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function(){c$=C(function(){this.id=0;this.info=this.bsAtoms=null;this.size=-1;this.colors=null;this.modelIndex=-2147483648;this.jmolName=null;this.translucency=this.argb=0;this.visible=!0;this.cacheID=this.rd=null;B(this,arguments)},J.adapter.readers.pymol,"JmolObject");F(c$,function(a,b,c,d){this.id=a;this.bsAtoms=c;this.info=d;this.jmolName=b},"~N,~S,JU.BS,~O");e(c$,"offset",function(a,b){if(0<a)switch(-2147483648!=this.modelIndex&&(this.modelIndex+=a),this.id){case 1610625028:case 12294:return;
case 4115:var c=this.info.intValue();0<=c&&(this.info=Integer.$valueOf(a+c));return;case 1073742032:for(var c=this.info.get("frames"),d=c.length;0<=--d;)c[d]+=a;return}if(!(0>=b))if(1060866==this.id)for(d=this.info.values().iterator();d.hasNext()&&((c=d.next())||1);)JU.BSUtil.offset(c,0,b);else null!=this.bsAtoms&&JU.BSUtil.offset(this.bsAtoms,0,b),null!=this.colors&&(c=this.colors[0],d=K(c.length+b,0),System.arraycopy(c,0,d,b,c.length),this.colors[0]=d)},"~N,~N");e(c$,"finalizeObject",function(a,
b,c,d){var f=b.sm,j=null;null!=this.bsAtoms&&(this.modelIndex=this.getModelIndex(b));switch(this.id){case 3145770:f.vwr.displayAtoms(this.bsAtoms,!1,!1,1276118017,!0);return;case 12295:d=f.vwr.getModelUndeletedAtomsBitSet(this.argb);JU.BSUtil.invertInPlace(d,f.vwr.getAtomCount());f.vwr.select(d,!1,0,!0);f.restrictSelected(!1,!0);return;case 1610625028:case 12294:null==this.bsAtoms?(null==this.info&&f.vwr.displayAtoms(null,!0,!1,0,!0),f.vwr.setObjectProp(this.info,this.id)):f.vwr.displayAtoms(this.bsAtoms,
1610625028==this.id,!1,1276118017,!0);return;case 1060866:f.vwr.defineAtomSets(this.info);return;case 1073742032:f.vwr.am.setMovie(this.info);return;case 4115:d=this.info.intValue();0<=d?f.vwr.setCurrentModelIndex(d):(f.vwr.setAnimationRange(-1,-1),f.vwr.setCurrentModelIndex(-1));return;case 1073742139:f.vwr.stm.saveScene(this.jmolName,this.info);f.vwr.stm.saveOrientation(this.jmolName,this.info.get("pymolView"));return;case 5:f.loadShape(this.id);f.setShapePropertyBs(this.id,"textLabels",this.info,
this.bsAtoms);return;case 1678770178:break;case 659488:case 1:if(-1!=this.size){f.setShapeSizeBs(1,this.size,null,this.bsAtoms);var e=f.getShapePropertyIndex(1,"sets",0)[1];a.setUniqueBonds(e,1==this.id);this.size=-1}this.id=1;break;case 1141899265:this.id=0;break;case 0:break;case 10:case 9:f.loadShape(this.id);a=b.getAtoms(3145764,null);JU.BSUtil.andNot(this.bsAtoms,a);break;case 16:f.loadShape(this.id);f.setShapePropertyBs(this.id,"ignore",JU.BSUtil.copyInvert(this.bsAtoms,f.vwr.getAtomCount()),
null);break;default:if(!this.visible)return}switch(this.id){case 23:f.vwr.setCGO(this.info);break;case 16:case 0:case 7:case 20:case 11:case 9:case 10:case 24:s(this.info,Array)&&(f.loadShape(this.id),f.setShapePropertyBs(this.id,"params",this.info,this.bsAtoms));break;case 6:if(0>this.modelIndex)return;f.loadShape(this.id);d=this.info;d.setModelSet(b);j=d.points;for(a=j.size();0<=--a;)j.get(a).mi=this.modelIndex;f.setShapePropertyBs(this.id,"measure",d,this.bsAtoms);return;case 135180:a=null==this.bsAtoms?
this.info:this.jmolName;if(0<=f.getShapeIdFromObjectName(a)){f.vwr.setObjectProp(a,1610625028);return}j=new JU.SB;j.append("isosurface ID ").append(JU.PT.esc(a));0>this.modelIndex&&(this.modelIndex=f.vwr.am.cmi);if(null==this.bsAtoms)j.append(" model ").append(b.am[this.modelIndex].getModelNumberDotted()).append(" color density sigma 1.0 ").append(JU.PT.esc(this.cacheID)).append(" ").append(JU.PT.esc(a)),d&&j.append(";isosurface cache");else{var e=this.info[0],g=this.info[1],g=" only",k=this.info[2],
l=this.info[3].floatValue(),m="";null==e&&(e="mesh nofill",m=" resolution 1.5");a=JU.PT.isOneOf(a,c);c=b.am[this.modelIndex].getModelNumberDotted();b=0>this.size?" sasurface ":" solvent ";j.append(" model ").append(c).append(m).append(" select ").append(JU.Escape.eBS(this.bsAtoms)).append(g).append("").append(b).appendF(Math.abs(this.size/1E3));a||(0==this.argb?j.append(" map property color"):j.append(";color isosurface ").append(JU.Escape.escapeColor(this.argb)));j.append(";isosurface frontOnly ").append(e);
0<this.translucency&&j.append(";color isosurface translucent "+this.translucency);null!=k&&!k.isEmpty()&&j.append(";isosurface slab within "+l+" {"+c+" and "+JU.Escape.eBS(k)+"}");d&&!a&&j.append(";isosurface cache")}break;case 1073742016:j=this.info;a=j.get(j.size()-2).toString();c=j.get(j.size()-1).toString();b=J.adapter.readers.pymol.PyMOLScene.floatAt(J.adapter.readers.pymol.PyMOLScene.listAt(j,3),0);e=J.adapter.readers.pymol.PyMOLScene.floatAt(J.adapter.readers.pymol.PyMOLScene.listAt(j,3),2);
j=new JU.SB;j.append(";isosurface ID ").append(JU.PT.esc(a)).append(" map ").append(JU.PT.esc(this.cacheID)).append(" ").append(JU.PT.esc(c)).append(";color isosurface range "+b+" "+e+";isosurface colorscheme rwb;set isosurfacekey true");0<this.translucency&&j.append(";color isosurface translucent "+this.translucency);d&&j.append(";isosurface cache");break;case 1073742018:this.modelIndex=f.vwr.am.cmi;e=this.info;a=e.get(e.size()-2).toString();j=new JU.SB;j.append("isosurface ID ").append(JU.PT.esc(a)).append(" model ").append(b.am[this.modelIndex].getModelNumberDotted()).append(" color ").append(JU.Escape.escapeColor(this.argb)).append("  ").append(JU.PT.esc(this.cacheID)).append(" ").append(JU.PT.esc(a)).append(" mesh nofill frontonly");
b=J.adapter.readers.pymol.PyMOLScene.floatAt(J.adapter.readers.pymol.PyMOLScene.listAt(J.adapter.readers.pymol.PyMOLScene.listAt(e,2),0),11);e=J.adapter.readers.pymol.PyMOLScene.listAt(J.adapter.readers.pymol.PyMOLScene.listAt(J.adapter.readers.pymol.PyMOLScene.listAt(e,2),0),12);if(0<b){g=new JU.P3;j.append(";isosurface slab within ").appendF(b).append(" [ ");for(b=e.size()-3;0<=b;b-=3)J.adapter.readers.pymol.PyMOLScene.pointAt(e,b,g),j.append(JU.Escape.eP(g));j.append(" ]")}d&&!JU.PT.isOneOf(a,
c)&&j.append(";isosurface cache");j.append(";set meshScale ").appendI(E(this.size/500));break;case 135271429:j=this.info;break;case 1113200654:f.loadShape(this.id=10),f.setShapePropertyBs(this.id,"putty",this.info,this.bsAtoms)}null!=j?f.vwr.runScript(j.toString()):((-1!=this.size||null!=this.rd)&&f.setShapeSizeBs(this.id,this.size,this.rd,this.bsAtoms),0!=this.argb&&f.setShapePropertyBs(this.id,"color",Integer.$valueOf(this.argb),this.bsAtoms),0<this.translucency?(f.setShapePropertyBs(this.id,"translucentLevel",
Float.$valueOf(this.translucency),this.bsAtoms),f.setShapePropertyBs(this.id,"translucency","translucent",this.bsAtoms)):null!=this.colors&&f.setShapePropertyBs(this.id,"colors",this.colors,this.bsAtoms))},"J.adapter.readers.pymol.PyMOLScene,JM.ModelSet,~S,~B");e(c$,"getModelIndex",function(a){if(null==this.bsAtoms)return-1;var b=this.bsAtoms.nextSetBit(0);b>=a.at.length&&System.out.println("PyMOL LOADING ERROR IN MERGE");return 0>b?-1:a.at[b].mi},"JM.ModelSet");e(c$,"setColors",function(a,b){this.colors=
[a,Float.$valueOf(b)]},"~A,~N");e(c$,"setSize",function(a){this.size=n(1E3*a)},"~N")});w("J.adapter.readers.pymol");z(["java.util.Hashtable","JU.BS"],"J.adapter.readers.pymol.PyMOLGroup",null,function(){c$=C(function(){this.object=this.list=this.objectNameID=this.name=null;this.visible=!0;this.occluded=!1;this.bsAtoms=null;this.type=0;this.parent=null;B(this,arguments)},J.adapter.readers.pymol,"PyMOLGroup");G(c$,function(){this.list=new java.util.Hashtable;this.bsAtoms=new JU.BS});F(c$,function(a){this.name=
a},"~S");e(c$,"addList",function(a){null==this.list.get(a.name)&&(this.list.put(a.name,a),a.parent=this)},"J.adapter.readers.pymol.PyMOLGroup");e(c$,"set",function(){});e(c$,"addGroupAtoms",function(a){this.bsAtoms.or(a);null!=this.parent&&this.parent.addGroupAtoms(this.bsAtoms);return this.bsAtoms},"JU.BS");t(c$,"toString",function(){return this.name})});w("J.adapter.readers.pymol");z(["J.api.JmolSceneGenerator","java.util.Hashtable","JU.BS","$.Lst","$.P3"],"J.adapter.readers.pymol.PyMOLScene","java.lang.Boolean $.Character $.Double $.Float JU.AU $.CU $.SB J.adapter.readers.pymol.JmolObject $.PyMOL $.PyMOLGroup J.atomdata.RadiusData J.c.VDW JM.Text JU.BSUtil $.C $.Escape $.Logger $.Point3fi".split(" "),
function(){c$=C(function(){this.vwr=null;this.pymolVersion=0;this.bsUniqueBonds=this.uniqueList=this.uniqueSettings=this.stateSettings=this.htStateSettings=this.settings=this.objectInfo=this.htObjectSettings=this.htMeasures=this.htObjectGroups=this.htObjectAtoms=this.htAtomMap=this.jmolObjects=this.moleculeNames=this.htHiddenObjects=this.htDefinedAtoms=this.htCarveSets=this.bsCartoon=this.objectSettings=this.groups=this.frameObj=this.colixes=this.labels=this.occludedObjects=this.atomColorList=this.ssMapAtom=
this.htSpacefill=this.bsNoSurface=this.bsHydrogen=this.bsLabeled=this.bsNonbonded=this.bsNucleic=this.bsHidden=null;this.transparency=this.stickTranslucency=this.sphereTranslucency=this.sphereScale=this.nonbondedTranslucency=this.nonbondedSize=this.meshWidth=this.labelSize=this.ribbonTranslucency=this.cartoonTranslucency=this.labelColor=this.labelFontId=this.sphereColor=this.ribbonColor=this.cartoonColor=this.surfaceColor=this.surfaceMode=this.dotColor=this.bgRgb=0;this.haveNucleicLadder=this.cartoonRockets=
this.cartoonLadderMode=!1;this.objectJmolName=this.objectNameID=this.objectName=this.labelPosition0=this.labelPosition=null;this.objectType=0;this.bsAtoms=null;this.objectHidden=!1;this.radii=this.newChain=this.sequenceNumbers=this.cartoonTypes=this.uniqueIDs=this.reader=null;this.stateCount=this.baseAtomIndex=this.baseModelIndex=0;this.mepList="";this.haveScenes=this.doCache=!1;this.bsCarve=null;this.solventAccessible=!1;this.bsStickBonds=this.bsLineBonds=null;this.currentAtomSetIndex=this.thisState=
0;this.surfaceInfoName=null;B(this,arguments)},J.adapter.readers.pymol,"PyMOLScene",null,J.api.JmolSceneGenerator);G(c$,function(){this.bsHidden=new JU.BS;this.bsNucleic=new JU.BS;this.bsNonbonded=new JU.BS;this.bsLabeled=new JU.BS;this.bsHydrogen=new JU.BS;this.bsNoSurface=new JU.BS;this.htSpacefill=new java.util.Hashtable;this.ssMapAtom=new java.util.Hashtable;this.atomColorList=new JU.Lst;this.occludedObjects=new java.util.Hashtable;this.labels=new java.util.Hashtable;this.bsCartoon=new JU.BS;
this.htCarveSets=new java.util.Hashtable;this.htDefinedAtoms=new java.util.Hashtable;this.htHiddenObjects=new java.util.Hashtable;this.moleculeNames=new JU.Lst;this.jmolObjects=new JU.Lst;this.htAtomMap=new java.util.Hashtable;this.htObjectAtoms=new java.util.Hashtable;this.htObjectGroups=new java.util.Hashtable;this.htMeasures=new java.util.Hashtable;this.htObjectSettings=new java.util.Hashtable;this.objectInfo=new java.util.Hashtable;this.htStateSettings=new java.util.Hashtable;this.labelPosition0=
new JU.P3;this.bsLineBonds=new JU.BS;this.bsStickBonds=new JU.BS});e(c$,"clearReaderData",function(){this.stateSettings=this.objectSettings=this.atomColorList=this.colixes=this.reader=null;this.haveScenes||(this.bsHidden=this.bsNucleic=this.bsNonbonded=this.bsLabeled=this.bsHydrogen=this.bsNoSurface=this.bsCartoon=this.occludedObjects=this.objectInfo=this.htHiddenObjects=this.htStateSettings=this.htObjectSettings=this.htObjectAtoms=this.htObjectGroups=this.htMeasures=this.htAtomMap=this.htSpacefill=
this.ssMapAtom=this.labels=this.groups=this.settings=null)});e(c$,"setUniqueBond",function(a,b){0>b||(null==this.uniqueList&&(this.uniqueList=new java.util.Hashtable,this.bsUniqueBonds=new JU.BS),this.uniqueList.put(Integer.$valueOf(a),Integer.$valueOf(b)),this.bsUniqueBonds.set(a))},"~N,~N");e(c$,"setStateCount",function(a){this.stateCount=a},"~N");F(c$,function(a,b,c,d,f,j,e,g,k,l){this.reader=a;this.vwr=b;this.settings=c;this.uniqueSettings=d;this.pymolVersion=f;this.haveScenes=j;this.baseAtomIndex=
e;this.baseModelIndex=g;this.doCache=k;this.surfaceInfoName=l+"##JmolSurfaceInfo##";this.setVersionSettings();c.trimToSize();this.bgRgb=J.adapter.readers.pymol.PyMOLScene.colorSetting(J.adapter.readers.pymol.PyMOLScene.listAt(c,6));J.adapter.readers.pymol.PyMOLScene.pointAt(J.adapter.readers.pymol.PyMOLScene.listAt(c,471).get(2),0,this.labelPosition0)},"J.api.PymolAtomReader,JV.Viewer,JU.Lst,java.util.Map,~N,~B,~N,~N,~B,~S");e(c$,"setReaderObjectInfo",function(a,b,c,d,f,j,e){this.objectName=a;this.objectHidden=
d;this.objectNameID=null==this.objectName?null:J.adapter.readers.pymol.PyMOLScene.fixName(this.objectName+e);this.objectSettings=new java.util.Hashtable;this.stateSettings=new java.util.Hashtable;null!=this.objectName&&(this.objectJmolName=J.adapter.readers.pymol.PyMOLScene.getJmolName(a),null!=c&&(this.htObjectGroups.put(this.objectName,c),this.htObjectGroups.put(this.objectNameID,c)),this.objectInfo.put(this.objectName,[this.objectNameID,Integer.$valueOf(b)]),null==this.htObjectSettings.get(this.objectName)&&
(J.adapter.readers.pymol.PyMOLScene.listToSettings(f,this.objectSettings),this.htObjectSettings.put(this.objectName,this.objectSettings)),null==this.htStateSettings.get(this.objectNameID)&&(J.adapter.readers.pymol.PyMOLScene.listToSettings(j,this.stateSettings),this.htStateSettings.put(this.objectNameID,this.stateSettings)));this.getObjectSettings()},"~S,~N,~S,~B,JU.Lst,JU.Lst,~S");c$.listToSettings=e(c$,"listToSettings",function(a,b){if(null!=a&&0!=a.size())for(var c=a.size();0<=--c;){var d=a.get(c);
b.put(d.get(0),d)}},"JU.Lst,java.util.Map");e(c$,"getObjectSettings",function(){this.transparency=this.floatSetting(138);this.dotColor=n(this.floatSetting(210));this.nonbondedSize=this.floatSetting(65);this.nonbondedTranslucency=this.floatSetting(524);this.sphereScale=this.floatSetting(155);this.cartoonColor=n(this.floatSetting(236));this.ribbonColor=n(this.floatSetting(235));this.sphereColor=n(this.floatSetting(173));this.cartoonTranslucency=this.floatSetting(279);this.ribbonTranslucency=this.floatSetting(666);
this.stickTranslucency=this.floatSetting(198);this.sphereTranslucency=this.floatSetting(172);this.cartoonLadderMode=this.booleanSetting(448);this.cartoonRockets=this.booleanSetting(180);this.surfaceMode=n(this.floatSetting(143));this.surfaceColor=n(this.floatSetting(144));this.solventAccessible=this.booleanSetting(338);this.meshWidth=this.floatSetting(90);var a=this.stringSetting(342).trim();0==a.length?this.bsCarve=null:(this.bsCarve=this.htCarveSets.get(a),null==this.bsCarve&&this.htCarveSets.put(a,
this.bsCarve=new JU.BS));this.labelPosition=new JU.P3;try{var b=this.getObjectSetting(471);J.adapter.readers.pymol.PyMOLScene.pointAt(J.adapter.readers.pymol.PyMOLScene.listAt(b,2),0,this.labelPosition)}catch(c){if(!x(c,Exception))throw c;}this.labelPosition.add(this.labelPosition0);this.labelColor=n(this.floatSetting(66));this.labelSize=this.floatSetting(453);this.labelFontId=n(this.floatSetting(328))});e(c$,"setAtomInfo",function(a,b,c,d,f){this.uniqueIDs=a;this.cartoonTypes=b;this.sequenceNumbers=
c;this.newChain=d;this.radii=f},"~A,~A,~A,~A,~A");e(c$,"setSceneObject",function(a,b){this.objectName=a;this.objectType=this.getObjectType(a);this.objectJmolName=J.adapter.readers.pymol.PyMOLScene.getJmolName(a);this.objectNameID=0==b&&0!=this.objectType?this.getObjectID(a):this.objectJmolName+"_"+b;this.bsAtoms=this.htObjectAtoms.get(a);this.objectSettings=this.htObjectSettings.get(a);this.stateSettings=this.htStateSettings.get(a+"_"+b);var c=this.htObjectGroups.get(a);this.objectHidden=this.htHiddenObjects.containsKey(a)||
null!=c&&!this.groups.get(c).visible;this.getObjectSettings()},"~S,~N");e(c$,"buildScene",function(a,b,c,d){var f=b.get(2),j=new java.util.Hashtable;j.put("pymolFrame",f);j.put("generator",this);j.put("name",a);f=J.adapter.readers.pymol.PyMOLScene.listAt(b,0);null!=f&&j.put("pymolView",this.getPymolView(f,!1));f=b.get(1);j.put("visibilities",f);for(var f="_scene_"+a+"_",e=Array(J.adapter.readers.pymol.PyMOL.REP_LIST.length),g=J.adapter.readers.pymol.PyMOL.REP_LIST.length;0<=--g;){var k=c.get(f+J.adapter.readers.pymol.PyMOL.REP_LIST[g]),
k=J.adapter.readers.pymol.PyMOLScene.listAt(k,5);null!=k&&0<k.size()&&(e[g]=J.adapter.readers.pymol.PyMOLScene.listToMap(k))}j.put("moleculeReps",e);f="_!c_"+a+"_";b=J.adapter.readers.pymol.PyMOLScene.listAt(b,3);c=b.size();e=Array(E(c/2));for(k=g=0;g<c;g+=2){var l=J.adapter.readers.pymol.PyMOLScene.intAt(b,g),m=d.get(f+l);null!=m&&1<m.size()&&(e[k++]=[Integer.$valueOf(l),m.get(1)])}j.put("colors",e);this.addJmolObject(1073742139,null,j).jmolName=a},"~S,JU.Lst,java.util.Map,java.util.Map");t(c$,"generateScene",
function(a){JU.Logger.info("PyMOLScene - generateScene "+a.get("name"));this.jmolObjects.clear();this.bsHidden.clearAll();this.occludedObjects.clear();this.htHiddenObjects.clear();this.thisState=a.get("pymolFrame").intValue();this.addJmolObject(4115,null,Integer.$valueOf(this.thisState-1));try{this.generateVisibilities(a.get("visibilities")),this.generateColors(a.get("colors")),this.generateShapes(a.get("moleculeReps")),this.finalizeVisibility(),this.offsetObjects(),this.finalizeObjects()}catch(b){if(x(b,
Exception))JU.Logger.info("PyMOLScene exception "+b),this.vwr.isJS||b.printStackTrace();else throw b;}},"java.util.Map");e(c$,"generateColors",function(a){if(null!=a)for(var b=a.length;0<=--b;){var c=a[b],d=c[0].intValue(),d=J.adapter.readers.pymol.PyMOL.getRGB(d),c=this.getSelectionAtoms(c[1],this.thisState,new JU.BS);this.addJmolObject(1141899265,c,null).argb=d}},"~A");e(c$,"getSelectionAtoms",function(a,b,c){if(null!=a)for(var d=a.size();0<=--d;)this.selectAllAtoms(J.adapter.readers.pymol.PyMOLScene.listAt(a,
d),b,c);return c},"JU.Lst,~N,JU.BS");e(c$,"selectAllAtoms",function(a,b,c){var d=a.get(0);this.setSceneObject(d,b);a=J.adapter.readers.pymol.PyMOLScene.listAt(a,1);var f=0==b?this.stateCount:b;for(b=0==b?1:b;b<=f;b++){var e=this.htAtomMap.get(J.adapter.readers.pymol.PyMOLScene.fixName(d+"_"+b));null!=e&&this.getBsAtoms(a,e,c)}},"JU.Lst,~N,JU.BS");e(c$,"generateVisibilities",function(a){if(null!=a){var b=new JU.BS;this.addJmolObject(12294,null,null);for(var c,d=this.groups.entrySet().iterator();d.hasNext()&&
((c=d.next())||1);)c.getValue().visible=!0;for(d=a.entrySet().iterator();d.hasNext()&&((c=d.next())||1);){var f=c.getKey();if(!f.equals("all")){var e=c.getValue(),h=1==J.adapter.readers.pymol.PyMOLScene.intAt(e,0)?1610625028:12294;12294==h&&this.htHiddenObjects.put(f,Boolean.TRUE);switch(this.getObjectType(f)){case 12:b=this.groups.get(f),null!=b&&(b.visible=1610625028==h)}}}this.setGroupVisibilities();for(d=a.entrySet().iterator();d.hasNext()&&((c=d.next())||1);)if(f=c.getKey(),!f.equals("all")&&
(this.setSceneObject(f,this.thisState),!this.objectHidden)){e=c.getValue();h=this.objectHidden?12294:1610625028;b=null;a=this.objectJmolName;switch(this.objectType){case 0:case 12:continue;case 1:b=this.vwr.getDefinedAtomSet(a);if(0>b.nextSetBit(0))continue;break;case 4:1610625028==h&&(f=this.htMeasures.get(f),null!=f&&this.addMeasurements(f,f[0].points.size(),null,this.getBS(J.adapter.readers.pymol.PyMOLScene.listAt(e,2)),J.adapter.readers.pymol.PyMOLScene.intAt(e,3),null,!0)),a+="_*"}this.addJmolObject(h,
b,a)}}},"java.util.Map");e(c$,"generateShapes",function(a){if(null!=a){this.addJmolObject(12295,null,null).argb=this.thisState-1;for(var b=0;b<this.moleculeNames.size();b++)if(this.setSceneObject(this.moleculeNames.get(b),this.thisState),!this.objectHidden){for(var c=Array(23),d=0;23>d;d++)c[d]=new JU.BS;for(d=a.length;0<=--d;){var f=a[d],f=null==f?null:f.get(this.objectName);null!=f&&this.selectAllAtoms(f,this.thisState,c[d])}this.createShapeObjects(c,!0,-1,-1)}}},"~A");e(c$,"getBS",function(a){for(var b=
new JU.BS,c=a.size();0<=--c;)b.set(J.adapter.readers.pymol.PyMOLScene.intAt(a,c));return b},"JU.Lst");e(c$,"getBsAtoms",function(a,b,c){for(var d=a.size();0<=--d;)c.set(b[J.adapter.readers.pymol.PyMOLScene.intAt(a,d)])},"JU.Lst,~A,JU.BS");c$.getColorPt=e(c$,"getColorPt",function(a){return s(a,Integer)?a.intValue():JU.CU.colorPtToFFRGB(J.adapter.readers.pymol.PyMOLScene.pointAt(a,0,J.adapter.readers.pymol.PyMOLScene.ptTemp))},"~O");c$.intAt=e(c$,"intAt",function(a,b){return a.get(b).intValue()},"JU.Lst,~N");
c$.colorSetting=e(c$,"colorSetting",function(a){return J.adapter.readers.pymol.PyMOLScene.getColorPt(a.get(2))},"JU.Lst");e(c$,"setReaderObjects",function(){this.clearReaderData();this.finalizeObjects();this.haveScenes||(this.bsUniqueBonds=this.bsStickBonds=this.bsLineBonds=this.uniqueSettings=null)});e(c$,"finalizeObjects",function(){this.vwr.setStringProperty("defaults","PyMOL");for(var a=0;a<this.jmolObjects.size();a++)try{this.jmolObjects.get(a).finalizeObject(this,this.vwr.ms,this.mepList,this.doCache)}catch(b){if(x(b,
Exception))System.out.println(b),this.vwr.isJS||b.printStackTrace();else throw b;}this.finalizeUniqueBonds();this.jmolObjects.clear()});e(c$,"offsetObjects",function(){for(var a=0;a<this.jmolObjects.size();a++)this.jmolObjects.get(a).offset(this.baseModelIndex,this.baseAtomIndex)});e(c$,"getJmolObject",function(a,b,c){0<this.baseAtomIndex&&(b=JU.BSUtil.copy(b));return new J.adapter.readers.pymol.JmolObject(a,this.objectNameID,b,c)},"~N,JU.BS,~O");e(c$,"addJmolObject",function(a,b,c){return this.addObject(this.getJmolObject(a,
b,c))},"~N,JU.BS,~O");e(c$,"getPymolView",function(a,b){for(var c=y(21,0),d=this.booleanSetting(84),f=this.booleanSetting(88),e=this.floatSetting(192),h=0,g=0,k=0;3>k;k++)c[h++]=J.adapter.readers.pymol.PyMOLScene.floatAt(a,g++);b&&g++;for(k=0;3>k;k++)c[h++]=J.adapter.readers.pymol.PyMOLScene.floatAt(a,g++);b&&g++;for(k=0;3>k;k++)c[h++]=J.adapter.readers.pymol.PyMOLScene.floatAt(a,g++);b&&(g+=5);for(k=0;8>k;k++)c[h++]=J.adapter.readers.pymol.PyMOLScene.floatAt(a,g++);g=this.booleanSetting(23);k=this.floatSetting(152);
c[h++]=g?k:-k;c[h++]=d?1:0;c[h++]=f?1:0;c[h++]=e;return c},"JU.Lst,~B");e(c$,"globalSetting",function(a){try{return this.settings.get(a).get(2).floatValue()}catch(b){if(x(b,Exception))return J.adapter.readers.pymol.PyMOL.getDefaultSetting(a,this.pymolVersion);throw b;}},"~N");e(c$,"addGroup",function(a,b,c){null==this.groups&&(this.groups=new java.util.Hashtable);var d=this.getGroup(this.objectName);d.object=a;d.objectNameID=this.objectNameID;d.visible=!this.objectHidden;d.type=c;d.visible||(this.occludedObjects.put(this.objectNameID,
Boolean.TRUE),this.htHiddenObjects.put(this.objectName,Boolean.TRUE));null!=b&&0!=b.length&&this.getGroup(b).addList(d);return d},"JU.Lst,~S,~N");e(c$,"getGroup",function(a){var b=this.groups.get(a);null==b&&(this.groups.put(a,b=new J.adapter.readers.pymol.PyMOLGroup(a)),this.defineAtoms(a,b.bsAtoms));return b},"~S");e(c$,"finalizeVisibility",function(){this.setGroupVisibilities();if(null!=this.groups)for(var a=this.jmolObjects.size();0<=--a;){var b=this.jmolObjects.get(a);null!=b.jmolName&&this.occludedObjects.containsKey(b.jmolName)&&
(b.visible=!1)}this.bsHidden.isEmpty()||this.addJmolObject(3145770,this.bsHidden,null)});e(c$,"setCarveSets",function(a){if(!this.htCarveSets.isEmpty())for(var b,c=this.htCarveSets.entrySet().iterator();c.hasNext()&&((b=c.next())||1);)this.getSelectionAtoms(J.adapter.readers.pymol.PyMOLScene.listAt(a.get(b.getKey()),5),0,b.getValue())},"java.util.Map");e(c$,"setGroupVisibilities",function(){if(null!=this.groups){for(var a=this.groups.values(),b=new JU.BS,c,a=a.iterator();a.hasNext()&&((c=a.next())||
1);)b.or(c.bsAtoms),null==c.parent?this.setGroupVisible(c,!0):c.list.isEmpty()&&c.addGroupAtoms(new JU.BS);this.defineAtoms("all",b)}});e(c$,"defineAtoms",function(a,b){this.htDefinedAtoms.put(J.adapter.readers.pymol.PyMOLScene.getJmolName(a),b)},"~S,JU.BS");c$.getJmolName=e(c$,"getJmolName",function(a){return"__"+J.adapter.readers.pymol.PyMOLScene.fixName(a)},"~S");e(c$,"createShapeObjects",function(a,b,c,d){if(0<=d){this.bsAtoms=JU.BSUtil.newBitSet2(c,d);var f;f=this.addJmolObject(1141899265,this.bsAtoms,
null);for(this.colixes=JU.AU.ensureLengthShort(this.colixes,d);--d>=c;)this.colixes[d]=this.atomColorList.get(d).intValue();f.setColors(this.colixes,0);f.setSize(0);f=this.addJmolObject(1,this.bsAtoms,null);f.setSize(0)}this.createShapeObject(7,a[7]);this.createShapeObject(0,a[0]);this.fixReps(a);this.createSpacefillObjects();for(d=0;23>d;d++)switch(d){case 7:case 0:continue;case 8:case 2:if(!b)continue;switch(this.surfaceMode){case 0:a[d].andNot(this.bsNoSurface);break;case 2:case 4:a[d].andNot(this.bsHydrogen);
break}default:this.createShapeObject(d,a[d])}this.bsAtoms=null},"~A,~B,~N,~N");e(c$,"addLabel",function(a,b,c,d,f){var e=n(this.getUniqueFloatDef(b,66,this.labelColor));-7==e||-6==e||0>e&&(e=c);c=y(7,0);if(null==d)d=this.getUniquePoint(b,471,null),null==d?d=this.labelPosition:d.add(this.labelPosition),J.adapter.readers.pymol.PyMOLScene.setLabelPosition(d,c);else for(b=0;7>b;b++)c[b]=J.adapter.readers.pymol.PyMOLScene.floatAt(d,b);this.labels.put(Integer.$valueOf(a),this.newTextLabel(f,c,e,this.labelFontId,
this.labelSize))},"~N,~N,~N,JU.Lst,~S");e(c$,"getUniqueFloatDef",function(a,b,c){var d;if(0>=a||null==(d=this.uniqueSettings.get(Integer.$valueOf((a<<10)+b))))return c;c=d.get(2).floatValue();JU.Logger.debugging&&JU.Logger.debug("Pymol unique setting for "+a+": ["+b+"] = "+c);return c},"~N,~N,~N");e(c$,"getUniquePoint",function(a,b,c){var d;if(0>=a||null==(d=this.uniqueSettings.get(Integer.$valueOf((a<<10)+b))))return c;c=new JU.P3;J.adapter.readers.pymol.PyMOLScene.pointAt(d.get(2),0,c);JU.Logger.info("Pymol unique setting for "+
a+": "+b+" = "+c);return c},"~N,~N,JU.P3");e(c$,"getObjectSetting",function(a){return this.objectSettings.get(Integer.$valueOf(a))},"~N");e(c$,"booleanSetting",function(a){return 0!=this.floatSetting(a)},"~N");e(c$,"floatSetting",function(a){try{return this.getSetting(a).get(2).floatValue()}catch(b){if(x(b,Exception))return J.adapter.readers.pymol.PyMOL.getDefaultSetting(a,this.pymolVersion);throw b;}},"~N");e(c$,"stringSetting",function(a){try{return this.getSetting(a).get(2).toString()}catch(b){if(x(b,
Exception))return null;throw b;}},"~N");e(c$,"getSetting",function(a){var b=null;null!=this.stateSettings&&(b=this.stateSettings.get(Integer.$valueOf(a)));null==b&&null!=this.objectSettings&&(b=this.objectSettings.get(Integer.$valueOf(a)));null==b&&(b=this.settings.get(a));return b},"~N");c$.pointAt=e(c$,"pointAt",function(a,b,c){c.set(J.adapter.readers.pymol.PyMOLScene.floatAt(a,b++),J.adapter.readers.pymol.PyMOLScene.floatAt(a,b++),J.adapter.readers.pymol.PyMOLScene.floatAt(a,b));return c},"JU.Lst,~N,JU.P3");
c$.floatAt=e(c$,"floatAt",function(a,b){return null==a?0:a.get(b).floatValue()},"JU.Lst,~N");c$.floatsAt=e(c$,"floatsAt",function(a,b,c,d){if(null==a)return null;for(var f=0;f<d;f++)c[f]=J.adapter.readers.pymol.PyMOLScene.floatAt(a,b++);return c},"JU.Lst,~N,~A,~N");c$.listAt=e(c$,"listAt",function(a,b){if(null==a||b>=a.size())return null;var c=a.get(b);return s(c,JU.Lst)?c:null},"JU.Lst,~N");c$.setLabelPosition=e(c$,"setLabelPosition",function(a,b){b[0]=1;b[1]=a.x;b[2]=a.y;b[3]=a.z;return b},"JU.P3,~A");
e(c$,"addCGO",function(a,b){a.addLast(this.objectName);var c=this.addJmolObject(23,null,a);c.argb=b;c.translucency=this.floatSetting(441);return J.adapter.readers.pymol.PyMOLScene.fixName(this.objectName)},"JU.Lst,~N");e(c$,"addMeasurements",function(a,b,c,d,f,e,h){var g=null==a,k=g?E(E(c.size()/3)/b):a.length;if(0==k)return!1;h=h&&d.get(3);var l=d.get(10);d=this.floatSetting(107)/20;0==d&&(d=0.05);l||(d=-5E-4);0>f&&(f=n(this.floatSetting(574)));l=J.adapter.readers.pymol.PyMOL.getRGB(f);l=JU.C.getColix(l);
f=0>this.labelColor?f:this.labelColor;g&&(a=Array(k),this.htMeasures.put(this.objectName,a));for(var m=JU.BSUtil.newAndSetBit(0),u=0,q=0;u<k;u++){var p,r;if(g){p=new JU.Lst;for(r=0;r<b;r++,q+=3)p.addLast(J.adapter.readers.pymol.PyMOLScene.pointAt(c,q,new JU.Point3fi));r=J.adapter.readers.pymol.PyMOLScene.floatsAt(J.adapter.readers.pymol.PyMOLScene.listAt(e,u),0,y(7,0),7);null==r&&(r=J.adapter.readers.pymol.PyMOLScene.setLabelPosition(this.labelPosition,y(7,0)));p=a[u]=this.vwr.newMeasurementData(this.objectNameID+
"_"+(u+1),p);p.note=this.objectName}else p=a[u],r=p.text.pymolOffset;var v=n(this.floatSetting(J.adapter.readers.pymol.PyMOLScene.MEAS_DIGITS[b-2])),v=b+": "+(h?"%0."+(0>v?1:v)+"VALUE":"");r=this.newTextLabel(v,r,f,n(this.floatSetting(328)),this.floatSetting(453));p.set(1060866,null,null,v,"angstroms",null,!1,!1,null,!1,n(2E3*d),l,r);this.addJmolObject(6,m,p)}return!0},"~A,~N,JU.Lst,JU.BS,~N,JU.Lst,~B");e(c$,"getViewScript",function(a){var b=new JU.SB;a=this.getPymolView(a,!0);b.append(";set translucent "+
(2!=this.globalSetting(213))+";set zshadePower 1;set traceAlpha "+(0!=this.globalSetting(111)));var c=this.cartoonRockets;b.append(";set cartoonRockets "+c);c&&b.append(";set rocketBarrels "+c);b.append(";set cartoonLadders "+this.haveNucleicLadder);b.append(";set ribbonBorder "+(0!=this.globalSetting(118)));b.append(";set cartoonFancy "+(0==this.globalSetting(118)));c="000000"+Integer.toHexString(this.bgRgb&16777215);c="[x"+c.substring(c.length-6)+"]";b.append(";background "+c);b.append(";moveto 0 PyMOL "+
JU.Escape.eAF(a));b.append(";save orientation 'default';");return b},"JU.Lst");e(c$,"getColix",function(a,b){var c=-7==a?8==JU.C.getBgContrast(this.bgRgb)?4:8:-6==a?JU.C.getBgContrast(this.bgRgb):JU.C.getColixO(Integer.$valueOf(J.adapter.readers.pymol.PyMOL.getRGB(a)));return JU.C.getColixTranslucent3(c,0<b,b)},"~N,~N");c$.colorSettingClamped=e(c$,"colorSettingClamped",function(a){return 6>a.size()||0==J.adapter.readers.pymol.PyMOLScene.intAt(a,4)?J.adapter.readers.pymol.PyMOLScene.colorSetting(a):
J.adapter.readers.pymol.PyMOLScene.getColorPt(a.get(5))},"JU.Lst");e(c$,"setAtomColor",function(a){this.atomColorList.addLast(Integer.$valueOf(this.getColix(a,0)))},"~N");e(c$,"setFrameObject",function(a,b){null!=b?this.frameObj=this.getJmolObject(a,null,b):null!=this.frameObj&&(this.frameObj.finalizeObject(this,this.vwr.ms,null,!1),this.frameObj=null)},"~N,~O");c$.fixName=e(c$,"fixName",function(a){a=a.toLowerCase().toCharArray();for(var b=a.length;0<=--b;)Character.isLetterOrDigit(a[b])||(a[b]=
"_");return String.valueOf(a)},"~S");e(c$,"getObjectID",function(a){return this.objectInfo.get(a)[0]},"~S");e(c$,"getObjectType",function(a){a=this.objectInfo.get(a);return null==a?0:a[1].intValue()},"~S");e(c$,"setAtomMap",function(a,b){this.htAtomMap.put(this.objectNameID,a);var c=this.htDefinedAtoms.get(this.objectJmolName);null==c&&(c=JU.BS.newN(b+a.length),JU.Logger.info("PyMOL molecule "+this.objectName),this.htDefinedAtoms.put(this.objectJmolName,c),this.htObjectAtoms.put(this.objectName,c),
this.moleculeNames.addLast(this.objectName));return c},"~A,~N");e(c$,"newTextLabel",function(a,b,c,d,f){var e;switch(d){default:case 11:case 12:case 13:case 14:e="SansSerif";break;case 0:case 1:e="Monospaced";break;case 9:case 10:case 15:case 16:case 17:case 18:e="Serif"}switch(d){default:d="Plain";break;case 6:case 12:case 16:case 17:d="Italic";break;case 7:case 10:case 13:d="Bold";break;case 8:case 14:case 18:d="BoldItalic"}f=this.vwr.getFont3D(e,d,0==f?12:1*f);return JM.Text.newLabel(this.vwr.gdata,
f,a,this.getColix(c,0),0,0,0,b)},"~S,~A,~N,~N,~N");e(c$,"setVersionSettings",function(){100>this.pymolVersion&&(this.addSetting(550,2,Integer.$valueOf(0)),this.addSetting(529,2,Integer.$valueOf(2)),this.addSetting(471,4,[1,1,0]),99>this.pymolVersion&&(this.addSetting(448,2,Integer.$valueOf(0)),this.addSetting(431,2,Integer.$valueOf(0)),this.addSetting(361,2,Integer.$valueOf(1))))});e(c$,"addSetting",function(a,b,c){var d=this.settings.size();if(d<=a)for(var f=a+1;--f>=d;)this.settings.addLast(null);
if(4==b){var d=c,e;c=e=new JU.Lst;for(f=0;3>f;f++)e.addLast(Double.$valueOf(d[f]))}f=new JU.Lst;f.addLast(Integer.$valueOf(a));f.addLast(Integer.$valueOf(b));f.addLast(c);this.settings.set(a,f)},"~N,~N,~O");e(c$,"fixReps",function(a){this.htSpacefill.clear();this.bsCartoon.clearAll();for(var b=this.bsAtoms.nextSetBit(0);0<=b;b=this.bsAtoms.nextSetBit(b+1)){var c=0,d=null==this.reader?this.uniqueIDs[b]:this.reader.getUniqueID(b);a[1].get(b)?c=(null==this.reader?this.radii[b]:this.reader.getVDW(b))*
this.getUniqueFloatDef(d,155,this.sphereScale):a[4].get(b)&&(c=this.nonbondedSize);0!=c&&(c=Float.$valueOf(c),d=this.htSpacefill.get(c),null==d&&this.htSpacefill.put(c,d=new JU.BS),d.set(b));c=null==this.reader?this.cartoonTypes[b]:this.reader.getCartoonType(b);if(a[5].get(b))switch(c){case 1:case 4:a[21].set(b);case -1:a[5].clear(b);this.bsCartoon.clear(b);break;case 7:a[22].set(b);a[5].clear(b);this.bsCartoon.clear(b);break;default:this.bsCartoon.set(b)}}a[5].and(this.bsCartoon);this.cleanSingletons(a[5]);
this.cleanSingletons(a[6]);this.cleanSingletons(a[21]);this.cleanSingletons(a[22]);this.bsCartoon.and(a[5])},"~A");e(c$,"cleanSingletons",function(a){if(!a.isEmpty()){a.and(this.bsAtoms);for(var b=new JU.BS,c=a.length(),d=0;;){for(var f=0,e=0,h=-2147483648,g=-2147483648,k=-2147483648;f<c;f++)(0>h||(null==this.reader?this.newChain[f]:this.reader.compareAtoms(h,f)))&&e++,k=null==this.reader?this.sequenceNumbers[f]:this.reader.getSequenceNumber(f),k!=g&&(g=k,e++),0==d?a.get(f)&&b.set(e):b.get(e)||a.clear(f),
h=f;if(2==++d)break;e=new JU.BS;for(f=b.nextSetBit(0);0<=f;f=b.nextSetBit(f+1))!b.get(f-1)&&!b.get(f+1)&&e.set(f);b.andNot(e)}}},"JU.BS");e(c$,"createShapeObject",function(a,b){if(!b.isEmpty()){var c=null;switch(a){case 11:b.and(this.bsNonbonded);if(b.isEmpty())break;this.setUniqueObjects(7,b,0,0,524,this.nonbondedTranslucency,0,this.nonbondedSize,0.5);break;case 4:case 1:this.setUniqueObjects(0,b,173,this.sphereColor,172,this.sphereTranslucency,155,this.sphereScale,1);break;case 19:var c=this.floatSetting(571),
d=n(this.floatSetting(570)),f=this.floatSetting(569);this.setUniqueObjects(20,b,570,d,571,c,569,f,50);break;case 9:this.setUniqueObjects(16,b,210,this.dotColor,0,0,155,this.sphereScale,1);break;case 2:c=this.floatSetting(344);c=this.addJmolObject(135180,b,[this.booleanSetting(156)?"FULLYLIT":"FRONTLIT",3==this.surfaceMode||4==this.surfaceMode?" only":"",this.bsCarve,Float.$valueOf(c)]);c.setSize(this.floatSetting(4)*(this.solventAccessible?-1:1));c.translucency=this.transparency;0<=this.surfaceColor&&
(c.argb=J.adapter.readers.pymol.PyMOL.getRGB(this.surfaceColor));c.modelIndex=this.currentAtomSetIndex;c.cacheID=this.surfaceInfoName;this.setUniqueObjects(24,b,144,this.surfaceColor,138,this.transparency,0,0,0);break;case 8:c=this.addJmolObject(135180,b,null);c.setSize(this.floatSetting(4));c.translucency=this.transparency;this.setUniqueObjects(24,b,144,this.surfaceColor,138,this.transparency,0,0,0);break;case 3:b.and(this.bsLabeled);if(b.isEmpty())break;this.addJmolObject(5,b,this.labels);break;
case 7:c=this.addJmolObject(659488,b,null);c.setSize(this.floatSetting(44)/15);d=n(this.floatSetting(526));0<=d&&(c.argb=J.adapter.readers.pymol.PyMOL.getRGB(d));break;case 0:c=this.addJmolObject(1,b,null);c.setSize(2*this.floatSetting(21));c.translucency=this.stickTranslucency;d=n(this.floatSetting(376));0<=d&&(c.argb=J.adapter.readers.pymol.PyMOL.getRGB(d));break;case 5:this.createCartoonObject("H",this.cartoonRockets?181:100);this.createCartoonObject("S",96);this.createCartoonObject("L",92);this.createCartoonObject(" ",
92);break;case 22:this.createPuttyObject(b);break;case 21:this.createTraceObject(b);break;case 6:this.createRibbonObject(b);break;default:JU.Logger.error("Unprocessed representation type "+a)}}},"~N,JU.BS");e(c$,"setUniqueObjects",function(a,b,c,d,f,e,h,g,k){for(var l=b.cardinality(),m=0==c?null:K(l,0),u=0==f?null:y(l,0),l=y(l,0),q=0,p=b.nextSetBit(0);0<=p;p=b.nextSetBit(p+1),q++){var r=null==this.reader?this.uniqueIDs[p]:this.reader.getUniqueID(p);if(null!=m){var v=n(this.getUniqueFloatDef(r,c,d));
0<v&&(m[q]=this.getColix(v,0))}null!=u&&(u[q]=this.getUniqueFloatDef(r,f,e));l[q]=this.getUniqueFloatDef(r,h,g)*k}return this.addJmolObject(a,b,[m,u,l])},"~N,JU.BS,~N,~N,~N,~N,~N,~N,~N");e(c$,"createSpacefillObjects",function(){for(var a,b=this.htSpacefill.entrySet().iterator();b.hasNext()&&((a=b.next())||1);){var c=a.getKey().floatValue(),d=a.getValue();this.addJmolObject(1141899265,d,null).rd=new J.atomdata.RadiusData(null,c,J.atomdata.RadiusData.EnumType.ABSOLUTE,J.c.VDW.AUTO)}this.htSpacefill.clear()});
e(c$,"createTraceObject",function(a){this.checkNucleicObject(a,!0);if(!a.isEmpty()){var b=this.floatSetting(103);a=this.setUniqueObjects(10,a,236,this.cartoonColor,0,0,0,0,0);a.setSize(2*b);a.translucency=this.cartoonTranslucency}},"JU.BS");e(c$,"checkNucleicObject",function(a,b){var c,d=JU.BSUtil.copy(this.bsNucleic);d.and(a);d.isEmpty()||(b&&this.cartoonLadderMode&&(this.haveNucleicLadder=!0),c=this.addJmolObject(11,d,null),c.translucency=this.cartoonTranslucency,c.setSize(2*this.floatSetting(103)),
a.andNot(d))},"JU.BS,~B");e(c$,"createPuttyObject",function(a){var b=[this.floatSetting(378),this.floatSetting(377),this.floatSetting(382),this.floatSetting(379),this.floatSetting(380),this.floatSetting(381),this.floatSetting(581)];this.addJmolObject(1113200654,a,b).translucency=this.cartoonTranslucency},"JU.BS");e(c$,"createRibbonObject",function(a){var b=1<this.floatSetting(19),c=2*this.floatSetting(20),d=this.floatSetting(327);0==c&&(c=0.1*this.floatSetting(106)*(b?1:1>=d?0.5:d));a=this.setUniqueObjects(b?
10:9,a,235,this.ribbonColor,0,0,0,0,0);a.setSize(c);a.translucency=this.ribbonTranslucency},"JU.BS");e(c$,"createCartoonObject",function(a,b){var c=JU.BSUtil.copy(this.ssMapAtom.get(a));if(null!=c&&(c.and(this.bsCartoon),!c.isEmpty())){if(a.equals(" ")&&(this.checkNucleicObject(c,!1),c.isEmpty()))return;c=this.setUniqueObjects(11,c,236,this.cartoonColor,0,0,0,0,0);c.setSize(2*this.floatSetting(b));c.translucency=this.cartoonTranslucency}},"~S,~N");e(c$,"addObject",function(a){this.jmolObjects.addLast(a);
return a},"J.adapter.readers.pymol.JmolObject");e(c$,"setGroupVisible",function(a,b){var c=b&&a.visible;if(!c){a.visible=!1;this.occludedObjects.put(a.objectNameID,Boolean.TRUE);this.htHiddenObjects.put(a.name,Boolean.TRUE);switch(a.type){case 1:this.bsHidden.or(a.bsAtoms);break;default:a.occluded=!0}for(var d,f=a.list.values().iterator();f.hasNext()&&((d=f.next())||1);)this.setGroupVisible(d,c)}},"J.adapter.readers.pymol.PyMOLGroup,~B");e(c$,"getSSMapAtom",function(a){var b=this.ssMapAtom.get(a);
null==b&&this.ssMapAtom.put(a,b=new JU.BS);return b},"~S");c$.listToMap=e(c$,"listToMap",function(a){for(var b=new java.util.Hashtable,c=a.size();0<=--c;){var d=J.adapter.readers.pymol.PyMOLScene.listAt(a,c);null!=d&&0<d.size()&&b.put(d.get(0),d)}return b},"JU.Lst");e(c$,"setAtomDefs",function(){this.setGroupVisibilities();for(var a=new java.util.Hashtable,b,c=this.htDefinedAtoms.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var d=b.getValue();d.isEmpty()||a.put(b.getKey(),d)}this.addJmolObject(1060866,
null,a);return a});e(c$,"needSelections",function(){return this.haveScenes||!this.htCarveSets.isEmpty()});e(c$,"setUniqueBonds",function(a,b){b?(this.bsStickBonds.or(a),this.bsStickBonds.andNot(this.bsLineBonds)):(this.bsLineBonds.or(a),this.bsLineBonds.andNot(this.bsStickBonds))},"JU.BS,~B");e(c$,"finalizeUniqueBonds",function(){if(null!=this.uniqueList)for(var a=this.vwr.getBondCount(),b=this.vwr.ms.bo,c=this.bsUniqueBonds.nextSetBit(0);0<=c;c=this.bsUniqueBonds.nextSetBit(c+1)){var d=NaN,f=this.uniqueList.get(Integer.$valueOf(c)).intValue();
this.bsLineBonds.get(c)?d=this.getUniqueFloatDef(f,44,NaN)/30:this.bsStickBonds.get(c)&&(d=this.getUniqueFloatDef(f,21,NaN));var e=n(this.getUniqueFloatDef(f,376,2147483647));2147483647!=e&&(e=J.adapter.readers.pymol.PyMOL.getRGB(e));var h=this.getUniqueFloatDef(f,64,NaN),f=this.getUniqueFloatDef(f,198,NaN);if(0>c||c>=a)break;this.setBondParameters(b[c],this.thisState-1,d,h,e,f)}});e(c$,"setBondParameters",function(a,b,c,d,f,e){0<=b&&a.atom1.mi!=b||(Float.isNaN(c)||(a.mad=M(2E3*c)),b=a.colix,2147483647!=
f&&(b=JU.C.getColix(f)),Float.isNaN(e)?a.colix!=b&&(a.colix=JU.C.copyColixTranslucency(a.colix,b)):a.colix=JU.C.getColixTranslucent3(b,0!=e,e),1==d?a.order|=98304:0==d&&(a.order|=65536))},"JM.Bond,~N,~N,~N,~N,~N");e(c$,"addMesh",function(a,b,c,d){a=this.addJmolObject(a,null,b);this.setSceneObject(c,-1);c=n(this.floatSetting(146));0>c&&(c=J.adapter.readers.pymol.PyMOLScene.intAt(J.adapter.readers.pymol.PyMOLScene.listAt(b,0),2));d||(a.setSize(this.meshWidth),a.argb=J.adapter.readers.pymol.PyMOL.getRGB(c));
a.translucency=this.transparency;a.cacheID=this.surfaceInfoName},"~N,JU.Lst,~S,~B");e(c$,"addIsosurface",function(a){a=this.addJmolObject(135180,null,a);a.cacheID=this.surfaceInfoName;return a},"~S");c$.ptTemp=c$.prototype.ptTemp=new JU.P3;A(c$,"MEAS_DIGITS",[530,531,532])});w("J.adapter.readers.pymol");z(["J.adapter.readers.pdb.PdbReader","J.api.PymolAtomReader","JU.BS","$.P3"],"J.adapter.readers.pymol.PyMOLReader","java.lang.Boolean java.util.Hashtable JU.Lst $.PT $.V3 J.adapter.readers.pymol.PickleReader $.PyMOL $.PyMOLScene J.adapter.smarter.Atom $.Bond $.Structure J.c.STR JU.BSUtil $.BoxInfo $.Logger".split(" "),
function(){c$=C(function(){this.allowSurface=!0;this.sourcePNGJ=this.isStateScript=this.doCache=this.doResize=!1;this.structureCount=this.stateCount=this.$ac=this.ac0=0;this.isHidden=!1;this.xyzMax=this.xyzMin=this.pymolScene=this.ssMapSeq=this.atomMap=this.bsBytesExcluded=this.bsStructureDefined=null;this.nModels=0;this.logging=!1;this.reps=null;this.isMovie=!1;this.pymolFrame=0;this.allStates=!1;this.pymolVersion=this.totalAtomCount=0;this.trajectoryStep=null;this.trajectoryPtr=0;this.mapObjects=
this.volumeData=this.objectName=null;this.haveMeasurements=!1;this.atoms=this.uniqueSettings=this.frames=null;this.haveScenes=!1;this.baseModelIndex=this.$baseAtomIndex=0;this.sceneOrder=null;this.bondCount=0;B(this,arguments)},J.adapter.readers.pymol,"PyMOLReader",J.adapter.readers.pdb.PdbReader,J.api.PymolAtomReader);G(c$,function(){this.bsStructureDefined=new JU.BS;this.xyzMin=JU.P3.new3(1E6,1E6,1E6);this.xyzMax=JU.P3.new3(-1E6,-1E6,-1E6);this.reps=Array(23)});t(c$,"setup",function(a,b,c){this.isBinary=
this.mustFinalizeModelSet=!0;this.setupASCR(a,b,c)},"~S,java.util.Map,~O");e(c$,"initializeReader",function(){this.$baseAtomIndex=this.htParams.get("baseAtomIndex").intValue();this.baseModelIndex=this.htParams.get("baseModelIndex").intValue();this.asc.setInfo("noAutoBond",Boolean.TRUE);this.asc.setAtomSetAuxiliaryInfo("pdbNoHydrogens",Boolean.TRUE);this.asc.setInfo("isPyMOL",Boolean.TRUE);this.isTrajectory&&(this.trajectorySteps=new JU.Lst);this.isStateScript=this.htParams.containsKey("isStateScript");
this.sourcePNGJ=this.htParams.containsKey("sourcePNGJ");this.doResize=this.checkFilterKey("DORESIZE");this.allowSurface=!this.checkFilterKey("NOSURFACE");(this.doCache=this.checkFilterKey("DOCACHE"))&&this.sourcePNGJ?this.doCache=!1:this.sourcePNGJ&&!this.doCache&&(this.sourcePNGJ=!1);this.doCache&&(this.bsBytesExcluded=new JU.BS);this.logging=!1;N(this,J.adapter.readers.pymol.PyMOLReader,"initializeReader",[])});t(c$,"processBinaryDocument",function(){var a=(new J.adapter.readers.pymol.PickleReader(this.binaryDoc,
this.vwr)).getMap(this.logging);this.process(a)});t(c$,"setAdditionalAtomParameters",function(){},"J.adapter.smarter.Atom");t(c$,"finalizeReader",function(){this.finalizeReaderPDB();this.asc.setTensors()});t(c$,"finalizeModelSet",function(){this.pymolScene.setReaderObjects();this.haveMeasurements&&(this.appendLoadNote(this.vwr.getMeasurementInfoAsString()),this.setLoadNote());if(this.haveScenes){for(var a=Array(this.sceneOrder.size()),b=a.length;0<=--b;)a[b]=this.sceneOrder.get(b);this.vwr.getModelSetAuxiliaryInfo().put("scenes",
a)}this.vwr.ms.setTrajectoryBs(JU.BSUtil.newBitSet2(this.baseModelIndex,this.vwr.ms.mc));this.isStateScript||this.pymolScene.setFrameObject(0,null);if(null!=this.bsBytesExcluded){for(var b=this.bsBytesExcluded.cardinality(),a=this.vwr.getFileAsBytes(this.filePath,null),c=H(a.length-b,0),b=this.bsBytesExcluded.nextClearBit(0),d=a.length,f=0;b<d;b=this.bsBytesExcluded.nextClearBit(b+1))c[f++]=a[b];this.vwr.cachePut(this.filePath,c)}});e(c$,"process",function(a){this.pymolVersion=a.get("version").intValue();
this.appendLoadNote("PyMOL version: "+this.pymolVersion);var b=this.fixSettings(J.adapter.readers.pymol.PyMOLReader.getMapList(a,"settings"));this.sceneOrder=J.adapter.readers.pymol.PyMOLReader.getMapList(a,"scene_order");this.haveScenes=this.getFrameScenes(a);var c=this.listAt(b,440);null!=c&&JU.Logger.info("PyMOL session file: "+c.get(2));this.setUniqueSettings(J.adapter.readers.pymol.PyMOLReader.getMapList(a,"unique_settings"));this.pymolScene=new J.adapter.readers.pymol.PyMOLScene(this,this.vwr,
b,this.uniqueSettings,this.pymolVersion,this.haveScenes,this.$baseAtomIndex,this.baseModelIndex,this.doCache,this.filePath);this.logging=0<this.vwr.getLogFileName().length;for(var b=J.adapter.readers.pymol.PyMOLReader.getMapList(a,"names"),d,f=a.entrySet().iterator();f.hasNext()&&((d=f.next())||1);)if(c=d.getKey(),JU.Logger.info(c),c.equals("names"))for(c=1;c<b.size();c++){var e=this.listAt(b,c);JU.Logger.info("  "+J.adapter.readers.pymol.PyMOLReader.stringAt(e,0))}if(this.logging){this.logging&&
this.vwr.log("$CLEAR$");for(f=a.entrySet().iterator();f.hasNext()&&((d=f.next())||1);)c=d.getKey(),"names".equals(c)||(this.vwr.log("\n==="+c+"==="),this.vwr.log(JU.PT.rep(d.getValue().toString(),"[","\n[")));this.vwr.log("\n===names===");for(c=1;c<b.size();c++){this.vwr.log("");d=b.get(c);this.vwr.log(" ="+d.get(0).toString()+"=");try{this.vwr.log(JU.PT.rep(d.toString(),"[","\n["))}catch(h){}}}this.addColors(J.adapter.readers.pymol.PyMOLReader.getMapList(a,"colors"),0!=this.pymolScene.globalSetting(214));
this.allStates=0!=this.pymolScene.globalSetting(49);this.pymolFrame=n(this.pymolScene.globalSetting(194));this.getAtomAndStateCount(b);this.pymolScene.setStateCount(this.stateCount);d=n(this.pymolScene.globalSetting(193));this.isMovie||this.pymolScene.setFrameObject(4115,this.allStates?Integer.$valueOf(-1):Integer.$valueOf(d-1));this.appendLoadNote("frame="+this.pymolFrame+" state="+d+" all_states="+this.allStates);if(!this.isStateScript&&this.doResize){f=c=0;try{c=J.adapter.readers.pymol.PyMOLReader.intAt(J.adapter.readers.pymol.PyMOLReader.getMapList(a,
"main"),0),f=J.adapter.readers.pymol.PyMOLReader.intAt(J.adapter.readers.pymol.PyMOLReader.getMapList(a,"main"),1)}catch(g){if(!x(g,Exception))throw g;}0<c&&0<f?(e="PyMOL dimensions width="+c+" height="+f,this.asc.setInfo("perferredWidthHeight",[c,f]),this.vwr.resizeInnerPanel(c,f)):e="PyMOL dimensions?";this.appendLoadNote(e)}var k;if(!this.isStateScript&&!this.allStates&&null!=(k=J.adapter.readers.pymol.PyMOLReader.getMapList(a,"movie")))c=J.adapter.readers.pymol.PyMOLReader.intAt(k,0),0<c&&this.processMovie(k,
c);0==this.totalAtomCount&&this.asc.newAtomSet();if(!(this.allStates&&-2147483648==this.desiredModelNumber))if(this.isMovie)switch(this.desiredModelNumber){case -2147483648:break;default:this.desiredModelNumber=this.frames[(0<this.desiredModelNumber&&this.desiredModelNumber<=this.frames.length?this.desiredModelNumber:this.pymolFrame)-1],this.pymolScene.setFrameObject(4115,Integer.$valueOf(this.desiredModelNumber-1))}else 0==this.desiredModelNumber&&(this.desiredModelNumber=d);k=b.size();for(d=0;d<
this.stateCount;d++)if(this.doGetModel(++this.nModels,null)){this.model(this.nModels);this.pymolScene.currentAtomSetIndex=this.asc.iSet;this.isTrajectory&&(this.trajectoryStep=Array(this.totalAtomCount),this.trajectorySteps.addLast(this.trajectoryStep),this.trajectoryPtr=0);for(c=1;c<k;c++)this.processObject(this.listAt(b,c),!0,d)}for(c=1;c<k;c++)this.processObject(this.listAt(b,c),!1,0);this.pymolScene.setReaderObjectInfo(null,0,null,!1,null,null,null);null!=this.mapObjects&&this.allowSurface&&this.processMeshes();
this.isTrajectory&&(this.appendLoadNote("PyMOL trajectories read: "+this.trajectorySteps.size()),this.asc.finalizeTrajectoryAs(this.trajectorySteps,null));this.processDefinitions();this.processSelectionsAndScenes(a);this.pymolScene.finalizeVisibility();this.isStateScript||(this.vwr.initialize(!0),this.addJmolScript(this.pymolScene.getViewScript(J.adapter.readers.pymol.PyMOLReader.getMapList(a,"view")).toString()));0==this.$ac&&this.asc.setInfo("dataOnly",Boolean.TRUE);this.pymolScene.offsetObjects()},
"java.util.Map");e(c$,"fixSettings",function(a){for(var b=a.size(),c=0;c<b;c++)for(var d=J.adapter.readers.pymol.PyMOLReader.intAt(a.get(c),0);c<d;)JU.Logger.info("PyMOL reader adding null settings #"+c),a.add(c++,new JU.Lst),b++;return a},"JU.Lst");e(c$,"getFrameScenes",function(a){if(null==this.sceneOrder)return!1;a=a.get("scene_dict");for(var b=0;b<this.sceneOrder.size();b++){var c=J.adapter.readers.pymol.PyMOLReader.stringAt(this.sceneOrder,b),c=J.adapter.readers.pymol.PyMOLReader.getMapList(a,
c);(null==c||null==c.get(2))&&this.sceneOrder.remove(b--)}return null!=this.sceneOrder&&0!=this.sceneOrder.size()},"java.util.Map");e(c$,"setUniqueSettings",function(a){this.uniqueSettings=new java.util.Hashtable;var b=0;if(null!=a&&0!=a.size())for(var c=a.size();0<=--c;){var d=a.get(c),f=J.adapter.readers.pymol.PyMOLReader.intAt(d,0);f>b&&(b=f);for(var d=d.get(1),e=d.size();0<=--e;){var h=d.get(e),g=(f<<10)+J.adapter.readers.pymol.PyMOLReader.intAt(h,0);this.uniqueSettings.put(Integer.$valueOf(g),
h);JU.Logger.info("PyMOL unique setting "+f+" "+h)}}return b},"JU.Lst");e(c$,"addColors",function(a,b){if(!(null==a||0==a.size()))for(var c=a.size();0<=--c;){var d=this.listAt(a,c);J.adapter.readers.pymol.PyMOL.addColor(d.get(1),b?J.adapter.readers.pymol.PyMOLScene.colorSettingClamped(d):J.adapter.readers.pymol.PyMOLScene.colorSetting(d))}},"JU.Lst,~B");e(c$,"getAtomAndStateCount",function(a){for(var b=0,c=1;c<a.size();c++){var d=this.listAt(a,c),f=J.adapter.readers.pymol.PyMOLReader.intAt(d,4);if(this.checkObject(d)&&
1==f){var e=this.listAt(d,5),d=this.listAt(e,4),f=d.size();f>this.stateCount&&(this.stateCount=f);for(var e=this.listAt(e,7).size(),h=0;h<f;h++){var g=this.listAt(d,h),g=this.listAt(g,3);null==g?this.isTrajectory=!1:(g=g.size(),b+=g,this.isTrajectory&&g!=e&&(this.isTrajectory=!1))}}}this.totalAtomCount=b;JU.Logger.info("PyMOL total atom count = "+this.totalAtomCount);JU.Logger.info("PyMOL state count = "+this.stateCount)},"JU.Lst");e(c$,"checkObject",function(a){this.objectName=J.adapter.readers.pymol.PyMOLReader.stringAt(a,
0);this.isHidden=1!=J.adapter.readers.pymol.PyMOLReader.intAt(a,2);return 0!=this.objectName.indexOf("_")},"JU.Lst");e(c$,"processMovie",function(a,b){var c=new java.util.Hashtable;c.put("frameCount",Integer.$valueOf(b));c.put("currentFrame",Integer.$valueOf(this.pymolFrame-1));for(var d=!1,f=!1,e=!1,h=this.listAt(a,4),g=h.size();0<=--g;)if(0!=J.adapter.readers.pymol.PyMOLReader.intAt(h,g)){this.frames=D(h.size(),0);for(e=this.frames.length;0<=--e;)this.frames[e]=J.adapter.readers.pymol.PyMOLReader.intAt(h,
e)+1;c.put("frames",this.frames);e=!0;break}for(var h=this.listAt(a,5),k,g=h.size();0<=--g;)if(null!=(k=J.adapter.readers.pymol.PyMOLReader.stringAt(h,g))&&1<k.length)if(h=J.adapter.readers.pymol.PyMOLReader.fixMovieCommands(h),null!=h){c.put("commands",h);d=!0;break}k=this.listAt(a,6);for(var l,g=k.size();0<=--g;)if(null!=(l=this.listAt(k,g))&&12<=l.size()&&null!=l.get(1))if(f=!0,k=J.adapter.readers.pymol.PyMOLReader.fixMovieViews(k),null!=k){c.put("views",k);break}this.appendLoadNote("PyMOL movie frameCount = "+
b);e&&(!d&&!f)&&(this.isMovie=!0,this.pymolScene.setReaderObjectInfo(null,0,null,!1,null,null,null),this.pymolScene.setFrameObject(1073742032,c))},"JU.Lst,~N");c$.fixMovieViews=e(c$,"fixMovieViews",function(a){return a},"JU.Lst");c$.fixMovieCommands=e(c$,"fixMovieCommands",function(a){return a},"JU.Lst");e(c$,"processObject",function(a,b,c){if(null!=a){var d=J.adapter.readers.pymol.PyMOLReader.intAt(a,4),f=a.get(a.size()-1);if(1==d==b&&this.checkObject(a)){var e=this.listAt(a,5),h=null;if(1==d){var g=
this.listAt(e,4),g=this.listAt(g,c),h=this.listAt(g,3);if(0<c&&(null==h||0==h.size()))return;h=this.listAt(g,7)}else if(0<c)return;JU.Logger.info("PyMOL model "+this.nModels+" Object "+this.objectName+(this.isHidden?" (hidden)":" (visible)"));var k=this.listAt(e,0),g=8>a.size()?null:J.adapter.readers.pymol.PyMOLReader.stringAt(a,6);" ".equals(g)&&(g=null);this.pymolScene.setReaderObjectInfo(this.objectName,d,g,this.isHidden,this.listAt(k,8),h,b?"_"+(c+1):"");h=null;k=null!=this.bsBytesExcluded;b=
null;switch(d){default:b=""+d;break;case -1:break;case 1:k=!1;h=this.processMolecule(e,c);break;case 4:k=!1;this.processMeasure(e);break;case 3:case 2:this.processMap(e,3==d,!1);break;case 8:this.processGadget(e);break;case 12:null==g&&(g="");break;case 6:b="CGO";this.processCGO(e);break;case 11:b="ALIGNEMENT";break;case 9:b="CALCULATOR";break;case 5:b="CALLBACK";break;case 10:b="SLICE";break;case 7:b="SURFACE"}if(null!=g||null!=h)a=this.pymolScene.addGroup(a,g,d),null!=h&&a.addGroupAtoms(h);k&&(a=
J.adapter.readers.pymol.PyMOLReader.intAt(f,0),f=J.adapter.readers.pymol.PyMOLReader.intAt(f,1),this.bsBytesExcluded.setBits(a,a+f),JU.Logger.info("cached PSE file excludes PyMOL object type "+d+" name="+this.objectName+" len="+f));null!=b&&JU.Logger.error("Unprocessed object type "+b+" "+this.objectName)}}},"JU.Lst,~B,~N");e(c$,"processCGO",function(a){if(!this.isStateScript&&!this.isHidden){var b=this.listAt(this.listAt(a,2),0);a=J.adapter.readers.pymol.PyMOL.getRGB(J.adapter.readers.pymol.PyMOLReader.intAt(this.listAt(a,
0),2));b=this.pymolScene.addCGO(b,a);null!=b&&this.appendLoadNote("CGO "+b)}},"JU.Lst");e(c$,"processGadget",function(a){this.objectName.endsWith("_e_pot")&&this.processMap(a,!0,!0)},"JU.Lst");e(c$,"processMap",function(a,b,c){if(b){if(this.sourcePNGJ||this.isHidden&&!c)return;null==this.mapObjects&&(this.mapObjects=new JU.Lst);this.mapObjects.addLast(a)}else null==this.volumeData&&(this.volumeData=new java.util.Hashtable),this.volumeData.put(this.objectName,a),!this.isHidden&&!this.isStateScript&&
this.pymolScene.addIsosurface(this.objectName);a.addLast(this.objectName)},"JU.Lst,~B,~B");e(c$,"processMeasure",function(a){if(!this.isStateScript&&!this.isHidden){JU.Logger.info("PyMOL measure "+this.objectName);var b=this.listAt(this.listAt(a,2),0),c,d=s(b.get(c=1),JU.Lst)?2:s(b.get(c=4),JU.Lst)?3:s(b.get(c=6),JU.Lst)?4:0;if(0!=d){var f=this.listAt(a,0);a=J.adapter.readers.pymol.PyMOLReader.getBsReps(this.listAt(f,3));c=this.listAt(b,c);var e=this.listAt(b,8),b=8<b.size(),f=J.adapter.readers.pymol.PyMOLReader.intAt(f,
2);this.pymolScene.addMeasurements(null,d,c,a,f,e,b)&&(this.haveMeasurements=!0)}}},"JU.Lst");e(c$,"processMolecule",function(a,b){var c=this.listAt(a,4),d=this.listAt(c,b),c=this.listAt(d,3),f=null==c?0:c.size();if(0==f)return null;this.$ac=this.ac0=this.asc.ac;var e=J.adapter.readers.pymol.PyMOLReader.intAt(a,3);if(0==e)return null;this.ssMapSeq=new java.util.Hashtable;0==b&&this.processMolCryst(this.listAt(a,10));var h=this.getBondList(this.listAt(a,6)),g=this.listAt(a,7);this.atomMap=D(e,0);for(var e=
this.pymolScene.setAtomMap(this.atomMap,this.ac0),k=0;23>k;k++)this.reps[k]=JU.BS.newN(1E3);k=this.listAt(d,2);d=this.listAt(d,8);if(0==b||!this.isTrajectory)for(var l=0;l<f;l++){var m=this.addAtom(g,J.adapter.readers.pymol.PyMOLReader.intAt(c,l),l,k,d,e,b);null!=m&&(this.trajectoryStep[this.trajectoryPtr++]=m)}this.addBonds(h);this.addMolStructures();this.atoms=this.asc.atoms;this.isStateScript||this.createShapeObjects();this.ssMapSeq=null;JU.Logger.info("reading "+(this.$ac-this.ac0)+" atoms");
JU.Logger.info("----------");return e},"JU.Lst,~N");e(c$,"processMolCryst",function(a){if(!(null==a||0==a.size())){var b=this.listAt(this.listAt(a,0),0),c=this.listAt(this.listAt(a,0),1);this.setUnitCell(this.floatAt(b,0),this.floatAt(b,1),this.floatAt(b,2),this.floatAt(c,0),this.floatAt(c,1),this.floatAt(c,2));this.setSpaceGroupName(J.adapter.readers.pymol.PyMOLReader.stringAt(a,1))}},"JU.Lst");e(c$,"getBondList",function(a){for(var b=new JU.Lst,c=this.pymolScene.booleanSetting(64)?0:65536,d=a.size(),
e=0;e<d;e++){var j=this.listAt(a,e),h=J.adapter.readers.pymol.PyMOLReader.intAt(j,2);if(1>h||3<h)h=1;var g=J.adapter.readers.pymol.PyMOLReader.intAt(j,0),k=J.adapter.readers.pymol.PyMOLReader.intAt(j,1),h=1<h&&0==c?h|98304:h|c,h=new J.adapter.smarter.Bond(g,k,h);h.uniqueID=6<j.size()&&0!=J.adapter.readers.pymol.PyMOLReader.intAt(j,6)?J.adapter.readers.pymol.PyMOLReader.intAt(j,5):-1;b.addLast(h)}return b},"JU.Lst");e(c$,"addAtom",function(a,b,c,d,e,j,h){this.atomMap[b]=-1;a=this.listAt(a,b);var g=
J.adapter.readers.pymol.PyMOLReader.intAt(a,0),k=J.adapter.readers.pymol.PyMOLReader.stringAt(a,1),l=J.adapter.readers.pymol.PyMOLReader.stringAt(a,2),m=J.adapter.readers.pymol.PyMOLReader.stringAt(a,6),n=J.adapter.readers.pymol.PyMOLReader.stringAt(a,5);3<n.length&&(n=n.substring(0,3));n.equals(" ")&&(n="UNK");var q=J.adapter.readers.pymol.PyMOLReader.stringAt(a,7);q.equals("A")&&(q="C");var p=0!=J.adapter.readers.pymol.PyMOLReader.intAt(a,19),k=this.vwr.getChainID(k),l=this.processAtom(new J.adapter.smarter.Atom,
m,l.charAt(0),n,k,g," ",p,q);if(!this.filterPDBAtom(l,this.fileAtomIndex++))return null;c*=3;q=this.floatAt(d,c);p=this.floatAt(d,++c);c=this.floatAt(d,++c);JU.BoxInfo.addPointXYZ(q,p,c,this.xyzMin,this.xyzMax,0);if(this.isTrajectory&&0<h)return null;h=0<=J.adapter.readers.pymol.PyMOLReader.nucleic.indexOf(n);null!=j&&j.set(this.$ac);j=J.adapter.readers.pymol.PyMOLReader.stringAt(a,9);d=J.adapter.readers.pymol.PyMOLReader.stringAt(a,10);if(-1E3<=g&&(!d.equals(" ")||m.equals("CA")||h))m=this.ssMapSeq.get(d),
null==m&&this.ssMapSeq.put(d,m=new JU.BS),m.set(g- -1E3),d+=k,m=this.ssMapSeq.get(d),null==m&&this.ssMapSeq.put(d,m=new JU.BS),m.set(g- -1E3);l.bfactor=this.floatAt(a,14);l.foccupancy=this.floatAt(a,15);l.radius=this.floatAt(a,16);0==l.radius&&(l.radius=1);l.partialCharge=this.floatAt(a,17);var n=J.adapter.readers.pymol.PyMOLReader.intAt(a,18),g=J.adapter.readers.pymol.PyMOLReader.getBsReps(this.listAt(a,20)),k=J.adapter.readers.pymol.PyMOLReader.intAt(a,21),r=J.adapter.readers.pymol.PyMOLReader.intAt(a,
22),v=J.adapter.readers.pymol.PyMOLReader.intAt(a,23),m=J.adapter.readers.pymol.PyMOLReader.intAt(a,24),s=0!=J.adapter.readers.pymol.PyMOLReader.intAt(a,25);d=40<a.size()&&1==J.adapter.readers.pymol.PyMOLReader.intAt(a,40)?J.adapter.readers.pymol.PyMOLReader.intAt(a,32):-1;l.vib=JU.V3.new3(d,v,NaN);46<a.size()&&(a=J.adapter.readers.pymol.PyMOLScene.floatsAt(a,41,y(8,0),6),this.asc.setAnisoBorU(l,a,12));this.pymolScene.setAtomColor(k);this.processAtom2(l,r,q,p,c,n);s||this.pymolScene.bsNonbonded.set(this.$ac);
j.equals(" ")||(this.pymolScene.bsLabeled.set(this.$ac),e=this.listAt(e,b),this.pymolScene.addLabel(this.$ac,d,k,e,j));this.isHidden&&this.pymolScene.bsHidden.set(this.$ac);h&&this.pymolScene.bsNucleic.set(this.$ac);for(e=0;21>e;e++)g.get(e)&&this.reps[e].set(this.$ac);l.elementSymbol.equals("H")&&this.pymolScene.bsHydrogen.set(this.$ac);0!=(m&J.adapter.readers.pymol.PyMOL.FLAG_NOSURFACE)&&this.pymolScene.bsNoSurface.set(this.$ac);this.atomMap[b]=this.$ac++;return null},"JU.Lst,~N,~N,JU.Lst,JU.Lst,JU.BS,~N");
e(c$,"addBonds",function(a){for(var b=a.size(),c=0;c<b;c++){var d=a.get(c);d.atomIndex1=this.atomMap[d.atomIndex1];d.atomIndex2=this.atomMap[d.atomIndex2];0>d.atomIndex1||0>d.atomIndex2||(this.pymolScene.setUniqueBond(this.bondCount++,d.uniqueID),this.asc.addBond(d))}},"JU.Lst");e(c$,"addMolStructures",function(){this.addMolSS("H",J.c.STR.HELIX);this.addMolSS("S",J.c.STR.SHEET);this.addMolSS("L",J.c.STR.TURN);this.addMolSS(" ",J.c.STR.NONE)});e(c$,"addMolSS",function(a,b){if(null!=this.ssMapSeq.get(a))for(var c=
-1,d=-1,e=0,j=this.asc.atoms,h=null,g=this.pymolScene.getSSMapAtom(a),k=this.$ac+1,l=-1,m=0,n=-1,q=-1,p=this.ac0;p<k;p++){p==this.$ac?m=0:(l=j[p].sequenceNumber,m=j[p].chainID,q=j[p].atomSetIndex);if(m!=e||q!=n){if(e=m,n=q,h=this.ssMapSeq.get(a+m),--p,0>c)continue}else if(null!=h&&-1E3<=l&&h.get(l- -1E3)){d=p;0>c&&(c=p);continue}else if(0>c)continue;if(b!==J.c.STR.NONE){m=this.bsStructureDefined.nextSetBit(c);if(0<=m&&m<=d)continue;this.bsStructureDefined.setBits(c,d+1);var m=new J.adapter.smarter.Structure(n,
b,b,b.toString(),++this.structureCount,b===J.c.STR.SHEET?1:0),r=j[c],s=j[d],t=this.asc.getAtomSetAtomIndex(q);m.set(r.chainID,r.sequenceNumber,r.insertionCode,s.chainID,s.sequenceNumber,s.insertionCode,c-t,d-t);this.asc.addStructure(m)}g.setBits(c,d+1);c=-1}},"~S,J.c.STR");e(c$,"createShapeObjects",function(){this.pymolScene.createShapeObjects(this.reps,this.allowSurface&&!this.isHidden,this.ac0,this.$ac)});e(c$,"processMeshes",function(){this.vwr.cachePut(this.pymolScene.surfaceInfoName,this.volumeData);
for(var a=this.mapObjects.size();0<=--a;){var b=this.mapObjects.get(a),c=b.get(b.size()-1).toString(),d=c.endsWith("_e_pot"),e,j;if(d){j=1073742016;var h=c.substring(0,c.length-3);e=h+"map";h=this.pymolScene.getObjectID(h+"chg");if(null==h)continue;b.addLast(h);this.pymolScene.mepList+=";"+h+";"}else j=1073742018,e=J.adapter.readers.pymol.PyMOLReader.stringAt(this.listAt(this.listAt(b,2),0),1);null!=this.volumeData.get(e)&&(b.addLast(e),this.volumeData.put(c,b),this.volumeData.put("__pymolSurfaceData__",
b),this.isStateScript||this.pymolScene.addMesh(j,b,c,d),this.appendLoadNote("PyMOL object "+c+" references map "+e))}});e(c$,"processDefinitions",function(){var a=this.vwr.getAtomDefs(this.pymolScene.setAtomDefs());2<a.length&&(a=a.substring(0,a.length-2));this.appendLoadNote(a)});e(c$,"processSelectionsAndScenes",function(a){if(this.pymolScene.needSelections()){var b=J.adapter.readers.pymol.PyMOLScene.listToMap(J.adapter.readers.pymol.PyMOLReader.getMapList(a,"names"));if(this.haveScenes){var c=
a.get("scene_dict");this.finalizeSceneData();a=J.adapter.readers.pymol.PyMOLScene.listToMap(J.adapter.readers.pymol.PyMOLReader.getMapList(a,"selector_secrets"));for(var d=0;d<this.sceneOrder.size();d++){var e=J.adapter.readers.pymol.PyMOLReader.stringAt(this.sceneOrder,d),j=J.adapter.readers.pymol.PyMOLReader.getMapList(c,e);null!=j&&(this.pymolScene.buildScene(e,j,b,a),this.appendLoadNote("scene: "+e))}}this.pymolScene.setCarveSets(b)}},"java.util.Map");e(c$,"finalizeSceneData",function(){for(var a=
D(this.$ac,0),b=D(this.$ac,0),c=D(this.$ac,0),d=O(this.$ac,!1),e=y(this.$ac,0),j=-2147483648,h=-2147483648,g=0;g<this.$ac;g++)if(a[g]=this.getCartoonType(g),b[g]=this.getUniqueID(g),c[g]=this.getSequenceNumber(g),e[g]=this.getVDW(g),j!=this.atoms[g].chainID||h!=this.atoms[g].atomSetIndex)d[g]=!0,j=this.atoms[g].chainID,h=this.atoms[g].atomSetIndex;this.pymolScene.setAtomInfo(b,a,c,d,e)});c$.intAt=e(c$,"intAt",function(a,b){return a.get(b).intValue()},"JU.Lst,~N");c$.stringAt=e(c$,"stringAt",function(a,
b){var c=a.get(b).toString();return 0==c.length?" ":c},"JU.Lst,~N");c$.getMapList=e(c$,"getMapList",function(a,b){return a.get(b)},"java.util.Map,~S");c$.getBsReps=e(c$,"getBsReps",function(a){for(var b=new JU.BS,c=Math.min(a.size(),21),d=0;d<c;d++)1==J.adapter.readers.pymol.PyMOLReader.intAt(a,d)&&b.set(d);return b},"JU.Lst");e(c$,"floatAt",function(a,b){return J.adapter.readers.pymol.PyMOLScene.floatAt(a,b)},"JU.Lst,~N");e(c$,"listAt",function(a,b){return J.adapter.readers.pymol.PyMOLScene.listAt(a,
b)},"JU.Lst,~N");t(c$,"getUniqueID",function(a){return n(this.atoms[a].vib.x)},"~N");t(c$,"getCartoonType",function(a){return n(this.atoms[a].vib.y)},"~N");t(c$,"getVDW",function(a){return this.atoms[a].radius},"~N");t(c$,"getSequenceNumber",function(a){return this.atoms[a].sequenceNumber},"~N");t(c$,"compareAtoms",function(a,b){return this.atoms[a].chainID!=this.atoms[b].chainID},"~N,~N");A(c$,"MIN_RESNO",-1E3,"nucleic"," A C G T U ADE THY CYT GUA URI DA DC DG DT DU ")})})(Clazz,Clazz.newLongArray,
Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,Clazz.makeConstructor,Clazz.defineEnumConstant,Clazz.exceptionOf,Clazz.newIntArray,Clazz.defineStatics,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,Clazz.p0p,Clazz.pu$h,Clazz.newShortArray,Clazz.innerTypeInstance,Clazz.isClassDefined,Clazz.prepareCallback,Clazz.newArray,
Clazz.castNullAs,Clazz.floatToShort,Clazz.superCall,Clazz.decorateAsType,Clazz.newBooleanArray,Clazz.newCharArray,Clazz.implementOf,Clazz.newDoubleArray,Clazz.overrideConstructor,Clazz.clone,Clazz.doubleToShort,Clazz.getInheritedLevel,Clazz.getParamsType,Clazz.isAF,Clazz.isAI,Clazz.isAS,Clazz.isASS,Clazz.isAP,Clazz.isAFloat,Clazz.isAII,Clazz.isAFF,Clazz.isAFFF,Clazz.tryToSearchAndExecute,Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,Clazz.overrideMethod,Clazz.declareAnonymous,
Clazz.cloneFinals);