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biojs-vis-pdbviewer

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A BioJS 2.0 component to view protein structures

github.com/sillitoe/biojs-vis-pdbviewer

sillitoe/biojs-vis-pdbviewer

2,617 lines • 1.36 MB
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"~N,~A");c(c$,"sub",function(a){this.sub33(a);this.m03-=a.m03;this.m13-=a.m13;this.m23-=a.m23;this.m30-=a.m30;this.m31-=a.m31;this.m32-=a.m32;this.m33-=a.m33},"JU.M4");c(c$,"transpose",function(){this.transpose33();var a=this.m03;this.m03=this.m30;this.m30=a;a=this.m13;this.m13=this.m31;this.m31=a;a=this.m23;this.m23=this.m32;this.m32=a});c(c$,"invertM",function(a){this.setM4(a);this.invert()},"JU.M4");c(c$,"invert",function(){var a=this.determinant4();0!=a&&(a=1/a,this.set(this.m11*(this.m22*this.m33-
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(this.m10*this.m22-this.m12*this.m20)+this.m00*(this.m12*this.m23-this.m13*this.m22),this.m13*(this.m20*this.m31-this.m21*this.m30)+this.m10*(this.m21*this.m33-this.m23*this.m31)+this.m11*(this.m23*this.m30-this.m20*this.m33),this.m23*(this.m00*this.m31-this.m01*this.m30)+this.m20*(this.m01*this.m33-this.m03*this.m31)+this.m21*(this.m03*this.m30-this.m00*this.m33),this.m33*(this.m00*this.m11-this.m01*this.m10)+this.m30*(this.m01*this.m13-this.m03*this.m11)+this.m31*(this.m03*this.m10-this.m00*this.m13),
this.m03*(this.m11*this.m20-this.m10*this.m21)+this.m00*(this.m13*this.m21-this.m11*this.m23)+this.m01*(this.m10*this.m23-this.m13*this.m20),this.m10*(this.m22*this.m31-this.m21*this.m32)+this.m11*(this.m20*this.m32-this.m22*this.m30)+this.m12*(this.m21*this.m30-this.m20*this.m31),this.m20*(this.m02*this.m31-this.m01*this.m32)+this.m21*(this.m00*this.m32-this.m02*this.m30)+this.m22*(this.m01*this.m30-this.m00*this.m31),this.m30*(this.m02*this.m11-this.m01*this.m12)+this.m31*(this.m00*this.m12-this.m02*
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"determinant4",function(){return(this.m00*this.m11-this.m01*this.m10)*(this.m22*this.m33-this.m23*this.m32)-(this.m00*this.m12-this.m02*this.m10)*(this.m21*this.m33-this.m23*this.m31)+(this.m00*this.m13-this.m03*this.m10)*(this.m21*this.m32-this.m22*this.m31)+(this.m01*this.m12-this.m02*this.m11)*(this.m20*this.m33-this.m23*this.m30)-(this.m01*this.m13-this.m03*this.m11)*(this.m20*this.m32-this.m22*this.m30)+(this.m02*this.m13-this.m03*this.m12)*(this.m20*this.m31-this.m21*this.m30)});c(c$,"scale",
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"]\n  ["+this.m20+"\t"+this.m21+"\t"+this.m22+"\t"+this.m23+"]\n  ["+this.m30+"\t"+this.m31+"\t"+this.m32+"\t"+this.m33+"] ]"})}),p("JU"),v(["java.io.OutputStream"],"JU.OC","java.io.BufferedWriter $.ByteArrayOutputStream $.FileOutputStream $.OutputStreamWriter JU.Base64 $.SB".split(" "),function(){c$=u(function(){this.bw=this.fileName=this.bytePoster=null;this.isLocalFile=!1;this.byteCount=0;this.closed=this.isCanceled=!1;this.type=this.sb=this.os=null;this.$isBase64=!1;this.bytes=this.os0=null;q(this,
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1,d)},"~S,~S,~N,~N")}),p("J.adapter.readers.molxyz"),v(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.XyzReader",["java.lang.Float","JU.Logger"],function(){c$=y(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 g=this.addAtomXYZSymName(d,1,null,null);this.setElementAndIsotope(g,d[0]);var c=4;switch(d.length){case 4:continue;case 5:case 6:case 8:case 9:if(0<=d[4].indexOf("."))g.partialCharge=this.parseFloatStr(d[4]);else{var e=this.parseIntStr(d[4]);-2147483648!=e&&(g.formalCharge=e)}switch(d.length){case 5:continue;case 6:g.radius=this.parseFloatStr(d[5]);continue;case 9:g.atomSerial=this.parseIntStr(d[8])}c++;
default:var e=this.parseFloatStr(d[c++]),j=this.parseFloatStr(d[c++]),d=this.parseFloatStr(d[c++]);if(Float.isNaN(e)||Float.isNaN(j)||Float.isNaN(d))continue;this.asc.addVibrationVector(g.index,e,j,d)}}}},"~N")}),p("J.adapter.smarter"),v(["JU.P3"],"J.adapter.smarter.Atom",["java.lang.Float","JU.AU","$.Lst","$.V3","JU.Vibration"],function(){c$=u(function(){this.index=this.atomSetIndex=0;this.bsSymmetry=null;this.atomSite=0;this.elementSymbol=null;this.elementNumber=-1;this.atomName=null;this.formalCharge=
-2147483648;this.partialCharge=NaN;this.vib=null;this.bfactor=NaN;this.foccupancy=1;this.radius=NaN;this.isHetero=!1;this.atomSerial=-2147483648;this.chainID=0;this.altLoc="\x00";this.group3=null;this.sequenceNumber=-2147483648;this.insertionCode="\x00";this.tensors=this.anisoBorU=null;this.ignoreSymmetry=!1;q(this,arguments)},J.adapter.smarter,"Atom",JU.P3,Cloneable);c(c$,"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=r(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");x(c$,"elementCharMasks",[1972292,-2147351151,-2146019271,-2130706430,1441792,-2147348464,25,-2147205008,-2147344384,0,-2147352576,1179905,548936,-2147434213,-2147221504,-2145759221,0,1056947,-2147339946,-2147477097,-2147483648,-2147483648,-2147483648,8388624,-2147483646,139264])}),p("J.adapter.smarter"),v(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["java.lang.Float","J.api.JmolAdapter"],
function(){c$=u(function(){this.iatom=0;this.atom=null;this.ac=0;this.bsAtoms=this.atoms=null;q(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);s(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$,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1095761940!=this.atom.vib.z?0:A(this.atom.vib.x)});h(c$,"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})}),p("J.adapter.smarter"),v(["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 $.SmarterJmolAdapter J.api.Interface JU.Logger".split(" "),function(){c$=u(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;q(this,arguments)},J.adapter.smarter,"AtomSetCollection");L(c$,function(){this.ascAuxiliaryInfo=new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=C(16,0);this.atomSetAtomIndexes=C(16,0);this.atomSetAtomCounts=C(16,0);this.atomSetBondCounts=
C(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSymbolicMap=new java.util.Hashtable});c(c$,"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$,"getGlobalBoolean",function(a){return this.getAtomSetCollectionAuxiliaryInfo(J.adapter.smarter.AtomSetCollection.globalBooleans[a])===
Boolean.TRUE},"~N");s(c$,function(a,b,d,g){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){g=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(g++,d[a]);1<g&&this.setInfo("isMultiFile",Boolean.TRUE)}else null!=
g&&(this.setInfo("isMultiFile",Boolean.TRUE),this.appendAtomSetCollectionList(g))},"~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.Lst");c(c$,"appendAtomSetCollectionList",function(a){var b=a.size();if(0==b)this.errorMessage="No file found!";else for(var d=0;d<b;d++){var g=a.get(d);r(g,JU.Lst)?this.appendAtomSetCollectionList(g):this.appendAtomSetCollection(d,g)}},"JU.Lst");c(c$,"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,g=0==this.trajectoryStepCount?null:this.trajectorySteps.get(this.trajectoryStepCount-1),c=0,e=0;c<this.ac;c++)if(null==this.bsAtoms||this.bsAtoms.get(c)){var j=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=g&&(j=J.adapter.smarter.AtomSetCollection.fixPeriodic(j,g[c]));b[e]=j;d&&(a[e]=this.atoms[c].vib);e++}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$,"appendAtomSetCollection",function(a,b){null!=b.reader&&b.reader.mustFinalizeModelSet&&this.readerList.addLast(b.reader);var d=this.ac;this.setInfo("loadState",b.getAtomSetCollectionAuxiliaryInfo("loadState"));if(null!=b.bsAtoms){null==this.bsAtoms&&(this.bsAtoms=new JU.BS);for(var g=b.bsAtoms.nextSetBit(0);0<=g;g=b.bsAtoms.nextSetBit(g+
1))this.bsAtoms.set(d+g)}for(var g=0,c=this.atomSetCount,e=0;e<b.atomSetCount;e++){this.newAtomSet();var j=(this.atomSetAuxiliaryInfo[this.iSet]=b.atomSetAuxiliaryInfo[e]).get("PDB_CONECT_firstAtom_count_max");null!=j&&(j[0]+=d);this.setAtomSetAuxiliaryInfo("title",b.collectionName);this.setAtomSetName(b.getAtomSetName(e));for(j=0;j<b.atomSetAtomCounts[e];j++){try{null!=this.bsAtoms&&this.bsAtoms.set(this.ac),this.newCloneAtom(b.atoms[g])}catch(k){if(D(k,Exception))this.errorMessage="appendAtomCollection error: "+
k;else throw k;}g++}this.atomSetNumbers[this.iSet]=0>a?this.iSet+1:1E6*(a+1)+b.atomSetNumbers[e]}for(g=0;g<b.bondCount;g++)e=b.bonds[g],this.addNewBondWithOrder(e.atomIndex1+d,e.atomIndex2+d,e.order);for(g=J.adapter.smarter.AtomSetCollection.globalBooleans.length;0<=--g;)b.getGlobalBoolean(g)&&this.setGlobalBoolean(g);for(g=0;g<b.structureCount;g++)d=b.structures[g],this.addStructure(d),d.modelStartEnd[0]+=c,d.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(c$,"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=C(this.ac,0),g=this.ac,a=this.atomSetCount;0<=--a;)for(var c=d[a].size();0<=--c;){var e=this.atoms[--g]=d[a].get(c);b[e.index]=g;e.index=g}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$,"reverseSets",function(a,b){for(var d=JU.AU.createArrayOfArrayList(this.atomSetCount),g=0;g<this.atomSetCount;g++)d[g]=new JU.Lst;for(g=0;g<b;g++){if(0>a[g].atomSetIndex)return;d[a[g].atomSetIndex].addLast(a[g])}for(g=this.atomSetCount;0<=--g;)for(var c=d[g].size();0<=--c;)a[--b]=d[g].get(c)},"~A,~N");c(c$,"reverseObject",function(a){for(var b=this.atomSetCount,d=w(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$,"reverseArray",function(a){for(var b=this.atomSetCount,d=w(b/2);0<=--d;)JU.AU.swapInt(a,d,b-1-d)},"~A");c(c$,"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 g;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[g=this.atoms[b].atomSetIndex].indexOf(c))d[g]+=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$,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=C(16,0);this.atomSetAuxiliaryInfo=Array(16);this.ascAuxiliaryInfo=new java.util.Hashtable;
this.atomSetCount=0;this.atomSetNumbers=C(16,0);this.atomSymbolicMap=new java.util.Hashtable;this.bonds=null;this.iSet=-1;this.xtalSymmetry=this.readerList=null;this.structures=Array(16);this.structureCount=0;this.vibrationSteps=this.trajectorySteps=null});c(c$,"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$,"removeAtomSet",function(a){null==this.bsAtoms&&(this.bsAtoms=new JU.BS,this.bsAtoms.setBits(0,this.ac));var b=this.atomSetAtomIndexes[a],d=b+this.atomSetAtomCounts[a];this.bsAtoms.clearBits(b,d);for(b=d;b<this.ac;b++)this.atoms[b].atomSetIndex--;for(b=a+1;b<this.atomSetCount;b++)this.atomSetAuxiliaryInfo[b-1]=this.atomSetAuxiliaryInfo[b],this.atomSetAtomIndexes[b-1]=this.atomSetAtomIndexes[b],this.atomSetBondCounts[b-1]=this.atomSetBondCounts[b],this.atomSetAtomCounts[b-
1]=this.atomSetAtomCounts[b],this.atomSetNumbers[b-1]=this.atomSetNumbers[b];for(b=d=0;b<this.structureCount;b++){var g=this.structures[b];g.modelStartEnd[0]==a&&g.modelStartEnd[1]==a&&(this.structures[b]=null,d++)}if(0<d){a=Array(this.structureCount-d);for(d=b=0;b<this.structureCount;b++)null!=this.structures[b]&&(a[d++]=this.structures[b]);this.structures=a}for(b=0;b<this.bondCount;b++)this.bonds[b].atomSetIndex=this.atoms[this.bonds[b].atomIndex1].atomSetIndex;this.atomSetAuxiliaryInfo[--this.atomSetCount]=
null},"~N");c(c$,"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 g=this.bonds[this.bondCount-b];this.addNewBondWithOrder(g.atomIndex1+a,g.atomIndex2+a,g.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(),
g=this.getLastAtomSetAtomIndex();this.newAtomSet();for(var c=0;c<d;++c){var e=this.newCloneAtom(this.atoms[g++]);null!=b&&e.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$,"addAtomWithMappedSerialNumber",
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this.getAtomFromName(b),d)},"~S,~S,~N");c(c$,"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],g=a.get(d),g=(null==g?0:g.intValue())+1;a.put(d,Integer.$valueOf(g))}}for(b=0;b<this.structureCount;b++)d=this.structures[b],1==d.strandCount&&(d.strandCount=a.get(d.structureID+" "+d.modelStartEnd[0]).intValue())}});c(c$,"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$,"addVibrationVectorWithSymmetry",function(a,b,d,g,c){if(c){c=this.atoms[a].atomSite;for(var e=this.atoms[a].atomSetIndex;a<this.ac&&this.atoms[a].atomSetIndex==e;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,b,d,g)}else this.addVibrationVector(a,b,d,g)},"~N,~N,~N,~N,~B");c(c$,"addVibrationVector",function(a,b,d,g){this.allowMultiple||(a%=this.ac);return this.atoms[a].vib=JU.V3.new3(b,d,g)},"~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$,"setU",function(a,b,d){var g=a.anisoBorU;null==g&&this.setAnisoBorU(a,g=M(8,0),8);g[b]=d},"J.adapter.smarter.Atom,~N,~N");c(c$,"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$,"finalizeTrajectory",function(){if(0!=this.trajectoryStepCount){var a=this.trajectorySteps.get(0),b=null==this.vibrationSteps?null:this.vibrationSteps.get(0),d=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(null!=this.vibrationSteps&&null!=b&&b.length<d||a.length<d)this.errorMessage="File cannot be loaded as a trajectory";else{for(var d=new JU.V3,g=0,c=0;g<this.ac;g++)if(null==this.bsAtoms||this.bsAtoms.get(g))null!=this.vibrationSteps&&
(this.atoms[g].vib=null==b?d:b[c]),null!=a[c]&&this.atoms[g].setT(a[c]),c++;this.setInfo("trajectorySteps",this.trajectorySteps);null!=this.vibrationSteps&&this.setInfo("vibrationSteps",this.vibrationSteps)}}});c(c$,"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$,"setAtomSetNames",function(a,b,d){for(var g=this.iSet;0<=--b&&
0<=g;--g)(null==d||!d.get(g))&&this.setAtomSetAuxiliaryInfoForSet("name",a,g)},"~S,~N,JU.BS");c(c$,"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$,"setAtomSetModelPropertyForSet",function(a,b,d){var g=this.getAtomSetAuxiliaryInfoValue(d,"modelProperties");
null==g&&this.setAtomSetAuxiliaryInfoForSet("modelProperties",g=new java.util.Properties,d);g.put(a,b);a.startsWith(".")&&g.put(a.substring(1),b)},"~S,~S,~N");c(c$,"setAtomProperties",function(a,b,d){r(b,String)&&!b.endsWith("\n")&&(b+="\n");0>d&&(d=this.iSet);var g=this.getAtomSetAuxiliaryInfoValue(d,"atomProperties");null==g&&this.setAtomSetAuxiliaryInfoForSet("atomProperties",g=new java.util.Hashtable,d);g.put(a,b)},"~S,~O,~N,~B");c(c$,"setAtomSetPartialCharges",function(a){if(!this.atomSetAuxiliaryInfo[this.iSet].containsKey(a))return!1;
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"~N");c(c$,"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,g){this.setAtomSetModelProperty("FreqValue",
d);d+=" "+(null==g?"cm^-1":g);g=(null==b?"":b+" ")+d;this.setAtomSetName(g);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 g},"~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$,"centralize",function(){for(var a=new JU.P3,b=0;b<this.atomSetCount;b++){var d=this.atomSetAtomCounts[b],g=this.atomSetAtomIndexes[b];a.set(0,0,0);for(var c=g+d;--c>=g;)a.add(this.atoms[c]);a.scale(1/d);for(c=g+d;--c>=g;)this.atoms[c].sub(a)}});c(c$,"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");x(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)}),p("J.adapter.smarter"),v(["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 $.Parser".split(" "),function(){c$=u(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;q(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);L(c$,function(){this.next=C(1,0);this.loadNote=new JU.SB});c(c$,"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),r(d,java.io.BufferedReader)?this.reader=d:r(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(!D(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");r(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),r(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=C(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]=
A(a.x);this.latticeCells[1]=A(a.y);this.latticeCells[2]=A(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=C(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=M(25,0);for(var a=25;0<=--a;)this.notionalUnitCell[a]=NaN;null!=this.ptSupercell&&(this.notionalUnitCell[22]=Math.max(1,A(this.ptSupercell.x)),this.notionalUnitCell[23]=Math.max(1,A(this.ptSupercell.y)),
this.notionalUnitCell[24]=Math.max(1,A(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,g,c,e){this.ignoreFileUnitCell||(this.clearUnitCell(),this.notionalUnitCell[0]=a,this.notionalUnitCell[1]=b,this.notionalUnitCell[2]=
d,0!=g&&(this.notionalUnitCell[3]=g),0!=c&&(this.notionalUnitCell[4]=c),0!=e&&(this.notionalUnitCell[5]=e),this.iHaveUnitCell=this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");c(c$,"addPrimitiveLatticeVector",function(a,b,d){if(!this.ignoreFileUnitCell){if(0==a)for(var g=0;6>g;g++)this.notionalUnitCell[g]=0;a=6+3*a;this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a]=b[d];if(Float.isNaN(this.notionalUnitCell[0]))for(a=0;6>a;a++)this.notionalUnitCell[a]=-1;this.iHaveUnitCell=
this.checkUnitCell(15)}},"~N,~A,~N");c(c$,"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$,"setTransform",function(a,b,d,g,c,e,j,k,l){null==this.matRot&&this.doSetOrientation&&(this.matRot=new JU.M3,a=JU.V3.new3(a,b,d),a.normalize(),this.matRot.setColumnV(0,a),a.set(g,c,e),a.normalize(),
this.matRot.setColumnV(1,a),a.set(j,k,l),a.normalize(),this.matRot.setColumnV(2,a),this.asc.setInfo("defaultOrientationMatrix",JU.M3.newM3(this.matRot)),g=JU.Quat.newM(this.matRot),this.asc.setInfo("defaultOrientationQuaternion",g),JU.Logger.info("defaultOrientationMatrix = "+this.matRot))},"~N,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"setAtomCoordXYZ",function(a,b,d,g){a.set(b,d,g);this.setAtomCoord(a)},"J.adapter.smarter.Atom,~N,~N,~N");c(c$,"setAtomCoordScaled",function(a,b,d,g){null==a&&(a=this.asc.addNewAtom());
this.setAtomCoordXYZ(a,this.parseFloatStr(b[d])*g,this.parseFloatStr(b[d+1])*g,this.parseFloatStr(b[d+2])*g);return a},"J.adapter.smarter.Atom,~A,~N,~N");c(c$,"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$,"addAtomXYZSymName",function(a,b,d,g){var c=this.asc.addNewAtom();null!=d&&(c.elementSymbol=d);null!=g&&(c.atomName=g);this.setAtomCoordTokens(c,a,b);return c},"~A,~N,~S,~S");
c(c$,"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$,"addSites",
function(a){this.asc.setAtomSetAuxiliaryInfo("pdbSites",a);var b="",d;for(a=a.entrySet().iterator();a.hasNext()&&((d=a.next())||1);){for(var g=d.getKey(),c=d.getValue(),e,j=g.length;0<=--j;)if(!Character.isLetterOrDigit(e=g.charAt(j))&&"'"!=e)g=g.substring(0,j)+"_"+g.substring(j+1);c=c.get("groups");0!=c.length&&(this.addSiteScript("@site_"+g+" "+c),this.addSiteScript("site_"+g+' = ["'+JU.PT.rep(c,",",'","')+'"]'),b+=',"site_'+g+'"')}0<b.length&&this.addSiteScript("site_list = ["+b.substring(1)+"]")},
"java.util.Map");c(c$,"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,g){if(0==d)this.fillDataBlock(a,g);else{g=a.length;for(var c=
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this.dzB,this.clipped),this.drawBackside&&this.line3d.plotLineDelta(this.shadesA[e],d,this.shadesB[e],c,this.xA-j,this.yA-k,this.zA+l,this.dxB,this.dyB,this.dzB,this.clipped);this.g3d.setZMargin(0);3==f&&this.renderSphericalEndcaps()}}},"~N,~N,~B,~B,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"renderBits",function(a,b,d,c,f,e,j,k,l,h,n,t){if(!(e>3*this.g3d.getRenderHeight())){var z=w(e/2)+1,F=Math.round(j),K=Math.round(k),r=Math.round(l),q=Math.round(h),s=Math.round(n),p=Math.round(t),u=this.g3d.clipCode3(F-z,
K-z,r-z),F=this.g3d.clipCode3(F+z,K+z,r+z),K=this.g3d.clipCode3(q-z,s-z,p-z),z=this.g3d.clipCode3(q+z,s+z,p+z);this.clipped=0!=(u|F|K|z);if(0==(u&z&F&K))if(this.dxBf=h-j,this.dyBf=n-k,this.dzBf=t-l,0==e||1==e)this.line3d.plotLineDelta(this.g3d.getColorArgbOrGray(a),d,this.g3d.getColorArgbOrGray(b),c,A(j),A(k),A(l),A(this.dxBf),A(this.dyBf),A(this.dzBf),this.clipped);else{0<e&&(this.diameter=e,this.xAf=j,this.yAf=k,this.zAf=l);this.drawBackside=!d&&!c&&(this.clipped||2==f||0==f);this.xA=A(this.xAf);
this.yA=A(this.yAf);this.zA=A(this.zAf);this.dxB=A(this.dxBf);this.dyB=A(this.dyBf);this.dzB=A(this.dzBf);this.shadesA=this.g3d.getShades(this.colixA=a);this.shadesB=this.g3d.getShades(this.colixB=b);this.endcaps=f;this.calcArgbEndcap(!0,!0);0<e&&this.generateBaseEllipsePrecisely(!1);2==f&&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,e=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,c,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[e],d,this.shadesB[e],c,this.xA-j,this.yA-k,this.zA+l,this.dxB,this.dyB,this.dzB,this.clipped);this.g3d.setZMargin(0);3==f&&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,c,f,e,j,k,l,h,n,t){if(!(c>3*this.g3d.getRenderHeight()))if(this.dxBf=k-(this.xAf=f),this.dyBf=
l-(this.yAf=e),this.dzBf=h-(this.zAf=j),this.xA=w(Math.floor(this.xAf)),this.yA=w(Math.floor(this.yAf)),this.zA=w(Math.floor(this.zAf)),this.dxB=w(Math.floor(this.dxBf)),this.dyB=w(Math.floor(this.dyBf)),this.dzB=w(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,A(k),A(l),A(h)),this.diameter=c,1>=c)1==c&&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(t);!t&&2==this.endcaps&&this.renderFlatEndcapPrecisely(!1);this.g3d.setZMargin(5);for(d=this.rasterCount;0<=--d;)h=this.txRaster[d],a=this.tyRaster[d],f=this.tzRaster[d],c=this.xAf+h,k=this.yAf+a,l=this.zAf-f,h=this.xAf-h,a=this.yAf-a,f=this.zAf+f,e=this.shadesA[0],this.tEndcapOpen&&0!=this.argbEndcap&&(this.g3d.plotPixelClippedScreened(this.argbEndcap,
b,A(c),A(k),A(l)),this.g3d.plotPixelClippedScreened(this.argbEndcap,b,A(h),A(a),A(f))),j=this.fp8ShadeIndexUp[d]>>8,0!=e&&(this.line3d.plotLineDeltaA(this.shadesA,b,this.shadesA,b,j,A(c),A(k),A(l),w(Math.ceil(this.xTip-c)),w(Math.ceil(this.yTip-k)),w(Math.ceil(this.zTip-l)),!0),n&&(this.line3d.plotLineDeltaA(this.shadesA,b,this.shadesA,b,j,A(c),A(k)+1,A(l),w(Math.ceil(this.xTip-c)),w(Math.ceil(this.yTip-k))+1,w(Math.ceil(this.zTip-l)),!0),this.line3d.plotLineDeltaA(this.shadesA,b,this.shadesA,b,j,
A(c)+1,A(k),A(l),w(Math.ceil(this.xTip-c))+1,w(Math.ceil(this.yTip-k)),w(Math.ceil(this.zTip-l)),!0)),!t&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDelta(e,b,e,b,A(h),A(a),A(f),w(Math.ceil(this.xTip-h)),w(Math.ceil(this.yTip-a)),w(Math.ceil(this.zTip-f)),!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]=w(Math.floor(this.txRaster[a])),this.yRaster[a]=w(Math.floor(this.tyRaster[a])),this.zRaster[a]=w(Math.floor(this.tzRaster[a]))},"~B");c(c$,"calcRotatedPoint",function(a,b,d){this.tRaster[b]=a;a*=3.141592653589793;var c=Math.sin(a)*this.cosTheta,f=Math.cos(a);a=this.radius*(c*this.cosPhi-f*this.sinPhi);c=this.radius*(c*this.sinPhi+f*this.cosPhi);f=this.radius2-(a*a+c*c);f=0<f?Math.sqrt(f):0;d?(this.txRaster[b]=a,this.tyRaster[b]=c,this.tzRaster[b]=
f):(this.tEvenDiameter?(this.xRaster[b]=w(a-0.5),this.yRaster[b]=w(c-0.5)):(this.xRaster[b]=w(a),this.yRaster[b]=w(c)),this.zRaster[b]=w(f+0.5));this.fp8ShadeIndexUp[b]=this.shader.getShadeFp8(a,c,f)},"~N,~N,~B");c(c$,"interpolate",function(a,b){var d=this.xRaster[b]-this.xRaster[a];0>d&&(d=-d);var c=this.yRaster[b]-this.yRaster[a];0>c&&(c=-c);if(!(1>=d+c)){for(var d=this.tRaster[a],c=this.tRaster[b],f=this.allocRaster(!1),e=4;0<=--e;){var j=(d+c)/2;this.calcRotatedPoint(j,f,!1);if(this.xRaster[f]==
this.xRaster[a]&&this.yRaster[f]==this.yRaster[a])this.fp8ShadeIndexUp[a]=this.fp8ShadeIndexUp[a]+this.fp8ShadeIndexUp[f]>>>1,d=j;else if(this.xRaster[f]==this.xRaster[b]&&this.yRaster[f]==this.yRaster[b])this.fp8ShadeIndexUp[b]=this.fp8ShadeIndexUp[b]+this.fp8ShadeIndexUp[f]>>>1,c=j;else{this.interpolate(a,f);this.interpolate(f,b);return}}this.xRaster[f]=this.xRaster[a];this.yRaster[f]=this.yRaster[b]}},"~N,~N");c(c$,"interpolatePrecisely",function(a,b){var d=w(Math.floor(this.txRaster[b]))-w(Math.floor(this.txRaster[a]));
0>d&&(d=-d);var c=w(Math.floor(this.tyRaster[b]))-w(Math.floor(this.tyRaster[a]));0>c&&(c=-c);if(!(1>=d+c)){for(var d=this.tRaster[a],c=this.tRaster[b],f=this.allocRaster(!0),e=4;0<=--e;){var j=(d+c)/2;this.calcRotatedPoint(j,f,!0);if(w(Math.floor(this.txRaster[f]))==w(Math.floor(this.txRaster[a]))&&w(Math.floor(this.tyRaster[f]))==w(Math.floor(this.tyRaster[a])))this.fp8ShadeIndexUp[a]=this.fp8ShadeIndexUp[a]+this.fp8ShadeIndexUp[f]>>>1,d=j;else if(w(Math.floor(this.txRaster[f]))==w(Math.floor(this.txRaster[b]))&&
w(Math.floor(this.tyRaster[f]))==w(Math.floor(this.tyRaster[b])))this.fp8ShadeIndexUp[b]=this.fp8ShadeIndexUp[b]+this.fp8ShadeIndexUp[f]>>>1,c=j;else{this.interpolatePrecisely(a,f);this.interpolatePrecisely(f,b);return}}this.txRaster[f]=this.txRaster[a];this.tyRaster[f]=this.tyRaster[b]}},"~N,~N");c(c$,"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$,"renderFlatEndcap",function(a){if(0!=this.dzB&&this.g3d.setC(this.colixEndcap)){var b=this.xA,d=this.yA,c=this.zA;if(a&&0>this.dzB){if(4==this.endcaps)return;b+=this.dxB;d+=this.dyB;c+=this.dzB}this.findMinMaxY();for(a=this.yMin;a<=this.yMax;++a){this.findMinMaxX(a);var f=this.xMax-this.xMin+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(f,b+this.xMin,d+a,c-this.zXMin-1,c-this.zXMax-1,null,null)}}},"~B");c(c$,"renderFlatEndcapPrecisely",
function(a){if(0!=this.dzBf&&this.g3d.setC(this.colixEndcap)){var b=this.xAf,d=this.yAf,c=this.zAf;a&&0>this.dzBf&&(b+=this.dxBf,d+=this.dyBf,c+=this.dzBf);a=A(b);d=A(d);c=A(c);this.findMinMaxY();for(b=this.yMin;b<=this.yMax;++b){this.findMinMaxX(b);var f=this.xMax-this.xMin+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(f,a+this.xMin,d+b,c-this.zXMin-1,c-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 c=b?this.dxBf:this.dxB,f=b?this.dyBf:this.dyB;0<=d||!a?(this.endcapShadeIndex=this.shader.getShadeIndex(-c,-f,d),this.colixEndcap=
this.colixA,d=this.shadesA):(this.endcapShadeIndex=this.shader.getShadeIndex(c,f,-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")}),p("J.g3d"),I(J.g3d,"G3DRenderer"),p("J.g3d"),v(["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 $.TextString JU.C".split(" "),
function(){c$=u(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;q(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);L(c$,function(){this.vectorAB=new JU.V3;this.vectorAC=new JU.V3;this.vectorNormal=new JU.V3;this.transformedVectors=Array(J.g3d.Graphics3D.normixCount);
for(var a=J.g3d.Graphics3D.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3;this.shadeIndexes=Q(J.g3d.Graphics3D.normixCount,0);this.shadeIndexes2Sided=Q(J.g3d.Graphics3D.normixCount,0)});h(c$,"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$,"setZMargin",function(a){this.zMargin=a},"~N");s(c$,function(){G(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$,"beginRendering",function(a,b,d,c){this.$currentlyRendering&&this.endRendering();this.renderLow=c;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=C(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$,"mergeBufferPixel",function(a,b,d,c){if(0!=d){var f=a[b];if(f!=d){0==f&&(f=c);c=f&16711935;var f=f&65280,e=d&16711935,j=d&65280;switch(d>>24&15){case 0:c=e;f=j;break;case 1:c=(e<<2)+(e<<1)+e+c>>3&16711935;f=(j<<2)+ +(j<<1)+j+f>>3&65280;break;case 2:c=(e<<1)+e+c>>2&16711935;f=(j<<1)+j+f>>2&65280;break;case 3:c=(e<<2)+e+(c<<1)+c>>3&16711935;f=(j<<2)+j+(f<<1)+f>>3&65280;break;case 4:c=c+e>>1&16711935;f=f+j>>1&65280;break;case 5:c=(e<<1)+e+(c<<2)+c>>3&16711935;f=(j<<1)+j+(f<<2)+f>>3&65280;break;
case 6:c=(c<<1)+c+e>>2&16711935;f=(f<<1)+f+j>>2&65280;break;case 7:c=(c<<2)+(c<<1)+c+e>>3&16711935,f=(f<<2)+(f<<1)+f+j>>3&65280}a[b]=4278190080|c|f}}},"~A,~N,~N,~N");h(c$,"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.$currentlyRendering)throw new NullPointerException;this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=Q(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});c(c$,"applyCustomAnaglyph",function(a){var b=a[0];a=a[1]&16777215;for(var d=this.anaglyphLength;0<=--d;){var c=
this.anaglyphChannelBytes[d]&255,c=(c|(c|c<<8)<<8)&a;this.pbuf[d]=this.pbuf[d]&b|c}},"~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,c){a?(this.setZShade2(b,d,c),this.pixel=new J.g3d.PixelatorShaded(this)):this.pixel=new J.g3d.Pixelator(this)},"~B,~N,~N,~N");c(c$,"downsampleFullSceneAntialiasing",function(a){var b=this.width,d=0,c=0,f=this.bgcolor;
a&&(f+=255==(f&255)?-1:1);for(var e=this.pbuf.length;0<=--e;)0==this.pbuf[e]&&(this.pbuf[e]=f);f&=16777215;for(e=this.windowHeight;0<=--e;c+=b)for(var j=this.windowWidth;0<=--j;++d){var k=(this.pbuf[c]>>2&1061109567)+(this.pbuf[c++ +b]>>2&1061109567)+(this.pbuf[c]>>2&1061109567)+(this.pbuf[c++ +b]>>2&1061109567),k=k+((k&3233857728)>>6);this.pbuf[d]=k&16777215|4278190080}if(a){d=c=0;for(e=this.windowHeight;0<=--e;c+=b)for(j=this.windowWidth;0<=--j;++d,++c)a=Math.min(this.zbuf[c],this.zbuf[c+b]),a=
Math.min(a,this.zbuf[++c]),a=Math.min(a,this.zbuf[c+b]),2147483647!=a&&(a>>=1),this.zbuf[d]=this.pbuf[d]==f?2147483647:a;this.antialiasThisFrame=!1;this.setWidthHeight(!1)}},"~B");c(c$,"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 c=0!=d;this.isScreened=c&&30720==d;if(!this.checkTranslucent(c&&!this.isScreened))return!1;this.aap=this.$isPass2||!c;this.$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$,"drawFilledCircle",function(a,b,d,c,f,e){if(!this.isClippedZ(e)){var j=w((d+1)/2),j=c<j||c+j>=this.width||f<j||f+j>=this.height;if(!j||!this.isClippedXY(d,c,f))0!=a&&this.setC(a)&&(j?this.circle3d.plotCircleCenteredClipped(c,f,e,d):this.circle3d.plotCircleCenteredUnclipped(c,f,e,d)),0!=b&&this.setC(b)&&
(j?this.circle3d.plotFilledCircleCenteredClipped(c,f,e,d):this.circle3d.plotFilledCircleCenteredUnclipped(c,f,e,d))}},"~N,~N,~N,~N,~N,~N");h(c$,"volumeRender4",function(a,b,d,c){if(1==a)this.plotPixelClippedXYZ(b,d,c);else if(!this.isClippedZ(c)){var f=w((a+1)/2),f=b<f||b+f>=this.width||d<f||d+f>=this.height;if(!f||!this.isClippedXY(a,b,d))f?this.circle3d.plotFilledCircleCenteredClipped(b,d,c,a):this.circle3d.plotFilledCircleCenteredUnclipped(b,d,c,a)}},"~N,~N,~N,~N");h(c$,"fillSphereXYZ",function(a,
b,d,c){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,b,d,c);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,!this.aap,a,b,d,c,null,null,null,-1,null,this.aap)},"~N,~N,~N,~N");h(c$,"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$,"fillEllipsoid",function(a,b,d,c,f,e,j,k,l,h,n){switch(e){case 1:this.plotPixelClippedArgb(this.argbCurrent,d,c,f);return;case 0:return}e<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,!this.aap,e,d,c,f,j,k,l,h,n,this.aap)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");
h(c$,"drawRect",function(a,b,d,c,f,e){if(!(0!=c&&this.isClippedZ(c))){c=f-1;e-=1;f=a+c;var j=b+e;0<=b&&b<this.height&&this.drawHLine(a,b,d,c);0<=j&&j<this.height&&this.drawHLine(a,j,d,c);0<=a&&a<this.width&&this.drawVLine(a,b,d,e);0<=f&&f<this.width&&this.drawVLine(f,b,d,e)}},"~N,~N,~N,~N,~N,~N");c(c$,"drawHLine",function(a,b,d,c){0>c&&(a+=c,c=-c);0>a&&(c+=a,a=0);a+c>=this.width&&(c=this.width-1-a);var f=a+this.width*b;if(this.aap)for(a=0;a<=c;a++)d<this.zbuf[f]&&this.addPixel(f,d,this.argbCurrent),
f++;else{b=0!=((a^b)&1);for(a=0;a<=c;a++)(b=!b)&&d<this.zbuf[f]&&this.addPixel(f,d,this.argbCurrent),f++}},"~N,~N,~N,~N");c(c$,"drawVLine",function(a,b,d,c){0>c&&(b+=c,c=-c);0>b&&(c+=b,b=0);b+c>=this.height&&(c=this.height-1-b);var f=a+this.width*b;if(this.aap)for(a=0;a<=c;a++)d<this.zbuf[f]&&this.addPixel(f,d,this.argbCurrent),f+=this.width;else{b=0!=((a^b)&1);for(a=0;a<=c;a++)(b=!b)&&d<this.zbuf[f]&&this.addPixel(f,d,this.argbCurrent),f+=this.width}},"~N,~N,~N,~N");h(c$,"fillRect",function(a,b,
d,c,f,e){if(!this.isClippedZ(c)){if(0>a){f+=a;if(0>=f)return;a=0}if(a+f>this.width&&(f=this.width-a,0>=f))return;if(0>b){e+=b;if(0>=e)return;b=0}for(b+e>this.height&&(e=this.height-b);0<=--e;)this.plotPixelsUnclippedCount(f,a,b++,d)}},"~N,~N,~N,~N,~N,~N");h(c$,"drawString",function(a,b,d,c,f,e,j){this.currentShadeIndex=0;null!=a&&(this.isClippedZ(e)||this.drawStringNoSlab(a,b,d,c,f,j))},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");h(c$,"drawStringNoSlab",function(a,b,d,c,f,e){if(null!=a){null==this.strings&&
(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));var j=new J.g3d.TextString;j.setText(a,null==b?this.currentFont:this.currentFont=b,this.argbCurrent,JU.C.isColixTranslucent(e)?this.getColorArgbOrGray(e)&16777215|(e&30720)<<13:0,d,c,f);this.strings[this.stringCount++]=j}},"~S,javajs.awt.Font,~N,~N,~N,~N");h(c$,"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$,"plotText",function(a,b,d,c,f,e,j,k){J.g3d.TextRenderer.plot(a,b,d,c,f,e,j,this,k,this.antialiasThisFrame)},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.api.JmolRendererInterface");h(c$,"drawImage",function(a,b,d,c,f,e,j,k){null==a||(0==j||0==k||this.isClippedZ(f))||
this.plotImage(b,d,c,a,null,e,j,k)},"~O,~N,~N,~N,~N,~N,~N,~N");h(c$,"plotImage",function(a,b,d,c,f,e,j,k){this.setC(e);this.$isPass2||(this.translucencyMask=-1);0==e&&(this.argbCurrent=0);J.g3d.ImageRenderer.plotImage(a,b,d,c,this,f,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$,"drawPoints",function(a,b,d){if(1<d)for(var c=0.8*d*d,f=-d;f<d;f++)for(var e=-d;e<d;e++)f*f+e*e>c||(this.plotPoints(a,b,f,e),this.plotPoints(a,b,f,e));else this.plotPoints(a,b,0,0)},"~N,~A,~N");h(c$,"drawDashedLine",function(a,b,d,c){this.line3d.plotDashedLine(this.argbCurrent,!this.aap,a,b,d.x,d.y,d.z,c.x,c.y,c.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,c,f,e){this.line3d.plotLine(this.argbCurrent,!this.aap,this.argbCurrent,!this.aap,a,b,d,c,f,e,!0)},"~N,~N,~N,~N,~N,~N");h(c$,"drawLine",function(a,b,d,c,f,e,j,k){this.setC(a)||(a=0);var l=!this.aap,h=this.argbCurrent;this.setC(b)||(b=0);0==a&&0==b||this.line3d.plotLine(h,l,this.argbCurrent,!this.aap,d,c,f,e,j,k,!0)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"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$,"fillCylinderXYZ",function(a,b,d,c,f,e,j,k,l,h){this.setC(a)||(a=0);var n=!this.aap;this.setC(b)||(b=0);0==a&&0==b||this.cylinder3d.render(a,b,n,!this.aap,d,c,f,e,j,k,l,h)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen",function(a,b,d,c,f,e,j,k){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d,c,f,e,j,k)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen3I",function(a,
b,d,c){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d.x,d.y,d.z,c.x,c.y,c.z)},"~N,~N,JU.P3i,JU.P3i,JU.P3,JU.P3,~N");h(c$,"fillCylinder",function(a,b,d,c){this.cylinder3d.render(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d.x,d.y,d.z,c.x,c.y,c.z)},"~N,~N,JU.P3i,JU.P3i");h(c$,"fillCylinderBits",function(a,b,d,c){this.cylinder3d.renderBits(this.colixCurrent,this.colixCurrent,!this.aap,!this.aap,a,b,d.x,d.y,d.z,c.x,c.y,c.z)},"~N,~N,JU.P3,JU.P3");h(c$,
"fillConeScreen",function(a,b,d,c,f){this.cylinder3d.renderCone(this.colixCurrent,!this.aap,a,b,d.x,d.y,d.z,c.x,c.y,c.z,!1,f)},"~N,~N,JU.P3i,JU.P3i,~B");h(c$,"fillConeSceen3f",function(a,b,d,c){this.cylinder3d.renderCone(this.colixCurrent,!this.aap,a,b,d.x,d.y,d.z,c.x,c.y,c.z,!0,!1)},"~N,~N,JU.P3,JU.P3");h(c$,"drawHermite4",function(a,b,d,c,f){this.hermite3d.renderHermiteRope(!1,a,0,0,0,b,d,c,f)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawHermite7",function(a,b,d,c,f,e,j,k,l,h,n,t,z){if(0==z)this.hermite3d.renderHermiteRibbon(a,
b,d,c,f,e,j,k,l,h,n,t,0);else{this.hermite3d.renderHermiteRibbon(a,b,d,c,f,e,j,k,l,h,n,t,1);var F=this.colixCurrent;this.setC(z);this.hermite3d.renderHermiteRibbon(a,b,d,c,f,e,j,k,l,h,n,t,-1);this.setC(F)}},"~B,~B,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,~N,~N");h(c$,"fillHermite",function(a,b,d,c,f,e,j,k){this.hermite3d.renderHermiteRope(!0,a,b,d,c,f,e,j,k)},"~N,~N,~N,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawTriangle3C",function(a,b,d,c,f,e,j){1==(j&1)&&this.drawLine(b,c,a.x,
a.y,a.z,d.x,d.y,d.z);2==(j&2)&&this.drawLine(c,e,d.x,d.y,d.z,f.x,f.y,f.z);4==(j&4)&&this.drawLine(b,e,a.x,a.y,a.z,f.x,f.y,f.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");h(c$,"drawTriangle3I",function(a,b,d,c){1==(c&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==(c&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==(c&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$,"fillTriangleTwoSided",function(a,b,d,c,f,e,j,k,l,h){this.setColorNoisy(this.getShadeIndex(a));this.triangle3d.fillTriangleXYZ(b,d,c,f,e,j,k,l,h,!1)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillTriangle3f",function(a,b,d,c){var f=this.getShadeIndexP3(a,b,d);c?this.setColorNoisy(f):this.setColor(this.shadesCurrent[f]);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,c,f,e,j,k,l,h){if(!this.$isPass2&&d==e&&d==l&&b==f&&b==k)this.setTriangleColixAndShadeIndex(b,this.getShadeIndex(d)),b=!1;else{if(!this.setTriangleTranslucency(b,f,k))return;this.triangle3d.setGouraud(this.getShades(b)[this.getShadeIndex(d)],this.getShades(f)[this.getShadeIndex(e)],this.getShades(k)[this.getShadeIndex(l)]);b=!0}this.triangle3d.fillTriangleP3if(a,c,j,h,b)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N,~N");
h(c$,"fillTriangle3CN",function(a,b,d,c,f,e,j,k,l){if(!this.$isPass2&&d==e&&d==l&&b==f&&b==k)this.setTriangleColixAndShadeIndex(b,this.getShadeIndex(d)),b=!1;else{if(!this.setTriangleTranslucency(b,f,k))return;this.triangle3d.setGouraud(this.getShades(b)[this.getShadeIndex(d)],this.getShades(f)[this.getShadeIndex(e)],this.getShades(k)[this.getShadeIndex(l)]);b=!0}this.triangle3d.fillTriangleP3i(a,c,j,b)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");c(c$,"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(w((a+b+d)/3))&30720)<<13|16777215;return!0},"~N,~N,~N");h(c$,"drawQuadrilateral",function(a,b,d,c,f){this.setC(a);this.drawLineAB(b,d);this.drawLineAB(d,c);this.drawLineAB(c,f);this.drawLineAB(f,b)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"fillQuadrilateral",
function(a,b,d,c){this.setColorNoisy(this.getShadeIndexP3(a,b,d));this.triangle3d.fillTriangleP3f(a,b,d,!1);this.triangle3d.fillTriangleP3f(a,d,c,!1)},"JU.P3,JU.P3,JU.P3,JU.P3");h(c$,"fillQuadrilateral3i",function(a,b,d,c,f,e,j,k,l,h,n,t){this.fillTriangle3CN(a,b,d,c,f,e,j,k,l);this.fillTriangle3CN(a,b,d,j,k,l,h,n,t)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");h(c$,"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$,"plotPixelClippedArgb",function(a,b,d,c){this.isClipped3(b,d,c)||(b=d*this.width+b,c<this.zbuf[b]&&this.addPixel(b,c,a))},"~N,~N,~N,~N");h(c$,"plotImagePixel",function(a,b,d,c,f,e){this.isClipped(b,d)||(b=d*this.width+b,c<this.zbuf[b]&&this.shadeTextPixel(b,c,a,e,f))},"~N,~N,~N,~N,~N,~N");c(c$,"plotPixelClippedScreened",function(a,b,d,c,f){!this.isClipped3(d,
c,f)&&!(b&&0!=((d^c)&1))&&(b=c*this.width+d,f<this.zbuf[b]&&this.addPixel(b,f,a))},"~N,~B,~N,~N,~N");c(c$,"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$,"plotPixelUnclippedArgb",function(a,b,d,c){b=d*this.width+b;c<this.zbuf[b]&&this.addPixel(b,c,a)},"~N,~N,~N,~N");c(c$,"plotPixelsClipped",function(a,b,d,c){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 f=d*this.width+
b;a=f+a;var e=1;this.aap||(e=2,0!=((b^d)&1)&&++f);for(;f<a;)c<this.zbuf[f]&&this.addPixel(f,c,this.argbCurrent),f+=e}},"~N,~N,~N,~N");c(c$,"plotPixelsClippedRaster",function(a,b,d,c,f,e,j){if(!(0>=a||0>d||d>=this.height||b>=this.width||c<this.slab&&f<this.slab||c>this.depth&&f>this.depth)){var k=(b<<16)+(d<<1)^858993459,l=(c<<10)+512;c=f-c;f=w(a/2);c=JU.GData.roundInt(w(((c<<10)+(0<=c?f:-f))/a));if(0>b){b=-b;l+=c*b;a-=b;if(0>=a)return;b=0}a+b>this.width&&(a=this.width-b);f=0!=((b^d)&1);b=d*this.width+
b;if(null==e)for(;0<=--a;){if(this.aap||!0==(f=!f))j=l>>10,j>=this.slab&&(j<=this.depth&&j<this.zbuf[b])&&(k=(k<<16)+(k<<1)+k&2147483647,e=k>>16&7,this.addPixel(b,j,0==e?this.argbNoisyDn:1==e?this.argbNoisyUp:this.argbCurrent));++b;l+=c}else{k=e.r<<8;d=w((j.r-e.r<<8)/a);var h=e.g,n=w((j.g-h)/a);e=e.b;for(var t=w((j.b-e)/a);0<=--a;){if(this.aap||(f=!f))j=l>>10,j>=this.slab&&(j<=this.depth&&j<this.zbuf[b])&&this.addPixel(b,j,4278190080|k&16711680|h&65280|e>>8&255);++b;l+=c;k+=d;h+=n;e+=t}}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");
c(c$,"plotPixelsUnclippedRaster",function(a,b,d,c,f,e,j){if(!(0>=a)){var k=((b<<16)+(d<<1)^858993459)&2147483647,l=0!=((b^d)&1),h=(c<<10)+512;c=f-c;f=w(a/2);c=JU.GData.roundInt(w(((c<<10)+(0<=c?f:-f))/a));b=d*this.width+b;if(null==e)for(;0<=--a;){if(this.aap||(l=!l))j=h>>10,j<this.zbuf[b]&&(k=(k<<16)+(k<<1)+k&2147483647,e=k>>16&7,this.addPixel(b,j,0==e?this.argbNoisyDn:1==e?this.argbNoisyUp:this.argbCurrent));++b;h+=c}else{k=e.r<<8;d=JU.GData.roundInt(w((j.r-e.r<<8)/a));f=e.g;var n=JU.GData.roundInt(w((j.g-
f)/a));e=e.b;for(var t=JU.GData.roundInt(w((j.b-e)/a));0<=--a;){if(this.aap||(l=!l))j=h>>10,j<this.zbuf[b]&&this.addPixel(b,j,4278190080|k&16711680|f&65280|e>>8&255);++b;h+=c;k+=d;f+=n;e+=t}}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsUnclippedCount",function(a,b,d,c){var f=d*this.width+b;if(this.aap)for(;0<=--a;)c<this.zbuf[f]&&this.addPixel(f,c,this.argbCurrent),++f;else if(a=f+a,!(0!=((b^d)&1)&&++f==a)){do c<this.zbuf[f]&&this.addPixel(f,c,this.argbCurrent),f+=2;while(f<a)}},"~N,~N,~N,~N");
c(c$,"plotPoints",function(a,b,d,c){for(a*=3;0<a;){var f=b[--a],e=b[--a]+c,j=b[--a]+d;if(!this.isClipped3(j,e,f)){var k=e*this.width+j++;f<this.zbuf[k]&&this.addPixel(k,f,this.argbCurrent);this.antialiasThisFrame&&(k=e*this.width+j,!this.isClipped3(j,e,f)&&f<this.zbuf[k]&&this.addPixel(k,f,this.argbCurrent),k=++e*this.width+j,!this.isClipped3(j,e,f)&&f<this.zbuf[k]&&this.addPixel(k,f,this.argbCurrent),k=e*this.width+--j,!this.isClipped3(j,e,f)&&f<this.zbuf[k]&&this.addPixel(k,f,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 c=this.transformedVectors[d];a.rotate2(b[d],c);this.shadeIndexes[d]=this.shader.getShadeB(c.x,-c.y,c.z);this.shadeIndexes2Sided[d]=0<=c.z?this.shadeIndexes[d]:this.shader.getShadeB(-c.x,c.y,-c.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,c,f){b=this.isAntialiased();this.setC(0>f?10:100<f?11:23);f=Math.max(Math.min(this.width,Math.round(c.x)),0);d=Math.max(Math.min(this.height,Math.round(c.y)),0);var e=Math.round(c.z)+1,j=b?8:4,k=b?20:10;b=b?2:1;this.drawRect(f-j,d,e,0,k,b);this.drawRect(f,d-j,e,0,b,k);this.drawRect(f-j,d-j,e,0,k,k);j=k;k>>=1;this.setC(a[1]<c.x?21:11);this.drawRect(f-j,d,e,0,k,b);this.setC(a[0]>c.x?21:11);this.drawRect(f+k,d,e,0,k,b);this.setC(a[3]<c.y?21:11);this.drawRect(f,d-j,e,0,b,k);this.setC(a[2]>
c.y?21:11);this.drawRect(f,d+k,e,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,c,f){switch(f){case 8:this.addPixel(a,b,d);return}0!=c&&J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,c,this.bgcolor);f+=this.translucencyLog;7<f||(J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,d&16777215|f<<24,this.bgcolor),this.zbuf[a]=b)},"~N,~N,~N,~N,~N");x(c$,"sort",null);c$.normixCount=c$.prototype.normixCount=
JU.Normix.getNormixCount();x(c$,"nullShadeIndex",50)}),p("J.g3d"),c$=y(J.g3d,"ImageRenderer"),c$.plotImage=c(c$,"plotImage",function(a,b,d,c,f,e,j,k,l,h){k=(j=-2147483648==a)?f.bgcolor:k;j&&(a=0,d=2147483646,l=f.width,h=f.height);0>=a+l||(a>=f.width||0>=b+h||b>=f.height)||(c=f.apiPlatform.drawImageToBuffer(null,f.platform.offscreenImage,c,l,h,j?k:0),null!=c&&(null!=e||0>a||a+l>f.width||0>b||b+h>f.height?J.g3d.ImageRenderer.plotImageClipped(a,b,d,f,e,l,h,c,k):J.g3d.ImageRenderer.plotImageUnClipped(a,
b,d,f,l,h,c,k)))},"~N,~N,~N,~O,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B,~N,~N,~N"),c$.plotImageClipped=c(c$,"plotImageClipped",function(a,b,d,c,f,e,j,k,l){null==f&&(f=c);for(var h=c=0;c<j;c++)for(var n=0;n<e;n++){var t=k[h++];f.plotImagePixel(t,a+n,b+c,d,8,l)}},"~N,~N,~N,J.g3d.Graphics3D,J.api.JmolRendererInterface,~N,~N,~A,~N"),c$.plotImageUnClipped=c(c$,"plotImageUnClipped",function(a,b,d,c,f,e,j){var k=c.zbuf,l=c.width;a=b*l+a;for(var h=b=0,n=0;b<e;){for(;h<f;)d<k[a]&&c.addPixel(a,d,j[n]),
++n,++h,++a;++b;h-=f;a+=l-f}},"~N,~N,~N,J.g3d.Graphics3D,~N,~N,~A,~N"),p("J.g3d"),v(["java.util.Hashtable"],"J.g3d.LineRenderer",["java.lang.Float","JU.BS","JU.Logger"],function(){c$=u(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;q(this,arguments)},J.g3d,"LineRenderer");L(c$,function(){this.lineCache=new java.util.Hashtable});
s(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"setLineBits",function(a,b){this.slope=0!=a?b/a:0<=b?3.4028235E38:-3.4028235E38;this.nBits=(this.lineTypeX=1>=this.slope&&-1<=this.slope)?this.g3d.getRenderWidth():this.g3d.getRenderHeight();if(!this.getCachedLine()){this.lineBits=JU.BS.newN(this.nBits);b=Math.abs(b);a=Math.abs(a);if(b>a){var d=a;a=b;b=d}for(var d=0,c=a+a,f=b+b,e=0;e<this.nBits;e++)d+=f,d>a&&(this.lineBits.set(e),d-=c);this.lineCache.put(this.slopeKey,this.lineBits);
this.nCached++}},"~N,~N");c(c$,"clearLineCache",function(){this.lineCache.clear();this.nCached=0});c(c$,"plotLine",function(a,b,d,c,f,e,j,k,l,h,n){this.x1t=f;this.x2t=k;this.y1t=e;this.y2t=l;this.z1t=j;this.z2t=h;if(n)switch(this.getTrimmedLine()){case 0:n=!1;break;case 2:return}this.plotLineClipped(a,b,d,c,f,e,j,k-f,l-e,h-j,n,0,0)},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDelta",function(a,b,d,c,f,e,j,k,l,h,n){this.x1t=f;this.x2t=f+k;this.y1t=e;this.y2t=e+l;this.z1t=j;this.z2t=j+h;if(n)switch(this.getTrimmedLine()){case 2:return;
case 0:n=!1}this.plotLineClipped(a,b,d,c,f,e,j,k,l,h,n,0,0)},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaA",function(a,b,d,c,f,e,j,k,l,h,n,t){this.x1t=e;this.x2t=e+l;this.y1t=j;this.y2t=j+h;this.z1t=k;this.z2t=k+n;if(t)switch(this.getTrimmedLine()){case 2:return;case 0:t=!1}this.plotLineClippedA(a,b,d,c,f,e,j,k,l,h,n,t,0,0)},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaBits",function(a,b,d,c,f,e,j,k,l,h,n,t){this.x1t=e;this.x2t=e+l;this.y1t=j;this.y2t=j+h;this.z1t=k;this.z2t=
k+n;t&&2==this.getTrimmedLine()||this.plotLineClippedBits(a,b,d,c,f,e,j,k,l,h,n,0,0)},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotDashedLine",function(a,b,d,c,f,e,j,k,l,h,n){this.x1t=f;this.x2t=k;this.y1t=e;this.y2t=l;this.z1t=j;this.z2t=h;if(n)switch(this.getTrimmedLine()){case 2:return;case 0:n=!1}this.plotLineClipped(a,b,a,b,f,e,j,k-f,l-e,h-j,n,d,c)},"~N,~B,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"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,c=this.g3d.depth;do{if(0!=(this.cc1&this.cc2))return 2;var f=this.x2t-this.x1t,e=this.y2t-
this.y1t,j=this.z2t-this.z1t;0!=this.cc1?(0!=(this.cc1&8)?(this.y1t+=A(-this.x1t*e/f),this.z1t+=A(-this.x1t*j/f),this.x1t=0):0!=(this.cc1&4)?(this.y1t+=A((a-this.x1t)*e/f),this.z1t+=A((a-this.x1t)*j/f),this.x1t=a):0!=(this.cc1&2)?(this.x1t+=A(-this.y1t*f/e),this.z1t+=A(-this.y1t*j/e),this.y1t=0):0!=(this.cc1&1)?(this.x1t+=A((b-this.y1t)*f/e),this.z1t+=A((b-this.y1t)*j/e),this.y1t=b):0!=(this.cc1&32)?(this.x1t+=A((d-this.z1t)*f/j),this.y1t+=A((d-this.z1t)*e/j),this.z1t=d):(this.x1t+=A((c-this.z1t)*
f/j),this.y1t+=A((c-this.z1t)*e/j),this.z1t=c),this.cc1=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(this.cc2&8)?(this.y2t+=A(-this.x2t*e/f),this.z2t+=A(-this.x2t*j/f),this.x2t=0):0!=(this.cc2&4)?(this.y2t+=A((a-this.x2t)*e/f),this.z2t+=A((a-this.x2t)*j/f),this.x2t=a):0!=(this.cc2&2)?(this.x2t+=A(-this.y2t*f/e),this.z2t+=A(-this.y2t*j/e),this.y2t=0):0!=(this.cc2&1)?(this.x2t+=A((b-this.y2t)*f/e),this.z2t+=A((b-this.y2t)*j/e),this.y2t=b):0!=(this.cc2&32)?(this.x2t+=A((d-this.z2t)*f/j),this.y2t+=
A((d-this.z2t)*e/j),this.z2t=d):(this.x2t+=A((c-this.z2t)*f/j),this.y2t+=A((c-this.z2t)*e/j),this.z2t=c),this.cc2=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(this.cc1|this.cc2));return 1});c(c$,"plotLineClipped",function(a,b,d,c,f,e,j,k,l,h,n,t,z){var F=this.g3d.zbuf,K=this.g3d.getRenderWidth(),r=0;0==t&&(z=2147483647,t=1);var q=e*K+f,s=this.g3d.bufferSize,p=0!=((f^e)&1);0!=a&&(!n&&0<=q&&q<s&&j<F[q]&&(!b||(p=!p)))&&this.g3d.addPixel(q,j,a);if(!(0==k&&0==l)){n=1;var u=K;f+=k;var v=e+
l;0>k&&(k=-k,n=-1);0>l&&(l=-l,u=-K);K=k+k;e=l+l;j<<=10;if(l<=k){var A=k-1;0>h&&(A=-A);h=w(((h<<10)+A)/k);l=0;A=Math.abs(f-this.x2t)-1;f=Math.abs(f-this.x1t)-1;for(var v=k-1,y=w(v/2);--v>=A&&!(v==y&&(b=c,a=d,0==a));){q+=n;j+=h;l+=e;l>k&&(q+=u,l-=K,p=!p);if(0!=a&&v<f&&0<=q&&q<s&&r<z&&(!b||(p=!p))){var B=j>>10;B<F[q]&&this.g3d.addPixel(q,B,a)}r=(r+1)%t}}else{A=l-1;0>h&&(A=-A);h=w(((h<<10)+A)/l);k=0;A=Math.abs(v-this.y2t)-1;f=Math.abs(v-this.y1t)-1;v=l-1;for(y=w(v/2);--v>=A&&!(v==y&&(b=c,a=d,0==a));){q+=
u;j+=h;k+=K;k>l&&(q+=n,k-=e,p=!p);if(0!=a&&v<f&&0<=q&&q<s&&r<z&&(!b||(p=!p)))B=j>>10,B<F[q]&&this.g3d.addPixel(q,B,a);r=(r+1)%t}}}},"~N,~B,~N,~B,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedA",function(a,b,d,c,f,e,j,k,l,h,n,t,z,F){var K=this.g3d.zbuf,r=this.g3d.getRenderWidth(),q=0;0==z&&(F=2147483647,z=1);var p=j*r+e,s=this.g3d.bufferSize,u=63>f?f+1:f,v=0<f?f-1:f,A=a[u],y=a[v],B=d[f],u=d[u];d=d[v];a=a[f];f=b;var x=0!=((e^j)&1);0!=a&&(!t&&0<=p&&p<s&&k<K[p]&&(!f||(x=!x)))&&this.g3d.addPixel(p,
k,a);if(!(0==l&&0==h)){t=1;var v=r,C=e+l,D=j+h;0>l&&(l=-l,t=-1);0>h&&(h=-h,v=-r);j=l+l;e=h+h;k<<=10;if(h<=l){var G=l-1;0>n&&(G=-G);n=w(((n<<10)+G)/l);h=0;for(var G=Math.abs(C-this.x2t)-1,C=Math.abs(C-this.x1t)-1,D=l-1,H=w(D/2);--D>=G;){if(D==H){a=B;if(0==a)break;A=u;y=d;if((f=c)&&!b)var x=w(p/r),E=p%r,x=0==((E^x)&1)}p+=t;k+=n;h+=e;h>l&&(p+=v,h-=j,x=!x);if(0!=a&&D<C&&0<=p&&p<s&&q<F&&(!f||(x=!x)))if(E=k>>10,E<K[p]){var I=this.shader.nextRandom8Bit();this.g3d.addPixel(p,E,85>I?y:170<I?A:a)}q=(q+1)%z}}else{G=
h-1;0>n&&(G=-G);n=w(((n<<10)+G)/h);l=0;G=Math.abs(D-this.y2t)-1;C=Math.abs(D-this.y1t)-1;D=h-1;for(H=w(D/2);--D>=G;){if(D==H){a=B;if(0==a)break;A=u;y=d;if((f=c)&&!b)x=w(p/r),E=p%r,x=0==((E^x)&1)}p+=v;k+=n;l+=j;l>h&&(p+=t,l-=e,x=!x);if(0!=a&&D<C&&0<=p&&p<s&&q<F&&(!f||(x=!x)))E=k>>10,E<K[p]&&(I=this.g3d.shader.nextRandom8Bit(),this.g3d.addPixel(p,E,85>I?y:170<I?A:a));q=(q+1)%z}}}},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedBits",function(a,b,d,c,f,e,j,k,l,h,n,t,z){var F=this.g3d.zbuf,
K=this.g3d.width,r=0;0==t&&(z=2147483647,t=1);var q=63>f?f+1:f,p=0<f?f-1:f,s=a[f],u=a[q],v=a[p];f=d[f];q=d[q];d=d[p];var p=b,y=0!=((e^j)&1);a=j*K+e;var B=this.g3d.bufferSize,x,D,C,G,E;this.lineTypeX?(x=e,D=this.x1t,C=this.x2t,e+=w(l/2),G=j=0<=l?1:-1,E=0<=h?K:-K,l=n/Math.abs(l)):(x=j,D=this.y1t,C=this.y2t,e=j+w(h/2),j=0<=h?1:-1,G=0<=h?K:-K,E=0<=l?1:-1,l=n/Math.abs(h));h=!1;for(n=x;;n+=j,x+=j){n==D&&(h=!0);if(n==e){s=f;if(0==s)break;u=q;v=d;if((p=c)&&!b)y=w(a/K),y=0==((a%K^y)&1)}if(0!=s&&(h&&0<=a&&
a<B&&r<z&&(!p||(y=!y)))&&k<F[a]){var H=this.shader.nextRandom8Bit();this.g3d.addPixel(a,A(k),85>H?v:170<H?u:s)}if(n==C)break;r=(r+1)%t;for(a+=G;0>x;)x+=this.nBits;this.lineBits.get(x%this.nBits)&&(a+=E);k+=l}},"~A,~B,~A,~B,~N,~N,~N,~N,~N,~N,~N,~N,~N");x(c$,"VISIBILITY_UNCLIPPED",0,"VISIBILITY_CLIPPED",1,"VISIBILITY_OFFSCREEN",2)}),p("J.g3d"),v(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){c$=u(function(){this.g=null;q(this,arguments)},J.g3d,"Pixelator");s(c$,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.$isPass2){var c=this.g.zbufT[a];if(b<c){var f=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=f&&c-b>this.g.zMargin)&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,f,this.g.bgcolor);this.g.zbufT[a]=b;this.g.pbufT[a]=d&this.g.translucencyMask}else b!=c&&!this.g.translucentCoverOnly&&
b-c>this.g.zMargin&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,d&this.g.translucencyMask,this.g.bgcolor)}else this.g.zbuf[a]=b,this.g.pbuf[a]=d},"~N,~N,~N")}),p("J.g3d"),v(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){c$=y(J.g3d,"PixelatorShaded",J.g3d.Pixelator);h(c$,"addPixel",function(a,b,d){if(!(b>this.g.zDepth)){if(b<=this.g.zDepth&&b>=this.g.zSlab){var c=(d&65280)>>8,f=(d&16711680)>>16,e=d&4278190080,j=(this.g.zDepth-b)/(this.g.zDepth-this.g.zSlab);if(1<this.g.zShadePower)for(var k=
0;k<this.g.zShadePower;k++)j*=j;d=this.g.zShadeR+A(j*((d&255)-this.g.zShadeR));c=this.g.zShadeG+A(j*(c-this.g.zShadeG));f=this.g.zShadeB+A(j*(f-this.g.zShadeB));d=f<<16|c<<8|d|e}this.addPixel1(a,b,d)}},"~N,~N,~N")}),p("J.g3d"),c$=u(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;q(this,arguments)},J.g3d,"Platform3D"),s(c$,function(a){this.apiPlatform=a},"javajs.api.GenericPlatform"),c(c$,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))}),c(c$,"allocateTBuffers",function(a){this.bufferSizeT=a?this.bufferSize:this.windowSize;this.zBufferT=C(this.bufferSizeT,0);this.pBufferT=C(this.bufferSizeT,0)},"~B"),c(c$,"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=C(this.bufferSize,0);this.pBuffer=C(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$,"setBackgroundTransparent",function(a){J.g3d.Platform3D.backgroundTransparent=
a},"~B"),x(c$,"backgroundTransparent",!1),p("J.g3d"),v(["JU.P3"],"J.g3d.SphereRenderer",["JU.GData"],function(){c$=u(function(){this.shader=this.g3d=null;this.diameter=this.z=this.y=this.x=this.maxZ=this.minZ=this.maxY=this.minY=this.maxX=this.minX=0;this.tScreened=!1;this.mDeriv=this.coef=this.mat=this.zroot=this.shades=null;this.selectedOctant=0;this.octantPoints=null;this.planeShade=0;this.zbuf=null;this.offsetPbufBeginLine=this.slab=this.depth=this.height=this.width=0;this.addAllPixels=!1;this.dxyz=
this.planeShades=this.ptTemp=null;this.z0=0;q(this,arguments)},J.g3d,"SphereRenderer");L(c$,function(){this.zroot=$(2,0);this.ptTemp=new JU.P3;this.planeShades=C(3,0);this.dxyz=M(3,3,0)});s(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"render",function(a,b,d,c,f,e,j,k,l,h,n,t){if(1!=e&&(this.width=this.g3d.width,this.height=this.g3d.height,49<d&&(d&=-2),!this.g3d.isClippedXY(d,c,f))){var z=d+1>>1;this.minX=c-z;this.maxX=c+z;this.minY=f-z;this.maxY=f+z;this.slab=this.g3d.slab;
this.depth=this.g3d.depth;this.minZ=e-z;this.maxZ=e+z;this.maxZ<this.slab||this.minZ>this.depth||(this.shader.nOut=this.shader.nIn=0,this.zbuf=this.g3d.zbuf,this.addAllPixels=t,this.offsetPbufBeginLine=this.width*f+c,this.x=c,this.y=f,this.z=e,this.diameter=d,this.tScreened=b,this.shades=a,this.mat=j,null!=j&&(this.coef=k,this.mDeriv=l,this.selectedOctant=h,this.octantPoints=n),null!=j||128<d?(this.renderLarge(),null!=j&&(this.octantPoints=this.mDeriv=this.coef=this.mat=null)):(a=this.shader.sphereShapeCache[d-
1],null==a&&(a=this.createSphereShape(d)),0>this.minX||this.maxX>=this.width||0>this.minY||this.maxY>=this.height||this.minZ<this.slab||e>this.depth?this.renderShapeClipped(a,c,f,e,d):this.renderShapeUnclipped(a,c,f,e,d)),this.zbuf=this.shades=null)}},"~A,~B,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A,~B");c(c$,"createSphereShape",function(a){for(var b=this.shader,d=0,c=0!=(a&1),f=a/2,e=f*f,j=w((a+1)/2),k=c?0:0.5,l=0;l<j;++l,++k)for(var h=k*k,n=c?0:0.5,t=0;t<j;++t,++n){var z=n*n,z=e-h-z;0<=z&&++d}for(var d=
C(d,0),F=0,k=c?0:0.5,l=0;l<j;++l,++k){h=k*k;n=c?0:0.5;for(t=0;t<j;++t,++n)if(z=n*n,z=e-h-z,0<=z){var K=Math.sqrt(z),z=A(K),r=b.getShadeN(n,k,K,f),q=b.getShadeN(-n,k,K,f),p=b.getShadeN(n,-k,K,f),K=b.getShadeN(-n,-k,K,f),z=z|r<<7|q<<13|p<<19|K<<25;d[F++]=z}d[F-1]|=2147483648}return b.sphereShapeCache[a-1]=d},"~N");c(c$,"renderShapeUnclipped",function(a,b,d,c,f){var e=0,j=1-(f&1),k=this.offsetPbufBeginLine,l=k-j*this.width;f=w((f+1)/2);var h=this.shades,n=this.g3d,t=this.zbuf,z=this.width;if(this.tScreened){b=
(b^d)&1;d=b^j;b=b|(b^j)<<1|d<<2|(d^j)<<3;do{F=k;K=k-j;r=l;q=l-j;d=b=~b;do p=a[e++],s=c-(p&127),0!=(d&1)&&s<t[F]&&n.addPixel(F,s,h[p>>7&63]),0!=(d&2)&&s<t[K]&&n.addPixel(K,s,h[p>>13&63]),0!=(d&4)&&s<t[r]&&n.addPixel(r,s,h[p>>19&63]),0!=(d&8)&&s<t[q]&&n.addPixel(q,s,h[p>>25&63]),++F,--K,++r,--q,d=~d;while(0<=p);k+=z;l-=z}while(0<--f)}else{do{var F=k,K=k-j,r=l,q=l-j,p;do{p=a[e++];var s=c-(p&127);s<t[F]&&n.addPixel(F,s,h[p>>7&63]);s<t[K]&&n.addPixel(K,s,h[p>>13&63]);s<t[r]&&n.addPixel(r,s,h[p>>19&63]);
s<t[q]&&n.addPixel(q,s,h[p>>25&63]);++F;--K;++r;--q}while(0<=p);k+=z;l-=z}while(0<--f)}},"~A,~N,~N,~N,~N");c(c$,"renderShapeClipped",function(a,b,d,c,f){var e=0,j=1-(f&1),k=this.offsetPbufBeginLine,l=k-j*this.width;f=w((f+1)/2);var h=d,n=d-j,t=(b<<16)+(d<<1)^858993459;d=(b^d)&1;var z=d^j;d=d|(d^j)<<1|z<<2|(z^j)<<3;var z=this.shades,F=this.g3d,p=this.zbuf;do{var r=0<=h&&h<this.height,q=0<=n&&n<this.height,s=k,u=k-j,v=l,A=l-j,y,x=d=~d,B=b,D=b-j;do{var C=0<=D&&D<this.width,G=0<=B&&B<this.width;y=a[e++];
var E;E=y&127;var H;c<this.slab?(H=c+E,E=H>=this.slab):(H=c-E,E=H<this.slab);E&&(H=this.slab);if(H>=this.slab&&H<=this.depth){if(r){if(G&&(this.addAllPixels||0!=(x&1))&&H<p[s]){var I=E?44+(t>>7&7):y>>7&63;F.addPixel(s,H,z[I])}if(C&&(this.addAllPixels||0!=(x&2))&&H<p[u])I=E?44+(t>>13&7):y>>13&63,F.addPixel(u,H,z[I])}if(q){if(G&&(!this.tScreened||0!=(x&4))&&H<p[v])I=E?44+(t>>19&7):y>>19&63,F.addPixel(v,H,z[I]);if(C&&(!this.tScreened||0!=(x&8))&&H<p[A])I=E?44+(t>>25&7):y>>25&63,F.addPixel(A,H,z[I])}}++s;
--u;++v;--A;++B;--D;x=~x;E&&(t=(t<<16)+(t<<1)+t&2147483647)}while(0<=y);k+=this.width;l-=this.width;++h;--n}while(0<--f)},"~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=w(this.diameter/2),c=this.x+d*a,f=(0>this.x?
-1:this.x<this.width?0:1)+(0>c?-2:c<this.width?0:2);-3==f||3==f||(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==f&&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$,"renderQuadrantUnclipped",function(a,b,d){for(var c=a*a,f=2*a+1,e=0==((this.x^this.y)&1),j=0>d?-this.width:this.width,k=this.offsetPbufBeginLine,l=0,h=0;h<=c;h+=l+ ++l,k+=j)for(var n=k,t=
e=!e,z=c-h,F=this.z-a,p=w((l*d+a<<8)/f),r=0,q=0;q<=z;q+=r+ ++r,n+=b)if((this.addAllPixels||(t=!t))&&!(this.zbuf[n]<=F))if(F=w(Math.sqrt(z-q)),F=this.z-F,!(this.zbuf[n]<=F)){var s=w((r*b+a<<8)/f);this.g3d.addPixel(n,F,this.shades[this.shader.sphereShadeIndexes[(p<<8)+s]])}},"~N,~N,~N");c(c$,"renderQuadrantClipped",function(a,b,d){for(var c=null!=this.mat,f=0<=this.selectedOctant,e=a*a,j=2*a+1,k=0>d?-this.width:this.width,h=this.offsetPbufBeginLine,m=(this.x<<16)+(this.y<<1)^858993459,n=this.y,t=0,
z=0,F=0,p=0;p<=e;p+=F+ ++F,h+=k,n+=d)if(0>n){if(0>d)break}else if(n>=this.height){if(0<d)break}else{var r=e-(c?0:p),q=this.x;c||(t=w((F*d+a<<8)/j));for(var m=(m<<16)+(m<<1)+m&2147483647,s=-1,u=1,v=h,A=0,y=0;y<=r;y+=A+ ++A,v+=b,q+=b)if(0>q){if(0>b)break}else if(q>=this.width){if(0<b)break}else if(!(this.tScreened&&0!=((q^n)&1))){var x;if(c){if(!J.g3d.SphereRenderer.getQuardricZ(q,n,this.coef,this.zroot)){if(0<=s)break;continue}s=this.z<this.slab?1:0;x=w(this.zroot[s]);0==x&&(x=this.z);u=2;this.z0=
x;if(f){this.ptTemp.set(q-this.x,n-this.y,x-this.z);this.mat.rotate(this.ptTemp);JU.GData.getScreenOctant(this.ptTemp)==this.selectedOctant&&(z=this.getPlaneShade(q,n,this.zroot),x=w(this.zroot[0]),u=3);var B=this.z<this.slab?x>=this.slab:x<this.slab;B&&(this.z0=x=this.slab,u=0)}if(x<this.slab||x>this.depth||this.zbuf[v]<=this.z0)continue}else{x=w(Math.sqrt(r-y));x=this.z+(this.z<this.slab?x:-x);if(B=this.z<this.slab?x>=this.slab:x<this.slab)x=this.slab,u=0;if(x<this.slab||x>this.depth||this.zbuf[v]<=
x)continue}switch(u){case 0:z=44+(m>>8&7);m=(m<<16)+(m<<1)+m&2147483647;u=1;break;case 2:z=this.shader.getEllipsoidShade(q,n,this.zroot[s],a,this.mDeriv);break;case 3:this.g3d.clearPixel(v,this.z0);break;default:z=w((A*b+a<<8)/j),z=this.shader.sphereShadeIndexes[(t<<8)+z]}this.g3d.addPixel(v,x,this.shades[z])}m=(m+q+n|1)&2147483647}},"~N,~N,~N");c$.getQuardricZ=c(c$,"getQuardricZ",function(a,b,d,c){var f=(d[4]*a+d[5]*b+d[8])/d[2]/2;a=f*f-(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]=-f-a;c[1]=-f+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,f,e=3.4028235E38,
j=0;3>j;j++)if(0!=(f=this.dxyz[j][2]))f=this.z+(-this.dxyz[j][0]*(a-this.x)-this.dxyz[j][1]*(b-this.y))/f,f<e&&(e=f,c=j);3==c&&(c=0,e=this.z);d[0]=e;return this.planeShades[c]},"~N,~N,~A");x(c$,"maxOddSizeSphere",49,"maxSphereDiameter",1E3,"maxSphereDiameter2",2E3,"SHADE_SLAB_CLIPPED",47)}),p("J.g3d"),v(["java.util.Hashtable"],"J.g3d.TextRenderer",["JU.CU"],function(){c$=u(function(){this.size=this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=null;this.isInvalid=!1;q(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,f,e,j,k,h,m){if(0==e.length)return 0;if(0<=e.indexOf("<su")||0<=e.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,b,d,c,f,e,j,k,h,m);var n=j.getAscent();b-=n;e=J.g3d.TextRenderer.getPlotText3D(a,b,k,e,j,m);if(e.isInvalid)return e.width;m&&0==(c&12632256)&&(c|=263172);null!=
h||0>a||a+e.width>k.width||0>b||b+e.height>k.height?J.g3d.TextRenderer.plotClipped(a,b,d,c,f,k,h,e.mapWidth,e.height,e.tmap):J.g3d.TextRenderer.plotUnclipped(a,b,d,c,f,k,e.mapWidth,e.height,e.tmap);return e.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,f,e,j,k,h,m){for(var n=0,t=e.length,z=Math.round(0.25*j.getHeight()),F=-Math.round(0.3*j.getHeight()),q=0,p=0;p<t;p++){if("<"==e.charAt(p)){if(p+
5<t&&e.substring(p,p+6).equals("<color")){var q=c,r=e.indexOf(">",p);if(0>r)continue;c=JU.CU.getArgbFromString(e.substring(p+7,r).trim());p=r;continue}if(p+7<t&&e.substring(p,p+8).equals("</color>")){p+=7;c=q;continue}if(p+4<t&&e.substring(p,p+5).equals("<sub>")){p+=4;b+=z;continue}if(p+4<t&&e.substring(p,p+5).equals("<sup>")){p+=4;b+=F;continue}if(p+5<t&&e.substring(p,p+6).equals("</sub>")){p+=5;b-=z;continue}if(p+5<t&&e.substring(p,p+6).equals("</sup>")){p+=5;b-=F;continue}}r=J.g3d.TextRenderer.plot(a+
n,b,d,c,f,e.substring(p,p+1),j,k,h,m);n+=r}return n},"~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,f,e,j,k,h){var m=0,n=e.zbuf,t=e.width;a=b*t+a;for(b=0;b<k;b++){for(var z=0;z<j;z++){var F=h[m++];0!=F&&d<n[a]&&e.shadeTextPixel(a,d,c,f,F);a++}a+=t-j}},"~N,~N,~N,~N,~N,J.g3d.Graphics3D,~N,~N,~A");c$.plotClipped=c(c$,"plotClipped",function(a,b,d,c,f,e,j,k,h,m){null==j&&(j=e);for(var n=e=0;n<h;n++)for(var t=0;t<
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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,f),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&&e.put(f,j);m&&(k.setTranslucency(c,f,d),j.put(c,k));J.g3d.TextRenderer.working=!1;return k},"~N,~N,J.g3d.Graphics3D,~S,javajs.awt.Font,~B");c(c$,"setTranslucency",function(a,b,d){a=d.apiPlatform.getTextPixels(a,b,d.platform.getGraphicsForTextOrImage(this.mapWidth,this.height),d.platform.offscreenImage,
this.mapWidth,this.height,this.ascent);if(null!=a){this.tmap=Q(this.size,0);for(b=a.length;0<=--b;)d=a[b]&255,0!=d&&(this.tmap[b]=J.g3d.TextRenderer.translucency[d>>5])}},"~S,javajs.awt.Font,J.g3d.Graphics3D");x(c$,"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}),p("J.g3d"),c$=y(J.g3d,"TextSorter",null,java.util.Comparator),h(c$,"compare",function(a,b){return null==
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"JU.Rgb16"],"J.g3d.TriangleRenderer",["JU.GData"],function(){c$=u(function(){this.rgb16t2=this.rgb16t1=this.rgb16sGouraud=this.rgb16sE=this.rgb16sW=this.azE=this.axE=this.azW=this.axW=this.az=this.ay=this.ax=this.g3d=null;q(this,arguments)},J.g3d,"TriangleRenderer",null,J.g3d.G3DRenderer);L(c$,function(){this.ax=C(3,0);this.ay=C(3,0);this.az=C(3,0);this.axW=C(64,0);this.azW=C(64,0);this.axE=C(64,0);this.azE=C(64,0);this.rgb16t1=new JU.Rgb16;this.rgb16t2=new JU.Rgb16});s(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(!D(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);
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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$,"fillTriangleP3if",function(a,b,d,c,f){this.ax[0]=a.x;this.ax[1]=b.x;this.ax[2]=d.x;this.ay[0]=a.y;this.ay[1]=b.y;this.ay[2]=d.y;this.az[0]=a.z;this.az[1]=b.z;this.az[2]=d.z;J.g3d.TriangleRenderer.adjustVertex(this.ax,c);J.g3d.TriangleRenderer.adjustVertex(this.ay,c);J.g3d.TriangleRenderer.adjustVertex(this.az,c);this.fillTriangleB(f)},"JU.P3i,JU.P3i,JU.P3i,~N,~B");c$.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]),f=0!=(b|d|c);if(!(f&&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 e=d,d=c,c=e;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 n,t;a?(n=this.rgb16sW,t=this.rgb16sE):n=t=null;e=k-j;0==e?(this.ax[d]<this.ax[b]&&(e=d,d=b,b=e),this.generateRaster(m,b,c,this.axW,this.azW,0,n),this.generateRaster(m,d,c,this.axE,this.azE,0,t)):k==h?(this.ax[c]<this.ax[d]&&(e=d,d=c,c=e),this.generateRaster(m,b,d,this.axW,this.azW,0,n),this.generateRaster(m,b,c,this.axE,this.azE,0,t)):(k=this.ax[c]-this.ax[b],h=JU.GData.roundInt(w(m/2)),0>k&&(h=-h),this.ax[b]+w((k*e+h)/m)<this.ax[d]?
(this.generateRaster(m,b,c,this.axW,this.azW,0,n),this.generateRaster(e+1,b,d,this.axE,this.azE,0,t),this.generateRaster(m-e,d,c,this.axE,this.azE,e,t)):(this.generateRaster(e+1,b,d,this.axW,this.azW,0,n),this.generateRaster(m-e,d,c,this.axW,this.azW,e,n),this.generateRaster(m,b,c,this.axE,this.azE,0,t)));this.g3d.setZMargin(5);a?this.fillRasterG(j,m,f,this.g3d.$isPass2?1:0):this.fillRaster(j,m,f,this.g3d.$isPass2?1:0);this.g3d.setZMargin(0)}}}},"~B");c(c$,"reallocRasterArrays",function(a){a=a+31&
-32;this.axW=C(a,0);this.azW=C(a,0);this.axE=C(a,0);this.azE=C(a,0);this.rgb16sW=this.reallocRgb16s(this.rgb16sW,a);this.rgb16sE=this.reallocRgb16s(this.rgb16sE,a)},"~N");c(c$,"generateRaster",function(a,b,d,c,f,e,j){var k=this.ax[b],h=this.az[b],m=this.ax[d]-k,n=this.az[d]-h,t,z,F;0<=m?(t=1,z=m,F=0):(t=-1,z=-m,F=1-a);var h=(h<<10)+512,p=JU.GData.roundInt(w(a/2));0>n&&(p=-p);n=w(((n<<10)+p)/a);z<=a?p=0:(p=JU.GData.roundInt(w(m/a)),z%=a);for(var q=0,m=e;q<a;h+=n,++m,++q)c[m]=k,f[m]=h>>10,k+=p,F+=z,
0<F&&(k+=t,F-=a);if(null!=j){c=this.rgb16t1;c.setRgb(this.rgb16sGouraud[b]);b=this.rgb16t2;b.diffDiv(this.rgb16sGouraud[d],c,a);m=e;for(a=e+a;m<a;++m)j[m].setAndIncrement(c,b)}},"~N,~N,~N,~A,~A,~N,~A");c(c$,"fillRaster",function(a,b,d,c){var f=0;0>a&&(b+=a,f-=a,a=0);a+b>this.g3d.height&&(b=this.g3d.height-a);if(d)for(;--b>=c;++a,++f){d=this.axW[f];var e=this.axE[f]-d+1-c;0<e&&this.g3d.plotPixelsClippedRaster(e,d,a,this.azW[f],this.azE[f],null,null)}else for(;--b>=c;++a,++f)e=this.axE[f]-(d=this.axW[f])+
1-c,1==c&&0>e&&(e=1,d--),0<e&&this.g3d.plotPixelsUnclippedRaster(e,d,a,this.azW[f],this.azE[f],null,null)},"~N,~N,~B,~N");c(c$,"fillRasterG",function(a,b,d,c){var f=0;0>a&&(b+=a,f-=a,a=0);a+b>this.g3d.height&&(b=this.g3d.height-a);if(d)for(;--b>=c;++a,++f){d=this.axW[f];var e=this.axE[f]-d+1-c;0<e&&this.g3d.plotPixelsClippedRaster(e,d,a,this.azW[f],this.azE[f],this.rgb16sW[f],this.rgb16sE[f])}else for(;--b>=c;++a,++f)e=this.axE[f]-(d=this.axW[f])+1-c,1==c&&0>e&&(e=1,d--),0<e&&this.g3d.plotPixelsUnclippedRaster(e,
d,a,this.azW[f],this.azE[f],this.rgb16sW[f],this.rgb16sE[f])},"~N,~N,~B,~N");x(c$,"DEFAULT",64)}),p("J.i18n"),v(["J.api.Translator","java.util.Hashtable","J.i18n.Language","$.Resource"],"J.i18n.GT",["java.text.MessageFormat","JU.Logger"],function(){c$=u(function(){this.resources=null;this.resourceCount=0;this.doTranslate=!0;this.language=null;q(this,arguments)},J.i18n,"GT",null,J.api.Translator);s(c$,function(){});h(c$,"translate",function(a){return J.i18n.GT._(a)},"~S");s(c$,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,f=null,e=this.language.indexOf("_");if(0<=e&&(d=d.substring(0,e),c=this.language,0<=(e=c.indexOf("_",++e))))c=c.substring(0,e),f=this.language;if(null==(this.language=this.getSupported(f))&&
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=f=null;switch(this.language.length){default:f=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===f&&(c=null);"en_US".equals(c)||
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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=w(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>f&&(f=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,n=!c&&0>this.vectorT2.x,t=null!=e&&0<e.length,z,F,p=Array(1),q=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(w(Math.floor(this.pointT2.x)),w(Math.floor(this.pointT2.y)),A(a),z=w(Math.floor(this.pointT2.x+this.vectorT2.x)),
F=w(Math.floor(this.pointT2.y+this.vectorT2.y)),A(a),f),t&&(this.draw000||0!=k))){p[0]=Float.$valueOf(0==k?0:k*j);var r=JU.Txt.sprintf(e[q%e.length],"f",p);this.drawString(z,F,A(a),4,n,c,m,w(Math.floor(this.pointT2.y)),r)}this.pointT.add(this.vectorT);k+=d;a+=b;q++}}}},"JU.Point3fi,JU.Point3fi,~N,~N,~N,~A");c(c$,"drawLine",function(a,b,d,c,f,e,j){return this.drawLine2(a,b,d,c,f,e,j)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawLine2",function(a,b,d,c,f,e,j){this.pt0i.set(a,b,d);this.pt1i.set(c,f,e);if(this.dotsOrDashes)null!=
this.dashDots&&this.drawDashed(a,b,d,c,f,e,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 w((j+1)/2)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawString",function(a,b,d,c,f,e,j,k,h){if(null!=h){var m=this.font3d.stringWidth(h),n=this.font3d.getAscent();a=f?a-(w(c/2)+2+m):e?a-(w(c/2)+2+w(m/2)):a+(w(c/2)+2);f=b;f=j?f+w(n/2):0==k||k<b?f+n:f-w(c/2);b=d-c-2;1>b&&(b=1);this.g3d.drawString(h,this.font3d,a,f,b,b,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");
c(c$,"drawDashed",function(a,b,d,c,f,e,j){if(!(null==j||0>this.width)){var k=j[0];c-=a;f-=b;e-=d;var h=0,m=j===J.render.FontLineShapeRenderer.ndots,n=m||j===J.render.FontLineShapeRenderer.sixdots;if(n){var t=(c*c+f*f)/(this.width*this.width);m?(k=Math.sqrt(t)/1.5,h=A(k)+3):8>t?j=J.render.FontLineShapeRenderer.twodots:32>t&&(j=J.render.FontLineShapeRenderer.fourdots)}var t=j[1],z=j[2],F=this.colixA,p=0==z?this.colixB:this.colixA;0==h&&(h=j.length);for(var q=0,r=3;r<h;r++){var q=m?q+1:j[r],s=w(Math.floor(a+
c*q/k)),u=w(Math.floor(b+f*q/k)),v=w(Math.floor(d+e*q/k));if(n)this.s1.set(s,u,v),r==t?this.g3d.setC(this.colixA):r==z&&this.g3d.setC(this.colixB),this.g3d.fillSphereI(this.width,this.s1);else{r==t&&(F=this.colixB);q=j[++r];r==z&&(p=this.colixB);var x=w(Math.floor(a+c*q/k)),y=w(Math.floor(b+f*q/k)),B=w(Math.floor(d+e*q/k));this.fillCylinder(F,p,2,this.width,s,u,v,x,y,B)}}}},"~N,~N,~N,~N,~N,~N,~A");c(c$,"fillCylinder",function(a,b,d,c,f,e,j,k,h,m){this.asLineOnly?this.g3d.drawLine(a,b,f,e,j,k,h,m):
this.g3d.fillCylinderXYZ(a,b,d,!this.isExport||1==this.mad?c:this.mad,f,e,j,k,h,m)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");x(c$,"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])}),p("J.render"),v(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["JU.C"],function(){c$=y(J.render,"FrankRenderer",J.render.ShapeRenderer);h(c$,"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=A(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,w(3*b/2));return!1})}),p("J.render"),v(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["J.api.Interface","JU.Logger","JV.JC"],function(){c$=u(function(){this.bsTranslucent=this.renderers=this.shapeManager=this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;q(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);L(c$,function(){this.bsTranslucent=JU.BS.newN(36)});s(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 f=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 e=this.vwr.getRubberBandSelection();null!=e&&a.setC(this.vwr.cm.colixRubberband)&&a.drawRect(e.x,e.y,0,0,e.width,e.height)}null==this.renderers&&
(this.renderers=Array(36));c=null;for(e=0;36>e&&a.currentlyRendering();++e){var j=this.shapeManager.getShape(e);null!=j&&(f&&(c="rendering "+JV.JC.getShapeClassName(e,!1),JU.Logger.startTimer(c)),(d||this.bsTranslucent.get(e))&&this.getRenderer(e).renderShape(a,b,j)&&this.bsTranslucent.set(e),f&&JU.Logger.checkTimer(c,!1))}a.renderAllStrings(null)}catch(k){if(D(k,Exception))this.vwr.isJS||k.printStackTrace(),JU.Logger.error("rendering error? "+k);else throw k;}},"JU.GData,JM.ModelSet,~B,~A");h(c$,
"renderExport",function(a,b,d){a=this.vwr.getBoolean(603979934);this.vwr.finalizeTransformParameters();this.shapeManager.finalizeAtoms(null,null);var c=this.vwr.initializeExporter(d);if(null==c)return JU.Logger.error("Cannot export "+d.get("type")),null;c.renderBackground(c);null==this.renderers&&(this.renderers=Array(36));d=null;for(var f=0;36>f;++f){var e=this.shapeManager.getShape(f);null!=e&&(a&&(d="rendering "+JV.JC.getShapeClassName(f,!1),JU.Logger.startTimer(d)),this.getRenderer(f).renderShape(c,
b,e),a&&JU.Logger.checkTimer(d,!1))}c.renderAllStrings(c);return c.finalizeOutput()},"JU.GData,JM.ModelSet,java.util.Map")}),p("J.render"),v(null,"J.render.ShapeRenderer",["JV.JC"],function(){c$=u(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;q(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")}),p("J.render"),v(["J.render.FontLineShapeRenderer",
"JU.BS","$.P3","$.V3"],"J.render.SticksRenderer",["java.lang.Float","J.c.PAL","JM.Bond","JU.C","$.Edge"],function(){c$=u(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;q(this,arguments)},J.render,"SticksRenderer",J.render.FontLineShapeRenderer);L(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=A(this.vwr.tm.scaleToScreen(w((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=w(this.width/8)+3;a=this.width+a;d=this.yA-w((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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case 10:case 15:return JS.SV.iValue(a);case 8:return a.value.length();case 9:return JU.Measure.distanceToPlane(a.value,JS.SV.pt0);case 11:var b=new JU.P3;a.value.rotate(b);return b.length();case 12:return b=new JU.P3,a.value.rotTrans(b),b.length();default:return 0}},"JS.T");c$.sValue=c(c$,"sValue",function(a){if(null==a)return"";var b;switch(a.tok){case 1048589:return"true";case 1048588:return"false";case 2:return""+a.intValue;case 10:return b=JS.SV.bsSelectToken(a),r(a.value,JM.BondSet)?JU.Escape.eBond(b):
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c(c$,"coordinateInRange",function(a,b,d,c,f){this.vwr.tm.transformPtScr(d,f);a=(a-f.x)*(a-f.x)+(b-f.y)*(b-f.y);return a<c?a:-1},"~N,~N,JU.T3,~N,JU.P3i");c(c$,"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$,
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function(a,b,d){if("type"===a)this.myMask=b.intValue();else if("reportAll"===a)this.reportAll=!0;else if("reset"===a)this.selectedBonds=this.bsColixSet=this.bsSizeSet=this.bsOrderSet=null;else if("bondOrder"===a){null==this.bsOrderSet&&(this.bsOrderSet=new JU.BS);a=b.shortValue();for(d=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(65535,d);d.hasNext();)this.bsOrderSet.set(d.nextIndex()),d.next().setOrder(a)}else if("color"===a)if(null==this.bsColixSet&&
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d.getAtom2().setClickable(this.vf))}});h(c$,"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 f=new java.util.Hashtable;f.put("pt",d);f.put("index",
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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$,"isWithinFourBonds",function(a){if(this.mi!=a.mi)return!1;if(this.isCovalentlyBonded(a))return!0;
for(var b=a.bonds,d=0;d<b.length;d++){var c=b[d].getOtherAtom(a);if(this.isCovalentlyBonded(c))return!0;for(var f=0;f<this.bonds.length;f++)if(this.bonds[f].getOtherAtom(this).isCovalentlyBonded(c))return!0}return!1},"JM.Atom");h(c$,"findAtomsLike",function(a){return this.group.chain.model.ms.vwr.getAtomBitSet(a)},"~S");x(c$,"VIBRATION_VECTOR_FLAG",1,"IS_HETERO_FLAG",2,"FLAG_MASK",3,"RADIUS_MAX",16,"RADIUS_GLOBAL",16.1,"MAD_GLOBAL",32200)}),p("JM"),v(["java.lang.Float","JU.BS","$.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 $.Vibration JV.JC".split(" "),function(){c$=u(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;O("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();
this.bsClickable=this.bsVisible=null;this.haveBSClickable=this.haveBSVisible=!1;this.bsModulated=null;q(this,arguments)},JM,"AtomCollection");L(c$,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=
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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$,"getAtomicCharges",function(){for(var a=M(this.ac,0),b=this.ac;0<=--b;)a[b]=
this.at[b].getElementNumber();return a});c(c$,"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=C(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,f=0;f<this.ac;f++)if(this.bsSurface.get(f))this.surfaceDistance100s[f]=0;else{for(var e=3.4028235E38,j=this.at[f],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()+'"');e=Math.min(h,e)}h=this.surfaceDistance100s[f]=w(Math.floor(100*e));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,h)}return c},"JU.BS,~N");c(c$,"setAtomCoord2",function(a,b,d){var c=null,f=null,e=null,j=0,k=1;if(r(d,JU.P3))c=d;else if(r(d,JU.Lst)){e=d;if(0==(k=e.size()))return;j=1}else if(JU.PT.isAP(d)){f=d;if(0==(k=f.length))return;j=2}else return;
d=0;if(null!=a)for(var h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){switch(j){case 1:if(d>=k)return;c=e.get(d++);break;case 2:if(d>=k)return;c=f[d++]}switch(b){case 1146095626:this.setAtomCoord(h,c.x,c.y,c.z);break;case 1146095627:this.at[h].setFractionalCoordTo(c,!0);this.taintAtom(h,2);break;case 1146095629:this.at[h].setFractionalCoordTo(c,!1);this.taintAtom(h,2);break;case 1146095631:this.setAtomVibrationVector(h,c)}}},"JU.BS,~N,~O");c(c$,"setAtomVibrationVector",function(a,b){this.setVibrationVector(a,
b);this.taintAtom(a,12)},"~N,JU.T3");c(c$,"setAtomCoord",function(a,b,d,c){if(!(0>a||a>=this.ac)){var f=this.at[a];f.set(b,d,c);this.fixTrajectory(f);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"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$,"setAtomCoordRelative",function(a,
b,d,c){if(!(0>a||a>=this.ac)){var f=this.at[a];f.add3(b,d,c);this.fixTrajectory(f);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"setAtomsCoordRelative",function(a,b,d,c){if(null!=a)for(var f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))this.setAtomCoordRelative(f,b,d,c)},"JU.BS,~N,~N,~N");c(c$,"setAPa",function(a,b,d,c,f,e,j){var k=0;if(!(null!=e&&0==e.length||null==a)){for(var h=null!=e&&e.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!=e){if(k>=
e.length)return;c=e[k++];d=A(c)}else if(null!=j){if(k>=j.length)return;f=j[k++]}var n=this.at[m];switch(b){case 1087375362:this.taintAtom(m,0);this.setAtomName(m,f);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,f);break;case 1112541185:case 1112541205:this.setAtomCoord(m,c,n.y,n.z);break;case 1112541186:case 1112541206:this.setAtomCoord(m,n.x,c,n.z);break;
case 1112541187:case 1112541207:this.setAtomCoord(m,n.x,n.y,c);break;case 1112541202:case 1112541203:case 1112541204:this.setVibrationVector2(m,b,c);break;case 1112541188:case 1112541189:case 1112541190:n.setFractionalCoord(b,c,!0);this.taintAtom(m,2);break;case 1112541191:case 1112541192:case 1112541193:n.setFractionalCoord(b,c,!1);this.taintAtom(m,2);break;case 1095763978:case 1087375365:this.setElement(n,d);break;case 1632634891:n.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(f,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);n.madAtom=Y(2E3*c);break;case 1114638363:this.vwr.slm.setSelectedAtom(n.i,0!=c);break;case 1112541199:this.setBFactor(m,
c)&&this.taintAtom(m,9);break;case 1095763991:n.setValence(d);this.taintAtom(m,10);break;case 1649412120:n.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$,"setVibrationVector",function(a,b){if(!Float.isNaN(b.x)&&!Float.isNaN(b.y)&&!Float.isNaN(b.z)){if(null==
this.vibrations||this.vibrations.length<a)this.vibrations=Array(this.at.length);r(b,JU.Vibration)?this.vibrations[a]=b:(null==this.vibrations[a]&&(this.vibrations[a]=new JU.Vibration),this.vibrations[a].setT(b));this.at[a].setVibrationVector()}},"~N,JU.T3");c(c$,"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$,"setAtomNumber",function(a,b){null==this.atomSerials&&(this.atomSerials=C(this.at.length,0));this.atomSerials[a]=b;return!0},"~N,~N");c(c$,"setAtomSeqID",function(a,b){null==this.atomSeqIDs&&
(this.atomSeqIDs=C(this.at.length,0));this.atomSeqIDs[a]=b;return!0},"~N,~N");c(c$,"setOccupancy",function(a,b){if(null==this.occupancies){if(100==b)return!1;this.occupancies=M(this.at.length,0);for(var d=this.at.length;0<=--d;)this.occupancies[d]=100}this.occupancies[a]=b;return!0},"~N,~N");c(c$,"setPartialCharge",function(a,b){if(Float.isNaN(b))return!1;if(null==this.partialCharges){if(0==b&&!Float.$valueOf(b).equals(JM.AtomCollection.MINUSZERO))return!1;this.partialCharges=M(this.at.length,0)}this.partialCharges[a]=
b;return!0},"~N,~N");c(c$,"setBondingRadius",function(a,b){if(Float.isNaN(b))return!1;null==this.bondingRadii&&(this.bondingRadii=M(this.at.length,0));this.bondingRadii[a]=b;return!0},"~N,~N");c(c$,"setBFactor",function(a,b){if(Float.isNaN(b))return!1;if(null==this.bfactor100s){if(0==b&&null==this.bfactor100s)return!1;this.bfactor100s=V(this.at.length,0)}this.bfactor100s[a]=ka(100*(-327.68>b?-327.68:327.67<b?327.67:b)+(0>b?-0.5:0.5));return!0},"~N,~N");c(c$,"setHydrophobicity",function(a,b){if(Float.isNaN(b))return!1;
if(null==this.hydrophobicities){this.hydrophobicities=M(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$,"setAtomData",function(a,b,d,c){var f=null,e=null;switch(a){case 2:this.loadCoordinates(d,!1,!c);return;case 12:this.loadCoordinates(d,!0,!0);return;case 15:f=M(this.ac,0),e=JU.BS.newN(this.ac)}c=JU.Parser.markLines(d,";");var j=0;try{for(var k=JU.PT.parseInt(d.substring(0,
c[0]-1)),h=1;h<=k;h++){var m=JU.PT.getTokens(JU.PT.parseTrimmed(d.substring(c[h],c[h+1]-1))),n=JU.PT.parseInt(m[0])-1;if(!(0>n||n>=this.ac)){var t=this.at[n];j++;var z=m.length-1,F=JU.PT.parseFloat(m[z]);switch(a){case 15:f[n]=F;e.set(n);continue;case 13:this.setAtomNumber(n,A(F));break;case 14:this.setAtomSeqID(n,A(F));break;case 0:this.setAtomName(n,m[z]);break;case 1:this.setAtomType(n,m[z]);break;case 3:t.setAtomicAndIsotopeNumber(A(F));t.setPaletteID(J.c.PAL.CPK.id);t.setColixAtom(this.vwr.getColixAtomPalette(t,
J.c.PAL.CPK.id));break;case 4:t.setFormalCharge(A(F));break;case 5:this.setHydrophobicity(n,F);break;case 6:this.setBondingRadius(n,F);break;case 8:this.setPartialCharge(n,F);break;case 9:this.setBFactor(n,F);break;case 10:t.setValence(A(F));break;case 11:t.setRadius(F)}this.taintAtom(n,a)}}15==a&&0<j&&this.vwr.setData(b,[b,f,e,Integer.$valueOf(1)],0,0,0,0,0)}catch(p){if(D(p,Exception))JU.Logger.error("AtomCollection.loadData error: "+p);else throw p;}},"~N,~S,~S,~B");c(c$,"loadCoordinates",function(a,
b,d){var c=JU.Parser.markLines(a,";"),f=b?new JU.V3:null;try{for(var e=JU.PT.parseInt(a.substring(0,c[0]-1)),j=1;j<=e;j++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[j],c[j+1]))),h=JU.PT.parseInt(k[0])-1,m=JU.PT.parseFloat(k[3]),n=JU.PT.parseFloat(k[4]),t=JU.PT.parseFloat(k[5]);b?(f.set(m,n,t),this.setAtomVibrationVector(h,f)):(this.setAtomCoord(h,m,n,t),d||this.untaint(h,2))}}catch(z){if(D(z,Exception))JU.Logger.error("Frame.loadCoordinate error: "+z);else throw z;}},"~S,~B,~B");c(c$,
"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$,"findNearest2",function(a,b,d,c,f){for(var e=null,j=this.ac;0<=--j;)if(!(null!=c&&c.get(j))){var k=this.at[j];k.isClickable()&&this.isCursorOnTopOf(k,a,b,f,e)&&(e=k)}d[0]=e},"~N,~N,~A,JU.BS,~N");c(c$,"isCursorOnTopOf",function(a,b,d,c,f){return 1<a.sZ&&!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(b,d,c,f)},"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=C(this.ac,0);var d=0!=(b&2);d&&(a.atomRadius=M(this.ac,0));for(var c=0!=(b&16),f=0;f<this.ac;f++){var e=this.at[f];e.isDeleted()||!c&&0<=a.modelIndex&&e.mi!=a.firstModelIndex?
(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(f)):(a.atomicNumber[f]=e.getElementNumber(),a.lastModelIndex=e.mi,d&&(a.atomRadius[f]=this.getWorkingRadius(e,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,f){var e=new JU.V3,j=new JU.V3,k=Array(this.ac),h=this.vwr.getDeletedAtoms(),m,n=0;if(null!=a)for(var t=a.nextSetBit(0);0<=t;t=a.nextSetBit(t+1))if(!(null!=h&&h.get(t))){var z=this.at[t],
F=z.getElementNumber();if(!(c&&6!=F)){var p=6>=F?1.1:10>=F?1:1.3;switch(F){case 7:case 8:p=1}if(!(d&&0<z.getCovalentHydrogenCount())&&(m=this.getImplicitHydrogenCount(z,!1),0!=m)){var q=this.aaRet[0],r=this.aaRet[2],s=this.aaRet[3];k[t]=Array(m);var u=0;if(0==s)switch(m){case 4:e.set(0.635,0.635,0.635),m=JU.P3.newP(e),m.add(z),k[t][u++]=m,null!=f&&f.addLast(z);case 3:e.set(-0.635,-0.635,0.635),m=JU.P3.newP(e),m.add(z),k[t][u++]=m,null!=f&&f.addLast(z);case 2:e.set(-0.635,0.635,-0.635),m=JU.P3.newP(e),
m.add(z),k[t][u++]=m,null!=f&&f.addLast(z);case 1:e.set(0.635,-0.635,-0.635),m=JU.P3.newP(e),m.add(z),k[t][u++]=m,null!=f&&f.addLast(z)}else switch(m){case 3:this.getHybridizationAndAxes(t,F,e,j,"sp3b",!1,!0);m=new JU.P3;m.scaleAdd2(p,e,z);k[t][u++]=m;null!=f&&f.addLast(z);this.getHybridizationAndAxes(t,F,e,j,"sp3c",!1,!0);m=new JU.P3;m.scaleAdd2(p,e,z);k[t][u++]=m;null!=f&&f.addLast(z);this.getHybridizationAndAxes(t,F,e,j,"sp3d",!1,!0);m=new JU.P3;m.scaleAdd2(p,e,z);k[t][u++]=m;null!=f&&f.addLast(z);
break;case 2:r=2==r||5==F||1==s&&4==q||7==F&&this.isAdjacentSp2(z);this.getHybridizationAndAxes(t,F,e,j,r?"sp2b":3==q?"sp3c":"lpa",!1,!0);m=JU.P3.newP(e);m.scaleAdd2(p,e,z);k[t][u++]=m;null!=f&&f.addLast(z);this.getHybridizationAndAxes(t,F,e,j,r?"sp2c":3==q?"sp3d":"lpb",!1,!0);m=JU.P3.newP(e);m.scaleAdd2(p,e,z);k[t][u++]=m;null!=f&&f.addLast(z);break;case 1:switch(q-s){case 1:if(8==F&&z===z.getGroup().getCarbonylOxygenAtom()){k[t]=null;continue}null!=this.getHybridizationAndAxes(t,F,e,j,2==r||5==
F||7==F&&this.isAdjacentSp2(z)?"sp2c":"sp3d",!0,!1)?(m=JU.P3.newP(e),m.scaleAdd2(p,e,z),k[t][u++]=m,null!=f&&f.addLast(z)):k[t]=[];break;case 2:this.getHybridizationAndAxes(t,F,e,j,4==q?"sp2c":"sp2b",!1,!1);m=JU.P3.newP(e);m.scaleAdd2(p,e,z);k[t][u++]=m;null!=f&&f.addLast(z);break;case 3:this.getHybridizationAndAxes(t,F,e,j,"spb",!1,!0),m=JU.P3.newP(e),m.scaleAdd2(p,e,z),k[t][u++]=m,null!=f&&f.addLast(z)}}n+=u}}}b[0]=n;return k},"JU.BS,~A,~B,~B,JU.Lst");c(c$,"isAdjacentSp2",function(a){for(var b=
a.bonds,d=0;d<b.length;d++)for(var c=b[d].getOtherAtom(a).bonds,f=0;f<c.length;f++)switch(c[f].order){case 515:case 514:case 2:case 3:return!0}return!1},"JM.Atom");c(c$,"getImplicitHydrogenCount",function(a,b){var d=a.getTargetValence();if(0>d)return 0;var c=a.getFormalCharge();null==this.aaRet&&(this.aaRet=C(4,0));this.aaRet[0]=d;this.aaRet[1]=c;this.aaRet[2]=0;this.aaRet[3]=a.getCovalentBondCount();var f=this.am[a.mi],f=f.isBioModel&&!f.isPdbWithMultipleBonds?a.group.getGroup3():null;null!=f&&0==
c&&JV.JC.getAminoAcidValenceAndCharge(f,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$,"fixFormalCharges",function(a){for(var b=0,d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1)){var c=this.at[d],f=this.getImplicitHydrogenCount(c,!0);if(0!=f){var e=c.getFormalCharge(),f=e-f;c.setFormalCharge(f);this.taintAtom(d,4);JU.Logger.debugging&&JU.Logger.debug("atom "+c+" formal charge "+e+" -> "+
f);b++}}return b},"JU.BS");c(c$,"getHybridizationAndAxes",function(a,b,d,c,f,e,j){var k=0<f.length&&"-"==f.charAt(0)?f.substring(1):f;if(0<=f.indexOf("d")&&!f.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,d,c,k);f=this.at[a];0==b&&(b=f.getElementNumber());var h=this.getAttached(f,4,e),m=h.length,n=k.charCodeAt(k.length-1)-97;if(0>n||6<n)n=0;d.set(0,0,0);c.set(0,0,0);for(var t=Array(4),z=0;z<m;z++)t[z]=JU.V3.newVsub(f,h[z]),t[z].normalize(),d.add(t[z]);0<m&&c.setT(t[0]);z=!1;a=new JU.V3;
if(3<=m){2.984513>c.angle(t[1])?a.cross(c,t[1]):a.cross(c,t[2]);a.normalize();var p=new JU.V3;2.984513>t[1].angle(t[2])?p.cross(t[1],t[2]):p.cross(c,t[2]);p.normalize();z=0.95<=Math.abs(p.dot(a))}var q=0==k.indexOf("sp3"),r=!q&&0==k.indexOf("sp2"),s=!q&&!r&&0==k.indexOf("sp"),u=0==k.indexOf("p"),v=0==k.indexOf("lp"),p=null;if(e){if(0==m)return null;if(q){if(3<n||4<m)return null}else if(r){if(2<n||3<m)return null}else if(s&&(1<n||2<m))return null;switch(m){case 1:if(1==b&&!q)return null;if(q){p="sp3";
break}switch(h[0].getCovalentBondCount()){case 1:if(2!=h[0].getValence()){p="sp";break}case 2:p=s?"sp":"sp2";break;case 3:if(!r&&!u)return null;p="sp2"}break;case 2:if(0.1>d.length()){if(0<=k.indexOf("2")||0<=k.indexOf("3"))return null;p="sp";break}p=q?"sp3":"sp2";if(0==k.indexOf("sp"))break;if(v){p="lp";break}p=k;break;default:if(z)p="sp2";else{if(v&&3==m){p="lp";break}p="sp3"}}if(null==p)return null;if(0==k.indexOf("p")){if("sp3"===p)return null}else if(0>k.indexOf(p))return null}if(n<m&&!k.startsWith("p")&&
!k.startsWith("l"))return d.sub2(h[n],f),d.normalize(),p;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(z=0;z<h[0].bonds.length;z++)if(h[0].bonds[z].isCovalent()&&h[0].getBondedAtomIndex(z)!=f.i&&(c.sub2(h[0],h[0].bonds[z].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!=n&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(d.x,d.y,d.z,2.09439507*(2==n?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(z=0;z<k.length;z++)if(k[z].isCovalent()&&
(b=k[z].getOtherAtom(j),b!==f)){a.sub2(b,j);break}a.cross(a,c);if(0.1<a.length()||2!=b.getCovalentBondCount())break;f=j;j=b}0.1<a.length()?(d.cross(a,c),d.normalize(),1==n&&d.scale(-1),d.scale(JM.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,c,d),u&&(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),r?(c.cross(c,d),1==n&&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];(f=3==b.getCovalentBondCount())||(f=3==(b=h[1]).getCovalentBondCount());if(f){this.getHybridizationAndAxes(b.i,0,c,d,"pz",!1,j);k.equals("px")&&c.scale(-1);d.setT(t[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(r){c.cross(d,a);break}if(q||v){a.normalize();d.normalize();k.equals("lp")||(0==n||2==n?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(!z){c.cross(d,c);break}d.setT(a);0>d.z&&j&&(d.scale(-1),c.scale(-1))}c.normalize();d.normalize();return p},"~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 f=c.startsWith("dsp3"),
e=c.charCodeAt(c.length-1)-97;if(null!=b&&(!f&&(5<e||!c.startsWith("d2sp3"))||f&&4<e))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=e>=j,h=w(j*(j-1)/2),m=JU.AU.newInt2(h),n=C(3,0),h=C(3,h,0),t=0,p=0,F=0;F<j-1;F++)for(var q=F+1;q<j;q++){var r=JU.Measure.computeAngleABC(c[F],a,c[q],!0),r=105>r?0:150<=r?2:1;h[r][n[r]]=t;n[r]++;m[t++]=[F,q];0==F&&1==r&&p++}t=100*n[0]+10*n[1]+n[2];if(null==b)switch(t){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==p%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(t){default:return null;
case 201:break;case 210:case 330:case 411:case 631:if(!f)return null;break;case 300:case 402:case 501:case 802:case 1203:if(f)return null}if(k)if(f)switch(n[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==e&&b.scale(-1);n=this.findNotAttached(j,m,h[2],n[2]);F=n.nextSetBit(0);d.sub2(c[F],a);d.normalize();d.scale(0.5);b.scaleAdd2(JM.AtomCollection.sqrt3_2,b,d);e=-1;break;case 1:4==e?(d=m[h[1][0]],b.add2(c[d[0]],c[d[1]]),b.scaleAdd2(-2,a,b),e=-1):(n=this.findNotAttached(j,
m,h[1],n[1]),e=n.nextSetBit(0));break;default:n=this.findNotAttached(j,m,h[1],n[1]),e=n.nextSetBit(0)}else{t=!1;if(4==j)switch(n[2]){case 1:n=this.findNotAttached(j,m,h[2],n[2]);F=n.nextSetBit(0);e=4==e?F:n.nextSetBit(F+1);break;default:t=!0}else{n=this.findNotAttached(j,m,h[2],n[2]);F=n.nextSetBit(0);for(q=j;q<e&&0<=F;q++)F=n.nextSetBit(F+1);-1==F?t=!0:e=F}t&&(b.sub2(c[m[h[0][0]][0]],a),d.sub2(c[m[h[0][0]][1]],a),b.cross(b,d),4==e&&b.scale(-1),e=-1)}0<=e&&b.sub2(c[e],a);k&&b.scale(-1);b.normalize();
return f?"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,f=0,e=0;e<c.length;e++)c[e].isCovalent()&&(b[f++]=c[e].getOtherAtom(a));d&&java.util.Arrays.sort(b,N(JM.AtomCollection.AtomSorter,this,null))}return b},"JM.Atom,~N,~B");c(c$,"findNotAttached",function(a,b,d,c){var f=JU.BS.newN(a);f.setBits(0,a);for(var e=0;e<a;e++)for(var j=0;j<c;j++){var k=b[d[j]];(k[0]==e||k[1]==e)&&f.clear(e)}return f},
"~N,~A,~A,~N");c(c$,"getAtomBitsMDa",function(a,b){var d=new JU.BS,c,f;c=r(b,Integer)?b.intValue():0;var e=0;switch(a){case 1613758488:return this.getWaterAtoms(d);case 1095761939:for(e=this.ac;0<=--e;)this.at[e].getResno()==c&&d.set(e);break;case 1297090050:for(e=this.ac;0<=--e;)this.at[e].getSymOp()==c&&d.set(e);break;case 1095763969:for(e=this.ac;0<=--e;)this.at[e].getAtomNumber()==c&&d.set(e);break;case 1087375362:c=","+b+",";for(e=this.ac;0<=--e;)f=this.at[e].getAtomName(),0<=c.indexOf(f)&&0<=
c.indexOf(","+f+",")&&d.set(e);break;case 1087375361:c=","+b+",";for(e=this.ac;0<=--e;)f=this.at[e].getAtomType(),0<=c.indexOf(f)&&0<=c.indexOf(","+f+",")&&d.set(e);break;case 1048613:for(e=this.ac;0<=--e;)this.at[e].getGroupID()==c&&d.set(e);break;case 1048609:return JU.BSUtil.copy(this.getChainBits(c));case 1048614:return JU.BSUtil.copy(this.getSeqcodeBits(c,!0));case 1613758470:for(e=this.ac;0<=--e;)this.at[e].isHetero()&&d.set(e);break;case 1613758476:for(e=this.ac;0<=--e;)1==this.at[e].getElementNumber()&&
d.set(e);break;case 3145741:for(e=this.ac;0<=--e;)this.at[e].isLeadAtom()&&d.set(e);break;case 3145744:for(e=this.ac;0<=--e;)this.at[e].isProtein()&&d.set(e);break;case 3145764:for(e=this.ac;0<=--e;)this.at[e].isCarbohydrate()&&d.set(e);break;case 137363467:case 3145760:f=137363467==a?J.c.STR.HELIX:J.c.STR.SHEET;for(e=this.ac;0<=--e;)this.at[e].isWithinStructure(f)&&d.set(e);break;case 3145742:for(e=this.ac;0<=--e;)this.at[e].isNucleic()&&d.set(e);break;case 3145732:for(e=this.ac;0<=--e;)this.at[e].isDna()&&
d.set(e);break;case 3145750:for(e=this.ac;0<=--e;)this.at[e].isRna()&&d.set(e);break;case 3145746:for(e=this.ac;0<=--e;)this.at[e].isPurine()&&d.set(e);break;case 3145748:for(e=this.ac;0<=--e;)this.at[e].isPyrimidine()&&d.set(e);break;case 1087375365:c=b;f=new JU.BS;for(e=c.nextSetBit(0);0<=e;e=c.nextSetBit(e+1))f.set(this.getElementNumber(e));for(e=this.ac;0<=--e;)f.get(this.getElementNumber(e))&&d.set(e);break;case 1095761941:c=b;f=new JU.BS;for(e=c.nextSetBit(0);0<=e;e=c.nextSetBit(e+1))f.set(this.at[e].atomSite);
for(e=this.ac;0<=--e;)f.get(this.at[e].atomSite)&&d.set(e);break;case 1073741824:return this.getIdentifierOrNull(b);case 1048608:c=b.toUpperCase();0<=c.indexOf("\\?")&&(c=JU.PT.rep(c,"\\?","\u0001"));(f=c.startsWith("?*"))&&(c=c.substring(1));for(e=this.ac;0<=--e;)this.isAtomNameMatch(this.at[e],c,f,f)&&d.set(e);break;case 1048607:for(e=this.ac;0<=--e;)this.at[e].isAltLoc(b)&&d.set(e);break;case 1048612:return this.getSpecName(b)}if(0>e)return d;c=b;var j;f=c.nextSetBit(0);if(0>f)return d;e=0;switch(a){case 1087373318:for(e=
f;0<=e;e=c.nextSetBit(e+1))f=this.at[e].getGroup().selectAtoms(d),f>e&&(e=f);break;case 1095766030:for(e=f;0<=e;e=c.nextSetBit(e+1))if(!d.get(e)){j=this.at[e].mi;d.set(e);for(f=e;0<=--f;)if(this.at[f].mi==j)d.set(f);else break;for(;++e<this.ac;)if(this.at[e].mi==j)d.set(e);else break}break;case 1087373316:c=JU.BSUtil.copy(b);for(e=c.nextSetBit(0);0<=e;e=c.nextSetBit(e+1))this.at[e].getChain().setAtomBitSet(d),c.andNot(d);break;case 1095761937:for(e=f;0<=e;e=c.nextSetBit(e+1))if(!d.get(e)){j=this.at[e].getPolymerIndexInModel();
d.set(e);for(f=e;0<=--f;)if(this.at[f].getPolymerIndexInModel()==j)d.set(f);else break;for(;++e<this.ac;)if(this.at[e].getPolymerIndexInModel()==j)d.set(e);else break}break;case 1641025539:for(e=f;0<=e;e=c.nextSetBit(e+1))if(!d.get(e)){j=this.at[e].getGroup().getStructure();d.set(e);for(f=e;0<=--f;)if(this.at[f].getGroup().getStructure()===j)d.set(f);else break;for(;++e<this.ac;)if(this.at[e].getGroup().getStructure()===j)d.set(e);else break}}0==e&&JU.Logger.error("MISSING getAtomBits entry for "+
JS.T.nameOf(a));return d},"~N,~O");c(c$,"getWaterAtoms",function(a){for(var b=C(2,0),d,c=this.ac;0<=--c;){var f=this.at[c].getGroupID();if(42<=f&&45>f)a.set(c);else if(8==(d=this.at[c]).getElementNumber()&&2==d.getCovalentBondCount()){for(var f=d.getBonds(),e=0,j,k=f.length;0<=--k&&3>e;)if(f[k].isCovalent()&&1==(j=f[k].getOtherAtom(d)).getElementNumber())b[e++%2]=j.i;2==e&&(a.set(b[1]),a.set(b[0]),a.set(c))}}return a},"JU.BS");c(c$,"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 f=c;c<d&&Character.isDigit(a.charAt(c));)++c;var e=0;try{e=Integer.parseInt(a.substring(f,c))}catch(j){if(D(j,NumberFormatException))return null;throw j;}f=" ";c<d&&"^"==a.charAt(c)&&++c<d&&(f=
a.charAt(c));e=JM.Group.getSeqcodeFor(e,f);e=this.getSeqcodeBits(e,!1);if(null==e){" "!=f&&(e=this.getSeqcodeBits(Character.toUpperCase(a.charAt(c)).charCodeAt(0),!1));if(null==e)return null;c++}b.and(e);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 f=this.ac;0<=--f;){var e=this.at[f].getGroup3(!0);if(null!=e&&0<e.length){if(JU.Txt.isMatch(e,a,b,!0)){null==d&&(d=JU.BS.newN(f+1));for(d.set(f);0<=--f&&this.at[f].getGroup3(!0).equals(e);)d.set(f);f++}}else this.isAtomNameMatch(this.at[f],a,b,c)&&(null==d&&(d=JU.BS.newN(f+1)),d.set(f))}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),f=2147483647!=c,e=!0,j=JM.Group.getInsertionCodeChar(a);switch(j){case "?":for(var k=this.ac;0<=--k;){var h=this.at[k].getSeqcode();if(!f||c==JM.Group.getSeqNumberFor(h)&&0!=JM.Group.getInsertionCodeFor(h))d.set(k),e=!1}break;default:for(k=this.ac;0<=--k;)if(h=this.at[k].getSeqcode(),a==h||!f&&a==JM.Group.getInsertionCodeFor(h)||"*"==j&&c==JM.Group.getSeqNumberFor(h))d.set(k),e=!1}return!e||
b?d:null},"~N,~B");c(c$,"getChainBits",function(a){var b=256>a&&this.vwr.getBoolean(603979823);b||(a=JM.AtomCollection.chainToUpper(a));for(var d=new JU.BS,c=JU.BS.newN(this.ac),f,e=c.nextClearBit(0);e<this.ac;e=c.nextClearBit(e+1)){var j=this.at[e].getChain();a==(f=j.chainID)||!b&&a==JM.AtomCollection.chainToUpper(f)?(j.setAtomBitSet(d),c.or(d)):j.setAtomBitSet(c)}return d},"~N");c$.chainToUpper=c(c$,"chainToUpper",function(a){return String.fromCharCode(a).toUpperCase().charCodeAt(0)},"~N");c(c$,
"getAtomIndices",function(a){for(var b=0,d=C(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$,"getAtomsNearPlane",function(a,b){for(var d=new JU.BS,c=this.ac;0<=--c;){var f=this.at[c],e=JU.Measure.distanceToPlane(b,f);(0<a&&-0.1<=e&&e<=a||0>a&&0.1>=e&&e>=a||0==a&&0.01>Math.abs(e))&&d.set(f.i)}return d},"~N,JU.P4");c(c$,"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 f=this.ac;0<=--f;)for(var e=this.at[f],j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))if(e.distance(b[j])<a){c.set(f);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.$valueOf(this.getAtomNumber(a)));
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c.atomIndex1=a;c.atomIndex2=-1;c.modelIndex=this.at[a].mi;this.addTensor(c,c.type);null!=c.altType&&this.addTensor(c,c.altType)}}},"~N,JU.Lst");c$.getTensorList=c(c$,"getTensorList",function(a){for(var b=-1,d=!1,c=a.size(),f=c;0<=--f;){var e=a.get(f);e.forThermalEllipsoid?b=f:2==e.iType&&(d=!0)}var j=Array((0<=b||!d?0:1)+c);if(0<=b&&(j[0]=a.get(b),1==a.size()))return j;if(d){b=0;for(f=c;0<=--f;)e=a.get(f),e.forThermalEllipsoid||(j[++b]=e)}else for(f=0;f<c;f++)j[f]=a.get(f);return j},"JU.Lst");c(c$,
"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 f=d[c];if(null!=f&&(b.equals(f.type)||b.equals(f.altType)))return f}}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(){E(self.c$);c$=u(function(){S(this,arguments);q(this,arguments)},JM.AtomCollection,"AtomSorter",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.i>b.i?1:a.i<b.i?-1:0},"JM.Atom,JM.Atom");c$=H()};c$.MINUSZERO=c$.prototype.MINUSZERO=Float.$valueOf(-0);x(c$,"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$.prototype.vRef=JU.V3.new3(3.14159,2.71828,1.41421);x(c$,"almost180",2.984513)}),p("JM"),v(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){c$=u(function(){this.bspf=this.cubeIterator=null;this.isZeroBased=this.hemisphereOnly=this.threadSafe=!1;this.modelIndex=2147483647;this.atomIndex=-1;this.distanceSquared=this.zeroBase=0;this.bsSelected=null;this.checkGreater=this.isGreaterOnly=!1;this.radiusData=null;this.vdw1=0;this.isVdw=
!1;this.vwr=this.atoms=null;this.iNext=0;q(this,arguments)},JM,"AtomIteratorWithinModel",null,J.api.AtomIndexIterator);s(c$,function(){});c(c$,"initialize",function(a,b,d,c,f,e){this.bspf=a;this.bsSelected=b;this.isGreaterOnly=d;this.isZeroBased=c;this.hemisphereOnly=f;this.threadSafe=e;this.cubeIterator=null},"J.bspt.Bspf,JU.BS,~B,~B,~B,~B");h(c$,"setModel",function(a,b,d,c,f,e,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!=e){this.atomIndex=0>e?-1:c;if(this.isVdw=null!=j)this.radiusData=j,this.atoms=a.at,this.vwr=a.vwr,e=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(f,e)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");h(c$,"setCenter",function(a,b){this.setCenter2(a,b)},"JU.T3,~N");
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this.cubeIterator.nextElement(),this.iNext=a.i,!0;this.iNext=-1;return!1});h(c$,"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$,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)})}),p("JM"),v(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){c$=u(function(){this.center=this.bsModels=null;this.distance=0;q(this,arguments)},JM,"AtomIteratorWithinModelSet",JM.AtomIteratorWithinModel);
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"JV.JC"],"JM.Bond",["JU.C"],function(){c$=u(function(){this.atom2=this.atom1=null;this.shapeVisibilityFlags=this.colix=this.mad=0;q(this,arguments)},JM,"Bond",JU.Edge);s(c$,function(a,b,d,c,f){G(this,JM.Bond,[]);this.atom1=a;this.atom2=b;this.colix=f;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$,"getIdentity",function(){return this.index+1+" "+this.getOrderNumberAsString()+" "+this.atom1.getInfo()+" -- "+this.atom2.getInfo()+" "+this.atom1.distance(this.atom2)});
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c(c$,"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",
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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)}),p("JM"),v(["JM.AtomCollection","JU.BS"],"JM.BondCollection","JU.AU JM.Bond $.BondIteratorSelected $.HBond JU.BSUtil $.Edge $.Logger".split(" "),function(){c$=u(function(){this.molecules=null;this.moleculeCount=0;this.bo=null;this.bondCount=0;this.freeBonds=this.numCached=null;this.haveWarned=!1;this.defaultCovalentMad=
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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 f=this.bo[c],
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r(this.bo[a],JM.HBond)&&(this.bo[a].energy=e))):(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,e)).index);null!=f&&f.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,f){d=JM.Bond.isOrderH(d)?new JM.HBond(a,b,d,c,0,f):new JM.Bond(a,b,d,c,0);this.addBondToAtom(a,d);this.addBondToAtom(b,
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0});c(c$,"getDefaultMadFromOrder",function(a){return JM.Bond.isOrderH(a)?1:32768==a?w(Math.floor(2E3*this.vwr.getFloat(570425406))):this.defaultCovalentMad},"~N");c(c$,"deleteConnections",function(a,b,d,c,f,e,j){var k=0>a,h=0>b,m=k||h;a=this.fixD(a,k);b=this.fixD(b,h);var n=new JU.BS,t=0,p=d|=131072;!j&&JM.Bond.isOrderH(d)&&(d=30720);if(e)e=c;else{e=new JU.BS;for(var q=c.nextSetBit(0);0<=q;q=c.nextSetBit(q+1)){var r=this.at[q];if(null!=r.bonds)for(var s=r.bonds.length;0<=--s;)f.get(r.getBondedAtomIndex(s))&&
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c$.formatLabelBond=c(c$,"formatLabelBond",function(a,b,d,c,f,e){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",f,e);JM.LabelToken.formatLabelAtomArray(a,b.atom2,d,"2",f,e);return JM.LabelToken.getLabel(d)},"JV.Viewer,JM.Bond,~A,java.util.Map,~A,JU.P3");c$.formatLabelMeasure=
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function(a,b){for(var d=0;d<a.length;d++){var c=a[d];if(null==c)break;if(null!=c.key){var f=b.get(c.key);c.text=r(f,Float)?c.format(f.floatValue(),null,null):c.format(NaN,f,null)}}},"~A,java.util.Map");c$.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$,"setToken",function(a,b,d,c,f,e){var j=d.pt+1;if(j>=c)return j;var k;"-"==b.charAt(j)&&(d.alignLeft=!0,++j);j<c&&"0"==b.charAt(j)&&
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this.getAtom(1),c=this.getAtom(2),d=(d.getVanderwaalsRadiusFloat(this.vwr,a.vdwType)+c.getVanderwaalsRadiusFloat(this.vwr,a.vdwType))*a.value;return b<=d}return 3.4028235E38==a.values[0]||b>=a.values[0]&&b<=a.values[1]},"J.atomdata.RadiusData,~N");c(c$,"isIntramolecular",function(a,b){for(var d=-1,c=1;c<=b;c++){var f=this.getAtomIndex(c);if(!(0>f))if(f=a[f].getMoleculeNumber(!1),0>d)d=f;else if(f!=d)return!1}return!0},"~A,~N");c(c$,"isMin",function(a){var b=this.getAtom(1),d=this.getAtom(2),c=A(100*
d.distanceSquared(b)),b=b.getAtomName(),d=d.getAtomName(),d=0>b.compareTo(d)?b+d:d+b;a=a.get(d);return null!=a&&c==a.intValue()},"java.util.Map");x(c$,"NMR_NOT",0,"NMR_DC",1,"NMR_JC",2)}),p("JM"),v(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["java.lang.Float","JU.BS","$.Lst","JM.Measurement","JU.BSUtil"],function(){c$=u(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;q(this,arguments)},JM,"MeasurementData",null,J.api.JmolMeasurementClient);s(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,f,e,j,k,h,m,n,t,p){this.ms=this.vwr.ms;this.tokAction=a;2<=this.points.size()&&(r(this.points.get(0),JU.BS)&&r(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=f;this.tickInfo=e;this.mustBeConnected=j;this.mustNotBeConnected=k;this.intramolecular=h;this.isAll=m;this.mad=n;this.colix=t;this.text=p;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$,"getMeasurements",function(a,b){if(b){this.minArray=M(this.points.get(0).cardinality(),0);for(var d=0;d<this.minArray.length;d++)this.minArray[d]=-0;this.define(null,this.ms);return this.minArray}if(a)return this.measurements=new JU.Lst,this.define(null,this.ms),this.measurements;this.measurementStrings=new JU.Lst;this.define(null,this.ms);return this.measurementStrings},"~B,~B");
c(c$,"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,f=Array(4),e=C(5,0),j=(new JM.Measurement).setPoints(b,e,f,null);j.setCount(d);for(var k=-1,h=0;h<d;h++){var m=this.points.get(h);if(r(m,JU.BS)){k=m.cardinality();if(0==k)return;1<k&&(c=0);k=h;0==h&&(this.iFirstAtom=0);e[h+1]=m.nextSetBit(0)}else f[h]=m,e[h+1]=-2-h}this.nextMeasure(0,k,j,c)}},"J.api.JmolMeasurementClient,JM.ModelSet");c(c$,"nextMeasure",function(a,b,d,c){if(a>b)d.isValid()&&
((!this.mustBeConnected||d.isConnected(this.atoms,a))&&(!this.mustNotBeConnected||!d.isConnected(this.atoms,a))&&(null==this.intramolecular||d.isIntramolecular(this.atoms,a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(d);else{var f=this.points.get(a),e=d.countPlusIndices,j=0==a?2147483647:e[a];if(0>j)this.nextMeasure(a+1,b,d,c);else{for(var k=!1,h=f.nextSetBit(0),m=0;0<=h;h=f.nextSetBit(h+1),m++)if(h!=j){var n=this.atoms[h].getModelIndex();if(0<=c&&this.justOneModel)if(0==
a)c=n;else if(c!=n)continue;e[a+1]=h;0==a&&(this.iFirstAtom=m);k=!0;this.nextMeasure(a+1,b,d,c)}k||this.nextMeasure(a+1,b,d,c)}}},"~N,~N,JM.Measurement,~N")}),p("JM"),v(["JM.Measurement"],"JM.MeasurementPending",null,function(){c$=u(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;q(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$,"addPoint",function(a,b,d){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==b){if(0<this.getIndexOf(a))return d&&(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=
this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(b))return d&&(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=!0;this.count=this.numSet+1;this.pts[a]=b;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;d&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);return this.count},"~N,JU.Point3fi,~B")}),p("JM"),v(["JU.BS","$.SB"],"JM.Model",["java.util.Hashtable",
"JU.AU","JU.BSUtil"],function(){c$=u(function(){this.ms=null;this.hydrogenCount=this.fileIndex=this.modelIndex=0;this.hasRasmolHBonds=this.isPdbWithMultipleBonds=this.isBioModel=!1;this.loadState="";this.loadScript=null;this.isModelKit=!1;this.dataFrames=null;this.dataSourceFrame=-1;this.jmolFrameType=this.jmolData=null;this.ac=this.firstAtomIndex=0;this.bsAtomsDeleted=this.bsAtoms=null;this.trajectoryBaseIndex=0;this.isTrajectory=!1;this.bondCount=this.selectedTrajectory=-1;this.nInsertions=this.nAltLocs=
this.moleculeCount=this.firstMoleculeIndex=0;this.groupCount=-1;this.chainCount=0;this.chains=null;this.biosymmetryCount=0;this.properties=this.auxiliaryInfo=null;this.defaultRotationRadius=0;this.orientation=this.biosymmetry=this.defaultStructure=null;this.isJmolDataFrame=this.structureTainted=!1;this.frameDelay=0;this.dssrCache=this.simpleCage=null;q(this,arguments)},JM,"Model");L(c$,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$,"getBondCount",function(){if(0<=this.bondCount)return this.bondCount;var a=this.ms.bo;this.bondCount=
0;for(var b=this.ms.bondCount;0<=--b;)a[b].atom1.mi==this.modelIndex&&this.bondCount++;return this.bondCount});s(c$,function(){});c(c$,"set",function(a,b,d,c,f,e){this.ms=a;this.dataSourceFrame=this.modelIndex=b;this.trajectoryBaseIndex=(this.isTrajectory=0<=d)?d:b;null==e&&(e=new java.util.Hashtable);this.auxiliaryInfo=e;e.containsKey("biosymmetryCount")&&(this.biosymmetryCount=e.get("biosymmetryCount").intValue(),this.biosymmetry=e.get("biosymmetry"));this.properties=f;null==c?this.jmolFrameType=
"modelSet":(this.jmolData=c,this.isJmolDataFrame=!0,e.put("jmolData",c),e.put("title",c),this.jmolFrameType=0<=c.indexOf("ramachandran")?"ramachandran":0<=c.indexOf("quaternion")?"quaternion":"data");return this},"JM.ModelSet,~N,~N,~S,java.util.Properties,java.util.Map");c(c$,"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})}),p("JM"),v(["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 $.Logger".split(" "),
function(){c$=u(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.$mergeGroups=this.htGroup1=null;this.iChain=0;this.structuresDefinedInFile=this.vStereo=null;q(this,arguments)},JM,"ModelLoader");
L(c$,function(){this.specialAtomIndexes=C(JV.JC.ATOMID_MAX,0);this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});s(c$,function(a,b,d,c,f,e){this.vwr=a;this.ms=new JM.ModelSet(a,b);var j=a.getModelAdapter();this.mergeModelSet=f;(this.merging=null!=this.mergeModelSet&&0<this.mergeModelSet.ac)?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);null==e?(this.initializeInfo(b,null),this.createModelSet(null,
null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||(this.ms.canSkipLoad=!1),a=j.getAtomSetCollectionAuxiliaryInfo(c),a.put("loadScript",d),this.initializeInfo(j.getFileTypeName(c).toLowerCase().intern(),a),this.createModelSet(j,c,e))},"JV.Viewer,~S,JU.SB,~O,JM.ModelSet,JU.BS");c(c$,"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=
C(32,0);this.firstAtomIndexes=C(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 f=this.mergeModelSet.trajectorySteps.size();0<=
--f;)this.mergeModelSet.vibrationSteps.addLast(null)}for(f=0;f<this.ms.trajectorySteps.size();f++)this.mergeModelSet.trajectorySteps.addLast(this.ms.trajectorySteps.get(f)),this.mergeModelSet.vibrationSteps.addLast(null==this.ms.vibrationSteps?null:this.ms.vibrationSteps.get(f))}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.')),f=this.ms.getInfoM("defaultOrientationQuaternion"),
null!=f&&(JU.Logger.info("defaultOrientationQuaternion = "+f),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&&(f=a.getAtomSetAuxiliaryInfo(b,0),this.ms.setInfo(this.baseModelIndex,"initialAtomCount",f.get("initialAtomCount")),this.ms.setInfo(this.baseModelIndex,"initialBondCount",
f.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 e=this.vwr.rd;d=this.ms.ac;c=this.ms.at;for(f=this.baseAtomIndex;f<d;f++)c[f].setMadAtom(this.vwr,
e);e=this.ms.am;for(f=e[this.baseModelIndex].firstAtomIndex;f<d;f++)e[c[f].mi].bsAtoms.set(f);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$,"setDefaultRendering",function(a){if(!this.isPyMOLsession){for(var b=new JU.SB,d=this.ms.mc,c=this.ms.am,f=this.baseModelIndex;f<d;f++)c[f].isBioModel&&c[f].getDefaultLargePDBRendering(b,
a);0!=b.length()&&(b.append("select *;"),a=this.ms.getInfoM("jmolscript"),null==a&&(a=""),b.append(a),this.ms.msInfo.put("jmolscript",b.toString()))}},"~N");c(c$,"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 f,d=d.entrySet().iterator();d.hasNext()&&((f=d.next())||1);){var e=f.getKey(),j=f.getValue(),k=this.ms.getModelAtomBitSetIncludingDeleted(b,!0);if(this.doAddHydrogens)var h=
null!=c&&JU.PT.isOneOf(e,c),j=this.jbr.fixPropertyValue(k,j,h);e="property_"+e.toLowerCase();JU.Logger.info("creating "+e+" for model "+this.ms.getModelName(b));this.vwr.setData(e,[e,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,f=0;f<this.adapterModelCount;++f,++c){var e=a.getAtomSetNumber(b,f),j=a.getAtomSetName(b,f),k=a.getAtomSetAuxiliaryInfo(b,f);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?""+e%1E6:"");this.setModelNameNumberProperties(c,d,j,e,h,k,this.jmolData)&&(this.group3Lists[c+1]=JV.JC.getGroup3List(),this.group3Counts[c+1]=C(JV.JC.getGroup3Count()+10,0),null==this.group3Lists[0]&&(this.group3Lists[0]=JV.JC.getGroup3List(),this.group3Counts[0]=C(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"));f=this.ms.msInfo.remove("loadState");e=this.ms.msInfo.remove("loadScript");if(0>e.indexOf("Viewer.AddHydrogens")||!d.isModelKit){j=JU.PT.split(f,"\n");k=new JU.SB;for(f=0;f<j.length;f++)h=d.loadState.indexOf(j[f]),(0>h||h!=d.loadState.lastIndexOf(j[f]))&&k.append(j[f]).appendC("\n");d.loadState+=d.loadScript.toString()+k.toString();d.loadScript=new JU.SB;d.loadScript.append("  ").appendSB(e).append(";\n")}if(this.isTrajectory){f=
this.ms.mc-c+1;JU.Logger.info(f+" trajectory steps read");this.ms.setInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(f));d=this.adapterModelCount;for(f=c;f<this.ms.mc;f++,d++)this.ms.am[f]=this.ms.am[this.baseModelCount],this.ms.modelNumbers[f]=a.getAtomSetNumber(b,d),this.ms.modelNames[f]=a.getAtomSetName(b,d),this.structuresDefinedInFile.set(f)}this.finalizeModels(this.baseModelCount)},"J.api.JmolAdapter,~O");c(c$,"setModelNameNumberProperties",function(a,b,d,c,f,e,j){var k=null!=
e&&Boolean.TRUE===e.get("isPDB");this.appendNew?(this.ms.am[a]=k?this.jbr.getBioModel(a,b,j,f,e):(new JM.Model).set(this.ms,a,b,j,f,e),this.ms.modelNumbers[a]=c,this.ms.modelNames[a]=d):(b=e.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$,"finalizeModels",function(a){var b=this.ms.mc;if(b!=a){var d,c=0,f=-1,e=this.ms.modelNumbers,j=this.ms.modelNames;if(this.isTrajectory)for(var k=
a;++k<this.ms.mc;)e[k]=e[k-1]+1;if(0<a){if(1E6>e[0])for(k=0;k<a;k++)0==j[k].length&&(j[k]=""+e[k]),e[k]+=1E6,this.ms.modelNumbersForAtomLabel[k]="1."+(k+1);var h=e[a-1],h=h-h%1E6;1E6>e[a]&&(h+=1E6);for(k=a;k<b;k++)e[k]+=h}for(var m=this.ms.am,k=a;k<b;++k)if(this.ms.setInfo(k,"fileType",this.ms.modelSetTypeName),null!=this.fileHeader&&this.ms.setInfo(k,"fileHeader",this.fileHeader),h=w(e[k]/1E6),h!=f&&(c=0,f=h),c++,0==h?(d=""+this.ms.getModelNumber(k),h=1):d=h+"."+c,this.ms.modelNumbersForAtomLabel[k]=
d,m[k].fileIndex=h-1,this.ms.modelFileNumbers[k]=1E6*h+c,null==j[k]||0==j[k].length)j[k]=d;if(this.merging)for(k=0;k<a;k++)m[k].ms=this.ms;for(k=0;k<b;k++)this.ms.setInfo(k,"modelName",j[k]),this.ms.setInfo(k,"modelNumber",Integer.$valueOf(e[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,f=!1,e=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(;e.hasNext();){j++;var h=e.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,f=c&&this.doAddHydrogens,
null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var h=e.getGroup3(),m=e.getChainID();this.checkNewGroup(a,m,h,e.getSequenceNumber(),e.getInsertionCode(),f,!1);m=e.getElementNumber();f&&1==JU.Elements.getElementNumber(m)&&this.jbr.setHaveHsAlready(!0);var n=e.getAtomName(),t=f?this.getPdbCharge(h,n):e.getFormalCharge();this.addAtom(c,e.getSymmetry(),e.getAtomSite(),e.getUniqueID(),m,n,t,e.getPartialCharge(),e.getTensors(),e.getOccupancy(),e.getBfactor(),e.getXYZ(),e.getIsHetero(),e.getSerial(),e.getSeqID(),
h,e.getVib(),e.getAltLoc(),e.getRadius())}0<this.groupCount&&f&&this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain?1:0);d=-1;c=null;f=this.ms.at;for(e=0;e<this.ms.ac;e++)f[e].mi!=d&&(d=f[e].mi,k[d].firstAtomIndex=e,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,f,e,j,k,h,m,n,t,p,q,r,s,u,v,w){var x=0;null!=e&&(a&&0<=e.indexOf("*")&&(e=e.$replace("*","'")),x=JV.JC.lookupSpecialAtomID(e),a&&(2==x&&"CA".equalsIgnoreCase(s))&&(x=0));a=this.ms.addAtom(this.iModel,this.nullGroup,f,e,q,r,d,t,w,u,j,k,m,n,h,p,x,b);a.setAltLoc(v);this.htAtomMap.put(c,a)},"~B,JU.BS,~N,~O,~N,~S,~N,~N,JU.Lst,~N,~N,JU.P3,~B,~N,~N,~S,JU.V3,~S,~N");c(c$,"checkNewGroup",function(a,b,d,c,f,e,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||f!=this.currentGroupInsertionCode||k!==this.currentGroup3){0<this.groupCount&&e&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!j?1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=
c;this.currentGroupInsertionCode=f;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,f);++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 f=!1;d.hasNext();){var e=d.getEncodedOrder(),j=
e,k=this.bondAtoms(d.getAtomUniqueID1(),d.getAtomUniqueID2(),j);null!=k&&(1<j&&(1025!=j&&1041!=j)&&(f=!0),j=d.getRadius(),0<j&&k.setMad(Y(2E3*j)),j=d.getColix(),0<=j&&k.setColix(j),k.order|=e&98304)}f&&(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 f=this.ms.getInfoM("unitCells");null!=f&&(c=f.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$,"initializeBonding",function(){var a=null==this.ms.getInfoM("someModelsHaveCONECT")?null:new JU.BS;null!=a&&this.ms.setPdbConectBonding(this.baseAtomIndex,this.baseModelIndex,a);var b=0,d=this.vwr.getBoolean(603979794),c=this.vwr.getBoolean(603979798),f=this.vwr.getBoolean(603979846),e=null,j=!1,k=this.ms.mc,h=this.ms.am;if(!this.noAutoBond)for(var m=this.baseModelIndex;m<k;m++){var b=h[m].bsAtoms.cardinality(),n=this.ms.getInfoI(m,"initialBondCount"),
t=h[m].isBioModel;0>n&&(n=this.ms.bondCount);var p=this.ms.getInfoB(m,"hasSymmetry");if(f||c&&(0==n||t&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||n<w(b/2))||p&&!d&&!this.ms.getInfoB(m,"hasBonds")))if(j=!0,this.merging||1<k)null==e&&(e=JU.BS.newN(this.ms.ac)),(m==this.baseModelIndex||!this.isTrajectory)&&e.or(h[m].bsAtoms)}j?(this.modulationOn&&this.ms.setModulation(null,!0,null,!1),this.ms.autoBondBs4(e,e,a,null,this.ms.defaultCovalentMad,this.vwr.getBoolean(603979874)),JU.Logger.info("ModelSet: autobonding; use  autobond=false  to not generate bonds automatically")):
(this.ms.initializeBspf(),JU.Logger.info("ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation"))});c(c$,"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]=C(0,0))}});c(c$,"distinguishAndPropagateGroup",function(a,b,d,c,f,e){var j=e-1;if(j<f)throw new NullPointerException;var k=this.ms.at[f].mi,h=null==d||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(b,d,c,f,e,
k,this.specialAtomIndexes,this.ms.at);null==h?(h=(new JM.Group).setGroup(b,d,c,f,j),c="o>"):c=h.isProtein()?"p>":h.isNucleic()?"n>":h.isCarbohydrate()?"c>":"o>";null!=d&&(this.countGroup(k,c,d),h.isNucleic()&&(d=null==this.htGroup1?null:this.htGroup1.get(d),null!=d&&(h.group1=d.charAt(0))));this.addGroup(b,h);this.groups[a]=h;h.setGroupIndex(a);for(a=e;--a>=f;)this.ms.at[a].setGroup(h)},"~N,JM.Chain,~S,~N,~N,~N");c(c$,"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$,"countGroup",function(a,b,d){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var f=(d+"   ").substring(0,3),e=this.group3Lists[c].indexOf(f);0>e&&(this.group3Lists[c]+=",["+f+"]",e=this.group3Lists[c].indexOf(f),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][w(e/6)]++;e=this.group3Lists[c].indexOf(",["+f);0<=e&&(this.group3Lists[c]=this.group3Lists[c].substring(0,
e)+b+this.group3Lists[c].substring(e+2));0<=a&&this.countGroup(-1,b,d)}},"~N,~S,~S");c(c$,"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 f=JU.JmolMolecule.getBranchBitSet(this.ms.at,d.atom2.i,a,null,
d.atom1.i,!1,!0);f.set(d.atom2.i);for(var e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))this.ms.at[e].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$,"set2dZ",function(a,b){var d=JU.BS.newN(b),c=new JU.BS,f=new JU.V3,e=JU.V3.new3(0,1,0),j=new JU.V3,k=new JU.BS;k.setBits(a,b);for(var h=a;h<b;h++)!d.get(h)&&!c.get(h)&&(c=this.getBranch2dZ(h,-1,k,c,f,e,j),d.or(c))},"~N,~N");c(c$,"getBranch2dZ",function(a,b,d,c,f,e,j){c=JU.BS.newN(this.ms.ac);
if(0>a)return c;var h=new JU.BS;h.or(d);0<=b&&h.clear(b);JM.ModelLoader.setBranch2dZ(this.ms.at[a],c,h,f,e,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,f,e){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 h=a.bonds[j];h.isHydrogen()||(h=h.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,h,c,f,e),JM.ModelLoader.setBranch2dZ(h,b,d,c,f,e))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setAtom2dZ=c(c$,
"setAtom2dZ",function(a,b,d,c,f){d.sub2(b,a);d.z=0;d.normalize();f.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,f){if(null==c)return null;var e=a.getModelAdapter(),j=new JU.P3,h=b.at,l=a.getFloat(570425363);if(null!=b.unitCells)for(var m=f.nextSetBit(0);0<=m;m=f.nextSetBit(m+1))if(null!=h[m].getAtomSymmetry()){l=-l;break}for(var m=-1,n=0,t=JU.BSUtil.cardinalityOf(f)==a.getAtomCount(),p=e.getAtomIterator(c);p.hasNext();){var q=
p.getXYZ();if(!Float.isNaN(q.x+q.y+q.z))if(1146095626==d){m=f.nextSetBit(m+1);if(0>m)break;n++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+m+": "+h[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(l,j,q,-1);q.and(f);if(t)if(n=JU.BSUtil.cardinalityOf(q),0==n){JU.Logger.warn("createAtomDataSet: no atom found at position "+j);continue}else 1<n&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+n+" atoms found at position "+
j);switch(d){case 1146095631:var r=p.getVib();if(null==r)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+j+" vib: "+r);b.setAtomCoords(q,1146095631,r);break;case 1129318401:b.setAtomProperty(q,d,0,p.getOccupancy(),null,null,null);break;case 1112541196:b.setAtomProperty(q,d,0,p.getPartialCharge(),null,null,null);break;case 1112541199:b.setAtomProperty(q,d,0,p.getBfactor(),null,null,null)}}}switch(d){case 1146095631:b=e.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+b);a.setStringProperty("_vibrationName",
b);break;case 1146095626:if(JU.Logger.info(n+" atom positions read"),b.recalculateLeadMidpointsAndWingVectors(-1),n==b.ac)return"boundbox {*};reset"}return null},"JV.Viewer,JM.ModelSet,~N,~O,JU.BS");x(c$,"defaultGroupCount",32)}),p("JM"),v("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 $.Txt JV.JC".split(" "),
function(){c$=u(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;q(this,arguments)},JM,"ModelSet",JM.BondCollection);L(c$,function(){this.closest=
Array(1);this.am=Array(1);this.modelNumbers=C(1,0);this.modelFileNumbers=C(1,0);this.modelNumbersForAtomLabel=Array(1);this.modelNames=Array(1);this.frameTitles=Array(1);this.ptTemp=new JU.P3;this.boxInfo=new JU.BoxInfo;this.boxInfo.addBoundBoxPoint(JU.P3.new3(-10,-10,-10));this.boxInfo.addBoundBoxPoint(JU.P3.new3(10,10,10));this.stateScripts=new JU.Lst;this.selectedMolecules=new JU.BS;this.ptTemp1=new JU.P3;this.ptTemp2=new JU.P3;this.matTemp=new JU.M3;this.matInv=new JU.M3;this.mat4=new JU.M4;this.mat4t=
new JU.M4;this.vTemp=new JU.V3});s(c$,function(a,b){G(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,f,e,j){var h=new JU.BS,l=new JU.V3,m=this.am[a].firstAtomIndex,n=m+this.getAtomCountInModel(a);if(0==f)for(var t=0;m<n&&t<d.length;m++,t++)this.at[m].mi=b,null!=d[t]&&(j?this.at[m].setFractionalCoordTo(d[t],!0):this.at[m].setT(d[t]),null!=this.vibrationSteps&&(null!=e&&null!=e[t]&&(l=e[t]),this.setVibrationVector(m,l)),h.set(m));
else{e=new JU.P3;l=Math.min(d.length,c.length);for(t=0;m<n&&t<l;m++,t++)this.at[m].mi=b,null==d[t]||null==c[t]||(e.sub2(c[t],d[t]),e.scaleAdd2(f,e,d[t]),j?this.at[m].setFractionalCoordTo(e,!0):this.at[m].setT(e),h.set(m))}this.initializeBspf();this.validateBspfForModel(a,!1);this.recalculateLeadMidpointsAndWingVectors(a);this.sm.refreshShapeTrajectories(a,h,null);this.am[a].hasRasmolHBonds&&(this.am[a].clearRasmolHydrogenBonds(null),this.am[a].getRasmolHydrogenBonds(h,h,null,!1,2147483647,!1,null))},
"~N,~N,~A,~A,~N,~A,~B");c(c$,"getFrameOffsets",function(a){if(null==a)return null;for(var b=Array(this.mc),d=0;d<this.mc;d++)b[d]=new JU.P3;for(var c=0,f=0,e=b[0],j=null!=this.trajectorySteps&&this.trajectorySteps.size()==this.mc,h=j?this.mc:1,l=0;l<h;l++){j&&this.setTrajectory(l);for(d=0;d<=this.ac;d++){if(d==this.ac||this.at[d].mi!=c){0<f&&(e.scale(-1/f),0!=c&&e.sub(b[0]),f=0);if(d==this.ac)break;c=this.at[d].mi;e=b[c]}a.get(d)&&(e.add(this.at[d]),f++)}}b[0].set(0,0,0);return b},"JU.BS");c(c$,"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,f){var e=new JU.BS;a=JU.BSUtil.copyInvert(this.modelsOf(a,e),this.mc);if(!f)return this.calculateStructuresAllExcept(a,b,d,c,!1,!1);for(f=0;f<this.mc;f++)a.get(f)||this.am[f].clearBioPolymers();this.calculatePolymers(null,0,0,a);b=this.calculateStructuresAllExcept(a,b,d,c,!0,!1);this.vwr.shm.resetBioshapes(e);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$,"getPointGroupAsString",function(a,b,d,c,f){return this.calculatePointGroupForFirstModel(a,!0,b,!1,d,c,f)},"JU.BS,~B,~S,~N,~N");c(c$,"calculatePointGroupForFirstModel",function(a,b,d,c,f,e,j){var h=this.vwr.am.cmi,l=null==a?-1:a.nextSetBit(0);0>h&&0<=l&&(h=this.at[l].getModelIndex());0>h&&(h=this.vwr.getVisibleFramesBitSet().nextSetBit(0),
a=null);var m=this.vwr.getModelUndeletedAtomsBitSet(h);null!=a&&m.and(a);l=m.nextSetBit(0);0>l&&(m=this.vwr.getModelUndeletedAtomsBitSet(h),l=m.nextSetBit(0));a=this.vwr.shm.getShapePropertyIndex(18,"mad",l);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(h,d,c,
f,e,j);return c?b:(1<this.mc?"frame "+this.getModelNumberDotted(h)+"; ":"")+b},"JU.BS,~B,~B,~B,~S,~N,~N");c(c$,"modelsOf",function(a,b){for(var d=JU.BS.newN(this.mc),c=null==a,f=c?this.ac-1:a.nextSetBit(0);0<=f;f=c?f-1:a.nextSetBit(f+1)){var e=this.am[this.at[f].mi].trajectoryBaseIndex;this.isJmolDataFrameForModel(e)||(d.set(e),b.set(f))}return d},"JU.BS,JU.BS");c(c$,"getDefaultStructure",function(a,b){for(var d=this.modelsOf(a,b),c=new JU.SB,f=d.nextSetBit(0);0<=f;f=d.nextSetBit(f+1))this.am[f].isBioModel&&
null!=this.am[f].defaultStructure&&c.append(this.am[f].defaultStructure);return c.toString()},"JU.BS,JU.BS");c(c$,"makeConnections",function(a,b,d,c,f,e,j,h,l,m){if(1073741852==c&&2048!=d){var n="connect ";0.1!=a&&(n+=a+" ");1E8!=b&&(n+=b+" ");this.addStateScript(n,h?f:null,h?null:f,h?null:e," auto",!1,!0)}this.moleculeCount=0;return this.makeConnections2(a,b,d,c,f,e,j,h,l,m)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"setPdbConectBonding",function(a,b,d){for(var c=this.vwr.getMadBond();b<this.mc;b++){var f=
this.getInfo(b,"PDB_CONECT_bonds");if(null!=f){var e=f.size();this.setInfo(b,"initialBondCount",Integer.$valueOf(e));for(var j=this.getInfo(b,"PDB_CONECT_firstAtom_count_max"),h=j[0]+a,l=h+j[1],j=j[2],m=C(j+1,0),n=h;n<l;n++)if(0<(h=this.atomSerials[n]))m[h]=n+1;for(l=0;l<e;l++){var n=f.get(l),t=n[0],h=n[1],n=n[2];0>t||(0>h||t>j||h>j)||(t=m[t]-1,h=m[h]-1,0>t||0>h||(null!=d&&(this.at[t].isHetero()&&d.set(t),this.at[h].isHetero()&&d.set(h)),this.checkValencesAndBond(this.at[t],this.at[h],n,2048==n?1:
c,null)))}}}},"~N,~N,JU.BS");c(c$,"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),f=this.am,b=new JU.BS,e=d=0;d<this.mc;d++)a.get(d)?(this.getAtomCountInModel(d),b.or(this.getModelAtomBitSetIncludingDeleted(d,
!1))):(this.am[d].modelIndex=e,c[e++]=this.am[d]);this.am=c;var j=this.mc,h=this.getBondsForSelectedAtoms(b,!0);this.deleteBonds(h,!0);for(e=d=0;d<j;d++)if(a.get(d)){var l=f[d].ac;if(0!=l){var m=f[d].bsAtoms,n=f[d].firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,m);this.deleteModel(e,n,l,m,h);for(var t=j;--t>d;)f[t].fixIndices(e,l,m);this.vwr.shm.deleteShapeAtoms([c,this.at,[e,n,l]],m);this.mc--}}else e++;this.deleteModel(-1,0,0,null,null);return b},"JU.BS");c(c$,"setAtomProperty",function(a,
b,d,c,f,e,j){switch(b){case 1115297793:case 1113200642:case 1113200647:case 1113200649:case 1113200650:case 1650071565:case 1113200654:if(4<c&&(c=4),null!=e){d=M(this.ac,0);try{var h=a.nextSetBit(0);for(f=0;0<=h;h=a.nextSetBit(h+1))d[h]=e[f++]}catch(l){if(D(l,Exception))return;throw l;}e=d}case 1113200646:case 1113200652:h=null;d=0;null==e?(16<c&&(c=16.1),0>c&&(c=0),d=w(Math.floor(2E3*c))):h=new J.atomdata.RadiusData(e,0,null,null);this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(b),d,h,a);return}this.setAPm(a,
b,d,c,f,e,j)},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"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$,"addHydrogens",function(a,b){var d=this.mc-1,c=new JU.BS;if(this.isTrajectory(d)||1<this.am[d].getGroupCount())return c;this.growAtomArrays(this.ac+b.length);var f=this.vwr.rd,e=this.getDefaultMadFromOrder(1);this.am[d].dssrCache=
null;for(var j=0,h=this.am[d].ac+1;j<a.size();j++,h++){var l=a.get(j),m=this.addAtom(d,l.group,1,"H"+h,h,l.getSeqID(),h,b[j],NaN,null,0,0,100,NaN,null,!1,0,null);m.setMadAtom(this.vwr,f);c.set(m.i);this.bondAtoms(l,m,1,e,null,0,!1,!1)}this.sm.loadDefaultShapes(this);return c},"JU.Lst,~A");c(c$,"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$,"getPlaneIntersection",function(a,b,d,c,f){var e=null;switch(a){case 1614417948:if(null==f)return null;e=f.getCanonicalCopy(d,!0);break;case 1679429641:e=this.boxInfo.getCanonicalCopy(d)}a=new JU.Lst;a.addLast(e);return this.intersectPlane(b,a,c)},"~N,JU.P4,~N,~N,J.api.SymmetryInterface");c(c$,"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(r(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$,"calculatePolymers",function(a,b,d,c){if(this.isPDB)for(var f=!this.vwr.getBoolean(603979892),e=0;e<this.mc;e++)if((null==c||!c.get(e))&&this.am[e].isBioModel){this.am[e].calculatePolymers(a,b,d,c,f);break}},"~A,~N,~N,JU.BS");c(c$,"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 f=
0;f<this.am[b].chains[c].groupCount;f++)a[d]=this.am[b].chains[c].groups[f],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$,"calcRotationRadius",function(a,b){if(this.isJmolDataFrameForModel(a)){var d=this.am[a].defaultRotationRadius;return 0==d?10:d}for(var d=0,c=this.ac;0<=--c;)if(this.isJmolDataFrameForAtom(this.at[c]))for(a=this.at[c].mi;0<=c&&this.at[c].mi==a;)c--;else{var f=this.at[c],f=b.distance(f)+this.getRadiusVdwJmol(f);f>d&&(d=f)}return 0==d?10:d},"~N,JU.P3");c(c$,"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,f=c?this.ac-1:a.nextSetBit(0);0<=f;f=c?f-1:a.nextSetBit(f+1))d++,this.isJmolDataFrameForAtom(this.at[f])||b.addBoundBoxPoint(this.at[f]);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 f=this.at[c],f=b.distance(f)+this.getRadiusVdwJmol(f);f>d&&(d=f)}return 0==d?10:d},"JU.BS");c(c$,"getCenterAndPoints",function(a,b){for(var d,c,f=b?1:0,e=a.size();0<=--e;){var j=a.get(e);d=j[0];r(j[1],JU.BS)?(c=j[1],f+=Math.min(d.cardinality(),c.cardinality())):f+=Math.min(d.cardinality(),j[1].length)}var h=P(2,f,null);b&&(h[0][0]=new JU.P3,h[1][0]=new JU.P3);for(e=a.size();0<=--e;)if(j=a.get(e),d=j[0],r(j[1],JU.BS)){c=j[1];for(var j=d.nextSetBit(0),l=c.nextSetBit(0);0<=
j&&0<=l;j=d.nextSetBit(j+1),l=c.nextSetBit(l+1))h[0][--f]=this.at[j],h[1][f]=this.at[l],b&&(h[0][0].add(this.at[j]),h[1][0].add(this.at[l]))}else{c=j[1];j=d.nextSetBit(0);for(l=0;0<=j&&l<c.length;j=d.nextSetBit(j+1),l++)h[0][--f]=this.at[j],h[1][f]=c[l],b&&(h[0][0].add(this.at[j]),h[1][0].add(c[l]))}b&&(h[0][0].scale(1/(h[0].length-1)),h[1][0].scale(1/(h[1].length-1)));return h},"JU.Lst,~B");c(c$,"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,f,e,j){this.setAPa(a,b,d,c,f,e,j);switch(b){case 1095763991:case 1632634891:this.vwr.getBoolean(603979944)&&this.assignAromaticBonds()}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"addStateScript",function(a,b,d,c,f,e,j){var h=this.vwr.am.cmi;
e?(this.thisStateModel!=h&&(a="frame "+(0>h?"all #"+h:this.getModelNumberDotted(h))+";\n  "+a),this.thisStateModel=h):this.thisStateModel=-1;a=new JM.StateScript(this.thisStateModel,a,b,d,c,f,j);a.isValid()&&this.stateScripts.addLast(a);return a},"~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");c(c$,"calculateStructuresAllExcept",function(a,b,d,c,f,e){this.freezeModels();var j="";a=JU.BSUtil.copyInvert(a,this.mc);f&&this.setDefaultStructure(a);for(var h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1))j+=this.am[h].calculateStructures(b,
d,c,f,e);f&&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,f=this.getModelBS(a,!1);this.setDefaultStructure(f);for(var e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1)){c!=e-1&&(d=-1);var d=this.at[e].group.setProteinStructureType(b,
d),j=this.at[e].mi;this.proteinStructureTainted=this.am[j].structureTainted=!0;c=e=this.at[e].group.lastAtomIndex}d=C(this.mc,0);for(e=0;e<this.ac;)j=this.at[e].mi,f.get(j)?(c=this.at[e].getStrucNo(),1E3>c&&c>d[j]&&(d[j]=c),e=this.at[e].group.lastAtomIndex+1):e=this.am[j].firstAtomIndex+this.am[j].ac;for(e=0;e<this.ac;)j=this.at[e].mi,f.get(j)?(1E3<this.at[e].getStrucNo()&&this.at[e].group.setStrucNo(++d[j]),e=this.at[e].group.lastAtomIndex+1):e=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$,"getConformation",function(a,b,d){for(var c=new JU.BS,f=this.mc;0<=--f;)if(f==
a||0>a){var e=this.getAltLocListInModel(f),j=this.getAltLocCountInModel(f);if(!(0<b&&b>=j)){var h=this.vwr.getModelUndeletedAtomsBitSet(f);if(0<=b&&!this.am[f].getPdbConformation(h,b))for(;0<=--j;)j!=b&&h.andNot(this.getAtomBitsMDa(1048607,e.substring(j,j+1)));0<=h.nextSetBit(0)&&(c.or(h),d&&this.am[f].setConformation(h))}}return c},"~N,~N,~B");c(c$,"getHeteroList",function(a){for(var b=new java.util.Hashtable,d=!1,c=this.mc;0<=--c;)if(0>a||c==a){var f=this.getInfo(c,"hetNames");if(null!=f)for(var d=
!0,e,f=f.entrySet().iterator();f.hasNext()&&((e=f.next())||1);){var j=e.getKey();b.put(j,e.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 r(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$,"getModelBS",function(a,b){for(var d=
new JU.BS,c=0,f=null==a,c=f?0:a.nextSetBit(0);0<=c&&c<this.ac;c=f?c+1:a.nextSetBit(c+1)){d.set(c=this.at[c].mi);if(b)for(var e=this.am[c].trajectoryBaseIndex,j=0;j<this.mc;j++)this.am[j].trajectoryBaseIndex==e&&d.set(j);c=this.am[c].firstAtomIndex+this.am[c].ac-1}return d},"JU.BS,~B");c(c$,"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$,"fillAtomData",function(a,b){if(0!=(b&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);a.atomMolecule=C(this.ac,0);for(var d,c=0;c<this.molecules.length;c++){d=a.bsMolecules[c]=this.molecules[c].atomList;for(var f=d.nextSetBit(0);0<=f;f=d.nextSetBit(f+1))a.atomMolecule[f]=
c}}0!=(b&8)?(d=C(1,0),a.hAtomRadius=this.vwr.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,d,!1,!0,null),a.hydrogenAtomCount=d[0]):(a.firstAtomIndex=0>a.modelIndex?null==a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.am[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=0==this.ac?0:this.at[a.firstAtomIndex].mi,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,b))},"J.atomdata.AtomData,~N");c(c$,"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(!r(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$,"modelFileNumberFromFloat",function(a){var b=w(Math.floor(a));for(a=w(Math.floor(1E4*(a-b+1E-5)));0!=a&&0==a%10;)a/=10;return 1E6*b+a},"~N");c(c$,"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 f=0;f<this.mc;++f)this.am[f].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,f,e,j){for(var h=null==b||a.equals(b),l=this.mc;0<=
--l;)this.am[l].isBioModel&&this.am[l].trajectoryBaseIndex==l&&(null==d&&(this.am[l].clearRasmolHydrogenBonds(a),h||this.am[l].clearRasmolHydrogenBonds(b)),this.am[l].getRasmolHydrogenBonds(a,b,d,c,f,e,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,f=new JU.Lst,e=a.nextSetBit(0);0<=e&&c<b;e=a.nextSetBit(e+1)){var j=this.at[e].group,h=j.getQuaternion(d);if(null==h&&(-2147483648==j.seqcode&&(h=j.getQuaternionFrame(this.at)),null==h))continue;c++;f.addLast(h);e=j.lastAtomIndex}return f.toArray(Array(f.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==r(this.vibrations[d],
J.api.JmolModulationSet)))return d;return-1},"~N,~N");c(c$,"getModulationList",function(a,b,d){var c=new JU.Lst;if(null!=this.vibrations)for(var f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))r(this.vibrations[f],J.api.JmolModulationSet)?c.addLast(this.vibrations[f].getModulation(b,d)):c.addLast(null);return c},"JU.BS,~S,JU.P3");c(c$,"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$,"calculateMolecularDipole",function(a,b){if(null!=b){var d=b.nextSetBit(0);if(0>d)return null;a=this.at[d].getModelIndex()}if(null==this.partialCharges||0>a)return null;var c=
d=0,f=0,e=0,j=new JU.V3,h=new JU.V3;null==b&&(b=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var l=b.nextSetBit(0);0<=l;l=b.nextSetBit(l+1))if(!(this.at[l].mi!=a||this.at[l].isDeleted())){var m=this.partialCharges[l];0>m?(c++,e+=m,h.scaleAdd2(m,this.at[l],h)):0<m&&(d++,f+=m,j.scaleAdd2(m,this.at[l],j))}if(0.01<Math.abs(f+e))return JU.Logger.info("Dipole calculation requires balanced charges: "+f+" "+e),null;if(0==c||0==d)return null;j.add(h);j.scale(4.8);return j},"~N,JU.BS");c(c$,"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,f){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,f)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");c(c$,"getSelectedAtomIterator",function(a,b,d,c,f){this.initializeBspf();
if(f){f=this.getModelBS(a,!1);for(var e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))this.initializeBspt(e);f=new JM.AtomIteratorWithinModelSet(f)}else f=new JM.AtomIteratorWithinModel;f.initialize(this.bspf,a,b,d,c,this.vwr.isParallel());return f},"JU.BS,~B,~B,~B,~B");h(c$,"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$,"getAtomBitsMaybeDeleted",function(a,b){var d,c;switch(a){default:return this.getAtomBitsMDa(a,b);case 1073741925:return this.getAnnotationBits("domains",1073741925,b);case 1073742189:return this.getAnnotationBits("validation",1073742189,b);case 1073741916:return this.getAnnotationBits("dssr",1073741916,b);case 1678770178:case 1048585:return this.getAtomBitsMDb(a,
b);case 1073741864:return this.getBasePairBits(b);case 1679429641:var f=this.getBoxInfo(b,1);c=this.getAtomsWithin(f.getBoundBoxCornerVector().length()+1E-4,f.getBoundBoxCenter(),null,-1);for(d=c.nextSetBit(0);0<=d;d=c.nextSetBit(d+1))f.isWithin(this.at[d])||c.clear(d);return c;case 1095761925:c=new JU.BS;d=b;this.ptTemp1.set(d[0]/1E3,d[1]/1E3,d[2]/1E3);for(d=this.ac;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,!1)&&c.set(d);return c;case 1095761926:c=JU.BSUtil.newBitSet2(0,this.ac);d=
b;f=[w(d[0]/1E3)-1,w(d[1]/1E3)-1,w(d[2]/1E3)-1,w(d[0]/1E3),w(d[1]/1E3),w(d[2]/1E3),0];for(d=this.mc;0<=--d;){var e=this.getUnitCell(d);null==e?JU.BSUtil.andNot(c,this.am[d].bsAtoms):c.andNot(e.notInCentroid(this,this.am[d].bsAtoms,f))}return c;case 3145754:c=b.nextSetBit(0);if(0>c)return new JU.BS;if(this.at[c].group.$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 f=d[0],e=
d[1],j=d[2];c=new JU.BS;var h=this.vwr.getBoolean(603979823);0<=j&&(256>j&&!h)&&(j=JM.AtomCollection.chainToUpper(j));for(d=this.mc;0<=--d;)this.am[d].isBioModel&&this.am[d].selectSeqcodeRange(f,e,j,c,h);return c;case 3145772:c=JU.BS.newN(this.ac);f=-1;e=0;for(d=this.ac;0<=--d;)if(h=this.at[d],j=h.getAtomSymmetry(),null!=j){if(h.mi!=f){f=h.mi;if(null==this.getModelCellRange(f))continue;e=this.getModelSymmetryCount(f)}for(var h=0,l=e;0<=--l;)if(j.get(l)&&1<++h){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$,"getAnnotationBits",function(a,b,d){for(var c=new JU.BS,f=this.vwr.getAnnotationParser(),e,j=this.mc;0<=--j;)null!=(e=this.getInfo(j,a))&&c.or(f.getAtomBits(this.vwr,d,this.getCachedAnnotationMap(j,a+" V ",e),this.am[j].dssrCache,
b,j,this.am[j].bsAtoms));return c},"~S,~N,~S");c(c$,"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=r(d,JS.SV)?d:this.vwr.evaluateExpressionAsVariable(d),a.put(b,c));return r(c,JS.SV)?c:null},"~N,~S,~O");c(c$,"isInLatticeCell",function(a,b,d,c){var f=this.getUnitCell(this.at[a].mi);d.setT(this.at[a]);return null!=f&&f.checkUnitCell(f,b,d,c)},"~N,JU.P3,JU.P3,~B");
c(c$,"getAtomsWithinRadius",function(a,b,d,c){var f=new JU.BS,e=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 h=b.nextSetBit(0);0<=h;h=b.nextSetBit(h+1))for(var l=this.mc;0<=--l;)e.get(l)&&(0>a?this.getAtomsWithin(a,this.at[h].getFractionalUnitCoordPt(!0,d),f,-1):(this.setIteratorForAtom(j,l,h,a,c),j.addAtoms(f)))}else{f.or(b);for(h=b.nextSetBit(0);0<=h;h=b.nextSetBit(h+1))0>a?this.getAtomsWithin(a,
this.at[h],f,this.at[h].mi):(this.setIteratorForAtom(j,-1,h,a,c),j.addAtoms(f))}j.release();return f},"~N,JU.BS,~B,J.atomdata.RadiusData");c(c$,"getGroupsWithin",function(a,b){for(var d=this.getIterativeModels(!1),c=new JU.BS,f=this.mc;0<=--f;)d.get(f)&&this.am[f].isBioModel&&this.am[f].getGroupsWithin(a,b,c);return c},"~N,JU.BS");c(c$,"getAtomsWithin",function(a,b,d,c){null==d&&(d=new JU.BS);if(0>a){a=-a;for(var f=this.ac;0<=--f;){var e=this.at[f];0<=c&&this.at[f].mi!=c||!d.get(f)&&e.getFractionalUnitDistance(b,
this.ptTemp1,this.ptTemp2)<=a&&d.set(e.i)}return d}c=this.getIterativeModels(!0);f=this.getSelectedAtomIterator(null,!1,!1,!1,!1);for(e=this.mc;0<=--e;)c.get(e)&&(this.setIteratorForAtom(f,-1,this.am[e].firstAtomIndex,-1,null),f.setCenter(b,a),f.addAtoms(d));f.release();return d},"~N,JU.P3,JU.BS,~N");c(c$,"getBasePairBits",function(a){var b=new JU.BS;if(0!=a.length%2)return b;var d=null,c=null,b=new JU.Lst;if(0==a.length)d=c=this.vwr.getAllAtoms(),this.calcRasmolHydrogenBonds(d,c,b,!0,1,!1,null);
else for(var f=0;f<a.length;)d=this.getSequenceBits(a.substring(f,++f),null),0!=d.cardinality()&&(c=this.getSequenceBits(a.substring(f,++f),null),0!=c.cardinality()&&this.calcRasmolHydrogenBonds(d,c,b,!0,1,!1,null));a=new JU.BS;for(f=b.size();0<=--f;)d=b.get(f),a.set(d.atom1.i),a.set(d.atom2.i);return this.getAtomBitsMDb(1087373318,a)},"~S");c(c$,"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$,"deleteBonds",function(a,b){if(!b)for(var d=new JU.BS,c=new JU.BS,f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var e=this.bo[f].atom1;this.am[e.mi].isModelKit||(d.clearAll(),c.clearAll(),d.set(e.i),c.set(this.bo[f].getAtomIndex2()),this.addStateScript("connect ",null,d,c,"delete",!1,!0))}this.dBb(a,b)},"JU.BS,~B");c(c$,"makeConnections2",function(a,b,d,c,f,e,j,h,l,m){null==j&&(j=new JU.BS);var n=65535==d,t=131071==d;t&&(d=1);var p=JM.Bond.isOrderH(d),q=!1,r=!1,s=!1,
u=!1;switch(c){case 12291:return this.deleteConnections(a,b,d,f,e,h,t);case 603979874:case 1073741852:if(515!=d)return this.autoBond(f,e,j,h,p,603979874==c);r=u=!0;break;case 1087373321:q=r=!0;break;case 1073742025:r=!0;break;case 1073741904:s=!0}c=!q||n;n=!q&&!n;this.defaultCovalentMad=this.vwr.getMadBond();var t=0>a,v=0>b,w=t||v,x=!h||0.1!=a||1E8!=b;x&&(a=this.fixD(a,t),b=this.fixD(b,v));var A=this.getDefaultMadFromOrder(d),y=0,B=0,C=null,E=null,G=null,H="\x00",I=d|131072;try{for(var M=f.nextSetBit(0);0<=
M;M=f.nextSetBit(M+1)){if(h)C=this.bo[M],E=C.atom1,G=C.atom2;else{E=this.at[M];if(E.isDeleted())continue;H=this.isModulated(M)?"\x00":E.altloc}for(var L=h?0:e.nextSetBit(0);0<=L;L=e.nextSetBit(L+1)){if(h)L=2147483646;else{if(L==M)continue;G=this.at[L];if(E.mi!=G.mi||G.isDeleted())continue;if("\x00"!=H&&H!=G.altloc&&"\x00"!=G.altloc)continue;C=E.getBond(G)}if(!((null==C?r:s)||x&&!this.isInRange(E,G,a,b,t,v,w)))if(null==C)j.set(this.bondAtoms(E,G,d,A,j,m,l,!0).index),y++;else if(n&&(C.setOrder(d),this.bsAromatic.clear(C.index)),
c||d==C.order||I==C.order||p&&C.isHydrogen())j.set(C.index),B++}}}catch(N){if(!D(N,Exception))throw N;}u&&this.assignAromaticBondsBs(!0,j);q||this.sm.setShapeSizeBs(1,-2147483648,null,j);return[y,B]},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"autoBondBs4",function(a,b,d,c,f,e){if(e)return this.autoBond_Pre_11_9_24(a,b,d,c,f);if(0==this.ac)return 0;0==f&&(f=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();e=this.vwr.getFloat(570425348);var j=this.vwr.getFloat(570425364),j=j*j,h=0;this.showRebondTimes&&
JU.Logger.startTimer("autobond");var l=-1,m=null==a,n,t;m?(t=0,n=null):(a.equals(b)?n=a:(n=JU.BSUtil.copy(a),n.or(b)),t=n.nextSetBit(0));for(var p=this.getSelectedAtomIterator(null,!1,!1,!0,!1),q=!1;0<=t&&t<this.ac;t=m?t+1:n.nextSetBit(t+1)){var r=m||a.get(t),s=m||b.get(t),u=this.at[t];if(!u.isDeleted()){var v=u.mi;if(v!=l){l=v;if(this.isJmolDataFrameForModel(v)){t=this.am[v].firstAtomIndex+this.am[v].ac-1;continue}q=this.getInfoB(v,"autoBondUsingOccupation")}v=u.getBondingRadius();if(0!=v){var w=
null!=d&&d.get(t);for(this.setIteratorForAtom(p,-1,t,v+this.maxBondingRadius+e,null);p.hasNext();){var x=this.at[p.next()];if(!x.isDeleted()){var y=x.i,A=m||a.get(y),B=m||b.get(y);!A&&!B||(!(r&&B||s&&A)||w&&d.get(y)||q&&null!=this.occupancies&&50>this.occupancies[t]!=50>this.occupancies[y])||(y=JM.BondCollection.getBondOrderFull(v,x.getBondingRadius(),p.foundDistance2(),j,e),0<y&&this.checkValencesAndBond(u,x,y,f,c)&&h++)}}p.release()}}}this.showRebondTimes&&JU.Logger.checkTimer("autoBond",!1);return h},
"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B");c(c$,"autoBond_Pre_11_9_24",function(a,b,d,c,f){if(0==this.ac)return 0;0==f&&(f=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var e=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 n=null==a||a.get(m),t=null==b||b.get(m);if(n||t){var p=this.at[m];if(!p.isDeleted()){var q=p.mi;if(q!=l&&(l=q,this.isJmolDataFrameForModel(q))){for(;0<=--m&&this.at[m].mi==q;);m++;continue}var r=p.getBondingRadius();
if(0!=r){var s=r+this.maxBondingRadius+e;this.initializeBspt(q);q=this.bspf.getCubeIterator(q);for(q.initialize(p,s,!0);q.hasMoreElements();)if(s=q.nextElement(),!(s===p||s.isDeleted())){var u=s.i,v=null==a||a.get(u),w=null==b||b.get(u);if(!(!v&&!w||null!=d&&d.get(u)&&d.get(m)))if(n&&w||t&&v)u=JM.BondCollection.getBondOrderFull(r,s.getBondingRadius(),q.foundDistance2(),j,e),0<u&&this.checkValencesAndBond(p,s,u,f,c)&&h++}q.release()}}}}return h},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(c$,"autoBond",function(a,
b,d,c,f,e){if(c){c=a;a=new JU.BS;b=new JU.BS;for(var j=c.nextSetBit(0);0<=j;j=c.nextSetBit(j+1))a.set(this.bo[j].atom1.i),b.set(this.bo[j].atom2.i)}return[f?this.autoHbond(a,b,!1):this.autoBondBs4(a,b,null,d,this.vwr.getMadBond(),e),0]},"JU.BS,JU.BS,JU.BS,~B,~B,~B");c(c$,"autoHbond",function(a,b,d){if(d){for(var c=this.getModelBS(a,!1),f=c.nextSetBit(0);0<=f&&d;f=c.nextSetBit(f+1))d=!this.am[f].hasRasmolHBonds;if(d)return 0}d=!1;for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))if(1==this.at[f].getElementNumber()){d=
!0;break}c=new JU.BS;f=this.vwr.getBoolean(603979853);if(null==b||f&&!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 e=null;if(!d){e=new JU.BS;for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))switch(this.at[f].atomID){case 64:case 4:case 14:case 15:case 16:case 17:e.set(f)}}var j=this.vwr.getFloat(570425361),
h=3.141592653589793*this.vwr.getFloat(570425360)/180,l=j*j,m=JM.ModelSet.hbondMin*JM.ModelSet.hbondMin,n=j>JM.ModelSet.hbondMin?m:l,t=j>JM.ModelSet.hbondMin?JM.ModelSet.hbondMin:j,p=0,q=0,r=new JU.V3,s=new JU.V3;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var u=null,v=null;b=this.getSelectedAtomIterator(b,!1,!1,!1,!1);for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var w=this.at[f],x=w.getElementNumber(),y=1==x;if(!(!y&&(d||7!=x&&8!=x)||y&&!d)){var A,B,C;if(y){x=w.bonds;
if(null==x)continue;C=!1;for(A=0;A<x.length&&!C;A++)C=x[A].getOtherAtom(w).getElementNumber(),C=7==C||8==C;if(!C)continue;B=t;x=1;A=n;C=!1}else B=j,x=m,A=l,C=e.get(f);for(this.setIteratorForAtom(b,-1,w.i,B,null);b.hasNext();){B=this.at[b.next()];var D=B.getElementNumber();if(!(B===w||!y&&7!=D&&8!=D||y&&1==D||(q=b.foundDistance2())<x||q>A||C&&e.get(B.i)||w.isBonded(B))){if(0<h){r.sub2(w,B);if(null==(v=JM.ModelSet.checkMinAttachedAngle(w,h,r,s,d)))continue;r.scale(-1);if(null==(u=JM.ModelSet.checkMinAttachedAngle(B,
h,r,s,d)))continue}var D=0,E;y&&!Float.isNaN(u.x)&&!Float.isNaN(v.x)?(E=4096,D=JM.HBond.getEnergy(Math.sqrt(q),u.distance(w),u.distance(v),B.distance(v))/1E3):E=2048;c.set(this.addHBond(w,B,E,D));p++}}}}b.release();this.sm.setShapeSizeBs(1,-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return d?p:-p},"JU.BS,JU.BS,~B");c$.checkMinAttachedAngle=c(c$,"checkMinAttachedAngle",function(a,b,d,c,f){var e=a.bonds;if(null==e||0==e.length)return JU.P3.new3(NaN,0,0);for(var j=null,
h=3.4028235E38,l=e.length;0<=--l;)if(e[l].isCovalent()){var m=e[l].getOtherAtom(a);if(f||1!=m.getElementNumber()){c.sub2(a,m);var n=c.angle(d);if(n<b)return null;n<h&&(j=m,h=n)}}return j},"JM.Atom,~N,JU.V3,JU.V3,~B");c(c$,"setStructureIndexes",function(){for(var a,b=0,d=-1,c=-1,f=-1,e=0;e<this.ac;e++){if((c=this.at[e].mi)!=f)b=0,f=c,d=-1;if((a=this.at[e].getStrucNo())!=d&&0!=a)this.at[e].getGroup().setStrucNo(++b),d=b}});c(c$,"getProteinStructureState",function(a,b,d,c){if(!this.isPDB)return"";for(var f=
0;f<this.mc;f++)if(this.am[f].isBioModel)return this.am[f].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$,"getAtomsConnected",function(a,b,d,c){for(var f=r(c,JM.BondSet),e=f?new JM.BondSet:new JU.BS,j=C(this.ac,0),h,l=30720==d,m=65535==
d,n=0;n<this.bondCount;n++){var t=this.bo[n];if(m||t.is(d)||l&&t.isHydrogen())f?e.set(n):(c.get(t.atom1.i)&&(j[h=t.atom2.i]++,e.set(h)),c.get(t.atom2.i)&&(j[h=t.atom1.i]++,e.set(h)))}if(f)return e;d=0==a;for(h=this.ac;0<=--h;)c=j[h],c<a||c>b?e.clear(h):d&&0==c&&e.set(h);return e},"~N,~N,~N,JU.BS");c(c$,"getSymTemp",function(a){return null==this.symTemp||a?this.symTemp=J.api.Interface.getSymmetry():this.symTemp},"~B");c(c$,"createModels",function(a){a=this.mc+a;var b=JU.AU.arrayCopyObject(this.am,
a);this.validateBspf(!1);this.modelNumbers=JU.AU.arrayCopyI(this.modelNumbers,a);this.modelFileNumbers=JU.AU.arrayCopyI(this.modelFileNumbers,a);this.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.modelNumbersForAtomLabel,a);this.modelNames=JU.AU.arrayCopyS(this.modelNames,a);this.frameTitles=JU.AU.arrayCopyS(this.frameTitles,a);for(var d=w(this.getModelFileNumber(this.mc-1)/1E6)+1,c=this.mc,f=0;c<a;c++)this.modelNumbers[c]=c+this.mc,this.modelFileNumbers[c]=1E6*d+ ++f,this.modelNumbersForAtomLabel[c]=
this.modelNames[c]=d+"."+f;this.thisStateModel=-1;d=this.getInfoM("group3Lists");null!=d&&(c=this.getInfoM("group3Counts"),d=JU.AU.arrayCopyS(d,a),c=JU.AU.arrayCopyII(c,a),this.msInfo.put("group3Lists",d),this.msInfo.put("group3Counts",c));this.unitCells=JU.AU.arrayCopyObject(this.unitCells,a);for(c=this.mc;c<a;c++)b[c]=(new JM.Model).set(this,c,-1,null,null,null),b[c].loadState=" model create #"+c+";";this.am=b;this.mc=a},"~N");c(c$,"deleteModel",function(a,b,d,c,f){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 e=this.getInfoM("group3Lists"),j=this.getInfoM("group3Counts"),
h=a+1;if(null!=e&&null!=e[h])for(var l=w(e[h].length/6);0<=--l;)0<j[h][l]&&(j[0][l]-=j[h][l],0==j[0][l]&&(e[0]=e[0].substring(0,6*l)+",["+e[0].substring(6*l+2)));null!=e&&(this.msInfo.put("group3Lists",JU.AU.deleteElements(e,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,f,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$,"getMoInfo",function(a){for(var b=new JU.SB,d=0;d<this.mc;d++)if(!(0<=a&&d!=a)){var c=this.vwr.getModelAuxiliaryInfoValue(d,"moData");if(null!=c){var c=c.get("mos"),f=null==c?0:c.size();if(0!=f)for(;0<=--f;){var e=c.get(f),j=e.get("type");null==j&&(j="");var h=e.get("energyUnits");null==h&&(h="");var l=e.get("occupancy");null!=l&&(j="occupancy "+l.floatValue()+" "+j);l=e.get("symmetry");null!=l&&(j+=l);l=""+e.get("energy");Float.isNaN(JU.PT.parseFloat(l))?
b.append(JU.Txt.sprintf("model %-2s;  mo %-2i # %s\n","sis",[this.getModelNumberDotted(d),Integer.$valueOf(f+1),j])):b.append(JU.Txt.sprintf("model %-2s;  mo %-2i # energy %-8.3f %s %s\n","sifss",[this.getModelNumberDotted(d),Integer.$valueOf(f+1),e.get("energy"),h,j]))}}}return b.toString()},"~N");c(c$,"assignAtom",function(a,b,d){null==b&&(b="C");var c=this.at[a],f=new JU.BS,e=1==c.getElementNumber(),f=JU.Elements.elementNumberFromSymbol(b,!0),j=!1;if(0<f)this.setElement(c,f),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()&&(e?b=1.5:!e&&1==f&&(b=1));0!=b&&(e=JU.V3.newVsub(c,this.at[c.getBondedAtomIndex(0)]),j=e.length(),e.normalize(),e.scale(b-j),
this.setAtomCoordRelative(a,e.x,e.y,e.z));a=JU.BSUtil.newAndSetBit(a);1!=f&&d&&(this.validateBspf(!1),f=this.getAtomsWithinRadius(1,a,!1,null),f.andNot(a),0<=f.nextSetBit(0)&&this.vwr.deleteAtoms(f,!1),f=this.vwr.getModelUndeletedAtomsBitSet(c.mi),f.andNot(this.getAtomBitsMDa(1613758476,null)),this.makeConnections2(0.1,1.8,1,1073741904,a,f,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 f=this.am[this.at[c].mi];f.firstAtomIndex==a[c]&&(f.firstAtomIndex=c);f.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(f=this.atomTensorList[c]=this.atomTensorList[a[c]],null!=f)for(var e=f.length;0<=--e;){var j=f[e];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,f,e,j,h,l,m,n,t,p,q,r,s,u,v){j=(new JM.Atom).setAtom(a,this.ac,h,l,v,j,d,n,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,p);this.setPartialCharge(this.ac,t);null!=r&&this.setAtomTensors(this.ac,r);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=u;0==u&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern())}-2147483648!=f&&(null==this.atomSerials&&(this.atomSerials=C(this.at.length,0)),this.atomSerials[this.ac]=f);0!=e&&(null==this.atomSeqIDs&&(this.atomSeqIDs=C(this.at.length,0)),this.atomSeqIDs[this.ac]=
e);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=
C(this.ac,0));null==this.atomNames&&(this.atomNames=Array(this.ac));for(var c=this.isXYZ&&this.vwr.getBoolean(603979978),f=2147483647,e=1;a<this.ac;++a){var j=this.at[a];j.mi!=f&&(f=j.mi,e=c?0:1);if(a>=-b){if(0==this.atomSerials[a]||0>b)this.atomSerials[a]=a<b?d.atomSerials[a]:e;if(null==this.atomNames[a]||0>b)this.atomNames[a]=(j.getElementSymbol()+this.atomSerials[a]).intern()}(!this.am[f].isModelKit||0<j.getElementNumber()&&!j.isDeleted())&&e++}},"~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 f=A(c[0]),e=0>f;e&&(f=-1-f);var j=A(c[1]);if(!(0>j||f>=this.ac||j>=this.ac)){var h=2<c.length?A(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[f].getBond(this.at[j]),null!=
c&&b.set(c.index)):this.bondAtoms(this.at[f],this.at[j],h,l,null,4<c.length?c[4]:0,e,!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,f=null,e=0;e<this.mc;e++){var j=this.getInfo(e,"modelID"),h=a.startsWith("~")?"~"+this.getModelNumberDotted(e):null;if(!(null==h&&null==j&&null==(j=this.getModelTitle(e)))){b&&(f=this.getModelFileName(e),f.endsWith("#molfile")?j=f:(f+="#",j=f+j));if(a.equalsIgnoreCase(j)||a.equalsIgnoreCase(h))return d?this.vwr.getJDXBaseModelIndex(e):e;null!=f&&a.startsWith(f)&&(c=-2)}}return null==
f&&!b?-2:c},"~S");c(c$,"getAuxiliaryInfo",function(a){var b=this.msInfo;if(null==b)return null;for(var d=new JU.Lst,c=0;c<this.mc;++c)if(null==a||a.get(c)){var f=this.getModelAuxiliaryInfo(c);d.addLast(f)}b.put("models",d);return b},"JU.BS");c(c$,"getDihedralMap",function(a){for(var b=new JU.Lst,d=a.length,c=null,f=null,e=null,j=null,h=d-1;0<=--h;)for(var l=d;--l>h;)if(c=this.at[a[h]],f=this.at[a[l]],c.isBonded(f))for(var m=d;0<=--m;)if(m!=h&&m!=l&&(e=this.at[a[m]]).isBonded(c))for(var n=d;0<=--n;)if(n!=
h&&n!=l&&n!=m&&(j=this.at[a[n]]).isBonded(f)){var t=C(4,0);t[0]=e.i;t[1]=c.i;t[2]=f.i;t[3]=j.i;b.addLast(t)}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$,"setModulation",function(a,b,d,c){if(null==this.bsModulated)if(b)this.bsModulated=new JU.BS;else if(null==a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var f=this.vwr.getFloat(1276121113),e=!1,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){var h=this.getVibration(j,!1);r(h,J.api.JmolModulationSet)&&
(h.setModTQ(this.at[j],b,d,c,f),null!=this.bsModulated&&this.bsModulated.setBitTo(j,b),e=!0)}e||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(c$,"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 f=Array(3375),c=0,e=new JU.P4,j=-7;7>=j;j++)for(var h=-7;7>=h;h++)for(var l=0;14>=l;l++,c++)1<(f[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-
f[j].lengthSquared()),Float.isNaN(l)&&(l=0),e.set4(f[j].x,f[j].y,f[j].z,l),this.vOrientations[j]=JU.Quat.newP4(e)}for(var f=new JU.P3,e=3.4028235E38,m=null,n=null,j=0;j<c;j++){var l=this.vOrientations[j],t=new JU.BoxInfo;t.setMargin(0);for(h=d;0<=h;h=b.nextSetBit(h+1))t.addBoundBoxPoint(l.transformP2(this.at[h],f));switch(a){default:case 1313866249:case 1073741863:h=(t.bbCorner1.x-t.bbCorner0.x)*(t.bbCorner1.y-t.bbCorner0.y)*(t.bbCorner1.z-t.bbCorner0.z);break;case 1112541205:h=t.bbCorner1.x-t.bbCorner0.x;
break;case 1112541206:h=t.bbCorner1.y-t.bbCorner0.y;break;case 1112541207:h=t.bbCorner1.z-t.bbCorner0.z}h<e&&(m=l,n=t,e=h)}if(1313866249!=a&&1073741863!=a)return m.toString();l=JU.Quat.newQ(m);d=n.bbCorner1.x-n.bbCorner0.x;c=n.bbCorner1.y-n.bbCorner0.y;j=n.bbCorner1.z-n.bbCorner0.z;d<c&&(f.set(0,0,1),l=JU.Quat.newVA(f,90).mulQ(l),h=d,d=c,c=h);c<j&&(j>d&&(f.set(0,1,0),l=JU.Quat.newVA(f,90).mulQ(l),h=d,d=j,j=h),f.set(1,0,0),l=JU.Quat.newVA(f,90).mulQ(l),h=c,c=j,j=h);return 1313866249==a?e+"\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$,"getBsBranches",function(a){for(var b=w(a.length/6),d=Array(b),c=new java.util.Hashtable,f=0,e=0;f<b;f++,e+=6)if(!(1>Math.abs(a[e+5]-a[e+4]))){var j=A(a[e+1]),h=A(a[e+2]),l=""+j+"_"+h;if(!c.containsKey(l)){c.put(l,Boolean.TRUE);
for(var l=this.vwr.getBranchBitSet(h,j,!0),m=this.at[j].bonds,j=this.at[j],n=0;n<m.length;n++){var t=m[n];if(t.isCovalent()&&(t=t.getOtherAtom(j).i,t!=h&&l.get(t))){l=null;break}}d[f]=l}}return d},"~A");c(c$,"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$,"moveAtoms",function(a,b,d,c,f,e,j){if(!j){null==a?this.matTemp.setM3(b):(this.matInv.setM3(b),this.matInv.invert(),this.ptTemp.set(0,0,0),this.matTemp.mul2(a,b),this.matTemp.mul2(this.matInv,this.matTemp));e?(this.vTemp.setT(f),this.mat4.setIdentity(),this.mat4.setTranslation(this.vTemp),this.mat4t.setToM3(this.matTemp),this.mat4.mul(this.mat4t),this.mat4t.setIdentity(),this.vTemp.scale(-1),this.mat4t.setTranslation(this.vTemp),this.mat4.mul(this.mat4t)):this.mat4.setToM3(this.matTemp);
for(a=c.nextSetBit(0);0<=a;a=c.nextSetBit(a+1))e?this.mat4.rotTrans(this.at[a]):(this.ptTemp.add(this.at[a]),this.mat4.rotTrans(this.at[a]),this.ptTemp.sub(this.at[a])),this.taintAtom(a,2);e||(this.ptTemp.scale(1/c.cardinality()),null==d&&(d=new JU.V3),d.add(this.ptTemp))}if(null!=d){for(a=c.nextSetBit(0);0<=a;a=c.nextSetBit(a+1))this.at[a].add(d);j||(this.mat4t.setIdentity(),this.mat4t.setTranslation(d),this.mat4.mul2(this.mat4t,this.mat4))}this.recalculatePositionDependentQuantities(c,this.mat4)},
"JU.M3,JU.M3,JU.V3,JU.BS,JU.P3,~B,~B");c(c$,"setDihedrals",function(a,b,d){var c=w(a.length/6);1<d&&(d=1);for(var f=0,e=0;f<c;f++,e+=6){var j=b[f];if(!(null==j||j.isEmpty())){var h=this.at[A(a[e+1])],l=JU.V3.newVsub(this.at[A(a[e+2])],h),l=JU.A4.newVA(l,-((a[e+5]-a[e+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$,"invertSelected",function(a,b,d,c,f){if(null!=
a)for(var e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1)){d=2*(a.x-this.at[e].x);c=2*(a.y-this.at[e].y);var j=2*(a.z-this.at[e].z);this.setAtomCoordRelative(e,d,c,j)}else if(null!=b){a=JU.V3.new3(b.x,b.y,b.z);a.normalize();for(var h=Math.sqrt(b.x*b.x+b.y*b.y+b.z*b.z),e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))j=2*-JU.Measure.distanceToPlaneD(b,h,this.at[e]),d=a.x*j,c=a.y*j,j*=a.z,this.setAtomCoordRelative(e,d,c,j)}else if(0<=d&&(b=this.at[d],a=b.bonds,null!=a)){f=new JU.BS;j=new JU.Lst;h=this.vwr.getModelUndeletedAtomsBitSet(b.mi);
for(e=0;e<a.length;e++){var l=a[e].getOtherAtom(b);c.get(l.i)?f.or(JU.JmolMolecule.getBranchBitSet(this.at,l.i,h,null,d,!0,!0)):j.addLast(l)}0!=j.size()&&(a=JU.Measure.getCenterAndPoints(j)[0],e=JU.V3.newVsub(b,a),e=JU.Quat.newVA(e,180),this.moveAtoms(null,e.getMatrix(),null,f,b,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS,JU.BS");c(c$,"setMSInfo",function(a,b){this.msInfo.put(a,b)},"~S,~O");x(c$,"hbondMin",2.5)}),p("JM"),v(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){c$=u(function(){this.rotationMatrix=
this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=null;this.cameraY=this.cameraX=this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.vwr=this.pymolView=this.moveToText=null;q(this,arguments)},JM,"Orientation");L(c$,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});s(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$,"restore",function(a,b){b?(this.vwr.setBooleanProperty("windowCentered",this.windowCenteredFlag),this.vwr.setBooleanProperty("navigationMode",this.navigationMode),null==this.pymolView?this.vwr.moveTo(this.vwr.eval,a,this.center,null,NaN,this.rotationMatrix,this.zoom,this.xTrans,this.yTrans,this.rotationRadius,this.navCenter,this.xNav,this.yNav,this.navDepth,this.cameraDepth,this.cameraX,this.cameraY):this.vwr.tm.moveToPyMOL(this.vwr.eval,a,this.pymolView)):this.vwr.tm.setRotation(this.rotationMatrix);
return!0},"~N,~B")}),p("JM"),v(null,"JM.StateScript",["JU.SB","JU.BSUtil","$.Escape"],function(){c$=u(function(){this.modelIndex=0;this.script2=this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;q(this,arguments)},JM,"StateScript");s(c$,function(a,b,d,c,f,e,j){this.modelIndex=a;this.script1=b;this.bsBonds=JU.BSUtil.copy(d);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(f);this.script2=e;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$,"setModelIndex",function(a){this.modelIndex=a},"~N")}),p("JM"),c$=u(function(){this.id=
"";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=0;this.signFactor=1;this.reference=null;q(this,arguments)},JM,"TickInfo"),s(c$,function(a){this.ticks=a},"JU.P3"),p("JU"),v(["JU.P3","$.P3i","$.V3"],"JU.BoxInfo",["JU.Lst","$.Measure","$.P4","JU.Point3fi"],function(){c$=u(function(){this.bbVertices=this.bbVector=this.bbCenter=this.bbCorner1=this.bbCorner0=null;this.isScaleSet=!1;this.margin=0;q(this,arguments)},JU,"BoxInfo");L(c$,function(){this.bbCorner0=new JU.P3;this.bbCorner1=
new JU.P3;this.bbCenter=new JU.P3;this.bbVector=new JU.V3;this.bbVertices=Array(8);for(var a=8;0<=--a;)this.bbVertices[a]=new JU.Point3fi;for(a=0;8>a;a++)JU.BoxInfo.unitBboxPoints[a]=JU.P3.new3(-1,-1,-1),JU.BoxInfo.unitBboxPoints[a].scaleAdd2(2,JU.BoxInfo.unitCubePoints[a],JU.BoxInfo.unitBboxPoints[a])});s(c$,function(){this.reset()});c(c$,"intersectPlane",function(a,b,d,c){var f=new JU.Lst;f.addLast(this.getCanonicalCopy(d));return a.intersectPlane(b,f,c)},"JM.ModelSet,JU.P4,~N,~N");c(c$,"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,f=0;8>f;f++)d.add(a[f]);d.scale(0.125);for(f=0;8>f;f++)c.sub2(a[f],d),c.scale(b),a[f].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,f=new JU.V3,e=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++)e.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(e,j,h,d,c,f,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]),f=JU.P3.newP(a[2]),e=JU.P3.newP(a[4]);c.sub(d);f.sub(d);e.sub(d);null!=b&&d.add(b);return[d,c,f,e]},"~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-
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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$,"isWithin",function(a){this.isScaleSet||this.setBbcage(1);return a.x>=this.bbCorner0.x&&a.x<=this.bbCorner1.x&&a.y>=this.bbCorner0.y&&a.y<=this.bbCorner1.y&&a.z>=this.bbCorner0.z&&a.z<=this.bbCorner1.z},"JU.P3");x(c$,"bbcageTickEdges","z\x00\x00yx\x00\x00\x00\x00\x00\x00\x00".split(""),
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a||null==b)){for(var f=b.length(),e=JU.BS.newN(f),j=!1,h=!1,l=d,m=0,n=0;m<f&&n<c;m++)b.get(m)?(h&&e.set(m),l=d,j=!1):a.get(n++)?(e.set(m),l&&(l=!1,h=j=!0)):l&&!j&&(h=!1);a.clearAll();a.or(e)}},"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),f=a.nextSetBit(0);f>=b;f=a.nextSetBit(f+1))c.set(f+d);JU.BSUtil.copy2(c,a)}},"JU.BS,~N,~N");c$.setMapBitSet=c(c$,"setMapBitSet",function(a,b,d,c){var f;a.containsKey(c)?f=a.get(c):a.put(c,f=new JU.BS);
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new JU.Int2IntHash(256);x(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])}),p("JU"),v(null,"JU.ColorEncoder","java.lang.Boolean $.Float java.util.Hashtable JU.AU $.CU $.Lst $.PT J.c.PAL JU.C $.Escape $.Logger JV.JC".split(" "),function(){c$=u(function(){this.argbsAmino=this.argbsShapely=this.argbsRwb=this.argbsRoygb=this.argbsCpk=
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0<=JU.Measure.distanceToPlane(e,a);JU.Measure.getPlaneThroughPoints(b,f,d,j,h,l,e);if(n!=0<=JU.Measure.distanceToPlane(e,a))return!1;JU.Measure.getPlaneThroughPoints(d,f,c,j,h,l,e);if(n!=0<=JU.Measure.distanceToPlane(e,a))return!1;JU.Measure.getPlaneThroughPoints(b,d,c,j,h,l,e);a=JU.Measure.distanceToPlane(e,a);if(m)return n==0<=a;f=JU.Measure.distanceToPlane(e,f);return 0>=f*a||Math.abs(f)>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,f=a.z,e=a.w,j=b.x,h=b.y,l=b.z,m=b.w,n=JU.V3.new3(d,c,f),t=JU.V3.new3(j,h,l),p=new JU.V3;p.cross(n,t);var n=Math.abs(p.x),t=Math.abs(p.y),q=Math.abs(p.z);switch(n>t?n>q?1:3:t>q?2:3){case 1:n=0;t=c*l-h*f;if(0.01>Math.abs(t))return null;f=(f*m-l*e)/t;d=(h*e-m*c)/t;break;case 2:t=d*l-j*f;if(0.01>Math.abs(t))return null;n=(f*m-l*e)/t;f=0;d=(j*e-m*d)/t;break;default:t=d*h-j*c;if(0.01>Math.abs(t))return null;n=(c*m-h*e)/t;f=(j*e-m*d)/t;d=0}c=new JU.Lst;c.addLast(JU.P3.new3(n,
f,d));p.normalize();c.addLast(p);return c},"JU.P4,JU.P4");c$.getIntersection=c(c$,"getIntersection",function(a,b,d,c,f,e){JU.Measure.getPlaneProjection(a,d,c,f);f.set(d.x,d.y,d.z);f.normalize();null==b&&(b=JU.V3.newV(f));d=b.dot(f);if(0.01>Math.abs(d))return null;e.sub2(c,a);c.scaleAdd2(e.dot(f)/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 c=new JU.Quat;if(1==a[0].length||a[0].length!=a[1].length)return c;
var g=a[0].length-1;if(2>g)return c;for(var f=0,e=0,j=0,h=0,l=0,m=0,n=0,p=0,q=0,r=new JU.P3,s=new JU.P3,g=g+1;1<=--g;){var u=a[1][g];r.sub2(a[0][g],a[0][0]);s.sub2(u,a[0][1]);f+=r.x*s.x;e+=r.x*s.y;j+=r.x*s.z;h+=r.y*s.x;l+=r.y*s.y;m+=r.y*s.z;n+=r.z*s.x;p+=r.z*s.y;q+=r.z*s.z}b[0]=JU.Measure.getRmsd(a,c);c=$(4,4,0);c[0][0]=f+l+q;c[0][1]=c[1][0]=m-p;c[0][2]=c[2][0]=n-j;c[0][3]=c[3][0]=e-h;c[1][1]=f-l-q;c[1][2]=c[2][1]=e+h;c[1][3]=c[3][1]=n+j;c[2][2]=-f+l-q;c[2][3]=c[3][2]=m+p;c[3][3]=-f-l+q;f=javajs.api.Interface.getInterface("JU.Eigen").setM(c).getEigenvectorsFloatTransposed()[3];
c=JU.Quat.newP4(JU.P4.new4(f[1],f[2],f[3],f[0]));b[1]=JU.Measure.getRmsd(a,c);return c},"~A,~A");c$.getTransformMatrix4=c(c$,"getTransformMatrix4",function(a,b,c,g){a=JU.Measure.getCenterAndPoints(a);var f=JU.Measure.getCenterAndPoints(b);b=M(2,0);var e=JU.Measure.calculateQuaternionRotation([a,f],b),f=JU.V3.newVsub(f[0],a[0]);c.setMV(e.getMatrix(),f);null!=g&&g.setT(a[0]);return b[1]},"JU.Lst,JU.Lst,JU.M4,JU.P3");c$.getCenterAndPoints=c(c$,"getCenterAndPoints",function(a){var b=a.size(),c=Array(b+
1);c[0]=new JU.P3;if(0<b){for(var g=0;g<b;g++)c[0].add(c[g+1]=a.get(g));c[0].scale(1/b)}return c},"JU.Lst");c$.getRmsd=c(c$,"getRmsd",function(a,b){for(var c=0,g=a[0],f=a[1],e=g[0],j=f[0],h=g.length-1,l=new JU.P3,m=h+1;1<=--m;)l.sub2(g[m],e),b.transformP2(l,l).add(j),c+=l.distanceSquared(f[m]);return Math.sqrt(c/h)},"~A,JU.Quat");x(c$,"radiansPerDegree",0.017453292519943295);c$.axisY=c$.prototype.axisY=JU.V3.new3(0,1,0)}),p("JU"),v(null,"JU.MeshSurface","java.lang.Float java.util.Hashtable JU.AU $.BS $.Lst $.Measure $.P3 $.P4 $.PT $.SB JU.BSUtil $.BoxInfo $.C $.Escape $.Geodesic $.TempArray".split(" "),
function(){c$=u(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;q(this,arguments)},JU,"MeshSurface");s(c$,function(){});c$.newMesh=c(c$,"newMesh",function(a,b,c,g,f,e){var j=new JU.MeshSurface;j.pis=g;a?j.altVertices=b:j.vs=b;j.vc=0==c?b.length:c;j.normals=
f;j.normalCount=0==e&&null!=f?f.length:e;return j},"~B,~A,~N,~A,~A,~N");c$.newSlab=c(c$,"newSlab",function(a,b,c,g,f,e){var j=new JU.MeshSurface;j.vs=a;j.vvs=c;j.vc=b;j.pis=g;j.pc=f;j.checkCount=e;return j},"~A,~N,~A,~A,~N,~N");c(c$,"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$,"addTriangle",function(a,b,c){this.addPolygon([a,b,c],null)},"~N,~N,~N");c(c$,"addQuad",function(a,b,c,g){this.haveQuads=!0;this.addPolygon([a,b,c,g],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,c){0==this.vc?this.vvs=M(25,
0):this.vc>=this.vvs.length&&(this.vvs=JU.AU.doubleLengthF(this.vvs));this.vvs[this.vc]=b;return this.addV(a,c)},"JU.T3,~N,~B");c(c$,"addTriangleCheck",function(a,b,c,g,f,e){return null==this.vs||null!=this.vvs&&(Float.isNaN(this.vvs[a])||Float.isNaN(this.vvs[b])||Float.isNaN(this.vvs[c]))||Float.isNaN(this.vs[a].x)||Float.isNaN(this.vs[b].x)||Float.isNaN(this.vs[c].x)?-1:this.addPolygonV3(a,b,c,g,f,e,null)},"~N,~N,~N,~N,~N,~N");c(c$,"addPolygonV3",function(a,b,c,g,f,e,j){return 2==this.checkCount?
this.addPolygonC([a,b,c,g,f],e,j):this.addPolygon([a,b,c,g],j)},"~N,~N,~N,~N,~N,~N,JU.BS");c(c$,"addPolygonC",function(a,b,c){if(0!=b){if(null==this.pcs||0==this.pc)this.lastColor=0;b=b==this.lastColor?this.lastColix:this.lastColix=JU.C.getColix(this.lastColor=b);this.setPolygonColix(this.pc,b)}return this.addPolygon(a,c)},"~A,~N,JU.BS");c(c$,"addPolygon",function(a,b){var c=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 c},"~A,JU.BS");c(c$,"setPolygonColix",function(a,b){null==this.pcs?this.pcs=V(25,0):a>=this.pcs.length&&(this.pcs=JU.AU.doubleLengthShort(this.pcs));this.pcs[a]=b},"~N,~N");c(c$,"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$,"setSlab",function(a,b,c,g,f){this.bsSlabDisplay=a;this.bsSlabGhost=b;this.slabMeshType=c.equalsIgnoreCase("mesh")?1073742018:1073741938;this.slabColix=JU.C.getColixTranslucent3(JU.C.getColixS(g),!0,f)},"JU.BS,JU.BS,~S,~S,~N");c(c$,
"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$,"resetTransPolygons",function(){for(var a=JU.C.isColixTranslucent(this.colix),b=JU.C.getColixTranslucencyFractional(this.colix),c=0;c<this.pc;c++)this.bsTransPolygons.get(c)&&
this.setABC(c)&&(this.vcs[this.iA]=JU.C.getColixTranslucent3(this.vcs[this.iA],a,b),this.vcs[this.iB]=JU.C.getColixTranslucent3(this.vcs[this.iB],a,b),this.vcs[this.iC]=JU.C.getColixTranslucent3(this.vcs[this.iC],a,b));this.polygonTranslucencies=this.bsTransPolygons=null});c(c$,"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 c=JU.PT.split(a.substring(6,a.length-
1),",");return JU.TempArray.getSlabObjectType(1679429641,[JU.Escape.uP(c[0]),JU.Escape.uP(c[1]),JU.Escape.uP(c[2]),JU.Escape.uP(c[3])],b,null)}var g=JU.Escape.uP(a);if(r(g,JU.P4))return JU.TempArray.getSlabObjectType(135266319,g,b,null)}catch(f){if(!D(f,Exception))throw f;}return null},"~S,~B");c(c$,"slabPolygonsList",function(a,b){for(var c=0;c<a.size()&&this.slabPolygons(a.get(c),b);c++);},"JU.Lst,~B");c(c$,"slabPolygons",function(a,b){if(0>this.polygonCount0)return!1;var c=a[0].intValue();if(1048587==
c||1073741872==c){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==c)return!1}var g=a[1],f=a[2].booleanValue()&&1073741872!=c;if(f&&!b)return!1;var e=
a[3],j=null!=e;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=e[0].intValue(),
this.slabColix=e[1].shortValue(),f=!1,this.colix=JU.C.getColixTranslucent3(this.colix,!1,0));e=new JU.SB;e.append(f?" cap ":" slab ");if(j){e.append("translucent ").appendF(JU.C.getColixTranslucencyFractional(this.slabColix)).append(" ");var h=JU.C.getHexCode(this.slabColix);null!=h&&e.append(h).append(" ");1073742018==this.slabMeshType&&e.append("mesh ")}switch(c){case 1073741872:e.append("brillouin");this.slabBrillouin(g);break;case 3:this.getIntersection(0,null,null,null,null,g,null,f,!1,3,j);
break;case 135266319:e.append(JU.Escape.eP4(g));this.getIntersection(0,g,null,null,null,null,null,f,!1,135266319,j);break;case 1614417948:case 1679429641:e.append("within ").append(JU.Escape.eAP(g));g=JU.BoxInfo.getFacesFromCriticalPoints(g);for(h=0;h<g.length;h++)this.getIntersection(0,g[h],null,null,null,null,null,f,!1,135266319,j);break;case 135270408:this.getIntersection(0,null,null,null,g,null,null,!1,!1,32,j);break;case 135266325:case 1073742114:case 1073742018:switch(h=g[0].floatValue(),c){case 135266325:c=
g[1];g=g[2];e.append("within ").appendF(h).append(null==g?JU.Escape.e(c):JU.Escape.e(g));this.getIntersection(h,null,c,null,null,null,null,f,!1,0<h?1276118018:1073742154,j);break;case 1073742114:if(null==this.vvs)return!1;c=g[1].floatValue();e.append("within range ").appendF(h).append(" ").appendF(c);g=c<h?JU.BSUtil.copy(this.bsSlabDisplay):null;this.getIntersection(h,null,null,null,null,null,null,f,!1,32,j);h=null==g?null:JU.BSUtil.copy(this.bsSlabDisplay);JU.BSUtil.copy2(g,this.bsSlabDisplay);this.getIntersection(c,
null,null,null,null,null,null,f,!1,64,j);null!=h&&this.bsSlabDisplay.or(h);break;case 1073742018:this.getIntersection(0,null,null,null,null,null,g[1],f,!1,0>h?32:64,j)}}f=e.toString();null==this.slabOptions&&(this.slabOptions=new JU.SB);0>this.slabOptions.indexOf(f)&&this.slabOptions.append(0<this.slabOptions.length()?"; ":"").append(this.meshType).append(f);return!0},"~A,~B");c(c$,"slabBrillouin",function(){},"~A");c(c$,"addIntersectionVertex",function(a,b,c,g,f,e,j){j=e>j?j+"_"+e:e+"_"+j;if(0<=
e&&(e=f.get(j),null!=e))return e.intValue();null!=this.vertexSource&&(this.vc>=this.vertexSource.length&&(this.vertexSource=JU.AU.doubleLengthI(this.vertexSource)),this.vertexSource[this.vc]=c);null!=this.vertexSets&&(this.vc>=this.vertexSets.length&&(this.vertexSets=JU.AU.doubleLengthI(this.vertexSets)),this.vertexSets[this.vc]=g);a=this.addVCVal(a,b,!0);f.put(j,Integer.$valueOf(a));return a},"JU.T3,~N,~N,~N,java.util.Map,~N,~N");c(c$,"getIntersection",function(a,b,c,g,f,e,j,h,l,m,n){var p=null==
g,q=null;if(null==f)if(3==m&&null!=e){if(null==this.vertexSource)return;f=M(this.vc,0);for(j=0;j<this.vc;j++)-1==(f[j]=this.vertexSource[j])&&System.out.println("meshsurface hmm")}else f=this.vvs;var r=new java.util.Hashtable;if(null!=c||n)h=!1;var s=M(2,0),u=M(2,0),v=Math.abs(a),w,x,y,A,B,D,E=0,G=0,H=0,I=0,L=h?new JU.Lst:null;if(0==this.pc)for(j=this.mergeVertexCount0;j<this.vc;j++)(Float.isNaN(f[j])||0<JU.MeshSurface.checkSlab(m,this.vs[j],f[j],a,b,c,e))&&this.bsSlabDisplay.clear(j);else{var N=
this.pc;for(j=this.mergePolygonCount0;j<N;j++)if(this.setABC(j)){var O=null!=this.bsSlabGhost&&this.bsSlabGhost.get(j)?this.bsSlabGhost:this.bsSlabDisplay,P=this.pis[j][3],Q=2==this.checkCount?this.pis[j][4]:0,S=this.vs[this.iA],T=this.vs[this.iB],U=this.vs[this.iC];A=f[this.iA];B=f[this.iB];D=f[this.iC];null!=this.vertexSource&&(E=this.vertexSource[this.iA],G=this.vertexSource[this.iB],H=this.vertexSource[this.iC]);null!=this.vertexSets&&(I=this.vertexSets[this.iA]);w=JU.MeshSurface.checkSlab(m,
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3>f||0<=a.indexOf(b.substring(1,f-1)):a.endsWith(b.substring(1));if(j)return a.startsWith(b.substring(0,f-1))}for(var h=a.length,l="????",m=4;m<h;)l+=l,m+=4;c&&(e&&(b=l+b.substring(1),f+=m-1),j&&(b=b.substring(0,f-1)+l,f+=m-1));if(f<h)return!1;for(c=0;f>h;){if(g&&"?"==b.charAt(c))++c;else if("?"!=b.charAt(c+f-1))return!1;--f}for(g=h;0<=--g;)if(f=b.charAt(c+g),"?"!=f&&(h=a.charAt(g),f!=h&&("\u0001"!=f||"?"!=h)))return!1;return!0},"~S,~S,~B,~B");c$.replaceQuotedStrings=c(c$,"replaceQuotedStrings",function(a,
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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});x(c$,"twoPI",6.283185307179586,"TYPE_MODULATION",0,"TYPE_VIBRATION",-1,"TYPE_SPIN",-2,"TYPE_DISPLACEMENT",-3)}),p("JV"),v(["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 $.JmolBinding".split(" "),
function(){c$=u(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;O("JV.ActionManager.MotionPoint")||JV.ActionManager.$ActionManager$MotionPoint$();this.dragGesture=null;O("JV.ActionManager.Gesture")||JV.ActionManager.$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;q(this,arguments)},JV,"ActionManager",null,javajs.api.EventManager);L(c$,function(){this.dragGesture=N(JV.ActionManager.Gesture,this,null,20);this.current=new JV.MouseState("current");this.moved=new JV.MouseState("moved");this.clicked=new JV.MouseState("clicked");this.pressed=new JV.MouseState("pressed");
this.dragged=new JV.MouseState("dragged");this.rectRubber=new JU.Rectangle});c(c$,"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 c=JV.ActionManager.getActionFromName(b),g=JV.binding.Binding.getMouseActionStr(a);0!=g&&(0<=c?this.b.bindAction(g,c):this.b.bindName(g,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 c=JV.ActionManager.getActionFromName(b),g=JV.binding.Binding.getMouseActionStr(a);0<=c?this.b.unbindAction(g,c):0!=g&&this.b.unbindName(g,b);null==b&&this.b.unbindUserAction(a)}},"~S,~S");c$.newAction=c(c$,"newAction",function(a,b,c){JV.ActionManager.actionInfo[a]=c;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$,"setCurrent",function(a,b,c,g){this.vwr.hoverOff();this.current.set(a,b,c,g)},"~N,~N,~N,~N");c(c$,"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(!D(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 c=8464|this.moved.modifiers;!this.labelMode&&!this.b.isUserAction(c)&&this.checkMotionRotateZoom(c,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,c,g){this.setCurrent(a,b,c,0);g&&this.exitMeasurementMode("mouseExit")},"~N,~N,~N,~B");c(c$,"setMouseActions",function(a,b,c){this.pressAction=JV.binding.Binding.getMouseAction(a,
b,c?5:4);this.dragAction=JV.binding.Binding.getMouseAction(a,b,1);this.clickAction=JV.binding.Binding.getMouseAction(a,b,2)},"~N,~N,~B");h(c$,"mouseAction",function(a,b,c,g,f,e){if(this.vwr.getMouseEnabled())switch(JU.Logger.debuggingHigh&&0!=a&&this.vwr.showString("mouse action: "+a+" "+e+" "+JV.binding.Binding.getMouseActionName(JV.binding.Binding.getMouseAction(f,e,a),!1),!1),a){case 0:this.setCurrent(b,c,g,e);this.moved.setCurrent(this.current,0);if(null!=this.mp||this.hoverActive){this.clickAction=
JV.binding.Binding.getMouseAction(this.clickedCount,e,0);this.checkClickAction(c,g,b,0);break}if(this.isZoomArea(c)){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,c,g,e,b,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.vwr.checkInMotion(1),this.setCurrent(b,c,g,e));this.pressAction=JV.binding.Binding.getMouseAction(this.pressedCount,e,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(c,g,b);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,e,!1);a=c-this.dragged.x;f=g-this.dragged.y;this.setCurrent(b,c,g,e);this.dragged.setCurrent(this.current,-1);32!=this.apm&&this.exitMeasurementMode(null);this.dragGesture.add(this.dragAction,c,g,b);this.checkDragWheelAction(this.dragAction,c,g,a,f,b,1);
break;case 5:this.setMouseActions(this.pressedCount,e,!0);this.setCurrent(b,c,g,e);this.vwr.spinXYBy(0,0,0);e=!this.pressed.check(this.xyRange,c,g,e,b,9223372036854775E3);this.checkReleaseAction(c,g,b,e);break;case 3:if(this.vwr.isApplet()&&!this.vwr.hasFocus())break;this.setCurrent(b,this.current.x,this.current.y,e);this.checkDragWheelAction(JV.binding.Binding.getMouseAction(0,e,3),this.current.x,this.current.y,0,g,b,3);break;case 2:this.setMouseMode();this.clickedCount=1<f?f:this.clicked.check(0,
0,0,e,b,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(b,c,g,e);this.setMouseActions(this.clickedCount,e,!1);this.clicked.setCurrent(this.current,this.clickedCount);this.vwr.setFocus();if(9!=this.apm&&this.bnd(JV.binding.Binding.getMouseAction(1,e,4),31))break;this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,e,2);this.checkClickAction(c,g,b,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(c$,"checkPressedAction",function(a,b,c){var g=JV.binding.Binding.getButtonMods(this.pressAction),
f=this.bnd(JV.binding.Binding.getMouseAction(1,g,4),31);if(0!=g){this.pressAction=this.vwr.notifyMouseClicked(a,b,this.pressAction,4);if(0==this.pressAction)return;g=JV.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,g,!1);JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));if(this.drawMode&&(this.bnd(this.dragAction,8)||this.bnd(this.dragAction,9))||this.labelMode&&this.bnd(this.dragAction,10))this.vwr.checkObjectDragged(-2147483648,
0,a,b,this.dragAction);else{this.checkUserAction(this.pressAction,a,b,0,0,c,4);c=!1;switch(this.apm){case 32:c=this.bnd(this.clickAction,0);break;case 28:c=this.bnd(this.dragAction,7)||this.bnd(this.dragAction,14);break;case 26:case 36:case 27:c=this.bnd(this.dragAction,7)||this.bnd(this.dragAction,27)||this.bnd(this.dragAction,14);break;case 29:c=this.bnd(this.dragAction,11)||this.bnd(this.dragAction,14);break;case 30:c=this.bnd(this.dragAction,12)||this.bnd(this.dragAction,27)||this.bnd(this.dragAction,
14)}if(c){if(this.dragAtomIndex=this.vwr.findNearestAtomIndexMovable(a,b,!0),0<=this.dragAtomIndex&&(32==this.apm||31==this.apm)&&this.vwr.isAtomAssignable(this.dragAtomIndex))this.enterMeasurementMode(this.dragAtomIndex),this.mp.addPoint(this.dragAtomIndex,null,!1)}else this.bnd(this.pressAction,23)?(f="j",this.vwr.getBoolean(603979883)&&(f=this.vwr.checkObjectClicked(a,b,this.LEFT_CLICKED),f=null!=f&&"bond".equals(f.get("type"))?"b":0<=this.vwr.findNearestAtomIndex(a,b)?"a":"m"),this.vwr.popupMenu(a,
b,f)):this.dragSelectedMode?(this.haveSelection=!0,f&&(this.haveSelection=0<=this.vwr.findNearestAtomIndexMovable(a,b,!0)),this.haveSelection&&(this.bnd(this.dragAction,13)||this.bnd(this.dragAction,14))&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1)):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(c$,"checkDragWheelAction",function(a,b,c,g,f,e,j){var h=JV.binding.Binding.getButtonMods(a);if(0!=h){h=this.vwr.notifyMouseClicked(b,c,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,c,g,f,e,j)){if(0<=this.vwr.getRotateBondIndex()){if(this.bnd(a,26)){this.vwr.moveSelected(g,f,-2147483648,b,c,null,!1,!1);return}this.bnd(a,25)||this.vwr.setRotateBondIndex(-1)}e=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(g,
!0),this.getDegrees(f,!1),null):this.vwr.moveSelected(g,f,this.bnd(a,14)?-f:-2147483648,-2147483648,-2147483648,null,!0,!1);return;case 36:case 27:case 30:e=this.vwr.ms.getAtoms(3145754,JU.BSUtil.newAndSetBit(this.dragAtomIndex)),36==this.apm&&e.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(g,!0),this.getDegrees(f,!1),e);
else{switch(this.apm){case 36:case 27:case 30:this.vwr.select(e,!1,0,!0)}this.vwr.moveAtomWithHydrogens(this.dragAtomIndex,g,f,this.bnd(a,14)?-f:-2147483648,e)}return}0<=this.dragAtomIndex&&1==j&&this.bnd(this.clickAction,0)&&32==this.apm?(a=this.vwr.findNearestAtomIndexMovable(b,c,!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=c,this.vwr.refresh(3,"assignNew"))):!this.drawMode&&!this.labelMode&&this.bnd(a,45)?this.vwr.translateXYBy(g,f):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(g,
!0),this.getDegrees(f,!1),null):this.vwr.moveSelected(g,f,-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,c,a)):this.checkMotionRotateZoom(a,b,g,f,!0)?this.vwr.tm.slabEnabled&&this.checkSlideZoom(a)?this.vwr.slabDepthByPixels(f):this.vwr.zoomBy(f):this.bnd(a,25)?this.vwr.rotateXYBy(this.getDegrees(g,!0),this.getDegrees(f,!1)):this.bnd(a,
29)?0==g&&1<Math.abs(f)?(this.setMotion(8,!0),this.vwr.zoomBy(f+(0<f?-1:1))):0==f&&1<Math.abs(g)&&(this.setMotion(13,!0),this.vwr.rotateZBy(-g+(0<g?1:-1),2147483647,2147483647)):this.bnd(a,46)?this.zoomByFactor(f,2147483647,2147483647):this.bnd(a,28)?(this.setMotion(13,!0),this.vwr.rotateZBy(-g,2147483647,2147483647)):this.vwr.tm.slabEnabled&&(this.bnd(a,6)?this.vwr.depthByPixels(f):this.bnd(a,38)?this.vwr.slabByPixels(f):this.bnd(a,39)&&this.vwr.slabDepthByPixels(f))}},"~N,~N,~N,~N,~N,~N,~N");c(c$,
"checkReleaseAction",function(a,b,c,g){JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));this.vwr.checkInMotion(0);this.vwr.setInMotion(!1);this.vwr.setCursor(0);this.dragGesture.add(this.dragAction,a,b,c);g&&this.vwr.setRotateBondIndex(-2147483648);0<=this.dragAtomIndex&&(29==this.apm||30==this.apm)&&this.minimize(!0);if(32==this.apm&&this.bnd(this.clickAction,0))null==this.mp||0>this.dragAtomIndex||this.assignNew(a,b);else if(this.dragAtomIndex=-1,
this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=this.b.name.equals("drag"),this.rectRubber.x=2147483647,g&&this.vwr.notifyMouseClicked(a,b,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.drawMode&&(this.bnd(this.dragAction,8)||this.bnd(this.dragAction,9))||this.labelMode&&this.bnd(this.dragAction,10))this.vwr.checkObjectDragged(2147483647,0,a,b,this.dragAction);else if(this.dragSelectedMode&&(this.bnd(this.dragAction,13)&&this.haveSelection)&&
this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1),(!g||!this.checkUserAction(this.pressAction,a,b,0,0,c,5))&&this.vwr.getBoolean(603979780)&&this.bnd(this.dragAction,44))a=this.getExitRate(),0<a&&this.vwr.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.vwr.g.logGestures&&this.vwr.log("$NOW$ swipe "+this.dragGesture+" "+a)},"~N,~N,~N,~B");c(c$,"checkClickAction",function(a,b,c,g){if(this.vwr.haveModelSet()){if(0<g){if(this.checkUserAction(this.clickAction,
a,b,0,0,c,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}}c=null;var f=!1,e=!1,j=null;this.drawMode||(j=this.vwr.checkObjectClicked(a,b,this.clickAction),null!=
j&&(f="bond".equals(j.get("type")),e="isosurface".equals(j.get("type")),c=this.getPoint(j)));f&&(g=1);if(!(null!=c&&Float.isNaN(c.x))){var h=this.findNearestAtom(a,b,c,0<g);if(0==g&&32!=this.apm)null!=this.mp&&((null!=c||0==this.mp.getIndexOf(h))&&this.mp.addPoint(h,c,!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(f){if(this.bnd(this.clickAction,34==this.bondPickingMode||33==this.bondPickingMode?0:5)){this.bondPicked(j.get("index").intValue());return}}else{if(e)return;if(32!=this.apm&&null!=this.mp&&this.bnd(this.clickAction,20)){this.atomOrPointPicked(h,c);4==this.addToMeasurement(h,c,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,37)){null!=this.mp?
(this.addToMeasurement(h,c,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(h),this.addToMeasurement(h,c,!0));this.atomOrPointPicked(h,c);return}}this.isSelectAction(this.clickAction)?e||this.atomOrPointPicked(h,c):this.bnd(this.clickAction,24)&&0>h&&this.reset()}}}},"~N,~N,~N,~N");c(c$,"checkUserAction",function(a,b,c,g,f,e,j){if(!this.b.isUserAction(a))return!1;for(var h=!1,l,m=this.b.getBindings(),n=a+"\t",
p,q=m.keySet().iterator();q.hasNext()&&((p=q.next())||1);)if(0==p.indexOf(n)&&JU.PT.isAS(l=m.get(p))){var r=l[1],s=null;if(0<=r.indexOf("_ATOM")){var u=this.findNearestAtom(b,c,null,!0),r=JU.PT.rep(r,"_ATOM","({"+(0<=u?""+u:"")+"})");0<=u&&(r=JU.PT.rep(r,"_POINT",JU.Escape.eP(this.vwr.ms.at[u])))}if(!this.drawMode&&(0<=r.indexOf("_POINT")||0<=r.indexOf("_OBJECT")||0<=r.indexOf("_BOND"))){u=this.vwr.checkObjectClicked(b,c,a);if(null!=u&&null!=(s=u.get("pt")))u.get("type").equals("bond")&&(r=JU.PT.rep(r,
"_BOND","[{"+u.get("index")+"}]")),r=JU.PT.rep(r,"_POINT",JU.Escape.eP(s)),r=JU.PT.rep(r,"_OBJECT",JU.Escape.escapeMap(u));r=JU.PT.rep(r,"_BOND","[{}]");r=JU.PT.rep(r,"_OBJECT","{}")}r=JU.PT.rep(r,"_POINT","{}");r=JU.PT.rep(r,"_ACTION",""+a);r=JU.PT.rep(r,"_X",""+b);r=JU.PT.rep(r,"_Y",""+(this.vwr.getScreenHeight()-c));r=JU.PT.rep(r,"_DELTAX",""+g);r=JU.PT.rep(r,"_DELTAY",""+f);r=JU.PT.rep(r,"_TIME",""+e);r=JU.PT.rep(r,"_MODE",""+j);r.startsWith("+:")&&(h=!0,r=r.substring(2));this.vwr.evalStringQuiet(r)}return!h},
"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkMotionRotateZoom",function(a,b,c,g,f){b=this.checkSlideZoom(a);var e=this.bnd(a,25),j=this.bnd(a,29);if(!b&&!e&&!j)return!1;a=(c=j&&(0==c||Math.abs(g)>5*Math.abs(c)))||this.isZoomArea(this.moved.x)||this.bnd(a,46)?8:e||j?13:this.bnd(a,1)?12:0;this.setMotion(a,f);return c||b},"~N,~N,~N,~N,~B");c(c$,"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,c,g){a=this.drawMode||null!=c?-1:this.vwr.findNearestAtomIndexMovable(a,b,!1);return 0<=a&&(g||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,c){if(-1==a&&null==b||null==this.mp)return this.exitMeasurementMode(null),0;var g=this.mp.count;-2147483648!=this.mp.traceX&&2==g&&this.mp.setCount(g=1);return 4==g&&!c?g: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$,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),b=this.measurementQueued.getAtomIndex(2);if(!(0>a||0>b))try{var c=this.vwr.getSmilesOpt(null,a,b,!1,!0,!1,!1,!1);this.vwr.setStatusMeasuring("measureSequence",-2,c,0)}catch(g){if(D(g,Exception))JU.Logger.error(g.toString());else throw g;}});c(c$,"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$,"queueAtom",function(a,b){var c=this.measurementQueued.addPoint(a,b,!0);0<=a&&this.vwr.setStatusAtomPicked(a,"Atom #"+c+":"+this.vwr.getAtomInfo(a),null);return c},"~N,JU.Point3fi");c(c$,"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$,"zoomByFactor",
function(a,b,c){0!=a&&(this.setMotion(8,!0),this.vwr.zoomByFactor(Math.pow(this.mouseWheelFactor,a),b,c),this.vwr.setInMotion(!1))},"~N,~N,~N");c(c$,"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 c=2;switch(this.apm){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var g=8==this.apm,c=25==this.apm;if(!this.bnd(this.clickAction,
g?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;g=g||this.measurementQueued.isConnected(this.vwr.ms.at,2)?" DELETE":c?"STRUTS":"";this.runScript("connect "+this.measurementQueued.getMeasurementScript(" ",!0)+g);this.resetMeasurement();return;case 21:c++;case 20:c++;case 18:case 19:case 22:if(!this.bnd(this.clickAction,20))return;
if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>c)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);this.queueAtom(a,b);g=this.measurementQueued.count;1==g&&(this.vwr.setPicked(-1),this.vwr.setPicked(a));if(g<c)return;22==this.apm?this.getSequence():(this.vwr.setStatusMeasuring("measurePicked",c,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.apm||4==this.pickingStyleMeasure)&&this.runScript("measure "+
this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();return}g=null!=this.mp&&1!=this.apm?1:this.apm;switch(g){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(g){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 c=this.vwr.getAtomBitSet("connected(atomIndex="+a+") and !within(SMARTS,'[r50,R]')"),f=c.cardinality();switch(f){case 0:case 1:return;case 3:case 4:for(var e=C(f,0),j=C(f,0),h=0,g=c.nextSetBit(0);0<=g;g=c.nextSetBit(g+1),h++)e[h]=this.vwr.getBranchBitSet(g,a,!0).cardinality(),j[h]=g;for(h=0;h<f-2;h++){for(var l=
-2147483648,m=0,g=0;g<f;g++)e[g]>=l&&c.get(j[g])&&(m=j[g],l=e[g]);c.clear(m)}}this.vwr.undoMoveActionClear(a,2,!0);this.vwr.invertSelected(null,null,a,c);this.vwr.setStatusAtomPicked(a,"inverted: "+JU.Escape.eBS(c),null)}return;case 7:this.bnd(this.clickAction,4)&&(c=JU.BSUtil.newAndSetBit(a),this.vwr.deleteAtoms(c,!1),this.vwr.setStatusAtomPicked(a,"deleted: "+JU.Escape.eBS(c),null));return}g="atomindex="+a;switch(this.apm){default:return;case 9:this.selectAtoms(g);break;case 10:this.selectAtoms("within(group, "+
g+")");break;case 11:this.selectAtoms("within(chain, "+g+")");break;case 13:this.selectAtoms("within(polymer, "+g+")");break;case 14:this.selectAtoms("within(structure, "+g+")");break;case 12:this.selectAtoms("within(molecule, "+g+")");break;case 16:this.selectAtoms("within(model, "+g+")");break;case 17:this.selectAtoms("visible and within(element, "+g+")");break;case 15:this.selectAtoms("visible and within(site, "+g+")")}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 c="assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'"';this.isPickAtomAssignCharge?(c+=";{atomindex="+this.dragAtomIndex+"}.label='%C'; ",this.vwr.undoMoveActionClear(this.dragAtomIndex,
4,!0)):this.vwr.undoMoveActionClear(-1,4146,!0);this.runScript(c)}else this.isPickAtomAssignCharge||(this.vwr.undoMoveActionClear(-1,4146,!0),c=this.vwr.ms.at[this.dragAtomIndex],1==c.getElementNumber()?this.runScript("assign atom ({"+this.dragAtomIndex+'}) "X"'):(c=JU.P3.new3(a,b,c.sZ),this.vwr.tm.unTransformPoint(c,c),this.runScript("assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'" '+JU.Escape.eP(c))));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 c=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 g=this.measurementQueued.count;if(1==g)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)g=this.queueAtom(b,a);2>g?c?this.vwr.scriptStatus(1==g?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==g?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")):(g=this.measurementQueued.getMeasurementScript(" ",!1),c?this.runScript("spin"+g+" "+this.vwr.getInt(553648157)):this.runScript("draw symop"+g+";show symop"+g))}},"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 c=this.vwr.getAtomBitSetEval(null,b+("("+a+")"));this.vwr.select(c,!1,0,!1);this.vwr.refresh(3,"selections set")}catch(g){if(!D(g,Exception))throw g;}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(){E(self.c$);c$=u(function(){S(this,arguments);this.time=this.y=this.x=this.index=0;q(this,arguments)},JV.ActionManager,"MotionPoint");c(c$,"set",function(a,b,c,g){this.index=a;this.x=b;this.y=c;this.time=g},"~N,~N,~N,~N");h(c$,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});c$=H()};c$.$ActionManager$Gesture$=function(){E(self.c$);
c$=u(function(){S(this,arguments);this.action=0;this.nodes=null;this.time0=this.ptNext=0;q(this,arguments)},JV.ActionManager,"Gesture");s(c$,function(a){this.nodes=Array(a);for(var b=0;b<a;b++)this.nodes[b]=N(JV.ActionManager.MotionPoint,this,null)},"~N");c(c$,"setAction",function(a,b){this.action=a;this.ptNext=0;this.time0=b;for(var c=0;c<this.nodes.length;c++)this.nodes[c].index=-1},"~N,~N");c(c$,"add",function(a,b,c,g){this.action=a;this.getNode(this.ptNext).set(this.ptNext,b,c,g-this.time0);this.ptNext++;
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return Math.sqrt(f*f+e*e)/(c.time-g.time)},"~N,~N");c(c$,"getDX",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),g=this.getNode(this.ptNext-a-b);return c.x-g.x},"~N,~N");c(c$,"getDY",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),g=this.getNode(this.ptNext-a-b);return c.y-g.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 c=a+1;0<=--c&&!(0<=this.getNode(this.ptNext-c-b).index););return c},"~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$=H()};x(c$);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",
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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})"),
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"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"));x(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(" ");
x(c$,"pickingStyleNames",null);JV.ActionManager.pickingStyleNames="toggle selectOrToggle extendedSelect drag measure measureoff".$plit(" ");x(c$,"MAX_DOUBLE_CLICK_MILLIS",700,"MININUM_GESTURE_DELAY_MILLISECONDS",10,"SLIDE_ZOOM_X_PERCENT",98,"DEFAULT_MOUSE_DRAG_FACTOR",1,"DEFAULT_MOUSE_WHEEL_FACTOR",1.15,"DEFAULT_GESTURE_SWIPE_FACTOR",1)}),p("JV"),v(["JU.BS","J.c.ANIM"],"JV.AnimationManager",["J.api.Interface","JU.BSUtil"],function(){c$=u(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=
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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=A(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 c;this.setModel(b,!0);c=b+1;this.currentMorphModel=b+a;c==b||(0>c||0>b)||this.vwr.ms.morphTrajectories(b,c,a)}},"~N");c(c$,"setModel",function(a,b){0>a&&this.stopThread(!1);
var c=this.cmi,g=this.vwr.ms,f=null==g?0:g.mc;if(1==f)this.cmi=a=0;else if(0>a||a>=f)a=-1;var g=null,e=!1;if(this.cmi!=a){if(0<f){var f=this.vwr.ms,j=f.isJmolDataFrameForModel(a),h=f.isJmolDataFrameForModel(this.cmi);h&&f.setJmolDataFrame(null,-1,this.cmi);-1!=this.cmi&&this.vwr.saveModelOrientation();if(h||j)g=f.getJmolFrameType(a)+" "+a+" <--  "+this.cmi+" "+f.getJmolFrameType(this.cmi),e=f.getJmolDataSourceFrame(a)==f.getJmolDataSourceFrame(this.cmi)}this.cmi=a;null!=g&&(0<=a&&this.vwr.restoreModelOrientation(a),
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c(c$,"setAnimationRange",function(a,b){var c=this.getFrameCount();0>a&&(a=0);0>b&&(b=c);a>=c&&(a=c-1);b>=c&&(b=c-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>=
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b){a=a.$replace("\\","/");var c=a.indexOf("|");0<=c&&(a=a.substring(0,c));c=null;(c=Jmol.Cache.get(a))||(c=this.cache.get(a));return b&&r(c,String)?null:c},"~S,~B");c(c$,"cacheClear",function(){JU.Logger.info("cache cleared");this.cache.clear();this.clearPngjCache(null)});c(c$,"cacheFileByNameAdd",function(a,b){if(null==a||!b&&a.equalsIgnoreCase(""))return this.cacheClear(),-1;var c;if(b){a=this.vwr.resolveDatabaseFormat(a);c=this.getFileAsBytes(a,null,!0);if(r(c,String))return 0;this.cachePut(a,
c)}else{if(a.endsWith("*"))return JU.AU.removeMapKeys(this.cache,a.substring(0,a.length-1));c=this.cache.remove(a.$replace("\\","/"))}return null==c?0:(r(c,String),c.length)},"~S,~B");c(c$,"cacheList",function(){for(var a=new java.util.Hashtable,b,c=this.cache.entrySet().iterator();c.hasNext()&&((b=c.next())||1);)a.put(b.getKey(),Integer.$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 c=this.getBufferedInputStreamOrErrorMessageFromName(a,null,!1,!1,b,!1,!0);if(r(c,String))return c;try{c=JU.Rdr.getStreamAsBytes(c,null)}catch(g){if(D(g,java.io.IOException))try{c.close()}catch(f){if(!D(f,java.io.IOException))throw f;}else throw g;}return null==c?"":JU.Rdr.fixUTF(c)},"~S,~A");x(c$,"SIMULATION_PROTOCOL","http://SIMULATION/","URL_LOCAL",4,"urlPrefixes",["http:","https:","sftp:","ftp:","file:"]);c$.scriptFilePrefixes=
c$.prototype.scriptFilePrefixes=['/*file*/"','FILE0="','FILE1="']}),p("JV"),v(["java.util.Hashtable","JU.P3","J.c.AXES","$.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 $.Viewer".split(" "),function(){c$=u(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;q(this,arguments)},
JV,"GlobalSettings");L(c$,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.axesMode=J.c.AXES.BOUNDBOX;this.objColors=C(8,0);this.objStateOn=ba(8,!1);this.objMad=C(8,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,[30,90,-15,95]);this.structureList.put(J.c.STR.SHEET,[-180,-10,70,180,-180,-45,-180,-130,140,180,90,180]);this.structureList.put(J.c.STR.HELIX,[-160,0,-100,45])});s(c$,function(a,b,c){this.vwr=a;this.registerAllValues(b,
c)},"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 c,g=0,f=J.c.CBK.values();g<f.length&&((c=f[g])||1);g++)this.resetValue(c.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$,"setUnits",function(a){var b=this.measureDistanceUnits,c=this.energyUnits;a.equalsIgnoreCase("angstroms")?this.measureDistanceUnits="angstroms":a.equalsIgnoreCase("nanometers")||a.equalsIgnoreCase("nm")?
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"kcal");b.equalsIgnoreCase(this.measureDistanceUnits)?c.equalsIgnoreCase(this.energyUnits)||this.setO("energyUnits",this.energyUnits):this.setO("measurementUnits",this.measureDistanceUnits)},"~S");c(c$,"isJmolVariable",function(a){return"_"==a.charAt(0)||this.htNonbooleanParameterValues.containsKey(a=a.toLowerCase())||this.htBooleanParameterFlags.containsKey(a)||0<=JV.GlobalSettings.unreportedProperties.indexOf(";"+a+";")},"~S");c(c$,"resetValue",function(a,b){this.setO(a,null==b?"":b.getParameter(a,
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"set minBondDistance "+this.minBondDistance);this.app(b,"set minimizationCriterion  "+this.minimizationCriterion);this.app(b,"set minimizationSteps  "+this.minimizationSteps);this.app(b,"set pdbAddHydrogens "+(null!=a&&a.get("pdbNoHydrogens")!==Boolean.TRUE?this.pdbAddHydrogens:!1));this.app(b,"set pdbGetHeader "+this.pdbGetHeader);this.app(b,"set pdbSequential "+this.pdbSequential);this.app(b,"set percentVdwAtom "+this.percentVdwAtom);this.app(b,"set smallMoleculeMaxAtoms "+this.smallMoleculeMaxAtoms);
this.app(b,"set smartAromatic "+this.smartAromatic);this.zeroBasedXyzRasmol&&this.app(b,"set zeroBasedXyzRasmol true");return b.toString()},"java.util.Map");c(c$,"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=w(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:w(a/6)+1},"~S");c$.getGroup3Count=c(c$,"getGroup3Count",function(){if(0<JV.JC.group3Count)return JV.JC.group3Count;
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case 1113200652:return 7;case 1113200646:return 8;case 1115297793:return 9;case 1113200654:return 10;case 1113200642:return 11;case 1650071565:return 12;case 1113200647:return 13;case 1113200649:return 14;case 1113200650:return 15;case 1113198595:return 16;case 135175:return 17;case 135198:return 18;case 1113198597:return 19;case 1113198596:return 20;case 135192:return 21;case 135174:return 23;case 135176:return 22;case 135180:return 24;case 135402505:return 25;case 135182:return 26;case 1183762:return 27;
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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)}),p("JV"),v(null,"JV.ModelManager",["JM.ModelLoader"],function(){c$=u(function(){this.fileName=this.modelSetPathName=this.modelSet=this.vwr=null;q(this,arguments)},JV,"ModelManager");s(c$,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,c,g,f,e){var h=null;e?(h=this.modelSet.modelSetName,h.equals("zapped")?h=null:0>h.indexOf(" (modified)")&&(h+=" (modified)")):null==g?this.zap():(this.modelSetPathName=a,this.fileName=b);null!=g&&(null==h&&(h=this.vwr.getModelAdapter().getAtomSetCollectionName(g),null!=h&&(h=h.trim(),0==h.length&&
(h=null)),null==h&&(h=JV.ModelManager.reduceFilename(b))),new JM.ModelLoader(this.vwr,h,c,g,e?this.modelSet:null,f));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$,"createAtomDataSet",function(a,b){return JM.ModelLoader.createAtomDataSet(this.vwr,this.modelSet,
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g||this.vwr.reportSelection(J.i18n.GT.i(J.i18n.GT._("{0} atoms hidden"),this.bsHidden.cardinality()))},"JM.ModelSet,JU.BS,~N,~B");c(c$,"hide",function(a,b,c,g){JV.SelectionManager.setBitSet(this.bsHidden,b,c);null!=a&&a.setBsHidden(this.bsHidden);g||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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v(["JU.BS"],"JV.ShapeManager","java.lang.Boolean JU.P3 J.api.Interface J.c.PAL $.VDW JM.Atom JU.BSUtil JV.JC".split(" "),function(){c$=u(function(){this.navigationCrossHairMinMax=this.bsRenderableAtoms=this.vwr=this.shapes=this.ms=this.gdata=null;q(this,arguments)},JV,"ShapeManager");L(c$,function(){this.bsRenderableAtoms=new JU.BS;this.navigationCrossHairMinMax=C(4,0)});s(c$,function(a){this.vwr=a;this.gdata=a.gdata},"JV.Viewer");c(c$,"findNearestShapeAtomIndex",function(a,b,c,g){if(null!=this.shapes)for(var f=
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"set size");(null==c?0!=b:0!=c.value)&&this.loadShape(a);null!=this.shapes[a]&&this.shapes[a].setShapeSizeRD(b,c,g);this.vwr.setShapeErrorState(-1,null)}},"~N,~N,J.atomdata.RadiusData,JU.BS");c(c$,"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$,"setShapePropertyBs",function(a,b,c,g){null==this.shapes||null==this.shapes[a]||(null==g&&(g=this.vwr.bsA()),this.vwr.setShapeErrorState(a,
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b,c,g,f)))return h;return null},"~N,~N,~N,JU.BS,~B");c(c$,"checkObjectDragged",function(a,b,c,g,f,e,h){for(var k=!1,l=0<h?h+1:36;!k&&h<l;++h)null!=this.shapes[h]&&(k=this.shapes[h].checkObjectDragged(a,b,c,g,f,e));return k},"~N,~N,~N,~N,~N,JU.BS,~N");c(c$,"checkObjectHovered",function(a,b,c,g){var f=this.shapes[1];if(g&&null!=f&&f.checkObjectHovered(a,b,c))return!0;for(g=0;g<JV.ShapeManager.hoverable.length;g++)if(f=this.shapes[JV.ShapeManager.hoverable[g]],null!=f&&f.checkObjectHovered(a,b,c))return!0;
return!1},"~N,~N,JU.BS,~B");c(c$,"deleteShapeAtoms",function(a,b){if(null!=this.shapes)for(var c=0;36>c;c++)null!=this.shapes[c]&&this.setShapePropertyBs(c,"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,c){a=JV.JC.shapeTokenIndex(a);if(0>a||null==this.shapes[a])return 0;
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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$,"setModelVisibility",function(){var a=this.shapes;if(!(null==a||null==a[0])){for(var b=this.vwr.getVisibleFramesBitSet(),c=8;32>c;c++)null!=a[c]&&a[c].setVisibilityFlags(b);for(var g=this.vwr.getBoolean(603979922),f=this.vwr.getDeletedAtoms(),e=this.ms.at,c=this.ms.ac;0<=--c;){var h=e[c];h.shapeVisibilityFlags&=-64;if(!(null!=f&&f.get(c)||
!g&&1==h.getElementNumber())){var k=h.getModelIndex();b.get(k)&&(k=1,this.ms.isAtomHidden(c)||(k|=8,0!=h.madAtom&&(k|=16),h.setShapeVisibility(k,!0)))}}for(c=0;36>c;++c)b=a[c],null!=b&&b.setModelClickability()}});c(c$,"finalizeAtoms",function(a,b){var c=this.vwr,g=c.tm,f=this.bsRenderableAtoms,e=this.gdata;if(null!=a){var h=this.ms.getAtomSetCenter(a),k=new JU.P3;g.transformPt3f(h,k);k.add(b);g.unTransformPoint(k,k);k.sub(h);c.setAtomCoordsRelative(k,a);b.set(0,0,0)}this.ms.getRenderable(f);for(var l=
this.ms.vibrations,m=null!=l&&g.vibrationOn,h=this.ms.at,n=f.nextSetBit(0);0<=n;n=f.nextSetBit(n+1)){var k=h[n],p=m&&k.hasVibration()?g.transformPtVib(k,l[n]):g.transformPt(k);k.sX=p.x;k.sY=p.y;k.sZ=p.z;var q=Math.abs(k.madAtom);q==JM.Atom.MAD_GLOBAL&&(q=A(2E3*c.getFloat(1141899265)));k.sD=Y(c.tm.scaleToScreen(p.z,q))}if(g.slabEnabled){n=c.getBoolean(603979940);g=c.getBoolean(603979939);l=e.getSlab();m=e.getDepth();if(n){p=this.ms.getMolecules();q=this.ms.getMoleculeCountInModel(-1);for(n=0;n<q;n++){var r=
p[n],s=0,k=r.firstAtomIndex;if(f.get(k)){for(;s<r.ac&&!e.isClippedZ(h[k].sZ-(h[k].sD>>1));s++,k++);if(s!=r.ac){k=r.firstAtomIndex;for(s=0;s<r.ac;s++)f.clear(k),h[k++].sZ=0}}}}for(n=f.nextSetBit(0);0<=n;n=this.bsRenderableAtoms.nextSetBit(n+1))if(k=h[n],e.isClippedZ(k.sZ-(g?h[n].sD>>1:0)))k.setClickable(0),p=w((g?-1:1)*k.sD/2),(k.sZ+p<l||k.sZ-p>m||!e.isInDisplayRange(k.sX,k.sY))&&f.clear(n)}if(0==this.ms.getAtomCount()||!c.getShowNavigationPoint())return null;c=2147483647;e=-2147483648;g=2147483647;
l=-2147483648;for(n=f.nextSetBit(0);0<=n;n=f.nextSetBit(n+1))k=h[n],k.sX<c&&(c=k.sX),k.sX>e&&(e=k.sX),k.sY<g&&(g=k.sY),k.sY>l&&(l=k.sY);this.navigationCrossHairMinMax[0]=c;this.navigationCrossHairMinMax[1]=e;this.navigationCrossHairMinMax[2]=g;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$,"restrictSelected",function(a,b){var c=this.vwr.getSelectedAtomsNoSubset();if(b){this.vwr.invertSelection();var g=this.vwr.getSelectionSubset();null!=g&&(c=this.vwr.getSelectedAtomsNoSubset(),c.and(g),this.vwr.select(c,!1,0,!0),JU.BSUtil.invertInPlace(c,this.vwr.getAtomCount()),c.and(g))}JU.BSUtil.andNot(c,this.vwr.getDeletedAtoms());g=this.vwr.getBoolean(603979812);a||this.vwr.setBooleanProperty("bondModeOr",!0);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",
Integer.$valueOf(32768),null);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(1023),null);for(var f=this.vwr.bsA(),e=21;0<=--e;)6!=e&&null!=this.getShape(e)&&this.setShapeSizeBs(e,0,null,f);null!=this.getShape(21)&&this.setShapePropertyBs(21,"delete",f,null);this.setLabel(null,f);a||this.vwr.setBooleanProperty("bondModeOr",g);this.vwr.select(c,!1,0,!0)},"~B,~B");x(c$,"hoverable",[30,25,24,22,35]);c$.clickableMax=c$.prototype.clickableMax=JV.ShapeManager.hoverable.length-
1}),p("JV"),v(["java.util.Hashtable"],"JV.StateManager","java.util.Arrays JU.BS $.SB JM.Orientation JU.BSUtil JV.GlobalSettings".split(" "),function(){c$=u(function(){this.saved=this.vwr=null;this.lastCoordinates=this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=this.lastContext=this.lastOrientation="";O("JV.StateManager.Scene")||JV.StateManager.$StateManager$Scene$();O("JV.StateManager.Connections")||JV.StateManager.$StateManager$Connections$();O("JV.StateManager.Connection")||
JV.StateManager.$StateManager$Connection$();q(this,arguments)},JV,"StateManager");L(c$,function(){this.saved=new java.util.Hashtable});c$.getVariableList=c(c$,"getVariableList",function(a,b,c,g){var f=new JU.SB,e=0,h=Array(a.size()),k;for(a=a.entrySet().iterator();a.hasNext()&&((k=a.next())||1);){var l=k.getKey(),m=k.getValue();if((c||!l.startsWith("site_"))&&(!g||"@"==l.charAt(0)))h[e++]=l+("@"==l.charAt(0)?" "+m.asString():" = "+JV.StateManager.varClip(l,m.escape(),b))}java.util.Arrays.sort(h,0,
e);for(b=0;b<e;b++)null!=h[b]&&f.append("  ").append(h[b]).append(";\n");0==e&&!g&&f.append("# --no global user variables defined--;\n");return f.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:w(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");s(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 c,g=a.entrySet().iterator();g.hasNext()&&((c=g.next())||1);)if(c.getKey().equalsIgnoreCase(b))return c.getValue();return null},"java.util.Map,~S");c(c$,"listSavedStates",function(){for(var a="",b,c=this.saved.keySet().iterator();c.hasNext()&&((b=c.next())||1);)a+="\n"+b;return a});c(c$,"deleteSavedType",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();)b.next().startsWith(a)&&
b.remove()},"~S");c(c$,"deleteSaved",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();){var c=b.next();(c.startsWith(a)||c.endsWith("_"+a)&&c.indexOf("_")==c.lastIndexOf("_"+a))&&b.remove()}},"~S");c(c$,"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$,"getSavedOrientationText",function(a){var b;if(null!=a)return b=this.getOrientationFor(a),null==b?"":b.getMoveToText(!0);a=new JU.SB;for(var c=this.saved.entrySet().iterator();c.hasNext()&&((b=c.next())||1);)b.getKey().startsWith("Orientation_")&&a.append(b.getValue().getMoveToText(!0));return a.toString()},"~S");c(c$,"saveScene",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Scene_");
else{var c=N(JV.StateManager.Scene,this,null,b);c.saveName=this.lastScene="Scene_"+a;this.saved.put(c.saveName,c)}},"~S,java.util.Map");c(c$,"restoreScene",function(a,b){var c=JV.StateManager.getNoCase(this.saved,0<a.length?"Scene_"+a:this.lastScene);return null!=c&&c.restore(b)},"~S,~N");c(c$,"saveOrientation",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Orientation_");else{var c=new JM.Orientation(this.vwr,a.equalsIgnoreCase("default"),b);c.saveName=this.lastOrientation="Orientation_"+
a;this.saved.put(c.saveName,c)}},"~S,~A");c(c$,"restoreOrientation",function(a,b,c){a=this.getOrientationFor(a);return null!=a&&a.restore(b,c)},"~S,~N,~B");c(c$,"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$,"saveBonds",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Bonds_");else{var b=N(JV.StateManager.Connections,this,null);b.saveName=this.lastConnections="Bonds_"+a;this.saved.put(b.saveName,b)}},"~S");c(c$,"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,c){0<
c&&b.length>c&&(b=b.substring(0,c)+" #...more ("+b.length+" bytes -- use SHOW "+a+" or MESSAGE @"+a+" to view)");return b},"~S,~S,~N");c$.$StateManager$Scene$=function(){E(self.c$);c$=u(function(){S(this,arguments);this.scene=this.saveName=null;q(this,arguments)},JV.StateManager,"Scene");s(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$=H()};c$.$StateManager$Connections$=function(){E(self.c$);c$=u(function(){S(this,arguments);this.saveName=null;this.bondCount=0;this.connections=null;q(this,arguments)},JV.StateManager,"Connections");s(c$,function(){var a=this.b$["JV.StateManager"].vwr.ms;if(null!=a){this.bondCount=a.bondCount;this.connections=Array(this.bondCount+1);for(var a=a.bo,b=this.bondCount;0<=--b;){var c=a[b];this.connections[b]=N(JV.StateManager.Connection,this,null,c.getAtomIndex1(),c.getAtomIndex2(),c.mad,
c.colix,c.order,c.getEnergy(),c.getShapeVisibilityFlags())}}});c(c$,"restore",function(){var a=this.b$["JV.StateManager"].vwr.ms;if(null==a)return!1;a.deleteAllBonds();for(var b=this.bondCount;0<=--b;){var c=this.connections[b],g=a.getAtomCount();c.atomIndex1>=g||c.atomIndex2>=g||(g=a.bondAtoms(a.at[c.atomIndex1],a.at[c.atomIndex2],c.order,c.mad,null,c.energy,!1,!0),g.setColix(c.colix),g.setShapeVisibilityFlags(c.shapeVisibilityFlags))}for(c=this.bondCount;0<=--c;)a.getBondAt(c).setIndex(c);this.b$["JV.StateManager"].vwr.setShapeProperty(1,
"reportAll",null);return!0});c$=H()};c$.$StateManager$Connection$=function(){E(self.c$);c$=u(function(){S(this,arguments);this.shapeVisibilityFlags=this.energy=this.order=this.colix=this.mad=this.atomIndex2=this.atomIndex1=0;q(this,arguments)},JV.StateManager,"Connection");s(c$,function(a,b,c,g,f,e,h){this.atomIndex1=a;this.atomIndex2=b;this.mad=c;this.colix=g;this.order=f;this.energy=e;this.shapeVisibilityFlags=h},"~N,~N,~N,~N,~N,~N,~N");c$=H()};x(c$,"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      ")}),p("JV"),v(["java.util.Hashtable"],"JV.StatusManager","java.lang.Boolean $.Float javajs.awt.Dimension JU.Lst $.PT J.api.Interface J.c.CBK JU.Logger".split(" "),function(){c$=u(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;q(this,arguments)},JV,"StatusManager");L(c$,function(){this.messageQueue=new java.util.Hashtable;this.jmolScriptCallbacks=new java.util.Hashtable});s(c$,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$,"setStatusChanged",function(a,b,c,g){if(this.recordStatus(a)){var f=new JU.Lst;f.addLast(Integer.$valueOf(++this.statusPtr));f.addLast(a);f.addLast(Integer.$valueOf(b));f.addLast(c);b=g?null:this.messageQueue.get(a);null==b?this.messageQueue.put(a,b=new JU.Lst):b.size()==JV.StatusManager.MAXIMUM_QUEUE_LENGTH&&
b.remove(0);b.addLast(f)}},"~S,~N,~O,~B");c(c$,"getStatusChanged",function(a){var b=0<a.length&&"-"==a.charAt(0),c=0<a.length&&"+"==a.charAt(0),g=!1;b?this.statusList=JU.PT.rep(this.statusList,a.substring(1,a.length),""):(a=JU.PT.rep(a,"+",""),this.statusList.equals(a)||c&&0<=this.statusList.indexOf(a)?g=!0:(c||(this.statusList=""),this.statusList+=a,JU.Logger.debugging&&JU.Logger.debug("StatusManager messageQueue = "+this.statusList)));a=new JU.Lst;if(g)for(var f,g=this.messageQueue.entrySet().iterator();g.hasNext()&&
((f=g.next())||1);)a.addLast(f.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 c=
J.c.CBK.getCallback(a);if(null!=c){var g=null==b?0:7<b.length&&0==b.toLowerCase().indexOf("script:")?7:11<b.length&&0==b.toLowerCase().indexOf("jmolscript:")?11:0;0==g?this.jmolScriptCallbacks.remove(c):this.jmolScriptCallbacks.put(c,b.substring(g).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 c=b?this.jmolScriptCallback(J.c.CBK.APPLETREADY):
null;this.notifyEnabled(J.c.CBK.APPLETREADY)&&this.cbl.notifyCallback(J.c.CBK.APPLETREADY,[c,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$,"setStatusAtomPicked",function(a,b,c){var g=this.jmolScriptCallback(J.c.CBK.PICK);JU.Logger.info("setStatusAtomPicked("+a+","+b+")");this.setStatusChanged("atomPicked",
a,b,!1);this.notifyEnabled(J.c.CBK.PICK)&&this.cbl.notifyCallback(J.c.CBK.PICK,[g,b,Integer.$valueOf(a),c])},"~N,~S,java.util.Map");c(c$,"setStatusClicked",function(a,b,c,g,f){var e=this.jmolScriptCallback(J.c.CBK.CLICK);if(!this.notifyEnabled(J.c.CBK.CLICK))return c;f=[c,f];this.cbl.notifyCallback(J.c.CBK.CLICK,[e,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),Integer.$valueOf(g),f]);return f[0]},"~N,~N,~N,~N,~N");c(c$,"setStatusResized",function(a,b){var c=this.jmolScriptCallback(J.c.CBK.RESIZE);
this.notifyEnabled(J.c.CBK.RESIZE)&&this.cbl.notifyCallback(J.c.CBK.RESIZE,[c,Integer.$valueOf(a),Integer.$valueOf(b)])},"~N,~N");c(c$,"setStatusAtomHovered",function(a,b){var c=this.jmolScriptCallback(J.c.CBK.HOVER);this.notifyEnabled(J.c.CBK.HOVER)&&this.cbl.notifyCallback(J.c.CBK.HOVER,[c,b,Integer.$valueOf(a)])},"~N,~S");c(c$,"setStatusObjectHovered",function(a,b,c){var g=this.jmolScriptCallback(J.c.CBK.HOVER);this.notifyEnabled(J.c.CBK.HOVER)&&this.cbl.notifyCallback(J.c.CBK.HOVER,[g,b,Integer.$valueOf(-1),
a,Float.$valueOf(c.x),Float.$valueOf(c.y),Float.$valueOf(c.z)])},"~S,~S,JU.T3");c(c$,"setFileLoadStatus",function(a,b,c,g,f,e,h){null==a&&"resetUndo".equals(b)&&(b=this.vwr.getProperty("DATA_API","getAppConsole",null),null!=b&&b.zap(),b=this.vwr.getZapName());this.setStatusChanged("fileLoaded",f,a,!1);null!=g&&this.setStatusChanged("fileLoadError",f,g,!1);var k=this.jmolScriptCallback(J.c.CBK.LOADSTRUCT);e&&this.notifyEnabled(J.c.CBK.LOADSTRUCT)&&(e=this.vwr.getP("_smilesString"),0!=e.length&&(b=
e),this.cbl.notifyCallback(J.c.CBK.LOADSTRUCT,[k,a,b,c,g,Integer.$valueOf(f),this.vwr.getP("_modelNumber"),this.vwr.getModelNumberDotted(this.vwr.getModelCount()-1),h]))},"~S,~S,~S,~S,~N,~B,Boolean");c(c$,"setStatusFrameChanged",function(a,b,c,g,f,e,h){if(null!=this.vwr.ms){var k=this.vwr.am.animationOn,l=k?-2-f:f;this.setStatusChanged("frameChanged",l,0<=f?this.vwr.getModelNumberDotted(f):"",!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,c,g,f],h,Float.$valueOf(e)]);null!=this.vwr.jmolpopup&&!k&&this.vwr.jmolpopup.jpiUpdateComputedMenus()}},"~N,~N,~N,~N,~N,~N,~S");c(c$,"setStatusDragDropped",function(a,b,c,g){this.setStatusChanged("dragDrop",0,"",!1);var f=this.jmolScriptCallback(J.c.CBK.DRAGDROP);if(!this.notifyEnabled(J.c.CBK.DRAGDROP))return!1;this.cbl.notifyCallback(J.c.CBK.DRAGDROP,[f,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),g]);return!0},"~N,~N,~N,~S");c(c$,"setScriptEcho",function(a,b){if(null!=
a){this.setStatusChanged("scriptEcho",0,a,!1);var c=this.jmolScriptCallback(J.c.CBK.ECHO);this.notifyEnabled(J.c.CBK.ECHO)&&this.cbl.notifyCallback(J.c.CBK.ECHO,[c,a,Integer.$valueOf(b?1:0)])}},"~S,~B");c(c$,"setStatusMeasuring",function(a,b,c,g){this.setStatusChanged(a,b,c,!1);var f=null;a.equals("measureCompleted")?(JU.Logger.info("measurement["+b+"] = "+c),f=this.jmolScriptCallback(J.c.CBK.MEASURE)):a.equals("measurePicked")&&(this.setStatusChanged("measurePicked",b,c,!1),JU.Logger.info("measurePicked "+
b+" "+c));this.notifyEnabled(J.c.CBK.MEASURE)&&this.cbl.notifyCallback(J.c.CBK.MEASURE,[f,c,Integer.$valueOf(b),a,Float.$valueOf(g)])},"~S,~N,~S,~N");c(c$,"notifyError",function(a,b,c){var g=this.jmolScriptCallback(J.c.CBK.ERROR);this.notifyEnabled(J.c.CBK.ERROR)&&this.cbl.notifyCallback(J.c.CBK.ERROR,[g,a,b,this.vwr.getShapeErrorState(),c])},"~S,~S,~S");c(c$,"notifyMinimizationStatus",function(a,b,c,g,f){var e=this.jmolScriptCallback(J.c.CBK.MINIMIZATION);this.notifyEnabled(J.c.CBK.MINIMIZATION)&&
this.cbl.notifyCallback(J.c.CBK.MINIMIZATION,[e,a,b,c,g,f])},"~S,Integer,Float,Float,~S");c(c$,"setScriptStatus",function(a,b,c,g){if(-1>c){var f=-2-c;this.setStatusChanged("scriptStarted",f,b,!1);a="script "+f+" started"}else if(null==a)return;var f=0==c?this.jmolScriptCallback(J.c.CBK.SCRIPT):null,e="Script completed"===a;if(this.recordStatus("script")){var h=null!=g;this.setStatusChanged(h?"scriptError":"scriptStatus",0,a,!1);if(h||e)this.setStatusChanged("scriptTerminated",1,"Jmol script terminated"+
(h?" unsuccessfully: "+a:" successfully"),!1)}e&&(this.vwr.getBoolean(603979880)&&this.vwr.getBoolean(603979825))&&(a=[null,"script <exiting>",b,Integer.$valueOf(-1),g],this.notifyEnabled(J.c.CBK.SCRIPT)&&this.cbl.notifyCallback(J.c.CBK.SCRIPT,a),this.processScript(a),a="Jmol script completed.");a=[f,a,b,Integer.$valueOf(e?-1:c),g];this.notifyEnabled(J.c.CBK.SCRIPT)&&this.cbl.notifyCallback(J.c.CBK.SCRIPT,a);this.processScript(a)},"~S,~S,~N,~S");c(c$,"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,c){(0!=c||this.notifyEnabled(J.c.CBK.SYNC))&&this.cbl.notifyCallback(J.c.CBK.SYNC,[null,a,b,Integer.$valueOf(c)])},"~S,~S,~N");c(c$,"modifySend",function(a,b,c,g){this.notifyEnabled(J.c.CBK.STRUCTUREMODIFIED)&&this.cbl.notifyCallback(J.c.CBK.STRUCTUREMODIFIED,
[null,Integer.$valueOf(c),Integer.$valueOf(a),Integer.$valueOf(b),g])},"~N,~N,~N,~S");c(c$,"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$,"functionXY",function(a,b,c){return null==this.jsl?M(Math.abs(b),Math.abs(c),0):this.jsl.functionXY(a,
b,c)},"~S,~N,~N");c(c$,"functionXYZ",function(a,b,c,g){return null==this.jsl?M(Math.abs(b),Math.abs(c),Math.abs(c),0):this.jsl.functionXYZ(a,b,c,g)},"~S,~N,~N,~N");c(c$,"jsEval",function(a){return null==this.jsl?"":this.jsl.eval(a)},"~S");c(c$,"createImage",function(a,b,c,g,f){return null==this.jsl?null:this.jsl.createImage(a,b,null==c?g:c,f)},"~S,~S,~S,~A,~N");c(c$,"getRegistryInfo",function(){return null==this.jsl?null:this.jsl.getRegistryInfo()});c(c$,"dialogAsk",function(a,b){var c=a.equals("Save Image"),
g=J.api.Interface.getOption("dialog.Dialog");if(null==g)return null;g.setupUI(!1);c&&g.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);var f=g.getFileNameFromDialog(this.vwr,a,b);c&&null!=f&&(this.qualityJPG=g.getQuality("JPG"),this.qualityPNG=g.getQuality("PNG"),c=g.getType(),null!=c&&(this.imageType=c));return f},"~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");x(c$,"MAXIMUM_QUEUE_LENGTH",16,"SYNC_OFF",0,"SYNC_DRIVER",1,"SYNC_SLAVE",2,"SYNC_DISABLE",3,"SYNC_ENABLE",4,"SYNC_STEREO",5)}),p("JV"),v("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 $.Logger".split(" "),function(){c$=u(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;q(this,arguments)},JV,"TransformManager");L(c$,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=new JU.P3;this.matrixTemp=new JU.M4;this.vectorTemp=new JU.V3;this.fixedRotationOffset=new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;
this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.pointT2=new JU.P3;this.rotationAxis=new JU.V3;this.fixedTranslation=new JU.P3;this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=new JU.M4;this.point3fScreenTemp=new JU.P3;this.point3iScreenTemp=new JU.P3i;
this.ptVibTemp=new JU.Point3fi;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.c.STER.NONE;this.matrixStereo=new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=new JU.P3});s(c$,function(){});c$.getTransformManager=c(c$,"getTransformManager",function(a,b,c,g){g=g?J.api.Interface.getInterface("JV.TransformManager4D"):new JV.TransformManager;g.vwr=a;g.setScreenParameters(b,
c,!0,!1,!0,!0);return g},"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,c){if(0==a&&0==b)null!=this.spinThread&&this.spinIsGesture&&this.clearSpin();else{this.clearSpin();var g=JU.P3.newP(this.fixedRotationCenter),f=new JU.P3;this.transformPt3f(g,f);a=JU.P3.new3(-b,a,0);a.add(f);this.unTransformPoint(a,a);this.vwr.setInMotion(!1);this.rotateAboutPointsInternal(null,a,g,10*c,NaN,!1,!0,null,!0,null,null,null)}},"~N,~N,~N");c(c$,"rotateXYBy",function(a,b,c){this.rotate3DBall(a,b,c)},"~N,~N,JU.BS");c(c$,"rotateZBy",function(a,b,c){2147483647!=
b&&2147483647!=c&&this.resetXYCenter(b,c);this.rotateZRadians(a/57.29577951308232)},"~N,~N,~N");c(c$,"applyRotation",function(a,b,c,g,f){null==c?this.matrixRotate.mul2(a,this.matrixRotate):(this.vwr.moveAtoms(a,this.matrixRotate,g,this.internalRotationCenter,b,c,f),null!=g&&this.internalRotationCenter.add(g))},"JU.M3,~B,JU.BS,JU.V3,~B");c(c$,"rotate3DBall",function(a,b,c){this.matrixTemp3.setAsBallRotation(0.017453292,-b,-a)&&this.applyRotation(this.matrixTemp3,!1,c,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,c,g,f,e,h){null!=b&&this.moveRotationCenter(b,!0);this.setSpinOff();this.setNavOn(!1);if(this.vwr.isHeadless()){if(e&&3.4028235E38==f)return!1;e=!1}if(Float.isNaN(g)||0==g||0==f)return!1;null!=b&&this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(c);this.rotationRate=g;if(e)return this.fixedRotationAxis.setVA(c,0.017453292*g),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=
h,this.setSpin(a,!0,f,null,null,h,!1),!1;a=0.017453292*f;this.fixedRotationAxis.setVA(c,f);this.rotateAxisAngleRadiansFixed(a,h);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,c,g,f,e,h,k,l,m,n,p){this.setSpinOff();this.setNavOn(!1);if(null==p&&(null==m||0.001>m.length())&&
(!h||0==f||Float.isNaN(g)||0==g)&&(h||0==f))return!1;var q=null;null==p&&(q=JU.V3.newVsub(c,b),e&&q.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(q),this.internalTranslation=null==m?null:JU.V3.newV(m));b=null!=k;if(h)return null==p?(h=w(Math.abs(f)/Math.abs(g)*this.spinFps+0.5),Float.isNaN(f)?this.rotationRate=g:(this.rotationRate=f/h*this.spinFps,null!=m&&this.internalTranslation.scale(1/h)),this.internalRotationAxis.setVA(q,0.017453292*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),
this.isSpinInternal=!0,this.isSpinFixed=!1,this.isSpinSelected=b):f=g,this.setSpin(a,!0,f,n,p,k,l),null!=p||null!=k;a=0.017453292*f;this.internalRotationAxis.setVA(q,a);this.rotateAxisAngleRadiansInternal(a,k);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,c){null==c?this.translateXYBy(a,b):(this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1),this.fixedTranslation.x=a,this.fixedTranslation.y=b,this.setFixedRotationCenter(c))},"~N,~N,JU.P3");
c(c$,"percentToPixels",function(a,b){switch(a){case "x":return w(Math.floor(b/100*this.width));case "y":return w(Math.floor(b/100*this.height));case "z":return w(Math.floor(b/100*this.screenPixelCount))}return 0},"~S,~N");c(c$,"angstromsToPixels",function(a){return w(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$,"resetXYCenter",function(a,b){if(!(2147483647==a||2147483647==b)){this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1);var c=new JU.P3;this.transformPt3f(this.fixedRotationCenter,c);c.set(a,b,c.z);this.unTransformPoint(c,c);this.fixedTranslation.set(a,b,0);this.setFixedRotationCenter(c)}},"~N,~N");c(c$,"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$,"getCameraFactors",function(){this.aperatureAngle=
360*Math.atan2(this.screenPixelCount/2,this.referencePlaneOffset)/3.141592653589793;this.cameraDistanceFromCenter=this.referencePlaneOffset/this.scalePixelsPerAngstrom;var a=JU.P3.new3(w(this.screenWidth/2),w(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(w(this.screenWidth/2),w(this.screenHeight/2),0);this.vwr.tm.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);var c=JU.P3.new3(w(this.screenWidth/2),w(this.screenHeight/2),this.cameraDistanceFromCenter*
this.scalePixelsPerAngstrom);this.vwr.tm.unTransformPoint(c,c);c.sub(this.fixedRotationCenter);b.add(c);System.out.println("TM no "+this.navigationOffset+" rpo "+this.referencePlaneOffset+" aa "+this.aperatureAngle+" sppa "+this.scalePixelsPerAngstrom+" vr "+this.visualRange+" sw/vr "+this.screenWidth/this.visualRange+" "+a+" "+this.fixedRotationCenter);return[a,b,this.fixedRotationCenter,JU.P3.new3(this.cameraDistanceFromCenter,this.aperatureAngle,this.scalePixelsPerAngstrom)]});c(c$,"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 c=0>a?-a/100:a;0!=c&&(this.cameraDepthSetting=c,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$,"setScreenParameters0",function(a,b,c,g,f,e){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=c,this.width=(this.antialias=g)?2*a:a,this.height=g?2*b:b,this.scaleFitToScreen(!1,c,f,e))},"~N,~N,~B,~B,~B,~B");c(c$,"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$,"scaleFitToScreen",function(a,b,c,g){0==this.width||0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*(a?0.5:this.xTranslationFraction),this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),g&&this.resetNavigationPoint(c),this.zoomHeight&&
(b=this.height>this.width),this.screenPixelCount=b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");c(c$,"scaleToScreen",function(a,b){if(0==b||2>a)return 0;var c=this.scaleToPerspective(a,b*this.scalePixelsPerAngstrom/1E3);return 0<c?c:1},"~N,~N");c(c$,"unscaleToScreen",function(a,b){var c=b/this.scalePixelsPerAngstrom;return this.perspectiveDepth?c/this.getPerspectiveFactor(a):
c},"~N,~N");c(c$,"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):w(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=A(this.pointT2.z)}catch(a){if(!D(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$,"zValueFromPercent",function(a){return w(Math.floor((1-a/50)*this.modelRadiusPixels+this.modelCenterOffset))},
"~N");c(c$,"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(D(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$,"transformPoints",function(a,b,c){for(;0<=
--a;)c[a].setT(this.transformPt(b[a]))},"~N,~A,~A");c(c$,"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,c){a.setTempPoint(b,this.vibrationT,Float.isNaN(c)?this.vibrationScale:c,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=w(Math.floor(a.x/100*this.screenWidth)),this.point3iScreenTemp.y=w(Math.floor((1-a.y/100)*this.screenHeight))):(this.point3iScreenTemp.x=A(a.x),
this.point3iScreenTemp.y=this.screenHeight-A(a.y));this.antialias&&(this.point3iScreenTemp.x<<=1,this.point3iScreenTemp.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.point3fScreenTemp);this.point3iScreenTemp.z=A(this.point3fScreenTemp.z);return this.point3iScreenTemp},"JU.T3");c(c$,"applyPerspective",function(a,b){this.getScreenTemp(a);var c=this.point3fScreenTemp.z;Float.isNaN(c)?(!this.haveNotifiedNaN&&JU.Logger.debugging&&JU.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=
!0,c=this.point3fScreenTemp.z=1):0>=c&&(c=this.point3fScreenTemp.z=1);switch(this.mode){case 1:this.point3fScreenTemp.x-=this.navigationShiftXY.x;this.point3fScreenTemp.y-=this.navigationShiftXY.y;break;case 2:this.point3fScreenTemp.x+=this.perspectiveShiftXY.x,this.point3fScreenTemp.y+=this.perspectiveShiftXY.y}this.perspectiveDepth&&(c=this.getPerspectiveFactor(c),this.point3fScreenTemp.x*=c,this.point3fScreenTemp.y*=c);switch(this.mode){case 1:this.point3fScreenTemp.x+=this.navigationOffset.x;
this.point3fScreenTemp.y+=this.navigationOffset.y;break;case 2:this.point3fScreenTemp.x-=this.perspectiveShiftXY.x,this.point3fScreenTemp.y-=this.perspectiveShiftXY.y;case 0:this.point3fScreenTemp.x+=this.fixedRotationOffset.x,this.point3fScreenTemp.y+=this.fixedRotationOffset.y}Float.isNaN(this.point3fScreenTemp.x)&&!this.haveNotifiedNaN&&(JU.Logger.debugging&&JU.Logger.debug("NaN found in transformPoint "),this.haveNotifiedNaN=!0);this.point3iScreenTemp.set(A(this.point3fScreenTemp.x),A(this.point3fScreenTemp.y),
A(this.point3fScreenTemp.z));if(null!=b&&(null!=this.slabPlane&&0<b.x*this.slabPlane.x+b.y*this.slabPlane.y+b.z*this.slabPlane.z+this.slabPlane.w||null!=this.depthPlane&&0>b.x*this.depthPlane.x+b.y*this.depthPlane.y+b.z*this.depthPlane.z+this.depthPlane.w))this.point3iScreenTemp.z=1;return this.point3iScreenTemp},"JU.T3,JU.T3");c(c$,"transformVector",function(a,b){this.matrixTransform.rotate2(a,b)},"JU.V3,JU.V3");c(c$,"move",function(a,b,c,g,f,e,h){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread");
this.movetoThread.setManager(this,this.vwr,[b,g,[c,f,e,h]]);0<e&&this.movetoThread.setEval(a);this.movetoThread.run()},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(c$,"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$,"moveToPyMOL",function(a,b,c){var g=JU.M3.newA9(c);g.invert();var f=c[9],e=-c[10],h=-c[11],k=JU.P3.new3(c[12],c[13],c[14]),l=c[15],m=c[16],n=c[17];this.setPerspectiveDepth(!(0<=n));var n=Math.abs(n)/2,p=Math.tan(3.141592653589793*n/180),n=h*p,p=0.5/p-0.5,q=50/n;0<l&&(l=50+A((h-l)*q),h=50+A((h-m)*q),this.setSlabEnabled(!0),this.slabToPercent(l),this.depthToPercent(h),21==c.length&&(m=0!=c[18],q=0!=c[19],c=c[20],this.setZShadeEnabled(m),m&&(q?this.vwr.setIntProperty("zSlab",A(Math.min(100,
l+c*(h-l)))):this.vwr.setIntProperty("zSlab",A((l+h)/2)),this.vwr.setIntProperty("zDepth",h))));this.moveTo(a,b,k,null,0,g,100,NaN,NaN,n,null,NaN,NaN,NaN,p,f,e);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(c$,"moveTo",function(a,b,c,g,f,e,h,k,l,m,n,p,q,r,s,u,v){if(null==e)if(e=new JU.M3,g=JU.V3.newV(g),Float.isNaN(f))e.m00=NaN;else if(0.01>f&&-0.01<f)e.setScale(1);else{if(0==g.x&&0==g.y&&0==g.z)return;var w=new JU.A4;w.setVA(g,f/57.29577951308232);e.setAA(w)}u==this.cameraSetting.x&&(u=NaN);v==
this.cameraSetting.y&&(v=NaN);s==this.cameraDepth&&(s=NaN);Float.isNaN(u)||(k=50*u/m/this.width*this.screenPixelCount);Float.isNaN(v)||(l=50*v/m/this.height*this.screenPixelCount);f=null==c?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(m);if(0>=b)this.setAll(c,e,n,h,k,l,m,f,r,p,q,s,u,v),this.vwr.moveUpdate(b),this.vwr.finalizeTransformParameters();else try{null==this.movetoThread&&(this.movetoThread=J.api.Interface.getOption("thread.MoveToThread"));var x=this.movetoThread.setManager(this,
this.vwr,[c,e,n,[b,h,k,l,m,f,r,p,q,s,u,v]]);0>=x||this.vwr.g.waitForMoveTo?(0<x&&this.movetoThread.setEval(a),this.movetoThread.run(),this.vwr.isSingleThreaded||(this.movetoThread=null)):this.movetoThread.start()}catch(y){if(!D(y,Exception))throw y;}},"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 c=new JU.SB;c.append("moveto ");b&&c.append("/* time, axisAngle */ ");c.appendF(a);c.append(" ").append(this.getRotationText());b&&c.append(" /* zoom, translation */ ");JV.TransformManager.truncate2(c,this.zmPctSet);JV.TransformManager.truncate2(c,this.getTranslationXPercent());JV.TransformManager.truncate2(c,this.getTranslationYPercent());c.append(" ");b&&c.append(" /* center, rotationRadius */ ");c.append(this.getCenterText());c.append(" ").appendF(this.modelRadius);c.append(this.getNavigationText(b));
b&&c.append(" /* cameraDepth, cameraX, cameraY */ ");JV.TransformManager.truncate2(c,this.cameraDepth);JV.TransformManager.truncate2(c,this.cameraSetting.x);JV.TransformManager.truncate2(c,this.cameraSetting.y);c.append(";");return c.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,c=-(57.29577951308232*Math.asin(b)),g;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,
this.matrixRotate.m11)),g=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,this.matrixRotate.m22),g=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!=c&&(a.append("; rotate y"),JV.TransformManager.truncate2(a,c));0!=g&&(a.append("; rotate z"),JV.TransformManager.truncate2(a,g));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,
c=this.vwr.ms.getInfoM("defaultOrientationMatrix");null==c?c=this.matrixRotate:(c=JU.M3.newM3(c),c.invert(),c.mul2(this.matrixRotate,c));var g=c.m22,f=57.29577951308232*Math.acos(g);0.999<g||-0.999>g?(g=57.29577951308232*Math.atan2(c.m10,c.m11),c=0):(g=57.29577951308232*Math.atan2(c.m21,-c.m20),c=57.29577951308232*Math.atan2(c.m12,c.m02));0!=g&&(0!=f&&0!=c&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");b.append("reset");b.append(";center ").append(this.getCenterText());0!=g&&(b.append("; rotate z"),
JV.TransformManager.truncate2(b,g));0!=f&&(b.append("; rotate y"),JV.TransformManager.truncate2(b,f));0!=c&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,c));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$,"setSpinXYZ",function(a,b,c){Float.isNaN(a)||
(this.spinX=a);Float.isNaN(b)||(this.spinY=b);Float.isNaN(c)||(this.spinZ=c);(this.isSpinInternal||this.isSpinFixed)&&this.clearSpin()},"~N,~N,~N");c(c$,"setSpinFps",function(a){0>=a?a=1:50<a&&(a=50);this.spinFps=a},"~N");c(c$,"setNavXYZ",function(a,b,c){Float.isNaN(a)||(this.navX=a);Float.isNaN(b)||(this.navY=b);Float.isNaN(c)||(this.navZ=c)},"~N,~N,~N");c(c$,"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$,"setSpin",function(a,b,c,g,f,e,h){this.navOn&&b&&this.setNavOn(!1);this.spinOn!=b&&(this.spinOn=b,this.vwr.g.setB("_spinning",b),b?null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread"),this.spinThread.setManager(this,this.vwr,[Float.$valueOf(c),g,f,e,h?Boolean.TRUE:null]),this.spinIsGesture=h,null==e&&null==f?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$,"setVibrationPeriod",function(a){if(Float.isNaN(a))a=this.vibrationPeriod;else if(0==a)this.vibrationPeriodMs=this.vibrationPeriod=0;else{this.vibrationPeriod=Math.abs(a);this.vibrationPeriodMs=A(1E3*this.vibrationPeriod);if(0<a)return;a=-a}this.setVibrationOn(0<a&&0<=this.vwr.modelGetLastVibrationIndex(this.vwr.am.cmi,
0))},"~N");c(c$,"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=
!0):(null!=this.vibrationThread&&(this.vibrationThread.interrupt(),this.vibrationThread=null),this.vibrationOn=!1,this.vibrationT.x=0)},"~B");c(c$,"clearVibration",function(){this.setVibrationOn(!1);this.vibrationScale=0});c(c$,"setStereoMode2",function(a){this.stereoMode=J.c.STER.CUSTOM;this.stereoColors=a},"~A");c(c$,"setStereoMode",function(a){this.stereoColors=null;this.stereoMode=a},"J.c.STER");c(c$,"setStereoDegrees",function(a){this.stereoDegrees=a;this.stereoRadians=0.017453292*a},"~N");c(c$,
"getStereoRotationMatrix",function(a){this.stereoFrame=a;if(!a)return this.matrixRotate;this.matrixTemp3.setAsYRotation(-this.stereoRadians);this.matrixStereo.mul2(this.matrixTemp3,this.matrixRotate);return this.matrixStereo},"~B");c(c$,"isWindowCentered",function(){return this.windowCentered});c(c$,"setWindowCentered",function(a){this.windowCentered=a;this.resetNavigationPoint(!0)},"~B");c(c$,"getRotationCenter",function(){return this.fixedRotationCenter});c(c$,"getRotationRadius",function(){return this.modelRadius});
c(c$,"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$,"setCenterAt",function(a,b){var c=JU.P3.newP(b);switch(a){case 96:c.add(this.vwr.ms.getAverageAtomPoint());break;case 1679429641:c.add(this.vwr.getBoundBoxCenter());break;case 1073741826:c.setT(this.rotationCenterDefault)}this.setRotationCenterAndRadiusXYZ(c,!0);this.resetFitToScreen(!0)},"~N,JU.P3");c(c$,"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 c=this.getPerspectiveFactor(this.untransformedPoint.z);
this.untransformedPoint.x/=c;this.untransformedPoint.y/=c}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=
!0,this.mode=1):(1==this.mode?(this.navMode=1,this.slabPercentSetting=0,this.perspectiveDepth=!0):a&&(this.slabPercentSetting=100),this.vwr.setFloatProperty("slabRange",0),a&&this.setSlabEnabled(1==this.mode),this.zoomFactor=3.4028235E38,this.zmPctSet=this.zmPct)},"~B");c(c$,"setNavigatePt",function(a){this.navigationCenter.setT(a);this.navMode=3;this.navigating=!0;this.finalizeTransformParameters();this.navigating=!1},"JU.P3");c(c$,"getNavigationCenter",function(){return this.navigationCenter});
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$,"setScreenParameters",function(a,b,c,g,f,e){var h=1==this.mode?JU.P3.newP(this.navigationCenter):null,k=JU.P3.newP(this.navigationOffset);k.x/=this.width;k.y/=this.height;this.setScreenParameters0(a,b,c,g,f,e);null!=h&&(this.navigationCenter.setT(h),this.navTranslatePercentOrTo(-1,k.x*this.width,k.y*this.height),this.setNavigatePt(h))},"~N,~N,~B,~B,~B,~B");c(c$,"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,c){!(0>=a)&&this.zoomEnabled&&(1!=this.mode?(this.zoomRatio=a,this.zmPctSet*=a,this.resetXYCenter(b,c)):this.getNav()&&this.nav.zoomByFactor(a,b,c))},"~N,~N,~N");c(c$,"setNavigationOffsetRelative",function(){this.getNav()&&
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h);Float.isNaN(k)||(this.scaleDefaultPixelsPerAngstrom=k);!Float.isNaN(f)&&!Float.isNaN(e)&&(this.translateToPercent("x",f),this.translateToPercent("y",e));1==this.mode&&(!Float.isNaN(m)&&!Float.isNaN(n)&&this.navTranslatePercentOrTo(0,m,n),Float.isNaN(l)||this.setNavigationDepthPercent(l))},"JU.P3,JU.M3,JU.P3,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");x(c$,"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)}),p("JV"),v("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 $.TransformManager JV.binding.Binding".split(" "),
function(){c$=u(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;q(this,arguments)},JV,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,javajs.api.PlatformViewer]);L(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);T(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,c,g,f,e,h,k){var l=new java.util.Hashtable;
l.put("display",a);l.put("adapter",b);l.put("statusListener",h);l.put("platform",k);l.put("options",e);l.put("fullName",c);l.put("documentBase",g);l.put("codeBase",f);return new JV.Viewer(l)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,javajs.api.GenericPlatform");s(c$,function(a){G(this,JV.Viewer,[]);this.setOptions(a)},"java.util.Map");c(c$,"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$,"getSymmetryInfo",function(a,b,c,g,f,e,h){return this.getPropertyManager().getSymmetryInfo(a,b,c,g,f,e,h)},"JU.BS,~S,~N,JU.P3,JU.P3,~S,~N");h(c$,"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 c=a.get("codePath");null==c&&(c="../java/");JV.Viewer.appletCodeBase=c.toString();JV.Viewer.appletIdiomaBase=JV.Viewer.appletCodeBase.substring(0,JV.Viewer.appletCodeBase.lastIndexOf("/",JV.Viewer.appletCodeBase.length-2)+1)+"idioma";c=a.get("documentBase");
JV.Viewer.appletDocumentBase=null==c?"":c.toString();c=a.get("options");this.commandOptions=null==c?"":c.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.$isSignedApplet=this.isJNLP||this.checkOption2("signedApplet","-signed"))||this.checkOption2("applet",
"-applet");this.allowScripting=!this.checkOption2("noscripting","-noscripting");var g=this.fullName.indexOf("__");this.htmlName=0>g?this.fullName:this.fullName.substring(0,g);this.appletName=JU.PT.split(this.htmlName+"_","_")[0];this.syncId=0>g?"":this.fullName.substring(g+2,this.fullName.length-2);this.access=this.checkOption2("access:READSPT","-r")?JV.Viewer.ACCESS.READSPT:this.checkOption2("access:NONE","-R")?JV.Viewer.ACCESS.NONE:JV.Viewer.ACCESS.ALL;(this.$isPreviewOnly=a.containsKey("previewOnly"))&&
a.remove("previewOnly");this.isPrintOnly=this.checkOption2("printOnly","-p");c=a.get("platform");g="unknown";null==c&&(c=this.commandOptions.contains("platform=")?this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");if(r(c,String)){g=c;this.isJS=(this.isWebGL=0<=g.indexOf(".awtjs."))||0<=g.indexOf(".awtjs2d.");var c=null,f="?";self.Jmol&&(c=Jmol._applets[this.htmlName.split("_object")[0]],f=Jmol._version);null!=f&&(this.html5Applet=c,JV.Viewer.strJavaVersion=
f,JV.Viewer.strJavaVendor="Java2Script "+(this.isWebGL?"(WebGL)":"(HTML5)"));c=J.api.Interface.getInterface(g)}this.apiPlatform=c;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);c=a.get("graphicsAdapter");null==c&&!this.isWebGL&&(c=J.api.Interface.getOption("g3d.Graphics3D"));this.gdata=null==c?new JU.GData:c;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);
g=a.containsKey("4DMouse");this.tm=JV.TransformManager.getTransformManager(this,2147483647,0,g);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);c=a.get("repaintManager");null==c&&(c=J.api.Interface.getOption("render.RepaintManager"));null!=c&&!c.equals("")&&(this.rm=c).set(this,this.shm);this.initialize(!0);this.fm=new JV.FileManager(this);this.definedAtomSets=new java.util.Hashtable;this.setJmolStatusListener(b);this.$isApplet?(JU.Logger.info("vwrOptions: \n"+JU.Escape.escapeMap(this.vwrOptions)),b=this.vwrOptions.get("documentLocation"),
!this.isJS&&(null!=b&&b.startsWith("file:/"))&&(b=b.substring(0,b.substring(0,(b+"?").indexOf("?")).lastIndexOf("/")),JU.Logger.info("setting current directory to "+b),this.cd(b)),b=JV.Viewer.appletDocumentBase,g=b.indexOf("#"),0<=g&&(b=b.substring(0,g)),g=b.lastIndexOf("?"),0<=g&&(b=b.substring(0,g)),g=b.lastIndexOf("/"),0<=g&&(b=b.substring(0,g)),JV.Viewer.jsDocumentBase=b,this.fm.setAppletContext(JV.Viewer.appletDocumentBase),a=a.get("appletProxy"),null!=a&&this.setStringProperty("appletProxy",
a),this.$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"),c=a.get("headlistMaxTimeMs"),null==c&&(c=Integer.$valueOf(6E4)),this.setTimeout(""+Math.random(),c.intValue(),"exitJmol")));this.useCommandThread=!this.isHeadless()&&this.checkOption2("useCommandThread","-threaded");this.setStartupBooleans();this.setIntProperty("_nProcessors",JV.Viewer.nProcessors);
this.isSilent||JU.Logger.info("(C) 2012 Jmol Development\nJmol Version: "+JV.Viewer.getJmolVersion()+"\njava.vendor: "+JV.Viewer.strJavaVendor+"\njava.version: "+JV.Viewer.strJavaVersion+"\nos.name: "+JV.Viewer.strOSName+"\nAccess: "+this.access+"\nmemory: "+this.getP("_memory")+"\nprocessors available: "+JV.Viewer.nProcessors+"\nuseCommandThread: "+this.useCommandThread+(!this.$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(!D(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$,"setCenterBitSet",function(a,b){var c=0<JU.BSUtil.cardinalityOf(a)?this.ms.getAtomSetCenter(a):null;this.isJmolDataFrame()||this.tm.setNewRotationCenter(c,b)},"JU.BS,~B");c(c$,"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,c,g,f,e,h){this.tm.move(a,b,c,g,f,e,h);this.moveUpdate(e)},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(c$,"moveTo",function(a,b,c,g,f,e,h,k,l,m,n,p,q,r,s,u,v){this.haveDisplay||(b=0);this.setTainted(!0);this.tm.moveTo(a,b,c,g,f,e,h,k,l,m,n,p,q,r,s,u,v)},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.V3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(c$,"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$,"processMultitouchEvent",function(a,b,c,g,f,e){this.actionManager.processMultitouchEvent(a,b,c,g,f,e)},"~N,~N,~N,~N,JU.P3,~N");
c(c$,"zoomBy",function(a){this.mouseEnabled&&this.tm.zoomBy(a);this.refresh(2,this.sm.syncingMouse?"Mouse: zoomBy "+a:"")},"~N");c(c$,"zoomByFactor",function(a,b,c){this.mouseEnabled&&this.tm.zoomByFactor(a,b,c);this.refresh(2,!this.sm.syncingMouse?"":"Mouse: zoomByFactor "+a+(2147483647==b?"":" "+b+" "+c))},"~N,~N,~N");c(c$,"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$,"spinXYBy",function(a,
b,c){this.mouseEnabled&&this.tm.spinXYBy(a,b,c);0==a&&0==b||this.refresh(2,this.sm.syncingMouse?"Mouse: spinXYBy "+a+" "+b+" "+c:"")},"~N,~N,~N");c(c$,"rotateZBy",function(a,b,c){this.mouseEnabled&&this.tm.rotateZBy(a,b,c);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateZBy "+a+(2147483647==b?"":" "+b+" "+c):"")},"~N,~N,~N");c(c$,"rotateSelected",function(a,b,c){this.isJmolDataFrame()||(this.mouseEnabled&&(this.tm.rotateXYBy(a,b,this.setMovableBitSet(c,!1)),this.refreshMeasures(!0)),this.refresh(2,
this.sm.syncingMouse?"Mouse: rotateMolecule "+a+" "+b:""))},"~N,~N,JU.BS");c(c$,"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$,"translate",function(a,b,c,g){var f="\x00"==c?A(b):"%"==c?this.tm.percentToPixels(a,b):this.tm.angstromsToPixels(b*("n"==c?10:1));if(null!=g){if(0==f)return;this.tm.setSelectedTranslation(g,a,f)}else switch(a){case "X":case "x":"\x00"==c?this.tm.translateToPercent("x",b):this.tm.translateXYBy(f,0);break;case "Y":case "y":"\x00"==c?this.tm.translateToPercent("y",b):this.tm.translateXYBy(0,f);break;case "Z":case "z":"\x00"==c?this.tm.translateToPercent("z",
b):this.tm.translateZBy(f)}this.refresh(1,"Viewer:translate()")},"~S,~N,~S,JU.BS");h(c$,"getZoomPercent",function(){return A(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$,"slabDepthByPixels",
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b){if(JU.PT.isOneOf(a,";x;y;z;fps;X;Y;Z;FPS;")){var c="x;y;z;fps;X;Y;Z;FPS".indexOf(a);switch(c){case 0:this.tm.setSpinXYZ(b,NaN,NaN);break;case 2:this.tm.setSpinXYZ(NaN,b,NaN);break;case 4:this.tm.setSpinXYZ(NaN,NaN,b);break;default:this.tm.setSpinFps(b);break;case 10:this.tm.setNavXYZ(b,NaN,NaN);break;case 12:this.tm.setNavXYZ(NaN,b,NaN);break;case 14:this.tm.setNavXYZ(NaN,NaN,b);break;case 16:this.tm.setNavFps(b)}this.g.setI((10>c?"spin":"nav")+a,b)}},"~S,~N");c(c$,"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 c=JV.StateManager.getObjectIdFromName(a);if(0>c)a.equalsIgnoreCase("axes")&&(this.setObjectArgb("axis1",b),this.setObjectArgb("axis2",b),this.setObjectArgb("axis3",b));else{this.g.objColors[c]=b;switch(c){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,c){var g=JV.StateManager.getObjectIdFromName(b.equalsIgnoreCase("axes")?"axis":b);if(!(0>g)){if(-2==c||-4==c){var f=c+3;c=this.getObjectMad(g);0==c&&
(c=f)}this.g.setB("show"+b,0!=c);this.g.objStateOn[g]=0!=c;0!=c&&(this.g.objMad[g]=c,this.setShapeSize(a,c,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,c){this.g.propertyColorScheme=a;a.startsWith("translucent ")&&(b=!0,a=a.substring(12).trim());this.cm.setPropertyColorScheme(a,b,c)},"~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,c,g){b&&(a=this.getUndeletedGroupAtomBits(a));this.slm.select(a,c,g);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$,"displayAtoms",function(a,b,c,g,f){c&&(a=this.getUndeletedGroupAtomBits(a));b?this.slm.display(this.ms,a,g,f):this.slm.hide(this.ms,a,g,f)},"JU.BS,~B,~B,~N,~B");c(c$,"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$,"getDefinedAtomSet",function(a){a=this.definedAtomSets.get(a.toLowerCase());return r(a,JU.BS)?a:new JU.BS},"~S");h(c$,"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$,"clearSelection",function(){this.slm.clearSelection(!0);this.g.setB("hideNotSelected",
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case 553648144:return this.g.dotScale;case 553648146:return this.g.helixStep;case 553648151:return this.g.meshScale;case 553648153:return this.g.minPixelSelRadius;case 553648154:return this.g.percentVdwAtom;case 553648157:return this.g.pickingSpinRate;case 553648166:return this.g.ribbonAspectRatio;case 536870922:return this.g.scriptDelay;case 553648170:return this.g.smallMoleculeMaxAtoms;case 553648184:return this.g.strutSpacing}JU.Logger.error("viewer.getInt("+JS.T.nameOf(a)+") - not listed");return 0},
"~N");c(c$,"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 c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 603979776:this.setBooleanPropertyTok(a,c,JS.SV.newV(4,b).asBoolean());break;case 553648128:this.setIntPropertyTok(a,c,JS.SV.newV(4,b).asInt());break;case 570425344:this.setFloatPropertyTok(a,c,JU.PT.parseFloat(b));break;
default:this.setStringPropertyTok(a,c,b)}}},"~S,~S");c(c$,"setStringPropertyTok",function(a,b,c){switch(b){case 545259521:this.setAnimationMode(c);return;case 545259569:this.g.nmrPredictFormat=c;break;case 545259548:this.g.defaultDropScript=c;break;case 545259571:c=this.fm.setPathForAllFiles(c);break;case 545259558:this.setUnits(c,!1);return;case 545259560:this.g.forceField=c="UFF".equalsIgnoreCase(c)?"UFF":"MMFF";this.minimizer=null;break;case 545259570:this.g.nmrUrlFormat=c;break;case 545259568:this.setUnits(c,
!0);return;case 545259566:this.g.loadLigandFormat=c;break;case 545259543:this.g.defaultLabelPDB=c;break;case 545259544:this.g.defaultLabelXYZ=c;break;case 545259549:this.g.defaultLoadFilter=c;break;case 545259567:c=this.getOutputManager().setLogFile(c);if(null==c)return;break;case 545259559:break;case 545259524:this.g.atomTypes=c;break;case 545259538:break;case 545259576:this.g.pickLabel=c;break;case 545259580:this.g.quaternionFrame=2==c.length&&c.startsWith("R")?c.substring(0,2):""+(c.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(c);return;case 545259564:new J.i18n.GT(this,c);b=J.i18n.GT.getLanguage();this.modelkitPopup=null;null!=this.jmolpopup&&(this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.getPopupMenu());this.sm.setCallbackFunction("language",b);c=J.i18n.GT.getLanguage();break;case 545259565:this.g.loadFormat=c;break;case 545259534:this.setObjectColor("background",
c);return;case 545259528:this.setObjectColor("axis1",c);return;case 545259530:this.setObjectColor("axis2",c);return;case 545259532:this.setObjectColor("axis3",c);return;case 545259536:this.setObjectColor("boundbox",c);return;case 545259586:this.setObjectColor("unitcell",c);return;case 545259578:this.setPropertyColorScheme(c,!1,!1);break;case 545259562:this.shm.loadShape(34);this.setShapeProperty(34,"atomLabel",c);break;case 545259547:this.g.defaultDistanceLabel=c;break;case 545259542:this.g.defaultAngleLabel=
c;break;case 545259554:this.g.defaultTorsionLabel=c;break;case 545259550:this.g.defaultLoadScript=c;break;case 545259522:this.fm.setAppletProxy(c);break;case 545259546:null==c&&(c="");c=c.$replace("\\","/");this.g.defaultDirectory=c;break;case 545259561:this.g.helpPath=c;break;case 545259552:!c.equalsIgnoreCase("RasMol")&&!c.equalsIgnoreCase("PyMOL")&&(c="Jmol");this.setDefaultsType(c);break;case 545259545:this.setDefaultColors(c.equalsIgnoreCase("rasmol"));return;case 545259572:this.setPickingMode(c,
0);return;case 545259574:this.setPickingStyle(c,0);return;case 545259540:break;default:if(a.toLowerCase().endsWith("callback")){this.sm.setCallbackFunction(a,0==c.length||c.equalsIgnoreCase("none")?null:c);break}if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(4,c));return}}this.g.setO(a,c)},"~S,~N,~S");h(c$,"setFloatProperty",function(a,b){if(!Float.isNaN(b))if("_"==a.charAt(0))this.g.setF(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,
c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 553648128:this.setIntPropertyTok(a,c,A(b));break;default:this.setFloatPropertyTok(a,c,b)}}},"~S,~N");c(c$,"setFloatPropertyTok",function(a,b,c){switch(b){case 570425366:this.ms.setModulation(null,!1,null,!1);this.g.modulationScale=c=Math.max(0.1,c);this.ms.setModulation(null,!0,null,!1);break;case 570425381:this.g.particleRadius=Math.abs(c);break;case 570425356:this.g.drawFontSize=c;break;case 570425358:this.g.exportScale=
c;break;case 570425403:this.g.starWidth=c;break;case 570425369:this.g.multipleBondRadiusFactor=c;break;case 570425370:this.g.multipleBondSpacing=c;break;case 570425393:this.tm.setSlabRange(c);break;case 570425365:this.g.minimizationCriterion=c;break;case 570425359:this.haveDisplay&&this.actionManager.setGestureSwipeFactor(c);break;case 570425367:this.haveDisplay&&this.actionManager.setMouseDragFactor(c);break;case 570425368:this.haveDisplay&&this.actionManager.setMouseWheelFactor(c);break;case 570425408:this.g.strutLengthMaximum=
c;break;case 570425406:this.g.strutDefaultRadius=c;break;case 570425376:this.setSpin("X",A(c));break;case 570425378:this.setSpin("Y",A(c));break;case 570425380:this.setSpin("Z",A(c));break;case 570425371:if(Float.isNaN(c))return;this.setSpin("FPS",A(c));break;case 570425363:this.g.loadAtomDataTolerance=c;break;case 570425360:this.g.hbondsAngleMinimum=c;break;case 570425361:this.g.hbondsDistanceMaximum=c;break;case 570425382:this.g.pointGroupDistanceTolerance=c;break;case 570425384:this.g.pointGroupLinearTolerance=
c;break;case 570425357:this.g.ellipsoidAxisDiameter=c;break;case 570425398:this.setSpin("x",A(c));break;case 570425400:this.setSpin("y",A(c));break;case 570425402:this.setSpin("z",A(c));break;case 570425396:this.setSpin("fps",A(c));break;case 570425352:this.g.defaultDrawArrowScale=c;break;case 570425354:this.g.defaultTranslucent=c;break;case 570425346:this.setAxesScale(c);break;case 570425416:this.tm.setVisualRange(c);this.refresh(1,"set visualRange");break;case 570425372:this.setNavigationDepthPercent(c);
break;case 570425374:this.g.navigationSpeed=c;break;case 570425373:this.tm.setNavigationSlabOffsetPercent(c);break;case 570425350:this.tm.setCameraDepthPercent(c,!1);this.refresh(1,"set cameraDepth");return;case 570425388:this.setRotationRadius(c,!0);return;case 570425362:this.g.hoverDelayMs=A(1E3*c);break;case 570425392:this.g.sheetSmoothing=c;break;case 570425355:c=JV.Viewer.checkFloatRange(c,-10,10);this.g.dipoleScale=c;break;case 570425404:this.tm.setStereoDegrees(c);break;case 1649410049:this.setVectorScale(c);
return;case 570425412:this.setVibrationPeriod(c);return;case 570425414:this.setVibrationScale(c);return;case 570425348:this.setBondTolerance(c);return;case 570425364:this.setMinBondDistance(c);return;case 570425390:this.tm.setScaleAngstromsPerInch(c);break;case 570425394:c=JV.Viewer.checkFloatRange(c,0,10);this.g.solventProbeRadius=c;break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(3,Float.$valueOf(c)));return}}this.g.setF(a,c)},
"~S,~N,~N");h(c$,"setIntProperty",function(a,b){if(-2147483648!=b)if("_"==a.charAt(0))this.g.setI(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 570425344:this.setFloatPropertyTok(a,c,b);break;default:this.setIntPropertyTok(a,c,b)}}},"~S,~N");c(c$,"setIntPropertyTok",function(a,b,c){switch(b){case 553648138:c=0==c?0:1;this.g.bondingVersion=JU.Elements.bondingVersion=
c;break;case 553648137:this.g.celShadingPower=c;this.gdata.setCelPower(c);break;case 553648129:this.gdata.setAmbientOcclusion(c);break;case 553648158:this.g.platformSpeed=Math.min(Math.max(c,0),10);break;case 553648151:this.g.meshScale=c;break;case 553648153:this.g.minPixelSelRadius=c;break;case 553648149:this.g.isosurfacePropertySmoothingPower=c;break;case 553648165:this.g.repaintWaitMs=c;break;case 553648170:this.g.smallMoleculeMaxAtoms=c;break;case 553648152:this.g.minimizationSteps=c;break;case 553648184:this.g.strutSpacing=
c;break;case 553648156:c=JV.Viewer.checkIntRange(c,0,1E3);this.gdata.setPhongExponent(c);break;case 553648146:this.g.helixStep=c;this.ms.setHaveStraightness(!1);break;case 553648144:this.g.dotScale=c;break;case 553648143:this.g.dotDensity=c;break;case 553648140:this.g.delayMaximumMs=c;break;case 553648150:JU.Logger.setLogLevel(c);JU.Logger.info("logging level set to "+c);this.g.setI("logLevel",c);null!=this.eval&&this.eval.setDebugging();return;case 553648134:switch(J.c.AXES.getAxesMode(c)){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,c);return;case 553648182:this.setStrandCount(12,c);return;case 553648180:this.setStrandCount(13,c);return;case 553648155:return;case 536870922:this.g.scriptDelay=c;break;case 553648176:c=0>c?JV.Viewer.checkIntRange(c,-10,-1):JV.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPower(c);break;case 553648172:c=JV.Viewer.checkIntRange(-c,-10,
-1);this.gdata.setSpecularPower(c);break;case 553648136:this.setMarBond(c);return;case 536870924:this.setBooleanPropertyTok(a,b,1==c);return;case 553648174:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPercent(c);break;case 553648142:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setDiffusePercent(c);break;case 553648130:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setAmbientPercent(c);break;case 553648186:this.tm.zDepthToPercent(c);break;case 553648188:this.tm.zSlabToPercent(c);break;
case 554176526:this.tm.depthToPercent(c);break;case 554176565:this.tm.slabToPercent(c);break;case 553648190:this.g.zShadePower=Math.max(c,1);break;case 553648166:this.g.ribbonAspectRatio=c;break;case 553648157:this.g.pickingSpinRate=1>c?1:c;break;case 553648132:this.setAnimationFps(c);return;case 553648154:this.setPercentVdwAtom(c);break;case 553648147:this.g.hermiteLevel=c;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(c));return}}this.g.setI(a,c)},"~S,~N,~N");c$.checkIntRange=c(c$,"checkIntRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");c$.checkFloatRange=c(c$,"checkFloatRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");h(c$,"setBooleanProperty",function(a,b){if("_"==a.charAt(0))this.g.setB(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,"");break;case 553648128:this.setIntPropertyTok(a,c,b?1:0);break;case 570425344:this.setFloatPropertyTok(a,
c,b?1:0);break;default:this.setBooleanPropertyTok(a,c,b)}}},"~S,~B");c(c$,"setBooleanPropertyTok",function(a,b,c){var g=!0;switch(b){case 603979938:this.g.showUnitCellInfo=c;break;case 603979937:this.g.showUnitCellDetails=c;break;case 603979848:g=!1;break;case 603979972:this.g.vectorsCentered=c;break;case 603979811:this.g.backboneSteps=c;break;case 603979819:(this.g.cartoonRibose=c)&&this.getBoolean(603979816)&&this.setBooleanPropertyTok("cartoonBaseEdges",603979816,!1);break;case 603979837:this.g.ellipsoidArrows=
c;break;case 603979967:this.g.translucent=c;break;case 603979818:this.g.cartoonLadders=c;break;case 603979968:b=this.g.twistedSheets;this.g.twistedSheets=c;b!=c&&this.checkCoordinatesChanged();break;case 603979822:this.g.celShading=c;this.gdata.setCel(c);break;case 603979817:this.g.cartoonFancy=c;break;case 603979934:this.g.showTiming=c;break;case 603979973:this.g.vectorSymmetry=c;break;case 603979870:this.g.isosurfaceKey=c;break;case 603979889:this.g.partialDots=c;break;case 603979874:this.g.legacyAutoBonding=
c;break;case 603979826:this.g.defaultStructureDSSP=c;break;case 603979834:this.g.dsspCalcHydrogen=c;break;case 603979782:(this.g.allowModelkit=c)||this.setModelKitMode(!1);break;case 603979883:this.setModelKitMode(c);break;case 603979885:this.g.multiProcessor=c&&1<JV.Viewer.nProcessors;break;case 603979884:this.g.monitorEnergy=c;break;case 603979853:this.g.hbondsRasmol=c;break;case 603979881:this.g.minimizationRefresh=c;break;case 603979882:this.g.minimizationSilent=c;break;case 603979869:c&&(this.$isKiosk=
!0,this.g.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));break;case 603979974:this.g.waitForMoveTo=c;break;case 603979876:this.g.logCommands=!0;break;case 603979877:this.g.logGestures=!0;break;case 603979784:this.g.allowMultiTouch=c;break;case 603979894:this.g.preserveState=c;this.ms.setPreserveState(c);this.undoClear();break;case 603979955:this.g.strutsMultiple=c;break;case 603979842:break;case 603979939:this.g.slabByAtom=c;break;case 603979940:this.g.slabByMolecule=
c;break;case 603979902:this.g.saveProteinStructureState=c;break;case 603979780:this.g.allowGestures=c;break;case 603979868:this.g.imageState=c;break;case 603979970:this.g.useMinimizationThread=c;break;case 603979781:this.g.disablePopupMenu&&(c=!1);this.g.allowKeyStrokes=c;break;case 603979831:this.g.dragSelected=c;this.showSelected=!1;break;case 603979924:this.g.showKeyStrokes=c;break;case 603979844:this.g.fontCaching=c;break;case 603979796:this.g.atomPicking=c;break;case 603979814:this.highlight(null);
this.g.bondPicking=c;break;case 603979906:this.g.selectAllModels=c;break;case 603979880:this.g.messageStyleChime=c;break;case 603979892:this.g.pdbSequential=c;break;case 603979890:this.g.pdbAddHydrogens=c;break;case 603979891:this.g.pdbGetHeader=c;break;case 603979838:this.g.ellipsoidAxes=c;break;case 603979836:this.g.ellipsoidArcs=c;break;case 603979839:this.g.ellipsoidBall=c;break;case 603979840:this.g.ellipsoidDots=c;break;case 603979841:this.g.ellipsoidFill=c;break;case 603979845:this.g.fontScaling=
c;break;case 603979956:this.setSyncTarget(0,c);break;case 603979958:this.setSyncTarget(1,c);break;case 603979976:this.g.wireframeRotation=c;break;case 603979871:this.g.isosurfacePropertySmoothing=c;break;case 603979833:this.g.drawPicking=c;break;case 603979786:case 603979790:case 603979788:this.setAntialias(b,c);break;case 603979944:this.g.smartAromatic=c;break;case 603979794:this.setApplySymmetryToBonds(c);break;case 603979792:this.g.appendNew=c;break;case 603979800:this.g.autoFps=c;break;case 603979971:JU.DF.setUseNumberLocalization(this.g.useNumberLocalization=
c);break;case 603979918:case 1611272202:a="showFrank";this.setFrankOn(c);break;case 1613758488:a="solventProbe";this.g.solventOn=c;break;case 603979948:this.g.solventOn=c;break;case 603979785:this.g.allowRotateSelected=c;break;case 603979783:this.g.allowMoveAtoms=c;this.g.allowRotateSelected=c;this.g.dragSelected=c;this.showSelected=!1;break;case 536870922:this.setIntPropertyTok("showScript",b,c?1:0);return;case 603979778:this.g.allowEmbeddedScripts=c;break;case 603979888:this.g.navigationPeriodic=
c;break;case 603979984:this.tm.setZShadeEnabled(c);return;case 603979832:this.haveDisplay&&(this.g.drawHover=c);break;case 603979887:this.setNavigationMode(c);break;case 603979886:return;case 603979860:this.g.hideNavigationPoint=c;break;case 603979930:this.g.showNavigationPointAlways=c;break;case 603979896:this.setRefreshing(c);break;case 603979872:this.g.justifyMeasurements=c;break;case 603979952:this.g.ssbondsBackbone=c;break;case 603979852:this.g.hbondsBackbone=c;break;case 603979854:this.g.hbondsSolid=
c;break;case 536870924:this.gdata.setSpecular(c);break;case 603979942:this.tm.setSlabEnabled(c);return;case 603979980:this.tm.setZoomEnabled(c);return;case 603979864:this.g.highResolutionFlag=c;break;case 603979966:this.g.traceAlpha=c;break;case 603979983:this.g.zoomLarge=c;this.tm.setZoomHeight(this.g.zoomHeight,c);break;case 603979982:this.g.zoomHeight=c;this.tm.setZoomHeight(c,this.g.zoomLarge);break;case 603979873:J.i18n.GT.setDoTranslate(c);break;case 603979862:this.slm.setHideNotSelected(c);
break;case 603979904:this.setScriptQueue(c);break;case 603979830:this.g.dotSurface=c;break;case 603979829:this.g.dotsSelectedOnly=c;break;case 1611141171:this.setSelectionHalos(c);break;case 603979910:this.g.rasmolHydrogenSetting=c;break;case 603979908:this.g.rasmolHeteroSetting=c;break;case 603979928:this.g.showMultipleBonds=c;break;case 603979920:this.g.showHiddenSelectionHalos=c;break;case 603979975:this.tm.setWindowCentered(c);break;case 603979828:this.g.displayCellParameters=c;break;case 603979960:this.g.testFlag1=
c;break;case 603979962:this.g.testFlag2=c;break;case 603979964:this.g.testFlag3=c;break;case 603979965:this.jmolTest();this.g.testFlag4=c;break;case 603979898:this.g.ribbonBorder=c;break;case 603979816:(this.g.cartoonBaseEdges=c)&&this.getBoolean(603979819)&&this.setBooleanPropertyTok("cartoonRibose",603979819,!1);break;case 603979820:this.g.cartoonRockets=c;break;case 603979900:this.g.rocketBarrels=c;break;case 603979850:this.gdata.setGreyscaleMode(this.g.greyscaleRendering=c);break;case 603979879:this.g.measurementLabels=
c;break;case 603979810:this.setAxesModeMolecular(!c);return;case 603979804:this.setAxesModeMolecular(c);return;case 603979808:this.setAxesModeUnitCell(c);return;case 603979806:this.setAxesOrientationRasmol(c);return;case 603979824:this.setStringPropertyTok("defaultcolorscheme",545259545,c?"rasmol":"jmol");return;case 603979825:this.setDebugScript(c);return;case 603979893:this.setPerspectiveDepth(c);return;case 603979798:this.setAutoBond(c);return;case 603979914:this.setShowAxes(c);return;case 603979916:this.setShowBbcage(c);
return;case 603979922:this.setShowHydrogens(c);return;case 603979926:this.setShowMeasurements(c);return;case 603979936:this.setShowUnitCell(c);return;case 603979812:g=!1;this.g.bondModeOr=c;break;case 603979978:g=!1;this.g.zeroBasedXyzRasmol=c;this.reset(!0);break;case 603979895:g=!1;this.g.rangeSelected=c;break;case 603979878:g=!1;this.g.measureAllModels=c;break;case 603979954:g=!1;this.sm.setAllowStatusReporting(c);break;case 603979823:g=!1;this.g.chainCaseSensitive=c;break;case 603979858:g=!1;
this.g.hideNameInPopup=c;break;case 603979827:g=!1;this.g.disablePopupMenu=c;break;case 603979846:g=!1;this.g.forceAutoBond=c;break;default:if(!this.g.htBooleanParameterFlags.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.getBoolean(c));return}}this.g.setB(a,c);g&&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$,"showParameter",function(a,b,c){c=""+this.g.getParameterEscaped(a,c);(b||0>c.indexOf("<not defined>"))&&this.showString(a+" = "+c,!1)},"~S,~B,~N");
c(c$,"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$,"makeConnections",function(a,b,c,g,f,e,h,k,l,m){this.clearModelDependentObjects();this.clearMinimization();return this.ms.makeConnections(a,b,c,g,f,e,h,k,l,m)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");h(c$,"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$,"getFont3D",function(a,b,c){return this.gdata.getFont3DFSS(a,b,c)},"~S,~S,~N");c(c$,"formatText",function(a){if(0>a.indexOf("@{")&&0>a.indexOf("%{"))return a;var b=a,c=0<=b.indexOf("\\");c&&(b=JU.PT.rep(b,"\\%","\u0001"),b=JU.PT.rep(b,"\\@","\u0002"),c=!b.equals(a));
for(var b=JU.PT.rep(b,"%{","@{"),g;0<=(a=b.indexOf("@{"));){a++;var f=a+1;g=b.length;a=JU.Txt.ichMathTerminator(b,a,g);if(a>=g)return b;g=b.substring(f,a);if(0==g.length)return b;g=this.evaluateExpression(g);r(g,JU.P3)&&(g=JU.Escape.eP(g));b=b.substring(0,f-2)+g.toString()+b.substring(a+1)}c&&(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,c){this.setFloatProperty("stereoDegrees",c);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$,"getProperty",function(a,b,c){if(!"DATA_API".equals(a))return this.getPropertyManager().getProperty(a,b,c);switch("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........".indexOf(b)){case 0:return this.scriptCheckRet(c,
!0);case 20:return null==this.appConsole?"":this.appConsole.getText();case 40:return this.showEditor(c),null;case 60:return this.scriptEditorVisible=c.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:r(c,J.api.JmolAppConsoleInterface)?this.appConsole=c:null!=c&&!c.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=c&&c.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!=c&&c.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=c;case 140:return this.getSpaceGroupInfo(null);case 160:return this.g.disablePopupMenu=
!0,null;case 180:return this.g.defaultDirectory;case 200:return r(c,String)?this.getMenu(c):this.getPopupMenu();case 220:return this.shm.getProperty(c)}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$,
"getModelExtract",function(a,b,c,g){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),b,c,g)},"~O,~B,~B,~S");c(c$,"setTainted",function(a){this.isTainted=this.axesAreTainted=a&&(this.refreshing||this.creatingImage)},"~B");c(c$,"notifyMouseClicked",function(a,b,c,g){var f=JV.binding.Binding.getButtonMods(c),e=JV.binding.Binding.getClickCount(c);this.g.setI("_mouseX",a);this.g.setI("_mouseY",this.dimScreen.height-b);this.g.setI("_mouseAction",c);this.g.setI("_mouseModifiers",f);
this.g.setI("_clickCount",e);return this.sm.setStatusClicked(a,this.dimScreen.height-b,c,e,g)},"~N,~N,~N,~N");c(c$,"checkObjectClicked",function(a,b,c){return this.shm.checkObjectClicked(a,b,c,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,c,g,f){var e=0;switch(this.getPickingMode()){case 2:e=
5;break;case 4:e=22}this.shm.checkObjectDragged(a,b,c,g,f,this.getVisibleFramesBitSet(),e)&&(this.refresh(1,"checkObjectDragged"),22==e&&this.scriptEcho(this.getShapeProperty(22,"command")))},"~N,~N,~N,~N,~N");c(c$,"rotateAxisAngleAtCenter",function(a,b,c,g,f,e,h){(a=this.tm.rotateAxisAngleAtCenter(a,b,c,g,f,e,h))&&this.refresh(-1,"rotateAxisAngleAtCenter");return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,c,g,f,e,h,k,l,m){if(this.isHeadless()){if(e&&
3.4028235E38==f)return!1;e=!1}(a=this.tm.rotateAboutPointsInternal(a,b,c,g,f,!1,e,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$,"startSpinningAxis",function(a,b,c){this.tm.spinOn||this.tm.navOn?(this.tm.setSpinOff(),this.tm.setNavOn(!1)):this.tm.rotateAboutPointsInternal(null,a,b,this.g.pickingSpinRate,3.4028235E38,c,!0,null,!1,null,null,null)},"JU.T3,JU.T3,~B");c(c$,"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 c="";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_"))c='{selected}.label("%{'+b+'}")';else{if(b.equalsIgnoreCase("CML"))return this.getModelCml(this.getAtomBitSet(a),2147483647,!0);c=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")||(c=JU.PT.rep(c,"selected",a));return this.evaluateExpression(c)},"~S,~S");c(c$,"getModelCml",function(a,b,c){return this.getPropertyManager().getModelCml(a,b,c)},"JU.BS,~N,~B");c(c$,"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$,"setAtomProperty",
function(a,b,c,g,f,e,h){1649412120==b&&this.shm.deleteVdwDependentShapes(a);this.clearMinimization();this.ms.setAtomProperty(a,b,c,g,f,e,h);switch(b){case 1112541185:case 1112541186:case 1112541187:case 1112541188:case 1112541189:case 1112541190:case 1112539153:case 1112539154:case 1112539155:case 1087375365:this.refreshMeasures(!0)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"checkCoordinatesChanged",function(){this.ms.recalculatePositionDependentQuantities(null,null);this.refreshMeasures(!0)});c(c$,"setAtomCoords",
function(a,b,c){0!=a.cardinality()&&(this.ms.setAtomCoords(a,b,c),this.checkMinimization(),this.sm.setStatusAtomMoved(a))},"JU.BS,~N,~O");c(c$,"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$,"invertSelected",function(a,b,c,g){var f=this.bsA();0!=f.cardinality()&&(this.ms.invertSelected(a,b,c,g,f),this.checkMinimization(),this.sm.setStatusAtomMoved(f))},"JU.P3,JU.P4,~N,JU.BS");c(c$,"moveAtoms",function(a,b,c,g,f,e,h){0!=e.cardinality()&&(this.ms.moveAtoms(a,b,c,e,g,f,h),this.checkMinimization(),this.sm.setStatusAtomMoved(e))},"JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B");
c(c$,"moveSelected",function(a,b,c,g,f,e,h,k){0!=c&&(-2147483648==g&&(this.rotateBondIndex=-1),this.isJmolDataFrame()||(-2147483648==a?(this.showSelected=!0,this.shm.loadShape(8),this.refresh(6,"moveSelected")):2147483647==a?this.showSelected&&(this.showSelected=!1,this.refresh(6,"moveSelected")):this.movingSelected||(this.movingSelected=!0,this.stopMinimization(),0<=this.rotateBondIndex&&-2147483648!=g?this.actionRotateBond(a,b,g,f):(e=this.setMovableBitSet(e,!k),0!=e.cardinality()&&(h?(g=this.ms.getAtomSetCenter(e),
this.tm.finalizeTransformParameters(),f=this.g.antialiasDisplay?2:1,h=this.tm.transformPt(g),a=-2147483648!=c?JU.P3.new3(h.x,h.y,h.z+c+0.5):JU.P3.new3(h.x+a*f+0.5,h.y+b*f+0.5,h.z),b=new JU.P3,this.tm.unTransformPoint(a,b),b.sub(g),this.setAtomCoordsRelative(b,e)):this.tm.rotateXYBy(a,b,e))),this.refresh(2,""),this.movingSelected=!1)))},"~N,~N,~N,~N,~N,JU.BS,~B,~B");c(c$,"highlightBond",function(a,b){if(!b||this.hoverEnabled){var c=null;if(0<=a){var g=this.ms.bo[a],c=g.getAtomIndex2();if(!this.isAtomAssignable(c))return;
c=JU.BSUtil.newAndSetBit(c);c.set(g.getAtomIndex1())}this.highlight(c);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,c,g){if(!(0>this.rotateBondIndex)){var f=this.bsRotateBranch,e,h;if(null==f){h=this.ms.bo[this.rotateBondIndex];e=h.getAtom1();h=h.getAtom2();this.undoMoveActionClear(e.i,2,!0);c=JU.P3.new3(c,g,w((e.sZ+h.sZ)/2));this.tm.unTransformPoint(c,c);if(1==h.getCovalentBondCount()||c.distance(e)<c.distance(h)&&1!=e.getCovalentBondCount())g=e,e=h,h=g;if(90<JU.Measure.computeAngleABC(c,e,h,!0)||90<JU.Measure.computeAngleABC(c,h,e,!0))f=this.getBranchBitSet(h.i,e.i,!0);if(null!=f){c=0;for(g=e.getBonds().length;0<=
--g;)if(f.get(e.getBondedAtomIndex(g))&&2==++c){f=null;break}}null==f&&(f=this.ms.getMoleculeBitSetForAtom(e.i));this.bsRotateBranch=f;this.rotatePrev1=e.i;this.rotatePrev2=h.i}else e=this.ms.at[this.rotatePrev1],h=this.ms.at[this.rotatePrev2];c=JU.V3.new3(h.sX-e.sX,h.sY-e.sY,0);a=JU.V3.new3(a,b,0);c.cross(c,a);a=(0<c.z?1:-1)*a.length();f=JU.BSUtil.copy(f);f.andNot(this.slm.getMotionFixedAtoms());this.rotateAboutPointsInternal(this.eval,e,h,0,a,!1,f,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,c){var g=null;if(0==a.indexOf("file:"))g=this.getFileAsString(a.substring(5),!1);else if(0!=a.indexOf("data2d_"))return this.sm.functionXY(a,b,c);b=Math.abs(b);c=Math.abs(c);if(null==g){a=this.getDataFloat2D(a);if(null!=a)return a;g=""}a=M(b,c,0);var f=M(b*c,0);JU.Parser.parseStringInfestedFloatArray(g,null,f);for(var e=g=0;g<b;g++)for(var h=0;h<c;h++)a[g][h]=f[e++];return a},"~S,~N,~N");
c(c$,"functionXYZ",function(a,b,c,g){var f=null;if(0==a.indexOf("file:"))f=this.getFileAsString(a.substring(5),!1);else if(0!=a.indexOf("data3d_"))return this.sm.functionXYZ(a,b,c,g);b=Math.abs(b);c=Math.abs(c);g=Math.abs(g);if(null==f){a=this.getDataFloat3D(a);if(null!=a)return a;f=""}a=M(b,c,g,0);var e=M(b*c*g,0);JU.Parser.parseStringInfestedFloatArray(f,null,e);for(var h=f=0;f<b;f++)for(var k=0;k<c;k++)for(var l=0;l<g;l++)a[f][k][l]=e[h++];return a},"~S,~N,~N,~N");h(c$,"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$,"getNMRPredict",function(a){var b=this.getModelExtract("selected",!0,!1,"V2000"),c=b.indexOf("\n"),b="Jmol "+JV.Viewer.version_date+b.substring(c);return a?(this.$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$,"getChemicalInfo",function(a,b){var c=null,g="/";switch(null==b?1073742035:b.tok){case 1073741977:g="I";break;case 1073741978:g="K";break;case 1073742159:g="T";break;case 1073742160:g="S";break;case 1073742035:g="N";break;default:c=JS.SV.sValue(b)}var f=
this.setLoadFormat("_"+a,g,!1);"/"==g&&(f+=JU.PT.rep(c," ","%20"));return this.getFileAsString4(f,-1,!1,!1,!1)},"~S,JS.T");c(c$,"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(D(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 g=new java.util.Hashtable;g.put("fileName",a);g.put("type",b);g.put("text",this.getStateInfo());r(c,Array)?g.put("scripts",c):r(c,JU.Lst)&&g.put("imageData",c);return this.getOutputManager().outputToFile(g)},"~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=C(JU.Elements.elementNumberMax,0);this.userVdws=M(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 g=this.slm.deleteAtoms(a);
this.setTainted(!0);this.sm.modifySend(c,this.ms.at[c].mi,-4,"OK");return g}return this.deleteModels(this.ms.at[c].mi,a)},"JU.BS,~B");c(c$,"deleteModels",function(a,b){this.clearModelDependentObjects();this.sm.modifySend(-1,a,5,"deleting model "+this.getModelNumberDotted(a));this.setCurrentModelIndexClear(0,!1);this.am.setAnimationOn(!1);var c=JU.BSUtil.copy(this.getDeletedAtoms()),g=null==b?JU.BSUtil.newAndSetBit(a):this.ms.getModelBS(b,!1),g=this.ms.deleteModels(g);this.slm.processDeletedModelAtoms(g);
null!=this.eval&&this.eval.deleteAtomsInVariables(g);this.setAnimationRange(0,0);this.clearRepaintManager(-1);this.am.clear();this.am.initializePointers(1);this.setCurrentModelIndexClear(1<this.getModelCount()?-1:0,1<this.getModelCount());this.hoverAtomIndex=-1;this.setFileLoadStatus(J.c.FIL.DELETED,null,null,null,null,null);this.refreshMeasures(!0);null!=c&&g.andNot(c);this.sm.modifySend(-1,a,-5,"OK");return JU.BSUtil.cardinalityOf(g)},"~N,JU.BS");c(c$,"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$,"deleteModelAtoms",function(a,b,c,g){this.sm.modifySend(-1,a,1,"delete atoms "+JU.Escape.eBS(g));JU.BSUtil.deleteBits(this.getFrameOffsets(),g);this.setFrameOffsets(this.getFrameOffsets());this.getDataManager().deleteModelAtoms(b,c,g);this.sm.modifySend(-1,a,-1,"OK")},"~N,~N,~N,JU.BS");c(c$,"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,g){return this.ms.getPointGroupAsString(this.bsA(),a,b,c,g)},"~B,~S,~N,~N");c(c$,"loadImageData",function(a,b,c,g){null==a&&this.scriptEcho(b);null==c?this.setBackgroundImage(null==a?
null:b,a):(this.shm.loadShape(30),this.setShapeProperty(30,"text",b),null!=a&&this.setShapeProperty(30,"image",a));this.isJS&&null!=g&&(g.mustResumeEval=!0,this.eval.resumeEval(g))},"~O,~S,~S,JS.ScriptContext");c(c$,"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(g){}}},"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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