==a&&(a=this.vwr.bsA());null!=this.shapes[24]&&this.shapes[24].setProperty("deleteVdw",null,a);null!=this.shapes[25]&&this.shapes[25].setProperty("deleteVdw",null,a)},"JU.BS");c(c$,"getAtomShapeValue",function(a,b,d){a=JV.JC.shapeTokenIndex(a);if(0>a||null==this.shapes[a])return 0;
d=this.shapes[a].getSize(d);if(0==d){if(0==(b.shapeVisibilityFlags&this.shapes[a].vf))return 0;d=this.shapes[a].getSizeG(b)}return d/2E3},"~N,JM.Group,~N");c(c$,"getObjectMap",function(a,b){if(null!=this.shapes)for(var d=Boolean.$valueOf(b),c=16;29>c;++c)this.getShapePropertyData(c,"getNames",[a,d])},"java.util.Map,~B");c(c$,"getProperty",function(a){return a.equals("getShapes")?this.shapes:null},"~O");c(c$,"getRenderableBitSet",function(){return this.bsRenderableAtoms});c(c$,"getShape",function(a){return null==
this.shapes?null:this.shapes[a]},"~N");c(c$,"mergeShapes",function(a){if(null!=a)if(null==this.shapes)this.shapes=a;else for(var b=0;b<a.length;++b)null!=a[b]&&(null==this.shapes[b]&&this.loadShape(b),this.shapes[b].merge(a[b]))},"~A");c(c$,"resetBioshapes",function(a){if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].isBioShape&&(this.shapes[b].setModelSet(this.ms),this.shapes[b].setShapeSizeRD(0,null,a),this.shapes[b].setProperty("color",J.c.PAL.NONE,
a))},"JU.BS");c(c$,"setAtomLabel",function(a,b){null!=this.shapes&&(this.loadShape(5),this.shapes[5].setProperty("label:"+a,Integer.$valueOf(b),null))},"~S,~N");c(c$,"setModelVisibility",function(){var a=this.shapes;if(!(null==a||null==a[0])){for(var b=this.vwr.getVisibleFramesBitSet(),d=8;32>d;d++)null!=a[d]&&a[d].setVisibilityFlags(b);for(var c=this.vwr.getBoolean(603979922),g=this.vwr.getDeletedAtoms(),f=this.ms.at,d=this.ms.ac;0<=--d;){var j=f[d];j.shapeVisibilityFlags&=-64;if(!(null!=g&&g.get(d)||
!c&&1==j.getElementNumber())){var h=j.getModelIndex();b.get(h)&&(h=1,this.ms.isAtomHidden(d)||(h|=8,0!=j.madAtom&&(h|=16),j.setShapeVisibility(h,!0)))}}for(d=0;36>d;++d)b=a[d],null!=b&&b.setModelClickability()}});c(c$,"finalizeAtoms",function(a,b){var d=this.vwr,c=d.tm,g=this.bsRenderableAtoms,f=this.gdata;if(null!=a){var j=this.ms.getAtomSetCenter(a),h=new JU.P3;c.transformPt3f(j,h);h.add(b);c.unTransformPoint(h,h);h.sub(j);d.setAtomCoordsRelative(h,a);b.set(0,0,0)}this.ms.getRenderable(g);for(var l=
this.ms.vibrations,m=null!=l&&c.vibrationOn,j=this.ms.at,r=g.nextSetBit(0);0<=r;r=g.nextSetBit(r+1)){var h=j[r],n=m&&h.hasVibration()?c.transformPtVib(h,l[r]):c.transformPt(h);h.sX=n.x;h.sY=n.y;h.sZ=n.z;var p=Math.abs(h.madAtom);p==JM.Atom.MAD_GLOBAL&&(p=z(2E3*d.getFloat(1141899265)));h.sD=Y(d.tm.scaleToScreen(n.z,p))}if(c.slabEnabled){r=d.getBoolean(603979940);c=d.getBoolean(603979939);l=f.getSlab();m=f.getDepth();if(r){n=this.ms.getMolecules();p=this.ms.getMoleculeCountInModel(-1);for(r=0;r<p;r++){var s=
n[r],t=0,h=s.firstAtomIndex;if(g.get(h)){for(;t<s.ac&&!f.isClippedZ(j[h].sZ-(j[h].sD>>1));t++,h++);if(t!=s.ac){h=s.firstAtomIndex;for(t=0;t<s.ac;t++)g.clear(h),j[h++].sZ=0}}}}for(r=g.nextSetBit(0);0<=r;r=this.bsRenderableAtoms.nextSetBit(r+1))if(h=j[r],f.isClippedZ(h.sZ-(c?j[r].sD>>1:0)))h.setClickable(0),n=q((c?-1:1)*h.sD/2),(h.sZ+n<l||h.sZ-n>m||!f.isInDisplayRange(h.sX,h.sY))&&g.clear(r)}if(0==this.ms.getAtomCount()||!d.getShowNavigationPoint())return null;d=2147483647;f=-2147483648;c=2147483647;
l=-2147483648;for(r=g.nextSetBit(0);0<=r;r=g.nextSetBit(r+1))h=j[r],h.sX<d&&(d=h.sX),h.sX>f&&(f=h.sX),h.sY<c&&(c=h.sY),h.sY>l&&(l=h.sY);this.navigationCrossHairMinMax[0]=d;this.navigationCrossHairMinMax[1]=f;this.navigationCrossHairMinMax[2]=c;this.navigationCrossHairMinMax[3]=l;return this.navigationCrossHairMinMax},"JU.BS,JU.P3");c(c$,"setModelSet",function(a){this.ms=this.vwr.ms=a},"JM.ModelSet");c(c$,"checkInheritedShapes",function(){null!=this.shapes[24]&&this.setShapePropertyBs(24,"remapInherited",
null,null)});c(c$,"restrictSelected",function(a,b){var d=this.vwr.getSelectedAtomsNoSubset();if(b){this.vwr.invertSelection();var c=this.vwr.getSelectionSubset();null!=c&&(d=this.vwr.getSelectedAtomsNoSubset(),d.and(c),this.vwr.select(d,!1,0,!0),JU.BSUtil.invertInPlace(d,this.vwr.getAtomCount()),d.and(c))}JU.BSUtil.andNot(d,this.vwr.getDeletedAtoms());c=this.vwr.getBoolean(603979812);a||this.vwr.setBooleanProperty("bondModeOr",!0);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",
Integer.$valueOf(32768),null);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(1023),null);for(var g=this.vwr.bsA(),f=21;0<=--f;)6!=f&&null!=this.getShape(f)&&this.setShapeSizeBs(f,0,null,g);null!=this.getShape(21)&&this.setShapePropertyBs(21,"delete",g,null);this.setLabel(null,g);a||this.vwr.setBooleanProperty("bondModeOr",c);this.vwr.select(d,!1,0,!0)},"~B,~B");C(c$,"hoverable",[30,25,24,22,35]);c$.clickableMax=c$.prototype.clickableMax=JV.ShapeManager.hoverable.length-
1});n("JV");w(["java.util.Hashtable"],"JV.StateManager","java.util.Arrays JU.BS $.SB JM.Orientation JU.BSUtil JV.GlobalSettings".split(" "),function(){c$=t(function(){this.saved=this.vwr=null;this.lastCoordinates=this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=this.lastContext=this.lastOrientation="";N("JV.StateManager.Scene")||JV.StateManager.$StateManager$Scene$();N("JV.StateManager.Connections")||JV.StateManager.$StateManager$Connections$();N("JV.StateManager.Connection")||
JV.StateManager.$StateManager$Connection$();s(this,arguments)},JV,"StateManager");K(c$,function(){this.saved=new java.util.Hashtable});c$.getVariableList=c(c$,"getVariableList",function(a,b,d,c){var g=new JU.SB,f=0,j=Array(a.size()),h;for(a=a.entrySet().iterator();a.hasNext()&&((h=a.next())||1);){var l=h.getKey(),m=h.getValue();if((d||!l.startsWith("site_"))&&(!c||"@"==l.charAt(0)))j[f++]=l+("@"==l.charAt(0)?" "+m.asString():" = "+JV.StateManager.varClip(l,m.escape(),b))}java.util.Arrays.sort(j,0,
f);for(b=0;b<f;b++)null!=j[b]&&g.append("  ").append(j[b]).append(";\n");0==f&&!c&&g.append("# --no global user variables defined--;\n");return g.toString()},"java.util.Map,~N,~B,~B");c$.getObjectIdFromName=c(c$,"getObjectIdFromName",function(a){if(null==a)return-1;a="background axis1      axis2      axis3      boundbox   unitcell   frank      ".indexOf(a.toLowerCase());return 0>a?a:q(a/11)},"~S");c$.getObjectNameFromId=c(c$,"getObjectNameFromId",function(a){return 0>a||8<=a?null:"background axis1      axis2      axis3      boundbox   unitcell   frank      ".substring(11*
a,11*a+11).trim()},"~N");u(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"getGlobalSettings",function(a,b){return new JV.GlobalSettings(this.vwr,a,b)},"JV.GlobalSettings,~B");c(c$,"clear",function(a){this.vwr.setShowAxes(!1);this.vwr.setShowBbcage(!1);this.vwr.setShowUnitCell(!1);a.clear()},"JV.GlobalSettings");c(c$,"setCrystallographicDefaults",function(){this.vwr.setAxesModeUnitCell(!0);this.vwr.setShowAxes(!0);this.vwr.setShowUnitCell(!0);this.vwr.setBooleanProperty("perspectiveDepth",!1)});c(c$,
"setCommonDefaults",function(){this.vwr.setBooleanProperty("perspectiveDepth",!0);this.vwr.setFloatProperty("bondTolerance",0.45);this.vwr.setFloatProperty("minBondDistance",0.4);this.vwr.setIntProperty("bondingVersion",0);this.vwr.setBooleanProperty("translucent",!0)});c(c$,"setJmolDefaults",function(){this.setCommonDefaults();this.vwr.setStringProperty("defaultColorScheme","Jmol");this.vwr.setBooleanProperty("axesOrientationRasmol",!1);this.vwr.setBooleanProperty("zeroBasedXyzRasmol",!1);this.vwr.setIntProperty("percentVdwAtom",
23);this.vwr.setIntProperty("bondRadiusMilliAngstroms",150);this.vwr.setVdwStr("auto")});c(c$,"setRasMolDefaults",function(){this.setCommonDefaults();this.vwr.setStringProperty("defaultColorScheme","RasMol");this.vwr.setBooleanProperty("axesOrientationRasmol",!0);this.vwr.setBooleanProperty("zeroBasedXyzRasmol",!0);this.vwr.setIntProperty("percentVdwAtom",0);this.vwr.setIntProperty("bondRadiusMilliAngstroms",1);this.vwr.setVdwStr("Rasmol")});c(c$,"setPyMOLDefaults",function(){this.setCommonDefaults();
this.vwr.setStringProperty("measurementUnits","ANGSTROMS");this.vwr.setBooleanProperty("zoomHeight",!0)});c$.getNoCase=c(c$,"getNoCase",function(a,b){for(var d,c=a.entrySet().iterator();c.hasNext()&&((d=c.next())||1);)if(d.getKey().equalsIgnoreCase(b))return d.getValue();return null},"java.util.Map,~S");c(c$,"listSavedStates",function(){for(var a="",b,d=this.saved.keySet().iterator();d.hasNext()&&((b=d.next())||1);)a+="\n"+b;return a});c(c$,"deleteSavedType",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();)b.next().startsWith(a)&&
b.remove()},"~S");c(c$,"deleteSaved",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();){var d=b.next();(d.startsWith(a)||d.endsWith("_"+a)&&d.indexOf("_")==d.lastIndexOf("_"+a))&&b.remove()}},"~S");c(c$,"saveSelection",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Selected_"):(a=this.lastSelected="Selected_"+a,this.saved.put(a,JU.BSUtil.copy(b)))},"~S,JU.BS");c(c$,"restoreSelection",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Selected_"+a:this.lastSelected);
if(null==a)return this.vwr.select(new JU.BS,!1,0,!1),!1;this.vwr.select(a,!1,0,!1);return!0},"~S");c(c$,"saveState",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("State_"):(a=this.lastState="State_"+a,this.saved.put(a,this.vwr.getStateInfo()))},"~S");c(c$,"getSavedState",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"State_"+a:this.lastState);return null==a?"":a},"~S");c(c$,"saveStructure",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Shape_"):(a=this.lastShape=
"Shape_"+a,this.saved.put(a,this.vwr.getStructureState()))},"~S");c(c$,"getSavedStructure",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Shape_"+a:this.lastShape);return null==a?"":a},"~S");c(c$,"saveCoordinates",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Coordinates_"):(a=this.lastCoordinates="Coordinates_"+a,this.saved.put(a,this.vwr.getCoordinateState(b)))},"~S,JU.BS");c(c$,"getSavedCoordinates",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?
"Coordinates_"+a:this.lastCoordinates);return null==a?"":a},"~S");c(c$,"getOrientation",function(){return new JM.Orientation(this.vwr,!1,null)});c(c$,"getSavedOrientationText",function(a){var b;if(null!=a)return b=this.getOrientationFor(a),null==b?"":b.getMoveToText(!0);a=new JU.SB;for(var d=this.saved.entrySet().iterator();d.hasNext()&&((b=d.next())||1);)b.getKey().startsWith("Orientation_")&&a.append(b.getValue().getMoveToText(!0));return a.toString()},"~S");c(c$,"saveScene",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Scene_");
else{var d=M(JV.StateManager.Scene,this,null,b);d.saveName=this.lastScene="Scene_"+a;this.saved.put(d.saveName,d)}},"~S,java.util.Map");c(c$,"restoreScene",function(a,b){var d=JV.StateManager.getNoCase(this.saved,0<a.length?"Scene_"+a:this.lastScene);return null!=d&&d.restore(b)},"~S,~N");c(c$,"saveOrientation",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Orientation_");else{var d=new JM.Orientation(this.vwr,a.equalsIgnoreCase("default"),b);d.saveName=this.lastOrientation="Orientation_"+
a;this.saved.put(d.saveName,d)}},"~S,~A");c(c$,"restoreOrientation",function(a,b,d){a=this.getOrientationFor(a);return null!=a&&a.restore(b,d)},"~S,~N,~B");c(c$,"getOrientationFor",function(a){return JV.StateManager.getNoCase(this.saved,0<a.length?"Orientation_"+a:this.lastOrientation)},"~S");c(c$,"saveContext",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Context_"):this.saved.put(this.lastContext="Context_"+a,b)},"~S,~O");c(c$,"getContext",function(a){return this.saved.get(0==
a.length?this.lastContext:"Context_"+a)},"~S");c(c$,"saveBonds",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Bonds_");else{var b=M(JV.StateManager.Connections,this,null);b.saveName=this.lastConnections="Bonds_"+a;this.saved.put(b.saveName,b)}},"~S");c(c$,"restoreBonds",function(a){this.vwr.clearModelDependentObjects();a=JV.StateManager.getNoCase(this.saved,0<a.length?"Bonds_"+a:this.lastConnections);return null!=a&&a.restore()},"~S");c$.varClip=c(c$,"varClip",function(a,b,d){0<
d&&b.length>d&&(b=b.substring(0,d)+" #...more ("+b.length+" bytes -- use SHOW "+a+" or MESSAGE @"+a+" to view)");return b},"~S,~S,~N");c$.$StateManager$Scene$=function(){G(self.c$);c$=t(function(){Q(this,arguments);this.scene=this.saveName=null;s(this,arguments)},JV.StateManager,"Scene");u(c$,function(a){this.scene=a},"java.util.Map");c(c$,"restore",function(a){var b=this.scene.get("generator");null!=b&&b.generateScene(this.scene);b=this.scene.get("pymolView");return null!=b&&this.b$["JV.StateManager"].vwr.tm.moveToPyMOL(this.b$["JV.StateManager"].vwr.eval,
a,b)},"~N");c$=F()};c$.$StateManager$Connections$=function(){G(self.c$);c$=t(function(){Q(this,arguments);this.saveName=null;this.bondCount=0;this.connections=null;s(this,arguments)},JV.StateManager,"Connections");u(c$,function(){var a=this.b$["JV.StateManager"].vwr.ms;if(null!=a){this.bondCount=a.bondCount;this.connections=Array(this.bondCount+1);for(var a=a.bo,b=this.bondCount;0<=--b;){var d=a[b];this.connections[b]=M(JV.StateManager.Connection,this,null,d.getAtomIndex1(),d.getAtomIndex2(),d.mad,
d.colix,d.order,d.getEnergy(),d.getShapeVisibilityFlags())}}});c(c$,"restore",function(){var a=this.b$["JV.StateManager"].vwr.ms;if(null==a)return!1;a.deleteAllBonds();for(var b=this.bondCount;0<=--b;){var d=this.connections[b],c=a.getAtomCount();d.atomIndex1>=c||d.atomIndex2>=c||(c=a.bondAtoms(a.at[d.atomIndex1],a.at[d.atomIndex2],d.order,d.mad,null,d.energy,!1,!0),c.setColix(d.colix),c.setShapeVisibilityFlags(d.shapeVisibilityFlags))}for(d=this.bondCount;0<=--d;)a.getBondAt(d).setIndex(d);this.b$["JV.StateManager"].vwr.setShapeProperty(1,
"reportAll",null);return!0});c$=F()};c$.$StateManager$Connection$=function(){G(self.c$);c$=t(function(){Q(this,arguments);this.shapeVisibilityFlags=this.energy=this.order=this.colix=this.mad=this.atomIndex2=this.atomIndex1=0;s(this,arguments)},JV.StateManager,"Connection");u(c$,function(a,b,d,c,g,f,j){this.atomIndex1=a;this.atomIndex2=b;this.mad=d;this.colix=c;this.order=g;this.energy=f;this.shapeVisibilityFlags=j},"~N,~N,~N,~N,~N,~N,~N");c$=F()};C(c$,"OBJ_BACKGROUND",0,"OBJ_AXIS1",1,"OBJ_AXIS2",
2,"OBJ_AXIS3",3,"OBJ_BOUNDBOX",4,"OBJ_UNITCELL",5,"OBJ_FRANK",6,"OBJ_MAX",8,"objectNameList","background axis1      axis2      axis3      boundbox   unitcell   frank      ")});n("JV");w(["java.util.Hashtable"],"JV.StatusManager","java.lang.Boolean $.Float javajs.awt.Dimension JU.Lst $.PT J.api.Interface J.c.CBK JU.Logger".split(" "),function(){c$=t(function(){this.cbl=this.jsl=this.vwr=null;this.statusList="";this.allowStatusReporting=!1;this.messageQueue=null;this.statusPtr=0;this.jmolScriptCallbacks=
null;this.minSyncRepeatMs=100;this.stereoSync=this.syncDisabled=this.isSynced=this.drivingSync=this.syncingMouse=this.syncingScripts=!1;this.qualityPNG=this.qualityJPG=-1;this.imageType=null;s(this,arguments)},JV,"StatusManager");K(c$,function(){this.messageQueue=new java.util.Hashtable;this.jmolScriptCallbacks=new java.util.Hashtable});u(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"setAllowStatusReporting",function(a){this.allowStatusReporting=a},"~B");c(c$,"getStatusList",function(){return this.statusList});
c(c$,"getMessageQueue",function(){return this.messageQueue});c(c$,"recordStatus",function(a){return this.allowStatusReporting&&0<this.statusList.length&&(this.statusList.equals("all")||0<=this.statusList.indexOf(a))},"~S");c(c$,"setStatusChanged",function(a,b,d,c){if(this.recordStatus(a)){var g=new JU.Lst;g.addLast(Integer.$valueOf(++this.statusPtr));g.addLast(a);g.addLast(Integer.$valueOf(b));g.addLast(d);b=c?null:this.messageQueue.get(a);null==b?this.messageQueue.put(a,b=new JU.Lst):b.size()==JV.StatusManager.MAXIMUM_QUEUE_LENGTH&&
b.remove(0);b.addLast(g)}},"~S,~N,~O,~B");c(c$,"getStatusChanged",function(a){var b=0<a.length&&"-"==a.charAt(0),d=0<a.length&&"+"==a.charAt(0),c=!1;b?this.statusList=JU.PT.rep(this.statusList,a.substring(1,a.length),""):(a=JU.PT.rep(a,"+",""),this.statusList.equals(a)||d&&0<=this.statusList.indexOf(a)?c=!0:(d||(this.statusList=""),this.statusList+=a,JU.Logger.debugging&&JU.Logger.debug("StatusManager messageQueue = "+this.statusList)));a=new JU.Lst;if(c)for(var g,c=this.messageQueue.entrySet().iterator();c.hasNext()&&
((g=c.next())||1);)a.addLast(g.getValue());this.messageQueue.clear();this.statusPtr=0;return a},"~S");c(c$,"setJmolStatusListener",function(a,b){this.jsl=a;this.cbl=null==b?a:b},"J.api.JmolStatusListener,J.api.JmolCallbackListener");c(c$,"setJmolCallbackListener",function(a){this.cbl=a},"J.api.JmolCallbackListener");c(c$,"jmolScriptCallback",function(a){a=this.jmolScriptCallbacks.get(a);null!=a&&this.vwr.evalStringQuietSync(a,!0,!1);return a},"J.c.CBK");c(c$,"setCallbackFunction",function(a,b){var d=
J.c.CBK.getCallback(a);if(null!=d){var c=null==b?0:7<b.length&&0==b.toLowerCase().indexOf("script:")?7:11<b.length&&0==b.toLowerCase().indexOf("jmolscript:")?11:0;0==c?this.jmolScriptCallbacks.remove(d):this.jmolScriptCallbacks.put(d,b.substring(c).trim())}null!=this.cbl&&this.cbl.setCallbackFunction(a,b)},"~S,~S");c(c$,"notifyEnabled",function(a){return null!=this.cbl&&this.cbl.notifyEnabled(a)},"J.c.CBK");c(c$,"setStatusAppletReady",function(a,b){var d=b?this.jmolScriptCallback(J.c.CBK.APPLETREADY):
null;this.notifyEnabled(J.c.CBK.APPLETREADY)&&this.cbl.notifyCallback(J.c.CBK.APPLETREADY,[d,a,Boolean.$valueOf(b),null])},"~S,~B");c(c$,"setStatusAtomMoved",function(a){var b=this.jmolScriptCallback(J.c.CBK.ATOMMOVED);this.setStatusChanged("atomMoved",-1,a,!1);this.notifyEnabled(J.c.CBK.ATOMMOVED)&&this.cbl.notifyCallback(J.c.CBK.ATOMMOVED,[b,a])},"JU.BS");c(c$,"setStatusAtomPicked",function(a,b,d){var c=this.jmolScriptCallback(J.c.CBK.PICK);JU.Logger.info("setStatusAtomPicked("+a+","+b+")");this.setStatusChanged("atomPicked",
a,b,!1);this.notifyEnabled(J.c.CBK.PICK)&&this.cbl.notifyCallback(J.c.CBK.PICK,[c,b,Integer.$valueOf(a),d])},"~N,~S,java.util.Map");c(c$,"setStatusClicked",function(a,b,d,c,g){var f=this.jmolScriptCallback(J.c.CBK.CLICK);if(!this.notifyEnabled(J.c.CBK.CLICK))return d;g=[d,g];this.cbl.notifyCallback(J.c.CBK.CLICK,[f,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(d),Integer.$valueOf(c),g]);return g[0]},"~N,~N,~N,~N,~N");c(c$,"setStatusResized",function(a,b){var d=this.jmolScriptCallback(J.c.CBK.RESIZE);
this.notifyEnabled(J.c.CBK.RESIZE)&&this.cbl.notifyCallback(J.c.CBK.RESIZE,[d,Integer.$valueOf(a),Integer.$valueOf(b)])},"~N,~N");c(c$,"setStatusAtomHovered",function(a,b){var d=this.jmolScriptCallback(J.c.CBK.HOVER);this.notifyEnabled(J.c.CBK.HOVER)&&this.cbl.notifyCallback(J.c.CBK.HOVER,[d,b,Integer.$valueOf(a)])},"~N,~S");c(c$,"setStatusObjectHovered",function(a,b,d){var c=this.jmolScriptCallback(J.c.CBK.HOVER);this.notifyEnabled(J.c.CBK.HOVER)&&this.cbl.notifyCallback(J.c.CBK.HOVER,[c,b,Integer.$valueOf(-1),
a,Float.$valueOf(d.x),Float.$valueOf(d.y),Float.$valueOf(d.z)])},"~S,~S,JU.T3");c(c$,"setFileLoadStatus",function(a,b,d,c,g,f,j){null==a&&"resetUndo".equals(b)&&(b=this.vwr.getProperty("DATA_API","getAppConsole",null),null!=b&&b.zap(),b=this.vwr.getZapName());this.setStatusChanged("fileLoaded",g,a,!1);null!=c&&this.setStatusChanged("fileLoadError",g,c,!1);var h=this.jmolScriptCallback(J.c.CBK.LOADSTRUCT);f&&this.notifyEnabled(J.c.CBK.LOADSTRUCT)&&(f=this.vwr.getP("_smilesString"),0!=f.length&&(b=
f),this.cbl.notifyCallback(J.c.CBK.LOADSTRUCT,[h,a,b,d,c,Integer.$valueOf(g),this.vwr.getP("_modelNumber"),this.vwr.getModelNumberDotted(this.vwr.getModelCount()-1),j]))},"~S,~S,~S,~S,~N,~B,Boolean");c(c$,"setStatusFrameChanged",function(a,b,d,c,g,f,j){if(null!=this.vwr.ms){var h=this.vwr.am.animationOn,l=h?-2-g:g;this.setStatusChanged("frameChanged",l,0<=g?this.vwr.getModelNumberDotted(g):"",!1);var m=this.jmolScriptCallback(J.c.CBK.ANIMFRAME);this.notifyEnabled(J.c.CBK.ANIMFRAME)&&this.cbl.notifyCallback(J.c.CBK.ANIMFRAME,
[m,[l,a,b,d,c,g],j,Float.$valueOf(f)]);null!=this.vwr.jmolpopup&&!h&&this.vwr.jmolpopup.jpiUpdateComputedMenus()}},"~N,~N,~N,~N,~N,~N,~S");c(c$,"setStatusDragDropped",function(a,b,d,c){this.setStatusChanged("dragDrop",0,"",!1);var g=this.jmolScriptCallback(J.c.CBK.DRAGDROP);if(!this.notifyEnabled(J.c.CBK.DRAGDROP))return!1;this.cbl.notifyCallback(J.c.CBK.DRAGDROP,[g,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(d),c]);return!0},"~N,~N,~N,~S");c(c$,"setScriptEcho",function(a,b){if(null!=
a){this.setStatusChanged("scriptEcho",0,a,!1);var d=this.jmolScriptCallback(J.c.CBK.ECHO);this.notifyEnabled(J.c.CBK.ECHO)&&this.cbl.notifyCallback(J.c.CBK.ECHO,[d,a,Integer.$valueOf(b?1:0)])}},"~S,~B");c(c$,"setStatusMeasuring",function(a,b,d,c){this.setStatusChanged(a,b,d,!1);var g=null;a.equals("measureCompleted")?(JU.Logger.info("measurement["+b+"] = "+d),g=this.jmolScriptCallback(J.c.CBK.MEASURE)):a.equals("measurePicked")&&(this.setStatusChanged("measurePicked",b,d,!1),JU.Logger.info("measurePicked "+
b+" "+d));this.notifyEnabled(J.c.CBK.MEASURE)&&this.cbl.notifyCallback(J.c.CBK.MEASURE,[g,d,Integer.$valueOf(b),a,Float.$valueOf(c)])},"~S,~N,~S,~N");c(c$,"notifyError",function(a,b,d){var c=this.jmolScriptCallback(J.c.CBK.ERROR);this.notifyEnabled(J.c.CBK.ERROR)&&this.cbl.notifyCallback(J.c.CBK.ERROR,[c,a,b,this.vwr.getShapeErrorState(),d])},"~S,~S,~S");c(c$,"notifyMinimizationStatus",function(a,b,d,c,g){var f=this.jmolScriptCallback(J.c.CBK.MINIMIZATION);this.notifyEnabled(J.c.CBK.MINIMIZATION)&&
this.cbl.notifyCallback(J.c.CBK.MINIMIZATION,[f,a,b,d,c,g])},"~S,Integer,Float,Float,~S");c(c$,"setScriptStatus",function(a,b,d,c){if(-1>d){var g=-2-d;this.setStatusChanged("scriptStarted",g,b,!1);a="script "+g+" started"}else if(null==a)return;var g=0==d?this.jmolScriptCallback(J.c.CBK.SCRIPT):null,f="Script completed"===a;if(this.recordStatus("script")){var j=null!=c;this.setStatusChanged(j?"scriptError":"scriptStatus",0,a,!1);if(j||f)this.setStatusChanged("scriptTerminated",1,"Jmol script terminated"+
(j?" unsuccessfully: "+a:" successfully"),!1)}f&&(this.vwr.getBoolean(603979880)&&this.vwr.getBoolean(603979825))&&(a=[null,"script <exiting>",b,Integer.$valueOf(-1),c],this.notifyEnabled(J.c.CBK.SCRIPT)&&this.cbl.notifyCallback(J.c.CBK.SCRIPT,a),this.processScript(a),a="Jmol script completed.");a=[g,a,b,Integer.$valueOf(f?-1:d),c];this.notifyEnabled(J.c.CBK.SCRIPT)&&this.cbl.notifyCallback(J.c.CBK.SCRIPT,a);this.processScript(a)},"~S,~S,~N,~S");c(c$,"processScript",function(a){var b=a[3].intValue();
null!=this.vwr.scriptEditor&&(0<b?this.vwr.scriptEditor.notifyScriptTermination():0>b?-2==b&&this.vwr.scriptEditor.notifyScriptStart():this.vwr.scriptEditor.isVisible()&&0<a[2].length&&this.vwr.scriptEditor.notifyContext(this.vwr.getScriptContext("SE notify"),a));null!=this.vwr.appConsole&&0==b&&this.vwr.appConsole.sendConsoleMessage(null==a[1]?null:a[1].toString())},"~A");c(c$,"doSync",function(){return this.isSynced&&this.drivingSync&&!this.syncDisabled});c(c$,"setSync",function(a){this.syncingMouse?
null!=a&&this.syncSend(a,"*",0):this.syncingScripts||this.syncSend("!"+this.vwr.tm.getMoveToText(this.minSyncRepeatMs/1E3,!1),"*",0)},"~S");c(c$,"setSyncDriver",function(a){this.stereoSync&&4!=a&&(this.syncSend("SET_GRAPHICS_OFF","*",0),this.stereoSync=!1);switch(a){case 4:if(!this.syncDisabled)return;this.syncDisabled=!1;break;case 3:this.syncDisabled=!0;break;case 5:this.stereoSync=this.isSynced=this.drivingSync=!0;break;case 1:this.isSynced=this.drivingSync=!0;break;case 2:this.drivingSync=!1;
this.isSynced=!0;break;default:this.isSynced=this.drivingSync=!1}JU.Logger.debugging&&JU.Logger.debug(this.vwr.appletName+" sync mode="+a+"; synced? "+this.isSynced+"; driving? "+this.drivingSync+"; disabled? "+this.syncDisabled)},"~N");c(c$,"syncSend",function(a,b,d){(0!=d||this.notifyEnabled(J.c.CBK.SYNC))&&this.cbl.notifyCallback(J.c.CBK.SYNC,[null,a,b,Integer.$valueOf(d)])},"~S,~S,~N");c(c$,"modifySend",function(a,b,d,c){this.notifyEnabled(J.c.CBK.STRUCTUREMODIFIED)&&this.cbl.notifyCallback(J.c.CBK.STRUCTUREMODIFIED,
[null,Integer.$valueOf(d),Integer.$valueOf(a),Integer.$valueOf(b),c])},"~N,~N,~N,~S");c(c$,"getSyncMode",function(){return!this.isSynced?0:this.drivingSync?1:2});c(c$,"showUrl",function(a){null!=this.jsl&&this.jsl.showUrl(a)},"~S");c(c$,"clearConsole",function(){null!=this.vwr.appConsole&&this.vwr.appConsole.sendConsoleMessage(null);null!=this.jsl&&this.cbl.notifyCallback(J.c.CBK.MESSAGE,null)});c(c$,"functionXY",function(a,b,d){return null==this.jsl?L(Math.abs(b),Math.abs(d),0):this.jsl.functionXY(a,
b,d)},"~S,~N,~N");c(c$,"functionXYZ",function(a,b,d,c){return null==this.jsl?L(Math.abs(b),Math.abs(d),Math.abs(d),0):this.jsl.functionXYZ(a,b,d,c)},"~S,~N,~N,~N");c(c$,"jsEval",function(a){return null==this.jsl?"":this.jsl.eval(a)},"~S");c(c$,"createImage",function(a,b,d,c,g){return null==this.jsl?null:this.jsl.createImage(a,b,null==d?c:d,g)},"~S,~S,~S,~A,~N");c(c$,"getRegistryInfo",function(){return null==this.jsl?null:this.jsl.getRegistryInfo()});c(c$,"dialogAsk",function(a,b){var d=a.equals("Save Image"),
c=J.api.Interface.getOption("dialog.Dialog");if(null==c)return null;c.setupUI(!1);d&&c.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);var g=c.getFileNameFromDialog(this.vwr,a,b);d&&null!=g&&(this.qualityJPG=c.getQuality("JPG"),this.qualityPNG=c.getQuality("PNG"),d=c.getType(),null!=d&&(this.imageType=d));return g},"~S,~S");c(c$,"getJspecViewProperties",function(a){return null==this.jsl?null:this.jsl.getJSpecViewProperty(null==a||0==a.length?"":":"+a)},"~S");c(c$,"resizeInnerPanel",function(a,
b){return null==this.jsl?new javajs.awt.Dimension(a,b):this.jsl.resizeInnerPanel("preferredWidthHeight "+a+" "+b+";")},"~N,~N");C(c$,"MAXIMUM_QUEUE_LENGTH",16,"SYNC_OFF",0,"SYNC_DRIVER",1,"SYNC_SLAVE",2,"SYNC_DISABLE",3,"SYNC_ENABLE",4,"SYNC_STEREO",5)});n("JV");w("JU.A4 $.M3 $.M4 $.P3 $.P3i $.V3 J.c.STER JU.Point3fi".split(" "),"JV.TransformManager","java.lang.Boolean $.Float java.util.Hashtable JU.P4 $.Quat $.SB J.api.Interface JU.Escape $.Logger".split(" "),function(){c$=t(function(){this.spinThread=
this.vibrationThread=this.movetoThread=this.vwr=null;this.perspectiveModel=11;this.modelRadiusPixels=this.modelRadius=this.modelCenterOffset=this.cameraDistanceFromCenter=this.aperatureAngle=this.referencePlaneOffset=this.cameraScaleFactor=0;this.navigationShiftXY=this.navigationOffset=this.navigationCenter=null;this.navigationDepth=0;this.vectorTemp=this.matrixTemp=null;this.haveNotifiedNaN=!1;this.spinX=0;this.spinY=30;this.spinZ=0;this.spinFps=30;this.navZ=this.navY=this.navX=0;this.navFps=NaN;
this.doTransform4D=this.isSpinSelected=this.isSpinFixed=this.isSpinInternal=!1;this.rotationCenterDefault=this.perspectiveShiftXY=this.perspectiveOffset=this.fixedRotationCenter=this.fixedRotationOffset=null;this.rotationRadiusDefault=0;this.internalRotationCenter=this.internalTranslation=this.internalRotationAxis=this.fixedRotationAxis=null;this.internalRotationAngle=0;this.rotationAxis=this.pointT2=this.vectorT2=this.vectorT=this.axisangleT=this.matrixTemp4=this.matrixTemp3=this.matrixRotate=null;
this.rotationRate=0;this.cameraSetting=this.camera=this.fixedTranslation=null;this.yTranslationFraction=this.xTranslationFraction=0.5;this.previousY=this.previousX=this.prevZoomSetting=0;this.zoomEnabled=!0;this.zmPctSet=this.zmPct=100;this.zoomRatio=0;this.zShadeEnabled=this.internalSlab=this.slabEnabled=!1;this.depthPercentSetting=this.slabPercentSetting=0;this.zSlabPercentSetting=50;this.zDepthPercentSetting=0;this.zSlabPoint=null;this.slabRange=this.zDepthValue=this.zSlabValue=this.depthValue=
this.slabValue=0;this.depthPlane=this.slabPlane=null;this.perspectiveDepth=!0;this.scale3D=!1;this.cameraDepthSetting=this.cameraDepth=3;this.visualRange=0;this.cameraDistance=1E3;this.scale3DAngstromsPerInch=this.scaleDefaultPixelsPerAngstrom=this.scalePixelsPerAngstrom=this.screenPixelCount=this.height=this.width=0;this.zoomHeight=this.useZoomLarge=this.antialias=!1;this.screenHeight=this.screenWidth=0;this.ptVibTemp=this.point3iScreenTemp=this.point3fScreenTemp=this.matrixTransformInv=this.matrixTransform=
null;this.navigating=!1;this.defaultMode=this.mode=0;this.matrixTest=this.aaTest1=this.ptTest3=this.ptTest2=this.ptTest1=this.untransformedPoint=null;this.vibrationOn=this.spinIsGesture=this.navOn=this.spinOn=!1;this.vibrationScale=this.vibrationPeriodMs=this.vibrationPeriod=0;this.stereoColors=this.stereoMode=this.vibrationT=null;this.stereoDegrees=NaN;this.stereoRadians=0;this.stereoFrame=!1;this.matrixStereo=null;this.windowCentered=!1;this.ptOffset=this.bsSelectedAtoms=this.frameOffset=this.frameOffsets=
null;this.navMode=1;this.zoomFactor=3.4028235E38;this.navigationSlabOffset=0;this.nav=null;s(this,arguments)},JV,"TransformManager");K(c$,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=new JU.P3;this.matrixTemp=new JU.M4;this.vectorTemp=new JU.V3;this.fixedRotationOffset=new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;
this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.pointT2=new JU.P3;this.rotationAxis=new JU.V3;this.fixedTranslation=new JU.P3;this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=new JU.M4;this.point3fScreenTemp=new JU.P3;this.point3iScreenTemp=new JU.P3i;
this.ptVibTemp=new JU.Point3fi;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.c.STER.NONE;this.matrixStereo=new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=new JU.P3});u(c$,function(){});c$.getTransformManager=c(c$,"getTransformManager",function(a,b,d,c){c=c?J.api.Interface.getInterface("JV.TransformManager4D"):new JV.TransformManager;c.vwr=a;c.setScreenParameters(b,
d,!0,!1,!0,!0);return c},"JV.Viewer,~N,~N,~B");c(c$,"homePosition",function(a){a&&this.setSpinOff();this.setNavOn(!1);this.navFps=10;this.navX=this.navY=this.navZ=0;this.rotationCenterDefault.setT(this.vwr.getBoundBoxCenter());this.setFixedRotationCenter(this.rotationCenterDefault);this.rotationRadiusDefault=this.setRotationRadius(0,!0);this.windowCentered=!0;this.setRotationCenterAndRadiusXYZ(null,!0);this.resetRotation();a=this.vwr.ms.getInfoM("defaultOrientationMatrix");null!=a&&this.setRotation(a);
this.setZoomEnabled(!0);this.zoomToPercent(this.vwr.g.modelKitMode?50:100);this.zmPct=this.zmPctSet;this.slabReset();this.resetFitToScreen(!0);this.vwr.isJmolDataFrame()?this.fixedRotationCenter.set(0,0,0):this.vwr.g.axesOrientationRasmol&&this.matrixRotate.setAsXRotation(3.141592653589793);this.vwr.stm.saveOrientation("default",null);1==this.mode&&this.setNavigationMode(!0)},"~B");c(c$,"setRotation",function(a){a.isRotation()?this.matrixRotate.setM3(a):this.resetRotation()},"JU.M3");c(c$,"resetRotation",
function(){this.matrixRotate.setScale(1)});c(c$,"clearThreads",function(){this.clearVibration();this.clearSpin();this.setNavOn(!1);this.stopMotion()});c(c$,"clear",function(){this.fixedRotationCenter.set(0,0,0);this.navigating=!1;this.zSlabPoint=this.depthPlane=this.slabPlane=null;this.resetNavigationPoint(!0)});c(c$,"setFixedRotationCenter",function(a){null!=a&&this.fixedRotationCenter.setT(a)},"JU.P3");c(c$,"setRotationPointXY",function(a){a=this.transformPt(a);this.fixedTranslation.set(a.x,a.y,
0)},"JU.P3");c(c$,"spinXYBy",function(a,b,d){if(0==a&&0==b)null!=this.spinThread&&this.spinIsGesture&&this.clearSpin();else{this.clearSpin();var c=JU.P3.newP(this.fixedRotationCenter),g=new JU.P3;this.transformPt3f(c,g);a=JU.P3.new3(-b,a,0);a.add(g);this.unTransformPoint(a,a);this.vwr.setInMotion(!1);this.rotateAboutPointsInternal(null,a,c,10*d,NaN,!1,!0,null,!0,null,null,null)}},"~N,~N,~N");c(c$,"rotateXYBy",function(a,b,d){this.rotate3DBall(a,b,d)},"~N,~N,JU.BS");c(c$,"rotateZBy",function(a,b,d){2147483647!=
b&&2147483647!=d&&this.resetXYCenter(b,d);this.rotateZRadians(a/57.29577951308232)},"~N,~N,~N");c(c$,"applyRotation",function(a,b,d,c,g){null==d?this.matrixRotate.mul2(a,this.matrixRotate):(this.vwr.moveAtoms(a,this.matrixRotate,c,this.internalRotationCenter,b,d,g),null!=c&&this.internalRotationCenter.add(c))},"JU.M3,~B,JU.BS,JU.V3,~B");c(c$,"rotate3DBall",function(a,b,d){this.matrixTemp3.setAsBallRotation(0.017453292,-b,-a)&&this.applyRotation(this.matrixTemp3,!1,d,null,!1)},"~N,~N,JU.BS");c(c$,
"rotateXRadians",function(a,b){this.applyRotation(this.matrixTemp3.setAsXRotation(a),!1,b,null,!1)},"~N,JU.BS");c(c$,"rotateYRadians",function(a,b){this.applyRotation(this.matrixTemp3.setAsYRotation(a),!1,b,null,!1)},"~N,JU.BS");c(c$,"rotateZRadians",function(a){this.applyRotation(this.matrixTemp3.setAsZRotation(a),!1,null,null,!1)},"~N");c(c$,"rotateAxisAngle",function(a,b){this.axisangleT.setVA(a,b);this.rotateAxisAngle2(this.axisangleT,null)},"JU.V3,~N");c(c$,"rotateAxisAngle2",function(a,b){this.applyRotation(this.matrixTemp3.setAA(a),
!1,b,null,!1)},"JU.A4,JU.BS");c(c$,"rotateAxisAngleAtCenter",function(a,b,d,c,g,f,j){null!=b&&this.moveRotationCenter(b,!0);this.setSpinOff();this.setNavOn(!1);if(this.vwr.isHeadless()){if(f&&3.4028235E38==g)return!1;f=!1}if(Float.isNaN(c)||0==c||0==g)return!1;null!=b&&this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(d);this.rotationRate=c;if(f)return this.fixedRotationAxis.setVA(d,0.017453292*c),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=
j,this.setSpin(a,!0,g,null,null,j,!1),!1;a=0.017453292*g;this.fixedRotationAxis.setVA(d,g);this.rotateAxisAngleRadiansFixed(a,j);return!0},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAxisAngleRadiansFixed",function(a,b){this.axisangleT.setAA(this.fixedRotationAxis);this.axisangleT.angle=a;this.rotateAxisAngle2(this.axisangleT,b)},"~N,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,d,c,g,f,j,h,l,m,r,n){this.setSpinOff();this.setNavOn(!1);if(null==n&&(null==m||0.001>m.length())&&
(!j||0==g||Float.isNaN(c)||0==c)&&(j||0==g))return!1;var p=null;null==n&&(p=JU.V3.newVsub(d,b),f&&p.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(p),this.internalTranslation=null==m?null:JU.V3.newV(m));b=null!=h;if(j)return null==n?(j=q(Math.abs(g)/Math.abs(c)*this.spinFps+0.5),Float.isNaN(g)?this.rotationRate=c:(this.rotationRate=g/j*this.spinFps,null!=m&&this.internalTranslation.scale(1/j)),this.internalRotationAxis.setVA(p,0.017453292*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),
this.isSpinInternal=!0,this.isSpinFixed=!1,this.isSpinSelected=b):g=c,this.setSpin(a,!0,g,r,n,h,l),null!=n||null!=h;a=0.017453292*g;this.internalRotationAxis.setVA(p,a);this.rotateAxisAngleRadiansInternal(a,h);return!1},"J.api.JmolScriptEvaluator,JU.T3,JU.T3,~N,~N,~B,~B,JU.BS,~B,JU.V3,JU.Lst,~A");c(c$,"rotateAxisAngleRadiansInternal",function(a,b){this.internalRotationAngle=a;this.vectorT.set(this.internalRotationAxis.x,this.internalRotationAxis.y,this.internalRotationAxis.z);this.matrixRotate.rotate2(this.vectorT,
this.vectorT2);this.axisangleT.setVA(this.vectorT2,a);this.applyRotation(this.matrixTemp3.setAA(this.axisangleT),!0,b,this.internalTranslation,1E6<a);null==b&&this.getNewFixedRotationCenter()},"~N,JU.BS");c(c$,"getNewFixedRotationCenter",function(){this.axisangleT.setAA(this.internalRotationAxis);this.axisangleT.angle=-this.internalRotationAngle;this.matrixTemp4.setToAA(this.axisangleT);this.vectorT.setT(this.internalRotationCenter);this.pointT2.sub2(this.fixedRotationCenter,this.vectorT);var a=new JU.P3;
this.matrixTemp4.rotTrans2(this.pointT2,a);a.add(this.vectorT);this.setRotationCenterAndRadiusXYZ(a,!1)});c(c$,"setTranslationFractions",function(){this.xTranslationFraction=this.fixedTranslation.x/this.width;this.yTranslationFraction=this.fixedTranslation.y/this.height});c(c$,"centerAt",function(a,b,d){null==d?this.translateXYBy(a,b):(this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1),this.fixedTranslation.x=a,this.fixedTranslation.y=b,this.setFixedRotationCenter(d))},"~N,~N,JU.P3");
c(c$,"percentToPixels",function(a,b){switch(a){case "x":return q(Math.floor(b/100*this.width));case "y":return q(Math.floor(b/100*this.height));case "z":return q(Math.floor(b/100*this.screenPixelCount))}return 0},"~S,~N");c(c$,"angstromsToPixels",function(a){return q(Math.floor(this.scalePixelsPerAngstrom*a))},"~N");c(c$,"translateXYBy",function(a,b){this.fixedTranslation.x+=a;this.fixedTranslation.y+=b;this.setTranslationFractions()},"~N,~N");c(c$,"setCamera",function(a,b){this.cameraSetting.set(a,
b,0==a&&0==b?0:1)},"~N,~N");c(c$,"translateToPercent",function(a,b){switch(a){case "x":this.xTranslationFraction=0.5+b/100;this.fixedTranslation.x=this.width*this.xTranslationFraction;break;case "y":this.yTranslationFraction=0.5+b/100;this.fixedTranslation.y=this.height*this.yTranslationFraction;break;case "z":1==this.mode&&this.setNavigationDepthPercent(b)}},"~S,~N");c(c$,"getTranslationXPercent",function(){return 0==this.width?0:100*(this.fixedTranslation.x-this.width/2)/this.width});c(c$,"getTranslationYPercent",
function(){return 0==this.height?0:100*(this.fixedTranslation.y-this.height/2)/this.height});c(c$,"getTranslationZPercent",function(){return 0});c(c$,"getTranslationScript",function(){var a="",b=this.getTranslationXPercent();0!=b&&(a+="translate x "+b+";");b=this.getTranslationYPercent();0!=b&&(a+="translate y "+b+";");return a});c(c$,"getOrientationText",function(a){switch(a){case 4130:return this.getMoveToText(1,!1);case 1073742132:return this.getRotationQuaternion().toString();case 1073742178:return a=
new JU.SB,JV.TransformManager.truncate2(a,this.getTranslationXPercent()),JV.TransformManager.truncate2(a,this.getTranslationYPercent()),a.toString();default:return this.getMoveToText(1,!0)+"\n#OR\n"+this.getRotateZyzText(!0)}},"~N");c(c$,"getOrientationInfo",function(){var a=new java.util.Hashtable;a.put("moveTo",this.getMoveToText(1,!1));a.put("center","center "+this.getCenterText());a.put("centerPt",this.fixedRotationCenter);var b=new JU.A4;this.getAxisAngle(b);a.put("axisAngle",b);a.put("quaternion",
JU.Quat.newAA(b).toPoint4f());a.put("rotationMatrix",this.matrixRotate);a.put("rotateZYZ",this.getRotateZyzText(!1));a.put("rotateXYZ",this.getRotateXyzText());a.put("transXPercent",Float.$valueOf(this.getTranslationXPercent()));a.put("transYPercent",Float.$valueOf(this.getTranslationYPercent()));a.put("zoom",Float.$valueOf(this.zmPct));a.put("modelRadius",Float.$valueOf(this.modelRadius));1==this.mode&&(a.put("navigationCenter","navigate center "+JU.Escape.eP(this.navigationCenter)),a.put("navigationOffsetXPercent",
Float.$valueOf(this.getNavigationOffsetPercent("X"))),a.put("navigationOffsetYPercent",Float.$valueOf(this.getNavigationOffsetPercent("Y"))),a.put("navigationDepthPercent",Float.$valueOf(this.getNavigationDepthPercent())));return a});c(c$,"getAxisAngle",function(a){a.setM(this.matrixRotate)},"JU.A4");c(c$,"getTransformText",function(){return this.matrixRotate.toString()});c(c$,"getMatrixRotate",function(){return JU.M3.newM3(this.matrixRotate)});c(c$,"getRotation",function(a){a.setM3(this.matrixRotate)},
"JU.M3");c(c$,"zoomBy",function(a){20<a?a=20:-20>a&&(a=-20);var b=a*this.zmPctSet/50;0==b&&(b=0<a?1:0>b?-1:0);this.zoomRatio=(b+this.zmPctSet)/this.zmPctSet;this.zmPctSet+=b},"~N");c(c$,"getZoomPercentFloat",function(){return this.zmPct});c(c$,"zoomToPercent",function(a){this.zmPctSet=a;this.zoomRatio=0},"~N");c(c$,"translateZBy",function(a){a>=this.screenPixelCount||(a=this.scalePixelsPerAngstrom/(1-1*a/this.screenPixelCount),a>=this.screenPixelCount||(a=100*(a/this.scaleDefaultPixelsPerAngstrom),
this.zoomRatio=a/this.zmPctSet,this.zmPctSet=a))},"~N");c(c$,"resetXYCenter",function(a,b){if(!(2147483647==a||2147483647==b)){this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1);var d=new JU.P3;this.transformPt3f(this.fixedRotationCenter,d);d.set(a,b,d.z);this.unTransformPoint(d,d);this.fixedTranslation.set(a,b,0);this.setFixedRotationCenter(d)}},"~N,~N");c(c$,"zoomByPercent",function(a){var b=a*this.zmPctSet/100;0==b&&(b=0>a?-1:1);this.zoomRatio=(b+this.zmPctSet)/this.zmPctSet;
this.zmPctSet+=b},"~N");c(c$,"setScaleAngstromsPerInch",function(a){if(this.scale3D=0<a)this.scale3DAngstromsPerInch=a;this.perspectiveDepth=!this.scale3D},"~N");c(c$,"setZslabPoint",function(a){this.zSlabPoint=null==a?null:JU.P3.newP(a)},"JU.P3");c(c$,"getZShadeStart",function(){return this.zShadeEnabled?this.zDepthValue:0});c(c$,"setSlabRange",function(a){this.slabRange=a},"~N");c(c$,"setSlabEnabled",function(a){this.slabEnabled=a;this.vwr.g.setB("slabEnabled",a)},"~B");c(c$,"setZShadeEnabled",
function(a){this.zShadeEnabled=a;this.vwr.g.setB("zShade",a)},"~B");c(c$,"setZoomEnabled",function(a){this.zoomEnabled=a;this.vwr.g.setB("zoomEnabled",a)},"~B");c(c$,"slabReset",function(){this.slabToPercent(100);this.depthToPercent(0);this.slabPlane=this.depthPlane=null;this.setSlabEnabled(!1);this.setZShadeEnabled(!1)});c(c$,"getSlabPercentSetting",function(){return this.slabPercentSetting});c(c$,"slabByPercentagePoints",function(a){this.slabPlane=null;this.slabPercentSetting+=a;this.slabDepthChanged();
this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1)},"~N");c(c$,"slabDepthChanged",function(){this.vwr.g.setI("slab",this.slabPercentSetting);this.vwr.g.setI("depth",this.depthPercentSetting)});c(c$,"depthByPercentagePoints",function(a){this.depthPlane=null;this.depthPercentSetting+=a;this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1);this.slabDepthChanged()},"~N");c(c$,"slabDepthByPercentagePoints",
function(a){this.depthPlane=this.slabPlane=null;this.slabPercentSetting+=a;this.depthPercentSetting+=a;this.slabDepthChanged()},"~N");c(c$,"slabToPercent",function(a){this.vwr.setFloatProperty("slabRange",0);this.slabPercentSetting=a;this.slabPlane=null;this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1);this.slabDepthChanged()},"~N");c(c$,"depthToPercent",function(a){this.vwr.g.setI("depth",a);this.depthPercentSetting=a;this.slabPercentSetting<=
this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1);this.slabDepthChanged()},"~N");c(c$,"zSlabToPercent",function(a){this.zSlabPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zDepthPercentSetting=a)},"~N");c(c$,"zDepthToPercent",function(a){this.zDepthPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zSlabPercentSetting=a)},"~N");c(c$,"slabInternal",function(a,b){b?(this.depthPlane=a,this.depthPercentSetting=0):(this.slabPlane=
a,this.slabPercentSetting=100)},"JU.P4,~B");c(c$,"setSlabDepthInternal",function(a){this.finalizeTransformParameters();a?this.depthPlane=null:this.slabPlane=null;this.slabInternal(this.getSlabDepthPlane(a),a)},"~B");c(c$,"getSlabDepthPlane",function(a){if(a){if(null!=this.depthPlane)return this.depthPlane}else if(null!=this.slabPlane)return this.slabPlane;var b=this.matrixTransform;return JU.P4.new4(-b.m20,-b.m21,-b.m22,-b.m23+(a?this.depthValue:this.slabValue))},"~B");c(c$,"getCameraFactors",function(){this.aperatureAngle=
360*Math.atan2(this.screenPixelCount/2,this.referencePlaneOffset)/3.141592653589793;this.cameraDistanceFromCenter=this.referencePlaneOffset/this.scalePixelsPerAngstrom;var a=JU.P3.new3(q(this.screenWidth/2),q(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(q(this.screenWidth/2),q(this.screenHeight/2),0);this.vwr.tm.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);var d=JU.P3.new3(q(this.screenWidth/2),q(this.screenHeight/2),this.cameraDistanceFromCenter*
this.scalePixelsPerAngstrom);this.vwr.tm.unTransformPoint(d,d);d.sub(this.fixedRotationCenter);b.add(d);System.out.println("TM no "+this.navigationOffset+" rpo "+this.referencePlaneOffset+" aa "+this.aperatureAngle+" sppa "+this.scalePixelsPerAngstrom+" vr "+this.visualRange+" sw/vr "+this.screenWidth/this.visualRange+" "+a+" "+this.fixedRotationCenter);return[a,b,this.fixedRotationCenter,JU.P3.new3(this.cameraDistanceFromCenter,this.aperatureAngle,this.scalePixelsPerAngstrom)]});c(c$,"setPerspectiveDepth",
function(a){this.perspectiveDepth!=a&&(this.perspectiveDepth=a,this.vwr.g.setB("perspectiveDepth",a),this.resetFitToScreen(!1))},"~B");c(c$,"getPerspectiveDepth",function(){return this.perspectiveDepth});c(c$,"setCameraDepthPercent",function(a,b){this.resetNavigationPoint(b);var d=0>a?-a/100:a;0!=d&&(this.cameraDepthSetting=d,this.vwr.g.setF("cameraDepth",this.cameraDepthSetting),this.cameraDepth=NaN)},"~N,~B");c(c$,"getCameraDepth",function(){return this.cameraDepthSetting});c(c$,"setVisualRange",
function(a){this.visualRange=a},"~N");c(c$,"setScreenParameters0",function(a,b,d,c,g,f){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=d,this.width=(this.antialias=c)?2*a:a,this.height=c?2*b:b,this.scaleFitToScreen(!1,d,g,f))},"~N,~N,~B,~B,~B,~B");c(c$,"setAntialias",function(a){var b=this.antialias!=a;this.width=(this.antialias=a)?2*this.screenWidth:this.screenWidth;this.height=this.antialias?2*this.screenHeight:this.screenHeight;b&&this.scaleFitToScreen(!1,this.useZoomLarge,
!1,!1)},"~B");c(c$,"defaultScaleToScreen",function(a){return this.screenPixelCount/2/a},"~N");c(c$,"resetFitToScreen",function(a){this.scaleFitToScreen(a,this.vwr.g.zoomLarge,!0,!0)},"~B");c(c$,"scaleFitToScreen",function(a,b,d,c){0==this.width||0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*(a?0.5:this.xTranslationFraction),this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),c&&this.resetNavigationPoint(d),this.zoomHeight&&
(b=this.height>this.width),this.screenPixelCount=b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");c(c$,"scaleToScreen",function(a,b){if(0==b||2>a)return 0;var d=this.scaleToPerspective(a,b*this.scalePixelsPerAngstrom/1E3);return 0<d?d:1},"~N,~N");c(c$,"unscaleToScreen",function(a,b){var d=b/this.scalePixelsPerAngstrom;return this.perspectiveDepth?d/this.getPerspectiveFactor(a):
d},"~N,~N");c(c$,"scaleToPerspective",function(a,b){return this.perspectiveDepth?b*this.getPerspectiveFactor(a):b},"~N,~N");c(c$,"getMatrixtransform",function(){return this.matrixTransform});c(c$,"setNavigationMode",function(a){this.mode=a&&this.canNavigate()?1:this.defaultMode;this.resetNavigationPoint(!0)},"~B");c(c$,"isNavigating",function(){return this.navigating||this.navOn});c(c$,"finalizeTransformParameters",function(){this.haveNotifiedNaN=!1;this.fixedRotationOffset.setT(this.fixedTranslation);
this.camera.setT(this.cameraSetting);this.internalSlab=this.slabEnabled&&(null!=this.slabPlane||null!=this.depthPlane);var a=this.getZoomSetting();this.zmPct!=a&&(this.zmPct=a,this.vwr.g.fontCaching||this.vwr.gdata.clearFontCache());this.calcCameraFactors();this.calcTransformMatrix();1==this.mode?this.calcNavigationPoint():this.calcSlabAndDepthValues()});c(c$,"getZoomSetting",function(){5>this.zmPctSet&&(this.zmPctSet=5);2E5<this.zmPctSet&&(this.zmPctSet=2E5);return this.zoomEnabled||1==this.mode?
this.zmPctSet:100});c(c$,"calcSlabAndDepthValues",function(){this.slabValue=1>this.slabRange?this.zValueFromPercent(this.slabPercentSetting):q(Math.floor(this.modelCenterOffset*this.slabRange/(2*this.modelRadius)*(this.zmPctSet/100)));this.depthValue=this.zValueFromPercent(this.depthPercentSetting);this.zSlabPercentSetting==this.zDepthPercentSetting?(this.zSlabValue=this.slabValue,this.zDepthValue=this.depthValue):(this.zSlabValue=this.zValueFromPercent(this.zSlabPercentSetting),this.zDepthValue=
this.zValueFromPercent(this.zDepthPercentSetting));if(null!=this.zSlabPoint)try{this.transformPt3f(this.zSlabPoint,this.pointT2),this.zSlabValue=z(this.pointT2.z)}catch(a){if(!y(a,Exception))throw a;}this.vwr.g.setO("_slabPlane",JU.Escape.eP4(this.getSlabDepthPlane(!1)));this.vwr.g.setO("_depthPlane",JU.Escape.eP4(this.getSlabDepthPlane(!0)));this.slabEnabled||(this.slabValue=0,this.depthValue=2147483647)});c(c$,"zValueFromPercent",function(a){return q(Math.floor((1-a/50)*this.modelRadiusPixels+this.modelCenterOffset))},
"~N");c(c$,"calcTransformMatrix",function(){this.matrixTransform.setIdentity();this.vectorTemp.sub2(this.frameOffset,this.fixedRotationCenter);this.matrixTransform.setTranslation(this.vectorTemp);this.matrixTemp.setToM3(this.stereoFrame?this.matrixStereo:this.matrixRotate);this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTemp.setIdentity();this.matrixTemp.m00=this.matrixTemp.m11=this.matrixTemp.m22=this.scalePixelsPerAngstrom;this.matrixTemp.m11=this.matrixTemp.m22=-this.scalePixelsPerAngstrom;
this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTransform.m23+=this.modelCenterOffset;try{this.matrixTransformInv.invertM(this.matrixTransform)}catch(a){if(y(a,Exception))System.out.println("ERROR INVERTING matrixTransform!");else throw a;}});c(c$,"rotatePoint",function(a,b){this.matrixRotate.rotate2(a,b);b.y=-b.y},"JU.T3,JU.T3");c(c$,"getScreenTemp",function(a){this.matrixTransform.rotTrans2(a,this.point3fScreenTemp)},"JU.T3");c(c$,"transformPoints",function(a,b,d){for(;0<=
--a;)d[a].setT(this.transformPt(b[a]))},"~N,~A,~A");c(c$,"transformPtScr",function(a,b){b.setT(this.transformPt(a))},"JU.T3,JU.P3i");c(c$,"transformPtNoClip",function(a,b){this.applyPerspective(a,null);b.setT(this.point3fScreenTemp)},"JU.P3,JU.P3");c(c$,"transformPt",function(a){return this.applyPerspective(a,this.internalSlab?a:null)},"JU.T3");c(c$,"transformPtVib",function(a,b){this.ptVibTemp.setT(a);return this.applyPerspective(this.getVibrationPoint(b,this.ptVibTemp,NaN),a)},"JU.P3,JU.Vibration");
c(c$,"getVibrationPoint",function(a,b,d){a.setTempPoint(b,this.vibrationT,Float.isNaN(d)?this.vibrationScale:d,this.vwr.g.modulationScale);return b},"JU.Vibration,JU.T3,~N");c(c$,"transformPt3f",function(a,b){this.applyPerspective(a,a);b.setT(this.point3fScreenTemp)},"JU.T3,JU.P3");c(c$,"transformPt2D",function(a){-3.4028235E38==a.z?(this.point3iScreenTemp.x=q(Math.floor(a.x/100*this.screenWidth)),this.point3iScreenTemp.y=q(Math.floor((1-a.y/100)*this.screenHeight))):(this.point3iScreenTemp.x=z(a.x),
this.point3iScreenTemp.y=this.screenHeight-z(a.y));this.antialias&&(this.point3iScreenTemp.x<<=1,this.point3iScreenTemp.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.point3fScreenTemp);this.point3iScreenTemp.z=z(this.point3fScreenTemp.z);return this.point3iScreenTemp},"JU.T3");c(c$,"applyPerspective",function(a,b){this.getScreenTemp(a);var d=this.point3fScreenTemp.z;Float.isNaN(d)?(!this.haveNotifiedNaN&&JU.Logger.debugging&&JU.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=
!0,d=this.point3fScreenTemp.z=1):0>=d&&(d=this.point3fScreenTemp.z=1);switch(this.mode){case 1:this.point3fScreenTemp.x-=this.navigationShiftXY.x;this.point3fScreenTemp.y-=this.navigationShiftXY.y;break;case 2:this.point3fScreenTemp.x+=this.perspectiveShiftXY.x,this.point3fScreenTemp.y+=this.perspectiveShiftXY.y}this.perspectiveDepth&&(d=this.getPerspectiveFactor(d),this.point3fScreenTemp.x*=d,this.point3fScreenTemp.y*=d);switch(this.mode){case 1:this.point3fScreenTemp.x+=this.navigationOffset.x;
this.point3fScreenTemp.y+=this.navigationOffset.y;break;case 2:this.point3fScreenTemp.x-=this.perspectiveShiftXY.x,this.point3fScreenTemp.y-=this.perspectiveShiftXY.y;case 0:this.point3fScreenTemp.x+=this.fixedRotationOffset.x,this.point3fScreenTemp.y+=this.fixedRotationOffset.y}Float.isNaN(this.point3fScreenTemp.x)&&!this.haveNotifiedNaN&&(JU.Logger.debugging&&JU.Logger.debug("NaN found in transformPoint "),this.haveNotifiedNaN=!0);this.point3iScreenTemp.set(z(this.point3fScreenTemp.x),z(this.point3fScreenTemp.y),
z(this.point3fScreenTemp.z));if(null!=b&&(null!=this.slabPlane&&0<b.x*this.slabPlane.x+b.y*this.slabPlane.y+b.z*this.slabPlane.z+this.slabPlane.w||null!=this.depthPlane&&0>b.x*this.depthPlane.x+b.y*this.depthPlane.y+b.z*this.depthPlane.z+this.depthPlane.w))this.point3iScreenTemp.z=1;return this.point3iScreenTemp},"JU.T3,JU.T3");c(c$,"transformVector",function(a,b){this.matrixTransform.rotate2(a,b)},"JU.V3,JU.V3");c(c$,"move",function(a,b,d,c,g,f,j){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread");
this.movetoThread.setManager(this,this.vwr,[b,c,[d,g,f,j]]);0<f&&this.movetoThread.setEval(a);this.movetoThread.run()},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(c$,"isInPosition",function(a,b){if(Float.isNaN(b))return!0;this.aaTest1.setVA(a,b/57.29577951308232);this.ptTest1.set(4.321,1.23456,3.14159);this.getRotation(this.matrixTest);this.matrixTest.rotate2(this.ptTest1,this.ptTest2);this.matrixTest.setAA(this.aaTest1).rotate2(this.ptTest1,this.ptTest3);return 0.1>this.ptTest3.distance(this.ptTest2)},
"JU.V3,~N");c(c$,"moveToPyMOL",function(a,b,d){var c=JU.M3.newA9(d);c.invert();var g=d[9],f=-d[10],j=-d[11],h=JU.P3.new3(d[12],d[13],d[14]),l=d[15],m=d[16],r=d[17];this.setPerspectiveDepth(!(0<=r));var r=Math.abs(r)/2,n=Math.tan(3.141592653589793*r/180),r=j*n,n=0.5/n-0.5,q=50/r;0<l&&(l=50+z((j-l)*q),j=50+z((j-m)*q),this.setSlabEnabled(!0),this.slabToPercent(l),this.depthToPercent(j),21==d.length&&(m=0!=d[18],q=0!=d[19],d=d[20],this.setZShadeEnabled(m),m&&(q?this.vwr.setIntProperty("zSlab",z(Math.min(100,
l+d*(j-l)))):this.vwr.setIntProperty("zSlab",z((l+j)/2)),this.vwr.setIntProperty("zDepth",j))));this.moveTo(a,b,h,null,0,c,100,NaN,NaN,r,null,NaN,NaN,NaN,n,g,f);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(c$,"moveTo",function(a,b,d,c,g,f,j,h,l,m,r,n,q,p,s,t,u){if(null==f)if(f=new JU.M3,c=JU.V3.newV(c),Float.isNaN(g))f.m00=NaN;else if(0.01>g&&-0.01<g)f.setScale(1);else{if(0==c.x&&0==c.y&&0==c.z)return;var v=new JU.A4;v.setVA(c,g/57.29577951308232);f.setAA(v)}t==this.cameraSetting.x&&(t=NaN);u==
this.cameraSetting.y&&(u=NaN);s==this.cameraDepth&&(s=NaN);Float.isNaN(t)||(h=50*t/m/this.width*this.screenPixelCount);Float.isNaN(u)||(l=50*u/m/this.height*this.screenPixelCount);g=null==d?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(m);if(0>=b)this.setAll(d,f,r,j,h,l,m,g,p,n,q,s,t,u),this.vwr.moveUpdate(b),this.vwr.finalizeTransformParameters();else try{null==this.movetoThread&&(this.movetoThread=J.api.Interface.getOption("thread.MoveToThread"));var w=this.movetoThread.setManager(this,
this.vwr,[d,f,r,[b,j,h,l,m,g,p,n,q,s,t,u]]);0>=w||this.vwr.g.waitForMoveTo?(0<w&&this.movetoThread.setEval(a),this.movetoThread.run(),this.vwr.isSingleThreaded||(this.movetoThread=null)):this.movetoThread.start()}catch(z){if(!y(z,Exception))throw z;}},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.T3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(c$,"stopMotion",function(){this.movetoThread=null});c(c$,"getRotationQuaternion",function(){return JU.Quat.newM(this.matrixRotate)});c(c$,"getRotationText",function(){this.axisangleT.setM(this.matrixRotate);
var a=57.29577951308232*this.axisangleT.angle,b=new JU.SB;this.vectorT.set(this.axisangleT.x,this.axisangleT.y,this.axisangleT.z);if(0.01>a)return"{0 0 1 0}";this.vectorT.normalize();this.vectorT.scale(1E3);b.append("{");JV.TransformManager.truncate0(b,this.vectorT.x);JV.TransformManager.truncate0(b,this.vectorT.y);JV.TransformManager.truncate0(b,this.vectorT.z);JV.TransformManager.truncate2(b,a);b.append("}");return b.toString()});c(c$,"getMoveToText",function(a,b){this.finalizeTransformParameters();
var d=new JU.SB;d.append("moveto ");b&&d.append("/* time, axisAngle */ ");d.appendF(a);d.append(" ").append(this.getRotationText());b&&d.append(" /* zoom, translation */ ");JV.TransformManager.truncate2(d,this.zmPctSet);JV.TransformManager.truncate2(d,this.getTranslationXPercent());JV.TransformManager.truncate2(d,this.getTranslationYPercent());d.append(" ");b&&d.append(" /* center, rotationRadius */ ");d.append(this.getCenterText());d.append(" ").appendF(this.modelRadius);d.append(this.getNavigationText(b));
b&&d.append(" /* cameraDepth, cameraX, cameraY */ ");JV.TransformManager.truncate2(d,this.cameraDepth);JV.TransformManager.truncate2(d,this.cameraSetting.x);JV.TransformManager.truncate2(d,this.cameraSetting.y);d.append(";");return d.toString()},"~N,~B");c(c$,"getCenterText",function(){return JU.Escape.eP(this.fixedRotationCenter)});c(c$,"getRotateXyzText",function(){var a=new JU.SB,b=this.matrixRotate.m20,d=-(57.29577951308232*Math.asin(b)),c;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,
this.matrixRotate.m11)),c=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,this.matrixRotate.m22),c=57.29577951308232*Math.atan2(this.matrixRotate.m10,this.matrixRotate.m00));a.append("reset");a.append(";center ").append(this.getCenterText());0!=b&&(a.append("; rotate x"),JV.TransformManager.truncate2(a,b));0!=d&&(a.append("; rotate y"),JV.TransformManager.truncate2(a,d));0!=c&&(a.append("; rotate z"),JV.TransformManager.truncate2(a,c));a.append(";");this.addZoomTranslationNavigationText(a);
return a.toString()});c(c$,"addZoomTranslationNavigationText",function(a){100!=this.zmPct&&(a.append(" zoom"),JV.TransformManager.truncate2(a,this.zmPct),a.append(";"));var b=this.getTranslationXPercent();0!=b&&(a.append(" translate x"),JV.TransformManager.truncate2(a,b),a.append(";"));b=this.getTranslationYPercent();0!=b&&(a.append(" translate y"),JV.TransformManager.truncate2(a,b),a.append(";"));if(this.modelRadius!=this.rotationRadiusDefault||10==this.modelRadius)a.append(" set rotationRadius"),
JV.TransformManager.truncate2(a,this.modelRadius),a.append(";");1==this.mode&&(a.append("navigate 0 center ").append(JU.Escape.eP(this.navigationCenter)),a.append(";navigate 0 translate"),JV.TransformManager.truncate2(a,this.getNavigationOffsetPercent("X")),JV.TransformManager.truncate2(a,this.getNavigationOffsetPercent("Y")),a.append(";navigate 0 depth "),JV.TransformManager.truncate2(a,this.getNavigationDepthPercent()),a.append(";"))},"JU.SB");c(c$,"getRotateZyzText",function(a){var b=new JU.SB,
d=this.vwr.ms.getInfoM("defaultOrientationMatrix");null==d?d=this.matrixRotate:(d=JU.M3.newM3(d),d.invert(),d.mul2(this.matrixRotate,d));var c=d.m22,g=57.29577951308232*Math.acos(c);0.999<c||-0.999>c?(c=57.29577951308232*Math.atan2(d.m10,d.m11),d=0):(c=57.29577951308232*Math.atan2(d.m21,-d.m20),d=57.29577951308232*Math.atan2(d.m12,d.m02));0!=c&&(0!=g&&0!=d&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");b.append("reset");b.append(";center ").append(this.getCenterText());0!=c&&(b.append("; rotate z"),
JV.TransformManager.truncate2(b,c));0!=g&&(b.append("; rotate y"),JV.TransformManager.truncate2(b,g));0!=d&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,d));b.append(";");this.addZoomTranslationNavigationText(b);return b.toString()},"~B");c$.truncate0=c(c$,"truncate0",function(a,b){a.appendC(" ");a.appendI(Math.round(b))},"JU.SB,~N");c$.truncate2=c(c$,"truncate2",function(a,b){a.appendC(" ");a.appendF(Math.round(100*b)/100)},"JU.SB,~N");c(c$,"setSpinXYZ",function(a,b,d){Float.isNaN(a)||
(this.spinX=a);Float.isNaN(b)||(this.spinY=b);Float.isNaN(d)||(this.spinZ=d);(this.isSpinInternal||this.isSpinFixed)&&this.clearSpin()},"~N,~N,~N");c(c$,"setSpinFps",function(a){0>=a?a=1:50<a&&(a=50);this.spinFps=a},"~N");c(c$,"setNavXYZ",function(a,b,d){Float.isNaN(a)||(this.navX=a);Float.isNaN(b)||(this.navY=b);Float.isNaN(d)||(this.navZ=d)},"~N,~N,~N");c(c$,"clearSpin",function(){this.setSpinOff();this.setNavOn(!1);this.isSpinFixed=this.isSpinInternal=!1});c(c$,"setSpinOn",function(){this.setSpin(null,
!0,3.4028235E38,null,null,null,!1)});c(c$,"setSpinOff",function(){this.setSpin(null,!1,3.4028235E38,null,null,null,!1)});c(c$,"setSpin",function(a,b,d,c,g,f,j){this.navOn&&b&&this.setNavOn(!1);this.spinOn!=b&&(this.spinOn=b,this.vwr.g.setB("_spinning",b),b?null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread"),this.spinThread.setManager(this,this.vwr,[Float.$valueOf(d),c,g,f,j?Boolean.TRUE:null]),this.spinIsGesture=j,null==f&&null==g?this.spinThread.start():(this.spinThread.setEval(a),
this.spinThread.run())):null!=this.spinThread&&(this.spinThread.reset(),this.spinThread=null))},"J.api.JmolScriptEvaluator,~B,~N,JU.Lst,~A,JU.BS,~B");c(c$,"setNavOn",function(a){if(!Float.isNaN(this.navFps)){var b=this.navOn;a&&this.spinOn&&this.setSpin(null,!1,0,null,null,null,!1);this.navOn=a;this.vwr.g.setB("_navigating",a);a||this.navInterrupt();a?(0==this.navX&&(0==this.navY&&0==this.navZ)&&(this.navZ=1),0==this.navFps&&(this.navFps=10),null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread"),
this.spinThread.setManager(this,this.vwr,null),this.spinThread.start())):b&&null!=this.spinThread&&(this.spinThread.interrupt(),this.spinThread=null)}},"~B");c(c$,"setVibrationScale",function(a){this.vibrationScale=a},"~N");c(c$,"setVibrationPeriod",function(a){if(Float.isNaN(a))a=this.vibrationPeriod;else if(0==a)this.vibrationPeriodMs=this.vibrationPeriod=0;else{this.vibrationPeriod=Math.abs(a);this.vibrationPeriodMs=z(1E3*this.vibrationPeriod);if(0<a)return;a=-a}this.setVibrationOn(0<a&&0<=this.vwr.modelGetLastVibrationIndex(this.vwr.am.cmi,
0))},"~N");c(c$,"setVibrationT",function(a){this.vibrationT.x=a;0==this.vibrationScale&&(this.vibrationScale=this.vwr.g.vibrationScale)},"~N");c(c$,"isVibrationOn",function(){return this.vibrationOn});c(c$,"setVibrationOn",function(a){a?1>this.vwr.getModelCount()?(this.vibrationOn=!1,this.vibrationT.x=0):(null==this.vibrationThread&&(this.vibrationThread=J.api.Interface.getOption("thread.VibrationThread"),this.vibrationThread.setManager(this,this.vwr,null),this.vibrationThread.start()),this.vibrationOn=
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c(c$,"setRotationRadius",function(a,b){a=this.modelRadius=0>=a?this.vwr.calcRotationRadius(this.fixedRotationCenter):a;b&&this.vwr.setRotationRadius(a,!1);return a},"~N,~B");c(c$,"setRotationCenterAndRadiusXYZ",function(a,b){this.resetNavigationPoint(!1);null==a?(this.setFixedRotationCenter(this.rotationCenterDefault),this.modelRadius=this.rotationRadiusDefault):(this.setFixedRotationCenter(a),b&&this.windowCentered&&(this.modelRadius=this.vwr.calcRotationRadius(this.fixedRotationCenter)))},"JU.P3,~B");
c(c$,"setNewRotationCenter",function(a,b){null==a&&(a=this.rotationCenterDefault);this.windowCentered?(this.translateToPercent("x",0),this.translateToPercent("y",0),this.setRotationCenterAndRadiusXYZ(a,!0),b&&this.resetFitToScreen(!0)):this.moveRotationCenter(a,!0)},"JU.P3,~B");c(c$,"moveRotationCenter",function(a,b){this.setRotationCenterAndRadiusXYZ(a,!1);b&&this.setRotationPointXY(this.fixedRotationCenter)},"JU.P3,~B");c(c$,"setCenter",function(){this.setRotationCenterAndRadiusXYZ(this.fixedRotationCenter,
!0)});c(c$,"setCenterAt",function(a,b){var d=JU.P3.newP(b);switch(a){case 96:d.add(this.vwr.ms.getAverageAtomPoint());break;case 1679429641:d.add(this.vwr.getBoundBoxCenter());break;case 1073741826:d.setT(this.rotationCenterDefault)}this.setRotationCenterAndRadiusXYZ(d,!0);this.resetFitToScreen(!0)},"~N,JU.P3");c(c$,"setFrameOffset",function(a){null==this.frameOffsets||0>a||a>=this.frameOffsets.length?this.frameOffset.set(0,0,0):this.frameOffset.setT(this.frameOffsets[a])},"~N");c(c$,"setFrameOffsets",
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this.referencePlaneOffset=this.cameraDistance+this.screenPixelCount/2;this.scalePixelsPerAngstrom=this.scale3D&&!this.perspectiveDepth&&1!=this.mode?72/this.scale3DAngstromsPerInch*(this.antialias?2:1):this.screenPixelCount/this.visualRange;1!=this.mode&&(this.mode=0==this.camera.z?0:2);this.perspectiveShiftXY.set(0==this.camera.z?0:100*(this.camera.x*this.scalePixelsPerAngstrom/this.screenWidth),0==this.camera.z?0:100*(this.camera.y*this.scalePixelsPerAngstrom/this.screenHeight),0);this.modelRadiusPixels=
this.modelRadius*this.scalePixelsPerAngstrom;var a=2*this.modelRadius/this.visualRange*this.referencePlaneOffset;if(1==this.mode)this.calcNavCameraFactors(a);else{this.zoomFactor=3.4028235E38;this.modelCenterOffset=this.referencePlaneOffset;if(!this.scale3D||this.perspectiveDepth)this.scalePixelsPerAngstrom*=this.modelCenterOffset/a*this.zmPct/100;this.modelRadiusPixels=this.modelRadius*this.scalePixelsPerAngstrom}});c(c$,"calcNavCameraFactors",function(a){3.4028235E38==this.zoomFactor?(1E4<this.zmPct&&
(this.zmPct=1E4),this.modelCenterOffset=100*a/this.zmPct):this.prevZoomSetting!=this.zmPctSet&&(this.modelCenterOffset=0==this.zoomRatio?100*a/this.zmPctSet:this.modelCenterOffset+(1-this.zoomRatio)*this.referencePlaneOffset,this.navMode=-1);this.prevZoomSetting=this.zmPctSet;this.zoomFactor=this.modelCenterOffset/this.referencePlaneOffset;this.zmPct=0==this.zoomFactor?1E4:100*(a/this.modelCenterOffset)},"~N");c(c$,"getPerspectiveFactor",function(a){return 0>=a?this.referencePlaneOffset:this.referencePlaneOffset/
a},"~N");c(c$,"unTransformPoint",function(a,b){this.untransformedPoint.setT(a);switch(this.mode){case 1:this.untransformedPoint.x-=this.navigationOffset.x;this.untransformedPoint.y-=this.navigationOffset.y;break;case 2:this.point3fScreenTemp.x+=this.perspectiveShiftXY.x,this.point3fScreenTemp.y+=this.perspectiveShiftXY.y;case 0:this.untransformedPoint.x-=this.fixedRotationOffset.x,this.untransformedPoint.y-=this.fixedRotationOffset.y}if(this.perspectiveDepth){var d=this.getPerspectiveFactor(this.untransformedPoint.z);
this.untransformedPoint.x/=d;this.untransformedPoint.y/=d}switch(this.mode){case 1:this.untransformedPoint.x+=this.navigationShiftXY.x;this.untransformedPoint.y+=this.navigationShiftXY.y;break;case 2:this.untransformedPoint.x-=this.perspectiveShiftXY.x,this.untransformedPoint.y-=this.perspectiveShiftXY.y}this.matrixTransformInv.rotTrans2(this.untransformedPoint,b)},"JU.T3,JU.T3");c(c$,"canNavigate",function(){return!0});c(c$,"resetNavigationPoint",function(a){5>this.zmPct&&1!=this.mode?(this.perspectiveDepth=
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c(c$,"getNavigationDepthPercent",function(){return this.navigationDepth});c(c$,"setNavigationSlabOffsetPercent",function(a){this.vwr.g.setF("navigationSlab",a);this.calcCameraFactors();this.navigationSlabOffset=a/50*this.modelRadiusPixels},"~N");c(c$,"getNavigationOffset",function(){this.transformPt3f(this.navigationCenter,this.navigationOffset);return this.navigationOffset});c(c$,"getNavPtHeight",function(){return this.height/2});c(c$,"getNavigationOffsetPercent",function(a){this.getNavigationOffset();
return 0==this.width||0==this.height?0:"X"==a?100*(this.navigationOffset.x-this.width/2)/this.width:100*(this.navigationOffset.y-this.getNavPtHeight())/this.height},"~S");c(c$,"getNavigationText",function(a){a=a?" /* navigation center, translation, depth */ ":" ";if(1!=this.mode)return a+"{0 0 0} 0 0 0";this.getNavigationOffset();return a+JU.Escape.eP(this.navigationCenter)+" "+this.getNavigationOffsetPercent("X")+" "+this.getNavigationOffsetPercent("Y")+" "+this.getNavigationDepthPercent()},"~B");
c(c$,"setScreenParameters",function(a,b,d,c,g,f){var j=1==this.mode?JU.P3.newP(this.navigationCenter):null,h=JU.P3.newP(this.navigationOffset);h.x/=this.width;h.y/=this.height;this.setScreenParameters0(a,b,d,c,g,f);null!=j&&(this.navigationCenter.setT(j),this.navTranslatePercentOrTo(-1,h.x*this.width,h.y*this.height),this.setNavigatePt(j))},"~N,~N,~B,~B,~B,~B");c(c$,"navInterrupt",function(){null!=this.nav&&this.nav.interrupt()});c(c$,"getNav",function(){if(null!=this.nav)return!0;this.nav=J.api.Interface.getOption("navigate.Navigator");
if(null==this.nav)return!1;this.nav.set(this,this.vwr);return!0});c(c$,"navigateList",function(a,b){this.getNav()&&this.nav.navigateList(a,b)},"J.api.JmolScriptEvaluator,JU.Lst");c(c$,"navigateAxis",function(a,b){this.getNav()&&this.nav.navigateAxis(a,b)},"JU.V3,~N");c(c$,"zoomByFactor",function(a,b,d){!(0>=a)&&this.zoomEnabled&&(1!=this.mode?(this.zoomRatio=a,this.zmPctSet*=a,this.resetXYCenter(b,d)):this.getNav()&&this.nav.zoomByFactor(a,b,d))},"~N,~N,~N");c(c$,"setNavigationOffsetRelative",function(){this.getNav()&&
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this.nav.getNavigationState():""});c(c$,"setZoomHeight",function(a,b){this.zoomHeight=a;this.scaleFitToScreen(!1,b,!1,!0)},"~B,~B");c(c$,"setAll",function(a,b,d,c,g,f,j,h,l,m,r,n,q,p){Float.isNaN(b.m00)||this.setRotation(b);null!=a&&this.moveRotationCenter(a,!this.windowCentered);null!=d&&1==this.mode&&this.navigationCenter.setT(d);Float.isNaN(n)||this.setCameraDepthPercent(n,!1);!Float.isNaN(q)&&!Float.isNaN(p)&&this.setCamera(q,p);Float.isNaN(c)||this.zoomToPercent(c);Float.isNaN(j)||(this.modelRadius=
j);Float.isNaN(h)||(this.scaleDefaultPixelsPerAngstrom=h);!Float.isNaN(g)&&!Float.isNaN(f)&&(this.translateToPercent("x",g),this.translateToPercent("y",f));1==this.mode&&(!Float.isNaN(m)&&!Float.isNaN(r)&&this.navTranslatePercentOrTo(0,m,r),Float.isNaN(l)||this.setNavigationDepthPercent(l))},"JU.P3,JU.M3,JU.P3,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");C(c$,"degreesPerRadian",57.29577951308232,"DEFAULT_NAV_FPS",10,"DEFAULT_SPIN_Y",30,"DEFAULT_SPIN_FPS",30,"MAXIMUM_ZOOM_PERCENTAGE",2E5,"MAXIMUM_ZOOM_PERSPECTIVE_DEPTH",
1E4,"MODE_STANDARD",0,"MODE_NAVIGATION",1,"MODE_PERSPECTIVE_PYMOL",2,"DEFAULT_PERSPECTIVE_MODEL",11,"NAV_MODE_IGNORE",-2,"NAV_MODE_ZOOMED",-1,"NAV_MODE_NONE",0,"NAV_MODE_RESET",1,"NAV_MODE_NEWXY",2,"NAV_MODE_NEWXYZ",3,"NAV_MODE_NEWZ",4)});n("JV");w("java.lang.Enum javajs.api.PlatformViewer J.api.JmolViewer J.atomdata.AtomDataServer java.util.Hashtable javajs.awt.Dimension JU.Lst J.atomdata.RadiusData J.c.VDW JU.CommandHistory".split(" "),"JV.Viewer","java.io.Reader java.lang.Boolean $.Character $.Float JU.BS $.CU $.DF $.Measure $.P3 $.P3i $.PT $.Rdr $.SB $.V3 J.adapter.smarter.SmarterJmolAdapter J.api.Interface $.JmolAppConsoleInterface J.c.ANIM $.AXES $.FIL $.STER J.i18n.GT JS.SV $.T J.thread.TimeoutThread JU.BSUtil $.C $.Elements $.Escape $.GData $.JmolMolecule $.Logger $.Parser $.TempArray $.Txt JV.ActionManager $.AnimationManager $.ColorManager $.FileManager $.JC $.ModelManager $.SelectionManager $.ShapeManager $.StateManager $.StatusManager $.TransformManager JV.binding.Binding".split(" "),
function(){c$=t(function(){this.queueOnHold=this.isSingleThreaded=this.isWebGL=this.isJS=this.haveDisplay=this.autoExit=!1;this.fullName="";this.fm=this.ms=this.definedAtomSets=this.compiler=null;this.mustRender=this.listCommands=this.isSyntaxCheck=this.isSyntaxAndFileCheck=this.isJNLP=this.$isApplet=!1;this.insertedCommand=this.appletName=this.htmlName="";this.tm=this.sm=this.g=this.rm=this.slm=this.shm=this.dm=this.cm=this.am=this.actionManager=this.html5Applet=this.gdata=null;this.logFilePath=
this.syncId="";this.useCommandThread=this.$noGraphicsAllowed=this.multiTouch=this.isSilent=this.isSignedAppletLocal=this.$isSignedApplet=this.isPrintOnly=this.allowScripting=!1;this.tempArray=this.eval=this.scm=this.stm=this.mm=this.commandHistory=this.access=this.modelAdapter=this.display=this.vwrOptions=this.commandOptions=null;this.$isPreviewOnly=this.allowArrayDotNotation=!1;this.mouseEnabled=!0;this.noneSelected=!1;this.frameOffsets=this.bsFrameOffsets=this.jsc=this.smilesMatcher=this.minimizer=
this.annotationParser=this.ligandModelSet=this.ligandModels=this.mouse=null;this.motionEventNumber=0;this.inMotion=!1;this.refreshing=!0;this.axesAreTainted=!1;this.dimScreen=null;this.maximumSize=2147483647;this.imageFontScaling=1;this.gRight=null;this.isStereoSlave=!1;this.jsParams=this.captureParams=null;this.antialiased=!1;this.hoverAtomIndex=-1;this.hoverText=null;this.hoverEnabled=!0;this.currentCursor=0;this.ptTemp=null;this.prevFrame=-2147483648;this.prevMorphModel=0;this.haveJDX=!1;this.rd=
this.jsv=null;this.frankOn=!0;this.scriptEditorVisible=!1;this.pm=this.headlessImageParams=this.modelkitPopup=this.jmolpopup=this.scriptEditor=this.appConsole=null;this.isTainted=!0;this.showSelected=this.movingSelected=!1;this.rotatePrev2=this.rotatePrev1=this.rotateBondIndex=-1;this.bsRotateBranch=null;this.creatingImage=!1;this.errorMessageUntranslated=this.errorMessage=this.defaultVdw=this.userVdwMars=this.userVdws=this.bsUserVdws=this.outputManager=null;this.currentShapeID=-1;this.localFunctions=
this.currentShapeState=null;this.privateKey=0;this.$isKiosk=!1;this.executor=null;this.displayLoadErrors=!0;this.$isParallel=!1;this.actionStatesRedo=this.actionStates=null;this.stateScriptVersionInt=0;this.logFileName=this.nmrCalculation=this.chainList=this.chainMap=this.timeouts=this.jsExporter3D=null;s(this,arguments)},JV,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,javajs.api.PlatformViewer]);K(c$,function(){this.commandHistory=new JU.CommandHistory;this.dimScreen=new javajs.awt.Dimension(0,
0);this.rd=new J.atomdata.RadiusData(null,0,null,null);this.defaultVdw=J.c.VDW.JMOL;this.localFunctions=new java.util.Hashtable;this.privateKey=Math.random();this.actionStates=new JU.Lst;this.actionStatesRedo=new JU.Lst;this.chainMap=new java.util.Hashtable;this.chainList=new JU.Lst});c(c$,"finalize",function(){JU.Logger.debugging&&JU.Logger.debug("vwr finalize "+this);R(this,JV.Viewer,"finalize",[])});c(c$,"hasDisplay",function(){return this.haveDisplay});h(c$,"isApplet",function(){return this.$isApplet});
c(c$,"setInsertedCommand",function(a){this.insertedCommand=a},"~S");c(c$,"getActionManager",function(){return this.actionManager});c(c$,"getLogFilePath",function(){return this.logFilePath});c(c$,"isSignedApplet",function(){return this.$isSignedApplet});c$.getJmolVersion=h(c$,"getJmolVersion",function(){return null==JV.Viewer.version_date?JV.Viewer.version_date=JV.JC.version+"  "+JV.JC.date:JV.Viewer.version_date});c$.allocateViewer=c(c$,"allocateViewer",function(a,b,d,c,g,f,j,h){var l=new java.util.Hashtable;
l.put("display",a);l.put("adapter",b);l.put("statusListener",j);l.put("platform",h);l.put("options",f);l.put("fullName",d);l.put("documentBase",c);l.put("codeBase",g);return new JV.Viewer(l)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,javajs.api.GenericPlatform");u(c$,function(a){E(this,JV.Viewer,[]);this.setOptions(a)},"java.util.Map");c(c$,"getStatusManager",function(){return this.sm});c(c$,"haveAccess",function(a){return this.access===a},"JV.Viewer.ACCESS");
h(c$,"getModelAdapter",function(){null==this.modelAdapter&&(this.modelAdapter=new J.adapter.smarter.SmarterJmolAdapter);return this.modelAdapter});c(c$,"getSymmetryInfo",function(a,b,d,c,g,f,j){return this.getPropertyManager().getSymmetryInfo(a,b,d,c,g,f,j)},"JU.BS,~S,~N,JU.P3,JU.P3,~S,~N");h(c$,"getSmartsMatch",function(a,b){null==b&&(b=this.bsA());return this.getSmilesMatcher().getSubstructureSet(a,this.ms.at,this.getAtomCount(),b,!0,!1)},"~S,JU.BS");c(c$,"getViewerOptions",function(){return this.vwrOptions});
c(c$,"setOptions",function(a){this.vwrOptions=a;JU.Logger.debugging&&JU.Logger.debug("Viewer constructor "+this);this.modelAdapter=a.get("adapter");var b=a.get("statusListener");this.fullName=a.get("fullName");null==this.fullName&&(this.fullName="");var d=a.get("codePath");null==d&&(d="../java/");JV.Viewer.appletCodeBase=d.toString();JV.Viewer.appletIdiomaBase=JV.Viewer.appletCodeBase.substring(0,JV.Viewer.appletCodeBase.lastIndexOf("/",JV.Viewer.appletCodeBase.length-2)+1)+"idioma";d=a.get("documentBase");
JV.Viewer.appletDocumentBase=null==d?"":d.toString();d=a.get("options");this.commandOptions=null==d?"":d.toString();(a.containsKey("debug")||0<=this.commandOptions.indexOf("-debug"))&&JU.Logger.setLogLevel(5);this.$isApplet&&a.containsKey("maximumSize")&&this.setMaximumSize(a.get("maximumSize").intValue());(this.isJNLP=this.checkOption2("isJNLP","-jnlp"))&&JU.Logger.info("setting JNLP mode TRUE");this.$isApplet=(this.$isSignedApplet=this.isJNLP||this.checkOption2("signedApplet","-signed"))||this.checkOption2("applet",
"-applet");this.allowScripting=!this.checkOption2("noscripting","-noscripting");var c=this.fullName.indexOf("__");this.htmlName=0>c?this.fullName:this.fullName.substring(0,c);this.appletName=JU.PT.split(this.htmlName+"_","_")[0];this.syncId=0>c?"":this.fullName.substring(c+2,this.fullName.length-2);this.access=this.checkOption2("access:READSPT","-r")?JV.Viewer.ACCESS.READSPT:this.checkOption2("access:NONE","-R")?JV.Viewer.ACCESS.NONE:JV.Viewer.ACCESS.ALL;(this.$isPreviewOnly=a.containsKey("previewOnly"))&&
a.remove("previewOnly");this.isPrintOnly=this.checkOption2("printOnly","-p");d=a.get("platform");c="unknown";null==d&&(d=this.commandOptions.contains("platform=")?this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");if(p(d,String)){c=d;this.isJS=(this.isWebGL=0<=c.indexOf(".awtjs."))||0<=c.indexOf(".awtjs2d.");var d=null,g="?";self.Jmol&&(d=Jmol._applets[this.htmlName.split("_object")[0]],g=Jmol._version);null!=g&&(this.html5Applet=d,JV.Viewer.strJavaVersion=
g,JV.Viewer.strJavaVendor="Java2Script "+(this.isWebGL?"(WebGL)":"(HTML5)"));d=J.api.Interface.getInterface(c)}this.apiPlatform=d;this.display=a.get("display");this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.$noGraphicsAllowed=this.checkOption2("noGraphics","-n");this.haveDisplay=this.isWebGL||null!=this.display&&!this.$noGraphicsAllowed&&!this.isHeadless()&&!this.checkOption2("isDataOnly","\x00");this.$noGraphicsAllowed=(new Boolean(this.$noGraphicsAllowed&null==this.display)).valueOf();
this.haveDisplay?(this.mustRender=!0,this.multiTouch=this.checkOption2("multiTouch","-multitouch"),this.isWebGL||(this.display=document.getElementById(this.display))):this.display=null;this.apiPlatform.setViewer(this,this.display);d=a.get("graphicsAdapter");null==d&&!this.isWebGL&&(d=J.api.Interface.getOption("g3d.Graphics3D"));this.gdata=null==d?new JU.GData:d;this.gdata.initialize(this.apiPlatform);this.stm=new JV.StateManager(this);this.cm=new JV.ColorManager(this,this.gdata);this.sm=new JV.StatusManager(this);
c=a.containsKey("4DMouse");this.tm=JV.TransformManager.getTransformManager(this,2147483647,0,c);this.slm=new JV.SelectionManager(this);this.haveDisplay&&(this.actionManager=this.multiTouch?J.api.Interface.getOption("multitouch.ActionManagerMT"):new JV.ActionManager,this.actionManager.setViewer(this,this.commandOptions+"-multitouch-"+a.get("multiTouch")),this.mouse=this.apiPlatform.getMouseManager(this.privateKey,this.display),this.multiTouch&&!this.checkOption2("-simulated","-simulated")&&this.apiPlatform.setTransparentCursor(this.display));
this.mm=new JV.ModelManager(this);this.shm=new JV.ShapeManager(this);this.tempArray=new JU.TempArray;this.am=new JV.AnimationManager(this);d=a.get("repaintManager");null==d&&(d=J.api.Interface.getOption("render.RepaintManager"));null!=d&&!d.equals("")&&(this.rm=d).set(this,this.shm);this.initialize(!0);this.fm=new JV.FileManager(this);this.definedAtomSets=new java.util.Hashtable;this.setJmolStatusListener(b);this.$isApplet?(JU.Logger.info("vwrOptions: \n"+JU.Escape.escapeMap(this.vwrOptions)),b=this.vwrOptions.get("documentLocation"),
!this.isJS&&(null!=b&&b.startsWith("file:/"))&&(b=b.substring(0,b.substring(0,(b+"?").indexOf("?")).lastIndexOf("/")),JU.Logger.info("setting current directory to "+b),this.cd(b)),b=JV.Viewer.appletDocumentBase,c=b.indexOf("#"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("?"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("/"),0<=c&&(b=b.substring(0,c)),JV.Viewer.jsDocumentBase=b,this.fm.setAppletContext(JV.Viewer.appletDocumentBase),a=a.get("appletProxy"),null!=a&&this.setStringProperty("appletProxy",
a),this.$isSignedApplet?(this.logFilePath=JU.PT.rep(JV.Viewer.appletCodeBase,"file://",""),this.logFilePath=JU.PT.rep(this.logFilePath,"file:/",""),0<=this.logFilePath.indexOf("//")?this.logFilePath=null:this.isSignedAppletLocal=!0):this.isJS||(this.logFilePath=null)):(this.gdata.setBackgroundTransparent(this.checkOption2("backgroundTransparent","-b")),(this.isSilent=this.checkOption2("silent","-i"))&&JU.Logger.setLogLevel(3),this.isSyntaxCheck=(this.isSyntaxAndFileCheck=this.checkOption2("checkLoad",
"-C"))||this.checkOption2("check","-c"),this.listCommands=this.checkOption2("listCommands","-l"),this.autoExit=this.checkOption2("exit","-x"),this.cd("."),this.isHeadless()&&(this.headlessImageParams=a.get("headlessImage"),d=a.get("headlistMaxTimeMs"),null==d&&(d=Integer.$valueOf(6E4)),this.setTimeout(""+Math.random(),d.intValue(),"exitJmol")));this.useCommandThread=!this.isHeadless()&&this.checkOption2("useCommandThread","-threaded");this.setStartupBooleans();this.setIntProperty("_nProcessors",JV.Viewer.nProcessors);
this.isSilent||JU.Logger.info("(C) 2012 Jmol Development\nJmol Version: "+JV.Viewer.getJmolVersion()+"\njava.vendor: "+JV.Viewer.strJavaVendor+"\njava.version: "+JV.Viewer.strJavaVersion+"\nos.name: "+JV.Viewer.strOSName+"\nAccess: "+this.access+"\nmemory: "+this.getP("_memory")+"\nprocessors available: "+JV.Viewer.nProcessors+"\nuseCommandThread: "+this.useCommandThread+(!this.$isApplet?"":"\nappletId:"+this.htmlName+(this.$isSignedApplet?" (signed)":"")));this.zap(!1,!0,!1);this.g.setO("language",
J.i18n.GT.getLanguage());this.stm.setJmolDefaults();JU.Elements.covalentVersion=1;this.allowArrayDotNotation=!0},"java.util.Map");c(c$,"setDisplay",function(a){this.display=a;this.apiPlatform.setViewer(this,a)},"~O");c(c$,"newMeasurementData",function(a,b){return J.api.Interface.getInterface("JM.MeasurementData").init(a,this,b)},"~S,JU.Lst");c(c$,"getDataManager",function(){return null==this.dm?this.dm=J.api.Interface.getInterface("JV.DataManager").set(this):this.dm});c(c$,"getScriptManager",function(){if(this.allowScripting&&
null==this.scm){this.scm=J.api.Interface.getInterface("JS.ScriptManager");if(null==this.scm)return this.allowScripting=!1,null;this.eval=this.scm.setViewer(this);this.useCommandThread&&this.scm.startCommandWatcher(!0)}return this.scm});c(c$,"checkOption2",function(a,b){return this.vwrOptions.containsKey(a)||0<=this.commandOptions.indexOf(b)},"~S,~S");c(c$,"isPreviewOnly",function(){return this.$isPreviewOnly});c(c$,"isHeadless",function(){return this.apiPlatform.isHeadless()});c(c$,"setStartupBooleans",
function(){this.setBooleanProperty("_applet",this.$isApplet);this.setBooleanProperty("_jspecview",!1);this.setBooleanProperty("_signedApplet",this.$isSignedApplet);this.setBooleanProperty("_headless",this.apiPlatform.isHeadless());this.setStringProperty("_restrict",'"'+this.access+'"');this.setBooleanProperty("_useCommandThread",this.useCommandThread)});c(c$,"noGraphicsAllowed",function(){return this.$noGraphicsAllowed});c(c$,"getExportDriverList",function(){return this.haveAccess(JV.Viewer.ACCESS.ALL)?
this.g.getParameter("exportDrivers",!0):""});c(c$,"getHtmlName",function(){return this.htmlName});h(c$,"getDisplay",function(){return this.display});h(c$,"dispose",function(){this.gRight=null;null!=this.mouse&&(this.actionManager.dispose(),this.mouse.dispose(),this.mouse=null);this.clearScriptQueue();this.clearThreads();this.haltScriptExecution();null!=this.scm&&this.scm.clear(!0);this.gdata.destroy();null!=this.jmolpopup&&this.jmolpopup.jpiDispose();null!=this.modelkitPopup&&this.modelkitPopup.jpiDispose();
try{null!=this.appConsole&&(this.appConsole.dispose(),this.appConsole=null),null!=this.scriptEditor&&(this.scriptEditor.dispose(),this.scriptEditor=null)}catch(a){if(!y(a,Exception))throw a;}});c(c$,"reset",function(a){this.ms.calcBoundBoxDimensions(null,1);this.axesAreTainted=!0;this.tm.homePosition(a);this.ms.setCrystallographicDefaults()?this.stm.setCrystallographicDefaults():this.setAxesModeMolecular(!1);this.prevFrame=-2147483648;this.tm.spinOn||this.refresh(-1,"Viewer:homePosition()")},"~B");
h(c$,"homePosition",function(){this.evalString("reset spin")});c(c$,"initialize",function(a){this.g=this.stm.getGlobalSettings(this.g,a);this.setStartupBooleans();this.g.setI("_width",this.dimScreen.width);this.g.setI("_height",this.dimScreen.height);this.haveDisplay&&(this.g.setB("_is2D",this.isJS&&!this.isWebGL),this.g.setB("_multiTouchClient",this.actionManager.isMTClient()),this.g.setB("_multiTouchServer",this.actionManager.isMTServer()));this.cm.resetElementColors();this.setObjectColor("background",
"black");this.setObjectColor("axis1","red");this.setObjectColor("axis2","green");this.setObjectColor("axis3","blue");this.gdata.setAmbientPercent(this.g.ambientPercent);this.gdata.setDiffusePercent(this.g.diffusePercent);this.gdata.setSpecular(this.g.specular);this.gdata.setCel(this.g.celShading);this.gdata.setCelPower(this.g.celShadingPower);this.gdata.setSpecularPercent(this.g.specularPercent);this.gdata.setSpecularPower(-this.g.specularExponent);this.gdata.setPhongExponent(this.g.phongExponent);
this.gdata.setSpecularPower(this.g.specularPower);null!=this.ms&&this.am.setAnimationOn(!1);this.am.setAnimationFps(this.g.animationFps);this.sm.setAllowStatusReporting(this.g.statusReporting);this.setBooleanProperty("antialiasDisplay",this.g.antialiasDisplay);this.setTransformManagerDefaults()},"~B");c(c$,"saveModelOrientation",function(){this.ms.saveModelOrientation(this.am.cmi,this.stm.getOrientation())});c(c$,"restoreModelOrientation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,
!0)},"~N");c(c$,"restoreModelRotation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!1)},"~N");c(c$,"getGLmolView",function(){var a=this.tm;return{center:a.fixedRotationCenter,quaternion:a.getRotationQuaternion(),xtrans:a.xTranslationFraction,ytrans:a.yTranslationFraction,scale:a.scalePixelsPerAngstrom,zoom:a.zoomPercent,cameraDistance:a.cameraDistance,pixelCount:a.screenPixelCount,perspective:a.perspectiveDepth,width:a.width,height:a.height}});c(c$,"setRotationRadius",function(a,
b){b&&(a=this.tm.setRotationRadius(a,!1));this.ms.setRotationRadius(this.am.cmi,a)&&this.g.setF("rotationRadius",a)},"~N,~B");c(c$,"setCenterBitSet",function(a,b){var d=0<JU.BSUtil.cardinalityOf(a)?this.ms.getAtomSetCenter(a):null;this.isJmolDataFrame()||this.tm.setNewRotationCenter(d,b)},"JU.BS,~B");c(c$,"setNewRotationCenter",function(a){this.isJmolDataFrame()||this.tm.setNewRotationCenter(a,!0)},"JU.P3");c(c$,"navigate",function(a,b){this.isJmolDataFrame()||(this.tm.navigateKey(a,b),!this.tm.vibrationOn&&
0!=a&&this.refresh(1,"Viewer:navigate()"))},"~N,~N");c(c$,"move",function(a,b,d,c,g,f,j){this.tm.move(a,b,d,c,g,f,j);this.moveUpdate(f)},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(c$,"moveTo",function(a,b,d,c,g,f,j,h,l,m,r,n,q,p,s,t,u){this.haveDisplay||(b=0);this.setTainted(!0);this.tm.moveTo(a,b,d,c,g,f,j,h,l,m,r,n,q,p,s,t,u)},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.V3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(c$,"moveUpdate",function(a){0<a?this.requestRepaintAndWait("moveUpdate"):
0==a&&this.setSync()},"~N");c(c$,"navigatePt",function(a){this.tm.setNavigatePt(a);this.setSync()},"JU.P3");c(c$,"navigateAxis",function(a,b){this.tm.navigateAxis(a,b);this.setSync()},"JU.V3,~N");c(c$,"navTranslatePercent",function(a,b){this.isJmolDataFrame()||(this.tm.navTranslatePercentOrTo(0,a,b),this.setSync())},"~N,~N");c(c$,"setMouseEnabled",function(a){this.mouseEnabled=a},"~B");h(c$,"processMultitouchEvent",function(a,b,d,c,g,f){this.actionManager.processMultitouchEvent(a,b,d,c,g,f)},"~N,~N,~N,~N,JU.P3,~N");
c(c$,"zoomBy",function(a){this.mouseEnabled&&this.tm.zoomBy(a);this.refresh(2,this.sm.syncingMouse?"Mouse: zoomBy "+a:"")},"~N");c(c$,"zoomByFactor",function(a,b,d){this.mouseEnabled&&this.tm.zoomByFactor(a,b,d);this.refresh(2,!this.sm.syncingMouse?"":"Mouse: zoomByFactor "+a+(2147483647==b?"":" "+b+" "+d))},"~N,~N,~N");c(c$,"rotateXYBy",function(a,b){this.mouseEnabled&&this.tm.rotateXYBy(a,b,null);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateXYBy "+a+" "+b:"")},"~N,~N");c(c$,"spinXYBy",function(a,
b,d){this.mouseEnabled&&this.tm.spinXYBy(a,b,d);0==a&&0==b||this.refresh(2,this.sm.syncingMouse?"Mouse: spinXYBy "+a+" "+b+" "+d:"")},"~N,~N,~N");c(c$,"rotateZBy",function(a,b,d){this.mouseEnabled&&this.tm.rotateZBy(a,b,d);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateZBy "+a+(2147483647==b?"":" "+b+" "+d):"")},"~N,~N,~N");c(c$,"rotateSelected",function(a,b,d){this.isJmolDataFrame()||(this.mouseEnabled&&(this.tm.rotateXYBy(a,b,this.setMovableBitSet(d,!1)),this.refreshMeasures(!0)),this.refresh(2,
this.sm.syncingMouse?"Mouse: rotateMolecule "+a+" "+b:""))},"~N,~N,JU.BS");c(c$,"setMovableBitSet",function(a,b){null==a&&(a=this.bsA());a=JU.BSUtil.copy(a);JU.BSUtil.andNot(a,this.getMotionFixedAtoms());b&&!this.g.allowMoveAtoms&&(a=this.ms.getMoleculeBitSet(a));return a},"JU.BS,~B");c(c$,"translateXYBy",function(a,b){this.mouseEnabled&&this.tm.translateXYBy(a,b);this.refresh(2,this.sm.syncingMouse?"Mouse: translateXYBy "+a+" "+b:"")},"~N,~N");h(c$,"rotateFront",function(){this.tm.resetRotation();
this.refresh(1,"Viewer:rotateFront()")});c(c$,"translate",function(a,b,d,c){var g="\x00"==d?z(b):"%"==d?this.tm.percentToPixels(a,b):this.tm.angstromsToPixels(b*("n"==d?10:1));if(null!=c){if(0==g)return;this.tm.setSelectedTranslation(c,a,g)}else switch(a){case "X":case "x":"\x00"==d?this.tm.translateToPercent("x",b):this.tm.translateXYBy(g,0);break;case "Y":case "y":"\x00"==d?this.tm.translateToPercent("y",b):this.tm.translateXYBy(0,g);break;case "Z":case "z":"\x00"==d?this.tm.translateToPercent("z",
b):this.tm.translateZBy(g)}this.refresh(1,"Viewer:translate()")},"~S,~N,~S,JU.BS");h(c$,"getZoomPercent",function(){return z(this.tm.getZoomSetting())});h(c$,"getZoomPercentFloat",function(){return this.tm.getZoomPercentFloat()});c(c$,"getMaxZoomPercent",function(){return 2E5});c(c$,"slabByPixels",function(a){this.tm.slabByPercentagePoints(a);this.refresh(3,"slabByPixels")},"~N");c(c$,"depthByPixels",function(a){this.tm.depthByPercentagePoints(a);this.refresh(3,"depthByPixels")},"~N");c(c$,"slabDepthByPixels",
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b){if(JU.PT.isOneOf(a,";x;y;z;fps;X;Y;Z;FPS;")){var d="x;y;z;fps;X;Y;Z;FPS".indexOf(a);switch(d){case 0:this.tm.setSpinXYZ(b,NaN,NaN);break;case 2:this.tm.setSpinXYZ(NaN,b,NaN);break;case 4:this.tm.setSpinXYZ(NaN,NaN,b);break;default:this.tm.setSpinFps(b);break;case 10:this.tm.setNavXYZ(b,NaN,NaN);break;case 12:this.tm.setNavXYZ(NaN,b,NaN);break;case 14:this.tm.setNavXYZ(NaN,NaN,b);break;case 16:this.tm.setNavFps(b)}this.g.setI((10>d?"spin":"nav")+a,b)}},"~S,~N");c(c$,"getSpinState",function(){return this.getStateCreator().getSpinState(!1)});
c(c$,"getOrientationText",function(a,b){switch(a){case 1313866249:case 1073741863:case 1112541205:case 1112541206:case 1112541207:case 135270418:return this.ms.getBoundBoxOrientation(a,this.bsA());case 1073742035:return this.stm.getSavedOrientationText(b);default:return this.tm.getOrientationText(a)}},"~N,~S");c(c$,"getCurrentColorRange",function(){return this.cm.getPropertyColorRange()});c(c$,"setDefaultColors",function(a){this.cm.setDefaultColors(a);this.g.setB("colorRasmol",a);this.g.setO("defaultColorScheme",
a?"rasmol":"jmol")},"~B");c(c$,"getColorArgbOrGray",function(a){return this.gdata.getColorArgbOrGray(a)},"~N");c(c$,"setElementArgb",function(a,b){this.g.setO("=color "+JU.Elements.elementNameFromNumber(a),JU.Escape.escapeColor(b));this.cm.setElementArgb(a,b)},"~N,~N");h(c$,"setVectorScale",function(a){this.g.setF("vectorScale",a);this.g.vectorScale=a},"~N");h(c$,"setVibrationScale",function(a){this.tm.setVibrationScale(a);this.g.vibrationScale=a;this.g.setF("vibrationScale",a)},"~N");c(c$,"setVibrationOff",
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b){var d=JV.StateManager.getObjectIdFromName(a);if(0>d)a.equalsIgnoreCase("axes")&&(this.setObjectArgb("axis1",b),this.setObjectArgb("axis2",b),this.setObjectArgb("axis3",b));else{this.g.objColors[d]=b;switch(d){case 0:this.gdata.setBackgroundArgb(b),this.cm.setColixBackgroundContrast(b)}this.g.setO(a+"Color",JU.Escape.escapeColor(b))}},"~S,~N");c(c$,"setBackgroundImage",function(a,b){this.g.backgroundImageFileName=a;this.gdata.setBackgroundImage(b)},"~S,~O");c(c$,"getObjectColix",function(a){a=this.g.objColors[a];
return 0==a?this.getColixBackgroundContrast():JU.C.getColix(a)},"~N");c(c$,"getFontState",function(a,b){return this.getStateCreator().getFontState(a,b)},"~S,javajs.awt.Font");h(c$,"setColorBackground",function(a){this.setObjectColor("background",a)},"~S");h(c$,"getBackgroundArgb",function(){return this.g.objColors[0]});c(c$,"setObjectMad",function(a,b,d){var c=JV.StateManager.getObjectIdFromName(b.equalsIgnoreCase("axes")?"axis":b);if(!(0>c)){if(-2==d||-4==d){var g=d+3;d=this.getObjectMad(c);0==d&&
(d=g)}this.g.setB("show"+b,0!=d);this.g.objStateOn[c]=0!=d;0!=d&&(this.g.objMad[c]=d,this.setShapeSize(a,d,null))}},"~N,~S,~N");c(c$,"getObjectMad",function(a){return this.g.objStateOn[a]?this.g.objMad[a]:0},"~N");c(c$,"setPropertyColorScheme",function(a,b,d){this.g.propertyColorScheme=a;a.startsWith("translucent ")&&(b=!0,a=a.substring(12).trim());this.cm.setPropertyColorScheme(a,b,d)},"~S,~B,~B");c(c$,"getPropertyColorScheme",function(){return this.g.propertyColorScheme});c(c$,"getColixBackgroundContrast",
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function(a){return this.cm.getColixForPropertyValue(a)},"~N");c(c$,"getColorPointForPropertyValue",function(a){return JU.CU.colorPtFromInt(this.gdata.getColorArgbOrGray(this.cm.getColixForPropertyValue(a)),null)},"~N");c(c$,"select",function(a,b,d,c){b&&(a=this.getUndeletedGroupAtomBits(a));this.slm.select(a,d,c);this.shm.setShapeSizeBs(1,2147483647,null,null)},"JU.BS,~B,~N,~B");h(c$,"setSelectionSet",function(a){this.select(a,!1,0,!0)},"JU.BS");c(c$,"selectBonds",function(a){this.shm.setShapeSizeBs(1,
2147483647,null,a)},"JU.BS");c(c$,"displayAtoms",function(a,b,d,c,g){d&&(a=this.getUndeletedGroupAtomBits(a));b?this.slm.display(this.ms,a,c,g):this.slm.hide(this.ms,a,c,g)},"JU.BS,~B,~B,~N,~B");c(c$,"getUndeletedGroupAtomBits",function(a){a=this.ms.getAtoms(1087373318,a);JU.BSUtil.andNot(a,this.slm.getDeletedAtoms());return a},"JU.BS");c(c$,"reportSelection",function(a){this.ms.getSelectionHaloEnabled()&&this.setTainted(!0);(this.isScriptQueued()||this.g.debugScript)&&this.scriptStatus(a)},"~S");
c(c$,"clearAtomSets",function(){this.setSelectionSubset(null);this.definedAtomSets.clear()});c(c$,"getDefinedAtomSet",function(a){a=this.definedAtomSets.get(a.toLowerCase());return p(a,JU.BS)?a:new JU.BS},"~S");h(c$,"selectAll",function(){this.slm.selectAll(!1)});c(c$,"setNoneSelected",function(a){this.noneSelected=a},"~B");c(c$,"getNoneSelected",function(){return this.noneSelected?Boolean.TRUE:Boolean.FALSE});h(c$,"clearSelection",function(){this.slm.clearSelection(!0);this.g.setB("hideNotSelected",
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null,JU.Rdr.getBR(d),f),j=p(h,String),j||(h=this.getModelAdapter().getAtomSetCollection(h),j=p(h,String),null!=g&&!j&&this.scriptEcho(this.getModelAdapter().getAtomSetCollectionAuxiliaryInfo(h).get("modelLoadNote")))));return j?(this.scriptEcho(h.toString()),this.ligandModels.put(a,Boolean.FALSE),null):h},"~S,~S,~S,~S");c(c$,"openFileFull",function(a,b,d,c){if(null==a||0<=a.indexOf("[]"))return null;var g="openFile("+a+")";JU.Logger.startTimer(g);d=this.setLoadParameters(d,b);var f=a.startsWith("@"),
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case 553648144:return this.g.dotScale;case 553648146:return this.g.helixStep;case 553648151:return this.g.meshScale;case 553648153:return this.g.minPixelSelRadius;case 553648154:return this.g.percentVdwAtom;case 553648157:return this.g.pickingSpinRate;case 553648166:return this.g.ribbonAspectRatio;case 536870922:return this.g.scriptDelay;case 553648170:return this.g.smallMoleculeMaxAtoms;case 553648184:return this.g.strutSpacing}JU.Logger.error("viewer.getInt("+JS.T.nameOf(a)+") - not listed");return 0},
"~N");c(c$,"getDelayMaximumMs",function(){return this.haveDisplay?this.g.delayMaximumMs:1});c(c$,"getHermiteLevel",function(){return this.tm.spinOn?0:this.g.hermiteLevel});c(c$,"getHoverDelay",function(){return this.g.modelKitMode?20:this.g.hoverDelayMs});h(c$,"getBoolean",function(a){switch(a){case 1074790662:return this.ms.getMSInfoB("isPDB");case 603979780:return this.g.allowGestures;case 603979784:return this.g.allowMultiTouch;case 603979785:return this.g.allowRotateSelected;case 603979792:return this.g.appendNew;
case 603979794:return this.g.applySymmetryToBonds;case 603979796:return this.g.atomPicking;case 603979798:return this.g.autoBond;case 603979800:return this.g.autoFps;case 603979806:return this.g.axesOrientationRasmol;case 603979811:return this.g.backboneSteps;case 603979812:return this.g.bondModeOr;case 603979816:return this.g.cartoonBaseEdges;case 603979817:return this.g.cartoonFancy;case 603979818:return this.g.cartoonLadders;case 603979819:return this.g.cartoonRibose;case 603979820:return this.g.cartoonRockets;
case 603979823:return this.g.chainCaseSensitive||0<this.chainList.size();case 603979825:return this.g.debugScript;case 603979826:return this.g.defaultStructureDSSP;case 603979827:return this.g.disablePopupMenu;case 603979828:return this.g.displayCellParameters;case 603979830:return this.g.dotSurface;case 603979829:return this.g.dotsSelectedOnly;case 603979833:return this.g.drawPicking;case 603979844:return this.g.fontCaching;case 603979845:return this.g.fontScaling;case 603979846:return this.g.forceAutoBond;
case 603979848:return!1;case 603979850:return this.g.greyscaleRendering;case 603979852:return this.g.hbondsBackbone;case 603979853:return this.g.hbondsRasmol;case 603979854:return this.g.hbondsSolid;case 1613758470:return this.g.rasmolHeteroSetting;case 603979858:return this.g.hideNameInPopup;case 603979864:return this.g.highResolutionFlag;case 1613758476:return this.g.rasmolHydrogenSetting;case 603979870:return this.g.isosurfaceKey;case 603979872:return this.g.justifyMeasurements;case 603979874:return this.g.legacyAutoBonding;
case 603979875:return this.g.legacyHAddition;case 603979877:return this.g.logGestures;case 603979878:return this.g.measureAllModels;case 603979879:return this.g.measurementLabels;case 603979880:return this.g.messageStyleChime;case 603979883:return this.g.modelKitMode;case 603979887:return this.g.navigationMode;case 603979888:return this.g.navigationPeriodic;case 603979889:return this.g.partialDots;case 603979892:return this.g.pdbSequential;case 603979894:return this.g.preserveState;case 603979898:return this.g.ribbonBorder;
case 603979900:return this.g.rocketBarrels;case 603979906:return this.g.selectAllModels;case 603979920:return this.g.showHiddenSelectionHalos;case 603979922:return this.g.showHydrogens;case 603979926:return this.g.showMeasurements;case 603979928:return this.g.showMultipleBonds;case 603979934:return this.g.showTiming;case 603979938:return this.g.showUnitCellInfo;case 603979937:return this.g.showUnitCellDetails;case 603979939:return this.g.slabByAtom;case 603979940:return this.g.slabByMolecule;case 603979944:return this.g.smartAromatic;
case 1613758488:return this.g.solventOn;case 603979952:return this.g.ssbondsBackbone;case 603979955:return this.g.strutsMultiple;case 603979966:return this.g.traceAlpha;case 603979967:return this.g.translucent;case 603979968:return this.g.twistedSheets;case 603979972:return this.g.vectorsCentered;case 603979973:return this.g.vectorSymmetry;case 603979974:return this.g.waitForMoveTo;case 603979978:return this.g.zeroBasedXyzRasmol}JU.Logger.error("viewer.getBoolean("+JS.T.nameOf(a)+") - not listed");
return!1},"~N");c(c$,"allowEmbeddedScripts",function(){return this.g.allowEmbeddedScripts&&!this.$isPreviewOnly});c(c$,"getDragSelected",function(){return this.g.dragSelected&&!this.g.modelKitMode});c(c$,"getBondPicking",function(){return this.g.bondPicking||this.g.modelKitMode});c(c$,"useMinimizationThread",function(){return this.g.useMinimizationThread&&!this.autoExit});h(c$,"getFloat",function(a){switch(a){case 1141899265:return this.g.particleRadius;case 570425346:return this.g.axesScale;case 570425348:return this.g.bondTolerance;
case 570425354:return this.g.defaultTranslucent;case 570425352:return this.g.defaultDrawArrowScale;case 570425355:return this.g.dipoleScale;case 570425356:return this.g.drawFontSize;case 570425358:return this.g.exportScale;case 570425360:return this.g.hbondsAngleMinimum;case 570425361:return this.g.hbondsDistanceMaximum;case 570425363:return this.g.loadAtomDataTolerance;case 570425364:return this.g.minBondDistance;case 1276121113:return this.g.modulationScale;case 570425370:return this.g.multipleBondSpacing;
case 570425369:return this.g.multipleBondRadiusFactor;case 570425374:return this.g.navigationSpeed;case 570425382:return this.g.pointGroupDistanceTolerance;case 570425384:return this.g.pointGroupLinearTolerance;case 570425388:return this.tm.getRotationRadius();case 570425392:return this.g.sheetSmoothing;case 570425394:return this.g.solventProbeRadius;case 570425403:return this.g.starWidth;case 570425406:return this.g.strutDefaultRadius;case 570425408:return this.g.strutLengthMaximum;case 1649410049:return this.g.vectorScale;
case 570425412:return this.g.vibrationPeriod}JU.Logger.error("viewer.getFloat("+JS.T.nameOf(a)+") - not listed");return 0},"~N");h(c$,"setStringProperty",function(a,b){if(null!=b)if("_"==a.charAt(0))this.g.setO(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 603979776:this.setBooleanPropertyTok(a,d,JS.SV.newV(4,b).asBoolean());break;case 553648128:this.setIntPropertyTok(a,d,JS.SV.newV(4,b).asInt());break;case 570425344:this.setFloatPropertyTok(a,d,JU.PT.parseFloat(b));break;
default:this.setStringPropertyTok(a,d,b)}}},"~S,~S");c(c$,"setStringPropertyTok",function(a,b,d){switch(b){case 545259521:this.setAnimationMode(d);return;case 545259569:this.g.nmrPredictFormat=d;break;case 545259548:this.g.defaultDropScript=d;break;case 545259571:d=this.fm.setPathForAllFiles(d);break;case 545259558:this.setUnits(d,!1);return;case 545259560:this.g.forceField=d="UFF".equalsIgnoreCase(d)?"UFF":"MMFF";this.minimizer=null;break;case 545259570:this.g.nmrUrlFormat=d;break;case 545259568:this.setUnits(d,
!0);return;case 545259566:this.g.loadLigandFormat=d;break;case 545259543:this.g.defaultLabelPDB=d;break;case 545259544:this.g.defaultLabelXYZ=d;break;case 545259549:this.g.defaultLoadFilter=d;break;case 545259567:d=this.getOutputManager().setLogFile(d);if(null==d)return;break;case 545259559:break;case 545259524:this.g.atomTypes=d;break;case 545259538:break;case 545259576:this.g.pickLabel=d;break;case 545259580:this.g.quaternionFrame=2==d.length&&d.startsWith("R")?d.substring(0,2):""+(d.toLowerCase()+
"p").charAt(0);JU.PT.isOneOf(this.g.quaternionFrame,"RC;RP;a;b;c;n;p;q;x;")||(this.g.quaternionFrame="p");this.ms.setHaveStraightness(!1);break;case 545259555:this.setVdwStr(d);return;case 545259564:new J.i18n.GT(this,d);b=J.i18n.GT.getLanguage();this.modelkitPopup=null;null!=this.jmolpopup&&(this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.getPopupMenu());this.sm.setCallbackFunction("language",b);d=J.i18n.GT.getLanguage();break;case 545259565:this.g.loadFormat=d;break;case 545259534:this.setObjectColor("background",
d);return;case 545259528:this.setObjectColor("axis1",d);return;case 545259530:this.setObjectColor("axis2",d);return;case 545259532:this.setObjectColor("axis3",d);return;case 545259536:this.setObjectColor("boundbox",d);return;case 545259586:this.setObjectColor("unitcell",d);return;case 545259578:this.setPropertyColorScheme(d,!1,!1);break;case 545259562:this.shm.loadShape(34);this.setShapeProperty(34,"atomLabel",d);break;case 545259547:this.g.defaultDistanceLabel=d;break;case 545259542:this.g.defaultAngleLabel=
d;break;case 545259554:this.g.defaultTorsionLabel=d;break;case 545259550:this.g.defaultLoadScript=d;break;case 545259522:this.fm.setAppletProxy(d);break;case 545259546:null==d&&(d="");d=d.$replace("\\","/");this.g.defaultDirectory=d;break;case 545259561:this.g.helpPath=d;break;case 545259552:!d.equalsIgnoreCase("RasMol")&&!d.equalsIgnoreCase("PyMOL")&&(d="Jmol");this.setDefaultsType(d);break;case 545259545:this.setDefaultColors(d.equalsIgnoreCase("rasmol"));return;case 545259572:this.setPickingMode(d,
0);return;case 545259574:this.setPickingStyle(d,0);return;case 545259540:break;default:if(a.toLowerCase().endsWith("callback")){this.sm.setCallbackFunction(a,0==d.length||d.equalsIgnoreCase("none")?null:d);break}if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(4,d));return}}this.g.setO(a,d)},"~S,~N,~S");h(c$,"setFloatProperty",function(a,b){if(!Float.isNaN(b))if("_"==a.charAt(0))this.g.setF(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,
d,""+b);break;case 603979776:this.setBooleanPropertyTok(a,d,0!=b);break;case 553648128:this.setIntPropertyTok(a,d,z(b));break;default:this.setFloatPropertyTok(a,d,b)}}},"~S,~N");c(c$,"setFloatPropertyTok",function(a,b,d){switch(b){case 570425366:this.ms.setModulation(null,!1,null,!1);this.g.modulationScale=d=Math.max(0.1,d);this.ms.setModulation(null,!0,null,!1);break;case 570425381:this.g.particleRadius=Math.abs(d);break;case 570425356:this.g.drawFontSize=d;break;case 570425358:this.g.exportScale=
d;break;case 570425403:this.g.starWidth=d;break;case 570425369:this.g.multipleBondRadiusFactor=d;break;case 570425370:this.g.multipleBondSpacing=d;break;case 570425393:this.tm.setSlabRange(d);break;case 570425365:this.g.minimizationCriterion=d;break;case 570425359:this.haveDisplay&&this.actionManager.setGestureSwipeFactor(d);break;case 570425367:this.haveDisplay&&this.actionManager.setMouseDragFactor(d);break;case 570425368:this.haveDisplay&&this.actionManager.setMouseWheelFactor(d);break;case 570425408:this.g.strutLengthMaximum=
d;break;case 570425406:this.g.strutDefaultRadius=d;break;case 570425376:this.setSpin("X",z(d));break;case 570425378:this.setSpin("Y",z(d));break;case 570425380:this.setSpin("Z",z(d));break;case 570425371:if(Float.isNaN(d))return;this.setSpin("FPS",z(d));break;case 570425363:this.g.loadAtomDataTolerance=d;break;case 570425360:this.g.hbondsAngleMinimum=d;break;case 570425361:this.g.hbondsDistanceMaximum=d;break;case 570425382:this.g.pointGroupDistanceTolerance=d;break;case 570425384:this.g.pointGroupLinearTolerance=
d;break;case 570425357:this.g.ellipsoidAxisDiameter=d;break;case 570425398:this.setSpin("x",z(d));break;case 570425400:this.setSpin("y",z(d));break;case 570425402:this.setSpin("z",z(d));break;case 570425396:this.setSpin("fps",z(d));break;case 570425352:this.g.defaultDrawArrowScale=d;break;case 570425354:this.g.defaultTranslucent=d;break;case 570425346:this.setAxesScale(d);break;case 570425416:this.tm.setVisualRange(d);this.refresh(1,"set visualRange");break;case 570425372:this.setNavigationDepthPercent(d);
break;case 570425374:this.g.navigationSpeed=d;break;case 570425373:this.tm.setNavigationSlabOffsetPercent(d);break;case 570425350:this.tm.setCameraDepthPercent(d,!1);this.refresh(1,"set cameraDepth");return;case 570425388:this.setRotationRadius(d,!0);return;case 570425362:this.g.hoverDelayMs=z(1E3*d);break;case 570425392:this.g.sheetSmoothing=d;break;case 570425355:d=JV.Viewer.checkFloatRange(d,-10,10);this.g.dipoleScale=d;break;case 570425404:this.tm.setStereoDegrees(d);break;case 1649410049:this.setVectorScale(d);
return;case 570425412:this.setVibrationPeriod(d);return;case 570425414:this.setVibrationScale(d);return;case 570425348:this.setBondTolerance(d);return;case 570425364:this.setMinBondDistance(d);return;case 570425390:this.tm.setScaleAngstromsPerInch(d);break;case 570425394:d=JV.Viewer.checkFloatRange(d,0,10);this.g.solventProbeRadius=d;break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(3,Float.$valueOf(d)));return}}this.g.setF(a,d)},
"~S,~N,~N");h(c$,"setIntProperty",function(a,b){if(-2147483648!=b)if("_"==a.charAt(0))this.g.setI(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,d,""+b);break;case 603979776:this.setBooleanPropertyTok(a,d,0!=b);break;case 570425344:this.setFloatPropertyTok(a,d,b);break;default:this.setIntPropertyTok(a,d,b)}}},"~S,~N");c(c$,"setIntPropertyTok",function(a,b,d){switch(b){case 553648138:d=0==d?0:1;this.g.bondingVersion=JU.Elements.bondingVersion=
d;break;case 553648137:this.g.celShadingPower=d;this.gdata.setCelPower(d);break;case 553648129:this.gdata.setAmbientOcclusion(d);break;case 553648158:this.g.platformSpeed=Math.min(Math.max(d,0),10);break;case 553648151:this.g.meshScale=d;break;case 553648153:this.g.minPixelSelRadius=d;break;case 553648149:this.g.isosurfacePropertySmoothingPower=d;break;case 553648165:this.g.repaintWaitMs=d;break;case 553648170:this.g.smallMoleculeMaxAtoms=d;break;case 553648152:this.g.minimizationSteps=d;break;case 553648184:this.g.strutSpacing=
d;break;case 553648156:d=JV.Viewer.checkIntRange(d,0,1E3);this.gdata.setPhongExponent(d);break;case 553648146:this.g.helixStep=d;this.ms.setHaveStraightness(!1);break;case 553648144:this.g.dotScale=d;break;case 553648143:this.g.dotDensity=d;break;case 553648140:this.g.delayMaximumMs=d;break;case 553648150:JU.Logger.setLogLevel(d);JU.Logger.info("logging level set to "+d);this.g.setI("logLevel",d);null!=this.eval&&this.eval.setDebugging();return;case 553648134:switch(J.c.AXES.getAxesMode(d)){case J.c.AXES.MOLECULAR:this.setAxesModeMolecular(!0);
break;case J.c.AXES.BOUNDBOX:this.setAxesModeMolecular(!1);break;case J.c.AXES.UNITCELL:this.setAxesModeUnitCell(!0)}return;case 553648178:this.setStrandCount(0,d);return;case 553648182:this.setStrandCount(12,d);return;case 553648180:this.setStrandCount(13,d);return;case 553648155:return;case 536870922:this.g.scriptDelay=d;break;case 553648176:d=0>d?JV.Viewer.checkIntRange(d,-10,-1):JV.Viewer.checkIntRange(d,0,100);this.gdata.setSpecularPower(d);break;case 553648172:d=JV.Viewer.checkIntRange(-d,-10,
-1);this.gdata.setSpecularPower(d);break;case 553648136:this.setMarBond(d);return;case 536870924:this.setBooleanPropertyTok(a,b,1==d);return;case 553648174:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setSpecularPercent(d);break;case 553648142:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setDiffusePercent(d);break;case 553648130:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setAmbientPercent(d);break;case 553648186:this.tm.zDepthToPercent(d);break;case 553648188:this.tm.zSlabToPercent(d);break;
case 554176526:this.tm.depthToPercent(d);break;case 554176565:this.tm.slabToPercent(d);break;case 553648190:this.g.zShadePower=Math.max(d,1);break;case 553648166:this.g.ribbonAspectRatio=d;break;case 553648157:this.g.pickingSpinRate=1>d?1:d;break;case 553648132:this.setAnimationFps(d);return;case 553648154:this.setPercentVdwAtom(d);break;case 553648147:this.g.hermiteLevel=d;break;case 553648145:case 553648148:case 553648160:case 553648159:case 553648162:case 553648164:break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a)){this.g.setUserVariable(a,
JS.SV.newI(d));return}}this.g.setI(a,d)},"~S,~N,~N");c$.checkIntRange=c(c$,"checkIntRange",function(a,b,d){return a<b?b:a>d?d:a},"~N,~N,~N");c$.checkFloatRange=c(c$,"checkFloatRange",function(a,b,d){return a<b?b:a>d?d:a},"~N,~N,~N");h(c$,"setBooleanProperty",function(a,b){if("_"==a.charAt(0))this.g.setB(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,d,"");break;case 553648128:this.setIntPropertyTok(a,d,b?1:0);break;case 570425344:this.setFloatPropertyTok(a,
d,b?1:0);break;default:this.setBooleanPropertyTok(a,d,b)}}},"~S,~B");c(c$,"setBooleanPropertyTok",function(a,b,d){var c=!0;switch(b){case 603979938:this.g.showUnitCellInfo=d;break;case 603979937:this.g.showUnitCellDetails=d;break;case 603979848:c=!1;break;case 603979972:this.g.vectorsCentered=d;break;case 603979811:this.g.backboneSteps=d;break;case 603979819:(this.g.cartoonRibose=d)&&this.getBoolean(603979816)&&this.setBooleanPropertyTok("cartoonBaseEdges",603979816,!1);break;case 603979837:this.g.ellipsoidArrows=
d;break;case 603979967:this.g.translucent=d;break;case 603979818:this.g.cartoonLadders=d;break;case 603979968:b=this.g.twistedSheets;this.g.twistedSheets=d;b!=d&&this.checkCoordinatesChanged();break;case 603979822:this.g.celShading=d;this.gdata.setCel(d);break;case 603979817:this.g.cartoonFancy=d;break;case 603979934:this.g.showTiming=d;break;case 603979973:this.g.vectorSymmetry=d;break;case 603979870:this.g.isosurfaceKey=d;break;case 603979889:this.g.partialDots=d;break;case 603979874:this.g.legacyAutoBonding=
d;break;case 603979826:this.g.defaultStructureDSSP=d;break;case 603979834:this.g.dsspCalcHydrogen=d;break;case 603979782:(this.g.allowModelkit=d)||this.setModelKitMode(!1);break;case 603979883:this.setModelKitMode(d);break;case 603979885:this.g.multiProcessor=d&&1<JV.Viewer.nProcessors;break;case 603979884:this.g.monitorEnergy=d;break;case 603979853:this.g.hbondsRasmol=d;break;case 603979881:this.g.minimizationRefresh=d;break;case 603979882:this.g.minimizationSilent=d;break;case 603979869:d&&(this.$isKiosk=
!0,this.g.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));break;case 603979974:this.g.waitForMoveTo=d;break;case 603979876:this.g.logCommands=!0;break;case 603979877:this.g.logGestures=!0;break;case 603979784:this.g.allowMultiTouch=d;break;case 603979894:this.g.preserveState=d;this.ms.setPreserveState(d);this.undoClear();break;case 603979955:this.g.strutsMultiple=d;break;case 603979842:break;case 603979939:this.g.slabByAtom=d;break;case 603979940:this.g.slabByMolecule=
d;break;case 603979902:this.g.saveProteinStructureState=d;break;case 603979780:this.g.allowGestures=d;break;case 603979868:this.g.imageState=d;break;case 603979970:this.g.useMinimizationThread=d;break;case 603979781:this.g.disablePopupMenu&&(d=!1);this.g.allowKeyStrokes=d;break;case 603979831:this.g.dragSelected=d;this.showSelected=!1;break;case 603979924:this.g.showKeyStrokes=d;break;case 603979844:this.g.fontCaching=d;break;case 603979796:this.g.atomPicking=d;break;case 603979814:this.highlight(null);
this.g.bondPicking=d;break;case 603979906:this.g.selectAllModels=d;break;case 603979880:this.g.messageStyleChime=d;break;case 603979892:this.g.pdbSequential=d;break;case 603979890:this.g.pdbAddHydrogens=d;break;case 603979891:this.g.pdbGetHeader=d;break;case 603979838:this.g.ellipsoidAxes=d;break;case 603979836:this.g.ellipsoidArcs=d;break;case 603979839:this.g.ellipsoidBall=d;break;case 603979840:this.g.ellipsoidDots=d;break;case 603979841:this.g.ellipsoidFill=d;break;case 603979845:this.g.fontScaling=
d;break;case 603979956:this.setSyncTarget(0,d);break;case 603979958:this.setSyncTarget(1,d);break;case 603979976:this.g.wireframeRotation=d;break;case 603979871:this.g.isosurfacePropertySmoothing=d;break;case 603979833:this.g.drawPicking=d;break;case 603979786:case 603979790:case 603979788:this.setAntialias(b,d);break;case 603979944:this.g.smartAromatic=d;break;case 603979794:this.setApplySymmetryToBonds(d);break;case 603979792:this.g.appendNew=d;break;case 603979800:this.g.autoFps=d;break;case 603979971:JU.DF.setUseNumberLocalization(this.g.useNumberLocalization=
d);break;case 603979918:case 1611272202:a="showFrank";this.setFrankOn(d);break;case 1613758488:a="solventProbe";this.g.solventOn=d;break;case 603979948:this.g.solventOn=d;break;case 603979785:this.g.allowRotateSelected=d;break;case 603979783:this.g.allowMoveAtoms=d;this.g.allowRotateSelected=d;this.g.dragSelected=d;this.showSelected=!1;break;case 536870922:this.setIntPropertyTok("showScript",b,d?1:0);return;case 603979778:this.g.allowEmbeddedScripts=d;break;case 603979888:this.g.navigationPeriodic=
d;break;case 603979984:this.tm.setZShadeEnabled(d);return;case 603979832:this.haveDisplay&&(this.g.drawHover=d);break;case 603979887:this.setNavigationMode(d);break;case 603979886:return;case 603979860:this.g.hideNavigationPoint=d;break;case 603979930:this.g.showNavigationPointAlways=d;break;case 603979896:this.setRefreshing(d);break;case 603979872:this.g.justifyMeasurements=d;break;case 603979952:this.g.ssbondsBackbone=d;break;case 603979852:this.g.hbondsBackbone=d;break;case 603979854:this.g.hbondsSolid=
d;break;case 536870924:this.gdata.setSpecular(d);break;case 603979942:this.tm.setSlabEnabled(d);return;case 603979980:this.tm.setZoomEnabled(d);return;case 603979864:this.g.highResolutionFlag=d;break;case 603979966:this.g.traceAlpha=d;break;case 603979983:this.g.zoomLarge=d;this.tm.setZoomHeight(this.g.zoomHeight,d);break;case 603979982:this.g.zoomHeight=d;this.tm.setZoomHeight(d,this.g.zoomLarge);break;case 603979873:J.i18n.GT.setDoTranslate(d);break;case 603979862:this.slm.setHideNotSelected(d);
break;case 603979904:this.setScriptQueue(d);break;case 603979830:this.g.dotSurface=d;break;case 603979829:this.g.dotsSelectedOnly=d;break;case 1611141171:this.setSelectionHalos(d);break;case 603979910:this.g.rasmolHydrogenSetting=d;break;case 603979908:this.g.rasmolHeteroSetting=d;break;case 603979928:this.g.showMultipleBonds=d;break;case 603979920:this.g.showHiddenSelectionHalos=d;break;case 603979975:this.tm.setWindowCentered(d);break;case 603979828:this.g.displayCellParameters=d;break;case 603979960:this.g.testFlag1=
d;break;case 603979962:this.g.testFlag2=d;break;case 603979964:this.g.testFlag3=d;break;case 603979965:this.jmolTest();this.g.testFlag4=d;break;case 603979898:this.g.ribbonBorder=d;break;case 603979816:(this.g.cartoonBaseEdges=d)&&this.getBoolean(603979819)&&this.setBooleanPropertyTok("cartoonRibose",603979819,!1);break;case 603979820:this.g.cartoonRockets=d;break;case 603979900:this.g.rocketBarrels=d;break;case 603979850:this.gdata.setGreyscaleMode(this.g.greyscaleRendering=d);break;case 603979879:this.g.measurementLabels=
d;break;case 603979810:this.setAxesModeMolecular(!d);return;case 603979804:this.setAxesModeMolecular(d);return;case 603979808:this.setAxesModeUnitCell(d);return;case 603979806:this.setAxesOrientationRasmol(d);return;case 603979824:this.setStringPropertyTok("defaultcolorscheme",545259545,d?"rasmol":"jmol");return;case 603979825:this.setDebugScript(d);return;case 603979893:this.setPerspectiveDepth(d);return;case 603979798:this.setAutoBond(d);return;case 603979914:this.setShowAxes(d);return;case 603979916:this.setShowBbcage(d);
return;case 603979922:this.setShowHydrogens(d);return;case 603979926:this.setShowMeasurements(d);return;case 603979936:this.setShowUnitCell(d);return;case 603979812:c=!1;this.g.bondModeOr=d;break;case 603979978:c=!1;this.g.zeroBasedXyzRasmol=d;this.reset(!0);break;case 603979895:c=!1;this.g.rangeSelected=d;break;case 603979878:c=!1;this.g.measureAllModels=d;break;case 603979954:c=!1;this.sm.setAllowStatusReporting(d);break;case 603979823:c=!1;this.g.chainCaseSensitive=d;break;case 603979858:c=!1;
this.g.hideNameInPopup=d;break;case 603979827:c=!1;this.g.disablePopupMenu=d;break;case 603979846:c=!1;this.g.forceAutoBond=d;break;default:if(!this.g.htBooleanParameterFlags.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.getBoolean(d));return}}this.g.setB(a,d);c&&this.setTainted(!0)},"~S,~N,~B");c(c$,"setModelKitMode",function(a){if(null!=this.actionManager&&this.allowScripting){if(a||this.g.modelKitMode)this.setPickingMode(null,a?33:1),this.setPickingMode(null,a?32:1);var b=this.g.modelKitMode!=
a;this.g.modelKitMode=a;this.highlight(null);a?(this.setNavigationMode(!1),this.selectAll(),this.setAtomPickingOption("C"),this.setBondPickingOption("p"),this.$isApplet||this.popupMenu(0,0,"m"),b&&this.sm.setCallbackFunction("modelkit","ON"),this.g.modelKitMode=!0,0==this.getAtomCount()&&this.zap(!1,!0,!0)):(this.actionManager.setPickingMode(-1),this.setStringProperty("pickingStyle","toggle"),this.setBooleanProperty("bondPicking",!1),b&&this.sm.setCallbackFunction("modelkit","OFF"))}},"~B");c(c$,
"setSmilesString",function(a){null==a?this.g.removeParam("_smilesString"):this.g.setO("_smilesString",a)},"~S");c(c$,"removeUserVariable",function(a){this.g.removeUserVariable(a);a.endsWith("callback")&&this.sm.setCallbackFunction(a,null)},"~S");c(c$,"isJmolVariable",function(a){return this.g.isJmolVariable(a)},"~S");c(c$,"jmolTest",function(){});c(c$,"showParameter",function(a,b,d){d=""+this.g.getParameterEscaped(a,d);(b||0>d.indexOf("<not defined>"))&&this.showString(a+" = "+d,!1)},"~S,~B,~N");
c(c$,"showString",function(a,b){this.isScriptQueued()&&((!this.isSilent||b)&&!this.isJS)&&JU.Logger.warn(a);this.scriptEcho(a)},"~S,~B");c(c$,"getAllSettings",function(a){return this.getStateCreator().getAllSettings(a)},"~S");c(c$,"getBindingInfo",function(a){return this.haveDisplay?this.actionManager.getBindingInfo(a):""},"~S");c(c$,"getIsosurfacePropertySmoothing",function(a){return a?this.g.isosurfacePropertySmoothingPower:this.g.isosurfacePropertySmoothing?1:0},"~B");c(c$,"setNavigationDepthPercent",
function(a){this.tm.setNavigationDepthPercent(a);this.refresh(1,"set navigationDepth")},"~N");c(c$,"getShowNavigationPoint",function(){return!this.g.navigationMode||!this.tm.canNavigate()?!1:this.tm.isNavigating()&&!this.g.hideNavigationPoint||this.g.showNavigationPointAlways||this.getInMotion(!0)});c(c$,"getCurrentSolventProbeRadius",function(){return this.g.solventOn?this.g.solventProbeRadius:0});c(c$,"getTestFlag",function(a){switch(a){case 1:return this.g.testFlag1;case 2:return this.g.testFlag2;
case 3:return this.g.testFlag3;case 4:return this.g.testFlag4}return!1},"~N");h(c$,"setPerspectiveDepth",function(a){this.tm.setPerspectiveDepth(a)},"~B");h(c$,"setAxesOrientationRasmol",function(a){this.g.setB("axesOrientationRasmol",a);this.g.axesOrientationRasmol=a;this.reset(!0)},"~B");c(c$,"setAxesScale",function(a){a=JV.Viewer.checkFloatRange(a,-100,100);this.g.axesScale=a;this.axesAreTainted=!0},"~N");c(c$,"getAxisPoints",function(){this.shm.loadShape(33);return 0==this.getObjectMad(1)||this.g.axesMode!==
J.c.AXES.UNITCELL||this.getShapeProperty(33,"axesTypeXY").booleanValue()||null!=this.getShapeProperty(33,"origin")?null:this.getShapeProperty(33,"axisPoints")});c(c$,"resetError",function(){this.g.removeParam("_errormessage")});c(c$,"setAxesModeMolecular",function(a){this.g.axesMode=a?J.c.AXES.MOLECULAR:J.c.AXES.BOUNDBOX;this.axesAreTainted=!0;this.g.removeParam("axesunitcell");this.g.removeParam(a?"axeswindow":"axesmolecular");this.g.setI("axesMode",this.g.axesMode.getCode());this.g.setB(a?"axesMolecular":
"axesWindow",!0)},"~B");c(c$,"setAxesModeUnitCell",function(a){this.g.axesMode=a?J.c.AXES.UNITCELL:J.c.AXES.BOUNDBOX;this.axesAreTainted=!0;this.g.removeParam("axesmolecular");this.g.removeParam(a?"axeswindow":"axesunitcell");this.g.setB(a?"axesUnitcell":"axesWindow",!0);this.g.setI("axesMode",this.g.axesMode.getCode())},"~B");h(c$,"getPerspectiveDepth",function(){return this.tm.getPerspectiveDepth()});h(c$,"setSelectionHalos",function(a){null==this.ms||a==this.ms.getSelectionHaloEnabled()||(this.g.setB("selectionHalos",
a),this.shm.loadShape(8),this.ms.setSelectionHaloEnabled(a))},"~B");c(c$,"getSelectionHaloEnabled",function(a){var b=this.ms.getSelectionHaloEnabled()||a&&this.showSelected;a&&(this.showSelected=!1);return b},"~B");c(c$,"setStrandCount",function(a,b){b=JV.Viewer.checkIntRange(b,0,20);switch(a){case 12:this.g.strandCountForStrands=b;break;case 13:this.g.strandCountForMeshRibbon=b;break;default:this.g.strandCountForStrands=b,this.g.strandCountForMeshRibbon=b}this.g.setI("strandCount",b);this.g.setI("strandCountForStrands",
this.g.strandCountForStrands);this.g.setI("strandCountForMeshRibbon",this.g.strandCountForMeshRibbon)},"~N,~N");c(c$,"getStrandCount",function(a){return 12==a?this.g.strandCountForStrands:this.g.strandCountForMeshRibbon},"~N");c(c$,"setNavigationMode",function(a){this.g.navigationMode=a;this.tm.setNavigationMode(a)},"~B");c(c$,"setTransformManagerDefaults",function(){this.tm.setCameraDepthPercent(this.g.defaultCameraDepth,!0);this.tm.setPerspectiveDepth(this.g.defaultPerspectiveDepth);this.tm.setStereoDegrees(-5);
this.tm.setVisualRange(this.g.visualRange);this.tm.setSpinOff();this.tm.setVibrationPeriod(0);this.tm.setFrameOffsets(this.frameOffsets)});h(c$,"setAutoBond",function(a){this.g.setB("autobond",a);this.g.autoBond=a},"~B");c(c$,"makeConnections",function(a,b,d,c,g,f,h,k,l,m){this.clearModelDependentObjects();this.clearMinimization();return this.ms.makeConnections(a,b,d,c,g,f,h,k,l,m)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");h(c$,"rebond",function(){this.rebondState(!1)});c(c$,"rebondState",function(a){this.clearModelDependentObjects();
this.ms.deleteAllBonds();a=a&&this.g.legacyAutoBonding;this.ms.autoBondBs4(null,null,null,null,this.getMadBond(),a);this.addStateScript(a?"set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;":"connect;",!1,!0)},"~B");h(c$,"setPercentVdwAtom",function(a){this.g.setI("percentVdwAtom",a);this.g.percentVdwAtom=a;this.rd.value=a/100;this.rd.factorType=J.atomdata.RadiusData.EnumType.FACTOR;this.rd.vdwType=J.c.VDW.AUTO;this.shm.setShapeSizeBs(0,0,this.rd,null)},"~N");h(c$,"getMadBond",function(){return 2*
this.g.bondRadiusMilliAngstroms});h(c$,"setShowHydrogens",function(a){this.g.setB("showHydrogens",a);this.g.showHydrogens=a},"~B");h(c$,"setShowBbcage",function(a){this.setObjectMad(31,"boundbox",a?-4:0);this.g.setB("showBoundBox",a)},"~B");h(c$,"getShowBbcage",function(){return 0!=this.getObjectMad(4)});c(c$,"setShowUnitCell",function(a){this.setObjectMad(32,"unitcell",a?-2:0);this.g.setB("showUnitCell",a)},"~B");c(c$,"getShowUnitCell",function(){return 0!=this.getObjectMad(5)});h(c$,"setShowAxes",
function(a){this.setObjectMad(33,"axes",a?-2:0);this.g.setB("showAxes",a)},"~B");h(c$,"getShowAxes",function(){return 0!=this.getObjectMad(1)});h(c$,"setFrankOn",function(a){this.$isPreviewOnly&&(a=!1);this.frankOn=a;this.setObjectMad(35,"frank",a?1:0)},"~B");c(c$,"getShowFrank",function(){return this.$isPreviewOnly||this.$isApplet&&this.creatingImage?!1:this.$isSignedApplet&&!this.isSignedAppletLocal&&!this.isJS||this.frankOn});h(c$,"setShowMeasurements",function(a){this.g.setB("showMeasurements",
a);this.g.showMeasurements=a},"~B");c(c$,"setUnits",function(a,b){this.g.setUnits(a);b&&(this.g.setUnits(a),this.setShapeProperty(6,"reformatDistances",null))},"~S,~B");h(c$,"setRasmolDefaults",function(){this.setDefaultsType("RasMol")});h(c$,"setJmolDefaults",function(){this.setDefaultsType("Jmol")});c(c$,"setDefaultsType",function(a){a.equalsIgnoreCase("RasMol")?this.stm.setRasMolDefaults():a.equalsIgnoreCase("PyMOL")?this.stm.setPyMOLDefaults():(this.stm.setJmolDefaults(),this.setIntProperty("bondingVersion",
0),this.shm.setShapeSizeBs(0,0,this.rd,this.getAllAtoms()))},"~S");c(c$,"setAntialias",function(a,b){switch(a){case 603979786:this.g.antialiasDisplay=b;break;case 603979790:this.g.antialiasTranslucent=b;break;case 603979788:this.g.antialiasImages=b;return}this.resizeImage(0,0,!1,!1,!0)},"~N,~B");c(c$,"allocTempPoints",function(a){return this.tempArray.allocTempPoints(a)},"~N");c(c$,"freeTempPoints",function(a){this.tempArray.freeTempPoints(a)},"~A");c(c$,"allocTempScreens",function(a){return this.tempArray.allocTempScreens(a)},
"~N");c(c$,"freeTempScreens",function(a){this.tempArray.freeTempScreens(a)},"~A");c(c$,"allocTempEnum",function(a){return this.tempArray.allocTempEnum(a)},"~N");c(c$,"freeTempEnum",function(a){this.tempArray.freeTempEnum(a)},"~A");c(c$,"getFont3D",function(a,b,d){return this.gdata.getFont3DFSS(a,b,d)},"~S,~S,~N");c(c$,"formatText",function(a){if(0>a.indexOf("@{")&&0>a.indexOf("%{"))return a;var b=a,d=0<=b.indexOf("\\");d&&(b=JU.PT.rep(b,"\\%","\u0001"),b=JU.PT.rep(b,"\\@","\u0002"),d=!b.equals(a));
for(var b=JU.PT.rep(b,"%{","@{"),c;0<=(a=b.indexOf("@{"));){a++;var g=a+1;c=b.length;a=JU.Txt.ichMathTerminator(b,a,c);if(a>=c)return b;c=b.substring(g,a);if(0==c.length)return b;c=this.evaluateExpression(c);p(c,JU.P3)&&(c=JU.Escape.eP(c));b=b.substring(0,g-2)+c.toString()+b.substring(a+1)}d&&(b=JU.PT.rep(b,"\u0002","@"),b=JU.PT.rep(b,"\u0001","%"));return b},"~S");c(c$,"getElementSymbol",function(a){return this.ms.getElementSymbol(a)},"~N");c(c$,"getElementNumber",function(a){return this.ms.getElementNumber(a)},
"~N");h(c$,"getAtomName",function(a){return this.ms.getAtomName(a)},"~N");h(c$,"getAtomNumber",function(a){return this.ms.getAtomNumber(a)},"~N");h(c$,"getAtomPoint3f",function(a){return this.ms.at[a]},"~N");h(c$,"getAtomRadius",function(a){return this.ms.getAtomRadius(a)},"~N");h(c$,"getAtomArgb",function(a){return this.gdata.getColorArgbOrGray(this.ms.getAtomColix(a))},"~N");h(c$,"getAtomModelIndex",function(a){return this.ms.at[a].mi},"~N");h(c$,"getBondRadius",function(a){return this.ms.getBondRadius(a)},
"~N");h(c$,"getBondOrder",function(a){return this.ms.getBondOrder(a)},"~N");h(c$,"getBondArgb1",function(a){return this.gdata.getColorArgbOrGray(this.ms.getBondColix1(a))},"~N");h(c$,"getBondModelIndex",function(a){return this.ms.getBondModelIndex(a)},"~N");h(c$,"getBondArgb2",function(a){return this.gdata.getColorArgbOrGray(this.ms.getBondColix2(a))},"~N");h(c$,"getPolymerLeadMidPoints",function(a,b){return this.ms.getPolymerLeadMidPoints(a,b)},"~N,~N");c(c$,"getAtomGroupQuaternions",function(a,
b){return this.ms.getAtomGroupQuaternions(a,b,this.getQuaternionFrame())},"JU.BS,~N");c(c$,"setStereoMode",function(a,b,d){this.setFloatProperty("stereoDegrees",d);this.setBooleanProperty("greyscaleRendering",b.isBiColor());null!=a?this.tm.setStereoMode2(a):this.tm.setStereoMode(b)},"~A,J.c.STER,~N");c(c$,"isStereoDouble",function(){return this.tm.stereoMode===J.c.STER.DOUBLE});c(c$,"getChimeInfo",function(a){return this.getPropertyManager().getChimeInfo(a,this.bsA())},"~N");c(c$,"getModelFileInfo",
function(){return this.getPropertyManager().getModelFileInfo(this.getVisibleFramesBitSet())});c(c$,"getModelFileInfoAll",function(){return this.getPropertyManager().getModelFileInfo(null)});h(c$,"getProperty",function(a,b,d){if(!"DATA_API".equals(a))return this.getPropertyManager().getProperty(a,b,d);switch("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........".indexOf(b)){case 0:return this.scriptCheckRet(d,
!0);case 20:return null==this.appConsole?"":this.appConsole.getText();case 40:return this.showEditor(d),null;case 60:return this.scriptEditorVisible=d.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:p(d,J.api.JmolAppConsoleInterface)?this.appConsole=d:null!=d&&!d.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=d&&d.booleanValue())&&(this.isJS&&(this.appConsole=J.api.Interface.getOption("consolejs.AppletConsole")),null!=this.appConsole&&this.appConsole.start(this)),
this.scriptEditor=this.isJS||null==this.appConsole?null:this.appConsole.getScriptEditor(),this.appConsole;case 100:return null==this.appConsole&&(null!=d&&d.booleanValue())&&(this.getProperty("DATA_API","getAppConsole",Boolean.TRUE),this.scriptEditor=null==this.appConsole?null:this.appConsole.getScriptEditor()),this.scriptEditor;case 120:return null!=this.jmolpopup&&this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.menuStructure=d;case 140:return this.getSpaceGroupInfo(null);case 160:return this.g.disablePopupMenu=
!0,null;case 180:return this.g.defaultDirectory;case 200:return p(d,String)?this.getMenu(d):this.getPopupMenu();case 220:return this.shm.getProperty(d)}JU.Logger.error("ERROR in getProperty DATA_API: "+b);return null},"~S,~S,~O");c(c$,"showEditor",function(a){var b=this.getProperty("DATA_API","getScriptEditor",Boolean.TRUE);null!=b&&b.show(a)},"~A");c(c$,"getPropertyManager",function(){null==this.pm&&(this.pm=J.api.Interface.getInterface("JV.PropertyManager")).setViewer(this);return this.pm});c(c$,
"getModelExtract",function(a,b,d,c){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),b,d,c)},"~O,~B,~B,~S");c(c$,"setTainted",function(a){this.isTainted=this.axesAreTainted=a&&(this.refreshing||this.creatingImage)},"~B");c(c$,"notifyMouseClicked",function(a,b,d,c){var g=JV.binding.Binding.getButtonMods(d),f=JV.binding.Binding.getClickCount(d);this.g.setI("_mouseX",a);this.g.setI("_mouseY",this.dimScreen.height-b);this.g.setI("_mouseAction",d);this.g.setI("_mouseModifiers",g);
this.g.setI("_clickCount",f);return this.sm.setStatusClicked(a,this.dimScreen.height-b,d,f,c)},"~N,~N,~N,~N");c(c$,"checkObjectClicked",function(a,b,d){return this.shm.checkObjectClicked(a,b,d,this.getVisibleFramesBitSet(),this.g.drawPicking)},"~N,~N,~N");c(c$,"checkObjectHovered",function(a,b){return 0<=a&&null!=this.shm&&this.shm.checkObjectHovered(a,b,this.getVisibleFramesBitSet(),this.getBondPicking())},"~N,~N");c(c$,"checkObjectDragged",function(a,b,d,c,g){var f=0;switch(this.getPickingMode()){case 2:f=
5;break;case 4:f=22}this.shm.checkObjectDragged(a,b,d,c,g,this.getVisibleFramesBitSet(),f)&&(this.refresh(1,"checkObjectDragged"),22==f&&this.scriptEcho(this.getShapeProperty(22,"command")))},"~N,~N,~N,~N,~N");c(c$,"rotateAxisAngleAtCenter",function(a,b,d,c,g,f,h){(a=this.tm.rotateAxisAngleAtCenter(a,b,d,c,g,f,h))&&this.refresh(-1,"rotateAxisAngleAtCenter");return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,d,c,g,f,h,k,l,m){if(this.isHeadless()){if(f&&
3.4028235E38==g)return!1;f=!1}(a=this.tm.rotateAboutPointsInternal(a,b,d,c,g,!1,f,h,!1,k,l,m))&&this.refresh(-1,"rotateAxisAboutPointsInternal");return a},"J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.Lst,~A");c(c$,"startSpinningAxis",function(a,b,d){this.tm.spinOn||this.tm.navOn?(this.tm.setSpinOff(),this.tm.setNavOn(!1)):this.tm.rotateAboutPointsInternal(null,a,b,this.g.pickingSpinRate,3.4028235E38,d,!0,null,!1,null,null,null)},"JU.T3,JU.T3,~B");c(c$,"getModelDipole",function(){return this.ms.getModelDipole(this.am.cmi)});
c(c$,"calculateMolecularDipole",function(a){return this.ms.calculateMolecularDipole(this.am.cmi,a)},"JU.BS");c(c$,"setDefaultLattice",function(a){Float.isNaN(a.x+a.y+a.z)||this.g.ptDefaultLattice.setT(a);this.g.setO("defaultLattice",JU.Escape.eP(a))},"JU.P3");c(c$,"getDefaultLattice",function(){return this.g.ptDefaultLattice});c(c$,"getData",function(a,b){var d="";if(b.equalsIgnoreCase("MOL")||b.equalsIgnoreCase("SDF")||b.equalsIgnoreCase("V2000")||b.equalsIgnoreCase("V3000")||b.equalsIgnoreCase("XYZVIB")||
b.equalsIgnoreCase("CD")||b.equalsIgnoreCase("JSON"))return this.getModelExtract(a,!1,!1,b);if(0==b.toLowerCase().indexOf("property_"))d='{selected}.label("%{'+b+'}")';else{if(b.equalsIgnoreCase("CML"))return this.getModelCml(this.getAtomBitSet(a),2147483647,!0);d=b.equalsIgnoreCase("PDB")?'{selected and not hetero}.label("ATOM  %5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  ").lines+{selected and hetero}.label("HETATM%5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  ").lines':
b.equalsIgnoreCase("XYZRN")?'"" + {selected}.size + "\n\n"+{selected}.label("%-2e %8.3x %8.3y %8.3z %4.2[vdw] 1 [%n]%r.%a#%i").lines':b.startsWith("USER:")?'{selected}.label("'+b.substring(5)+'").lines':'"" + {selected}.size + "\n\n"+{selected}.label("%-2e %10.5x %10.5y %10.5z").lines'}a.equals("selected")||(d=JU.PT.rep(d,"selected",a));return this.evaluateExpression(d)},"~S,~S");c(c$,"getModelCml",function(a,b,d){return this.getPropertyManager().getModelCml(a,b,d)},"JU.BS,~N,~B");c(c$,"getPdbAtomData",
function(a,b){return this.getPropertyManager().getPdbAtomData(null==a?this.bsA():a,b)},"JU.BS,JU.OC");c(c$,"isJmolDataFrame",function(){return this.ms.isJmolDataFrameForModel(this.am.cmi)});c(c$,"setFrameTitle",function(a,b){this.ms.setFrameTitle(JU.BSUtil.newAndSetBit(a),b)},"~N,~S");c(c$,"setFrameTitleObj",function(a){this.shm.loadShape(30);this.ms.setFrameTitle(this.getVisibleFramesBitSet(),a)},"~O");c(c$,"getFrameTitle",function(){return this.ms.getFrameTitle(this.am.cmi)});c(c$,"setAtomProperty",
function(a,b,d,c,g,f,h){1649412120==b&&this.shm.deleteVdwDependentShapes(a);this.clearMinimization();this.ms.setAtomProperty(a,b,d,c,g,f,h);switch(b){case 1112541185:case 1112541186:case 1112541187:case 1112541188:case 1112541189:case 1112541190:case 1112539153:case 1112539154:case 1112539155:case 1087375365:this.refreshMeasures(!0)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"checkCoordinatesChanged",function(){this.ms.recalculatePositionDependentQuantities(null,null);this.refreshMeasures(!0)});c(c$,"setAtomCoords",
function(a,b,d){0!=a.cardinality()&&(this.ms.setAtomCoords(a,b,d),this.checkMinimization(),this.sm.setStatusAtomMoved(a))},"JU.BS,~N,~O");c(c$,"setAtomCoordsRelative",function(a,b){null==b&&(b=this.bsA());0!=b.cardinality()&&(this.ms.setAtomCoordsRelative(a,b),this.checkMinimization(),this.sm.setStatusAtomMoved(b))},"JU.T3,JU.BS");c(c$,"invertAtomCoordPt",function(a,b){this.ms.invertSelected(a,null,-1,null,b);this.checkMinimization();this.sm.setStatusAtomMoved(b)},"JU.P3,JU.BS");c(c$,"invertAtomCoordPlane",
function(a,b){this.ms.invertSelected(null,a,-1,null,b);this.checkMinimization();this.sm.setStatusAtomMoved(b)},"JU.P4,JU.BS");c(c$,"invertSelected",function(a,b,d,c){var g=this.bsA();0!=g.cardinality()&&(this.ms.invertSelected(a,b,d,c,g),this.checkMinimization(),this.sm.setStatusAtomMoved(g))},"JU.P3,JU.P4,~N,JU.BS");c(c$,"moveAtoms",function(a,b,d,c,g,f,h){0!=f.cardinality()&&(this.ms.moveAtoms(a,b,d,f,c,g,h),this.checkMinimization(),this.sm.setStatusAtomMoved(f))},"JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B");
c(c$,"moveSelected",function(a,b,d,c,g,f,h,k){0!=d&&(-2147483648==c&&(this.rotateBondIndex=-1),this.isJmolDataFrame()||(-2147483648==a?(this.showSelected=!0,this.shm.loadShape(8),this.refresh(6,"moveSelected")):2147483647==a?this.showSelected&&(this.showSelected=!1,this.refresh(6,"moveSelected")):this.movingSelected||(this.movingSelected=!0,this.stopMinimization(),0<=this.rotateBondIndex&&-2147483648!=c?this.actionRotateBond(a,b,c,g):(f=this.setMovableBitSet(f,!k),0!=f.cardinality()&&(h?(c=this.ms.getAtomSetCenter(f),
this.tm.finalizeTransformParameters(),g=this.g.antialiasDisplay?2:1,h=this.tm.transformPt(c),a=-2147483648!=d?JU.P3.new3(h.x,h.y,h.z+d+0.5):JU.P3.new3(h.x+a*g+0.5,h.y+b*g+0.5,h.z),b=new JU.P3,this.tm.unTransformPoint(a,b),b.sub(c),this.setAtomCoordsRelative(b,f)):this.tm.rotateXYBy(a,b,f))),this.refresh(2,""),this.movingSelected=!1)))},"~N,~N,~N,~N,~N,JU.BS,~B,~B");c(c$,"highlightBond",function(a,b){if(!b||this.hoverEnabled){var d=null;if(0<=a){var c=this.ms.bo[a],d=c.getAtomIndex2();if(!this.isAtomAssignable(d))return;
d=JU.BSUtil.newAndSetBit(d);d.set(c.getAtomIndex1())}this.highlight(d);this.refresh(3,"highlightBond")}},"~N,~B");c(c$,"highlight",function(a){null!=a&&this.shm.loadShape(8);this.setShapeProperty(8,"highlight",a)},"JU.BS");c(c$,"setRotateBondIndex",function(a){if(0<=this.rotateBondIndex||!(0>a))this.rotatePrev1=-1,this.bsRotateBranch=null,-2147483648!=a&&(this.rotateBondIndex=a,this.highlightBond(a,!1))},"~N");c(c$,"getRotateBondIndex",function(){return this.rotateBondIndex});c(c$,"actionRotateBond",
function(a,b,d,c){if(!(0>this.rotateBondIndex)){var g=this.bsRotateBranch,f,h;if(null==g){h=this.ms.bo[this.rotateBondIndex];f=h.getAtom1();h=h.getAtom2();this.undoMoveActionClear(f.i,2,!0);d=JU.P3.new3(d,c,q((f.sZ+h.sZ)/2));this.tm.unTransformPoint(d,d);if(1==h.getCovalentBondCount()||d.distance(f)<d.distance(h)&&1!=f.getCovalentBondCount())c=f,f=h,h=c;if(90<JU.Measure.computeAngleABC(d,f,h,!0)||90<JU.Measure.computeAngleABC(d,h,f,!0))g=this.getBranchBitSet(h.i,f.i,!0);if(null!=g){d=0;for(c=f.getBonds().length;0<=
--c;)if(g.get(f.getBondedAtomIndex(c))&&2==++d){g=null;break}}null==g&&(g=this.ms.getMoleculeBitSetForAtom(f.i));this.bsRotateBranch=g;this.rotatePrev1=f.i;this.rotatePrev2=h.i}else f=this.ms.at[this.rotatePrev1],h=this.ms.at[this.rotatePrev2];d=JU.V3.new3(h.sX-f.sX,h.sY-f.sY,0);a=JU.V3.new3(a,b,0);d.cross(d,a);a=(0<d.z?1:-1)*a.length();g=JU.BSUtil.copy(g);g.andNot(this.slm.getMotionFixedAtoms());this.rotateAboutPointsInternal(this.eval,f,h,0,a,!1,g,null,null,null)}},"~N,~N,~N,~N");c(c$,"refreshMeasures",
function(a){this.setShapeProperty(6,"refresh",null);a&&this.stopMinimization()},"~B");c(c$,"functionXY",function(a,b,d){var c=null;if(0==a.indexOf("file:"))c=this.getFileAsString(a.substring(5),!1);else if(0!=a.indexOf("data2d_"))return this.sm.functionXY(a,b,d);b=Math.abs(b);d=Math.abs(d);if(null==c){a=this.getDataFloat2D(a);if(null!=a)return a;c=""}a=L(b,d,0);var g=L(b*d,0);JU.Parser.parseStringInfestedFloatArray(c,null,g);for(var f=c=0;c<b;c++)for(var h=0;h<d;h++)a[c][h]=g[f++];return a},"~S,~N,~N");
c(c$,"functionXYZ",function(a,b,d,c){var g=null;if(0==a.indexOf("file:"))g=this.getFileAsString(a.substring(5),!1);else if(0!=a.indexOf("data3d_"))return this.sm.functionXYZ(a,b,d,c);b=Math.abs(b);d=Math.abs(d);c=Math.abs(c);if(null==g){a=this.getDataFloat3D(a);if(null!=a)return a;g=""}a=L(b,d,c,0);var f=L(b*d*c,0);JU.Parser.parseStringInfestedFloatArray(g,null,f);for(var h=g=0;g<b;g++)for(var k=0;k<d;k++)for(var l=0;l<c;l++)a[g][k][l]=f[h++];return a},"~S,~N,~N,~N");h(c$,"extractMolData",function(a){if(null==
a){a=this.am.cmi;if(0>a)return null;a=this.getModelNumberDotted(a)}return this.getModelExtract(a,!0,!1,"V2000")},"~S");c(c$,"getNMRPredict",function(a){var b=this.getModelExtract("selected",!0,!1,"V2000"),d=b.indexOf("\n"),b="Jmol "+JV.Viewer.version_date+b.substring(d);return a?(this.$isApplet?this.showUrl(this.g.nmrUrlFormat+b):(this.syncScript("true","*",0),this.syncScript("H1Simulate:",".",0)),null):this.getFileAsString(this.g.nmrPredictFormat+b,!1)},"~B");c(c$,"getHelp",function(a){0>this.g.helpPath.indexOf("?")?
(0<a.length&&0!=a.indexOf("?")&&(a="?search="+JU.PT.rep(a," ","%20")),a+=(0==a.length?"?ver=":"&ver=")+JV.JC.version):a="&"+a;this.showUrl(this.g.helpPath+a)},"~S");c(c$,"show2D",function(a){this.showUrl(this.setLoadFormat("_"+a,"2",!1))},"~S");c(c$,"getChemicalInfo",function(a,b){var d=null,c="/";switch(null==b?1073742035:b.tok){case 1073741977:c="I";break;case 1073741978:c="K";break;case 1073742159:c="T";break;case 1073742160:c="S";break;case 1073742035:c="N";break;default:d=JS.SV.sValue(b)}var g=
this.setLoadFormat("_"+a,c,!1);"/"==c&&(g+=JU.PT.rep(d," ","%20"));return this.getFileAsString4(g,-1,!1,!1,!1)},"~S,JS.T");c(c$,"addCommand",function(a){!this.autoExit&&(this.haveDisplay&&this.getPreserveState())&&this.commandHistory.addCommand(JU.PT.replaceAllCharacters(a,"\r\n\t"," "))},"~S");c(c$,"removeCommand",function(){return this.commandHistory.removeCommand()});h(c$,"getSetHistory",function(a){return this.commandHistory.getSetHistory(a)},"~N");c(c$,"getOutputChannel",function(a,b){return this.getOutputManager().getOutputChannel(a,
b)},"~S,~A");h(c$,"writeTextFile",function(a,b){var c=new java.util.Hashtable;c.put("fileName",a);c.put("type","txt");c.put("text",b);this.outputToFile(c)},"~S,~S");h(c$,"clipImageOrPasteText",function(a){return!this.haveAccess(JV.Viewer.ACCESS.ALL)?"no":this.getOutputManager().clipImageOrPasteText(a)},"~S");h(c$,"getClipboardText",function(){if(!this.haveAccess(JV.Viewer.ACCESS.ALL))return"no";try{return this.getOutputManager().getClipboardText()}catch(a){if(y(a,Error))return J.i18n.GT._("clipboard is not accessible -- use signed applet");
throw a;}});c(c$,"processWriteOrCapture",function(a){return this.getOutputManager().processWriteOrCapture(a)},"java.util.Map");c(c$,"createZip",function(a,b,c){var e=new java.util.Hashtable;e.put("fileName",a);e.put("type",b);e.put("text",this.getStateInfo());p(c,Array)?e.put("scripts",c):p(c,JU.Lst)&&e.put("imageData",c);return this.getOutputManager().outputToFile(e)},"~S,~S,~O");h(c$,"outputToFile",function(a){return this.getOutputManager().outputToFile(a)},"java.util.Map");c(c$,"getOutputManager",
function(){return null!=this.outputManager?this.outputManager:(this.outputManager=J.api.Interface.getInterface("JV.OutputManager"+(this.isJS&&!this.isWebGL?"JS":"Awt"))).setViewer(this,this.privateKey)});c(c$,"setSyncTarget",function(a,b){switch(a){case 0:this.sm.syncingMouse=b;break;case 1:this.sm.syncingScripts=b;break;case 2:this.sm.syncSend(b?"GET_GRAPHICS":"SET_GRAPHICS_OFF","*",0);Float.isNaN(this.tm.stereoDegrees)&&this.setFloatProperty("stereoDegrees",-5);b&&(this.setBooleanProperty("_syncMouse",
!1),this.setBooleanProperty("_syncScript",!1));return}!this.sm.syncingScripts&&!this.sm.syncingMouse&&this.refresh(-1,"set sync")},"~N,~B");h(c$,"syncScript",function(a,b,c){this.getStateCreator().syncScript(a,b,c)},"~S,~S,~N");h(c$,"getModelIndexFromId",function(a){return this.ms.getModelIndexFromId(a)},"~S");c(c$,"setSyncDriver",function(a){this.sm.setSyncDriver(a)},"~N");c(c$,"getPartialCharges",function(){return this.ms.getPartialCharges()});c(c$,"setProteinType",function(a,b){this.ms.setProteinType(null==
b?this.bsA():b,a)},"J.c.STR,JU.BS");h(c$,"getBondPoint3f1",function(a){return this.ms.getBondAtom1(a)},"~N");h(c$,"getBondPoint3f2",function(a){return this.ms.getBondAtom2(a)},"~N");c(c$,"getVanderwaalsMar",function(a){return this.defaultVdw===J.c.VDW.USER?this.userVdwMars[a]:JU.Elements.getVanderwaalsMar(a,this.defaultVdw)},"~N");c(c$,"getVanderwaalsMarType",function(a,b){if(null==b)b=this.defaultVdw;else switch(b){case J.c.VDW.AUTO:case J.c.VDW.AUTO_BABEL:case J.c.VDW.AUTO_JMOL:case J.c.VDW.AUTO_RASMOL:this.defaultVdw!==
J.c.VDW.AUTO&&(b=this.defaultVdw)}b===J.c.VDW.USER&&null==this.bsUserVdws&&(b=J.c.VDW.JMOL);return b===J.c.VDW.USER?this.userVdwMars[a&127]:JU.Elements.getVanderwaalsMar(a,b)},"~N,J.c.VDW");c(c$,"setVdwStr",function(a){a=J.c.VDW.getVdwType(a);null==a&&(a=J.c.VDW.AUTO);switch(a){case J.c.VDW.JMOL:case J.c.VDW.BABEL:case J.c.VDW.RASMOL:case J.c.VDW.AUTO:case J.c.VDW.USER:break;default:a=J.c.VDW.JMOL}a!==this.defaultVdw&&(a===J.c.VDW.USER&&null==this.bsUserVdws)&&this.setUserVdw(this.defaultVdw);this.defaultVdw=
a;this.g.setO("defaultVDW",a.getVdwLabel())},"~S");c(c$,"setUserVdw",function(a){this.userVdwMars=D(JU.Elements.elementNumberMax,0);this.userVdws=L(JU.Elements.elementNumberMax,0);this.bsUserVdws=new JU.BS;a===J.c.VDW.USER&&(a=J.c.VDW.JMOL);for(var b=1;b<JU.Elements.elementNumberMax;b++)this.userVdwMars[b]=JU.Elements.getVanderwaalsMar(b,a),this.userVdws[b]=this.userVdwMars[b]/1E3},"J.c.VDW");c(c$,"getDefaultVdwNameOrData",function(a,b,c){switch(a){case -2147483648:return this.defaultVdw.getVdwLabel();
case 2147483647:if(null==(c=this.bsUserVdws))return"";b=J.c.VDW.USER}if(null==b||b===J.c.VDW.AUTO)b=this.defaultVdw;b===J.c.VDW.USER&&null==this.bsUserVdws&&this.setUserVdw(this.defaultVdw);return this.getDataManager().getDefaultVdwNameOrData(b,c)},"~N,J.c.VDW,JU.BS");c(c$,"deleteAtoms",function(a,b){var c=null==a?-1:a.nextSetBit(0);if(0>c)return 0;this.clearModelDependentObjects();if(!b){this.sm.modifySend(c,this.ms.at[c].mi,4,"deleting atom "+this.getAtomName(c));this.ms.deleteAtoms(a);var e=this.slm.deleteAtoms(a);
this.setTainted(!0);this.sm.modifySend(c,this.ms.at[c].mi,-4,"OK");return e}return this.deleteModels(this.ms.at[c].mi,a)},"JU.BS,~B");c(c$,"deleteModels",function(a,b){this.clearModelDependentObjects();this.sm.modifySend(-1,a,5,"deleting model "+this.getModelNumberDotted(a));this.setCurrentModelIndexClear(0,!1);this.am.setAnimationOn(!1);var c=JU.BSUtil.copy(this.getDeletedAtoms()),e=null==b?JU.BSUtil.newAndSetBit(a):this.ms.getModelBS(b,!1),e=this.ms.deleteModels(e);this.slm.processDeletedModelAtoms(e);
null!=this.eval&&this.eval.deleteAtomsInVariables(e);this.setAnimationRange(0,0);this.clearRepaintManager(-1);this.am.clear();this.am.initializePointers(1);this.setCurrentModelIndexClear(1<this.getModelCount()?-1:0,1<this.getModelCount());this.hoverAtomIndex=-1;this.setFileLoadStatus(J.c.FIL.DELETED,null,null,null,null,null);this.refreshMeasures(!0);null!=c&&e.andNot(c);this.sm.modifySend(-1,a,-5,"OK");return JU.BSUtil.cardinalityOf(e)},"~N,JU.BS");c(c$,"deleteBonds",function(a){var b=this.ms.getBondModelIndex(a.nextSetBit(0));
this.sm.modifySend(-1,b,2,"delete bonds "+JU.Escape.eBond(a));this.ms.deleteBonds(a,!1);this.sm.modifySend(-1,b,-2,"OK")},"JU.BS");c(c$,"deleteModelAtoms",function(a,b,c,e){this.sm.modifySend(-1,a,1,"delete atoms "+JU.Escape.eBS(e));JU.BSUtil.deleteBits(this.getFrameOffsets(),e);this.setFrameOffsets(this.getFrameOffsets());this.getDataManager().deleteModelAtoms(b,c,e);this.sm.modifySend(-1,a,-1,"OK")},"~N,~N,~N,JU.BS");c(c$,"getDeletedAtoms",function(){return this.slm.getDeletedAtoms()});c(c$,"getQuaternionFrame",
function(){return this.g.quaternionFrame.charAt(2==this.g.quaternionFrame.length?1:0)});c(c$,"calculatePointGroup",function(){return this.ms.calculatePointGroup(this.bsA())});c(c$,"getPointGroupInfo",function(a){return this.ms.getPointGroupInfo(this.getAtomBitSet(a))},"~O");c(c$,"getPointGroupAsString",function(a,b,c,e){return this.ms.getPointGroupAsString(this.bsA(),a,b,c,e)},"~B,~S,~N,~N");c(c$,"loadImageData",function(a,b,c,e){null==a&&this.scriptEcho(b);null==c?this.setBackgroundImage(null==a?
null:b,a):(this.shm.loadShape(30),this.setShapeProperty(30,"text",b),null!=a&&this.setShapeProperty(30,"image",a));this.isJS&&null!=e&&(e.mustResumeEval=!0,this.eval.resumeEval(e))},"~O,~S,~S,JS.ScriptContext");c(c$,"cd",function(a){null==a?a=".":0==a.length&&(this.setStringProperty("defaultDirectory",""),a=".");a=this.fm.getDefaultDirectory(a+(a.equals("=")?"":a.endsWith("/")?"X.spt":"/X.spt"));0<a.length&&this.setStringProperty("defaultDirectory",a);this.fm.getFilePath(a+"/",!0,!1).startsWith("file:/")&&
JV.FileManager.setLocalPath(this,a,!1);return a},"~S");c(c$,"setErrorMessage",function(a,b){this.errorMessageUntranslated=b;null!=a&&this.eval.stopScriptThreads();return this.errorMessage=a},"~S,~S");h(c$,"getErrorMessage",function(){return this.errorMessage});h(c$,"getErrorMessageUn",function(){return null==this.errorMessageUntranslated?this.errorMessage:this.errorMessageUntranslated});c(c$,"setShapeErrorState",function(a,b){this.currentShapeID=a;this.currentShapeState=b},"~N,~S");c(c$,"getShapeErrorState",
function(){if(0>this.currentShapeID)return"";null!=this.ms&&this.shm.releaseShape(this.currentShapeID);this.clearRepaintManager(this.currentShapeID);return JV.JC.getShapeClassName(this.currentShapeID,!1)+" "+this.currentShapeState});c(c$,"handleError",function(a,b){try{b&&this.zapMsg(""+a),this.undoClear(),0==JU.Logger.getLogLevel()&&JU.Logger.setLogLevel(4),this.setCursor(0),this.setBooleanProperty("refreshing",!0),this.fm.setPathForAllFiles(""),JU.Logger.error("vwr handling error condition: "+a+
"  "),this.isJS||a.printStackTrace(),this.notifyError("Error","doClear="+b+"; "+a,""+a)}catch(c){try{JU.Logger.error("Could not notify error "+a+": due to "+c)}catch(e){}}},"Error,~B");c(c$,"getAtomicCharges",function(){return this.ms.getAtomicCharges()});c(c$,"getFunctions",function(a){return a?JV.Viewer.staticFunctions:this.localFunctions},"~B");c(c$,"removeFunction",function(a){a=a.toLowerCase();null!=this.getFunction(a)&&(JV.Viewer.staticFunctions.remove(a),this.localFunctions.remove(a))},"~S");
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c(c$,"addFunction",function(a){var b=a.getName();(JV.Viewer.isStaticFunction(b)?JV.Viewer.staticFunctions:this.localFunctions).put(b,a)},"J.api.JmolScriptFunction");c(c$,"getFunctionCalls",function(a){return this.getStateCreator().getFunctionCalls(a)},"~S");c(c$,"warn",function(a){this.isPrintOnly||JU.Logger.warn(a)},"~S");c(c$,"getMoInfo",function(a){return this.ms.getMoInfo(a)},"~N");c(c$,"checkPrivateKey",function(a){return a==this.privateKey},"~N");c(c$,"bindAction",function(a,b){this.haveDisplay&&
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n("JSV.common");w(["java.lang.Enum","JSV.common.Coordinate"],"JSV.common.Annotation",["java.lang.Double","JU.CU"],function(){c$=t(function(){this.text="";this.is2D=this.$isPixels=!1;this.offsetY=this.offsetX=0;this.spec=null;s(this,arguments)},JSV.common,"Annotation",JSV.common.Coordinate);c(c$,"setA",function(a,b,c,e,g,f,h,k){this.set(a,b);this.spec=c;this.text=e;this.$isPixels=g;this.is2D=f;this.offsetX=h;this.offsetY=k;return this},"~N,~N,JSV.common.Spectrum,~S,~B,~B,~N,~N");c(c$,"setSpec",function(a){this.spec=
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0,k=1):(k=0,l=1);break;case 3:case 4:g=c.get(2),'"'==g.charAt(0)?(l=2,k=4==m?3:-1):(k=2,l=4==m?3:-1),g=c.get(2),'"'==g.charAt(0)?(l=2,k=-1):(k=2,l=-1)}if(null==e&&(0>f||0>h||0>l||0>k))return null;var r=0>f?e.getXVal():Double.$valueOf(c.get(f)).doubleValue(),n=0>h?e.getYVal():Double.$valueOf(c.get(h)).doubleValue(),q=0>k?e.getColor():a.getColor1(JU.CU.getArgbFromString(c.get(k))),p;0>l?p=e.text:(p=c.get(l),'"'==p.charAt(0)&&(p=p.substring(1,p.length-1)));return(new JSV.common.ColoredAnnotation).setCA(r,
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this.getColor3(255,255,255);this.elementColors=new java.util.Hashtable;this.setColor(JSV.common.ScriptToken.TITLECOLOR,JSV.common.ColorParameters.BLACK);this.setColor(JSV.common.ScriptToken.UNITSCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.SCALECOLOR,JSV.common.ColorParameters.BLACK);this.setColor(JSV.common.ScriptToken.COORDINATESCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.GRIDCOLOR,JSV.common.ColorParameters.LIGHT_GRAY);this.setColor(JSV.common.ScriptToken.PLOTCOLOR,
JSV.common.ColorParameters.BLUE);this.setColor(JSV.common.ScriptToken.PLOTAREACOLOR,JSV.common.ColorParameters.WHITE);this.setColor(JSV.common.ScriptToken.BACKGROUNDCOLOR,this.getColor3(192,192,192));this.setColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.PEAKTABCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR,JSV.common.ColorParameters.DARK_GRAY);for(var a=0;8>a;a++)JSV.common.ColorParameters.defaultPlotColors[a]=
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c(c$,"setElementColors",function(a){this.displayFontName=a.displayFontName;var b;for(a=a.elementColors.entrySet().iterator();a.hasNext()&&((b=a.next())||1);)this.setColor(b.getKey(),b.getValue());return this},"JSV.common.ColorParameters");c(c$,"getColorFromString",function(a){return this.getColor1(JU.CU.getArgbFromString(a))},"~S");c(c$,"getPlotColors",function(a){if(null==a)return this.plotColors[0]=this.getElementColor(JSV.common.ScriptToken.PLOTCOLOR),this.plotColors;a=new java.util.StringTokenizer(a,
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this.displayFontName=b:this.displayFontName}return null},"JSV.common.ScriptToken,~S");C(c$,"BLACK",null,"RED",null,"LIGHT_GRAY",null,"DARK_GRAY",null,"BLUE",null,"WHITE",null);c$.defaultPlotColors=c$.prototype.defaultPlotColors=Array(8);c$.defaultPlotColorNames=c$.prototype.defaultPlotColorNames="black darkGreen darkred orange magenta cyan maroon darkGray".split(" ")});n("JSV.common");c$=B(JSV.common,"CoordComparator",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.getXVal()>b.getXVal()?
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function(a,b,c){JSV.common.Coordinate.applyScale(a,1/b,1/c)},"~A,~N,~N");c$.applyScale=c(c$,"applyScale",function(a,b,c){if(1!=b||1!=c)for(var e=0;e<a.length;e++)a[e].setXVal(a[e].getXVal()*b),a[e].setYVal(a[e].getYVal()*c)},"~A,~N,~N");c$.applyShiftReference=c(c$,"applyShiftReference",function(a,b,c,e,g,f,h){if(!(b>a.length||0>b)){switch(h){case 0:g=a[a.length-b].getXVal()-g*f;break;case 1:g=c-g*f;break;case 2:g=e+g}for(c=0;c<a.length;c++)b=a[c],b.setXVal(b.getXVal()-g),a[c]=b}},"~A,~N,~N,~N,~N,~N,~N");
c$.getMinX=c(c$,"getMinX",function(a,b,c){for(var e=1.7976931348623157E308;b<c;b++){var g=a[b].getXVal();g<e&&(e=g)}return e},"~A,~N,~N");c$.getMinX=c(c$,"getMinX",function(a,b){for(var c=1.7976931348623157E308,e=0;e<a.size();e++){var g=a.get(e).getXYCoords(),g=JSV.common.Coordinate.getMinX(g,b.getStartingPointIndex(e),b.getEndingPointIndex(e));g<c&&(c=g)}return c},"JU.Lst,JSV.common.ViewData");c$.getMaxX=c(c$,"getMaxX",function(a,b,c){for(var e=-1.7976931348623157E308;b<c;b++){var g=a[b].getXVal();
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e=0;e<a.size();e++){var g=a.get(e).getUserYFactor(),f=a.get(e).getYRef(),h=a.get(e).getXYCoords(),g=(JSV.common.Coordinate.getMinY(h,b.getStartingPointIndex(e),b.getEndingPointIndex(e))-f)*g+f;g<c&&(c=g)}return c},"JU.Lst,JSV.common.ViewData");c$.getMaxY=c(c$,"getMaxY",function(a,b,c){for(var e=-1.7976931348623157E308;b<c;b++){var g=a[b].getYVal();g>e&&(e=g)}return e},"~A,~N,~N");c$.getMaxYUser=c(c$,"getMaxYUser",function(a,b){for(var c=-1.7976931348623157E308,e=0;e<a.size();e++){var g=a.get(e).getUserYFactor(),
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c),b)},"~N,~N,~N");c$.getNearestIndexForX=c(c$,"getNearestIndexForX",function(a,b){var c=(new JSV.common.Coordinate).set(b,0),c=java.util.Arrays.binarySearch(a,c,JSV.common.Coordinate.c);0>c&&(c=-1-c);return 0>c?0:c>a.length-1?a.length-1:c},"~A,~N");c$.findXForPeakNearest=c(c$,"findXForPeakNearest",function(a,b,c){b=JSV.common.Coordinate.getNearestIndexForX(a,b);for(c=c?-1:1;b<a.length-1&&0<c*(a[b+1].yVal-a[b].yVal);)b++;for(;1<=b&&0<c*(a[b-1].yVal-a[b].yVal);)b--;return 0==b||b==a.length-1?a[b].xVal:
JSV.common.Coordinate.parabolicInterpolation(a,b)},"~A,~N,~B");c$.parabolicInterpolation=c(c$,"parabolicInterpolation",function(a,b){var c=a[b-1].yVal,e=a[b+1].yVal;return a[b].xVal+(c-e)/2/(c-2*a[b].yVal+e)*(a[b+1].xVal-a[b].xVal)},"~A,~N");c$.getPickedCoordinates=c(c$,"getPickedCoordinates",function(a,b,c,e){if(null==b)return!1;var g=b.getXVal();c.setXVal(g);c.setYVal(b.getYVal());if(null==e)return!0;b=JSV.common.Coordinate.getNearestIndexForX(a,g);e.setXVal(a[b].getXVal());e.setYVal(a[b].getYVal());
return!0},"~A,JSV.common.Coordinate,JSV.common.Coordinate,JSV.common.Coordinate");c$.shiftX=c(c$,"shiftX",function(a,b){for(var c=a.length;0<=--c;)a[c].xVal+=b},"~A,~N");c$.getNearestXWithYAbove=c(c$,"getNearestXWithYAbove",function(a,b,c,e,g){b=JSV.common.Coordinate.getNearestIndexForX(a,b);var f=e?-1:1;if(g)for(;b<a.length&&0>f*(a[b].yVal-c);)b++;else for(;0<=b&&0>f*(a[b].yVal-c);)b--;return-1==b||b==a.length?NaN:JSV.common.Coordinate.findXForPeakNearest(a,a[b].getXVal(),e)},"~A,~N,~N,~B,~B");c$.c=
c$.prototype.c=new JSV.common.CoordComparator});n("JSV.common");w(["java.lang.Enum"],"JSV.common.ExportType",null,function(){c$=B(JSV.common,"ExportType",Enum);c$.getType=c(c$,"getType",function(a){a=a.toUpperCase();if(a.equalsIgnoreCase("Original..."))return JSV.common.ExportType.SOURCE;if(a.startsWith("XML"))return JSV.common.ExportType.AML;for(var b,c=0,e=JSV.common.ExportType.values();c<e.length&&((b=e[c])||1);c++)if(b.name().equals(a))return b;return JSV.common.ExportType.UNK},"~S");c$.isExportMode=
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"JSV.common.GraphSet","java.lang.Boolean $.Double $.Float JU.DF $.PT JSV.common.Annotation $.ColorParameters $.ColoredAnnotation $.ImageView $.Integral $.IntegralData $.Measurement $.MeasurementData $.PanelData $.Parameters $.PeakData $.PeakPickEvent $.PlotWidget $.ScaleData $.ScriptToken $.Spectrum $.ViewData JU.Logger".split(" "),function(){c$=t(function(){this.gs2dLinkedY=this.gs2dLinkedX=null;this.cur1D2Locked=!1;this.spectra=this.highlights=null;this.allowStacking=this.isSplittable=!0;this.widgets=
this.graphsTemp=this.pendingIntegral=this.pendingMeasurement=this.lastAnnotation=this.selectedSpectrumIntegrals=this.selectedSpectrumMeasurements=this.annotations=null;this.haveSingleYScale=this.isLinked=!1;this.iSpectrumClicked=this.iSpectrumMovedTo=0;this.iSpectrumSelected=-1;this.stackSelected=!1;this.viewData=this.bsSelected=null;this.reversePlot=!1;this.nSplit=1;this.yStackOffsetPercent=0;this.showAllStacked=!0;this.pd=this.imageView=this.viewList=null;this.sticky2Dcursor=!1;this.nSpectra=0;
this.fracY=this.fracX=1;this.fY0=this.fX0=0;this.cur2Dy=this.cur1D2x2=this.cur1D2x1=this.cur2Dx1=this.cur2Dx0=this.pin2Dy01=this.pin2Dx01=this.pin2Dy1=this.pin2Dy0=this.pin2Dx1=this.pin2Dx0=this.pin1Dy01=this.pin1Dx01=this.pin1Dy1=this.pin1Dy0=this.pin1Dx1=this.pin1Dx0=this.zoomBox2D=this.zoomBox1D=null;this.xPixels0=this.xPixel10=this.yPixels=this.xPixels=this.yPixel000=this.yPixel11=this.xPixel11=this.yPixel00=this.xPixel00=this.yHArrows=this.xHArrows=this.xVArrows=this.yPixel1=this.xPixel1=this.yPixel0=
this.xPixel0=0;this.allowStackedYScale=!0;this.drawXAxisLeftToRight=!1;this.xAxisLeftToRight=!0;this.iPreviousSpectrumClicked=-1;this.zoomEnabled=this.$haveSelectedSpectrum=!1;this.currentZoomIndex=0;this.lastClickX=NaN;this.lastPixelX=2147483647;this.bottom=this.left=this.top=this.right=this.width=this.height=0;this.coordTemp=this.piMouseOver=null;this.FONT_PLAIN=0;this.FONT_BOLD=1;this.FONT_ITALIC=2;this.is2DSpectrum=!1;this.selectedIntegral=this.selectedMeasurement=null;this.lastXMax=NaN;this.lastSpecClicked=
-1;this.inPlotMove=!1;this.xPixelMovedTo2=this.xPixelMovedTo=-1;this.xValueMovedTo=this.yValueMovedTo=0;this.haveLeftRightArrows=!1;this.yPixelPlot1=this.yPixelPlot0=this.xPixelPlot0=this.xPixelPlot1=0;this.nextClickForSetPeak=!1;this.mapX=null;N("JSV.common.GraphSet.Highlight")||JSV.common.GraphSet.$GraphSet$Highlight$();this.triggered=!0;this.gMain=this.g2d=this.plotColors=this.image2D=this.jsvp=this.aIntegrationRatios=this.dialogs=null;s(this,arguments)},JSV.common,"GraphSet",null,JSV.common.XYScaleConverter);
K(c$,function(){this.highlights=new JU.Lst;this.spectra=new JU.Lst;this.graphsTemp=new JU.Lst;this.bsSelected=new JU.BS;this.coordTemp=new JSV.common.Coordinate;this.mapX=new java.util.Hashtable});u(c$,function(a){this.pd=a;this.jsvp=a.jsvp;this.g2d=a.g2d},"JSV.common.PanelData");c(c$,"setSpectrumMovedTo",function(a){return this.iSpectrumMovedTo=a},"~N");c(c$,"setSpectrumClicked",function(a){this.stackSelected=this.showAllStacked;if(0>a||this.iSpectrumClicked!=a)this.lastClickX=NaN,this.lastPixelX=
2147483647;this.iSpectrumClicked=this.setSpectrumSelected(this.setSpectrumMovedTo(a))},"~N");c(c$,"setSpectrumSelected",function(a){var b=a!=this.iSpectrumSelected;this.iSpectrumSelected=a;b&&this.getCurrentView();return this.iSpectrumSelected},"~N");c(c$,"closeDialogsExcept",function(a){if(null!=this.dialogs)for(var b,c=this.dialogs.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var e=b.getValue();p(e,JSV.dialog.JSVDialog)&&(a===JSV.common.Annotation.AType.NONE||e.getAType()!==a)&&e.setVisible(!1)}},
"JSV.common.Annotation.AType");c(c$,"dispose",function(){this.widgets=this.graphsTemp=this.imageView=this.pendingMeasurement=this.lastAnnotation=this.annotations=this.viewList=this.viewData=this.spectra=null;this.disposeImage();if(null!=this.dialogs)for(var a,b=this.dialogs.entrySet().iterator();b.hasNext()&&((a=b.next())||1);){var c=a.getValue();p(c,JSV.dialog.JSVDialog)&&c.dispose()}this.dialogs=null});c(c$,"isDrawNoSpectra",function(){return-2147483648==this.iSpectrumSelected});c(c$,"getFixedSelectedSpectrumIndex",
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b){b&&this.isSplittable?(this.nSplit=this.nSpectra,this.showAllStacked=!1,this.setSpectrumClicked(this.iSpectrumSelected),this.pd.currentSplitPoint=this.iSpectrumSelected):(this.nSplit=1,this.showAllStacked=this.allowStacking&&!b,this.setSpectrumClicked(this.iSpectrumSelected));this.stackSelected=!1;JSV.common.GraphSet.setFractionalPositions(this.pd,a,JSV.common.PanelData.LinkMode.NONE)},"JU.Lst,~B");c(c$,"setPositionForFrame",function(a){0>a&&(a=0);var b=this.height-50;this.xPixel00=q(this.width*
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q(this.top/2);this.yPixel1=this.yPixel11-q(this.bottom/2);this.yPixels=this.yPixel1-this.yPixel0+1;null!=this.imageView&&this.is2DSpectrum&&(this.setImageWindow(),this.pd.display1D?(this.xPixels=q(Math.floor(0.8*(this.pd.display1D?1*(this.xPixels0-this.imageView.xPixels)/this.xPixels0:1)*this.xPixels0)),this.xPixel1=this.xPixel0+this.xPixels-1):(this.xPixels=0,this.xPixel1=this.imageView.xPixel0-30))},"~N");c(c$,"hasPoint",function(a,b){return a>=this.xPixel00&&a<=this.xPixel11&&b>=this.yPixel000&&
b<=this.yPixel11*this.nSplit},"~N,~N");c(c$,"isInPlotRegion",function(a,b){return a>=this.xPixel0&&a<=this.xPixel1&&b>=this.yPixel0&&b<=this.yPixel1},"~N,~N");c(c$,"getSplitPoint",function(a){return Math.max(0,Math.min(q((a-this.yPixel000)/(this.yPixel11-this.yPixel00)),this.nSplit-1))},"~N");c(c$,"isSplitWidget",function(a,b){return this.isSplittable&&a>=this.xPixel11-20&&b>=this.yPixel00+1&&a<=this.xPixel11-10&&b<=this.yPixel00+11},"~N,~N");c(c$,"initGraphSet",function(a,b){null==JSV.common.GraphSet.veryLightGrey&&
(JSV.common.GraphSet.veryLightGrey=this.g2d.getColor3(200,200,200));this.setPlotColors(JSV.common.ColorParameters.defaultPlotColors);this.xAxisLeftToRight=this.getSpectrumAt(0).shouldDisplayXAxisIncreasing();this.setDrawXAxis();var c=D(this.nSpectra,0),e=D(this.nSpectra,0);this.bsSelected.setBits(0,this.nSpectra);this.allowStackedYScale=!0;0>=b&&(b=2147483647);this.isSplittable=1<this.nSpectra;this.showAllStacked=(this.allowStacking=this.spectra.get(0).isStackable())&&1<this.nSpectra;for(var g=0;g<
this.nSpectra;g++){var f=this.spectra.get(g).getXYCoords().length-1;c[g]=JSV.common.Coordinate.intoRange(a,0,f);e[g]=JSV.common.Coordinate.intoRange(b,0,f);this.allowStackedYScale=(new Boolean(this.allowStackedYScale&(this.spectra.get(g).getYUnits().equals(this.spectra.get(0).getYUnits())&&this.spectra.get(g).getUserYFactor()==this.spectra.get(0).getUserYFactor()))).valueOf()}this.getView(0,0,0,0,c,e,null,null);this.viewList=new JU.Lst;this.viewList.addLast(this.viewData)},"~N,~N");c(c$,"getView",
function(a,b,c,e,g,f,h,k){var l=0==this.graphsTemp.size()?this.spectra:this.graphsTemp,m=this.getSpectrumAt(0).getSubSpectra(),r=null==m||2==m.size()&&m.get(1).isImaginary(),n=!this.getSpectrumAt(0).is1D();r&&c==e?l=this.spectra:c==e&&(this.viewData=new JSV.common.ViewData(m,c,e,this.getSpectrum().isContinuous()),l=null);null!=l&&(this.viewData=new JSV.common.ViewData(l,c,e,g,f,this.getSpectrumAt(0).isContinuous(),n),a!=b&&this.getScale().setXRange(a,b));null!=h&&(JSV.common.ScaleData.copyScaleFactors(h,
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this.setDrawXAxis()},"~B");c(c$,"setDrawXAxis",function(){this.drawXAxisLeftToRight=(new Boolean(this.xAxisLeftToRight^this.reversePlot)).valueOf();for(var a=0;a<this.spectra.size();a++)this.spectra.get(a).setExportXAxisDirection(this.drawXAxisLeftToRight)});c(c$,"isInTopBar",function(a,b){return a==this.fixX(a)&&b>this.pin1Dx0.yPixel0-2&&b<this.pin1Dx0.yPixel1},"~N,~N");c(c$,"isInTopBar2D",function(a,b){return null!=this.imageView&&a==this.imageView.fixX(a)&&b>this.pin2Dx0.yPixel0-2&&b<this.pin2Dx0.yPixel1},
"~N,~N");c(c$,"isInRightBar",function(a,b){return b==this.fixY(b)&&a>this.pin1Dy0.xPixel1&&a<this.pin1Dy0.xPixel0+2},"~N,~N");c(c$,"isInRightBar2D",function(a,b){return null!=this.imageView&&b==this.fixY(b)&&a>this.pin2Dy0.xPixel1&&a<this.pin2Dy0.xPixel0+2},"~N,~N");c(c$,"toX0",function(a){return this.viewList.get(0).getScale().toX0(this.fixX(a),this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");c(c$,"toY0",function(a){return this.viewList.get(0).getScale().toY0(this.fixY(a),this.yPixel0,
this.yPixel1)},"~N");h(c$,"toX",function(a){return null!=this.imageView&&this.imageView.isXWithinRange(a)?this.imageView.toX(a):this.getScale().toX(this.fixX(a),this.xPixel1,this.drawXAxisLeftToRight)},"~N");h(c$,"toY",function(a){return this.getScale().toY(a,this.yPixel0)},"~N");c(c$,"toPixelX",function(a){return this.getScale().toPixelX(a,this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");c(c$,"toPixelY",function(a){return this.getScale().toPixelY(a,this.yPixel1)},"~N");c(c$,"toPixelX0",
function(a){return this.viewList.get(0).getScale().toPixelX0(a,this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");c(c$,"toPixelY0",function(a){return this.fixY(this.viewList.get(0).getScale().toPixelY0(a,this.yPixel0,this.yPixel1))},"~N");c(c$,"fixX",function(a){return JSV.common.Coordinate.intoRange(a,this.xPixel0,this.xPixel1)},"~N");c(c$,"fixY",function(a){return JSV.common.Coordinate.intoRange(a,this.yPixel0,this.yPixel1)},"~N");c(c$,"getXPixel0",function(){return this.xPixel0});c(c$,
"getXPixels",function(){return this.xPixels});h(c$,"getYPixels",function(){return this.yPixels});c(c$,"getScale",function(){return this.viewData.getScale()});c(c$,"toPixelYint",function(a){return this.yPixel1-q(Double.isNaN(a)?-2147483648:this.yPixels*a)},"~N");c(c$,"findAnnotation2D",function(a){for(var b=this.annotations.size();0<=--b;){var c=this.annotations.get(b);if(this.isNearby(c,a,this.imageView,10))return c}return null},"JSV.common.Coordinate");c(c$,"addAnnotation",function(a,b){null==this.annotations&&
(this.annotations=new JU.Lst);for(var c=!1,e=this.annotations.size();0<=--e;)if(a.is2D?this.isNearby(this.annotations.get(e),a,this.imageView,10):a.equals(this.annotations.get(e)))c=!0,this.annotations.remove(e);0<a.text.length&&(!c||!b)&&this.annotations.addLast(a)},"JSV.common.Annotation,~B");c(c$,"setImageWindow",function(){this.imageView.setPixelWidthHeight(q((this.pd.display1D?0.6:1)*this.xPixels0),this.yPixels);this.imageView.setXY0(this.getSpectrumAt(0),q(Math.floor(this.xPixel10-this.imageView.xPixels)),
this.yPixel0)});c(c$,"findNearestMaxMin",function(){if(1<this.nSpectra&&0>this.iSpectrumClicked)return!1;this.xValueMovedTo=this.getSpectrum().findXForPeakNearest(this.xValueMovedTo);this.setXPixelMovedTo(this.xValueMovedTo,1.7976931348623157E308,0,0);return!Double.isNaN(this.xValueMovedTo)});c(c$,"setXPixelMovedTo",function(a,b,c,e){1.7976931348623157E308==a&&1.7976931348623157E308==b?(this.xPixelMovedTo=c,this.xPixelMovedTo2=e,this.isLinked&&this.sticky2Dcursor&&this.pd.setlinkedXMove(this,this.toX(this.xPixelMovedTo),
!1)):(1.7976931348623157E308!=a&&(this.xPixelMovedTo=this.toPixelX(a),this.fixX(this.xPixelMovedTo)!=this.xPixelMovedTo&&(this.xPixelMovedTo=-1),this.xPixelMovedTo2=-1,1E10!=a&&this.setSpectrumClicked(this.getFixedSelectedSpectrumIndex())),1.7976931348623157E308!=b&&(this.xPixelMovedTo2=this.toPixelX(b)))},"~N,~N,~N,~N");c(c$,"processPendingMeasurement",function(a,b,c){if(this.isInPlotRegion(a,b)){var e=this.toX(a),g=this.toY(b),f=e;switch(c){case 0:this.pendingMeasurement.setPt2(this.toX(a),this.toY(b));
break;case 3:case 2:if(0>this.iSpectrumClicked)break;var h=this.spectra.get(this.iSpectrumClicked);this.setScale(this.iSpectrumClicked);3!=c&&(c=this.findMeasurement(this.selectedSpectrumMeasurements,a,b,1),null!=c?(e=c.getXVal(),g=c.getYVal()):null!=(c=this.findMeasurement(this.selectedSpectrumMeasurements,a,b,2))?(e=c.getXVal2(),g=c.getYVal2()):e=this.getNearestPeak(h,e,g));this.pendingMeasurement=(new JSV.common.Measurement).setM1(e,g,h);this.pendingMeasurement.setPt2(f,g);this.pd.repaint();break;
case 1:case -2:case -3:for(f=null!=this.pendingMeasurement&&this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,-1));f;){this.setScale(this.getSpectrumIndex(this.pendingMeasurement.spec));if(3!=c){if(!this.findNearestMaxMin()){f=!1;break}a=this.xPixelMovedTo}e=this.toX(a);g=this.toY(b);this.pendingMeasurement.setPt2(e,g);if(0==this.pendingMeasurement.text.length){f=!1;break}this.setMeasurement(this.pendingMeasurement);if(1!=c){f=!1;break}this.setSpectrumClicked(this.getSpectrumIndex(this.pendingMeasurement.spec));
this.pendingMeasurement=(new JSV.common.Measurement).setM1(e,g,this.pendingMeasurement.spec);break}f||(this.pendingMeasurement=null);this.pd.repaint();break;case 5:this.findNearestMaxMin()?(a=this.getFixedSelectedSpectrumIndex(),Double.isNaN(this.lastXMax)||this.lastSpecClicked!=a||null==this.pendingMeasurement?(this.lastXMax=this.xValueMovedTo,this.lastSpecClicked=a,this.pendingMeasurement=(new JSV.common.Measurement).setM1(this.xValueMovedTo,this.yValueMovedTo,this.spectra.get(a))):(this.pendingMeasurement.setPt2(this.xValueMovedTo,
this.yValueMovedTo),0<this.pendingMeasurement.text.length&&this.setMeasurement(this.pendingMeasurement),this.pendingMeasurement=null,this.lastXMax=NaN)):this.lastXMax=NaN}}else this.pendingMeasurement=null},"~N,~N,~N");c(c$,"checkIntegralNormalizationClick",function(a,b){if(null==this.selectedSpectrumIntegrals)return!1;var c=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5);if(null==c)return!1;this.selectedIntegral=c;this.pd.normalizeIntegral();this.updateDialog(JSV.common.Annotation.AType.Integration,
-1);this.setSpectrumClicked(this.getSpectrumIndex(c.spec));return!0},"~N,~N");c(c$,"getNearestPeak",function(a,b,c){var e=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),b,c,a.isInverted(),!1);a=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),b,c,a.isInverted(),!0);return Double.isNaN(e)?a:Double.isNaN(a)?e:Math.abs(e-b)<Math.abs(a-b)?e:a},"JSV.common.Spectrum,~N,~N");c(c$,"findMeasurement",function(a,b,c,e){if(null==a||0==a.size())return null;if(0==e){var g=this.findMeasurement(a,
b,c,-1);return null!=g||p(a.get(0),JSV.common.Integral)?g:this.findMeasurement(a,b,c,-2)}for(var f=a.size();0<=--f;){var g=a.get(f),h,k,l,m;p(g,JSV.common.Integral)?(h=k=this.toPixelX(g.getXVal2()),l=this.toPixelYint(g.getYVal()),m=this.toPixelYint(g.getYVal2())):(h=this.toPixelX(g.getXVal()),k=this.toPixelX(g.getXVal2()),l=m=-2==e?this.yPixel1-2:this.toPixelY(g.getYVal()));switch(e){case 1:if(4>Math.abs(b-h)+Math.abs(c-l))return g;break;case 2:if(4>Math.abs(b-k)+Math.abs(c-m))return g;break;case -5:l=
m=q((l+m)/2),k=h+20;default:if(JSV.common.GraphSet.isOnLine(b,c,h,l,k,m))return g}}return null},"JSV.common.MeasurementData,~N,~N,~N");c(c$,"setMeasurement",function(a){var b=this.getSpectrumIndex(a.spec),c=this.getDialog(JSV.common.Annotation.AType.Measurements,b);null==c&&this.addDialog(b,JSV.common.Annotation.AType.Measurements,c=new JSV.common.MeasurementData(JSV.common.Annotation.AType.Measurements,a.spec));c.getData().addLast(a.copyM());this.updateDialog(JSV.common.Annotation.AType.Measurements,
-1)},"JSV.common.Measurement");c(c$,"checkArrowUpDownClick",function(a,b){var c=!1,e=this.isArrowClick(a,b,3)?JSV.common.GraphSet.RT2:this.isArrowClick(a,b,4)?1/JSV.common.GraphSet.RT2:0;if(0!=e){1<this.nSplit&&this.setSpectrumSelected(this.iSpectrumMovedTo);if((1==this.nSpectra||0<=this.iSpectrumSelected)&&this.spectra.get(this.getFixedSelectedSpectrumIndex()).isTransmittance())e=1/e;this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,e);c=!0}else this.isArrowClick(a,b,-1)&&
(this.resetViewCompletely(),c=!0);c&&(null!=this.imageView&&(this.update2dImage(!1),this.resetPinsFromView()),this.pd.taintedAll=!0);return c},"~N,~N");c(c$,"resetViewCompletely",function(){this.clearViews();this.showAllStacked&&!this.stackSelected&&this.closeDialogsExcept(JSV.common.Annotation.AType.NONE);this.viewData.resetScaleFactors();this.updateDialogs()});c(c$,"checkArrowLeftRightClick",function(a,b){if(this.haveLeftRightArrows){var c=this.isArrowClick(a,b,1)?-1:this.isArrowClick(a,b,2)?1:
0;if(0!=c)return this.setSpectrumClicked((this.iSpectrumSelected+c)%this.nSpectra),!0;if(this.isArrowClick(a,b,0)){if(this.showAllStacked)return this.showAllStacked=!1,this.setSpectrumClicked(this.getFixedSelectedSpectrumIndex()),!0;this.showAllStacked=this.allowStacking;this.setSpectrumSelected(-1);this.stackSelected=!1}}return!1},"~N,~N");c(c$,"isArrowClick",function(a,b,c){switch(c){case 3:case 4:case -1:return c=q((this.yPixel00+this.yPixel11)/2)+15*(3==c?-1:4==c?1:0),10>Math.abs(this.xVArrows-
a)&&10>Math.abs(c-b);case 1:case 2:case 0:return c=this.xHArrows+15*(1==c?-1:2==c?1:0),10>Math.abs(c-a)&&10>Math.abs(this.yHArrows-b)}return!1},"~N,~N,~N");c(c$,"setWidgetValueByUser",function(a){var b;b=a===this.cur2Dy?""+this.imageView.toSubspectrumIndex(a.yPixel0):a===this.pin1Dx01?""+Math.min(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal())+" - "+Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()):a===this.pin1Dy01?""+Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal())+" - "+Math.max(this.pin1Dy0.getYVal(),
this.pin1Dy1.getYVal()):a===this.pin2Dx01?""+Math.min(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal())+" - "+Math.max(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal()):a===this.pin2Dy01?""+q(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+q(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):""+a.getValue();b=this.pd.getInput("New value?","Set Slider",b);if(null!=b){b=b.trim();try{if(a===this.pin1Dx01||a===this.pin1Dy01||a===this.pin2Dx01||a===this.pin2Dy01){var c=b.indexOf("-",1);
if(!(0>c)){var e=Double.$valueOf(b.substring(0,c)).doubleValue(),g=Double.$valueOf(b.substring(c+1)).doubleValue();a===this.pin1Dx01?this.doZoom(e,this.pin1Dy0.getYVal(),g,this.pin1Dy1.getYVal(),!0,!1,!1,!0,!0):a===this.pin1Dy01?this.doZoom(this.pin1Dx0.getXVal(),e,this.pin1Dx1.getXVal(),g,null==this.imageView,null==this.imageView,!1,!1,!0):a===this.pin2Dx01?(this.imageView.setView0(this.imageView.toPixelX0(e),this.pin2Dy0.yPixel0,this.imageView.toPixelX0(g),this.pin2Dy1.yPixel0),this.doZoom(e,this.pin1Dy0.getYVal(),
g,this.pin1Dy1.getYVal(),!1,!1,!1,!0,!0)):a===this.pin2Dy01&&(this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.toPixelY0(e),this.pin2Dx1.xPixel0,this.imageView.toPixelY0(g)),this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!1,!0))}}else{var f=Double.$valueOf(b).doubleValue();a.isXtype?(g=a===this.pin1Dx0||a===this.cur2Dx0||a===this.pin2Dx0?this.pin1Dx1.getXVal():
this.pin1Dx0.getXVal(),this.doZoom(f,0,g,0,!a.is2D,!1,!1,!0,!0)):a===this.cur2Dy?this.setCurrentSubSpectrum(q(f)):a===this.pin2Dy0||a===this.pin2Dy1?(g=a===this.pin2Dy0?this.pin2Dy1.yPixel0:this.pin2Dy0.yPixel0,this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.subIndexToPixelY(q(f)),this.pin2Dx1.xPixel0,g)):(g=a===this.pin1Dy0?this.pin1Dy1.getYVal():this.pin1Dy0.getYVal(),this.doZoom(this.pin1Dx0.getXVal(),f,this.pin1Dx1.getXVal(),g,null==this.imageView,null==this.imageView,!1,!1,!0))}}catch(h){if(!y(h,
Exception))throw h;}}},"JSV.common.PlotWidget");c(c$,"removeAllHighlights",function(a){if(null==a)this.highlights.clear();else for(var b=this.highlights.size();0<=--b;)this.highlights.get(b).spectrum===a&&this.highlights.remove(b)},"JSV.common.Spectrum");c(c$,"setCoordClicked",function(a,b,c){0==c&&(this.nextClickForSetPeak=!1);if(Double.isNaN(b))return this.pd.coordClicked=null,this.pd.coordsClicked=null;this.pd.coordClicked=(new JSV.common.Coordinate).set(this.lastClickX=b,c);this.pd.coordsClicked=
this.getSpectrum().getXYCoords();this.pd.xPixelClicked=this.lastPixelX=a;return this.pd.coordClicked},"~N,~N,~N");c(c$,"setWidgets",function(a,b,c){if(a||null==this.pin1Dx0)null==this.zoomBox1D?this.newPins():this.resetPinPositions();this.setDerivedPins(b);this.setPinSliderPositions(c)},"~B,~N,~B");c(c$,"newPins",function(){this.zoomBox1D=new JSV.common.PlotWidget("zoomBox1D");this.pin1Dx0=new JSV.common.PlotWidget("pin1Dx0");this.pin1Dx1=new JSV.common.PlotWidget("pin1Dx1");this.pin1Dy0=new JSV.common.PlotWidget("pin1Dy0");
this.pin1Dy1=new JSV.common.PlotWidget("pin1Dy1");this.pin1Dx01=new JSV.common.PlotWidget("pin1Dx01");this.pin1Dy01=new JSV.common.PlotWidget("pin1Dy01");this.cur1D2x1=new JSV.common.PlotWidget("cur1D2x1");this.cur1D2x1.color=JSV.common.ScriptToken.PEAKTABCOLOR;this.cur1D2x2=new JSV.common.PlotWidget("cur1D2x2");this.cur1D2x2.color=JSV.common.ScriptToken.PEAKTABCOLOR;if(null!=this.imageView){this.zoomBox2D=new JSV.common.PlotWidget("zoomBox2D");this.pin2Dx0=new JSV.common.PlotWidget("pin2Dx0");this.pin2Dx1=
new JSV.common.PlotWidget("pin2Dx1");this.pin2Dy0=new JSV.common.PlotWidget("pin2Dy0");this.pin2Dy1=new JSV.common.PlotWidget("pin2Dy1");this.pin2Dx01=new JSV.common.PlotWidget("pin2Dx01");this.pin2Dy01=new JSV.common.PlotWidget("pin2Dy01");this.cur2Dx0=new JSV.common.PlotWidget("cur2Dx0");this.cur2Dx1=new JSV.common.PlotWidget("cur2Dx1");this.cur2Dy=new JSV.common.PlotWidget("cur2Dy");this.pin2Dy0.setY(0,this.imageView.toPixelY0(0));var a=this.getSpectrumAt(0).getSubSpectra().size();this.pin2Dy1.setY(a,
this.imageView.toPixelY0(a))}this.setWidgetX(this.pin1Dx0,this.getScale().minX);this.setWidgetX(this.pin1Dx1,this.getScale().maxX);this.setWidgetY(this.pin1Dy0,this.getScale().minY);this.setWidgetY(this.pin1Dy1,this.getScale().maxY);this.widgets=[this.zoomBox1D,this.zoomBox2D,this.pin1Dx0,this.pin1Dx01,this.pin1Dx1,this.pin1Dy0,this.pin1Dy01,this.pin1Dy1,this.pin2Dx0,this.pin2Dx01,this.pin2Dx1,this.pin2Dy0,this.pin2Dy01,this.pin2Dy1,this.cur2Dx0,this.cur2Dx1,this.cur2Dy,this.cur1D2x1,this.cur1D2x2]});
c(c$,"setWidgetX",function(a,b){a.setX(b,this.toPixelX0(b))},"JSV.common.PlotWidget,~N");c(c$,"setWidgetY",function(a,b){a.setY(b,this.toPixelY0(b))},"JSV.common.PlotWidget,~N");c(c$,"resetPinsFromView",function(){null!=this.pin1Dx0&&(this.setWidgetX(this.pin1Dx0,this.getScale().minXOnScale),this.setWidgetX(this.pin1Dx1,this.getScale().maxXOnScale),this.setWidgetY(this.pin1Dy0,this.getScale().minYOnScale),this.setWidgetY(this.pin1Dy1,this.getScale().maxYOnScale))});c(c$,"resetPinPositions",function(){this.resetX(this.pin1Dx0);
this.resetY(this.pin1Dy0);this.resetY(this.pin1Dy1);null==this.imageView?(null!=this.gs2dLinkedX&&this.resetX(this.cur1D2x1),null!=this.gs2dLinkedY&&this.resetX(this.cur1D2x2)):(this.pin2Dy0.setY(this.pin2Dy0.getYVal(),this.imageView.toPixelY0(this.pin2Dy0.getYVal())),this.pin2Dy1.setY(this.pin2Dy1.getYVal(),this.imageView.toPixelY0(this.pin2Dy1.getYVal())))});c(c$,"resetX",function(a){this.setWidgetX(a,a.getXVal())},"JSV.common.PlotWidget");c(c$,"resetY",function(a){this.setWidgetY(a,a.getYVal())},
"JSV.common.PlotWidget");c(c$,"setPinSliderPositions",function(a){this.pin1Dx0.yPixel0=this.pin1Dx1.yPixel0=this.pin1Dx01.yPixel0=this.yPixel0-5;this.pin1Dx0.yPixel1=this.pin1Dx1.yPixel1=this.pin1Dx01.yPixel1=this.yPixel0;this.cur1D2x1.yPixel1=this.cur1D2x2.yPixel1=this.yPixel0-5;this.cur1D2x1.yPixel0=this.cur1D2x2.yPixel0=this.yPixel1+6;null==this.imageView?(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=this.pin1Dy01.xPixel0=this.xPixel1+5,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=
this.xPixel1):(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=this.pin1Dy01.xPixel0=this.imageView.xPixel1+15,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=this.imageView.xPixel1+10,this.pin2Dx0.yPixel0=this.pin2Dx1.yPixel0=this.pin2Dx01.yPixel0=this.yPixel0-5,this.pin2Dx0.yPixel1=this.pin2Dx1.yPixel1=this.pin2Dx01.yPixel1=this.yPixel0,this.pin2Dy0.xPixel0=this.pin2Dy1.xPixel0=this.pin2Dy01.xPixel0=this.imageView.xPixel1+5,this.pin2Dy0.xPixel1=this.pin2Dy1.xPixel1=this.pin2Dy01.xPixel1=
this.imageView.xPixel1,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=this.yPixel1+6,this.cur2Dx0.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=this.yPixel1+6,this.cur2Dx1.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dy.xPixel0=a?q((this.xPixel1+this.imageView.xPixel0)/2):this.imageView.xPixel0-6,this.cur2Dy.xPixel1=this.imageView.xPixel1+5)},"~B");c(c$,"setDerivedPins",function(a){this.triggered=!0;null!=this.gs2dLinkedX&&this.cur1D2x1.setX(this.cur1D2x1.getXVal(),
this.toPixelX(this.cur1D2x1.getXVal()));null!=this.gs2dLinkedY&&this.cur1D2x2.setX(this.cur1D2x2.getXVal(),this.toPixelX(this.cur1D2x2.getXVal()));this.pin1Dx01.setX(0,q((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2));this.pin1Dy01.setY(0,q((this.pin1Dy0.yPixel0+this.pin1Dy1.yPixel0)/2));this.pin1Dx01.setEnabled(Math.min(this.pin1Dx0.xPixel0,this.pin1Dx1.xPixel0)>this.xPixel0||Math.max(this.pin1Dx0.xPixel0,this.pin1Dx1.xPixel0)<this.xPixel1);this.pin1Dy01.setEnabled(Math.min(this.pin1Dy0.yPixel0,
this.pin1Dy1.yPixel0)>Math.min(this.toPixelY(this.getScale().minY),this.toPixelY(this.getScale().maxY))||Math.max(this.pin1Dy0.yPixel0,this.pin1Dy1.yPixel0)<Math.max(this.toPixelY(this.getScale().minY),this.toPixelY(this.getScale().maxY)));if(null!=this.imageView){var b=this.pin1Dx0.getXVal();this.cur2Dx0.setX(b,this.imageView.toPixelX(b));b=this.pin1Dx1.getXVal();this.cur2Dx1.setX(b,this.imageView.toPixelX(b));b=this.imageView.toX(this.imageView.xPixel0);this.pin2Dx0.setX(b,this.imageView.toPixelX0(b));
b=this.imageView.toX(this.imageView.xPixel1);this.pin2Dx1.setX(b,this.imageView.toPixelX0(b));this.pin2Dx01.setX(0,q((this.pin2Dx0.xPixel0+this.pin2Dx1.xPixel0)/2));b=this.imageView.imageHeight-1-this.imageView.yView1;this.pin2Dy0.setY(b,this.imageView.toPixelY0(b));b=this.imageView.imageHeight-1-this.imageView.yView2;this.pin2Dy1.setY(b,this.imageView.toPixelY0(b));this.pin2Dy01.setY(0,q((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2));this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=this.imageView.subIndexToPixelY(a);
this.pin2Dx01.setEnabled(Math.min(this.pin2Dx0.xPixel0,this.pin2Dx1.xPixel0)!=this.imageView.xPixel0||Math.max(this.pin2Dx0.xPixel0,this.pin2Dx1.xPixel1)!=this.imageView.xPixel1);this.pin2Dy01.setEnabled(Math.min(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel0)!=this.yPixel0||Math.max(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel1)!=this.yPixel1)}},"~N");c(c$,"doZoom",function(a,b,c,e,g,f,h,k,l){a==c?(a=this.getScale().minXOnScale,c=this.getScale().maxXOnScale):this.isLinked&&k&&this.pd.doZoomLinked(this,a,
c,l,h,g);a>c&&(k=a,a=c,c=k);b>e&&(k=b,b=e,e=k);k=!g&&null!=this.imageView&&(this.imageView.minZ!=b||this.imageView.maxZ!=e);if(this.zoomEnabled||k){if(h){if(!this.getScale().isInRangeX(a)&&!this.getScale().isInRangeX(c))return;this.getScale().isInRangeX(a)?this.getScale().isInRangeX(c)||(c=this.getScale().maxX):a=this.getScale().minX}this.pd.taintedAll=!0;h=this.viewData.getScaleData();var m=D(this.nSpectra,0),r=D(this.nSpectra,0);this.graphsTemp.clear();var n=this.getSpectrumAt(0).getSubSpectra(),
n=null==n||2==n.size();if(this.getSpectrumAt(0).is1D()&&!n){if(this.graphsTemp.addLast(this.getSpectrum()),!JSV.common.ScaleData.setDataPointIndices(this.graphsTemp,a,c,3,m,r))return}else if(!JSV.common.ScaleData.setDataPointIndices(this.spectra,a,c,3,m,r))return;if(n=b==e)g=!k&&g?g=this.getScale().spectrumScaleFactor:1,1E-4>Math.abs(g-1)&&(b=this.getScale().minYOnScale,e=this.getScale().maxYOnScale);g=null;if(n||f)this.getCurrentView(),g=this.viewData.getNewScales(this.iSpectrumSelected,n,b,e);this.getView(a,
c,b,e,m,r,h,g);this.setXPixelMovedTo(1E10,1.7976931348623157E308,0,0);this.setWidgetX(this.pin1Dx0,a);this.setWidgetX(this.pin1Dx1,c);this.setWidgetY(this.pin1Dy0,b);this.setWidgetY(this.pin1Dy1,e);null==this.imageView?this.updateDialogs():(a=this.getSpectrumAt(0).getSubIndex(),c=this.imageView.fixSubIndex(a),c!=a&&this.setCurrentSubSpectrum(c),k&&this.update2dImage(!1));l&&this.addCurrentZoom()}},"~N,~N,~N,~N,~B,~B,~B,~B,~B");c(c$,"updateDialogs",function(){this.updateDialog(JSV.common.Annotation.AType.PeakList,
-1);this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)});c(c$,"setCurrentSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.setCurrentSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(c$,"addCurrentZoom",function(){if(this.viewList.size()>this.currentZoomIndex+1)for(var a=this.viewList.size()-1;a>this.currentZoomIndex;a--)this.viewList.remove(a);this.viewList.addLast(this.viewData);
this.currentZoomIndex++});c(c$,"setZoomTo",function(a){this.currentZoomIndex=a;this.viewData=this.viewList.get(a);this.resetPinsFromView()},"~N");c(c$,"clearViews",function(){this.isLinked&&this.pd.clearLinkViews(this);this.setZoom(0,0,0,0);for(var a=this.viewList.size();1<=--a;)this.viewList.remove(a)});c(c$,"drawAll",function(a,b,c,e,g,f){this.g2d=this.pd.g2d;this.gMain=a;var h=this.getSpectrumAt(0).getSubIndex();this.is2DSpectrum=!this.getSpectrumAt(0).is1D()&&(this.isLinked||this.pd.getBoolean(JSV.common.ScriptToken.DISPLAY2D))&&
(null!=this.imageView||this.get2DImage());null!=this.imageView&&f&&(this.pd.isPrinting&&this.g2d!==this.pd.g2d0&&this.g2d.newGrayScaleImage(a,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,this.imageView.getBuffer()),this.is2DSpectrum&&this.setPositionForFrame(e),this.draw2DImage());var k=this.stackSelected||!this.showAllStacked?this.iSpectrumSelected:-1,l=!this.showAllStacked||1==this.nSpectra||0<=k,m=null==this.imageView||this.pd.display1D,r=0<=k?1:0,n=this.getFixedSelectedSpectrumIndex();
if(m&&f&&(this.fillBox(a,this.xPixel0,this.yPixel0,this.xPixel1,this.yPixel1,JSV.common.ScriptToken.PLOTAREACOLOR),0>k)){l=!0;for(k=0;k<this.nSpectra;k++)this.doPlot(k,e)&&0!=r++&&(l=(new Boolean(l&this.viewData.areYScalesSame(k-1,k))).valueOf())}var q=1==this.nSpectra?0:!this.showAllStacked?this.iSpectrumMovedTo:this.iSpectrumSelected;c=c===a?b:c;if(f){var k=!this.isLinked&&this.isSplittable&&(1==this.nSplit||this.pd.currentSplitPoint==e),p=this.zoomEnabled&&!this.isDrawNoSpectra()&&this.pd.isCurrentGraphSet(this)&&
this.spectra.get(0).isScalable()&&(k||1==this.nSpectra)&&(1==this.nSplit||this.pd.currentSplitPoint==this.iSpectrumMovedTo);this.drawFrame(a,q,k,this.isSplittable,p)}if(this.pd.isCurrentGraphSet(this)&&e==this.pd.currentSplitPoint&&(2>r||0<=this.iSpectrumSelected))this.$haveSelectedSpectrum=!0;this.haveSingleYScale=this.showAllStacked&&1<this.nSpectra?this.allowStackedYScale&&l:!0;if(m){l=z(this.yPixels*(this.yStackOffsetPercent/100));this.haveLeftRightArrows=!1;for(p=k=0;k<this.nSpectra;k++)if(this.doPlot(k,
e)){var q=this.stackSelected&&0<=this.iSpectrumSelected&&this.iSpectrumSelected!=k,s=!this.reversePlot&&this.getShowAnnotation(JSV.common.Annotation.AType.Integration,k)&&(!this.showAllStacked||this.iSpectrumSelected==k)?this.getDialog(JSV.common.Annotation.AType.Integration,k).getData():null;this.setScale(k);var t=this.spectra.get(k);1<this.nSplit&&(n=k);var u=!q&&(1==this.nSplit||this.showAllStacked||this.iSpectrumSelected==e),v=u&&this.$haveSelectedSpectrum&&k==n;u&&(this.resetPinsFromView(),this.drawWidgets(b,
c,h,g,m,v,!1));this.haveSingleYScale&&(k==n&&f)&&(this.drawGrid(a),this.pd.isPrinting&&1<this.nSplit&&this.drawSpectrumSource(a,k));u&&this.drawWidgets(b,c,h,!1,m,v,!0);!this.isDrawNoSpectra()&&((1==this.nSpectra||0<=this.iSpectrumSelected)&&(this.haveSingleYScale&&k==n||this.showAllStacked&&this.stackSelected&&k==this.iSpectrumSelected))&&this.drawHighlightsAndPeakTabs(b,c,k);if(f){if((1==r&&0>this.iSpectrumSelected||this.iSpectrumSelected==k&&this.pd.isCurrentGraphSet(this))&&this.pd.titleOn&&!this.pd.titleDrawn)this.pd.drawTitle(a,
this.height,this.width,this.pd.getDrawTitle(this.pd.isPrinting)),this.pd.titleDrawn=!0;this.haveSingleYScale&&k==n&&(this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.YUNITSON)&&this.drawYUnits(a))}u=t.isContinuous();v=(1<this.nSplit?k==this.iSpectrumMovedTo:this.isLinked||k==n)&&!this.pd.isPrinting&&t.isContinuous();f&&this.drawSpectrum(a,k,p,q,s,u,v);this.drawMeasurements(b,k);null!=this.pendingMeasurement&&this.pendingMeasurement.spec===
t&&this.drawMeasurement(b,this.pendingMeasurement);v&&0<=this.xPixelMovedTo&&this.drawSpectrumPointer(b,t,p,s);1<this.nSpectra&&(1==this.nSplit&&this.pd.isCurrentGraphSet(this)&&f)&&(this.haveLeftRightArrows=!0,this.pd.isPrinting||(this.setScale(0),q=this.iSpectrumSelected,2!=this.nSpectra&&(this.setPlotColor(a,(q+this.nSpectra-1)%this.nSpectra),this.fillArrow(a,1,this.yHArrows,this.xHArrows-9,!0),this.setCurrentBoxColor(a),this.fillArrow(a,1,this.yHArrows,this.xHArrows-9,!1)),0<=q&&(this.setPlotColor(a,
q),this.fillCircle(a,this.xHArrows,this.yHArrows,!0)),this.setCurrentBoxColor(a),this.fillCircle(a,this.xHArrows,this.yHArrows,!1),this.setPlotColor(a,(q+1)%this.nSpectra),this.fillArrow(a,2,this.yHArrows,this.xHArrows+9,!0),this.setCurrentBoxColor(a),this.fillArrow(a,2,this.yHArrows,this.xHArrows+9,!1)));p-=l}f&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&this.drawXScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.XUNITSON)&&this.drawXUnits(a))}else f&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&
this.drawXScale(a,this.imageView),this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this.imageView),0<=h&&this.draw2DUnits(a)),this.drawWidgets(b,c,h,g,m,!0,!1),this.drawWidgets(b,c,h,g,m,!0,!0);null!=this.annotations&&this.drawAnnotations(b,this.annotations,null)},"~O,~O,~O,~N,~B,~B");c(c$,"drawSpectrumSource",function(a,b){this.pd.printFilePath(a,this.pd.thisWidth-this.pd.right,this.yPixel0,this.spectra.get(b).getFilePath())},"~O,~N");c(c$,"doPlot",function(a,b){var c=this.stackSelected&&
0<=this.iSpectrumSelected&&this.iSpectrumSelected!=a,e=this.showAllStacked||-1==this.iSpectrumSelected||this.iSpectrumSelected==a;return 1<this.nSplit?a==b:e&&(!this.pd.isPrinting||!c)},"~N,~N");c(c$,"drawSpectrumPointer",function(a,b,c,e){this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);var g=this.pd.integralShiftMode;null!=e&&((!this.pd.ctrlPressed||this.pd.isIntegralDrag)&&!this.isOnSpectrum(this.pd.mouseX,this.pd.mouseY,-1)?e=null:0==g&&(g=this.getShiftMode(this.pd.mouseX,this.pd.mouseY)));
var f=this.yValueMovedTo;this.yValueMovedTo=null==e?b.getYValueAt(this.xValueMovedTo):e.getPercentYValueAt(this.xValueMovedTo);this.setCoordStr(this.xValueMovedTo,this.yValueMovedTo);0!=g?(this.setPlotColor(a,0),b=0>g?this.yPixelPlot0:this.yPixelPlot1,this.drawHandle(a,0>g?this.xPixelPlot1:this.xPixelPlot0,b,!1)):(null!=e&&this.g2d.setStrokeBold(a,!0),Double.isNaN(f)||null!=this.pendingMeasurement?(this.g2d.drawLine(a,this.xPixelMovedTo,this.yPixel0,this.xPixelMovedTo,this.yPixel1),0<=this.xPixelMovedTo2&&
this.g2d.drawLine(a,this.xPixelMovedTo2,this.yPixel0,this.xPixelMovedTo2,this.yPixel1),this.yValueMovedTo=NaN):(b=null==e?c+this.toPixelY(this.yValueMovedTo):this.toPixelYint(this.yValueMovedTo/100),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixelMovedTo,b-10,this.xPixelMovedTo,b+10)),null!=e&&this.g2d.setStrokeBold(a,!1))},"~O,JSV.common.Spectrum,~N,JSV.common.IntegralData");c(c$,"setScale",function(a){this.viewData.setScale(a,this.xPixels,this.yPixels,this.spectra.get(a).isInverted())},"~N");c(c$,
"draw2DUnits",function(a){var b=this.getSpectrumAt(0).nucleusX,c=this.getSpectrumAt(0).nucleusY;this.setColorFromToken(a,JSV.common.ScriptToken.PLOTCOLOR);this.drawUnits(a,b,this.imageView.xPixel1+5*this.pd.scalingFactor,this.yPixel1,1,1);this.drawUnits(a,c,this.imageView.xPixel0-5*this.pd.scalingFactor,this.yPixel0,1,0)},"~O");c(c$,"drawPeakTabs",function(a,b,c){var e=1==this.nSpectra||0<=this.iSpectrumSelected?c.getPeakList():null;if(null!=e&&0<e.size()){null!=this.piMouseOver&&this.piMouseOver.spectrum===
c&&this.pd.isMouseUp()?(this.g2d.setGraphicsColor(b,this.g2d.getColor4(240,240,240,140)),this.drawPeak(b,this.piMouseOver,0),c.setHighlightedPeak(this.piMouseOver)):c.setHighlightedPeak(null);this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);for(b=e.size();0<=--b;){var g=e.get(b);this.drawPeak(a,g,g===c.getSelectedPeak()?14:7)}}},"~O,~O,JSV.common.Spectrum");c(c$,"drawPeak",function(a,b,c){if(!this.pd.isPrinting){var e=b.getXMin(),g=b.getXMax();e!=g&&this.drawBar(a,b,e,g,null,c)}},"~O,JSV.common.PeakInfo,~N");
c(c$,"drawWidgets",function(a,b,c,e,g,f,h){this.setWidgets(e,c,g);if(!this.pd.isPrinting||!(null==this.imageView?!this.cur1D2Locked:this.sticky2Dcursor)){!this.pd.isPrinting&&!h&&(g?(this.fillBox(a,this.xPixel0,this.pin1Dx0.yPixel1,this.xPixel1,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin1Dx0.xPixel0,this.pin1Dx0.yPixel1,this.pin1Dx1.xPixel0,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.PLOTCOLOR)):(this.fillBox(a,this.imageView.xPixel0,this.pin2Dx0.yPixel1,this.imageView.xPixel1,
this.pin2Dx0.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dx0.xPixel0,this.pin2Dx0.yPixel1,this.pin2Dx1.xPixel0,this.pin2Dx1.yPixel1+2,JSV.common.ScriptToken.PLOTCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,this.yPixel1,this.pin2Dy1.xPixel1+2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,this.pin2Dy0.yPixel1,this.pin2Dy1.xPixel1+2,this.pin2Dy1.yPixel0,JSV.common.ScriptToken.PLOTCOLOR)),this.fillBox(a,this.pin1Dy0.xPixel1,this.yPixel1,this.pin1Dy1.xPixel1+
2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),f&&this.fillBox(a,this.pin1Dy0.xPixel1,this.pin1Dy0.yPixel1,this.pin1Dy1.xPixel1+2,this.pin1Dy1.yPixel0,JSV.common.ScriptToken.PLOTCOLOR));for(c=0;c<this.widgets.length;c++)if(e=this.widgets[c],!(null==e||!e.isPinOrCursor&&!this.zoomEnabled)){var k=e===this.cur1D2x1||e===this.cur1D2x2||e===this.cur2Dx0||e===this.cur2Dx1||e===this.cur2Dy;if((e.isPin||!e.isPinOrCursor)!=h){if(e.is2D){if(e===this.cur2Dx0&&!g)continue}else{var l=e===this.pin1Dy0||e===this.pin1Dy1||
e===this.pin1Dy01;if(null!=this.imageView&&g==l||l&&!f||e===this.cur1D2x1&&null==this.gs2dLinkedX||e===this.cur1D2x2&&null==this.gs2dLinkedY||e===this.zoomBox1D&&(this.pd.isIntegralDrag||0!=this.pd.integralShiftMode))if(!this.isLinked||null!=this.imageView)continue}if(!this.pd.isPrinting||k)e.isPinOrCursor?(this.setColorFromToken(a,e.color),this.g2d.drawLine(a,e.xPixel0,e.yPixel0,e.xPixel1,e.yPixel1),e.isVisible=!0,e.isPin&&this.drawHandle(a,e.xPixel0,e.yPixel0,!e.isEnabled)):e.xPixel1!=e.xPixel0&&
this.fillBox(b,e.xPixel0,e.yPixel0,e.xPixel1,e.yPixel1,e===this.zoomBox1D&&this.pd.shiftPressed?JSV.common.ScriptToken.ZOOMBOXCOLOR2:JSV.common.ScriptToken.ZOOMBOXCOLOR)}}}},"~O,~O,~N,~B,~B,~B,~B");c(c$,"drawBar",function(a,b,c,e,g,f){var h=e+c,k=Math.abs(e-c),l=Math.abs(this.toX(this.xPixel1)-this.toX(this.xPixel0));0<f&&k>l/20&&(k=l/20,c=h/2-k,e=h/2+k);c=this.toPixelX(c);e=this.toPixelX(e);c>e&&(h=c,c=e,e=h);c=this.fixX(c);e=this.fixX(e);3>e-c&&(c-=2,e+=2);null!=b&&b.setPixelRange(c,e);0==f?this.fillBox(a,
c,this.yPixel0,e,this.yPixel0+this.yPixels,g):(this.fillBox(a,c,this.yPixel0,e,this.yPixel0+3,g),null!=b&&(c=q((c+e)/2),this.fillBox(a,c-1,this.yPixel0,c+1,this.yPixel0+f,g)))},"~O,JSV.common.PeakInfo,~N,~N,JSV.common.ScriptToken,~N");c(c$,"drawSpectrum",function(a,b,c,e,g,f,h){var k=this.spectra.get(b);this.drawPlot(a,b,k,f,c,e,null,h);null!=g&&(this.haveIntegralDisplayed(b)&&this.drawPlot(a,b,k,!0,c,!1,g,!0),this.drawIntegralValues(a,b,c));null!=this.getIntegrationRatios(b)&&this.drawAnnotations(a,
this.getIntegrationRatios(b),JSV.common.ScriptToken.INTEGRALPLOTCOLOR)},"~O,~N,~N,~B,JSV.common.IntegralData,~B,~B");c(c$,"getMeasurements",function(a,b){var c=this.getDialog(a,b);return null==c||0==c.getData().size()||!c.getState()?null:c.getData()},"JSV.common.Annotation.AType,~N");c(c$,"drawPlot",function(a,b,c,e,g,f,h,k){var l=null==h?c.getXYCoords():this.getIntegrationGraph(b).getXYCoords(),m=null!=h;h=null==h?null:h.getBitSet();k=!m&&!f&&null!=this.pendingIntegral&&this.pendingIntegral.spec===
this.spectra.get(b)||null!=c.fillColor&&k;f=f?-2:m?-1:!this.allowStacking?0:b;this.setPlotColor(a,f);var n=!0,q=this.toPixelY(0);m?k=(new Boolean(k&q==this.fixY(q))).valueOf():q=this.fixY(q);var p=this.viewData.getStartingPointIndex(b);b=this.viewData.getEndingPointIndex(b);if(e){b--;var s=!k&&this.g2d.canDoLineTo();s&&this.g2d.doStroke(a,!0);var t=!1;for(e=p;e<=b;e++){var u=l[e],v=l[e+1],w=m?this.toPixelYint(u.getYVal()):this.toPixelY(u.getYVal());if(-2147483648!=w){var y=m?this.toPixelYint(v.getYVal()):
this.toPixelY(v.getYVal());if(-2147483648!=y){var z=this.toPixelX(u.getXVal()),B=this.toPixelX(v.getXVal()),w=this.fixY(g+w),y=this.fixY(g+y);m&&(e==p&&(this.xPixelPlot1=z,this.yPixelPlot0=w),this.xPixelPlot0=B,this.yPixelPlot1=y);if(!(B==z&&w==y))if(k&&(!m||this.pendingIntegral.overlaps(u.getXVal(),v.getXVal())))m?(this.g2d.setGraphicsColor(a,this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR)),this.g2d.drawLine(a,z,q,z,w)):(this.g2d.setGraphicsColor(a,c.fillColor),this.g2d.fillRect(a,z,Math.min(q,
w),B-z,Math.abs(q-w))),this.setPlotColor(a,f);else if(!(w==y&&w==this.yPixel0)&&(null!=h&&h.get(e)!=n&&(n=h.get(e),!this.pd.isPrinting&&0!=this.pd.integralShiftMode?this.setPlotColor(a,0):n?this.setColorFromToken(a,JSV.common.ScriptToken.INTEGRALPLOTCOLOR):this.setPlotColor(a,-3)),!this.pd.isPrinting||n))t?this.g2d.lineTo(a,B,y):(this.g2d.drawLine(a,z,w,B,y),t=s)}}}s&&this.g2d.doStroke(a,!1)}else{for(e=p;e<=b;e++)c=l[e],y=this.toPixelY(c.getYVal()),-2147483648!=y&&(z=this.toPixelX(c.getXVal()),w=
this.toPixelY(Math.max(this.getScale().minYOnScale,0)),w=this.fixY(g+w),y=this.fixY(g+y),w==y&&(w==this.yPixel0||w==this.yPixel1)||this.g2d.drawLine(a,z,w,z,y));this.getScale().isYZeroOnScale()&&(g+=this.toPixelY(this.getScale().spectrumYRef),g==this.fixY(g)&&this.g2d.drawLine(a,this.xPixel1,g,this.xPixel0,g))}},"~O,~N,JSV.common.Spectrum,~B,~N,~B,JSV.common.IntegralData,~B");c(c$,"drawFrame",function(a,b,c,e,g){if(!this.pd.gridOn||this.pd.isPrinting)if(this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR),
this.g2d.drawRect(a,this.xPixel0,this.yPixel0,this.xPixels,this.yPixels),this.pd.isPrinting)return;this.setCurrentBoxColor(a);g&&(0<=b&&(this.setPlotColor(a,b),this.fillArrow(a,3,this.xVArrows,q((this.yPixel00+this.yPixel11)/2)-9,!0),this.fillArrow(a,4,this.xVArrows,q((this.yPixel00+this.yPixel11)/2)+9,!0),this.setCurrentBoxColor(a)),this.fillArrow(a,3,this.xVArrows,q((this.yPixel00+this.yPixel11)/2)-9,!1),this.fillCircle(a,this.xVArrows,q((this.yPixel00+this.yPixel11)/2),!1),this.fillArrow(a,4,this.xVArrows,
q((this.yPixel00+this.yPixel11)/2)+9,!1));if(null==this.imageView&&c){b=this.xPixel00+10;c=this.xPixel11-10;g=this.yPixel00+1;var f=this.yPixel11-2;this.g2d.drawLine(a,b,g,c,g);this.g2d.drawLine(a,c,g,c,f);this.g2d.drawLine(a,b,f,c,f);e&&this.fillBox(a,c-10,g,c,g+10,null)}},"~O,~N,~B,~B,~B");c(c$,"drawGrid",function(a){if(this.pd.gridOn&&null==this.imageView){this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR);var b;if(Double.isNaN(this.getScale().firstX)){b=this.getScale().maxXOnScale+this.getScale().steps[0]/
2;for(var c=this.getScale().minXOnScale;c<b;c+=this.getScale().steps[0]){var e=this.toPixelX(c);this.g2d.drawLine(a,e,this.yPixel0,e,this.yPixel1)}}else{b=1.0001*this.getScale().maxXOnScale;for(c=this.getScale().firstX;c<=b;c+=this.getScale().steps[0])e=this.toPixelX(c),this.g2d.drawLine(a,e,this.yPixel0,e,this.yPixel1)}for(c=this.getScale().firstY;c<this.getScale().maxYOnScale+this.getScale().steps[1]/2;c+=this.getScale().steps[1])b=this.toPixelY(c),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixel0,
b,this.xPixel1,b)}},"~O");c(c$,"drawXScale",function(a,b){this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);this.pd.isPrinting&&this.g2d.drawLine(a,b.getXPixel0(),this.yPixel1,b.getXPixel0()+b.getXPixels()-1,this.yPixel1);for(var c=this.getScale().precision[0],e=this.pd.setFont(a,b.getXPixels(),0,this.pd.isPrinting?10:12,!1),g=this.yPixel1,f=this.yPixel1+4*this.pd.scalingFactor,h=this.yPixel1+2*this.pd.scalingFactor,e=e.getHeight(),k=b.toPixelX(this.getScale().steps[0])-b.toPixelX(0),l=
Math.abs(0.95*k),m=this.getScale().firstX-this.getScale().steps[0],n=1.0001*(this.getScale().maxXOnScale+this.getScale().steps[0]),p=0;2>p;p++){1==p&&JSV.common.ScaleData.fixScale(this.mapX);for(var s=1E10,t=m;t<=n;t+=this.getScale().steps[0]){var k=b.toPixelX(t),u=Double.$valueOf(t),v;switch(p){case 0:v=JU.DF.formatDecimalDbl(t,c);this.mapX.put(u,v);this.drawTick(a,k,g,f,b);k=Math.abs(s-t);s=this.getScale().minorTickCounts[0];if(0!=s){k/=s;for(v=1;v<s;v++)this.drawTick(a,b.toPixelX(t-v*k),g,h,b)}s=
t;continue;case 1:v=this.mapX.get(u);if(null==v||k!=b.fixX(k))continue;var u=this.pd.getStringWidth(v),w=k+q(u/2)==b.fixX(k+q(u/2))?2:0;0<w&&this.g2d.drawString(a,v,k-q(u/w),f+e);t+=Math.floor(u/l)*this.getScale().steps[0]}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(c$,"drawTick",function(a,b,c,e,g){b==g.fixX(b)&&this.g2d.drawLine(a,b,c,b,e)},"~O,~N,~N,~N,JSV.common.XYScaleConverter");c(c$,"drawYScale",function(a,b){var c=b.getScale(),e=c.precision[1],g=this.pd.setFont(a,b.getXPixels(),
0,this.pd.isPrinting?10:12,!1).getHeight(),f=c.maxYOnScale+c.steps[1]/2,h=-2147483648;this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);for(var k=0;2>k;k++){1==k&&JSV.common.ScaleData.fixScale(this.mapX);for(var l=c.firstY;l<f;l+=c.steps[1]){var m=Double.$valueOf(l),n=b.getXPixel0(),p=b.toPixelY(l);if(p==b.fixY(p)){var s;0==k&&this.g2d.drawLine(a,n,p,n-3*this.pd.scalingFactor,p);if(!(Math.abs(p-h)<=g))switch(h=p,k){case 0:s=JU.DF.formatDecimalDbl(l,e);this.mapX.put(m,s);break;case 1:s=this.mapX.get(m);
if(null==s)continue;s.startsWith("0")&&s.contains("E")&&(s="0");this.g2d.drawString(a,s,n-4*this.pd.scalingFactor-this.pd.getStringWidth(s),p+q(g/3))}}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(c$,"drawXUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!0);null!=b&&this.drawUnits(a,b,this.xPixel1+25*this.pd.scalingFactor,this.yPixel1+5*this.pd.scalingFactor,1,1)},"~O");c(c$,"drawUnits",function(a,b,c,e,g,f){this.setColorFromToken(a,JSV.common.ScriptToken.UNITSCOLOR);this.pd.setFont(a,
(null==this.imageView?this:this.imageView).getXPixels(),2,10,!1);this.g2d.drawString(a,b,q(c-this.pd.getStringWidth(b)*g),q(e+this.pd.getFontHeight()*f))},"~O,~S,~N,~N,~N,~N");c(c$,"drawYUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!1);null!=b&&this.drawUnits(a,b,(this.pd.isPrinting?30:5)*this.pd.scalingFactor,this.yPixel0+(this.pd.isPrinting?0:5)*this.pd.scalingFactor,0,-1)},"~O");c(c$,"drawHighlightsAndPeakTabs",function(a,b,c){var e=this.getMeasurements(JSV.common.Annotation.AType.PeakList,
c),g=this.spectra.get(c);if(this.pd.isPrinting)null!=e&&(this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR),this.printPeakList(a,g,e));else{if(null==e){for(var f=0;f<this.highlights.size();f++){var h=this.highlights.get(f);h.spectrum===g&&(this.pd.setHighlightColor(h.color),this.drawBar(b,null,h.x1,h.x2,JSV.common.ScriptToken.HIGHLIGHTCOLOR,0))}this.drawPeakTabs(a,b,g)}if(null!=e){b=g.isInverted()?this.yPixel1-10*this.pd.scalingFactor:this.yPixel0;this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);
for(f=e.size();0<=--f;)g=e.get(f),g=this.toPixelX(g.getXVal()),this.g2d.drawLine(a,g,b,g,b+10*this.pd.scalingFactor);this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,c))&&(b=this.toPixelY(e.getThresh()),b==this.fixY(b)&&!this.pd.isPrinting&&this.g2d.drawLine(a,this.xPixel0,b,this.xPixel1,b))}}},"~O,~O,~N");c(c$,"printPeakList",function(a,b,c){var e=c.getMeasurementListArray(null);if(0!=e.length){this.pd.setFont(a,this.xPixels,0,8,!1);for(var g=this.pd.getFontHeight(),f=D(c.size(),
0),h=D(c.size(),0),k=0,l=5*this.pd.scalingFactor,m=10*this.pd.scalingFactor,n=15*this.pd.scalingFactor,p=25*this.pd.scalingFactor,s=0;s<e.length;s++)h[s]=this.toPixelX(Double.parseDouble(e[s][1])),0==s?f[s]=h[s]:(f[s]=Math.max(f[s-1]+g,h[s]+g),k+=f[s]-h[s]);k/=2*e.length;f[0]-k<this.xPixel0+p&&(k=f[0]-(this.xPixel0+p));for(s=0;s<e.length;s++)f[s]-=k;s=b.isInverted();b=this.pd.getStringWidth("99.9999");for(var k=6<=e[0].length?this.pd.getStringWidth("99.99"):0,p=s?-1:1,t=(s?this.yPixel1:this.yPixel0)+
p*(k+b+n),s=0;s<e.length;s++)this.g2d.drawLine(a,f[s],t,f[s],t+l*p),this.g2d.drawLine(a,f[s],t+l*p,h[s],t+m*p),this.g2d.drawLine(a,h[s],t+m*p,h[s],t+n*p),0<k&&0<e[s][4].length&&this.g2d.drawLine(a,q((f[s]+f[s-1])/2),t-b+l,q((f[s]+f[s-1])/2),t-b-l);t-=2*p*this.pd.scalingFactor;0<k&&(this.drawStringRotated(a,-90,f[0]-n,t,"  ppm"),this.drawStringRotated(a,-90,f[0]-n,t-b-l," Hz"));for(s=c.size();0<=--s;)this.drawStringRotated(a,-90*p,f[s]+q(p*g/3),t,e[s][1]),0<k&&0<e[s][4].length&&(c=q((f[s]+f[s-1])/
2)+q(g/3),this.drawStringRotated(a,-90,c,t-b-l,e[s][4]))}},"~O,JSV.common.Spectrum,JSV.common.PeakData");c(c$,"drawStringRotated",function(a,b,c,e,g){this.g2d.drawStringRotated(a,g,c,e,b)},"~O,~N,~N,~N,~S");c(c$,"drawAnnotations",function(a,b,c){this.pd.setFont(a,this.xPixels,1,12,!1);for(var e=b.size();0<=--e;){var g=b.get(e);this.setAnnotationColor(a,g,c);var f=(g.is2D?this.imageView:this).toPixelX(g.getXVal()),h=g.isPixels()?q(this.yPixel0+10*this.pd.scalingFactor-g.getYVal()):g.is2D?this.imageView.subIndexToPixelY(q(g.getYVal())):
this.toPixelY(g.getYVal());this.g2d.drawString(a,g.text,f+g.offsetX*this.pd.scalingFactor,h-g.offsetY*this.pd.scalingFactor)}},"~O,JU.Lst,JSV.common.ScriptToken");c(c$,"drawIntegralValues",function(a,b,c){var e=this.getMeasurements(JSV.common.Annotation.AType.Integration,b);if(null!=e){this.pd.isPrinting?this.pd.setFont(a,this.xPixels,0,8,!1):this.pd.setFont(a,this.xPixels,1,12,!1);this.setColorFromToken(a,JSV.common.ScriptToken.INTEGRALPLOTCOLOR);var g=this.pd.getFontHeight();this.g2d.setStrokeBold(a,
!0);for(var f=e.size();0<=--f;){var h=e.get(f);if(0!=h.getValue()){var k=this.toPixelX(h.getXVal2()),l=c*this.pd.scalingFactor+this.toPixelYint(h.getYVal()),m=c*this.pd.scalingFactor+this.toPixelYint(h.getYVal2());k!=this.fixX(k)||(l!=this.fixY(l)||m!=this.fixY(m))||(this.pd.isPrinting||this.g2d.drawLine(a,k,l,k,m),this.g2d.drawString(a,"  "+h.text,k,q((l+m)/2)+q(g/3)))}}this.g2d.setStrokeBold(a,!1)}b==this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumIntegrals=e)},"~O,~N,~N");c(c$,"drawMeasurements",
function(a,b){var c=this.getMeasurements(JSV.common.Annotation.AType.Measurements,b);if(null!=c)for(var e=c.size();0<=--e;)this.drawMeasurement(a,c.get(e));b==this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumMeasurements=c)},"~O,~N");c(c$,"drawMeasurement",function(a,b){if(!(0==b.text.length&&b!==this.pendingMeasurement)){this.pd.setFont(a,this.xPixels,1,12,!1);this.g2d.setGraphicsColor(a,b===this.pendingMeasurement?this.pd.getColor(JSV.common.ScriptToken.PEAKTABCOLOR):this.pd.BLACK);var c=
this.toPixelX(b.getXVal()),e=this.toPixelY(b.getYVal()),g=this.toPixelX(b.getXVal2());if(!Double.isNaN(b.getXVal())&&!(c!=this.fixX(c)||g!=this.fixX(g))){var f=2<=Math.abs(c-g),h=this.getScale().isYZeroOnScale()&&b.spec.isHNMR(),k=q((c+g)/2);this.g2d.setStrokeBold(a,!0);f&&this.g2d.drawLine(a,c,e,g,e);h&&this.g2d.drawLine(a,c+1,this.yPixel1-1,g,this.yPixel1-1);this.g2d.setStrokeBold(a,!1);f&&this.g2d.drawString(a,b.text,k+b.offsetX,e-b.offsetY);h&&(this.g2d.drawLine(a,c,this.yPixel1,c,this.yPixel1-
6*this.pd.scalingFactor),this.g2d.drawLine(a,g,this.yPixel1,g,this.yPixel1-6*this.pd.scalingFactor))}}},"~O,JSV.common.Measurement");c(c$,"getPinSelected",function(a,b){if(null!=this.widgets)for(var c=0;c<this.widgets.length;c++)if(null!=this.widgets[c]&&this.widgets[c].isPinOrCursor&&this.widgets[c].selected(a,b))return this.widgets[c];return null},"~N,~N");c(c$,"set2DCrossHairs",function(a,b){var c;if(a==this.imageView.fixX(a)&&b==this.fixY(b)&&(this.pin1Dx1.setX(c=this.imageView.toX(a),this.toPixelX(c)),
this.cur2Dx1.setX(c,a),this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b)),this.isLinked)){var e=this.imageView.toY(b);this.pd.set2DCrossHairsLinked(this,c,e,!this.sticky2Dcursor)}},"~N,~N");c(c$,"reset2D",function(a){a?(this.imageView.setView0(this.imageView.xPixel0,this.pin2Dy0.yPixel0,this.imageView.xPixel1,this.pin2Dy1.yPixel0),this.doZoom(0,this.getScale().minY,0,this.getScale().maxY,!0,!1,!1,!1,!0)):this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.yPixel0,this.pin2Dx1.xPixel0,
this.imageView.yPixel1)},"~B");c(c$,"setAnnotationText",function(a){var b=this.pd.getInput("New text?","Set Label",a.text);if(null==b)return!1;0==b.length?this.annotations.removeObj(a):a.text=b;return!0},"JSV.common.Annotation");c(c$,"checkIntegral",function(a,b,c){var e=this.getDialog(JSV.common.Annotation.AType.Integration,-1);null!=e&&(a=e.getData().addIntegralRegion(a,b),c&&p(e,JSV.dialog.JSVDialog)&&e.update(null,0,0),this.selectedSpectrumIntegrals=null,this.pendingIntegral=c?null:a)},"~N,~N,~B");
c(c$,"setToolTipForPixels",function(a,b){var c=this.getPinSelected(a,b),e=this.getScale().precision[0],g=this.getScale().precision[1];if(null!=c)this.setStartupPinTip()||(c===this.pin1Dx01||c===this.pin2Dx01?e=JU.DF.formatDecimalDbl(Math.min(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),e)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),e):c===this.pin1Dy01?e=JU.DF.formatDecimalDbl(Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()),g)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dy0.getYVal(),
this.pin1Dy1.getYVal()),g):c===this.cur2Dy?(c=this.imageView.toSubspectrumIndex(c.yPixel0),e=this.get2DYLabel(c,e)):e=c===this.pin2Dy01?""+q(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+q(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):c.isXtype?JU.DF.formatDecimalDbl(c.getXVal(),e):c.is2D?""+q(c.getYVal()):JU.DF.formatDecimalDbl(c.getYVal(),g),this.pd.setToolTipText(e));else{if(null!=this.imageView){if(this.imageView.fixX(a)==a&&this.fixY(b)==b){c=this.imageView.toSubspectrumIndex(b);
e=JU.DF.formatDecimalDbl(this.imageView.toX(a),e)+" "+this.getSpectrum().getAxisLabel(!0)+",  "+this.get2DYLabel(c,e);this.pd.setToolTipText(this.pd.display1D?e:"");this.pd.coordStr=e;return}if(!this.pd.display1D){this.pd.setToolTipText("");this.pd.coordStr="";return}}var c=this.toX(this.fixX(a)),e=null!=this.imageView&&this.imageView.isXWithinRange(a)?this.imageView.toSubspectrumIndex(this.fixY(b)):this.toY(this.fixY(b)),g=this.setCoordStr(c,e),f=this.getFixedSelectedSpectrumIndex();this.isInPlotRegion(a,
b)?1!=this.nSpectra&&this.haveIntegralDisplayed(f)&&(e=this.getIntegrationGraph(f).getPercentYValueAt(c),g+=", "+JU.DF.formatDecimalDbl(e,1)):e=NaN;this.pd.setToolTipText(null!=this.pendingMeasurement||null!=this.selectedMeasurement||null!=this.selectedIntegral?this.pd.hasFocus()?"Press ESC to delete "+(null!=this.selectedIntegral?"integral, DEL to delete all visible, or N to normalize":null==this.pendingMeasurement?'"'+this.selectedMeasurement.text+'" or DEL to delete all visible':"measurement"):
"":Double.isNaN(e)?null:g)}},"~N,~N");c(c$,"setCoordStr",function(a,b){var c=JU.DF.formatDecimalDbl(a,this.getScale().precision[0]);this.pd.coordStr="("+c+(this.haveSingleYScale||0<=this.iSpectrumSelected?", "+JU.DF.formatDecimalDbl(b,this.getScale().precision[1]):"")+")";return c},"~N,~N");c(c$,"setStartupPinTip",function(){if(null==this.pd.startupPinTip)return!1;this.pd.setToolTipText(this.pd.startupPinTip);this.pd.startupPinTip=null;return!0});c(c$,"get2DYLabel",function(a,b){var c=this.getSpectrumAt(0).getSubSpectra().get(a);
return JU.DF.formatDecimalDbl(c.getY2D(),b)+(c.y2DUnits.equals("HZ")?" HZ ("+JU.DF.formatDecimalDbl(c.getY2DPPM(),b)+" PPM)":"")},"~N,~N");c(c$,"isOnSpectrum",function(a,b,c){var e=null,g=!0,f=0>c;if(f){e=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==e)return!1;e=e.getData().getXYCoords();c=this.getFixedSelectedSpectrumIndex()}else{this.setScale(c);var h=this.spectra.get(c),e=h.xyCoords,g=h.isContinuous()}var h=c*z(this.yPixels*(this.yStackOffsetPercent/100)),k=this.viewData.getStartingPointIndex(c);
c=this.viewData.getEndingPointIndex(c);if(g)for(g=k;g<c;g++){var l=e[g],m=e[g+1],k=this.toPixelX(l.getXVal()),n=this.toPixelX(m.getXVal()),l=f?this.toPixelYint(l.getYVal()):this.toPixelY(l.getYVal()),m=f?this.toPixelYint(m.getYVal()):this.toPixelY(m.getYVal());if(!(-2147483648==l||-2147483648==m))if(l=this.fixY(l)-h,m=this.fixY(m)-h,JSV.common.GraphSet.isOnLine(a,b,k,l,n,m))return!0}else for(g=k;g<=c;g++)if(f=e[g],m=this.toPixelY(f.getYVal()),-2147483648!=m&&(k=this.toPixelX(f.getXVal()),l=this.toPixelY(Math.max(this.getScale().minYOnScale,
0)),l=this.fixY(l),m=this.fixY(m),!(l==m&&(l==this.yPixel0||l==this.yPixel1))&&JSV.common.GraphSet.isOnLine(a,b,k,l,k,m)))return!0;return!1},"~N,~N,~N");c$.distance=c(c$,"distance",function(a,b){return Math.sqrt(a*a+b*b)},"~N,~N");c$.findCompatibleGraphSet=c(c$,"findCompatibleGraphSet",function(a,b){for(var c=0;c<a.size();c++)if(JSV.common.Spectrum.areXScalesCompatible(b,a.get(c).getSpectrum(),!1,!1))return a.get(c);return null},"JU.Lst,JSV.common.Spectrum");c$.isGoodEvent=c(c$,"isGoodEvent",function(a,
b,c){return null==b?5<Math.abs(a.xPixel1-a.xPixel0)&&5<Math.abs(a.yPixel1-a.yPixel0):c?5<Math.abs(a.xPixel0-b.xPixel0):5<Math.abs(a.yPixel0-b.yPixel0)},"JSV.common.PlotWidget,JSV.common.PlotWidget,~B");c$.isOnLine=c(c$,"isOnLine",function(a,b,c,e,g,f){var h=Math.abs(c-a);if(2>h&&2>Math.abs(e-b))return!0;var k=g-a;if(2>Math.abs(k)&&2>Math.abs(f-b))return!0;var l=e-f;if(2<Math.abs(l)&&e<b==f<b)return!1;var m=c-g;return 2<Math.abs(m)&&c<a==g<a?!1:JSV.common.GraphSet.distance(h,e-b)+JSV.common.GraphSet.distance(k,
b-f)<JSV.common.GraphSet.distance(m,l)+2},"~N,~N,~N,~N,~N,~N");c$.setFractionalPositions=c(c$,"setFractionalPositions",function(a,b,c){var e=b.size(),g=0,f=0;a.isLinked=c!==JSV.common.PanelData.LinkMode.NONE;if(c===JSV.common.PanelData.LinkMode.NONE){for(var h=0;h<e;h++)c=b.get(h),g+=(c.getSpectrumAt(0).is1D(),1)*c.nSplit;g=1/g;for(h=0;h<e;h++)c=b.get(h),c.isLinked=!1,a=c.getSpectrumAt(0).is1D()?g:1*g,c.fX0=0,c.fY0=f,c.fracX=1,c.fracY=a,f+=a*c.nSplit}else{var g=null,k=-1;if(2==e||3==e)for(h=0;h<e;h++)if(c=
b.get(h),!c.getSpectrum().is1D()){g=c;0<=k&&(h=-2);k=h;break}if(-2==k||-1==k&&2!=e)JSV.common.GraphSet.setFractionalPositions(a,b,JSV.common.PanelData.LinkMode.NONE);else for(h=0;h<e;h++)c=b.get(h),c.isLinked=!0,a=c.getSpectrumAt(0),a.is1D()?(null!=g&&(k=g.getSpectrumAt(0),JSV.common.Spectrum.areLinkableX(a,k)&&(c.gs2dLinkedX=g),JSV.common.Spectrum.areLinkableY(a,k)&&(c.gs2dLinkedY=g)),c.fX0=0,c.fY0=f,c.fracX=null==g?1:0.5,c.fracY=3==e||null==g?0.5:1,f+=0.5):(c.fX0=0.5,c.fY0=0,c.fracX=0.5,c.fracY=
1)}},"JSV.common.PanelData,JU.Lst,JSV.common.PanelData.LinkMode");c(c$,"addAnnotation",function(a,b){if(0==a.size()||1==a.size()&&a.get(0).equalsIgnoreCase("none"))return this.lastAnnotation=this.annotations=null;4>a.size()&&null==this.lastAnnotation&&(this.lastAnnotation=this.getAnnotation((this.getScale().maxXOnScale+this.getScale().minXOnScale)/2,(this.getScale().maxYOnScale+this.getScale().minYOnScale)/2,b,!1,!1,0,0));var c=this.getAnnotation(a,this.lastAnnotation);if(null==c)return null;if(null==
this.annotations&&1==a.size()&&'"'==a.get(0).charAt(0))return c=c.text,this.getSpectrum().setTitle(c),c;this.lastAnnotation=c;this.addAnnotation(c,!1);return null},"JU.Lst,~S");c(c$,"addHighlight",function(a,b,c,e){null==c&&(c=this.getSpectrumAt(0));a=M(JSV.common.GraphSet.Highlight,this,null,a,b,c,null==e?this.pd.getColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR):e);this.highlights.contains(a)||this.highlights.addLast(a)},"~N,~N,JSV.common.Spectrum,javajs.api.GenericColor");c(c$,"addPeakHighlight",
function(a){for(var b=this.spectra.size();0<=--b;){var c=this.spectra.get(b);this.removeAllHighlights(c);if(!(null==a||a.isClearAll()||c!==a.spectrum)){var e=a.toString();if(null!=e){var g=JU.PT.getQuotedAttribute(e,"xMin"),e=JU.PT.getQuotedAttribute(e,"xMax");if(null==g||null==e)break;g=JU.PT.parseFloat(g);e=JU.PT.parseFloat(e);if(Float.isNaN(g)||Float.isNaN(e))break;this.pd.addHighlight(this,g,e,c,200,140,140,100);c.setSelectedPeak(a);!this.getScale().isInRangeX(g)&&!(this.getScale().isInRangeX(e)||
g<this.getScale().minX&&this.getScale().maxX<e)&&this.setZoomTo(0)}}}},"JSV.common.PeakInfo");c(c$,"advanceSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.advanceSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(c$,"checkSpectrumClickedEvent",function(a,b,c){if(this.nextClickForSetPeak)return!1;if(0<c&&this.checkArrowLeftRightClick(a,b))return!0;if(1<c||(null!=this.pendingMeasurement||
!this.isInPlotRegion(a,b))||0==c&&(c=this.isOnSpectrum(a,b,-1),this.pd.integralShiftMode=c?this.getShiftMode(a,b):0,this.pd.isIntegralDrag=0==this.pd.integralShiftMode&&(c||this.haveIntegralDisplayed(-1)&&null!=this.findMeasurement(this.getIntegrationGraph(-1),a,b,0)),0!=this.pd.integralShiftMode)||!this.showAllStacked)return!1;this.stackSelected=!1;for(c=0;c<this.nSpectra;c++)if(this.isOnSpectrum(a,b,c))return this.setSpectrumClicked(this.iPreviousSpectrumClicked=c),!1;if(this.isDialogOpen())return!1;
this.setSpectrumClicked(-1);return this.stackSelected=!1},"~N,~N,~N");c(c$,"getShiftMode",function(a,b){return this.isStartEndIntegral(a,!1)?b:this.isStartEndIntegral(a,!0)?-b:0},"~N,~N");c(c$,"isDialogOpen",function(){return this.isVisible(this.getDialog(JSV.common.Annotation.AType.Integration,-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,-1))});c(c$,"isStartEndIntegral",function(a,b){return b?
20>this.xPixelPlot1-a:20>a-this.xPixelPlot0},"~N,~B");c(c$,"checkWidgetEvent",function(a,b,c){if(this.zoomEnabled&&this.triggered)if(this.triggered=!1,c)2==this.pd.clickCount&&null==this.pendingMeasurement?(-1==this.iSpectrumClicked&&0<=this.iPreviousSpectrumClicked&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),this.processPendingMeasurement(a,b,2)):null==this.pendingMeasurement&&(c=this.getPinSelected(a,b),null==c&&(b=this.fixY(b),a<this.xPixel1?(this.pd.shiftPressed&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),
a=this.fixX(a),this.zoomBox1D.setX(this.toX(a),a),this.zoomBox1D.yPixel0=b,c=this.zoomBox1D):null!=this.imageView&&a<this.imageView.xPixel1&&(this.zoomBox2D.setX(this.imageView.toX(a),this.imageView.fixX(a)),this.zoomBox2D.yPixel0=b,c=this.zoomBox2D)),this.pd.thisWidget=c);else if(this.nextClickForSetPeak=!1,c=this.pd.thisWidget,null!=c)if(c===this.zoomBox1D)this.zoomBox1D.xPixel1=this.fixX(a),this.zoomBox1D.yPixel1=this.fixY(b),this.pd.isIntegralDrag&&this.zoomBox1D.xPixel0!=this.zoomBox1D.xPixel1&&
this.checkIntegral(this.zoomBox1D.getXVal(),this.toX(this.zoomBox1D.xPixel1),!1);else if(c===this.zoomBox2D)this.zoomBox2D.xPixel1=this.imageView.fixX(a),this.zoomBox2D.yPixel1=this.fixY(b);else if(c===this.cur2Dy)b=this.fixY(b),this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=b,this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b));else if(!(c===this.cur2Dx0||c===this.cur2Dx1))if(c===this.pin1Dx0||c===this.pin1Dx1||c===this.pin1Dx01){a=this.fixX(a);c.setX(this.toX0(a),a);if(c===this.pin1Dx01){c=
a-q((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2);a=this.pin1Dx0.xPixel0+c;b=this.pin1Dx1.xPixel0+c;if(0==c||this.fixX(a)!=a||this.fixX(b)!=b)return;this.pin1Dx0.setX(this.toX0(a),a);this.pin1Dx1.setX(this.toX0(b),b)}this.doZoom(this.pin1Dx0.getXVal(),0,this.pin1Dx1.getXVal(),0,!0,!1,!1,!0,!1)}else if(c===this.pin1Dy0||c===this.pin1Dy1||c===this.pin1Dy01){b=this.fixY(b);c.setY(this.toY0(b),b);if(c===this.pin1Dy01){c=b-q((this.pin1Dy0.yPixel0+this.pin1Dy1.yPixel0)/2)+1;b=this.pin1Dy0.yPixel0+c;a=
this.pin1Dy1.yPixel0+c;c=this.toY0(b);var e=this.toY0(a);if(Math.min(c,e)==this.getScale().minY||Math.max(c,e)==this.getScale().maxY)return;this.pin1Dy0.setY(c,b);this.pin1Dy1.setY(e,a)}this.doZoom(0,this.pin1Dy0.getYVal(),0,this.pin1Dy1.getYVal(),null==this.imageView,null==this.imageView,!1,!1,!1)}else if(c===this.pin2Dx0||c===this.pin2Dx1||c===this.pin2Dx01){a=this.imageView.fixX(a);c.setX(this.imageView.toX0(a),a);if(c===this.pin2Dx01){c=a-q((this.pin2Dx0.xPixel0+this.pin2Dx1.xPixel0)/2)+1;a=this.pin2Dx0.xPixel0+
c;b=this.pin2Dx1.xPixel0+c;if(this.imageView.fixX(a)!=a||this.imageView.fixX(b)!=b)return;this.pin2Dx0.setX(this.imageView.toX0(a),a);this.pin2Dx1.setX(this.imageView.toX0(b),b)}JSV.common.GraphSet.isGoodEvent(this.pin2Dx0,this.pin2Dx1,!0)?(this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,this.pin2Dx1.xPixel0,this.pin2Dy1.yPixel0),this.doZoom(this.pin2Dx0.getXVal(),this.getScale().minY,this.pin2Dx1.getXVal(),this.getScale().maxY,!1,!1,!1,!0,!1)):this.reset2D(!0)}else if(c===this.pin2Dy0||
c===this.pin2Dy1||c===this.pin2Dy01){b=this.fixY(b);c.setY(this.imageView.toSubspectrumIndex(b),b);if(c===this.pin2Dy01){c=b-q((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2)+1;b=this.pin2Dy0.yPixel0+c;a=this.pin2Dy1.yPixel0+c;if(b!=this.fixY(b)||a!=this.fixY(a))return;this.pin2Dy0.setY(this.imageView.toSubspectrumIndex(b),b);this.pin2Dy1.setY(this.imageView.toSubspectrumIndex(a),a)}JSV.common.GraphSet.isGoodEvent(this.pin2Dy0,this.pin2Dy1,!1)?this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,
this.pin2Dx1.xPixel1,this.pin2Dy1.yPixel1):this.reset2D(!1)}},"~N,~N,~B");c(c$,"clearIntegrals",function(){this.checkIntegral(NaN,0,!1)});c(c$,"clearMeasurements",function(){this.removeDialog(this.getFixedSelectedSpectrumIndex(),JSV.common.Annotation.AType.Measurements)});c$.createGraphSetsAndSetLinkMode=c(c$,"createGraphSetsAndSetLinkMode",function(a,b,c,e,g,f){for(var h=new JU.Lst,k=0;k<c.size();k++){var l=c.get(k),m=f===JSV.common.PanelData.LinkMode.NONE?JSV.common.GraphSet.findCompatibleGraphSet(h,
l):null;null==m&&h.addLast(m=new JSV.common.GraphSet(b.getPanelData()));m.addSpec(l)}JSV.common.GraphSet.setFractionalPositions(a,h,f);for(k=h.size();0<=--k;)h.get(k).initGraphSet(e,g),JU.Logger.info("JSVGraphSet "+(k+1)+" nSpectra = "+h.get(k).nSpectra);return h},"JSV.common.PanelData,JSV.api.JSVPanel,JU.Lst,~N,~N,JSV.common.PanelData.LinkMode");c(c$,"drawGraphSet",function(a,b,c,e,g,f,h,k,l,m,n){this.zoomEnabled=this.pd.getBoolean(JSV.common.ScriptToken.ENABLEZOOM);this.height=g*this.pd.scalingFactor;
this.width=e*this.pd.scalingFactor;this.left=f*this.pd.scalingFactor;this.right=h*this.pd.scalingFactor;this.top=k*this.pd.scalingFactor;this.bottom=l*this.pd.scalingFactor;this.$haveSelectedSpectrum=!1;this.selectedSpectrumMeasurements=this.selectedSpectrumIntegrals=null;if(!this.pd.isPrinting&&null!=this.widgets)for(e=0;e<this.widgets.length;e++)null!=this.widgets[e]&&(this.widgets[e].isVisible=!1);for(e=0;e<this.nSplit;e++)this.setPositionForFrame(e),this.drawAll(a,b,c,e,m||1<this.nSplit,n);this.setPositionForFrame(1<
this.nSplit?this.pd.currentSplitPoint:0)},"~O,~O,~O,~N,~N,~N,~N,~N,~N,~B,~B");c(c$,"escapeKeyPressed",function(a){null!=this.zoomBox1D&&(this.zoomBox1D.xPixel0=this.zoomBox1D.xPixel1=0);null!=this.zoomBox2D&&(this.zoomBox2D.xPixel0=this.zoomBox2D.xPixel1=0);this.inPlotMove&&(null!=this.pendingMeasurement?this.pendingMeasurement=null:(this.pendingMeasurement=this.pd.thisWidget=null,null!=this.selectedSpectrumMeasurements&&null!=this.selectedMeasurement&&(a?this.selectedSpectrumMeasurements.clear(this.getScale().minXOnScale,
this.getScale().maxXOnScale):this.selectedSpectrumMeasurements.removeObj(this.selectedMeasurement),this.selectedMeasurement=null,this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)),null!=this.selectedSpectrumIntegrals&&null!=this.selectedIntegral&&(a?this.selectedSpectrumIntegrals.clear(this.getScale().minXOnScale,this.getScale().maxXOnScale):this.selectedSpectrumIntegrals.removeObj(this.selectedIntegral),this.selectedIntegral=null,this.updateDialog(JSV.common.Annotation.AType.Integration,
-1))))},"~B");c$.findGraphSet=c(c$,"findGraphSet",function(a,b,c){for(var e=a.size();0<=--e;)if(a.get(e).hasPoint(b,c))return a.get(e);return null},"JU.Lst,~N,~N");c(c$,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.spectra.size()&&null==(b=this.spectra.get(c).findMatchingPeakInfo(a));c++);return b},"JSV.common.PeakInfo");c(c$,"getCurrentSpectrumIndex",function(){return 1==this.nSpectra?0:this.iSpectrumSelected});c(c$,"getSelectedIntegral",function(){return this.selectedIntegral});c(c$,
"getShowAnnotation",function(a,b){var c=this.getDialog(a,b);return null!=c&&c.getState()},"JSV.common.Annotation.AType,~N");c(c$,"hasFileLoaded",function(a){for(var b=this.spectra.size();0<=--b;)if(this.spectra.get(b).getFilePathForwardSlash().equals(a))return!0;return!1},"~S");c(c$,"haveSelectedSpectrum",function(){return this.$haveSelectedSpectrum});c(c$,"mouseClickedEvent",function(a,b,c,e){this.selectedIntegral=this.selectedMeasurement=null;var g=this.nextClickForSetPeak;this.nextClickForSetPeak=
!1;if(!this.checkArrowUpDownClick(a,b))if(this.lastClickX=NaN,this.lastPixelX=2147483647,this.isSplitWidget(a,b))this.splitStack(this.pd.graphSets,1==this.nSplit);else{var f=this.getPinSelected(a,b);if(null!=f)this.setWidgetValueByUser(f);else if(f=null!=this.imageView&&a==this.imageView.fixX(a)&&b==this.fixY(b),2==c&&(-1==this.iSpectrumClicked&&0<=this.iPreviousSpectrumClicked)&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),!f&&e)this.setSpectrumClicked(this.iPreviousSpectrumClicked),null!=
this.pendingMeasurement?this.processPendingMeasurement(a,b,-3):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,b,3);else if(this.lastXMax=NaN,2==c)f?(this.sticky2Dcursor&&this.addAnnotation(this.getAnnotation(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b),this.pd.coordStr,!1,!0,5,5),!0),this.sticky2Dcursor=!this.sticky2Dcursor,this.set2DCrossHairs(a,b)):this.isInTopBar(a,b)?this.doZoom(this.toX0(this.xPixel0),0,this.toX0(this.xPixel1),0,!0,!1,!1,!0,!0):this.isInRightBar(a,b)?
this.doZoom(this.getScale().minXOnScale,this.viewList.get(0).getScale().minYOnScale,this.getScale().maxXOnScale,this.viewList.get(0).getScale().maxYOnScale,!0,!0,!1,!1,!1):this.isInTopBar2D(a,b)?this.reset2D(!0):this.isInRightBar2D(a,b)?this.reset2D(!1):null!=this.pendingMeasurement?this.processPendingMeasurement(a,b,-2):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,b,2);else if(f){if(null!=this.annotations&&(c=(new JSV.common.Coordinate).set(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b)),
c=this.findAnnotation2D(c),null!=c&&this.setAnnotationText(c)))return;this.sticky2Dcursor=!1;this.set2DCrossHairs(a,b)}else{if(this.isInPlotRegion(a,b)){if(null!=this.selectedSpectrumIntegrals&&this.checkIntegralNormalizationClick(a,b))return;if(null!=this.pendingMeasurement){this.processPendingMeasurement(a,b,1);return}this.setCoordClicked(a,this.toX(a),this.toY(b));this.updateDialog(JSV.common.Annotation.AType.PeakList,-1);if(g){this.shiftSpectrum(NaN,NaN);return}}else this.setCoordClicked(0,NaN,
0);this.pd.notifyPeakPickedListeners(null)}}},"~N,~N,~N,~B");c(c$,"updateDialog",function(a,b){var c=this.getDialog(a,b);if(null!=c&&this.isVisible(c)){var e=this.toX(this.xPixel1)-this.toX(this.xPixel0),g=this.getSpectrum().isInverted()?this.yPixel1-this.pd.mouseY:this.pd.mouseY-this.yPixel0;c.update(this.pd.coordClicked,e,g)}},"JSV.common.Annotation.AType,~N");c(c$,"isVisible",function(a){return p(a,JSV.dialog.JSVDialog)&&a.isVisible()},"JSV.api.AnnotationData");c(c$,"mouseReleasedEvent",function(a,
b){if(null!=this.pendingMeasurement)2>Math.abs(this.toPixelX(this.pendingMeasurement.getXVal())-a)&&(this.pendingMeasurement=null),this.processPendingMeasurement(a,b,-2),this.setToolTipForPixels(a,b);else if(0!=this.pd.integralShiftMode)this.pd.integralShiftMode=0,this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0;else{0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo);var c=this.pd.thisWidget;if(this.pd.isIntegralDrag)JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,null,!0)&&this.checkIntegral(this.toX(this.zoomBox1D.xPixel0),
this.toX(this.zoomBox1D.xPixel1),!0),this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0=0,this.pendingIntegral=null,this.pd.isIntegralDrag=!1;else if(c===this.zoomBox2D)JSV.common.GraphSet.isGoodEvent(this.zoomBox2D,null,!0)&&(this.imageView.setZoom(this.zoomBox2D.xPixel0,this.zoomBox2D.yPixel0,this.zoomBox2D.xPixel1,this.zoomBox2D.yPixel1),this.zoomBox2D.xPixel1=this.zoomBox2D.xPixel0,this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+
this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!0,!0));else if(c===this.zoomBox1D){if(JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,null,!0)){var c=this.zoomBox1D.xPixel1,e=this.pd.shiftPressed;this.doZoom(this.toX(this.zoomBox1D.xPixel0),e?this.toY(this.zoomBox1D.yPixel0):0,this.toX(c),e?this.toY(this.zoomBox1D.yPixel1):0,!0,e,!0,!0,!0);this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0}}else(c===this.pin1Dx0||c===this.pin1Dx1||c===this.cur2Dx0||c===this.cur2Dx1)&&this.addCurrentZoom()}},"~N,~N");
c(c$,"mouseMovedEvent",function(a,b){if(1<this.nSpectra){var c=this.getSplitPoint(b);this.setPositionForFrame(c);this.setSpectrumMovedTo(1<this.nSplit?c:this.iSpectrumSelected);0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo)}this.inPlotMove=this.isInPlotRegion(a,b);this.setXPixelMovedTo(1.7976931348623157E308,1.7976931348623157E308,this.inPlotMove?a:-1,-1);this.inPlotMove&&(this.xValueMovedTo=this.toX(this.xPixelMovedTo),this.yValueMovedTo=this.getSpectrum().getYValueAt(this.xValueMovedTo));
if(0!=this.pd.integralShiftMode){var c=this.getDialog(JSV.common.Annotation.AType.Integration,-1),e=c.getData().getXYCoords(),e=e[0<this.pd.integralShiftMode?e.length-1:0].getYVal();c.getData().shiftY(this.pd.integralShiftMode,this.toPixelYint(e)+b-(0<this.pd.integralShiftMode?this.yPixelPlot1:this.yPixelPlot0),this.yPixel0,this.yPixels)}else this.pd.isIntegralDrag||(null!=this.pendingMeasurement?(this.processPendingMeasurement(a,b,0),this.setToolTipForPixels(a,b)):(this.selectedMeasurement=this.inPlotMove&&
null!=this.selectedSpectrumMeasurements?this.findMeasurement(this.selectedSpectrumMeasurements,a,b,0):null,this.selectedIntegral=null,this.inPlotMove&&(null!=this.selectedSpectrumIntegrals&&null==this.selectedMeasurement)&&(this.selectedIntegral=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,0),null==this.selectedIntegral&&(this.selectedIntegral=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5))),this.setToolTipForPixels(a,b),null==this.imageView?(this.piMouseOver=null,c=1<this.nSplit?
this.iSpectrumMovedTo:this.iSpectrumClicked,!this.isDrawNoSpectra()&&0<=c&&(c=this.spectra.get(c),null!=c.getPeakList()&&(this.coordTemp.setXVal(this.toX(a)),this.coordTemp.setYVal(this.toY(b)),this.piMouseOver=c.findPeakByCoord(a,this.coordTemp)))):!this.pd.display1D&&this.sticky2Dcursor&&this.set2DCrossHairs(a,b)))},"~N,~N");c(c$,"nextView",function(){this.currentZoomIndex+1<this.viewList.size()&&this.setZoomTo(this.currentZoomIndex+1)});c(c$,"previousView",function(){0<this.currentZoomIndex&&this.setZoomTo(this.currentZoomIndex-
1)});c(c$,"resetView",function(){this.setZoomTo(0)});c(c$,"removeAllHighlights",function(){this.removeAllHighlights(null)});c(c$,"removeHighlight",function(a){this.highlights.remove(a)},"~N");c(c$,"removeHighlight",function(a,b){for(var c=this.highlights.size();0<=--c;){var e=this.highlights.get(c);e.x1==a&&e.x2==b&&this.highlights.remove(c)}},"~N,~N");c(c$,"scaleYBy",function(a){if(null!=this.imageView||this.zoomEnabled)this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,a),
null!=this.imageView&&(this.update2dImage(!1),this.resetPinsFromView()),this.pd.refresh()},"~N");c(c$,"selectSpectrum",function(a,b,c){for(var e=!1,g=this.spectra.size();0<=--g;)if((null==a||this.getSpectrumAt(g).getFilePathForwardSlash().equals(a))&&this.getSpectrumAt(g).matchesPeakTypeModel(b,c))this.setSpectrumSelected(g),1<this.nSplit&&this.splitStack(this.pd.graphSets,!0),e=!0;1<this.nSpectra&&(!e&&0<=this.iSpectrumSelected&&!this.pd.isCurrentGraphSet(this))&&this.setSpectrumSelected(-2147483648);
return e},"~S,~S,~S");c(c$,"selectPeakByFileIndex",function(a,b,c){for(var e,g=this.spectra.size();0<=--g;)if(null!=(e=this.getSpectrumAt(g).selectPeakByFileIndex(a,b,c)))return e;return null},"~S,~S,~S");c(c$,"setSelected",function(a){0>a?(this.bsSelected.clearAll(),this.setSpectrumClicked(-1)):(this.bsSelected.set(a),this.setSpectrumClicked(1==this.bsSelected.cardinality()?a:-1),1<this.nSplit&&0<=a&&(this.pd.currentSplitPoint=a))},"~N");c(c$,"setSelectedIntegral",function(a){var b=this.selectedIntegral.getSpectrum();
this.getIntegrationGraph(this.getSpectrumIndex(b)).setSelectedIntegral(this.selectedIntegral,a)},"~N");c(c$,"setShowAnnotation",function(a,b){var c=this.getDialog(a,-1);if(null==c)null!=b&&b!==Boolean.TRUE||(a===JSV.common.Annotation.AType.PeakList||a===JSV.common.Annotation.AType.Integration||a===JSV.common.Annotation.AType.Measurements)&&this.pd.showDialog(a);else if(null==b)p(c,JSV.dialog.JSVDialog)?c.setVisible(!1):c.setState(!c.getState());else{var e=b.booleanValue();c.setState(e);(e||p(c,JSV.dialog.JSVDialog))&&
this.pd.showDialog(a)}},"JSV.common.Annotation.AType,Boolean");c(c$,"checkIntegral",function(a,b){if(!this.getSpectrum().canIntegrate()||this.reversePlot)return!1;var c=this.getFixedSelectedSpectrumIndex(),e=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==b)return!0;switch(JSV.common.IntegralData.IntMode.getMode(b.toUpperCase())){case JSV.common.IntegralData.IntMode.ON:this.integrate(c,a);break;case JSV.common.IntegralData.IntMode.OFF:this.integrate(c,null);break;case JSV.common.IntegralData.IntMode.TOGGLE:this.integrate(c,
null==e?a:null);break;case JSV.common.IntegralData.IntMode.AUTO:null==e&&(this.checkIntegral(a,"ON"),e=this.getDialog(JSV.common.Annotation.AType.Integration,-1));null!=e&&e.getData().autoIntegrate();break;case JSV.common.IntegralData.IntMode.LIST:this.pd.showDialog(JSV.common.Annotation.AType.Integration);break;case JSV.common.IntegralData.IntMode.MARK:null==e&&(this.checkIntegral(a,"ON"),e=this.getDialog(JSV.common.Annotation.AType.Integration,-1));null!=e&&e.getData().addMarks(b.substring(4).trim());
break;case JSV.common.IntegralData.IntMode.MIN:if(null!=e)try{var g=Double.parseDouble(JSV.common.ScriptToken.getTokens(b).get(1));e.getData().setMinimumIntegral(g)}catch(f){if(!y(f,Exception))throw f;}break;case JSV.common.IntegralData.IntMode.UPDATE:null!=e&&e.getData().update(a)}this.updateDialog(JSV.common.Annotation.AType.Integration,-1);return!0},"JSV.common.Parameters,~S");c(c$,"setSpectrum",function(a,b){b&&1<this.nSplit?1<this.nSplit&&this.setSpectrumClicked(a):(this.setSpectrumClicked(a),
this.showAllStacked=this.stackSelected=!1);0<=a&&this.dialogsToFront(this.getSpectrum())},"~N,~B");c(c$,"setSpectrumJDX",function(a){var b=this.getFixedSelectedSpectrumIndex();this.spectra.remove(b);this.spectra.add(b,a);this.pendingMeasurement=null;this.clearViews();this.viewData.newSpectrum(this.spectra)},"JSV.common.Spectrum");c(c$,"setZoom",function(a,b,c,e){this.setZoomTo(0);0==a&&0==c&&0==b&&0==e?(this.newPins(),this.imageView=null,this.getScale(),this.getScale()):this.doZoom(a,b,c,e,!0,b!=
e,!1,!0,!0)},"~N,~N,~N,~N");c(c$,"shiftSpectrum",function(a,b){var c=this.getSpectrum();if(!c.isNMR()||!c.is1D())return!1;if(1.7976931348623157E308==b||1.7976931348623157E308==a)a=-c.addSpecShift(0);else{if(4.9E-324==b)return this.nextClickForSetPeak=!0,this.jsvp.showMessage("Click on or beside a peak to set its chemical shift.","Set Reference"),!1;if(Double.isNaN(a)||4.9E-324==a){var e=4.9E-324==a?this.lastClickX:this.getNearestPeak(c,this.lastClickX,this.toY(this.pd.mouseY));if(Double.isNaN(e))return!1;
if(Double.isNaN(b))try{var g=this.pd.getInput("New chemical shift (set blank to reset)","Set Reference",""+e).trim();b=0==g.length?e-c.addSpecShift(0):Double.parseDouble(g)}catch(f){if(y(f,Exception))return!1;throw f;}a=b-e}}if(0==a)return!1;c.addSpecShift(a);if(null!=this.annotations)for(e=this.annotations.size();0<=--e;)this.annotations.get(e).spec===c&&this.annotations.get(e).addSpecShift(a);if(null!=this.dialogs)for(var h,e=this.dialogs.entrySet().iterator();e.hasNext()&&((h=e.next())||1);)h.getValue().getSpectrum()===
c&&h.getValue().setSpecShift(a);this.getScale().addSpecShift(a);Double.isNaN(this.lastClickX)||(this.lastClickX+=a);this.updateDialogs();this.doZoom(0,this.getScale().minYOnScale,0,this.getScale().maxYOnScale,!0,!0,!1,!0,!1);this.pd.repaint();return!0},"~N,~N");c(c$,"toPeak",function(a){a*=this.drawXAxisLeftToRight?1:-1;Double.isNaN(this.lastClickX)&&(this.lastClickX=this.lastPixelX=0);var b=this.getSpectrum(),c=this.setCoordClicked(this.lastPixelX,this.lastClickX,0);a=b.setNextPeak(c,a);0>a||(a=
b.getPeakList().get(a),b.setSelectedPeak(a),this.setCoordClicked(a.getXPixel(),a.getX(),0),this.pd.notifyPeakPickedListeners(new JSV.common.PeakPickEvent(this.jsvp,this.pd.coordClicked,a)))},"~N");c(c$,"scaleSelectedBy",function(a){for(var b=this.bsSelected.nextSetBit(0);0<=b;b=this.bsSelected.nextSetBit(b+1))this.viewData.scaleSpectrum(b,a)},"~N");h(c$,"toString",function(){return"gs: "+this.nSpectra+" "+this.spectra+" "+this.spectra.get(0).getFilePath()});c(c$,"setXPointer",function(a,b){null!=
a&&this.setSpectrumClicked(this.getSpectrumIndex(a));this.xValueMovedTo=this.lastClickX=b;this.lastPixelX=this.toPixelX(b);this.setXPixelMovedTo(b,1.7976931348623157E308,0,0);this.yValueMovedTo=NaN},"JSV.common.Spectrum,~N");c(c$,"setXPointer2",function(a,b){null!=a&&this.setSpectrumClicked(this.getSpectrumIndex(a));this.setXPixelMovedTo(1.7976931348623157E308,b,0,0)},"JSV.common.Spectrum,~N");c(c$,"hasCurrentMeasurement",function(a){return null!=(a===JSV.common.Annotation.AType.Integration?this.selectedSpectrumIntegrals:
this.selectedSpectrumMeasurements)},"JSV.common.Annotation.AType");c(c$,"getDialog",function(a,b){-1==b&&(b=this.getCurrentSpectrumIndex());return null==this.dialogs||0>b?null:this.dialogs.get(a+"_"+b)},"JSV.common.Annotation.AType,~N");c(c$,"removeDialog",function(a,b){null!=this.dialogs&&0<=a&&this.dialogs.remove(b+"_"+a)},"~N,JSV.common.Annotation.AType");c(c$,"addDialog",function(a,b,c){null==this.dialogs&&(this.dialogs=new java.util.Hashtable);a=b+"_"+a;c.setGraphSetKey(a);this.dialogs.put(a,
c);return c},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");c(c$,"removeDialog",function(a){var b=a.getGraphSetKey();this.dialogs.remove(b);a=a.getData();null!=a&&this.dialogs.put(b,a)},"JSV.dialog.JSVDialog");c(c$,"getPeakListing",function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;var e=this.getDialog(JSV.common.Annotation.AType.PeakList,-1);if(null==e){if(!c)return null;this.addDialog(a,JSV.common.Annotation.AType.PeakList,e=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,
this.getSpectrum()))}e.getData().setPeakList(b,-2147483648,this.viewData.getScale());p(e,JSV.dialog.JSVDialog)&&e.setFields();return e.getData()},"~N,JSV.common.Parameters,~B");c(c$,"setPeakListing",function(a){var b=this.getDialog(JSV.common.Annotation.AType.PeakList,-1),c=p(b,JSV.dialog.JSVDialog)?b:null;(null==a?null==c||!c.isVisible():a.booleanValue())?this.pd.showDialog(JSV.common.Annotation.AType.PeakList):p(b,JSV.dialog.JSVDialog)&&b.setVisible(!1)},"Boolean");c(c$,"haveIntegralDisplayed",
function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null!=a&&a.getState()},"~N");c(c$,"getIntegrationGraph",function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null==a?null:a.getData()},"~N");c(c$,"setIntegrationRatios",function(a){var b=this.getFixedSelectedSpectrumIndex();null==this.aIntegrationRatios&&(this.aIntegrationRatios=Array(this.nSpectra));this.aIntegrationRatios[b]=JSV.common.IntegralData.getIntegrationRatiosFromString(this.getSpectrum(),
a)},"~S");c(c$,"getIntegrationRatios",function(a){return null==this.aIntegrationRatios?null:this.aIntegrationRatios[a]},"~N");c(c$,"integrate",function(a,b){var c=this.getSpectrumAt(a);if(null==b||!c.canIntegrate())return this.removeDialog(a,JSV.common.Annotation.AType.Integration),!1;this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(c,b));return!0},"~N,JSV.common.Parameters");c(c$,"getIntegration",function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;
var e=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==e){if(!c)return null;e=this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(this.getSpectrum(),b))}return e.getData()},"~N,JSV.common.Parameters,~B");c(c$,"getMeasurementInfo",function(a,b){var c;switch(a){case JSV.common.Annotation.AType.PeakList:c=this.getPeakListing(b,null,!1);break;case JSV.common.Annotation.AType.Integration:c=this.getIntegration(b,null,!1);break;default:return null}if(null==
c)return null;var e=new java.util.Hashtable;c.getInfo(e);return e},"JSV.common.Annotation.AType,~N");c(c$,"getInfo",function(a,b){var c=new java.util.Hashtable;if("viewInfo".equalsIgnoreCase(a))return this.getScale().getInfo(c);var e=new JU.Lst;c.put("spectra",e);for(var g=0;g<this.nSpectra;g++)if(!(0<=b&&g!=b)){var f=this.spectra.get(g),h=f.getInfo(a);if(0<=b&&null!=a&&(2==h.size()||a.equalsIgnoreCase("id")))return 2==h.size()&&h.remove("id"),h;JSV.common.Parameters.putInfo(a,h,"type",f.getDataType());
JSV.common.Parameters.putInfo(a,h,"titleLabel",f.getTitleLabel());JSV.common.Parameters.putInfo(a,h,"filePath",f.getFilePath().$replace("\\","/"));JSV.common.Parameters.putInfo(a,h,"PeakList",JSV.common.Parameters.isMatch(a,"PeakList")?this.getMeasurementInfo(JSV.common.Annotation.AType.PeakList,g):null);JSV.common.Parameters.putInfo(a,h,"Integration",JSV.common.Parameters.isMatch(a,"Integration")?this.getMeasurementInfo(JSV.common.Annotation.AType.Integration,g):null);if(0<=b)return h;e.addLast(h)}return c},
"~S,~N");c(c$,"getTitle",function(a){return 1==this.nSpectra||0<=this.iSpectrumSelected&&(!a||1==this.nSplit)?this.getSpectrum().getTitle():null},"~B");c(c$,"getCurrentView",function(){this.setScale(this.getFixedSelectedSpectrumIndex());return this.viewData.getScale()});c(c$,"set2DXY",function(a,b,c){var e;null!=this.gs2dLinkedX&&(e=this.toPixelX(a),e!=this.fixX(e)&&(e=-2147483648,a=1.7976931348623157E308),this.cur1D2x1.setX(a,e));null!=this.gs2dLinkedY&&(e=this.toPixelX(b),e!=this.fixX(e)&&(e=-2147483648,
b=1.7976931348623157E308),this.cur1D2x2.setX(b,e));this.cur1D2Locked=c},"~N,~N,~B");c(c$,"dialogsToFront",function(a){if(null!=this.dialogs){null==a&&(a=this.getSpectrum());for(var b,c=this.dialogs.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var e=b.getValue();this.isVisible(e)&&(null==a?e.setVisible(!0):e.setFocus(e.getSpectrum()===a))}}},"JSV.common.Spectrum");c(c$,"setPlotColors",function(a){var b=a;if(b.length>this.nSpectra)a=Array(this.nSpectra),System.arraycopy(b,0,a,0,this.nSpectra),
b=a;else if(this.nSpectra>b.length){a=Array(this.nSpectra);var c=this.nSpectra-b.length;System.arraycopy(b,0,a,0,b.length);for(var e=0,b=b.length;e<c;e++,b++)a[b]=this.generateRandomColor();b=a}this.plotColors=b},"~O");c(c$,"disposeImage",function(){null!=this.image2D&&this.image2D.parentNode.removeChild(this.image2D);this.plotColors=this.highlights=this.pd=this.jsvp=this.image2D=null});c(c$,"generateRandomColor",function(){for(;;){var a=q(255*Math.random()),b=q(255*Math.random()),c=q(255*Math.random()),
a=this.g2d.getColor3(a,b,c);if(0!=a.getRGB())return a}});c(c$,"setPlotColor0",function(a){this.plotColors[0]=a},"~O");c(c$,"getPlotColor",function(a){return a>=this.plotColors.length?null:this.plotColors[a]},"~N");c(c$,"setColorFromToken",function(a,b){null!=b&&this.g2d.setGraphicsColor(a,b===JSV.common.ScriptToken.PLOTCOLOR?this.plotColors[0]:this.pd.getColor(b))},"~O,JSV.common.ScriptToken");c(c$,"setPlotColor",function(a,b){var c;switch(b){case -3:c=JSV.common.GraphSet.veryLightGrey;break;case -2:c=
this.pd.BLACK;break;case -1:c=this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR);break;default:c=this.plotColors[b]}this.g2d.setGraphicsColor(a,c)},"~O,~N");c(c$,"draw2DImage",function(){null!=this.imageView&&this.g2d.drawGrayScaleImage(this.gMain,this.image2D,this.imageView.xPixel0,this.imageView.yPixel0,this.imageView.xPixel0+this.imageView.xPixels-1,this.imageView.yPixel0+this.imageView.yPixels-1,this.imageView.xView1,this.imageView.yView1,this.imageView.xView2,this.imageView.yView2)});
c(c$,"get2DImage",function(){this.imageView=new JSV.common.ImageView;this.imageView.set(this.viewList.get(0).getScale());if(!this.update2dImage(!0))return!1;this.imageView.resetZoom();return this.sticky2Dcursor=!0});c(c$,"update2dImage",function(a){this.imageView.set(this.viewData.getScale());var b=this.getSpectrumAt(0),c=this.imageView.get2dBuffer(b,!a);if(null==c)return this.imageView=this.image2D=null,!1;a&&(c=this.imageView.adjustView(b,this.viewData),this.imageView.resetView());this.image2D=
this.g2d.newGrayScaleImage(this.gMain,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,c);this.setImageWindow();return!0},"~B");c(c$,"getAnnotation",function(a,b,c,e,g,f,h){return(new JSV.common.ColoredAnnotation).setCA(a,b,this.getSpectrum(),c,this.pd.BLACK,e,g,f,h)},"~N,~N,~S,~B,~B,~N,~N");c(c$,"getAnnotation",function(a,b){return JSV.common.Annotation.getColoredAnnotation(this.g2d,this.getSpectrum(),a,b)},"JU.Lst,JSV.common.Annotation");c(c$,"fillBox",function(a,b,c,e,g,f){this.setColorFromToken(a,
f);this.g2d.fillRect(a,Math.min(b,e),Math.min(c,g),Math.abs(b-e),Math.abs(c-g))},"~O,~N,~N,~N,~N,JSV.common.ScriptToken");c(c$,"drawHandle",function(a,b,c,e){e?this.g2d.drawRect(a,b-2,c-2,4,4):this.g2d.fillRect(a,b-2,c-2,5,5)},"~O,~N,~N,~B");c(c$,"setCurrentBoxColor",function(a){this.g2d.setGraphicsColor(a,this.pd.BLACK)},"~O");c(c$,"fillArrow",function(a,b,c,e,g){var f=1;switch(b){case 1:case 3:f=-1}c=[c-5,c-5,c+5,c+5,c+8,c,c-8];e=[e+5*f,e-f,e-f,e+5*f,e+5*f,e+10*f,e+5*f];switch(b){case 1:case 2:g?
this.g2d.fillPolygon(a,e,c,7):this.g2d.drawPolygon(a,e,c,7);break;case 3:case 4:g?this.g2d.fillPolygon(a,c,e,7):this.g2d.drawPolygon(a,c,e,7)}},"~O,~N,~N,~N,~B");c(c$,"fillCircle",function(a,b,c,e){e?this.g2d.fillCircle(a,b-4,c-4,8):this.g2d.drawCircle(a,b-4,c-4,8)},"~O,~N,~N,~B");c(c$,"setAnnotationColor",function(a,b,c){null!=c?this.setColorFromToken(a,c):(c=null,p(b,JSV.common.ColoredAnnotation)&&(c=b.getColor()),null==c&&(c=this.pd.BLACK),this.g2d.setGraphicsColor(a,c))},"~O,JSV.common.Annotation,JSV.common.ScriptToken");
c(c$,"setSolutionColor",function(a,b,c){for(var e=0;e<this.nSpectra;e++){var g=this.spectra.get(e),f=b||!g.canShowSolutionColor()?-1:a.getColour(g,c);g.setFillColor(-1==f?null:this.pd.vwr.parameters.getColor1(f))}},"JSV.api.VisibleInterface,~B,~B");c(c$,"setIRMode",function(a,b){for(var c=0;c<this.nSpectra;c++){var e=this.spectra.get(c);if(e.dataType.equals(b)){var g=JSV.common.Spectrum.taConvert(e,a);g!==e&&this.pd.setSpecForIRMode(g)}}},"JSV.common.Spectrum.IRMode,~S");c$.$GraphSet$Highlight$=function(){G(self.c$);
c$=t(function(){Q(this,arguments);this.x2=this.x1=0;this.spectrum=this.color=null;s(this,arguments)},JSV.common.GraphSet,"Highlight");h(c$,"toString",function(){return"highlight "+this.x1+" "+this.x2+" "+this.spectrum});u(c$,function(a,b,c,e){this.x1=a;this.x2=b;this.color=e;this.spectrum=c},"~N,~N,JSV.common.Spectrum,javajs.api.GenericColor");h(c$,"equals",function(a){return!p(a,JSV.common.GraphSet.Highlight)?!1:a.x1==this.x1&&a.x2==this.x2},"~O");c$=F()};C(c$,"ARROW_RESET",-1,"ARROW_HOME",0,"ARROW_LEFT",
1,"ARROW_RIGHT",2,"ARROW_UP",3,"ARROW_DOWN",4);c$.RT2=c$.prototype.RT2=Math.sqrt(2);C(c$,"veryLightGrey",null,"minNumOfPointsForZoom",3,"MIN_DRAG_PIXELS",5,"ONLINE_CUTOFF",2)});n("JSV.common");w(["JSV.common.XYScaleConverter"],"JSV.common.ImageView",["java.lang.Double","JSV.common.Coordinate","$.ScaleData"],function(){c$=t(function(){this.buf2d=null;this.yView2=this.xView2=this.yView1=this.xView1=this.yPixelZoom2=this.xPixelZoom2=this.yPixelZoom1=this.xPixelZoom1=this.yPixels=this.xPixels=this.imageHeight=
this.imageWidth=this.yPixel1=this.xPixel1=this.yPixel0=this.xPixel0=this.averageGray=this.grayFactorLast=0;this.minX=NaN;this.maxZ=this.minZ=this.maxY=this.minY=this.maxX=0;this.scaleData=null;s(this,arguments)},JSV.common,"ImageView",null,JSV.common.XYScaleConverter);c(c$,"set",function(a){Double.isNaN(this.minX)&&(this.minX=a.minX,this.maxX=a.maxX);this.minZ=a.minY;this.maxZ=a.maxY;this.scaleData=new JSV.common.ScaleData},"JSV.common.ScaleData");c(c$,"setZoom",function(a,b,c,e){this.xPixelZoom1=
Math.min(a,c);this.yPixelZoom1=Math.min(b,e);this.xPixelZoom2=Math.max(a,c);this.yPixelZoom2=Math.max(b,e);this.setView()},"~N,~N,~N,~N");c(c$,"setXY0",function(a,b,c){this.xPixel0=b;this.yPixel0=c;this.xPixel1=this.xPixel0+this.xPixels-1;this.yPixel1=this.yPixel0+this.yPixels-1;this.setMinMaxY(a)},"JSV.common.Spectrum,~N,~N");c(c$,"setPixelWidthHeight",function(a,b){this.xPixels=a;this.yPixels=b},"~N,~N");c(c$,"resetView",function(){this.yView1=this.xView1=0;this.xView2=this.imageWidth-1;this.yView2=
this.imageHeight-1});c(c$,"setView",function(){0==this.xPixelZoom1&&this.resetZoom();var a=this.toImageX(this.xPixelZoom1),b=this.toImageY(this.yPixelZoom1),c=this.toImageX(this.xPixelZoom2),e=this.toImageY(this.yPixelZoom2);this.xView1=Math.min(a,c);this.yView1=Math.min(b,e);this.xView2=Math.max(a,c);this.yView2=Math.max(b,e);this.setScaleData();this.resetZoom()});c(c$,"resetZoom",function(){this.xPixelZoom1=this.xPixel0;this.yPixelZoom1=this.yPixel0;this.xPixelZoom2=this.xPixel1;this.yPixelZoom2=
this.yPixel1});c(c$,"toImageX",function(a){return this.xView1+q(Math.floor((a-this.xPixel0)/(this.xPixels-1)*(this.xView2-this.xView1)))},"~N");c(c$,"toImageY",function(a){return this.yView1+q(Math.floor((a-this.yPixel0)/(this.yPixels-1)*(this.yView2-this.yView1)))},"~N");c(c$,"toImageX0",function(a){return JSV.common.Coordinate.intoRange(q((1*a-this.xPixel0)/(this.xPixels-1)*(this.imageWidth-1)),0,this.imageWidth-1)},"~N");c(c$,"toImageY0",function(a){return JSV.common.Coordinate.intoRange(q((1*
a-this.yPixel0)/(this.yPixels-1)*(this.imageHeight-1)),0,this.imageHeight-1)},"~N");c(c$,"isXWithinRange",function(a){return a>=this.xPixel0-5&&a<this.xPixel0+this.xPixels+5},"~N");c(c$,"toSubspectrumIndex",function(a){return JSV.common.Coordinate.intoRange(this.imageHeight-1-this.toImageY(a),0,this.imageHeight-1)},"~N");c(c$,"toX0",function(a){return this.maxX+(this.minX-this.maxX)*(this.fixX(a)-this.xPixel0)/(this.xPixels-1)},"~N");c(c$,"toPixelX0",function(a){return this.xPixel1-q((a-this.minX)/
(this.maxX-this.minX)*(this.xPixels-1))},"~N");c(c$,"toPixelY0",function(a){return this.yPixel1-q(a/(this.imageHeight-1)*(this.yPixels-1))},"~N");c(c$,"subIndexToPixelY",function(a){return this.yPixel0+q(1*(this.imageHeight-1-a-this.yView1)/(this.yView2-this.yView1)*(this.yPixels-1))},"~N");c(c$,"fixSubIndex",function(a){return JSV.common.Coordinate.intoRange(a,this.imageHeight-1-this.yView2,this.imageHeight-1-this.yView1)},"~N");c(c$,"setView0",function(a,b,c,e){a=this.toImageX0(a);b=this.toImageY0(b);
c=this.toImageX0(c);e=this.toImageY0(e);this.xView1=Math.min(a,c);this.yView1=Math.min(b,e);this.xView2=Math.max(a,c);this.yView2=Math.max(b,e);this.resetZoom()},"~N,~N,~N,~N");c(c$,"get2dBuffer",function(a,b){var c=a.getSubSpectra();if(null==c||!c.get(0).isContinuous())return null;var e=a.getXYCoords(),g=c.size();this.imageWidth=e.length;this.imageHeight=g;var f=255/(this.maxZ-this.minZ);if(!b&&null!=this.buf2d&&f==this.grayFactorLast)return this.buf2d;this.grayFactorLast=f;for(var h=this.imageWidth*
this.imageHeight,k=D(h,0),l=0,m=0;m<g;m++){var n=c.get(m).xyCoords;if(n.length!=e.length)return null;for(var p=c.get(m).getUserYFactor(),s=0;s<e.length;s++){var t=n[s].getYVal(),t=255-JSV.common.Coordinate.intoRange(q((t*p-this.minZ)*f),0,255);k[--h]=t;l+=t}}this.averageGray=1-l/(this.imageWidth*this.imageHeight)/255;System.out.println("Average gray = "+this.averageGray);return this.buf2d=k},"JSV.common.Spectrum,~B");c(c$,"adjustView",function(a,b){for(var c=0,e=!1;((e=0.05>this.averageGray)||0.3<
this.averageGray)&&10>c++;)b.scaleSpectrum(-2,e?2:0.5),this.set(b.getScale()),this.get2dBuffer(a,!1);return this.buf2d},"JSV.common.Spectrum,JSV.common.ViewData");c(c$,"getBuffer",function(){return this.buf2d});c(c$,"setMinMaxY",function(a){a=a.getSubSpectra();var b=a.get(0);this.maxY=b.getY2D();this.minY=a.get(a.size()-1).getY2D();b.y2DUnits.equalsIgnoreCase("Hz")&&(this.maxY/=b.freq2dY,this.minY/=b.freq2dY);this.setScaleData()},"JSV.common.Spectrum");c(c$,"setScaleData",function(){this.scaleData.minY=
this.minY;this.scaleData.maxY=this.maxY;this.scaleData.setYScale(this.toY(this.yPixel0),this.toY(this.yPixel1),!1,!1)});h(c$,"fixX",function(a){return a<this.xPixel0?this.xPixel0:a>this.xPixel1?this.xPixel1:a},"~N");h(c$,"fixY",function(a){return JSV.common.Coordinate.intoRange(a,this.yPixel0,this.yPixel1)},"~N");h(c$,"getScale",function(){return this.scaleData});h(c$,"toX",function(a){return this.maxX+(this.minX-this.maxX)*this.toImageX(this.fixX(a))/(this.imageWidth-1)},"~N");h(c$,"toY",function(a){a=
this.toSubspectrumIndex(a);return this.maxY+(this.minY-this.maxY)*a/(this.imageWidth-1)},"~N");h(c$,"toPixelX",function(a){var b=this.toX(this.xPixel0),c=this.toX(this.xPixel1);return this.xPixel0+q((a-b)/(c-b)*(this.xPixels-1))},"~N");h(c$,"toPixelY",function(a){return q(this.yPixel0+(a-this.scaleData.minYOnScale)/(this.scaleData.maxYOnScale-this.scaleData.minYOnScale)*this.yPixels)},"~N");h(c$,"getXPixels",function(){return this.xPixels});h(c$,"getYPixels",function(){return this.yPixels});h(c$,
"getXPixel0",function(){return this.xPixel0});C(c$,"DEFAULT_MIN_GRAY",0.05,"DEFAULT_MAX_GRAY",0.3)});n("JSV.common");w(["JSV.common.Measurement"],"JSV.common.Integral",null,function(){c$=B(JSV.common,"Integral",JSV.common.Measurement);c(c$,"setInt",function(a,b,c,e,g,f){this.setA(a,b,c,"",!1,!1,0,6);this.setPt2(g,f);this.setValue(e);return this},"~N,~N,JSV.common.Spectrum,~N,~N,~N")});n("JSV.common");c$=B(JSV.common,"IntegralComparator",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.getXVal()<
b.getXVal()?-1:a.getXVal()>b.getXVal()?1:0},"JSV.common.Measurement,JSV.common.Measurement");n("JSV.common");w(["java.lang.Enum","JSV.common.MeasurementData","$.IntegralComparator"],"JSV.common.IntegralData","java.lang.Double java.util.Collections $.StringTokenizer JU.AU $.BS $.DF $.Lst $.PT JSV.common.Annotation $.Coordinate $.Integral $.ScriptToken".split(" "),function(){c$=t(function(){this.intRange=this.percentOffset=this.percentMinY=0;this.normalizationFactor=1;this.integralTotal=this.offset=
this.percentRange=0;this.haveRegions=!1;this.xyCoords=null;s(this,arguments)},JSV.common,"IntegralData",JSV.common.MeasurementData);c(c$,"getPercentMinimumY",function(){return this.percentMinY});c(c$,"getPercentOffset",function(){return this.percentOffset});c(c$,"getIntegralFactor",function(){return this.intRange});u(c$,function(a,b,c,e){E(this,JSV.common.IntegralData,[JSV.common.Annotation.AType.Integration,e]);this.percentMinY=a;this.percentOffset=b;this.percentRange=c;this.calculateIntegral()},
"~N,~N,~N,JSV.common.Spectrum");u(c$,function(a,b){E(this,JSV.common.IntegralData,[JSV.common.Annotation.AType.Integration,a]);null==b?this.autoIntegrate():(this.percentOffset=b.integralOffset,this.percentRange=b.integralRange,this.calculateIntegral())},"JSV.common.Spectrum,JSV.common.Parameters");c(c$,"update",function(a){this.update(a.integralMinY,a.integralOffset,a.integralRange)},"JSV.common.Parameters");c(c$,"update",function(a,b,c){var e=this.percentRange;if(!(0>=c||c==this.percentRange&&b==
this.percentOffset)){this.percentOffset=b;this.percentRange=c;this.checkRange();a=c/100/this.integralTotal;b/=100;for(var g=0;g<this.xyCoords.length;g++){var f=this.xyCoords[g].getYVal(),f=(f-this.offset)/this.intRange;this.xyCoords[g].setYVal(f*a+b)}1!=this.normalizationFactor&&(this.normalizationFactor*=e/c);if(this.haveRegions)for(g=this.size();0<=--g;)c=this.get(g),e=this.getYValueAt(c.getXVal()),f=this.getYValueAt(c.getXVal2()),c.setYVal(e),c.setYVal2(f),c.setValue(100*Math.abs(f-e)*this.normalizationFactor);
this.intRange=a;this.offset=b}},"~N,~N,~N");c(c$,"getYValueAt",function(a){return JSV.common.Coordinate.getYValueAt(this.xyCoords,a)},"~N");c(c$,"addIntegralRegion",function(a,b){if(Double.isNaN(a))return this.haveRegions=!1,this.clear(),null;if(a==b)return null;var c=this.getYValueAt(a),e=this.getYValueAt(b);this.haveRegions=!0;c=(new JSV.common.Integral).setInt(a,c,this.spec,100*Math.abs(e-c)*this.normalizationFactor,b,e);this.clear(a,b);this.addLast(c);java.util.Collections.sort(this,JSV.common.IntegralData.c);
return c},"~N,~N");h(c$,"setSpecShift",function(a){JSV.common.Coordinate.shiftX(this.xyCoords,a);for(var b=this.size();1<=--b;)this.get(b).addSpecShift(a)},"~N");c(c$,"addMarks",function(a){a=JU.PT.rep(" "+a,","," ");a=JU.PT.rep(a," -"," #");a=JU.PT.rep(a,"--","-#");a=a.$replace("-","^");a=a.$replace("#","-");a=JSV.common.ScriptToken.getTokens(a);for(var b=0;b<a.size();b++)try{var c=a.get(b),e=0,g=c.indexOf("^");if(!(0>g)){var f=c.indexOf(":");f>g&&(e=Double.$valueOf(c.substring(f+1).trim()).doubleValue(),
c=c.substring(0,f).trim());var h=Double.$valueOf(c.substring(0,g).trim()).doubleValue(),k=Double.$valueOf(c.substring(g+1).trim()).doubleValue();0==k&&0==h&&this.clear();if(k!=h){var l=this.addIntegralRegion(Math.max(k,h),Math.min(k,h));null!=l&&0<e&&this.setSelectedIntegral(l,e)}}}catch(m){if(!y(m,Exception))throw m;}},"~S");c(c$,"calculateIntegral",function(){var a=this.spec.getXYCoords();this.xyCoords=Array(a.length);this.integralTotal=0;this.checkRange();for(var b=1E100,c=0;c<a.length;c++){var e=
a[c].getYVal();e<b&&0<=e&&(b=e)}for(c=0;c<a.length;c++)e=a[c].getYVal(),-1.7976931348623157E308<e&&(this.integralTotal+=e-b);this.intRange=this.percentRange/100/this.integralTotal;this.offset=this.percentOffset/100;for(var g=0,c=a.length;0<=--c;)e=a[c].getYVal(),-1.7976931348623157E308<e&&(g+=e-b),this.xyCoords[c]=(new JSV.common.Coordinate).set(a[c].getXVal(),g*this.intRange+this.offset);return this.xyCoords});c(c$,"checkRange",function(){this.percentOffset=Math.max(5,this.percentOffset);this.percentRange=
Math.max(10,this.percentRange)});c$.getIntegrationRatiosFromString=c(c$,"getIntegrationRatiosFromString",function(a,b){for(var c=new JU.Lst,e=new java.util.StringTokenizer(b,",");e.hasMoreTokens();){var g=e.nextToken(),g=new java.util.StringTokenizer(g,":"),g=(new JSV.common.Annotation).setA(Double.parseDouble(g.nextToken()),0,a,g.nextToken(),!0,!1,0,0);c.addLast(g)}return c},"JSV.common.Spectrum,~S");c(c$,"getXYCoords",function(){return this.xyCoords});c(c$,"getPercentYValueAt",function(a){return 100*
this.getYValueAt(a)},"~N");c(c$,"dispose",function(){this.xyCoords=this.spec=null});c(c$,"setSelectedIntegral",function(a,b){var c=a.getValue();this.factorAllIntegrals(0>=b?1/this.normalizationFactor:b/c,0>=b)},"JSV.common.Measurement,~N");c(c$,"factorAllIntegrals",function(a,b){for(var c=0;c<this.size();c++){var e=this.get(c);e.setValue(a*e.getValue())}this.normalizationFactor=b?1:this.normalizationFactor*a},"~N,~B");c(c$,"getBitSet",function(){var a=JU.BS.newN(this.xyCoords.length);if(0==this.size())return a.setBits(0,
this.xyCoords.length),a;for(var b=this.size();0<=--b;){var c=this.get(b),e=JSV.common.Coordinate.getNearestIndexForX(this.xyCoords,c.getXVal()),c=JSV.common.Coordinate.getNearestIndexForX(this.xyCoords,c.getXVal2());a.setBits(Math.min(e,c),Math.max(e,c))}return a});h(c$,"getMeasurementListArray",function(){for(var a=Array(this.size()),b=0,c=this.size();0<=--c;)a[b++]=[""+b,JU.DF.formatDecimalDbl(this.get(c).getXVal(),2),JU.DF.formatDecimalDbl(this.get(c).getXVal2(),2),this.get(c).text];return a},
"~S");h(c$,"getMeasurementListArrayReal",function(){for(var a=JU.AU.newDouble2(this.size()),b=0,c=this.size();0<=--c;b++)a[b]=[this.get(c).getXVal(),this.get(c).getXVal2(),this.get(c).getValue()];return a},"~S");h(c$,"getDataHeader",function(){return JSV.common.IntegralData.$HEADER});c(c$,"shiftY",function(a,b,c,e){b=q(100*(c+e-b)/e);0>a&&(b-=this.percentOffset);0>a?this.update(0,this.percentOffset,b):this.update(0,b,this.percentRange)},"~N,~N,~N,~N");c(c$,"autoIntegrate",function(){null==this.xyCoords&&
this.calculateIntegral();if(0!=this.xyCoords.length){this.clear();for(var a=-1,b=0,c=this.xyCoords[this.xyCoords.length-1].getYVal(),e=this.xyCoords.length-1;0<=--e;){var g=this.xyCoords[e].getYVal();b++;1E-4>g-c&&0>a?g<c&&(c=g,b=0):0>a?(a=e+Math.min(b,20),c=g,b=0):1E-4>g-c?(1==b&&(c=g),20<=b&&(this.addIntegralRegion(this.xyCoords[a].getXVal(),this.xyCoords[e].getXVal()),a=-1,c=g,b=0)):(b=0,c=g)}0<this.spec.nH&&this.factorAllIntegrals(this.spec.nH/this.percentRange,!1)}});c(c$,"getInfo",function(a){a.put("offset",
Double.$valueOf(this.myParams.integralOffset));a.put("range",Double.$valueOf(this.myParams.integralRange));a.put("normalizationFactor",Double.$valueOf(this.normalizationFactor));a.put("integralTotal",Double.$valueOf(this.integralTotal));R(this,JSV.common.IntegralData,"getInfo",[a])},"java.util.Map");c(c$,"setMinimumIntegral",function(a){for(var b=this.size();0<=--b;)this.get(b).getValue()<a&&this.remove(b)},"~N");G(self.c$);c$=B(JSV.common.IntegralData,"IntMode",Enum);c$.getMode=c(c$,"getMode",function(a){for(var b,
c=0,e=JSV.common.IntegralData.IntMode.values();c<e.length&&((b=e[c])||1);c++)if(a.startsWith(b.name()))return b;return JSV.common.IntegralData.IntMode.ON},"~S");v(c$,"OFF",0,[]);v(c$,"ON",1,[]);v(c$,"TOGGLE",2,[]);v(c$,"AUTO",3,[]);v(c$,"LIST",4,[]);v(c$,"MARK",5,[]);v(c$,"MIN",6,[]);v(c$,"UPDATE",7,[]);c$=F();C(c$,"DEFAULT_OFFSET",30,"DEFAULT_RANGE",50,"DEFAULT_MINY",0.1);c$.c=c$.prototype.c=new JSV.common.IntegralComparator;c$.$HEADER=c$.prototype.$HEADER=["peak","start/ppm","end/ppm","value"]});
n("JSV.common");w(["java.lang.Enum","JSV.source.JDXDataObject","JU.Lst"],"JSV.common.Spectrum","java.lang.Boolean $.Double java.util.Hashtable JU.PT JSV.common.Coordinate $.Parameters $.PeakInfo JSV.source.JDXSourceStreamTokenizer JU.Logger".split(" "),function(){c$=t(function(){this.highlightedPeak=this.selectedPeak=this.piUnitsY=this.piUnitsX=this.peakList=this.subSpectra=null;this.currentSubSpectrumIndex=this.specShift=0;this.$isForcedSubset=!1;this.id="";this.convertedSpectrum=null;this.userYFactor=
1;this.exportXAxisLeftToRight=!1;this.fillColor=null;s(this,arguments)},JSV.common,"Spectrum",JSV.source.JDXDataObject);K(c$,function(){this.peakList=new JU.Lst});h(c$,"finalize",function(){System.out.println("JDXSpectrum "+this+" finalized "+this.title)});c(c$,"dispose",function(){});c(c$,"isForcedSubset",function(){return this.$isForcedSubset});c(c$,"setId",function(a){this.id=a},"~S");u(c$,function(){E(this,JSV.common.Spectrum,[]);this.headerTable=new JU.Lst;this.xyCoords=[];this.parent=this});
c(c$,"copy",function(){var a=new JSV.common.Spectrum;this.copyTo(a);a.setPeakList(this.peakList,this.piUnitsX,null);a.fillColor=this.fillColor;return a});c(c$,"getXYCoords",function(){return this.getCurrentSubSpectrum().xyCoords});c(c$,"getPeakList",function(){return this.peakList});c(c$,"setPeakList",function(a,b,c){this.peakList=a;this.piUnitsX=b;this.piUnitsY=c;for(b=a.size();0<=--b;)this.peakList.get(b).spectrum=this;JU.Logger.debugging&&JU.Logger.info("Spectrum "+this.getTitle()+" peaks: "+a.size());
return a.size()},"JU.Lst,~S,~S");c(c$,"selectPeakByFileIndex",function(a,b,c){if(null!=this.peakList&&0<this.peakList.size()&&(null==c||this.sourceID.equals(b)))for(var e=0;e<this.peakList.size();e++)if(this.peakList.get(e).checkFileIndex(a,b,c))return System.out.println("selecting peak by FileIndex "+this+" "+this.peakList.get(e)),this.selectedPeak=this.peakList.get(e);return null},"~S,~S,~S");c(c$,"selectPeakByFilePathTypeModel",function(a,b,c){if(null!=this.peakList&&0<this.peakList.size())for(var e=
0;e<this.peakList.size();e++)if(this.peakList.get(e).checkFileTypeModel(a,b,c))return System.out.println("selecting peak byFilePathTypeModel "+this+" "+this.peakList.get(e)),this.selectedPeak=this.peakList.get(e);return null},"~S,~S,~S");c(c$,"matchesPeakTypeModel",function(a,b){if(a.equals("ID"))return this.sourceID.equalsIgnoreCase(b);if(null!=this.peakList&&0<this.peakList.size())for(var c=0;c<this.peakList.size();c++)if(this.peakList.get(c).checkTypeModel(a,b))return!0;return!1},"~S,~S");c(c$,
"setSelectedPeak",function(a){this.selectedPeak=a},"JSV.common.PeakInfo");c(c$,"setHighlightedPeak",function(a){this.highlightedPeak=a},"JSV.common.PeakInfo");c(c$,"getSelectedPeak",function(){return this.selectedPeak});c(c$,"getModelPeakInfoForAutoSelectOnLoad",function(){if(null!=this.peakList)for(var a=0;a<this.peakList.size();a++)if(this.peakList.get(a).autoSelectOnLoad())return this.peakList.get(a);return null});c(c$,"getAssociatedPeakInfo",function(a,b){this.selectedPeak=this.findPeakByCoord(a,
b);return null==this.selectedPeak?this.getBasePeakInfo():this.selectedPeak},"~N,JSV.common.Coordinate");c(c$,"findPeakByCoord",function(a,b){if(null!=b&&null!=this.peakList&&0<this.peakList.size()){for(var c=b.getXVal(),e=-1,g=1E100,f=0;f<this.peakList.size();f++){var h=this.peakList.get(f).checkRange(a,c);h<g&&(g=h,e=f)}if(0<=e)return this.peakList.get(e)}return null},"~N,JSV.common.Coordinate");c(c$,"getPeakTitle",function(){return null!=this.selectedPeak?this.selectedPeak.getTitle():null!=this.highlightedPeak?
this.highlightedPeak.getTitle():this.getTitleLabel()});c(c$,"getTitleLabel",function(){var a=null==this.peakList||0==this.peakList.size()?this.getQualifiedDataType():this.peakList.get(0).getType();return(null!=a&&0<a.length?a+" ":"")+this.getTitle()});c(c$,"setNextPeak",function(a,b){if(null==this.peakList||0==this.peakList.size())return-1;for(var c=a.getXVal()+1E-6*b,e=-1,g=-1,f=1.7976931348623157E308*b,h=0,k=this.peakList.size();0<=--k;){var l=this.peakList.get(k).getX();0<b?l>c&&l<f?(e=k,f=l):
l<c&&l-c<h&&(g=k,h=l-c):l<c&&l>f?(e=k,f=l):l>c&&l-c>h&&(g=k,h=l-c)}if(0>e){if(0>g)return-1;e=g}return e},"JSV.common.Coordinate,~N");c(c$,"getPercentYValueAt",function(a){return!this.isContinuous()?NaN:this.getYValueAt(a)},"~N");c(c$,"getYValueAt",function(a){return JSV.common.Coordinate.getYValueAt(this.xyCoords,a)},"~N");c(c$,"setUserYFactor",function(a){this.userYFactor=a},"~N");c(c$,"getUserYFactor",function(){return this.userYFactor});c(c$,"getConvertedSpectrum",function(){return this.convertedSpectrum});
c(c$,"setConvertedSpectrum",function(a){this.convertedSpectrum=a},"JSV.common.Spectrum");c$.taConvert=c(c$,"taConvert",function(a,b){if(!a.isContinuous())return a;switch(b){case JSV.common.Spectrum.IRMode.NO_CONVERT:return a;case JSV.common.Spectrum.IRMode.TO_ABS:if(!a.isTransmittance())return a;break;case JSV.common.Spectrum.IRMode.TO_TRANS:if(!a.isAbsorbance())return a}var c=a.getConvertedSpectrum();return null!=c?c:a.isAbsorbance()?JSV.common.Spectrum.toT(a):JSV.common.Spectrum.toA(a)},"JSV.common.Spectrum,JSV.common.Spectrum.IRMode");
c$.toT=c(c$,"toT",function(a){if(!a.isAbsorbance())return null;var b=a.getXYCoords(),c=Array(b.length);JSV.common.Coordinate.isYInRange(b,0,4)||(b=JSV.common.Coordinate.normalise(b,0,4));for(var e=0;e<b.length;e++)c[e]=(new JSV.common.Coordinate).set(b[e].getXVal(),JSV.common.Spectrum.toTransmittance(b[e].getYVal()));return JSV.common.Spectrum.newSpectrum(a,c,"TRANSMITTANCE")},"JSV.common.Spectrum");c$.toA=c(c$,"toA",function(a){if(!a.isTransmittance())return null;for(var b=a.getXYCoords(),c=Array(b.length),
e=JSV.common.Coordinate.isYInRange(b,-2,2),g=0;g<b.length;g++)c[g]=(new JSV.common.Coordinate).set(b[g].getXVal(),JSV.common.Spectrum.toAbsorbance(b[g].getYVal(),e));return JSV.common.Spectrum.newSpectrum(a,c,"ABSORBANCE")},"JSV.common.Spectrum");c$.newSpectrum=c(c$,"newSpectrum",function(a,b,c){var e=a.copy();e.setOrigin("JSpecView Converted");e.setOwner("JSpecView Generated");e.setXYCoords(b);e.setYUnits(c);a.setConvertedSpectrum(e);e.setConvertedSpectrum(a);return e},"JSV.common.Spectrum,~A,~S");
c$.toAbsorbance=c(c$,"toAbsorbance",function(a,b){return Math.min(4,b?2-JSV.common.Spectrum.log10(a):-JSV.common.Spectrum.log10(a))},"~N,~B");c$.toTransmittance=c(c$,"toTransmittance",function(a){return 0>=a?1:Math.pow(10,-a)},"~N");c$.log10=c(c$,"log10",function(a){return Math.log(a)/Math.log(10)},"~N");c$.process=c(c$,"process",function(a,b){if(b===JSV.common.Spectrum.IRMode.TO_ABS||b===JSV.common.Spectrum.IRMode.TO_TRANS)for(var c=0;c<a.size();c++)a.set(c,JSV.common.Spectrum.taConvert(a.get(c),
b));return!0},"JU.Lst,JSV.common.Spectrum.IRMode");c(c$,"getSubSpectra",function(){return this.subSpectra});c(c$,"getCurrentSubSpectrum",function(){return null==this.subSpectra?this:this.subSpectra.get(this.currentSubSpectrumIndex)});c(c$,"advanceSubSpectrum",function(a){return this.setCurrentSubSpectrum(this.currentSubSpectrumIndex+a)},"~N");c(c$,"setCurrentSubSpectrum",function(a){return this.currentSubSpectrumIndex=JSV.common.Coordinate.intoRange(a,0,this.subSpectra.size()-1)},"~N");c(c$,"addSubSpectrum",
function(a,b){if(!b&&(2>this.numDim||this.blockID!=a.blockID)||!JSV.common.Spectrum.allowSubSpec(this,a))return!1;this.$isForcedSubset=b;null==this.subSpectra&&(this.subSpectra=new JU.Lst,this.addSubSpectrum(this,!0));this.subSpectra.addLast(a);a.parent=this;return!0},"JSV.common.Spectrum,~B");c(c$,"getSubIndex",function(){return null==this.subSpectra?-1:this.currentSubSpectrumIndex});c(c$,"setExportXAxisDirection",function(a){this.exportXAxisLeftToRight=a},"~B");c(c$,"isExportXAxisLeftToRight",function(){return this.exportXAxisLeftToRight});
c(c$,"getInfo",function(a){var b=new java.util.Hashtable;if("id".equalsIgnoreCase(a))return b.put(a,this.id),b;b.put("id",this.id);JSV.common.Parameters.putInfo(a,b,"specShift",Double.$valueOf(this.specShift));var c="header".equals(a);if(!c&&null!=a)for(var e=this.headerTable.size();0<=--e;){var g=this.headerTable.get(e);if(g[0].equalsIgnoreCase(a)||g[2].equalsIgnoreCase(a))return b.put(a,g[1]),b}for(var g=new java.util.Hashtable,f=this.getHeaderRowDataAsArray(),e=0;e<f.length;e++){var h=JSV.source.JDXSourceStreamTokenizer.cleanLabel(f[e][0]);
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this.apiPlatform.isSingleThreaded();this.panelNodes=new JU.Lst;this.repaintManager=new JSV.common.RepaintManager(this);b||this.setPopupMenu(!0,!0)},"JSV.api.ScriptInterface,~B,~B");c(c$,"setPopupMenu",function(a,b){this.popupAllowMenu=a;this.popupZoomEnabled=b},"~B,~B");c(c$,"showMenu",function(a,b){if(this.popupAllowMenu){if(null==this.jsvpPopupMenu)try{this.jsvpPopupMenu=this.getPlatformInterface("Popup"),this.jsvpPopupMenu.jpiInitialize(this,this.isApplet?"appletMenu":"appMenu"),this.jsvpPopupMenu.setEnabled(this.popupAllowMenu,
this.popupZoomEnabled)}catch(c){if(y(c,Exception)){JU.Logger.error(c+" initializing popup menu");return}throw c;}this.jsvpPopupMenu.jpiShow(a,b)}},"~N,~N");c(c$,"runScriptNow",function(a){this.scriptLevelCount++;null==a&&(a="");a=a.trim();if(a.startsWith("!"))a=a.substring(1).trim();else if(a.startsWith(">"))return JU.Logger.error(a),!0;if(0<=a.indexOf("<PeakData"))return this.syncScript(a),!0;JU.Logger.info("RUNSCRIPT "+a);var b=!0,c=10;a=new JSV.common.ScriptTokenizer(a,!0);for(var e=null;null!=
a&&a.hasMoreTokens()&&0<c&&b;){var g=a.nextToken(),f=new JSV.common.ScriptTokenizer(g,!1),h=JSV.common.ScriptToken.getKey(f);if(null!=h){var k=JSV.common.ScriptToken.getScriptToken(h),f=JSV.common.ScriptToken.getValue(k,f,g);try{switch(k){case JSV.common.ScriptToken.UNKNOWN:JU.Logger.info("Unrecognized parameter: "+h);--c;break;default:if(null==this.selectedPanel)break;this.parameters.set(this.pd(),k,f);this.si.siUpdateBoolean(k,JSV.common.Parameters.isTrue(f));break;case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:this.si.siExecSetCallback(k,
f);break;case JSV.common.ScriptToken.DEFAULTLOADSCRIPT:f=JU.PT.rep(f,"''",'"');this.defaultLoadScript=0<f.length?f:null;break;case JSV.common.ScriptToken.DEFAULTNMRNORMALIZATION:this.nmrMaxY=JU.PT.parseFloat(f);break;case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(f);break;case JSV.common.ScriptToken.CLOSE:this.execClose(f);break;case JSV.common.ScriptToken.DEBUG:JU.Logger.setLogLevel(f.toLowerCase().equals("high")?6:JSV.common.Parameters.isTrue(f)?5:4);break;
case JSV.common.ScriptToken.GETPROPERTY:var l=null==this.selectedPanel?null:this.getPropertyAsJavaObject(f);null!=l&&this.selectedPanel.showMessage(JU.PT.toJSON(null,l),f);break;case JSV.common.ScriptToken.HIDDEN:this.si.siExecHidden(JSV.common.Parameters.isTrue(f));break;case JSV.common.ScriptToken.INTEGRATIONRATIOS:this.integrationRatios=f;this.execIntegrate(null);break;case JSV.common.ScriptToken.INTERFACE:this.interfaceOverlaid=this.checkOvelayInterface(f);break;case JSV.common.ScriptToken.INTEGRALOFFSET:case JSV.common.ScriptToken.INTEGRALRANGE:this.execSetIntegralParameter(k,
Double.parseDouble(f));break;case JSV.common.ScriptToken.JMOL:this.si.syncToJmol(f);break;case JSV.common.ScriptToken.JSV:this.syncScript(JU.PT.trimQuotes(f));break;case JSV.common.ScriptToken.LOAD:if(0==f.length){null!=this.defaultLoadScript&&this.runScriptNow(this.defaultLoadScript);break}this.load(f,(null==this.defaultLoadScript?"":this.defaultLoadScript+";")+a.getRemainingScript());e=null==this.selectedPanel?null:this.si.siLoaded(f);a=null;break;case JSV.common.ScriptToken.LOADIMAGINARY:this.loadImaginary=
JSV.common.Parameters.isTrue(f);break;case JSV.common.ScriptToken.PEAK:this.execPeak(f);break;case JSV.common.ScriptToken.PEAKLIST:this.execPeakList(f);break;case JSV.common.ScriptToken.SCALEBY:this.scaleSelectedBy(this.panelNodes,f);break;case JSV.common.ScriptToken.SCRIPT:if(f.equals("")||f.toLowerCase().startsWith("inline"))this.execScriptInline(f);else{var m=JSV.common.JSVFileManager.getFileAsString(f);null!=m&&100>this.scriptLevelCount&&this.runScriptNow(m)}break;case JSV.common.ScriptToken.SELECT:this.execSelect(f);
break;case JSV.common.ScriptToken.SPECTRUM:case JSV.common.ScriptToken.SPECTRUMNUMBER:this.setSpectrum(f)||(b=!1);break;case JSV.common.ScriptToken.STACKOFFSETY:this.execOverlayOffsetY(JU.PT.parseInt(""+JU.PT.parseFloat(f)));break;case JSV.common.ScriptToken.TEST:this.si.siExecTest(f);break;case JSV.common.ScriptToken.OVERLAY:case JSV.common.ScriptToken.VIEW:this.execView(f,!0);break;case JSV.common.ScriptToken.HIGHLIGHT:b=this.highlight(g);break;case JSV.common.ScriptToken.FINDX:case JSV.common.ScriptToken.GETSOLUTIONCOLOR:case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:case JSV.common.ScriptToken.IRMODE:case JSV.common.ScriptToken.LABEL:case JSV.common.ScriptToken.LINK:case JSV.common.ScriptToken.OVERLAYSTACKED:case JSV.common.ScriptToken.PRINT:case JSV.common.ScriptToken.SETPEAK:case JSV.common.ScriptToken.SETX:case JSV.common.ScriptToken.SHIFTX:case JSV.common.ScriptToken.SHOWERRORS:case JSV.common.ScriptToken.SHOWMEASUREMENTS:case JSV.common.ScriptToken.SHOWMENU:case JSV.common.ScriptToken.SHOWKEY:case JSV.common.ScriptToken.SHOWPEAKLIST:case JSV.common.ScriptToken.SHOWINTEGRATION:case JSV.common.ScriptToken.SHOWPROPERTIES:case JSV.common.ScriptToken.SHOWSOURCE:case JSV.common.ScriptToken.YSCALE:case JSV.common.ScriptToken.WRITE:case JSV.common.ScriptToken.ZOOM:if(this.isClosed()){b=
!1;break}switch(k){case JSV.common.ScriptToken.FINDX:this.pd().findX(null,Double.parseDouble(f));break;case JSV.common.ScriptToken.GETSOLUTIONCOLOR:this.show("solutioncolor"+f.toLowerCase());break;case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:this.execIntegrate(f);break;case JSV.common.ScriptToken.IRMODE:this.execIRMode(f);break;case JSV.common.ScriptToken.LABEL:this.pd().addAnnotation(JSV.common.ScriptToken.getTokens(f));break;case JSV.common.ScriptToken.LINK:this.pd().linkSpectra(JSV.common.PanelData.LinkMode.getMode(f));
break;case JSV.common.ScriptToken.OVERLAYSTACKED:this.pd().splitStack(!JSV.common.Parameters.isTrue(f));break;case JSV.common.ScriptToken.PRINT:e=this.execWrite(null);break;case JSV.common.ScriptToken.SETPEAK:this.pd().shiftSpectrum(NaN,f.equalsIgnoreCase("NONE")?1.7976931348623157E308:f.equalsIgnoreCase("?")?4.9E-324:Double.parseDouble(f));break;case JSV.common.ScriptToken.SETX:this.pd().shiftSpectrum(4.9E-324,Double.parseDouble(f));break;case JSV.common.ScriptToken.SHIFTX:this.pd().shiftSpectrum(f.equalsIgnoreCase("NONE")?
1.7976931348623157E308:Double.parseDouble(f),NaN);break;case JSV.common.ScriptToken.SHOWERRORS:this.show("errors");break;case JSV.common.ScriptToken.SHOWINTEGRATION:this.pd().showAnnotation(JSV.common.Annotation.AType.Integration,JSV.common.Parameters.getTFToggle(f));break;case JSV.common.ScriptToken.SHOWKEY:this.setOverlayLegendVisibility(JSV.common.Parameters.getTFToggle(f),!0);break;case JSV.common.ScriptToken.SHOWMEASUREMENTS:this.pd().showAnnotation(JSV.common.Annotation.AType.Measurements,JSV.common.Parameters.getTFToggle(f));
break;case JSV.common.ScriptToken.SHOWMENU:this.showMenu(-2147483648,0);break;case JSV.common.ScriptToken.SHOWPEAKLIST:this.pd().showAnnotation(JSV.common.Annotation.AType.PeakList,JSV.common.Parameters.getTFToggle(f));break;case JSV.common.ScriptToken.SHOWPROPERTIES:this.show("properties");break;case JSV.common.ScriptToken.SHOWSOURCE:this.show("source");break;case JSV.common.ScriptToken.YSCALE:this.setYScale(f);break;case JSV.common.ScriptToken.WINDOW:this.si.siNewWindow(JSV.common.Parameters.isTrue(f),
!1);break;case JSV.common.ScriptToken.WRITE:e=this.execWrite(f);break;case JSV.common.ScriptToken.ZOOM:b=this.execZoom(f)}}}catch(n){if(y(n,Exception))e=n.toString(),JU.Logger.error(n.toString()),b=!1,--c;else throw n;}}}this.scriptLevelCount--;this.si.siExecScriptComplete(e,!0);return b},"~S");c(c$,"execClose",function(a){var b=!a.startsWith("!");b||(a=a.substring(1));this.close(JU.PT.trimQuotes(a));(!b||0==this.panelNodes.size())&&this.si.siValidateAndRepaint(!0)},"~S");c(c$,"checkOvelayInterface",
function(a){return a.equalsIgnoreCase("single")||a.equalsIgnoreCase("overlay")},"~S");c(c$,"execPeak",function(a){try{var b=JSV.common.ScriptToken.getTokens(a);a=' type="'+b.get(0).toUpperCase()+'" _match="'+JU.PT.trimQuotes(b.get(1).toUpperCase())+'"';2<b.size()&&b.get(2).equalsIgnoreCase("all")&&(a+=' title="ALL"');this.processPeakPickEvent(new JSV.common.PeakInfo(a),!1)}catch(c){if(!y(c,Exception))throw c;}},"~S");c(c$,"execPeakList",function(a){var b=this.parameters,c=JSV.common.Parameters.getTFToggle(a);
if(0>a.indexOf("="))this.isClosed()||this.pd().getPeakListing(null,c);else for(var c=JSV.common.ScriptToken.getTokens(a),e=c.size();0<=--e;){a=c.get(e);var g=a.indexOf("=");if(!(0>=g)){var f=a.substring(0,g);a=a.substring(g+1);try{f.startsWith("thr")?b.peakListThreshold=Double.$valueOf(a).doubleValue():f.startsWith("int")&&(b.peakListInterpolation=a.equalsIgnoreCase("none")?"NONE":"parabolic"),this.isClosed()||this.pd().getPeakListing(b,Boolean.TRUE)}catch(h){if(!y(h,Exception))throw h;}}}},"~S");
c(c$,"highlight",function(a){var b=JSV.common.ScriptToken.getTokens(a),c=b.size();switch(c){case 3:case 5:case 6:case 7:break;case 2:case 4:if(b.get(c-1).equalsIgnoreCase("OFF"))break;default:return!1}if(!this.isClosed()){a=JU.PT.parseFloat(1<c?b.get(1):"");var e=JU.PT.parseFloat(2<c?b.get(2):""),g=this.getRGB(3<c?b.get(3):"100"),f=this.getRGB(4<c?b.get(4):"100"),h=this.getRGB(5<c?b.get(5):"100"),b=this.getRGB(6<c?b.get(6):"100");Float.isNaN(a)||Float.isNaN(e)?this.pd().removeAllHighlights():(this.pd().removeHighlight(a,
e),0>b&&(b=150),0<=g&&(0<=f&&0<=h)&&this.pd().addHighlight(null,a,e,null,g,f,h,b));this.repaint(!0)}return!0},"~S");c(c$,"getRGB",function(a){a=JU.PT.parseFloat(a);return z(Float.isNaN(a)?-1:1<a?a:255*a)},"~S");c(c$,"execZoom",function(a){var b=0,c=0,e=0,g=0;a=JU.PT.rep(a," - "," ").$replace(","," ");a=JSV.common.ScriptToken.getTokens(a);switch(a.size()){default:return!1;case 0:return b=this.pd().getCurrentGraphSet().getCurrentView(),a=Math.round(100*b.minXOnScale)/100+","+Math.round(100*b.maxXOnScale)/
100,a=this.selectedPanel.getInput("Enter zoom range x1 x2","Zoom",a),null==a||this.execZoom(a);case 1:return a=a.get(0),a.equalsIgnoreCase("next")?this.pd().nextView():a.toLowerCase().startsWith("prev")?this.pd().previousView():a.equalsIgnoreCase("out")?this.pd().resetView():a.equalsIgnoreCase("clear")&&this.pd().clearAllView(),!0;case 2:b=Double.parseDouble(a.get(0));c=Double.parseDouble(a.get(1));break;case 4:b=Double.parseDouble(a.get(0)),e=Double.parseDouble(a.get(1)),c=Double.parseDouble(a.get(2)),
g=Double.parseDouble(a.get(3))}this.pd().setZoom(b,e,c,g);return!0},"~S");c(c$,"scaleSelectedBy",function(a,b){try{for(var c=Double.parseDouble(b),e=a.size();0<=--e;)a.get(e).pd().scaleSelectedBy(c)}catch(g){if(!y(g,Exception))throw g;}},"JU.Lst,~S");c(c$,"pd",function(){return null==this.selectedPanel?null:this.selectedPanel.getPanelData()});c(c$,"isClosed",function(){return null==this.pd()});c(c$,"execSelect",function(a){if(a.startsWith("ID ")){if(!this.isClosed())try{this.pd().selectSpectrum(null,
"ID",JU.PT.trimQuotes(a.substring(3)),!0)}catch(b){if(!y(b,Exception))throw b;}}else{for(var c=this.panelNodes,e=c.size();0<=--e;)c.get(e).pd().selectFromEntireSet(-2147483648);c=new JU.Lst;this.fillSpecList(a,c,!1)}},"~S");c(c$,"execView",function(a,b){if(a.equals(""))this.checkOverlay();else{var c=new JU.Lst,e=this.fillSpecList(a,c,!0);0<c.size()&&this.si.siOpenDataOrFile(null,e,c,e,-1,-1,!1,null,null);b||this.si.siValidateAndRepaint(!1)}},"~S,~B");c(c$,"execIRMode",function(a){for(var b=JSV.common.Spectrum.IRMode.getMode(a),
c=this.pd().getSpectrum().dataType,e=this.panelNodes.size();0<=--e;)this.panelNodes.get(e).pd().setIRMode(b,c);this.setIRmode(a)},"~S");c(c$,"execIntegrate",function(a){this.isClosed()||(this.pd().checkIntegral(this.parameters,a),null!=this.integrationRatios&&this.pd().setIntegrationRatios(this.integrationRatios),this.integrationRatios=null,this.repaint(!0))},"~S");c(c$,"repaint",function(a){this.selectedPanel.doRepaint(a)},"~B");c(c$,"execSetIntegralParameter",function(a,b){var c=this.parameters;
switch(a){case JSV.common.ScriptToken.INTEGRALRANGE:c.integralRange=b;break;case JSV.common.ScriptToken.INTEGRALOFFSET:c.integralOffset=b}this.isClosed()||this.pd().checkIntegral(this.parameters,"update")},"JSV.common.ScriptToken,~N");c(c$,"setYScale",function(a){var b=JSV.common.ScriptToken.getTokens(a),c=0,e=!1;1<b.size()&&b.get(0).equalsIgnoreCase("ALL")&&(e=!0,c++);a=Double.parseDouble(b.get(c++));b=Double.parseDouble(b.get(c));if(e){e=this.pd().getSpectrum();for(c=this.panelNodes.size();0<=--c;){var g=
this.panelNodes.get(c);g.source===this.currentSource&&JSV.common.Spectrum.areXScalesCompatible(e,g.getSpectrum(),!1,!1)&&g.pd().setZoom(0,a,0,b)}}else this.pd().setZoom(0,a,0,b)},"~S");c(c$,"setOverlayLegendVisibility",function(a,b){b&&(this.overlayLegendVisible=null==a?!this.overlayLegendVisible:a===Boolean.TRUE);for(var c=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes),e=this.panelNodes.size();0<=--e;)this.showOverlayLegend(this.panelNodes.get(e),this.panelNodes.get(e)===c&&this.overlayLegendVisible)},
"Boolean,~B");c(c$,"showOverlayLegend",function(a,b){var c=a.legend;null==c&&b&&(c=a.setLegend(1<a.pd().getNumberOfSpectraInCurrentSet()&&1==a.pd().getNumberOfGraphSets()?this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null):null));null!=c&&c.setVisible(b)},"JSV.common.PanelNode,~B");c(c$,"syncScript",function(a){a.equals("TEST")&&(a=JSV.common.JSViewer.testScript);JU.Logger.info("JSViewer.syncScript Jmol>JSV "+a);if(0>a.indexOf("<PeakData"))a.startsWith("JSVSTR:")?this.si.syncToJmol(a):
(this.runScriptNow(a),0<=a.indexOf("#SYNC_PEAKS")&&this.syncPeaksAfterSyncScript());else{JU.Logger.info(">>toJSV>> "+a);var b=JU.PT.getQuotedAttribute(a,"sourceID"),c,e,g,f;if(null==b){e=JU.PT.getQuotedAttribute(a,"file");g=JU.PT.getQuotedAttribute(a,"index");if(null==e||null==g)return;e=JU.PT.rep(e,"#molfile","");c=JU.PT.getQuotedAttribute(a,"model");b=JU.PT.getQuotedAttribute(a,"src");f=null!=b&&b.startsWith("Jmol")?null:this.returnFromJmolModel;if(null!=c&&null!=f&&!c.equals(f)){JU.Logger.info("JSV ignoring model "+
c+"; should be "+f);return}this.returnFromJmolModel=null;if(0==this.panelNodes.size()||!this.checkFileAlreadyLoaded(e))JU.Logger.info("file "+e+" not found -- JSViewer closing all and reopening"),this.si.siSyncLoad(e);a=JU.PT.getQuotedAttribute(a,"type");f=null}else e=null,g=c=b,f=","+JU.PT.getQuotedAttribute(a,"atom")+",",a="ID";g=this.selectPanelByPeak(e,g,f);f=this.pd();f.selectSpectrum(e,a,c,!0);this.si.siSendPanelChange();f.addPeakHighlight(g);this.repaint(!0);(null==b||null!=g&&null!=g.getAtoms())&&
this.si.syncToJmol(this.jmolSelect(g))}},"~S");c(c$,"syncPeaksAfterSyncScript",function(){var a=this.currentSource;if(null!=a)try{var b="file="+JU.PT.esc(a.getFilePath()),c=a.getSpectra().get(0).getPeakList(),e=new JU.SB;e.append("[");for(var g=c.size(),a=0;a<g;a++){var f=c.get(a).toString(),f=f+" "+b;e.append(JU.PT.esc(f));0<a&&e.append(",")}e.append("]");this.si.syncToJmol("Peaks: "+e)}catch(h){if(!y(h,Exception))throw h;}});c(c$,"checkFileAlreadyLoaded",function(a){if(this.isClosed())return!1;
if(this.pd().hasFileLoaded(a))return!0;for(var b=this.panelNodes.size();0<=--b;)if(this.panelNodes.get(b).pd().hasFileLoaded(a))return this.si.siSetSelectedPanel(this.panelNodes.get(b).jsvp),!0;return!1},"~S");c(c$,"selectPanelByPeak",function(a,b,c){if(null==this.panelNodes)return null;for(var e=null,g=this.panelNodes.size();0<=--g;)this.panelNodes.get(g).pd().addPeakHighlight(null);e=this.pd().selectPeakByFileIndex(a,b,c);if(null!=e)this.setNode(JSV.common.PanelNode.findNode(this.selectedPanel,
this.panelNodes));else for(g=this.panelNodes.size();0<=--g;){var f=this.panelNodes.get(g);if(null!=(e=f.pd().selectPeakByFileIndex(a,b,c))){this.setNode(f);break}}return e},"~S,~S,~S");c(c$,"processPeakPickEvent",function(a){if(p(a,JSV.common.PeakInfo)){var b=this.pd().findMatchingPeakInfo(a);if(null==b){if(!"ALL".equals(a.getTitle()))return;for(var c=null,e=0;e<this.panelNodes.size();e++)if(null!=(b=this.panelNodes.get(e).pd().findMatchingPeakInfo(a))){c=this.panelNodes.get(e);break}if(null==c)return;
this.setNode(c)}a=b}else this.si.siSetSelectedPanel(a.getSource()),a=a.getPeakInfo();this.pd().addPeakHighlight(a);this.syncToJmol(a);a.isClearAll()?this.repaint(!1):this.pd().selectSpectrum(a.getFilePath(),a.getType(),a.getModel(),!0);this.si.siCheckCallbacks(a.getTitle())},"~O,~B");c(c$,"newStructToJmol",function(a){JU.Logger.info("sending new structure to Jmol:\n"+a);this.si.syncToJmol("struct:"+a)},"~S");c(c$,"syncToJmol",function(a){this.repaint(!0);this.returnFromJmolModel=a.getModel();this.si.syncToJmol(this.jmolSelect(a))},
"JSV.common.PeakInfo");c(c$,"sendPanelChange",function(){var a=this.pd(),b=a.getSpectrum(),c=b.getSelectedPeak();null==c&&(c=b.getModelPeakInfoForAutoSelectOnLoad());null==c&&(c=b.getBasePeakInfo());a.addPeakHighlight(c);JU.Logger.info(Thread.currentThread()+"JSViewer sendFrameChange "+this.selectedPanel);this.syncToJmol(c)});c(c$,"jmolSelect",function(a){var b="IR".equals(a.getType())||"RAMAN".equals(a.getType())?"vibration ON; selectionHalos OFF;":"vibration OFF; selectionhalos "+(null==a.getAtoms()?
"OFF":"ON");return"Select: "+a+' script="'+b+' " sourceID="'+this.pd().getSpectrum().sourceID+'"'},"JSV.common.PeakInfo");c(c$,"getPropertyAsJavaObject",function(a){var b=new java.util.Hashtable;if("SOURCEID".equalsIgnoreCase(a))return b.put(a,null==this.pd()?"":this.pd().getSpectrum().sourceID),b;if(null!=a&&a.startsWith("DATA_"))return b.put(a,""+JSV.common.JSVFileManager.htCorrelationCache.get(a.substring(5))),b;var c=!1;if(null!=a&&a.toUpperCase().startsWith("ALL ")||"all".equalsIgnoreCase(a))a=
a.substring(3).trim(),c=!0;"".equals(a)&&(a=null);var e=this.pd().getInfo(!0,a);if(!c&&null!=e)return e;null!=e&&b.put("current",e);c=new JU.Lst;for(e=0;e<this.panelNodes.size();e++)null!=this.panelNodes.get(e).jsvp&&c.addLast(this.panelNodes.get(e).getInfo(a));b.put("items",c);return b},"~S");c(c$,"getCoordinate",function(){if(!this.isClosed()){var a=this.pd().getClickedCoordinate();if(null!=a)return a.getXVal()+" "+a.getYVal()}return""});c(c$,"fillSpecList",function(a,b,c){var e,g=null,f=a.equalsIgnoreCase("NONE");
if(f||a.equalsIgnoreCase("all"))a="*";if(0>a.indexOf("*")){e=a.$plit(" ");a=new JU.SB;for(var h=0;h<e.length;h++){var k=e[h].indexOf(".");k!=e[h].lastIndexOf(".")&&(e[h]=e[h].substring(0,k+1)+e[h].substring(k+1).$replace(".","_"));a.append(e[h]).append(" ")}a=a.toString().trim()}if(a.equals("*"))e=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes));else if(a.startsWith('"')||a.startsWith("'"))e=JSV.common.ScriptToken.getTokens(a);else if(a=JU.PT.rep(a,"_",
" _ "),a=JU.PT.rep(a,"-"," - "),e=JSV.common.ScriptToken.getTokens(a),g=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes)),0==g.size())return null;var l=this.isClosed()?"1.":JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes).id,l=l.substring(0,l.indexOf(".")+1);a=new JU.SB;for(var m=e.size(),n=null,h=0;h<m;h++){var p=e.get(h),k=NaN,q=-1;h+1<m&&e.get(h+1).equals("*")?(h+=2,k=Double.parseDouble(e.get(h))):h+1<m&&e.get(h+1).equals("_")&&(h+=
2,q=Integer.parseInt(e.get(h)));if(p.equals("-")){null==n&&(n=g.get(0));p=h+1==m?g.get(g.size()-1):e.get(++h);p.contains(".")||(p=l+p);for(k=0;k<g.size()&&!g.get(k).equals(n);)k++;for(k++;k<g.size()&&!n.equals(p);){var s=JSV.common.PanelNode.findNodeById(n=g.get(k++),this.panelNodes);b.addLast(s.pd().getSpectrumAt(0));a.append(",").append(n)}}else if(p.startsWith("'")&&p.endsWith("'")&&(p='"'+JU.PT.trim(p,"'")+'"'),p.startsWith('"'))for(var p=JU.PT.trim(p,'"'),q=this.panelNodes.size(),t=0;t<q;t++){if(s=
this.panelNodes.get(t),null!=s.fileName&&s.fileName.startsWith(p)||null!=s.frameTitle&&s.frameTitle.startsWith(p))this.addSpecToList(s.pd(),k,-1,b,c),a.append(",").append(s.id)}else p.contains(".")||(p=l+p),s=JSV.common.PanelNode.findNodeById(p,this.panelNodes),null!=s&&(n=p,this.addSpecToList(s.pd(),k,q,b,c),a.append(",").append(p),0<q&&a.append(".").appendI(q))}c&&0<b.size()&&(s=JSV.common.PanelNode.findNodeById(a.substring(1),this.panelNodes),null!=s&&(this.setNode(s),b.clear()));return f?"NONE":
0<a.length()?a.toString().substring(1):null},"~S,JU.Lst,~B");c(c$,"addSpecToList",function(a,b,c,e,g){g?(a.getSpectrumAt(0).setUserYFactor(Double.isNaN(b)?1:b),a.addToList(c-1,e)):a.selectFromEntireSet(c-1)},"JSV.common.PanelData,~N,~N,JU.Lst,~B");c(c$,"getSolutionColor",function(a){var b=this.pd().getSpectrum(),c=b.canShowSolutionColor()?JSV.common.JSViewer.getInterface("JSV.common.Visible"):null;return null==c?-1:c.getColour(b,a)},"~B");c(c$,"openDataOrFile",function(a,b,c,e,g,f,h,k){if("NONE".equals(b))return this.close("View*"),
0;this.si.writeStatus("");var l=null,m=null,n=null,p=!1;null!=e&&e.startsWith("cache://")&&(a=Jmol.Cache.get(b=e));if(null!=a)try{n=b,m=l=JSV.common.JSVFileManager.getFullPathName(b)}catch(q){if(!y(q,JSV.exception.JSVException))throw q;}else if(null!=c)p=!0,m=n=l="View"+ ++this.nViews;else if(null!=e)try{this.recentURL=l=(new java.net.URL(JSV.common.JSVFileManager.appletDocumentBase,e,null)).toString(),n=JSV.common.JSVFileManager.getTagName(l)}catch(s){if(y(s,java.net.MalformedURLException))l=this.apiPlatform.newFile(e),
n=l.getName(),m=l=l.getFullPath(),this.recentURL=null;else throw s;}b=-1;if(0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,l))||0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,e)))return p?(--this.nViews,this.setNode(this.panelNodes.get(b))):this.si.writeStatus(l+" is already open"),-1;!h&&!p&&this.close("all");this.si.setCursor(3);try{this.si.siSetCurrentSource(p?JSV.source.JDXSource.createView(c):JSV.source.JDXReader.createJDXSource(JSV.common.JSVFileManager.getBufferedReaderForData(a),l,this.obscureTitleFromUser===
Boolean.TRUE,this.loadImaginary,g,f,this.nmrMaxY))}catch(t){if(y(t,Exception))return alert(t.toString()),this.si.setCursor(0),this.isApplet&&this.selectedPanel.showMessage(t.toString(),"Error Opening File"),-3;throw t;}this.si.setCursor(0);System.gc();null==m?(m=this.currentSource.getFilePath(),null!=m&&(n=m.substring(m.lastIndexOf("/")+1))):this.currentSource.setFilePath(m);null==k&&!p&&(k=m);null!=k&&this.currentSource.setID(k);this.si.siSetLoaded(n,m);a=this.currentSource.getJDXSpectrum(0);if(null==
a)return-4;c=this.currentSource.getSpectra();JSV.common.Spectrum.process(c,this.irMode);c=this.interfaceOverlaid||a.isAutoOverlayFromJmolClick();p||c&&this.currentSource.isCompoundSource?this.combineSpectra(p?e:null):this.splitSpectra();this.pd().taintedAll=!0;p||this.si.siUpdateRecentMenus(l);return 0},"~O,~S,JU.Lst,~S,~N,~N,~B,~S");c(c$,"close",function(a){var b=0,c=null==a?-2:a.indexOf(">");0<c&&(b=JU.PT.parseInt(a.substring(c+1).trim()),a=a.substring(0,c).trim());"*".equals(a)&&(a="all");var e=
"all"===a;if(null==a||0==b&&a.equalsIgnoreCase("all"))this.closeSource(null);else{var g=a.equalsIgnoreCase("views"),c=new JU.Lst;a=a.$replace("\\","/");var f=this.panelNodes.size(),b=f-b;if(a.endsWith("*"))for(a=a.substring(0,a.length-1);0<=--f;)this.panelNodes.get(f).fileName.startsWith(a)&&c.addLast(this.panelNodes.get(f).source);else if(a.equalsIgnoreCase("selected"))for(a=null;0<=--f;)e=this.panelNodes.get(f).source,this.panelNodes.get(f).isSelected&&(null==a||a!==e)&&c.addLast(e),a=e;else if(e||
g||a.equalsIgnoreCase("simulations"))for(a=0;0<=--f&&a<b;){if(e||(g?this.panelNodes.get(f).isView:this.panelNodes.get(f).isSimulation))c.addLast(this.panelNodes.get(f).source),a++}else e=0==a.length?this.currentSource:JSV.common.PanelNode.findSourceByNameOrId(a,this.panelNodes),null!=e&&c.addLast(e);for(f=c.size();0<=--f;)this.closeSource(c.get(f));null==this.selectedPanel&&0<this.panelNodes.size()&&this.si.siSetSelectedPanel(JSV.common.PanelNode.getLastFileFirstNode(this.panelNodes))}},"~S");c(c$,
"load",function(a,b){var c=JSV.common.ScriptToken.getTokens(a),e=c.get(0),g=null,f=0;e.equalsIgnoreCase("ID")&&(g=JU.PT.trimQuotes(c.get(1)),e=c.get(2),f=2);var h=e.equalsIgnoreCase("APPEND"),k=e.equalsIgnoreCase("CHECK");(h||k)&&f++;0<f&&(e=c.get(f));null==b&&(b=this.defaultLoadScript);e.equals("?")?this.openFileFromDialog(h,!1,!1,b):e.equals("http://?")?this.openFileFromDialog(h,!0,!1,null):e.equals("$?")?this.openFileFromDialog(h,!0,!0,null):(e.equalsIgnoreCase("MOL")&&(e="http://SIMULATION/MOL="+
JU.PT.trimQuotes(c.get(++f))),!k&&!h&&(e.equals('""')&&null!=this.currentSource&&(e=this.currentSource.getFilePath()),this.close("all")),e=JU.PT.trimQuotes(e),e.startsWith("$")&&(e="http://SIMULATION/"+e.substring(1)),k=f+1<c.size()?Integer.$valueOf(c.get(++f)).intValue():-1,c=f+1<c.size()?Integer.$valueOf(c.get(++f)).intValue():k,this.si.siOpenDataOrFile(null,null,null,e,k,c,h,b,g))},"~S,~S");c(c$,"combineSpectra",function(a){var b=this.currentSource,c=b.getSpectra(),c=this.si.siGetNewJSVPanel2(c);
c.setTitle(b.getTitle());c.getTitle().equals("")&&(c.getPanelData().setViewTitle(b.getFilePath()),c.setTitle(a));this.si.siSetPropertiesFromPreferences(c,!0);this.spectraTree.createTree(++this.fileCount,b,[c]).getPanelNode().isView=!0;b=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);b.setFrameTitle(a);b.isView=!0;this.autoShowLegend&&1==this.pd().getNumberOfGraphSets()&&b.setLegend(this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null));this.si.siSetMenuEnables(b,!1)},"~S");
c(c$,"closeSource",function(a){for(var b=this.spectraTree.getRootNode(),c=null==a?null:a.getFilePath(),e=new JU.Lst,b=b.children();b.hasMoreElements();){var g=b.nextElement();if(null==c||g.getPanelNode().source.getFilePath().equals(c)){for(var f=g.children();f.hasMoreElements();){var h=f.nextElement();e.addLast(h);this.panelNodes.removeObj(h.getPanelNode())}e.addLast(g);if(null!=c)break}}this.spectraTree.deleteNodes(e);null==a&&(null!=this.currentSource&&this.currentSource.dispose(),this.currentSource=
null,null!=this.selectedPanel&&this.selectedPanel.dispose());this.currentSource===a&&(this.si.siSetSelectedPanel(null),this.si.siSetCurrentSource(null));for(e=c=0;e<this.panelNodes.size();e++)b=JU.PT.parseFloat(this.panelNodes.get(e).id),b>=c+1&&(c=q(Math.floor(b)));this.fileCount=c;System.gc();JU.Logger.checkMemory();this.si.siSourceClosed(a)},"JSV.source.JDXSource");c(c$,"setFrameAndTreeNode",function(a){null==this.panelNodes||(0>a||a>=this.panelNodes.size())||this.setNode(this.panelNodes.get(a))},
"~N");c(c$,"selectFrameNode",function(a){a=JSV.common.PanelNode.findNode(a,this.panelNodes);if(null==a)return null;this.spectraTree.setPath(this.spectraTree.newTreePath(a.treeNode.getPath()));this.setOverlayLegendVisibility(null,!1);return a},"JSV.api.JSVPanel");c(c$,"setSpectrum",function(a){if(0<=a.indexOf(".")){a=JSV.common.PanelNode.findNodeById(a,this.panelNodes);if(null==a)return!1;this.setNode(a)}else{a=JU.PT.parseInt(a);if(0>=a)return this.checkOverlay(),!1;this.setFrameAndTreeNode(a-1)}return!0},
"~S");c(c$,"splitSpectra",function(){for(var a=this.currentSource,b=a.getSpectra(),c=Array(b.size()),e=null,g=0;g<b.size();g++)e=b.get(g),e=this.si.siGetNewJSVPanel(e),this.si.siSetPropertiesFromPreferences(e,!0),c[g]=e;this.spectraTree.createTree(++this.fileCount,a,c);this.si.siGetNewJSVPanel(null);a=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);this.si.siSetMenuEnables(a,!0)});c(c$,"selectedTreeNode",function(a){null!=a&&(a.isLeaf()?this.setNode(a.getPanelNode()):System.out.println("not a leaf"),
this.si.siSetCurrentSource(a.getPanelNode().source))},"JSV.api.JSVTreeNode");c(c$,"dispose",function(){this.fileHelper=null;null!=this.viewDialog&&this.viewDialog.dispose();this.viewDialog=null;null!=this.overlayLegendDialog&&this.overlayLegendDialog.dispose();this.overlayLegendDialog=null;null!=this.jsvpPopupMenu&&(this.jsvpPopupMenu.jpiDispose(),this.jsvpPopupMenu=null);if(null!=this.panelNodes)for(var a=this.panelNodes.size();0<=--a;)this.panelNodes.get(a).dispose(),this.panelNodes.remove(a)});
c(c$,"runScript",function(a){null==this.scriptQueue?this.si.siProcessCommand(a):this.scriptQueue.addLast(a)},"~S");c(c$,"requestRepaint",function(){null!=this.selectedPanel&&this.repaintManager.refresh()});c(c$,"repaintDone",function(){this.repaintManager.repaintDone()});c(c$,"checkOverlay",function(){null!=this.mainPanel&&this.markSelectedPanels(this.panelNodes,this.mainPanel.getCurrentPanelIndex());this.viewDialog=this.getDialog(JSV.common.Annotation.AType.Views,null)});c(c$,"markSelectedPanels",
function(a,b){for(var c=a.size();0<=--c;)a.get(c).isSelected=b==c},"JU.Lst,~N");c(c$,"execOverlayOffsetY",function(a){if(-2147483648==a){if(null==this.selectedPanel)return;a=this.selectedPanel.getInput("Enter a vertical offset in percent for stacked plots","Overlay",""+this.recentStackPercent);a=JU.PT.parseFloat(a);if(Float.isNaN(a))return;a=z(a)}this.recentStackPercent=a;this.parameters.viewOffset=a;this.isClosed()&&this.pd().setYStackOffsetPercent(a)},"~N");c(c$,"execScriptInline",function(a){0<
a.length&&(a=a.substring(6).trim());0==a.length&&(a=this.selectedPanel.getInput("Enter a JSpecView script","Script",this.recentScript));null!=a&&(this.recentScript=a,this.runScriptNow(a))},"~S");c(c$,"setDisplay",function(a){this.apiPlatform.setViewer(this,this.display=a);var b=D(2,0);this.apiPlatform.getFullScreenDimensions(a,b);this.setScreenDimension(b[0],b[1])},"~O");c(c$,"setScreenDimension",function(a,b){b=Math.min(b,this.maximumSize);a=Math.min(a,this.maximumSize);this.dimScreen.width==a&&
this.dimScreen.height==b||this.resizeImage(a,b)},"~N,~N");c(c$,"resizeImage",function(a,b){0<a?(this.dimScreen.width=a,this.dimScreen.height=b):(a=0==this.dimScreen.width?this.dimScreen.width=500:this.dimScreen.width,b=0==this.dimScreen.height?this.dimScreen.height=500:this.dimScreen.height);this.g2d.setWindowParameters(a,b)},"~N,~N");c(c$,"updateJS",function(){null!=this.selectedPanel&&this.selectedPanel.paintComponent(this.apiPlatform.getGraphics(null))});c(c$,"processMouseEvent",function(a,b,c,
e,g){return null!=this.selectedPanel&&this.selectedPanel.processMouseEvent(a,b,c,e,g)},"~N,~N,~N,~N,~N");c(c$,"processTwoPointGesture",function(a){this.isClosed()||this.selectedPanel.processTwoPointGesture(a)},"~A");c(c$,"getApplet",function(){return this.html5Applet});c(c$,"openFileAsyncSpecial",function(a){var b=null==this.currentSource?"NO":this.getDialogManager().getDialogInput(this,"Do you want to append this file? (Answer NO to replace.)","Drag/Drop Action",3,null,null,"YES");null!=b&&(b=b.toLowerCase().startsWith("y")?
"append":"",this.runScript("load "+b+' "'+a+'"'))},"~S,~N");c(c$,"getHeight",function(){return this.dimScreen.height});c(c$,"getWidth",function(){return this.dimScreen.width});c(c$,"getPlatformInterface",function(a){return JSV.common.JSViewer.getInterface("JSV."+(this.isJS?"js2d.Js":"java.Awt")+a)},"~S");c(c$,"getDialogManager",function(){if(null!=this.dialogManager)return this.dialogManager;this.dialogManager=this.getPlatformInterface("DialogManager");return this.dialogManager.set(this)});c(c$,"getDialog",
function(a,b){switch(a){case JSV.common.Annotation.AType.Integration:return JSV.common.JSViewer.getInterface("JSV.dialog.IntegrationDialog").setParams("Integration for "+b,this,b);case JSV.common.Annotation.AType.Measurements:return JSV.common.JSViewer.getInterface("JSV.dialog.MeasurementsDialog").setParams("Measurements for "+b,this,b);case JSV.common.Annotation.AType.PeakList:return JSV.common.JSViewer.getInterface("JSV.dialog.PeakListDialog").setParams("Peak List for "+b,this,b);case JSV.common.Annotation.AType.OverlayLegend:return this.overlayLegendDialog=
JSV.common.JSViewer.getInterface("JSV.dialog.OverlayLegendDialog").setParams(this.pd().getViewTitle(),this,null);case JSV.common.Annotation.AType.Views:return this.viewDialog=JSV.common.JSViewer.getInterface("JSV.dialog.ViewsDialog").setParams("View/Combine/Close Spectra",this,null);default:return null}},"JSV.common.Annotation.AType,JSV.common.Spectrum");c(c$,"show",function(a){this.getDialogManager();if(a.equals("properties"))this.dialogManager.showProperties(null,this.pd().getSpectrum());else if(a.equals("errors"))this.dialogManager.showSourceErrors(null,
this.currentSource);else if(a.equals("source"))null==this.currentSource?0<this.panelNodes.size()&&this.dialogManager.showMessageDialog(null,"Please Select a Spectrum","Select Spectrum",0):this.dialogManager.showSource(this,this.pd().getSpectrum().getFilePath());else if(a.startsWith("solutioncolorfill"))if(0<=a.indexOf("all"))for(var b=this.panelNodes.size();0<=--b;)this.panelNodes.get(b).pd().setSolutionColor(a);else this.pd().setSolutionColor(a);else a.startsWith("solutioncolor")&&(a=this.getSolutionColorStr(0>
a.indexOf("false")),a="background-color:rgb("+a+")'><br />Predicted Solution Colour- RGB("+a+")<br /><br />",this.isJS?this.dialogManager.showMessage(this,"<div style='width:100%;height:100%;"+a+"</div>","Predicted Colour"):this.selectedPanel.showMessage("<html><body style='"+a+"</body></html>","Predicted Colour"))},"~S");c(c$,"getDialogPrint",function(a){if(!this.isJS)try{var b=this.getPlatformInterface("PrintDialog").set(this.offWindowFrame,this.lastPrintLayout,a).getPrintLayout();null!=b&&(this.lastPrintLayout=
b);return b}catch(c){if(!y(c,Exception))throw c;}return new JSV.common.PrintLayout},"~B");c(c$,"setIRmode",function(a){this.irMode=a.equals("AtoT")?JSV.common.Spectrum.IRMode.TO_TRANS:a.equals("TtoA")?JSV.common.Spectrum.IRMode.TO_ABS:JSV.common.Spectrum.IRMode.getMode(a)},"~S");c(c$,"getOptionFromDialog",function(a,b,c){return this.getDialogManager().getOptionFromDialog(null,a,this.selectedPanel,b,c)},"~A,~S,~S");c(c$,"print",function(a){return this.execWrite('PDF "'+a+'"')},"~S");c(c$,"execWrite",
function(a){this.isJS&&null==a&&(a="PDF");a=JSV.common.JSViewer.getInterface("JSV.export.Exporter").write(this,null==a?null:JSV.common.ScriptToken.getTokens(a),!1);this.si.writeStatus(a);return a},"~S");c(c$,"$export",function(a,b){null==a&&(a="XY");var c=this.pd(),e=c.getNumberOfSpectraInCurrentSet();if(-1>b||b>=e)return"Maximum spectrum index (0-based) is "+(e-1)+".";c=0>b?c.getSpectrum():c.getSpectrumAt(b);try{return JSV.common.JSViewer.getInterface("JSV.export.Exporter").exportTheSpectrum(this,
JSV.common.ExportType.getType(a),null,c,0,c.getXYCoords().length-1,null,!1)}catch(g){if(y(g,Exception))return JU.Logger.error(g.toString()),null;throw g;}},"~S,~N");h(c$,"postByteArray",function(a,b){return JSV.common.JSVFileManager.postByteArray(a,b)},"~S,~A");c(c$,"getOutputChannel",function(a,b){for(;a.startsWith("/");)a=a.substring(1);return(new JU.OC).setParams(this,a,!b,null)},"~S,~B");c$.getInterface=c(c$,"getInterface",function(a){try{var b=Z._4Name(a);return null==b?null:b.newInstance()}catch(c){if(y(c,
Exception))return JU.Logger.error("Interface.java Error creating instance for "+a+": \n"+c),null;throw c;}},"~S");c(c$,"showMessage",function(a){null!=this.selectedPanel&&null!=a&&this.selectedPanel.showMessage(a,null)},"~S");c(c$,"openFileFromDialog",function(a,b,c,e){var g=null;c?(g=this.fileHelper.getUrlFromDialog("Enter the name or identifier of a compound",this.recentSimulation),null!=g&&(this.recentSimulation=g,this.load((a?"APPEND ":"")+'"$'+g+'"',e))):b?(g=this.fileHelper.getUrlFromDialog("Enter the URL of a JCAMP-DX File",
null==this.recentURL?this.recentOpenURL:this.recentURL),null!=g&&(this.recentOpenURL=g,this.load((a?"APPEND ":"")+'"'+g+'"',e))):(b=[Boolean.$valueOf(a),e],b=this.fileHelper.showFileOpenDialog(this.mainPanel,b),null!=b&&this.openFile(b.getFullPath(),!a))},"~B,~B,~B,~S");c(c$,"openFile",function(a,b){if(b&&null!=this.panelNodes){var c=JSV.common.PanelNode.findSourceByNameOrId((new java.io.File(a)).getAbsolutePath(),this.panelNodes);null!=c&&this.closeSource(c)}this.si.siOpenDataOrFile(null,null,null,
a,-1,-1,!0,this.defaultLoadScript,null)},"~S,~B");c(c$,"selectPanel",function(a,b){var c=-1;if(null!=b){for(var e=b.size();0<=--e;){var g=b.get(e).jsvp;g===a?c=e:(g.setEnabled(!1),g.setFocusable(!1),g.getPanelData().closeAllDialogsExcept(JSV.common.Annotation.AType.NONE))}this.markSelectedPanels(b,c)}return c},"JSV.api.JSVPanel,JU.Lst");c(c$,"checkAutoIntegrate",function(){this.autoIntegrate&&this.pd().integrateAll(this.parameters)});c(c$,"parseInitScript",function(a){null==a&&(a="");a=new JSV.common.ScriptTokenizer(a,
!0);for(JU.Logger.debugging&&JU.Logger.info("Running in DEBUG mode");a.hasMoreTokens();){var b=a.nextToken(),c=new JSV.common.ScriptTokenizer(b,!1),e=c.nextToken();e.equalsIgnoreCase("SET")&&(e=c.nextToken());var e=e.toUpperCase(),g=JSV.common.ScriptToken.getScriptToken(e),b=JSV.common.ScriptToken.getValue(g,c,b);JU.Logger.info("KEY-> "+e+" VALUE-> "+b+" : "+g);try{switch(g){default:this.parameters.set(null,g,b);break;case JSV.common.ScriptToken.UNKNOWN:break;case JSV.common.ScriptToken.APPLETID:this.fullName=
this.appletName+"__"+(this.appletName=b)+"__";e=null;"undefined"!=typeof Jmol&&(e=Jmol._applets[b]);this.html5Applet=e;break;case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(b);break;case JSV.common.ScriptToken.COMPOUNDMENUON:this.allowCompoundMenu=Boolean.parseBoolean(b);break;case JSV.common.ScriptToken.APPLETREADYCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:this.si.siExecSetCallback(g,
b);break;case JSV.common.ScriptToken.ENDINDEX:this.initialEndIndex=Integer.parseInt(b);break;case JSV.common.ScriptToken.INTERFACE:this.checkOvelayInterface(b);break;case JSV.common.ScriptToken.IRMODE:this.setIRmode(b);break;case JSV.common.ScriptToken.MENUON:this.allowMenu=Boolean.parseBoolean(b);break;case JSV.common.ScriptToken.OBSCURE:null==this.obscureTitleFromUser&&(this.obscureTitleFromUser=Boolean.$valueOf(b));break;case JSV.common.ScriptToken.STARTINDEX:this.initialStartIndex=Integer.parseInt(b);
break;case JSV.common.ScriptToken.SYNCID:this.fullName=this.appletName+"__"+(this.syncID=b)+"__"}}catch(f){if(!y(f,Exception))throw f;}}},"~S");c(c$,"getSolutionColorStr",function(a){a=JU.CU.colorPtFromInt(this.getSolutionColor(a),null);return z(a.x)+","+z(a.y)+","+z(a.z)},"~B");C(c$,"sourceLabel","Original...","FILE_OPEN_OK",0,"FILE_OPEN_ALREADY",-1,"FILE_OPEN_ERROR",-3,"FILE_OPEN_NO_DATA",-4,"OVERLAY_DIALOG",-1,"OVERLAY_OFFSET",99,"PORTRAIT",1,"PAGE_EXISTS",0,"NO_SUCH_PAGE",1,"testScript",'<PeakData  index="1" title="" model="~1.1" type="1HNMR" xMin="3.2915" xMax="3.2965" atoms="15,16,17,18,19,20" multiplicity="" integral="1"> src="JPECVIEW" file="http://SIMULATION/$caffeine"',
"NLEVEL_MAX",100)});n("JSV.common");w(["JSV.common.Annotation","$.Coordinate"],"JSV.common.Measurement",null,function(){c$=t(function(){this.pt2=null;this.value=0;s(this,arguments)},JSV.common,"Measurement",JSV.common.Annotation);K(c$,function(){this.pt2=new JSV.common.Coordinate});c(c$,"setM1",function(a,b,c){this.setA(a,b,c,"",!1,!1,0,6);this.setPt2(this.getXVal(),this.getYVal());return this},"~N,~N,JSV.common.Spectrum");c(c$,"copyM",function(){var a=new JSV.common.Measurement;a.setA(this.getXVal(),
this.getYVal(),this.spec,this.text,!1,!1,this.offsetX,this.offsetY);a.setPt2(this.pt2.getXVal(),this.pt2.getYVal());return a});c(c$,"setPt2",function(a,b){this.spec=a;b&&this.setPt2(this.getXVal(),this.getYVal());return this},"JSV.common.Spectrum,~B");c(c$,"setPt2",function(a,b){this.pt2.setXVal(a);this.pt2.setYVal(b);this.value=Math.abs(a-this.getXVal());this.text=this.spec.setMeasurementText(this)},"~N,~N");c(c$,"getSpectrum",function(){return this.spec});c(c$,"setValue",function(a){this.value=
a;this.text=this.spec.setMeasurementText(this)},"~N");c(c$,"getValue",function(){return this.value});c(c$,"getXVal2",function(){return this.pt2.getXVal()});c(c$,"getYVal2",function(){return this.pt2.getYVal()});h(c$,"addSpecShift",function(a){this.setXVal(this.getXVal()+a);this.pt2.setXVal(this.pt2.getXVal()+a)},"~N");c(c$,"setYVal2",function(a){this.pt2.setYVal(a)},"~N");c(c$,"overlaps",function(a,b){return Math.min(this.getXVal(),this.getXVal2())<Math.max(a,b)&&Math.max(this.getXVal(),this.getXVal2())>
Math.min(a,b)},"~N,~N");h(c$,"toString",function(){return"["+this.getXVal()+","+this.pt2.getXVal()+"]"})});n("JSV.common");w(["JU.Lst","JSV.api.AnnotationData"],"JSV.common.MeasurementData",["JU.AU","$.DF","JSV.common.Annotation","$.Parameters"],function(){c$=t(function(){this.units=this.spec=this.type=null;this.precision=0;this.myParams=null;this.isON=!0;this.key=null;s(this,arguments)},JSV.common,"MeasurementData",JU.Lst,JSV.api.AnnotationData);u(c$,function(a,b){E(this,JSV.common.MeasurementData,
[]);this.type=a;this.spec=b;this.myParams=(new JSV.common.Parameters).setName("MeasurementData")},"JSV.common.Annotation.AType,JSV.common.Spectrum");c(c$,"getMeasurements",function(){return this});h(c$,"getAType",function(){return this.type});h(c$,"getState",function(){return this.isON});h(c$,"setState",function(a){this.isON=a},"~B");c(c$,"setMeasurements",function(){},"JU.Lst");h(c$,"getParameters",function(){return this.myParams});c(c$,"getDataHeader",function(){return JSV.common.MeasurementData.HEADER});
c(c$,"getMeasurementListArray",function(a){this.units=a;var b=this.getMeasurementListArrayReal(a),c=this.spec.isNMR()?4:2;a=this.spec.isHNMR()&&a.equals("ppm")?4:2;for(var e=Array(this.size()),g=this.size();0<=--g;)e[g]=[""+(g+1),JU.DF.formatDecimalDbl(b[g][0],c),JU.DF.formatDecimalDbl(b[g][1],c),JU.DF.formatDecimalDbl(b[g][2],a)];return e},"~S");c(c$,"getMeasurementListArrayReal",function(a){a=this.spec.isNMR()&&a.equalsIgnoreCase("HZ");for(var b=JU.AU.newDouble2(this.size()),c=0,e=this.size();0<=
--e;){var g=this.get(e).getValue();a&&(g*=this.spec.observedFreq);b[c++]=[this.get(e).getXVal(),this.get(e).getXVal2(),g]}return b},"~S");c$.checkParameters=c(c$,"checkParameters",function(a,b){if(0==a.size())return!1;var c=a.getParameters();switch(a.getAType()){case JSV.common.Annotation.AType.PeakList:return b.peakListInterpolation.equals(c.peakListInterpolation)&&b.peakListThreshold==c.peakListThreshold}return!1},"JSV.common.MeasurementData,JSV.common.ColorParameters");h(c$,"getSpectrum",function(){return this.spec});
h(c$,"getData",function(){return this});c(c$,"clear",function(a,b){for(var c=this.size();0<=--c;){var e=this.get(c);(0==e.text.length||e.overlaps(a,b))&&this.remove(c)}},"~N,~N");h(c$,"setSpecShift",function(a){for(var b=this.size();0<=--b;){var c=this.get(b),e=c.getXVal()+a;c.setXVal(e);c.setValue(e);c.text=JU.DF.formatDecimalDbl(e,this.precision)}},"~N");h(c$,"getGraphSetKey",function(){return this.key});h(c$,"setGraphSetKey",function(a){this.key=a},"~S");h(c$,"isVisible",function(){return!0});
c(c$,"getInfo",function(a){a.put("header",this.getDataHeader());a.put("table",this.getMeasurementListArrayReal("ppm"));null!=this.units&&a.put("units",this.units)},"java.util.Map");c$.HEADER=c$.prototype.HEADER=["","start","end","value"]});n("JSV.common");w(["java.lang.Enum","javajs.api.EventManager","java.util.Hashtable","JU.Lst"],"JSV.common.PanelData","java.lang.Boolean $.Double javajs.awt.Font JU.CU JSV.api.JSVGraphics JSV.common.Annotation $.Coordinate $.GraphSet $.JSVFileManager $.JSVersion $.JSViewer $.MeasurementData $.Parameters $.PeakPickEvent $.ScriptToken $.Spectrum $.SubSpecChangeEvent $.ZoomEvent JSV.dialog.JSVDialog JU.Logger".split(" "),
function(){c$=t(function(){this.graphSets=this.jsvp=this.options=this.currentGraphSet=this.listeners=this.vwr=this.g2d0=this.g2d=null;this.currentSplitPoint=0;this.coordsClicked=this.coordClicked=this.thisWidget=null;this.isIntegralDrag=this.drawXAxisLeftToRight=this.shiftPressed=this.ctrlPressed=!1;this.xAxisLeftToRight=!0;this.scalingFactor=1;this.integralShiftMode=0;this.left=60;this.right=50;this.coordStr="";this.startupPinTip="Click to set.";this.title=null;this.endIndex=this.startIndex=this.thisHeight=
this.thisWidth=this.nSpectra=this.clickCount=0;this.titleFontName=this.displayFontName=this.viewTitle=this.commonFilePath=null;this.isPrinting=!1;this.doReset=!0;this.printingFontName=null;this.printGraphPosition="default";this.isLinked=this.display1D=this.titleDrawn=!1;this.spectra=this.printJobTitle=null;this.taintedAll=!0;this.mouseState=this.currentFont=null;this.titleOn=this.gridOn=!1;this.mouseY=this.mouseX=0;this.linking=!1;this.xPixelClicked=0;this.gMain=this.optionsSaved=this.bgcolor=this.BLACK=
this.zoomBoxColor2=this.zoomBoxColor=this.highlightColor=this.unitsColor=this.titleColor=this.scaleColor=this.plotAreaColor=this.peakTabColor=this.integralPlotColor=this.gridColor=this.coordinatesColor=null;s(this,arguments)},JSV.common,"PanelData",null,javajs.api.EventManager);K(c$,function(){this.listeners=new JU.Lst;this.options=new java.util.Hashtable});u(c$,function(a,b){this.vwr=b;this.jsvp=a;this.g2d=this.g2d0=b.g2d;this.BLACK=this.g2d.getColor1(0);this.highlightColor=this.g2d.getColor4(255,
0,0,200);this.zoomBoxColor=this.g2d.getColor4(150,150,100,130);this.zoomBoxColor2=this.g2d.getColor4(150,100,100,130)},"JSV.api.JSVPanel,JSV.common.JSViewer");c(c$,"addListener",function(a){this.listeners.contains(a)||this.listeners.addLast(a)},"JSV.api.PanelListener");c(c$,"getCurrentGraphSet",function(){return this.currentGraphSet});c(c$,"dispose",function(){this.jsvp=null;for(var a=0;a<this.graphSets.size();a++)this.graphSets.get(a).dispose();this.listeners=this.options=this.thisWidget=this.coordsClicked=
this.coordClicked=this.currentGraphSet=this.currentFont=this.graphSets=null});c(c$,"setViewTitle",function(a){this.viewTitle=a},"~S");c(c$,"getViewTitle",function(){return null==this.viewTitle?this.getTitle():this.viewTitle});c(c$,"getInfo",function(a,b){var c=new java.util.Hashtable,e=null;if(a)return this.currentGraphSet.getInfo(b,this.getCurrentSpectrumIndex());for(var g,e=this.options.entrySet().iterator();e.hasNext()&&((g=e.next())||1);)JSV.common.Parameters.putInfo(b,c,g.getKey().name(),g.getValue());
JSV.common.Parameters.putInfo(b,c,"type",this.getSpectrumAt(0).getDataType());JSV.common.Parameters.putInfo(b,c,"title",this.title);JSV.common.Parameters.putInfo(b,c,"nSets",Integer.$valueOf(this.graphSets.size()));e=new JU.Lst;for(g=this.graphSets.size();0<=--g;)e.addLast(this.graphSets.get(g).getInfo(b,-1));c.put("sets",e);return c},"~B,~S");c(c$,"setBooleans",function(a,b){if(null==b)for(var c,e=a.getBooleans().entrySet().iterator();e.hasNext()&&((c=e.next())||1);)this.setBooleans(a,c.getKey());
else this.setBoolean(b,a.getBoolean(b))},"JSV.common.Parameters,JSV.common.ScriptToken");c(c$,"setBoolean",function(a,b){this.taintedAll=!0;if(a===JSV.common.ScriptToken.REVERSEPLOT)this.currentGraphSet.setReversePlot(b);else switch(this.options.put(a,Boolean.$valueOf(b)),a){case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:this.doReset=!0}},"JSV.common.ScriptToken,~B");c(c$,"getBoolean",function(a){if(a===JSV.common.ScriptToken.REVERSEPLOT)return this.currentGraphSet.reversePlot;
if(null==this.options)return!1;a=this.options.get(a);return null!=a&&p(a,Boolean)&&a===Boolean.TRUE},"JSV.common.ScriptToken");c(c$,"setFontName",function(a,b){switch(a){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.displayFontName=b;break;case JSV.common.ScriptToken.TITLEFONTNAME:this.titleFontName=b}null!=b&&this.options.put(a,b)},"JSV.common.ScriptToken,~S");c(c$,"getDisplay1D",function(){return this.display1D});c(c$,"initOne",function(a){this.spectra=new JU.Lst;this.spectra.addLast(a);this.initMany(this.spectra,
0,0)},"JSV.common.Spectrum");c(c$,"initMany",function(a,b,c){this.startIndex=b;this.endIndex=c;this.nSpectra=a.size();this.spectra=a;this.commonFilePath=a.get(0).getFilePath();for(b=0;b<this.nSpectra;b++)if(!this.commonFilePath.equalsIgnoreCase(a.get(b).getFilePath())){this.commonFilePath=null;break}this.setGraphSets(JSV.common.PanelData.LinkMode.NONE)},"JU.Lst,~N,~N");c(c$,"setGraphSets",function(a){this.graphSets=JSV.common.GraphSet.createGraphSetsAndSetLinkMode(this,this.jsvp,this.spectra,this.startIndex,
this.endIndex,a);this.currentGraphSet=this.graphSets.get(0);this.title=this.getSpectrum().getTitleLabel()},"JSV.common.PanelData.LinkMode");c(c$,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.graphSets.size()&&null==(b=this.graphSets.get(c).findMatchingPeakInfo(a));c++);return b},"JSV.common.PeakInfo");c(c$,"integrateAll",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).integrate(-1,a)},"JSV.common.ColorParameters");c(c$,"getNumberOfGraphSets",function(){return this.graphSets.size()});
c(c$,"getTitle",function(){return this.title});c(c$,"refresh",function(){this.doReset=!0});c(c$,"addAnnotation",function(a){a=this.currentGraphSet.addAnnotation(a,this.getTitle());null!=a&&(this.title=a)},"JU.Lst");c(c$,"addPeakHighlight",function(a){for(var b=0;b<this.graphSets.size();b++)this.graphSets.get(b).addPeakHighlight(a)},"JSV.common.PeakInfo");c(c$,"selectPeakByFileIndex",function(a,b,c){var e=this.currentGraphSet.selectPeakByFileIndex(a,b,c);if(null==e)for(var g=this.graphSets.size();0<=
--g&&!(this.graphSets.get(g)!==this.currentGraphSet&&null!=(e=this.graphSets.get(g).selectPeakByFileIndex(a,b,c))););return e},"~S,~S,~S");c(c$,"setPlotColors",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).setPlotColors(a)},"~A");c(c$,"selectSpectrum",function(a,b,c,e){e&&this.currentGraphSet.selectSpectrum(a,b,c);if("ID".equals(b))this.jumpToSpectrumIndex(this.getCurrentSpectrumIndex(),!0);else for(e=0;e<this.graphSets.size();e++)this.graphSets.get(e)!==this.currentGraphSet&&
this.graphSets.get(e).selectSpectrum(a,b,c)},"~S,~S,~S,~B");c(c$,"hasFileLoaded",function(a){for(var b=this.graphSets.size();0<=--b;)if(this.graphSets.get(b).hasFileLoaded(a))return!0;return!1},"~S");c(c$,"clearAllView",function(){for(var a=this.graphSets.size();0<=--a;)this.graphSets.get(a).resetViewCompletely()});c(c$,"drawGraph",function(a,b,c,e,g,f){var h;this.gMain=a;this.display1D=!this.isLinked&&this.getBoolean(JSV.common.ScriptToken.DISPLAY1D);var k=40,l=50,m=this.isPrinting||this.doReset||
this.thisWidth!=e||this.thisHeight!=g;m&&(this.taintedAll=!0);this.taintedAll&&this.g2d.fillBackground(c,this.bgcolor);b!==a&&(this.g2d.fillBackground(b,null),a!==c&&this.g2d.fillBackground(a,null),this.g2d.setStrokeBold(a,!1));this.isPrinting?(k*=3,l*=3,this.scalingFactor=10,h=!1):(this.scalingFactor=1,h=this.getBoolean(JSV.common.ScriptToken.COORDINATESON),this.titleOn=this.getBoolean(JSV.common.ScriptToken.TITLEON),this.gridOn=this.getBoolean(JSV.common.ScriptToken.GRIDON));this.titleDrawn=this.doReset=
!1;this.thisWidth=e;this.thisHeight=g;for(var n=this.graphSets.size();0<=--n;)this.graphSets.get(n).drawGraphSet(a,b,c,e,g,this.left,this.right,k,l,m,this.taintedAll);this.titleOn&&(!this.titleDrawn&&this.taintedAll)&&this.drawTitle(a,g*this.scalingFactor,e*this.scalingFactor,this.getDrawTitle(this.isPrinting));h&&null!=this.coordStr&&this.drawCoordinates(b,k,this.thisWidth-this.right,k-20);f&&this.taintedAll&&(c=null!=this.commonFilePath?this.commonFilePath:1==this.graphSets.size()&&null!=this.currentGraphSet.getTitle(!0)?
this.getSpectrum().getFilePath():null,null!=c&&this.printFilePath(a,this.left,g,c));this.isPrinting&&this.printVersion(a,g);this.taintedAll=this.isPrinting||a===b},"~O,~O,~O,~N,~N,~B");c(c$,"drawCoordinates",function(a,b,c,e){this.g2d.setGraphicsColor(a,this.coordinatesColor);b=this.setFont(a,this.jsvp.getWidth(),0,12,!0);this.g2d.drawString(a,this.coordStr,c-b.stringWidth(this.coordStr),e)},"~O,~N,~N,~N");c(c$,"setFont",function(a,b,c,e,g){return this.g2d.setFont(a,this.getFont(a,b,c,e,g))},"~O,~N,~N,~N,~B");
c(c$,"printFilePath",function(a,b,c,e){b*=this.scalingFactor;c*=this.scalingFactor;0<e.indexOf("?")&&(e=e.substring(e.indexOf("?")+1));e=e.substring(e.lastIndexOf("/")+1);e=e.substring(e.lastIndexOf("\\")+1);this.g2d.setGraphicsColor(a,this.BLACK);var g=this.setFont(a,1E3,0,9,!0);b!=this.left*this.scalingFactor&&(b-=g.stringWidth(e));this.g2d.drawString(a,e,b,c-g.getHeight())},"~O,~N,~N,~S");c(c$,"printVersion",function(a,b){this.g2d.setGraphicsColor(a,this.BLACK);var c=this.setFont(a,100,0,12,!0),
e=this.jsvp.getApiPlatform().getDateFormat(null)+" JSpecView "+JSV.common.JSVersion.VERSION_SHORT,g=c.stringWidth(e);this.g2d.drawString(a,e,(this.thisWidth-this.right)*this.scalingFactor-g,b*this.scalingFactor-3*c.getHeight())},"~O,~N");c(c$,"drawTitle",function(a,b,c,e){e=e.$replace("\n"," ");var g=this.getFont(a,c,this.isPrinting||this.getBoolean(JSV.common.ScriptToken.TITLEBOLDON)?1:0,14,!0),f=g.stringWidth(e);f>c&&(g=q(14*c/f),10>g&&(g=10),g=this.getFont(a,c,this.isPrinting||this.getBoolean(JSV.common.ScriptToken.TITLEBOLDON)?
1:0,g,!0));this.g2d.setGraphicsColor(a,this.titleColor);this.setCurrentFont(this.g2d.setFont(a,g));this.g2d.drawString(a,e,this.isPrinting?this.left*this.scalingFactor:5,b-q(g.getHeight()*(this.isPrinting?2:0.5)))},"~O,~N,~N,~S");c(c$,"setCurrentFont",function(a){this.currentFont=a},"javajs.awt.Font");c(c$,"getFontHeight",function(){return this.currentFont.getAscent()});c(c$,"getStringWidth",function(a){return this.currentFont.stringWidth(a)},"~S");c(c$,"selectFromEntireSet",function(a){for(var b=
0,c=0;b<this.graphSets.size();b++)if(-2147483648==a)this.graphSets.get(b).setSelected(-1);else for(var e=this.graphSets.get(b).spectra,g=0;g<e.size();g++,c++)(0>a||a==c)&&this.graphSets.get(b).setSelected(g)},"~N");c(c$,"addToList",function(a,b){for(var c=0;c<this.spectra.size();c++)(0>a||c==a)&&b.addLast(this.spectra.get(c))},"~N,JU.Lst");c(c$,"scaleSelectedBy",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).scaleSelectedBy(a)},"~N");c(c$,"setCurrentGraphSet",function(a,
b,c){b=1<a.nSplit?a.getSplitPoint(b):a.getCurrentSpectrumIndex();var e=this.currentGraphSet!==a,g=e||this.currentSplitPoint!=b;this.currentGraphSet=a;this.currentSplitPoint=b;(e||1<a.nSplit&&g)&&this.setSpectrum(b,!0);if(!e){e=a.checkSpectrumClickedEvent(this.mouseX,this.mouseY,c);if(!e)return;this.currentSplitPoint=b=a.getCurrentSpectrumIndex();this.setSpectrum(b,!0)}this.jumpToSpectrumIndex(b,e||1<a.nSplit&&g)},"JSV.common.GraphSet,~N,~N");c(c$,"jumpToSpectrum",function(a){a=this.currentGraphSet.getSpectrumIndex(a);
this.jumpToSpectrumIndex(a,!0)},"JSV.common.Spectrum");c(c$,"jumpToSpectrumIndex",function(a,b){if(!(0>a||a>=this.currentGraphSet.nSpectra)){this.currentSplitPoint=a;b&&this.setSpectrum(this.currentSplitPoint,1<this.currentGraphSet.nSplit);var c=this.getSpectrum();this.notifySubSpectrumChange(c.getSubIndex(),c)}},"~N,~B");c(c$,"splitStack",function(a){this.currentGraphSet.splitStack(this.graphSets,a)},"~B");c(c$,"getNumberOfSpectraInCurrentSet",function(){return this.currentGraphSet.nSpectra});c(c$,
"getSourceID",function(){return this.getSpectrumAt(0).sourceID});c(c$,"getStartingPointIndex",function(a){return this.currentGraphSet.viewData.getStartingPointIndex(a)},"~N");c(c$,"getEndingPointIndex",function(a){return this.currentGraphSet.viewData.getEndingPointIndex(a)},"~N");c(c$,"haveSelectedSpectrum",function(){return this.currentGraphSet.haveSelectedSpectrum()});c(c$,"getShowAnnotation",function(a){return this.currentGraphSet.getShowAnnotation(a,-1)},"JSV.common.Annotation.AType");c(c$,"showAnnotation",
function(a,b){this.currentGraphSet.setShowAnnotation(a,b)},"JSV.common.Annotation.AType,Boolean");c(c$,"setYStackOffsetPercent",function(a){this.currentGraphSet.yStackOffsetPercent=a},"~N");c(c$,"setSpectrum",function(a,b){this.currentGraphSet.setSpectrum(a,b)},"~N,~B");c(c$,"getSpectrum",function(){return this.currentGraphSet.getSpectrum()});c(c$,"setSpecForIRMode",function(a){this.taintedAll=!0;var b=this.currentGraphSet.getSpectrum();this.currentGraphSet.setSpectrumJDX(a);for(var c=0;c<this.spectra.size();c++)this.spectra.get(c)===
b&&this.spectra.set(c,a)},"JSV.common.Spectrum");c(c$,"isShowAllStacked",function(){return this.currentGraphSet.showAllStacked});c(c$,"getCurrentSpectrumIndex",function(){return this.currentGraphSet.getCurrentSpectrumIndex()});c(c$,"getSpectrumAt",function(a){return null==this.currentGraphSet?null:this.currentGraphSet.getSpectrumAt(a)},"~N");c(c$,"addHighlight",function(a,b,c,e,g,f,h,k){(null==a?this.currentGraphSet:a).addHighlight(b,c,e,this.g2d.getColor4(g,f,h,k))},"JSV.common.GraphSet,~N,~N,JSV.common.Spectrum,~N,~N,~N,~N");
c(c$,"removeHighlight",function(a,b){this.currentGraphSet.removeHighlight(a,b)},"~N,~N");c(c$,"removeAllHighlights",function(){this.currentGraphSet.removeAllHighlights()});c(c$,"setZoom",function(a,b,c,e){this.currentGraphSet.setZoom(a,b,c,e);this.taintedAll=this.doReset=!0;this.notifyListeners(new JSV.common.ZoomEvent)},"~N,~N,~N,~N");c(c$,"resetView",function(){this.currentGraphSet.resetView()});c(c$,"previousView",function(){this.currentGraphSet.previousView()});c(c$,"nextView",function(){this.currentGraphSet.nextView()});
c(c$,"getSelectedIntegral",function(){return this.currentGraphSet.getSelectedIntegral()});c(c$,"advanceSubSpectrum",function(a){this.currentGraphSet.advanceSubSpectrum(a)},"~N");c(c$,"setSelectedIntegral",function(a){this.currentGraphSet.setSelectedIntegral(a)},"~N");c(c$,"scaleYBy",function(a){this.currentGraphSet.scaleYBy(a)},"~N");c(c$,"toPeak",function(a){this.currentGraphSet.toPeak(a)},"~N");c(c$,"getClickedCoordinate",function(){return this.coordClicked});c(c$,"getPickedCoordinates",function(a,
b){return JSV.common.Coordinate.getPickedCoordinates(this.coordsClicked,this.coordClicked,a,b)},"JSV.common.Coordinate,JSV.common.Coordinate");c(c$,"shiftSpectrum",function(a,b){return this.currentGraphSet.shiftSpectrum(a,b)},"~N,~N");c(c$,"findX",function(a,b){this.currentGraphSet.setXPointer(a,b)},"JSV.common.Spectrum,~N");c(c$,"setXPointers",function(a,b,c,e){this.currentGraphSet.setXPointer(a,b);this.currentGraphSet.setXPointer2(c,e)},"JSV.common.Spectrum,~N,JSV.common.Spectrum,~N");c(c$,"isCurrentGraphSet",
function(a){return a===this.currentGraphSet},"JSV.common.GraphSet");c(c$,"repaint",function(){this.jsvp.doRepaint(!1)});c(c$,"setToolTipText",function(a){this.jsvp.setToolTipText(a)},"~S");c(c$,"setHighlightColor",function(a){this.setColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR,a)},"javajs.api.GenericColor");c(c$,"getInput",function(a,b,c){return this.jsvp.getInput(a,b,c)},"~S,~S,~S");c(c$,"getFont",function(a,b,c,e,g){e*=this.scalingFactor;g?400>b&&(e=b*e/400):250>b&&(e=b*e/250);b=this.jsvp.getFontFaceID(this.isPrinting?
this.printingFontName:this.displayFontName);return this.currentFont=javajs.awt.Font.createFont3D(b,c,e,e,this.jsvp.getApiPlatform(),a)},"~O,~N,~N,~N,~B");c(c$,"notifySubSpectrumChange",function(a,b){this.notifyListeners(new JSV.common.SubSpecChangeEvent(a,null==b?null:b.getTitleLabel()))},"~N,JSV.common.Spectrum");c(c$,"notifyPeakPickedListeners",function(a){null==a&&(a=new JSV.common.PeakPickEvent(this.jsvp,this.coordClicked,this.getSpectrum().getAssociatedPeakInfo(this.xPixelClicked,this.coordClicked)));
this.notifyListeners(a)},"JSV.common.PeakPickEvent");c(c$,"notifyListeners",function(a){for(var b=0;b<this.listeners.size();b++)null!=this.listeners.get(b)&&this.listeners.get(b).panelEvent(a)},"~O");c(c$,"escapeKeyPressed",function(a){this.currentGraphSet.escapeKeyPressed(a)},"~B");c(c$,"hasFocus",function(){return this.jsvp.hasFocus()});c(c$,"isMouseUp",function(){return this.mouseState===JSV.common.PanelData.Mouse.UP});c(c$,"doMouseMoved",function(a,b){this.mouseX=a;this.mouseY=b;this.mouseState=
JSV.common.PanelData.Mouse.UP;this.clickCount=0;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&c.mouseMovedEvent(a,b)},"~N,~N");c(c$,"doMousePressed",function(a,b){this.mouseState=JSV.common.PanelData.Mouse.DOWN;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&(this.setCurrentGraphSet(c,b,0),this.clickCount=++this.clickCount%3,c.checkWidgetEvent(a,b,!0))},"~N,~N");c(c$,"doMouseDragged",function(a,b){this.isIntegralDrag=(new Boolean(this.isIntegralDrag|this.ctrlPressed)).valueOf();
this.mouseState=JSV.common.PanelData.Mouse.DOWN;JSV.common.GraphSet.findGraphSet(this.graphSets,a,b)===this.currentGraphSet&&(this.currentGraphSet.checkWidgetEvent(a,b,!1),this.currentGraphSet.mouseMovedEvent(a,b))},"~N,~N");c(c$,"doMouseReleased",function(a,b,c){this.mouseState=JSV.common.PanelData.Mouse.UP;!(null==this.thisWidget&&null==this.currentGraphSet.pendingMeasurement)&&c&&(this.currentGraphSet.mouseReleasedEvent(a,b),this.thisWidget=null,this.isIntegralDrag=!1,this.integralShiftMode=0)},
"~N,~N,~B");c(c$,"doMouseClicked",function(a,b,c){var e=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=e&&(this.setCurrentGraphSet(e,b,this.clickCount),e.mouseClickedEvent(a,b,this.clickCount,c),this.repaint())},"~N,~N,~B");c(c$,"hasCurrentMeasurements",function(a){return this.currentGraphSet.hasCurrentMeasurement(a)},"JSV.common.Annotation.AType");c(c$,"getDialog",function(a){return this.currentGraphSet.getDialog(a,-1)},"JSV.common.Annotation.AType");c(c$,"addDialog",function(a,b,c){this.currentGraphSet.addDialog(a,
b,c)},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");c(c$,"getPeakListing",function(a,b){null!=a&&this.currentGraphSet.getPeakListing(-1,a,!0);this.currentGraphSet.setPeakListing(b)},"JSV.common.Parameters,Boolean");c(c$,"checkIntegral",function(a,b){this.currentGraphSet.checkIntegral(a,b)},"JSV.common.Parameters,~S");c(c$,"setIntegrationRatios",function(a){this.currentGraphSet.setIntegrationRatios(a)},"~S");c(c$,"getView",function(){return this.currentGraphSet.getCurrentView()});c(c$,"closeAllDialogsExcept",
function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).closeDialogsExcept(a)},"JSV.common.Annotation.AType");c(c$,"removeDialog",function(a){this.currentGraphSet.removeDialog(a)},"JSV.dialog.JSVDialog");c(c$,"normalizeIntegral",function(){var a=this.getSelectedIntegral();if(null!=a){var b=a.text;0==b.length&&(b=""+a.getValue());a=this.getInput("Enter a new value for this integral","Normalize Integral",b);try{this.setSelectedIntegral(Double.parseDouble(a))}catch(c){if(!y(c,Exception))throw c;
}}});c(c$,"getDrawTitle",function(a){var b=null;a?b=this.printJobTitle:1==this.nSpectra?b=this.getSpectrum().getPeakTitle():null!=this.viewTitle?(null!=this.currentGraphSet.getTitle(!1)&&(b=this.getSpectrum().getPeakTitle()),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();0<=b.indexOf("\n")&&(b=b.substring(0,b.indexOf("\n")).trim());return b},"~B");c(c$,"getPrintJobTitle",function(a){var b=null;1==this.nSpectra?b=this.getSpectrum().getTitle():null!=this.viewTitle?(1==this.graphSets.size()&&
(b=this.currentGraphSet.getTitle(a)),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();0<=b.indexOf("\n")?b=b.substring(0,b.indexOf("\n")).trim():b.startsWith("$")&&(b=b.substring(1));return b},"~B");c(c$,"linkSpectra",function(a){a===JSV.common.PanelData.LinkMode.ALL&&(a=2==this.nSpectra?JSV.common.PanelData.LinkMode.AB:3==this.nSpectra?JSV.common.PanelData.LinkMode.ABC:JSV.common.PanelData.LinkMode.NONE);a!==JSV.common.PanelData.LinkMode.NONE&&a.toString().length!=this.nSpectra||this.setGraphSets(a)},
"JSV.common.PanelData.LinkMode");c(c$,"doZoomLinked",function(a,b,c,e,g,f){if(!this.linking){this.linking=!0;for(var h=a.getSpectrumAt(0),k=this.graphSets.size();0<=--k;){var l=this.graphSets.get(k);l!==a&&JSV.common.Spectrum.areXScalesCompatible(h,this.graphSets.get(k).getSpectrumAt(0),!1,!0)&&l.doZoom(b,0,c,0,f,!1,g,!1,e)}this.linking=!1}},"JSV.common.GraphSet,~N,~N,~B,~B,~B");c(c$,"clearLinkViews",function(a){if(!this.linking){this.linking=!0;for(var b=a.getSpectrum(),c=this.graphSets.size();0<=
--c;){var e=this.graphSets.get(c);e!==a&&JSV.common.Spectrum.areXScalesCompatible(b,this.graphSets.get(c).getSpectrum(),!1,!0)&&e.clearViews()}this.linking=!1}},"JSV.common.GraphSet");c(c$,"setlinkedXMove",function(a,b,c){if(!this.linking){this.linking=!0;for(var e=a.getSpectrum(),g=this.graphSets.size();0<=--g;){var f=this.graphSets.get(g);f!==a&&JSV.common.Spectrum.areXScalesCompatible(e,this.graphSets.get(g).getSpectrum(),!1,!0)&&null==f.imageView&&(c?f.setXPixelMovedTo(1.7976931348623157E308,
b,0,0):f.setXPixelMovedTo(b,1.7976931348623157E308,0,0))}this.linking=!1}},"JSV.common.GraphSet,~N,~B");c(c$,"set2DCrossHairsLinked",function(a,b,c,e){for(var g=this.graphSets.size();0<=--g;){var f=this.graphSets.get(g);f!==a&&f.set2DXY(b,c,e)}},"JSV.common.GraphSet,~N,~N,~B");c(c$,"dialogsToFront",function(a){this.currentGraphSet.dialogsToFront(a)},"JSV.common.Spectrum");c(c$,"setColor",function(a,b){null!=b&&this.options.put(a,JU.CU.toRGBHexString(b));switch(a){case JSV.common.ScriptToken.BACKGROUNDCOLOR:this.jsvp.setBackgroundColor(this.bgcolor=
b);this.taintedAll=!0;break;case JSV.common.ScriptToken.COORDINATESCOLOR:this.coordinatesColor=b;break;case JSV.common.ScriptToken.GRIDCOLOR:this.gridColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:this.highlightColor=b;255==this.highlightColor.getOpacity255()&&this.highlightColor.setOpacity255(150);break;case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:this.integralPlotColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.PEAKTABCOLOR:this.peakTabColor=b;this.taintedAll=
!0;break;case JSV.common.ScriptToken.PLOTCOLOR:for(var c=this.graphSets.size();0<=--c;)this.graphSets.get(c).setPlotColor0(b);this.taintedAll=!0;break;case JSV.common.ScriptToken.PLOTAREACOLOR:this.plotAreaColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.SCALECOLOR:this.scaleColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.TITLECOLOR:this.titleColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.UNITSCOLOR:this.unitsColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.ZOOMBOXCOLOR:this.zoomBoxColor=
b;break;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:this.zoomBoxColor2=b;break;default:JU.Logger.warn("AwtPanel --- unrecognized color: "+a)}},"JSV.common.ScriptToken,javajs.api.GenericColor");c(c$,"getColor",function(a){switch(a){default:return JU.Logger.error("awtgraphset missing color "+a),this.BLACK;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:return this.zoomBoxColor2;case JSV.common.ScriptToken.ZOOMBOXCOLOR:return this.zoomBoxColor;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:return this.highlightColor;
case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:return this.integralPlotColor;case JSV.common.ScriptToken.GRIDCOLOR:return this.gridColor;case JSV.common.ScriptToken.PEAKTABCOLOR:return this.peakTabColor;case JSV.common.ScriptToken.PLOTAREACOLOR:return this.plotAreaColor;case JSV.common.ScriptToken.SCALECOLOR:return this.scaleColor;case JSV.common.ScriptToken.TITLECOLOR:return this.titleColor;case JSV.common.ScriptToken.UNITSCOLOR:return this.unitsColor}},"JSV.common.ScriptToken");c(c$,"getOverlayLegendData",
function(){for(var a=this.currentGraphSet.nSpectra,b=Array(a),c=this.getSpectrumAt(0).getFilePath(),e=this.getSpectrumAt(a-1).getFilePath(),c=!c.equals(e),e=0;e<a;e++){var g=Array(3),f=this.getSpectrumAt(e);this.title=f.getTitle();c&&(this.title=JSV.common.JSVFileManager.getTagName(f.getFilePath())+" - "+this.title);f=this.getCurrentPlotColor(e);g[0]=new Integer(e+1);g[1]=f;g[2]=" "+this.title;b[e]=g}return b});c(c$,"setColorOrFont",function(a,b){if(null==b){for(var c,e=a.elementColors.entrySet().iterator();e.hasNext()&&
((c=e.next())||1);)this.setColorOrFont(a,c.getKey());this.setColorOrFont(a,JSV.common.ScriptToken.DISPLAYFONTNAME);this.setColorOrFont(a,JSV.common.ScriptToken.TITLEFONTNAME)}else{switch(b){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.setFontName(b,a.displayFontName);return;case JSV.common.ScriptToken.TITLEFONTNAME:this.setFontName(b,a.titleFontName);return}this.setColor(b,a.getElementColor(b))}},"JSV.common.ColorParameters,JSV.common.ScriptToken");c(c$,"getCurrentPlotColor",function(a){return this.currentGraphSet.getPlotColor(a)},
"~N");c(c$,"setPrint",function(a,b){null==a?(this.options.putAll(this.optionsSaved),this.optionsSaved=null):(this.printJobTitle=a.title,this.printingFontName=b,this.printGraphPosition=a.position,this.optionsSaved=new java.util.Hashtable,this.optionsSaved.putAll(this.options),this.gridOn=a.showGrid,this.titleOn=a.showTitle,this.setBoolean(JSV.common.ScriptToken.XSCALEON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.XUNITSON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.YSCALEON,a.showYScale),
this.setBoolean(JSV.common.ScriptToken.YUNITSON,a.showYScale))},"JSV.common.PrintLayout,~S");c(c$,"showDialog",function(a){var b=this.getDialog(a);this.closeAllDialogsExcept(a);if(null!=b&&p(b,JSV.dialog.JSVDialog))return b.reEnable();var c=this.getCurrentSpectrumIndex();if(0>c)return this.jsvp.showMessage("To enable "+a+" first select a spectrum by clicking on it.",""+a),null;var e=this.getSpectrum(),g=this.vwr.getDialog(a,e);null==b&&a===JSV.common.Annotation.AType.Measurements&&(b=new JSV.common.MeasurementData(JSV.common.Annotation.AType.Measurements,
e));null!=b&&g.setData(b);this.addDialog(c,a,g);g.reEnable();return g},"JSV.common.Annotation.AType");c(c$,"printPdf",function(a,b){var c=!b.layout.equals("landscape");this.print(a,c?b.imageableHeight:b.imageableWidth,c?b.imageableWidth:b.imageableHeight,b.imageableX,b.imageableY,b.paperHeight,b.paperWidth,c,0)},"JSV.api.JSVGraphics,JSV.common.PrintLayout");c(c$,"print",function(a,b,c,e,g,f,h,k,l){this.g2d=this.g2d0;if(0==l)return this.isPrinting=!0,l=!1,p(a,JSV.api.JSVGraphics)&&(this.g2d=a,a=this.gMain),
this.printGraphPosition.equals("default")?k?(b=450,c=280):(b=280,c=450):this.printGraphPosition.equals("fit to page")?l=!0:k?(b=450,c=280,e=q(q(h-c)/2),g=q(q(f-b)/2)):(b=280,c=450,g=q(q(h-280)/2),e=q(q(f-450)/2)),this.g2d.translateScale(a,e,g,0.1),this.taintedAll=!0,this.drawGraph(a,a,a,q(c),q(b),l),this.isPrinting=!1,0;this.isPrinting=!1;return 1},"~O,~N,~N,~N,~N,~N,~N,~B,~N");h(c$,"keyPressed",function(a,b){if(this.isPrinting)return!1;this.checkKeyControl(a,!0);switch(a){case 27:case 127:case 8:return this.escapeKeyPressed(27!=
a),this.isIntegralDrag=!1,this.repaint(),!0}var c=0,e=!1;if(0==b)switch(a){case 37:case 39:this.doMouseMoved(39==a?++this.mouseX:--this.mouseX,this.mouseY);this.repaint();e=!0;break;case 33:case 34:c=33==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;e=!0;break;case 40:case 38:e=40==a?-1:1,null==this.getSpectrumAt(0).getSubSpectra()?this.notifySubSpectrumChange(e,null):(this.advanceSubSpectrum(e),this.repaint()),e=!0}else if(this.checkMod(a,2))switch(a){case 40:case 38:case 45:case 61:c=61==
a||38==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;e=!0;break;case 37:case 39:this.toPeak(39==a?1:-1),e=!0}0!=c&&(this.scaleYBy(c),this.repaint());return e},"~N,~N");h(c$,"keyReleased",function(a){this.isPrinting||this.checkKeyControl(a,!1)},"~N");h(c$,"keyTyped",function(a,b){if(this.isPrinting)return!1;switch(a){case "n":if(0!=b)break;this.normalizeIntegral();return!0;case 26:if(2!=b)break;this.previousView();this.repaint();return!0;case 25:if(2!=b)break;this.nextView();this.repaint();return!0}return!1},
"~N,~N");h(c$,"mouseAction",function(a,b,c,e,g,f){if(!this.isPrinting)switch(a){case 4:if(!this.checkMod(f,16))break;this.doMousePressed(c,e);break;case 5:this.doMouseReleased(c,e,this.checkMod(f,16));this.repaint();break;case 1:this.doMouseDragged(c,e);this.repaint();break;case 0:this.jsvp.getFocusNow(!1);if(0!=(f&28)){this.doMouseDragged(c,e);this.repaint();break}this.doMouseMoved(c,e);null!=this.coordStr&&this.repaint();break;case 2:if(this.checkMod(f,4)){this.jsvp.showMenu(c,e);break}this.ctrlPressed=
!1;this.doMouseClicked(c,e,this.updateControlPressed(f))}},"~N,~N,~N,~N,~N,~N");c(c$,"checkMod",function(a,b){return(a&b)==b},"~N,~N");c(c$,"checkKeyControl",function(a,b){switch(a){case 17:case 157:this.ctrlPressed=b;break;case 16:this.shiftPressed=b}},"~N,~B");c(c$,"updateControlPressed",function(a){return this.ctrlPressed=(new Boolean(this.ctrlPressed|(this.checkMod(a,2)||this.checkMod(a,20)))).valueOf()},"~N");h(c$,"mouseEnterExit",function(a,b,c,e){if(e)this.thisWidget=null,this.isIntegralDrag=
!1,this.integralShiftMode=0;else try{this.jsvp.getFocusNow(!1)}catch(g){if(y(g,Exception))System.out.println("pd "+this+" cannot focus");else throw g;}},"~N,~N,~N,~B");c(c$,"setSolutionColor",function(a){var b=0<=a.indexOf("none"),c=0>a.indexOf("false");if(0>a.indexOf("all"))b=b?-1:this.vwr.getSolutionColor(c),this.getSpectrum().setFillColor(-1==b?null:this.vwr.parameters.getColor1(b));else{a=JSV.common.JSViewer.getInterface("JSV.common.Visible");for(var e=this.graphSets.size();0<=--e;)this.graphSets.get(e).setSolutionColor(a,
b,c)}},"~S");c(c$,"setIRMode",function(a,b){for(var c=this.graphSets.size();0<=--c;)this.graphSets.get(c).setIRMode(a,b)},"JSV.common.Spectrum.IRMode,~S");G(self.c$);c$=B(JSV.common.PanelData,"LinkMode",Enum);c$.getMode=c(c$,"getMode",function(a){if(a.equals("*"))return JSV.common.PanelData.LinkMode.ALL;for(var b,c=0,e=JSV.common.PanelData.LinkMode.values();c<e.length&&((b=e[c])||1);c++)if(b.name().equalsIgnoreCase(a))return b;return JSV.common.PanelData.LinkMode.NONE},"~S");v(c$,"ALL",0,[]);v(c$,
"NONE",1,[]);v(c$,"AB",2,[]);v(c$,"ABC",3,[]);c$=F();G(self.c$);c$=B(JSV.common.PanelData,"Mouse",Enum);v(c$,"UP",0,[]);v(c$,"DOWN",1,[]);c$=F();C(c$,"defaultPrintHeight",450,"defaultPrintWidth",280,"topMargin",40,"bottomMargin",50,"leftMargin",60,"rightMargin",50)});n("JSV.common");w(null,"JSV.common.PanelNode",["JU.SB","JSV.common.Parameters"],function(){c$=t(function(){this.legend=this.id=this.jsvp=this.fileName=this.source=this.treeNode=null;this.isSimulation=this.isView=this.isSelected=!1;this.frameTitle=
null;s(this,arguments)},JSV.common,"PanelNode");u(c$,function(a,b,c,e){this.id=a;this.source=c;this.fileName=b;this.isSimulation=0<=c.getFilePath().indexOf("http://SIMULATION/");this.jsvp=e;null!=e&&(this.pd().getSpectrumAt(0).setId(a),this.frameTitle=e.getTitle())},"~S,~S,JSV.source.JDXSource,JSV.api.JSVPanel");c(c$,"setTreeNode",function(a){this.treeNode=a},"JSV.api.JSVTreeNode");c(c$,"getTreeNode",function(){return this.treeNode});c(c$,"dispose",function(){this.source.dispose();null!=this.jsvp&&
this.jsvp.dispose();this.legend=this.jsvp=this.source=null});c(c$,"pd",function(){return this.jsvp.getPanelData()});c(c$,"getSpectrum",function(){return this.pd().getSpectrum()});c(c$,"setLegend",function(a){null!=this.legend&&this.legend.dispose();return this.legend=a},"JSV.dialog.JSVDialog");h(c$,"toString",function(){return(null==this.id?"":this.id+": ")+(null==this.frameTitle?this.fileName:this.frameTitle)});c$.findSourceByNameOrId=c(c$,"findSourceByNameOrId",function(a,b){for(var c=b.size();0<=
--c;){var e=b.get(c);if(a.equals(e.id)||a.equalsIgnoreCase(e.source.getFilePath()))return e.source}for(c=b.size();0<=--c;)if(e=b.get(c),a.equals(e.fileName))return e.source;return null},"~S,JU.Lst");c$.findNodeById=c(c$,"findNodeById",function(a,b){if(null!=a)for(var c=b.size();0<=--c;)if(a.equals(b.get(c).id)||a.equals(b.get(c).frameTitle))return b.get(c);return null},"~S,JU.Lst");c$.findNode=c(c$,"findNode",function(a,b){for(var c=b.size();0<=--c;)if(b.get(c).jsvp===a)return b.get(c);return null},
"JSV.api.JSVPanel,JU.Lst");c$.getSpectrumListAsString=c(c$,"getSpectrumListAsString",function(a){for(var b=new JU.SB,c=0;c<a.size();c++){var e=a.get(c);e.isView||b.append(" ").append(e.id)}return b.toString().trim()},"JU.Lst");c$.isOpen=c(c$,"isOpen",function(a,b){if(null!=b)for(var c=a.size();0<=--c&&!b.equals(a.get(c).source.getFilePath())&&!b.equals(a.get(c).frameTitle););return-1},"JU.Lst,~S");c(c$,"setFrameTitle",function(a){this.frameTitle=a},"~S");c$.getLastFileFirstNode=c(c$,"getLastFileFirstNode",
function(a){for(var b=a.size(),c=0==b?null:a.get(b-1),b=b-1;0<=--b&&a.get(b).source===c.source;)c=a.get(b);return null==c?null:c.jsvp},"JU.Lst");c(c$,"getInfo",function(a){var b=this.pd().getInfo(!1,a);JSV.common.Parameters.putInfo(a,b,"panelId",this.id);JSV.common.Parameters.putInfo(a,b,"panelFileName",this.fileName);JSV.common.Parameters.putInfo(a,b,"panelSource",this.source.getFilePath());return b},"~S")});n("JSV.common");w(null,"JSV.common.Parameters",["java.lang.Boolean","java.util.Hashtable",
"JSV.common.ScriptToken"],function(){c$=t(function(){this.name=null;this.integralMinY=0.1;this.integralRange=50;this.integralOffset=30;this.integralDrawAll=!1;this.viewOffset=0;this.peakListThreshold=NaN;this.peakListInterpolation="parabolic";this.precision=2;this.htBooleans=null;s(this,arguments)},JSV.common,"Parameters");u(c$,function(){this.htBooleans=new java.util.Hashtable;this.setBoolean(JSV.common.ScriptToken.TITLEON,!0);this.setBoolean(JSV.common.ScriptToken.ENABLEZOOM,!0);this.setBoolean(JSV.common.ScriptToken.DISPLAY2D,
!0);this.setBoolean(JSV.common.ScriptToken.COORDINATESON,!0);this.setBoolean(JSV.common.ScriptToken.GRIDON,!0);this.setBoolean(JSV.common.ScriptToken.XSCALEON,!0);this.setBoolean(JSV.common.ScriptToken.YSCALEON,!0);this.setBoolean(JSV.common.ScriptToken.XUNITSON,!0);this.setBoolean(JSV.common.ScriptToken.YUNITSON,!0)});c(c$,"setName",function(a){this.name=a;return this},"~S");c(c$,"getBooleans",function(){return this.htBooleans});c(c$,"setBoolean",function(a,b){this.htBooleans.put(a,Boolean.$valueOf(b));
return b},"JSV.common.ScriptToken,~B");c(c$,"getBoolean",function(a){return Boolean.TRUE===this.htBooleans.get(a)},"JSV.common.ScriptToken");c$.isTrue=c(c$,"isTrue",function(a){return 0==a.length||Boolean.parseBoolean(a)},"~S");c$.getTFToggle=c(c$,"getTFToggle",function(a){return a.equalsIgnoreCase("TOGGLE")?null:JSV.common.Parameters.isTrue(a)?Boolean.TRUE:Boolean.FALSE},"~S");c(c$,"setP",function(a,b,c){switch(b){default:return;case JSV.common.ScriptToken.COORDINATESON:case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:case JSV.common.ScriptToken.ENABLEZOOM:case JSV.common.ScriptToken.GRIDON:case JSV.common.ScriptToken.REVERSEPLOT:case JSV.common.ScriptToken.TITLEON:case JSV.common.ScriptToken.TITLEBOLDON:case JSV.common.ScriptToken.XSCALEON:case JSV.common.ScriptToken.XUNITSON:case JSV.common.ScriptToken.YSCALEON:case JSV.common.ScriptToken.YUNITSON:c=
JSV.common.Parameters.getTFToggle(c);if(null!=c){this.setBoolean(b,c.booleanValue());break}if(null==a)return;c=!a.getBoolean(b);switch(b){case JSV.common.ScriptToken.XSCALEON:this.setBoolean(JSV.common.ScriptToken.XUNITSON,c);a.setBoolean(JSV.common.ScriptToken.XUNITSON,c);break;case JSV.common.ScriptToken.YSCALEON:this.setBoolean(JSV.common.ScriptToken.YUNITSON,c),a.setBoolean(JSV.common.ScriptToken.YUNITSON,c)}this.setBoolean(b,c)}null!=a&&a.setBooleans(this,b)},"JSV.common.PanelData,JSV.common.ScriptToken,~S");
c$.isMatch=c(c$,"isMatch",function(a,b){return null==a||b.equalsIgnoreCase(a)},"~S,~S");c$.putInfo=c(c$,"putInfo",function(a,b,c,e){null!=e&&JSV.common.Parameters.isMatch(a,c)&&b.put(null==a?c:a,e)},"~S,java.util.Map,~S,~O")});n("JSV.common");w(["JSV.common.MeasurementData"],"JSV.common.PeakData",["java.lang.Double","JU.DF","JSV.common.Coordinate","$.PeakPick"],function(){c$=t(function(){this.maxY=this.minY=this.thresh=0;s(this,arguments)},JSV.common,"PeakData",JSV.common.MeasurementData);c(c$,"getThresh",
function(){return this.thresh});h(c$,"getDataHeader",function(){return this.spec.isHNMR()?JSV.common.PeakData.HNMR_HEADER:["peak",this.spec.getXUnits(),this.spec.getYUnits()]});h(c$,"getMeasurementListArray",function(){for(var a=Array(this.size()),b=[-1E100,1E100,1E100],c,e=0,g=this.size();0<=--g;e++)c=this.spec.getPeakListArray(this.get(g),b,this.maxY),a[e]=2==c.length?[""+(e+1),JU.DF.formatDecimalDbl(c[0],2),JU.DF.formatDecimalDbl(c[1],4)]:[""+(e+1),JU.DF.formatDecimalDbl(c[0],4),JU.DF.formatDecimalDbl(c[1],
4),JU.DF.formatDecimalDbl(c[2],2),0==c[3]?"":JU.DF.formatDecimalDbl(c[3],2),0==c[4]?"":JU.DF.formatDecimalDbl(c[4],2),0==c[5]?"":JU.DF.formatDecimalDbl(c[5],2)];return a},"~S");h(c$,"getMeasurementListArrayReal",function(){for(var a=X(this.size(),0),b=[-1E100,1E100,1E100],c=0,e=this.size();0<=--e;c++)a[c]=this.spec.getPeakListArray(this.get(e),b,this.maxY);return a},"~S");c(c$,"getInfo",function(a){a.put("interpolation",this.myParams.peakListInterpolation);a.put("threshold",Double.$valueOf(this.myParams.peakListThreshold));
R(this,JSV.common.PeakData,"getInfo",[a])},"java.util.Map");c(c$,"setPeakList",function(a,b,c){this.precision=-2147483648==b?this.spec.getDefaultUnitPrecision():b;var e=this.spec.getXYCoords();if(!(3>e.length)){this.clear();null!=a&&(this.myParams.peakListInterpolation=a.peakListInterpolation,this.myParams.peakListThreshold=a.peakListThreshold);a=this.myParams.peakListInterpolation.equals("parabolic");var g=this.spec.isInverted();this.minY=c.minYOnScale;this.maxY=c.maxYOnScale;var f=c.minXOnScale;
c=c.maxXOnScale;this.thresh=this.myParams.peakListThreshold;Double.isNaN(this.thresh)&&(this.thresh=this.myParams.peakListThreshold=(this.minY+this.maxY)/2);var h=0,k=[e[0].getYVal(),h=e[1].getYVal(),0],l=0;if(g)for(g=2;g<e.length;g++){var m=k[g%3]=e[g].getYVal();if(h<this.thresh&&(k[(g-2)%3]>h&&h<m)&&(h=a?JSV.common.Coordinate.parabolicInterpolation(e,g-1):e[g-1].getXVal(),h>=f||h<=c))if(h=(new JSV.common.PeakPick).setValue(h,m,this.spec,null,0),this.addLast(h),100==++l)break;h=m}else for(g=2;g<
e.length;g++){m=k[g%3]=e[g].getYVal();if(h>this.thresh&&(k[(g-2)%3]<h&&h>m)&&(h=a?JSV.common.Coordinate.parabolicInterpolation(e,g-1):e[g-1].getXVal(),h>=f&&h<=c&&(h=(new JSV.common.PeakPick).setValue(h,m,this.spec,JU.DF.formatDecimalDbl(h,b),h),this.addLast(h),100==++l)))break;h=m}}},"JSV.common.Parameters,~N,JSV.common.ScaleData");c$.HNMR_HEADER=c$.prototype.HNMR_HEADER="peak shift/ppm intens shift/hz diff/hz 2-diff 3-diff".split(" ")});n("JSV.common");w(null,"JSV.common.PeakInfo",["JU.PT"],function(){c$=
t(function(){this.px1=this.px0=this.yMax=this.yMin=this.xMax=this.xMin=0;this.atomKey=this._match=this.spectrum=this.id=this.atoms=this.model=this.title=this.filePathForwardSlash=this.file=this.index=this.type2=this.type=this.stringInfo=null;s(this,arguments)},JSV.common,"PeakInfo");u(c$,function(){});u(c$,function(a){this.stringInfo=a;this.type=JU.PT.getQuotedAttribute(a,"type");null==this.type&&(this.type="");this.type=this.type.toUpperCase();var b=this.type.indexOf("/");this.type2=0>b?"":JSV.common.PeakInfo.fixType(this.type.substring(this.type.indexOf("/")+
1));this.type=0<=b?JSV.common.PeakInfo.fixType(this.type.substring(0,b))+"/"+this.type2:JSV.common.PeakInfo.fixType(this.type);this.id=JU.PT.getQuotedAttribute(a,"id");this.index=JU.PT.getQuotedAttribute(a,"index");this.file=JU.PT.getQuotedAttribute(a,"file");System.out.println("pi file="+this.file);this.filePathForwardSlash=null==this.file?null:this.file.$replace("\\","/");this.model=JU.PT.getQuotedAttribute(a,"model");a.contains('baseModel=""')||(this.atoms=JU.PT.getQuotedAttribute(a,"atoms"));
this.atomKey=","+this.atoms+",";this.title=JU.PT.getQuotedAttribute(a,"title");this._match=JU.PT.getQuotedAttribute(a,"_match");this.xMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMax"));this.xMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMin"));this.yMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMax"));this.yMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMin"))},"~S");c(c$,"isClearAll",function(){return null==this.spectrum});c(c$,"getType",function(){return this.type});c(c$,"getAtoms",
function(){return this.atoms});c(c$,"getXMax",function(){return this.xMax});c(c$,"getXMin",function(){return this.xMin});c(c$,"getYMin",function(){return this.yMin});c(c$,"getYMax",function(){return this.yMax});c(c$,"getX",function(){return(this.xMax+this.xMin)/2});c(c$,"getMatch",function(){return this._match});c$.fixType=c(c$,"fixType",function(a){return a.equals("HNMR")?"1HNMR":a.equals("CNMR")?"13CNMR":a},"~S");h(c$,"toString",function(){return this.stringInfo});c(c$,"getIndex",function(){return this.index});
c(c$,"getTitle",function(){return this.title});c(c$,"checkFileIndex",function(a,b,c){return null!=c?0<=this.atomKey.indexOf(c):b.equals(this.index)&&(a.equals(this.file)||a.equals(this.filePathForwardSlash))},"~S,~S,~S");c(c$,"checkFileTypeModel",function(a,b,c){return a.equals(this.file)&&this.checkModel(c)&&this.type.endsWith(b)},"~S,~S,~S");c(c$,"checkTypeModel",function(a,b){return this.checkType(a)&&this.checkModel(b)},"~S,~S");c(c$,"checkModel",function(a){return null!=a&&a.equals(this.model)},
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function(){return this.file});c(c$,"autoSelectOnLoad",function(){return this.type.startsWith("GC")});c(c$,"setPixelRange",function(a,b){this.px0=a;this.px1=b},"~N,~N");c(c$,"checkRange",function(a,b){return(2147483647!=a?this.px0<=a&&this.px1>=a:b>=this.xMin&&b<=this.xMax)?Math.abs(b-this.getX()):1E100},"~N,~N");c(c$,"getXPixel",function(){return q((this.px0+this.px1)/2)});c$.nullPeakInfo=c$.prototype.nullPeakInfo=new JSV.common.PeakInfo});n("JSV.common");w(["JSV.common.Measurement"],"JSV.common.PeakPick",
null,function(){c$=B(JSV.common,"PeakPick",JSV.common.Measurement);c(c$,"setValue",function(a,b,c,e,g){null==e?(this.set(a,b),this.setPt2(c,!1)):(this.setA(a,b,c,e,!1,!1,0,6),this.value=g,this.setPt2(this.getXVal(),this.getYVal()));return this},"~N,~N,JSV.common.Spectrum,~S,~N")});n("JSV.common");w(["java.util.EventObject"],"JSV.common.PeakPickEvent",null,function(){c$=t(function(){this.peakInfo=this.coord=null;s(this,arguments)},JSV.common,"PeakPickEvent",java.util.EventObject);u(c$,function(a,b,
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null;this.maxY=this.minY=this.maxYOnScale=this.minYOnScale=0;this.isShiftZoomedY=!1;this.spectrumScaleFactor=1;this.spectrumYRef=0;this.userYFactor=1;this.yFactorForScale=this.xFactorForScale=this.maxY2D=this.minY2D=this.firstY=0;s(this,arguments)},JSV.common,"ScaleData");K(c$,function(){this.precision=D(2,0);this.exportPrecision=D(2,0);this.steps=X(2,0);this.minorTickCounts=D(2,0)});u(c$,function(){});u(c$,function(a,b){this.startDataPointIndex=a;this.endDataPointIndex=b;this.pointCount=this.endDataPointIndex-
this.startDataPointIndex+1},"~N,~N");u(c$,function(a,b,c,e,g){this.minX=JSV.common.Coordinate.getMinX(a,b,c);this.maxX=JSV.common.Coordinate.getMaxX(a,b,c);this.minY=JSV.common.Coordinate.getMinY(a,b,c);0<this.minY&&!e&&(this.minY=0);this.maxY=JSV.common.Coordinate.getMaxY(a,b,c);this.setScale(e,g)},"~A,~N,~N,~B,~B");c(c$,"setScale",function(a,b){this.setXScale();a||(this.maxXOnScale+=this.steps[0]/2);this.setYScale(this.minY,this.maxY,!0,b)},"~B,~B");c(c$,"setXScale",function(){var a=this.setScaleParams(this.minX,
this.maxX,0);this.firstX=Math.floor(this.minX/a)*a;1E-4<Math.abs((this.minX-this.firstX)/a)&&(this.firstX+=a);this.minXOnScale=this.minX;this.maxXOnScale=this.maxX});c(c$,"isYZeroOnScale",function(){return this.minYOnScale<this.spectrumYRef&&this.maxYOnScale>this.spectrumYRef});c(c$,"setYScale",function(a,b,c,e){0==a&&0==b&&(b=1);this.isShiftZoomedY&&(a=this.minYOnScale,b=this.maxYOnScale);var g=this.setScaleParams(a,b,1),f=e?g/2:g/4;e=e?g/4:g/2;this.isShiftZoomedY||(this.minYOnScale=0==a?0:c?f*Math.floor(a/
f):a,this.maxYOnScale=c?e*Math.ceil(1.05*b/e):b);this.firstY=0==a?0:Math.floor(a/f)*f;if(0>this.minYOnScale&&0<this.maxYOnScale)for(this.firstY=0;this.firstY-g>this.minYOnScale;)this.firstY-=g;else 0!=this.minYOnScale&&1E-4<Math.abs((a-this.firstY)/f)&&(this.firstY+=f);c&&(this.initMinYOnScale=this.minYOnScale,this.initMaxYOnScale=this.maxYOnScale,this.initMinY=a,this.initMaxY=b)},"~N,~N,~B,~B");c(c$,"scale2D",function(a){var b=this.maxY-this.minY;1==a?(this.maxY=this.initMaxY,this.minY=this.initMinY):
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1-b):3<b?-2:0;a=0;for(e=Math.pow(10,e-b);e>JSV.common.ScaleData.NTICKS[a];)a++;this.steps[c]=Math.pow(10,b)*JSV.common.ScaleData.NTICKS[a];e=Math.log10(Math.abs(100010*this.steps[c]));b=e-Math.floor(e);for(a=e=0;a<JSV.common.ScaleData.NTICKS.length;a++)if(0.001>Math.abs(b-JSV.common.ScaleData.LOGTICKS[a])){e=JSV.common.ScaleData.NTICKS[a];break}this.minorTickCounts[c]=e;return this.steps[c]},"~N,~N,~N");c(c$,"isInRangeX",function(a){return a>=this.minX&&a<=this.maxX},"~N");c(c$,"addSpecShift",function(a){this.specShift+=
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Double.$valueOf(this.maxYOnScale));a.put("minorTickCountX",Integer.$valueOf(this.minorTickCounts[0]));a.put("xStep",Double.$valueOf(this.steps[0]));return a},"java.util.Map");c(c$,"setMinMax",function(a,b,c,e){this.minX=a;this.maxX=b;this.minY=c;this.maxY=e},"~N,~N,~N,~N");c(c$,"toX",function(a,b,c){return this.toXScaled(a,b,c,this.xFactorForScale)},"~N,~N,~B");c(c$,"toX0",function(a,b,c,e){return this.toXScaled(a,c,e,(this.maxXOnScale-this.minXOnScale)/(c-b))},"~N,~N,~N,~B");c(c$,"toXScaled",function(a,
b,c,e){return c?this.maxXOnScale-(b-a)*e:this.minXOnScale+(b-a)*e},"~N,~N,~B,~N");c(c$,"toPixelX",function(a,b,c,e){return this.toPixelXScaled(a,b,c,e,this.xFactorForScale)},"~N,~N,~N,~B");c(c$,"toPixelX0",function(a,b,c,e){return this.toPixelXScaled(a,b,c,e,(this.maxXOnScale-this.minXOnScale)/(c-b))},"~N,~N,~N,~B");c(c$,"toPixelXScaled",function(a,b,c,e,g){a=q((a-this.minXOnScale)/g);return e?b+a:c-a},"~N,~N,~N,~B,~N");c(c$,"toY",function(a,b){return this.maxYOnScale+(b-a)*this.yFactorForScale},
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e=(e-this.thisScale.minYOnScale)/(this.thisScale.maxYOnScale-this.thisScale.minYOnScale);c=Array(this.scaleData.length);for(var g=0;g<this.scaleData.length;g++)c[g]=0<=a&&g!=a?this.scaleData[g]:new JSV.common.ScaleData;JSV.common.ScaleData.copyScaleFactors(this.scaleData,c);JSV.common.ScaleData.copyYScales(this.scaleData,c);for(g=0;g<this.scaleData.length;g++)0<=a&&g!=a||(c[g].isShiftZoomedY=!0,c[g].minYOnScale=this.scaleData[g].minYOnScale*(1-b)+b*this.scaleData[g].maxYOnScale,c[g].maxYOnScale=this.scaleData[g].minYOnScale*
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break;case JSV.common.Annotation.AType.NONE:return;case JSV.common.Annotation.AType.PeakList:this.skipCreate||(this.setThreshold(NaN),this.createData());this.skipCreate=!1;break;case JSV.common.Annotation.AType.Views:this.vwr.parameters.viewOffset=Double.parseDouble(a[0])}this.loadData();this.checkEnables();this.jsvp.doRepaint(!0)}catch(e){if(!y(e,Exception))throw e;}},"~A");c(c$,"done",function(){null!=this.jsvp&&null!=this.$spec&&this.jsvp.getPanelData().removeDialog(this);null!=this.xyData&&this.xyData.setState(this.isON);
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this.xyData&&this.createData();a=this.xyData.getMeasurementListArray(null);b=this.xyData.getDataHeader();c=[40,65,50,50,50,50,50];this.createTable(a,b,c);this.setTableSelectionEnabled(!0);break;case JSV.common.Annotation.AType.OverlayLegend:b=["No.","Plot Color","Title"],a=this.vwr.selectedPanel.getPanelData().getOverlayLegendData(),c=[30,60,250],this.createTable(a,b,c),this.setTableSelectionEnabled(!0)}});c(c$,"createData",function(){switch(this.type){case JSV.common.Annotation.AType.Integration:this.xyData=
new JSV.common.IntegralData(this.$spec,this.myParams);this.iSelected=-1;break;case JSV.common.Annotation.AType.PeakList:try{var a=Double.parseDouble(this.dialog.getText(this.txt1));this.myParams.peakListThreshold=a;this.myParams.peakListInterpolation=this.dialog.getSelectedItem(this.combo1).toString();this.myParams.precision=this.precision;var b=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,this.$spec);b.setPeakList(this.myParams,this.precision,this.jsvp.getPanelData().getView());this.xyData=
b;this.loadData()}catch(c){if(!y(c,Exception))throw c;}}});c(c$,"setPrecision",function(a){this.precision=this.formatOptions[a]},"~N");c(c$,"tableSelect",function(a){if("true".equals(this.getField(a,"adjusting")))this.iColSelected=this.iRowSelected=-1,System.out.println("adjusting"+a);else{var b=JU.PT.parseInt(this.getField(a,"index"));switch("ROW COL ROWCOL".indexOf(this.getField(a,"selector"))){case 8:this.iColSelected=JU.PT.parseInt(this.getField(a,"index2"));case 0:this.iRowSelected=b;System.out.println("r set to "+
b);break;case 4:this.iColSelected=b,System.out.println("c set to "+b)}0<=this.iColSelected&&0<=this.iRowSelected&&this.tableCellSelect(this.iRowSelected,this.iColSelected)}},"~S");c(c$,"getField",function(a,b){a+="&";var c="&"+b+"=",e=a.indexOf(c);return 0>e?null:a.substring(e+c.length,a.indexOf("&",e+1))},"~S,~S")});n("JSV.exception");w(["java.lang.Exception"],"JSV.exception.JSVException",null,function(){c$=B(JSV.exception,"JSVException",Exception)});n("JSV.js2d");c$=B(JSV.js2d,"Display");c$.getFullScreenDimensions=
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"~O,~N,~N");c$.toIntARGB=c(c$,"toIntARGB",function(a){for(var b=q(a.length/4),c=D(b,0),e=0,g=0;e<b;g++)c[e++]=a[g++]<<16|a[g++]<<8|a[g++]|4278190080;return c},"~A");c$.fromIntARGB=c(c$,"fromIntARGB",function(a,b){for(var c=b.length>>2,e=0,g=0;e<c;e++)b[g++]=a[e]>>16&255,b[g++]=a[e]>>8&255,b[g++]=a[e]&255,b[g++]=255},"~A,~A");c$.getTextPixels=c(c$,"getTextPixels",function(a,b,c,e,g,f){c.fillStyle="#000000";c.fillRect(0,0,e,g);c.fillStyle="#FFFFFF";c.font=b.font;c.fillText(a,0,f);return JSV.js2d.Image.grabPixels(c,
e,g)},"~S,javajs.awt.Font,~O,~N,~N,~N");c$.allocateRgbImage=c(c$,"allocateRgbImage",function(a,b,c,e,g,f){null==f&&(f={width:a,height:b});f.buf32=c},"~N,~N,~A,~N,~B,~O");c$.getStaticGraphics=c(c$,"getStaticGraphics",function(a){return JSV.js2d.Image.getGraphics(a)},"~O,~B");c$.getGraphics=c(c$,"getGraphics",function(a){return a.getContext("2d")},"~O");c$.drawImage=c(c$,"drawImage",function(a,b,c,e){this.fromIntARGB(b.buf32,b.buf8);a.putImageData(b.imgdata,c,e)},"~O,~O,~N,~N,~N,~N");n("JSV.js2d");
w(["javajs.api.GenericFileInterface"],"JSV.js2d.JsFile",["JU.PT","JSV.common.JSVFileManager"],function(){c$=t(function(){this.fullName=this.name=null;s(this,arguments)},JSV.js2d,"JsFile",null,javajs.api.GenericFileInterface);c$.newFile=c(c$,"newFile",function(a){return new JSV.js2d.JsFile(a)},"~S");u(c$,function(a){this.name=a.$replace("\\","/");this.fullName=a;!this.fullName.startsWith("/")&&0>JSV.common.JSVFileManager.urlTypeIndex(a)&&(this.fullName=JSV.common.JSVFileManager.jsDocumentBase+"/"+
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e=c[1];this.vwr.si.siOpenDataOrFile(String.instantialize(b),"cache://"+a,null,null,-1,-1,g,null,null);null!=e&&this.vwr.runScript(e)}},"~S,~O,~A");h(c$,"getUrlFromDialog",function(a,b){return prompt(a,b)},"~S,~S")});n("JSV.js2d");c$=B(JSV.js2d,"JsFont");c$.newFont=c(c$,"newFont",function(a,b,c,e,g){a=a.equals("Monospaced")?"Courier":a.startsWith("Sans")?"Sans-Serif":"Serif";return(b?"bold ":"")+(c?"italic ":"")+e+g+" "+a},"~S,~B,~B,~N,~S");c$.getFontMetrics=c(c$,"getFontMetrics",function(a,b){b.font!=
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a.setYLabel(this.yLabel);a.setXYCoords(this.xyCoords);a.setContinuous(this.continuous);a.setIncreasing(this.xIncreases);a.observedFreq=this.observedFreq;a.observedNucl=this.observedNucl;a.offset=this.offset;a.dataPointNum=this.dataPointNum;a.shiftRefType=this.shiftRefType;a.$isHZtoPPM=this.$isHZtoPPM;a.numDim=this.numDim;a.nucleusX=this.nucleusX;a.nucleusY=this.nucleusY;a.freq2dX=this.freq2dX;a.freq2dY=this.freq2dY;a.setFilePath(this.filePath);a.nH=this.nH},"JSV.source.JDXDataObject");c(c$,"getTypeLabel",
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c(c$,"getPeakListArray",function(a,b,c){var e=a.getXVal();a=a.getYVal();this.isNMR()&&(a/=c);c=Math.abs(e-b[0]);b[0]=e;var g=c+b[1];b[1]=c;var f=g+b[2];b[2]=g;return this.isNMR()?[e,a,e*this.observedFreq,20<c*this.observedFreq?0:c*this.observedFreq,20<g*this.observedFreq?0:g*this.observedFreq,20<f*this.observedFreq?0:f*this.observedFreq]:[e,a]},"JSV.common.Measurement,~A,~N");C(c$,"ERROR",1.7976931348623157E308,"SCALE_NONE",0,"SCALE_TOP",1,"SCALE_BOTTOM",2,"SCALE_TOP_BOTTOM",3,"gyroData",[1,42.5774806,
2,6.53590131,3,45.4148,3,32.436,6,6.2661,7,16.5483,9,5.9842,10,4.5752,11,13.663,13,10.70839657,14,3.07770646,15,4.3172657,17,5.7742,19,40.07757016,21,3.3631,23,11.26952167,25,2.6083,27,11.1031,29,8.4655,31,17.2514409,33,3.2717,35,4.1765,37,3.4765,37,5.819,39,3.46,39,1.9893,40,2.4737,41,1.0919,43,2.8688,45,10.3591,47,2.4041,49,2.4048,50,4.2505,51,11.2133,53,2.4115,55,10.5763,57,1.3816,59,10.077,61,3.8114,63,11.2982,65,12.103,67,2.6694,69,10.2478,71,13.0208,73,1.4897,75,7.315,77,8.1571,79,10.7042,81,
11.5384,83,1.6442,85,4.1254,87,13.9811,87,1.8525,89,2.0949,91,3.9748,93,10.4523,95,2.7874,97,2.8463,99,9.6294,99,1.9553,101,2.1916,103,1.3477,105,1.957,107,1.7331,109,1.9924,111,9.0692,113,9.4871,113,9.3655,115,9.3856,115,14.0077,117,15.261,119,15.966,121,10.2551,123,5.5532,123,11.2349,125,13.5454,127,8.5778,129,11.8604,131,3.5159,133,5.6234,135,4.2582,137,4.7634,138,5.6615,139,6.0612,137,4.88,139,5.39,141,2.37,141,13.0359,143,2.319,145,1.429,143,11.59,147,5.62,147,1.7748,149,14631,151,10.5856,153,
4.6745,155,1.312,157,1.72,159,10.23,161,1.4654,163,2.0508,165,9.0883,167,1.2281,169,3.531,171,7.5261,173,2.073,175,4.8626,176,3.451,177,1.7282,179,1.0856,180,4.087,181,5.1627,183,1.7957,185,9.7176,187,9.817,187,0.9856,189,3.3536,191,0.7658,191,0.8319,195,9.2922,197,0.7406,199,7.7123,201,2.8469,203,24.7316,205,24.9749,207,9.034,209,6.963,209,11.7,211,9.16,223,5.95,223,1.3746,225,11.187,227,5.6,229,1.4,231,10.2,235,0.83,237,9.57,239,3.09,243,4.6,1E100])});n("JSV.source");w(null,"JSV.source.JDXDecompressor",
["java.lang.Double","JSV.common.Coordinate","JU.Logger"],function(){c$=t(function(){this.lineNumber=this.ich=this.nPoints=this.deltaX=this.yFactor=this.xFactor=0;this.t=null;this.dx=this.firstX=0;this.maxY=4.9E-324;this.minY=1.7976931348623157E308;this.debugging=!1;this.xyCoords=null;this.ipt=0;this.lastLine=this.line=null;this.lineLen=0;this.errorLog=null;this.lastDif=this.difVal=-2147483648;this.yval=this.xval=this.dupCount=0;this.firstLastX=null;s(this,arguments)},JSV.source,"JDXDecompressor");
c(c$,"getMinY",function(){return this.minY});c(c$,"getMaxY",function(){return this.maxY});u(c$,function(a,b,c,e,g,f){this.t=a;this.firstX=b;this.xFactor=c;this.yFactor=e;this.deltaX=g;this.nPoints=f;this.lineNumber=a.labelLineNo;this.debugging=JU.Logger.isActiveLevel(6)},"JSV.source.JDXSourceStreamTokenizer,~N,~N,~N,~N,~N");c(c$,"addPoint",function(a){if(this.ipt==this.xyCoords.length){var b=Array(2*this.ipt);System.arraycopy(this.xyCoords,0,b,0,this.ipt);this.xyCoords=b}b=a.getYVal();b>this.maxY?
this.maxY=b:b<this.minY&&(this.minY=b);this.debugging&&this.logError("Coord: "+this.ipt+a);this.xyCoords[this.ipt++]=a;this.firstLastX[1]=a.getXVal()},"JSV.common.Coordinate");c(c$,"decompressData",function(a,b){this.errorLog=a;this.firstLastX=b;this.debugging&&this.logError("firstX="+this.firstX+" xFactor="+this.xFactor+" yFactor="+this.yFactor+" deltaX="+this.deltaX+" nPoints="+this.nPoints);this.testAlgorithm();this.xyCoords=Array(this.nPoints);var c=Math.abs(0.35*this.deltaX),e=Math.abs(1.4*this.deltaX),
g=Math.abs(0.6*this.deltaX);try{for(;null!=(this.line=this.t.readLineTrimmed())&&0>this.line.indexOf("##");)if(this.lineNumber++,this.debugging&&this.logError(this.lineNumber+"\t"+this.line),0!=(this.lineLen=this.line.length)){this.ich=0;var f=-2147483648!=this.lastDif;this.xval=this.getValueDelim()*this.xFactor;0==this.ipt&&(b[0]=this.xval,this.dx=this.firstX-this.xval);this.xval+=this.dx;var h=(new JSV.common.Coordinate).set(this.xval,(this.yval=this.getYValue())*this.yFactor);if(0==this.ipt)this.addPoint(h);
else{var k=this.xyCoords[this.ipt-1],l=Math.abs(k.getXVal()-h.getXVal());if(f&&l<c){this.xyCoords[this.ipt-1]=h;var m=k.getYVal(),n=h.getYVal();n!=m&&this.logError(this.lastLine+"\n"+this.line+"\nY-value Checkpoint Error! Line "+this.lineNumber+" for y1="+n+" y0="+m)}else this.addPoint(h),(l<g||l>e)&&this.logError(this.lastLine+"\n"+this.line+"\nX-sequence Checkpoint Error! Line "+this.lineNumber+" |x1-x0|="+l+" instead of "+Math.abs(this.deltaX)+" for x1="+h.getXVal()+" x0="+k.getXVal())}for(;this.ich<
this.lineLen||-2147483648!=this.difVal||0<this.dupCount;)this.xval+=this.deltaX,Double.isNaN(this.yval=this.getYValue())||this.addPoint((new JSV.common.Coordinate).set(this.xval,this.yval*this.yFactor));this.lastLine=this.line}}catch(p){if(!y(p,java.io.IOException))throw p;}this.nPoints!=this.ipt&&(this.logError("Decompressor did not find "+this.nPoints+" points -- instead "+this.ipt),c=Array(this.ipt),System.arraycopy(this.xyCoords,0,c,0,this.ipt),this.xyCoords=c);return 0<this.deltaX?this.xyCoords:
JSV.common.Coordinate.reverse(this.xyCoords)},"JU.SB,~A");c(c$,"logError",function(a){this.debugging&&JU.Logger.debug(a);this.errorLog.append(a).appendC("\n")},"~S");c(c$,"getYValue",function(){if(0<this.dupCount)return--this.dupCount,this.yval=-2147483648==this.lastDif?this.yval:this.yval+this.lastDif;if(-2147483648!=this.difVal)return this.yval+=this.difVal,this.lastDif=this.difVal,this.difVal=-2147483648,this.yval;if(this.ich==this.lineLen)return NaN;var a=this.line.charAt(this.ich);this.debugging&&
JU.Logger.info(""+a);switch(a){case "%":this.difVal=0;break;case "J":case "K":case "L":case "M":case "N":case "O":case "P":case "Q":case "R":this.difVal=a.charCodeAt(0)-73;break;case "j":case "k":case "l":case "m":case "n":case "o":case "p":case "q":case "r":this.difVal=105-a.charCodeAt(0);break;case "S":case "T":case "U":case "V":case "W":case "X":case "Y":case "Z":this.dupCount=a.charCodeAt(0)-82;break;case "s":this.dupCount=9;break;case "+":case "-":case ".":case "0":case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":case "@":case "A":case "B":case "C":case "D":case "E":case "F":case "G":case "H":case "I":case "a":case "b":case "c":case "d":case "e":case "f":case "g":case "h":case "i":return this.lastDif=
-2147483648,this.getValue();case "?":return this.lastDif=-2147483648,NaN;default:return this.ich++,this.lastDif=-2147483648,this.getYValue()}this.ich++;-2147483648!=this.difVal?this.difVal=this.getDifDup(this.difVal):this.dupCount=this.getDifDup(this.dupCount)-1;return this.getYValue()});c(c$,"getDifDup",function(a){var b=this.ich;this.next();var c=a+this.line.substring(b,this.ich);return b==this.ich?a:Integer.$valueOf(c).intValue()},"~N");c(c$,"getValue",function(){var a=this.ich;if(this.ich==this.lineLen)return NaN;
var a=this.line.charAt(this.ich),b=0;switch(a){case "+":case "-":case ".":case "0":case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":return this.getValueDelim();case "@":case "A":case "B":case "C":case "D":case "E":case "F":case "G":case "H":case "I":b=a.charCodeAt(0)-64;a=++this.ich;break;case "a":case "b":case "c":case "d":case "e":case "f":case "g":case "h":case "i":b=96-a.charCodeAt(0);a=++this.ich;break;default:return this.ich++,this.getValue()}this.next();return Double.$valueOf(b+
this.line.substring(a,this.ich)).doubleValue()});c(c$,"getValueDelim",function(){for(var a=this.ich,b="\x00";this.ich<this.lineLen&&0<=" ,\t\n".indexOf(b=this.line.charAt(this.ich));)this.ich++;var c=1;switch(b){case "-":c=-1;case "+":a=++this.ich}b=this.next();if("E"==b&&this.ich+3<this.lineLen)switch(this.line.charAt(this.ich+1)){case "-":case "+":this.ich+=4,this.ich<this.lineLen&&("0"<=(b=this.line.charAt(this.ich))&&"9">=b)&&this.ich++}return c*Double.$valueOf(this.line.substring(a,this.ich)).doubleValue()});
c(c$,"next",function(){for(;this.ich<this.lineLen&&0>"+-%@ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrs? ,\t\n".indexOf(this.line.charAt(this.ich));)this.ich++;return this.ich==this.lineLen?"\x00":this.line.charAt(this.ich)});c(c$,"testAlgorithm",function(){});C(c$,"allDelim","+-%@ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrs? ,\t\n","WHITE_SPACE"," ,\t\n")});n("JSV.source");w(["JU.Lst"],"JSV.source.JDXHeader",null,function(){c$=t(function(){this.title="";this.jcampdx="5.01";this.origin=this.dataClass=
this.dataType="";this.owner="PUBLIC DOMAIN";this.time=this.date=this.longDate="";this.headerTable=this.qualifiedType=null;s(this,arguments)},JSV.source,"JDXHeader");K(c$,function(){this.headerTable=new JU.Lst});c(c$,"setTitle",function(a){this.title=a},"~S");c(c$,"setJcampdx",function(a){this.jcampdx=a},"~S");c(c$,"setDataType",function(a){this.dataType=a},"~S");c(c$,"setDataClass",function(a){this.dataClass=a},"~S");c(c$,"setOrigin",function(a){this.origin=a},"~S");c(c$,"setOwner",function(a){this.owner=
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this.qualifiedType=JSV.source.JDXHeader.getTypeName(this.dataType):this.qualifiedType});c(c$,"getJcampdx",function(){return this.jcampdx});c(c$,"getDataType",function(){return this.dataType});c(c$,"getOrigin",function(){return this.origin});c(c$,"getOwner",function(){return this.owner});c(c$,"getLongDate",function(){return this.longDate});c(c$,"getDate",function(){return this.date});c(c$,"getTime",function(){return this.time});c(c$,"getDataClass",function(){return this.dataClass});c(c$,"setHeaderTable",
function(a){this.headerTable=a},"JU.Lst");c(c$,"getHeaderTable",function(){return this.headerTable});c(c$,"getHeaderRowDataAsArray",function(a,b){var c=Array((a?6:5)+this.headerTable.size()+b),e=0;c[e++]=["##TITLE",this.title];c[e++]=["##JCAMP-DX",this.jcampdx];c[e++]=["##DATA TYPE",this.dataType];a&&(c[e++]=["##DATA CLASS",this.dataClass]);c[e++]=["##ORIGIN",this.origin];c[e++]=["##OWNER",this.owner];for(var g=0;g<this.headerTable.size();g++)c[e++]=this.getRow(g);return c},"~B,~N");c(c$,"getRow",
function(a){a=this.headerTable.get(a);return[a[0],JU.PT.rep(a[1],"<","&lt;")]},"~N");C(c$,"typeNames","ND NMR SPECTRUM   NMR;NMR SPECTRUM      NMR;INFRARED SPECTRUM IR;MASS SPECTRUM     MS;RAMAN SPECTRUM    RAMAN;GAS CHROMATOGRAM  GC;UV/VIS SPECTRUM   UV/VIS".split(";"))});n("JSV.source");w(["J.api.JmolJDXMOLReader"],"JSV.source.JDXReader","java.io.BufferedReader $.StringReader java.lang.Double $.Float java.util.Hashtable $.StringTokenizer JU.Lst $.PT $.SB JSV.api.JSVZipReader JSV.common.Coordinate $.JSVFileManager $.JSViewer $.PeakInfo $.Spectrum JSV.exception.JSVException JSV.source.JDXDecompressor $.JDXSource $.JDXSourceStreamTokenizer JU.Logger".split(" "),
function(){c$=t(function(){this.nmrMaxY=NaN;this.errorLog=this.t=this.source=null;this.isZipFile=this.done=this.obscure=!1;this.filePath=null;this.loadImaginary=!0;this.isTabularData=this.isSimulation=!1;this.blockID=this.nSpec=this.lastSpec=this.firstSpec=0;this.peakData=this.acdMolFile=this.acdAssignments=this.modelSpectrum=this.reader=this.mpr=null;s(this,arguments)},JSV.source,"JDXReader",null,J.api.JmolJDXMOLReader);c$.getVarList=c(c$,"getVarList",function(a){a=JSV.source.JDXReader.VAR_LIST_TABLE[0].indexOf(a);
return JSV.source.JDXReader.VAR_LIST_TABLE[1].substring(a+1,a+12).trim()},"~S");u(c$,function(a,b,c,e,g,f){a=JU.PT.trimQuotes(a);if(this.isSimulation=null!=a&&a.startsWith("http://SIMULATION/"))this.nmrMaxY=Float.isNaN(f)?1E4:f;this.filePath=a;this.obscure=b;this.firstSpec=e;this.lastSpec=g;this.loadImaginary=c},"~S,~B,~B,~N,~N,~N");c$.createJDXSourceFromStream=c(c$,"createJDXSourceFromStream",function(a,b,c,e){return JSV.source.JDXReader.createJDXSource(JSV.common.JSVFileManager.getBufferedReaderForInputStream(a),
"stream",b,c,-1,-1,e)},"java.io.InputStream,~B,~B,~N");c$.createJDXSource=c(c$,"createJDXSource",function(a,b,c,e,g,f,h){var k=null;try{null==a&&(a=JSV.common.JSVFileManager.getBufferedReaderFromName(b,"##TITLE"));a.mark(400);var l=$(400,"\x00");a.read(l,0,400);a.reset();var k=String.instantialize(l),m=k.indexOf("#"),n=k.indexOf("<");if(0>m||0<=n&&n<m){var p=k.toLowerCase(),p=p.contains("<animl")||p.contains("<!doctype technique")?"AnIML":p.contains("xml-cml")?"CML":null;c=null;null!=p&&(c=JSV.common.JSViewer.getInterface("JSV.source."+
p+"Reader").getSource(b,a));a.close();if(null==c)throw JU.Logger.error(k+"..."),new JSV.exception.JSVException("File type not recognized");return c}return(new JSV.source.JDXReader(b,c,e,g,f,h)).getJDXSource(a)}catch(q){if(y(q,Exception))throw null!=a&&a.close(),null!=k&&JU.Logger.error(k+"..."),a=q.getMessage(),new JSV.exception.JSVException("Error reading data: "+a);throw q;}},"java.io.BufferedReader,~S,~B,~B,~N,~N,~N");c(c$,"getJDXSource",function(a){this.source=new JSV.source.JDXSource(0,this.filePath);
this.isZipFile=p(a,JSV.api.JSVZipReader);this.t=new JSV.source.JDXSourceStreamTokenizer(a);this.errorLog=new JU.SB;for(var b=a=null,c=!1;!this.done&&"##TITLE".equals(this.t.peakLabel());){c=!0;null!=a&&!this.isZipFile&&this.errorLog.append("Warning - file is a concatenation without LINK record -- does not conform to IUPAC standards!\n");for(var e=new JSV.common.Spectrum,g=new JU.Lst;!this.done&&null!=(a=this.t.getLabel())&&null!=(b=this.getValue(a));)if(this.isTabularData){this.setTabularDataType(e,
a);if(!this.processTabularData(e,g))throw new JSV.exception.JSVException("Unable to read JDX file");this.addSpectrum(e,!1);e=null}else a.equals("##DATATYPE")&&b.toUpperCase().equals("LINK")?(this.getBlockSpectra(g),e=null):a.equals("##NTUPLES")||a.equals("##VARNAME")?(this.getNTupleSpectra(g,e,a),e=null):(null==e&&(e=new JSV.common.Spectrum),this.readDataLabel(e,a,b,this.errorLog,this.obscure)||(JSV.source.JDXReader.addHeader(g,this.t.rawLabel,b),this.checkCustomTags(e,a,b)))}if(!c)throw new JSV.exception.JSVException("##TITLE record not found");
this.source.setErrorLog(this.errorLog.toString());return this.source},"~O");c(c$,"getValue",function(a){var b=this.isTabularDataLabel(a)?"":this.t.getValue();return"##END".equals(a)?null:b},"~S");c(c$,"isTabularDataLabel",function(a){return this.isTabularData=0<="##DATATABLE##PEAKTABLE##XYDATA##XYPOINTS#".indexOf(a+"#")},"~S");c(c$,"addSpectrum",function(a,b){if(!this.loadImaginary&&a.isImaginary())return JU.Logger.info("FileReader skipping imaginary spectrum -- use LOADIMAGINARY TRUE to load this spectrum."),
!0;if(null!=this.acdAssignments){if(!a.dataType.equals("MASS SPECTRUM")&&!a.isContinuous())return JU.Logger.info("Skipping ACD Labs line spectrum for "+a),!0;if(0<this.acdAssignments.size())try{this.mpr.setACDAssignments(a.title,a.getTypeLabel(),this.source.peakCount,this.acdAssignments,this.acdMolFile)}catch(c){if(y(c,Exception))JU.Logger.info("Failed to create peak data: "+c);else throw c;}null!=this.acdMolFile&&JSV.common.JSVFileManager.htCorrelationCache.put("mol",this.acdMolFile)}Float.isNaN(this.nmrMaxY)?
1E4<=a.getMaxY()&&a.doNormalize(1E3):a.doNormalize(this.nmrMaxY);this.isSimulation&&a.setSimulated(this.filePath);this.nSpec++;if(0<this.firstSpec&&this.nSpec<this.firstSpec)return!0;if(0<this.lastSpec&&this.nSpec>this.lastSpec)return!(this.done=!0);a.setBlockID(this.blockID);this.source.addJDXSpectrum(null,a,b);return!0},"JSV.common.Spectrum,~B");c(c$,"getBlockSpectra",function(a){JU.Logger.debug("--JDX block start--");for(var b="",c=null,e=0==this.source.type,g=!1;null!=(b=this.t.getLabel())&&!b.equals("##TITLE");)c=
this.getValue(b),e&&!JSV.source.JDXReader.readHeaderLabel(this.source,b,c,this.errorLog,this.obscure)&&JSV.source.JDXReader.addHeader(a,this.t.rawLabel,c),b.equals("##BLOCKS")&&100<JU.PT.parseInt(c)&&0>=this.firstSpec&&(g=!0);c=this.getValue(b);if(!"##TITLE".equals(b))throw new JSV.exception.JSVException("Unable to read block source");e&&this.source.setHeaderTable(a);this.source.type=1;this.source.isCompoundSource=!0;e=new JSV.common.Spectrum;a=new JU.Lst;this.readDataLabel(e,b,c,this.errorLog,this.obscure);
try{for(var f;null!=(f=this.t.getLabel());){if(null==(c=this.getValue(f))&&"##END".equals(b)){JU.Logger.debug("##END= "+this.t.getValue());break}b=f;if(this.isTabularData){if(this.setTabularDataType(e,b),!this.processTabularData(e,a))throw new JSV.exception.JSVException("Unable to read Block Source");}else{if(b.equals("##DATATYPE")&&c.toUpperCase().equals("LINK"))this.getBlockSpectra(a),b=e=null;else if(b.equals("##NTUPLES")||b.equals("##VARNAME"))this.getNTupleSpectra(a,e,b),e=null,b="";if(this.done)break;
if(null==e){e=new JSV.common.Spectrum;a=new JU.Lst;if(""===b)continue;if(null==b){b="##END";continue}}if(null==c){if(0<e.getXYCoords().length&&!this.addSpectrum(e,g))return this.source;e=new JSV.common.Spectrum;a=new JU.Lst}else this.readDataLabel(e,b,c,this.errorLog,this.obscure)||(JSV.source.JDXReader.addHeader(a,this.t.rawLabel,c),this.checkCustomTags(e,b,c))}}}catch(h){if(y(h,Exception))throw new JSV.exception.JSVException(h.getMessage());throw h;}this.addErrorLogSeparator();this.source.setErrorLog(this.errorLog.toString());
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break}if(c.equals("##PAGE"))k=this.t.getValue();else{if(null==l&&(l=new JSV.common.Spectrum,b.copyTo(l),l.setTitle(b.getTitle()),!l.is1D())){var n=k.indexOf("=");if(0<=n)try{l.setY2D(Double.parseDouble(k.substring(n+1).trim()));var p=k.substring(0,n).trim(),q=g.indexOf(p);0<=q&&l.setY2DUnits(f.get("##UNITS").get(q))}catch(s){if(!y(s,Exception))throw s;}}n=new JU.Lst;for(l.setHeaderTable(n);!c.equals("##DATATABLE");)JSV.source.JDXReader.addHeader(n,this.t.rawLabel,this.t.getValue()),c=this.t.getLabel();
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!0;case 40:return a.yFactor=Double.parseDouble(c),!0;case 50:return a.setXUnits(c),!0;case 60:return a.setYUnits(c),!0;case 70:a.setXLabel(c);break;case 80:a.setYLabel(c);break;case 90:return a.numDim=Integer.parseInt(c),!0;case 100:0!=a.shiftRefType&&(1.7976931348623157E308==a.offset&&(a.offset=Double.parseDouble(c)),a.dataPointNum=1,a.shiftRefType=1);break;default:if(17>b.length)break;if(b.equals("##.OBSERVEFREQUENCY "))return a.observedFreq=Double.parseDouble(c),!0;if(b.equals("##.OBSERVENUCLEUS "))return a.setObservedNucleus(c),
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a.yFactor=Double.parseDouble(g.get(c));g=b.get("##LAST");a.fileLastX=Double.parseDouble(g.get(f));g=b.get("##FIRST");a.fileFirstX=Double.parseDouble(g.get(f));g=b.get("##VARDIM");a.nPointsFile=Integer.parseInt(g.get(f));g=b.get("##UNITS");a.setXUnits(g.get(f));a.setYUnits(g.get(c));null==a.nucleusX&&null!=(g=b.get("##.NUCLEUS"))?(a.setNucleusAndFreq(g.get(0),!1),a.setNucleusAndFreq(g.get(f),!0)):null==a.nucleusX&&(a.nucleusX="?");this.decompressData(a,e);return!0}return a.dataClass.equals("PEAKTABLE")||
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var g=new JSV.source.JDXDecompressor(this.t,a.fileFirstX,a.xFactor,a.yFactor,e,a.nPointsFile),f=X(2,0),h=System.currentTimeMillis(),k=g.decompressData(this.errorLog,f);JU.Logger.debugging&&JU.Logger.debug("decompression time = "+(System.currentTimeMillis()-h)+" ms");a.setXYCoords(k);h=g.getMinY();null!=b&&(h<b[0]&&(b[0]=h),h=g.getMaxY(),h>b[1]&&(b[1]=h));g=Double.isNaN(a.freq2dX)?a.observedFreq:a.freq2dX;1.7976931348623157E308!=a.offset&&(1.7976931348623157E308!=g&&a.dataType.toUpperCase().contains("SPECTRUM"))&&
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this.modelSpectrum=a;b="##$MODELS ##$PEAKS  ##$SIGNALS##$MOLFILE##PEAKASSI##$UVIRASS##$MSFRAGM".indexOf(b);if(0>b)return!1;this.getMpr().set(this,this.filePath,null);try{switch(this.reader=new java.io.BufferedReader(new java.io.StringReader(c)),b){case 0:this.mpr.readModels();break;case 10:case 20:this.peakData=new JU.Lst;this.source.peakCount+=this.mpr.readPeaks(20==b,this.source.peakCount);break;case 30:this.acdAssignments=new JU.Lst;this.acdMolFile=JU.PT.rep(c,"$$ Empty String","");break;case 40:case 50:case 60:this.acdAssignments=
this.mpr.readACDAssignments(a.nPointsFile,40==b);break}}catch(e){if(y(e,Exception))throw new JSV.exception.JSVException(e.getMessage());throw e;}finally{this.reader=null}return!0},"JSV.common.Spectrum,~S,~S");c(c$,"getMpr",function(){return null==this.mpr?this.mpr=JSV.common.JSViewer.getInterface("J.jsv.JDXMOLParser"):this.mpr});h(c$,"rd",function(){return this.reader.readLine()});h(c$,"setSpectrumPeaks",function(a,b,c){this.modelSpectrum.setPeakList(this.peakData,b,c);this.modelSpectrum.isNMR()&&
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c(c$,"dispose",function(){this.jdxSpectra=this.headerTable=null});u(c$,function(a,b){E(this,JSV.source.JDXSource,[]);this.type=a;this.setFilePath(b);this.headerTable=new JU.Lst;this.jdxSpectra=new JU.Lst;this.isCompoundSource=0!=a},"~N,~S");c(c$,"getJDXSpectrum",function(a){return this.jdxSpectra.size()<=a?null:this.jdxSpectra.get(a)},"~N");c(c$,"addJDXSpectrum",function(a,b,c){null==a&&(a=this.filePath);b.setFilePath(a);a=this.jdxSpectra.size();(0==a||!this.jdxSpectra.get(a-1).addSubSpectrum(b,c))&&
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c$.ptNonWhite=c(c$,"ptNonWhite",function(a,b,c){for(;b<c&&Character.isWhitespace(a.charAt(b));)b++;return b},"JU.SB,~N,~N");c$.ptNonSpace=c(c$,"ptNonSpace",function(a,b,c){for(;b<c&&(" "==a.charAt(b)||"\t"==a.charAt(b));)b++;return b},"JU.SB,~N,~N");c$.ptNonSpaceRev=c(c$,"ptNonSpaceRev",function(a,b){for(;0<=--b&&(" "==a.charAt(b)||"\t"==a.charAt(b)););return b},"JU.SB,~N")});n("JSV.tree");w(["JSV.api.JSVTree"],"JSV.tree.SimpleTree",["JSV.common.JSVFileManager","$.PanelNode","JSV.tree.SimpleTreeModel",
"$.SimpleTreeNode","$.SimpleTreePath"],function(){c$=t(function(){this.selectedPath=this.vwr=this.spectraTreeModel=this.rootNode=this.si=null;s(this,arguments)},JSV.tree,"SimpleTree",null,JSV.api.JSVTree);h(c$,"getRootNode",function(){return this.rootNode});u(c$,function(a){this.vwr=a;this.rootNode=new JSV.tree.SimpleTreeNode("Spectra",null);this.spectraTreeModel=new JSV.tree.SimpleTreeModel(this.rootNode)},"JSV.common.JSViewer");c(c$,"valueChanged",function(){this.vwr.selectedTreeNode(this.getLastSelectedPathComponent())});
c(c$,"getLastSelectedPathComponent",function(){return null==this.selectedPath?null:this.selectedPath.getLastPathComponent()});h(c$,"setSelectedPanel",function(a,b){if(null!=b){var c=JSV.common.PanelNode.findNode(b,this.vwr.panelNodes).treeNode;this.setSelectionPath(this.vwr.spectraTree.newTreePath(c.getPath()))}},"JSV.api.ScriptInterface,JSV.api.JSVPanel");c(c$,"setSelectionPath",function(a){this.selectedPath=a;this.valueChanged()},"JSV.api.JSVTreePath");h(c$,"createTree",function(a,b,c){var e=this.vwr.spectraTree,
g=e.getRootNode(),f=this.vwr.panelNodes,h=JSV.common.JSVFileManager.getTagName(b.getFilePath()),k=new JSV.common.PanelNode(null,h,b,null),l=new JSV.tree.SimpleTreeNode(h,k);k.setTreeNode(l);e.spectraTreeModel.insertNodeInto(l,g,g.getChildCount());for(g=0;g<c.length;g++){var k=new JSV.common.PanelNode(a+"."+(g+1),h,b,c[g]),m=new JSV.tree.SimpleTreeNode(k.toString(),k);k.setTreeNode(m);f.addLast(k);e.spectraTreeModel.insertNodeInto(m,l,l.getChildCount())}this.vwr.selectFrameNode(c[0]);return l},"~N,JSV.source.JDXSource,~A");
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