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"$.Lst","$.V3","JU.Vibration"],function(){c$=r(function(){this.index=this.atomSetIndex=0;this.bsSymmetry=null;this.atomSite=0;this.elementSymbol=null;this.elementNumber=-1;this.atomName=null;this.formalCharge=-2147483648;this.partialCharge=NaN;this.vib=null;this.bfactor=NaN;this.foccupancy=1;this.radius=NaN;this.isHetero=!1;this.atomSerial=-2147483648;this.chainID=0;this.altLoc="\x00";this.group3=null;this.sequenceNumber=-2147483648;this.insertionCode="\x00";this.tensors=this.anisoBorU=null;this.ignoreSymmetry=
!1;n(this,arguments)},J.adapter.smarter,"Atom",JU.P3,Cloneable);c(c$,"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");t(c$,function(){H(this,J.adapter.smarter.Atom,[]);this.set(NaN,NaN,NaN)});c(c$,"getClone",function(){var a=this.clone();null!=this.vib&&(a.vib=q(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$,"getElementSymbol",function(){if(null==this.elementSymbol&&null!=this.atomName){for(var a=this.atomName.length,b=0,d=String.fromCharCode(0);b<a&&!J.adapter.smarter.Atom.isValidSymChar1(d=this.atomName.charAt(b));)++b;switch(a-b){case 0:break;default:if(a=this.atomName.charAt(b+1),J.adapter.smarter.Atom.isValidSymNoCase(d,a)){this.elementSymbol=
""+d+a;break}case 1:J.adapter.smarter.Atom.isValidSym1(d)&&(this.elementSymbol=""+d)}}return this.elementSymbol});c$.isValidSym1=c(c$,"isValidSym1",function(a){return"A"<=a&&"Z">=a&&0>J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");c$.isValidSym2=c(c$,"isValidSym2",function(a,b){return"A"<=a&&"Z">=a&&"a"<=b&&"z">=b&&0!=(J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]>>b.charCodeAt(0)-97&1)},"~S,~S");c$.isValidSymNoCase=c(c$,"isValidSymNoCase",function(a,b){return J.adapter.smarter.Atom.isValidSym2(a,
"a">b?String.fromCharCode(b.charCodeAt(0)+32):b)},"~S,~S");c$.isValidSymChar1=c(c$,"isValidSymChar1",function(a){return"A"<=a&&"Z">=a&&0!=J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");F(c$,"elementCharMasks",A(-1,[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]))});u("J.adapter.smarter");
x(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["java.lang.Float","J.api.JmolAdapter"],function(){c$=r(function(){this.iatom=0;this.atom=null;this.ac=0;this.bsAtoms=this.atoms=null;n(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);t(c$,function(a){this.ac=a.ac;this.atoms=a.atoms;this.bsAtoms=a.bsAtoms;this.iatom=0},"J.adapter.smarter.AtomSetCollection");j(c$,"hasNext",function(){if(this.iatom==this.ac)return!1;for(;null==(this.atom=this.atoms[this.iatom++])||
null!=this.bsAtoms&&!this.bsAtoms.get(this.atom.index);)if(this.iatom==this.ac)return!1;this.atoms[this.iatom-1]=null;return!0});j(c$,"getAtomSetIndex",function(){return this.atom.atomSetIndex});j(c$,"getSymmetry",function(){return this.atom.bsSymmetry});j(c$,"getAtomSite",function(){return this.atom.atomSite+1});j(c$,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});j(c$,"getElementNumber",function(){return 0<this.atom.elementNumber?this.atom.elementNumber:J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});
j(c$,"getAtomName",function(){return this.atom.atomName});j(c$,"getFormalCharge",function(){return this.atom.formalCharge});j(c$,"getPartialCharge",function(){return this.atom.partialCharge});j(c$,"getTensors",function(){return this.atom.tensors});j(c$,"getRadius",function(){return this.atom.radius});j(c$,"getVib",function(){return null==this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});j(c$,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1094713365!=
this.atom.vib.z?0:B(this.atom.vib.x)});j(c$,"getBfactor",function(){return this.atom.bfactor});j(c$,"getOccupancy",function(){return 100*this.atom.foccupancy});j(c$,"getIsHetero",function(){return this.atom.isHetero});j(c$,"getSerial",function(){return this.atom.atomSerial});j(c$,"getChainID",function(){return this.atom.chainID});j(c$,"getAltLoc",function(){return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc)});j(c$,"getGroup3",function(){return this.atom.group3});j(c$,"getSequenceNumber",
function(){return this.atom.sequenceNumber});j(c$,"getInsertionCode",function(){return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode)});j(c$,"getXYZ",function(){return this.atom})});u("J.adapter.smarter");x(["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.BSUtil $.Logger".split(" "),function(){c$=r(function(){this.atoms=
this.atomSetInfo=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;n(this,arguments)},J.adapter.smarter,"AtomSetCollection");O(c$,function(){this.atomSetInfo=new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=A(16,0);this.atomSetAtomIndexes=
A(16,0);this.atomSetAtomCounts=A(16,0);this.atomSetBondCounts=A(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSymbolicMap=new java.util.Hashtable});c(c$,"setCollectionName",function(a){if(null!=a&&0<(a=a.trim()).length)this.collectionName=a},"~S");c(c$,"clearGlobalBoolean",function(a){this.atomSetInfo.remove(J.adapter.smarter.AtomSetCollection.globalBooleans[a])},"~N");c(c$,"setGlobalBoolean",function(a){this.setInfo(J.adapter.smarter.AtomSetCollection.globalBooleans[a],Boolean.TRUE)},"~N");
c(c$,"getGlobalBoolean",function(a){return this.atomSetInfo.get(J.adapter.smarter.AtomSetCollection.globalBooleans[a])===Boolean.TRUE},"~N");t(c$,function(a,b,d,f){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){f=0;this.readerList=new JU.Lst;for(a=0;a<d.length;a++)null!=d[a]&&(0<d[a].ac||
null!=d[a].reader&&d[a].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(f++,d[a]);1<f&&this.setInfo("isMultiFile",Boolean.TRUE)}else null!=f&&(this.setInfo("isMultiFile",Boolean.TRUE),this.appendAtomSetCollectionList(f))},"~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.Lst");c(c$,"appendAtomSetCollectionList",function(a){var b=a.size();if(0==b)this.errorMessage="No file found!";else for(var d=0;d<b;d++){var f=a.get(d);q(f,JU.Lst)?this.appendAtomSetCollectionList(f):this.appendAtomSetCollection(d,
f)}},"JU.Lst");c(c$,"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,f=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 h=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=
f&&(h=J.adapter.smarter.AtomSetCollection.fixPeriodic(h,f[c]));b[e]=h;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$,"appendAtomSetCollection",function(a,b){null!=b.reader&&b.reader.mustFinalizeModelSet&&this.readerList.addLast(b.reader);var d=this.ac;this.setInfo("loadState",b.atomSetInfo.get("loadState"));
if(null!=b.bsAtoms){null==this.bsAtoms&&(this.bsAtoms=new JU.BS);for(var f=b.bsAtoms.nextSetBit(0);0<=f;f=b.bsAtoms.nextSetBit(f+1))this.bsAtoms.set(d+f)}for(var f=0,c=this.atomSetCount,e=0;e<b.atomSetCount;e++){this.newAtomSet();var h=(this.atomSetAuxiliaryInfo[this.iSet]=b.atomSetAuxiliaryInfo[e]).get("PDB_CONECT_firstAtom_count_max");null!=h&&(h[0]+=d);this.setCurrentModelInfo("title",b.collectionName);this.setAtomSetName(b.getAtomSetName(e));for(h=0;h<b.atomSetAtomCounts[e];h++){try{null!=this.bsAtoms&&
this.bsAtoms.set(this.ac),this.newCloneAtom(b.atoms[f])}catch(k){if(E(k,Exception))this.errorMessage="appendAtomCollection error: "+k;else throw k;}f++}this.atomSetNumbers[this.iSet]=0>a?this.iSet+1:1E6*(a+1)+b.atomSetNumbers[e]}for(f=0;f<b.bondCount;f++)e=b.bonds[f],this.addNewBondWithOrder(e.atomIndex1+d,e.atomIndex2+d,e.order);for(f=J.adapter.smarter.AtomSetCollection.globalBooleans.length;0<=--f;)b.getGlobalBoolean(f)&&this.setGlobalBoolean(f);for(f=0;f<b.structureCount;f++)d=b.structures[f],
this.addStructure(d),d.modelStartEnd[0]+=c,d.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(c$,"setNoAutoBond",function(){this.setInfo("noAutoBond",Boolean.TRUE)});c(c$,"freeze",function(a){1==this.atomSetCount&&null==this.collectionName&&(this.collectionName=this.getAtomSetAuxiliaryInfoValue(0,"name"));a&&this.reverseAtomSets();1<this.trajectoryStepCount&&this.finalizeTrajectory();this.getList(!0);this.getList(!1);for(a=0;a<this.atomSetCount;a++)this.setModelInfoForSet("initialAtomCount",
Integer.$valueOf(this.atomSetAtomCounts[a]),a),this.setModelInfoForSet("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=A(this.ac,0),f=this.ac,a=this.atomSetCount;0<=--a;)for(var c=d[a].size();0<=--c;){var e=this.atoms[--f]=d[a].get(c);b[e.index]=f;e.index=f}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$,"reverseSets",function(a,b){for(var d=JU.AU.createArrayOfArrayList(this.atomSetCount),f=0;f<this.atomSetCount;f++)d[f]=new JU.Lst;for(f=0;f<b;f++){if(0>a[f].atomSetIndex)return;d[a[f].atomSetIndex].addLast(a[f])}for(f=this.atomSetCount;0<=--f;)for(var c=d[f].size();0<=--c;)a[--b]=d[f].get(c)},"~A,~N");c(c$,"reverseObject",function(a){for(var b=
this.atomSetCount,d=y(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$,"reverseArray",function(a){for(var b=this.atomSetCount,d=y(b/2);0<=--d;)JU.AU.swapInt(a,d,b-1-d)},"~A");c(c$,"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 f;
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[f=this.atoms[b].atomSetIndex].indexOf(c))d[f]+=c}a=a?"altLocs":"insertionCodes";for(b=0;b<this.atomSetCount;b++)0<d[b].length&&this.setModelInfoForSet(a,d[b],b)}},"~B");c(c$,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=
A(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSetInfo=new java.util.Hashtable;this.atomSetCount=0;this.atomSetNumbers=A(16,0);this.atomSymbolicMap=new java.util.Hashtable;this.bonds=null;this.iSet=-1;this.xtalSymmetry=this.readerList=null;this.structures=Array(16);this.structureCount=0;this.vibrationSteps=this.trajectorySteps=null});c(c$,"discardPreviousAtoms",function(){for(var a=this.ac;0<=--a;)this.atoms[a]=null;this.ac=0;this.atomSymbolicMap.clear();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$,"removeCurrentAtomSet",function(){if(!(0>this.iSet)){var a=this.atomSetAtomIndexes[this.iSet];null!=this.bsAtoms&&this.bsAtoms.clearBits(a,this.ac);this.ac=a;this.atomSetAtomCounts[this.iSet]=0;this.iSet--;this.atomSetCount--;this.reader.doCheckUnitCell=!1}});c(c$,"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$,"cloneAtomSetWithBonds",function(a){var b=this.atomSetBondCounts[a?this.iSet:0];a=a?this.cloneLastAtomSet():this.cloneFirstAtomSet(0);if(0<a)for(var d=0;d<b;d++){var f=this.bonds[this.bondCount-
b];this.addNewBondWithOrder(f.atomIndex1+a,f.atomIndex2+a,f.order)}},"~B");c(c$,"cloneLastAtomSet",function(){return this.cloneLastAtomSetFromPoints(0,null)});c(c$,"cloneLastAtomSetFromPoints",function(a,b){if(!this.allowMultiple)return 0;var d=0<a?a:this.getLastAtomSetAtomCount(),f=this.getLastAtomSetAtomIndex();this.newAtomSet();for(var c=0;c<d;++c){var e=this.newCloneAtom(this.atoms[f++]);null!=b&&e.setT(b[c])}return d},"~N,~A");c(c$,"getLastAtomSetAtomCount",function(){return this.atomSetAtomCounts[this.iSet]});
c(c$,"getLastAtomSetAtomIndex",function(){return this.ac-this.atomSetAtomCounts[this.iSet]});c(c$,"addNewAtom",function(){return this.addAtom(new J.adapter.smarter.Atom)});c(c$,"addAtom",function(a){this.ac==this.atoms.length&&(this.atoms=2E5<this.ac?JU.AU.ensureLength(this.atoms,this.ac+5E4):JU.AU.doubleLength(this.atoms));0==this.atomSetCount&&this.newAtomSet();a.index=this.ac;this.atoms[this.ac++]=a;a.atomSetIndex=this.iSet;a.atomSite=this.atomSetAtomCounts[this.iSet]++;return a},"J.adapter.smarter.Atom");
c(c$,"addAtomWithMappedName",function(a){var b=this.addAtom(a).atomName;null!=b&&this.atomSymbolicMap.put(b,a)},"J.adapter.smarter.Atom");c(c$,"addAtomWithMappedSerialNumber",function(a){var b=this.addAtom(a).atomSerial;-2147483648!=b&&this.atomSymbolicMap.put(""+b,a)},"J.adapter.smarter.Atom");c(c$,"getAtomFromName",function(a){return this.atomSymbolicMap.get(a)},"~S");c(c$,"getAtomIndex",function(a){a=this.atomSymbolicMap.get(a);return null==a?-1:a.index},"~S");c(c$,"addNewBondWithOrder",function(a,
b,d){0<=a&&(a<this.ac&&0<=b&&b<this.ac&&a!=b)&&this.addBond(new J.adapter.smarter.Bond(a,b,d))},"~N,~N,~N");c(c$,"addNewBondFromNames",function(a,b,d){this.addNewBondWithOrderA(this.getAtomFromName(a),this.getAtomFromName(b),d)},"~S,~S,~N");c(c$,"addNewBondWithOrderA",function(a,b,d){null!=a&&null!=b&&this.addNewBondWithOrder(a.index,b.index,d)},"J.adapter.smarter.Atom,J.adapter.smarter.Atom,~N");c(c$,"addBond",function(a){0<this.trajectoryStepCount||(0>a.atomIndex1||0>a.atomIndex2||0>a.order||a.atomIndex1==
a.atomIndex2||this.atoms[a.atomIndex1].atomSetIndex!=this.atoms[a.atomIndex2].atomSetIndex?JU.Logger.debugging&&JU.Logger.debug(">>>>>>BAD BOND:"+a.atomIndex1+"-"+a.atomIndex2+" order="+a.order):(this.bondCount==this.bonds.length&&(this.bonds=JU.AU.arrayCopyObject(this.bonds,this.bondCount+1024)),this.bonds[this.bondCount++]=a,this.atomSetBondCounts[this.iSet]++))},"J.adapter.smarter.Bond");c(c$,"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],f=a.get(d),f=(null==f?0:f.intValue())+1;a.put(d,Integer.$valueOf(f))}}for(b=0;b<this.structureCount;b++)d=this.structures[b],1==d.strandCount&&(d.strandCount=a.get(d.structureID+" "+d.modelStartEnd[0]).intValue())}});
c(c$,"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$,"addVibrationVectorWithSymmetry",function(a,b,d,f,c){if(c){c=this.atoms[a].atomSite;for(var e=this.atoms[a].atomSetIndex;a<this.ac&&this.atoms[a].atomSetIndex==e;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,b,d,f)}else this.addVibrationVector(a,b,d,f)},"~N,~N,~N,~N,~B");
c(c$,"addVibrationVector",function(a,b,d,f){this.allowMultiple||(a%=this.ac);return this.atoms[a].vib=JU.V3.new3(b,d,f)},"~N,~N,~N,~N");c(c$,"setCoordinatesAreFractional",function(a){this.coordinatesAreFractional=a;this.setCurrentModelInfo("coordinatesAreFractional",Boolean.$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 f=a.anisoBorU;null==f&&this.setAnisoBorU(a,
f=I(8,0),8);f[b]=d},"J.adapter.smarter.Atom,~N,~N");c(c$,"getXSymmetry",function(){null==this.xtalSymmetry&&(this.xtalSymmetry=J.api.Interface.getOption("adapter.smarter.XtalSymmetry",this.reader.vwr,"file").set(this.reader));return this.xtalSymmetry});c(c$,"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$,"setInfo",function(a,b){null==b?this.atomSetInfo.remove(a):this.atomSetInfo.put(a,b)},"~S,~O");c(c$,"setAtomSetCollectionPartialCharges",function(a){if(!this.atomSetInfo.containsKey(a))return!1;for(var b=this.atomSetInfo.get(a),d=b.size(),f=this.ac;0<=--f;)this.atoms[f].partialCharge=b.get(f%d).floatValue();JU.Logger.info("Setting partial charges type "+a);return!0},"~S");c(c$,"mapPartialCharge",function(a,b){this.getAtomFromName(a).partialCharge=b},"~S,~N");c$.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$,"finalizeTrajectory",
function(){if(0!=this.trajectoryStepCount){var a=this.trajectorySteps.get(0),b=null==this.vibrationSteps?null:this.vibrationSteps.get(0),d=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(null!=this.vibrationSteps&&null!=b&&b.length<d||a.length<d)this.errorMessage="File cannot be loaded as a trajectory";else{for(var d=new JU.V3,f=0,c=0;f<this.ac;f++)if(null==this.bsAtoms||this.bsAtoms.get(f))null!=this.vibrationSteps&&(this.atoms[f].vib=null==b?d:b[c]),null!=a[c]&&this.atoms[f].setT(a[c]),
c++;this.setInfo("trajectorySteps",this.trajectorySteps);null!=this.vibrationSteps&&this.setInfo("vibrationSteps",this.vibrationSteps)}}});c(c$,"newAtomSet",function(){this.newAtomSetClear(!0)});c(c$,"newAtomSetClear",function(a){!this.allowMultiple&&0<=this.iSet&&this.reader.discardPreviousAtoms();this.bondIndex0=this.bondCount;this.isTrajectory&&this.reader.discardPreviousAtoms();this.iSet=this.atomSetCount++;this.atomSetCount>this.atomSetNumbers.length&&(this.atomSetAtomIndexes=JU.AU.doubleLengthI(this.atomSetAtomIndexes),
this.atomSetAtomCounts=JU.AU.doubleLengthI(this.atomSetAtomCounts),this.atomSetBondCounts=JU.AU.doubleLengthI(this.atomSetBondCounts),this.atomSetAuxiliaryInfo=JU.AU.doubleLength(this.atomSetAuxiliaryInfo));this.atomSetAtomIndexes[this.iSet]=this.ac;this.atomSetCount+this.trajectoryStepCount>this.atomSetNumbers.length&&(this.atomSetNumbers=JU.AU.doubleLengthI(this.atomSetNumbers));this.isTrajectory?this.atomSetNumbers[this.iSet+this.trajectoryStepCount]=this.atomSetCount+this.trajectoryStepCount:
this.atomSetNumbers[this.iSet]=this.atomSetCount;a&&this.atomSymbolicMap.clear();this.setCurrentModelInfo("title",this.collectionName)},"~B");c(c$,"getAtomSetAtomIndex",function(a){0>a&&System.out.println("??");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$,"setAtomSetName",function(a){if(null!=a)if(this.isTrajectory)this.setTrajectoryName(a);
else{var b=0>this.iSet?null:this.getAtomSetName(this.iSet);this.setModelInfoForSet("name",a,this.iSet);null!=this.reader&&(0<a.length&&!a.equals(b))&&this.reader.appendLoadNote(a);this.allowMultiple||this.setCollectionName(a)}},"~S");c(c$,"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$,"setCurrentAtomSetNumber",function(a){this.setAtomSetNumber(this.iSet+(this.isTrajectory?this.trajectoryStepCount:0),a)},"~N");c(c$,"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 f=this.getAtomSetAuxiliaryInfoValue(d,"modelProperties");null==f&&this.setModelInfoForSet("modelProperties",f=new java.util.Properties,
d);f.put(a,b);a.startsWith(".")&&f.put(a.substring(1),b)},"~S,~S,~N");c(c$,"setAtomProperties",function(a,b,d){q(b,String)&&!b.endsWith("\n")&&(b+="\n");0>d&&(d=this.iSet);var f=this.getAtomSetAuxiliaryInfoValue(d,"atomProperties");null==f&&this.setModelInfoForSet("atomProperties",f=new java.util.Hashtable,d);f.put(a,b)},"~S,~O,~N,~B");c(c$,"setAtomSetPartialCharges",function(a){if(!this.atomSetAuxiliaryInfo[this.iSet].containsKey(a))return!1;a=this.getAtomSetAuxiliaryInfoValue(this.iSet,a);for(var b=
a.size();0<=--b;)this.atoms[b].partialCharge=a.get(b).floatValue();return!0},"~S");c(c$,"getAtomSetAuxiliaryInfoValue",function(a,b){return this.atomSetAuxiliaryInfo[0<=a?a:this.iSet].get(b)},"~N,~S");c(c$,"setCurrentModelInfo",function(a,b){this.setModelInfoForSet(a,b,this.iSet)},"~S,~O");c(c$,"setModelInfoForSet",function(a,b,d){0>d||(null==this.atomSetAuxiliaryInfo[d]&&(this.atomSetAuxiliaryInfo[d]=new java.util.Hashtable),null==b?this.atomSetAuxiliaryInfo[d].remove(a):this.atomSetAuxiliaryInfo[d].put(a,
b))},"~S,~O,~N");c(c$,"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$,"setAtomSetEnergy",
function(a,b){0>this.iSet||(JU.Logger.info("Energy for model "+(this.iSet+1)+" = "+a),this.setCurrentModelInfo("EnergyString",a),this.setCurrentModelInfo("Energy",Float.$valueOf(b)),this.setAtomSetModelProperty("Energy",""+b))},"~S,~N");c(c$,"setAtomSetFrequency",function(a,b,d,f,c){this.setAtomSetModelProperty("FreqValue",f);f+=" "+(null==c?"cm^-1":c);c=(null==d?"":d+" ")+f;this.setAtomSetName(c);this.setAtomSetModelProperty("Frequency",f);this.setAtomSetModelProperty("Mode",""+a);this.setModelInfoForSet("vibrationalMode",
Integer.$valueOf(a),this.iSet);null!=d&&this.setAtomSetModelProperty("FrequencyLabel",d);this.setAtomSetModelProperty(".PATH",(null==b?"":b+J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR+"Frequencies")+"Frequencies");return c},"~N,~S,~S,~S,~S");c(c$,"getBondList",function(){for(var a=Array(this.bondCount),b=0;b<this.bondCount;b++)a[b]=v(-1,[this.atoms[this.bonds[b].atomIndex1].atomName,this.atoms[this.bonds[b].atomIndex2].atomName,""+this.bonds[b].order]);return a});c(c$,"centralize",function(){for(var a=
new JU.P3,b=0;b<this.atomSetCount;b++){var d=this.atomSetAtomCounts[b],f=this.atomSetAtomIndexes[b];a.set(0,0,0);for(var c=f+d;--c>=f;)a.add(this.atoms[c]);a.scale(1/d);for(c=f+d;--c>=f;)this.atoms[c].sub(a)}});c(c$,"mergeTrajectories",function(a){if(this.isTrajectory&&a.isTrajectory&&null==this.vibrationSteps){for(var b=0;b<a.trajectoryStepCount;b++)this.trajectorySteps.add(this.trajectoryStepCount++,a.trajectorySteps.get(b));this.setInfo("trajectorySteps",this.trajectorySteps);this.setInfo("ignoreUnitCell",
a.atomSetInfo.get("ignoreUnitCell"))}},"J.adapter.smarter.AtomSetCollection");c(c$,"removeAtomSet",function(a){null==this.bsAtoms&&(this.bsAtoms=JU.BSUtil.newBitSet2(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=0;b<this.bondCount;b++)this.bonds[b].atomSetIndex=this.atoms[this.bonds[b].atomIndex1].atomSetIndex;this.atomSetAuxiliaryInfo[--this.atomSetCount]=null;for(b=d=0;b<this.structureCount;b++){var f=this.structures[b];f.modelStartEnd[0]==a&&f.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}},"~N");c(c$,"removeLastUnselectedAtoms",function(){for(var a=this.ac,b=0,d=this.getLastAtomSetAtomIndex(),f=0,c=d;c<a;c++)this.bsAtoms.get(c)?(0<b&&(this.atoms[this.atoms[c].index=c-b]=this.atoms[c],this.atoms[c]=null),f++):(b++,this.ac--,this.atoms[c]=null);this.atomSetAtomCounts[this.iSet]=f;0==f?(this.iSet--,this.atomSetCount--):this.bsAtoms.setBits(d,d+f)});c(c$,"checkNoEmptyModel",function(){for(;0<this.atomSetCount&&0==this.atomSetAtomCounts[this.atomSetCount-
1];)this.atomSetCount--});F(c$,"globalBooleans",v(-1,"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)});u("J.adapter.smarter");x(["javajs.api.GenericLineReader","JU.SB"],"J.adapter.smarter.AtomSetCollectionReader","java.io.BufferedReader java.lang.Boolean $.Float $.NullPointerException javajs.api.GenericBinaryDocument JU.BS $.Lst $.M3 $.P3 $.PT $.Quat $.T4 $.V3 J.adapter.smarter.Atom $.AtomSetCollection J.api.Interface $.JmolAdapter JU.BSUtil $.Logger".split(" "),
function(){c$=r(function(){this.requiresBSFilter=this.debugging=this.isBinary=!1;this.dssr=this.validation=this.domains=this.trajectorySteps=this.htParams=this.readerName=this.binaryDoc=this.reader=this.asc=this.primitiveToCrystal=null;this.isConcatenated=!1;this.addedDataKey=this.addedData=null;this.fixJavaFloat=!0;this.next=this.prevline=this.line=this.lstNCS=this.thisBiomolecule=null;this.ptLine=0;this.fillRange=this.latticeCells=this.latticeType=null;this.iHaveSymmetryOperators=this.iHaveUnitCell=
this.doProcessLines=!1;this.continuing=!0;this.vwr=null;this.isMolecular=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=this.useFileModelNumbers=!1;this.calculationType="?";this.sgName=null;this.ignoreFileSpaceGroupName=this.ignoreFileUnitCell=
!1;this.unitCellParams=null;this.desiredModelNumber=-2147483648;this.out=this.symmetry=null;this.doPackUnitCell=this.iHaveFractionalCoordinates=!1;this.ptSupercell=null;this.forcePacked=this.mustFinalizeModelSet=!1;this.packingError=0.02;this.isPrimitive=this.rotateHexCell=!1;this.modDim=0;this.loadNote=null;this.merging=this.fileCoordinatesAreFractional=this.doConvertToFractional=!1;this.symmetryRange=0;this.firstLastStep=null;this.lastModelNumber=2147483647;this.desiredSpaceGroupIndex=-1;this.fileScaling=
null;this.latticeScaling=NaN;this.unitCellOffset=this.fileOffsetFractional=this.fileOffset=null;this.unitCellOffsetFractional=!1;this.fileName=this.filePath=this.moreUnitCellInfo=null;this.stateScriptVersionInt=2147483647;this.baseAtomIndex=0;this.haveModel=this.isFinalized=!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.isDSSP1=this.ignoreStructure=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.strSupercell=
null;this.vibsFractional=!1;this.siteScript=this.previousScript=null;n(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);O(c$,function(){this.next=A(1,0);this.loadNote=new JU.SB});c(c$,"setup",function(a,b,d){this.setupASCR(a,b,d)},"~S,java.util.Map,~O");c(c$,"setupASCR",function(a,b,d){null!=a&&(this.debugging=JU.Logger.debugging,this.htParams=b,this.filePath=""+b.get("fullPathName"),a=this.filePath.lastIndexOf("/"),this.fileName=this.filePath.substring(a+
1),q(d,java.io.BufferedReader)?this.reader=d:q(d,javajs.api.GenericBinaryDocument)&&(this.binaryDoc=d))},"~S,java.util.Map,~O");c(c$,"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.finalizeSubclassReader();
this.isFinalized||this.finalizeReaderASCR()}catch(a){JU.Logger.info("Reader error: "+a),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.$valueOf(a))}catch(b){if(!E(b,
Exception))throw b;}});c(c$,"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$,"finalizeSubclassReader",function(){});c(c$,"finalizeReaderASCR",function(){this.isFinalized=!0;if(0<this.asc.atomSetCount){1==this.asc.atomSetCount&&this.asc.setCurrentModelInfo("dbName",this.htParams.get("dbName"));this.applySymmetryAndSetTrajectory();this.asc.finalizeStructures();this.doCentralize&&this.asc.centralize();null!=this.fillRange&&this.asc.setInfo("boundbox",this.fillRange);var a=this.asc.getAtomSetAuxiliaryInfo(0);if(null!=a){if(null!=this.domains){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)for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),
a.put("validation",this.validation);if(null!=this.dssr){a.put("dssrJSON",Boolean.TRUE);for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("dssr",this.dssr)}}}this.fixJavaFloat||this.asc.setInfo("legacyJavaFloat",Boolean.TRUE);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$,"setModelPDB",function(a){a?this.asc.setGlobalBoolean(4):this.asc.clearGlobalBoolean(4);this.asc.setCurrentModelInfo("isPDB",a?Boolean.TRUE:null)},"~B");c(c$,"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.$valueOf(this.asc.ac));null!=this.bsFilter&&(this.htParams.put("filteredAtomCount",Integer.$valueOf(JU.BSUtil.cardinalityOf(this.bsFilter))),this.htParams.put("bsFilter",this.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.setModelInfoForSet("fileName",
this.filePath,d),this.asc.setModelInfoForSet("fileType",b,d);this.asc.freeze(this.reverseModels);if(null!=this.asc.errorMessage)return this.asc.errorMessage+"\nfor file "+this.filePath+"\ntype "+a;if((null==this.asc.bsAtoms?0==this.asc.ac:0>this.asc.bsAtoms.nextSetBit(0))&&0>b.indexOf("DataOnly")&&null==this.asc.atomSetInfo.get("dataOnly"))return"No atoms found\nfor file "+this.filePath+"\ntype "+a;this.fixBaseIndices();return this.asc});c(c$,"setError",function(a){var b;b=a.getMessage?a.getMessage():
a.toString();this.asc.errorMessage=null==this.line?"Error reading file at end of file \n"+b:"Error reading file at line "+this.ptLine+":\n"+this.line+"\n"+b;a.printStackTrace()},"Throwable");c(c$,"initialize",function(){this.htParams.containsKey("baseAtomIndex")&&(this.baseAtomIndex=this.htParams.get("baseAtomIndex").intValue());this.initializeSymmetry();this.vwr=this.htParams.remove("vwr");this.htParams.containsKey("stateScriptVersionInt")&&(this.stateScriptVersionInt=this.htParams.get("stateScriptVersionInt").intValue());
var a=this.htParams.get("packingError");null!=a?this.packingError=a.floatValue():null!=this.htParams.get("legacyJavaFloat")&&(this.fixJavaFloat=!1);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.requiresBSFilter?this.htParams.get("bsFilter"):null;this.setFilter(null);this.fillRange=this.htParams.get("fillRange");null!=this.strSupercell&&!this.checkFilterKey("NOPACK")&&(this.forcePacked=!0);a=this.htParams.get("supercell");q(a,JU.P3)?(a=this.ptSupercell=
a,this.strSupercell=B(a.x)+"a,"+B(a.y)+"b,"+B(a.z)+"c"):q(a,String)&&(this.strSupercell=a);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),q(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.useFileModelNumbers=this.htParams.containsKey("useFileModelNumbers")||this.checkFilterKey("USEFILEMODELNUMBERS");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.addExplicitLatticeVector(0,a,0),this.addExplicitLatticeVector(1,a,3),this.addExplicitLatticeVector(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");this.dssr=this.htParams.get("dssr");this.isConcatenated=this.htParams.containsKey("concatenate")});c(c$,"initializeSymmetryOptions",function(){this.latticeCells=A(4,0);this.doApplySymmetry=!1;var a=this.htParams.get("lattice");if(null==a||0==a.length()){if(!this.forcePacked&&null==this.strSupercell)return;
a=JU.P3.new3(1,1,1)}this.latticeCells[0]=B(a.x);this.latticeCells[1]=B(a.y);this.latticeCells[2]=B(a.z);q(a,JU.T4)&&(this.latticeCells[3]=B(a.w));if((this.doCentroidUnitCell=this.htParams.containsKey("centroid"))&&(-1==this.latticeCells[2]||0==this.latticeCells[2]))this.latticeCells[2]=1;a=this.forcePacked||this.htParams.containsKey("packed");this.centroidPacked=this.doCentroidUnitCell&&a;this.doPackUnitCell=!this.doCentroidUnitCell&&(a||0>this.latticeCells[2]);this.doApplySymmetry=0<this.latticeCells[0]&&
0<this.latticeCells[1];this.doApplySymmetry||(this.latticeCells=A(3,0))});c(c$,"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.discardPreviousAtoms();this.haveModel=(new Boolean(this.haveModel|d)).valueOf();d&&(this.doProcessLines=!0);return d},"~N,~S");c(c$,"discardPreviousAtoms",function(){this.asc.discardPreviousAtoms()});c(c$,"initializeSymmetry",function(){this.previousSpaceGroup=this.sgName;this.previousUnitCell=this.unitCellParams;this.iHaveUnitCell=this.ignoreFileUnitCell;if(!this.ignoreFileUnitCell){this.unitCellParams=I(26,0);for(var a=25;0<=--a;)this.unitCellParams[a]=NaN;this.unitCellParams[25]=
this.latticeScaling;this.symmetry=null}this.ignoreFileSpaceGroupName||(this.sgName="unspecified!");this.doCheckUnitCell=!1});c(c$,"newAtomSet",function(a){0<=this.asc.iSet?(this.asc.newAtomSet(),this.asc.setCollectionName("<collection of "+(this.asc.iSet+1)+" models>")):this.asc.setCollectionName(a);this.asc.setModelInfoForSet("name",a,Math.max(0,this.asc.iSet));this.asc.setAtomSetName(a)},"~S");c(c$,"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.unitCellParams=this.previousUnitCell);return d},"~N,~A");c(c$,"setSpaceGroupName",function(a){this.ignoreFileSpaceGroupName||null==a||(a=a.trim(),a.equals(this.sgName)||(a.equals("P1")||JU.Logger.info("Setting space group name to "+a),this.sgName=a))},"~S");c(c$,"setSymmetryOperator",function(a){if(this.ignoreFileSymmetryOperators)return-1;var b=this.asc.getXSymmetry().addSpaceGroupOperation(a,
!0);0>b&&JU.Logger.warn("Skippings symmetry operation "+a);this.iHaveSymmetryOperators=!0;return b},"~S");c(c$,"initializeCartesianToFractional",function(){for(var a=0;16>a;a++)if(!Float.isNaN(this.unitCellParams[6+a]))return;for(a=0;16>a;a++)this.unitCellParams[6+a]=0==a%5?1:0;this.nMatrixElements=0});c(c$,"clearUnitCell",function(){if(!this.ignoreFileUnitCell){for(var a=6;22>a;a++)this.unitCellParams[a]=NaN;this.checkUnitCell(6)}});c(c$,"setUnitCellItem",function(a,b){if(!this.ignoreFileUnitCell&&
!(0==a&&1==b||3==a&&0==b))!Float.isNaN(b)&&(6<=a&&Float.isNaN(this.unitCellParams[6]))&&this.initializeCartesianToFractional(),this.unitCellParams[a]=b,this.debugging&&JU.Logger.debug("setunitcellitem "+a+" "+b),6>a||Float.isNaN(b)?this.iHaveUnitCell=this.checkUnitCell(6):12==++this.nMatrixElements&&(this.iHaveUnitCell=this.checkUnitCell(22))},"~N,~N");c(c$,"setUnitCell",function(a,b,d,f,c,e){this.ignoreFileUnitCell||(this.clearUnitCell(),this.unitCellParams[0]=a,this.unitCellParams[1]=b,this.unitCellParams[2]=
d,0!=f&&(this.unitCellParams[3]=f),0!=c&&(this.unitCellParams[4]=c),0!=e&&(this.unitCellParams[5]=e),this.iHaveUnitCell=this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");c(c$,"addExplicitLatticeVector",function(a,b,d){if(!this.ignoreFileUnitCell){if(0==a)for(var f=0;6>f;f++)this.unitCellParams[f]=0;a=6+3*a;this.unitCellParams[a++]=b[d++];this.unitCellParams[a++]=b[d++];this.unitCellParams[a]=b[d];if(Float.isNaN(this.unitCellParams[0]))for(a=0;6>a;a++)this.unitCellParams[a]=-1;this.iHaveUnitCell=this.checkUnitCell(15)}},
"~N,~A,~N");c(c$,"checkUnitCell",function(a){for(var b=0;b<a;b++)if(Float.isNaN(this.unitCellParams[b]))return!1;if(22==a&&1==this.unitCellParams[0]&&1==this.unitCellParams[1]&&1==this.unitCellParams[2]&&1==this.unitCellParams[6]&&1==this.unitCellParams[11]&&1==this.unitCellParams[16])return!1;this.doApplySymmetry&&(this.getSymmetry(),this.doConvertToFractional=!this.fileCoordinatesAreFractional);return!0},"~N");c(c$,"getSymmetry",function(){if(!this.iHaveUnitCell)return null;null==this.symmetry&&
(this.getNewSymmetry().setUnitCell(this.unitCellParams,!1),this.checkUnitCellOffset());null==this.symmetry?this.iHaveUnitCell=!1:this.symmetry.setSpaceGroupName(this.sgName);return this.symmetry});c(c$,"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$,"fractionalizeCoordinates",function(a){if(null!=this.getSymmetry()){var b=this.asc.atoms;if(a)for(var d=this.asc.ac;0<=--d;)this.symmetry.toFractional(b[d],!1);else for(d=this.asc.ac;0<=--d;)this.symmetry.toCartesian(b[d],!1);this.setFractionalCoordinates(a)}},"~B");c(c$,"getNewSymmetry",function(){return this.symmetry=this.getInterface("JS.Symmetry")});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.ignoreStructure=this.checkFilterKey("DSSP");this.isDSSP1=this.checkFilterKey("DSSP1");
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.strSupercell=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.parseIntAt(this.filter,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("LATTICESCALING="),null!=a&&25<this.unitCellParams.length&&(this.unitCellParams[25]=this.latticeScaling=this.parseFloatStr(a)),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,f,c,e,h,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(f,c,e),a.normalize(),this.matRot.setColumnV(1,a),a.set(h,k,l),a.normalize(),this.matRot.setColumnV(2,a),this.asc.setInfo("defaultOrientationMatrix",JU.M3.newM3(this.matRot)),f=JU.Quat.newM(this.matRot),this.asc.setInfo("defaultOrientationQuaternion",f),JU.Logger.info("defaultOrientationMatrix = "+this.matRot))},"~N,~N,~N,~N,~N,~N,~N,~N,~N");
c(c$,"setAtomCoordXYZ",function(a,b,d,f){a.set(b,d,f);this.setAtomCoord(a)},"J.adapter.smarter.Atom,~N,~N,~N");c(c$,"setAtomCoordScaled",function(a,b,d,f){null==a&&(a=this.asc.addNewAtom());this.setAtomCoordXYZ(a,this.parseFloatStr(b[d])*f,this.parseFloatStr(b[d+1])*f,this.parseFloatStr(b[d+2])*f);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,f){var c=this.asc.addNewAtom();null!=d&&(c.elementSymbol=d);null!=f&&(c.atomName=f);this.setAtomCoordTokens(c,a,b);return c},"~A,~N,~S,~S");c(c$,"setAtomCoord",function(a){var b=this.doConvertToFractional&&!this.fileCoordinatesAreFractional&&null!=this.getSymmetry();null!=this.fileScaling&&(a.x=a.x*this.fileScaling.x+this.fileOffset.x,a.y=a.y*this.fileScaling.y+this.fileOffset.y,a.z=a.z*this.fileScaling.z+this.fileOffset.z);b&&(this.symmetry.haveUnitCell()||
this.symmetry.setUnitCell(this.unitCellParams,!1),this.symmetry.toFractional(a,!1),this.iHaveFractionalCoordinates=!0);this.fixJavaFloat&&this.fileCoordinatesAreFractional&&JU.PT.fixPtFloats(a,1E5);this.doCheckUnitCell=!0},"J.adapter.smarter.Atom");c(c$,"addSites",function(a){this.asc.setCurrentModelInfo("pdbSites",a);var b="",d;for(a=a.entrySet().iterator();a.hasNext()&&((d=a.next())||1);){for(var f=d.getKey(),c=d.getValue(),e,h=f.length;0<=--h;)if(!JU.PT.isLetterOrDigit(e=f.charAt(h))&&"'"!=e)f=
f.substring(0,h)+"_"+f.substring(h+1);c=c.get("groups");0!=c.length&&(this.addSiteScript("@site_"+f+" "+c),this.addSiteScript("site_"+f+' = ["'+JU.PT.rep(c,",",'","')+'"]'),b+=',"site_'+f+'"')}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.getSymmetry()):
null;null==a&&this.asc.setTensors();this.isTrajectory&&this.asc.setTrajectory();null!=this.moreUnitCellInfo&&(this.asc.setCurrentModelInfo("moreUnitCellInfo",this.moreUnitCellInfo),this.moreUnitCellInfo=null);this.finalizeSubclassSymmetry(null!=a);this.initializeSymmetry();return a});c(c$,"finalizeSubclassSymmetry",function(){},"~B");c(c$,"doPreSymmetry",function(){});c(c$,"finalizeMOData",function(a){this.asc.setCurrentModelInfo("moData",a);null!=a&&(a=a.get("mos"),null!=a&&JU.Logger.info(a.size()+
" molecular orbitals read in model "+this.asc.atomSetCount))},"java.util.Map");c$.getElementSymbol=c(c$,"getElementSymbol",function(a){return J.api.JmolAdapter.getElementSymbol(a)},"~N");c(c$,"fillDataBlock",function(a,b){for(var d=a.length,f=0;f<d;f++)a[f]=JU.PT.getTokens(this.discardLinesUntilNonBlank()),a[f].length<b&&--f},"~A,~N");c(c$,"fillFloatArray",function(a,b,d){for(var f=[],c=0,e=0;e<d.length;e++){for(;null!=f&&c>=f.length;){null==a&&(a=this.rd());if(0==b)f=JU.PT.getTokens(a);else{f=Array(y(a.length/
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(c?3*p:p)-1,L=0,q=0;q<p;q++){++G;var n=l[G];")"==n.charAt(0)&&(n=n.substring(1));var n=this.parseFloatStr(n),t=this.parseFloatStr(c?l[++G]:z[G]),r=this.parseFloatStr(c?l[++G]:w[G]);if(!f[q]){var u=null==k?h:k[h];0>u||(u+=a+d*L++,this.debugging&&JU.Logger.debug("atom "+u+" vib"+L+": "+n+" "+t+" "+r),this.asc.addVibrationVectorWithSymmetry(u,n,t,r,m))}}}},"~N,~N,~N,~A,~B,~N,~N,~A,~N,~A");c(c$,"fillDataBlockFixed",function(a,b,d,f){if(0==d)this.fillDataBlock(a,f);else for(var c=a.length,e=0;e<c;e++){this.discardLinesUntilNonBlank();
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77;c$.PALETTE_ALTLOC=14;c$.PALETTE_INSERTION=15;c$.PALETTE_JMOL=16;c$.PALETTE_RASMOL=17;c$.PALETTE_TYPE=18;c$.PALETTE_ENERGY=19;c$.PALETTE_PROPERTY=84;c$.PALETTE_VARIABLE=85;c$.PALETTE_STRAIGHTNESS=86;c$.PALETTE_POLYMER=87;c$.PALETTE_NUCLEIC=24;c$.argbsCpkRasmol=A(-1,[16716947,33554431,50315467,62005794,83951360,113821896,126849023,149946368,165324064,184549631,203590434,226525328,249210144,268412160,285198386,285277952,343965840,377520272,411074704,427851920,452961536,480586282,497363498,514140714,
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"getId",function(){return this.id});c(c$,"getColor",function(){return this.color});c$.getProteinStructureType=c(c$,"getProteinStructureType",function(a){for(var b,d=0,f=J.c.STR.values();d<f.length&&((b=f[d])||1);d++)if(a.equalsIgnoreCase(b.name()))return b.isProtein()?b:J.c.STR.NOT;return J.c.STR.NOT},"~S");c(c$,"getBioStructureTypeName",function(a){return 0>this.id?"":a&&this.isProtein()?"protein":this.name()},"~B");c(c$,"isProtein",function(){return 0<=this.id&&3>=this.id||7<=this.id});D(c$,"NOT",
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"VDW",Enum);t(c$,function(a,b,d){this.pt=a;this.type=b;this.type2=d},"~N,~S,~S");c(c$,"getVdwLabel",function(){return null==this.type?this.type2:this.type});c$.getVdwType=c(c$,"getVdwType",function(a){if(null!=a)for(var b,d=0,f=J.c.VDW.values();d<f.length&&((b=f[d])||1);d++)if(a.equalsIgnoreCase(b.type))return b;return null},"~S");c$.getVdwType2=c(c$,"getVdwType2",function(a){if(null!=a)for(var b,d=0,f=J.c.VDW.values();d<f.length&&((b=f[d])||1);d++)if(a.equalsIgnoreCase(b.type2))return b;return null},
"~S");D(c$,"JMOL",0,[0,"Jmol",null]);D(c$,"BABEL",1,[1,"Babel",null]);D(c$,"RASMOL",2,[2,"RasMol",null]);D(c$,"BABEL21",3,[3,"Babel21",null]);D(c$,"AUTO_JMOL",4,[0,null,"Jmol"]);D(c$,"AUTO_BABEL",5,[1,null,"Babel"]);D(c$,"AUTO_RASMOL",6,[2,null,"RasMol"]);D(c$,"AUTO",7,[0,"Auto",null]);D(c$,"USER",8,[-1,"User",null]);D(c$,"ADPMAX",9,[-1,null,"adpmax"]);D(c$,"ADPMIN",10,[-1,null,"adpmin"]);D(c$,"HYDRO",11,[-1,null,"hydrophobic"]);D(c$,"BONDING",12,[-1,null,"bondingradius"]);D(c$,"TEMP",13,[-1,null,
"temperature"]);D(c$,"NOJMOL",14,[-1,null,null]);D(c$,"NADA",15,[-1,null,null])});u("J.g3d");x(["JU.P3i"],"J.g3d.CylinderRenderer",["JU.AU","$.P3"],function(){c$=r(function(){this.shader=this.line3d=this.g3d=null;this.colixB=this.colixA=0;this.shadesB=this.shadesA=null;this.dzBf=this.dyBf=this.dxBf=this.zAf=this.yAf=this.xAf=this.dzB=this.dyB=this.dxB=this.zA=this.yA=this.xA=0;this.tEvenDiameter=!1;this.endcaps=this.diameter=0;this.endCapHidden=!1;this.sinPhi=this.cosPhi=this.cosTheta=this.radius2=
this.radius=this.endcapShadeIndex=this.colixEndcap=this.argbEndcap=this.zEndcap=this.yEndcap=this.xEndcap=0;this.clipped=!1;this.rasterCount=0;this.ptB0i=this.ptA0i=this.ptB0=this.ptA0=this.xyzfRaster=this.xyztRaster=null;this.zTip=this.yTip=this.xTip=0;n(this,arguments)},J.g3d,"CylinderRenderer");O(c$,function(){this.xyztRaster=v(-1,[I(32,0),I(32,0),I(32,0),I(32,0)]);this.xyzfRaster=v(-1,[A(32,0),A(32,0),A(32,0),A(32,0)]);this.ptA0i=new JU.P3i;this.ptB0i=new JU.P3i});t(c$,function(a){this.g3d=a;
this.line3d=a.line3d;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"renderOld",function(a,b,d,f,c,e,h,k,l,j,m){var p=y(c/2)+1,z=this.g3d,w=z.clipCode3(e-p,h-p,k-p),G=z.clipCode3(e+p,h+p,k+p),L=z.clipCode3(l-p,j-p,m-p),p=z.clipCode3(l+p,j+p,m+p),q=w|G|L|p;this.clipped=0!=q;if(!(-1==q||0!=(w&p&G&L)))if(this.dxB=l-e,this.dyB=j-h,this.dzB=m-k,1>=c)this.line3d.plotLineDeltaOld(z.getColorArgbOrGray(a),z.getColorArgbOrGray(b),e,h,k,this.dxB,this.dyB,this.dzB,this.clipped);else{l=0==d&&(this.clipped||2==
f||0==f);this.diameter=c;this.xA=e;this.yA=h;this.zA=k;this.endcaps=f;this.shadesA=z.getShades(this.colixA=a);this.shadesB=z.getShades(this.colixB=b);this.calcArgbEndcap(!0,!1);this.calcCosSin(this.dxB,this.dyB,this.dzB);this.calcPoints(3,!1);this.interpolate(0,1,this.xyzfRaster,this.xyztRaster);this.interpolate(1,2,this.xyzfRaster,this.xyztRaster);k=this.xyzfRaster;2==f&&this.renderFlatEndcap(!0,!1,k);z.setZMargin(5);a=z.width;b=z.zbuf;c=k[0];e=k[1];h=k[2];k=k[3];j=z.pixel;for(m=this.rasterCount;0<=
--m;)w=k[m]>>8,G=w>>1,L=c[m],p=e[m],q=h[m],this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(z.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+L,this.yEndcap+p,this.zEndcap-q-1,a,b,j),z.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-L,this.yEndcap-p,this.zEndcap+q-1,a,b,j)):(z.plotPixelUnclipped(this.argbEndcap,this.xEndcap+L,this.yEndcap+p,this.zEndcap-q-1,a,b,j),z.plotPixelUnclipped(this.argbEndcap,this.xEndcap-L,this.yEndcap-p,this.zEndcap+q-1,a,b,j))),this.line3d.plotLineDeltaAOld(this.shadesA,
this.shadesB,d,w,this.xA+L,this.yA+p,this.zA-q,this.dxB,this.dyB,this.dzB,this.clipped),l&&this.line3d.plotLineDeltaOld(this.shadesA[G],this.shadesB[G],this.xA-L,this.yA-p,this.zA+q,this.dxB,this.dyB,this.dzB,this.clipped);z.setZMargin(0);3==f&&this.renderSphericalEndcaps()}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"renderBitsFloat",function(a,b,d,f,c,e,h){var k=this.g3d;null==this.ptA0&&(this.ptA0=new JU.P3,this.ptB0=new JU.P3);this.ptA0.setT(e);var l=y(c/2)+1,j=Math.round(e.x),m=Math.round(e.y),
p=Math.round(e.z),z=Math.round(h.x),w=Math.round(h.y),G=Math.round(h.z),L=k.clipCode3(j-l,m-l,p-l),j=k.clipCode3(j+l,m+l,p+l),m=k.clipCode3(z-l,w-l,G-l),l=k.clipCode3(z+l,w+l,G+l),z=L|j|m|l;this.clipped=0!=z;if(!(-1==z||0!=(L&l&j&m))){this.dxBf=h.x-e.x;this.dyBf=h.y-e.y;this.dzBf=h.z-e.z;0<c&&(this.diameter=c,this.xAf=e.x,this.yAf=e.y,this.zAf=e.z);e=0==d&&(this.clipped||2==f||0==f);this.xA=B(this.xAf);this.yA=B(this.yAf);this.zA=B(this.zAf);this.dxB=B(this.dxBf);this.dyB=B(this.dyBf);this.dzB=B(this.dzBf);
this.shadesA=k.getShades(this.colixA=a);this.shadesB=k.getShades(this.colixB=b);this.endcaps=f;this.calcArgbEndcap(!0,!0);z=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);2==f&&this.renderFlatEndcap(!0,!0,z);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;b=k.zbuf;h=z[0];L=z[1];l=z[2];z=z[3];for(w=this.rasterCount;0<=--w;){var G=z[w]>>8,j=G>>1,m=h[w],p=L[w],q=l[w];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(k.plotPixelClippedArgb(this.argbEndcap,
this.xEndcap+m,this.yEndcap+p,this.zEndcap-q-1,a,b,c),k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-m,this.yEndcap-p,this.zEndcap+q-1,a,b,c)):(k.plotPixelUnclipped(this.argbEndcap,this.xEndcap+m,this.yEndcap+p,this.zEndcap-q-1,a,b,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-m,this.yEndcap-p,this.zEndcap+q-1,a,b,c)));this.ptA0.set(this.xA+m,this.yA+p,this.zA-q);this.ptB0.setT(this.ptA0);this.ptB0.x+=this.dxB;this.ptB0.y+=this.dyB;this.ptB0.z+=this.dzB;this.line3d.plotLineDeltaABitsFloat(this.shadesA,
this.shadesB,G,this.ptA0,this.ptB0,d,this.clipped);e&&(this.ptA0.set(this.xA-m,this.yA-p,this.zA+q),this.ptB0.setT(this.ptA0),this.ptB0.x+=this.dxB,this.ptB0.y+=this.dyB,this.ptB0.z+=this.dzB,this.line3d.plotLineDeltaABitsFloat(this.shadesA,this.shadesB,j,this.ptA0,this.ptB0,d,this.clipped))}k.setZMargin(0);3==f&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;this.zAf+=this.dzBf}},"~N,~N,~N,~N,~N,JU.P3,JU.P3");c(c$,"renderBits",function(a,b,d,f,c,e,h){var k=this.g3d;if(0==c||
1==c)this.line3d.plotLineBits(k.getColorArgbOrGray(a),k.getColorArgbOrGray(b),e,h,0,0,!1);else{this.ptA0i.setT(e);var l=y(c/2)+1,j=e.x,m=e.y,p=e.z,z=h.x,w=h.y,G=h.z,L=k.clipCode3(j-l,m-l,p-l),j=k.clipCode3(j+l,m+l,p+l),m=k.clipCode3(z-l,w-l,G-l),l=k.clipCode3(z+l,w+l,G+l),z=L|j|m|l;this.clipped=0!=z;if(!(-1==z||0!=(L&l&j&m))){this.dxBf=h.x-e.x;this.dyBf=h.y-e.y;this.dzBf=h.z-e.z;0<c&&(this.diameter=c,this.xAf=e.x,this.yAf=e.y,this.zAf=e.z);e=0==d&&(this.clipped||2==f||0==f);this.xA=B(this.xAf);this.yA=
B(this.yAf);this.zA=B(this.zAf);this.dxB=B(this.dxBf);this.dyB=B(this.dyBf);this.dzB=B(this.dzBf);this.shadesA=k.getShades(this.colixA=a);this.shadesB=k.getShades(this.colixB=b);this.endcaps=f;this.calcArgbEndcap(!0,!0);z=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);2==f&&this.renderFlatEndcap(!0,!0,z);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;b=k.zbuf;h=z[0];L=z[1];l=z[2];z=z[3];for(w=this.rasterCount;0<=--w;){var G=z[w]>>8,j=G>>1,m=h[w],p=L[w],
q=l[w];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+m,this.yEndcap+p,this.zEndcap-q-1,a,b,c),k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-m,this.yEndcap-p,this.zEndcap+q-1,a,b,c)):(k.plotPixelUnclipped(this.argbEndcap,this.xEndcap+m,this.yEndcap+p,this.zEndcap-q-1,a,b,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-m,this.yEndcap-p,this.zEndcap+q-1,a,b,c)));this.ptA0i.set(this.xA+m,this.yA+p,this.zA-q);this.ptB0i.setT(this.ptA0i);
this.ptB0i.x+=this.dxB;this.ptB0i.y+=this.dyB;this.ptB0i.z+=this.dzB;this.line3d.plotLineDeltaABitsInt(this.shadesA,this.shadesB,G,this.ptA0i,this.ptB0i,d,this.clipped);e&&(this.ptA0i.set(this.xA-m,this.yA-p,this.zA+q),this.ptB0i.setT(this.ptA0i),this.ptB0i.x+=this.dxB,this.ptB0i.y+=this.dyB,this.ptB0i.z+=this.dzB,this.line3d.plotLineDeltaABitsInt(this.shadesA,this.shadesB,j,this.ptA0i,this.ptB0i,d,this.clipped))}k.setZMargin(0);3==f&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;
this.zAf+=this.dzBf}}},"~N,~N,~N,~N,~N,JU.P3i,JU.P3i");c(c$,"renderConeOld",function(a,b,d,f,c,e,h,k,l,j,m){this.dxBf=h-(this.xAf=f);this.dyBf=k-(this.yAf=c);this.dzBf=l-(this.zAf=e);this.xA=y(Math.floor(this.xAf));this.yA=y(Math.floor(this.yAf));this.zA=y(Math.floor(this.zAf));this.dxB=y(Math.floor(this.dxBf));this.dyB=y(Math.floor(this.dyBf));this.dzB=y(Math.floor(this.dzBf));this.xTip=h;this.yTip=k;this.zTip=l;this.shadesA=this.g3d.getShades(this.colixA=a);var p=this.shader.getShadeIndex(this.dxB,
this.dyB,-this.dzB);a=this.g3d;f=a.pixel;c=a.width;e=a.zbuf;a.plotPixelClippedArgb(this.shadesA[p],B(h),B(k),B(l),c,e,f);this.diameter=d;if(1>=d)1==d&&this.line3d.plotLineDeltaOld(this.colixA,this.colixA,this.xA,this.yA,this.zA,this.dxB,this.dyB,this.dzB,this.clipped);else{this.endcaps=b;this.calcArgbEndcap(!1,!0);this.generateBaseEllipsePrecisely(m);!m&&2==this.endcaps&&this.renderFlatEndcap(!1,!0,this.xyzfRaster);a.setZMargin(5);b=this.xyztRaster[0];d=this.xyztRaster[1];h=this.xyztRaster[2];k=this.xyzfRaster[3];
l=this.shadesA;for(var p=this.endCapHidden&&0!=this.argbEndcap,z=this.rasterCount;0<=--z;){var w=b[z],G=d[z],L=h[z],q=k[z]>>8,n=this.xAf+w,t=this.yAf+G,u=this.zAf-L,w=this.xAf-w,G=this.yAf-G,L=this.zAf+L,r=l[0];p&&(a.plotPixelClippedArgb(this.argbEndcap,B(n),B(t),B(u),c,e,f),a.plotPixelClippedArgb(this.argbEndcap,B(w),B(G),B(L),c,e,f));0!=r&&(this.line3d.plotLineDeltaAOld(l,l,0,q,B(n),B(t),B(u),y(Math.ceil(this.xTip-n)),y(Math.ceil(this.yTip-t)),y(Math.ceil(this.zTip-u)),!0),j&&(this.line3d.plotLineDeltaAOld(l,
l,0,q,B(n),B(t)+1,B(u),y(Math.ceil(this.xTip-n)),y(Math.ceil(this.yTip-t))+1,y(Math.ceil(this.zTip-u)),!0),this.line3d.plotLineDeltaAOld(l,l,0,q,B(n)+1,B(t),B(u),y(Math.ceil(this.xTip-n))+1,y(Math.ceil(this.yTip-t)),y(Math.ceil(this.zTip-u)),!0)),!m&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDeltaOld(r,r,B(w),B(G),B(L),y(Math.ceil(this.xTip-w)),y(Math.ceil(this.yTip-G)),y(Math.ceil(this.zTip-L)),!0))}a.setZMargin(0)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B,~B");c(c$,"generateBaseEllipsePrecisely",
function(a){this.calcCosSin(this.dxBf,this.dyBf,this.dzBf);this.calcPoints(a?2:3,!0);this.interpolatePrecisely(0,1,this.xyzfRaster,this.xyztRaster);a||this.interpolatePrecisely(1,2,this.xyzfRaster,this.xyztRaster);for(a=3;0<=--a;)for(var b=this.rasterCount;0<=--b;)this.xyzfRaster[a][b]=y(Math.floor(this.xyztRaster[a][b]))},"~B");c(c$,"calcPoints",function(a,b){this.calcRotatedPoint(0,0,b,this.xyzfRaster,this.xyztRaster);this.calcRotatedPoint(0.5,1,b,this.xyzfRaster,this.xyztRaster);3==(this.rasterCount=
a)&&this.calcRotatedPoint(1,2,b,this.xyzfRaster,this.xyztRaster)},"~N,~B");c(c$,"calcCosSin",function(a,b,d){var f=a*a+b*b;if(0==f)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var c=Math.sqrt(f),f=Math.sqrt(f+d*d);this.cosTheta=d/f;this.cosPhi=a/c;this.sinPhi=b/c}},"~N,~N,~N");c(c$,"calcRotatedPoint",function(a,b,d,f,c){c[3][b]=a;a*=3.141592653589793;var e=Math.sin(a)*this.cosTheta,h=Math.cos(a);a=this.radius*(e*this.cosPhi-h*this.sinPhi);e=this.radius*(e*this.sinPhi+h*this.cosPhi);h=this.radius2-
(a*a+e*e);h=0<h?Math.sqrt(h):0;d?(c[0][b]=a,c[1][b]=e,c[2][b]=h):(this.tEvenDiameter?(f[0][b]=y(a-0.5),f[1][b]=y(e-0.5)):(f[0][b]=y(a),f[1][b]=y(e)),f[2][b]=y(h+0.5));f[3][b]=this.shader.getShadeFp8(a,e,h)},"~N,~N,~B,~A,~A");c(c$,"allocRaster",function(a,b,d){if(this.rasterCount>=b[0].length)for(;this.rasterCount>=b[0].length;){for(var f=4;0<=--f;)b[f]=JU.AU.doubleLengthI(b[f]);d[3]=JU.AU.doubleLengthF(d[3])}if(a)for(;this.rasterCount>=d[0].length;)for(f=3;0<=--f;)d[f]=JU.AU.doubleLengthF(d[f]);return this.rasterCount++},
"~B,~A,~A");c(c$,"interpolate",function(a,b,d,f){var c=d[0],e=d[1],c=c[b]-c[a];0>c&&(c=-c);e=e[b]-e[a];0>e&&(e=-e);if(!(1>=c+e)){for(var h=this.allocRaster(!1,d,f),c=d[0],e=d[1],k=d[3],l=f[3][a],j=f[3][b],m=4;0<=--m;){var p=(l+j)/2;this.calcRotatedPoint(p,h,!1,d,f);if(c[h]==c[a]&&e[h]==e[a])k[a]=k[a]+k[h]>>>1,l=p;else if(c[h]==c[b]&&e[h]==e[b])k[b]=k[b]+k[h]>>>1,j=p;else{this.interpolate(a,h,d,f);this.interpolate(h,b,d,f);return}}c[h]=c[a];e[h]=e[b]}},"~N,~N,~A,~A");c(c$,"interpolatePrecisely",function(a,
b,d,f){var c=f[0],e=f[1],h=y(Math.floor(c[b]))-y(Math.floor(c[a]));0>h&&(h=-h);e=y(Math.floor(e[b]))-y(Math.floor(e[a]));0>e&&(e=-e);if(!(1>=h+e)){for(var e=f[3],h=e[a],k=e[b],l=this.allocRaster(!0,d,f),c=f[0],e=f[1],j=d[3],m=4;0<=--m;){var p=(h+k)/2;this.calcRotatedPoint(p,l,!0,d,f);if(y(Math.floor(c[l]))==y(Math.floor(c[a]))&&y(Math.floor(e[l]))==y(Math.floor(e[a])))j[a]=j[a]+j[l]>>>1,h=p;else if(y(Math.floor(c[l]))==y(Math.floor(c[b]))&&y(Math.floor(e[l]))==y(Math.floor(e[b])))j[b]=j[b]+j[l]>>>
1,k=p;else{this.interpolatePrecisely(a,l,d,f);this.interpolatePrecisely(l,b,d,f);return}}c[l]=c[a];e[l]=e[b]}},"~N,~N,~A,~A");c(c$,"renderFlatEndcap",function(a,b,d){var f,c;if(b){if(0==this.dzBf||!this.g3d.setC(this.colixEndcap))return;b=this.xAf;f=this.yAf;c=this.zAf;a&&0>this.dzBf&&(b+=this.dxBf,f+=this.dyBf,c+=this.dzBf);b=B(b);f=B(f);c=B(c)}else{if(0==this.dzB||!this.g3d.setC(this.colixEndcap))return;b=this.xA;f=this.yA;c=this.zA;a&&0>this.dzB&&(b+=this.dxB,f+=this.dyB,c+=this.dzB)}var e=d[1][0];
a=d[1][0];var h=0,k=0,l=d[0],j=d[1];d=d[2];for(var m=this.rasterCount;0<--m;){var p=j[m];p<e?e=p:p>a?a=p:(p=-p,p<e?e=p:p>a&&(a=p))}for(p=e;p<=a;++p){for(var e=2147483647,z=-2147483648,m=this.rasterCount;0<=--m;){if(j[m]==p){var w=l[m];w<e&&(e=w,h=d[m]);w>z&&(z=w,k=d[m])}j[m]==-p&&(w=-l[m],w<e&&(e=w,h=-d[m]),w>z&&(z=w,k=-d[m]))}m=z-e+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(m,b+e,f+p,c-h-1,c-k-1,null,null)}},"~B,~B,~A");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.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;this.endCapHidden=!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 f=b?this.dxBf:this.dxB,c=b?this.dyBf:this.dyB;0<=d||!a?(this.endcapShadeIndex=this.shader.getShadeIndex(-f,-c,d),this.colixEndcap=this.colixA,d=this.shadesA):(this.endcapShadeIndex=this.shader.getShadeIndex(f,c,-d),this.colixEndcap=this.colixB,d=this.shadesB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB);56<this.endcapShadeIndex&&(this.endcapShadeIndex=56);this.argbEndcap=d[this.endcapShadeIndex];this.endCapHidden=1==this.endcaps}},"~B,~B")});u("J.g3d");
N(J.g3d,"G3DRenderer");u("J.g3d");x(["J.api.JmolRendererInterface","JU.GData","JU.P3i","$.V3"],"J.g3d.Graphics3D","java.lang.NullPointerException java.util.Arrays javajs.awt.Font JU.AU J.api.Interface J.c.STER J.g3d.CylinderRenderer $.LineRenderer $.Pixelator $.PixelatorScreened $.PixelatorShaded $.PixelatorT $.Platform3D $.SphereRenderer $.TextRenderer $.TextString JU.C $.Normix".split(" "),function(){c$=r(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.$haveTranslucentObjects=this.twoPass=!1;this.zbufT=this.zbuf=this.pbufT=this.pbuf=null;this.translucencyMask=0;this.renderLow=!1;this.shadesCurrent=null;this.anaglyphLength=0;this.pixelShaded=this.pixelScreened=this.pixelT0=this.pixel0=this.pixel=null;this.zMargin=0;this.aobuf=null;this.translucencyLog=this.lastRawColor=this.currentShadeIndex=0;this.wasScreened=
!1;this.saveDiffuse=this.saveAmbient=0;this.shadeIndexes2Sided=this.shadeIndexes=this.vectorNormal=this.vectorAC=this.vectorAB=this.sC=this.sB=this.sA=null;this.pass2Flag01=0;n(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);O(c$,function(){this.sA=new JU.P3i;this.sB=new JU.P3i;this.sC=new JU.P3i;this.vectorAB=new JU.V3;this.vectorAC=new JU.V3;this.vectorNormal=new JU.V3;this.shadeIndexes=P(JU.GData.normixCount,0);this.shadeIndexes2Sided=P(JU.GData.normixCount,0)});j(c$,
"isWebGL",function(){return!1});j(c$,"clear",function(){this.stringCount=0;this.strings=null;J.g3d.TextRenderer.clearFontCache()});j(c$,"destroy",function(){this.releaseBuffers();this.graphicsForMetrics=this.pixelScreened=this.pixelT0=this.pixel=this.pixel0=this.pixelShaded=this.platform=null});c(c$,"setZMargin",function(a){this.zMargin=a},"~N");t(c$,function(){H(this,J.g3d.Graphics3D,[]);for(var a=JU.GData.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3});j(c$,"initialize",function(a,b){this.vwr=
a;this.apiPlatform=b;this.platform=new J.g3d.Platform3D(b);this.pixel=this.pixel0=new J.g3d.Pixelator(this);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)},"JV.Viewer,javajs.awt.GenericPlatform");j(c$,"addRenderer",function(a){switch(a){case 1073741880:null==this.circle3d&&(this.circle3d=this.getRenderer("Circle"));break;case 553648146:null==this.hermite3d&&
(this.hermite3d=this.getRenderer("Hermite"));case 1073742182:null==this.triangle3d&&(this.triangle3d=this.getRenderer("Triangle"),this.triangle3d.isOrthographic=!this.vwr.tm.perspectiveDepth)}},"~N");c(c$,"getRenderer",function(a){a=J.api.Interface.getOption("g3d."+a+"Renderer",this.vwr,"render");if(null==a)throw new NullPointerException("Interface");a.set(this,this);return a},"~S");j(c$,"setWindowParameters",function(a,b,d){this.setWinParams(a,b,d);this.currentlyRendering&&this.endRendering()},"~N,~N,~B");
j(c$,"checkTranslucent",function(a){a&&(this.$haveTranslucentObjects=!0);return!this.twoPass||this.twoPass&&this.isPass2==a},"~B");j(c$,"beginRendering",function(a,b,d,f){this.currentlyRendering&&this.endRendering();this.renderLow=f;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.line3d.isOrthographic=!this.vwr.tm.perspectiveDepth;null!=this.triangle3d&&(this.triangle3d.isOrthographic=!this.vwr.tm.perspectiveDepth);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=this.pass2Flag01=0;this.$haveTranslucentObjects=
this.wasScreened=!1;this.pixel=this.pixel0;this.pixel.bgcolor=this.bgcolor;this.translucentCoverOnly=!b;null==this.pbuf&&(this.platform.allocateBuffers(this.windowWidth,this.windowHeight,this.antialiasThisFrame,d),this.pbuf=this.platform.pBuffer,this.zbuf=this.platform.zBuffer,this.aobuf=null,this.pixel0.setBuf(),null!=this.pixelT0&&this.pixelT0.setBuf(),null!=this.pixelShaded&&this.pixelShaded.setBuf());this.setWidthHeight(this.antialiasThisFrame);null!=this.pixelScreened&&(this.pixelScreened.width=
this.width);this.platform.clearBuffer();null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,null,0,0,0);this.textY=0},"JU.M3,~B,~B,~B");j(c$,"setBackgroundTransparent",function(a){null!=this.platform&&this.platform.setBackgroundTransparent(a)},"~B");c(c$,"releaseBuffers",function(){this.aobuf=this.zbufT=this.pbufT=this.zbuf=this.pbuf=null;this.platform.releaseBuffers();this.line3d.clearLineCache()});j(c$,"setPass2",function(a){if(!this.$haveTranslucentObjects||
!this.currentlyRendering)return!1;this.isPass2=!0;this.pass2Flag01=1;this.colixCurrent=0;if(null==this.pbufT||this.antialias2!=a)this.platform.allocateTBuffers(a),this.pbufT=this.platform.pBufferT,this.zbufT=this.platform.zBufferT;this.antialias2=a;this.antialiasThisFrame&&!this.antialias2&&this.downsampleFullSceneAntialiasing(!0);this.platform.clearTBuffer();null==this.pixelT0&&(this.pixelT0=new J.g3d.PixelatorT(this));null==this.pixel.p0?this.pixel=this.pixelT0:this.pixel.p0=this.pixelT0;return!0},
"~B");j(c$,"endRendering",function(){if(this.currentlyRendering){if(null!=this.pbuf){if(this.isPass2&&null!=this.pbufT)for(var a=this.pbufT.length;0<=--a;)this.pbuf[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pbuf[a],this.pbufT[a],this.bgcolor);this.pixel===this.pixelShaded&&0==this.pixelShaded.zShadePower&&this.pixelShaded.showZBuffer();this.antialiasThisFrame&&this.downsampleFullSceneAntialiasing(!1)}this.platform.setBackgroundColor(this.bgcolor);this.platform.notifyEndOfRendering();this.currentlyRendering=
this.isPass2=!1}});c$.mergeBufferPixel=c(c$,"mergeBufferPixel",function(a,b,d){if(0==b||a==b)return a;0==a&&(a=d);d=a&16711935;a&=65280;var f=b&16711935,c=b&65280;switch(b>>24&15){case 0:d=f;a=c;break;case 1:d=(f<<2)+(f<<1)+f+d>>3&16711935;a=(c<<2)+ +(c<<1)+c+a>>3&65280;break;case 2:d=(f<<1)+f+d>>2&16711935;a=(c<<1)+c+a>>2&65280;break;case 3:d=(f<<2)+f+(d<<1)+d>>3&16711935;a=(c<<2)+c+(a<<1)+a>>3&65280;break;case 4:d=d+f>>1&16711935;a=a+c>>1&65280;break;case 5:d=(f<<1)+f+(d<<2)+d>>3&16711935;a=(c<<
1)+c+(a<<2)+a>>3&65280;break;case 6:d=(d<<1)+d+f>>2&16711935;a=(a<<1)+a+c>>2&65280;break;case 7:d=(d<<2)+(d<<1)+d+f>>3&16711935,a=(a<<2)+(a<<1)+a+c>>3&65280}return 4278190080|d|a},"~N,~N,~N");j(c$,"getScreenImage",function(a){var b=this.platform.bufferedImage;a&&this.releaseBuffers();return b},"~B");j(c$,"applyAnaglygh",function(a,b){switch(a){case J.c.STER.REDCYAN:for(var d=this.anaglyphLength;0<=--d;){var f=this.anaglyphChannelBytes[d]&255;this.pbuf[d]=this.pbuf[d]&4294901760|f<<8|f}break;case J.c.STER.CUSTOM:for(var f=
b[0],c=b[1]&16777215,d=this.anaglyphLength;0<=--d;){var e=this.anaglyphChannelBytes[d]&255,e=(e|(e|e<<8)<<8)&c;this.pbuf[d]=this.pbuf[d]&f|e}break;case J.c.STER.REDBLUE:for(d=this.anaglyphLength;0<=--d;)f=this.anaglyphChannelBytes[d]&255,this.pbuf[d]=this.pbuf[d]&4294901760|f;break;case J.c.STER.REDGREEN:for(d=this.anaglyphLength;0<=--d;)this.pbuf[d]=this.pbuf[d]&4294901760|(this.anaglyphChannelBytes[d]&255)<<8}},"J.c.STER,~A");j(c$,"snapshotAnaglyphChannelBytes",function(){if(this.currentlyRendering)throw new NullPointerException;
this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=P(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});j(c$,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});j(c$,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});j(c$,"setSlabAndZShade",function(a,b,d,f,c){this.setSlab(a);this.setDepth(b);
d<f?(null==this.pixelShaded&&(this.pixelShaded=new J.g3d.PixelatorShaded(this)),this.pixel=this.pixelShaded.set(d,f,c)):this.pixel=this.pixel0},"~N,~N,~N,~N,~N");c(c$,"downsampleFullSceneAntialiasing",function(a){var b=this.bgcolor;a&&(b+=255==(b&255)?-1:1);J.g3d.Graphics3D.downsample2d(this.pbuf,this.windowWidth,this.windowHeight,b);a&&(J.g3d.Graphics3D.downsample2dZ(this.pbuf,this.zbuf,this.windowWidth,this.windowHeight,b),this.antialiasThisFrame=!1,this.setWidthHeight(!1))},"~B");c$.downsample2d=
c(c$,"downsample2d",function(a,b,d,f){var c=b<<1;if(0!=f){f&=16777215;for(var e=a.length;0<=--e;)0==a[e]&&(a[e]=f)}for(var h=(f>>2&1061109567)<<2,h=h+((h&3233857728)>>6),k=0,l=0,e=d;0<=--e;l+=c)for(d=b;0<=--d;++k){var j=(a[l]>>2&1061109567)+(a[l++ +c]>>2&1061109567)+(a[l]>>2&1061109567)+(a[l++ +c]>>2&1061109567),j=j+((j&3233857728)>>6);j==h&&(j=f);a[k]=j&16777215|4278190080}},"~A,~N,~N,~N");c$.downsample2dZ=c(c$,"downsample2dZ",function(a,b,d,f,c){for(var e=d<<1,h=0,k=0;0<=--f;k+=e)for(var l=d;0<=
--l;++h,++k){var j=Math.min(b[k],b[k+e]),j=Math.min(j,b[++k]),j=Math.min(j,b[k+e]);2147483647!=j&&(j>>=1);b[h]=a[h]==c?2147483647:j}},"~A,~A,~N,~N,~N");c(c$,"hasContent",function(){return this.platform.hasContent()});j(c$,"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 f=0!=d,c=f&&30720==d;this.setScreened(c);if(!this.checkTranslucent(f&&!c))return!1;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$,"setScreened",function(a){this.wasScreened!=a&&((this.wasScreened=a)?(null==this.pixelScreened&&(this.pixelScreened=
new J.g3d.PixelatorScreened(this,this.pixel0)),null==this.pixel.p0?this.pixel=this.pixelScreened:this.pixel.p0=this.pixelScreened):null==this.pixel.p0||this.pixel===this.pixelScreened?this.pixel=this.isPass2?this.pixelT0:this.pixel0:this.pixel.p0=this.isPass2?this.pixelT0:this.pixel0);return this.pixel},"~B");j(c$,"drawFilledCircle",function(a,b,d,f,c,e){if(!this.isClippedZ(e)){var h=y((d+1)/2),h=f<h||f+h>=this.width||c<h||c+h>=this.height;if(!h||!this.isClippedXY(d,f,c))0!=a&&this.setC(a)&&(h?this.isClippedXY(d,
f,c)||this.circle3d.plotCircleCenteredClipped(f,c,e,d):this.circle3d.plotCircleCenteredUnclipped(f,c,e,d)),0!=b&&this.setC(b)&&(h?this.circle3d.plotFilledCircleCenteredClipped(f,c,e,d):this.circle3d.plotFilledCircleCenteredUnclipped(f,c,e,d))}},"~N,~N,~N,~N,~N,~N");j(c$,"volumeRender4",function(a,b,d,f){if(1==a)this.plotPixelClippedArgb(this.argbCurrent,b,d,f,this.width,this.zbuf,this.pixel);else if(!this.isClippedZ(f)){var c=y((a+1)/2),c=b<c||b+c>=this.width||d<c||d+c>=this.height;if(!c||!this.isClippedXY(a,
b,d))c?this.circle3d.plotFilledCircleCenteredClipped(b,d,f,a):this.circle3d.plotFilledCircleCenteredUnclipped(b,d,f,a)}},"~N,~N,~N,~N");j(c$,"fillSphereXYZ",function(a,b,d,f){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,b,d,f,this.width,this.zbuf,this.pixel);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,a,b,d,f,null,null,null,-1,null)},"~N,~N,~N,~N");j(c$,"volumeRender",function(a){a?(this.saveAmbient=this.getAmbientPercent(),this.saveDiffuse=
this.getDiffusePercent(),this.setAmbientPercent(100),this.setDiffusePercent(0),this.addRenderer(1073741880)):(this.setAmbientPercent(this.saveAmbient),this.setDiffusePercent(this.saveDiffuse))},"~B");j(c$,"fillSphereI",function(a,b){this.fillSphereXYZ(a,b.x,b.y,b.z)},"~N,JU.P3i");j(c$,"fillSphereBits",function(a,b){this.fillSphereXYZ(a,Math.round(b.x),Math.round(b.y),Math.round(b.z))},"~N,JU.P3");j(c$,"fillEllipsoid",function(a,b,d,f,c,e,h,k,l,j,m){switch(e){case 1:this.plotPixelClippedArgb(this.argbCurrent,
d,f,c,this.width,this.zbuf,this.pixel);return;case 0:return}e<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,e,d,f,c,h,k,l,j,m)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");j(c$,"drawRect",function(a,b,d,f,c,e){if(!(0!=f&&this.isClippedZ(f))){f=c-1;e-=1;c=a+f;var h=b+e;0<=b&&b<this.height&&this.drawHLine(a,b,d,f);0<=h&&h<this.height&&this.drawHLine(a,h,d,f);0<=a&&a<this.width&&this.drawVLine(a,b,d,e);0<=c&&c<this.width&&this.drawVLine(c,b,d,e)}},"~N,~N,~N,~N,~N,~N");
c(c$,"drawHLine",function(a,b,d,f){0>f&&(a+=f,f=-f);0>a&&(f+=a,a=0);a+f>=this.width&&(f=this.width-1-a);var c=this.pixel,e=this.argbCurrent;a+=this.width*b;for(b=0;b<=f;b++)d<this.zbuf[a]&&c.addPixel(a,d,e),a++},"~N,~N,~N,~N");c(c$,"drawVLine",function(a,b,d,f){0>f&&(b+=f,f=-f);0>b&&(f+=b,b=0);b+f>=this.height&&(f=this.height-1-b);a+=this.width*b;b=this.pixel;for(var c=this.argbCurrent,e=0;e<=f;e++)d<this.zbuf[a]&&b.addPixel(a,d,c),a+=this.width},"~N,~N,~N,~N");j(c$,"fillTextRect",function(a,b,d,
f,c,e){if(!this.isClippedZ(f)){f=this.width;if(0>a){c+=a;if(0>=c)return;a=0}if(a+c>f&&(c=f-a,0>=c))return;if(0>b){e+=b;if(0>=e)return;b=0}b+e>this.height&&(e=this.height-b);for(var h=this.argbCurrent,k=this.zbuf,l=this.pixel;0<=--e;)this.plotPixelsUnclippedCount(h,c,a,b++,d,f,k,l)}},"~N,~N,~N,~N,~N,~N");j(c$,"drawString",function(a,b,d,f,c,e,h){this.currentShadeIndex=0;null!=a&&(this.isClippedZ(e)||this.drawStringNoSlab(a,b,d,f,c,h))},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");j(c$,"drawStringNoSlab",function(a,
b,d,f,c,e){if(null!=a){null==this.strings&&(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));var h=new J.g3d.TextString;h.setText(a,null==b?this.currentFont:this.currentFont=b,this.argbCurrent,JU.C.isColixTranslucent(e)?this.getColorArgbOrGray(e)&16777215|(e&30720)<<13:0,d,f,c);this.strings[this.stringCount++]=h}},"~S,javajs.awt.Font,~N,~N,~N,~N");j(c$,"renderAllStrings",function(a){if(null!=this.strings){2<=this.stringCount&&(null==J.g3d.Graphics3D.sort&&
(J.g3d.Graphics3D.sort=new J.g3d.TextString),java.util.Arrays.sort(this.strings,J.g3d.Graphics3D.sort));for(var b=0;b<this.stringCount;b++){var d=this.strings[b];this.plotText(d.x,d.y,d.z,d.argb,d.bgargb,d.text,d.font,a)}this.strings=null;this.stringCount=0}},"~O");j(c$,"plotText",function(a,b,d,f,c,e,h,k){J.g3d.TextRenderer.plot(a,b,d,f,c,e,h,this,k,this.antialiasThisFrame)},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.api.JmolRendererInterface");j(c$,"drawImage",function(a,b,d,f,c,e,h,k){null!=a&&(0<h&&
0<k&&!this.isClippedZ(c))&&this.plotImage(b,d,f,a,null,e,h,k)},"~O,~N,~N,~N,~N,~N,~N,~N");j(c$,"plotImage",function(a,b,d,f,c,e,h,k){this.setC(e);this.isPass2||(this.translucencyMask=-1);0==e&&(this.argbCurrent=0);var l=-2147483648==a;e=l?this.bgcolor:this.argbCurrent;l&&(a=0,d=2147483646,h=this.width,k=this.height);if(!(0>=a+h||a>=this.width||0>=b+k||b>=this.height))if(f=this.apiPlatform.drawImageToBuffer(null,this.platform.offscreenImage,f,h,k,l?e:0),null!=f){var l=this.zbuf,j=this.width,m=this.pixel,
p=this.height,z=this.translucencyLog;if(null==c&&0<=a&&a+h<=j&&0<=b&&b+k<=p){var w=0,G=0;for(a=b*j+a;w<k;w++,a+=j-h)for(var L=0;L<h;L++,G++,a++)if(d<l[a]){var q=f[G];-16777216==(q&4278190080)&&m.addPixel(a,d,q)}}else{null==c&&(c=this);for(G=w=0;w<k;w++)for(L=0;L<h;L++)q=f[G++],-16777216==(q&4278190080)&&c.plotImagePixel(q,a+L,b+w,d,8,e,j,p,l,m,z)}}},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");j(c$,"setFontFid",function(a){this.currentFont=javajs.awt.Font.getFont3D(a)},"~N");j(c$,"setFont",
function(a){this.currentFont=a},"javajs.awt.Font");j(c$,"drawPixel",function(a,b,d){this.plotPixelClippedArgb(this.argbCurrent,a,b,d,this.width,this.zbuf,this.pixel)},"~N,~N,~N");j(c$,"drawPoints",function(a,b,d){if(1<d)for(var f=0.8*d*d,c=-d;c<d;c++)for(var e=-d;e<d;e++)c*c+e*e>f||(this.plotPoints(a,b,c,e),this.plotPoints(a,b,c,e));else this.plotPoints(a,b,0,0)},"~N,~A,~N");j(c$,"drawDashedLineBits",function(a,b,d,f){this.setScreeni(d,this.sA);this.setScreeni(f,this.sB);this.line3d.plotLineBits(this.argbCurrent,
this.argbCurrent,this.sA,this.sB,a,b,!0)},"~N,~N,JU.P3,JU.P3");c(c$,"setScreeni",function(a,b){b.x=Math.round(a.x);b.y=Math.round(a.y);b.z=Math.round(a.z)},"JU.P3,JU.P3i");j(c$,"drawLineXYZ",function(a,b,d,f,c,e){this.line3d.plotLineOld(this.argbCurrent,this.argbCurrent,a,b,d,f,c,e)},"~N,~N,~N,~N,~N,~N");j(c$,"drawLine",function(a,b,d,f,c,e,h,k){this.setC(a)||(a=0);var l=this.argbCurrent;this.setC(b)||(b=0);(0!=a||0!=b)&&this.line3d.plotLineOld(l,this.argbCurrent,d,f,c,e,h,k)},"~N,~N,~N,~N,~N,~N,~N,~N");
j(c$,"drawLineBits",function(a,b,d,f){this.setC(a)||(a=0);var c=this.argbCurrent;this.setC(b)||(b=0);if(0!=a||0!=b)this.setScreeni(d,this.sA),this.setScreeni(f,this.sB),this.line3d.plotLineBits(c,this.argbCurrent,this.sA,this.sB,0,0,!1)},"~N,~N,JU.P3,JU.P3");j(c$,"drawLineAB",function(a,b){this.setScreeni(a,this.sA);this.setScreeni(b,this.sB);this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,0,0,!1)},"JU.P3,JU.P3");j(c$,"fillCylinderXYZ",function(a,b,d,f,c,e,h,k,l,j){if(!(f>
this.ht3)){var m=0;this.currentShadeIndex=0;this.setC(b)||(b=0);this.wasScreened&&(m=2);this.setC(a)||(a=0);this.wasScreened&&(m+=1);0==a&&0==b||this.cylinder3d.renderOld(a,b,m,d,f,c,e,h,k,l,j)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");j(c$,"fillCylinderScreen3I",function(a,b,d,f){b<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,this.colixCurrent,0,a,b,B(d.x),B(d.y),B(d.z),B(f.x),B(f.y),B(f.z))},"~N,~N,JU.P3,JU.P3,JU.P3,JU.P3,~N");j(c$,"fillCylinder",function(a,b,d,f){b<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,
this.colixCurrent,0,a,b,d.x,d.y,d.z,f.x,f.y,f.z)},"~N,~N,JU.P3i,JU.P3i");j(c$,"fillCylinderBits",function(a,b,d,f){b<=this.ht3&&(1!=d.z&&1!=f.z)&&(0==b||1==b?(this.setScreeni(d,this.sA),this.setScreeni(f,this.sB),this.line3d.plotLineBits(this.getColorArgbOrGray(this.colixCurrent),this.getColorArgbOrGray(this.colixCurrent),this.sA,this.sB,0,0,!1)):this.cylinder3d.renderBitsFloat(this.colixCurrent,this.colixCurrent,0,a,b,d,f))},"~N,~N,JU.P3,JU.P3");j(c$,"fillCylinderBits2",function(a,b,d,f,c,e){if(!(f>
this.ht3)){var h=0;this.currentShadeIndex=0;this.setC(b)||(b=0);this.wasScreened&&(h=2);this.setC(a)||(a=0);this.wasScreened&&(h+=1);0==a&&0==b||(this.setScreeni(c,this.sA),this.setScreeni(e,this.sB),this.cylinder3d.renderBits(a,b,h,d,f,this.sA,this.sB))}},"~N,~N,~N,~N,JU.P3,JU.P3");j(c$,"fillConeScreen3f",function(a,b,d,f,c){b<=this.ht3&&this.cylinder3d.renderConeOld(this.colixCurrent,a,b,d.x,d.y,d.z,f.x,f.y,f.z,!0,c)},"~N,~N,JU.P3,JU.P3,~B");j(c$,"drawHermite4",function(a,b,d,f,c){this.hermite3d.renderHermiteRope(!1,
a,0,0,0,b,d,f,c)},"~N,JU.P3,JU.P3,JU.P3,JU.P3");j(c$,"drawHermite7",function(a,b,d,f,c,e,h,k,l,j,m,p,z){if(0==z)this.hermite3d.renderHermiteRibbon(a,b,d,f,c,e,h,k,l,j,m,p,0);else{this.hermite3d.renderHermiteRibbon(a,b,d,f,c,e,h,k,l,j,m,p,1);var w=this.colixCurrent;this.setC(z);this.hermite3d.renderHermiteRibbon(a,b,d,f,c,e,h,k,l,j,m,p,-1);this.setC(w)}},"~B,~B,~N,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,~N,~N");j(c$,"fillHermite",function(a,b,d,f,c,e,h,k){this.hermite3d.renderHermiteRope(!0,
a,b,d,f,c,e,h,k)},"~N,~N,~N,~N,JU.P3,JU.P3,JU.P3,JU.P3");j(c$,"drawTriangle3C",function(a,b,d,f,c,e,h){1==(h&1)&&this.drawLine(b,f,a.x,a.y,a.z,d.x,d.y,d.z);2==(h&2)&&this.drawLine(f,e,d.x,d.y,d.z,c.x,c.y,c.z);4==(h&4)&&this.drawLine(b,e,a.x,a.y,a.z,c.x,c.y,c.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");j(c$,"fillTriangleTwoSided",function(a,b,d,c){this.setColorNoisy(this.getShadeIndex(a));this.fillTriangleP3f(b,d,c,!1)},"~N,JU.P3,JU.P3,JU.P3");c(c$,"fillTriangleP3f",function(a,b,d,c){this.setScreeni(a,
this.sA);this.setScreeni(b,this.sB);this.setScreeni(d,this.sC);this.triangle3d.fillTriangle(this.sA,this.sB,this.sC,c)},"JU.P3,JU.P3,JU.P3,~B");j(c$,"fillTriangle3f",function(a,b,d,c){var g=this.getShadeIndexP3(a,b,d,c);0>g||(c?this.setColorNoisy(g):this.setColor(this.shadesCurrent[g]),this.fillTriangleP3f(a,b,d,!1))},"JU.P3,JU.P3,JU.P3,~B");j(c$,"fillTriangle3i",function(a,b,d,c,g,e,h){h&&(c=this.vectorAB,c.set(b.x-a.x,b.y-a.y,b.z-a.z),null==d?c=this.shader.getShadeIndex(-c.x,-c.y,c.z):(this.vectorAC.set(d.x-
a.x,d.y-a.y,d.z-a.z),c.cross(c,this.vectorAC),c=0<=c.z?this.shader.getShadeIndex(-c.x,-c.y,c.z):this.shader.getShadeIndex(c.x,c.y,-c.z)),56<c&&(c=56),this.setColorNoisy(c));this.fillTriangleP3f(a,b,d,!1)},"JU.P3,JU.P3,JU.P3,JU.T3,JU.T3,JU.T3,~B");j(c$,"fillTriangle3CN",function(a,b,d,c,g,e,h,k,l){this.triangle3d.fillTriangle(a,c,h,this.checkGouraud(b,g,k,d,e,l))},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");j(c$,"fillTriangle3CNBits",function(a,b,d,c,g,e,h,k,l){this.fillTriangleP3f(a,c,h,this.checkGouraud(b,
g,k,d,e,l))},"JU.P3,~N,~N,JU.P3,~N,~N,JU.P3,~N,~N,~B");c(c$,"checkGouraud",function(a,b,d,c,g,e){if(!this.isPass2&&c==g&&c==e&&a==b&&a==d){b=this.getShadeIndex(c);if(a!=this.colixCurrent||this.currentShadeIndex!=b)this.currentShadeIndex=-1,this.setC(a),this.setColorNoisy(b);return!1}this.setTriangleTranslucency(a,b,d);this.triangle3d.setGouraud(this.getShades(a)[this.getShadeIndex(c)],this.getShades(b)[this.getShadeIndex(g)],this.getShades(d)[this.getShadeIndex(e)]);return!0},"~N,~N,~N,~N,~N,~N");
c(c$,"getShadeIndex",function(a){return-1E4==a||9999==a?J.g3d.Graphics3D.nullShadeIndex:0>a?this.shadeIndexes2Sided[~a]:this.shadeIndexes[a]},"~N");c(c$,"setTriangleTranslucency",function(a,b,d){this.isPass2&&(a&=14336,b&=14336,d&=14336,this.translucencyMask=(JU.GData.roundInt(y((a+b+d)/3))&30720)<<13|16777215)},"~N,~N,~N");j(c$,"fillQuadrilateral",function(a,b,d,c,g){g=this.getShadeIndexP3(a,b,d,g);0>g||(this.setColorNoisy(g),this.fillTriangleP3f(a,b,d,!1),this.fillTriangleP3f(a,d,c,!1))},"JU.P3,JU.P3,JU.P3,JU.P3,~B");
j(c$,"drawSurface",function(){},"JU.MeshSurface,~N");j(c$,"plotPixelClippedP3i",function(a){this.plotPixelClippedArgb(this.argbCurrent,a.x,a.y,a.z,this.width,this.zbuf,this.pixel)},"JU.P3i");c(c$,"plotPixelClippedArgb",function(a,b,d,c,g,e,h){this.isClipped3(b,d,c)||(b=d*g+b,c<e[b]&&h.addPixel(b,c,a))},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotPixelUnclipped",function(a,b,d,c,g,e,h){b=d*g+b;c<e[b]&&h.addPixel(b,c,a)},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotImagePixel",function(a,b,d,c,
g,e,h,k,l,j,m){0>b||(b>=h||0>d||d>=k)||j.addImagePixel(g,m,d*h+b,c,a,e)},"~N,~N,~N,~N,~N,~N,~N,~N,~A,~O,~N");c(c$,"plotPixelsClippedRaster",function(a,b,d,c,g,e,h){var k,l;if(!(0>=a||0>d||d>=this.height||b>=this.width||c<(l=this.slab)&&g<l||c>(k=this.depth)&&g>k)){var j=this.zbuf,m=(b<<16)+(d<<1)^858993459,p=(c<<10)+512;c=g-c;g=y(a/2);c=JU.GData.roundInt(y(((c<<10)+(0<=c?g:-g))/a));if(0>b){b=-b;p+=c*b;a-=b;if(0>=a)return;b=0}a+b>this.width&&(a=this.width-b);b=d*this.width+b;d=this.pixel;if(null==
e){e=this.argbNoisyDn;g=this.argbNoisyUp;for(var z=this.argbCurrent;0<=--a;){h=p>>10;if(h>=l&&h<=k&&h<j[b]){var m=(m<<16)+(m<<1)+m&2147483647,w=m>>16&7;d.addPixel(b,h,0==w?e:1==w?g:z)}++b;p+=c}}else{m=e.r<<8;g=y((h.r-e.r<<8)/a);z=e.g;w=y((h.g-z)/a);e=e.b;for(var G=y((h.b-e)/a);0<=--a;)h=p>>10,h>=l&&(h<=k&&h<j[b])&&d.addPixel(b,h,4278190080|m&16711680|z&65280|e>>8&255),++b,p+=c,m+=g,z+=w,e+=G}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsUnclippedRaster",function(a,b,d,c,g,e,h){if(!(0>=a)){var k=
((b<<16)+(d<<1)^858993459)&2147483647,l=(c<<10)+512;c=g-c;g=y(a/2);c=JU.GData.roundInt(y(((c<<10)+(0<=c?g:-g))/a));b=d*this.width+b;d=this.zbuf;g=this.pixel;if(null==e){e=this.argbNoisyDn;for(var j=this.argbNoisyUp,m=this.argbCurrent;0<=--a;){h=l>>10;if(h<d[b]){var k=(k<<16)+(k<<1)+k&2147483647,p=k>>16&7;g.addPixel(b,h,0==p?e:1==p?j:m)}++b;l+=c}}else{k=e.r<<8;j=JU.GData.roundInt(y((h.r-e.r<<8)/a));m=e.g;p=JU.GData.roundInt(y((h.g-m)/a));e=e.b;for(var z=JU.GData.roundInt(y((h.b-e)/a));0<=--a;)h=l>>
10,h<d[b]&&g.addPixel(b,h,4278190080|k&16711680|m&65280|e>>8&255),++b,l+=c,k+=j,m+=p,e+=z}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsClippedRasterBits",function(a,b,d,c,g,e,h,k,l){var j,m;if(!(0>=a||0>d||d>=this.height||b>=this.width||c<(m=this.slab)&&g<m||c>(j=this.depth)&&g>j)){c=this.zbuf;var p=(b<<16)+(d<<1)^858993459;if(0>b){a-=-b;if(0>=a)return;b=0}a+b>this.width&&(a=this.width-b);d=d*this.width+b;g=this.pixel;if(null==e){e=this.argbNoisyDn;for(var z=this.argbNoisyUp,w=this.argbCurrent;0<=
--a;){h=this.line3d.getZCurrent(k,l,b++);if(h>=m&&h<=j&&h<c[d]){var p=(p<<16)+(p<<1)+p&2147483647,G=p>>16&7;g.addPixel(d,h,2>G?e:6>G?z:w)}++d}}else{p=e.r<<8;z=y((h.r-e.r<<8)/a);w=e.g;G=y((h.g-w)/a);e=e.b;for(var L=y((h.b-e)/a);0<=--a;)h=this.line3d.getZCurrent(k,l,b++),h>=m&&(h<=j&&h<c[d])&&g.addPixel(d,h,4278190080|p&16711680|w&65280|e>>8&255),++d,p+=z,w+=G,e+=L}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(c$,"plotPixelsUnclippedRasterBits",function(a,b,d,c,g,e,h){if(!(0>=a)){var k=((b<<16)+(d<<
1)^858993459)&2147483647;d=d*this.width+b;var l=this.zbuf,j=this.pixel;if(null==c)for(var m=this.argbNoisyDn,p=this.argbNoisyUp,z=this.argbCurrent;0<=--a;)g=this.line3d.getZCurrent(e,h,b++),g<l[d]&&(k=(k<<16)+(k<<1)+k&2147483647,c=k>>16&7,j.addPixel(d,g,0==c?m:1==c?p:z)),++d;else{k=c.r<<8;m=JU.GData.roundInt(y((g.r-c.r<<8)/a));p=c.g;z=JU.GData.roundInt(y((g.g-p)/a));c=c.b;for(var w=JU.GData.roundInt(y((g.b-c)/a));0<=--a;)g=this.line3d.getZCurrent(e,h,b++),g<l[d]&&j.addPixel(d,g,4278190080|k&16711680|
p&65280|c>>8&255),++d,k+=m,p+=z,c+=w}}},"~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(c$,"plotPixelsUnclippedCount",function(a,b,d,c,g,e,h,k){for(d=c*e+d;0<=--b;)g<h[d]&&k.addPixel(d,g,a),++d},"~N,~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotPoints",function(a,b,d,c){var g=this.pixel,e=this.argbCurrent,h=this.zbuf,k=this.width,l=this.antialiasThisFrame;for(a*=3;0<a;){var j=b[--a],m=b[--a]+c,p=b[--a]+d;if(!this.isClipped3(p,m,j)){var z=m*k+p++;j<h[z]&&g.addPixel(z,j,e);l&&(z=m*k+p,!this.isClipped3(p,m,j)&&
j<h[z]&&g.addPixel(z,j,e),z=++m*k+p,!this.isClipped3(p,m,j)&&j<h[z]&&g.addPixel(z,j,e),z=m*k+--p,!this.isClipped3(p,m,j)&&j<h[z]&&g.addPixel(z,j,e))}}},"~N,~A,~N,~N");c(c$,"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");c(c$,"getShadeIndexP3",function(a,b,d,c){this.vectorAB.sub2(b,a);this.vectorAC.sub2(d,a);a=this.vectorNormal;a.cross(this.vectorAB,this.vectorAC);
return 0>a.z?this.shader.getShadeIndex(a.x,a.y,-a.z):c?-1:this.shader.getShadeIndex(-a.x,-a.y,a.z)},"JU.P3,JU.P3,JU.P3,~B");j(c$,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");j(c$,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,a.sY,a.sZ)},"JM.Atom,~N");j(c$,"getExportType",function(){return 0});j(c$,"getExportName",function(){return null});c(c$,"canDoTriangles",function(){return!0});
c(c$,"isCartesianExport",function(){return!1});j(c$,"initializeExporter",function(){return null},"JV.Viewer,~N,JU.GData,java.util.Map");j(c$,"finalizeOutput",function(){return null});j(c$,"drawBond",function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");j(c$,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(c$,"getPrivateKey",function(){return 0});j(c$,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});c(c$,"setRotationMatrix",function(a){for(var b=JU.Normix.getVertexVectors(),d=
JU.GData.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");j(c$,"renderCrossHairs",function(a,b,d,c,g){b=this.isAntialiased();this.setC(0>g?10:100<g?11:23);g=Math.max(Math.min(this.width,Math.round(c.x)),0);d=Math.max(Math.min(this.height,Math.round(c.y)),0);var e=Math.round(c.z)+1,h=b?8:4,k=b?20:10;b=b?2:1;this.drawRect(g-
h,d,e,0,k,b);this.drawRect(g,d-h,e,0,b,k);this.drawRect(g-h,d-h,e,0,k,k);h=k;k>>=1;this.setC(a[1]<c.x?21:11);this.drawRect(g-h,d,e,0,k,b);this.setC(a[0]>c.x?21:11);this.drawRect(g+k,d,e,0,k,b);this.setC(a[3]<c.y?21:11);this.drawRect(g,d-h,e,0,b,k);this.setC(a[2]>c.y?21:11);this.drawRect(g,d+k,e,0,b,k)},"~A,~N,~N,JU.P3,~N");j(c$,"initializeOutput",function(){return!1},"JV.Viewer,~N,java.util.Map");F(c$,"sort",null,"nullShadeIndex",50)});u("J.g3d");x(["J.g3d.PrecisionRenderer","java.util.Hashtable"],
"J.g3d.LineRenderer",["java.lang.Float","JU.BS"],function(){c$=r(function(){this.lineBits=this.shader=this.g3d=null;this.slope=0;this.lineTypeX=!1;this.nBits=0;this.slopeKey=this.lineCache=null;this.z2t=this.y2t=this.x2t=this.z1t=this.y1t=this.x1t=0;n(this,arguments)},J.g3d,"LineRenderer",J.g3d.PrecisionRenderer);O(c$,function(){this.lineCache=new java.util.Hashtable});t(c$,function(a){H(this,J.g3d.LineRenderer,[]);this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"setLineBits",function(a,
b){this.slope=0!=a?b/a:0<=b?3.4028235E38:-3.4028235E38;this.nBits=(this.lineTypeX=1>=this.slope&&-1<=this.slope)?this.g3d.width:this.g3d.height;this.slopeKey=Float.$valueOf(this.slope);if(this.lineCache.containsKey(this.slopeKey))this.lineBits=this.lineCache.get(this.slopeKey);else{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,g=b+b,e=0;e<this.nBits;e++)d+=g,d>a&&(this.lineBits.set(e),d-=c);this.lineCache.put(this.slopeKey,this.lineBits)}},
"~N,~N");c(c$,"clearLineCache",function(){this.lineCache.clear()});c(c$,"plotLineOld",function(a,b,d,c,g,e,h,k){this.x1t=d;this.x2t=e;this.y1t=c;this.y2t=h;this.z1t=g;this.z2t=k;var l=!0;switch(this.getTrimmedLineImpl()){case 0:l=!1;break;case 2:return}this.plotLineClippedOld(a,b,d,c,g,e-d,h-c,k-g,l,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"plotLineDeltaOld",function(a,b,d,c,g,e,h,k,l){this.x1t=d;this.x2t=d+e;this.y1t=c;this.y2t=c+h;this.z1t=g;this.z2t=g+k;if(l)switch(this.getTrimmedLineImpl()){case 2:return;
case 0:l=!1}this.plotLineClippedOld(a,b,d,c,g,e,h,k,l,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaAOld",function(a,b,d,c,g,e,h,k,l,j,m){this.x1t=g;this.x2t=g+k;this.y1t=e;this.y2t=e+l;this.z1t=h;this.z2t=h+j;if(m)switch(this.getTrimmedLineImpl()){case 2:return;case 0:m=!1}var p=this.g3d.zbuf,z=this.g3d.width,w=0,G=e*z+g,L=this.g3d.bufferSize,q=63>c?c+1:c,n=0<c?c-1:c,t=a[q],u=a[n],r=b[c],q=b[q];b=b[n];a=a[c];c=this.g3d.pixel;0!=d&&(c=this.g3d.setScreened(1==(d&1)),this.g3d.currentShadeIndex=
0);0!=a&&(!m&&0<=G&&G<L&&h<p[G])&&c.addPixel(G,h,a);if(!(0==k&&0==l)){m=1;n=z;g+=k;var v=e+l;0>k&&(k=-k,m=-1);0>l&&(l=-l,n=-z);z=k+k;e=l+l;h<<=10;if(l<=k){var x=k-1;0>j&&(x=-x);j=y(((j<<10)+x)/k);l=0;x=Math.abs(g-this.x2t)-1;g=Math.abs(g-this.x1t)-1;for(var v=k-1,B=y(v/2);--v>=x;){if(v==B){a=r;if(0==a)break;t=q;u=b;0!=d%3&&(c=this.g3d.setScreened(2==(d&2)),this.g3d.currentShadeIndex=0)}G+=m;h+=j;l+=e;l>k&&(G+=n,l-=z);if(0!=a&&v<g&&0<=G&&G<L&&2147483647>w){var A=h>>10;if(A<p[G]){var C=this.shader.nextRandom8Bit();
c.addPixel(G,A,85>C?u:170<C?t:a)}}w=(w+1)%1}}else{x=l-1;0>j&&(x=-x);j=y(((j<<10)+x)/l);k=0;x=Math.abs(v-this.y2t)-1;g=Math.abs(v-this.y1t)-1;v=l-1;for(B=y(v/2);--v>=x;){if(v==B){a=r;if(0==a)break;t=q;u=b;0!=d%3&&(c=this.g3d.setScreened(2==(d&2)),this.g3d.currentShadeIndex=0)}G+=n;h+=j;k+=z;k>l&&(G+=m,k-=e);0!=a&&(v<g&&0<=G&&G<L&&2147483647>w)&&(A=h>>10,A<p[G]&&(C=this.g3d.shader.nextRandom8Bit(),c.addPixel(G,A,85>C?u:170<C?t:a)));w=(w+1)%1}}}},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaABitsFloat",
function(a,b,d,c,g,e,h){var k=Math.round(c.x),l=Math.round(c.y),j=Math.round(c.z),m=Math.round(g.x),p=Math.round(g.y),z=Math.round(g.z),w=m-k,G=p-l;this.x1t=k;this.x2t=m;this.y1t=l;this.y2t=p;this.z1t=j;this.z2t=z;if(!(h&&2==this.getTrimmedLineImpl())){h=this.g3d.zbuf;var q=this.g3d.width,m=0,z=63>d?d+1:d,p=0<d?d-1:d,n=a[d],t=a[z],u=a[p];d=b[d];a=b[z];b=b[p];var p=l*q+k,z=this.g3d.bufferSize,r,v,x,A;this.lineTypeX?(r=k,v=this.x1t,x=this.x2t,k+=y(w/2),A=l=0<=w?1:-1,w=0<=G?q:-q,this.setRastABFloat(c.x,
c.z,g.x,g.z)):(r=l,v=this.y1t,x=this.y2t,k=l+y(G/2),l=0<=G?1:-1,A=0<=G?q:-q,w=0<=w?1:-1,this.setRastABFloat(c.y,c.z,g.y,g.z));c=j;g=n;j=t;G=u;t=!1;u=this.g3d.pixel;0!=e&&(u=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(n=r;;n+=l,r+=l){n==v&&(t=!0);if(n==k){g=d;if(0==g)break;j=a;G=b;0!=e%3&&(u=this.g3d.setScreened(2==(e&2)),this.g3d.currentShadeIndex=0)}0!=g&&(t&&0<=p&&p<z&&2147483647>m)&&(c=this.getZCurrent(this.a,this.b,n),c<h[p]&&(q=this.shader.nextRandom8Bit(),u.addPixel(p,B(c),
85>q?G:170<q?j:g)));if(n==x)break;m=(m+1)%1;for(p+=A;0>r;)r+=this.nBits;this.lineBits.get(r%this.nBits)&&(p+=w)}}},"~A,~A,~N,JU.P3,JU.P3,~N,~B");c(c$,"plotLineDeltaABitsInt",function(a,b,d,c,g,e,h){var k=c.x,l=c.y,j=c.z,m=g.x,p=g.y,z=g.z,w=m-k,G=p-l;this.x1t=k;this.x2t=m;this.y1t=l;this.y2t=p;this.z1t=j;this.z2t=z;if(!(h&&2==this.getTrimmedLineImpl())){h=this.g3d.zbuf;var q=this.g3d.width,m=0,z=63>d?d+1:d,p=0<d?d-1:d,n=a[d],t=a[z],u=a[p];d=b[d];a=b[z];b=b[p];var p=l*q+k,z=this.g3d.bufferSize,r,v,
x,A;this.lineTypeX?(r=k,v=this.x1t,x=this.x2t,k+=y(w/2),A=l=0<=w?1:-1,w=0<=G?q:-q,this.setRastAB(c.x,c.z,g.x,g.z)):(r=l,v=this.y1t,x=this.y2t,k=l+y(G/2),l=0<=G?1:-1,A=0<=G?q:-q,w=0<=w?1:-1,this.setRastAB(c.y,c.z,g.y,g.z));c=j;g=n;j=t;G=u;t=!1;u=this.g3d.pixel;0!=e&&(u=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(n=r;;n+=l,r+=l){n==v&&(t=!0);if(n==k){g=d;if(0==g)break;j=a;G=b;0!=e%3&&(u=this.g3d.setScreened(2==(e&2)),this.g3d.currentShadeIndex=0)}0!=g&&(t&&0<=p&&p<z&&2147483647>
m)&&(c=this.getZCurrent(this.a,this.b,n),c<h[p]&&(q=this.shader.nextRandom8Bit(),u.addPixel(p,B(c),85>q?G:170<q?j:g)));if(n==x)break;m=(m+1)%1;for(p+=A;0>r;)r+=this.nBits;this.lineBits.get(r%this.nBits)&&(p+=w)}}},"~A,~A,~N,JU.P3i,JU.P3i,~N,~B");c(c$,"plotLineBits",function(a,b,d,c,g,e,h){if(!(1>=d.z||1>=c.z)){var k=!0;this.x1t=d.x;this.y1t=d.y;this.z1t=d.z;this.x2t=c.x;this.y2t=c.y;this.z2t=c.z;switch(this.getTrimmedLineImpl()){case 2:return;case 0:k=!1;break;default:h&&(d.set(this.x1t,this.y1t,
this.z1t),c.set(this.x2t,this.y2t,this.z2t))}h=this.g3d.zbuf;var l=this.g3d.width,j=0;0==g&&(e=2147483647,g=1);var m=d.x,p=d.y,z=d.z,w=c.x-m,q=m+w,L=c.y-p,n=p+L,r=p*l+m,u=this.g3d.bufferSize,t=this.g3d.pixel;0!=a&&(!k&&0<=r&&r<u&&z<h[r])&&t.addPixel(r,z,a);if(!(0==w&&0==L)){var v=k=1,z=l;0>w&&(w=-w,k=-1);0>L&&(L=-L,z=-l,v=-1);var l=w+w,x=L+L;if(L<=w){this.setRastAB(d.x,d.z,c.x,c.z);p=0;d=Math.abs(q-this.x2t)-1;q=Math.abs(q-this.x1t)-1;n=w-1;for(c=y(n/2);--n>=d&&!(n==c&&(a=b,0==a));){r+=k;m+=k;p+=
x;p>w&&(r+=z,p-=l);if(0!=a&&n<q&&0<=r&&r<u&&j<e){var A=this.getZCurrent(this.a,this.b,m);A<h[r]&&t.addPixel(r,A,a)}j=(j+1)%g}}else{this.setRastAB(d.y,d.z,c.y,c.z);m=0;d=Math.abs(n-this.y2t)-1;q=Math.abs(n-this.y1t)-1;n=L-1;for(c=y(n/2);--n>=d&&!(n==c&&(a=b,0==a));)r+=z,p+=v,m+=l,m>L&&(r+=k,m-=x),0!=a&&(n<q&&0<=r&&r<u&&j<e)&&(A=this.getZCurrent(this.a,this.b,p),A<h[r]&&t.addPixel(r,A,a)),j=(j+1)%g}}}},"~N,~N,JU.P3i,JU.P3i,~N,~N,~B");c(c$,"getTrimmedLineImpl",function(){var a=this.g3d.clipCode3(this.x1t,
this.y1t,this.z1t),b=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t);if(0==(a|b))return 0;if(-1==(a|b))return 2;var d=this.g3d.xLast,c=this.g3d.yLast,g=this.g3d.slab,e=this.g3d.depth;do{if(0!=(a&b))return 2;var h=this.x2t-this.x1t,k=this.y2t-this.y1t,l=this.z2t-this.z1t;0!=a?(0!=(a&8)?(this.y1t+=B(-this.x1t*k/h),this.z1t+=B(-this.x1t*l/h),this.x1t=0):0!=(a&4)?(this.y1t+=B((d-this.x1t)*k/h),this.z1t+=B((d-this.x1t)*l/h),this.x1t=d):0!=(a&2)?(this.x1t+=B(-this.y1t*h/k),this.z1t+=B(-this.y1t*l/k),this.y1t=
0):0!=(a&1)?(this.x1t+=B((c-this.y1t)*h/k),this.z1t+=B((c-this.y1t)*l/k),this.y1t=c):0!=(a&32)?(this.x1t+=B((g-this.z1t)*h/l),this.y1t+=B((g-this.z1t)*k/l),this.z1t=g):(this.x1t+=B((e-this.z1t)*h/l),this.y1t+=B((e-this.z1t)*k/l),this.z1t=e),a=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(b&8)?(this.y2t+=B(-this.x2t*k/h),this.z2t+=B(-this.x2t*l/h),this.x2t=0):0!=(b&4)?(this.y2t+=B((d-this.x2t)*k/h),this.z2t+=B((d-this.x2t)*l/h),this.x2t=d):0!=(b&2)?(this.x2t+=B(-this.y2t*h/k),this.z2t+=B(-this.y2t*
l/k),this.y2t=0):0!=(b&1)?(this.x2t+=B((c-this.y2t)*h/k),this.z2t+=B((c-this.y2t)*l/k),this.y2t=c):0!=(b&32)?(this.x2t+=B((g-this.z2t)*h/l),this.y2t+=B((g-this.z2t)*k/l),this.z2t=g):(this.x2t+=B((e-this.z2t)*h/l),this.y2t+=B((e-this.z2t)*k/l),this.z2t=e),b=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(a|b));return 1});c(c$,"plotLineClippedOld",function(a,b,d,c,g,e,h,k,l,j,m){var p=this.g3d.zbuf,z=this.g3d.width,w=0;0==j&&(m=2147483647,j=1);var q=c*z+d,n=this.g3d.bufferSize,r=this.g3d.pixel;
0!=a&&(!l&&0<=q&&q<n&&g<p[q])&&r.addPixel(q,g,a);if(!(0==e&&0==h)){l=1;var u=z;d+=e;var t=c+h;0>e&&(e=-e,l=-1);0>h&&(h=-h,u=-z);z=e+e;c=h+h;g<<=10;if(h<=e){var v=e-1;0>k&&(v=-v);k=y(((k<<10)+v)/e);h=0;v=Math.abs(d-this.x2t)-1;d=Math.abs(d-this.x1t)-1;for(var t=e-1,x=y(t/2);--t>=v&&!(t==x&&(a=b,0==a));){q+=l;g+=k;h+=c;h>e&&(q+=u,h-=z);if(0!=a&&t<d&&0<=q&&q<n&&w<m){var A=g>>10;A<p[q]&&r.addPixel(q,A,a)}w=(w+1)%j}}else{v=h-1;0>k&&(v=-v);k=y(((k<<10)+v)/h);e=0;v=Math.abs(t-this.y2t)-1;d=Math.abs(t-this.y1t)-
1;t=h-1;for(x=y(t/2);--t>=v&&!(t==x&&(a=b,0==a));)q+=u,g+=k,e+=z,e>h&&(q+=l,e-=c),0!=a&&(t<d&&0<=q&&q<n&&w<m)&&(A=g>>10,A<p[q]&&r.addPixel(q,A,a)),w=(w+1)%j}}},"~N,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N");F(c$,"VISIBILITY_UNCLIPPED",0,"VISIBILITY_CLIPPED",1,"VISIBILITY_OFFSCREEN",2)});u("J.g3d");x(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){c$=r(function(){this.pb=this.zb=this.p0=this.g=null;this.bgcolor=this.width=0;n(this,arguments)},J.g3d,"Pixelator");t(c$,function(a){this.g=a;this.bgcolor=this.g.bgcolor;
this.setBuf()},"J.g3d.Graphics3D");c(c$,"setBuf",function(){this.zb=this.g.zbuf;this.pb=this.g.pbuf});c(c$,"clearPixel",function(a,b){this.zb[a]>b&&(this.zb[a]=2147483647)},"~N,~N");c(c$,"addPixel",function(a,b,d){this.zb[a]=b;this.pb[a]=d},"~N,~N,~N");c(c$,"addImagePixel",function(a,b,d,c,g,e){if(c<this.zb[d])switch(a){case 0:break;case 8:this.addPixel(d,c,g);break;default:a+=b,7>=a&&(b=this.pb[d],0!=e&&(b=J.g3d.Graphics3D.mergeBufferPixel(b,e,e)),b=J.g3d.Graphics3D.mergeBufferPixel(b,g&16777215|
a<<24,this.bgcolor),this.addPixel(d,c,b))}},"~N,~N,~N,~N,~N,~N")});u("J.g3d");x(["J.g3d.Pixelator"],"J.g3d.PixelatorT",["J.g3d.Graphics3D"],function(){c$=C(J.g3d,"PixelatorT",J.g3d.Pixelator);j(c$,"clearPixel",function(){},"~N,~N");j(c$,"addPixel",function(a,b,d){var c=this.g.zbufT[a];if(b<c){var g=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=g&&c-b>this.g.zMargin)&&(this.pb[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],g,this.g.bgcolor));this.g.zbufT[a]=b;this.g.pbufT[a]=d&this.g.translucencyMask}else b!=
c&&!this.g.translucentCoverOnly&&b-c>this.g.zMargin&&(this.pb[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],d&this.g.translucencyMask,this.g.bgcolor))},"~N,~N,~N")});u("J.g3d");x(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){c$=r(function(){this.tmp=this.bgRGB=null;this.zShadePower=this.zDepth=this.zSlab=0;n(this,arguments)},J.g3d,"PixelatorShaded",J.g3d.Pixelator);t(c$,function(a){H(this,J.g3d.PixelatorShaded,[a]);this.tmp=A(3,0)},"J.g3d.Graphics3D");c(c$,"set",function(a,b,d){this.bgcolor=
this.g.bgcolor;this.bgRGB=A(-1,[this.bgcolor&255,this.bgcolor>>8&255,this.g.bgcolor>>16&255]);this.zSlab=0>a?0:a;this.zDepth=0>b?0:b;this.zShadePower=d;this.p0=this.g.pixel0;return this},"~N,~N,~N");j(c$,"addPixel",function(a,b,d){if(!(b>this.zDepth)){if(b>=this.zSlab&&0<this.zShadePower){var c=this.tmp,g=this.bgRGB;c[0]=d;c[1]=d>>8;c[2]=d>>16;var e=(this.zDepth-b)/(this.zDepth-this.zSlab);if(1<this.zShadePower)for(var h=0;h<this.zShadePower;h++)e*=e;for(h=0;3>h;h++)c[h]=g[h]+B(e*((c[h]&255)-g[h]));
d=c[2]<<16|c[1]<<8|c[0]|d&4278190080}this.p0.addPixel(a,b,d)}},"~N,~N,~N");c(c$,"showZBuffer",function(){for(var a=this.p0.zb.length;0<=--a;)if(0!=this.p0.pb[a]){var b=B(Math.min(255,Math.max(0,255*(this.zDepth-this.p0.zb[a])/(this.zDepth-this.zSlab))));this.p0.pb[a]=4278190080|b|b<<8|b<<16}})});u("J.g3d");x(["J.g3d.Pixelator"],"J.g3d.PixelatorScreened",null,function(){c$=C(J.g3d,"PixelatorScreened",J.g3d.Pixelator);t(c$,function(a,b){H(this,J.g3d.PixelatorScreened,[a]);this.width=a.width;this.p0=
b},"J.g3d.Graphics3D,J.g3d.Pixelator");j(c$,"addPixel",function(a,b,d){a%this.width%2==y(a/this.width)%2&&this.p0.addPixel(a,b,d)},"~N,~N,~N")});u("J.g3d");c$=r(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;n(this,arguments)},
J.g3d,"Platform3D");t(c$,function(a){this.apiPlatform=a},"javajs.awt.GenericPlatform");c(c$,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))});c(c$,"allocateTBuffers",function(a){this.bufferSizeT=a?this.bufferSize:this.windowSize;this.zBufferT=A(this.bufferSizeT,0);this.pBufferT=A(this.bufferSizeT,0)},"~B");c(c$,"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=A(this.bufferSize,0);this.pBuffer=A(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$,"setBackgroundTransparent",function(a){J.g3d.Platform3D.backgroundTransparent=a},"~B");F(c$,
"backgroundTransparent",!1);u("J.g3d");c$=r(function(){this.b=this.a=0;this.isOrthographic=!1;n(this,arguments)},J.g3d,"PrecisionRenderer");c(c$,"getZCurrent",function(a,b,d){return Math.round(1.4E-45==a?b:this.isOrthographic?a*d+b:a/(b-d))},"~N,~N,~N");c(c$,"setRastABFloat",function(a,b,d,c){var g=c-b,e=d-a;0==g||0==e?(this.a=1.4E-45,this.b=b):this.isOrthographic?(this.a=g/e,this.b=b-this.a*a):(this.a=e*b*(c/g),this.b=(d*c-a*b)/g)},"~N,~N,~N,~N");c(c$,"setRastAB",function(a,b,d,c){var g=c-b,e=d-
a;1.4E-45==a||0==g||0==e?(this.a=1.4E-45,this.b=c):this.isOrthographic?(this.a=g/e,this.b=b-this.a*a):(this.a=e*b*(c/g),this.b=(d*c-a*b)/g)},"~N,~N,~N,~N");u("J.g3d");x(["JU.P3"],"J.g3d.SphereRenderer",null,function(){c$=r(function(){this.mDeriv=this.coef=this.mat=this.zroot=this.shader=this.g3d=null;this.planeShade=this.selectedOctant=0;this.zbuf=null;this.offsetPbufBeginLine=this.slab=this.depth=this.height=this.width=0;this.dxyz=this.planeShades=this.ptTemp=null;n(this,arguments)},J.g3d,"SphereRenderer");
O(c$,function(){this.zroot=Y(2,0);this.ptTemp=new JU.P3;this.planeShades=A(3,0);this.dxyz=I(3,3,0)});t(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"render",function(a,b,d,c,g,e,h,k,l,j){if(1!=g&&(49<b&&(b&=-2),!this.g3d.isClippedXY(b,d,c))){this.slab=this.g3d.slab;this.depth=this.g3d.depth;var m=b+1>>1,p=g-m;if(!(g+m<this.slab||p>this.depth)){var z=d-m,w=d+m,q=c-m,n=c+m;this.shader.nOut=this.shader.nIn=0;this.zbuf=this.g3d.zbuf;this.height=this.g3d.height;this.width=this.g3d.width;
this.offsetPbufBeginLine=this.width*c+d;var r=this.shader;this.mat=e;if(null!=e&&(this.coef=h,this.mDeriv=k,this.selectedOctant=l,null==r.ellipsoidShades&&r.createEllipsoidShades(),null!=j)){this.planeShade=-1;for(h=0;3>h;h++)if(m=this.dxyz[h][0]=j[h].x-d,k=this.dxyz[h][1]=j[h].y-c,l=this.dxyz[h][2]=j[h].z-g,this.planeShades[h]=r.getShadeIndex(m,k,-l),0==m&&0==k){this.planeShade=this.planeShades[h];break}}if(null!=e||128<b)this.renderQuadrant(-1,-1,d,c,g,b,a),this.renderQuadrant(-1,1,d,c,g,b,a),this.renderQuadrant(1,
-1,d,c,g,b,a),this.renderQuadrant(1,1,d,c,g,b,a),null!=e&&(this.mDeriv=this.coef=this.mat=null);else{var t=r.sphereShapeCache[b-1];if(null==t){t=0;e=0!=(b&1);j=b/2;k=j*j;m=y((b+1)/2);l=e?0:0.5;for(h=0;h<m;++h,++l)for(var u=l*l,v=e?0:0.5,x=0;x<m;++x,++v){var C=v*v,C=k-u-C;0<=C&&++t}var t=A(t,0),E=0;l=e?0:0.5;for(h=0;h<m;++h,++l){u=l*l;v=e?0:0.5;for(x=0;x<m;++x,++v)if(C=v*v,C=k-u-C,0<=C){var D=Math.sqrt(C),C=B(D),F=r.getShadeN(v,l,D,j),H=r.getShadeN(-v,l,D,j),I=r.getShadeN(v,-l,D,j),D=r.getShadeN(-v,
-l,D,j),C=C|F<<7|H<<13|I<<19|D<<25;t[E++]=C}t[E-1]|=2147483648}r.sphereShapeCache[b-1]=t}0>z||w>=this.width||0>q||n>=this.height||p<this.slab||g>this.depth?this.renderSphereClipped(t,d,c,g,b,a):this.renderSphereUnclipped(t,g,b,a)}this.zbuf=null}}},"~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");c(c$,"renderSphereUnclipped",function(a,b,d,c){var g=0,e=1-(d&1),h=this.offsetPbufBeginLine,k=h-e*this.width;d=y((d+1)/2);var l=this.zbuf,j=this.width,m=this.g3d.pixel;do{var p=h,z=h-e,w=k,q=k-e,n;do{n=a[g++];var r=
b-(n&127);r<l[p]&&m.addPixel(p,r,c[n>>7&63]);r<l[z]&&m.addPixel(z,r,c[n>>13&63]);r<l[w]&&m.addPixel(w,r,c[n>>19&63]);r<l[q]&&m.addPixel(q,r,c[n>>25&63]);++p;--z;++w;--q}while(0<=n);h+=j;k-=j}while(0<--d)},"~A,~N,~N,~A");c(c$,"renderSphereClipped",function(a,b,d,c,g,e){var h=this.width,k=this.height,l=0,j=1-(g&1),m=this.offsetPbufBeginLine,p=m-j*h;g=y((g+1)/2);var z=d,w=d-j;d=(b<<16)+(d<<1)^858993459;var q=this.zbuf,n=this.g3d.pixel,r=this.slab,t=this.depth;do{var u=0<=z&&z<k,v=0<=w&&w<k,x=m,A=m-j,
B=p,C=p-j,D,E=b,F=b-j;do{var H=0<=F&&F<h,I=0<=E&&E<h;D=a[l++];var M;M=D&127;var K;c<r?(K=c+M,M=K>=r):(K=c-M,M=K<r);M&&(K=r);if(K>=r&&K<=t){if(u){if(I&&K<q[x]){var N=M?44+(d>>7&7):D>>7&63;n.addPixel(x,K,e[N])}H&&K<q[A]&&(N=M?44+(d>>13&7):D>>13&63,n.addPixel(A,K,e[N]))}v&&(I&&K<q[B]&&(N=M?44+(d>>19&7):D>>19&63,n.addPixel(B,K,e[N])),H&&K<q[C]&&(N=M?44+(d>>25&7):D>>25&63,n.addPixel(C,K,e[N])))}++x;--A;++B;--C;++E;--F;M&&(d=(d<<16)+(d<<1)+d&2147483647)}while(0<=D);m+=h;p-=h;++z;--w}while(0<--g)},"~A,~N,~N,~N,~N,~A");
c(c$,"renderQuadrant",function(a,b,d,c,g,e,h){e=y(e/2);var k=d+e*a,l=(0>d?-1:d<this.width?0:1)+(0>k?-2:k<this.width?0:2);-3==l||3==l||(k=c+e*b,k=(0>c?-1:c<this.height?0:1)+(0>k?-2:k<this.height?0:2),-3==k||3==k||(null==this.mat&&0==l&&0==k&&g-e>=this.slab&&g<=this.depth?this.renderQuadrantUnclipped(e,a,b,g,h):this.renderQuadrantClipped(e,a,b,d,c,g,h)))},"~N,~N,~N,~N,~N,~N,~A");c(c$,"renderQuadrantUnclipped",function(a,b,d,c,g){for(var e=a*a,h=2*a+1,k=0>d?-this.width:this.width,l=this.offsetPbufBeginLine,
j=this.zbuf,m=this.g3d.pixel,p=this.shader.sphereShadeIndexes,z=0,w=0;w<=e;w+=z+ ++z,l+=k)for(var q=l,n=e-w,r=c-a,t=y((z*d+a<<8)/h),u=0,v=0;v<=n;v+=u+ ++u,q+=b)if(!(j[q]<=r)&&(r=y(Math.sqrt(n-v)),r=c-r,!(j[q]<=r))){var x=y((u*b+a<<8)/h);m.addPixel(q,r,g[p[(t<<8)+x]])}},"~N,~N,~N,~N,~A");c(c$,"renderQuadrantClipped",function(a,b,d,c,g,e,h){for(var k=null!=this.mat,l=0<=this.selectedOctant,j=a*a,m=2*a+1,p=0>d?-this.width:this.width,z=this.offsetPbufBeginLine,w=(c<<16)+(g<<1)^858993459,q=0,n=0,r=this.g3d.pixel,
t=0,u=this.height,v=this.width,x=this.zbuf,A=this.dxyz,B=this.slab,C=this.depth,D=this.ptTemp,E=this.coef,F=this.zroot,H=this.selectedOctant,I=this.shader,K=this.planeShades,M=I.sphereShadeIndexes,N=this.planeShade,O=this.mat,P=0,S=0,Q=g;S<=j;S+=P+ ++P,z+=p,Q+=d)if(0>Q){if(0>d)break}else if(Q>=u){if(0<d)break}else{var U=j-(k?0:S);k||(q=y((P*d+a<<8)/m));for(var w=(w<<16)+(w<<1)+w&2147483647,Z=c,W=0,V=0,Y=-1,$=1,X=z;V<=U;V+=W+ ++W,X+=b,Z+=b)if(0>Z){if(0>b)break}else if(Z>=v){if(0<b)break}else{var R;
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0,m),this.generateRaster(d-k,e,h,this.axW,this.azW,k,m),this.generateRaster(d,g,h,this.axE,this.azE,0,p)));this.g3d.setZMargin(5);g=this.g3d.pass2Flag01;e=1-g;h=0;0>b&&(d+=b,h-=b,b=0);b+d>this.g3d.height&&(d=this.g3d.height-b);if(c)if(a)for(;--d>=g;++b,++h)a=this.axE[h]-(c=this.axW[h])+e,0<a&&this.g3d.plotPixelsClippedRaster(a,c,b,this.azW[h],this.azE[h],this.rgb16sW[h],this.rgb16sE[h]);else for(;--d>=g;++b,++h)a=this.axE[h]-(c=this.axW[h])+e,1==g&&0>a&&(a=1,c--),0<a&&this.g3d.plotPixelsUnclippedRaster(a,
c,b,this.azW[h],this.azE[h],this.rgb16sW[h],this.rgb16sE[h]);else if(a)for(;--d>=g;++b,++h)a=this.axE[h]-(c=this.axW[h])+e,0<a&&this.g3d.plotPixelsClippedRasterBits(a,c,b,this.azW[h],this.azE[h],null,null,this.aa[h],this.bb[h]);else for(;--d>=g;++b,++h)a=this.axE[h]-(c=this.axW[h])+e,1==g&&0>a&&(a=1,c--),0<a&&this.g3d.plotPixelsUnclippedRasterBits(a,c,b,null,null,this.aa[h],this.bb[h]);this.g3d.setZMargin(0)}}}},"JU.P3i,JU.P3i,JU.P3i,~B");c(c$,"generateRaster",function(a,b,d,c,g,e,h){var k=this.ax[b],
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3,6,1,3,5,7,9,11]),"fourdots",A(-1,[13,3,5,2,5,8,11]),"twodots",A(-1,[12,3,4,3,9]))});u("J.render");x(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["JV.Viewer"],function(){c$=C(J.render,"FrankRenderer",J.render.ShapeRenderer);j(c$,"render",function(){var a=this.shape,b=this.vwr.getBooleanProperty("allowKeyStrokes"),d=this.vwr.getBoolean(603979883);this.colix=d?20:this.vwr.isSignedApplet?b||JV.Viewer.isJS&&!JV.Viewer.isWebGL?5:10:b?7:12;if(this.isExport||!this.vwr.getShowFrank()||!this.g3d.setC(this.colix))return!1;
if(this.vwr.frankOn&&!this.vwr.noFrankEcho)return this.vwr.noFrankEcho;this.vwr.noFrankEcho=!0;b=this.vwr.imageFontScaling;a.getFont(b);var b=B(a.frankWidth+4*b),c=a.frankDescent;this.g3d.drawStringNoSlab(a.frankString,a.font3d,this.vwr.gdata.width-b,this.vwr.gdata.height-c,0,0);d&&this.g3d.fillTextRect(0,0,0,0,2*c,y(3*b/2));return!1})});u("J.render");x(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["java.lang.NullPointerException","J.api.Interface","JU.Logger","JV.JC","$.Viewer"],
function(){c$=r(function(){this.bsTranslucent=this.renderers=this.shapeManager=this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;n(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);O(c$,function(){this.bsTranslucent=JU.BS.newN(37)});t(c$,function(){});j(c$,"set",function(a,b){this.vwr=a;this.shapeManager=b},"JV.Viewer,JV.ShapeManager");j(c$,"isRepaintPending",function(){return this.repaintPending});j(c$,"pushHoldRepaint",function(){++this.holdRepaint},"~S");j(c$,"popHoldRepaint",
function(a,b){--this.holdRepaint;0>=this.holdRepaint&&(this.holdRepaint=0,a&&(this.repaintPending=!0,this.repaintNow(b)))},"~B,~S");j(c$,"requestRepaintAndWait",function(){var a=null,a=self.Jmol&&Jmol._repaint?Jmol:null;null!=a&&(a._repaint(this.vwr.html5Applet,!1),this.repaintDone())},"~S");j(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.display)},
"~S");j(c$,"repaintDone",function(){this.repaintPending=!1});j(c$,"clear",function(a){if(null!=this.renderers)if(0<=a)this.renderers[a]=null;else for(a=0;37>a;++a)this.renderers[a]=null},"~N");c(c$,"getRenderer",function(a){if(null!=this.renderers[a])return this.renderers[a];var b=JV.JC.getShapeClassName(a,!0)+"Renderer";if(null==(b=J.api.Interface.getInterface(b,this.vwr,"render")))return null;b.setViewerG3dShapeID(this.vwr,a);return this.renderers[a]=b},"~N");j(c$,"render",function(a,b,d,c){null==
this.renderers&&(this.renderers=Array(37));this.getAllRenderers();try{var g=this.vwr.getBoolean(603979934);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.navigationDepthPercent);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);this.vwr.noFrankEcho=!0}c=null;for(e=0;37>e&&a.currentlyRendering;++e){var h=
this.shapeManager.getShape(e);null!=h&&(g&&(c="rendering "+JV.JC.getShapeClassName(e,!1),JU.Logger.startTimer(c)),(d||this.bsTranslucent.get(e))&&this.getRenderer(e).renderShape(a,b,h)&&this.bsTranslucent.set(e),g&&JU.Logger.checkTimer(c,!1))}a.renderAllStrings(null)}catch(k){if(E(k,Exception)){JV.Viewer.isJS||k.printStackTrace();if(this.vwr.async&&"Interface".equals(k.getMessage()))throw new NullPointerException;JU.Logger.error("rendering error? "+k)}else throw k;}},"JU.GData,JM.ModelSet,~B,~A");
c(c$,"getAllRenderers",function(){for(var a=!0,b=0;37>b;++b)null==this.shapeManager.getShape(b)||null!=this.getRenderer(b)||(a=this.repaintPending=!this.vwr.async);if(!a)throw new NullPointerException;});j(c$,"renderExport",function(a,b,d){this.shapeManager.finalizeAtoms(null,!0);a=this.vwr.initializeExporter(d);if(null==a)return JU.Logger.error("Cannot export "+d.get("type")),null;null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();d=null;try{var c=this.vwr.getBoolean(603979934);
a.renderBackground(a);for(var g=0;37>g;++g){var e=this.shapeManager.getShape(g);null!=e&&(c&&(d="rendering "+JV.JC.getShapeClassName(g,!1),JU.Logger.startTimer(d)),this.getRenderer(g).renderShape(a,b,e),c&&JU.Logger.checkTimer(d,!1))}a.renderAllStrings(a);d=a.finalizeOutput()}catch(h){if(E(h,Exception))JV.Viewer.isJS||h.printStackTrace(),JU.Logger.error("rendering error? "+h);else throw h;}return d},"JU.GData,JM.ModelSet,java.util.Map")});u("J.render");x(null,"J.render.ShapeRenderer",["JV.JC"],function(){c$=
r(function(){this.shape=this.ms=this.g3d=this.tm=this.vwr=null;this.exportType=this.mad=this.colix=this.shapeID=this.myVisibilityFlag=0;this.isExport=!1;n(this,arguments)},J.render,"ShapeRenderer");c(c$,"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.setup(a,b,d);a=this.render();this.exportType=0;this.isExport=
!1;return a},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");c(c$,"setup",function(a,b,d){this.g3d=a;this.ms=b;this.shape=d;this.exportType=a.getExportType();this.isExport=0!=this.exportType},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");c(c$,"isVisibleForMe",function(a){return a.isVisible(this.myVisibilityFlag|9)},"JM.Atom")});u("J.render");x(["J.render.FontLineShapeRenderer","JU.BS","$.P3","$.V3"],"J.render.SticksRenderer","java.lang.Float JU.A4 $.M3 J.c.PAL JU.C $.Edge".split(" "),
function(){c$=r(function(){this.showMultipleBonds=!1;this.multipleBondRadiusFactor=this.multipleBondSpacing=0;this.useBananas=this.bondsPerp=!1;this.modeMultipleBond=0;this.isCartesian=!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=this.rTheta=0;this.a4=this.rot=null;n(this,arguments)},J.render,"SticksRenderer",J.render.FontLineShapeRenderer);O(c$,function(){this.x=new JU.V3;this.y=new JU.V3;this.z=new JU.V3;this.p1=new JU.P3;this.p2=new JU.P3;this.bsForPass2=JU.BS.newN(64)});j(c$,"render",function(){var a=this.ms.bo;if(null==a)return!1;(this.isPass2=this.vwr.gdata.isPass2)||this.bsForPass2.clearAll();this.slabbing=
this.tm.slabEnabled;this.slabByAtom=this.vwr.getBoolean(603979939);this.endcaps=3;this.dashDots=this.vwr.getBoolean(603979893)?J.render.FontLineShapeRenderer.sixdots:J.render.FontLineShapeRenderer.dashes;this.isCartesian=1==this.exportType;this.getMultipleBondSettings(!1);this.wireframeOnly=!this.vwr.checkMotionRendering(1677721602);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.isPass2){if(!this.isExport)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.shapeVisibilityFlags&this.myVisibilityFlag)&&this.renderBond()&&(b=!0,this.bsForPass2.set(d));return b});c(c$,"getMultipleBondSettings",function(a){this.useBananas=this.vwr.getBoolean(603979886)&&
!a;this.multipleBondSpacing=a?0.15:this.vwr.getFloat(570425370);this.multipleBondRadiusFactor=a?0.4:this.vwr.getFloat(570425369);this.bondsPerp=this.useBananas||0<this.multipleBondSpacing&&0>this.multipleBondRadiusFactor;this.useBananas&&(this.multipleBondSpacing=0>this.multipleBondSpacing?0.4*-this.multipleBondSpacing:this.multipleBondSpacing);this.multipleBondRadiusFactor=Math.abs(this.multipleBondRadiusFactor);0==this.multipleBondSpacing&&this.isCartesian&&(this.multipleBondSpacing=0.2);this.modeMultipleBond=
this.vwr.g.modeMultipleBond;this.showMultipleBonds=0!=this.multipleBondSpacing&&0!=this.modeMultipleBond&&this.vwr.getBoolean(603979928)},"~B");c(c$,"renderBond",function(){var a,b;this.a=a=this.bond.atom1;this.b=b=this.bond.atom2;var d=this.bond.order&-131073;this.bondsBackbone&&(this.ssbondsBackbone&&0!=(d&256)?(this.a=this.a.group.getLeadAtomOr(this.a),this.b=this.b.group.getLeadAtomOr(this.b)):this.hbondsBackbone&&JU.Edge.isOrderH(d)&&(this.a=this.a.group.getLeadAtomOr(this.a),this.b=this.b.group.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)))return!1;if(this.slabbing){var c=this.vwr.gdata.isClippedZ(this.a.sZ);if(c&&this.vwr.gdata.isClippedZ(this.b.sZ)||this.slabByAtom&&(c||this.vwr.gdata.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.colixAtom;this.colixB=b.colixAtom;2==((this.colix=this.bond.colix)&-30721)?
(this.colix&=30720,this.colixA=JU.C.getColixInherited(this.colix|this.vwr.cm.getColixAtomPalette(a,J.c.PAL.CPK.id),this.colixA),this.colixB=JU.C.getColixInherited(this.colix|this.vwr.cm.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.renderPass2(this.colixA),c=!JU.C.renderPass2(this.colixB),!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 1025:case 1041:this.bondOrder=1;case 1:case 2:case 3:case 4:case 5:case 6: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)):JU.Edge.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=B(this.vwr.tm.scaleToScreen(y((this.zA+this.zB)/2),this.mad));this.wireframeOnly&&0<this.width&&(this.width=1);if(!this.isCartesian&&(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:switch(this.bondOrder){case 4:this.bondOrder=
2;d=this.multipleBondRadiusFactor;0==d&&1<this.width&&(this.width=y(0.5*this.width));d=this.multipleBondSpacing;0>d&&(this.multipleBondSpacing=0.3);this.drawBond(b);this.bondsPerp=!this.bondsPerp;this.bondOrder=2;this.drawBond(b>>2);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=d;break;case 5:this.bondOrder=3;d=this.multipleBondRadiusFactor;0==d&&1<this.width&&(this.width=y(0.5*this.width));d=this.multipleBondSpacing;0>d&&(this.multipleBondSpacing=0.2);this.drawBond(b);this.bondsPerp=!this.bondsPerp;
this.bondOrder=2;this.multipleBondSpacing*=1.5;this.drawBond(b>>3);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=d;break;case 6:this.bondOrder=4;d=this.multipleBondRadiusFactor;0==d&&1<this.width&&(this.width=y(0.5*this.width));d=this.multipleBondSpacing;0>d&&(this.multipleBondSpacing=0.15);this.drawBond(b);this.bondsPerp=!this.bondsPerp;this.bondOrder=2;this.multipleBondSpacing*=1.5;this.drawBond(b>>4);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=d;break;default:this.drawBond(b)}}return a});
c(c$,"drawBond",function(a){var b=0!=(a&1);if(this.isCartesian&&1==this.bondOrder&&!b)this.g3d.drawBond(this.a,this.b,this.colixA,this.colixB,this.endcaps,this.mad,-1);else{var d=0==this.dx&&0==this.dy;if(!d||!this.asLineOnly||this.isCartesian){var c=1<this.bondOrder&&0<this.multipleBondSpacing,g=c&&(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(d&&!c){a=y(this.width/8)+3;a=this.width+
a;b=this.yA-y((this.bondOrder-1)*a/2);do this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.xA,b,this.zA,this.xB,b,this.zB),b+=a;while(0<--this.bondOrder)}else if(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(c)if(g||this.z.setT(JU.P3.getUnlikely()),this.x.sub2(this.b,this.a),this.y.cross(this.x,this.z),
this.y.normalize(),Float.isNaN(this.y.x)&&(this.z.setT(JU.P3.getUnlikely()),this.y.cross(this.x,this.z),this.y.cross(this.y,this.x),this.y.normalize()),this.bondsPerp&&this.y.cross(this.y,this.x),this.y.scale(this.multipleBondSpacing),this.x.setT(this.y),this.x.scale((this.bondOrder-1)/2),this.useBananas)switch(this.drawBanana(this.a,this.b,this.x,0),this.bondOrder){case 4:this.drawBanana(this.a,this.b,this.x,90),this.drawBanana(this.a,this.b,this.x,-90);default:this.drawBanana(this.a,this.b,this.x,
180);break;case 3:this.drawBanana(this.a,this.b,this.x,120),this.drawBanana(this.a,this.b,this.x,-120)}else{this.p1.sub2(this.a,this.x);for(this.p2.sub2(this.b,this.x);;){this.isCartesian?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 if(this.mag2d=Math.round(Math.sqrt(this.dx*this.dx+this.dy*this.dy)),this.resetAxisCoordinates(),this.isCartesian&&3==this.bondOrder)this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB),this.stepAxisCoordinates(),this.x.sub2(this.b,
this.a),this.x.scale(0.05),this.p1.sub2(this.a,this.x),this.p2.add2(this.b,this.x),this.g3d.drawBond(this.p1,this.p2,this.colixA,this.colixB,this.endcaps,this.mad,-2),this.stepAxisCoordinates(),this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB);else for(;;){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=this.mag2d>>3;-1!=this.multipleBondSpacing&&0>this.multipleBondSpacing&&(a*=-this.multipleBondSpacing);a=this.width+a;this.dxStep=y(a*this.dy/this.mag2d);this.dyStep=y(a*-this.dx/this.mag2d);this.xAxis1=this.xA;this.yAxis1=this.yA;this.xAxis2=this.xB;this.yAxis2=this.yB;a=this.bondOrder-1;this.xAxis1-=y(this.dxStep*a/
2);this.yAxis1-=y(this.dyStep*a/2);this.xAxis2-=y(this.dxStep*a/2);this.yAxis2-=y(this.dyStep*a/2)});c(c$,"stepAxisCoordinates",function(){this.xAxis1+=this.dxStep;this.yAxis1+=this.dyStep;this.xAxis2+=this.dxStep;this.yAxis2+=this.dyStep});c(c$,"getAromaticDottedBondMask",function(){var a=this.b.findAromaticNeighbor(this.a.i);return null==a?1:0>this.dx*(a.sY-this.yA)-this.dy*(a.sX-this.xA)?2:1});c(c$,"drawBanana",function(a,b,d,c){this.g3d.addRenderer(553648146);this.vectorT.sub2(b,a);null==this.rot&&
(this.rot=new JU.M3,this.a4=new JU.A4);this.a4.setVA(this.vectorT,3.141592653589793*c/180);this.rot.setAA(this.a4);this.pointT.setT(a);this.pointT3.setT(b);this.pointT2.ave(a,b);this.rot.rotate2(d,this.vectorT);this.pointT2.add(this.vectorT);this.tm.transformPtScrT3(a,this.pointT);this.tm.transformPtScrT3(this.pointT2,this.pointT2);this.tm.transformPtScrT3(b,this.pointT3);a=Math.max(this.width,1);this.g3d.setC(this.colixA);this.g3d.fillHermite(5,a,a,a,this.pointT,this.pointT,this.pointT2,this.pointT3);
this.g3d.setC(this.colixB);this.g3d.fillHermite(5,a,a,a,this.pointT,this.pointT2,this.pointT3,this.pointT3)},"JM.Atom,JM.Atom,JU.V3,~N")});u("JS");x(["JS.T"],"JS.ContextToken",["java.util.Hashtable","JS.SV"],function(){c$=r(function(){this.name0=this.forVars=this.contextVariables=null;n(this,arguments)},JS,"ContextToken",JS.T);c$.newContext=c(c$,"newContext",function(a){a=a?JS.ContextToken.newCmd(1275335685,"{"):JS.ContextToken.newCmd(1275334681,"}");a.intValue=0;return a},"~B");c$.newCmd=c(c$,"newCmd",
function(a,b){var d=new JS.ContextToken;d.tok=a;d.value=b;return d},"~N,~O");c(c$,"addName",function(a){null==this.contextVariables&&(this.contextVariables=new java.util.Hashtable);this.contextVariables.put(a,JS.SV.newS("").setName(a))},"~S")});u("JS");x(null,"JS.ScriptContext",["java.util.Hashtable","JS.SV"],function(){c$=r(function(){this.aatoken=null;this.chk=this.allowJSThreads=!1;this.contextPath=" >> ";this.vars=null;this.displayLoadErrorsSave=!1;this.errorType=this.errorMessageUntranslated=
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b;break;case 1111492616:case 1111492613:this.y=b;break;case 1111492617:case 1111492614:this.z=b}null!=c&&c.toCartesian(this,d)},"~N,~N,~B");c(c$,"setFractionalCoordTo",function(a,b){this.setFractionalCoordPt(this,a,b)},"JU.P3,~B");c(c$,"setFractionalCoordPt",function(a,b,d){a.setT(b);b=this.getUnitCell();null!=b&&b.toCartesian(a,d&&!this.group.chain.model.isJmolDataFrame)},"JU.P3,JU.P3,~B");c(c$,"isCursorOnTopOf",function(a,b,d,c){var g=y(this.sD/2);g<d&&(g=d);d=g*g;g=this.sX-a;g*=g;if(g>d)return!1;
var e=this.sY-b;d-=g+e*e;if(0>d)return!1;if(null==c)return!0;var g=this.sZ,e=c.sZ,h=y(c.sD/2);if(g<e-h)return!0;a=c.sX-a;b=c.sY-b;b=h*h-(a*a+b*b);return g-Math.sqrt(d)<e-Math.sqrt(b)},"~N,~N,~N,JM.Atom");c(c$,"getInfo",function(){return this.getIdentity(!0)});c(c$,"getIdentityXYZ",function(a,b){b=this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!this.group.chain.model.ms.vwr.g.legacyJavaFloat,!1,b):this;return this.getIdentity(a)+" "+b.x+" "+b.y+" "+b.z},"~B,JU.P3");c(c$,"getIdentity",
function(a){var b=new JU.SB,d=this.getGroup3(!0);if(null!=d&&0<d.length&&(!d.equals("UNK")||this.group.chain.model.isBioModel)){b.append("[");b.append(d);b.append("]");d=this.group.getSeqcodeString();null!=d&&b.append(d);d=this.group.chain.chainID;if(0!=d&&32!=d){b.append(":");var c=this.getChainIDStr();256<=d&&(c=JU.PT.esc(c));b.append(c)}if(!a)return b.toString();b.append(".")}b.append(this.getAtomName());0==b.length()&&(b.append(this.getElementSymbolIso(!1)),b.append(" "),b.appendI(this.getAtomNumber()));
"\x00"!=this.altloc&&(b.append("%"),b.appendC(this.altloc));1<this.group.chain.model.ms.mc&&!this.group.chain.model.isJmolDataFrame&&(b.append("/"),b.append(this.getModelNumberForLabel()));b.append(" #");b.appendI(this.getAtomNumber());return b.toString()},"~B");j(c$,"getGroup3",function(a){var b=this.group.getGroup3();return a||null!=b&&0<b.length?b:"UNK"},"~B");j(c$,"getGroup1",function(a){var b=this.group.getGroup1();return"\x00"!=b?""+b:"\x00"!=a?""+a:""},"~S");j(c$,"getBioSmilesType",function(){return this.group.isProtein()?
"p":this.group.isDna()?"d":this.group.isRna()?"r":this.group.isCarbohydrate()?"c":" "});j(c$,"isPurine",function(){return this.group.isPurine()});j(c$,"isPyrimidine",function(){return this.group.isPyrimidine()});j(c$,"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,1040384!=a&&(this.shapeVisibilityFlags|=a))},"~N");c(c$,"checkVisible",function(){if(this.isVisible(2))return this.isVisible(4);var a=this.isVisible(9);if(a){a=this.shapeVisibilityFlags;if(0!=this.group.shapeVisibilityFlags&&(8192!=this.group.shapeVisibilityFlags||this.isLeadAtom()))a|=this.group.shapeVisibilityFlags;a&=-10;32==a&&0==this.clickabilityFlags&&(a=0);if(a=0!=a)this.shapeVisibilityFlags|=4}this.shapeVisibilityFlags|=2;return a});j(c$,"isLeadAtom",function(){return this.group.isLeadAtom(this.i)});
j(c$,"getChainID",function(){return this.group.chain.chainID});j(c$,"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$,"getModulation",function(){return this.group.chain.model.ms.getModulation(this.i)});c(c$,"getModelNumberForLabel",function(){return this.group.chain.model.ms.getModelNumberForAtomLabel(this.mi)});
c(c$,"getModelNumber",function(){return this.group.chain.model.ms.getModelNumber(this.mi)%1E6});j(c$,"getBioStructureTypeName",function(){return this.group.getProteinStructureType().getBioStructureTypeName(!0)});j(c$,"equals",function(a){return this===a},"~O");j(c$,"hashCode",function(){return this.i});c(c$,"findAromaticNeighbor",function(a){if(null==this.bonds)return null;for(var b=this.bonds.length;0<=--b;){var d=this.bonds[b],c=d.getOtherAtom(this);if(d.isAromatic()&&c.i!=a)return c}return null},
"~N");c(c$,"atomPropertyInt",function(a){switch(a){case 1094715393:return this.getAtomNumber();case 1094713365:return this.getSeqID();case 1094713346:return this.atomID;case 1094713368:return Math.max(0,this.altloc.charCodeAt(0)-32);case 1094713347:return this.i;case 1228931587:return this.getCovalentBondCount();case 1094713351:return this.group.chain.chainNo;case 1765808134:return this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom);case 1086326789:case 1094715402:return this.getElementNumber();
case 1094713353:return this.atomicAndIsotopeNumber;case 1228935687:return this.group.chain.model.fileIndex+1;case 1631586315:return this.getFormalCharge();case 1094713356:return this.group.groupID;case 1094713357:return this.group.groupIndex;case 1094717454:return this.getModelNumber();case -1094717454:return this.group.chain.model.ms.modelFileNumbers[this.mi];case 1094713359:return this.mi;case 1094713360:return this.getMoleculeNumber(!0);case 1094713361:return this.group.getMonomerIndex()+1;case 1128269825:return this.getOccupancy100();
case 1094713362:return this.group.getBioPolymerIndexInModel()+1;case 1094713363:return this.group.getBioPolymerLength();case 1665140738:return this.getRasMolRadius();case 1094715412:return this.getResno();case 1094713366:return this.getAtomSite();case 1639976963:return this.group.getProteinStructureType().getId();case 1237320707:return this.group.getProteinStructureSubType().getId();case 1094713367:return this.group.getStrucNo();case 1296041986:return this.getSymOp();case 1094715417:return this.getValence()}return 0},
"~N");c(c$,"getSymOp",function(){return null==this.atomSymmetry?0:this.atomSymmetry.nextSetBit(0)+1});c(c$,"atomPropertyFloat",function(a,b,d){switch(b){case 1111490561:return this.getADPMinMax(!0);case 1111490562:return this.getADPMinMax(!1);case 1111492609:case 1111492629:return this.x;case 1111492610:case 1111492630:return this.y;case 1111492611:case 1111492631:return this.z;case 1111490587:return this.group.chain.model.ms.getAtomicDSSRData(this.i);case 1114249217:case 1112152066:case 1112150019:case 1112150020:case 1112150021:case 1112152070:case 1112152071:case 1112152073:case 1112152074:case 1112152076:case 1649022989:case 1112152078:return a.shm.getAtomShapeValue(b,
this.group,this.i);case 1111492618:return this.getBondingRadius();case 1111490563:return a.getNMRCalculation().getChemicalShift(this);case 1111490564:return JU.Elements.getCovalentRadius(this.atomicAndIsotopeNumber);case 1111490565:case 1111490576:case 1111490574:return this.group.getGroupParameter(b);case 1111492615:case 1111492612:return this.getFractionalCoord(!a.g.legacyJavaFloat,"X",!1,d);case 1111492616:case 1111492613:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,d);case 1111492617:case 1111492614:return this.getFractionalCoord(!a.g.legacyJavaFloat,
"Z",!1,d);case 1113589786:return this.getHydrophobicity();case 1111490566:return a.getNMRCalculation().getMagneticShielding(this);case 1111490567:return this.getMass();case 1128269825:return this.getOccupancy100()/100;case 1111492619:return this.getPartialCharge();case 1111490569:case 1111490570:case 1111490568:if(this.group.chain.model.isJmolDataFrame&&this.group.chain.model.jmolFrameType.startsWith("plot ramachandran"))switch(b){case 1111490569:return this.getFractionalCoord(!a.g.legacyJavaFloat,
"X",!1,d);case 1111490570:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,d);case 1111490568:if(this.group.chain.model.isJmolDataFrame&&this.group.chain.model.jmolFrameType.equals("plot ramachandran"))return a=this.getFractionalCoord(!a.g.legacyJavaFloat,"Z",!1,d)-180,-180>a?360+a:a}return this.group.getGroupParameter(b);case 1665140738:case 1112152075:return this.getRadius();case 1111490571:return a.antialiased?y(this.sX/2):this.sX;case 1111490572:return a.getScreenHeight()-(a.antialiased?
y(this.sY/2):this.sY);case 1111490573:return a.antialiased?y(this.sZ/2):this.sZ;case 1113589787:return a.slm.isAtomSelected(this.i)?1:0;case 1111490575:return a.ms.getSurfaceDistanceMax(),this.getSurfaceDistance100()/100;case 1111492620:return this.getBfactor100()/100;case 1111490577:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"X",d);case 1111490578:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Y",d);case 1111490579:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Z",
d);case 1648363544:return this.getVanderwaalsRadiusFloat(a,J.c.VDW.AUTO);case 1648361473:return b=this.getVibrationVector(),null==b?0:b.length()*a.getFloat(1648361473);case 1111492626:return this.getVib("x");case 1111492627:return this.getVib("y");case 1111492628:return this.getVib("z");case 1111490583:return this.getVib("X");case 1111490584:return this.getVib("Y");case 1111490585:return this.getVib("Z");case 1111490586:return this.getVib("O");case 1111490580:return this.getVib("1");case 1111490581:return this.getVib("2");
case 1111490582:return this.getVib("3");case 1312817669:return this.getVolume(a,J.c.VDW.AUTO);case 1145047051:case 1145047053:case 1145045006:case 1145047052:case 1145047055:case 1145045008:case 1145047050:return a=this.atomPropertyTuple(a,b,d),null==a?-1:a.length()}return this.atomPropertyInt(b)},"JV.Viewer,~N,JU.P3");c(c$,"getVib",function(a){return this.group.chain.model.ms.getVibCoord(this.i,a)},"~S");c(c$,"getNominalMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getNaturalIsotope(this.getElementNumber())});
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case 1086324747:return d=this.group.getSeqcodeString(),null==d?"":d;case 1086324743:return this.getGroup1("\x00");case 1086324742:return this.getGroup3(!1);case 1086326789:return this.getElementSymbolIso(!0);case 1086324745:return this.getIdentity(!0);case 1086324746:return d=this.group.getInsertionCode(),"\x00"==d?"":""+d;case 1825200146:case 1287653388:return d=a.shm.getShapePropertyIndex(5,"label",this.i),null==d&&(d=""),d;case 1639976963:return this.group.getProteinStructureType().getBioStructureTypeName(!1);
case 1237320707:return this.group.getProteinStructureSubType().getBioStructureTypeName(!1);case 1086324749:return this.group.getStructureId();case 1086324748:return a.getHybridizationAndAxes(this.i,null,null,"d");case 1086326798:return this.getElementSymbolIso(!1);case 1088421903:return this.getSymmetryOperatorList(!0)}return""},"JV.Viewer,~N");j(c$,"getCIPChirality",function(a){var b=(this.formalChargeAndFlags&496)>>4;0==b&&(1<this.atomicAndIsotopeNumber&&a)&&(b=this.group.chain.model.ms.getAtomCIPChiralityCode(this),
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"atomPropertyTuple",function(a,b,d){switch(b){case 1073742329:return JU.P3.newP(this);case 1145047051:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d);case 1145047053:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d);case 1145045006:return this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d):this.getFractionalUnitCoordPt(!a.g.legacyJavaFloat,!1,d);case 1145047052:return JU.P3.new3(a.antialiased?y(this.sX/2):this.sX,a.getScreenHeight()-(a.antialiased?
y(this.sY/2):this.sY),a.antialiased?y(this.sZ/2):this.sZ);case 1145047055:return this.getVibrationVector();case 1145045008:return a=this.getModulation(),null==a?null:a.getV3();case 1145047050:return this;case 1765808134:return JU.CU.colorPtFromInt(this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom),d)}return null},"JV.Viewer,~N,JU.P3");j(c$,"getOffsetResidueAtom",function(a,b){return this.group.getAtomIndex(a,b)},"~S,~N");j(c$,"isCrossLinked",function(a){return this.group.isCrossLinked(a.group)},
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Exception))throw d;}return b},"~S");F(c$,"ATOM_INFRAME",1,"ATOM_VISSET",2,"ATOM_VISIBLE",4,"ATOM_NOTHIDDEN",8,"ATOM_NOFLAGS",-64,"ATOM_INFRAME_NOTHIDDEN",9,"ATOM_SHAPE_VIS_MASK",-10,"RADIUS_MAX",16,"RADIUS_GLOBAL",16.1,"MAD_GLOBAL",32200,"CHARGE_OFFSET",24,"FLAG_MASK",15,"VIBRATION_VECTOR_FLAG",1,"IS_HETERO_FLAG",2,"CIP_CHIRALITY_OFFSET",4,"CIP_CHIRALITY_MASK",496,"CIP_CHIRALITY_RULE_OFFSET",9,"CIP_CHIRALITY_RULE_MASK",3584,"CIP_MASK",4080)});u("JM");x(["JU.V3"],"JM.AtomCollection","java.lang.Float java.util.Arrays $.Hashtable JU.A4 $.AU $.BS $.Lst $.M3 $.Measure $.P3 $.PT J.api.Interface $.JmolModulationSet J.atomdata.RadiusData J.c.PAL $.VDW JM.Group JS.T JU.BSUtil $.Elements $.Escape $.Logger $.Parser $.Vibration".split(" "),
function(){c$=r(function(){this.at=this.bioModelset=this.g3d=this.vwr=null;this.ac=0;this.labeler=this.pointGroup=this.trajectory=null;this.maxVanderwaalsRadius=this.maxBondingRadius=1.4E-45;this.hasBfactorRange=!1;this.bfactor100Hi=this.bfactor100Lo=0;this.haveBSClickable=this.haveBSVisible=!1;this.bsSurface=null;this.surfaceDistanceMax=this.nSurfaceAtoms=0;this.averageAtomPoint=null;this.haveChirality=!1;this.bspf=null;this.canSkipLoad=this.preserveState=!0;this.haveStraightness=!1;this.aaRet=this.bsPartialCharges=
this.hydrophobicities=this.bondingRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.dssrData=this.atomSeqIDs=this.atomResnos=this.atomSerials=this.atomTypes=this.atomNames=this.tainted=this.surfaceDistance100s=this.atomTensors=this.atomTensorList=this.bsModulated=this.bsClickable=this.bsVisible=this.bsHidden=null;U("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();this.atomCapacity=0;n(this,arguments)},JM,"AtomCollection");c(c$,"setupAC",
function(){this.bsHidden=new JU.BS;this.bsVisible=new JU.BS;this.bsClickable=new JU.BS;null==JM.AtomCollection.userSettableValues&&(JM.AtomCollection.userSettableValues="atomName atomType coord element formalCharge hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals vibrationVector atomNo seqID resNo chain".$plit(" "))});c(c$,"releaseModelSetAC",function(){this.bfactor100s=this.occupancies=this.vibrations=this.atomSeqIDs=this.atomSerials=this.dssrData=this.atomResnos=this.atomTypes=
this.atomNames=this.tainted=this.bsSurface=this.surfaceDistance100s=this.bspf=this.g3d=this.vwr=this.at=null;this.resetPartialCharges();this.atomTensors=this.bondingRadii=null});c(c$,"mergeAtomArrays",function(a){this.tainted=a.tainted;this.atomNames=a.atomNames;this.atomTypes=a.atomTypes;this.atomResnos=a.atomResnos;this.dssrData=a.dssrData;this.atomSerials=a.atomSerials;this.atomSeqIDs=a.atomSeqIDs;this.vibrations=a.vibrations;this.occupancies=a.occupancies;this.bfactor100s=a.bfactor100s;this.bondingRadii=
a.bondingRadii;this.partialCharges=a.partialCharges;this.bsPartialCharges=a.bsPartialCharges;this.atomTensors=a.atomTensors;this.atomTensorList=a.atomTensorList;this.bsModulated=a.bsModulated;this.haveStraightness=!1;this.surfaceDistance100s=null},"JM.AtomCollection");c(c$,"getAtomPointVector",function(a){var b=new JU.Lst,d=this.ac;if(null!=a)for(var c=a.nextSetBit(0);0<=c&&c<d;c=a.nextSetBit(c+1))b.addLast(this.at[c]);return b},"JU.BS");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$,"getLabeler",function(){return null==this.labeler?
this.labeler=J.api.Interface.getInterface("JM.LabelToken",this.vwr,"ms"):this.labeler});c(c$,"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$,"getElementName",function(a){return JU.Elements.elementNameFromNumber(this.at[a].getAtomicAndIsotopeNumber())},"~N");c(c$,"getQuaternion",function(a,b){return 0>a?null:this.at[a].group.getQuaternion(b)},"~N,~S");c(c$,"getFirstAtomIndexFromAtomNumber",function(a,b){for(var d=
0;d<this.ac;d++){var c=this.at[d];if(c.getAtomNumber()==a&&b.get(c.mi))return d}return-1},"~N,JU.BS");c(c$,"setFormalCharges",function(a,b){if(null!=a){this.resetPartialCharges();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$,"getAtomicCharges",function(){for(var a=I(this.ac,0),b=this.ac;0<=--b;)a[b]=this.at[b].getElementNumber();return a});c(c$,"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",this.vwr,"ms").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=A(this.ac,0);this.nSurfaceAtoms=JU.BSUtil.cardinalityOf(this.bsSurface);if(0==this.nSurfaceAtoms||null==c||0==c.length)return c;for(var d=3.4028235E38==b?0:b,g=0;g<this.ac;g++)if(this.bsSurface.get(g))this.surfaceDistance100s[g]=0;else{for(var e=3.4028235E38,h=this.at[g],k=c.length;0<=--k;){var j=Math.abs(c[k].distance(h)-d);0>j&&JU.Logger.debugging&&JU.Logger.debug("draw d"+k+" "+JU.Escape.eP(c[k])+' "'+j+" ? "+h.getInfo()+'"');e=Math.min(j,
e)}j=this.surfaceDistance100s[g]=y(Math.floor(100*e));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,j)}return c},"JU.BS,~N");c(c$,"setAtomCoord2",function(a,b,d){var c=null,g=null,e=null,h=0,k=1;if(q(d,JU.P3))c=d;else if(q(d,JU.Lst)){e=d;if(0==(k=e.size()))return;h=1}else if(JU.AU.isAP(d)){g=d;if(0==(k=g.length))return;h=2}else return;d=0;if(null!=a)for(var j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){switch(h){case 1:if(d>=k)return;c=e.get(d++);break;case 2:if(d>=k)return;c=g[d++]}if(null!=
c)switch(b){case 1145047050:this.setAtomCoord(j,c.x,c.y,c.z);break;case 1145047051:this.at[j].setFractionalCoordTo(c,!0);this.taintAtom(j,2);break;case 1145047053:this.at[j].setFractionalCoordTo(c,!1);this.taintAtom(j,2);break;case 1145047055:this.setAtomVibrationVector(j,c)}}},"JU.BS,~N,~O");c(c$,"setAtomVibrationVector",function(a,b){this.setVibrationVector(a,b);this.taintAtom(a,12)},"~N,JU.T3");c(c$,"setAtomCoord",function(a,b,d,c){if(!(0>a||a>=this.ac)){var g=this.at[a];g.set(b,d,c);this.fixTrajectory(g);
this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"fixTrajectory",function(a){this.isTrajectory(a.mi)&&this.trajectory.fixAtom(a)},"JM.Atom");c(c$,"setAtomCoordRelative",function(a,b,d,c){if(!(0>a||a>=this.ac)){var g=this.at[a];g.add3(b,d,c);this.fixTrajectory(g);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"setAtomsCoordRelative",function(a,b,d,c){if(null!=a)for(var g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))this.setAtomCoordRelative(g,b,d,c)},"JU.BS,~N,~N,~N");c(c$,"setAPa",function(a,b,d,c,g,e,h){var k=0;
if(!(null!=e&&0==e.length||null==a)){for(var j=null!=e&&e.length==this.ac||null!=h&&h.length==this.ac,s=a.nextSetBit(0);0<=s;s=a.nextSetBit(s+1)){j&&(k=s);if(null!=e){if(k>=e.length)return;c=e[k++];if(Float.isNaN(c))continue;d=B(c)}else if(null!=h){if(k>=h.length)return;g=h[k++]}var m=this.at[s];switch(b){case 1086326786:this.setAtomName(s,g,!0);break;case 1086326785:this.setAtomType(s,g);break;case 1086326788:this.setChainID(s,g);break;case 1094715393:this.setAtomNumber(s,d,!0);break;case 1094713365:this.setAtomSeqID(s,
d);break;case 1111492609:case 1111492629:this.setAtomCoord(s,c,m.y,m.z);break;case 1111492610:case 1111492630:this.setAtomCoord(s,m.x,c,m.z);break;case 1111492611:case 1111492631:this.setAtomCoord(s,m.x,m.y,c);break;case 1111492626:case 1111492627:case 1111492628:this.setVibrationVector2(s,b,c);break;case 1111492612:case 1111492613:case 1111492614:m.setFractionalCoord(b,c,!0);this.taintAtom(s,2);break;case 1111492615:case 1111492616:case 1111492617:m.setFractionalCoord(b,c,!1);this.taintAtom(s,2);
break;case 1094715402:case 1086326789:this.setElement(m,d,!0);break;case 1631586315:this.resetPartialCharges();m.setFormalCharge(d);this.taintAtom(s,4);break;case 1113589786:this.setHydrophobicity(s,c);break;case 1128269825:2>c&&0.01<c&&(c*=100);this.setOccupancy(s,c,!0);break;case 1111492619:this.setPartialCharge(s,c,!0);break;case 1111492618:this.setBondingRadius(s,c);break;case 1111492620:this.setBFactor(s,c,!0);break;case 1094715412:this.setAtomResno(s,d);break;case 1825200146:case 1287653388:this.vwr.shm.setAtomLabel(g,
s);break;case 1665140738:case 1112152075:0>c?c=0:16<c&&(c=16.1);m.madAtom=aa(2E3*c);break;case 1113589787:this.vwr.slm.setSelectedAtom(m.i,0!=c);break;case 1094715417:m.setValence(d);this.taintAtom(s,10);break;case 1648363544:m.setRadius(c)?this.taintAtom(s,11):this.untaint(s,11);break;default:JU.Logger.error("unsettable atom property: "+JS.T.nameOf(b));return}}switch(b){case 1113589787:this.vwr.slm.setSelectedAtom(-1,!1);break;case 1665140738:case 1112152075:this.vwr.setShapeSize(0,2147483647,a)}}},
"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"getVibCoord",function(a,b){var d=null,c=null;switch(b){case "x":case "y":case "z":c=this.getVibration(a,!1);break;default:d=this.getModulation(a),null!=d&&(c=d.getVibration(!1),null==c&&(c=d))}if(null==c&&null==d)return NaN;switch(b){case "x":case "X":return c.x;case "y":case "Y":return c.y;case "z":case "Z":return c.z;case "O":return d.getModulation("O",null).floatValue();case "1":case "2":case "3":return d=d.getModulation("T",null),d="1"==b?d.x:"2"==b?d.y:d.z,d-
Math.floor(d);default:return NaN}},"~N,~S");c(c$,"getVibration",function(a,b){var d=null==this.vibrations?null:this.vibrations[a];return q(d,J.api.JmolModulationSet)?d.getVibration(b):null==d&&b?new JU.Vibration:d},"~N,~B");c(c$,"getModulation",function(a){a=null==this.vibrations?null:this.vibrations[a];return null!=a&&0<a.modDim?a:null},"~N");c(c$,"setVibrationVector",function(a,b){if(!Float.isNaN(b.x)&&!Float.isNaN(b.y)&&!Float.isNaN(b.z)){if(null==this.vibrations||this.vibrations.length<a)this.vibrations=
Array(this.at.length);q(b,JU.Vibration)?this.vibrations[a]=b:(null==this.vibrations[a]&&(this.vibrations[a]=new JU.Vibration),this.vibrations[a].setXYZ(b));this.at[a].setVibrationVector()}},"~N,JU.T3");c(c$,"setVibrationVector2",function(a,b,d){var c=this.getVibration(a,!0);if(null!=c){switch(b){case 1111492626:c.x=d;break;case 1111492627:c.y=d;break;case 1111492628:c.z=d}this.setAtomVibrationVector(a,c)}},"~N,~N,~N");c(c$,"setAtomName",function(a,b,d){if(!d||!b.equals(this.at[a].getAtomName())){var c=
this.am[this.at[a].mi].isBioModel?this.vwr.getJBR().lookupSpecialAtomID(b):0;this.at[a].atomID=c;0>=c&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[a]=b);d&&this.taintAtom(a,0)}},"~N,~S,~B");c(c$,"setAtomType",function(a,b){b.equals(this.at[a].getAtomType())||(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[a]=b)},"~N,~S");c(c$,"setChainID",function(a,b){if(!b.equals(this.at[a].getChainIDStr())){var d=this.at[a].getChainID(),d=this.getChainBits(d);
this.at[a].group.chain.chainID=this.vwr.getChainID(b,!0);for(var c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))this.taintAtom(c,16)}},"~N,~S");c(c$,"setAtomNumber",function(a,b,d){d&&b==this.at[a].getAtomNumber()||(null==this.atomSerials&&(this.atomSerials=A(this.at.length,0)),this.atomSerials[a]=b,d&&this.taintAtom(a,13))},"~N,~N,~B");c(c$,"setElement",function(a,b,d){d&&a.getElementNumber()==b||(a.setAtomicAndIsotopeNumber(b),a.paletteID=J.c.PAL.CPK.id,a.colixAtom=this.vwr.cm.getColixAtomPalette(a,
J.c.PAL.CPK.id),this.resetPartialCharges(),d&&this.taintAtom(a.i,3))},"JM.Atom,~N,~B");c(c$,"resetPartialCharges",function(){this.bsPartialCharges=this.partialCharges=null});c(c$,"setAtomResno",function(a,b){b!=this.at[a].getResno()&&(this.at[a].group.setResno(b),null==this.atomResnos&&(this.atomResnos=A(this.at.length,0)),this.atomResnos[a]=b,this.taintAtom(a,15))},"~N,~N");c(c$,"setAtomSeqID",function(a,b){b!=this.at[a].getSeqID()&&(null==this.atomSeqIDs&&(this.atomSeqIDs=A(this.at.length,0)),this.atomSeqIDs[a]=
b,this.taintAtom(a,14))},"~N,~N");c(c$,"setOccupancy",function(a,b,d){if(!(d&&b==this.at[a].getOccupancy100())){if(null==this.occupancies){if(100==b)return;this.occupancies=I(this.at.length,0);for(var c=this.at.length;0<=--c;)this.occupancies[c]=100}this.occupancies[a]=b;d&&this.taintAtom(a,7)}},"~N,~N,~B");c(c$,"setPartialCharge",function(a,b,d){if(!Float.isNaN(b)){if(null==this.partialCharges){this.bsPartialCharges=new JU.BS;if(0==b)return;this.partialCharges=I(this.at.length,0)}this.bsPartialCharges.set(a);
this.partialCharges[a]=b;d&&this.taintAtom(a,8)}},"~N,~N,~B");c(c$,"setBondingRadius",function(a,b){Float.isNaN(b)||b==this.at[a].getBondingRadius()||(null==this.bondingRadii&&(this.bondingRadii=I(this.at.length,0)),this.bondingRadii[a]=b,this.taintAtom(a,6))},"~N,~N");c(c$,"setBFactor",function(a,b,d){if(!(Float.isNaN(b)||d&&b==this.at[a].getBfactor100())){if(null==this.bfactor100s){if(0==b)return;this.bfactor100s=S(this.at.length,0)}this.bfactor100s[a]=ua(100*(-327.68>b?-327.68:327.67<b?327.67:
b)+(0>b?-0.5:0.5));d&&this.taintAtom(a,9)}},"~N,~N,~B");c(c$,"setHydrophobicity",function(a,b){if(!(Float.isNaN(b)||b==this.at[a].getHydrophobicity())){if(null==this.hydrophobicities){this.hydrophobicities=I(this.at.length,0);for(var d=0;d<this.at.length;d++)this.hydrophobicities[d]=JU.Elements.getHydrophobicity(this.at[d].group.groupID)}this.hydrophobicities[a]=b;this.taintAtom(a,5)}},"~N,~N");c(c$,"setAtomData",function(a,b,d,c){var g=null,e=null;switch(a){case 2:this.loadCoordinates(d,!1,!c);return;
case 12:this.loadCoordinates(d,!0,!0);return;case 17:g=I(this.ac,0),e=JU.BS.newN(this.ac)}c=JU.Parser.markLines(d,";");var h=0;try{for(var k=JU.PT.parseInt(d.substring(0,c[0]-1)),j=1;j<=k;j++){var s=JU.PT.getTokens(JU.PT.parseTrimmed(d.substring(c[j],c[j+1]-1))),m=JU.PT.parseInt(s[0])-1;if(!(0>m||m>=this.ac)){var p=this.at[m];h++;var z=s.length-1,w=JU.PT.parseFloat(s[z]);switch(a){case 17:g[m]=w;e.set(m);continue;case 0:this.setAtomName(m,s[z],!0);break;case 13:this.setAtomNumber(m,B(w),!0);break;
case 15:this.setAtomResno(m,B(w));break;case 14:this.setAtomSeqID(m,B(w));break;case 1:this.setAtomType(m,s[z]);break;case 16:this.setChainID(m,s[z]);break;case 3:p.setAtomicAndIsotopeNumber(B(w));p.paletteID=J.c.PAL.CPK.id;p.colixAtom=this.vwr.cm.getColixAtomPalette(p,J.c.PAL.CPK.id);break;case 4:p.setFormalCharge(B(w));break;case 5:this.setHydrophobicity(m,w);break;case 6:this.setBondingRadius(m,w);break;case 8:this.setPartialCharge(m,w,!0);break;case 9:this.setBFactor(m,w,!0);break;case 10:p.setValence(B(w));
break;case 11:p.setRadius(w)}this.taintAtom(m,a)}}17==a&&0<h&&this.vwr.setData(b,v(-1,[b,g,e,Integer.$valueOf(1)]),0,0,0,0,0)}catch(q){if(E(q,Exception))JU.Logger.error("AtomCollection.loadData error: "+q);else throw q;}},"~N,~S,~S,~B");c(c$,"loadCoordinates",function(a,b,d){var c=JU.Parser.markLines(a,";"),g=b?new JU.V3:null;try{for(var e=JU.PT.parseInt(a.substring(0,c[0]-1)),h=1;h<=e;h++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[h],c[h+1]))),j=JU.PT.parseInt(k[0])-1,s=k[3].equalsIgnoreCase("1.4E-45")?
1.4E-45:JU.PT.parseFloat(k[3]),m=k[4].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(k[4]),p=JU.PT.parseFloat(k[5]);b?(g.set(s,m,p),this.setAtomVibrationVector(j,g)):(this.setAtomCoord(j,s,m,p),d||this.untaint(j,2))}}catch(z){if(E(z,Exception))JU.Logger.error("Frame.loadCoordinate error: "+z);else throw z;}},"~S,~B,~B");c(c$,"validateBspf",function(a){null!=this.bspf&&(this.bspf.isValid=a);this.averageAtomPoint=null},"~B");c(c$,"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$,"getUserSettableType",function(a){var b=0==a.indexOf("property_");a=b?a.substring(9):a;for(var d=0;17>d;d++)if(JM.AtomCollection.userSettableValues[d].equalsIgnoreCase(a))return d;return b?17:-1},"~S");c(c$,"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(17)),null==this.tainted[b]&&(this.tainted[b]=JU.BS.newN(this.ac)),this.tainted[b].set(a));2==b&&this.taintModelCoord(a)},"~N,~N");c(c$,"taintModelCoord",function(a){a=this.am[this.at[a].mi];this.validateBspfForModel(a.trajectoryBaseIndex,!1);a.isBioModel&&a.resetDSSR(!0);this.pointGroup=null},"~N");c(c$,"untaint",function(a,b){this.preserveState&&(null==this.tainted||
null==this.tainted[b]||this.tainted[b].clear(a))},"~N,~N");c(c$,"setTaintedAtoms",function(a,b){if(this.preserveState){if(null==a){if(null==this.tainted)return;this.tainted[b]=null;return}null==this.tainted&&(this.tainted=Array(17));null==this.tainted[b]&&(this.tainted[b]=JU.BS.newN(this.ac));JU.BSUtil.copy2(a,this.tainted[b])}if(2==b){var d=a.nextSetBit(0);0<=d&&this.taintModelCoord(d)}},"JU.BS,~N");c(c$,"unTaintAtoms",function(a,b){if(!(null==this.tainted||null==this.tainted[b])){for(var d=a.nextSetBit(0);0<=
d;d=a.nextSetBit(d+1))this.tainted[b].clear(d);0>this.tainted[b].nextSetBit(0)&&(this.tainted[b]=null)}},"JU.BS,~N");c(c$,"findNearest2",function(a,b,d,c,g){for(var e=null,h=this.ac;0<=--h;)if(!(null!=c&&c.get(h))){var k=this.at[h];k.isClickable()&&this.isCursorOnTopOf(k,a,b,g,e)&&(e=k)}d[0]=e},"~N,~N,~A,JU.BS,~N");c(c$,"isCursorOnTopOf",function(a,b,d,c,g){return 1<a.sZ&&!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(b,d,c,g)},"JM.Atom,~N,~N,~N,JM.Atom");c(c$,
"fillADa",function(a,b){a.xyz=a.atoms=this.at;a.ac=this.ac;a.atomicNumber=A(this.ac,0);var d=0!=(b&2);d&&(a.atomRadius=I(this.ac,0));for(var c=0!=(b&16),g=0;g<this.ac;g++){var e=this.at[g];e.isDeleted()||!c&&0<=a.modelIndex&&e.mi!=a.firstModelIndex?(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(g)):(a.atomicNumber[g]=e.getElementNumber(),a.lastModelIndex=e.mi,d&&(a.atomRadius[g]=this.getWorkingRadius(e,a)))}},"J.atomdata.AtomData,~N");c(c$,"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,g){var e=new JU.V3,h=new JU.V3,k=Array(this.ac),j=this.vwr.slm.bsDeleted,s,m=0;if(null!=a)for(var p=a.nextSetBit(0);0<=p;p=a.nextSetBit(p+1))if(!(null!=j&&j.get(p))){var z=this.at[p],w=z.getElementNumber();if(!(c&&6!=w)){var q=6>=w?1.1:10>=w?1:1.3;switch(w){case 7:case 8:q=1}if(!(d&&0<z.getCovalentHydrogenCount())&&(s=this.getMissingHydrogenCount(z,!1),0!=s)){var n=this.aaRet[0],r=this.aaRet[2],t=this.aaRet[3];if(!(0==t&&z.isHetero())){k[p]=Array(s);var u=
0;if(0==t)switch(s){case 4:e.set(0.635,0.635,0.635),s=JU.P3.newP(e),s.add(z),k[p][u++]=s,null!=g&&g.addLast(z);case 3:e.set(-0.635,-0.635,0.635),s=JU.P3.newP(e),s.add(z),k[p][u++]=s,null!=g&&g.addLast(z);case 2:e.set(-0.635,0.635,-0.635),s=JU.P3.newP(e),s.add(z),k[p][u++]=s,null!=g&&g.addLast(z);case 1:e.set(0.635,-0.635,-0.635),s=JU.P3.newP(e),s.add(z),k[p][u++]=s,null!=g&&g.addLast(z)}else switch(s){case 3:this.getHybridizationAndAxes(p,w,e,h,"sp3b",!1,!0);s=new JU.P3;s.scaleAdd2(q,e,z);k[p][u++]=
s;null!=g&&g.addLast(z);this.getHybridizationAndAxes(p,w,e,h,"sp3c",!1,!0);s=new JU.P3;s.scaleAdd2(q,e,z);k[p][u++]=s;null!=g&&g.addLast(z);this.getHybridizationAndAxes(p,w,e,h,"sp3d",!1,!0);s=new JU.P3;s.scaleAdd2(q,e,z);k[p][u++]=s;null!=g&&g.addLast(z);break;case 2:r=2==r||5==w||1==t&&4==n||7==w&&this.isAdjacentSp2(z);this.getHybridizationAndAxes(p,w,e,h,r?"sp2b":3==n?"sp3c":"lpa",!1,!0);s=JU.P3.newP(e);s.scaleAdd2(q,e,z);k[p][u++]=s;null!=g&&g.addLast(z);this.getHybridizationAndAxes(p,w,e,h,r?
"sp2c":3==n?"sp3d":"lpb",!1,!0);s=JU.P3.newP(e);s.scaleAdd2(q,e,z);k[p][u++]=s;null!=g&&g.addLast(z);break;case 1:switch(n-t){case 1:if(8==w&&z===z.group.getCarbonylOxygenAtom()){k[p]=null;continue}null!=this.getHybridizationAndAxes(p,w,e,h,2==r||5==w||7==w&&(z.group.getNitrogenAtom()===z||this.isAdjacentSp2(z))?"sp2c":"sp3d",!0,!1)?(s=JU.P3.newP(e),s.scaleAdd2(q,e,z),k[p][u++]=s,null!=g&&g.addLast(z)):k[p]=[];break;case 2:this.getHybridizationAndAxes(p,w,e,h,4==n?"sp2c":"sp2b",!1,!1);s=JU.P3.newP(e);
s.scaleAdd2(q,e,z);k[p][u++]=s;null!=g&&g.addLast(z);break;case 3:this.getHybridizationAndAxes(p,w,e,h,"spb",!1,!0),s=JU.P3.newP(e),s.scaleAdd2(q,e,z),k[p][u++]=s,null!=g&&g.addLast(z)}}m+=u}}}}b[0]=m;return k},"JU.BS,~A,~B,~B,JU.Lst");c(c$,"isAdjacentSp2",function(a){for(var b=a.bonds,d=0;d<b.length;d++)for(var c=b[d].getOtherAtom(a).bonds,g=0;g<c.length;g++)switch(c[g].order){case 515:case 514:case 2:case 3:return!0}return!1},"JM.Atom");c(c$,"getMissingHydrogenCount",function(a,b){var d=a.getTargetValence();
if(0>d)return 0;var c=a.getFormalCharge(),g=a.getValence(),e=this.am[a.mi],e=e.isBioModel&&!e.isPdbWithMultipleBonds?a.group.getGroup3():null;null==this.aaRet&&(this.aaRet=A(5,0));this.aaRet[0]=d;this.aaRet[1]=c;this.aaRet[2]=0;this.aaRet[3]=a.getCovalentBondCount();this.aaRet[4]=null==e?0:g;null!=e&&0==c&&this.bioModelset.getAminoAcidValenceAndCharge(e,a.getAtomName(),this.aaRet)&&(d=this.aaRet[0],c=this.aaRet[1]);0!=c&&(d+=4==d?-Math.abs(c):c,this.aaRet[0]=d);d-=g;return 0>d&&!b?0:d},"JM.Atom,~B");
c(c$,"fixFormalCharges",function(a){for(var b=0,d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1)){var c=this.at[d],g=this.getMissingHydrogenCount(c,!0);if(0!=g){var e=c.getFormalCharge(),g=e-g;c.setFormalCharge(g);this.taintAtom(d,4);JU.Logger.debugging&&JU.Logger.debug("atom "+c+" formal charge "+e+" -> "+g);b++}}return b},"JU.BS");c(c$,"getHybridizationAndAxes",function(a,b,d,c,g,e,h){var k=0<g.length&&"-"==g.charAt(0)?g.substring(1):g;if(0<=g.indexOf("d")&&!g.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,
d,c,k);g=this.at[a];0==b&&(b=g.getElementNumber());var j=this.getAttached(g,4,e),s=j.length,m=k.charCodeAt(k.length-1)-97;if(0>m||6<m)m=0;d.set(0,0,0);c.set(0,0,0);for(var p=Array(4),q=0;q<s;q++)p[q]=JU.V3.newVsub(g,j[q]),p[q].normalize(),d.add(p[q]);0<s&&c.setT(p[0]);q=!1;a=new JU.V3;if(3<=s){2.984513>c.angle(p[1])?a.cross(c,p[1]):a.cross(c,p[2]);a.normalize();var w=new JU.V3;2.984513>p[1].angle(p[2])?w.cross(p[1],p[2]):w.cross(c,p[2]);w.normalize();q=0.95<=Math.abs(w.dot(a))}var n=0==k.indexOf("sp3"),
r=!n&&0==k.indexOf("sp2"),t=!n&&!r&&0==k.indexOf("sp"),u=0==k.indexOf("p"),v=0==k.indexOf("lp"),w=null;if(e){if(0==s)return null;if(n){if(3<m||4<s)return null}else if(r){if(2<m||3<s)return null}else if(t&&(1<m||2<s))return null;switch(s){case 1:if(1==b&&!n)return null;if(n){w="sp3";break}switch(j[0].getCovalentBondCount()){case 1:if(2!=j[0].getValence()){w="sp";break}case 2:w=t?"sp":"sp2";break;case 3:if(!r&&!u)return null;w="sp2"}break;case 2:if(0.1>d.length()){if(0<=k.indexOf("2")||0<=k.indexOf("3"))return null;
w="sp";break}w=n?"sp3":"sp2";if(0==k.indexOf("sp"))break;if(v){w="lp";break}w=k;break;default:if(q)w="sp2";else{if(v&&3==s){w="lp";break}w="sp3"}}if(null==w)return null;if(0==k.indexOf("p")){if("sp3"===w)return null}else if(0>k.indexOf(w))return null}if(m<s&&!k.startsWith("p")&&!k.startsWith("l"))return d.sub2(j[m],g),d.normalize(),w;switch(s){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(n){for(q=j[0].getBondCount();0<=--q;)if(j[0].bonds[q].isCovalent()&&j[0].getBondedAtomIndex(q)!=g.i&&(c.sub2(j[0],j[0].bonds[q].getOtherAtom(j[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!=m&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(d.x,d.y,d.z,2.09439507*
(2==m?1:-1))).rotate(c));d.setT(c);c.cross(a,d);break}a.cross(c,d);switch(j[0].getCovalentBondCount()){case 1:if(2!=j[0].getValence())break;case 2:h=j[0];c.setT(d);for(a.setT(JM.AtomCollection.vRef);null!=h&&2==h.getCovalentBondCount();){k=h.bonds;b=null;for(q=0;q<k.length;q++)if(k[q].isCovalent()&&(b=k[q].getOtherAtom(h),b!==g)){a.sub2(b,h);break}a.cross(a,c);if(0.1<a.length()||2!=b.getCovalentBondCount())break;g=h;h=b}0.1<a.length()?(d.cross(a,c),d.normalize(),1==m&&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(j[0].i,0,c,a,"pz",!1,h),a.setT(c),r?(c.cross(c,d),1==m&&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=j[0];(g=3==b.getCovalentBondCount())||(g=3==(b=j[1]).getCovalentBondCount());if(g){this.getHybridizationAndAxes(b.i,0,c,d,"pz",
!1,h);k.equals("px")&&c.scale(-1);d.setT(p[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(n||v){a.normalize();d.normalize();k.equals("lp")||(0==m||2==m?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(n)break;if(!q){c.cross(d,c);break}d.setT(a);0>d.z&&h&&(d.scale(-1),c.scale(-1))}c.normalize();d.normalize();return w},"~N,~N,JU.V3,JU.V3,~S,~B,~B");
c(c$,"getHybridizationAndAxesD",function(a,b,d,c){c.startsWith("sp3d2")&&(c="d2sp3"+(5==c.length?"a":c.substring(5)));c.startsWith("sp3d")&&(c="dsp3"+(4==c.length?"a":c.substring(4)));if(c.equals("d2sp3")||c.equals("dsp3"))c+="a";var g=c.startsWith("dsp3"),e=c.charCodeAt(c.length-1)-97;if(null!=b&&(!g&&(5<e||!c.startsWith("d2sp3"))||g&&4<e))return null;a=this.at[a];c=this.getAttached(a,6,!0);if(null==c)return null==b?null:"?";var h=c.length;if(3>h&&null!=b)return null;for(var k=e>=h,j=y(h*(h-1)/2),
s=JU.AU.newInt2(j),m=A(3,0),j=A(3,j,0),p=0,q=0,w=0;w<h-1;w++)for(var n=w+1;n<h;n++){var r=JU.Measure.computeAngleABC(c[w],a,c[n],!0),r=105>r?0:150<=r?2:1;j[r][m[r]]=p;m[r]++;s[p++]=A(-1,[w,n]);0==w&&1==r&&q++}p=100*m[0]+10*m[1]+m[2];if(null==b)switch(p){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==q%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(p){default:return null;case 201:break;case 210:case 330:case 411:case 631:if(!g)return null;break;case 300:case 402:case 501:case 802:case 1203:if(g)return null}if(k)if(g)switch(m[1]){case 0:b.sub2(c[s[j[0][0]][0]],
a);d.sub2(c[s[j[0][0]][1]],a);b.cross(b,d);b.normalize();4==e&&b.scale(-1);m=this.findNotAttached(h,s,j[2],m[2]);w=m.nextSetBit(0);d.sub2(c[w],a);d.normalize();d.scale(0.5);b.scaleAdd2(JM.AtomCollection.sqrt3_2,b,d);e=-1;break;case 1:4==e?(d=s[j[1][0]],b.add2(c[d[0]],c[d[1]]),b.scaleAdd2(-2,a,b),e=-1):(m=this.findNotAttached(h,s,j[1],m[1]),e=m.nextSetBit(0));break;default:m=this.findNotAttached(h,s,j[1],m[1]),e=m.nextSetBit(0)}else{p=!1;if(4==h)switch(m[2]){case 1:m=this.findNotAttached(h,s,j[2],
m[2]);w=m.nextSetBit(0);e=4==e?w:m.nextSetBit(w+1);break;default:p=!0}else{m=this.findNotAttached(h,s,j[2],m[2]);w=m.nextSetBit(0);for(n=h;n<e&&0<=w;n++)w=m.nextSetBit(w+1);-1==w?p=!0:e=w}p&&(b.sub2(c[s[j[0][0]][0]],a),d.sub2(c[s[j[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 g?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(c$,"getAttached",function(a,b,d){var c=a.getCovalentBondCount();if(c>b)return null;b=Array(c);if(0<c){for(var c=a.bonds,
g=0,e=0;e<c.length;e++)c[e].isCovalent()&&(b[g++]=c[e].getOtherAtom(a));d&&java.util.Arrays.sort(b,Q(JM.AtomCollection.AtomSorter,this,null))}return b},"JM.Atom,~N,~B");c(c$,"findNotAttached",function(a,b,d,c){var g=JU.BS.newN(a);g.setBits(0,a);for(var e=0;e<a;e++)for(var h=0;h<c;h++){var k=b[d[h]];(k[0]==e||k[1]==e)&&g.clear(e)}return g},"~N,~A,~A,~N");c(c$,"getAtomBitsMDa",function(a,b,d){var c=q(b,Integer)?b.intValue():0;switch(a){case 1086326786:case 1086326785:var g=1086326785==a,e=","+b+",";
for(a=this.ac;0<=--a;)b=g?this.at[a].getAtomType():this.at[a].getAtomName(),0<=e.indexOf(","+b+",")&&d.set(a);return d;case 1094715393:for(a=this.ac;0<=--a;)this.at[a].getAtomNumber()==c&&d.set(a);return d;case 2097155:for(a=this.ac;0<=--a;)0<this.at[a].getCovalentBondCount()&&d.set(a);return d;case 2097188:case 2097156:case 136314895:case 2097166:case 2097168:case 2097170:case 2097172:case 2097174:case 2097184:return this.haveBioModels?this.bioModelset.getAtomBitsBS(a,null,d):d;case 1612709900:c=
1;case 1094715402:for(a=this.ac;0<=--a;)this.at[a].getElementNumber()==c&&d.set(a);return d;case 1612709894:for(a=this.ac;0<=--a;)this.at[a].isHetero()&&d.set(a);return d;case 1073741824:return this.getIdentifierOrNull(b);case 2097165:for(a=this.ac;0<=--a;)this.at[a].isLeadAtom()&&d.set(a);return d;case 1094713362:case 1639976963:return this.haveBioModels?this.bioModelset.getAtomBitsBS(a,b,d):d;case 1094715412:for(a=this.ac;0<=--a;)this.at[a].getResno()==c&&d.set(a);return d;case 1612709912:b=A(2,
0);for(a=this.ac;0<=--a;)if(c=this.at[a].group.groupID,42<=c&&45>c)d.set(a);else if(8==(g=this.at[a]).getElementNumber()&&2==g.getCovalentBondCount()){for(var c=g.bonds,h=0,k=c.length;0<=--k&&3>h;)if(c[k].isCovalent()&&1==(e=c[k].getOtherAtom(g)).getElementNumber())b[h++%2]=e.i;2==h&&(d.set(b[1]),d.set(b[0]),d.set(a))}return d;case 1073742355:for(a=this.ac;0<=--a;)this.isAltLoc(this.at[a].altloc,b)&&d.set(a);return d;case 1073742356:g=b.toUpperCase();0<=g.indexOf("\\?")&&(g=JU.PT.rep(g,"\\?","\u0001"));
(e=g.startsWith("?*"))&&(g=g.substring(1));for(a=this.ac;0<=--a;)this.isAtomNameMatch(this.at[a],g,e,e)&&d.set(a);return d;case 1073742357:return JU.BSUtil.copy(this.getChainBits(c));case 1073742360:return this.getSpecName(b);case 1073742361:for(a=this.ac;0<=--a;)this.at[a].group.groupID==c&&d.set(a);return d;case 1073742362:return JU.BSUtil.copy(this.getSeqcodeBits(c,!0));case 5:for(a=this.ac;0<=--a;)this.at[a].group.getInsCode()==c&&d.set(a);return d;case 1296041986:for(a=this.ac;0<=--a;)this.at[a].getSymOp()==
c&&d.set(a);return d}e=b.nextSetBit(0);if(0>e)return d;switch(a){case 1094717454:g=JU.BSUtil.copy(b);for(a=e;0<=a;a=g.nextSetBit(a+1))d.or(this.am[this.at[a].mi].bsAtoms),g.andNot(d);return d;case 1086326788:g=JU.BSUtil.copy(b);for(a=e;0<=a;a=g.nextSetBit(a+1))this.at[a].group.chain.setAtomBits(d),g.andNot(d);return d;case 1086326789:g=new JU.BS;for(a=e;0<=a;a=b.nextSetBit(a+1))g.set(this.at[a].getElementNumber());for(a=this.ac;0<=--a;)g.get(this.at[a].getElementNumber())&&d.set(a);return d;case 1086324742:g=
JU.BSUtil.copy(b);for(a=e;0<=a;a=g.nextSetBit(a+1))this.at[a].group.setAtomBits(d),g.andNot(d);return d;case 1094713366:g=new JU.BS;for(a=e;0<=a;a=b.nextSetBit(a+1))g.set(this.at[a].atomSite);for(a=this.ac;0<=--a;)g.get(this.at[a].atomSite)&&d.set(a);return d}JU.Logger.error("MISSING getAtomBits entry for "+JS.T.nameOf(a));return d},"~N,~O,JU.BS");c(c$,"getChainBits",function(a){var b=this.vwr.getBoolean(603979822);0<=a&&(300>a&&!b)&&(a=this.chainToUpper(a));for(var d=new JU.BS,c=JU.BS.newN(this.ac),
g,e=c.nextClearBit(0);e<this.ac;e=c.nextClearBit(e+1)){var h=this.at[e].group.chain;a==(g=h.chainID)||!b&&0<=g&&300>g&&a==this.chainToUpper(g)?(h.setAtomBits(d),c.or(d)):h.setAtomBits(c)}return d},"~N");c(c$,"chainToUpper",function(a){return 97<=a&&122>=a?a-32:256<=a&&300>a?a-191:a},"~N");c(c$,"isAltLoc",function(a,b){if(null==b)return"\x00"==a;if(1!=b.length)return!1;var d=b.charAt(0);return"*"==d||"?"==d&&"\x00"!=a||a==d},"~S,~S");c(c$,"getSeqcodeBits",function(a,b){var d=new JU.BS,c=JM.Group.getSeqNumberFor(a),
g=2147483647!=c,e=!0,h=JM.Group.getInsertionCodeChar(a);switch(h){case "?":for(var k=this.ac;0<=--k;){var j=this.at[k].group.seqcode;if((!g||c==JM.Group.getSeqNumberFor(j))&&0!=JM.Group.getInsertionCodeFor(j))d.set(k),e=!1}break;default:for(k=this.ac;0<=--k;)if(j=this.at[k].group.seqcode,a==j||!g&&a==JM.Group.getInsertionCodeFor(j)||"*"==h&&c==JM.Group.getSeqNumberFor(j))d.set(k),e=!1}return!e||b?d:null},"~N,~B");c(c$,"getIdentifierOrNull",function(a){var b=this.getSpecNameOrNull(a,!1);0<=a.indexOf("\\?")&&
(a=JU.PT.rep(a,"\\?","\u0001"));return null!=b||0<a.indexOf("?")?b:0<a.indexOf("*")?this.getSpecNameOrNull(a,!0):this.haveBioModels?this.bioModelset.getIdentifierOrNull(a):null},"~S");c(c$,"getSpecName",function(a){var b=this.getSpecNameOrNull(a,!1);if(null!=b)return b;0<a.indexOf("*")&&(b=this.getSpecNameOrNull(a,!0));return null==b?new JU.BS:b},"~S");c(c$,"getSpecNameOrNull",function(a,b){var d=null;a=a.toUpperCase();0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));var c=a.startsWith("?*");
c&&(a=a.substring(1));for(var g=this.ac;0<=--g;){var e=this.at[g].getGroup3(!0);if(null!=e&&0<e.length){if(JU.PT.isMatch(e,a,b,!0)){null==d&&(d=JU.BS.newN(g+1));for(d.set(g);0<=--g&&this.at[g].getGroup3(!0).equals(e);)d.set(g);g++}}else this.isAtomNameMatch(this.at[g],a,b,c)&&(null==d&&(d=JU.BS.newN(g+1)),d.set(g))}return d},"~S,~B");c(c$,"isAtomNameMatch",function(a,b,d,c){return JU.PT.isMatch(a.getAtomName().toUpperCase(),b,d,c)},"JM.Atom,~S,~B,~B");c(c$,"getAtomIndices",function(a){for(var b=0,
d=A(this.ac,0),c=a.nextSetBit(0);0<=c&&c<this.ac;c=a.nextSetBit(c+1))d[c]=++b;return d},"JU.BS");c(c$,"getAtomsNearPlane",function(a,b){for(var d=new JU.BS,c=this.ac;0<=--c;){var g=this.at[c],e=JU.Measure.distanceToPlane(b,g);(0<a&&-0.1<=e&&e<=a||0>a&&0.1>=e&&e>=a||0==a&&0.01>Math.abs(e))&&d.set(g.i)}return d},"~N,JU.P4");c(c$,"clearVisibleSets",function(){this.haveBSClickable=this.haveBSVisible=!1});c(c$,"getAtomsInFrame",function(a){this.clearVisibleSets();a.clearAll();for(var b=this.ac;0<=--b;)this.at[b].isVisible(1)&&
a.set(b)},"JU.BS");c(c$,"getVisibleSet",function(a){if(a)this.vwr.setModelVisibility(),this.vwr.shm.finalizeAtoms(null,!0);else if(this.haveBSVisible)return this.bsVisible;this.bsVisible.clearAll();for(a=this.ac;0<=--a;)this.at[a].checkVisible()&&this.bsVisible.set(a);null!=this.vwr.shm.bsSlabbedInternal&&this.bsVisible.andNot(this.vwr.shm.bsSlabbedInternal);this.haveBSVisible=!0;return this.bsVisible},"~B");c(c$,"getClickableSet",function(a){if(a)this.vwr.setModelVisibility();else if(this.haveBSClickable)return this.bsClickable;
this.bsClickable.clearAll();for(a=this.ac;0<=--a;)this.at[a].isClickable()&&this.bsClickable.set(a);this.haveBSClickable=!0;return this.bsClickable},"~B");c(c$,"isModulated",function(a){return null!=this.bsModulated&&this.bsModulated.get(a)},"~N");c(c$,"deleteModelAtoms",function(a,b,d){this.at=JU.AU.deleteElements(this.at,a,b);this.ac=this.at.length;for(var c=a;c<this.ac;c++)this.at[c].i=c,this.at[c].mi--;null!=this.bsModulated&&JU.BSUtil.deleteBits(this.bsModulated,d);this.deleteAtomTensors(d);
this.atomNames=JU.AU.deleteElements(this.atomNames,a,b);this.atomTypes=JU.AU.deleteElements(this.atomTypes,a,b);this.atomResnos=JU.AU.deleteElements(this.atomResnos,a,b);this.atomSerials=JU.AU.deleteElements(this.atomSerials,a,b);this.atomSeqIDs=JU.AU.deleteElements(this.atomSeqIDs,a,b);this.dssrData=JU.AU.deleteElements(this.dssrData,a,b);this.bfactor100s=JU.AU.deleteElements(this.bfactor100s,a,b);this.hasBfactorRange=!1;this.occupancies=JU.AU.deleteElements(this.occupancies,a,b);this.resetPartialCharges();
this.atomTensorList=JU.AU.deleteElements(this.atomTensorList,a,b);this.vibrations=JU.AU.deleteElements(this.vibrations,a,b);this.nSurfaceAtoms=0;this.surfaceDistance100s=this.bsSurface=null;if(null!=this.tainted)for(a=0;17>a;a++)JU.BSUtil.deleteBits(this.tainted[a],d)},"~N,~N,JU.BS");c(c$,"getAtomIdentityInfo",function(a,b,d){b.put("_ipt",Integer.$valueOf(a));b.put("atomIndex",Integer.$valueOf(a));b.put("atomno",Integer.$valueOf(this.at[a].getAtomNumber()));b.put("info",this.getAtomInfo(a,null,d));
b.put("sym",this.at[a].getElementSymbol())},"~N,java.util.Map,JU.P3");c(c$,"getAtomTensorList",function(a){return 0>a||null==this.atomTensorList||a>=this.atomTensorList.length?null:this.atomTensorList[a]},"~N");c(c$,"deleteAtomTensors",function(a){if(null!=this.atomTensors){for(var b=new JU.Lst,d,c=this.atomTensors.keySet().iterator();c.hasNext()&&((d=c.next())||1);){for(var g=this.atomTensors.get(d),e=g.size();0<=--e;){var h=g.get(e);(a.get(h.atomIndex1)||0<=h.atomIndex2&&a.get(h.atomIndex2))&&g.removeItemAt(e)}0==
g.size()&&b.addLast(d)}for(e=b.size();0<=--e;)this.atomTensors.remove(b.get(e))}},"JU.BS");c(c$,"setCapacity",function(a){this.atomCapacity+=a},"~N");c(c$,"setAtomTensors",function(a,b){if(!(null==b||0==b.size())){null==this.atomTensors&&(this.atomTensors=new java.util.Hashtable);null==this.atomTensorList&&(this.atomTensorList=Array(this.at.length));this.atomTensorList=JU.AU.ensureLength(this.atomTensorList,this.at.length);this.atomTensorList[a]=JM.AtomCollection.getTensorList(b);for(var d=b.size();0<=
--d;){var c=b.get(d);c.atomIndex1=a;c.atomIndex2=-1;c.modelIndex=this.at[a].mi;this.addTensor(c,c.type);null!=c.altType&&this.addTensor(c,c.altType)}}},"~N,JU.Lst");c(c$,"addTensor",function(a,b){b=b.toLowerCase();var d=this.atomTensors.get(b);null==d&&(this.atomTensors.put(b,d=new JU.Lst),d.ensureCapacity(this.atomCapacity));d.addLast(a)},"JU.Tensor,~S");c$.getTensorList=c(c$,"getTensorList",function(a){for(var b=-1,d=!1,c=a.size(),g=c;0<=--g;){var e=a.get(g);e.forThermalEllipsoid?b=g:2==e.iType&&
(d=!0)}var h=Array((0<=b||!d?0:1)+c);if(0<=b&&(h[0]=a.get(b),1==a.size()))return h;if(d){b=0;for(g=c;0<=--g;)e=a.get(g),e.forThermalEllipsoid||(h[++b]=e)}else for(g=0;g<c;g++)h[g]=a.get(g);return h},"JU.Lst");c(c$,"getAtomTensor",function(a,b){var d=this.getAtomTensorList(a);if(null!=d&&null!=b){b=b.toLowerCase();for(var c=0;c<d.length;c++){var g=d[c];if(null!=g&&(b.equals(g.type)||b.equals(g.altType)))return g}}return null},"~N,~S");c(c$,"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(c$,"scaleVectorsToMax",function(a){if(null!=this.vibrations){for(var b=0,d=JU.BS.newN(this.ac),c=this.vibrations.length;0<=--c;){var g=this.getVibration(c,!1);if(null!=g&&(-1==g.modDim||-2==g.modDim))b=Math.max(b,g.length()),d.set(c)}if(!(b==a||0==b)){b=a/b;a=!1;for(c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1)){var g=
this.getVibration(c,!1),e=this.getModulation(c);if(null==e){if(0==b)return;g.scale(b)}else e.scaleVibration(b);a||(this.taintAtom(c,12),a=!0)}this.tainted[12].or(d)}}},"~N");c(c$,"getAtomsFromAtomNumberInFrame",function(a){for(var b=this.vwr.getFrameAtoms(),d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.at[d].getAtomNumber()!=a&&b.clear(d);return b},"~N");c(c$,"generateCrystalClass",function(a,b){var d=0>a||a>=this.ac?null:this.at[a].getUnitCell(),c=null!=b&&Float.isNaN(b.x);return null==d?new JU.Lst:
d.generateCrystalClass(c?null:null!=b?b:this.at[a])},"~N,JU.P3");c$.$AtomCollection$AtomSorter$=function(){K(self.c$);c$=r(function(){V(this,arguments);n(this,arguments)},JM.AtomCollection,"AtomSorter",null,java.util.Comparator);j(c$,"compare",function(a,b){return a.i>b.i?1:a.i<b.i?-1:0},"JM.Atom,JM.Atom");c$=M()};F(c$,"almost180",2.984513);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);F(c$,"userSettableValues",null,"TAINT_ATOMNAME",0,
"TAINT_ATOMTYPE",1,"TAINT_COORD",2,"TAINT_ELEMENT",3,"TAINT_FORMALCHARGE",4,"TAINT_HYDROPHOBICITY",5,"TAINT_BONDINGRADIUS",6,"TAINT_OCCUPANCY",7,"TAINT_PARTIALCHARGE",8,"TAINT_TEMPERATURE",9,"TAINT_VALENCE",10,"TAINT_VANDERWAALS",11,"TAINT_VIBRATION",12,"TAINT_ATOMNO",13,"TAINT_SEQID",14,"TAINT_RESNO",15,"TAINT_CHAIN",16,"TAINT_MAX",17)});u("JM");x(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){c$=r(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;n(this,arguments)},JM,"AtomIteratorWithinModel",null,J.api.AtomIndexIterator);t(c$,function(){});c(c$,"initialize",function(a,b,d,c,g,e){this.bspf=a;this.bsSelected=b;this.isGreaterOnly=d;this.isZeroBased=c;this.hemisphereOnly=g;this.threadSafe=
e;this.cubeIterator=null},"J.bspt.Bspf,JU.BS,~B,~B,~B,~B");j(c$,"setModel",function(a,b,d,c,g,e,h){this.threadSafe&&(b=-1-b);if(b!=this.modelIndex||null==this.cubeIterator)this.cubeIterator=this.bspf.getCubeIterator(b),this.modelIndex=b;this.zeroBase=this.isZeroBased?d:0;if(-2147483648!=e){this.atomIndex=0>e?-1:c;if(this.isVdw=null!=h)this.radiusData=h,this.atoms=a.at,this.vwr=a.vwr,e=h.factorType===J.atomdata.RadiusData.EnumType.OFFSET?5+h.value:5*h.value,this.vdw1=this.atoms[c].getVanderwaalsRadiusFloat(this.vwr,
h.vdwType);this.checkGreater=this.isGreaterOnly&&2147483647!=c;this.setCenter(g,e)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");j(c$,"setCenter",function(a,b){this.setCenter2(a,b)},"JU.T3,~N");c(c$,"setCenter2",function(a,b){null!=this.cubeIterator&&(this.cubeIterator.initialize(a,b,this.hemisphereOnly),this.distanceSquared=b*b)},"JU.T3,~N");j(c$,"hasNext",function(){return this.hasNext2()});c(c$,"hasNext2",function(){if(0<=this.atomIndex)for(;this.cubeIterator.hasMoreElements();){var a=
this.cubeIterator.nextElement();if((this.iNext=a.i)!=this.atomIndex&&(!this.checkGreater||this.iNext>this.atomIndex)&&(null==this.bsSelected||this.bsSelected.get(this.iNext)))return!0}else if(this.cubeIterator.hasMoreElements())return a=this.cubeIterator.nextElement(),this.iNext=a.i,!0;this.iNext=-1;return!1});j(c$,"next",function(){return this.iNext-this.zeroBase});j(c$,"foundDistance2",function(){return null==this.cubeIterator?-1:this.cubeIterator.foundDistance2()});j(c$,"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");j(c$,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)});j(c$,"getPosition",
function(){return null})});u("JM");x(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){c$=r(function(){this.center=this.bsModels=null;this.distance=0;n(this,arguments)},JM,"AtomIteratorWithinModelSet",JM.AtomIteratorWithinModel);t(c$,function(a){H(this,JM.AtomIteratorWithinModelSet,[]);this.bsModels=a},"JU.BS");j(c$,"setCenter",function(a,b){this.center=a;this.distance=b;this.set(0)},"JU.T3,~N");c(c$,"set",function(a){if(0>(this.modelIndex=this.bsModels.nextSetBit(a))||
null==(this.cubeIterator=this.bspf.getCubeIterator(this.modelIndex)))return!1;this.setCenter2(this.center,this.distance);return!0},"~N");j(c$,"hasNext",function(){return this.hasNext2()?!0:!this.set(this.modelIndex+1)?!1:this.hasNext()})});u("JM");x(["JU.Edge","JV.JC"],"JM.Bond",["JU.C"],function(){c$=r(function(){this.atom2=this.atom1=null;this.shapeVisibilityFlags=this.colix=this.mad=0;n(this,arguments)},JM,"Bond",JU.Edge);t(c$,function(a,b,d,c,g){this.atom1=a;this.atom2=b;this.colix=g;this.setOrder(d);
this.setMad(c)},"JM.Atom,JM.Atom,~N,~N,~N");c(c$,"setMad",function(a){this.mad=a;this.setShapeVisibility(0!=a)},"~N");c(c$,"setShapeVisibility",function(a){0!=(this.shapeVisibilityFlags&JM.Bond.myVisibilityFlag)!=a&&(this.atom1.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.atom2.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.shapeVisibilityFlags=a?this.shapeVisibilityFlags|JM.Bond.myVisibilityFlag:this.shapeVisibilityFlags&~JM.Bond.myVisibilityFlag)},"~B");c(c$,"getIdentity",function(){return this.index+
1+" "+JU.Edge.getBondOrderNumberFromOrder(this.order)+" "+this.atom1.getInfo()+" -- "+this.atom2.getInfo()+" "+this.atom1.distance(this.atom2)});j(c$,"isCovalent",function(){return 0!=(this.order&1023)});j(c$,"isHydrogen",function(){return JU.Edge.isOrderH(this.order)});c(c$,"isStereo",function(){return 0!=(this.order&1024)});c(c$,"isPartial",function(){return 0!=(this.order&224)});c(c$,"isAromatic",function(){return 0!=(this.order&512)});c(c$,"getEnergy",function(){return 0});c(c$,"getValence",function(){return!this.isCovalent()?
0:this.isPartial()||this.is(515)?1:this.order&7});c(c$,"deleteAtomReferences",function(){null!=this.atom1&&this.atom1.deleteBond(this);null!=this.atom2&&this.atom2.deleteBond(this);this.atom1=this.atom2=null});c(c$,"setTranslucent",function(a,b){this.colix=JU.C.getColixTranslucent3(this.colix,a,b)},"~B,~N");c(c$,"setOrder",function(a){16==this.atom1.getElementNumber()&&16==this.atom2.getElementNumber()&&(a|=256);512==a&&(a=515);this.order=a|this.order&131072},"~N");j(c$,"getAtomIndex1",function(){return this.atom1.i});
j(c$,"getAtomIndex2",function(){return this.atom2.i});j(c$,"getCovalentOrder",function(){return JU.Edge.getCovalentBondOrder(this.order)});c(c$,"getOtherAtom",function(a){return this.atom1===a?this.atom2:this.atom2===a?this.atom1:null},"JM.Atom");c(c$,"is",function(a){return(this.order&-131073)==a},"~N");j(c$,"getOtherNode",function(a){return this.atom1===a?this.atom2:this.atom2===a||null==a?this.atom1:null},"JU.SimpleNode");c(c$,"setAtropisomerOptions",function(a,b){var d=b.get(this.atom1.i),c=d?
b:a,d=d?a:b,g,e=2147483647,h=this.atom1.bonds;for(g=0;g<h.length;g++){var k=h[g].getOtherAtom(this.atom1);if(c.get(k.i)&&k!==this.atom2)break}if(g<h.length){h=this.atom2.bonds;for(e=0;e<h.length&&!(k=h[e].getOtherAtom(this.atom2),d.get(k.i)&&k!==this.atom1);e++);}this.order=2<g||e>=h.length||2<e?1:JU.Edge.getAtropismOrder(g+1,e+1)},"JU.BS,JU.BS");j(c$,"getCIPChirality",function(){return""},"~B");j(c$,"setCIPChirality",function(){},"~N");j(c$,"toString",function(){return this.atom1+" - "+this.atom2});
c$.myVisibilityFlag=c$.prototype.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(1)});u("JM");x(["JM.AtomCollection"],"JM.BondCollection","JU.AU $.BS JM.Bond $.BondIteratorSelected $.BondSet $.HBond JU.BSUtil $.C $.Edge $.Logger".split(" "),function(){c$=r(function(){this.bo=null;this.bondCount=0;this.molecules=this.freeBonds=this.numCached=null;this.defaultCovalentMad=this.moleculeCount=0;this.bsAromatic=this.bsAromaticDouble=this.bsAromaticSingle=null;this.haveHiddenBonds=!1;n(this,arguments)},JM,
"BondCollection",JM.AtomCollection);c(c$,"setupBC",function(){this.bsAromatic=new JU.BS;this.numCached=A(5,0);this.freeBonds=Array(5);for(var a=5;0<--a;)this.freeBonds[a]=Array(200);this.setupAC()});c(c$,"releaseModelSetBC",function(){this.freeBonds=this.bo=null;this.releaseModelSetAC()});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$,"getBondColix1",function(a){return JU.C.getColixInherited(this.bo[a].colix,this.bo[a].atom1.colixAtom)},"~N");c(c$,"getBondColix2",function(a){return JU.C.getColixInherited(this.bo[a].colix,this.bo[a].atom2.colixAtom)},"~N");c(c$,"getBondCountInModel",function(a){for(var b=0,d=this.bondCount;0<=--d;)this.bo[d].atom1.mi==a&&b++;return b},"~N");c(c$,"getBondsForSelectedAtoms",function(a,b){for(var d=new JU.BS,c=0;c<this.bondCount;++c){var g=this.bo[c],e=a.get(g.atom1.i),
g=a.get(g.atom2.i);(b?e||g:e&&g)&&d.set(c)}return d},"JU.BS,~B");c(c$,"bondAtoms",function(a,b,d,c,g,e,h,k){d=this.getOrAddBond(a,b,d,c,g,e,!0);k&&(d.order|=131072,h&&(a.group=b.group,a.group.addAtoms(a.i)));return d},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B,~B");c(c$,"getOrAddBond",function(a,b,d,c,g,e,h){if(131071==d||65535==d)d=1;a.isBonded(b)?(a=a.getBond(b).index,h&&(this.bo[a].setOrder(d),this.bo[a].setMad(c),q(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!=g&&g.set(a);return this.bo[a]},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B");c(c$,"setBond",function(a,b){return this.bo[b.index=a]=b},"~N,JM.Bond");c(c$,"bondMutually",function(a,b,d,c,g){d=JU.Edge.isOrderH(d)?new JM.HBond(a,b,d,c,0,g):new JM.Bond(a,b,d,c,0);this.addBondToAtom(a,d);this.addBondToAtom(b,d);return d},"JM.Atom,JM.Atom,~N,~N,~N");c(c$,"addBondToAtom",function(a,b){null==
a.bonds?(a.bonds=Array(1),a.bonds[0]=b):a.bonds=this.addToBonds(b,a.bonds)},"JM.Atom,JM.Bond");c(c$,"addToBonds",function(a,b){var d;if(null==b)d=0<this.numCached[1]?this.freeBonds[1][--this.numCached[1]]:Array(1),d[0]=a;else{var c=b.length;d=c+1;d=5>d&&0<this.numCached[d]?this.freeBonds[d][--this.numCached[d]]:Array(d);d[c]=a;for(var g=c;0<=--g;)d[g]=b[g];5>c&&200>this.numCached[c]&&(this.freeBonds[c][this.numCached[c]++]=b)}return d},"JM.Bond,~A");c(c$,"addHBond",function(a,b,d,c){this.bondCount==
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--a;){var b=this.bo[a];b.isAromatic()&&b.setOrder(515)}});c(c$,"assignAromaticBondsBs",function(a,b){a||(this.bsAromatic=new JU.BS);this.bsAromaticSingle=new JU.BS;this.bsAromaticDouble=new JU.BS;for(var d=null==b,c=d?this.bondCount-1:b.nextSetBit(0),g=c;0<=g;g=d?g-1:b.nextSetBit(g+1)){var e=this.bo[g];this.bsAromatic.get(g)&&e.setOrder(515);switch(e.order&-131073){case 515:if(!this.assignAromaticMustBeSingle(e.atom1)&&!this.assignAromaticMustBeSingle(e.atom2)){this.bsAromatic.set(g);break}e.order=
513;case 513:this.bsAromaticSingle.set(g);break;case 514:this.bsAromaticDouble.set(g)}}for(var c=(d=null==b)?this.bondCount-1:b.nextSetBit(0),h=new JU.BS,g=c;0<=g;g=d?g-1:b.nextSetBit(g+1))e=this.bo[g],e.is(515)&&(!this.bsAromaticDouble.get(g)&&!this.bsAromaticSingle.get(g))&&(h.set(g),8==e.atom1.getElementNumber()||8==e.atom2.getElementNumber()?this.assignAromaticDouble(e)||this.assignAromaticSingle(e):h.set(g));for(g=h.nextSetBit(0);0<=g;g=h.nextSetBit(g+1))this.assignAromaticDouble(e=this.bo[g])||
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null==a,c=d?this.bondCount-1:a.nextSetBit(0);0<=c;c=d?c-1:a.nextSetBit(c+1))if(b=this.bo[c],b.is(513)){var g,e=b.atom2,h,k=e.getElementNumber();7==k||8==k?(h=k,g=e,e=b.atom1,k=e.getElementNumber()):(g=b.atom1,h=g.getElementNumber());if(!(7!=h&&8!=h)){var j=g.getValence();if(!(0>j)){var s=g.getCovalentBondCount();g=g.getFormalCharge();switch(h){case 7:3==j&&(3==s&&1>g&&6==k&&3==e.getValence())&&b.setOrder(514);break;case 8:1==j&&(0==g&&(14==k||16==k))&&b.setOrder(514)}}}}},"JU.BS");c(c$,"getAtomBitsMDb",
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JU.Edge.getBondOrderNumberFromOrder(c.getCovalentOrder()).charCodeAt(0)-48+("p"==b?1:-1);3<d?d=1:0>d&&(d=3);break;default:return null}var g=new JU.BS;try{if(0==d){var e=new JU.BS;e.set(c.index);g.set(c.atom1.i);g.set(c.atom2.i);this.dBm(e,!1);return g}c.setOrder(d|131072);1!=c.atom1.getElementNumber()&&1!=c.atom2.getElementNumber()&&(this.removeUnnecessaryBonds(c.atom1,!1),this.removeUnnecessaryBonds(c.atom2,!1));g.set(c.atom1.i);g.set(c.atom2.i)}catch(h){if(E(h,Exception))JU.Logger.error("Exception in seBondOrder: "+
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j(c$,"nextIndex",function(){return this.iBond});j(c$,"next",function(){return this.bonds[this.iBond++]})});u("JM");x(["JU.BS"],"JM.BondSet",["JU.BSUtil"],function(){c$=r(function(){this.associatedAtoms=null;n(this,arguments)},JM,"BondSet",JU.BS);t(c$,function(){H(this,JM.BondSet,[])});c$.newBS=c(c$,"newBS",function(a,b){var d=new JM.BondSet;JU.BSUtil.copy2(a,d);d.associatedAtoms=b;return d},"JU.BS,~A")});u("JM");x(["JM.Structure"],"JM.Chain",null,function(){c$=r(function(){this.model=null;this.chainNo=
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d)/10:100*d;if(a.equals("au"))return b?Math.round(1E3*(d/0.5291772))/1E3:d/0.5291772;if(a.endsWith("khz"))return b?Math.round(d/10)/100:d/1E3}return b?Math.round(100*d)/100:d},"~S,~B");c$.nmrType=c(c$,"nmrType",function(a){return 0>a.indexOf("hz")?0:a.startsWith("dc_")||a.equals("khz")?1:2},"~S");c(c$,"formatAngle",function(a){var b=this.getLabelString();0<=b.indexOf("%V")&&(a=Math.round(10*a)/10);return this.formatString(a,"\u00b0",b)},"~N");c(c$,"getLabelString",function(){var a=this.countPlusIndices[0]+
":",b=null;if(null!=this.strFormat){if(0==this.strFormat.length)return null;b=2<this.strFormat.length&&0==this.strFormat.indexOf(a)?this.strFormat:null}null==b&&(this.strFormat=null,b=this.vwr.getDefaultMeasurementLabel(this.countPlusIndices[0]));0==b.indexOf(a)&&(b=b.substring(2));null==this.strFormat&&(this.strFormat=a+b);return b});c(c$,"formatString",function(a,b,d){return JM.LabelToken.formatLabelMeasure(this.vwr,this,d,a,b)},"~N,~S,~S");c(c$,"sameAsPoints",function(a,b){if(this.count!=a[0])return!1;
for(var d=!0,c=1;c<=this.count&&d;c++)d=this.countPlusIndices[c]==a[c];if(d)for(c=0;c<this.count&&d;c++)null!=b[c]&&(d=0.01>this.pts[c].distance(b[c]));if(d)return!0;switch(this.count){default:return!0;case 2:return this.sameAsIJ(a,b,1,2)&&this.sameAsIJ(a,b,2,1);case 3:return this.sameAsIJ(a,b,1,3)&&this.sameAsIJ(a,b,2,2)&&this.sameAsIJ(a,b,3,1);case 4:return this.sameAsIJ(a,b,1,4)&&this.sameAsIJ(a,b,2,3)&&this.sameAsIJ(a,b,3,2)&&this.sameAsIJ(a,b,4,1)}},"~A,~A");c(c$,"sameAsIJ",function(a,b,d,c){d=
this.countPlusIndices[d];a=a[c];return 0<=d||0<=a?d==a:0.01>this.pts[-2-d].distance(b[-2-a])},"~A,~A,~N,~N");c(c$,"sameAs",function(a,b){return this.sameAsIJ(this.countPlusIndices,this.pts,a,b)},"~N,~N");c(c$,"getMeasurement",function(a){if(null==this.countPlusIndices||2>this.count)return NaN;for(var b=this.count;0<=--b;)if(-1==this.countPlusIndices[b+1])return NaN;var b=null==a?this.getAtom(1):a[0],d=null==a?this.getAtom(2):a[1],c;switch(this.count){case 2:return b.distance(d);case 3:return c=null==
a?this.getAtom(3):a[2],JU.Measure.computeAngleABC(b,d,c,!0);case 4:return c=null==a?this.getAtom(3):a[2],a=null==a?this.getAtom(4):a[3],JU.Measure.computeTorsion(b,d,c,a,!0);default:return NaN}},"~A");c(c$,"getLabel",function(a,b,d){var c=this.countPlusIndices[a];return 0>c?(d?"modelIndex "+this.getAtom(a).mi+" ":"")+JU.Escape.eP(this.getAtom(a)):b?"({"+c+"})":this.vwr.getAtomInfo(c)},"~N,~B,~B");c(c$,"setModelIndex",function(a){if(null!=this.pts)for(var b=0;b<this.count;b++)null!=this.pts[b]&&(this.pts[b].mi=
a)},"~N");c(c$,"isValid",function(){return!(this.sameAs(1,2)||2<this.count&&this.sameAs(1,3)||4==this.count&&this.sameAs(2,4))});c$.find=c(c$,"find",function(a,b){for(var d=b.countPlusIndices,c=b.pts,g=a.size();0<=--g;)if(a.get(g).sameAsPoints(d,c))return g;return-1},"JU.Lst,JM.Measurement");c(c$,"isConnected",function(a,b){for(var d=-1,c=1;c<=b;c++){var g=this.getAtomIndex(c);if(!(0>g)){if(0<=d&&!a[g].isBonded(a[d]))return!1;d=g}}return!0},"~A,~N");c(c$,"getInfoAsString",function(a){var b=this.fixValue(a,
!0);a=new JU.SB;a.append(2==this.count?null==this.type?"distance":this.type:3==this.count?"angle":"dihedral");a.append(" \t").appendF(b);a.append(" \t").append(JU.PT.esc(this.strMeasurement));for(b=1;b<=this.count;b++)a.append(" \t").append(this.getLabel(b,!1,!1));null!=this.thisID&&a.append(" \t").append(this.thisID);return a.toString()},"~S");c(c$,"isInRange",function(a,b){if(a.factorType===J.atomdata.RadiusData.EnumType.FACTOR){var d=this.getAtom(1),c=this.getAtom(2),d=(d.getVanderwaalsRadiusFloat(this.vwr,
a.vdwType)+c.getVanderwaalsRadiusFloat(this.vwr,a.vdwType))*a.value;return b<=d}return 3.4028235E38==a.values[0]||b>=a.values[0]&&b<=a.values[1]},"J.atomdata.RadiusData,~N");c(c$,"isIntramolecular",function(a,b){for(var d=-1,c=1;c<=b;c++){var g=this.getAtomIndex(c);if(!(0>g))if(g=a[g].getMoleculeNumber(!1),0>d)d=g;else if(g!=d)return!1}return!0},"~A,~N");c(c$,"isMin",function(a){var b=this.getAtom(1),d=this.getAtom(2),c=B(100*d.distanceSquared(b)),b=b.getAtomName(),d=d.getAtomName(),d=0>b.compareTo(d)?
b+d:d+b;a=a.get(d);return null!=a&&c==a.intValue()},"java.util.Map");F(c$,"NMR_NOT",0,"NMR_DC",1,"NMR_JC",2)});u("JM");x(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["java.lang.Float","JU.BS","$.Lst","JM.Measurement","JU.BSUtil"],function(){c$=r(function(){this.points=this.measurements=this.measurementStrings=this.client=null;this.mustNotBeConnected=this.mustBeConnected=!1;this.tickInfo=null;this.tokAction=12290;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;n(this,arguments)},JM,"MeasurementData",null,J.api.JmolMeasurementClient);t(c$,function(){});c(c$,"init",function(a,b,d){this.vwr=b;this.points=d;this.thisID=a;return this},"~S,JV.Viewer,JU.Lst");c(c$,"setModelSet",function(a){this.ms=a;return this},"JM.ModelSet");c(c$,"set",function(a,b,d,c,g,e,h,k,j,s,m,p,n){this.ms=this.vwr.ms;this.tokAction=a;2<=
this.points.size()&&(q(this.points.get(0),JU.BS)&&q(this.points.get(1),JU.BS))&&(this.justOneModel=JU.BSUtil.haveCommon(this.vwr.ms.getModelBS(this.points.get(0),!1),this.vwr.ms.getModelBS(this.points.get(1),!1)));this.htMin=b;this.radiusData=d;this.strFormat=c;this.units=g;this.tickInfo=e;this.mustBeConnected=h;this.mustNotBeConnected=k;this.intramolecular=j;this.isAll=s;this.mad=m;this.colix=p;this.text=n;return this},"~N,java.util.Map,J.atomdata.RadiusData,~S,~S,JM.TickInfo,~B,~B,Boolean,~B,~N,~N,JM.Text");
c(c$,"processNextMeasure",function(a){var b=a.getMeasurement(null);if(!(null!=this.htMin&&!a.isMin(this.htMin)||null!=this.radiusData&&!a.isInRange(this.radiusData,b)))if(null==this.measurementStrings&&null==this.measurements){var d=this.minArray[this.iFirstAtom];a.value=b;b=a.fixValue(this.units,!1);this.minArray[this.iFirstAtom]=-Infinity==1/d?b:Math.min(d,b)}else null!=this.measurementStrings?this.measurementStrings.addLast(a.getStringUsing(this.vwr,this.strFormat,this.units)):this.measurements.addLast(Float.$valueOf(a.getMeasurement(null)))},
"JM.Measurement");c(c$,"getMeasurements",function(a,b){if(b){this.minArray=I(this.points.get(0).cardinality(),0);for(var d=0;d<this.minArray.length;d++)this.minArray[d]=-0;this.define(null,this.ms);return this.minArray}if(a)return this.measurements=new JU.Lst,this.define(null,this.ms),this.measurements;this.measurementStrings=new JU.Lst;this.define(null,this.ms);return this.measurementStrings},"~B,~B");c(c$,"define",function(a,b){this.client=null==a?this:a;this.atoms=b.at;var d=this.points.size();
if(!(2>d)){var c=-1,g=Array(4),e=A(5,0),h=(new JM.Measurement).setPoints(b,e,g,null);h.setCount(d);for(var k=-1,j=0;j<d;j++){var s=this.points.get(j);if(q(s,JU.BS)){k=s.cardinality();if(0==k)return;1<k&&(c=0);k=j;0==j&&(this.iFirstAtom=0);e[j+1]=s.nextSetBit(0)}else g[j]=s,e[j+1]=-2-j}this.nextMeasure(0,k,h,c)}},"J.api.JmolMeasurementClient,JM.ModelSet");c(c$,"nextMeasure",function(a,b,d,c){if(a>b)d.isValid()&&((!this.mustBeConnected||d.isConnected(this.atoms,a))&&(!this.mustNotBeConnected||!d.isConnected(this.atoms,
a))&&(null==this.intramolecular||d.isIntramolecular(this.atoms,a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(d);else{var g=this.points.get(a),e=d.countPlusIndices,h=0==a?2147483647:e[a];if(0>h)this.nextMeasure(a+1,b,d,c);else{for(var k=!1,j=g.nextSetBit(0),s=0;0<=j;j=g.nextSetBit(j+1),s++)if(j!=h){var m=this.atoms[j].mi;if(0<=c&&this.justOneModel)if(0==a)c=m;else if(c!=m)continue;e[a+1]=j;0==a&&(this.iFirstAtom=s);k=!0;this.nextMeasure(a+1,b,d,c)}k||this.nextMeasure(a+1,
b,d,c)}}},"~N,~N,JM.Measurement,~N")});u("JM");x(["JM.Measurement"],"JM.MeasurementPending",null,function(){c$=r(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;n(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$,"getIndexOf",
function(a){for(var b=1;b<=this.numSet;b++)if(this.countPlusIndices[b]==a)return b;return 0},"~N");j(c$,"setCount",function(a){this.setCountM(a);this.numSet=a},"~N");c(c$,"addPoint",function(a,b,d){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==b){if(0<this.getIndexOf(a))return d&&(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(b))return d&&
(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=!0;this.count=this.numSet+1;this.pts[a]=b;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;d&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);return this.count},"~N,JU.Point3fi,~B")});u("JM");x(["JU.BS","$.SB"],"JM.Model",["java.util.Hashtable","JU.AU","JU.BSUtil"],function(){c$=r(function(){this.mat4=this.ms=null;this.fileIndex=
this.modelIndex=0;this.isModelKit=this.isPdbWithMultipleBonds=this.isBioModel=!1;this.translation=this.dataFrames=this.biosymmetry=this.properties=this.auxiliaryInfo=this.orientation=this.dssrCache=this.simpleCage=this.chains=null;this.dataSourceFrame=-1;this.loadState="";this.loadScript=null;this.isTrajectory=this.isJmolDataFrame=this.structureTainted=this.hasRasmolHBonds=!1;this.act=this.insertionCount=this.altLocCount=this.trajectoryBaseIndex=0;this.bondCount=-1;this.chainCount=0;this.groupCount=
-1;this.firstMoleculeIndex=this.firstAtomIndex=this.biosymmetryCount=this.moleculeCount=this.hydrogenCount=0;this.bsAtomsDeleted=this.bsAtoms=null;this.frameDelay=this.defaultRotationRadius=0;this.selectedTrajectory=-1;this.bsCheck=this.pdbID=this.jmolFrameType=this.jmolData=null;this.hasChirality=!1;n(this,arguments)},JM,"Model");O(c$,function(){this.chains=Array(8);this.loadScript=new JU.SB;this.bsAtoms=new JU.BS;this.bsAtomsDeleted=new JU.BS});t(c$,function(){});c(c$,"set",function(a,b,d,c,g,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=g;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$,"getTrueAtomCount",function(){return this.bsAtoms.cardinality()-this.bsAtomsDeleted.cardinality()});c(c$,"isContainedIn",function(a){null==this.bsCheck&&(this.bsCheck=new JU.BS);this.bsCheck.or(a);this.bsCheck.and(this.bsAtoms);this.bsCheck.andNot(this.bsAtomsDeleted);return this.bsCheck.cardinality()==this.getTrueAtomCount()},"JU.BS");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});c(c$,"getChainCount",function(a){if(1<this.chainCount&&!a)for(a=0;a<this.chainCount;a++)if(0==this.chains[a].chainID)return this.chainCount-1;return this.chainCount},"~B");c(c$,"calcSelectedGroupsCount",function(a){for(var b=this.chainCount;0<=--b;)this.chains[b].calcSelectedGroupsCount(a)},"JU.BS");c(c$,
"getGroupCount",function(){if(0>this.groupCount){this.groupCount=0;for(var a=this.chainCount;0<=--a;)this.groupCount+=this.chains[a].groupCount}return this.groupCount});c(c$,"getChainAt",function(a){return a<this.chainCount?this.chains[a]:null},"~N");c(c$,"getChain",function(a){for(var b=this.chainCount;0<=--b;){var d=this.chains[b];if(d.chainID==a)return d}return null},"~N");c(c$,"resetDSSR",function(a){this.dssrCache=null;a&&this.auxiliaryInfo.remove("dssr")},"~B");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$,"freeze",function(){this.freezeM();return!1});c(c$,"freezeM",function(){for(var a=0;a<this.chainCount;a++)if(0==this.chains[a].groupCount){for(var b=
a+1;b<this.chainCount;b++)this.chains[b-1]=this.chains[b];this.chainCount--}this.chains=JU.AU.arrayCopyObject(this.chains,this.chainCount);this.groupCount=-1;this.getGroupCount();for(a=0;a<this.chainCount;++a)this.chains[a].groups=JU.AU.arrayCopyObject(this.chains[a].groups,this.chains[a].groupCount)})});u("JM");x(["java.util.Hashtable","JU.BS"],"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 JS.T JU.BSUtil $.Elements $.JmolMolecule $.Logger JV.JC".split(" "),
function(){c$=r(function(){this.modelSet0=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.isMutate=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=this.modulationTUV=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.$mergeGroups=this.htGroup1=null;this.iChain=0;this.structuresDefinedInFile=this.vStereo=null;n(this,arguments)},
JM,"ModelLoader");O(c$,function(){this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});t(c$,function(a,b,d,c,g,e){this.vwr=a;this.ms=new JM.ModelSet(a,b);var h=a.getModelAdapter();this.modelSet0=g;(this.merging=null!=g&&0<g.ac)?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);null==e?(this.initializeInfo(b,null),this.createModelSet(null,null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||
(this.ms.canSkipLoad=!1),a=h.getAtomSetCollectionAuxiliaryInfo(c),a.put("loadScript",d),this.initializeInfo(h.getFileTypeName(c).toLowerCase().intern(),a),this.createModelSet(h,c,e),null!=this.jbr&&this.jbr.setLoader(null),this.jbr=null)},"JV.Viewer,~S,JU.SB,~O,JM.ModelSet,JU.BS");c(c$,"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");this.ms.haveBioModels=this.ms.getMSInfoB("isPDB");
this.isMutate=this.ms.getMSInfoB("isMutate");this.ms.haveBioModels&&(this.jbr=this.vwr.getJBR().setLoader(this));this.jmolData=0==this.adapterModelCount?this.ms.getInfoM("jmolData"):null;this.fileHeader=this.ms.getInfoM("fileHeader");var d=this.ms.getInfoM("trajectorySteps");if(this.isTrajectory=null!=d)this.ms.trajectory=this.newTrajectory(this.ms,d);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")),b.containsKey("legacyJavaFloat")&&this.vwr.setBooleanProperty("legacyJavaFloat",!0));this.htGroup1=this.ms.getInfoM("htGroup1");d=this.ms.getInfoM("modulationOn");null!=d&&(this.modulationOn=!0,this.modulationTUV=d===Boolean.TRUE?null:d);this.noAutoBond=
this.ms.getMSInfoB("noAutoBond");this.doMinimize=(this.is2D=this.ms.getMSInfoB("is2D"))&&this.ms.getMSInfoB("doMinimize");this.adapterTrajectoryCount=this.isTrajectory?this.ms.trajectory.steps.size():0;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.haveBioModels=(new Boolean(this.ms.haveBioModels|this.modelSet0.haveBioModels)).valueOf(),this.ms.bioModelset=this.modelSet0.bioModelset,null!=this.ms.bioModelset&&this.ms.bioModelset.set(this.vwr,this.ms),this.ms.someModelsHaveSymmetry=(new Boolean(this.ms.someModelsHaveSymmetry|this.modelSet0.getMSInfoB("someModelsHaveSymmetry"))).valueOf(),this.someModelsHaveUnitcells=(new Boolean(this.someModelsHaveUnitcells|this.modelSet0.getMSInfoB("someModelsHaveUnitcells"))).valueOf(),
this.ms.someModelsHaveFractionalCoordinates=(new Boolean(this.ms.someModelsHaveFractionalCoordinates|this.modelSet0.getMSInfoB("someModelsHaveFractionalCoordinates"))).valueOf(),this.ms.someModelsHaveAromaticBonds=(new Boolean(this.ms.someModelsHaveAromaticBonds|this.modelSet0.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$,"newTrajectory",function(a,b){return J.api.Interface.getInterface("JM.Trajectory",this.vwr,"load").set(this.vwr,a,b)},"JM.ModelSet,JU.Lst");c(c$,"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.isMutate&&(!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=A(32,0);this.firstAtomIndexes=
A(32,0);this.currentChainID=2147483647;this.currentChain=null;this.currentGroupInsertionCode="\uffff";this.currentGroup3="xxxxx";this.iModel=-1;this.model=null;this.merging&&this.mergeTrajAndVib(this.modelSet0,this.ms);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.')),d=this.ms.getInfoM("defaultOrientationQuaternion"),null!=d&&(JU.Logger.info("defaultOrientationQuaternion = "+d),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&&(d=a.getAtomSetAuxiliaryInfo(b,0),this.ms.setInfo(this.baseModelIndex,"initialAtomCount",d.get("initialAtomCount")),this.ms.setInfo(this.baseModelIndex,"initialBondCount",d.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 g=this.vwr.rd;d=this.ms.ac;for(var c=this.ms.at,e=this.baseAtomIndex;e<d;e++)c[e].setMadAtom(this.vwr,g);g=this.ms.am;for(e=g[this.baseModelIndex].firstAtomIndex;e<d;e++)g[c[e].mi].bsAtoms.set(e);this.freeze();this.finalizeShapes();this.vwr.setModelSet(this.ms);this.setAtomProperties();null!=a&&
a.finish(b);null!=this.modelSet0&&this.modelSet0.releaseModelSet();this.modelSet0=null},"J.api.JmolAdapter,~O,JU.BS");c(c$,"mergeTrajAndVib",function(a,b){this.baseModelCount=a.mc;this.baseTrajectoryCount=0;null==a.trajectory&&this.isTrajectory&&this.newTrajectory(a,new JU.Lst);if(!(null==a.trajectory||0==a.mc)){this.baseTrajectoryCount=a.mc;for(var d=a.trajectory.steps.size(),c=d;c<this.baseTrajectoryCount;c++)a.trajectory.steps.addLast(null);if(this.isTrajectory){if(null==a.vibrationSteps){a.vibrationSteps=
new JU.Lst;for(c=d;0<=--c;)a.vibrationSteps.addLast(null)}d=b.trajectory.steps.size();for(c=0;c<d;c++)a.trajectory.steps.addLast(b.trajectory.steps.get(c)),a.vibrationSteps.addLast(null==b.vibrationSteps?null:b.vibrationSteps.get(c))}else b.trajectory=this.newTrajectory(b,null);b.vibrationSteps=a.vibrationSteps;b.trajectory.steps=a.trajectory.steps;a.trajectory=null}},"JM.ModelSet,JM.ModelSet");c(c$,"setDefaultRendering",function(a){if(!this.isPyMOLsession){for(var b=new JU.SB,d=this.ms.mc,c=this.ms.am,
g=this.baseModelIndex;g<d;g++)c[g].isBioModel&&c[g].getDefaultLargePDBRendering(b,a);0!=b.length()&&(b.append("select *;"),a=this.ms.getInfoM("jmolscript"),null==a&&(a=""),b.append(a),this.ms.msInfo.put("jmolscript",b.toString()))}},"~N");c(c$,"setAtomProperties",function(){for(var a=this.ms.mc,b=this.baseModelIndex;b<a;b++){var d=this.ms.getInfo(b,"atomProperties");null!=this.jmolData&&this.addJmolDataProperties(this.ms.am[b],this.ms.getInfo(b,"jmolDataProperties"));var c=this.ms.getInfo(b,"groupPropertyList");
this.ms.am[b].isBioModel&&null!=this.ms.getInfo(b,"dssr")&&this.vwr.getAnnotationParser(!0).setGroup1(this.ms,b);if(null!=d)for(var g,d=d.entrySet().iterator();d.hasNext()&&((g=d.next())||1);){var e=g.getKey(),h=g.getValue(),k=this.ms.getModelAtomBitSetIncludingDeleted(b,!0);if(this.doAddHydrogens)var j=null!=c&&JU.PT.isOneOf(e,c),h=this.jbr.fixPropertyValue(k,h,j);e="property_"+e.toLowerCase();JU.Logger.info("creating "+e+" for model "+this.ms.getModelName(b));this.vwr.setData(e,v(-1,[e,h,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.modelSet0.ac,this.ms.bondCount=this.modelSet0.bondCount,this.$mergeGroups=
this.modelSet0.getGroups(),this.groupCount=this.baseGroupIndex=this.$mergeGroups.length,this.ms.mergeModelArrays(this.modelSet0),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.modelSet0.mc;a++)(this.ms.am[a]=this.modelSet0.am[a]).ms=this.ms},"~N");c(c$,"mergeGroups",function(){var a=this.modelSet0.getAuxiliaryInfo(null),b=a.get("group3Lists"),a=a.get("group3Counts");
if(null!=b){for(var d=0;d<this.baseModelCount;d++)this.group3Lists[d+1]=b[d+1],this.group3Counts[d+1]=a[d+1],this.structuresDefinedInFile.set(d);this.group3Lists[0]=b[0];this.group3Counts[0]=a[0]}!this.appendNew&&this.ms.haveBioModels&&this.structuresDefinedInFile.clear(this.baseModelIndex)});c(c$,"iterateOverAllNewModels",function(a,b){this.group3Lists=Array(this.ms.mc+1);this.group3Counts=JU.AU.newInt2(this.ms.mc+1);this.structuresDefinedInFile=new JU.BS;this.merging&&this.mergeGroups();for(var d=
this.isTrajectory?this.baseTrajectoryCount:-1,c=this.baseModelIndex,g=0;g<this.adapterModelCount;++g,++c){var e=a.getAtomSetNumber(b,g),h=a.getAtomSetName(b,g),k=a.getAtomSetAuxiliaryInfo(b,g);k.containsKey("modelID")&&k.put("modelID0",k.get("modelID"));var j=k.get("modelProperties");this.vwr.setStringProperty("_fileType",k.get("fileType"));null==h&&(h=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,h,e,j,k,this.jmolData)}d=this.ms.am[this.baseModelIndex];this.vwr.setSmilesString(this.ms.msInfo.get("smilesString"));g=this.ms.msInfo.remove("loadState");e=this.ms.msInfo.remove("loadScript");if(0>e.indexOf("Viewer.AddHydrogens")||!d.isModelKit){h=JU.PT.split(g,"\n");k=new JU.SB;for(g=0;g<h.length;g++)j=d.loadState.indexOf(h[g]),(0>j||j!=d.loadState.lastIndexOf(h[g]))&&k.append(h[g]).appendC("\n");d.loadState+=d.loadScript.toString()+k.toString();
d.loadScript=new JU.SB;0<=e.indexOf("load append ")&&e.append("; set appendNew true");d.loadScript.append("  ").appendSB(e).append(";\n")}if(this.isTrajectory){g=this.ms.mc-c+1;JU.Logger.info(g+" trajectory steps read");this.ms.setInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(g));d=this.adapterModelCount;for(g=c;g<this.ms.mc;g++,d++)this.ms.am[g]=this.ms.am[this.baseModelCount],this.ms.modelNumbers[g]=a.getAtomSetNumber(b,d),this.ms.modelNames[g]=a.getAtomSetName(b,d),this.structuresDefinedInFile.set(g)}this.finalizeModels(this.baseModelCount)},
"J.api.JmolAdapter,~O");c(c$,"setModelNameNumberProperties",function(a,b,d,c,g,e,h){if(this.appendNew){var k=null!=e&&Boolean.TRUE===e.get("isPDB");this.ms.am[a]=k?this.jbr.getBioModel(a,b,h,g,e):(new JM.Model).set(this.ms,a,b,h,g,e);this.ms.modelNumbers[a]=c;this.ms.modelNames[a]=d;k&&this.jbr.setGroupLists(a)}else 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].altLocCount=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].insertionCount=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},"~N,~N,~S,~N,java.util.Properties,java.util.Map,~S");c(c$,"finalizeModels",
function(a){var b=this.ms.mc;if(b!=a){var d,c=0,g=-1,e=this.ms.modelNumbers,h=this.ms.modelNames;if(this.isTrajectory)for(var k=a;++k<this.ms.mc;)e[k]=e[k-1]+1;if(0<a){if(1E6>e[0])for(k=0;k<a;k++)0==h[k].length&&(h[k]=""+e[k]),e[k]+=1E6,this.ms.modelNumbersForAtomLabel[k]="1."+(k+1);var j=e[a-1],j=j-j%1E6;1E6>e[a]&&(j+=1E6);for(k=a;k<b;k++)e[k]+=j}for(var s=this.ms.am,k=a;k<b;++k)if(this.ms.setInfo(k,"fileType",this.ms.modelSetTypeName),null!=this.fileHeader&&this.ms.setInfo(k,"fileHeader",this.fileHeader),
j=y(e[k]/1E6),j!=g&&(c=0,g=j),c++,0==j?(d=""+this.ms.getModelNumber(k),j=1):d=j+"."+c,this.ms.modelNumbersForAtomLabel[k]=d,s[k].fileIndex=j-1,this.ms.modelFileNumbers[k]=1E6*j+c,null==h[k]||0==h[k].length)h[k]=d;if(this.merging)for(k=0;k<a;k++)s[k].ms=this.ms;for(k=0;k<b;k++)this.ms.setInfo(k,"modelName",h[k]),this.ms.setInfo(k,"modelNumber",Integer.$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,g=!1,e=a.getAtomIterator(b);this.ms.setCapacity(a.getAtomCount(b));var h=0,k=this.ms.am;0<this.ms.mc&&(this.nullGroup=(new JM.Group).setGroup(new JM.Chain(this.ms.am[this.baseModelIndex],32,0),"",0,-1,-1));for(;e.hasNext();){h++;var j=e.getAtomSetIndex()+this.baseModelIndex;j!=d&&(this.iChain=0,this.iModel=j,
this.model=k[j],this.currentChainID=2147483647,this.isNewChain=!0,k[j].bsAtoms.clearAll(),c=k[j].isBioModel,d=j,g=c&&this.doAddHydrogens,null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var j=e.getGroup3(),s=e.getChainID();this.checkNewGroup(a,s,j,e.getSequenceNumber(),e.getInsertionCode(),g,!1);s=e.getElementNumber();g&&1==JU.Elements.getElementNumber(s)&&this.jbr.setHaveHsAlready(!0);var m=e.getAtomName(),p=g?this.getPdbCharge(j,m):e.getFormalCharge();this.addAtom(c,e.getSymmetry(),e.getAtomSite(),
e.getUniqueID(),s,m,p,e.getPartialCharge(),e.getTensors(),e.getOccupancy(),e.getBfactor(),e.getXYZ(),e.getIsHetero(),e.getSerial(),e.getSeqID(),j,e.getVib(),e.getAltLoc(),e.getRadius())}0<this.groupCount&&g&&this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain?1:0);d=-1;c=null;g=this.ms.at;for(e=0;e<this.ms.ac;e++)g[e].mi!=d&&(d=g[e].mi,k[d].firstAtomIndex=e,j=this.ms.getDefaultVdwType(d),j!==c&&(JU.Logger.info("Default Van der Waals type for model set to "+j.getVdwLabel()),c=j));
JU.Logger.info(h+" atoms created")},"J.api.JmolAdapter,~O");c(c$,"addJmolDataProperties",function(a,b){if(null!=b)for(var d=a.bsAtoms,c=d.cardinality(),g,e=b.entrySet().iterator();e.hasNext()&&((g=e.next())||1);){var h=g.getKey(),k=g.getValue();if(k.length!=c)break;var j=h.startsWith("property_")?1715472409:JS.T.getTokFromName(h);switch(j){default:if(JS.T.tokAttr(j,2048)){this.vwr.setAtomProperty(d,j,0,0,null,k,null);break}case 1111492629:case 1111492630:case 1111492631:h="property_"+h;case 1715472409:this.vwr.setData(h,
v(-1,[h,k,d,Integer.$valueOf(1)]),0,0,0,0,0)}}},"JM.Model,java.util.Map");c(c$,"getPdbCharge",function(a,b){return a.equals("ARG")&&b.equals("NH1")||a.equals("LYS")&&b.equals("NZ")||a.equals("HIS")&&b.equals("ND1")?1:0},"~S,~S");c(c$,"addAtom",function(a,b,d,c,g,e,h,k,j,s,m,p,q,w,n,r,t,u,v){var x=0,y=null;if(null!=e){var A;if(0<=(A=e.indexOf("\x00")))y=e.substring(A+1),e=e.substring(0,A);a&&(0<=e.indexOf("*")&&(e=e.$replace("*","'")),x=this.vwr.getJBR().lookupSpecialAtomID(e),2==x&&"CA".equalsIgnoreCase(r)&&
(x=0))}a=this.ms.addAtom(this.iModel,this.nullGroup,g,e,y,w,n,d,p,v,t,h,k,s,m,j,q,x,b);a.altloc=u;this.htAtomMap.put(c,a)},"~B,JU.BS,~N,~O,~N,~S,~N,~N,JU.Lst,~N,~N,JU.P3,~B,~N,~N,~S,JU.V3,~S,~N");c(c$,"checkNewGroup",function(a,b,d,c,g,e,h){var k=null==d?null:d.intern();b!=this.currentChainID&&(this.currentChainID=b,this.currentChain=this.getOrAllocateChain(this.model,b),this.currentGroupInsertionCode="\uffff",this.currentGroupSequenceNumber=-1,this.currentGroup3="xxxx",this.isNewChain=!0);if(c!=
this.currentGroupSequenceNumber||g!=this.currentGroupInsertionCode||k!==this.currentGroup3){0<this.groupCount&&e&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!h?1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=c;this.currentGroupInsertionCode=g;for(this.currentGroup3=k;this.groupCount>=this.group3Of.length;)this.chainOf=JU.AU.doubleLength(this.chainOf),this.group3Of=JU.AU.doubleLengthS(this.group3Of),this.seqcodes=JU.AU.doubleLengthI(this.seqcodes),this.firstAtomIndexes=
JU.AU.doubleLengthI(this.firstAtomIndexes);this.firstAtomIndexes[this.groupCount]=this.ms.ac;this.chainOf[this.groupCount]=this.currentChain;this.group3Of[this.groupCount]=d;this.seqcodes[this.groupCount]=JM.Group.getSeqcodeFor(c,g);++this.groupCount}},"J.api.JmolAdapter,~N,~S,~N,~S,~B,~B");c(c$,"getOrAllocateChain",function(a,b){var d=a.getChain(b);if(null!=d)return d;a.chainCount==a.chains.length&&(a.chains=JU.AU.doubleLength(a.chains));return a.chains[a.chainCount++]=new JM.Chain(a,b,0==b||32==
b?0:++this.iChain)},"JM.Model,~N");c(c$,"iterateOverAllNewBonds",function(a,b){var d=a.getBondIterator(b);if(null!=d){var c=this.vwr.getMadBond();this.ms.defaultCovalentMad=null==this.jmolData?c:0;for(var g=!1;d.hasNext();){var e=d.getEncodedOrder(),h=e,k=this.bondAtoms(d.getAtomUniqueID1(),d.getAtomUniqueID2(),h);null!=k&&(1<h&&(1025!=h&&1041!=h)&&(g=!0),h=d.getRadius(),0<h&&k.setMad(aa(2E3*h)),h=d.getColix(),0<=h&&(k.colix=h),k.order|=e&98304)}g&&(this.ms.someModelsHaveSymmetry&&!this.vwr.getBoolean(603979794))&&
JU.Logger.info('ModelSet: use "set appletSymmetryToBonds TRUE " to apply the file-based multiple bonds to symmetry-generated atoms.');this.ms.defaultCovalentMad=c}},"J.api.JmolAdapter,~O");c(c$,"bondAtoms",function(a,b,d){var c=this.htAtomMap.get(a);if(null==c)return JU.Logger.error("bondAtoms cannot find atomUid1?:"+a),null;a=this.htAtomMap.get(b);if(null==a)return JU.Logger.error("bondAtoms cannot find atomUid2?:"+b),null;if(c.isBonded(a))return null;1025==d||1041==d?(b=this.ms.bondMutually(c,a,
this.is2D?d:1,this.ms.getDefaultMadFromOrder(1),0),null==this.vStereo&&(this.vStereo=new JU.Lst),this.vStereo.addLast(b)):(b=this.ms.bondMutually(c,a,d,this.ms.getDefaultMadFromOrder(d),0),b.isAromatic()&&(this.ms.someModelsHaveAromaticBonds=!0));this.ms.bondCount==this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount+250));this.ms.setBond(this.ms.bondCount++,b);return b},"~O,~O,~N");c(c$,"initializeUnitCellAndSymmetry",function(){this.someModelsAreModulated&&null==this.ms.bsModulated&&
(this.ms.bsModulated=new JU.BS);if(this.someModelsHaveUnitcells){this.ms.unitCells=Array(this.ms.mc);this.ms.haveUnitCells=!0;for(var a=null!=this.modelSet0&&null!=this.modelSet0.unitCells,b=0,d=0;b<this.ms.mc;b++)if(a&&b<this.baseModelCount)this.ms.unitCells[b]=this.modelSet0.unitCells[b];else{this.ms.unitCells[b]=J.api.Interface.getSymmetry(this.vwr,"file");var c=null;if(this.isTrajectory){var g=this.ms.getInfoM("unitCells");null!=g&&(c=g.get(d++))}this.ms.unitCells[b].setSymmetryInfo(b,this.ms.getModelAuxiliaryInfo(b),
c)}}if(this.appendNew&&this.ms.someModelsHaveSymmetry){this.ms.getAtoms(1088421903,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){for(var a=this.ms.at,d=-1,c=null,g=!1,e=!this.vwr.g.legacyJavaFloat,b=this.baseAtomIndex;b<this.ms.ac;b++)a[b].mi!=d&&(d=
a[b].mi,c=this.ms.getUnitCell(d),g=null!=c&&c.getCoordinatesAreFractional()),g&&(c=a[b].getUnitCell(),c.toCartesian(c.toSupercell(a[b]),!1),e&&JU.PT.fixPtFloats(a[b],1E4));for(b=this.baseModelIndex;b<this.ms.mc;b++)this.ms.isTrajectory(b)&&this.ms.trajectory.setUnitCell(b)}});c(c$,"initializeBonding",function(){var a=null==this.ms.getInfoM("someModelsHaveCONECT")?null:new JU.BS;null!=a&&this.ms.setPdbConectBonding(this.baseAtomIndex,this.baseModelIndex,a);var b=0,d=this.vwr.getBoolean(603979794),
c=this.vwr.getBoolean(603979798),g=this.vwr.getBoolean(603979846),e=null,h=!1,k=this.ms.mc,j=this.ms.am;if(!this.noAutoBond)for(var s=this.baseModelIndex;s<k;s++){var b=j[s].bsAtoms.cardinality(),m=this.ms.getInfoI(s,"initialBondCount"),p=j[s].isBioModel;0>m&&(m=this.ms.bondCount);if(g||c&&(0==m||p&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||m<y(b/2))||this.ms.getInfoB(s,"hasSymmetry")&&!d&&!this.ms.getInfoB(s,"hasBonds")))if(h=!0,this.merging||1<k)null==e&&(e=JU.BS.newN(this.ms.ac)),
(s==this.baseModelIndex||!this.isTrajectory)&&e.or(j[s].bsAtoms)}this.modulationOn&&this.ms.setModulation(null,!0,this.modulationTUV,!1);h?(this.ms.autoBondBs4(e,e,a,null,this.ms.defaultCovalentMad,this.vwr.getBoolean(603979873)),JU.Logger.info("ModelSet: autobonding; use  autobond=false  to not generate bonds automatically")):JU.Logger.info("ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation")});c(c$,"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]).chain.model.ms=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])-1);if(null!=this.group3Lists){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]=A(0,0))}});c(c$,"distinguishAndPropagateGroup",function(a,b,d,c,g,e){if(e<g)throw new NullPointerException;var h=null==d||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(b,d,c,g,e,this.specialAtomIndexes,this.ms.at);null==h?(h=(new JM.Group).setGroup(b,d,c,g,e),null!=this.jbr&&(h.groupID=this.jbr.getGroupID(d)),c="o>"):c=h.isProtein()?"p>":h.isNucleic()?"n>":h.isCarbohydrate()?"c>":"o>";null!=d&&(this.countGroup(this.ms.at[g].mi,c,d),h.isNucleic()&&
(d=null==this.htGroup1?null:this.htGroup1.get(d),null!=d&&(h.group1=d.charAt(0))));this.addGroup(b,h);this.groups[a]=h;h.groupIndex=a;for(a=e+1;--a>=g;)this.ms.at[a].group=h},"~N,JM.Chain,~S,~N,~N,~N");c(c$,"addGroup",function(a,b){a.groupCount==a.groups.length&&(a.groups=JU.AU.doubleLength(a.groups));a.groups[a.groupCount++]=b},"JM.Chain,JM.Group");c(c$,"countGroup",function(a,b,d){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var g=(d+"   ").substring(0,3),e=this.group3Lists[c].indexOf(g);
0>e&&(this.group3Lists[c]+=",["+g+"]",e=this.group3Lists[c].indexOf(g),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][y(e/6)]++;e=this.group3Lists[c].indexOf(",["+g);0<=e&&(this.group3Lists[c]=this.group3Lists[c].substring(0,e)+b+this.group3Lists[c].substring(e+2));0<=a&&this.countGroup(-1,b,d)}},"~N,~S,~S");c(c$,"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.modelSet0);this.findElementsPresent();this.ms.resetMolecules();this.currentChain=this.model=null;!this.ms.haveBioModels||this.isPyMOLsession||this.isMutate?this.ms.freezeModels():(a=this.vwr.getBoolean(603979826),a=this.ms.calculateStructuresAllExcept(this.structuresDefinedInFile,
a,!1,!0,!0,a,1405E3<=JV.JC.versionInt&&null==this.ms.getInfoM("DSSP1")?2:1),0<a.length&&JU.Logger.info(a))});c(c$,"findElementsPresent",function(){this.ms.elementsPresent=Array(this.ms.mc);for(var a=0;a<this.ms.mc;a++)this.ms.elementsPresent[a]=JU.BS.newN(64);for(a=this.ms.ac;0<=--a;){var b=this.ms.at[a].getAtomicAndIsotopeNumber();b>=JU.Elements.elementNumberMax&&(b=JU.Elements.elementNumberMax+JU.Elements.altElementIndexFromNumber(b));this.ms.elementsPresent[this.ms.at[a].mi].set(b)}});c(c$,"applyStereochemistry",
function(){this.set2dZ(this.baseAtomIndex,this.ms.ac);if(null!=this.vStereo){var a=new JU.BS;a.setBits(this.baseAtomIndex,this.ms.ac);for(var b=this.vStereo.size();0<=--b;){var d=this.vStereo.get(b),c=1025==d.order?3:-3;d.order=1;d.atom2.z!=d.atom1.z&&0>c==d.atom2.z<d.atom1.z&&(c/=3);var g=JU.JmolMolecule.getBranchBitSet(this.ms.at,d.atom2.i,a,null,d.atom1.i,!1,!0);g.set(d.atom2.i);for(var e=g.nextSetBit(0);0<=e;e=g.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$,"set2dZ",function(a,b){var d=JU.BS.newN(b),c=new JU.BS,g=new JU.V3,e=JU.V3.new3(0,1,0),h=new JU.V3,k=new JU.BS;k.setBits(a,b);for(var j=a;j<b;j++)!d.get(j)&&!c.get(j)&&(c=this.getBranch2dZ(j,-1,k,c,g,e,h),d.or(c))},"~N,~N");c(c$,"getBranch2dZ",function(a,b,d,c,g,e,h){c=JU.BS.newN(this.ms.ac);if(0>a)return c;var k=new JU.BS;k.or(d);0<=b&&k.clear(b);JM.ModelLoader.setBranch2dZ(this.ms.at[a],c,k,g,e,h);return c},"~N,~N,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");
c$.setBranch2dZ=c(c$,"setBranch2dZ",function(a,b,d,c,g,e){var h=a.i;if(d.get(h)&&(d.clear(h),b.set(h),null!=a.bonds))for(h=a.bonds.length;0<=--h;){var k=a.bonds[h];k.isHydrogen()||(k=k.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,k,c,g,e),JM.ModelLoader.setBranch2dZ(k,b,d,c,g,e))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setAtom2dZ=c(c$,"setAtom2dZ",function(a,b,d,c,g){d.sub2(b,a);d.z=0;d.normalize();g.cross(c,d);d=Math.acos(d.dot(c));b.z=a.z+0.8*Math.sin(4*d)},"JM.Atom,JM.Atom,JU.V3,JU.V3,JU.V3");
c(c$,"finalizeShapes",function(){this.ms.sm=this.vwr.shm;this.ms.sm.setModelSet(this.ms);this.ms.setBsHidden(this.vwr.slm.getHiddenSet());this.merging||this.ms.sm.resetShapes();this.ms.sm.loadDefaultShapes(this.ms);this.ms.someModelsHaveAromaticBonds&&this.vwr.getBoolean(603979944)&&this.ms.assignAromaticBondsBs(!1,null);this.merging&&1==this.baseModelCount&&this.ms.sm.setShapePropertyBs(6,"clearModelIndex",null,null)});c(c$,"undeleteAtom",function(a){this.ms.at[a].valence=0},"~N");c$.createAtomDataSet=
c(c$,"createAtomDataSet",function(a,b,d,c,g){if(null==c)return null;var e=a.getModelAdapter(),h=new JU.P3,k=b.at,j=a.getFloat(570425363);if(null!=b.unitCells)for(var s=g.nextSetBit(0);0<=s;s=g.nextSetBit(s+1))if(null!=k[s].atomSymmetry){j=-j;break}for(var s=-1,m=0,p=JU.BSUtil.cardinalityOf(g)==a.ms.ac,q=e.getAtomIterator(c);q.hasNext();){var w=q.getXYZ();if(!Float.isNaN(w.x+w.y+w.z))if(1145047050==d){s=g.nextSetBit(s+1);if(0>s)break;m++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+s+": "+k[s]+
" --\x3e ("+w.x+","+w.y+","+w.z);b.setAtomCoord(s,w.x,w.y,w.z)}else{h.setT(w);w=JU.BS.newN(b.ac);b.getAtomsWithin(j,h,w,-1);w.and(g);if(p)if(m=JU.BSUtil.cardinalityOf(w),0==m){JU.Logger.warn("createAtomDataSet: no atom found at position "+h);continue}else 1<m&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+m+" atoms found at position "+h);switch(d){case 1145047055:var n=q.getVib();if(null==n)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+h+" vib: "+n);b.setAtomCoords(w,1145047055,
n);break;case 1128269825:b.setAtomProperty(w,d,0,q.getOccupancy(),null,null,null);break;case 1111492619:b.setAtomProperty(w,d,0,q.getPartialCharge(),null,null,null);break;case 1111492620:b.setAtomProperty(w,d,0,q.getBfactor(),null,null,null)}}}switch(d){case 1145047055:b=e.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+b);a.setStringProperty("_vibrationName",b);break;case 1145047050:if(JU.Logger.info(m+" atom positions read"),b.recalculateLeadMidpointsAndWingVectors(-1),m==b.ac)return"boundbox {*};reset"}return null},
"JV.Viewer,JM.ModelSet,~N,~O,JU.BS");F(c$,"defaultGroupCount",32)});u("JM");x(["JM.BondCollection"],"JM.ModelSet","java.lang.Boolean $.Float java.util.Hashtable JU.A4 $.AU $.BS $.Lst $.M3 $.M4 $.Measure $.P3 $.P4 $.PT $.Quat $.SB $.V3 J.api.Interface $.JmolModulationSet J.atomdata.RadiusData J.bspt.Bspf J.c.PAL $.VDW JM.Atom $.AtomIteratorWithinModel $.AtomIteratorWithinModelSet $.HBond $.Model $.StateScript JS.ScriptCompiler JU.BSUtil $.BoxInfo $.Edge $.Elements $.Escape $.JmolMolecule $.Logger $.SimpleUnitCell JV.JC".split(" "),
function(){c$=r(function(){this.haveBioModels=!1;this.am=this.modelSetName=this.bsSymmetry=null;this.mc=0;this.unitCells=null;this.haveUnitCells=!1;this.elementsPresent=this.frameTitles=this.modelNames=this.modelNumbersForAtomLabel=this.modelFileNumbers=this.modelNumbers=this.closest=null;this.isXYZ=!1;this.msInfo=this.modelSetProperties=null;this.isBbcageDefault=this.someModelsHaveFractionalCoordinates=this.someModelsHaveAromaticBonds=this.someModelsHaveSymmetry=!1;this.stateScripts=this.boxInfo=
this.bboxAtoms=this.bboxModels=null;this.thisStateModel=0;this.selectedMolecules=this.vibrationSteps=null;this.showRebondTimes=!0;this.sm=this.bsAll=null;this.proteinStructureTainted=!1;this.vTemp=this.mat4t=this.mat4=this.matInv=this.matTemp=this.ptTemp2=this.ptTemp1=this.ptTemp=this.vOrientations=this.htPeaks=null;this.echoShapeActive=!1;this.defaultBBox=this.translations=this.modelSetTypeName=null;this.maxBondWarned=!1;n(this,arguments)},JM,"ModelSet",JM.BondCollection);c(c$,"getBoxInfo",function(){return this.boxInfo});
t(c$,function(a,b){H(this,JM.ModelSet,[]);this.vwr=a;this.modelSetName=b;this.selectedMolecules=new JU.BS;this.stateScripts=new JU.Lst;this.boxInfo=new JU.BoxInfo;this.boxInfo.addBoundBoxPoint(JU.P3.new3(-10,-10,-10));this.boxInfo.addBoundBoxPoint(JU.P3.new3(10,10,10));this.am=Array(1);this.modelNumbers=A(1,0);this.modelFileNumbers=A(1,0);this.modelNumbersForAtomLabel=Array(1);this.modelNames=Array(1);this.frameTitles=Array(1);this.closest=Array(1);this.ptTemp=new JU.P3;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;this.setupBC()},"JV.Viewer,~S");c(c$,"releaseModelSet",function(){this.am=null;this.unitCells=this.bsAll=this.bsSymmetry=this.am=this.closest[0]=null;this.releaseModelSetBC()});c(c$,"getEchoStateActive",function(){return this.echoShapeActive});c(c$,"setEchoStateActive",function(a){this.echoShapeActive=a},"~B");c(c$,"getModelSetTypeName",function(){return this.modelSetTypeName});c(c$,
"getModelNumberIndex",function(a,b,d){if(b){for(b=0;b<this.mc;b++)if(this.modelNumbers[b]==a||1E6>a&&this.modelNumbers[b]==1E6+a)return b;return-1}if(1E6>a)return a;for(b=0;b<this.mc;b++)if(this.modelFileNumbers[b]==a)return d&&this.isTrajectory(b)&&this.setTrajectory(b),b;return-1},"~N,~B,~B");c(c$,"getModelDataBaseName",function(a){for(var b=0;b<this.mc;b++)if(a.equals(this.am[b].bsAtoms))return this.getInfo(b,"dbName");return null},"JU.BS");c(c$,"setTrajectory",function(a){0<=a&&(this.isTrajectory(a)&&
this.at[this.am[a].firstAtomIndex].mi!=a)&&this.trajectory.setModel(a)},"~N");c(c$,"getBitSetTrajectories",function(){return null==this.trajectory?null:this.trajectory.getModelsSelected()});c(c$,"setTrajectoryBs",function(a){if(null!=this.trajectory)for(var b=0;b<this.mc;b++)a.get(b)&&this.setTrajectory(b)},"JU.BS");c(c$,"morphTrajectories",function(a,b,d){0<=a&&(0<=b&&this.isTrajectory(a)&&this.isTrajectory(b))&&this.trajectory.morph(a,b,d)},"~N,~N,~N");c(c$,"getTranslation",function(a){return null==
this.translations||a>=this.translations.length?null:this.translations[a]},"~N");c(c$,"translateModel",function(a,b){if(null==b){var d=this.getTranslation(a);null!=d&&(b=JU.P3.newP(d),b.scale(-1),this.translateModel(a,b),this.translations[a]=null)}else{if(null==this.translations||this.translations.length<=a)this.translations=Array(this.mc);null==this.translations[a]&&(this.translations[a]=new JU.P3);this.translations[a].add(b);for(var d=this.am[a].bsAtoms,c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))this.at[c].add(b)}},
"~N,JU.T3");c(c$,"getFrameOffsets",function(a,b){if(null==a){if(b)for(var d=this.mc;0<=--d;){var c=this.am[d];!c.isJmolDataFrame&&!c.isTrajectory&&this.translateModel(c.modelIndex,null)}return null}if(0>a.nextSetBit(0))return null;if(b){for(var g=JU.BSUtil.copy(a),e=null,h=new JU.P3,d=0;d<this.mc;d++){c=this.am[d];if(!c.isJmolDataFrame&&!c.isTrajectory){var k=g.nextSetBit(0);c.bsAtoms.get(k)&&(null==e?e=JU.P3.newP(this.at[k]):(h.sub2(e,this.at[k]),this.translateModel(d,h)))}g.andNot(c.bsAtoms)}return null}g=
Array(this.mc);for(d=this.mc;0<=--d;)g[d]=new JU.P3;var h=e=0,k=g[0],j=null!=this.trajectory&&this.trajectory.steps.size()==this.mc,s=j?this.mc:1;g[0].set(0,0,0);for(c=0;c<s;c++){j&&this.setTrajectory(c);for(d=0;d<=this.ac;d++){if(d==this.ac||this.at[d].mi!=e){0<h&&(k.scale(-1/h),0!=e&&k.sub(g[0]),h=0);if(d==this.ac)break;e=this.at[d].mi;k=g[e]}a.get(d)&&(k.add(this.at[d]),h++)}}return g},"JU.BS,~B");c(c$,"getAtoms",function(a,b){switch(a){default:return JU.BSUtil.andNot(this.getAtomBitsMaybeDeleted(a,
b),this.vwr.slm.bsDeleted);case 1073742358:var d=b.intValue(),c=this.getModelNumberIndex(d,!0,!0);return 0>c&&0<d?new JU.BS:this.vwr.getModelUndeletedAtomsBitSet(c);case 1275203608:return d=v(-1,[null,null,null]),this.vwr.shm.getShapePropertyData(21,"getCenters",d),null==d[1]?new JU.BS:d[1]}},"~N,~O");c(c$,"findNearestAtomIndex",function(a,b,d,c){if(0==this.ac)return-1;this.closest[0]=null;this.g3d.isAntialiased()&&(a<<=1,b<<=1);this.findNearest2(a,b,this.closest,d,c);this.sm.findNearestShapeAtomIndex(a,
b,this.closest,d);a=null==this.closest[0]?-1:this.closest[0].i;this.closest[0]=null;return a},"~N,~N,JU.BS,~N");c(c$,"calculatePointGroup",function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,null,0,0,null,null,null)},"JU.BS");c(c$,"getPointGroupInfo",function(a){return this.calculatePointGroupForFirstModel(a,!1,!0,null,0,0,null,null,null)},"JU.BS");c(c$,"getPointGroupAsString",function(a,b,d,c,g,e,h){return this.calculatePointGroupForFirstModel(a,!0,!1,b,d,c,g,e,h)},"JU.BS,~S,~N,~N,~A,JU.P3,~S");
c(c$,"calculatePointGroupForFirstModel",function(a,b,d,c,g,e,h,k,j){var s=this.pointGroup,m=J.api.Interface.getSymmetry(this.vwr,"ms"),p=null,q=!1,w=!1,n=!1,r=null!=h,t=this.vwr.am.cmi;if(!r)if(h=null==a?-1:a.nextSetBit(0),0>t&&0<=h&&(t=this.at[h].mi),0>t&&(t=this.vwr.getVisibleFramesBitSet().nextSetBit(0),a=null),p=this.vwr.getModelUndeletedAtomsBitSet(t),n=null!=a&&p.cardinality()!=a.cardinality(),null!=a&&p.and(a),h=p.nextSetBit(0),0>h&&(p=this.vwr.getModelUndeletedAtomsBitSet(t),h=p.nextSetBit(0)),
w=this.vwr.shm.getShapePropertyIndex(18,"mad",h),q=null!=w&&0!=w.intValue()||this.vwr.tm.vibrationOn,w=null!=c&&0<=c.toUpperCase().indexOf(":POLY")){s=v(-1,[Integer.$valueOf(h),null]);this.vwr.shm.getShapePropertyData(21,"points",s);h=s[1];if(null==h)return null;p=null;q=!1;s=null}else h=this.at;null!=c&&0<=c.indexOf(":")&&(c=c.substring(0,c.indexOf(":")));s=m.setPointGroup(s,k,h,p,q,r?0:this.vwr.getFloat(570425382),this.vwr.getFloat(570425384),n);!w&&!r&&(this.pointGroup=s);if(!b&&!d)return s.getPointGroupName();
b=s.getPointGroupInfo(t,j,d,c,g,e);return d?b:(1<this.mc?"frame "+this.getModelNumberDotted(t)+"; ":"")+b},"JU.BS,~B,~B,~S,~N,~N,~A,JU.P3,~S");c(c$,"getDefaultStructure",function(a,b){return this.haveBioModels?this.bioModelset.getAllDefaultStructures(a,b):""},"JU.BS,JU.BS");c(c$,"deleteModelBonds",function(a){a=this.getModelAtomBitSetIncludingDeleted(a,!1);this.makeConnections(0,3.4028235E38,131071,12291,a,a,null,!1,!1,0)},"~N");c(c$,"makeConnections",function(a,b,d,c,g,e,h,k,j,s){if(1073741852==
c&&2048!=d){var m="connect ";0.1!=a&&(m+=a+" ");1E8!=b&&(m+=b+" ");this.addStateScript(m,k?g:null,k?null:g,k?null:e," auto",!1,!0)}this.moleculeCount=0;return this.makeConnections2(a,b,d,c,g,e,h,k,j,s)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"setPdbConectBonding",function(a,b,d){for(var c=this.vwr.getMadBond();b<this.mc;b++){var g=this.getInfo(b,"PDB_CONECT_bonds");if(null!=g){var e=g.size();this.setInfo(b,"initialBondCount",Integer.$valueOf(e));for(var h=this.getInfo(b,"PDB_CONECT_firstAtom_count_max"),
k=h[0]+a,j=k+h[1],h=h[2],s=A(h+1,0),m=k;m<j;m++)if(0<(k=this.atomSerials[m]))s[k]=m+1;for(j=0;j<e;j++){var k=g.get(j),m=k[0],p=k[1],k=k[2];if(!(0>m||0>p||m>h||p>h))if(m=s[m]-1,p=s[p]-1,!(0>m||0>p)){var q=this.at[m],w=this.at[p];null!=d&&(q.isHetero()&&d.set(m),w.isHetero()&&d.set(p));if(q.altloc==w.altloc||"\x00"==q.altloc||"\x00"==w.altloc)this.getOrAddBond(q,w,k,2048==k?1:c,null,0,!1)}}}}},"~N,~N,JU.BS");c(c$,"deleteAllBonds",function(){this.moleculeCount=0;for(var a=this.stateScripts.size();0<=
--a;)this.stateScripts.get(a).isConnect()&&this.stateScripts.removeItemAt(a);this.deleteAllBonds2()});c(c$,"includeAllRelatedFrames",function(a){for(var b=0,d=0;d<this.mc;d++){var c=this.isTrajectory(d),g=c&&a.get(b=this.am[d].trajectoryBaseIndex);if(a.get(d)){if(c&&!g){a.set(b);this.includeAllRelatedFrames(a);break}}else(c||this.isJmolDataFrameForModel(d)&&a.get(this.am[d].dataSourceFrame))&&a.set(d)}},"JU.BS");c(c$,"deleteModels",function(a){this.includeAllRelatedFrames(a);var b=a.cardinality();
if(0==b)return null;this.moleculeCount=0;null!=this.msInfo&&this.msInfo.remove("models");for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.clearDataFrameReference(d);if(b==this.mc)return b=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.vwr.zap(!0,!1,!1),b;this.validateBspf(!1);for(var c=Array(this.mc-b),g=this.am,b=new JU.BS,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 h=this.mc,k=this.getBondsForSelectedAtoms(b,!0);this.deleteBonds(k,!0);for(e=d=0;d<h;d++)if(a.get(d)){var j=g[d].act;if(0!=j){var s=g[d].bsAtoms,m=g[d].firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,s);this.deleteModel(e,m,j,s,k);for(var p=h;--p>d;)g[p].fixIndices(e,j,s);this.vwr.shm.deleteShapeAtoms(v(-1,[c,this.at,A(-1,[e,m,j])]),s);this.mc--}}else e++;this.haveBioModels=!1;for(d=this.mc;0<=--d;)this.am[d].isBioModel&&(this.haveBioModels=!0,this.bioModelset.set(this.vwr,this));this.validateBspf(!1);
this.bsAll=null;this.resetMolecules();this.isBbcageDefault=!1;this.calcBoundBoxDimensions(null,1);return b},"JU.BS");c(c$,"resetMolecules",function(){this.molecules=null;this.moleculeCount=0;this.resetChirality()});c(c$,"resetChirality",function(){if(this.haveChirality)for(var a=-1,b=this.ac;0<=--b;){var d=this.at[b];d.setCIPChirality(0);d.mi!=a&&(this.am[a=d.mi].hasChirality=!1)}});c(c$,"deleteModel",function(a,b,d,c,g){if(!(0>a)){this.modelNumbers=JU.AU.deleteElements(this.modelNumbers,a,1);this.modelFileNumbers=
JU.AU.deleteElements(this.modelFileNumbers,a,1);this.modelNumbersForAtomLabel=JU.AU.deleteElements(this.modelNumbersForAtomLabel,a,1);this.modelNames=JU.AU.deleteElements(this.modelNames,a,1);this.frameTitles=JU.AU.deleteElements(this.frameTitles,a,1);this.thisStateModel=-1;var e=this.getInfoM("group3Lists"),h=this.getInfoM("group3Counts"),k=a+1;if(null!=e&&null!=e[k])for(var j=y(e[k].length/6);0<=--j;)0<h[k][j]&&(h[0][j]-=h[k][j],0==h[0][j]&&(e[0]=e[0].substring(0,6*j)+",["+e[0].substring(6*j+2)));
null!=e&&(this.msInfo.put("group3Lists",JU.AU.deleteElements(e,a,1)),this.msInfo.put("group3Counts",JU.AU.deleteElements(h,a,1)));null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(j=this.stateScripts.size();0<=--j;)this.stateScripts.get(j).deleteAtoms(a,g,c)||this.stateScripts.removeItemAt(j);this.deleteModelAtoms(b,d,c);this.vwr.deleteModelAtoms(a,b,d,c)}},"~N,~N,~N,JU.BS,JU.BS");c(c$,"setAtomProperty",function(a,b,d,c,g,e,h){switch(b){case 1114249217:case 1112152066:case 1112152071:case 1112152073:case 1112152074:case 1649022989:case 1112152078:if(4<
c&&(c=4),null!=e){d=I(this.ac,0);try{var k=a.nextSetBit(0);for(g=0;0<=k;k=a.nextSetBit(k+1))d[k]=e[g++]}catch(j){if(E(j,Exception))return;throw j;}e=d}case 1112152070:case 1112152076:k=null;d=0;null==e?(16<c&&(c=16.1),0>c&&(c=0),d=y(Math.floor(2E3*c))):k=new J.atomdata.RadiusData(e,0,null,null);this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(b),d,k,a);return}this.setAPm(a,b,d,c,g,e,h)},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"getFileData",function(a){if(0>a)return"";var b=this.getInfo(a,"fileData");if(null!=
b)return b;if(!this.getInfoB(a,"isCIF"))return this.getPDBHeader(a);b=this.vwr.getCifData(a);this.setInfo(a,"fileData",b);return b},"~N");c(c$,"addHydrogens",function(a,b){var d=this.mc-1,c=new JU.BS;if(this.isTrajectory(d)||1<this.am[d].getGroupCount())return c;this.growAtomArrays(this.ac+b.length);var g=this.vwr.rd,e=this.getDefaultMadFromOrder(1);this.am[d].resetDSSR(!1);for(var h=0,k=this.am[d].act+1;h<a.size();h++,k++){var j=a.get(h),s=this.addAtom(d,j.group,1,"H"+k,null,k,j.getSeqID(),k,b[h],
NaN,null,0,0,100,NaN,null,!1,0,null);s.setMadAtom(this.vwr,g);c.set(s.i);this.bondAtoms(j,s,1,e,null,0,!1,!1)}this.sm.loadDefaultShapes(this);return c},"JU.Lst,~A");c(c$,"mergeModelArrays",function(a){this.at=a.at;this.bo=a.bo;this.stateScripts=a.stateScripts;this.proteinStructureTainted=a.proteinStructureTainted;this.thisStateModel=-1;this.bsSymmetry=a.bsSymmetry;this.modelFileNumbers=a.modelFileNumbers;this.modelNumbersForAtomLabel=a.modelNumbersForAtomLabel;this.modelNames=a.modelNames;this.modelNumbers=
a.modelNumbers;this.frameTitles=a.frameTitles;this.haveChirality=a.haveChirality;null!=this.msInfo&&this.msInfo.remove("models");this.mergeAtomArrays(a)},"JM.ModelSet");c(c$,"getUnitCell",function(a){return 0>a||a>=this.mc?null:null!=this.am[a].simpleCage?this.am[a].simpleCage:null!=this.unitCells&&a<this.unitCells.length&&null!=this.unitCells[a]&&this.unitCells[a].haveUnitCell()?this.unitCells[a]:null!=this.getInfo(a,"unitCellParams")?(null==this.unitCells&&(this.unitCells=Array(this.mc)),this.haveUnitCells=
!0,this.unitCells[a]=this.vwr.getSymTemp().setSymmetryInfo(a,this.am[a].auxiliaryInfo,null)):null},"~N");c(c$,"setModelCage",function(a,b){0<=a&&a<this.mc&&(this.am[a].simpleCage=b,this.haveUnitCells=!0)},"~N,J.api.SymmetryInterface");c(c$,"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(q(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$,"getGroups",
function(){for(var a=0,b=0;b<this.mc;b++)a+=this.am[b].getGroupCount();for(var a=Array(a),d=b=0;b<this.mc;b++)for(var c=0;c<this.am[b].chainCount;c++)for(var g=0;g<this.am[b].chains[c].groupCount;g++)a[d]=this.am[b].chains[c].groups[g],a[d].groupIndex=d,d++;return a});c(c$,"getUnitCellParams",function(){var a=this.getUnitCell(0);return null==a?null:a.getUnitCellParams()});c(c$,"setCrystallographicDefaults",function(){return!this.haveBioModels&&this.someModelsHaveSymmetry&&this.someModelsHaveFractionalCoordinates});
c(c$,"getBoundBoxCenter",function(a){return this.isJmolDataFrameForModel(a)?new JU.P3:(null==this.getDefaultBoundBox()?this.boxInfo:this.defaultBBox).getBoundBoxCenter()},"~N");c(c$,"getBoundBoxCornerVector",function(){return this.boxInfo.getBoundBoxCornerVector()});c(c$,"getBBoxVertices",function(){return this.boxInfo.getBoundBoxVertices()});c(c$,"setBoundBox",function(a,b,d,c){this.isBbcageDefault=!1;this.bboxAtoms=this.bboxModels=null;this.boxInfo.setBoundBox(a,b,d,c)},"JU.T3,JU.T3,~B,~N");c(c$,
"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$,"findAtomsInRectangle",
function(a){for(var b=this.vwr.getVisibleFramesBitSet(),d=new JU.BS,c=this.ac;0<=--c;){var g=this.at[c];b.get(g.mi)?g.checkVisible()&&a.contains(g.sX,g.sY)&&d.set(c):c=this.am[g.mi].firstAtomIndex}return d},"JU.Rectangle");c(c$,"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,d){if(this.isJmolDataFrameForModel(a))return b=this.am[a].defaultRotationRadius,0==b?10:b;if(d&&null!=this.getDefaultBoundBox())return 1.2*(this.defaultBBox.getMaxDim()/2);d=0;for(var 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 a=this.at[c],a=b.distance(a)+this.getRadiusVdwJmol(a),a>d&&(d=a);return 0==d?10:d},"~N,JU.P3,~B");c(c$,"calcBoundBoxDimensions",function(a,b){null!=a&&0>a.nextSetBit(0)&&
(a=null);if(!(null==a&&this.isBbcageDefault||0==this.ac)){if(null==this.getDefaultBoundBox())this.bboxModels=this.getModelBS(this.bboxAtoms=JU.BSUtil.copy(a),!1),this.calcAtomsMinMax(a,this.boxInfo)==this.ac&&(this.isBbcageDefault=!0),null==a&&null!=this.unitCells&&this.calcUnitCellMinMax();else{var d=this.defaultBBox.getBoundBoxVertices();this.boxInfo.reset();for(var c=0;8>c;c++)this.boxInfo.addBoundBoxPoint(d[c])}this.boxInfo.setBbcage(b)}},"JU.BS,~N");c(c$,"getDefaultBoundBox",function(){var a=
this.getInfoM("boundbox");null==a?this.defaultBBox=null:(null==this.defaultBBox&&(this.defaultBBox=new JU.BoxInfo),this.defaultBBox.setBoundBoxFromOABC(a));return this.defaultBBox});c(c$,"getBoxInfo",function(a,b){if(null==a)return this.boxInfo;var d=new JU.BoxInfo;this.calcAtomsMinMax(a,d);d.setBbcage(b);return d},"JU.BS,~N");c(c$,"calcAtomsMinMax",function(a,b){b.reset();for(var d=0,c=null==a,g=c?this.ac-1:a.nextSetBit(0);0<=g;g=c?g-1:a.nextSetBit(g+1))d++,this.isJmolDataFrameForAtom(this.at[g])||
b.addBoundBoxPoint(this.at[g]);return d},"JU.BS,JU.BoxInfo");c(c$,"calcUnitCellMinMax",function(){for(var a=new JU.P3,b=0;b<this.mc;b++)if(this.unitCells[b].getCoordinatesAreFractional())for(var d=this.unitCells[b].getUnitCellVerticesNoOffset(),c=this.unitCells[b].getCartesianOffset(),g=0;8>g;g++)a.add2(c,d[g]),this.boxInfo.addBoundBoxPoint(a)});c(c$,"calcRotationRadiusBs",function(a){for(var b=this.getAtomSetCenter(a),d=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var g=this.at[c],g=b.distance(g)+
this.getRadiusVdwJmol(g);g>d&&(d=g)}return 0==d?10:d},"JU.BS");c(c$,"getCenterAndPoints",function(a,b){for(var d,c,g=b?1:0,e=a.size();0<=--e;){var h=a.get(e);d=h[0];q(h[1],JU.BS)?(c=h[1],g+=Math.min(d.cardinality(),c.cardinality())):g+=Math.min(d.cardinality(),h[1].length)}var k=v(2,g,null);b&&(k[0][0]=new JU.P3,k[1][0]=new JU.P3);for(e=a.size();0<=--e;)if(h=a.get(e),d=h[0],q(h[1],JU.BS)){c=h[1];for(var h=d.nextSetBit(0),j=c.nextSetBit(0);0<=h&&0<=j;h=d.nextSetBit(h+1),j=c.nextSetBit(j+1))k[0][--g]=
this.at[h],k[1][g]=this.at[j],b&&(k[0][0].add(this.at[h]),k[1][0].add(this.at[j]))}else{c=h[1];h=d.nextSetBit(0);for(j=0;0<=h&&j<c.length;h=d.nextSetBit(h+1),j++)k[0][--g]=this.at[h],k[1][g]=c[j],b&&(k[0][0].add(this.at[h]),k[1][0].add(c[j]))}b&&(k[0][0].scale(1/(k[0].length-1)),k[1][0].scale(1/(k[1].length-1)));return k},"JU.Lst,~B");c(c$,"getAtomSetCenter",function(a){for(var b=new JU.P3,d=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.isJmolDataFrameForAtom(this.at[c])||(d++,b.add(this.at[c]));
1<d&&b.scale(1/d);return b},"JU.BS");c(c$,"getAverageAtomPoint",function(){null==this.averageAtomPoint&&(this.averageAtomPoint=this.getAtomSetCenter(this.vwr.getAllAtoms()));return this.averageAtomPoint});c(c$,"setAPm",function(a,b,d,c,g,e,h){this.setAPa(a,b,d,c,g,e,h);switch(b){case 1094715417:case 1631586315:this.vwr.getBoolean(603979944)&&this.assignAromaticBondsBs(!0,null)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"addStateScript",function(a,b,d,c,g,e,h){var k=this.vwr.am.cmi;e?(this.thisStateModel!=
k&&(a="frame "+(0>k?"all #"+k:this.getModelNumberDotted(k))+";\n  "+a),this.thisStateModel=k):this.thisStateModel=-1;a=new JM.StateScript(this.thisStateModel,a,b,d,c,g,h);a.isValid()&&this.stateScripts.addLast(a);return a},"~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");c(c$,"freezeModels",function(){this.haveBioModels=!1;for(var a=this.mc;0<=--a;)this.haveBioModels=(new Boolean(this.haveBioModels|this.am[a].freeze())).valueOf()});c(c$,"getStructureList",function(){return this.vwr.getStructureList()});c(c$,"getInfoM",
function(a){return null==this.msInfo?null:this.msInfo.get(a)},"~S");c(c$,"getMSInfoB",function(a){a=this.getInfoM(a);return q(a,Boolean)&&a.booleanValue()},"~S");c(c$,"isTrajectory",function(a){return this.am[a].isTrajectory},"~N");c(c$,"isTrajectorySubFrame",function(a){return this.am[a].trajectoryBaseIndex!=a},"~N");c(c$,"isTrajectoryMeasurement",function(a){return null!=this.trajectory&&this.trajectory.hasMeasure(a)},"~A");c(c$,"getModelBS",function(a,b){var d=new JU.BS,c=0,g=null==a;b=(new Boolean(b&
null!=this.trajectory)).valueOf();for(c=g?0:a.nextSetBit(0);0<=c&&c<this.ac;c=g?c+1:a.nextSetBit(c+1))d.set(c=this.at[c].mi),b&&this.trajectory.getModelBS(c,d),c=this.am[c].firstAtomIndex+this.am[c].act-1;return d},"JU.BS,~B");c(c$,"getIterativeModels",function(a){for(var b=new JU.BS,d=0;d<this.mc;d++)if(a||!this.isJmolDataFrameForModel(d))this.isTrajectorySubFrame(d)||b.set(d);return b},"~B");c(c$,"fillAtomData",function(a,b){if(0!=(b&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);
a.atomMolecule=A(this.ac,0);for(var d,c=0;c<this.molecules.length;c++){d=a.bsMolecules[c]=this.molecules[c].atomList;for(var g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))a.atomMolecule[g]=c}}0!=(b&8)?(d=A(1,0),a.hAtomRadius=this.vwr.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,d,!1,!0,null),a.hydrogenAtomCount=d[0]):(a.firstAtomIndex=0>a.modelIndex?null==a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.am[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=
0==this.ac?0:this.at[a.firstAtomIndex].mi,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,b))},"J.atomdata.AtomData,~N");c(c$,"getModelNumberDotted",function(a){return 1>this.mc||a>=this.mc||0>a?"":JU.Escape.escapeModelFileNumber(this.modelFileNumbers[a])},"~N");c(c$,"getModelNumber",function(a){return this.modelNumbers[2147483647==a?this.mc-1:a]},"~N");c(c$,"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){0<=a&&a<this.mc&&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$,"getInfoI",function(a,b){var d=this.am[a].auxiliaryInfo;return null!=d&&d.containsKey(b)?d.get(b).intValue():-2147483648},"~N,~S");
c(c$,"getInsertionCountInModel",function(a){return this.am[a].insertionCount},"~N");c$.modelFileNumberFromFloat=c(c$,"modelFileNumberFromFloat",function(a){var b=y(Math.floor(a));for(a=y(Math.floor(1E4*(a-b+1E-5)));0!=a&&0==a%10;)a/=10;return 1E6*b+a},"~N");c(c$,"getChainCountInModelWater",function(a,b){if(0>a){for(var d=0,c=this.mc;0<=--c;)d+=this.am[c].getChainCount(b);return d}return this.am[a].getChainCount(b)},"~N,~B");c(c$,"getGroupCountInModel",function(a){if(0>a){a=0;for(var b=this.mc;0<=
--b;)a+=this.am[b].getGroupCount();return a}return this.am[a].getGroupCount()},"~N");c(c$,"calcSelectedGroupsCount",function(){for(var a=this.vwr.bsA(),b=this.mc;0<=--b;)this.am[b].calcSelectedGroupsCount(a)});c(c$,"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.getPDBHeader(a);a=this.getInfo(a,"fileHeader");null==a&&(a=this.modelSetName);return null!=a?a:"no header information found"},"~N");c(c$,"getAltLocCountInModel",function(a){return this.am[a].altLocCount},"~N");c(c$,"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){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&&a<this.vwr.ms.mc)for(var d,c=0>a||this.isTrajectory(a)||a>=this.mc-1?this.ac:this.am[a+1].firstAtomIndex,g=0>=a?0:this.am[a].firstAtomIndex;--c>=g;)if((0>a||this.at[c].mi==a)&&((1275072532==b||0==b)&&null!=(d=this.getModulation(c))||
(4166==b||0==b)&&null!=(d=this.getVibration(c,!1)))&&d.isNonzero())return c;return-1},"~N,~N");c(c$,"getModulationList",function(a,b,d){var c=new JU.Lst;if(null!=this.vibrations)for(var g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))q(this.vibrations[g],J.api.JmolModulationSet)?c.addLast(this.vibrations[g].getModulation(b,d)):c.addLast(Float.$valueOf("O"==b?NaN:-1));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].mi}if(0>
a)return null;var c=d=0,g=0,e=0,h=new JU.V3,k=new JU.V3;null==b&&(b=this.getModelAtomBitSetIncludingDeleted(-1,!1));this.vwr.getOrCalcPartialCharges(this.am[a].bsAtoms,null);for(var j=b.nextSetBit(0);0<=j;j=b.nextSetBit(j+1))if(!(this.at[j].mi!=a||this.at[j].isDeleted())){var s=this.partialCharges[j];0>s?(c++,e+=s,k.scaleAdd2(s,this.at[j],k)):0<s&&(d++,g+=s,h.scaleAdd2(s,this.at[j],h))}if(0.015<Math.abs(g+e))return JU.Logger.info("Dipole calculation requires balanced charges: "+g+" "+e),null;if(0==
c||0==d)return null;h.add(k);h.scale(4.8);return h},"~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$,"getMolecules",function(){if(0<this.moleculeCount)return this.molecules;null==this.molecules&&(this.molecules=Array(4));this.moleculeCount=0;for(var a=
null,b=Array(this.mc),d=null,c=0;c<this.mc;c++)b[c]=this.vwr.getModelUndeletedAtomsBitSet(c),a=this.am[c],a.moleculeCount=0,d=a.isBioModel?a.getBioBranches(d):null;this.molecules=JU.JmolMolecule.getMolecules(this.at,b,d,null);for(c=this.moleculeCount=this.molecules.length;0<=--c;)a=this.am[this.molecules[c].modelIndex],a.firstMoleculeIndex=c,a.moleculeCount++;return this.molecules});c(c$,"initializeBspf",function(){if(!(null!=this.bspf&&this.bspf.isValid)){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.isValid=!0;this.bspf=a}});c(c$,"initializeBspt",function(a){this.initializeBspf();this.bspf.isInitializedIndex(a)||
this.bspf.initialize(a,this.at,this.vwr.getModelUndeletedAtomsBitSet(a))},"~N");c(c$,"setIteratorForPoint",function(a,b,d,c){0>b?a.setCenter(d,c):(this.initializeBspt(b),a.setModel(this,b,this.am[b].firstAtomIndex,2147483647,d,c,null))},"J.api.AtomIndexIterator,~N,JU.T3,~N");c(c$,"setIteratorForAtom",function(a,b,d,c,g){0>b&&(b=this.at[d].mi);b=this.am[b].trajectoryBaseIndex;this.initializeBspt(b);a.setModel(this,b,this.am[b].firstAtomIndex,d,this.at[d],c,g)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");
c(c$,"getSelectedAtomIterator",function(a,b,d,c,g){this.initializeBspf();if(g){g=this.getModelBS(a,!1);for(var e=g.nextSetBit(0);0<=e;e=g.nextSetBit(e+1))this.initializeBspt(e);g=new JM.AtomIteratorWithinModelSet(g)}else g=new JM.AtomIteratorWithinModel;g.initialize(this.bspf,a,b,d,c,this.vwr.isParallel());return g},"JU.BS,~B,~B,~B,~B");j(c$,"getBondCountInModel",function(a){return 0>a?this.bondCount:this.am[a].getBondCount()},"~N");c(c$,"getAtomCountInModel",function(a){return 0>a?this.ac:this.am[a].act},
"~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$,"getAtomBitsMaybeDeleted",
function(a,b){var d,c;switch(a){default:return this.getAtomBitsMDa(a,b,new JU.BS);case 1073741925:case 1073742189:case 1111490587:case 1073742128:case 1073741863:case 1086324744:return c=new JU.BS,this.haveBioModels?this.bioModelset.getAtomBitsStr(a,b,c):c;case 1677721602:case 1073742331:return this.getAtomBitsMDb(a,b);case 1678381065:var g=this.getBoxInfo(b,1);c=this.getAtomsWithin(g.getBoundBoxCornerVector().length()+1E-4,g.getBoundBoxCenter(),null,-1);for(d=c.nextSetBit(0);0<=d;d=c.nextSetBit(d+
1))g.isWithin(this.at[d])||c.clear(d);return c;case 1094713349:c=new JU.BS;d=b;this.ptTemp1.set(d[0]/1E3,d[1]/1E3,d[2]/1E3);for(d=this.ac;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,!1)&&c.set(d);return c;case 1094713350:c=JU.BSUtil.newBitSet2(0,this.ac);d=b;g=A(-1,[y(d[0]/1E3)-1,y(d[1]/1E3)-1,y(d[2]/1E3)-1,y(d[0]/1E3),y(d[1]/1E3),y(d[2]/1E3),0]);for(d=this.mc;0<=--d;){var e=this.getUnitCell(d);null==e?JU.BSUtil.andNot(c,this.am[d].bsAtoms):c.andNot(e.notInCentroid(this,this.am[d].bsAtoms,
g))}return c;case 1094713360:return this.getMoleculeBitSet(b);case 1073742363:return this.getSelectCodeRange(b);case 2097196:c=JU.BS.newN(this.ac);g=-1;e=0;for(d=this.ac;0<=--d;){var h=this.at[d],k=h.atomSymmetry;if(null!=k){if(h.mi!=g){g=h.mi;if(null==this.getModelCellRange(g))continue;e=this.getModelSymmetryCount(g)}for(var h=0,j=e;0<=--j;)if(k.get(j)&&1<++h){c.set(d);break}}}return c;case 1088421903:return JU.BSUtil.copy(null==this.bsSymmetry?this.bsSymmetry=JU.BS.newN(this.ac):this.bsSymmetry);
case 1814695966:c=new JU.BS;if(null==this.vwr.getCurrentUnitCell())return c;this.ptTemp1.set(1,1,1);for(d=this.ac;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,!1)&&c.set(d);return c}},"~N,~O");c(c$,"getSelectCodeRange",function(a){var b=new JU.BS,d=a[0],c=a[1];a=a[2];var g=this.vwr.getBoolean(603979822);0<=a&&(300>a&&!g)&&(a=this.chainToUpper(a));for(var e=this.mc;0<=--e;)if(this.am[e].isBioModel)for(var h=this.am[e],k,j=h.chainCount;0<=--j;){var s=h.chains[j];if(-1==a||a==(k=s.chainID)||
!g&&0<k&&300>k&&a==this.chainToUpper(k))for(var m=s.groups,s=s.groupCount,p=0;0<=p;)p=JM.ModelSet.selectSeqcodeRange(m,s,p,d,c,b)}return b},"~A");c$.selectSeqcodeRange=c(c$,"selectSeqcodeRange",function(a,b,d,c,g,e){var h,k,j,s=!1;for(k=d;k<b&&a[k].seqcode!=c;k++);if(k==b){if(0<d)return-1;s=!0;j=2147483647;for(var m=b;0<=--m;)if((h=a[m].seqcode)>c&&h-c<j)k=m,j=h-c;if(2147483647==j)return-1}if(2147483647==g)c=b-1,s=!0;else{for(c=k;c<b&&a[c].seqcode!=g;c++);if(c==b){if(0<d)return-1;s=!0;j=2147483647;
for(m=k;m<b;m++)if((h=a[m].seqcode)<g&&g-h<j)c=m,j=g-h;if(2147483647==j)return-1}}for(m=k;m<=c;++m)a[m].setAtomBits(e);return s?-1:c+1},"~A,~N,~N,~N,~N,JU.BS");c(c$,"isInLatticeCell",function(a,b,d,c){var g=this.getUnitCell(this.at[a].mi);d.setT(this.at[a]);return null!=g&&g.checkUnitCell(g,b,d,c)},"~N,JU.P3,JU.P3,~B");c(c$,"getAtomsWithinRadius",function(a,b,d,c){var g=new JU.BS,e=this.getIterativeModels(!1);b=JU.BSUtil.andNot(b,this.vwr.slm.bsDeleted);var h=this.getSelectedAtomIterator(null,!1,
!1,!1,!1);if(d){d=!this.vwr.g.legacyJavaFloat;for(var k=new JU.P3,j=b.nextSetBit(0);0<=j;j=b.nextSetBit(j+1))for(var s=this.mc;0<=--s;)e.get(s)&&(0>a?this.getAtomsWithin(a,this.at[j].getFractionalUnitCoordPt(d,!0,k),g,-1):(this.setIteratorForAtom(h,s,j,a,c),h.addAtoms(g)))}else{g.or(b);for(j=b.nextSetBit(0);0<=j;j=b.nextSetBit(j+1))0>a?this.getAtomsWithin(a,this.at[j],g,this.at[j].mi):(this.setIteratorForAtom(h,-1,j,a,c),h.addAtoms(g))}h.release();return g},"~N,JU.BS,~B,J.atomdata.RadiusData");c(c$,
"getAtomsWithin",function(a,b,d,c){null==d&&(d=new JU.BS);if(0>a){a=-a;for(var g=this.ac;0<=--g;){var e=this.at[g];0<=c&&this.at[g].mi!=c||!d.get(g)&&e.getFractionalUnitDistance(b,this.ptTemp1,this.ptTemp2)<=a&&d.set(e.i)}return d}c=this.getIterativeModels(!0);g=this.getSelectedAtomIterator(null,!1,!1,!1,!1);for(e=this.mc;0<=--e;)c.get(e)&&!this.am[e].bsAtoms.isEmpty()&&(this.setIteratorForAtom(g,-1,this.am[e].firstAtomIndex,-1,null),g.setCenter(b,a),g.addAtoms(d));g.release();return d},"~N,JU.T3,JU.BS,~N");
c(c$,"deleteBonds",function(a,b){if(!b)for(var d=new JU.BS,c=new JU.BS,g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1)){var e=this.bo[g].atom1;this.am[e.mi].isModelKit||(d.clearAll(),c.clearAll(),d.set(e.i),c.set(this.bo[g].getAtomIndex2()),this.addStateScript("connect ",null,d,c,"delete",!1,!0))}this.dBb(a,b)},"JU.BS,~B");c(c$,"makeConnections2",function(a,b,d,c,g,e,h,k,j,s){null==h&&(h=new JU.BS);var m=65535==d,p=131071==d,q=65537==d;p&&(d=1);var w=JU.Edge.isOrderH(d),n=!1,r=!1,t=!1,u=!1;switch(c){case 12291:return this.deleteConnections(a,
b,d,g,e,k,p);case 603979873:case 1073741852:if(515!=d){if(k){a=g;g=new JU.BS;e=new JU.BS;for(var v=a.nextSetBit(0);0<=v;v=a.nextSetBit(v+1))g.set(this.bo[v].atom1.i),e.set(this.bo[v].atom2.i)}return A(-1,[w?this.autoHbond(g,e,!1):this.autoBondBs4(g,e,null,h,this.vwr.getMadBond(),603979873==c),0])}r=u=!0;break;case 1086324745:n=r=!0;break;case 1073742025:r=!0;break;case 1073741904:t=!0}c=!n||m;m=!n&&!m;this.defaultCovalentMad=this.vwr.getMadBond();var p=0>a,x=0>b,y=p||x,B=!k||0.1!=a||1E8!=b;B&&(a=
this.fixD(a,p),b=this.fixD(b,x));var C=this.getDefaultMadFromOrder(d),D=0,F=0,H=null,I=null,K=null,M="\x00",N=d|131072,O=0!=(d&512);try{for(v=g.nextSetBit(0);0<=v;v=g.nextSetBit(v+1)){if(k)H=this.bo[v],I=H.atom1,K=H.atom2;else{I=this.at[v];if(I.isDeleted())continue;M=this.isModulated(v)?"\x00":I.altloc}for(var P=k?0:e.nextSetBit(0);0<=P;P=e.nextSetBit(P+1)){if(k)P=2147483646;else{if(P==v)continue;K=this.at[P];if(I.mi!=K.mi||K.isDeleted())continue;if("\x00"!=M&&M!=K.altloc&&"\x00"!=K.altloc)continue;
H=I.getBond(K)}if(!(null==H?r:t)&&!(B&&!this.isInRange(I,K,a,b,p,x,y)||O&&!this.allowAromaticBond(H)))if(null==H)h.set(this.bondAtoms(I,K,d,C,h,s,j,!0).index),D++;else if(m&&(H.setOrder(d),q&&H.setAtropisomerOptions(g,e),this.bsAromatic.clear(H.index)),c||d==H.order||N==H.order||w&&H.isHydrogen())h.set(H.index),F++}}}catch(Q){if(!E(Q,Exception))throw Q;}u&&this.assignAromaticBondsBs(!0,h);n||this.sm.setShapeSizeBs(1,-2147483648,null,h);return A(-1,[D,F])},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");
c(c$,"autoBondBs4",function(a,b,d,c,g,e){if(e)return this.autoBond_Pre_11_9_24(a,b,d,c,g);if(0==this.ac)return 0;0==g&&(g=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();e=this.vwr.getFloat(570425348);var h=this.vwr.getFloat(570425364),h=h*h,k=0;this.showRebondTimes&&JU.Logger.startTimer("autobond");var j=-1,s=null==a,m,p;s?(p=0,m=null):(a.equals(b)?m=a:(m=JU.BSUtil.copy(a),m.or(b)),p=m.nextSetBit(0));for(var q=this.getSelectedAtomIterator(null,!1,!1,!0,!1),w=!1;0<=p&&p<this.ac;p=s?p+1:m.nextSetBit(p+
1)){var n=s||a.get(p),r=s||b.get(p),t=this.at[p];if(!t.isDeleted()){var u=t.mi;if(u!=j){j=u;if(this.isJmolDataFrameForModel(u)){p=this.am[u].firstAtomIndex+this.am[u].act-1;continue}w=this.getInfoB(u,"autoBondUsingOccupation")}u=t.getBondingRadius();if(0!=u){var v=null!=d&&d.get(p);for(this.setIteratorForAtom(q,-1,p,u+this.maxBondingRadius+e,null);q.hasNext();){var x=this.at[q.next()];if(!x.isDeleted()){var y=x.i,A=s||a.get(y),B=s||b.get(y);!A&&!B||(!(n&&B||r&&A)||v&&d.get(y)||w&&null!=this.occupancies&&
50>this.occupancies[p]!=50>this.occupancies[y])||(y=this.isBondable(u,x.getBondingRadius(),q.foundDistance2(),h,e)?1:0,0<y&&this.autoBondCheck(t,x,y,g,c)&&k++)}}q.release()}}}this.showRebondTimes&&JU.Logger.checkTimer("autoBond",!1);return k},"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B");c(c$,"isBondable",function(a,b,d,c,g){if(0==a||0==b||d<c)return!1;a=a+b+g;return d<=a*a},"~N,~N,~N,~N,~N");c(c$,"autoBondCheck",function(a,b,d,c,g){if(20<a.getCurrentBondCount()||20<b.getCurrentBondCount())return this.maxBondWarned||
JU.Logger.warn("maximum auto bond count reached"),this.maxBondWarned=!0,!1;var e=a.getFormalCharge();if(0!=e){var h=b.getFormalCharge();if(0>e&&0>h||0<e&&0<h)return!1}if(a.altloc!=b.altloc&&"\x00"!=a.altloc&&"\x00"!=b.altloc&&null==this.getModulation(a.i))return!1;this.getOrAddBond(a,b,d,c,g,0,!1);return!0},"JM.Atom,JM.Atom,~N,~N,JU.BS");c(c$,"autoBond_Pre_11_9_24",function(a,b,d,c,g){if(0==this.ac)return 0;0==g&&(g=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var e=this.vwr.getFloat(570425348),
h=this.vwr.getFloat(570425364),h=h*h,k=0;this.initializeBspf();for(var j=-1,s=this.ac;0<=--s;){var m=null==a||a.get(s),p=null==b||b.get(s);if(m||p){var q=this.at[s];if(!q.isDeleted()){var w=q.mi;if(w!=j&&(j=w,this.isJmolDataFrameForModel(w))){for(;0<=--s&&this.at[s].mi==w;);s++;continue}var n=q.getBondingRadius();if(0!=n){var r=n+this.maxBondingRadius+e;this.initializeBspt(w);w=this.bspf.getCubeIterator(w);for(w.initialize(q,r,!0);w.hasMoreElements();)if(r=w.nextElement(),!(r===q||r.isDeleted())){var t=
r.i,u=null==a||a.get(t),v=null==b||b.get(t);if(!(!u&&!v||null!=d&&d.get(t)&&d.get(s)))if(m&&v||p&&u)t=this.isBondable(n,r.getBondingRadius(),w.foundDistance2(),h,e)?1:0,0<t&&this.autoBondCheck(q,r,t,g,c)&&k++}w.release()}}}}return k},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(c$,"autoHbond",function(a,b,d){if(d){for(var c=this.getModelBS(a,!1),g=c.nextSetBit(0);0<=g&&d;g=c.nextSetBit(g+1))d=!this.am[g].hasRasmolHBonds;if(d)return 0}d=!1;for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))if(1==this.at[g].getElementNumber()){d=
!0;break}c=new JU.BS;g=this.vwr.getBoolean(603979853);if(null==b||g&&!d)return JU.Logger.info((null==b?"DSSP/DSSR ":"RasMol")+" pseudo-hbond calculation"),this.calcRasmolHydrogenBonds(a,b,null,!1,2147483647,!1,c),-c.cardinality();JU.Logger.info(d?"Standard Hbond calculation":"Jmol pseudo-hbond calculation");var e=null;if(!d){e=new JU.BS;for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))switch(this.at[g].atomID){case 64:case 4:case 14:case 15:case 16:case 17:e.set(g)}}var h=this.vwr.getFloat(570425361),
k;d?(h>JM.ModelSet.hbondMaxReal&&(h=JM.ModelSet.hbondMaxReal),k=1):k=JM.ModelSet.hbondMinRasmol*JM.ModelSet.hbondMinRasmol;var j=h*h,s=3.141592653589793*this.vwr.getFloat(570425360)/180,m=0,p=0,q=new JU.V3,n=new JU.V3;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var r=null,t=null;b=this.getSelectedAtomIterator(b,!1,!1,!1,!1);for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1)){var u=this.at[g],v=u.getElementNumber(),x=1==v;if(!(x?!d:d||7!=v&&8!=v)){if(x){var v=!1,y=u.bonds;
if(null==y)continue;for(var A=!1,B=0;!A&&B<y.length;B++)A=y[B].getOtherAtom(u).getElementNumber(),A=7==A||8==A;if(!A)continue}else v=e.get(g);for(this.setIteratorForAtom(b,-1,u.i,h,null);b.hasNext();)if(y=this.at[b.next()],B=y.getElementNumber(),!(y===u||(x?1==B:7!=B&&8!=B)||(p=b.foundDistance2())<k||p>j||v&&e.get(y.i)||u.isBonded(y))){if(0<s){q.sub2(u,y);if(null==(t=JM.ModelSet.checkMinAttachedAngle(u,s,q,n,d)))continue;q.scale(-1);if(null==(r=JM.ModelSet.checkMinAttachedAngle(y,s,q,n,d)))continue}B=
0;x&&!Float.isNaN(r.x)&&!Float.isNaN(t.x)?(A=4096,B=JM.HBond.getEnergy(Math.sqrt(p),r.distance(u),r.distance(t),y.distance(t))/1E3):A=2048;c.set(this.addHBond(u,y,A,B));m++}}}b.release();this.sm.setShapeSizeBs(1,-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return d?m:-m},"JU.BS,JU.BS,~B");c$.checkMinAttachedAngle=c(c$,"checkMinAttachedAngle",function(a,b,d,c,g){var e=a.bonds,h=!0,k=null;if(null!=e&&0<e.length)for(var j=3.4028235E38,s=e.length;0<=--s;)if(e[s].isCovalent()){var h=
!1,m=e[s].getOtherAtom(a);if(g||1!=m.getElementNumber()){c.sub2(a,m);var p=c.angle(d);if(p<b)return null;p<j&&(k=m,j=p)}}return h?JU.P3.new3(NaN,0,0):k},"JM.Atom,~N,JU.V3,JU.V3,~B");c(c$,"setStructureIndexes",function(){for(var a,b=0,d=-1,c=-1,g=-1,e=0;e<this.ac;e++){if((c=this.at[e].mi)!=g)b=0,g=c,d=-1;if((a=this.at[e].group.getStrucNo())!=d&&0!=a)this.at[e].group.setStrucNo(++b),d=b}});c(c$,"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$,"getSymmetryInfoAsString",function(){for(var a=(new JU.SB).append("Symmetry Information:"),b=0;b<this.mc;++b){a.append("\nmodel #").append(this.getModelNumberDotted(b)).append("; name=").append(this.getModelName(b)).append("\n");
var d=this.getUnitCell(b);a.append(null==d?"no symmetry information":d.getSymmetryInfoStr())}return a.toString()});c(c$,"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=y(this.modelFileNumbers[this.mc-1]/1E6)+1,c=this.mc,g=0;c<a;c++)this.modelNumbers[c]=c+this.mc,this.modelFileNumbers[c]=1E6*d+ ++g,this.modelNumbersForAtomLabel[c]=this.modelNames[c]=d+"."+g;this.thisStateModel=-1;d=this.getInfoM("group3Lists");null!=d&&(c=this.getInfoM("group3Counts"),d=JU.AU.arrayCopyS(d,a),c=JU.AU.arrayCopyII(c,a),this.msInfo.put("group3Lists",d),this.msInfo.put("group3Counts",c));this.unitCells=JU.AU.arrayCopyObject(this.unitCells,a);for(c=this.mc;c<a;c++)b[c]=(new JM.Model).set(this,
c,-1,null,null,null),b[c].loadState=" model create #"+c+";";this.am=b;this.mc=a},"~N");c(c$,"assignAtom",function(a,b,d,c){this.clearDB(a);null==b&&(b="C");var g=this.at[a],e=new JU.BS,h=1==g.getElementNumber(),e=JU.Elements.elementNumberFromSymbol(b,!0),k=!1;if(0<e)this.setElement(g,e,!c),this.vwr.shm.setShapeSizeBs(0,0,this.vwr.rd,JU.BSUtil.newAndSetBit(a)),this.setAtomName(a,b+g.getAtomNumber(),!c),this.vwr.getBoolean(603979883)&&(this.am[g.mi].isModelKit=!0),this.am[g.mi].isModelKit||this.taintAtom(a,
0);else if(b.equals("Pl"))g.setFormalCharge(g.getFormalCharge()+1);else if(b.equals("Mi"))g.setFormalCharge(g.getFormalCharge()-1);else if(b.equals("X"))k=!0;else if(!b.equals("."))return;c&&(this.removeUnnecessaryBonds(g,k),b=0,1==g.getCovalentBondCount()&&(h?b=1.5:!h&&1==e&&(b=1)),0!=b&&(c=JU.V3.newVsub(g,this.at[g.getBondedAtomIndex(0)]),h=c.length(),c.normalize(),c.scale(b-h),this.setAtomCoordRelative(a,c.x,c.y,c.z)),a=JU.BSUtil.newAndSetBit(a),1!=e&&d&&(this.validateBspf(!1),e=this.getAtomsWithinRadius(1,
a,!1,null),e.andNot(a),0<=e.nextSetBit(0)&&this.vwr.deleteAtoms(e,!1),e=this.vwr.getModelUndeletedAtomsBitSet(g.mi),e.andNot(this.getAtomBitsMDa(1612709900,null,new JU.BS)),this.makeConnections2(0.1,1.8,1,1073741904,a,e,null,!1,!1,0)),this.vwr.addHydrogens(a,!1,!0))},"~N,~S,~B,~B");c(c$,"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].$delete(b);for(d=0;d<this.mc;d++)this.am[d].bsAtomsDeleted.or(a),
this.am[d].bsAtomsDeleted.and(this.am[d].bsAtoms),this.am[d].resetDSSR(!1);this.deleteBonds(b,!1);this.validateBspf(!1)}},"JU.BS");c(c$,"clearDB",function(a){this.getModelAuxiliaryInfo(this.at[a].mi).remove("dbName")},"~N");c(c$,"adjustAtomArrays",function(a,b,d){this.ac=d;for(var c=b;c<d;c++){this.at[c]=this.at[a[c]];this.at[c].i=c;var g=this.am[this.at[c].mi];g.firstAtomIndex==a[c]&&(g.firstAtomIndex=c);g.bsAtoms.set(c)}if(null!=this.vibrations)for(c=b;c<d;c++)this.vibrations[c]=this.vibrations[a[c]];
if(null!=this.atomTensorList)for(c=b;c<d;c++)if(g=this.atomTensorList[c]=this.atomTensorList[a[c]],null!=g)for(var e=g.length;0<=--e;){var h=g[e];null!=h&&(h.atomIndex1=c)}if(null!=this.atomNames)for(c=b;c<d;c++)this.atomNames[c]=this.atomNames[a[c]];if(null!=this.atomTypes)for(c=b;c<d;c++)this.atomTypes[c]=this.atomTypes[a[c]];if(null!=this.atomResnos)for(c=b;c<d;c++)this.atomResnos[c]=this.atomResnos[a[c]];if(null!=this.atomSerials)for(c=b;c<d;c++)this.atomSerials[c]=this.atomSerials[a[c]];if(null!=
this.atomSeqIDs)for(c=b;c<d;c++)this.atomSeqIDs[c]=this.atomSeqIDs[a[c]];if(null!=this.bfactor100s)for(c=b;c<d;c++)this.bfactor100s[c]=this.bfactor100s[a[c]];if(null!=this.occupancies)for(c=b;c<d;c++)this.occupancies[c]=this.occupancies[a[c]];if(null!=this.partialCharges)for(c=b;c<d;c++)this.partialCharges[c]=this.partialCharges[a[c]]},"~A,~N,~N");c(c$,"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.atomResnos&&(this.atomResnos=JU.AU.arrayCopyI(this.atomResnos,a));null!=this.atomSerials&&(this.atomSerials=JU.AU.arrayCopyI(this.atomSerials,a));null!=this.atomSeqIDs&&(this.atomSeqIDs=JU.AU.arrayCopyI(this.atomSeqIDs,a))},"~N");c(c$,"addAtom",function(a,b,d,c,g,e,h,k,j,s,m,p,q,n,r,t,u,v,x){k=(new JM.Atom).setAtom(a,this.ac,j,s,x,k,d,p,u);this.am[a].act++;this.am[a].bsAtoms.set(this.ac);JU.Elements.isElement(d,1)&&this.am[a].hydrogenCount++;this.ac>=this.at.length&&this.growAtomArrays(this.ac+
100);this.at[this.ac]=k;this.setBFactor(this.ac,r,!1);this.setOccupancy(this.ac,n,!1);this.setPartialCharge(this.ac,q,!1);null!=t&&this.setAtomTensors(this.ac,t);k.group=b;k.colixAtom=this.vwr.cm.getColixAtomPalette(k,J.c.PAL.CPK.id);null!=c&&(null!=g&&(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[this.ac]=g),k.atomID=v,0==v&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern()));-2147483648!=e&&(null==this.atomSerials&&(this.atomSerials=
A(this.at.length,0)),this.atomSerials[this.ac]=e);0!=h&&(null==this.atomSeqIDs&&(this.atomSeqIDs=A(this.at.length,0)),this.atomSeqIDs[this.ac]=h);null!=m&&this.setVibrationVector(this.ac,m);this.ac++;return k},"~N,JM.Group,~N,~S,~S,~N,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.Lst,~B,~N,JU.BS");c(c$,"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 b=JU.PT.getQuotedStringAt(b.toString(),
0),JS.ScriptCompiler.unescapeString(b,0,b.length);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$,"setAtomNamesAndNumbers",function(a,b,d){0>b&&(a=this.am[this.at[a].mi].firstAtomIndex);null==this.atomSerials&&(this.atomSerials=A(this.ac,0));null==this.atomNames&&(this.atomNames=Array(this.ac));for(var c=this.isXYZ&&this.vwr.getBoolean(603979978),g=2147483647,e=1;a<this.ac;++a){var h=this.at[a];h.mi!=g&&(g=h.mi,e=c?0:1);if(a>=-b){if(0==this.atomSerials[a]||0>b)this.atomSerials[a]=a<b?d.atomSerials[a]:e;if(null==
this.atomNames[a]||0>b)this.atomNames[a]=(h.getElementSymbol()+this.atomSerials[a]).intern()}(!this.am[g].isModelKit||0<h.getElementNumber()&&!h.isDeleted())&&e++}},"~N,~N,JM.AtomCollection");c(c$,"setUnitCellOffset",function(a,b,d){null!=a&&(null==b?a.setOffset(d):a.setOffsetPt(b))},"J.api.SymmetryInterface,JU.T3,~N");c(c$,"connect",function(a){this.resetMolecules();for(var b=new JU.BS,d=0;d<a.length;d++){var c=a[d];if(!(null==c||2>c.length)){var g=B(c[0]),e=0>g;e&&(g=-1-g);var h=B(c[1]);if(!(0>
h||g>=this.ac||h>=this.ac)){var k=2<c.length?B(c[2]):1;0>k&&(k&=65535);var j=3<c.length?aa(1E3*a[d][3]):this.getDefaultMadFromOrder(k);0==k||0==j&&32768!=k&&!JU.Edge.isOrderH(k)?(c=this.at[g].getBond(this.at[h]),null!=c&&b.set(c.index)):this.bondAtoms(this.at[g],this.at[h],k,j,null,4<c.length?c[4]:0,e,!0)}}}0<=b.nextSetBit(0)&&this.deleteBonds(b,!1)},"~A");c(c$,"setFrameDelayMs",function(a,b){for(var d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.am[this.am[d].trajectoryBaseIndex].frameDelay=a},
"~N,JU.BS");c(c$,"getFrameDelayMs",function(a){return a<this.am.length&&0<=a?this.am[this.am[a].trajectoryBaseIndex].frameDelay:0},"~N");c(c$,"getModelIndexFromId",function(a){var b=0<=a.indexOf("#"),d=a.toLowerCase().endsWith(".basemodel");d&&(a=a.substring(0,a.length-10));for(var c=-1,g=null,e=0;e<this.mc;e++){var h=this.getInfo(e,"modelID"),k=a.startsWith("~")?"~"+this.getModelNumberDotted(e):null;if(!(null==k&&null==h&&null==(h=this.getModelTitle(e)))){b&&(g=this.getModelFileName(e),g.endsWith("#molfile")?
h=g:(g+="#",h=g+h));if(a.equalsIgnoreCase(h)||a.equalsIgnoreCase(k))return d?this.vwr.getJDXBaseModelIndex(e):e;null!=g&&a.startsWith(g)&&(c=-2)}}return null==g&&!b?-2:c},"~S");c(c$,"getAuxiliaryInfo",function(a){var b=this.msInfo;null==b&&(b=new java.util.Hashtable);if(null!=a||!b.containsKey("models")){for(var d=new JU.Lst,c=0;c<this.mc;++c)if(null==a||a.get(c)){var g=this.getModelAuxiliaryInfo(c);g.put("modelIndex",Integer.$valueOf(c));d.addLast(g)}b.put("models",d)}return b},"JU.BS");c(c$,"getDihedralMap",
function(a){for(var b=new JU.Lst,d=a.length,c=null,g=null,e=null,h=null,k=d-1;0<=--k;)for(var j=d;--j>k;)if(c=this.at[a[k]],g=this.at[a[j]],c.isBonded(g))for(var s=d;0<=--s;)if(s!=k&&s!=j&&(e=this.at[a[s]]).isBonded(c))for(var m=d;0<=--m;)if(m!=k&&m!=j&&m!=s&&(h=this.at[a[m]]).isBonded(g)){var p=A(4,0);p[0]=e.i;p[1]=c.i;p[2]=g.i;p[3]=h.i;b.addLast(p)}d=b.size();a=JU.AU.newInt2(d);for(k=d;0<=--k;)a[d-k-1]=b.get(k);return a},"~A");c(c$,"setModulation",function(a,b,d,c){if(null==this.bsModulated)if(b)this.bsModulated=
new JU.BS;else if(null==a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var g=this.vwr.getFloat(1275072532),e=!1,h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){var k=this.getModulation(h);null!=k&&(k.setModTQ(this.at[h],b,d,c,g),null!=this.bsModulated&&this.bsModulated.setBitTo(h,b),e=!0)}e||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(c$,"getBoundBoxOrientation",function(a,b){var d=0,c=0,g=0,e=null,h=null,k=b.nextSetBit(0),j=0;if(0<=k){c=null==this.vOrientations?0:this.vOrientations.length;
if(0==c){e=Array(3375);c=0;j=new JU.P4;for(d=-7;7>=d;d++)for(g=-7;7>=g;g++)for(var s=0;14>=s;s++,c++)1<(e[c]=JU.V3.new3(d/7,g/7,s/14)).length()&&--c;this.vOrientations=Array(c);for(d=c;0<=--d;)s=Math.sqrt(1-e[d].lengthSquared()),Float.isNaN(s)&&(s=0),j.set4(e[d].x,e[d].y,e[d].z,s),this.vOrientations[d]=JU.Quat.newP4(j)}var s=new JU.P3,j=3.4028235E38,m=null,p=new JU.BoxInfo;p.setMargin(1312817669==a?0:0.1);for(d=0;d<c;d++){e=this.vOrientations[d];p.reset();for(g=k;0<=g;g=b.nextSetBit(g+1))p.addBoundBoxPoint(e.transform2(this.at[g],
s));switch(a){default:case 1312817669:case 1073741864:case 1814695966:g=(p.bbCorner1.x-p.bbCorner0.x)*(p.bbCorner1.y-p.bbCorner0.y)*(p.bbCorner1.z-p.bbCorner0.z);break;case 1111492629:g=p.bbCorner1.x-p.bbCorner0.x;break;case 1111492630:g=p.bbCorner1.y-p.bbCorner0.y;break;case 1111492631:g=p.bbCorner1.z-p.bbCorner0.z}g<j&&(h=e,m=p,p=new JU.BoxInfo,p.setMargin(0.1),j=g)}switch(a){default:return h;case 1814695966:k=m.getBoundBoxVertices();k=v(-1,[k[0],k[4],k[2],k[1]]);h=h.inv();for(d=0;4>d;d++)h.transform2(k[d],
k[d]),0<d&&k[d].sub(k[0]);return k;case 1312817669:case 1073741864:e=JU.Quat.newQ(h),d=m.bbCorner1.x-m.bbCorner0.x,c=m.bbCorner1.y-m.bbCorner0.y,g=m.bbCorner1.z-m.bbCorner0.z,d<c&&(s.set(0,0,1),e=JU.Quat.newVA(s,90).mulQ(e),h=d,d=c,c=h),c<g&&(g>d&&(s.set(0,1,0),e=JU.Quat.newVA(s,90).mulQ(e),h=d,d=g,g=h),s.set(1,0,0),e=JU.Quat.newVA(s,90).mulQ(e),h=c,c=g,g=h)}}return 1312817669==a?j+"\t{"+d+" "+c+" "+g+"}\t"+b:1814695966==a?null:null==e||0==e.getTheta()?new JU.Quat:e},"~N,JU.BS");c(c$,"getUnitCellForAtom",
function(a){if(0>a||a>this.ac)return null;if(null!=this.bsModulated){var b=this.getModulation(a),b=null==b?null:b.getSubSystemUnitCell();if(null!=b)return b}return this.getUnitCell(this.at[a].mi)},"~N");c(c$,"clearCache",function(){for(var a=this.mc;0<=--a;)this.am[a].resetDSSR(!1)});c(c$,"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$,"getBsBranches",function(a){for(var b=y(a.length/6),d=Array(b),c=new java.util.Hashtable,g=0,e=0;g<b;g++,e+=6)if(!(1>Math.abs(a[e+5]-a[e+4]))){var h=B(a[e+1]),k=B(a[e+2]),j=""+h+"_"+k;if(!c.containsKey(j)){c.put(j,Boolean.TRUE);for(var j=this.vwr.getBranchBitSet(k,h,!0),s=this.at[h].bonds,h=this.at[h],m=0;m<s.length;m++){var p=s[m];if(p.isCovalent()&&(p=p.getOtherAtom(h).i,p!=k&&j.get(p))){j=null;break}}d[g]=j}}return d},"~A");c(c$,"recalculatePositionDependentQuantities",function(a,b){null!=
this.vwr.shm.getShape(21)&&this.vwr.shm.getShapePropertyData(21,"move",v(-1,[a,b]));this.haveStraightness&&this.calculateStraightnessAll();this.recalculateLeadMidpointsAndWingVectors(-1);for(var d=this.getModelBS(a,!1),c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))if(this.sm.notifyAtomPositionsChanged(c,a,b),null!=b){var g=this.am[c];g.isContainedIn(a)&&(null==g.mat4&&(g.mat4=JU.M4.newM4(null)),g.mat4.mul2(b,g.mat4))}this.averageAtomPoint=null},"JU.BS,JU.M4");c(c$,"moveAtoms",function(a,b,d,c,g,e,h,
k){if(null!=a){for(b=g.nextSetBit(0);0<=b;b=g.nextSetBit(b+1))a.rotTrans(this.at[b]),this.taintAtom(b,2);this.mat4.setM4(a);c=null}else if(!k){null==b?this.matTemp.setM3(d):(this.ptTemp.set(0,0,0),this.matInv.setM3(d),this.matInv.invert(),this.matTemp.mul2(b,d),this.matTemp.mul2(this.matInv,this.matTemp));h?(this.vTemp.setT(e),this.mat4.setIdentity(),this.mat4.setTranslation(this.vTemp),this.mat4t.setToM3(this.matTemp),this.mat4.mul(this.mat4t),this.mat4t.setIdentity(),this.vTemp.scale(-1),this.mat4t.setTranslation(this.vTemp),
this.mat4.mul(this.mat4t)):this.mat4.setToM3(this.matTemp);for(b=g.nextSetBit(0);0<=b;b=g.nextSetBit(b+1))h?this.mat4.rotTrans(this.at[b]):(this.ptTemp.add(this.at[b]),this.mat4.rotTrans(this.at[b]),this.ptTemp.sub(this.at[b])),this.taintAtom(b,2);h||(this.ptTemp.scale(1/g.cardinality()),null==c&&(c=new JU.V3),c.add(this.ptTemp))}if(null!=c){for(b=g.nextSetBit(0);0<=b;b=g.nextSetBit(b+1))this.at[b].add(c),this.taintAtom(b,2);k||(this.mat4t.setIdentity(),this.mat4t.setTranslation(c),this.mat4.mul2(this.mat4t,
this.mat4))}this.recalculatePositionDependentQuantities(g,this.mat4)},"JU.M4,JU.M3,JU.M3,JU.V3,JU.BS,JU.P3,~B,~B");c(c$,"setDihedrals",function(a,b,d){var c=y(a.length/6);1<d&&(d=1);for(var g=0,e=0;g<c;g++,e+=6){var h=b[g];if(!(null==h||h.isEmpty())){var k=this.at[B(a[e+1])],j=JU.V3.newVsub(this.at[B(a[e+2])],k),j=JU.A4.newVA(j,-((a[e+5]-a[e+4])*d)/57.29577951308232);this.matTemp.setAA(j);this.ptTemp.setT(k);for(k=h.nextSetBit(0);0<=k;k=h.nextSetBit(k+1))this.at[k].sub(this.ptTemp),this.matTemp.rotate(this.at[k]),
this.at[k].add(this.ptTemp),this.taintAtom(k,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 1111492626:case 1111492627:case 1111492628:case 1145047055:break;default:this.recalculatePositionDependentQuantities(a,null)}},
"JU.BS,~N,~O");c(c$,"invertSelected",function(a,b,d,c){this.resetChirality();if(null!=a)for(var g=c.nextSetBit(0);0<=g;g=c.nextSetBit(g+1)){var e=2*(a.x-this.at[g].x);d=2*(a.y-this.at[g].y);var h=2*(a.z-this.at[g].z);this.setAtomCoordRelative(g,e,d,h)}else if(null!=b){a=JU.V3.new3(b.x,b.y,b.z);a.normalize();for(var j=Math.sqrt(b.x*b.x+b.y*b.y+b.z*b.z),g=c.nextSetBit(0);0<=g;g=c.nextSetBit(g+1))h=2*-JU.Measure.distanceToPlaneD(b,j,this.at[g]),e=a.x*h,d=a.y*h,h*=a.z,this.setAtomCoordRelative(g,e,d,
h)}else if(0<=d&&(b=this.at[d],a=b.bonds,null!=a)){e=new JU.BS;h=new JU.Lst;j=this.vwr.getModelUndeletedAtomsBitSet(b.mi);for(g=0;g<a.length;g++){var l=a[g].getOtherAtom(b);c.get(l.i)?e.or(JU.JmolMolecule.getBranchBitSet(this.at,l.i,j,null,d,!0,!0)):h.addLast(l)}0!=h.size()&&(a=JU.Measure.getCenterAndPoints(h)[0],c=JU.V3.newVsub(b,a),c=JU.Quat.newVA(c,180),this.moveAtoms(null,null,c.getMatrix(),null,e,b,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS");c(c$,"getCellWeights",function(a){var b=null,d=a.nextSetBit(0),
c=-1;if(0<=d&&null!=this.getUnitCell(c=this.at[d].mi)){var g=new JU.P3;this.getModelAtomBitSetIncludingDeleted(c,!0).and(a);b=I(a.cardinality(),0);for(c=0;0<=d;d=a.nextSetBit(d+1))b[c++]=JU.SimpleUnitCell.getCellWeight(this.at[d].getFractionalUnitCoordPt(!0,!1,g))}return b},"JU.BS");c(c$,"getAtomGroupQuaternions",function(a,b,d){var c=0,g=new JU.Lst;a=JU.BSUtil.copy(a);for(var e=new JU.BS,h=a.nextSetBit(0);0<=h&&c<b;h=a.nextSetBit(h+1)){var j=this.at[h].group;j.setAtomBits(e);a.andNot(e);var l=j.getQuaternion(d);
if(null==l&&(this.am[this.at[h].mi].isBioModel||(l=j.getQuaternionFrame(this.at)),null==l))continue;c++;g.addLast(l)}return g.toArray(Array(g.size()))},"JU.BS,~N,~S");c(c$,"getConformation",function(a,b,d,c){var g=new JU.BS;if(0<=b)for(var e=this.mc;0<=--e;)if(!(e!=a&&0<=a)){var h=this.am[e],j=this.vwr.getModelUndeletedAtomsBitSet(a);null!=c&&j.and(c);if(!(0>j.nextSetBit(0)))if(b>=h.altLocCount)0==b&&g.or(j);else if(!this.am[e].isBioModel||!this.am[e].getConformation(b,d,j,g)){for(var l=this.getAltLocCountInModel(e),
h=this.getAltLocListInModel(e),s=new JU.BS;0<=--l;)l!=b&&j.andNot(this.getAtomBitsMDa(1073742355,h.substring(l,l+1),s));0<=j.nextSetBit(0)&&g.or(j)}}return g},"~N,~N,~B,JU.BS");c(c$,"getSequenceBits",function(a,b,d){return this.haveBioModels?this.bioModelset.getAllSequenceBits(a,b,d):d},"~S,JU.BS,JU.BS");c(c$,"getBioPolymerCountInModel",function(a){return this.haveBioModels?this.bioModelset.getBioPolymerCountInModel(a):0},"~N");c(c$,"getPolymerPointsAndVectors",function(a,b,d,c){this.haveBioModels&&
this.bioModelset.getAllPolymerPointsAndVectors(a,b,d,c)},"JU.BS,JU.Lst,~B,~N");c(c$,"recalculateLeadMidpointsAndWingVectors",function(a){this.haveBioModels&&this.bioModelset.recalculatePoints(a)},"~N");c(c$,"calcRasmolHydrogenBonds",function(a,b,d,c,g,e,h){this.haveBioModels&&this.bioModelset.calcAllRasmolHydrogenBonds(a,b,d,c,g,e,h,2)},"JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS");c(c$,"calculateStraightnessAll",function(){this.haveBioModels&&!this.haveStraightness&&this.bioModelset.calculateStraightnessAll()});
c(c$,"calculateStruts",function(a,b){return this.haveBioModels?this.bioModelset.calculateStruts(a,b):0},"JU.BS,JU.BS");c(c$,"getGroupsWithin",function(a,b){return this.haveBioModels?this.bioModelset.getGroupsWithinAll(a,b):new JU.BS},"~N,JU.BS");c(c$,"getProteinStructureState",function(a,b){return this.haveBioModels?this.bioModelset.getFullProteinStructureState(a,b):""},"JU.BS,~N");c(c$,"calculateStructures",function(a,b,d,c,g,e){return this.haveBioModels?this.bioModelset.calculateAllStuctures(a,
b,d,c,g,e):""},"JU.BS,~B,~B,~B,~B,~N");c(c$,"calculateStructuresAllExcept",function(a,b,d,c,g,e,h){this.freezeModels();return this.haveBioModels?this.bioModelset.calculateAllStructuresExcept(a,b,d,c,g,e,h):""},"JU.BS,~B,~B,~B,~B,~B,~N");c(c$,"recalculatePolymers",function(a){this.bioModelset.recalculateAllPolymers(a,this.getGroups())},"JU.BS");c(c$,"calculatePolymers",function(a,b,d,c){null!=this.bioModelset&&this.bioModelset.calculateAllPolymers(a,b,d,c)},"~A,~N,~N,JU.BS");c(c$,"calcSelectedMonomersCount",
function(){this.haveBioModels&&this.bioModelset.calcSelectedMonomersCount()});c(c$,"setProteinType",function(a,b){this.haveBioModels&&this.bioModelset.setAllProteinType(a,b)},"JU.BS,J.c.STR");c(c$,"setStructureList",function(a){this.haveBioModels&&this.bioModelset.setAllStructureList(a)},"java.util.Map");c(c$,"setConformation",function(a){this.haveBioModels&&this.bioModelset.setAllConformation(a);return a},"JU.BS");c(c$,"getHeteroList",function(a){a=this.haveBioModels?this.bioModelset.getAllHeteroList(a):
null;return null==a?this.getInfoM("hetNames"):a},"~N");c(c$,"getUnitCellPointsWithin",function(a,b,d,c){var g=new JU.Lst,e=null,h=null;c&&(e=new java.util.Hashtable,h=new JU.Lst,e.put("atoms",h),e.put("points",g));var j=null==b?-1:b.nextSetBit(0);b=this.vwr.getModelUndeletedAtomsBitSet(0>j?this.vwr.am.cmi:this.at[j].mi);0>j&&(j=b.nextSetBit(0));if(0<=j){var l=this.getUnitCellForAtom(j);if(null!=l){b=l.getIterator(this.vwr,this.at[j],this.at,b,a);for(null!=d&&b.setCenter(d,a);b.hasNext();)j=b.next(),
d=b.getPosition(),g.addLast(d),c&&h.addLast(Integer.$valueOf(j))}}return c?e:g},"~N,JU.BS,JU.P3,~B");c(c$,"calculateDssrProperty",function(a){if(null!=a){if(null==this.dssrData||this.dssrData.length<this.ac)this.dssrData=I(this.ac,0);for(var b=0;b<this.ac;b++)this.dssrData[b]=NaN;for(b=this.mc;0<=--b;)this.am[b].isBioModel&&this.am[b].getAtomicDSSRData(this.dssrData,a)}},"~S");c(c$,"getAtomicDSSRData",function(a){return null==this.dssrData||this.dssrData.length<=a?NaN:this.dssrData[a]},"~N");c(c$,
"getAtomCIPChiralityCode",function(a){this.haveChirality=!0;var b=this.am[a.mi];b.hasChirality||(this.calculateChiralityForAtoms(b.bsAtoms,!1),b.hasChirality=!0);return a.getCIPChiralityCode()},"JM.Atom");c(c$,"calculateChiralityForAtoms",function(a,b){this.haveChirality=!0;for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.at[d].setCIPChirality(0);J.api.Interface.getSymmetry(this.vwr,"ms").calculateCIPChiralityForAtoms(this.vwr,a);if(!b)return null;for(var c="",d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+
1))c+=this.at[d].getCIPChirality(!1);return c},"JU.BS,~B");F(c$,"hbondMinRasmol",2.5,"hbondMaxReal",3.5,"hbondHCMaxReal",3.2)});u("JM");x(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){c$=r(function(){this.rotationMatrix=this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=null;this.cameraY=this.cameraX=this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.vwr=this.pymolView=this.moveToText=
null;n(this,arguments)},JM,"Orientation");O(c$,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});t(c$,function(a,b,d){this.vwr=a;null!=d?(this.pymolView=d,this.moveToText="moveTo -1.0 PyMOL "+JU.Escape.eAF(d)):(a.finalizeTransformParameters(),b?(b=a.ms.getInfoM("defaultOrientationMatrix"),null==b?this.rotationMatrix.setScale(1):this.rotationMatrix.setM3(b)):a.tm.getRotation(this.rotationMatrix),this.xTrans=a.tm.getTranslationXPercent(),this.yTrans=a.tm.getTranslationYPercent(),
this.zoom=a.tm.getZoomSetting(),this.center.setT(a.tm.fixedRotationCenter),this.windowCenteredFlag=a.tm.isWindowCentered(),this.rotationRadius=a.getFloat(570425388),this.navigationMode=a.getBoolean(603979889),this.moveToText=a.tm.getMoveToText(-1,!1),this.navigationMode&&(this.xNav=a.tm.getNavigationOffsetPercent("X"),this.yNav=a.tm.getNavigationOffsetPercent("Y"),this.navDepth=a.tm.navigationDepthPercent,this.navCenter=JU.P3.newP(a.tm.navigationCenter)),0!=a.tm.camera.z&&(this.cameraDepth=a.tm.getCameraDepth(),
this.cameraX=a.tm.camera.x,this.cameraY=a.tm.camera.y))},"JV.Viewer,~B,~A");c(c$,"getMoveToText",function(a){return a?"   "+this.moveToText+"\n  save orientation "+JU.PT.esc(this.saveName.substring(12))+";\n":this.moveToText},"~B");c(c$,"restore",function(a,b){b?(this.vwr.setBooleanProperty("windowCentered",this.windowCenteredFlag),this.vwr.setBooleanProperty("navigationMode",this.navigationMode),null==this.pymolView?this.vwr.moveTo(this.vwr.eval,a,this.center,null,NaN,this.rotationMatrix,this.zoom,
this.xTrans,this.yTrans,this.rotationRadius,this.navCenter,this.xNav,this.yNav,this.navDepth,this.cameraDepth,this.cameraX,this.cameraY):this.vwr.tm.moveToPyMOL(this.vwr.eval,a,this.pymolView)):this.vwr.tm.setRotation(this.rotationMatrix);return!0},"~N,~B")});u("JM");x(null,"JM.StateScript",["JU.SB","JU.BSUtil","$.Escape"],function(){c$=r(function(){this.modelIndex=0;this.script2=this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;n(this,arguments)},JM,"StateScript");
t(c$,function(a,b,d,c,g,e,h){this.modelIndex=a;this.script1=b;this.bsBonds=JU.BSUtil.copy(d);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(g);this.script2=e;this.inDefinedStateBlock=h},"~N,~S,JU.BS,JU.BS,JU.BS,~S,~B");c(c$,"isValid",function(){return null!=this.script1&&0<this.script1.length&&(null==this.bsBonds||0<=this.bsBonds.nextSetBit(0))&&(null==this.bsAtoms1||0<=this.bsAtoms1.nextSetBit(0))&&(null==this.bsAtoms2||0<=this.bsAtoms2.nextSetBit(0))});j(c$,"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$,"setModelIndex",function(a){this.modelIndex=a},"~N")});u("JM");N(JM,"Structure");u("JM");c$=r(function(){this.id="";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=0;this.signFactor=1;this.reference=null;n(this,arguments)},JM,"TickInfo");t(c$,function(a){this.ticks=a},"JU.P3");u("JU");x(["JU.P3","$.V3"],"JU.BoxInfo",
["JU.Point3fi"],function(){c$=r(function(){this.bbVertices=this.bbVector=this.bbCenter=this.bbCorner1=this.bbCorner0=null;this.isScaleSet=!1;this.margin=0;n(this,arguments)},JU,"BoxInfo");O(c$,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=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])});t(c$,
function(){for(var a=8;0<=--a;)this.bbVertices[a]=new JU.Point3fi;this.reset()});c(c$,"reset",function(){this.isScaleSet=!1;this.bbCorner0.set(3.4028235E38,3.4028235E38,3.4028235E38);this.bbCorner1.set(-3.4028235E38,-3.4028235E38,-3.4028235E38)});c$.scaleBox=c(c$,"scaleBox",function(a,b){if(!(0==b||1==b)){for(var d=new JU.P3,c=new JU.V3,g=0;8>g;g++)d.add(a[g]);d.scale(0.125);for(g=0;8>g;g++)c.sub2(a[g],d),c.scale(b),a[g].add2(d,c)}},"~A,~N");c$.getVerticesFromOABC=c(c$,"getVerticesFromOABC",function(a){for(var b=
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F(c$,"toRadians",0.017453292,"INFO_DIMENSIONS",6,"INFO_GAMMA",5,"INFO_BETA",4,"INFO_ALPHA",3,"INFO_C",2,"INFO_B",1,"INFO_A",0,"SLOP",0.02,"SLOP1",0.98)});u("JU");x(null,"JU.TempArray",["java.lang.Boolean","$.Float","JU.P3","$.P3i"],function(){c$=r(function(){this.freeEnum=this.lengthsFreeEnum=this.freeScreens=this.lengthsFreeScreens=this.freePoints=this.lengthsFreePoints=null;n(this,arguments)},JU,"TempArray");O(c$,function(){this.lengthsFreePoints=A(6,0);this.freePoints=Array(6);this.lengthsFreeScreens=
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JV.ActionManager.newAction(16,"_navTranslate",J.i18n.GT.o(J.i18n.GT.$("translate navigation point (requires {0} and {1})"),v(-1,["set NAVIGATIONMODE","set picking NAVIGATE"]))),JV.ActionManager.newAction(17,"_pickAtom",J.i18n.GT.$("pick an atom")),JV.ActionManager.newAction(3,"_pickConnect",J.i18n.GT.o(J.i18n.GT.$("connect atoms (requires {0})"),"set picking CONNECT")),JV.ActionManager.newAction(18,"_pickIsosurface",J.i18n.GT.o(J.i18n.GT.$("pick an ISOSURFACE point (requires {0}"),"set DRAWPICKING")),
JV.ActionManager.newAction(19,"_pickLabel",J.i18n.GT.o(J.i18n.GT.$("pick a label to toggle it hidden/displayed (requires {0})"),"set picking LABEL")),JV.ActionManager.newAction(20,"_pickMeasure",J.i18n.GT.o(J.i18n.GT.$("pick an atom to include it in a measurement (after starting a measurement or after {0})"),"set picking DISTANCE/ANGLE/TORSION")),JV.ActionManager.newAction(21,"_pickNavigate",J.i18n.GT.o(J.i18n.GT.$("pick a point or atom to navigate to (requires {0})"),"set NAVIGATIONMODE")),JV.ActionManager.newAction(22,
"_pickPoint",J.i18n.GT.o(J.i18n.GT.$("pick a DRAW point (for measurements) (requires {0}"),"set DRAWPICKING")),JV.ActionManager.newAction(23,"_popupMenu",J.i18n.GT.$("pop up the full context menu")),JV.ActionManager.newAction(24,"_reset",J.i18n.GT.$("reset (when clicked off the model)")),JV.ActionManager.newAction(25,"_rotate",J.i18n.GT.$("rotate")),JV.ActionManager.newAction(26,"_rotateBranch",J.i18n.GT.o(J.i18n.GT.$("rotate branch around bond (requires {0})"),"set picking ROTATEBOND")),JV.ActionManager.newAction(27,
"_rotateSelected",J.i18n.GT.o(J.i18n.GT.$("rotate selected atoms (requires {0})"),"set DRAGSELECTED")),JV.ActionManager.newAction(28,"_rotateZ",J.i18n.GT.$("rotate Z")),JV.ActionManager.newAction(29,"_rotateZorZoom",J.i18n.GT.$("rotate Z (horizontal motion of mouse) or zoom (vertical motion of mouse)")),JV.ActionManager.newAction(30,"_select",J.i18n.GT.o(J.i18n.GT.$("select an atom (requires {0})"),"set pickingStyle EXTENDEDSELECT")),JV.ActionManager.newAction(31,"_selectAndDrag",J.i18n.GT.o(J.i18n.GT.$("select and drag atoms (requires {0})"),
"set DRAGSELECTED")),JV.ActionManager.newAction(32,"_selectAndNot",J.i18n.GT.o(J.i18n.GT.$("unselect this group of atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT")),JV.ActionManager.newAction(33,"_selectNone",J.i18n.GT.o(J.i18n.GT.$("select NONE (requires {0})"),"set pickingStyle EXTENDEDSELECT")),JV.ActionManager.newAction(34,"_selectOr",J.i18n.GT.o(J.i18n.GT.$("add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT")),JV.ActionManager.newAction(35,
"_selectToggle",J.i18n.GT.o(J.i18n.GT.$("toggle selection (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT/RASMOL")),JV.ActionManager.newAction(36,"_selectToggleOr",J.i18n.GT.o(J.i18n.GT.$("if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG")),JV.ActionManager.newAction(37,"_setMeasure",J.i18n.GT.$("pick an atom to initiate or conclude a measurement")),JV.ActionManager.newAction(38,"_slab",J.i18n.GT.o(J.i18n.GT.$("adjust slab (front plane; requires {0})"),
"SLAB ON")),JV.ActionManager.newAction(39,"_slabAndDepth",J.i18n.GT.o(J.i18n.GT.$("move slab/depth window (both planes; requires {0})"),"SLAB ON")),JV.ActionManager.newAction(40,"_slideZoom",J.i18n.GT.$("zoom (along right edge of window)")),JV.ActionManager.newAction(41,"_spinDrawObjectCCW",J.i18n.GT.o(J.i18n.GT.$("click on two points to spin around axis counterclockwise (requires {0})"),"set picking SPIN")),JV.ActionManager.newAction(42,"_spinDrawObjectCW",J.i18n.GT.o(J.i18n.GT.$("click on two points to spin around axis clockwise (requires {0})"),
"set picking SPIN")),JV.ActionManager.newAction(43,"_stopMotion",J.i18n.GT.o(J.i18n.GT.$("stop motion (requires {0})"),"set waitForMoveTo FALSE")),JV.ActionManager.newAction(44,"_swipe",J.i18n.GT.$("spin model (swipe and release button and stop motion simultaneously)")),JV.ActionManager.newAction(45,"_translate",J.i18n.GT.$("translate")),JV.ActionManager.newAction(46,"_wheelZoom",J.i18n.GT.$("zoom")))});c$.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$,"setBinding",function(a){this.b=a},"JV.binding.Binding");c(c$,"bnd",function(a,b){for(var d=b.length;0<=--d;)if(this.b.isBound(a,b[d]))return!0;
return!1},"~N,~A");c(c$,"isDrawOrLabelAction",function(a){return this.drawMode&&this.bnd(a,[8,9])||this.labelMode&&this.bnd(a,[10])},"~N");c$.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(this.vwr,"Pfaat"):this.pfaatBinding);break;case 3:this.b.name.equals("drag")||
this.setBinding(null==this.dragBinding?this.dragBinding=JV.binding.Binding.newBinding(this.vwr,"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(this.vwr,"Rasmol"):this.rasmolBinding);break;default:this.b!==this.jmolBinding&&this.setBinding(this.jmolBinding)}this.b.name.equals("drag")||(this.predragBinding=this.b)},"~N");c(c$,"setGestureSwipeFactor",
function(a){this.gestureSwipeFactor=a},"~N");c(c$,"setMouseDragFactor",function(a){this.mouseDragFactor=a},"~N");c(c$,"setMouseWheelFactor",function(a){this.mouseWheelFactor=a},"~N");c(c$,"setCurrent",function(a,b,d,c){this.vwr.hoverOff();this.current.set(a,b,d,c)},"~N,~N,~N,~N");c(c$,"getCurrentX",function(){return this.current.x});c(c$,"getCurrentY",function(){return this.current.y});c(c$,"setMouseMode",function(){this.drawMode=this.labelMode=!1;this.dragSelectedMode=this.vwr.getDragSelected();
this.measuresEnabled=!this.dragSelectedMode;if(!this.dragSelectedMode)switch(this.apm){default:return;case 32:this.measuresEnabled=!this.isPickAtomAssignCharge;return;case 4:this.drawMode=!0;this.measuresEnabled=!1;break;case 2:this.labelMode=!0;this.measuresEnabled=!1;break;case 9:this.measuresEnabled=!1;break;case 19:case 22:case 20:case 21:this.measuresEnabled=!1;return}this.exitMeasurementMode(null)});c(c$,"clearMouseInfo",function(){this.pressedCount=this.clickedCount=0;this.dragGesture.setAction(0,
0);this.exitMeasurementMode(null)});c(c$,"setDragAtomIndex",function(a){this.dragAtomIndex=a;this.setAtomsPicked(JU.BSUtil.newAndSetBit(a),"Label picked for atomIndex = "+a)},"~N");c(c$,"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(!E(b,Exception))throw b;}},"~B");c(c$,"setModeMouse",function(a){-1==a&&this.startHoverWatcher(!1)},"~N");
j(c$,"keyPressed",function(a,b){if(this.keyProcessing)return!1;this.vwr.hoverOff();this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&this.isAltKeyReleased&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1);this.isAltKeyReleased=!1;this.moved.modifiers|=8;break;case 16:this.dragged.modifiers|=1;this.moved.modifiers|=1;break;case 17:this.moved.modifiers|=2;break;case 27:this.exitMeasurementMode("escape")}var d=8464|this.moved.modifiers;!this.labelMode&&
!this.b.isUserAction(d)&&this.checkMotionRotateZoom(d,this.current.x,0,0,!1);if(this.vwr.getBoolean(603979889))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");j(c$,"keyReleased",function(a){switch(a){case 18:this.dragSelectedMode&&this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1);this.isAltKeyReleased=!0;this.moved.modifiers&=-9;break;case 16:this.moved.modifiers&=-2;break;case 17:this.moved.modifiers&=
-3}0==this.moved.modifiers&&this.vwr.setCursor(0);if(this.vwr.getBoolean(603979889))switch(a){case 38:case 40:case 37:case 39:this.vwr.navigate(0,0)}},"~N");j(c$,"mouseEnterExit",function(a,b,d,c){this.vwr.tm.stereoDoubleDTI&&(b<<=1);this.setCurrent(a,b,d,0);c&&this.exitMeasurementMode("mouseExit")},"~N,~N,~N,~B");c(c$,"setMouseActions",function(a,b,d){this.pressAction=JV.binding.Binding.getMouseAction(a,b,d?5:4);this.dragAction=JV.binding.Binding.getMouseAction(a,b,1);this.clickAction=JV.binding.Binding.getMouseAction(a,
b,2)},"~N,~N,~B");j(c$,"mouseAction",function(a,b,d,c,g,e){if(this.vwr.getMouseEnabled())switch(JU.Logger.debuggingHigh&&(0!=a&&this.vwr.getBoolean(603979960))&&this.vwr.showString("mouse action: "+a+" "+e+" "+JV.binding.Binding.getMouseActionName(JV.binding.Binding.getMouseAction(g,e,a),!1),!1),this.vwr.tm.stereoDoubleDTI&&(d<<=1),a){case 0:this.setCurrent(b,d,c,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(d,c,b,0);break}if(this.isZoomArea(d)){this.checkMotionRotateZoom(this.LEFT_DRAGGED,0,0,0,!1);break}8==this.vwr.currentCursor&&this.vwr.setCursor(0);break;case 4:this.setMouseMode();this.pressedCount=this.pressed.check(20,d,c,e,b,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.vwr.checkInMotion(1),this.setCurrent(b,d,c,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(d,c,b);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,e,!1);a=d-this.dragged.x;g=c-this.dragged.y;this.setCurrent(b,d,c,e);this.dragged.setCurrent(this.current,-1);this.dragGesture.add(this.dragAction,d,c,b);this.checkDragWheelAction(this.dragAction,d,c,a,g,b,1);break;case 5:this.setMouseActions(this.pressedCount,e,!0);this.setCurrent(b,d,c,e);this.vwr.spinXYBy(0,0,0);e=!this.pressed.check(this.xyRange,
d,c,e,b,9223372036854775E3);this.checkReleaseAction(d,c,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,c,b,3);break;case 2:this.setMouseMode();this.clickedCount=1<g?g:this.clicked.check(0,0,0,e,b,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(b,d,c,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(d,c,b,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(c$,"checkPressedAction",function(a,b,d){var c=JV.binding.Binding.getButtonMods(this.pressAction),g=this.bnd(JV.binding.Binding.getMouseAction(1,c,4),[31]);if(0!=c){this.pressAction=this.vwr.notifyMouseClicked(a,b,this.pressAction,4);if(0==
this.pressAction)return;c=JV.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,c,!1);JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));if(!this.isDrawOrLabelAction(this.dragAction)||!this.vwr.checkObjectDragged(-2147483648,0,a,b,this.dragAction)){this.checkUserAction(this.pressAction,a,b,0,0,d,4);d=!1;switch(this.apm){case 32:d=this.bnd(this.clickAction,[0]);break;case 28:d=this.bnd(this.dragAction,
[7,14]);break;case 26:case 36:case 27:d=this.bnd(this.dragAction,[7,14,27]);break;case 29:d=this.bnd(this.dragAction,[11,14]);break;case 30:d=this.bnd(this.dragAction,[11,14,27])}if(d){if(this.dragAtomIndex=this.vwr.findNearestAtomIndexMovable(a,b,!0),0<=this.dragAtomIndex&&(32==this.apm||31==this.apm)&&this.vwr.ms.isAtomAssignable(this.dragAtomIndex))this.enterMeasurementMode(this.dragAtomIndex),this.mp.addPoint(this.dragAtomIndex,null,!1)}else this.bnd(this.pressAction,[23])?(g="j",this.vwr.getBoolean(603979883)&&
(g=this.vwr.checkObjectClicked(a,b,this.LEFT_CLICKED),g=null!=g&&"bond".equals(g.get("type"))?"b":0<=this.vwr.findNearestAtomIndex(a,b)?"a":"m"),this.vwr.popupMenu(a,b,g)):this.dragSelectedMode?(this.haveSelection=!g||0<=this.vwr.findNearestAtomIndexMovable(a,b,!0))&&this.bnd(this.dragAction,[13,14])&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(c$,"checkDragWheelAction",function(a,b,d,c,g,
e,h){var j=JV.binding.Binding.getButtonMods(a);if(0!=j){j=this.vwr.notifyMouseClicked(b,d,JV.binding.Binding.getMouseAction(this.pressedCount,j,h),h);if(0==j)return;0<j&&(a=j)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.vwr.refresh(3,"rubberBand selection");else if(!this.checkUserAction(a,b,d,c,g,e,h)){if(0<=this.vwr.getRotateBondIndex()){if(this.bnd(a,[26])){this.vwr.moveSelected(c,g,-2147483648,b,d,null,!1,!1);return}this.bnd(a,[25])||this.vwr.setRotateBondIndex(-1)}e=null;if(0<=
this.dragAtomIndex&&2!=this.apm)switch(this.apm){case 26:this.dragSelected(a,c,g,!0);return;case 36:case 27:case 30:e=this.vwr.ms.getAtoms(1094713360,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(c,!0),this.getDegrees(g,!1),e);else{switch(this.apm){case 36:case 27:case 30:this.vwr.select(e,
!1,0,!0)}this.vwr.moveAtomWithHydrogens(this.dragAtomIndex,c,g,this.bnd(a,[14])?-g:-2147483648,e)}return}if(0<=this.dragAtomIndex&&1==h&&this.bnd(this.clickAction,[0])&&32==this.apm)a=this.vwr.findNearestAtomIndexMovable(b,d,!1),0<=a?(null!=this.mp?this.mp.setCount(1):this.measuresEnabled&&this.enterMeasurementMode(a),this.addToMeasurement(a,null,!0),this.mp.colix=20):null!=this.mp&&(this.mp.setCount(1),this.mp.colix=23),null!=this.mp&&(this.mp.traceX=b,this.mp.traceY=d,this.vwr.refresh(3,"assignNew"));
else if(!this.drawMode&&!this.labelMode&&this.bnd(a,[45]))this.vwr.translateXYBy(c,g);else if(this.dragSelectedMode&&this.haveSelection&&this.bnd(a,[13,27]))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.dragSelected(a,c,g,!1));else{if(this.isDrawOrLabelAction(a)&&(this.setMotion(13,!0),this.vwr.checkObjectDragged(this.dragged.x,this.dragged.y,b,d,
a)))return;if(this.checkMotionRotateZoom(a,b,c,g,!0))this.vwr.tm.slabEnabled&&this.bnd(a,[39])?this.vwr.slabDepthByPixels(g):this.vwr.zoomBy(g);else if(this.bnd(a,[25]))this.vwr.rotateXYBy(this.getDegrees(c,!0),this.getDegrees(g,!1));else if(this.bnd(a,[29]))0==c&&1<Math.abs(g)?(this.setMotion(8,!0),this.vwr.zoomBy(g+(0<g?-1:1))):0==g&&1<Math.abs(c)&&(this.setMotion(13,!0),this.vwr.rotateZBy(-c+(0<c?1:-1),2147483647,2147483647));else{if(this.vwr.tm.slabEnabled){if(this.bnd(a,[6])){this.vwr.depthByPixels(g);
return}if(this.bnd(a,[38])){this.vwr.slabByPixels(g);return}if(this.bnd(a,[39])){this.vwr.slabDepthByPixels(g);return}}this.bnd(a,[46])?this.zoomByFactor(g,2147483647,2147483647):this.bnd(a,[28])&&(this.setMotion(13,!0),this.vwr.rotateZBy(-c,2147483647,2147483647))}}}},"~N,~N,~N,~N,~N,~N,~N");c(c$,"dragSelected",function(a,b,d,c){this.setMotion(13,!0);this.bnd(a,[27])&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(b,!0),this.getDegrees(d,!1),null):this.vwr.moveSelected(b,
d,c&&this.bnd(a,[14])?-d:-2147483648,-2147483648,-2147483648,null,!0,!1)},"~N,~N,~N,~B");c(c$,"checkReleaseAction",function(a,b,d,c){JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));this.vwr.checkInMotion(0);this.vwr.setInMotion(!1);this.vwr.setCursor(0);this.dragGesture.add(this.dragAction,a,b,d);c&&this.vwr.setRotateBondIndex(-2147483648);0<=this.dragAtomIndex&&(29==this.apm||30==this.apm)&&this.minimize(!0);if(32==
this.apm&&this.bnd(this.clickAction,[0]))null==this.mp||0>this.dragAtomIndex||this.assignNew(a,b);else if(this.dragAtomIndex=-1,this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=this.b.name.equals("drag"),this.rectRubber.x=2147483647,c&&this.vwr.notifyMouseClicked(a,b,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.isDrawOrLabelAction(this.dragAction))this.vwr.checkObjectDragged(2147483647,0,a,b,this.dragAction);else if(this.haveSelection&&
(this.dragSelectedMode&&this.bnd(this.dragAction,[13]))&&this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1),(!c||!this.checkUserAction(this.pressAction,a,b,0,0,d,5))&&this.vwr.getBoolean(603979780)&&this.bnd(this.dragAction,[44]))a=this.getExitRate(),0<a&&this.vwr.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.vwr.g.logGestures&&this.vwr.log("$NOW$ swipe "+this.dragGesture+" "+a)},"~N,~N,~N,~B");c(c$,"checkClickAction",
function(a,b,d,c){if(0<c){if(this.checkUserAction(this.clickAction,a,b,0,0,d,32768))return;this.clickAction=this.vwr.notifyMouseClicked(a,b,this.clickAction,32768);if(0==this.clickAction)return}JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.clickAction,!1));if(this.bnd(this.clickAction,[2])){if(this.vwr.frankClicked(a,b)){this.vwr.popupMenu(-a,b,"j");return}if(this.vwr.frankClickedModelKit(a,b)){this.vwr.popupMenu(0,0,"m");return}}d=
null;var g=!1,e=!1,h=null;if(!this.drawMode&&(h=this.vwr.checkObjectClicked(a,b,this.clickAction),null!=h)){if(this.labelMode){this.pickLabel(h.get("atomIndex").intValue());return}g="bond".equals(h.get("type"));e="isosurface".equals(h.get("type"));d=this.getPoint(h)}g&&(c=1);if(!(null!=d&&Float.isNaN(d.x))){var j=this.findNearestAtom(a,b,d,0<c);if(0==c&&32!=this.apm)null!=this.mp&&((null!=d||0==this.mp.getIndexOf(j))&&this.mp.addPoint(j,d,!1),this.mp.haveModified&&this.vwr.setPendingMeasurement(this.mp),
this.vwr.refresh(3,"measurementPending"));else if(this.setMouseMode(),this.bnd(this.clickAction,[43])&&this.vwr.tm.stopMotion(),this.vwr.getBoolean(603979889)&&23==this.apm&&this.bnd(this.clickAction,[21]))this.vwr.navTranslatePercent(100*a/this.vwr.getScreenWidth()-50,100*b/this.vwr.getScreenHeight()-50);else{if(g){if(this.bnd(this.clickAction,[34==this.bondPickingMode||33==this.bondPickingMode?0:5])){this.bondPicked(h.get("index").intValue());return}}else{if(e)return;if(32!=this.apm&&null!=this.mp&&
this.bnd(this.clickAction,[20])){this.atomOrPointPicked(j,d);4==this.addToMeasurement(j,d,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,[37])){null!=this.mp?(this.addToMeasurement(j,d,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(j),this.addToMeasurement(j,d,!0));this.atomOrPointPicked(j,d);return}}this.isSelectAction(this.clickAction)?e||this.atomOrPointPicked(j,d):this.bnd(this.clickAction,
[24])&&0>j&&this.reset()}}},"~N,~N,~N,~N");c(c$,"pickLabel",function(a){var b=this.vwr.ms.at[a].atomPropertyString(this.vwr,1825200146);2==this.pressedCount?(b=this.vwr.apiPlatform.prompt("Set label for atomIndex="+a,b,null,!1),null!=b&&(this.vwr.shm.setAtomLabel(b,a),this.vwr.refresh(1,"label atom"))):this.setAtomsPicked(JU.BSUtil.newAndSetBit(a),"Label picked for atomIndex = "+a+": "+b)},"~N");c(c$,"checkUserAction",function(a,b,d,c,g,e,h){if(!this.b.isUserAction(a))return!1;for(var j=!1,l,s=this.b.getBindings(),
m=a+"\t",p,q=s.keySet().iterator();q.hasNext()&&((p=q.next())||1);)if(0==p.indexOf(m)&&JU.AU.isAS(l=s.get(p))){var n=l[1],r=null;if(0<=n.indexOf("_ATOM")){var t=this.findNearestAtom(b,d,null,!0),n=JU.PT.rep(n,"_ATOM","({"+(0<=t?""+t:"")+"})");0<=t&&(n=JU.PT.rep(n,"_POINT",JU.Escape.eP(this.vwr.ms.at[t])))}if(!this.drawMode&&(0<=n.indexOf("_POINT")||0<=n.indexOf("_OBJECT")||0<=n.indexOf("_BOND"))){t=this.vwr.checkObjectClicked(b,d,a);if(null!=t&&null!=(r=t.get("pt")))t.get("type").equals("bond")&&
(n=JU.PT.rep(n,"_BOND","[{"+t.get("index")+"}]")),n=JU.PT.rep(n,"_POINT",JU.Escape.eP(r)),n=JU.PT.rep(n,"_OBJECT",JU.Escape.escapeMap(t));n=JU.PT.rep(n,"_BOND","[{}]");n=JU.PT.rep(n,"_OBJECT","{}")}n=JU.PT.rep(n,"_POINT","{}");n=JU.PT.rep(n,"_ACTION",""+a);n=JU.PT.rep(n,"_X",""+b);n=JU.PT.rep(n,"_Y",""+(this.vwr.getScreenHeight()-d));n=JU.PT.rep(n,"_DELTAX",""+c);n=JU.PT.rep(n,"_DELTAY",""+g);n=JU.PT.rep(n,"_TIME",""+e);n=JU.PT.rep(n,"_MODE",""+h);n.startsWith("+:")&&(j=!0,n=n.substring(2));this.vwr.evalStringQuiet(n)}return!j},
"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkMotionRotateZoom",function(a,b,d,c,g){b=this.bnd(a,[40])&&this.isZoomArea(this.pressed.x);var e=this.bnd(a,[25]),h=this.bnd(a,[29]);if(!b&&!e&&!h)return!1;a=(d=h&&(0==d||Math.abs(c)>5*Math.abs(d)))||this.isZoomArea(this.moved.x)||this.bnd(a,[46])?8:e||h?13:this.bnd(a,[1])?12:0;this.setMotion(a,g);return d||b},"~N,~N,~N,~N,~B");c(c$,"getExitRate",function(){var a=this.dragGesture.getTimeDifference(2);return this.isMultiTouch?80<a?0:this.dragGesture.getSpeedPixelsPerMillisecond(2,
1):10<a?0:this.dragGesture.getSpeedPixelsPerMillisecond(4,2)});c(c$,"isRubberBandSelect",function(a){return this.rubberbandSelectionMode&&this.bnd(a&-8193|32768,[35,34,32])},"~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$,"getDegrees",function(a,b){return 180*(a/Math.min(500,b?this.vwr.getScreenWidth():this.vwr.getScreenHeight()))*this.mouseDragFactor},"~N,~B");c(c$,"isZoomArea",function(a){return a>98*this.vwr.getScreenWidth()*
(this.vwr.tm.stereoDoubleFull||this.vwr.tm.stereoDoubleDTI?2:1)/100},"~N");c(c$,"getPoint",function(a){var b=new JU.Point3fi;b.setT(a.get("pt"));b.mi=a.get("modelIndex").intValue();return b},"java.util.Map");c(c$,"findNearestAtom",function(a,b,d,c){a=this.drawMode||null!=d?-1:this.vwr.findNearestAtomIndexMovable(a,b,!1);return 0<=a&&(c||null==this.mp)&&!this.vwr.slm.isInSelectionSubset(a)?-1:a},"~N,~N,JU.Point3fi,~B");c(c$,"isSelectAction",function(a){return this.bnd(a,[17])||!this.drawMode&&!this.labelMode&&
1==this.apm&&this.bnd(a,[1])||this.dragSelectedMode&&this.bnd(this.dragAction,[27,13])||this.bnd(a,[22,35,32,34,36,30])},"~N");c(c$,"enterMeasurementMode",function(a){this.vwr.setPicked(a,!0);this.vwr.setCursor(1);this.vwr.setPendingMeasurement(this.mp=this.getMP());this.measurementQueued=this.mp},"~N");c(c$,"getMP",function(){return J.api.Interface.getInterface("JM.MeasurementPending",this.vwr,"mouse").set(this.vwr.ms)});c(c$,"addToMeasurement",function(a,b,d){if(-1==a&&null==b||null==this.mp)return this.exitMeasurementMode(null),
0;var c=this.mp.count;-2147483648!=this.mp.traceX&&2==c&&this.mp.setCount(c=1);return 4==c&&!d?c:this.mp.addPoint(a,b,!0)},"~N,JU.Point3fi,~B");c(c$,"resetMeasurement",function(){this.exitMeasurementMode(null);this.measurementQueued=this.getMP()});c(c$,"exitMeasurementMode",function(a){null!=this.mp&&(this.vwr.setPendingMeasurement(this.mp=null),this.vwr.setCursor(0),null!=a&&this.vwr.refresh(3,a))},"~S");c(c$,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),b=this.measurementQueued.getAtomIndex(2);
if(!(0>a||0>b))try{var d=this.vwr.getSmilesOpt(null,a,b,1048576,null);this.vwr.setStatusMeasuring("measureSequence",-2,d,0)}catch(c){if(E(c,Exception))JU.Logger.error(c.toString());else throw c;}});c(c$,"minimize",function(a){var b=this.dragAtomIndex;a&&(this.dragAtomIndex=-1);this.vwr.dragMinimizeAtom(b)},"~B");c(c$,"queueAtom",function(a,b){var d=this.measurementQueued.addPoint(a,b,!0);0<=a&&this.vwr.setStatusAtomPicked(a,"Atom #"+d+":"+this.vwr.getAtomInfo(a),null,!1);return d},"~N,JU.Point3fi");
c(c$,"setMotion",function(a,b){switch(this.vwr.currentCursor){case 3:break;default:this.vwr.setCursor(a)}b&&this.vwr.setInMotion(!0)},"~N,~B");c(c$,"zoomByFactor",function(a,b,d){0!=a&&(this.setMotion(8,!0),this.vwr.zoomByFactor(Math.pow(this.mouseWheelFactor,a),b,d),this.moved.setCurrent(this.current,0),this.vwr.setInMotion(!0),this.zoomTrigger=!0,this.startHoverWatcher(!0))},"~N,~N,~N");c(c$,"runScript",function(a){this.vwr.script(a)},"~S");c(c$,"atomOrPointPicked",function(a,b){if(0>a){this.resetMeasurement();
if(this.bnd(this.clickAction,[33])){this.runScript("select none");return}if(5!=this.apm&&6!=this.apm)return}var d=2;switch(this.apm){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var d=8==this.apm,c=25==this.apm;if(!this.bnd(this.clickAction,[d?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;d=d||this.measurementQueued.isConnected(this.vwr.ms.at,
2)?" DELETE":c?"STRUTS":"";this.runScript("connect "+this.measurementQueued.getMeasurementScript(" ",!0)+d);this.resetMeasurement();return;case 21:d++;case 20:d++;case 18:case 19:case 22:if(!this.bnd(this.clickAction,[20]))return;if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>d)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);this.queueAtom(a,b);c=this.measurementQueued.count;1==c&&this.vwr.setPicked(a,!0);if(c<d)return;
22==this.apm?this.getSequence():(this.vwr.setStatusMeasuring("measurePicked",d,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.apm||4==this.pickingStyleMeasure)&&this.runScript("measure "+this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();return}d=null!=this.mp&&1!=this.apm?1:this.apm;switch(d){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(d){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,!1);return;case 2:this.bnd(this.clickAction,[19])&&(this.runScript("set labeltoggle {atomindex="+a+"}"),this.pickLabel(a));return;case 31:this.bnd(this.clickAction,[0])&&(this.vwr.invertRingAt(a,!0),this.vwr.setStatusAtomPicked(a,"invert stereo for atomIndex="+a,null,!1));return;case 7:this.bnd(this.clickAction,
[4])&&(d=JU.BSUtil.newAndSetBit(a),this.vwr.deleteAtoms(d,!1),this.vwr.setStatusAtomPicked(a,"deleted: "+JU.Escape.eBS(d),null,!1));return}d="atomindex="+a;switch(this.apm){default:return;case 9:this.selectAtoms(d);break;case 10:this.selectAtoms("within(group, "+d+")");break;case 11:this.selectAtoms("within(chain, "+d+")");break;case 13:this.selectAtoms("within(polymer, "+d+")");break;case 14:this.selectAtoms("within(structure, "+d+")");break;case 12:this.selectAtoms("within(molecule, "+d+")");break;
case 16:this.selectAtoms("within(model, "+d+")");break;case 17:this.selectAtoms("visible and within(element, "+d+")");break;case 15:this.selectAtoms("visible and within(site, "+d+")")}this.vwr.clearClickCount();this.vwr.setStatusAtomPicked(a,null,null,!1)}},"~N,JU.Point3fi");c(c$,"assignNew",function(a,b){if(2==this.mp.count)this.vwr.undoMoveActionClear(-1,4146,!0),this.runScript("assign connect "+this.mp.getMeasurementScript(" ",!1));else if(this.pickAtomAssignType.equals("Xx"))this.exitMeasurementMode("bond dropped");
else if(this.pressed.inRange(this.xyRange,this.dragged.x,this.dragged.y)){var d="assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'"';this.isPickAtomAssignCharge?(d+=";{atomindex="+this.dragAtomIndex+"}.label='%C'; ",this.vwr.undoMoveActionClear(this.dragAtomIndex,4,!0)):this.vwr.undoMoveActionClear(-1,4146,!0);this.runScript(d)}else this.isPickAtomAssignCharge||(this.vwr.undoMoveActionClear(-1,4146,!0),d=this.vwr.ms.at[this.dragAtomIndex],1==d.getElementNumber()?this.runScript("assign atom ({"+
this.dragAtomIndex+'}) "X"'):(d=JU.P3.new3(a,b,d.sZ),this.vwr.tm.unTransformPoint(d,d),this.runScript("assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'" '+JU.Escape.eP(d))));this.exitMeasurementMode(null)},"~N,~N");c(c$,"bondPicked",function(a){33==this.bondPickingMode&&this.vwr.undoMoveActionClear(-1,4146,!0);switch(this.bondPickingMode){case 33:this.runScript("assign bond [{"+a+'}] "'+this.pickBondAssignType+'"');break;case 34:this.vwr.setRotateBondIndex(a);break;case 8:this.vwr.deleteBonds(JU.BSUtil.newAndSetBit(a))}},
"~N");c(c$,"checkTwoAtomAction",function(a,b){var d=5==this.apm;if(this.vwr.tm.spinOn||this.vwr.tm.navOn||null!=this.vwr.getPendingMeasurement())this.resetMeasurement(),this.vwr.tm.spinOn&&this.runScript("spin off");else{2<=this.measurementQueued.count&&this.resetMeasurement();var c=this.measurementQueued.count;if(1==c)if(null==a){if(this.measurementQueued.getAtomIndex(1)==b)return}else if(0==this.measurementQueued.getAtom(1).distance(a))return;if(0<=b||null!=a)c=this.queueAtom(b,a);2>c?d?this.vwr.scriptStatus(1==
c?J.i18n.GT.$("pick one more atom in order to spin the model around an axis"):J.i18n.GT.$("pick two atoms in order to spin the model around an axis")):this.vwr.scriptStatus(1==c?J.i18n.GT.$("pick one more atom in order to display the symmetry relationship"):J.i18n.GT.$("pick two atoms in order to display the symmetry relationship between them")):(c=this.measurementQueued.getMeasurementScript(" ",!1),d?this.runScript("spin"+c+" "+this.vwr.getInt(553648157)):this.runScript("draw symop "+c+";show symop "+
c))}},"JU.Point3fi,~N");c(c$,"reset",function(){this.runScript("!reset")});c(c$,"selectAtoms",function(a){if(!(null!=this.mp||this.selectionWorking)){this.selectionWorking=!0;var b=this.rubberbandSelectionMode||this.bnd(this.clickAction,[35])?"selected and not ("+a+") or (not selected) and ":this.bnd(this.clickAction,[32])?"selected and not ":this.bnd(this.clickAction,[34])?"selected or ":0==this.clickAction||this.bnd(this.clickAction,[36])?"selected tog ":this.bnd(this.clickAction,[30])?"":null;
if(null!=b)try{var d=this.vwr.getAtomBitSetEval(null,b+("("+a+")"));this.setAtomsPicked(d,"selected: "+JU.Escape.eBS(d));this.vwr.refresh(3,"selections set")}catch(c){if(!E(c,Exception))throw c;}this.selectionWorking=!1}},"~S");c(c$,"setAtomsPicked",function(a,b){this.vwr.select(a,!1,0,!1);this.vwr.setStatusAtomPicked(-1,b,null,!1)},"JU.BS,~S");c(c$,"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,!1)},"~N");j(c$,"keyTyped",
function(){return!1},"~N,~N");F(c$);c$.actionInfo=c$.prototype.actionInfo=Array(47);c$.actionNames=c$.prototype.actionNames=Array(47);F(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(" ");
F(c$,"pickingStyleNames",null);JV.ActionManager.pickingStyleNames="toggle selectOrToggle extendedSelect drag measure measureoff".$plit(" ");F(c$,"MAX_DOUBLE_CLICK_MILLIS",700,"MININUM_GESTURE_DELAY_MILLISECONDS",10,"SLIDE_ZOOM_X_PERCENT",98,"DEFAULT_MOUSE_DRAG_FACTOR",1,"DEFAULT_MOUSE_WHEEL_FACTOR",1.15,"DEFAULT_GESTURE_SWIPE_FACTOR",1);c$=r(function(){this.time=this.y=this.x=this.index=0;n(this,arguments)},JV,"MotionPoint");c(c$,"set",function(a,b,d,c){this.index=a;this.x=b;this.y=d;this.time=c},
"~N,~N,~N,~N");j(c$,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});c$=r(function(){this.action=0;this.nodes=null;this.time0=this.ptNext=0;this.vwr=null;n(this,arguments)},JV,"Gesture");t(c$,function(a,b){this.vwr=b;this.nodes=Array(a);for(var d=0;d<a;d++)this.nodes[d]=new JV.MotionPoint},"~N,JV.Viewer");c(c$,"setAction",function(a,b){this.action=a;this.ptNext=0;this.time0=b;for(var d=0;d<this.nodes.length;d++)this.nodes[d].index=-1},"~N,~N");c(c$,"add",function(a,
b,d,c){this.action=a;this.getNode(this.ptNext).set(this.ptNext,b,d,c-this.time0);this.ptNext++;return this.ptNext},"~N,~N,~N,~N");c(c$,"getTimeDifference",function(a){a=this.getPointCount2(a,0);if(2>a)return 0;var b=this.getNode(this.ptNext-1);a=this.getNode(this.ptNext-a);return b.time-a.time},"~N");c(c$,"getSpeedPixelsPerMillisecond",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b),g=360*((d.x-c.x)/this.vwr.getScreenWidth()),
e=360*((d.y-c.y)/this.vwr.getScreenHeight());return Math.sqrt(g*g+e*e)/(d.time-c.time)},"~N,~N");c(c$,"getDX",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b);return d.x-c.x},"~N,~N");c(c$,"getDY",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b);return d.y-c.y},"~N,~N");c(c$,"getPointCount",function(){return this.ptNext});c(c$,"getPointCount2",function(a,
b){a>this.nodes.length-b&&(a=this.nodes.length-b);for(var d=a+1;0<=--d&&!(0<=this.getNode(this.ptNext-d-b).index););return d},"~N,~N");c(c$,"getNode",function(a){return this.nodes[(a+this.nodes.length+this.nodes.length)%this.nodes.length]},"~N");j(c$,"toString",function(){return 0==this.nodes.length?""+this:JV.binding.Binding.getMouseActionName(this.action,!1)+" nPoints = "+this.ptNext+" "+this.nodes[0]})});u("JV");x(["JU.BS"],"JV.AnimationManager",["J.api.Interface","JU.BSUtil"],function(){c$=r(function(){this.vwr=
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0,a.group.getSelectedMonomerCount()-1,1,!1);case 77:return this.ce.getColorIndexFromPalette(c.getMoleculeIndex(a.i,!0),0,c.getMoleculeCountInModel(a.mi)-1,0,!1);case 14:return d=a.mi,this.ce.getColorIndexFromPalette(c.getAltLocIndexInModel(d,a.altloc),0,c.getAltLocCountInModel(d),0,!1);case 15:return d=a.mi,this.ce.getColorIndexFromPalette(c.getInsertionCodeIndexInModel(d,a.group.getInsertionCode()),0,c.getInsertionCountInModel(d),0,!1);case 16:c=a.getAtomicAndIsotopeNumber();d=this.getJmolOrRasmolArgb(c,
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f);b.put("fileTypes",e);a=this.newFilesReader(f,g,e,null,b,c);a.run();return a.getAtomSetCollection()},"~A,java.util.Map,~B");c(c$,"createAtomSetCollectionFromString",function(a,b,c){this.setLoadState(b);var f=0<=a.indexOf("Viewer.AddHydrogens")?this.getFileInfo():null;b=new J.io.FileReader(this.vwr,"string",null,null,null,JU.Rdr.getBR(a),b,c);b.run();null!=f&&this.setFileInfo(f);!c&&!q(b.getAtomSetCollection(),String)&&this.setFileInfo(v(-1,["5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63"===
a?"Jmol Model Kit":"string"]));return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(c$,"createAtomSeCollectionFromStrings",function(a,b,c,f){if(!c.containsKey("isData")){var g='"'+this.vwr.getDataSeparator()+'"',e='"'+(f?"append":"model")+' inline"',h=new JU.SB;h.append('set dataSeparator "~~~next file~~~";\ndata ').append(e);for(var j=0;j<a.length;j++)0<j&&h.append("~~~next file~~~"),h.append(a[j]);h.append("end ").append(e).append(";set dataSeparator ").append(g);b.appendSB(h)}this.setLoadState(c);
JU.Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");b=Array(a.length);g=Array(a.length);for(j=0;j<a.length;j++)b[j]="string["+j+"]",g[j]=JV.FileManager.newDataReader(this.vwr,a[j]);a=this.newFilesReader(b,b,null,g,c,f);a.run();return a.getAtomSetCollection()},"~A,JU.SB,java.util.Map,~B");c(c$,"createAtomSeCollectionFromArrayData",function(a,b,c){JU.Logger.info("FileManager.getAtomSetCollectionFromArrayData(Vector)");for(var f=a.size(),g=Array(f),e=Array(f),h=0;h<f;h++)g[h]="String["+
h+"]",e[h]=JV.FileManager.newDataReader(this.vwr,a.get(h));a=this.newFilesReader(g,g,null,e,b,c);a.run();return a.getAtomSetCollection()},"JU.Lst,java.util.Map,~B");c$.newDataReader=c(c$,"newDataReader",function(a,b){var c=q(b,String)?"String":JU.AU.isAS(b)?"Array":q(b,JU.Lst)?"List":null;return null==c?null:J.api.Interface.getInterface("JU."+c+"DataReader",a,"file").setData(b)},"JV.Viewer,~O");c(c$,"newFilesReader",function(a,b,c,f,g,e){var h=J.api.Interface.getOption("io.FilesReader",this.vwr,"file");
h.set(this,this.vwr,a,b,c,f,g,e);return h},"~A,~A,~A,~A,java.util.Map,~B");c(c$,"createAtomSetCollectionFromDOM",function(a,b){var c=J.api.Interface.getOption("io.DOMReadaer",this.vwr,"file");c.set(this,this.vwr,a,b);c.run();return c.getAtomSetCollection()},"~O,java.util.Map");c(c$,"createAtomSetCollectionFromReader",function(a,b,c,f){a=new J.io.FileReader(this.vwr,b,a,null,null,c,f,!1);a.run();return a.getAtomSetCollection()},"~S,~S,~O,java.util.Map");c(c$,"getBufferedInputStream",function(a){a=
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m){var p=Array(1),n=this.vwr.getImageAsBytes(m?"PNGJ":"PNG",0,0,-1,p);if(null!=p[0])return p[0];s?(g=n,a=JU.PT.rep(a,"?_","=_")):a=(new JU.SB).append(a).append("=").appendSB(JU.Base64.getBase64(n)).toString()}var r=JU.OC.urlTypeIndex(a),s=0<=r,m=null;if(s&&0<=(r=a.indexOf("?POST?")))m=a.substring(r+6),a=a.substring(0,r);var t=null!=this.appletDocumentBaseURL;if(t||s){t&&(s&&null!=this.appletProxy)&&(a=this.appletProxy+"?url="+this.urlEncode(a));var u=t?new java.net.URL(this.appletDocumentBaseURL,
a,null):new java.net.URL(ba("java.net.URL"),a,null);if(f)return null;a=u.toString();c&&0>a.toLowerCase().indexOf("password")&&JU.Logger.info("FileManager opening url "+a);l=this.vwr.apiPlatform.getURLContents(u,g,m,!1);n=null;if(q(l,JU.SB)){a=l;if(e&&!JU.Rdr.isBase64(a))return JU.Rdr.getBR(a.toString());n=JU.Rdr.getBytesFromSB(a)}else JU.AU.isAB(l)&&(n=l);null!=n&&(l=JU.Rdr.getBIS(n))}else if(!h||null==(b=this.cacheGet(a,!0)))c&&JU.Logger.info("FileManager opening file "+a),l=this.vwr.apiPlatform.getBufferedFileInputStream(a);
if(q(l,String))return l}j=null==b?l:JU.Rdr.getBIS(b);f&&(j.close(),j=null);return j}catch(v){if(E(v,Exception))try{null!=j&&j.close()}catch(x){if(!E(x,java.io.IOException))throw x;}else throw v;}return""+v},"~S,~S,~B,~B,~A,~B,~B");c$.getBufferedReaderForResource=c(c$,"getBufferedReaderForResource",function(a,b,c,f){f=a.vwrOptions.get("codePath")+c+f;if(a.async){a=a.fm.cacheGet(f,!1);if(null==a)throw new JV.JmolAsyncException(f);return JU.Rdr.getBufferedReader(JU.Rdr.getBIS(a),null)}return a.fm.getBufferedReaderOrErrorMessageFromName(f,
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[a+"|"+b[f],null]),this.getFileDataAsString(a,-1,!1,!1,!1),a[1];return""},"~S,~B,~S");c(c$,"getFullPathNameOrError",function(a,b,c){var f=this.getClassifiedName(JV.JC.fixProtocol(a),!0);if(null==f||null==f[0]||2>f.length)return v(-1,[null,"cannot read file name: "+a]);a=f[0];f=JV.FileManager.fixDOSName(f[0]);a=JU.Rdr.getZipRoot(a);b=this.getBufferedInputStreamOrErrorMessageFromName(a,f,!1,!b,null,!1,!b);c[0]=f;q(b,String)&&(c[1]=b);return b},"~S,~B,~A");c(c$,"getBufferedReaderOrErrorMessageFromName",
function(a,b,c,f){a=JV.JC.fixProtocol(a);var g=this.cacheGet(a,!1),e=JU.AU.isAB(g),h=e?g:null;if(a.startsWith("cache://")){if(null==g)return"cannot read "+a;if(e)h=g;else return JU.Rdr.getBR(g)}g=this.getClassifiedName(a,!0);if(null==g)return"cannot read file name: "+a;null!=b&&(b[0]=JV.FileManager.fixDOSName(g[0]));return this.getUnzippedReaderOrStreamFromName(g[0],h,!1,c,!1,f,null)},"~S,~A,~B,~B");c(c$,"getUnzippedReaderOrStreamFromName",function(a,b,c,f,g,e,h){if(e&&null==b){var j=a.endsWith(".spt")?
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!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.multipleBondBananas=!1;this.nboCharges=!0;this.cartoonRockets=this.cartoonBaseEdges=!1;this.cartoonBlockHeight=0.5;this.cipRule6Full=this.chainCaseSensitive=this.cartoonRibose=this.cartoonLadders=this.cartoonFancy=this.cartoonSteps=this.cartoonBlocks=!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.twistedSheets=!1;this.allowAudio=this.autoplayMovie=!0;this.allowGestures=!1;this.allowMultiTouch=this.allowModelkit=!0;this.hiddenLinesDashed=this.allowKeyStrokes=!1;this.animationFps=10;this.atomPicking=!0;this.autoFps=!1;this.axesMode=603979809;this.axesScale=2;this.axesOffset=
0;this.starWidth=0.05;this.bondPicking=!1;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=0;this.helpPath="https://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.saveProteinStructureState=!0;this.showModVecs=!1;this.showUnitCellDetails=!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.noDelay=!1;this.vectorScale=1;this.vectorsCentered=
this.vectorSymmetry=!1;this.vectorTrail=0;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.objMad10=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.bondingVersion=0;n(this,arguments)},JV,"GlobalSettings");O(c$,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.objColors=A(7,0);this.objStateOn=ha(7,!1);this.objMad10=A(7,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,I(-1,[30,90,-15,95]));this.structureList.put(J.c.STR.SHEET,I(-1,[-180,-10,70,180,
-180,-45,-180,-130,140,180,90,180]));this.structureList.put(J.c.STR.HELIX,I(-1,[-160,0,-100,45]))});t(c$,function(a,b,c){this.vwr=a;this.htNonbooleanParameterValues=new java.util.Hashtable;this.htBooleanParameterFlags=new java.util.Hashtable;this.htPropertyFlagsRemoved=new java.util.Hashtable;null!=b&&(c||(this.setO("_pngjFile",b.getParameter("_pngjFile",!1)),this.htUserVariables=b.htUserVariables),this.debugScript=b.debugScript,this.disablePopupMenu=b.disablePopupMenu,this.messageStyleChime=b.messageStyleChime,
this.defaultDirectory=b.defaultDirectory,this.autoplayMovie=b.autoplayMovie,this.allowAudio=b.allowAudio,this.allowGestures=b.allowGestures,this.allowModelkit=b.allowModelkit,this.allowMultiTouch=b.allowMultiTouch,this.allowKeyStrokes=b.allowKeyStrokes,this.legacyAutoBonding=b.legacyAutoBonding,this.legacyHAddition=b.legacyHAddition,this.legacyJavaFloat=b.legacyJavaFloat,this.bondingVersion=b.bondingVersion,this.platformSpeed=b.platformSpeed,this.useScriptQueue=b.useScriptQueue,this.showTiming=b.showTiming,
this.wireframeRotation=b.wireframeRotation,this.testFlag1=b.testFlag1,this.testFlag2=b.testFlag2,this.testFlag3=b.testFlag3,this.testFlag4=b.testFlag4);this.loadFormat=this.pdbLoadFormat=JV.JC.databases.get("pdb");this.pdbLoadLigandFormat=JV.JC.databases.get("ligand");this.nmrUrlFormat=JV.JC.databases.get("nmr");this.nmrPredictFormat=JV.JC.databases.get("nmrdb");this.smilesUrlFormat=JV.JC.databases.get("nci")+"/file?format=sdf&get3d=true";this.nihResolverFormat=JV.JC.databases.get("nci");this.pubChemFormat=
JV.JC.databases.get("pubchem");var f;c=0;for(var g=J.c.CBK.values();c<g.length&&((f=g[c])||1);c++)this.resetValue(f.name()+"Callback",b);this.setF("cameraDepth",3);this.setI("contextDepthMax",100);this.setI("depth",0);this.setF("gestureSwipeFactor",1);this.setB("hideNotSelected",!1);this.setI("historyLevel",0);this.setO("hoverLabel","");this.setB("isKiosk",a.isKiosk());this.setO("logFile",a.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.setB("perspectiveDepth",!0);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.setF("visualRange",5);this.setI("stereoDegrees",-5);this.setB("syncScript",a.sm.syncingScripts);this.setB("syncMouse",a.sm.syncingMouse);this.setB("syncStereo",a.sm.stereoSync);this.setB("windowCentered",!0);this.setB("zoomEnabled",!0);this.setI("_version",JV.JC.versionInt);
this.setO("_versionDate",JV.Viewer.getJmolVersion());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;Stl;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("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",603979808==this.axesMode?2:603979804==this.axesMode?1:0);this.setF("axesScale",this.axesScale);this.setF("axesOffset",this.axesOffset);this.setB("axesOrientationRasmol",this.axesOrientationRasmol);this.setF("cartoonBlockHeight",this.cartoonBlockHeight);this.setB("cartoonBlocks",this.cartoonBlocks);this.setB("cartoonSteps",this.cartoonSteps);this.setB("bondModeOr",this.bondModeOr);this.setB("bondPicking",this.bondPicking);this.setI("bondRadiusMilliAngstroms",this.bondRadiusMilliAngstroms);
this.setF("bondTolerance",this.bondTolerance);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("cipRule6Full",this.cipRule6Full);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.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.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("hiddenLinesDashed",this.hiddenLinesDashed);this.setB("highResolution",this.highResolutionFlag);this.setF("hoverDelay",this.hoverDelayMs/1E3);this.setB("imageState",this.imageState);this.setI("infoFontSize",this.infoFontSize);this.setB("isosurfaceKey",this.isosurfaceKey);this.setB("isosurfacePropertySmoothing",this.isosurfacePropertySmoothing);this.setI("isosurfacePropertySmoothingPower",this.isosurfacePropertySmoothingPower);this.setB("jmolInJSpecView",this.jmolInJSpecView);
this.setB("justifyMeasurements",this.justifyMeasurements);this.setB("legacyAutoBonding",this.legacyAutoBonding);this.setB("legacyHAddition",this.legacyHAddition);this.setB("legacyJavaFloat",this.legacyJavaFloat);this.setF("loadAtomDataTolerance",this.loadAtomDataTolerance);this.setO("loadFormat",this.loadFormat);this.setO("loadLigandFormat",this.pdbLoadLigandFormat);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.setB("multipleBondBananas",this.multipleBondBananas);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.setB("nboCharges",this.nboCharges);this.setB("noDelay",this.noDelay);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.setI("percentVdwAtom",this.percentVdwAtom);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("showModulationVectors",this.showModVecs);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("solventProbe",this.solventOn);this.setF("solventProbeRadius",this.solventProbeRadius);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.setI("vectorTrail",this.vectorTrail);this.setF("vibrationPeriod",
this.vibrationPeriod);this.setF("vibrationScale",this.vibrationScale);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.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.vwr.setPicked(-1,!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$,"setUnits",function(a){var b=this.measureDistanceUnits,c=this.energyUnits;a.equalsIgnoreCase("angstroms")?this.measureDistanceUnits="angstroms":a.equalsIgnoreCase("nanometers")||
a.equalsIgnoreCase("nm")?this.measureDistanceUnits="nanometers":a.equalsIgnoreCase("picometers")||a.equalsIgnoreCase("pm")?this.measureDistanceUnits="picometers":a.equalsIgnoreCase("bohr")||a.equalsIgnoreCase("au")?this.measureDistanceUnits="au":a.equalsIgnoreCase("vanderwaals")||a.equalsIgnoreCase("vdw")?this.measureDistanceUnits="vdw":a.toLowerCase().endsWith("hz")||a.toLowerCase().endsWith("khz")?this.measureDistanceUnits=a.toLowerCase():a.equalsIgnoreCase("kj")?this.energyUnits="kJ":a.equalsIgnoreCase("kcal")&&
(this.energyUnits="kcal");b.equalsIgnoreCase(this.measureDistanceUnits)?c.equalsIgnoreCase(this.energyUnits)||this.setO("energyUnits",this.energyUnits):this.setO("measurementUnits",this.measureDistanceUnits)},"~S");c(c$,"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$,"resetValue",function(a,b){this.setO(a,null==
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4294918208,4294934656,4294951104,4294967295,4292401407,4290032895,4287664383,4285295871,4282927359,4280558847,4278190335]),"argbsRwbScale",A(-1,[4294901760,4294905872,4294909984,4294914096,4294918208,4294922320,4294926432,4294930544,4294934656,4294938768,4294942880,4294946992,4294951104,4294955216,4294959328,4294967295,4292927743,4291875071,4290822399,4289769727,4288717055,4287664383,4286611711,4285559039,4284506367,4283453695,4282401023,4281348351,4280295679,4279243007,4278190335]));c$.FORMAL_CHARGE_COLIX_RED=
c$.prototype.FORMAL_CHARGE_COLIX_RED=JU.Elements.elementSymbols.length+JV.JC.altArgbsCpk.length;c$.PARTIAL_CHARGE_COLIX_RED=c$.prototype.PARTIAL_CHARGE_COLIX_RED=JV.JC.FORMAL_CHARGE_COLIX_RED+JV.JC.argbsFormalCharge.length;c$.PARTIAL_CHARGE_RANGE_SIZE=c$.prototype.PARTIAL_CHARGE_RANGE_SIZE=JV.JC.argbsRwbScale.length;F(c$,"argbsRoygbScale",A(-1,[4294901760,4294909952,4294918144,4294926336,4294934528,4294942720,4294950912,4294959104,4294963200,4294967040,4293980160,4292935424,4290838272,4288741120,
4286643968,4284546816,4282449664,4280352512,4278255360,4278255392,4278255424,4278255456,4278255488,4278255520,4278255552,4278255584,4278255615,4278247679,4278239487,4278231295,4278223103,4278214911,4278206719,4278198527,4278190335]),"argbsIsosurfacePositive",4283441312,"argbsIsosurfaceNegative",4288684112,"ATOMID_AMINO_NITROGEN",1,"ATOMID_ALPHA_CARBON",2,"ATOMID_CARBONYL_CARBON",3,"ATOMID_CARBONYL_OXYGEN",4,"ATOMID_O1",5,"ATOMID_ALPHA_ONLY_MASK",4,"ATOMID_PROTEIN_MASK",14,"ATOMID_O5_PRIME",6,"ATOMID_C5_PRIME",
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4,"GROUPID_CYSTEINE",5,"GROUPID_GLUTAMINE",6,"GROUPID_GLUTAMATE",7,"GROUPID_HISTIDINE",9,"GROUPID_LYSINE",12,"GROUPID_PROLINE",15,"GROUPID_TRYPTOPHAN",19,"GROUPID_AMINO_MAX",24,"GROUPID_NUCLEIC_MAX",42,"GROUPID_WATER",42,"GROUPID_SOLVENT_MIN",45,"GROUPID_ION_MIN",46,"GROUPID_ION_MAX",48,"predefinedVariable",v(-1,"@_1H _H & !(_2H,_3H);@_12C _C & !(_13C,_14C);@_14N _N & !(_15N);@solvent water, (_g>=45 & _g<48);@ligand _g=0|!(_g<46,protein,nucleic,water);@turn structure=1;@sheet structure=2;@helix structure=3;@helix310 substructure=7;@helixalpha substructure=8;@helixpi substructure=9;@bulges within(dssr,'bulges');@coaxStacks within(dssr,'coaxStacks');@hairpins within(dssr,'hairpins');@hbonds within(dssr,'hbonds');@helices within(dssr,'helices');@iloops within(dssr,'iloops');@isoCanonPairs within(dssr,'isoCanonPairs');@junctions within(dssr,'junctions');@kissingLoops within(dssr,'kissingLoops');@multiplets within(dssr,'multiplets');@nonStack within(dssr,'nonStack');@nts within(dssr,'nts');@pairs within(dssr,'pairs');@ssSegments within(dssr,'ssSegments');@stacks within(dssr,'stacks');@stems within(dssr,'stems')".split(";")),
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function(a,b){0>a?this.selectionChanged(!0):null!=this.bsSubset&&!this.bsSubset.get(a)||null!=this.bsDeleted&&this.bsDeleted.get(a)||(this.bsSelection.setBitTo(a,b),this.empty=b?0:-1)},"~N,~B");c(c$,"setSelectionSubset",function(a){this.bsSubset=a},"JU.BS");c(c$,"isInSelectionSubset",function(a){return 0>a||null==this.bsSubset||this.bsSubset.get(a)},"~N");c(c$,"invertSelection",function(){JU.BSUtil.invertInPlace(this.bsSelection,this.vwr.ms.ac);this.empty=0<this.bsSelection.length()?0:1;this.selectionChanged(!1)});
c(c$,"excludeSelectionSet",function(a){null==a||1==this.empty||(this.bsSelection.andNot(a),this.empty=-1)},"JU.BS");c(c$,"getSelectionCount",function(){if(1==this.empty)return 0;this.empty=1;var a;null==this.bsSubset?a=this.bsSelection:(this.bsTemp.clearAll(),this.bsTemp.or(this.bsSubset),this.bsTemp.and(this.bsSelection),a=this.bsTemp);a=a.cardinality();0<a&&(this.empty=0);return a});c(c$,"addListener",function(a){for(var b=this.listeners.length;0<=--b;)if(this.listeners[b]===a){this.listeners[b]=
null;break}for(var c=this.listeners.length,b=c;0<=--b;)if(null==this.listeners[b]){this.listeners[b]=a;return}this.listeners=0==this.listeners.length?Array(1):JU.AU.doubleLength(this.listeners);this.listeners[c]=a},"J.api.JmolSelectionListener");c(c$,"selectionChanged",function(a){this.hideNotSelected&&this.hide(this.vwr.ms,JU.BSUtil.copyInvert(this.bsSelection,this.vwr.ms.ac),0,a);if(!(a||0==this.listeners.length))for(a=this.listeners.length;0<=--a;)null!=this.listeners[a]&&this.listeners[a].selectionChanged(this.bsSelection)},
"~B");c(c$,"deleteAtoms",function(a){var b=JU.BSUtil.copy(a);null==this.bsDeleted?this.bsDeleted=b:(b.andNot(this.bsDeleted),this.bsDeleted.or(a));this.bsHidden.andNot(this.bsDeleted);this.bsSelection.andNot(this.bsDeleted);return b.cardinality()},"JU.BS");c(c$,"getSelectedAtoms",function(){if(null==this.bsSubset)return this.bsSelection;var a=JU.BSUtil.copy(this.bsSelection);a.and(this.bsSubset);return a});c(c$,"getSelectedAtomsNoSubset",function(){return JU.BSUtil.copy(this.bsSelection)});c(c$,"excludeAtoms",
function(a,b){null!=this.bsDeleted&&a.andNot(this.bsDeleted);!b&&null!=this.bsSubset&&(a=JU.BSUtil.copy(a)).and(this.bsSubset);return a},"JU.BS,~B");c(c$,"setMotionFixedAtoms",function(a){this.bsFixed.clearAll();null!=a&&this.bsFixed.or(a)},"JU.BS");c(c$,"getMotionFixedAtoms",function(){return this.bsFixed});F(c$,"TRUE",1,"FALSE",0,"UNKNOWN",-1)});u("JV");x(null,"JV.ShapeManager","java.lang.Boolean JU.BS $.P3 J.api.Interface J.c.PAL $.VDW JM.Atom JU.BSUtil JV.JC".split(" "),function(){c$=r(function(){this.navMinMax=
this.bsSlabbedInternal=this.bsRenderableAtoms=this.vwr=this.shapes=this.ms=null;n(this,arguments)},JV,"ShapeManager");O(c$,function(){this.navMinMax=A(4,0)});t(c$,function(a){this.vwr=a;this.bsRenderableAtoms=new JU.BS;this.bsSlabbedInternal=new JU.BS},"JV.Viewer");c(c$,"findNearestShapeAtomIndex",function(a,b,c,f){if(null!=this.shapes)for(var g=0;g<this.shapes.length&&null==c[0];++g)null!=this.shapes[g]&&this.shapes[g].findNearestAtomIndex(a,b,c,f)},"~N,~N,~A,JU.BS");c(c$,"getShapePropertyIndex",
function(a,b,c){if(null==this.shapes||null==this.shapes[a])return null;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getProperty(b,c);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~N");c(c$,"getShapePropertyData",function(a,b,c){if(null==this.shapes||null==this.shapes[a])return!1;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getPropertyData(b,c);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~A");c(c$,"getShapeIdFromObjectName",function(a){if(null!=this.shapes)for(var b=
16;30>b;++b)if(null!=this.shapes[b]&&0<=this.shapes[b].getIndexFromName(a))return b;return-1},"~S");c(c$,"loadDefaultShapes",function(a){this.ms=a;if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].setModelSet(a);this.loadShape(0);this.loadShape(1)},"JM.ModelSet");c(c$,"loadShape",function(a){if(null==this.shapes)return null;if(null!=this.shapes[a])return this.shapes[a];if(2==a||3==a||4==a)return null;var b=JV.JC.getShapeClassName(a,!1);if(null==(b=J.api.Interface.getInterface(b,
this.vwr,"shape")))return null;this.vwr.setShapeErrorState(a,"allocate");b.initializeShape(this.vwr,this.ms,a);this.vwr.setShapeErrorState(-1,null);return this.shapes[a]=b},"~N");c(c$,"notifyAtomPositionsChanged",function(a,b,c){var f=Integer.$valueOf(a);a=this.vwr.getModelUndeletedAtomsBitSet(a);for(var g=0;37>g;g++)null!=this.shapes[g]&&this.setShapePropertyBs(g,"refreshTrajectories",v(-1,[f,b,c]),a)},"~N,JU.BS,JU.M4");c(c$,"releaseShape",function(a){null!=this.shapes&&(this.shapes[a]=null)},"~N");
c(c$,"resetShapes",function(){this.shapes=Array(37)});c(c$,"setShapeSizeBs",function(a,b,c,f){if(null!=this.shapes){if(null==f&&(1!=a||2147483647!=b))f=this.vwr.bsA();null!=c&&(0!=c.value&&c.vdwType===J.c.VDW.TEMP)&&this.ms.getBfactor100Lo();this.vwr.setShapeErrorState(a,"set size");(null==c?0!=b:0!=c.value)&&this.loadShape(a);null!=this.shapes[a]&&this.shapes[a].setShapeSizeRD(b,c,f);this.vwr.setShapeErrorState(-1,null)}},"~N,~N,J.atomdata.RadiusData,JU.BS");c(c$,"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$,"setShapePropertyBs",function(a,b,c,f){null==this.shapes||null==this.shapes[a]||(null==f&&(f=this.vwr.bsA()),this.vwr.setShapeErrorState(a,"set "+b),this.shapes[a].setProperty(b.intern(),c,f),this.vwr.setShapeErrorState(-1,null))},"~N,~S,~O,JU.BS");c(c$,"checkFrankclicked",function(a,b){var c=this.shapes[36];return null!=c&&c.wasClicked(a,b)},"~N,~N");c(c$,
"checkObjectClicked",function(a,b,c,f,g){var e,h=null;if(2==this.vwr.getPickingMode())return this.shapes[5].checkObjectClicked(a,b,c,f,!1);if(0!=c&&this.vwr.getBondPicking()&&null!=(h=this.shapes[1].checkObjectClicked(a,b,c,f,!1)))return h;for(var j=0;j<JV.ShapeManager.clickableMax;j++)if(null!=(e=this.shapes[JV.ShapeManager.hoverable[j]])&&null!=(h=e.checkObjectClicked(a,b,c,f,g)))return h;return null},"~N,~N,~N,JU.BS,~B");c(c$,"checkObjectDragged",function(a,b,c,f,g,e,h){for(var j=!1,l=0<h?h+1:
37;!j&&h<l;++h)null!=this.shapes[h]&&(j=this.shapes[h].checkObjectDragged(a,b,c,f,g,e));return j},"~N,~N,~N,~N,~N,JU.BS,~N");c(c$,"checkObjectHovered",function(a,b,c,f){var g=this.shapes[1];if(f&&null!=g&&g.checkObjectHovered(a,b,c))return!0;for(f=0;f<JV.ShapeManager.hoverable.length;f++)if(g=this.shapes[JV.ShapeManager.hoverable[f]],null!=g&&g.checkObjectHovered(a,b,c))return!0;return!1},"~N,~N,JU.BS,~B");c(c$,"deleteShapeAtoms",function(a,b){if(null!=this.shapes)for(var c=0;37>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;c=this.shapes[a].getSize(c);if(0==c){if(0==(b.shapeVisibilityFlags&this.shapes[a].vf))return 0;c=this.shapes[a].getSizeG(b)}return c/
2E3},"~N,JM.Group,~N");c(c$,"replaceGroup",function(a,b){if(null!=this.shapes)for(var c=9;16>c;c++)null!=this.shapes[c]&&this.shapes[c].replaceGroup(a,b)},"JM.Group,JM.Group");c(c$,"getObjectMap",function(a,b){if(null!=this.shapes)for(var c=Boolean.$valueOf(b),f=16;30>f;++f)this.getShapePropertyData(f,"getNames",v(-1,[a,c]))},"java.util.Map,~B");c(c$,"getProperty",function(a){return a.equals("getShapes")?this.shapes:null},"~O");c(c$,"getShape",function(a){return null==this.shapes?null:this.shapes[a]},
"~N");c(c$,"resetBioshapes",function(a){if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].isBioShape&&(this.shapes[b].setModelSet(this.ms),this.shapes[b].setShapeSizeRD(0,null,a),this.shapes[b].setProperty("color",J.c.PAL.NONE,a))},"JU.BS");c(c$,"setAtomLabel",function(a,b){null!=this.shapes&&this.shapes[5].setProperty("label:"+a,Integer.$valueOf(b),null)},"~S,~N");c(c$,"setModelVisibility",function(){var a=this.shapes;if(!(null==a||null==a[0])){for(var b=
this.vwr.getVisibleFramesBitSet(),c=8;33>c;c++)null!=a[c]&&a[c].setModelVisibilityFlags(b);var a=this.vwr.getBoolean(603979922),f=this.vwr.slm.bsDeleted,g=this.ms.at;this.ms.clearVisibleSets();if(0<g.length)for(c=this.ms.ac;0<=--c;){var e=g[c];e.shapeVisibilityFlags&=-64;if(!(null!=f&&f.get(c))&&b.get(e.mi)){var h=1;if(!this.ms.isAtomHidden(c)&&(a||1!=e.getElementNumber()))h|=8,0!=e.madAtom&&(h|=16),e.setShapeVisibility(h,!0)}}this.setShapeVis()}});c(c$,"setShapeVis",function(){for(var a=0;37>a;++a){var b=
this.shapes[a];null!=b&&b.setAtomClickability()}});c(c$,"finalizeAtoms",function(a,b){var c=this.vwr,f=c.tm;b&&c.finalizeTransformParameters();if(null!=a){var g=this.ms.getAtomSetCenter(a),e=new JU.P3;f.transformPt3f(g,e);e.add(f.ptOffset);f.unTransformPoint(e,e);e.sub(g);c.setAtomCoordsRelative(e,a);f.ptOffset.set(0,0,0);f.bsSelectedAtoms=null}g=this.bsRenderableAtoms;this.ms.getAtomsInFrame(g);var h=this.ms.vibrations,j=null!=h&&f.vibrationOn,l=null!=this.ms.bsModulated&&null!=this.ms.occupancies,
n=this.ms.at,m,p=!1,q=this.bsSlabbedInternal;q.clearAll();for(var r=g.nextSetBit(0);0<=r;r=g.nextSetBit(r+1)){var e=n[r],t=j&&e.hasVibration()?f.transformPtVib(e,h[r]):f.transformPt(e);1==t.z&&(f.internalSlab&&f.xyzIsSlabbedInternal(e))&&q.set(r);e.sX=t.x;e.sY=t.y;e.sZ=t.z;var u=Math.abs(e.madAtom);u==JM.Atom.MAD_GLOBAL&&(u=B(2E3*c.getFloat(1140850689)));e.sD=aa(c.tm.scaleToScreen(t.z,u));if(l&&null!=h[r]&&-2147483648!=(m=h[r].getOccupancy100(j)))p=!0,e.setShapeVisibility(2,!1),0<=m&&50>m?e.setShapeVisibility(24,
!1):e.setShapeVisibility(8|(0<e.madAtom?16:0),!0),this.ms.occupancies[e.i]=Math.abs(m)}p&&this.setShapeVis();m=c.gdata;if(f.slabEnabled){r=c.getBoolean(603979940);f=c.getBoolean(603979939);h=m.slab;j=m.depth;if(r){l=this.ms.getMolecules();p=this.ms.getMoleculeCountInModel(-1);for(r=0;r<p;r++)if(q=l[r],t=0,e=q.firstAtomIndex,g.get(e)){for(;t<q.ac&&!m.isClippedZ(n[e].sZ-(n[e].sD>>1));t++,e++);if(t!=q.ac){e=q.firstAtomIndex;for(t=0;t<q.ac;t++)g.clear(e),n[e++].sZ=0}}}for(r=g.nextSetBit(0);0<=r;r=g.nextSetBit(r+
1))if(e=n[r],m.isClippedZ(e.sZ-(f?n[r].sD>>1:0)))e.setClickable(0),l=y((f?-1:1)*e.sD/2),(e.sZ+l<h||e.sZ-l>j||!m.isInDisplayRange(e.sX,e.sY))&&g.clear(r)}if(0==this.ms.ac||!c.getShowNavigationPoint())return null;c=2147483647;m=-2147483648;f=2147483647;h=-2147483648;for(r=g.nextSetBit(0);0<=r;r=g.nextSetBit(r+1))e=n[r],e.sX<c&&(c=e.sX),e.sX>m&&(m=e.sX),e.sY<f&&(f=e.sY),e.sY>h&&(h=e.sY);this.navMinMax[0]=c;this.navMinMax[1]=m;this.navMinMax[2]=f;this.navMinMax[3]=h;return this.navMinMax},"JU.BS,~B");
c(c$,"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.slm.getSelectedAtomsNoSubset();if(b){this.vwr.slm.invertSelection();var f=this.vwr.slm.bsSubset;null!=f&&(c=this.vwr.slm.getSelectedAtomsNoSubset(),c.and(f),this.vwr.select(c,!1,0,!0),JU.BSUtil.invertInPlace(c,this.vwr.ms.ac),c.and(f))}JU.BSUtil.andNot(c,this.vwr.slm.bsDeleted);
f=this.vwr.getBoolean(603979812);a||this.vwr.setBooleanProperty("bondModeOr",!0);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(32768),null);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(1023),null);for(var g=this.vwr.bsA(),e=21;0<=--e;)6!=e&&null!=this.getShape(e)&&this.setShapeSizeBs(e,0,null,g);null!=this.getShape(21)&&this.setShapePropertyBs(21,"off",g,null);this.setLabel(null,g);a||this.vwr.setBooleanProperty("bondModeOr",
f);this.vwr.select(c,!1,0,!0)},"~B,~B");F(c$,"hoverable",A(-1,[31,25,24,22,36]));c$.clickableMax=c$.prototype.clickableMax=JV.ShapeManager.hoverable.length-1});u("JV");x(["java.util.Hashtable"],["JV.Connection","$.Scene","$.StateManager","$.Connections"],["java.util.Arrays","JU.BS","$.SB","JM.Orientation","JU.BSUtil"],function(){c$=r(function(){this.saved=this.vwr=null;this.lastCoordinates=this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=this.lastContext=this.lastOrientation=
"";n(this,arguments)},JV,"StateManager");O(c$,function(){this.saved=new java.util.Hashtable});c$.getVariableList=c(c$,"getVariableList",function(a,b,c,f){var g=new JU.SB,e=0,h=Array(a.size()),j;for(a=a.entrySet().iterator();a.hasNext()&&((j=a.next())||1);){var l=j.getKey(),n=j.getValue();if((c||!l.startsWith("site_"))&&(!f||"@"==l.charAt(0)))h[e++]=l+("@"==l.charAt(0)?" "+n.asString():" = "+JV.StateManager.varClip(l,n.escape(),b))}java.util.Arrays.sort(h,0,e);for(b=0;b<e;b++)null!=h[b]&&g.append("  ").append(h[b]).append(";\n");
0==e&&!f&&g.append("# --no global user variables defined--;\n");return g.toString()},"java.util.Map,~N,~B,~B");c$.getObjectIdFromName=c(c$,"getObjectIdFromName",function(a){if(null==a)return-1;a="background axis1      axis2      axis3      boundbox   unitcell   frank      ".indexOf(a.toLowerCase());return 0>a?a:y(a/11)},"~S");c$.getObjectNameFromId=c(c$,"getObjectNameFromId",function(a){return 0>a||7<=a?null:"background axis1      axis2      axis3      boundbox   unitcell   frank      ".substring(11*
a,11*a+11).trim()},"~N");t(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"clear",function(a){this.vwr.setShowAxes(!1);this.vwr.setShowBbcage(!1);this.vwr.setShowUnitCell(!1);a.clear()},"JV.GlobalSettings");c(c$,"resetLighting",function(){this.vwr.setIntProperty("ambientPercent",45);this.vwr.setIntProperty("celShadingPower",10);this.vwr.setIntProperty("diffusePercent",84);this.vwr.setIntProperty("phongExponent",64);this.vwr.setIntProperty("specularExponent",6);this.vwr.setIntProperty("specularPercent",
22);this.vwr.setIntProperty("specularPower",40);this.vwr.setIntProperty("zDepth",0);this.vwr.setIntProperty("zShadePower",3);this.vwr.setIntProperty("zSlab",50);this.vwr.setBooleanProperty("specular",!0);this.vwr.setBooleanProperty("celShading",!1);this.vwr.setBooleanProperty("zshade",!1)});c(c$,"setCrystallographicDefaults",function(){this.vwr.setAxesMode(603979808);this.vwr.setShowAxes(!0);this.vwr.setShowUnitCell(!0);this.vwr.setBooleanProperty("perspectiveDepth",!1)});c(c$,"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$,"getNoCase",function(a,b){for(var c,f=a.entrySet().iterator();f.hasNext()&&((c=f.next())||1);)if(c.getKey().equalsIgnoreCase(b))return c.getValue();return null},"java.util.Map,~S");c(c$,"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$,"saveScene",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Scene_");
else{var c=new JV.Scene(b);c.saveName=this.lastScene="Scene_"+a;this.saved.put(c.saveName,c)}},"~S,java.util.Map");c(c$,"restoreScene",function(a,b){var c=JV.StateManager.getNoCase(this.saved,0<a.length?"Scene_"+a:this.lastScene);return null!=c&&c.restore(this.vwr,b)},"~S,~N");c(c$,"saveOrientation",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Orientation_");else{var c=new JM.Orientation(this.vwr,a.equalsIgnoreCase("default"),b);c.saveName=this.lastOrientation="Orientation_"+
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b&&b.zap(),b=this.vwr.getZapName());this.setStatusChanged("fileLoaded",g,a,!1);null!=f&&this.setStatusChanged("fileLoadError",g,f,!1);var j=this.jmolScriptCallback(J.c.CBK.LOADSTRUCT);e&&this.notifyEnabled(J.c.CBK.LOADSTRUCT)&&(e=this.vwr.getP("_smilesString"),0!=e.length&&(b=e),this.cbl.notifyCallback(J.c.CBK.LOADSTRUCT,v(-1,[j,a,b,c,f,Integer.$valueOf(g),this.vwr.getP("_modelNumber"),this.vwr.getModelNumberDotted(this.vwr.ms.mc-1),h])))},"~S,~S,~S,~S,~N,~B,Boolean");c(c$,"setStatusFrameChanged",
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this.jsl?null:this.jsl.getRegistryInfo()});c(c$,"dialogAsk",function(a,b,c){var f=a.equals("Save Image"),g=J.api.Interface.getOption("dialog.Dialog",this.vwr,"status");if(null==g)return null;g.setupUI(!1);f&&g.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);a=g.getFileNameFromDialog(this.vwr,a,b);f&&null!=a&&(this.qualityJPG=g.getQuality("JPG"),this.qualityPNG=g.getQuality("PNG"),f=g.getType(),null!=c&&(c.put("qualityJPG",Integer.$valueOf(this.qualityJPG)),c.put("qualityPNG",Integer.$valueOf(this.qualityPNG)),
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"JV.TransformManager","java.lang.Boolean $.Float java.util.Hashtable JU.P4 $.Quat $.SB J.api.Interface JU.Escape $.Logger".split(" "),function(){c$=r(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.navigationDepthPercent=
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.internalSlab=this.zShadeEnabled=this.slabEnabled=!1;this.depthValue=this.slabValue=
this.depthPercentSetting=this.slabPercentSetting=0;this.zSlabPercentSetting=50;this.zDepthPercentSetting=0;this.zSlabPoint=null;this.slabRange=this.zDepthValue=this.zSlabValue=0;this.depthPlane=this.slabPlane=null;this.perspectiveDepth=!0;this.scale3D=!1;this.cameraDepthSetting=this.cameraDepth=3;this.visualRangeAngstroms=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.iScrPt=this.fScrPt=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.stereoDoubleFull=
this.stereoDoubleDTI=!1;this.stereoDegrees=NaN;this.stereoRadians=0;this.stereoFrame=!1;this.matrixStereo=null;this.windowCentered=!1;this.ptOffset=this.bsSelectedAtoms=this.bsFrameOffsets=this.frameOffsets=this.frameOffset=null;this.navMode=1;this.zoomFactor=3.4028235E38;this.navigationSlabOffset=0;this.nav=null;n(this,arguments)},JV,"TransformManager");O(c$,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=new JU.P3;this.matrixTemp=new JU.M4;this.vectorTemp=
new JU.V3;this.fixedRotationOffset=new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.pointT2=new JU.P3;this.rotationAxis=new JU.V3;
this.fixedTranslation=new JU.P3;this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=new JU.M4;this.fScrPt=new JU.P3;this.iScrPt=new JU.P3i;this.ptVibTemp=new JU.Point3fi;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.c.STER.NONE;this.matrixStereo=new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=
new JU.P3});t(c$,function(){});c$.getTransformManager=c(c$,"getTransformManager",function(a,b,c,f){f=f?J.api.Interface.getInterface("JV.TransformManager4D",a,"tm"):new JV.TransformManager;f.vwr=a;f.setScreenParameters(b,c,!0,!1,!0,!0);return f},"JV.Viewer,~N,~N,~B");c(c$,"setDefaultPerspective",function(){this.setCameraDepthPercent(3,!0);this.setPerspectiveDepth(!0);this.setStereoDegrees(-5);this.visualRangeAngstroms=5;this.setSpinOff();this.setVibrationPeriod(0)});c(c$,"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$,"setFixedRotationCenter",function(a){null!=a&&this.fixedRotationCenter.setT(a)},"JU.T3");c(c$,"setRotationPointXY",function(a){a=this.transformPt(a);this.fixedTranslation.set(a.x,a.y,0)},"JU.P3");c(c$,"spinXYBy",function(a,b,c){if(0==a&&0==b)null!=this.spinThread&&this.spinIsGesture&&
this.clearSpin();else{this.clearSpin();var f=JU.P3.newP(this.fixedRotationCenter),g=new JU.P3;this.transformPt3f(f,g);a=JU.P3.new3(-b,a,0);a.add(g);this.unTransformPoint(a,a);this.vwr.setInMotion(!1);this.rotateAboutPointsInternal(null,a,f,10*c,NaN,!1,!0,null,!0,null,null,null,null)}},"~N,~N,~N");c(c$,"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,f,g,e){null==c?this.matrixRotate.mul2(a,this.matrixRotate):(this.vwr.moveAtoms(e,a,this.matrixRotate,f,this.internalRotationCenter,b,c,g),null!=f&&this.internalRotationCenter.add(f))},"JU.M3,~B,JU.BS,JU.V3,~B,JU.M4");c(c$,"rotate3DBall",function(a,b,c){this.matrixTemp3.setAsBallRotation(0.017453292,-b,-a)&&this.applyRotation(this.matrixTemp3,!1,c,null,!1,null)},"~N,~N,JU.BS");c(c$,"rotateXRadians",function(a,b){this.applyRotation(this.matrixTemp3.setAsXRotation(a),
!1,b,null,!1,null)},"~N,JU.BS");c(c$,"rotateYRadians",function(a,b){this.applyRotation(this.matrixTemp3.setAsYRotation(a),!1,b,null,!1,null)},"~N,JU.BS");c(c$,"rotateZRadians",function(a){this.applyRotation(this.matrixTemp3.setAsZRotation(a),!1,null,null,!1,null)},"~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,null)},"JU.A4,JU.BS");
c(c$,"rotateAxisAngleAtCenter",function(a,b,c,f,g,e,h){null!=b&&this.moveRotationCenter(b,!0);e&&this.setSpinOff();this.setNavOn(!1);if(this.vwr.headless){if(e&&3.4028235E38==g)return!1;e=!1}if(Float.isNaN(f)||0==f||0==g)return!1;null!=b&&this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(c);this.rotationRate=f;if(e)return this.fixedRotationAxis.setVA(c,0.017453292*f),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=h,this.setSpin(a,!0,g,null,null,
h,!1),3.4028235E38!=g;a=0.017453292*g;this.fixedRotationAxis.setVA(c,g);this.rotateAxisAngleRadiansFixed(a,h);return!0},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAxisAngleRadiansFixed",function(a,b){this.axisangleT.setAA(this.fixedRotationAxis);this.axisangleT.angle=a;this.rotateAxisAngle2(this.axisangleT,b)},"~N,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,c,f,g,e,h,j,l,n,m,p,q){h&&this.setSpinOff();this.setNavOn(!1);if(null==p&&(null==n||0.001>n.length())&&(h?
Float.isNaN(f)||0==f:0==g))return!1;var r=null;null==p&&(r=JU.V3.newVsub(c,b),e&&r.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(r),this.internalTranslation=null==n?null:JU.V3.newV(n));b=null!=j;if(h)return null==p?(0==g&&(g=NaN),Float.isNaN(g)?this.rotationRate=f:(q=y(Math.abs(g)/Math.abs(f)*this.spinFps+0.5),this.rotationRate=g/q*this.spinFps,null!=n&&this.internalTranslation.scale(1/q)),this.internalRotationAxis.setVA(r,0.017453292*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),
this.isSpinInternal=!0,this.isSpinFixed=!1,this.isSpinSelected=b):g=f,this.setSpin(a,!0,g,m,p,j,l),!Float.isNaN(g);a=0.017453292*g;this.internalRotationAxis.setVA(r,a);this.rotateAxisAngleRadiansInternal(a,j,q);return!1},"J.api.JmolScriptEvaluator,JU.T3,JU.T3,~N,~N,~B,~B,JU.BS,~B,JU.V3,JU.Lst,~A,JU.M4");c(c$,"rotateAxisAngleRadiansInternal",function(a,b,c){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,c);null==b&&this.getNewFixedRotationCenter()},"~N,JU.BS,JU.M4");c(c$,"getNewFixedRotationCenter",function(){this.axisangleT.setAA(this.internalRotationAxis);this.axisangleT.angle=-this.internalRotationAngle;this.matrixTemp4.setToAA(this.axisangleT);this.vectorT.setT(this.internalRotationCenter);this.pointT2.sub2(this.fixedRotationCenter,this.vectorT);
var a=this.matrixTemp4.rotTrans2(this.pointT2,new JU.P3);a.add(this.vectorT);this.setRotationCenterAndRadiusXYZ(a,!1)});c(c$,"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 y(Math.floor(b/100*this.width));case "y":return y(Math.floor(b/100*this.height));case "z":return y(Math.floor(b/100*this.screenPixelCount))}return 0},"~S,~N");c(c$,"angstromsToPixels",function(a){return y(Math.floor(this.scalePixelsPerAngstrom*a))},"~N");c(c$,"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$,"getTranslationScript",function(){var a="",b=this.getTranslationXPercent();0!=b&&(a+="translate x "+b+";");b=this.getTranslationYPercent();0!=b&&(a+="translate y "+b+";");return a});c(c$,"getOrientationText",function(a,b){switch(a){case 4129:return this.getMoveToText(1,!1);case 1073742132:var c=this.getRotationQ();b&&(c=c.inv());return c.toString();case 1073742178:var c=new JU.SB,f=this.getTranslationXPercent();
JV.TransformManager.truncate2(c,b?-f:f);f=this.getTranslationYPercent();JV.TransformManager.truncate2(c,b?-f:f);return c.toString();default:return this.getMoveToText(1,!0)+"\n#OR\n"+this.getRotateZyzText(!0)}},"~N,~B");c(c$,"getRotationQ",function(){return JU.Quat.newM(this.matrixRotate)});c(c$,"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;
b.setM(this.matrixRotate);a.put("axisAngle",b);a.put("quaternion",this.getRotationQ().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.$valueOf(this.navigationDepthPercent)));return a});c(c$,"getRotation",function(a){a.setM3(this.matrixRotate)},"JU.M3");c(c$,"setZoomHeight",function(a,b){this.zoomHeight=a;this.scaleFitToScreen(!1,b,!1,!0)},"~B,~B");c(c$,"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$,"zoomByFactor",function(a,b,c){!(0>=a)&&this.zoomEnabled&&(1!=this.mode?(this.zoomRatio=a,this.zmPctSet*=a,this.resetXYCenter(b,c)):this.getNav()&&this.nav.zoomByFactor(a,b,c))},"~N,~N,~N");c(c$,"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$,"setSlabRange",function(a){this.slabRange=a},"~N");c(c$,"setSlabEnabled",function(a){this.vwr.g.setB("slabEnabled",this.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$,"slabReset",function(){this.slabToPercent(100);this.depthToPercent(0);this.slabPlane=this.depthPlane=null;this.setSlabEnabled(!1);this.setZShadeEnabled(!1);this.slabDepthChanged()});c(c$,"getSlabPercentSetting",function(){return this.slabPercentSetting});c(c$,"slabDepthChanged",function(){this.vwr.g.setI("slab",this.slabPercentSetting);this.vwr.g.setI("depth",this.depthPercentSetting);this.finalizeTransformParameters()});
c(c$,"slabByPercentagePoints",function(a){this.slabPlane=null;if(!(0>a?this.slabPercentSetting<=Math.max(0,this.depthPercentSetting):100<=this.slabPercentSetting))this.slabPercentSetting+=a,this.slabDepthChanged(),this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1)},"~N");c(c$,"depthByPercentagePoints",function(a){this.depthPlane=null;if(!(0>a?0>=this.depthPercentSetting:this.depthPercentSetting>=Math.min(100,this.slabPercentSetting)))this.depthPercentSetting+=
a,this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1),this.slabDepthChanged()},"~N");c(c$,"slabDepthByPercentagePoints",function(a){this.depthPlane=this.slabPlane=null;if(!(0>a?this.slabPercentSetting<=Math.max(0,this.depthPercentSetting):this.depthPercentSetting>=Math.min(100,this.slabPercentSetting)))this.slabPercentSetting+=a,this.depthPercentSetting+=a,this.slabDepthChanged()},"~N");c(c$,"slabToPercent",function(a){this.slabPlane=null;this.vwr.setFloatProperty("slabRange",
0);this.slabPercentSetting=a;this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1);this.slabDepthChanged()},"~N");c(c$,"depthToPercent",function(a){this.depthPlane=null;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$,"slabInternal",function(a,b){b?(this.depthPlane=a,this.depthPercentSetting=0):(this.slabPlane=a,this.slabPercentSetting=100);this.slabDepthChanged()},"JU.P4,~B");c(c$,"setSlabDepthInternal",function(a){a?this.depthPlane=null:this.slabPlane=null;this.finalizeTransformParameters();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(y(this.screenWidth/
2),y(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(y(this.screenWidth/2),y(this.screenHeight/2),0);this.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);var c=JU.P3.new3(y(this.screenWidth/2),y(this.screenHeight/2),this.cameraDistanceFromCenter*this.scalePixelsPerAngstrom);this.unTransformPoint(c,c);c.sub(this.fixedRotationCenter);b.add(c);return v(-1,[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$,"setScreenParameters0",function(a,b,c,f,g,e){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=c,this.width=(this.antialias=f)?2*a:a,this.height=f?2*b:b,this.scaleFitToScreen(!1,c,g,e))},"~N,~N,~B,~B,~B,~B");c(c$,"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$,"scaleFitToScreen",function(a,b,c,f){0==this.width||0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*(a?0.5:this.xTranslationFraction),this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),f&&this.resetNavigationPoint(c),this.zoomHeight&&(b=this.height>this.width),this.screenPixelCount=
b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");c(c$,"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$,"setNavigationMode",function(a){this.mode=a?1:this.defaultMode;this.resetNavigationPoint(!0)},"~B");c(c$,"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$,"calcSlabAndDepthValues",function(){this.slabValue=1>this.slabRange?this.zValueFromPercent(this.slabPercentSetting):
y(Math.floor(this.modelCenterOffset*this.slabRange/(2*this.modelRadius)*(this.zmPctSet/100)));this.depthValue=this.zValueFromPercent(this.depthPercentSetting);this.zSlabPercentSetting==this.zDepthPercentSetting?(this.zSlabValue=this.slabValue,this.zDepthValue=this.depthValue):(this.zSlabValue=this.zValueFromPercent(this.zSlabPercentSetting),this.zDepthValue=this.zValueFromPercent(this.zDepthPercentSetting));if(null!=this.zSlabPoint)try{this.transformPt3f(this.zSlabPoint,this.pointT2),this.zSlabValue=
B(this.pointT2.z)}catch(a){if(!E(a,Exception))throw a;}this.vwr.g.setO("_slabPlane",JU.Escape.eP4(this.getSlabDepthPlane(!1)));this.vwr.g.setO("_depthPlane",JU.Escape.eP4(this.getSlabDepthPlane(!0)));this.slabEnabled||(this.slabValue=0,this.depthValue=2147483647)});c(c$,"zValueFromPercent",function(a){return y(Math.floor((1-a/50)*this.modelRadiusPixels+this.modelCenterOffset))},"~N");c(c$,"calcTransformMatrix",function(){this.matrixTransform.setIdentity();this.vectorTemp.sub2(this.frameOffset,this.fixedRotationCenter);
this.matrixTransform.setTranslation(this.vectorTemp);this.matrixTemp.setToM3(this.stereoFrame?this.matrixStereo:this.matrixRotate);this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTemp.setIdentity();this.matrixTemp.m00=this.matrixTemp.m11=this.matrixTemp.m22=this.scalePixelsPerAngstrom;this.matrixTemp.m11=this.matrixTemp.m22=-this.scalePixelsPerAngstrom;this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTransform.m23+=this.modelCenterOffset;try{this.matrixTransformInv.setM4(this.matrixTransform).invert()}catch(a){if(E(a,
Exception))System.out.println("ERROR INVERTING matrixTransform!");else throw a;}});c(c$,"rotatePoint",function(a,b){this.matrixRotate.rotate2(a,b);b.y=-b.y},"JU.T3,JU.T3");c(c$,"getScreenTemp",function(a){this.matrixTransform.rotTrans2(a,this.fScrPt)},"JU.T3");c(c$,"transformPtScr",function(a,b){b.setT(this.transformPt(a))},"JU.T3,JU.P3i");c(c$,"transformPtScrT3",function(a,b){this.transformPt(a);b.setT(this.fScrPt)},"JU.T3,JU.T3");c(c$,"transformPt3f",function(a,b){this.applyPerspective(a,a);b.setT(this.fScrPt)},
"JU.T3,JU.P3");c(c$,"transformPtNoClip",function(a,b){this.applyPerspective(a,null);b.setT(this.fScrPt)},"JU.T3,JU.T3");c(c$,"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){return a.setCalcPoint(b,this.vibrationT,Float.isNaN(c)?this.vibrationScale:c,this.vwr.g.modulationScale)},
"JU.Vibration,JU.T3,~N");c(c$,"transformPt2D",function(a){-3.4028235E38==a.z?(this.iScrPt.x=y(Math.floor(a.x/100*this.screenWidth)),this.iScrPt.y=y(Math.floor((1-a.y/100)*this.screenHeight))):(this.iScrPt.x=B(a.x),this.iScrPt.y=this.screenHeight-B(a.y));this.antialias&&(this.iScrPt.x<<=1,this.iScrPt.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.fScrPt);this.iScrPt.z=B(this.fScrPt.z);return this.iScrPt},"JU.T3");c(c$,"applyPerspective",function(a,b){this.getScreenTemp(a);var c=
this.fScrPt.z;Float.isNaN(c)?(!this.haveNotifiedNaN&&JU.Logger.debugging&&JU.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=!0,c=this.fScrPt.z=1):0>=c&&(c=this.fScrPt.z=1);switch(this.mode){case 1:this.fScrPt.x-=this.navigationShiftXY.x;this.fScrPt.y-=this.navigationShiftXY.y;break;case 2:this.fScrPt.x+=this.perspectiveShiftXY.x,this.fScrPt.y+=this.perspectiveShiftXY.y}this.perspectiveDepth&&(c=this.getPerspectiveFactor(c),this.fScrPt.x*=c,this.fScrPt.y*=c);switch(this.mode){case 1:this.fScrPt.x+=
this.navigationOffset.x;this.fScrPt.y+=this.navigationOffset.y;break;case 2:this.fScrPt.x-=this.perspectiveShiftXY.x,this.fScrPt.y-=this.perspectiveShiftXY.y;case 0:this.fScrPt.x+=this.fixedRotationOffset.x,this.fScrPt.y+=this.fixedRotationOffset.y}Float.isNaN(this.fScrPt.x)&&!this.haveNotifiedNaN&&(JU.Logger.debugging&&JU.Logger.debug("NaN found in transformPoint "),this.haveNotifiedNaN=!0);this.iScrPt.set(B(this.fScrPt.x),B(this.fScrPt.y),B(this.fScrPt.z));null!=b&&this.xyzIsSlabbedInternal(b)&&
(this.fScrPt.z=this.iScrPt.z=1);return this.iScrPt},"JU.T3,JU.T3");c(c$,"xyzIsSlabbedInternal",function(a){return null!=this.slabPlane&&0<a.x*this.slabPlane.x+a.y*this.slabPlane.y+a.z*this.slabPlane.z+this.slabPlane.w||null!=this.depthPlane&&0>a.x*this.depthPlane.x+a.y*this.depthPlane.y+a.z*this.depthPlane.z+this.depthPlane.w},"JU.T3");c(c$,"move",function(a,b,c,f,g,e,h){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm");this.movetoThread.setManager(this,this.vwr,v(-1,
[b,f,I(-1,[c,g,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 f=JU.M3.newA9(c);f.invert();var g=c[9],e=-c[10],h=-c[11],j=JU.P3.new3(c[12],c[13],c[14]),l=c[15],n=c[16],m=c[17];this.setPerspectiveDepth(!(0<=m));var m=Math.abs(m)/2,p=Math.tan(3.141592653589793*m/180),m=h*p,p=0.5/p-0.5,q=50/m;0<l&&(l=50+B((h-l)*q),h=50+B((h-n)*q),this.setSlabEnabled(!0),this.slabToPercent(l),this.depthToPercent(h),21==c.length&&(n=0!=c[18],q=0!=c[19],c=c[20],this.setZShadeEnabled(n),n&&(q?this.vwr.setIntProperty("zSlab",B(Math.min(100,l+c*(h-l)))):this.vwr.setIntProperty("zSlab",
B((l+h)/2)),this.vwr.setIntProperty("zDepth",h))));this.moveTo(a,b,j,null,0,f,100,NaN,NaN,m,null,NaN,NaN,NaN,p,g,e);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(c$,"moveTo",function(a,b,c,f,g,e,h,j,l,n,m,p,q,r,t,u,x){if(null==e)if(e=new JU.M3,f=JU.V3.newV(f),Float.isNaN(g))e.m00=NaN;else if(0.01>g&&-0.01<g)e.setScale(1);else{if(0==f.x&&0==f.y&&0==f.z)return;var y=new JU.A4;y.setVA(f,g/57.29577951308232);e.setAA(y)}u==this.cameraSetting.x&&(u=NaN);x==this.cameraSetting.y&&(x=NaN);t==this.cameraDepth&&
(t=NaN);Float.isNaN(u)||(j=50*u/n/this.width*this.screenPixelCount);Float.isNaN(x)||(l=50*x/n/this.height*this.screenPixelCount);g=null==c?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(n);if(0>=b)this.setAll(c,e,m,h,j,l,n,g,r,p,q,t,u,x),this.vwr.moveUpdate(b),this.vwr.finalizeTransformParameters();else try{null==this.movetoThread&&(this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm"));var A=this.movetoThread.setManager(this,this.vwr,v(-1,[c,e,m,I(-1,[b,h,
j,l,n,g,r,p,q,t,u,x])]));0>=A||this.vwr.g.waitForMoveTo?(0<A&&this.movetoThread.setEval(a),this.movetoThread.run(),this.vwr.isSingleThreaded||(this.movetoThread=null)):this.movetoThread.start()}catch(B){if(!E(B,Exception))throw B;}},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.T3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(c$,"setAll",function(a,b,c,f,g,e,h,j,l,n,m,p,q,r){Float.isNaN(b.m00)||this.setRotation(b);null!=a&&this.moveRotationCenter(a,!this.windowCentered);null!=c&&1==this.mode&&this.navigationCenter.setT(c);
Float.isNaN(p)||this.setCameraDepthPercent(p,!1);!Float.isNaN(q)&&!Float.isNaN(r)&&this.setCamera(q,r);Float.isNaN(f)||this.zoomToPercent(f);Float.isNaN(h)||(this.modelRadius=h);Float.isNaN(j)||(this.scaleDefaultPixelsPerAngstrom=j);!Float.isNaN(g)&&!Float.isNaN(e)&&(this.translateToPercent("x",g),this.translateToPercent("y",e));1==this.mode&&(!Float.isNaN(n)&&!Float.isNaN(m)&&this.navTranslatePercentOrTo(0,n,m),Float.isNaN(l)||this.setNavigationDepthPercent(l))},"JU.P3,JU.M3,JU.P3,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");
c(c$,"stopMotion",function(){this.movetoThread=null});c(c$,"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$,"getRotateXyzText",function(){var a=new JU.SB,b=this.matrixRotate.m20,
c=-(57.29577951308232*Math.asin(b)),f;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,this.matrixRotate.m11)),f=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,this.matrixRotate.m22),f=57.29577951308232*Math.atan2(this.matrixRotate.m10,this.matrixRotate.m00));a.append("reset");a.append(";center ").append(this.getCenterText());0!=b&&(a.append("; rotate x"),JV.TransformManager.truncate2(a,b));0!=c&&(a.append("; rotate y"),JV.TransformManager.truncate2(a,c));0!=f&&
(a.append("; rotate z"),JV.TransformManager.truncate2(a,f));a.append(";");this.addZoomTranslationNavigationText(a);return a.toString()});c(c$,"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.navigationDepthPercent),a.append(";"))},"JU.SB");c(c$,"getRotateZyzText",function(a){var b=new JU.SB,c=this.vwr.ms.getInfoM("defaultOrientationMatrix");null==c?c=this.matrixRotate:(c=JU.M3.newM3(c),c.invert(),c.mul2(this.matrixRotate,c));var f=c.m22,g=57.29577951308232*Math.acos(f);0.999<f||-0.999>f?(f=57.29577951308232*Math.atan2(c.m10,c.m11),c=0):(f=57.29577951308232*Math.atan2(c.m21,-c.m20),c=57.29577951308232*Math.atan2(c.m12,c.m02));0!=f&&(0!=g&&0!=c&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");
b.append("reset");b.append(";center ").append(this.getCenterText());0!=f&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,f));0!=g&&(b.append("; rotate y"),JV.TransformManager.truncate2(b,g));0!=c&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,c));b.append(";");this.addZoomTranslationNavigationText(b);return b.toString()},"~B");c$.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,f,g,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.vwr,"tm"),this.spinThread.setManager(this,this.vwr,v(-1,[Float.$valueOf(c),
f,g,e,h?Boolean.TRUE:null])),this.spinIsGesture=h,Float.isNaN(c)||3.4028235E38==c||!this.vwr.g.waitForMoveTo?this.spinThread.start():(this.spinThread.setEval(a),this.spinThread.run())):null!=this.spinThread&&(this.spinThread.reset(),this.spinThread=null))},"J.api.JmolScriptEvaluator,~B,~N,JU.Lst,~A,JU.BS,~B");c(c$,"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.vwr,"tm"),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=B(1E3*this.vibrationPeriod);if(0<a)return;a=-a}this.setVibrationOn(0<a&&0<=this.vwr.ms.getLastVibrationVector(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$,"setVibrationOn",function(a){a?1>this.vwr.ms.mc?(this.vibrationOn=
!1,this.vibrationT.x=0):(null==this.vibrationThread&&(this.vibrationThread=J.api.Interface.getOption("thread.VibrationThread",this.vwr,"tm"),this.vibrationThread.setManager(this,this.vwr,null),this.vibrationThread.start()),this.vibrationOn=!0):(null!=this.vibrationThread&&(this.vibrationThread.interrupt(),this.vibrationThread=null),this.vibrationOn=!1,this.vibrationT.x=0)},"~B");c(c$,"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;this.stereoDoubleDTI=a===J.c.STER.DTI;this.stereoDoubleFull=a===J.c.STER.DOUBLE},"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$,"setRotationRadius",function(a,b){a=this.modelRadius=0>=a?this.vwr.ms.calcRotationRadius(this.vwr.am.cmi,this.fixedRotationCenter,!0):a;b&&this.vwr.setRotationRadius(a,!1);return a},"~N,~B");c(c$,"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.ms.calcRotationRadius(this.vwr.am.cmi,this.fixedRotationCenter,!0)))},"JU.T3,~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",
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"~N,JU.P3");c(c$,"setFrameOffset",function(a){null==this.frameOffsets||0>a||a>=this.frameOffsets.length?this.frameOffset.set(0,0,0):this.frameOffset.setT(this.frameOffsets[a])},"~N");c(c$,"setSelectedTranslation",function(a,b,c){this.bsSelectedAtoms=a;switch(b){case "X":case "x":this.ptOffset.x+=c;break;case "Y":case "y":this.ptOffset.y+=c;break;case "Z":case "z":this.ptOffset.z+=c}},"JU.BS,~S,~N");c(c$,"setNavFps",function(a){this.navFps=a},"~N");c(c$,"calcCameraFactors",function(){Float.isNaN(this.cameraDepth)&&
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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.visualRangeAngstroms*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$,"unTransformPoint",function(a,b){this.untransformedPoint.setT(a);switch(this.mode){case 1:this.untransformedPoint.x-=this.navigationOffset.x;this.untransformedPoint.y-=this.navigationOffset.y;break;case 2:this.fScrPt.x+=this.perspectiveShiftXY.x,this.fScrPt.y+=this.perspectiveShiftXY.y;case 0:this.untransformedPoint.x-=this.fixedRotationOffset.x,
this.untransformedPoint.y-=this.fixedRotationOffset.y}if(this.perspectiveDepth){var c=this.getPerspectiveFactor(this.untransformedPoint.z);this.untransformedPoint.x/=c;this.untransformedPoint.y/=c}switch(this.mode){case 1:this.untransformedPoint.x+=this.navigationShiftXY.x;this.untransformedPoint.y+=this.navigationShiftXY.y;break;case 2:this.untransformedPoint.x-=this.perspectiveShiftXY.x,this.untransformedPoint.y-=this.perspectiveShiftXY.y}this.matrixTransformInv.rotTrans2(this.untransformedPoint,
b)},"JU.T3,JU.T3");c(c$,"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$,"setNavigatePt",function(a){this.navigationCenter.setT(a);this.navMode=3;this.navigating=!0;this.finalizeTransformParameters();
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f,g,e){var h=1==this.mode?JU.P3.newP(this.navigationCenter):null,j=JU.P3.newP(this.navigationOffset);j.x/=this.width;j.y/=this.height;this.setScreenParameters0(a,b,c,f,g,e);null!=h&&(this.navigationCenter.setT(h),this.navTranslatePercentOrTo(-1,j.x*this.width,j.y*this.height),this.setNavigatePt(h))},"~N,~N,~B,~B,~B,~B");c(c$,"navInterrupt",function(){null!=this.nav&&this.nav.interrupt()});c(c$,"getNav",function(){if(null!=this.nav)return!0;this.nav=J.api.Interface.getOption("navigate.Navigator",this.vwr,
"tm");if(null==this.nav)return!1;this.nav.set(this,this.vwr);return!0});c(c$,"navigateList",function(a,b){this.getNav()&&this.nav.navigateList(a,b)},"J.api.JmolScriptEvaluator,JU.Lst");c(c$,"navigateAxis",function(a,b){this.getNav()&&this.nav.navigateAxis(a,b)},"JU.V3,~N");c(c$,"setNavigationOffsetRelative",function(){this.getNav()&&this.nav.setNavigationOffsetRelative()});c(c$,"navigateKey",function(a,b){this.getNav()&&this.nav.navigateKey(a,b)},"~N,~N");c(c$,"setNavigationDepthPercent",function(a){this.getNav()&&
this.nav.setNavigationDepthPercent(a)},"~N");c(c$,"navTranslatePercentOrTo",function(a,b,c){this.getNav()&&this.nav.navTranslatePercentOrTo(a,b,c)},"~N,~N,~N");c(c$,"calcNavigationPoint",function(){this.getNav()&&this.nav.calcNavigationPoint()});c(c$,"getNavigationState",function(){return 1==this.mode&&this.getNav()?this.nav.getNavigationState():""});F(c$,"DEFAULT_SPIN_Y",30,"DEFAULT_SPIN_FPS",30,"DEFAULT_NAV_FPS",10,"DEFAULT_VISUAL_RANGE",5,"DEFAULT_STEREO_DEGREES",-5,"MODE_STANDARD",0,"MODE_NAVIGATION",
1,"MODE_PERSPECTIVE_PYMOL",2,"DEFAULT_PERSPECTIVE_MODEL",11,"DEFAULT_PERSPECTIVE_DEPTH",!0,"DEFAULT_CAMERA_DEPTH",3,"degreesPerRadian",57.29577951308232,"MAXIMUM_ZOOM_PERCENTAGE",2E5,"MAXIMUM_ZOOM_PERSPECTIVE_DEPTH",1E4,"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)});u("JV");x(["java.lang.Enum","javajs.awt.PlatformViewer","J.api.JmolViewer","J.atomdata.AtomDataServer","java.util.Hashtable"],"JV.Viewer","java.io.BufferedInputStream $.BufferedReader $.Reader java.lang.Boolean $.Character $.Float $.NullPointerException java.util.Arrays javajs.awt.Dimension JU.AU $.BS $.CU $.DF $.Lst $.Measure $.P3 $.P3i $.PT $.Quat $.Rdr $.SB $.V3 J.adapter.smarter.SmarterJmolAdapter J.api.Interface $.JmolAppConsoleInterface J.atomdata.RadiusData J.c.FIL $.STER $.VDW J.i18n.GT JM.ModelSet JS.SV $.T J.thread.TimeoutThread JU.BSUtil $.C $.CommandHistory $.Elements $.Escape $.GData $.JmolMolecule $.Logger $.Parser $.TempArray JV.ActionManager $.AnimationManager $.ColorManager $.FileManager $.GlobalSettings $.JC $.ModelManager $.SelectionManager $.ShapeManager $.StateManager $.StatusManager $.TransformManager JV.binding.Binding".split(" "),
function(){c$=r(function(){this.queueOnHold=this.isSingleThreaded=this.haveDisplay=this.autoExit=this.testAsync=!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.appletName=this.htmlName="";this.tryPt=0;this.insertedCommand="";this.tm=this.sm=this.g=this.rm=this.slm=this.shm=this.dm=this.cm=this.am=this.acm=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.async=this.allowArrayDotNotation=!1;this.errorMessageUntranslated=this.errorMessage=this.chainList=this.chainMap=this.rd=this.defaultVdw=this.actionStatesRedo=this.actionStates=this.dimScreen=
this.executor=null;this.privateKey=0;this.headless=this.isPreviewOnly=this.dataOnly=!1;this.lastData=this.jsc=this.smilesMatcher=this.minimizer=this.dssrParser=this.annotationParser=this.ligandModelSet=this.ligandModels=this.mouse=this.movableBitSet=null;this.motionEventNumber=0;this.inMotion=!1;this.refreshing=!0;this.axesAreTainted=!1;this.maximumSize=2147483647;this.gRight=null;this.isStereoSlave=!1;this.imageFontScaling=1;this.jsParams=this.captureParams=null;this.antialiased=!1;this.hoverAtomIndex=
-1;this.hoverText=null;this.hoverLabel="%U";this.hoverEnabled=!0;this.currentCursor=0;this.ptTemp=null;this.prevFrame=-2147483648;this.prevMorphModel=0;this.haveJDX=!1;this.jsv=null;this.selectionHalosEnabled=!1;this.noFrankEcho=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=this.atomHighlighted=
-1;this.bsRotateBranch=null;this.creatingImage=!1;this.userVdwMars=this.userVdws=this.bsUserVdws=this.outputManager=null;this.currentShapeID=-1;this.localFunctions=this.currentShapeState=null;this.$isKiosk=!1;this.displayLoadErrors=!0;this.$isParallel=!1;this.stateScriptVersionInt=0;this.timeouts=this.jsExporter3D=null;this.chainCaseSpecified=!1;this.nboParser=this.triangulator=this.jsonParser=this.jcm=this.jbr=this.jzt=this.logFileName=this.nmrCalculation=null;n(this,arguments)},JV,"Viewer",J.api.JmolViewer,
[J.atomdata.AtomDataServer,javajs.awt.PlatformViewer]);c(c$,"finalize",function(){JU.Logger.debugging&&JU.Logger.debug("vwr finalize "+this);W(this,JV.Viewer,"finalize",[])});c(c$,"setInsertedCommand",function(a){this.insertedCommand=a},"~S");c$.getJmolVersion=j(c$,"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,f,g,e,h,j){var l=new java.util.Hashtable;
l.put("display",a);l.put("adapter",b);l.put("statusListener",h);l.put("platform",j);l.put("options",e);l.put("fullName",c);l.put("documentBase",f);l.put("codeBase",g);return new JV.Viewer(l)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,javajs.awt.GenericPlatform");t(c$,function(a){H(this,JV.Viewer,[]);this.commandHistory=new JU.CommandHistory;this.dimScreen=new javajs.awt.Dimension(0,0);this.rd=new J.atomdata.RadiusData(null,0,null,null);this.defaultVdw=J.c.VDW.JMOL;
this.localFunctions=new java.util.Hashtable;this.privateKey=Math.random();this.actionStates=new JU.Lst;this.actionStatesRedo=new JU.Lst;this.chainMap=new java.util.Hashtable;this.chainList=new JU.Lst;this.setOptions(a)},"java.util.Map");c(c$,"haveAccess",function(a){return this.access===a},"JV.Viewer.ACCESS");j(c$,"getModelAdapter",function(){return null==this.modelAdapter?this.modelAdapter=new J.adapter.smarter.SmarterJmolAdapter:this.modelAdapter});j(c$,"getSmartsMatch",function(a,b){null==b&&(b=
this.bsA());return this.getSmilesMatcher().getSubstructureSet(a,this.ms.at,this.ms.ac,b,2)},"~S,JU.BS");c(c$,"getSmartsMatchForNodes",function(a,b){return this.getSmilesMatcher().getSubstructureSet(a,b,b.length,null,2)},"~S,~A");c(c$,"getSmartsMap",function(a,b){null==b&&(b=this.bsA());return this.getSmilesMatcher().getCorrelationMaps(a,this.ms.at,this.ms.ac,b,2)},"~S,JU.BS");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 f=this.fullName.indexOf("__");this.htmlName=
0>f?this.fullName:this.fullName.substring(0,f);this.appletName=JU.PT.split(this.htmlName+"_","_")[0];this.syncId=0>f?"":this.fullName.substring(f+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");this.dataOnly=this.checkOption2("isDataOnly",
"\x00");this.autoExit=this.checkOption2("exit","-x");c=a.get("platform");f="unknown";null==c&&(c=this.commandOptions.contains("platform=")?this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");if(q(c,String)){f=c;JV.Viewer.isWebGL=0<=f.indexOf(".awtjs.");JV.Viewer.isJS=JV.Viewer.isWebGL||0<=f.indexOf(".awtjs2d.");this.async=!this.dataOnly&&!this.autoExit&&(this.testAsync||JV.Viewer.isJS&&a.containsKey("async"));var c=null,g="?";self.Jmol&&(c=Jmol._applets[this.htmlName.split("_object")[0]],
g=Jmol._version);null!=g&&(this.html5Applet=c,JV.Viewer.strJavaVersion=g,JV.Viewer.strJavaVendor="Java2Script "+((this,JV.Viewer).isWebGL?"(WebGL)":"(HTML5)"));c=J.api.Interface.getInterface(f,this,"setOptions")}this.apiPlatform=c;this.display=a.get("display");this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.noGraphicsAllowed=this.checkOption2("noDisplay","-n");this.headless=this.apiPlatform.isHeadless();this.haveDisplay=JV.Viewer.isWebGL||null!=this.display&&!this.noGraphicsAllowed&&
!this.headless&&!this.dataOnly;this.noGraphicsAllowed=(new Boolean(this.noGraphicsAllowed&null==this.display)).valueOf();this.headless=(new Boolean(this.headless|this.noGraphicsAllowed)).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&&!JV.Viewer.isWebGL&&(c=J.api.Interface.getOption("g3d.Graphics3D",
this,"setOptions"));this.gdata=null==c&&(JV.Viewer.isWebGL||!JV.Viewer.isJS)?new JU.GData:c;this.gdata.initialize(this,this.apiPlatform);this.stm=new JV.StateManager(this);this.cm=new JV.ColorManager(this,this.gdata);this.sm=new JV.StatusManager(this);f=a.containsKey("4DMouse");this.tm=JV.TransformManager.getTransformManager(this,2147483647,0,f);this.slm=new JV.SelectionManager(this);this.haveDisplay&&(this.acm=this.multiTouch?J.api.Interface.getOption("multitouch.ActionManagerMT",null,null):new JV.ActionManager,
this.acm.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",this,
"setOptions"));if(JV.Viewer.isJS||null!=c&&!c.equals(""))(this.rm=c).set(this,this.shm);this.ms=new JM.ModelSet(this,null);this.initialize(!0,!1);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"),!JV.Viewer.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,f=b.indexOf("#"),0<=f&&(b=b.substring(0,f)),f=b.lastIndexOf("?"),0<=f&&(b=b.substring(0,f)),f=b.lastIndexOf("/"),0<=f&&(b=b.substring(0,f)),JV.Viewer.jsDocumentBase=b,this.fm.setAppletContext(JV.Viewer.appletDocumentBase),b=a.get("appletProxy"),null!=b&&this.setStringProperty("appletProxy",b),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):JV.Viewer.isJS||(this.logFilePath=null),new J.i18n.GT(this,a.get("language")),JV.Viewer.isJS&&this.acm.createActions()):(this.gdata.setBackgroundTransparent(this.checkOption2("backgroundTransparent","-b")),(this.isSilent=this.checkOption2("silent","-i"))&&JU.Logger.setLogLevel(3),this.headless&&!this.isSilent&&JU.Logger.info("Operating headless display="+this.display+" nographicsallowed="+this.noGraphicsAllowed),
this.isSyntaxCheck=(this.isSyntaxAndFileCheck=this.checkOption2("checkLoad","-C"))||this.checkOption2("check","-c"),this.listCommands=this.checkOption2("listCommands","-l"),this.cd("."),this.headless&&(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.headless&&this.checkOption2("useCommandThread","-threaded");this.setStartupBooleans();this.setIntProperty("_nProcessors",
JV.Viewer.nProcessors);this.isSilent||JU.Logger.info("(C) 2015 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.allowScripting&&
this.getScriptManager();this.zap(!1,!0,!1);this.g.setO("language",J.i18n.GT.getLanguage());this.g.setO("_hoverLabel",this.hoverLabel);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",this,"script").init(a,this,b)},"~S,JU.Lst");c(c$,"getDataManager",function(){return null==
this.dm?this.dm=J.api.Interface.getInterface("JV.DataManager",this,"script").set(this):this.dm});c(c$,"getScriptManager",function(){if(this.allowScripting&&null==this.scm){this.scm=J.api.Interface.getInterface("JS.ScriptManager",this,"setOptions");if(JV.Viewer.isJS&&null==this.scm)throw new NullPointerException;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$,"checkOption2",function(a,
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this.setWidthHeightVar();this.haveDisplay&&(this.g.setB("_is2D",JV.Viewer.isJS&&!JV.Viewer.isWebGL),this.g.setB("_multiTouchClient",this.acm.isMTClient()),this.g.setB("_multiTouchServer",this.acm.isMTServer()));this.cm.setDefaultColors(!1);this.setObjectColor("background","black");this.setObjectColor("axis1","red");this.setObjectColor("axis2","green");this.setObjectColor("axis3","blue");this.am.setAnimationOn(!1);this.am.setAnimationFps(this.g.animationFps);this.sm.playAudio(null);this.sm.allowStatusReporting=
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c(c$,"translateXYBy",function(a,b){this.tm.translateXYBy(a,b);this.refresh(2,this.sm.syncingMouse?"Mouse: translateXYBy "+a+" "+b:"")},"~N,~N");j(c$,"rotateFront",function(){this.tm.resetRotation();this.refresh(1,"Viewer:rotateFront()")});c(c$,"translate",function(a,b,c,f){var g="\x00"==c?B(b):"%"==c?this.tm.percentToPixels(a,b):this.tm.angstromsToPixels(b*("n"==c?10:1));if(null!=f){if(0==g)return;this.tm.setSelectedTranslation(f,a,g)}else switch(a){case "X":case "x":"\x00"==c?this.tm.translateToPercent("x",
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0<c.length&&a.put("filter",c)}c=b&&!this.g.appendNew&&0<this.ms.ac;a.put("baseAtomIndex",Integer.$valueOf(b?this.ms.ac:0));a.put("baseModelIndex",Integer.$valueOf(0==this.ms.ac?0:this.ms.mc+(c?-1:0)));c&&a.put("merging",Boolean.TRUE);return a},"java.util.Map,~B");j(c$,"openFileAsyncSpecial",function(a,b){this.getScriptManager().openFileAsync(a,b)},"~S,~N");j(c$,"openFile",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(null,a,null,null)},"~S");j(c$,"openFiles",function(a){this.zap(!0,
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c.length+") "+a+" ms");c=e.get("fullPathNames");n=e.get("fileTypes");h=h.toString();for(a=0;a<c.length;a++)b=c[a],null!=n&&null!=n[a]&&(b=n[a]+"::"+b),h=JU.PT.rep(h,"$FILENAME"+(a+1)+"$",JU.PT.esc(JV.FileManager.fixDOSName(b)));h=(new JU.SB).append(h)}else null==f?(null==h&&(h=(new JU.SB).append("load /*file*/$FILENAME$")),j=this.openFileFull(b,g,e,h)):j=q(f,java.io.Reader)||q(f,java.io.BufferedInputStream)||JU.AU.isAB(f)?this.fm.createAtomSetCollectionFromReader(a,b,f,this.setLoadParameters(e,g)):
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new java.util.Hashtable);this.ligandModelSet.put(a,Boolean.TRUE);null==this.ligandModels&&(this.ligandModels=new java.util.Hashtable);var h=a.indexOf("|");0<=h&&(a=a.substring(a.indexOf("|")+1));var j=null==f?this.ligandModels.get(a):null,g=null;if(q(j,Boolean))return null;if(null==j&&(null==f||0<=h))j=this.ligandModels.get(a+c);var h=!1,l=null==j;if(l){if(e){g=this.setLoadFormat("#"+a,"#",!1);if(0==g.length)return null;this.scriptEcho("fetching "+g);j=this.getFileAsString3(g,!1,null)}else this.scriptEcho("fetching "+
b),j=this.getFileAsString3(b,!1,null),f=null==f?-1:j.indexOf(f),0<=f&&(j=j.substring(0,f));(h=0==j.indexOf("java."))||this.ligandModels.put(a+c,j)}if(!e)return l||this.scriptEcho(b+" loaded from cache"),j;!h&&q(j,String)&&(b=j,0!=b.length&&(c=new java.util.Hashtable,c.put("modelOnly",Boolean.TRUE),j=this.getModelAdapter().getAtomSetCollectionReader("ligand",null,JU.Rdr.getBR(b),c),h=q(j,String),h||(j=this.getModelAdapter().getAtomSetCollection(j),h=q(j,String),null!=g&&!h&&this.scriptEcho(this.getModelAdapter().getAtomSetCollectionAuxiliaryInfo(j).get("modelLoadNote")))));
return h?(this.scriptEcho(j.toString()),this.ligandModels.put(a,Boolean.FALSE),null):j},"~S,~S,~S,~S");c(c$,"openFileFull",function(a,b,c,f){if(null==a||a.equals("String[]"))return null;var g,e="openFile("+a+")";JU.Logger.startTimer(e);c=this.setLoadParameters(c,b);var h=a.startsWith("@"),j=c.containsKey("fileData");0==a.indexOf("$")&&c.put("smilesString",a.substring(1));var l=a.equals("string")||a.equals("Jmol Model Kit");g=null;if(j){if(g=c.get("fileData"),c.containsKey("isData"))return e=this.loadInlineScript(g,
"\x00",b,c),this.lastData=this.g.preserveState?this.getDataManager().createFileData(g):null,e}else if(l){g=this.ms.getInlineData(-1);if(null==g)if(this.g.modelKitMode)g="5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63";else return"cannot find string data";null!=f&&c.put("loadScript",f=(new JU.SB).append(JU.PT.rep(f.toString(),"/*file*/$FILENAME$",'/*data*/data "model inline"\n'+g+'end "model inline"')))}null!=g?(b||this.zap(!0,!1,!1),!h&&(!j||l)&&this.getStateCreator().getInlineData(f,
g,b,this.g.defaultLoadFilter),g=this.fm.createAtomSetCollectionFromString(g,c,b)):g=this.fm.createAtomSetCollectionFromFile(a,c,b);JU.Logger.checkTimer(e,!1);return g},"~S,~B,java.util.Map,JU.SB");j(c$,"openStringInline",function(a){a=this.openStringInlineParamsAppend(a,null,!1);this.refresh(1,"openStringInline");return a},"~S");c(c$,"loadInline",function(a){return this.loadInlineScriptRepaint(a,this.g.inlineNewlineChar,!1)},"~S");c(c$,"loadInline",function(a,b){return this.loadInlineScriptRepaint(a,
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"~A,~B");c(c$,"loadInline",function(a,b){if(null==a||0==a.size())return null;b||this.zap(!0,!1,!1);for(var c=new JU.Lst,f=0;f<a.size();f++)c.addLast(a.get(f));c=this.fm.createAtomSeCollectionFromArrayData(c,this.setLoadParameters(null,b),b);c=this.createModelSetAndReturnError(c,b,null,new java.util.Hashtable);this.refresh(1,"loadInline");return c},"java.util.List,~B");c(c$,"loadInlineScript",function(a,b,c,f){if(null==a||0==a.length)return null;a=JV.Viewer.fixInlineString(a,b);0!=b.charCodeAt(0)&&
JU.Logger.info("loading model inline, "+a.length+" bytes, with newLine character "+b.charCodeAt(0)+" isAppend="+c);JU.Logger.debugging&&JU.Logger.debug(a);b=this.getDataSeparator();var g;if(null!=b&&""!==b&&0<=(g=a.indexOf(b))&&0>a.indexOf("# Jmol state")){for(var e=2;0<=(g=a.indexOf(b,g+1));)e++;var h=Array(e),j=0,l=0;for(g=0;g<e;g++)j=a.indexOf(b,l),0>j&&(j=a.length),h[g]=a.substring(l,j),l=j+b.length;return this.openStringsInlineParamsAppend(h,f,c)}return this.openStringInlineParamsAppend(a,f,
c)},"~S,~S,~B,java.util.Map");c$.fixInlineString=c(c$,"fixInlineString",function(a,b){var c;0<=a.indexOf("\\/n")&&(a=JU.PT.rep(a,"\n",""),a=JU.PT.rep(a,"\\/n","\n"),b=String.fromCharCode(0));if(0!=b.charCodeAt(0)&&"\n"!=b){var f=0<=a.indexOf("\n"),g=a.length;for(c=0;c<g&&" "==a.charAt(c);++c);c<g&&a.charAt(c)==b&&(a=a.substring(c+1));a=f?JU.PT.rep(a,""+b,""):a.$replace(b,"\n")}return a},"~S,~S");c(c$,"openStringInlineParamsAppend",function(a,b,c){var f=this.getModelAdapter().getFileTypeName(JU.Rdr.getBR(a));
if(null==f)return"unknown file type";if(f.equals("spt"))return"cannot open script inline";b=this.setLoadParameters(b,c);var f=b.get("loadScript"),g=b.containsKey("isData");null==f&&(f=new JU.SB);c||this.zap(!0,!1,!1);g||this.getStateCreator().getInlineData(f,a,c,this.g.defaultLoadFilter);a=this.fm.createAtomSetCollectionFromString(a,b,c);return this.createModelSetAndReturnError(a,c,f,b)},"~S,java.util.Map,~B");c(c$,"openStringsInlineParamsAppend",function(a,b,c){var f=new JU.SB;c||this.zap(!0,!1,
!1);a=this.fm.createAtomSeCollectionFromStrings(a,f,this.setLoadParameters(b,c),c);return this.createModelSetAndReturnError(a,c,f,b)},"~A,java.util.Map,~B");c(c$,"getInlineChar",function(){return this.g.inlineNewlineChar});c(c$,"getDataSeparator",function(){return this.g.getParameter("dataseparator",!0)});c(c$,"createModelSetAndReturnError",function(a,b,c,f){JU.Logger.startTimer("creating model");var g=this.fm.getFullPathName(!1),e=this.fm.getFileName();null==c&&(this.setBooleanProperty("preserveState",
!1),c=(new JU.SB).append('load "???"'));if(q(a,String))return this.setFileLoadStatus(J.c.FIL.NOT_LOADED,g,null,null,a,null),this.displayLoadErrors&&(!b&&!a.equals("#CANCELED#")&&!a.startsWith(JV.JC.READER_NOT_FOUND))&&this.zapMsg(a),a;b?this.clearAtomSets():this.g.modelKitMode&&!e.equals("Jmol Model Kit")&&this.setModelKitMode(!1);this.setFileLoadStatus(J.c.FIL.CREATING_MODELSET,g,e,null,null,null);this.pushHoldRepaintWhy("createModelSet");this.setErrorMessage(null,null);try{var h=new JU.BS;this.mm.createModelSet(g,
e,c,a,h,b);if(0<h.cardinality()){var j=this.ms.getInfoM("jmolscript");if(this.ms.getMSInfoB("doMinimize"))try{var l=f.get("eval");this.minimize(l,2147483647,0,h,null,0,!0,!0,!0,!0)}catch(n){if(!E(n,Exception))throw n;}else this.addHydrogens(h,!1,!0);null!=j&&this.ms.msInfo.put("jmolscript",j)}this.initializeModel(b)}catch(m){if(E(m,Error))this.handleError(m,!0),a=this.getShapeErrorState(),a="ERROR creating model: "+m+(0==a.length?"":"|"+a),this.zapMsg(a),this.setErrorMessage(a,null);else throw m;
}this.popHoldRepaint("createModelSet \u0001## REPAINT_IGNORE ##");a=this.getErrorMessage();this.setFileLoadStatus(J.c.FIL.CREATED,g,e,this.ms.modelSetName,a,f.get("async"));b&&(this.selectAll(),this.setTainted(!0),this.axesAreTainted=!0);JU.Logger.checkTimer("creating model",!1);System.gc();return a},"~O,~B,JU.SB,java.util.Map");c(c$,"loadAtomDataAndReturnError",function(a,b){if(q(a,String))return a;this.setErrorMessage(null,null);try{var c=this.mm.createAtomDataSet(a,b);switch(b){case 1145047050:null!=
c&&this.runScriptCautiously(c);break;case 4166:this.setStatusFrameChanged(!0,!1);break;case 1648363544:this.shm.deleteVdwDependentShapes(null)}}catch(f){if(E(f,Error))this.handleError(f,!0),c=this.getShapeErrorState(),c="ERROR adding atom data: "+f+(0==c.length?"":"|"+c),this.zapMsg(c),this.setErrorMessage(c,null),this.setParallel(!1);else throw f;}return this.getErrorMessage()},"~O,~N");c(c$,"getCurrentFileAsString",function(a){var b=this.fm.getFullPathName(!1);return b.equals("string")||b.equals("Jmol Model Kit")?
this.ms.getInlineData(this.am.cmi):b.equals("String[]")?b:"JSNode"===b?"<DOM NODE>":this.getFileAsString4(b,-1,!0,!1,!1,a)},"~S");c(c$,"getFullPathNameOrError",function(a){var b=Array(2);this.fm.getFullPathNameOrError(a,!1,b);return b},"~S");c(c$,"getFileAsString3",function(a,b,c){return this.getFileAsString4(a,-1,!1,!1,b,c)},"~S,~B,~S");c(c$,"getFileAsString4",function(a,b,c,f,g,e){if(null==a)return this.getCurrentFileAsString(e);a=v(-1,[a,null]);this.fm.getFileDataAsString(a,b,c,f,g);return a[1]},
"~S,~N,~B,~B,~B,~S");c(c$,"getAsciiFileOrNull",function(a){a=v(-1,[a,null]);return this.fm.getFileDataAsString(a,-1,!1,!1,!1)?a[1]:null},"~S");c(c$,"autoCalculate",function(a,b){switch(a){case 1111490575:this.ms.getSurfaceDistanceMax();break;case 1111490574:this.ms.calculateStraightnessAll();break;case 1111490587:this.ms.calculateDssrProperty(b)}},"~N,~S");c(c$,"calculateStraightness",function(){this.ms.haveStraightness=!1;this.ms.calculateStraightnessAll()});c(c$,"calculateSurface",function(a,b){null==
a&&(a=this.bsA());if(3.4028235E38==b||-1==b)this.ms.addStateScript("calculate surfaceDistance "+(3.4028235E38==b?"FROM":"WITHIN"),null,a,null,"",!1,!0);return this.ms.calculateSurface(a,b)},"JU.BS,~N");c(c$,"getStructureList",function(){return this.g.getStructureList()});c(c$,"setStructureList",function(a,b){this.g.setStructureList(a,b);this.ms.setStructureList(this.getStructureList())},"~A,J.c.STR");c(c$,"calculateStructures",function(a,b,c,f){null==a&&(a=this.bsA());return this.ms.calculateStructures(a,
b,!this.am.animationOn,this.g.dsspCalcHydrogen,c,f)},"JU.BS,~B,~B,~N");c(c$,"getAnnotationParser",function(a){return a?null==this.dssrParser?this.dssrParser=J.api.Interface.getOption("dssx.DSSR1",this,"script"):this.dssrParser:null==this.annotationParser?this.annotationParser=J.api.Interface.getOption("dssx.AnnotationParser",this,"script"):this.annotationParser},"~B");j(c$,"getSelectedAtomIterator",function(a,b,c,f){return this.ms.getSelectedAtomIterator(a,b,c,!1,f)},"JU.BS,~B,~B,~B");j(c$,"setIteratorForAtom",
function(a,b,c){this.ms.setIteratorForAtom(a,-1,b,c,null)},"J.api.AtomIndexIterator,~N,~N");j(c$,"setIteratorForPoint",function(a,b,c,f){this.ms.setIteratorForPoint(a,b,c,f)},"J.api.AtomIndexIterator,~N,JU.T3,~N");j(c$,"fillAtomData",function(a,b){a.programInfo="Jmol Version "+JV.Viewer.getJmolVersion();a.fileName=this.fm.getFileName();this.ms.fillAtomData(a,b)},"J.atomdata.AtomData,~N");c(c$,"addStateScript",function(a,b,c){return this.ms.addStateScript(a,null,null,null,null,b,c)},"~S,~B,~B");c(c$,
"getMinimizer",function(a){return null==this.minimizer&&a?(this.minimizer=J.api.Interface.getInterface("JM.Minimizer",this,"script")).setProperty("vwr",this):this.minimizer},"~B");c(c$,"getSmilesMatcher",function(){return null==this.smilesMatcher?this.smilesMatcher=J.api.Interface.getInterface("JS.SmilesMatcher",this,"script"):this.smilesMatcher});c(c$,"clearModelDependentObjects",function(){this.setFrameOffsets(null,!1);this.stopMinimization();this.smilesMatcher=this.minimizer=null});c(c$,"zap",
function(a,b,c){this.clearThreads();null==this.mm.modelSet?this.mm.zap():(this.ligandModelSet=null,this.clearModelDependentObjects(),this.fm.clear(),this.clearRepaintManager(-1),this.am.clear(),this.tm.clear(),this.slm.clear(),this.clearAllMeasurements(),this.clearMinimization(),this.gdata.clear(),this.mm.zap(),null!=this.scm&&this.scm.clear(!1),null!=this.nmrCalculation&&this.getNMRCalculation().setChemicalShiftReference(null,0),this.haveDisplay&&(this.mouse.clear(),this.clearTimeouts(),this.acm.clear()),
this.stm.clear(this.g),this.tempArray.clear(),this.chainMap.clear(),this.chainList.clear(),this.chainCaseSpecified=!1,this.definedAtomSets.clear(),this.lastData=null,null!=this.dm&&this.dm.clear(),this.setBooleanProperty("legacyjavafloat",!1),b&&(c&&this.g.removeParam("_pngjFile"),c&&this.g.modelKitMode&&(this.openStringInlineParamsAppend("5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63",null,!0),this.setRotationRadius(5,!0),this.setStringProperty("picking","assignAtom_C"),
this.setStringProperty("picking","assignBond_p")),this.undoClear()),System.gc());this.initializeModel(!1);a&&this.setFileLoadStatus(J.c.FIL.ZAPPED,null,b?"resetUndo":this.getZapName(),null,null,null);JU.Logger.debugging&&JU.Logger.checkMemory()},"~B,~B,~B");c(c$,"zapMsg",function(a){this.zap(!0,!0,!1);this.echoMessage(a)},"~S");c(c$,"echoMessage",function(a){this.shm.loadShape(31);this.setShapeProperty(31,"font",this.getFont3D("SansSerif","Plain",20));this.setShapeProperty(31,"target","error");this.setShapeProperty(31,
"text",a)},"~S");c(c$,"initializeModel",function(a){this.clearThreads();a?this.am.initializePointers(1):(this.reset(!0),this.selectAll(),this.rotatePrev1=this.rotateBondIndex=-1,this.movingSelected=!1,this.slm.noneSelected=Boolean.FALSE,this.setHoverEnabled(!0),this.setSelectionHalosEnabled(!1),this.tm.setCenter(),this.am.initializePointers(1),this.setBooleanProperty("multipleBondBananas",!1),this.ms.getMSInfoB("isPyMOL")||(this.clearAtomSets(),this.setCurrentModelIndex(0)),this.setBackgroundModelIndex(-1),
this.setFrankOn(this.getShowFrank()),this.startHoverWatcher(!0),this.setTainted(!0),this.finalizeTransformParameters())},"~B");c(c$,"startHoverWatcher",function(a){a&&this.inMotion||(!this.haveDisplay||a&&(!this.hoverEnabled&&!this.sm.haveHoverCallback()||this.am.animationOn))||this.acm.startHoverWatcher(a)},"~B");j(c$,"getModelSetPathName",function(){return this.mm.modelSetPathName});j(c$,"getModelSetFileName",function(){return null==this.mm.fileName?this.getZapName():this.mm.fileName});c(c$,"getUnitCellInfoText",
function(){var a=this.getCurrentUnitCell();return null==a?"not applicable":a.getUnitCellInfo()});c(c$,"getUnitCellInfo",function(a){var b=this.getCurrentUnitCell();return null==b?NaN:b.getUnitCellInfoType(a)},"~N");c(c$,"getV0abc",function(a){var b=this.getCurrentUnitCell();return null==b?null:b.getV0abc(a)},"~O");c(c$,"getPolymerPointsAndVectors",function(a,b){this.ms.getPolymerPointsAndVectors(a,b,this.g.traceAlpha,this.g.sheetSmoothing)},"JU.BS,JU.Lst");c(c$,"getHybridizationAndAxes",function(a,
b,c,f){return this.ms.getHybridizationAndAxes(a,0,b,c,f,!0,!0)},"~N,JU.V3,JU.V3,~S");c(c$,"getAllAtoms",function(){return this.getModelUndeletedAtomsBitSet(-1)});c(c$,"getModelUndeletedAtomsBitSet",function(a){return this.slm.excludeAtoms(this.ms.getModelAtomBitSetIncludingDeleted(a,!0),!1)},"~N");c(c$,"getModelUndeletedAtomsBitSetBs",function(a){return this.slm.excludeAtoms(this.ms.getModelAtomBitSetIncludingDeletedBs(a),!1)},"JU.BS");j(c$,"getBoundBoxCenter",function(){return this.ms.getBoundBoxCenter(this.am.cmi)});
c(c$,"calcBoundBoxDimensions",function(a,b){this.ms.calcBoundBoxDimensions(a,b);this.axesAreTainted=!0},"JU.BS,~N");j(c$,"getBoundBoxCornerVector",function(){return this.ms.getBoundBoxCornerVector()});c(c$,"getBoundBoxCenterX",function(){return y(this.dimScreen.width/2)});c(c$,"getBoundBoxCenterY",function(){return y(this.dimScreen.height/2)});j(c$,"getModelSetProperties",function(){return this.ms.modelSetProperties});j(c$,"getModelProperties",function(a){return this.ms.am[a].properties},"~N");j(c$,
"getModelSetAuxiliaryInfo",function(){return this.ms.getAuxiliaryInfo(null)});j(c$,"getModelNumber",function(a){return 0>a?a:this.ms.getModelNumber(a)},"~N");c(c$,"getModelFileNumber",function(a){return 0>a?0:this.ms.modelFileNumbers[a]},"~N");j(c$,"getModelNumberDotted",function(a){return 0>a?"0":this.ms.getModelNumberDotted(a)},"~N");j(c$,"getModelName",function(a){return this.ms.getModelName(a)},"~N");c(c$,"modelHasVibrationVectors",function(a){return 0<=this.ms.getLastVibrationVector(a,4166)},
"~N");c(c$,"getBondsForSelectedAtoms",function(a){return this.ms.getBondsForSelectedAtoms(a,this.g.bondModeOr||1==JU.BSUtil.cardinalityOf(a))},"JU.BS");c(c$,"frankClicked",function(a,b){return!this.g.disablePopupMenu&&this.getShowFrank()&&this.shm.checkFrankclicked(a,b)},"~N,~N");c(c$,"frankClickedModelKit",function(a,b){return!this.g.disablePopupMenu&&this.g.modelKitMode&&0<=a&&0<=b&&40>a&&80>b},"~N,~N");j(c$,"findNearestAtomIndex",function(a,b){return this.findNearestAtomIndexMovable(a,b,!1)},"~N,~N");
c(c$,"findNearestAtomIndexMovable",function(a,b,c){return!this.g.atomPicking?-1:this.ms.findNearestAtomIndex(a,b,c?this.slm.getMotionFixedAtoms():null,this.g.minPixelSelRadius)},"~N,~N,~B");c(c$,"toCartesian",function(a,b){var c=this.getCurrentUnitCell();null!=c&&(c.toCartesian(a,b),this.g.legacyJavaFloat||JU.PT.fixPtFloats(a,1E4))},"JU.T3,~B");c(c$,"toFractional",function(a,b){var c=this.getCurrentUnitCell();null!=c&&(c.toFractional(a,b),this.g.legacyJavaFloat||JU.PT.fixPtFloats(a,1E5))},"JU.T3,~B");
c(c$,"toUnitCell",function(a,b){var c=this.getCurrentUnitCell();null!=c&&c.toUnitCell(a,b)},"JU.P3,JU.P3");c(c$,"setCurrentCage",function(a){a=v(-1,[a,null]);this.shm.getShapePropertyData(24,"unitCell",a);this.ms.setModelCage(this.am.cmi,a[1])},"~S");c(c$,"addUnitCellOffset",function(a){var b=this.getCurrentUnitCell();null!=b&&a.add(b.getCartesianOffset())},"JU.P3");c(c$,"setAtomData",function(a,b,c,f){this.ms.setAtomData(a,b,c,f);2==a&&this.checkCoordinatesChanged();this.refreshMeasures(!0)},"~N,~S,~S,~B");
j(c$,"setCenterSelected",function(){this.setCenterBitSet(this.bsA(),!0)});c(c$,"setApplySymmetryToBonds",function(a){this.g.applySymmetryToBonds=a},"~B");j(c$,"setBondTolerance",function(a){this.g.setF("bondTolerance",a);this.g.bondTolerance=a},"~N");j(c$,"setMinBondDistance",function(a){this.g.setF("minBondDistance",a);this.g.minBondDistance=a},"~N");c(c$,"getAtomsNearPt",function(a,b){var c=new JU.BS;this.ms.getAtomsWithin(a,b,c,-1);return c},"~N,JU.P3");c(c$,"getBranchBitSet",function(a,b,c){return 0>
a||a>=this.ms.ac?new JU.BS:JU.JmolMolecule.getBranchBitSet(this.ms.at,a,this.getModelUndeletedAtomsBitSet(this.ms.at[a].mi),null,b,c,!0)},"~N,~N,~B");j(c$,"getElementsPresentBitSet",function(a){return this.ms.getElementsPresentBitSet(a)},"~N");c(c$,"getFileHeader",function(){return this.ms.getFileHeader(this.am.cmi)});c(c$,"getFileData",function(){return this.ms.getFileData(this.am.cmi)});c(c$,"getCifData",function(a){return this.readCifData(this.ms.getModelFileName(a),this.ms.getModelFileType(a).toUpperCase())},
"~N");c(c$,"readCifData",function(a,b){var c=null==a?this.ms.getModelFileName(this.am.cmi):a;if(null==b&&null!=c&&0<=c.toUpperCase().indexOf("BCIF")){c=this.fm.getBufferedInputStream(c);try{return J.api.Interface.getInterface("JU.MessagePackReader",this,"script").getMapForStream(c)}catch(f){if(E(f,Exception))return f.printStackTrace(),new java.util.Hashtable;throw f;}}c=null==a||0==a.length?this.getCurrentFileAsString("script"):this.getFileAsString3(a,!1,null);if(null==c||2>c.length)return null;c=
JU.Rdr.getBR(c);null==b&&(b=this.getModelAdapter().getFileTypeName(c));return null==b?null:this.readCifData(null,c,b)},"~S,~S");c(c$,"readCifData",function(a,b,c){null==b&&(b=this.getFileAsString(a));a=q(b,java.io.BufferedReader)?b:JU.Rdr.getBR(b);return JU.Rdr.readCifData(J.api.Interface.getInterface("CIF2".equals(c)?"J.adapter.readers.cif.Cif2DataParser":"JU.CifDataParser",this,"script"),a)},"~S,~O,~S");c(c$,"getStateCreator",function(){null==this.jsc&&(this.jsc=J.api.Interface.getInterface("JV.StateCreator",
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a&&this.setScreenDimension(a,b);return!0},"~N,~N");c(c$,"renderScreenImage",function(a,b,c){this.renderScreenImageStereo(a,!1,b,c)},"~O,~N,~N");c(c$,"getImage",function(a,b){var c=null;try{this.beginRendering(a,b),this.render(),this.gdata.endRendering(),c=this.gdata.getScreenImage(b)}catch(f){if(E(f,Error))this.gdata.getScreenImage(b),this.handleError(f,!1),this.setErrorMessage("Error during rendering: "+f,null);else if(E(f,Exception))System.out.println("render error"+f),JV.Viewer.isJS||f.printStackTrace();
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this.notifyViewerRepaintDone()):(this.rm.render(this.gdata,this.ms,!0,b),this.gdata.setPass2(a)&&(this.tm.setAntialias(a),this.rm.render(this.gdata,this.ms,!1,null),this.tm.setAntialias(this.antialiased)))}});c(c$,"drawImage",function(a,b,c,f,g){null!=a&&null!=b&&this.apiPlatform.drawImage(a,b,c,f,this.dimScreen.width,this.dimScreen.height,g);this.gdata.releaseScreenImage()},"~O,~O,~N,~N,~B");j(c$,"getScreenImageBuffer",function(a,b){if(JV.Viewer.isWebGL)return b?this.apiPlatform.allocateRgbImage(0,
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this.setShapeProperty(35,"label",a);this.setHoverEnabled(null!=a);this.g.setO("_hoverLabel",this.hoverLabel=a);!this.hoverEnabled&&!this.sm.haveHoverCallback()&&this.startHoverWatcher(!1)},"~S");c(c$,"setHoverEnabled",function(a){this.hoverEnabled=a;this.g.setB("_hoverEnabled",a)},"~B");c(c$,"hoverOn",function(a,b){this.g.removeParam("_objecthovered");this.g.setI("_atomhovered",a);this.g.setO("_hoverLabel",this.hoverLabel);this.g.setUserVariable("hovered",JS.SV.getVariable(JU.BSUtil.newAndSetBit(a)));
this.sm.haveHoverCallback()&&this.sm.setStatusAtomHovered(a,this.getAtomInfoXYZ(a,!1));if(this.hoverEnabled)if(this.g.modelKitMode)this.ms.isAtomAssignable(a)&&this.highlight(JU.BSUtil.newAndSetBit(a)),this.refresh(3,"hover on atom");else if(!(null!=this.eval&&this.isScriptExecuting()||a==this.hoverAtomIndex||0==this.g.hoverDelayMs)&&this.slm.isInSelectionSubset(a))this.shm.loadShape(35),b&&this.ms.at[a].isVisible(512)&&this.setShapeProperty(35,"specialLabel",J.i18n.GT.$("Drag to move label")),this.setShapeProperty(35,
"text",null),this.setShapeProperty(35,"target",Integer.$valueOf(a)),this.hoverText=null,this.hoverAtomIndex=a,this.refresh(3,"hover on atom")},"~N,~B");c(c$,"hoverOnPt",function(a,b,c,f,g){null!=this.eval&&this.isScriptExecuting()||(this.g.setO("_hoverLabel",this.hoverLabel),null!=f&&null!=g&&(this.g.setO("_objecthovered",f),this.g.setI("_atomhovered",-1),this.g.setUserVariable("hovered",JS.SV.getVariable(g)),this.sm.haveHoverCallback()&&this.sm.setStatusObjectHovered(f,c,g)),this.hoverEnabled&&(this.shm.loadShape(35),
this.setShapeProperty(35,"xy",JU.P3i.new3(a,b,0)),this.setShapeProperty(35,"target",null),this.setShapeProperty(35,"specialLabel",null),this.setShapeProperty(35,"text",c),this.hoverAtomIndex=-1,this.hoverText=c,this.refresh(3,"hover on point")))},"~N,~N,~S,~S,JU.T3");c(c$,"hoverOff",function(){try{if(this.g.modelKitMode&&this.highlight(null),this.hoverEnabled){var a=null!=this.hoverText||0<=this.hoverAtomIndex;0<=this.hoverAtomIndex&&(this.setShapeProperty(35,"target",null),this.hoverAtomIndex=-1);
null!=this.hoverText&&(this.setShapeProperty(35,"text",null),this.hoverText=null);this.setShapeProperty(35,"specialLabel",null);a&&this.refresh(3,"hover off")}}catch(b){if(!E(b,Exception))throw b;}});j(c$,"setDebugScript",function(a){this.g.debugScript=a;this.g.setB("debugScript",a);null!=this.eval&&this.eval.setDebugging()},"~B");c(c$,"clearClickCount",function(){this.setTainted(!0)});c(c$,"setCursor",function(a){if(!this.$isKiosk&&!(this.currentCursor==a||this.multiTouch||!this.haveDisplay))this.apiPlatform.setCursor(this.currentCursor=
a,this.display)},"~N");c(c$,"setPickingMode",function(a,b){if(this.haveDisplay){this.showSelected=!1;var c=null;if(null!=a){var f=a.indexOf("_");0<=f&&(c=a.substring(f+1),a=a.substring(0,f));b=JV.ActionManager.getPickingMode(a)}0>b&&(b=1);this.acm.setPickingMode(b);this.g.setO("picking",JV.ActionManager.getPickingModeName(this.acm.getAtomPickingMode()));if(!(null==c||0==c.length))switch(c=Character.toUpperCase(c.charAt(0))+(1==c.length?"":c.substring(1,2)),b){case 32:this.setAtomPickingOption(c);
break;case 33:this.setBondPickingOption(c);break;default:JU.Logger.error("Bad picking mode: "+a+"_"+c)}}},"~S,~N");c(c$,"getPickingMode",function(){return this.haveDisplay?this.acm.getAtomPickingMode():0});c(c$,"setPickingStyle",function(a,b){this.haveDisplay&&(null!=a&&(b=JV.ActionManager.getPickingStyleIndex(a)),0>b&&(b=0),this.acm.setPickingStyle(b),this.g.setO("pickingStyle",JV.ActionManager.getPickingStyleName(this.acm.getPickingStyle())))},"~S,~N");c(c$,"getDrawHover",function(){return this.haveDisplay&&
this.g.drawHover});c(c$,"getAtomInfo",function(a){null==this.ptTemp&&(this.ptTemp=new JU.P3);return 0<=a?this.ms.getAtomInfo(a,null,this.ptTemp):this.shm.getShapePropertyIndex(6,"pointInfo",-a)},"~N");c(c$,"getAtomInfoXYZ",function(a,b){var c=this.ms.at[a];if(b)return this.getChimeMessenger().getInfoXYZ(c);null==this.ptTemp&&(this.ptTemp=new JU.P3);return c.getIdentityXYZ(!0,this.ptTemp)},"~N,~B");c(c$,"setSync",function(){this.sm.doSync()&&this.sm.setSync(null)});j(c$,"setJmolCallbackListener",function(a){this.sm.cbl=
a},"J.api.JmolCallbackListener");j(c$,"setJmolStatusListener",function(a){this.sm.cbl=this.sm.jsl=a},"J.api.JmolStatusListener");c(c$,"getStatusChanged",function(a){return null==a?null:this.sm.getStatusChanged(a)},"~S");c(c$,"menuEnabled",function(){return!this.g.disablePopupMenu&&null!=this.getPopupMenu()});c(c$,"popupMenu",function(a,b,c){if(this.haveDisplay&&this.refreshing&&!this.isPreviewOnly&&!this.g.disablePopupMenu)switch(c){case "j":try{this.getPopupMenu(),this.jmolpopup.jpiShow(a,b)}catch(f){JU.Logger.info(f.toString()),
this.g.disablePopupMenu=!0}break;case "a":case "b":case "m":if(null==this.modelkitPopup&&null==(this.modelkitPopup=this.apiPlatform.getMenuPopup(null,c)))break;this.modelkitPopup.jpiShow(a,b)}},"~N,~N,~S");c(c$,"getMenu",function(a){this.getPopupMenu();return a.equals("\x00")?(this.popupMenu(this.dimScreen.width-120,0,"j"),"OK"):null==this.jmolpopup?"":this.jmolpopup.jpiGetMenuAsString("Jmol version "+JV.Viewer.getJmolVersion()+"|_GET_MENU|"+a)},"~S");c(c$,"getPopupMenu",function(){return this.g.disablePopupMenu?
null:null==this.jmolpopup&&(this.jmolpopup=this.allowScripting?this.apiPlatform.getMenuPopup(this.menuStructure,"j"):null,null==this.jmolpopup&&!this.async)?(this.g.disablePopupMenu=!0,null):this.jmolpopup.jpiGetMenuAsObject()});j(c$,"setMenu",function(a,b){b&&JU.Logger.info("Setting menu "+(0==a.length?"to Jmol defaults":"from file "+a));0==a.length?a=null:b&&(a=this.getFileAsString3(a,!1,null));this.getProperty("DATA_API","setMenu",a);this.sm.setCallbackFunction("menu",a)},"~S,~B");c(c$,"setStatusFrameChanged",
function(a){a&&(this.prevFrame=-2147483648);this.tm.setVibrationPeriod(NaN);var b=this.am.firstFrameIndex,c=this.am.lastFrameIndex,f=this.am.isMovie;a=this.am.cmi;b==c&&!f&&(a=b);var g=this.getModelFileNumber(a),e=this.am.cmi,h=g,j=g%1E6,l=f?b:this.getModelFileNumber(b),n=f?c:this.getModelFileNumber(c),m;f?m=""+(e+1):0==h?(m=this.getModelNumberDotted(b),b!=c&&(m+=" - "+this.getModelNumberDotted(c)),y(l/1E6)==y(n/1E6)&&(h=l)):m=this.getModelNumberDotted(a);0!=h&&(h=1E6>h?1:y(h/1E6));f||(this.g.setI("_currentFileNumber",
h),this.g.setI("_currentModelNumberInFile",j));b=this.am.currentMorphModel;this.g.setI("_currentFrame",e);this.g.setI("_morphCount",this.am.morphCount);this.g.setF("_currentMorphFrame",b);this.g.setI("_frameID",g);this.g.setI("_modelIndex",a);this.g.setO("_modelNumber",m);this.g.setO("_modelName",0>a?"":this.getModelName(a));g=0>a?"":this.ms.getModelTitle(a);this.g.setO("_modelTitle",null==g?"":g);this.g.setO("_modelFile",0>a?"":this.ms.getModelFileName(a));this.g.setO("_modelType",0>a?"":this.ms.getModelFileType(a));
e==this.prevFrame&&b==this.prevMorphModel||(this.prevFrame=e,this.prevMorphModel=b,g=this.getModelName(e),f?g=""+(""===g?e+1:this.am.caf+1)+": "+g:(f=""+this.getModelNumberDotted(e),g.equals(f)||(g=f+": "+g)),this.sm.setStatusFrameChanged(h,j,0>this.am.animationDirection?-l:l,0>this.am.currentDirection?-n:n,e,b,g),this.doHaveJDX()&&this.getJSV().setModel(a),JV.Viewer.isJS&&this.updateJSView(a,-1))},"~B,~B");c(c$,"doHaveJDX",function(){return this.haveJDX||(this.haveJDX=this.getBooleanProperty("_jspecview"))});
c(c$,"getJSV",function(){null==this.jsv&&(this.jsv=J.api.Interface.getOption("jsv.JSpecView",this,"script"),this.jsv.setViewer(this));return this.jsv});c(c$,"getJDXBaseModelIndex",function(a){return!this.doHaveJDX()?a:this.getJSV().getBaseModelIndex(a)},"~N");c(c$,"getJspecViewProperties",function(a){a=this.sm.getJspecViewProperties(""+a);null!=a&&(this.haveJDX=!0);return a},"~O");c(c$,"scriptEcho",function(a){JU.Logger.isActiveLevel(4)&&(System.out.println(a),this.sm.setScriptEcho(a,this.isScriptQueued()),
this.listCommands&&(null!=a&&0==a.indexOf("$["))&&JU.Logger.info(a))},"~S");c(c$,"isScriptQueued",function(){return null!=this.scm&&this.scm.isScriptQueued()});c(c$,"notifyError",function(a,b,c){this.g.setO("_errormessage",c);this.sm.notifyError(a,b,c)},"~S,~S,~S");c(c$,"jsEval",function(a){return""+this.sm.jsEval(a)},"~S");c(c$,"jsEvalSV",function(a){return JS.SV.getVariable(JV.Viewer.isJS?this.sm.jsEval(a):this.jsEval(a))},"~S");c(c$,"setFileLoadStatus",function(a,b,c,f,g,e){this.setErrorMessage(g,
null);this.g.setI("_loadPoint",a.getCode());var h=a!==J.c.FIL.CREATING_MODELSET;h&&this.setStatusFrameChanged(!1,!1);this.sm.setFileLoadStatus(b,c,f,g,a.getCode(),h,e);h&&(this.doHaveJDX()&&this.getJSV().setModel(this.am.cmi),JV.Viewer.isJS&&this.updateJSView(this.am.cmi,-2))},"J.c.FIL,~S,~S,~S,~S,Boolean");c(c$,"getZapName",function(){return this.g.modelKitMode?"Jmol Model Kit":"zapped"});c(c$,"setStatusMeasuring",function(a,b,c,f){this.sm.setStatusMeasuring(a,b,c,f)},"~S,~N,~S,~N");c(c$,"notifyMinimizationStatus",
function(){var a=this.getP("_minimizationStep"),b=this.getP("_minimizationForceField");this.sm.notifyMinimizationStatus(this.getP("_minimizationStatus"),q(a,String)?Integer.$valueOf(0):a,this.getP("_minimizationEnergy"),a.toString().equals("0")?Float.$valueOf(0):this.getP("_minimizationEnergyDiff"),b)});c(c$,"setStatusAtomPicked",function(a,b,c,f){f&&this.setSelectionSet(JU.BSUtil.newAndSetBit(a));null==b&&(b=this.g.pickLabel,b=0==b.length?this.getAtomInfoXYZ(a,this.g.messageStyleChime):this.ms.getAtomInfo(a,
b,this.ptTemp));this.setPicked(a,!1);0>a&&(f=this.getPendingMeasurement(),null!=f&&(b=b.substring(0,b.length-1)+',"'+f.getString()+'"]'));this.g.setO("_pickinfo",b);this.sm.setStatusAtomPicked(a,b,c);0>a||(1==this.sm.getSyncMode()&&this.doHaveJDX()&&this.getJSV().atomPicked(a),JV.Viewer.isJS&&this.updateJSView(this.ms.at[a].mi,a))},"~N,~S,java.util.Map,~B");c(c$,"setStatusDragDropped",function(a,b,c,f){0==a&&(this.g.setO("_fileDropped",f),this.g.setUserVariable("doDrop",JS.SV.vT));return!this.sm.setStatusDragDropped(a,
b,c,f)||this.getP("doDrop").toString().equals("true")},"~N,~N,~N,~S");c(c$,"setStatusResized",function(a,b){this.sm.setStatusResized(a,b)},"~N,~N");c(c$,"scriptStatus",function(a){this.setScriptStatus(a,"",0,null)},"~S");c(c$,"scriptStatusMsg",function(a,b){this.setScriptStatus(a,b,0,null)},"~S,~S");c(c$,"setScriptStatus",function(a,b,c,f){this.sm.setScriptStatus(a,b,c,f)},"~S,~S,~N,~S");j(c$,"showUrl",function(a){if(null!=a){if(0>a.indexOf(":")){var b=this.fm.getAppletDocumentBase();""===b&&(b=this.fm.getFullPathName(!1));
0<=b.indexOf("/")?b=b.substring(0,b.lastIndexOf("/")+1):0<=b.indexOf("\\")&&(b=b.substring(0,b.lastIndexOf("\\")+1));a=b+a}JU.Logger.info("showUrl:"+a);this.sm.showUrl(a)}},"~S");c(c$,"setMeshCreator",function(a){this.shm.loadShape(24);this.setShapeProperty(24,"meshCreator",a)},"~O");c(c$,"showConsole",function(a){if(this.haveDisplay)try{null==this.appConsole&&a&&this.getConsole(),this.appConsole.setVisible(!0)}catch(b){}},"~B");c(c$,"getConsole",function(){this.getProperty("DATA_API","getAppConsole",
Boolean.TRUE);return this.appConsole});j(c$,"getParameter",function(a){return this.getP(a)},"~S");c(c$,"getP",function(a){return this.g.getParameter(a,!0)},"~S");c(c$,"getPOrNull",function(a){return this.g.getParameter(a,!1)},"~S");c(c$,"unsetProperty",function(a){a=a.toLowerCase();(a.equals("all")||a.equals("variables"))&&this.fm.setPathForAllFiles("");this.g.unsetUserVariable(a)},"~S");j(c$,"notifyStatusReady",function(a){System.out.println("Jmol applet "+this.fullName+(a?" ready":" destroyed"));
a||this.dispose();this.sm.setStatusAppletReady(this.fullName,a)},"~B");j(c$,"getBooleanProperty",function(a){a=a.toLowerCase();if(this.g.htBooleanParameterFlags.containsKey(a))return this.g.htBooleanParameterFlags.get(a).booleanValue();if(a.endsWith("p!")){if(null==this.acm)return!1;var b=this.acm.getPickingState().toLowerCase();a=a.substring(0,a.length-2)+";";return 0<=b.indexOf(a)}if(a.equalsIgnoreCase("executionPaused"))return null!=this.eval&&this.eval.isPaused();if(a.equalsIgnoreCase("executionStepping"))return null!=
this.eval&&this.eval.isStepping();if(a.equalsIgnoreCase("haveBFactors"))return null!=this.ms.getBFactors();if(a.equalsIgnoreCase("colorRasmol"))return this.cm.isDefaultColorRasmol;if(a.equalsIgnoreCase("frank"))return this.getShowFrank();if(a.equalsIgnoreCase("spinOn"))return this.tm.spinOn;if(a.equalsIgnoreCase("isNavigating"))return this.tm.isNavigating();if(a.equalsIgnoreCase("showSelections"))return this.selectionHalosEnabled;if(this.g.htUserVariables.containsKey(a)){b=this.g.getUserVariable(a);
if(1073742335==b.tok)return!0;if(1073742334==b.tok)return!1}JU.Logger.error("vwr.getBooleanProperty("+a+") - unrecognized");return!1},"~S");j(c$,"getInt",function(a){switch(a){case 553648148:return this.g.infoFontSize;case 553648132:return this.am.animationFps;case 553648142:return this.g.dotDensity;case 553648143:return this.g.dotScale;case 553648145: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;case 553648185:return this.g.vectorTrail}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?
0:this.g.hermiteLevel});c(c$,"getHoverDelay",function(){return this.g.modelKitMode?20:this.g.hoverDelayMs});j(c$,"getBoolean",function(a){switch(a){case 603979891:return this.g.nboCharges;case 603979856:return this.g.hiddenLinesDashed;case 1073742086:return this.ms.getMSInfoB("isPDB");case 603979802:return this.g.autoplayMovie;case 603979797:return!this.headless&&this.g.allowAudio;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.cartoonSteps;case 603979810:return this.g.cartoonBlocks;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 603979822:return this.g.chainCaseSensitive||this.chainCaseSpecified;case 603979823:return this.g.cipRule6Full;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 1612709894:return this.g.rasmolHeteroSetting;case 603979858:return this.g.hideNameInPopup;case 603979864:return this.g.highResolutionFlag;case 1612709900:return this.g.rasmolHydrogenSetting;
case 603979867:return this.g.isosurfaceKey;case 603979869:return this.g.jmolInJSpecView;case 603979871:return this.g.justifyMeasurements;case 603979873:return this.g.legacyAutoBonding;case 603979874:return this.g.legacyHAddition;case 603979875:return this.g.legacyJavaFloat;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 603979886:return this.g.multipleBondBananas;
case 603979889:return this.g.navigationMode;case 603979890:return this.g.navigationPeriodic;case 603979893:return this.g.partialDots;case 603979896:return this.g.pdbSequential;case 603979898:return this.g.preserveState;case 603979900:return this.refreshing;case 603979901:return this.g.ribbonBorder;case 603979902:return this.g.rocketBarrels;case 603979892:return this.g.noDelay;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 603979927:return this.g.showModVecs;case 603979928:return this.g.showMultipleBonds;case 603979934:return this.g.showTiming;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 1612709912:return this.g.solventOn;case 603979952:return this.g.ssbondsBackbone;case 603979955:return this.g.strutsMultiple;case 603979960:return this.g.testFlag1;
case 603979962:return this.g.testFlag2;case 603979964:return this.g.testFlag3;case 603979965:return this.g.testFlag4;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 603979975: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});j(c$,"getFloat",function(a){switch(a){case 1140850689:return this.g.particleRadius;case 570425345:return this.g.axesOffset;case 570425346:return this.g.axesScale;
case 570425348:return this.g.bondTolerance;case 570425354:return this.g.defaultTranslucent;case 570425352:return this.g.defaultDrawArrowScale;case 570425355:return this.g.dipoleScale;case 570425356:return this.g.drawFontSize;case 570425358:return this.g.exportScale;case 570425360:return this.g.hbondsAngleMinimum;case 570425361:return this.g.hbondsDistanceMaximum;case 570425363:return this.g.loadAtomDataTolerance;case 570425364:return this.g.minBondDistance;case 1275072532:return this.g.modulationScale;
case 570425370:return this.g.multipleBondSpacing;case 570425369:return this.g.multipleBondRadiusFactor;case 570425374:return this.g.navigationSpeed;case 570425382:return this.g.pointGroupDistanceTolerance;case 570425384:return this.g.pointGroupLinearTolerance;case 570425388:return this.tm.modelRadius;case 570425392:return this.g.sheetSmoothing;case 570425394:return this.g.solventProbeRadius;case 570425403:return this.g.starWidth;case 570425406:return this.g.strutDefaultRadius;case 570425408:return this.g.strutLengthMaximum;
case 1648361473:return this.g.vectorScale;case 570425412:return this.g.vibrationPeriod;case 570425347:return this.g.cartoonBlockHeight}JU.Logger.error("viewer.getFloat("+JS.T.nameOf(a)+") - not listed");return 0},"~N");j(c$,"setStringProperty",function(a,b){if(!(null==b||null==a||0==a.length))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 545259570:this.g.nihResolverFormat=c;break;case 545259521:this.setAnimationMode(c);return;case 545259569:this.g.nmrPredictFormat=c;break;case 545259548:this.g.defaultDropScript=c;break;case 545259572:c=this.fm.setPathForAllFiles(c);break;case 545259559:this.setUnits(c,!1);return;case 545259561:this.g.forceField=
c="UFF".equalsIgnoreCase(c)?"UFF":"MMFF";this.minimizer=null;break;case 545259571:this.g.nmrUrlFormat=c;break;case 545259568:this.setUnits(c,!0);return;case 545259566:this.g.pdbLoadLigandFormat=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 545259560: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.haveStraightness=!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 545259563:this.shm.loadShape(35);this.setShapeProperty(35,"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 545259562: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 545259573: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");j(c$,"setFloatProperty",function(a,b){if(!Float.isNaN(b)&&!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setF(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 553648128:this.setIntPropertyTok(a,c,B(b));break;default:this.setFloatPropertyTok(a,c,b)}}},"~S,~N");c(c$,"setFloatPropertyTok",function(a,b,c){switch(b){case 570425347:this.g.cartoonBlockHeight=
c;break;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.acm.setGestureSwipeFactor(c);break;case 570425367:this.haveDisplay&&this.acm.setMouseDragFactor(c);break;case 570425368:this.haveDisplay&&this.acm.setMouseWheelFactor(c);break;case 570425408:this.g.strutLengthMaximum=c;break;case 570425406:this.g.strutDefaultRadius=c;break;case 570425376:this.setSpin("X",B(c));break;case 570425378:this.setSpin("Y",B(c));break;case 570425380:this.setSpin("Z",B(c));break;case 570425371:if(Float.isNaN(c))return;this.setSpin("FPS",
B(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",B(c));break;case 570425400:this.setSpin("y",B(c));break;case 570425402:this.setSpin("z",B(c));break;case 570425396:this.setSpin("fps",B(c));
break;case 570425352:this.g.defaultDrawArrowScale=c;break;case 570425354:this.g.defaultTranslucent=c;break;case 570425345:this.setAxesScale(b,c);break;case 570425346:this.setAxesScale(b,c);break;case 570425416:this.tm.visualRangeAngstroms=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=B(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 1648361473: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.newF(c));return}}this.g.setF(a,c)},"~S,~N,~N");j(c$,"setIntProperty",function(a,b){if(!(-2147483648==b||null==a||0==a.length))if("_"==a.charAt(0))this.g.setI(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,
c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 570425344:this.setFloatPropertyTok(a,c,b);break;default:this.setIntPropertyTok(a,c,b)}}},"~S,~N");c(c$,"setIntPropertyTok",function(a,b,c){switch(b){case 553648148:this.g.infoFontSize=Math.max(0,c);break;case 553648167:case 553648147:case 553648168:c=this.eval.setStatic(b,c);break;case 553648185:this.g.vectorTrail=c;break;case 553648138:c=0==c?0:1;this.g.bondingVersion=JU.Elements.bondingVersion=c;break;case 553648137: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 553648145:this.g.helixStep=c;this.ms.haveStraightness=!1;break;case 553648143:this.g.dotScale=c;break;case 553648142: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:this.setAxesMode(2==c?603979808:1==c?603979804:603979809);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 553648141: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=c=Math.max(c,0);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 553648146:this.g.hermiteLevel=c;break;case 553648144: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");j(c$,"setBooleanProperty",function(a,b){if(!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setB(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,"");break;case 553648128:this.setIntPropertyTok(a,c,b?1:0);break;case 570425344:this.setFloatPropertyTok(a,c,b?1:0);break;default:this.setBooleanPropertyTok(a,c,b)}}},"~S,~B");c(c$,"setBooleanPropertyTok",
function(a,b,c){var f=!0;switch(b){case 603979823:this.g.cipRule6Full=c;break;case 603979802:this.g.autoplayMovie=c;break;case 603979797:c=!1;this.g.allowAudio=c;break;case 603979892:this.g.noDelay=c;break;case 603979891:this.g.nboCharges=c;break;case 603979856:this.g.hiddenLinesDashed=c;break;case 603979886:this.g.multipleBondBananas=c;break;case 603979884:this.g.modulateOccupancy=c;break;case 603979875:this.g.legacyJavaFloat=c;break;case 603979927:this.g.showModVecs=c;break;case 603979937:this.g.showUnitCellDetails=
c;break;case 603979848:f=!1;break;case 603979972:this.g.vectorsCentered=c;break;case 603979810:this.g.cartoonBlocks=c;break;case 603979811:this.g.cartoonSteps=c;break;case 603979819:this.g.cartoonRibose=c;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 603979821: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 603979867:this.g.isosurfaceKey=c;break;case 603979893:this.g.partialDots=c;break;case 603979873: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 603979887:this.g.multiProcessor=c&&1<JV.Viewer.nProcessors;
break;case 603979885: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 603979866:c&&(this.$isKiosk=!0,this.g.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));break;case 603979975: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 603979898: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 603979903:this.g.saveProteinStructureState=c;break;case 603979780:this.g.allowGestures=c;break;case 603979865: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)?this.slm.setSelectionSubset(null):this.am.setSelectAllSubset(!1);break;case 603979880:this.g.messageStyleChime=c;break;case 603979896:this.g.pdbSequential=c;break;case 603979894:this.g.pdbAddHydrogens=
c;break;case 603979895: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 603979977:this.g.wireframeRotation=c;break;case 603979868: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 1612709912: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.showSelected=!1;break;case 536870922:this.setIntPropertyTok("showScript",b,c?1:0);return;case 603979778:this.g.allowEmbeddedScripts=c;break;case 603979890:this.g.navigationPeriodic=c;break;case 603979984:this.tm.setZShadeEnabled(c);return;case 603979832:this.haveDisplay&&(this.g.drawHover=c);break;case 603979889:this.setNavigationMode(c);break;case 603979888:return;
case 603979860:this.g.hideNavigationPoint=c;break;case 603979930:this.g.showNavigationPointAlways=c;break;case 603979900:this.setRefreshing(c);break;case 603979869:this.g.jmolInJSpecView=c;break;case 603979871: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 603979872: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.setSelectionHalosEnabled(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 603979976: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 603979901:this.g.ribbonBorder=
c;break;case 603979816:this.g.cartoonBaseEdges=c;break;case 603979820:this.g.cartoonRockets=c;break;case 603979902:this.g.rocketBarrels=c;break;case 603979850:this.gdata.setGreyscaleMode(this.g.greyscaleRendering=c);break;case 603979879:this.g.measurementLabels=c;break;case 603979809:case 603979804:case 603979808:this.setAxesMode(b);return;case 603979806:this.setAxesOrientationRasmol(c);return;case 603979824:this.setStringPropertyTok("defaultcolorscheme",545259545,c?"rasmol":"jmol");return;case 603979825:this.setDebugScript(c);
return;case 603979897: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:f=!1;this.g.bondModeOr=c;break;case 603979978:f=!1;this.g.zeroBasedXyzRasmol=c;this.reset(!0);break;case 603979899:f=!1;this.g.rangeSelected=c;break;case 603979878:f=
!1;this.g.measureAllModels=c;break;case 603979954:f=!1;this.sm.allowStatusReporting=c;break;case 603979822:f=!1;this.g.chainCaseSensitive=c;break;case 603979858:f=!1;this.g.hideNameInPopup=c;break;case 603979827:f=!1;this.g.disablePopupMenu=c;break;case 603979846:f=!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);f&&this.setTainted(!0)},"~S,~N,~B");c(c$,"setModelKitMode",
function(a){if(null!=this.acm&&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.ms.ac&&this.zap(!1,!0,!0)):(this.acm.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$,"jmolTest",function(){});c(c$,"showParameter",function(a,b,c){c=""+this.g.getParameterEscaped(a,c);(b||0>c.indexOf("<not defined>"))&&this.showString(a+
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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?!1:this.tm.isNavigating()&&!this.g.hideNavigationPoint||this.g.showNavigationPointAlways||this.getInMotion(!0)});c(c$,"getCurrentSolventProbeRadius",function(){return this.g.solventOn?this.g.solventProbeRadius:0});j(c$,"setPerspectiveDepth",function(a){this.tm.setPerspectiveDepth(a)},"~B");j(c$,
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this.g.removeParam("axeswindow");this.g.setB("axesMolecular",!0);a=1;break;case 603979809:this.g.removeParam("axesunitcell"),this.g.removeParam("axesmolecular"),this.g.setB("axesWindow",!0),a=0}this.g.setI("axesMode",a)},"~N");c(c$,"getSelectionHalosEnabled",function(){return this.selectionHalosEnabled});c(c$,"setSelectionHalosEnabled",function(a){this.selectionHalosEnabled!=a&&(this.g.setB("selectionHalos",a),this.shm.loadShape(8),this.selectionHalosEnabled=a)},"~B");c(c$,"getShowSelectedOnce",function(){var a=
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c(c$,"rebondState",function(a){this.clearModelDependentObjects();this.ms.deleteAllBonds();a=a&&this.g.legacyAutoBonding;this.ms.autoBondBs4(null,null,null,null,this.getMadBond(),a);this.addStateScript(a?"set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;":"connect;",!1,!0)},"~B");j(c$,"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");j(c$,"getMadBond",function(){return 2*this.g.bondRadiusMilliAngstroms});j(c$,"setShowHydrogens",function(a){this.g.setB("showHydrogens",a);this.g.showHydrogens=a},"~B");c(c$,"setShowBbcage",function(a){this.setObjectMad10(32,"boundbox",a?-4:0);this.g.setB("showBoundBox",a)},"~B");c(c$,"getShowBbcage",function(){return 0!=this.getObjectMad10(4)});c(c$,"setShowUnitCell",function(a){this.setObjectMad10(33,"unitcell",a?-2:0);this.g.setB("showUnitCell",a)},"~B");c(c$,"getShowUnitCell",
function(){return 0!=this.getObjectMad10(5)});c(c$,"setShowAxes",function(a){this.setObjectMad10(34,"axes",a?-2:0);this.g.setB("showAxes",a)},"~B");c(c$,"getShowAxes",function(){return 0!=this.getObjectMad10(1)});j(c$,"setFrankOn",function(a){this.isPreviewOnly&&(a=!1);this.frankOn=a;this.setObjectMad10(36,"frank",a?1:0)},"~B");c(c$,"getShowFrank",function(){return this.isPreviewOnly||this.isApplet&&this.creatingImage?!1:this.isSignedApplet&&!this.isSignedAppletLocal&&!JV.Viewer.isJS||this.frankOn});
j(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");j(c$,"setRasmolDefaults",function(){this.setDefaultsType("RasMol")});j(c$,"setJmolDefaults",function(){this.setDefaultsType("Jmol")});c(c$,"setDefaultsType",function(a){a.equalsIgnoreCase("RasMol")?this.stm.setRasMolDefaults():a.equalsIgnoreCase("PyMOL")?this.stm.setPyMOLDefaults():
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function(a){return this.tempArray.allocTempPoints(a)},"~N");c(c$,"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$,"getFont3D",function(a,b,c){return this.gdata.getFont3DFSS(a,
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c(c$,"getModelFileInfoAll",function(){return this.getPropertyManager().getModelFileInfo(null)});j(c$,"getProperty",function(a,b,c){if(!"DATA_API".equals(a))return this.getPropertyManager().getProperty(a,b,c);switch("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........getPreference.......".indexOf(b)){case 0:return this.scriptCheckRet(c,
!0);case 20:return null==this.appConsole?"":this.appConsole.getText();case 40:return this.showEditor(c),null;case 60:return this.scriptEditorVisible=c.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:q(c,J.api.JmolAppConsoleInterface)?this.appConsole=c:null!=c&&!c.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=c&&c.booleanValue())&&(JV.Viewer.isJS&&(this.appConsole=J.api.Interface.getOption("consolejs.AppletConsole",this,"script")),null!=this.appConsole&&this.appConsole.start(this)),
this.scriptEditor=JV.Viewer.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.getSymTemp().getSpaceGroupInfo(this.ms,
null,-1,!1);case 160:return this.g.disablePopupMenu=!0,null;case 180:return this.g.defaultDirectory;case 200:return q(c,String)?this.getMenu(c):this.getPopupMenu();case 220:return this.shm.getProperty(c);case 240:return this.sm.syncSend("getPreference",c,1)}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==
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22}return this.shm.checkObjectDragged(a,b,c,f,g,this.getVisibleFramesBitSet(),e)?(this.refresh(1,"checkObjectDragged"),22==e&&this.scriptEcho(this.getShapeProperty(22,"command")),!0):!1},"~N,~N,~N,~N,~N");c(c$,"rotateAxisAngleAtCenter",function(a,b,c,f,g,e,h){(a=this.tm.rotateAxisAngleAtCenter(a,b,c,f,g,e,h))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,c,f,g,e,h,j,l,n,m){if(this.headless){if(e&&3.4028235E38==g)return!1;
e=!1}(a=this.tm.rotateAboutPointsInternal(a,b,c,f,g,!1,e,h,!1,j,l,n,m))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.Lst,~A,JU.M4");c(c$,"startSpinningAxis",function(a,b,c){this.tm.spinOn||this.tm.navOn?(this.tm.setSpinOff(),this.tm.setNavOn(!1)):this.tm.rotateAboutPointsInternal(null,a,b,this.g.pickingSpinRate,3.4028235E38,c,!0,null,!1,null,null,null,null)},"JU.T3,JU.T3,~B");c(c$,"getModelDipole",function(){return this.ms.getModelDipole(this.am.cmi)});
c(c$,"calculateMolecularDipole",function(a){try{return this.ms.calculateMolecularDipole(this.am.cmi,a)}catch(b){if(E(b,JV.JmolAsyncException))return null!=this.eval&&this.eval.loadFileResourceAsync(b.getFileName()),null;throw b;}},"JU.BS");c(c$,"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$,"getDefaultLattice",function(){return this.g.ptDefaultLattice});c(c$,"getModelExtract",function(a,b,c,f){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),
b,c,f,!1)},"~O,~B,~B,~S");j(c$,"getData",function(a,b){return this.getModelFileData(a,b,!0)},"~S,~S");c(c$,"getModelFileData",function(a,b,c){return this.getPropertyManager().getAtomData(a,b,c)},"~S,~S,~B");c(c$,"getModelCml",function(a,b,c,f){return this.getPropertyManager().getModelCml(a,b,c,f,!1)},"JU.BS,~N,~B,~B");c(c$,"getPdbAtomData",function(a,b,c,f){return this.getPropertyManager().getPdbAtomData(null==a?this.bsA():a,b,c,f,!1)},"JU.BS,JU.OC,~B,~B");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$,"setFrameTitleObj",function(a){this.shm.loadShape(31);this.ms.setFrameTitle(this.getVisibleFramesBitSet(),a)},"~O");c(c$,"getFrameTitle",function(){return this.ms.getFrameTitle(this.am.cmi)});c(c$,"setAtomProperty",function(a,b,c,f,g,e,h){1648363544==b&&this.shm.deleteVdwDependentShapes(a);this.clearMinimization();this.ms.setAtomProperty(a,b,c,f,g,e,h);switch(b){case 1111492609:case 1111492610:case 1111492611:case 1111492612:case 1111492613:case 1111492614:case 1111490577:case 1111490578:case 1111490579:case 1086326789:this.refreshMeasures(!0)}},
"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"checkCoordinatesChanged",function(){this.ms.recalculatePositionDependentQuantities(null,null);this.refreshMeasures(!0)});c(c$,"setAtomCoords",function(a,b,c){a.isEmpty()||(this.ms.setAtomCoords(a,b,c),this.checkMinimization(),this.sm.setStatusAtomMoved(a))},"JU.BS,~N,~O");c(c$,"setAtomCoordsRelative",function(a,b){null==b&&(b=this.bsA());b.isEmpty()||(this.ms.setAtomCoordsRelative(a,b),this.checkMinimization(),this.sm.setStatusAtomMoved(b))},"JU.T3,JU.BS");c(c$,"invertAtomCoordPt",
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j;j=c.nextSetBit(j+1),h++)g[h]=this.getBranchBitSet(j,a,!0).cardinality(),e[h]=j;for(h=0;h<f-2;h++){for(var l=-2147483648,n=0,j=0;j<f;j++)g[j]>=l&&c.get(e[j])&&(n=e[j],l=g[j]);c.clear(n)}}b&&this.undoMoveActionClear(a,2,!0);this.invertSelected(null,null,a,c);b&&this.setStatusAtomPicked(a,"inverted: "+JU.Escape.eBS(c),null,!1)},"~N,~B");c(c$,"invertSelected",function(a,b,c,f){null==f&&(f=this.bsA());0!=f.cardinality()&&(this.ms.invertSelected(a,b,c,f),this.checkMinimization(),this.sm.setStatusAtomMoved(f))},
"JU.P3,JU.P4,~N,JU.BS");c(c$,"moveAtoms",function(a,b,c,f,g,e,h,j){h.isEmpty()||(this.ms.moveAtoms(a,b,c,f,h,g,e,j),this.checkMinimization(),this.sm.setStatusAtomMoved(h))},"JU.M4,JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B");c(c$,"moveSelected",function(a,b,c,f,g,e,h,j){0!=c&&(-2147483648==f&&(this.rotateBondIndex=-1),this.isJmolDataFrame()||(-2147483648==a?(this.showSelected=!0,this.movableBitSet=this.setMovableBitSet(null,!j),this.shm.loadShape(8),this.refresh(6,"moveSelected")):2147483647==a?this.showSelected&&
(this.showSelected=!1,this.movableBitSet=null,this.refresh(6,"moveSelected")):this.movingSelected||(this.movingSelected=!0,this.stopMinimization(),0<=this.rotateBondIndex&&-2147483648!=f?this.actionRotateBond(a,b,f,g):(e=this.setMovableBitSet(e,!j),e.isEmpty()||(h?(f=this.ms.getAtomSetCenter(e),this.tm.finalizeTransformParameters(),g=this.g.antialiasDisplay?2:1,h=this.tm.transformPt(f),a=-2147483648!=c?JU.P3.new3(h.x,h.y,h.z+c+0.5):JU.P3.new3(h.x+a*g+0.5,h.y+b*g+0.5,h.z),b=new JU.P3,this.tm.unTransformPoint(a,
b),b.sub(f),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$,"highlightBond",function(a,b){if(!b||this.hoverEnabled){var c=null;if(0<=a){var f=this.ms.bo[a],c=f.atom2.i;if(!this.ms.isAtomAssignable(c))return;c=JU.BSUtil.newAndSetBit(c);c.set(f.atom1.i)}this.highlight(c);this.refresh(3,"highlightBond")}},"~N,~B");c(c$,"highlight",function(a){this.atomHighlighted=null!=a&&1==a.cardinality()?a.nextSetBit(0):
-1;null==a?this.setCursor(0):(this.shm.loadShape(8),this.setCursor(12));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$,"actionRotateBond",function(a,b,c,f){if(!(0>this.rotateBondIndex)){var g=this.bsRotateBranch,e,h;if(null==g){h=this.ms.bo[this.rotateBondIndex];
e=h.atom1;h=h.atom2;this.undoMoveActionClear(e.i,2,!0);c=JU.P3.new3(c,f,y((e.sZ+h.sZ)/2));this.tm.unTransformPoint(c,c);if(1==h.getCovalentBondCount()||c.distance(e)<c.distance(h)&&1!=e.getCovalentBondCount())f=e,e=h,h=f;if(90<JU.Measure.computeAngleABC(c,e,h,!0)||90<JU.Measure.computeAngleABC(c,h,e,!0))g=this.getBranchBitSet(h.i,e.i,!0);if(null!=g){c=0;for(f=e.bonds.length;0<=--f;)if(g.get(e.getBondedAtomIndex(f))&&2==++c){g=null;break}}null==g&&(g=this.ms.getMoleculeBitSetForAtom(e.i));this.bsRotateBranch=
g;this.rotatePrev1=e.i;this.rotatePrev2=h.i}else e=this.ms.at[this.rotatePrev1],h=this.ms.at[this.rotatePrev2];c=JU.V3.new3(h.sX-e.sX,h.sY-e.sY,0);a=JU.V3.new3(a,b,0);c.cross(c,a);a=(0<c.z?1:-1)*a.length();g=JU.BSUtil.copy(g);g.andNot(this.slm.getMotionFixedAtoms());this.rotateAboutPointsInternal(this.eval,e,h,0,a,!1,g,null,null,null,null)}},"~N,~N,~N,~N");c(c$,"refreshMeasures",function(a){this.setShapeProperty(6,"refresh",null);a&&this.stopMinimization()},"~B");c(c$,"functionXY",function(a,b,c){var f=
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