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c(c$,"setRotationScale",function(a){this.m00=a.m00;this.m01=a.m01;this.m02=a.m02;this.m10=a.m10;this.m11=a.m11;this.m12=a.m12;this.m20=a.m20;this.m21=a.m21;this.m22=a.m22},"JU.M3");c(c$,"setRowA",function(a,b){3>a&&this.setRow33(a,b);switch(a){case 0:this.m03=b[3];return;case 1:this.m13=b[3];return;case 2:this.m23=b[3];return;case 3:this.m30=b[0];this.m31=b[1];this.m32=b[2];this.m33=b[3];return}this.err()},"~N,~A");h(c$,"getRow",function(a,b){3>a&&this.getRow33(a,b);switch(a){case 0:b[3]=this.m03;
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this.m13*(this.m22*this.m30-this.m20*this.m32)+this.m10*(this.m23*this.m32-this.m22*this.m33),this.m22*(this.m00*this.m33-this.m03*this.m30)+this.m23*(this.m02*this.m30-this.m00*this.m32)+this.m20*(this.m03*this.m32-this.m02*this.m33),this.m32*(this.m00*this.m13-this.m03*this.m10)+this.m33*(this.m02*this.m10-this.m00*this.m12)+this.m30*(this.m03*this.m12-this.m02*this.m13),this.m02*(this.m13*this.m20-this.m10*this.m23)+this.m03*(this.m10*this.m22-this.m12*this.m20)+this.m00*(this.m12*this.m23-this.m13*
this.m22),this.m13*(this.m20*this.m31-this.m21*this.m30)+this.m10*(this.m21*this.m33-this.m23*this.m31)+this.m11*(this.m23*this.m30-this.m20*this.m33),this.m23*(this.m00*this.m31-this.m01*this.m30)+this.m20*(this.m01*this.m33-this.m03*this.m31)+this.m21*(this.m03*this.m30-this.m00*this.m33),this.m33*(this.m00*this.m11-this.m01*this.m10)+this.m30*(this.m01*this.m13-this.m03*this.m11)+this.m31*(this.m03*this.m10-this.m00*this.m13),this.m03*(this.m11*this.m20-this.m10*this.m21)+this.m00*(this.m13*this.m21-
this.m11*this.m23)+this.m01*(this.m10*this.m23-this.m13*this.m20),this.m10*(this.m22*this.m31-this.m21*this.m32)+this.m11*(this.m20*this.m32-this.m22*this.m30)+this.m12*(this.m21*this.m30-this.m20*this.m31),this.m20*(this.m02*this.m31-this.m01*this.m32)+this.m21*(this.m00*this.m32-this.m02*this.m30)+this.m22*(this.m01*this.m30-this.m00*this.m31),this.m30*(this.m02*this.m11-this.m01*this.m12)+this.m31*(this.m00*this.m12-this.m02*this.m10)+this.m32*(this.m01*this.m10-this.m00*this.m11),this.m00*(this.m11*
this.m22-this.m12*this.m21)+this.m01*(this.m12*this.m20-this.m10*this.m22)+this.m02*(this.m10*this.m21-this.m11*this.m20));this.scale(a);return this});c(c$,"set",function(a,b,d,f,c,e,j,l,k,h,n,q,z,A,H,E){this.m00=a;this.m01=b;this.m02=d;this.m03=f;this.m10=c;this.m11=e;this.m12=j;this.m13=l;this.m20=k;this.m21=h;this.m22=n;this.m23=q;this.m30=z;this.m31=A;this.m32=H;this.m33=E},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"determinant4",function(){return(this.m00*this.m11-this.m01*this.m10)*
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a.m13*b.m33,a.m20*b.m00+a.m21*b.m10+a.m22*b.m20+a.m23*b.m30,a.m20*b.m01+a.m21*b.m11+a.m22*b.m21+a.m23*b.m31,a.m20*b.m02+a.m21*b.m12+a.m22*b.m22+a.m23*b.m32,a.m20*b.m03+a.m21*b.m13+a.m22*b.m23+a.m23*b.m33,a.m30*b.m00+a.m31*b.m10+a.m32*b.m20+a.m33*b.m30,a.m30*b.m01+a.m31*b.m11+a.m32*b.m21+a.m33*b.m31,a.m30*b.m02+a.m31*b.m12+a.m32*b.m22+a.m33*b.m32,a.m30*b.m03+a.m31*b.m13+a.m32*b.m23+a.m33*b.m33)},"JU.M4,JU.M4");c(c$,"transform",function(a){this.transform2(a,a)},"JU.T4");c(c$,"transform2",function(a,
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a.m00&&this.m01==a.m01&&this.m02==a.m02&&this.m03==a.m03&&this.m10==a.m10&&this.m11==a.m11&&this.m12==a.m12&&this.m13==a.m13&&this.m20==a.m20&&this.m21==a.m21&&this.m22==a.m22&&this.m23==a.m23&&this.m30==a.m30&&this.m31==a.m31&&this.m32==a.m32&&this.m33==a.m33},"~O");h(c$,"hashCode",function(){return JU.T3.floatToIntBits(this.m00)^JU.T3.floatToIntBits(this.m01)^JU.T3.floatToIntBits(this.m02)^JU.T3.floatToIntBits(this.m03)^JU.T3.floatToIntBits(this.m10)^JU.T3.floatToIntBits(this.m11)^JU.T3.floatToIntBits(this.m12)^
JU.T3.floatToIntBits(this.m13)^JU.T3.floatToIntBits(this.m20)^JU.T3.floatToIntBits(this.m21)^JU.T3.floatToIntBits(this.m22)^JU.T3.floatToIntBits(this.m23)^JU.T3.floatToIntBits(this.m30)^JU.T3.floatToIntBits(this.m31)^JU.T3.floatToIntBits(this.m32)^JU.T3.floatToIntBits(this.m33)});h(c$,"toString",function(){return"[\n  ["+this.m00+"\t"+this.m01+"\t"+this.m02+"\t"+this.m03+"]\n  ["+this.m10+"\t"+this.m11+"\t"+this.m12+"\t"+this.m13+"]\n  ["+this.m20+"\t"+this.m21+"\t"+this.m22+"\t"+this.m23+"]\n  ["+
this.m30+"\t"+this.m31+"\t"+this.m32+"\t"+this.m33+"] ]"});c(c$,"round",function(a){this.m00=this.rnd(this.m00,a);this.m01=this.rnd(this.m01,a);this.m02=this.rnd(this.m02,a);this.m03=this.rnd(this.m03,a);this.m10=this.rnd(this.m10,a);this.m11=this.rnd(this.m11,a);this.m12=this.rnd(this.m12,a);this.m13=this.rnd(this.m13,a);this.m20=this.rnd(this.m20,a);this.m21=this.rnd(this.m21,a);this.m22=this.rnd(this.m22,a);this.m23=this.rnd(this.m23,a);this.m30=this.rnd(this.m30,a);this.m31=this.rnd(this.m31,
a);this.m32=this.rnd(this.m32,a);this.m33=this.rnd(this.m33,a);return this},"~N");c(c$,"rnd",function(a,b){return Math.abs(a)<b?0:a},"~N,~N")});m("JU");x(["java.io.OutputStream","javajs.api.GenericOutputChannel"],"JU.OC","java.io.BufferedWriter $.ByteArrayOutputStream $.OutputStreamWriter java.lang.Float JU.Base64 $.SB".split(" "),function(){c$=w(function(){this.bw=this.fileName=this.bytePoster=null;this.isLocalFile=!1;this.byteCount=0;this.closed=this.isCanceled=!1;this.type=this.sb=this.os=null;
this.$isBase64=!1;this.bytes=this.os0=null;this.bigEndian=!0;s(this,arguments)},JU,"OC",java.io.OutputStream,javajs.api.GenericOutputChannel);p(c$,function(){I(this,JU.OC,[])});p(c$,function(a){I(this,JU.OC,[]);this.setParams(null,a,!1,null)},"~S");c(c$,"setParams",function(a,b,d,f){this.bytePoster=a;if(this.$isBase64=";base64,".equals(b))b=null,this.os0=f,f=null;this.fileName=b;this.os=f;this.isLocalFile=null!=b&&!JU.OC.isRemote(b);d&&(!this.$isBase64&&null!=f)&&(this.bw=new java.io.BufferedWriter(new java.io.OutputStreamWriter(f)));
return this},"javajs.api.BytePoster,~S,~B,java.io.OutputStream");h(c$,"isBigEndian",function(){return this.bigEndian});c(c$,"setBigEndian",function(a){this.bigEndian=a},"~B");c(c$,"setBytes",function(a){this.bytes=a;return this},"~A");c(c$,"getFileName",function(){return this.fileName});c(c$,"getName",function(){return null==this.fileName?null:this.fileName.substring(this.fileName.lastIndexOf("/")+1)});c(c$,"getByteCount",function(){return this.byteCount});c(c$,"setType",function(a){this.type=a},
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k=this.asc.ac;l<k;l++)d[l].partialCharge=0;for(var h=0,l=C(e[h++]);0<=--l;){var n=C(e[h++])+this.iatom0-1,q=e[h++];d[n].partialCharge=q;j++}}catch(z){l=this.asc.getLastAtomSetAtomIndex();for(k=this.asc.ac;l<k;l++)d[l].partialCharge=0;JU.Logger.error("error reading "+f+" field -- partial charges cleared")}JU.Logger.info(j+" partial charges read")}else if(f.toUpperCase().contains("ATOM_NAMES")){j=0;try{for(var A=JU.PT.getTokens(c),h=0,l=this.parseIntStr(A[h++]);0<=--l;){for(var H;-2147483648==(H=this.parseIntStr(A[h++])););
var n=H+this.iatom0-1,E=A[h++];E.equals(".")||(d[n].atomName=E);j++}}catch(u){JU.Logger.error("error reading "+f+" field")}JU.Logger.info(j+" atom names read")}},"java.util.Map,JU.Lst");c(c$,"addMolAtom",function(a,b,d,f,c,e,j){switch(b){case 0:break;case 1:d="1H";break;case 2:d="2H";break;case 3:d="3H";break;default:d=b+d}this.optimize2D&&0!=j&&(this.optimize2D=!1);b=new J.adapter.smarter.Atom;b.elementSymbol=d;b.formalCharge=f;this.setAtomCoordXYZ(b,c,e,j);-2147483648==a?this.asc.addAtom(b):(this.haveAtomSerials=
!0,b.atomSerial=a,this.asc.addAtomWithMappedSerialNumber(b))},"~N,~N,~S,~N,~N,~N,~N");c(c$,"fixOrder",function(a,b){switch(a){default:case 0:case -10:return 1;case 1:switch(b){case 1:return 1025;case 3:case 6:return 1041}break;case 2:case 3:break;case 4:return 515;case 5:return 66;case 6:return 513;case 7:return 514;case 8:case 9:return 33;case 14:return 4;case 15:return 5;case 16:return 6}return a},"~N,~N");c(c$,"addMolBond",function(a,b,d,f){d=this.fixOrder(d,f);this.haveAtomSerials?this.asc.addNewBondFromNames(a,
b,d):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(a)-1,this.iatom0+this.parseIntStr(b)-1,d)},"~S,~S,~N,~N")});m("J.adapter.readers.molxyz");x(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.XyzReader",["java.lang.Float","JU.Logger"],function(){c$=F(J.adapter.readers.molxyz,"XyzReader",J.adapter.smarter.AtomSetCollectionReader);h(c$,"checkLine",function(){var a=this.parseIntStr(this.line);if(-2147483648==a)return this.continuing=!1;this.vibrationNumber=++this.modelNumber;
if(0>=this.desiredVibrationNumber?this.doGetModel(this.modelNumber,null):this.doGetVibration(this.vibrationNumber)){this.rd();this.checkCurrentLineForScript();this.asc.newAtomSet();var b=this.line.trim();this.readAtoms(a);this.applySymmetryAndSetTrajectory();this.asc.setAtomSetName(b);if(this.isLastModel(this.modelNumber))return this.continuing=!1}else this.skipAtomSet(a);this.discardLinesUntilNonBlank();return!1});h(c$,"finalizeSubclassReader",function(){this.isTrajectory=!1;this.finalizeReaderASCR()});
c(c$,"skipAtomSet",function(a){for(this.rd();0<=--a;)this.rd()},"~N");c(c$,"readAtoms",function(a){for(var b=0;b<a;++b){this.rd();var d=this.getTokens();if(4>d.length)JU.Logger.warn("line cannot be read for XYZ atom data: "+this.line);else{var f=this.addAtomXYZSymName(d,1,null,null);this.setElementAndIsotope(f,d[0]);var c=4;switch(d.length){case 4:continue;case 5:case 6:case 8:case 9:if(0<=d[4].indexOf("."))f.partialCharge=this.parseFloatStr(d[4]);else{var e=this.parseIntStr(d[4]);-2147483648!=e&&
(f.formalCharge=e)}switch(d.length){case 5:continue;case 6:f.radius=this.parseFloatStr(d[5]);continue;case 9:f.atomSerial=this.parseIntStr(d[8])}c++;default:var e=this.parseFloatStr(d[c++]),j=this.parseFloatStr(d[c++]),d=this.parseFloatStr(d[c++]);if(Float.isNaN(e)||Float.isNaN(j)||Float.isNaN(d))continue;this.asc.addVibrationVector(f.index,e,j,d)}}}},"~N")});m("J.adapter.smarter");x(["JU.P3"],"J.adapter.smarter.Atom",["JU.AU","$.Lst","$.V3","JU.Vibration"],function(){c$=w(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.bondRadius=NaN;this.altLoc="\x00";this.group3=null;this.sequenceNumber=-2147483648;this.insertionCode="\x00";this.tensors=this.anisoBorU=null;this.ignoreSymmetry=!1;this.typeSymbol=null;s(this,arguments)},J.adapter.smarter,
"Atom",JU.P3,Cloneable);c(c$,"addTensor",function(a,b,d){if(null==a)return null;if(d||null==this.tensors)this.tensors=new JU.Lst;this.tensors.addLast(a);null!=b&&a.setType(b);return a},"JU.Tensor,~S,~B");p(c$,function(){I(this,J.adapter.smarter.Atom,[]);this.set(NaN,NaN,NaN)});c(c$,"getClone",function(){var a;try{a=this.clone()}catch(b){if(D(b,CloneNotSupportedException))return null;throw b;}null!=this.vib&&(a.vib=t(this.vib,JU.Vibration)?this.vib.clone():JU.V3.newV(a.vib));null!=this.anisoBorU&&
(a.anisoBorU=JU.AU.arrayCopyF(this.anisoBorU,-1));if(null!=this.tensors){a.tensors=new JU.Lst;for(var d=this.tensors.size();0<=--d;)a.tensors.addLast(this.tensors.get(d).copyTensor())}return a});c(c$,"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");c(c$,"copyTo",function(a,b){var d=b.newCloneAtom(this);d.setT(a);return d},"JU.P3,J.adapter.smarter.AtomSetCollection");G(c$,"elementCharMasks",B(-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]))});m("J.adapter.smarter");x(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["java.lang.Float","J.api.JmolAdapter"],function(){c$=w(function(){this.iatom=0;this.atom=null;this.ac=0;this.bsAtoms=this.atoms=null;s(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);p(c$,function(a){this.ac=
a.ac;this.atoms=a.atoms;this.bsAtoms=a.bsAtoms;this.iatom=0},"J.adapter.smarter.AtomSetCollection");h(c$,"hasNext",function(){if(this.iatom==this.ac)return!1;for(;null==(this.atom=this.atoms[this.iatom++])||null!=this.bsAtoms&&!this.bsAtoms.get(this.atom.index);)if(this.iatom==this.ac)return!1;this.atoms[this.iatom-1]=null;return!0});h(c$,"getAtomSetIndex",function(){return this.atom.atomSetIndex});h(c$,"getSymmetry",function(){return this.atom.bsSymmetry});h(c$,"getAtomSite",function(){return this.atom.atomSite+
1});h(c$,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});h(c$,"getElementNumber",function(){return 0<this.atom.elementNumber?this.atom.elementNumber:J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});h(c$,"getAtomName",function(){return this.atom.atomName});h(c$,"getFormalCharge",function(){return this.atom.formalCharge});h(c$,"getPartialCharge",function(){return this.atom.partialCharge});h(c$,"getTensors",function(){return this.atom.tensors});h(c$,"getRadius",
function(){return this.atom.radius});h(c$,"getBondRadius",function(){return this.atom.bondRadius});h(c$,"getVib",function(){return null==this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});h(c$,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1094713365!=this.atom.vib.z?0:C(this.atom.vib.x)});h(c$,"getBfactor",function(){return this.atom.bfactor});h(c$,"getOccupancy",function(){return 100*this.atom.foccupancy});h(c$,"getIsHetero",function(){return this.atom.isHetero});
h(c$,"getSerial",function(){return this.atom.atomSerial});h(c$,"getChainID",function(){return this.atom.chainID});h(c$,"getAltLoc",function(){return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc)});h(c$,"getGroup3",function(){return this.atom.group3});h(c$,"getSequenceNumber",function(){return this.atom.sequenceNumber});h(c$,"getInsertionCode",function(){return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode)});h(c$,"getXYZ",function(){return this.atom})});m("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 $.Logger".split(" "),function(){c$=w(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.readerList=null;this.atomMapAnyCase=!1;this.bsStructuredModels=null;this.haveAnisou=!1;this.baseSymmetryAtomCount=0;this.checkLatticeOnly=!1;this.xtalSymmetry=null;this.bondIndex0=0;this.checkSpecial=
!0;this.atomSymbolicMap=null;this.haveUnitCell=!1;this.vibScale=0;s(this,arguments)},J.adapter.smarter,"AtomSetCollection");O(c$,function(){this.atomSetInfo=new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=B(16,0);this.atomSetAtomIndexes=B(16,0);this.atomSetAtomCounts=B(16,0);this.atomSetBondCounts=B(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSymbolicMap=new java.util.Hashtable});c(c$,"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$,"getGlobalBoolean",function(a){return this.atomSetInfo.get(J.adapter.smarter.AtomSetCollection.globalBooleans[a])===Boolean.TRUE},"~N");p(c$,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);b=null==b?null:b.htParams.get("appendToModelIndex");null!=b&&this.setInfo("appendToModelIndex",b);if(null!=d){f=0;this.readerList=new JU.Lst;for(b=0;b<d.length;b++)null!=d[b]&&(0<d[b].ac||null!=d[b].reader&&d[b].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(f++,d[b]);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$,"appendAtomSetCollectionList",function(a){var b=a.size();if(0==b)this.errorMessage="No file found!";else for(var d=0;d<b;d++){var f=a.get(d);t(f,JU.Lst)?this.appendAtomSetCollectionList(f):this.appendAtomSetCollection(d,f)}},"JU.Lst");c(c$,"setTrajectory",function(){this.isTrajectory||(this.trajectorySteps=new JU.Lst);this.isTrajectory=
!0;var a=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(!(1>=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 j=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=f&&(j=J.adapter.smarter.AtomSetCollection.fixPeriodic(j,f[c]));b[e]=j;d&&(a[e]=this.atoms[c].vib);e++}if(d){if(null==
this.vibrationSteps){this.vibrationSteps=new JU.Lst;for(c=0;c<this.trajectoryStepCount;c++)this.vibrationSteps.addLast(null)}this.vibrationSteps.addLast(a)}this.trajectorySteps.addLast(b);this.trajectoryStepCount++}});c(c$,"appendAtomSetCollection",function(a,b){null!=b.reader&&b.reader.mustFinalizeModelSet&&this.readerList.addLast(b.reader);var d=this.ac;this.setInfo("loadState",b.atomSetInfo.get("loadState"));if(null!=b.bsAtoms){null==this.bsAtoms&&(this.bsAtoms=new JU.BS);for(var f=b.bsAtoms.nextSetBit(0);0<=
f;f=b.bsAtoms.nextSetBit(f+1))this.bsAtoms.set(d+f)}for(var f=0,c=this.atomSetCount,e=0;e<b.atomSetCount;e++){this.newAtomSet();var j=(this.atomSetAuxiliaryInfo[this.iSet]=b.atomSetAuxiliaryInfo[e]).get("PDB_CONECT_firstAtom_count_max");null!=j&&(j[0]+=d);this.setCurrentModelInfo("title",b.collectionName);this.setAtomSetName(b.getAtomSetName(e));for(j=0;j<b.atomSetAtomCounts[e];j++)null!=this.bsAtoms&&this.bsAtoms.set(this.ac),this.newCloneAtom(b.atoms[f]),f++;this.atomSetNumbers[this.iSet]=0>a?this.iSet+
1:1E6*(a+1)+b.atomSetNumbers[e]}for(f=0;f<b.bondCount;f++)e=b.bonds[f],this.addNewBondWithOrder(e.atomIndex1+d,e.atomIndex2+d,e.order);for(f=J.adapter.smarter.AtomSetCollection.globalBooleans.length;0<=--f;)b.getGlobalBoolean(f)&&this.setGlobalBoolean(f);for(f=0;f<b.structureCount;f++)d=b.structures[f],this.addStructure(d),d.modelStartEnd[0]+=c,d.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(c$,"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=B(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=u(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$,"reverseArray",function(a){for(var b=this.atomSetCount,d=u(b/2);0<=--d;)JU.AU.swapInt(a,
d,b-1-d)},"~A");c(c$,"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$,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=B(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSetInfo=new java.util.Hashtable;this.atomSetCount=0;this.atomSetNumbers=B(16,0);this.atomSymbolicMap=new java.util.Hashtable;this.bonds=null;this.iSet=-1;this.xtalSymmetry=this.readerList=null;this.structures=
Array(16);this.structureCount=0;this.vibrationSteps=this.trajectorySteps=null});c(c$,"discardPreviousAtoms",function(){for(var a=this.ac;0<=--a;)this.atoms[a]=null;this.ac=0;this.atomSymbolicMap.clear();this.atomMapAnyCase=!1;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$,"setAtomMapAnyCase",function(){this.atomMapAnyCase=!0;var a=new java.util.Hashtable;a.putAll(this.atomSymbolicMap);for(var b,d=this.atomSymbolicMap.entrySet().iterator();d.hasNext()&&((b=d.next())||1);){var f=b.getKey(),c=f.toUpperCase();c.equals(f)||a.put(c,b.getValue())}this.atomSymbolicMap=a});
c(c$,"getAtomIndex",function(a){var b=this.atomSymbolicMap.get(a);null==b&&this.atomMapAnyCase&&(b=this.atomSymbolicMap.get(a.toUpperCase()));return null==b?-1:b.index},"~S");c(c$,"addNewBondWithOrder",function(a,b,d){var f=null;0<=a&&(a<this.ac&&0<=b&&b<this.ac&&a!=b)&&(f=new J.adapter.smarter.Bond(a,b,d),this.addBond(f));return f},"~N,~N,~N");c(c$,"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$,"setU",function(a,b,d){var f=a.anisoBorU;null==f&&this.setAnisoBorU(a,f=L(8,0),8);f[b]=d},"J.adapter.smarter.Atom,~N,~N");c(c$,"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);0==this.ac&&(this.ac=a.length)}}});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.atomMapAnyCase=!1);this.setCurrentModelInfo("title",this.collectionName)},"~B");c(c$,"getAtomSetAtomIndex",function(a){0>a&&Zystem.out.println("??");return this.atomSetAtomIndexes[a]},
"~N");c(c$,"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){t(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$,"checkNoEmptyModel",function(){for(;0<this.atomSetCount&&0==this.atomSetAtomCounts[this.atomSetCount-1];)this.atomSetCount--});G(c$,"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)});m("J.adapter.smarter");x(["javajs.api.GenericLineReader","JU.SB"],"J.adapter.smarter.AtomSetCollectionReader","java.io.BufferedReader java.lang.Boolean $.Double $.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 $.Logger".split(" "),
function(){c$=w(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.paramsLattice=this.moreUnitCellInfo=null;this.paramsPacked=this.paramsCentroid=!1;this.fileName=this.filePath=null;this.baseBondIndex=this.baseAtomIndex=0;this.stateScriptVersionInt=2147483647;this.haveModel=this.isFinalized=!1;this.previousUnitCell=this.previousSpaceGroup=null;this.nMatrixElements=0;this.filter=this.bsFilter=this.matUnitCellOrientation=this.ucItems=
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.strSupercell=null;this.allow_a_len_1=!1;this.ms=this.matRot=this.filter2=this.filter1=null;this.vibsFractional=!1;this.siteScript=this.previousScript=null;s(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);O(c$,function(){this.next=B(1,0);this.loadNote=new JU.SB});c(c$,"setup",function(a,b,d){this.setupASCR(a,b,d)},"~S,java.util.Map,~O");c(c$,"setupASCR",function(a,b,d){null!=a&&(this.debugging=JU.Logger.debugging,this.htParams=
b,this.filePath=""+b.get("fullPathName"),a=this.filePath.lastIndexOf("/"),this.fileName=this.filePath.substring(a+1),t(d,java.io.BufferedReader)?this.reader=d:t(d,javajs.api.GenericBinaryDocument)&&(this.binaryDoc=d))},"~S,java.util.Map,~O");c(c$,"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$,"fixBaseIndices",function(){try{var a=this.htParams.get("baseModelIndex").intValue();this.baseAtomIndex+=this.asc.ac;this.baseBondIndex+=this.asc.bondCount;
a+=this.asc.atomSetCount;this.htParams.put("baseAtomIndex",Integer.$valueOf(this.baseAtomIndex));this.htParams.put("baseBondIndex",Integer.$valueOf(this.baseBondIndex));this.htParams.put("baseModelIndex",Integer.$valueOf(a))}catch(b){if(!D(b,Exception))throw b;}});c(c$,"readDataObject",function(a){this.initialize();this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);this.initializeReader();this.processDOM(a);return this.finish()},"~O");c(c$,"processDOM",function(){},"~O");
c(c$,"processBinaryDocument",function(){});c(c$,"initializeReader",function(){});c(c$,"checkLine",function(){return!0});c(c$,"checkLastModel",function(){if(this.isLastModel(this.modelNumber)&&this.doProcessLines)return this.continuing=this.doProcessLines=!1;this.doProcessLines=!1;return!0});c(c$,"isLastModel",function(a){return 0<this.desiredModelNumber||a>=this.lastModelNumber},"~N");c(c$,"appendLoadNote",function(a){null==a?this.loadNote=new JU.SB:(this.loadNote.append(a).append("\n"),JU.Logger.info(a))},
"~S");c(c$,"initializeTrajectoryFile",function(){this.asc.addAtom(new J.adapter.smarter.Atom);this.trajectorySteps=this.htParams.get("trajectorySteps");null==this.trajectorySteps&&this.htParams.put("trajectorySteps",this.trajectorySteps=new JU.Lst)});c(c$,"finalizeSubclassReader",function(){});c(c$,"finalizeReaderASCR",function(){this.isFinalized=!0;if(0<this.asc.atomSetCount){1==this.asc.atomSetCount&&(this.asc.setCurrentModelInfo("dbName",this.htParams.get("dbName")),this.asc.setCurrentModelInfo("auxFiles",
this.htParams.get("auxFiles")));this.applySymmetryAndSetTrajectory();this.asc.finalizeStructures();this.doCentralize&&this.asc.centralize();null!=this.fillRange&&this.asc.setInfo("boundbox",this.fillRange);var a=this.asc.getAtomSetAuxiliaryInfo(0);if(null!=a){if(null!=this.domains){this.asc.setGlobalBoolean(5);var b=this.domains.getMapKeys(2,!0),d=b.indexOf("{ ",2);0<=d&&(b=b.substring(d+2));d=b.indexOf("_metadata");0>d&&(d=b.indexOf("metadata"));0<=d&&(b=b.substring(0,d));b=JU.PT.rep(JU.PT.replaceAllCharacters(b,
"{}","").trim(),"\n","\n  ")+"\n\nUse SHOW DOMAINS for details.";this.appendLoadNote("\nDomains loaded:\n   "+b);for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("domains",this.domains)}if(null!=this.validation)for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("validation",this.validation);if(null!=this.dssr){a.put("dssrJSON",Boolean.TRUE);for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("dssr",this.dssr)}}}this.fixJavaFloat||
this.asc.setInfo("legacyJavaFloat",Boolean.TRUE);this.setLoadNote()});c(c$,"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=a.getMessage();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.htParams.containsKey("baseBondIndex")&&(this.baseBondIndex=this.htParams.get("baseBondIndex").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");t(a,JU.P3)?(a=this.ptSupercell=a,this.strSupercell=C(a.x)+"a,"+C(a.y)+"b,"+C(a.z)+"c"):t(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),t(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.paramsLattice=this.htParams.get("lattice");this.paramsCentroid=
this.htParams.containsKey("centroid");this.paramsPacked=this.htParams.containsKey("packed");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=B(4,0);this.doApplySymmetry=!1;var a=this.paramsLattice;if(null==a||0==a.length()){if(!this.forcePacked&&null==this.strSupercell)return;
a=JU.P3.new3(1,1,1)}this.latticeCells[0]=C(a.x);this.latticeCells[1]=C(a.y);this.latticeCells[2]=C(a.z);t(a,JU.T4)&&(this.latticeCells[3]=C(a.w));if((this.doCentroidUnitCell=this.paramsCentroid)&&(-1==this.latticeCells[2]||0==this.latticeCells[2]))this.latticeCells[2]=1;a=this.forcePacked||this.paramsPacked;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=B(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$,"initializeSymmetry",function(){this.previousSpaceGroup=this.sgName;this.previousUnitCell=this.unitCellParams;this.iHaveUnitCell=this.ignoreFileUnitCell;if(!this.ignoreFileUnitCell){this.unitCellParams=L(26,0);for(var a=25;0<=--a;)this.unitCellParams[a]=NaN;this.unitCellParams[25]=this.latticeScaling;this.symmetry=null}this.ignoreFileSpaceGroupName||
(this.sgName="unspecified!");this.doCheckUnitCell=!1});c(c$,"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(),0==a.length||(a.equals("HM:")||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){this.ignoreFileUnitCell||(0==a&&1==b&&!this.allow_a_len_1||3==a&&0==b?(null==this.ucItems&&
(this.ucItems=L(6,0)),this.ucItems[a]=b):(null!=this.ucItems&&6>a&&(this.ucItems[a]=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");this.allow_a_len_1=this.checkFilterKey("TOPOS");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("!.");if(this.filter.startsWith("_")||0<=this.filter.indexOf(";_"))this.filterElement=this.checkFilterKey("_");this.filterGroup3=this.checkFilterKey("[");this.filterChain=this.checkFilterKey(":");this.filterAltLoc=this.checkFilterKey("%");if(this.filterEveryNth=this.checkFilterKey("/="))this.filterN=this.parseIntAt(this.filter,this.filter.indexOf("/=")+2);else if(this.filter.startsWith("=")||0<=this.filter.indexOf(";="))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("/=");if(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$,"checkFilterKey",function(a){return null!=this.filter&&0<=this.filter.indexOf(a)},"~S");c(c$,"checkAndRemoveFilterKey",function(a){if(!this.checkFilterKey(a))return!1;this.filter=JU.PT.rep(this.filter,a,"");3>this.filter.length&&(this.filter=null);return!0},"~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);this.appendLoadNote("This model is 2D. Its 3D structure will be generated.")});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,j,l,k){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(j,l,k),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");
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J.adapter.smarter.Resolver.gulpContainsRecords,J.adapter.smarter.Resolver.espressoContainsRecords,J.adapter.smarter.Resolver.siestaContainsRecords,J.adapter.smarter.Resolver.xcrysDenContainsRecords,J.adapter.smarter.Resolver.mopacArchiveContainsRecords,J.adapter.smarter.Resolver.abinitContainsRecords,J.adapter.smarter.Resolver.gaussianFchkContainsRecords,J.adapter.smarter.Resolver.inputContainsRecords,J.adapter.smarter.Resolver.aflowContainsRecords,J.adapter.smarter.Resolver.magCifContainsRecords,
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this.xEndcap-E,this.yEndcap-q,this.zEndcap+m-1,a,b,h))),this.line3d.plotLineDeltaAOld(this.shadesA,this.shadesB,d,A,this.xA+E,this.yA+q,this.zA-m,this.dxB,this.dyB,this.dzB,this.clipped),k&&this.line3d.plotLineDeltaOld(this.shadesA[H],this.shadesB[H],this.xA-E,this.yA-q,this.zA+m,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,j){var l=this.g3d;null==this.ptA0&&(this.ptA0=
new JU.P3,this.ptB0=new JU.P3);this.ptA0.setT(e);var k=u(c/2)+1,h=Math.round(e.x),n=Math.round(e.y),q=Math.round(e.z),z=Math.round(j.x),A=Math.round(j.y),H=Math.round(j.z),E=l.clipCode3(h-k,n-k,q-k),h=l.clipCode3(h+k,n+k,q+k),n=l.clipCode3(z-k,A-k,H-k),k=l.clipCode3(z+k,A+k,H+k),z=E|h|n|k;this.clipped=0!=z;if(!(-1==z||0!=(E&k&h&n))){this.dxBf=j.x-e.x;this.dyBf=j.y-e.y;this.dzBf=j.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=C(this.xAf);
this.yA=C(this.yAf);this.zA=C(this.zAf);this.dxB=C(this.dxBf);this.dyB=C(this.dyBf);this.dzB=C(this.dzBf);this.shadesA=l.getShades(this.colixA=a);this.shadesB=l.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);l.setZMargin(5);c=l.pixel;a=l.width;b=l.zbuf;j=z[0];E=z[1];k=z[2];z=z[3];for(A=this.rasterCount;0<=--A;){var H=z[A]>>8,h=H>>1,n=j[A],
q=E[A],m=k[A];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(l.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+n,this.yEndcap+q,this.zEndcap-m-1,a,b,c),l.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-n,this.yEndcap-q,this.zEndcap+m-1,a,b,c)):(l.plotPixelUnclipped(this.argbEndcap,this.xEndcap+n,this.yEndcap+q,this.zEndcap-m-1,a,b,c),l.plotPixelUnclipped(this.argbEndcap,this.xEndcap-n,this.yEndcap-q,this.zEndcap+m-1,a,b,c)));this.ptA0.set(this.xA+n,this.yA+q,this.zA-m);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,H,this.ptA0,this.ptB0,d,this.clipped);e&&(this.ptA0.set(this.xA-n,this.yA-q,this.zA+m),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,h,this.ptA0,this.ptB0,d,this.clipped))}l.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,j){var l=this.g3d;if(0==c||1==c)this.line3d.plotLineBits(l.getColorArgbOrGray(a),l.getColorArgbOrGray(b),e,j,0,0,!1);else{this.ptA0i.setT(e);var k=u(c/2)+1,h=e.x,n=e.y,q=e.z,z=j.x,A=j.y,H=j.z,E=l.clipCode3(h-k,n-k,q-k),h=l.clipCode3(h+k,n+k,q+k),n=l.clipCode3(z-k,A-k,H-k),k=l.clipCode3(z+k,A+k,H+k),z=E|h|n|k;this.clipped=0!=z;if(!(-1==z||0!=(E&k&h&n))){this.dxBf=j.x-e.x;this.dyBf=j.y-e.y;this.dzBf=j.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=C(this.xAf);this.yA=C(this.yAf);this.zA=C(this.zAf);this.dxB=C(this.dxBf);this.dyB=C(this.dyBf);this.dzB=C(this.dzBf);this.shadesA=l.getShades(this.colixA=a);this.shadesB=l.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);l.setZMargin(5);c=l.pixel;a=l.width;
b=l.zbuf;j=z[0];E=z[1];k=z[2];z=z[3];for(A=this.rasterCount;0<=--A;){var H=z[A]>>8,h=H>>1,n=j[A],q=E[A],m=k[A];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(l.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+n,this.yEndcap+q,this.zEndcap-m-1,a,b,c),l.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-n,this.yEndcap-q,this.zEndcap+m-1,a,b,c)):(l.plotPixelUnclipped(this.argbEndcap,this.xEndcap+n,this.yEndcap+q,this.zEndcap-m-1,a,b,c),l.plotPixelUnclipped(this.argbEndcap,this.xEndcap-n,this.yEndcap-
q,this.zEndcap+m-1,a,b,c)));this.ptA0i.set(this.xA+n,this.yA+q,this.zA-m);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,H,this.ptA0i,this.ptB0i,d,this.clipped);e&&(this.ptA0i.set(this.xA-n,this.yA-q,this.zA+m),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,h,this.ptA0i,this.ptB0i,
d,this.clipped))}l.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$,"renderConeOld",function(a,b,d,f,c,e,j,l,k,h,n){this.dxBf=j-(this.xAf=f);this.dyBf=l-(this.yAf=c);this.dzBf=k-(this.zAf=e);this.xA=u(Math.floor(this.xAf));this.yA=u(Math.floor(this.yAf));this.zA=u(Math.floor(this.zAf));this.dxB=u(Math.floor(this.dxBf));this.dyB=u(Math.floor(this.dyBf));this.dzB=u(Math.floor(this.dzBf));this.xTip=j;
this.yTip=l;this.zTip=k;this.shadesA=this.g3d.getShades(this.colixA=a);var q=this.shader.getShadeIndex(this.dxB,this.dyB,-this.dzB);a=this.g3d;f=a.pixel;c=a.width;e=a.zbuf;a.plotPixelClippedArgb(this.shadesA[q],C(j),C(l),C(k),c,e,f);this.diameter=d;if(1>=d)1==d&&this.line3d.plotLineDeltaOld(this.colixA,this.colixA,this.xA,this.yA,this.zA,this.dxB,this.dyB,this.dzB,this.clipped);else{this.endcaps=b;this.calcArgbEndcap(!1,!0);this.generateBaseEllipsePrecisely(n);!n&&2==this.endcaps&&this.renderFlatEndcap(!1,
!0,this.xyzfRaster);a.setZMargin(5);b=this.xyztRaster[0];d=this.xyztRaster[1];j=this.xyztRaster[2];l=this.xyzfRaster[3];k=this.shadesA;for(var q=this.endCapHidden&&0!=this.argbEndcap,z=this.rasterCount;0<=--z;){var A=b[z],H=d[z],E=j[z],m=l[z]>>8,t=this.xAf+A,p=this.yAf+H,s=this.zAf-E,A=this.xAf-A,H=this.yAf-H,E=this.zAf+E,w=k[0];q&&(a.plotPixelClippedArgb(this.argbEndcap,C(t),C(p),C(s),c,e,f),a.plotPixelClippedArgb(this.argbEndcap,C(A),C(H),C(E),c,e,f));0!=w&&(this.line3d.plotLineDeltaAOld(k,k,0,
m,C(t),C(p),C(s),u(Math.ceil(this.xTip-t)),u(Math.ceil(this.yTip-p)),u(Math.ceil(this.zTip-s)),!0),h&&(this.line3d.plotLineDeltaAOld(k,k,0,m,C(t),C(p)+1,C(s),u(Math.ceil(this.xTip-t)),u(Math.ceil(this.yTip-p))+1,u(Math.ceil(this.zTip-s)),!0),this.line3d.plotLineDeltaAOld(k,k,0,m,C(t)+1,C(p),C(s),u(Math.ceil(this.xTip-t))+1,u(Math.ceil(this.yTip-p)),u(Math.ceil(this.zTip-s)),!0)),!n&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDeltaOld(w,w,C(A),C(H),C(E),u(Math.ceil(this.xTip-A)),u(Math.ceil(this.yTip-
H)),u(Math.ceil(this.zTip-E)),!0))}a.setZMargin(0)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B,~B");c(c$,"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]=u(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$,"calcRotatedPoint",function(a,b,d,f,c){c[3][b]=a;a*=3.141592653589793;var e=Math.sin(a)*this.cosTheta,
j=Math.cos(a);a=this.radius*(e*this.cosPhi-j*this.sinPhi);e=this.radius*(e*this.sinPhi+j*this.cosPhi);j=this.radius2-(a*a+e*e);j=0<j?Math.sqrt(j):0;d?(c[0][b]=a,c[1][b]=e,c[2][b]=j):(this.tEvenDiameter?(f[0][b]=u(a-0.5),f[1][b]=u(e-0.5)):(f[0][b]=u(a),f[1][b]=u(e)),f[2][b]=u(j+0.5));f[3][b]=this.shader.getShadeFp8(a,e,j)},"~N,~N,~B,~A,~A");c(c$,"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$,"interpolate",function(a,b,d,f){var c=d[0],e=d[1],c=c[b]-c[a];0>c&&(c=-c);e=e[b]-e[a];0>e&&(e=-e);if(!(1>=c+e)){for(var j=this.allocRaster(!1,d,f),c=d[0],e=d[1],l=d[3],k=f[3][a],h=f[3][b],n=4;0<=--n;){var q=(k+h)/2;this.calcRotatedPoint(q,j,!1,d,f);if(c[j]==c[a]&&e[j]==e[a])l[a]=l[a]+l[j]>>>1,k=q;else if(c[j]==c[b]&&e[j]==e[b])l[b]=l[b]+l[j]>>>
1,h=q;else{this.interpolate(a,j,d,f);this.interpolate(j,b,d,f);return}}c[j]=c[a];e[j]=e[b]}},"~N,~N,~A,~A");c(c$,"interpolatePrecisely",function(a,b,d,f){var c=f[0],e=f[1],j=u(Math.floor(c[b]))-u(Math.floor(c[a]));0>j&&(j=-j);e=u(Math.floor(e[b]))-u(Math.floor(e[a]));0>e&&(e=-e);if(!(1>=j+e)){for(var e=f[3],j=e[a],l=e[b],k=this.allocRaster(!0,d,f),c=f[0],e=f[1],h=d[3],n=4;0<=--n;){var q=(j+l)/2;this.calcRotatedPoint(q,k,!0,d,f);if(u(Math.floor(c[k]))==u(Math.floor(c[a]))&&u(Math.floor(e[k]))==u(Math.floor(e[a])))h[a]=
h[a]+h[k]>>>1,j=q;else if(u(Math.floor(c[k]))==u(Math.floor(c[b]))&&u(Math.floor(e[k]))==u(Math.floor(e[b])))h[b]=h[b]+h[k]>>>1,l=q;else{this.interpolatePrecisely(a,k,d,f);this.interpolatePrecisely(k,b,d,f);return}}c[k]=c[a];e[k]=e[b]}},"~N,~N,~A,~A");c(c$,"renderFlatEndcap",function(a,b,d){var f,c;if(b){if(0==this.dzBf||!this.g3d.setC(this.colixEndcap))return;b=this.xAf;f=this.yAf;c=this.zAf;a&&0>this.dzBf&&(b+=this.dxBf,f+=this.dyBf,c+=this.dzBf);b=C(b);f=C(f);c=C(c)}else{if(0==this.dzB||!this.g3d.setC(this.colixEndcap))return;
b=this.xA;f=this.yA;c=this.zA;a&&0>this.dzB&&(b+=this.dxB,f+=this.dyB,c+=this.dzB)}var e=d[1][0];a=d[1][0];var j=0,l=0,k=d[0],h=d[1];d=d[2];for(var n=this.rasterCount;0<--n;){var q=h[n];q<e?e=q:q>a?a=q:(q=-q,q<e?e=q:q>a&&(a=q))}for(q=e;q<=a;++q){for(var e=2147483647,z=-2147483648,n=this.rasterCount;0<=--n;){if(h[n]==q){var A=k[n];A<e&&(e=A,j=d[n]);A>z&&(z=A,l=d[n])}h[n]==-q&&(A=-k[n],A<e&&(e=A,j=-d[n]),A>z&&(z=A,l=-d[n]))}n=z-e+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(n,
b+e,f+q,c-j-1,c-l-1,null,null)}},"~B,~B,~A");c(c$,"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$,"calcArgbEndcap",function(a,b){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;this.endCapHidden=!1;var d=b?
this.dzBf:this.dzB;if(!(3==this.endcaps||0==d)){this.xEndcap=this.xA;this.yEndcap=this.yA;this.zEndcap=this.zA;var f=b?this.dxBf:this.dxB,c=b?this.dyBf:this.dyB;0<=d||!a?(this.endcapShadeIndex=this.shader.getShadeIndex(-f,-c,d),this.colixEndcap=this.colixA,d=this.shadesA):(this.endcapShadeIndex=this.shader.getShadeIndex(f,c,-d),this.colixEndcap=this.colixB,d=this.shadesB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB);56<this.endcapShadeIndex&&(this.endcapShadeIndex=56);this.argbEndcap=
d[this.endcapShadeIndex];this.endCapHidden=1==this.endcaps}},"~B,~B")});m("J.g3d");K(J.g3d,"G3DRenderer");m("J.g3d");x(["J.api.JmolRendererInterface","JU.GData","JU.P3i","$.V3"],"J.g3d.Graphics3D","java.lang.NullPointerException java.util.Arrays JU.AU J.api.Interface J.c.STER J.g3d.CylinderRenderer $.LineRenderer $.Pixelator $.PixelatorScreened $.PixelatorShaded $.PixelatorT $.Platform3D $.SphereRenderer $.TextRenderer $.TextString JU.C $.Font $.Normix".split(" "),function(){c$=w(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.$haveTranslucentObjects=this.twoPass=!1;this.zbufT=this.zbuf=this.pbufT=this.pbuf=null;this.translucencyMask=0;this.renderLow=!1;this.shadesCurrent=null;this.anaglyphLength=0;this.pixelShaded=this.pixelScreened=this.pixelT0=this.pixel0=this.pixel=null;this.zMargin=0;this.aobuf=null;
this.translucencyLog=this.lastRawColor=this.currentShadeIndex=0;this.wasScreened=!1;this.saveDiffuse=this.saveAmbient=0;this.shadeIndexes2Sided=this.shadeIndexes=this.vectorNormal=this.vectorAC=this.vectorAB=this.sC=this.sB=this.sA=null;this.pass2Flag01=0;s(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);O(c$,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)});h(c$,"isWebGL",function(){return!1});h(c$,"clear",function(){this.stringCount=0;this.strings=null;J.g3d.TextRenderer.clearFontCache()});h(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");p(c$,function(){I(this,J.g3d.Graphics3D,[]);for(var a=JU.GData.normixCount;0<=--a;)this.transformedVectors[a]=
new JU.V3});h(c$,"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,J.api.GenericPlatform");h(c$,"addRenderer",function(a){switch(a){case 1073741880:null==this.circle3d&&(this.circle3d=this.getRenderer("Circle"));
break;case 553648145:null==this.hermite3d&&(this.hermite3d=this.getRenderer("Hermite"));case 1073742182:null==this.triangle3d&&(this.triangle3d=this.getRenderer("Triangle"),this.triangle3d.isOrthographic=!this.vwr.tm.perspectiveDepth)}},"~N");c(c$,"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");h(c$,"setWindowParameters",function(a,b,d){this.setWinParams(a,b,d);this.currentlyRendering&&
this.endRendering()},"~N,~N,~B");h(c$,"checkTranslucent",function(a){a&&(this.$haveTranslucentObjects=!0);return!this.twoPass||this.twoPass&&this.isPass2==a},"~B");h(c$,"beginRendering",function(a,b,d,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.$haveTranslucentObjects=
this.wasScreened=!1;this.pixel=this.pixel0;this.pixel.bgcolor=this.bgcolor;this.translucentCoverOnly=!b;null==this.pbuf&&(this.platform.allocateBuffers(this.windowWidth,this.windowHeight,this.antialiasThisFrame,d),this.pbuf=this.platform.pBuffer,this.zbuf=this.platform.zBuffer,this.aobuf=null,this.pixel0.setBuf(),null!=this.pixelT0&&this.pixelT0.setBuf(),null!=this.pixelShaded&&this.pixelShaded.setBuf());this.setWidthHeight(this.antialiasThisFrame);null!=this.pixelScreened&&(this.pixelScreened.width=
this.width);this.platform.clearBuffer();null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,null,0,0,0);this.textY=0},"JU.M3,~B,~B,~B");h(c$,"setBackgroundTransparent",function(a){null!=this.platform&&this.platform.setBackgroundTransparent(a)},"~B");c(c$,"releaseBuffers",function(){this.aobuf=this.zbufT=this.pbufT=this.zbuf=this.pbuf=null;this.platform.releaseBuffers();this.line3d.clearLineCache()});h(c$,"setPass2",function(a){if(!this.$haveTranslucentObjects||
!this.currentlyRendering)return!1;this.isPass2=!0;this.pass2Flag01=1;this.colixCurrent=0;if(null==this.pbufT||this.antialias2!=a)this.platform.allocateTBuffers(a),this.pbufT=this.platform.pBufferT,this.zbufT=this.platform.zBufferT;this.antialias2=a;this.antialiasThisFrame&&!this.antialias2&&this.downsampleFullSceneAntialiasing(!0);this.platform.clearTBuffer();null==this.pixelT0&&(this.pixelT0=new J.g3d.PixelatorT(this));null==this.pixel.p0?this.pixel=this.pixelT0:this.pixel.p0=this.pixelT0;return!0},
"~B");h(c$,"endRendering",function(){if(this.currentlyRendering){if(null!=this.pbuf){if(this.isPass2&&null!=this.pbufT)for(var a=this.pbufT.length;0<=--a;)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");h(c$,"getScreenImage",function(a){var b=this.platform.bufferedImage;a&&this.releaseBuffers();return b},"~B");h(c$,"applyAnaglygh",function(a,b){switch(a){case J.c.STER.REDCYAN: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");h(c$,"snapshotAnaglyphChannelBytes",function(){if(this.currentlyRendering)throw new NullPointerException;
this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=P(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});h(c$,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});h(c$,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});h(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 j=(f>>2&1061109567)<<2,j=j+((j&3233857728)>>6),l=0,k=0,e=d;0<=--e;k+=c)for(d=b;0<=--d;++l){var h=(a[k]>>2&1061109567)+(a[k++ +c]>>2&1061109567)+(a[k]>>2&1061109567)+(a[k++ +c]>>2&1061109567),h=h+((h&3233857728)>>6);h==j&&(h=f);a[l]=h&16777215|4278190080}},"~A,~N,~N,~N");c$.downsample2dZ=c(c$,"downsample2dZ",function(a,b,d,f,c){for(var e=d<<1,j=0,l=0;0<=--f;l+=e)for(var k=d;0<=
--k;++j,++l){var h=Math.min(b[l],b[l+e]),h=Math.min(h,b[++l]),h=Math.min(h,b[l+e]);2147483647!=h&&(h>>=1);b[j]=a[j]==c?2147483647:h}},"~A,~A,~N,~N,~N");c(c$,"hasContent",function(){return this.platform.hasContent()});h(c$,"setC",function(a){var b=JU.C.isColixLastAvailable(a);if(!b&&a==this.colixCurrent&&-1==this.currentShadeIndex)return!0;var d=a&30720;if(16384==d)return!1;this.renderLow&&(d=0);var 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$,"setScreened",function(a){this.wasScreened!=a&&((this.wasScreened=a)?(null==this.pixelScreened&&(this.pixelScreened=
new J.g3d.PixelatorScreened(this,this.pixel0)),null==this.pixel.p0?this.pixel=this.pixelScreened:this.pixel.p0=this.pixelScreened):null==this.pixel.p0||this.pixel===this.pixelScreened?this.pixel=this.isPass2?this.pixelT0:this.pixel0:this.pixel.p0=this.isPass2?this.pixelT0:this.pixel0);return this.pixel},"~B");h(c$,"drawFilledCircle",function(a,b,d,f,c,e){if(!this.isClippedZ(e)){var j=u((d+1)/2),j=f<j||f+j>=this.width||c<j||c+j>=this.height;if(!j||!this.isClippedXY(d,f,c))0!=a&&this.setC(a)&&(j?this.isClippedXY(d,
f,c)||this.circle3d.plotCircleCenteredClipped(f,c,e,d):this.circle3d.plotCircleCenteredUnclipped(f,c,e,d)),0!=b&&this.setC(b)&&(j?this.circle3d.plotFilledCircleCenteredClipped(f,c,e,d):this.circle3d.plotFilledCircleCenteredUnclipped(f,c,e,d))}},"~N,~N,~N,~N,~N,~N");h(c$,"volumeRender4",function(a,b,d,f){if(1==a)this.plotPixelClippedArgb(this.argbCurrent,b,d,f,this.width,this.zbuf,this.pixel);else if(!this.isClippedZ(f)){var c=u((a+1)/2),c=b<c||b+c>=this.width||d<c||d+c>=this.height;if(!c||!this.isClippedXY(a,
b,d))c?this.circle3d.plotFilledCircleCenteredClipped(b,d,f,a):this.circle3d.plotFilledCircleCenteredUnclipped(b,d,f,a)}},"~N,~N,~N,~N");h(c$,"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");h(c$,"volumeRender",function(a){a?(this.saveAmbient=this.getAmbientPercent(),this.saveDiffuse=
this.getDiffusePercent(),this.setAmbientPercent(100),this.setDiffusePercent(0),this.addRenderer(1073741880)):(this.setAmbientPercent(this.saveAmbient),this.setDiffusePercent(this.saveDiffuse))},"~B");h(c$,"fillSphereI",function(a,b){this.fillSphereXYZ(a,b.x,b.y,b.z)},"~N,JU.P3i");h(c$,"fillSphereBits",function(a,b){this.fillSphereXYZ(a,Math.round(b.x),Math.round(b.y),Math.round(b.z))},"~N,JU.P3");h(c$,"fillEllipsoid",function(a,b,d,f,c,e,j,l,k,h,n){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,j,l,k,h,n)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");h(c$,"drawRect",function(a,b,d,f,c,e){if(!(0!=f&&this.isClippedZ(f))){f=c-1;e-=1;c=a+f;var j=b+e;0<=b&&b<this.height&&this.drawHLine(a,b,d,f);0<=j&&j<this.height&&this.drawHLine(a,j,d,f);0<=a&&a<this.width&&this.drawVLine(a,b,d,e);0<=c&&c<this.width&&this.drawVLine(c,b,d,e)}},"~N,~N,~N,~N,~N,~N");
c(c$,"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$,"drawVLine",function(a,b,d,f){0>f&&(b+=f,f=-f);0>b&&(f+=b,b=0);b+f>=this.height&&(f=this.height-1-b);a+=this.width*b;b=this.pixel;for(var c=this.argbCurrent,e=0;e<=f;e++)d<this.zbuf[a]&&b.addPixel(a,d,c),a+=this.width},"~N,~N,~N,~N");h(c$,"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 j=this.argbCurrent,l=this.zbuf,k=this.pixel;0<=--e;)this.plotPixelsUnclippedCount(j,c,a,b++,d,f,l,k)}},"~N,~N,~N,~N,~N,~N");h(c$,"drawString",function(a,b,d,f,c,e,j){this.currentShadeIndex=0;null!=a&&(this.isClippedZ(e)||this.drawStringNoSlab(a,b,d,f,c,j))},"~S,JU.Font,~N,~N,~N,~N,~N");h(c$,"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 j=new J.g3d.TextString;j.setText(a,null==b?this.currentFont:this.currentFont=b,this.argbCurrent,JU.C.isColixTranslucent(e)?this.getColorArgbOrGray(e)&16777215|(e&30720)<<13:0,d,f,c);this.strings[this.stringCount++]=j}},"~S,JU.Font,~N,~N,~N,~N");h(c$,"renderAllStrings",function(a){if(null!=this.strings){2<=this.stringCount&&(null==J.g3d.Graphics3D.sort&&
(J.g3d.Graphics3D.sort=new J.g3d.TextString),java.util.Arrays.sort(this.strings,J.g3d.Graphics3D.sort));for(var b=0;b<this.stringCount;b++){var d=this.strings[b];this.plotText(d.x,d.y,d.z,d.argb,d.bgargb,d.text,d.font,a)}this.strings=null;this.stringCount=0}},"~O");h(c$,"plotText",function(a,b,d,f,c,e,j,l){J.g3d.TextRenderer.plot(a,b,d,f,c,e,j,this,l,this.antialiasThisFrame)},"~N,~N,~N,~N,~N,~S,JU.Font,J.api.JmolRendererInterface");h(c$,"drawImage",function(a,b,d,f,c,e,j,l){null!=a&&(0<j&&0<l&&!this.isClippedZ(c))&&
this.plotImage(b,d,f,a,null,e,j,l)},"~O,~N,~N,~N,~N,~N,~N,~N");h(c$,"plotImage",function(a,b,d,f,c,e,j,l){this.setC(e);this.isPass2||(this.translucencyMask=-1);0==e&&(this.argbCurrent=0);var k=-2147483648==a;e=k?this.bgcolor:this.argbCurrent;k&&(a=0,d=2147483646,j=this.width,l=this.height);if(!(0>=a+j||a>=this.width||0>=b+l||b>=this.height))if(f=this.apiPlatform.drawImageToBuffer(null,this.platform.offscreenImage,f,j,l,k?e:0),null!=f){var k=this.zbuf,h=this.width,n=this.pixel,q=this.height,z=this.translucencyLog;
if(null==c&&0<=a&&a+j<=h&&0<=b&&b+l<=q){var A=0,H=0;for(a=b*h+a;A<l;A++,a+=h-j)for(var E=0;E<j;E++,H++,a++)if(d<k[a]){var m=f[H];-16777216==(m&4278190080)&&n.addPixel(a,d,m)}}else{null==c&&(c=this);for(H=A=0;A<l;A++)for(E=0;E<j;E++)m=f[H++],-16777216==(m&4278190080)&&c.plotImagePixel(m,a+E,b+A,d,8,e,h,q,k,n,z)}}},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");h(c$,"setFontFid",function(a){this.currentFont=JU.Font.getFont3D(a)},"~N");h(c$,"setFont",function(a){this.currentFont=a},"JU.Font");h(c$,
"drawPixel",function(a,b,d){this.plotPixelClippedArgb(this.argbCurrent,a,b,d,this.width,this.zbuf,this.pixel)},"~N,~N,~N");h(c$,"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");h(c$,"drawDashedLineBits",function(a,b,d,f){this.isAntialiased()&&(a+=a,b+=b);this.setScreeni(d,this.sA);this.setScreeni(f,this.sB);this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,
this.sA,this.sB,a,b,!0);this.isAntialiased()&&(Math.abs(d.x-f.x)<Math.abs(d.y-f.y)?(this.sA.x+=1,this.sB.x+=1):(this.sA.y+=1,this.sB.y+=1),this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,a,b,!0))},"~N,~N,JU.P3,JU.P3");c(c$,"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");h(c$,"drawLineXYZ",function(a,b,d,f,c,e){this.line3d.plotLineOld(this.argbCurrent,this.argbCurrent,a,b,d,f,c,e)},"~N,~N,~N,~N,~N,~N");h(c$,"drawLine",
function(a,b,d,f,c,e,j,l){this.setC(a)||(a=0);var k=this.argbCurrent;this.setC(b)||(b=0);(0!=a||0!=b)&&this.line3d.plotLineOld(k,this.argbCurrent,d,f,c,e,j,l)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"drawLineBits",function(a,b,d,f){this.setC(a)||(a=0);var c=this.argbCurrent;this.setC(b)||(b=0);if(0!=a||0!=b)this.setScreeni(d,this.sA),this.setScreeni(f,this.sB),this.line3d.plotLineBits(c,this.argbCurrent,this.sA,this.sB,0,0,!1)},"~N,~N,JU.P3,JU.P3");h(c$,"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");h(c$,"fillCylinderXYZ",function(a,b,d,f,c,e,j,l,k,h){if(!(f>this.ht3)){var n=0;this.currentShadeIndex=0;this.setC(b)||(b=0);this.wasScreened&&(n=2);this.setC(a)||(a=0);this.wasScreened&&(n+=1);0==a&&0==b||this.cylinder3d.renderOld(a,b,n,d,f,c,e,j,l,k,h)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen3I",function(a,b,d,f){b<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,
this.colixCurrent,0,a,b,C(d.x),C(d.y),C(d.z),C(f.x),C(f.y),C(f.z))},"~N,~N,JU.P3,JU.P3,JU.P3,JU.P3,~N");h(c$,"fillCylinder",function(a,b,d,f){b<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,this.colixCurrent,0,a,b,d.x,d.y,d.z,f.x,f.y,f.z)},"~N,~N,JU.P3i,JU.P3i");h(c$,"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");h(c$,"fillCylinderBits2",function(a,b,d,f,c,e){if(!(f>this.ht3)){var j=0;this.currentShadeIndex=0;this.setC(b)||(b=0);this.wasScreened&&(j=2);this.setC(a)||(a=0);this.wasScreened&&(j+=1);0==a&&0==b||(this.setScreeni(c,this.sA),this.setScreeni(e,this.sB),this.cylinder3d.renderBits(a,b,j,d,f,this.sA,this.sB))}},"~N,~N,~N,~N,JU.P3,JU.P3");h(c$,"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");h(c$,"drawHermite4",function(a,b,d,f,c){this.hermite3d.renderHermiteRope(!1,a,0,0,0,b,d,f,c)},"~N,JU.P3,JU.P3,JU.P3,JU.P3");h(c$,"drawHermite7",function(a,b,d,f,c,e,j,l,k,h,n,q,z){if(0==z)this.hermite3d.renderHermiteRibbon(a,b,d,f,c,e,j,l,k,h,n,q,0);else{this.hermite3d.renderHermiteRibbon(a,b,d,f,c,e,j,l,k,h,n,q,1);var A=this.colixCurrent;this.setC(z);this.hermite3d.renderHermiteRibbon(a,
b,d,f,c,e,j,l,k,h,n,q,-1);this.setC(A)}},"~B,~B,~N,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,~N,~N");h(c$,"fillHermite",function(a,b,d,f,c,e,j,l){this.hermite3d.renderHermiteRope(!0,a,b,d,f,c,e,j,l)},"~N,~N,~N,~N,JU.P3,JU.P3,JU.P3,JU.P3");h(c$,"drawTriangle3C",function(a,b,d,f,c,e,j){1==(j&1)&&this.drawLine(b,f,a.x,a.y,a.z,d.x,d.y,d.z);2==(j&2)&&this.drawLine(f,e,d.x,d.y,d.z,c.x,c.y,c.z);4==(j&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");h(c$,"fillTriangleTwoSided",
function(a,b,d,f){this.setColorNoisy(this.getShadeIndex(a));this.fillTriangleP3f(b,d,f,!1)},"~N,JU.P3,JU.P3,JU.P3");c(c$,"fillTriangleP3f",function(a,b,d,f){this.setScreeni(a,this.sA);this.setScreeni(b,this.sB);this.setScreeni(d,this.sC);this.triangle3d.fillTriangle(this.sA,this.sB,this.sC,f)},"JU.P3,JU.P3,JU.P3,~B");h(c$,"fillTriangle3f",function(a,b,d,f){var c=this.getShadeIndexP3(a,b,d,f);0>c||(f?this.setColorNoisy(c):this.setColor(this.shadesCurrent[c]),this.fillTriangleP3f(a,b,d,!1))},"JU.P3,JU.P3,JU.P3,~B");
h(c$,"fillTriangle3i",function(a,b,d,f,c,e,j){j&&(f=this.vectorAB,f.set(b.x-a.x,b.y-a.y,b.z-a.z),null==d?f=this.shader.getShadeIndex(-f.x,-f.y,f.z):(this.vectorAC.set(d.x-a.x,d.y-a.y,d.z-a.z),f.cross(f,this.vectorAC),f=0<=f.z?this.shader.getShadeIndex(-f.x,-f.y,f.z):this.shader.getShadeIndex(f.x,f.y,-f.z)),56<f&&(f=56),this.setColorNoisy(f));this.fillTriangleP3f(a,b,d,!1)},"JU.P3,JU.P3,JU.P3,JU.T3,JU.T3,JU.T3,~B");h(c$,"fillTriangle3CN",function(a,b,d,f,c,e,j,l,k){this.triangle3d.fillTriangle(a,f,
j,this.checkGouraud(b,c,l,d,e,k))},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");h(c$,"fillTriangle3CNBits",function(a,b,d,f,c,e,j,l,k){this.fillTriangleP3f(a,f,j,this.checkGouraud(b,c,l,d,e,k))},"JU.P3,~N,~N,JU.P3,~N,~N,JU.P3,~N,~N,~B");c(c$,"checkGouraud",function(a,b,d,f,c,e){if(!this.isPass2&&f==c&&f==e&&a==b&&a==d){b=this.getShadeIndex(f);if(a!=this.colixCurrent||this.currentShadeIndex!=b)this.currentShadeIndex=-1,this.setC(a),this.setColorNoisy(b);return!1}this.setTriangleTranslucency(a,b,d);this.triangle3d.setGouraud(this.getShades(a)[this.getShadeIndex(f)],
this.getShades(b)[this.getShadeIndex(c)],this.getShades(d)[this.getShadeIndex(e)]);return!0},"~N,~N,~N,~N,~N,~N");c(c$,"getShadeIndex",function(a){return-1E4==a||9999==a?J.g3d.Graphics3D.nullShadeIndex:0>a?this.shadeIndexes2Sided[~a]:this.shadeIndexes[a]},"~N");c(c$,"setTriangleTranslucency",function(a,b,d){this.isPass2&&(a&=14336,b&=14336,d&=14336,this.translucencyMask=(JU.GData.roundInt(u((a+b+d)/3))&30720)<<13|16777215)},"~N,~N,~N");h(c$,"fillQuadrilateral",function(a,b,d,f,c){c=this.getShadeIndexP3(a,
b,d,c);0>c||(this.setColorNoisy(c),this.fillTriangleP3f(a,b,d,!1),this.fillTriangleP3f(a,d,f,!1))},"JU.P3,JU.P3,JU.P3,JU.P3,~B");h(c$,"drawSurface",function(){},"JU.MeshSurface,~N");h(c$,"plotPixelClippedP3i",function(a){this.plotPixelClippedArgb(this.argbCurrent,a.x,a.y,a.z,this.width,this.zbuf,this.pixel)},"JU.P3i");c(c$,"plotPixelClippedArgb",function(a,b,d,f,c,e,j){this.isClipped3(b,d,f)||(b=d*c+b,f<e[b]&&j.addPixel(b,f,a))},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotPixelUnclipped",function(a,
b,d,f,c,e,j){b=d*c+b;f<e[b]&&j.addPixel(b,f,a)},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotImagePixel",function(a,b,d,f,c,e,j,l,k,h,n){0>b||(b>=j||0>d||d>=l)||h.addImagePixel(c,n,d*j+b,f,a,e)},"~N,~N,~N,~N,~N,~N,~N,~N,~A,~O,~N");c(c$,"plotPixelsClippedRaster",function(a,b,d,f,c,e,j){var l,k;if(!(0>=a||0>d||d>=this.height||b>=this.width||f<(k=this.slab)&&c<k||f>(l=this.depth)&&c>l)){var h=this.zbuf,n=(b<<16)+(d<<1)^858993459,q=(f<<10)+512;f=c-f;c=u(a/2);f=JU.GData.roundInt(u(((f<<10)+(0<=f?c:-c))/
a));if(0>b){b=-b;q+=f*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;c=this.argbNoisyUp;for(var z=this.argbCurrent;0<=--a;){j=q>>10;if(j>=k&&j<=l&&j<h[b]){var n=(n<<16)+(n<<1)+n&2147483647,A=n>>16&7;d.addPixel(b,j,0==A?e:1==A?c:z)}++b;q+=f}}else{n=e.r<<8;c=u((j.r-e.r<<8)/a);z=e.g;A=u((j.g-z)/a);e=e.b;for(var H=u((j.b-e)/a);0<=--a;)j=q>>10,j>=k&&(j<=l&&j<h[b])&&d.addPixel(b,j,4278190080|n&16711680|z&65280|e>>8&255),++b,q+=f,n+=
c,z+=A,e+=H}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsUnclippedRaster",function(a,b,d,f,c,e,j){if(!(0>=a)){var l=((b<<16)+(d<<1)^858993459)&2147483647,k=(f<<10)+512;f=c-f;c=u(a/2);f=JU.GData.roundInt(u(((f<<10)+(0<=f?c:-c))/a));b=d*this.width+b;d=this.zbuf;c=this.pixel;if(null==e){e=this.argbNoisyDn;for(var h=this.argbNoisyUp,n=this.argbCurrent;0<=--a;){j=k>>10;if(j<d[b]){var l=(l<<16)+(l<<1)+l&2147483647,q=l>>16&7;c.addPixel(b,j,0==q?e:1==q?h:n)}++b;k+=f}}else{l=e.r<<8;h=JU.GData.roundInt(u((j.r-
e.r<<8)/a));n=e.g;q=JU.GData.roundInt(u((j.g-n)/a));e=e.b;for(var z=JU.GData.roundInt(u((j.b-e)/a));0<=--a;)j=k>>10,j<d[b]&&c.addPixel(b,j,4278190080|l&16711680|n&65280|e>>8&255),++b,k+=f,l+=h,n+=q,e+=z}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsClippedRasterBits",function(a,b,d,f,c,e,j,l,k){var h,n;if(!(0>=a||0>d||d>=this.height||b>=this.width||f<(n=this.slab)&&c<n||f>(h=this.depth)&&c>h)){f=this.zbuf;var q=(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;c=this.pixel;if(null==e){e=this.argbNoisyDn;for(var z=this.argbNoisyUp,A=this.argbCurrent;0<=--a;){j=this.line3d.getZCurrent(l,k,b++);if(j>=n&&j<=h&&j<f[d]){var q=(q<<16)+(q<<1)+q&2147483647,H=q>>16&7;c.addPixel(d,j,2>H?e:6>H?z:A)}++d}}else{q=e.r<<8;z=u((j.r-e.r<<8)/a);A=e.g;H=u((j.g-A)/a);e=e.b;for(var E=u((j.b-e)/a);0<=--a;)j=this.line3d.getZCurrent(l,k,b++),j>=n&&(j<=h&&j<f[d])&&c.addPixel(d,j,4278190080|q&16711680|A&65280|e>>8&255),++d,q+=z,A+=H,e+=E}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");
c(c$,"plotPixelsUnclippedRasterBits",function(a,b,d,f,c,e,j){if(!(0>=a)){var l=((b<<16)+(d<<1)^858993459)&2147483647;d=d*this.width+b;var k=this.zbuf,h=this.pixel;if(null==f)for(var n=this.argbNoisyDn,q=this.argbNoisyUp,z=this.argbCurrent;0<=--a;)c=this.line3d.getZCurrent(e,j,b++),c<k[d]&&(l=(l<<16)+(l<<1)+l&2147483647,f=l>>16&7,h.addPixel(d,c,0==f?n:1==f?q:z)),++d;else{l=f.r<<8;n=JU.GData.roundInt(u((c.r-f.r<<8)/a));q=f.g;z=JU.GData.roundInt(u((c.g-q)/a));f=f.b;for(var A=JU.GData.roundInt(u((c.b-
f)/a));0<=--a;)c=this.line3d.getZCurrent(e,j,b++),c<k[d]&&h.addPixel(d,c,4278190080|l&16711680|q&65280|f>>8&255),++d,l+=n,q+=z,f+=A}}},"~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(c$,"plotPixelsUnclippedCount",function(a,b,d,f,c,e,j,l){for(d=f*e+d;0<=--b;)c<j[d]&&l.addPixel(d,c,a),++d},"~N,~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotPoints",function(a,b,d,f){var c=this.pixel,e=this.argbCurrent,j=this.zbuf,l=this.width,k=this.antialiasThisFrame;for(a*=3;0<a;){var h=b[--a],n=b[--a]+f,q=b[--a]+d;if(!this.isClipped3(q,
n,h)){var z=n*l+q++;h<j[z]&&c.addPixel(z,h,e);k&&(z=n*l+q,!this.isClipped3(q,n,h)&&h<j[z]&&c.addPixel(z,h,e),z=++n*l+q,!this.isClipped3(q,n,h)&&h<j[z]&&c.addPixel(z,h,e),z=n*l+--q,!this.isClipped3(q,n,h)&&h<j[z]&&c.addPixel(z,h,e))}}},"~N,~A,~N,~N");c(c$,"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$,"getShadeIndexP3",function(a,b,d,f){this.vectorAB.sub2(b,
a);this.vectorAC.sub2(d,a);a=this.vectorNormal;a.cross(this.vectorAB,this.vectorAC);return 0>a.z?this.shader.getShadeIndex(a.x,a.y,-a.z):f?-1:this.shader.getShadeIndex(-a.x,-a.y,a.z)},"JU.P3,JU.P3,JU.P3,~B");h(c$,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");h(c$,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,a.sY,a.sZ)},"JM.Atom,~N");h(c$,"getExportType",function(){return 0});
h(c$,"getExportName",function(){return null});c(c$,"canDoTriangles",function(){return!0});c(c$,"isCartesianExport",function(){return!1});h(c$,"initializeExporter",function(){return null},"JV.Viewer,~N,JU.GData,java.util.Map");h(c$,"finalizeOutput",function(){return null});h(c$,"drawBond",function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");h(c$,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(c$,"getPrivateKey",function(){return 0});h(c$,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});
c(c$,"setRotationMatrix",function(a){for(var b=JU.Normix.getVertexVectors(),d=JU.GData.normixCount;0<=--d;){var f=this.transformedVectors[d];a.rotate2(b[d],f);this.shadeIndexes[d]=this.shader.getShadeB(f.x,-f.y,f.z);this.shadeIndexes2Sided[d]=0<=f.z?this.shadeIndexes[d]:this.shader.getShadeB(-f.x,f.y,-f.z)}},"JU.M3");h(c$,"renderCrossHairs",function(a,b,d,f,c){b=this.isAntialiased();this.setC(0>c?10:100<c?11:23);c=Math.max(Math.min(this.width,Math.round(f.x)),0);d=Math.max(Math.min(this.height,Math.round(f.y)),
0);var e=Math.round(f.z)+1,j=b?8:4,l=b?20:10;b=b?2:1;this.drawRect(c-j,d,e,0,l,b);this.drawRect(c,d-j,e,0,b,l);this.drawRect(c-j,d-j,e,0,l,l);j=l;l>>=1;this.setC(a[1]<f.x?21:11);this.drawRect(c-j,d,e,0,l,b);this.setC(a[0]>f.x?21:11);this.drawRect(c+l,d,e,0,l,b);this.setC(a[3]<f.y?21:11);this.drawRect(c,d-j,e,0,b,l);this.setC(a[2]>f.y?21:11);this.drawRect(c,d+l,e,0,b,l)},"~A,~N,~N,JU.P3,~N");h(c$,"initializeOutput",function(){return!1},"JV.Viewer,~N,java.util.Map");G(c$,"sort",null,"nullShadeIndex",
50)});m("J.g3d");x(["J.g3d.PrecisionRenderer","java.util.Hashtable"],"J.g3d.LineRenderer",["java.lang.Float","JU.BS"],function(){c$=w(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;s(this,arguments)},J.g3d,"LineRenderer",J.g3d.PrecisionRenderer);O(c$,function(){this.lineCache=new java.util.Hashtable});p(c$,function(a){I(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,f=a+a,c=b+b,e=0;e<this.nBits;e++)d+=c,d>a&&(this.lineBits.set(e),
d-=f);this.lineCache.put(this.slopeKey,this.lineBits)}},"~N,~N");c(c$,"clearLineCache",function(){this.lineCache.clear()});c(c$,"plotLineOld",function(a,b,d,f,c,e,j,l){this.x1t=d;this.x2t=e;this.y1t=f;this.y2t=j;this.z1t=c;this.z2t=l;var k=!0;switch(this.getTrimmedLineImpl()){case 0:k=!1;break;case 2:return}this.plotLineClippedOld(a,b,d,f,c,e-d,j-f,l-c,k,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"plotLineDeltaOld",function(a,b,d,f,c,e,j,l,k){this.x1t=d;this.x2t=d+e;this.y1t=f;this.y2t=f+j;this.z1t=c;
this.z2t=c+l;if(k)switch(this.getTrimmedLineImpl()){case 2:return;case 0:k=!1}this.plotLineClippedOld(a,b,d,f,c,e,j,l,k,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaAOld",function(a,b,d,f,c,e,j,l,k,h,n){this.x1t=c;this.x2t=c+l;this.y1t=e;this.y2t=e+k;this.z1t=j;this.z2t=j+h;if(n)switch(this.getTrimmedLineImpl()){case 2:return;case 0:n=!1}var q=this.g3d.zbuf,z=this.g3d.width,A=0,H=e*z+c,E=this.g3d.bufferSize,m=63>f?f+1:f,t=0<f?f-1:f,p=a[m],s=a[t],w=b[f],m=b[m];b=b[t];a=a[f];f=this.g3d.pixel;
0!=d&&(f=this.g3d.setScreened(1==(d&1)),this.g3d.currentShadeIndex=0);0!=a&&(!n&&0<=H&&H<E&&j<q[H])&&f.addPixel(H,j,a);if(!(0==l&&0==k)){n=1;t=z;c+=l;var v=e+k;0>l&&(l=-l,n=-1);0>k&&(k=-k,t=-z);z=l+l;e=k+k;j<<=10;if(k<=l){var x=l-1;0>h&&(x=-x);h=u(((h<<10)+x)/l);k=0;x=Math.abs(c-this.x2t)-1;c=Math.abs(c-this.x1t)-1;for(var v=l-1,y=u(v/2);--v>=x;){if(v==y){a=w;if(0==a)break;p=m;s=b;0!=d%3&&(f=this.g3d.setScreened(2==(d&2)),this.g3d.currentShadeIndex=0)}H+=n;j+=h;k+=e;k>l&&(H+=t,k-=z);if(0!=a&&v<c&&
0<=H&&H<E&&2147483647>A){var B=j>>10;if(B<q[H]){var C=this.shader.nextRandom8Bit();f.addPixel(H,B,85>C?s:170<C?p:a)}}A=(A+1)%1}}else{x=k-1;0>h&&(x=-x);h=u(((h<<10)+x)/k);l=0;x=Math.abs(v-this.y2t)-1;c=Math.abs(v-this.y1t)-1;v=k-1;for(y=u(v/2);--v>=x;){if(v==y){a=w;if(0==a)break;p=m;s=b;0!=d%3&&(f=this.g3d.setScreened(2==(d&2)),this.g3d.currentShadeIndex=0)}H+=t;j+=h;l+=z;l>k&&(H+=n,l-=e);0!=a&&(v<c&&0<=H&&H<E&&2147483647>A)&&(B=j>>10,B<q[H]&&(C=this.g3d.shader.nextRandom8Bit(),f.addPixel(H,B,85>C?
s:170<C?p:a)));A=(A+1)%1}}}},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaABitsFloat",function(a,b,d,f,c,e,j){var l=Math.round(f.x),k=Math.round(f.y),h=Math.round(f.z),n=Math.round(c.x),q=Math.round(c.y),z=Math.round(c.z),A=n-l,H=q-k;this.x1t=l;this.x2t=n;this.y1t=k;this.y2t=q;this.z1t=h;this.z2t=z;if(!(j&&2==this.getTrimmedLineImpl())){j=this.g3d.zbuf;var E=this.g3d.width,n=0,z=63>d?d+1:d,q=0<d?d-1:d,m=a[d],t=a[z],p=a[q];d=b[d];a=b[z];b=b[q];var q=k*E+l,z=this.g3d.bufferSize,s,w,v,x;this.lineTypeX?
(s=l,w=this.x1t,v=this.x2t,l+=u(A/2),x=k=0<=A?1:-1,A=0<=H?E:-E,this.setRastABFloat(f.x,f.z,c.x,c.z)):(s=k,w=this.y1t,v=this.y2t,l=k+u(H/2),k=0<=H?1:-1,x=0<=H?E:-E,A=0<=A?1:-1,this.setRastABFloat(f.y,f.z,c.y,c.z));f=h;c=m;h=t;H=p;t=!1;p=this.g3d.pixel;0!=e&&(p=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(m=s;;m+=k,s+=k){m==w&&(t=!0);if(m==l){c=d;if(0==c)break;h=a;H=b;0!=e%3&&(p=this.g3d.setScreened(2==(e&2)),this.g3d.currentShadeIndex=0)}0!=c&&(t&&0<=q&&q<z&&2147483647>n)&&(f=this.getZCurrent(this.a,
this.b,m),f<j[q]&&(E=this.shader.nextRandom8Bit(),p.addPixel(q,C(f),85>E?H:170<E?h:c)));if(m==v)break;n=(n+1)%1;for(q+=x;0>s;)s+=this.nBits;this.lineBits.get(s%this.nBits)&&(q+=A)}}},"~A,~A,~N,JU.P3,JU.P3,~N,~B");c(c$,"plotLineDeltaABitsInt",function(a,b,d,f,c,e,j){var l=f.x,k=f.y,h=f.z,n=c.x,q=c.y,z=c.z,A=n-l,H=q-k;this.x1t=l;this.x2t=n;this.y1t=k;this.y2t=q;this.z1t=h;this.z2t=z;if(!(j&&2==this.getTrimmedLineImpl())){j=this.g3d.zbuf;var E=this.g3d.width,n=0,z=63>d?d+1:d,q=0<d?d-1:d,m=a[d],t=a[z],
s=a[q];d=b[d];a=b[z];b=b[q];var q=k*E+l,z=this.g3d.bufferSize,p,w,v,x;this.lineTypeX?(p=l,w=this.x1t,v=this.x2t,l+=u(A/2),x=k=0<=A?1:-1,A=0<=H?E:-E,this.setRastAB(f.x,f.z,c.x,c.z)):(p=k,w=this.y1t,v=this.y2t,l=k+u(H/2),k=0<=H?1:-1,x=0<=H?E:-E,A=0<=A?1:-1,this.setRastAB(f.y,f.z,c.y,c.z));f=h;c=m;h=t;H=s;t=!1;s=this.g3d.pixel;0!=e&&(s=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(m=p;;m+=k,p+=k){m==w&&(t=!0);if(m==l){c=d;if(0==c)break;h=a;H=b;0!=e%3&&(s=this.g3d.setScreened(2==(e&
2)),this.g3d.currentShadeIndex=0)}0!=c&&(t&&0<=q&&q<z&&2147483647>n)&&(f=this.getZCurrent(this.a,this.b,m),f<j[q]&&(E=this.shader.nextRandom8Bit(),s.addPixel(q,C(f),85>E?H:170<E?h:c)));if(m==v)break;n=(n+1)%1;for(q+=x;0>p;)p+=this.nBits;this.lineBits.get(p%this.nBits)&&(q+=A)}}},"~A,~A,~N,JU.P3i,JU.P3i,~N,~B");c(c$,"plotLineBits",function(a,b,d,f,c,e,j){if(!(1>=d.z||1>=f.z)){var l=!0;this.x1t=d.x;this.y1t=d.y;this.z1t=d.z;this.x2t=f.x;this.y2t=f.y;this.z2t=f.z;switch(this.getTrimmedLineImpl()){case 2:return;
case 0:l=!1;break;default:j&&(d.set(this.x1t,this.y1t,this.z1t),f.set(this.x2t,this.y2t,this.z2t))}j=this.g3d.zbuf;var k=this.g3d.width,h=0;0==c&&(e=2147483647,c=1);var n=d.x,q=d.y,z=d.z,A=f.x-n,H=n+A,E=f.y-q,m=q+E,p=q*k+n,t=this.g3d.bufferSize,s=this.g3d.pixel;0!=a&&(!l&&0<=p&&p<t&&z<j[p])&&s.addPixel(p,z,a);if(!(0==A&&0==E)){var w=l=1,z=k;0>A&&(A=-A,l=-1);0>E&&(E=-E,z=-k,w=-1);var k=A+A,v=E+E;if(E<=A){this.setRastAB(d.x,d.z,f.x,f.z);q=0;d=Math.abs(H-this.x2t)-1;H=Math.abs(H-this.x1t)-1;m=A-1;for(f=
u(m/2);--m>=d&&!(m==f&&(a=b,0==a));){p+=l;n+=l;q+=v;q>A&&(p+=z,q-=k);if(0!=a&&m<H&&0<=p&&p<t&&h<e){var x=this.getZCurrent(this.a,this.b,n);x<j[p]&&s.addPixel(p,x,a)}h=(h+1)%c}}else{this.setRastAB(d.y,d.z,f.y,f.z);n=0;d=Math.abs(m-this.y2t)-1;H=Math.abs(m-this.y1t)-1;m=E-1;for(f=u(m/2);--m>=d&&!(m==f&&(a=b,0==a));)p+=z,q+=w,n+=k,n>E&&(p+=l,n-=v),0!=a&&(m<H&&0<=p&&p<t&&h<e)&&(x=this.getZCurrent(this.a,this.b,q),x<j[p]&&s.addPixel(p,x,a)),h=(h+1)%c}}}},"~N,~N,JU.P3i,JU.P3i,~N,~N,~B");c(c$,"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,f=this.g3d.yLast,c=this.g3d.slab,e=this.g3d.depth;do{if(0!=(a&b))return 2;var j=this.x2t-this.x1t,l=this.y2t-this.y1t,k=this.z2t-this.z1t;0!=a?(0!=(a&8)?(this.y1t+=C(-this.x1t*l/j),this.z1t+=C(-this.x1t*k/j),this.x1t=0):0!=(a&4)?(this.y1t+=C((d-this.x1t)*l/j),this.z1t+=C((d-this.x1t)*k/j),this.x1t=d):0!=(a&2)?(this.x1t+=C(-this.y1t*
j/l),this.z1t+=C(-this.y1t*k/l),this.y1t=0):0!=(a&1)?(this.x1t+=C((f-this.y1t)*j/l),this.z1t+=C((f-this.y1t)*k/l),this.y1t=f):0!=(a&32)?(this.x1t+=C((c-this.z1t)*j/k),this.y1t+=C((c-this.z1t)*l/k),this.z1t=c):(this.x1t+=C((e-this.z1t)*j/k),this.y1t+=C((e-this.z1t)*l/k),this.z1t=e),a=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(b&8)?(this.y2t+=C(-this.x2t*l/j),this.z2t+=C(-this.x2t*k/j),this.x2t=0):0!=(b&4)?(this.y2t+=C((d-this.x2t)*l/j),this.z2t+=C((d-this.x2t)*k/j),this.x2t=d):0!=(b&2)?(this.x2t+=
C(-this.y2t*j/l),this.z2t+=C(-this.y2t*k/l),this.y2t=0):0!=(b&1)?(this.x2t+=C((f-this.y2t)*j/l),this.z2t+=C((f-this.y2t)*k/l),this.y2t=f):0!=(b&32)?(this.x2t+=C((c-this.z2t)*j/k),this.y2t+=C((c-this.z2t)*l/k),this.z2t=c):(this.x2t+=C((e-this.z2t)*j/k),this.y2t+=C((e-this.z2t)*l/k),this.z2t=e),b=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(a|b));return 1});c(c$,"plotLineClippedOld",function(a,b,d,f,c,e,j,l,k,h,n){var q=this.g3d.zbuf,z=this.g3d.width,A=0;0==h&&(n=2147483647,h=1);var H=
f*z+d,E=this.g3d.bufferSize,m=this.g3d.pixel;0!=a&&(!k&&0<=H&&H<E&&c<q[H])&&m.addPixel(H,c,a);if(!(0==e&&0==j)){k=1;var p=z;d+=e;var t=f+j;0>e&&(e=-e,k=-1);0>j&&(j=-j,p=-z);z=e+e;f=j+j;c<<=10;if(j<=e){var s=e-1;0>l&&(s=-s);l=u(((l<<10)+s)/e);j=0;s=Math.abs(d-this.x2t)-1;d=Math.abs(d-this.x1t)-1;for(var t=e-1,w=u(t/2);--t>=s&&!(t==w&&(a=b,0==a));){H+=k;c+=l;j+=f;j>e&&(H+=p,j-=z);if(0!=a&&t<d&&0<=H&&H<E&&A<n){var v=c>>10;v<q[H]&&m.addPixel(H,v,a)}A=(A+1)%h}}else{s=j-1;0>l&&(s=-s);l=u(((l<<10)+s)/j);
e=0;s=Math.abs(t-this.y2t)-1;d=Math.abs(t-this.y1t)-1;t=j-1;for(w=u(t/2);--t>=s&&!(t==w&&(a=b,0==a));)H+=p,c+=l,e+=z,e>j&&(H+=k,e-=f),0!=a&&(t<d&&0<=H&&H<E&&A<n)&&(v=c>>10,v<q[H]&&m.addPixel(H,v,a)),A=(A+1)%h}}},"~N,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N");G(c$,"VISIBILITY_UNCLIPPED",0,"VISIBILITY_CLIPPED",1,"VISIBILITY_OFFSCREEN",2)});m("J.g3d");x(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){c$=w(function(){this.pb=this.zb=this.p0=this.g=null;this.bgcolor=this.width=0;s(this,arguments)},J.g3d,"Pixelator");
p(c$,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,f,c,e){if(f<this.zb[d])switch(a){case 0:break;case 8:this.addPixel(d,f,c);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,c&16777215|a<<24,this.bgcolor),this.addPixel(d,f,b))}},"~N,~N,~N,~N,~N,~N")});m("J.g3d");x(["J.g3d.Pixelator"],"J.g3d.PixelatorT",["J.g3d.Graphics3D"],function(){c$=F(J.g3d,"PixelatorT",J.g3d.Pixelator);h(c$,"clearPixel",function(){},"~N,~N");h(c$,"addPixel",function(a,b,d){var f=this.g.zbufT[a];if(b<f){var c=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=c&&f-b>this.g.zMargin)&&(this.pb[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],c,this.g.bgcolor));
this.g.zbufT[a]=b;this.g.pbufT[a]=d&this.g.translucencyMask}else b!=f&&!this.g.translucentCoverOnly&&b-f>this.g.zMargin&&(this.pb[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],d&this.g.translucencyMask,this.g.bgcolor))},"~N,~N,~N")});m("J.g3d");x(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){c$=w(function(){this.tmp=this.bgRGB=null;this.zShadePower=this.zDepth=this.zSlab=0;s(this,arguments)},J.g3d,"PixelatorShaded",J.g3d.Pixelator);p(c$,function(a){I(this,J.g3d.PixelatorShaded,[a]);
this.tmp=B(3,0)},"J.g3d.Graphics3D");c(c$,"set",function(a,b,d){this.bgcolor=this.g.bgcolor;this.bgRGB=B(-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");h(c$,"addPixel",function(a,b,d){if(!(b>this.zDepth)){if(b>=this.zSlab&&0<this.zShadePower){var f=this.tmp,c=this.bgRGB;f[0]=d;f[1]=d>>8;f[2]=d>>16;var e=(this.zDepth-b)/(this.zDepth-this.zSlab);if(1<this.zShadePower)for(var j=
0;j<this.zShadePower;j++)e*=e;for(j=0;3>j;j++)f[j]=c[j]+C(e*((f[j]&255)-c[j]));d=f[2]<<16|f[1]<<8|f[0]|d&4278190080}this.p0.addPixel(a,b,d)}},"~N,~N,~N");c(c$,"showZBuffer",function(){for(var a=this.p0.zb.length;0<=--a;)if(0!=this.p0.pb[a]){var b=C(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}})});m("J.g3d");x(["J.g3d.Pixelator"],"J.g3d.PixelatorScreened",null,function(){c$=F(J.g3d,"PixelatorScreened",J.g3d.Pixelator);p(c$,
function(a,b){I(this,J.g3d.PixelatorScreened,[a]);this.width=a.width;this.p0=b},"J.g3d.Graphics3D,J.g3d.Pixelator");h(c$,"addPixel",function(a,b,d){a%this.width%2==u(a/this.width)%2&&this.p0.addPixel(a,b,d)},"~N,~N,~N")});m("J.g3d");c$=w(function(){this.bufferSizeT=this.bufferSize=this.bufferHeight=this.bufferWidth=this.windowSize=this.windowHeight=this.windowWidth=0;this.zBufferT=this.zBuffer=this.pBufferT=this.pBuffer=this.bufferedImage=null;this.heightOffscreen=this.widthOffscreen=0;this.apiPlatform=
this.graphicsForTextOrImage=this.offscreenImage=null;s(this,arguments)},J.g3d,"Platform3D");p(c$,function(a){this.apiPlatform=a},"J.api.GenericPlatform");c(c$,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))});c(c$,"allocateTBuffers",function(a){this.bufferSizeT=a?this.bufferSize:this.windowSize;this.zBufferT=B(this.bufferSizeT,0);this.pBufferT=B(this.bufferSizeT,0)},"~B");c(c$,"allocateBuffers",function(a,b,d,f){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=B(this.bufferSize,0);this.pBuffer=B(this.bufferSize,0);this.bufferedImage=this.apiPlatform.allocateRgbImage(this.windowWidth,this.windowHeight,this.pBuffer,this.windowSize,J.g3d.Platform3D.backgroundTransparent,f)},"~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$,"setBackgroundTransparent",function(a){J.g3d.Platform3D.backgroundTransparent=
a},"~B");G(c$,"backgroundTransparent",!1);m("J.g3d");c$=w(function(){this.b=this.a=0;this.isOrthographic=!1;s(this,arguments)},J.g3d,"PrecisionRenderer");c(c$,"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$,"setRastABFloat",function(a,b,d,f){var c=f-b,e=d-a;0==c||0==e?(this.a=1.4E-45,this.b=b):this.isOrthographic?(this.a=c/e,this.b=b-this.a*a):(this.a=e*b*(f/c),this.b=(d*f-a*b)/c)},"~N,~N,~N,~N");c(c$,"setRastAB",function(a,b,d,f){var c=
f-b,e=d-a;1.4E-45==a||0==c||0==e?(this.a=1.4E-45,this.b=f):this.isOrthographic?(this.a=c/e,this.b=b-this.a*a):(this.a=e*b*(f/c),this.b=(d*f-a*b)/c)},"~N,~N,~N,~N");m("J.g3d");x(["JU.P3"],"J.g3d.SphereRenderer",null,function(){c$=w(function(){this.mDeriv=this.coef=this.mat=this.zroot=this.shader=this.g3d=null;this.planeShade=this.selectedOctant=0;this.zbuf=null;this.offsetPbufBeginLine=this.slab=this.depth=this.height=this.width=0;this.dxyz=this.planeShades=this.ptTemp=null;s(this,arguments)},J.g3d,
"SphereRenderer");O(c$,function(){this.zroot=Q(2,0);this.ptTemp=new JU.P3;this.planeShades=B(3,0);this.dxyz=L(3,3,0)});p(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"render",function(a,b,d,f,c,e,j,l,k,h){if(1!=c&&(49<b&&(b&=-2),!this.g3d.isClippedXY(b,d,f))){this.slab=this.g3d.slab;this.depth=this.g3d.depth;var n=b+1>>1,q=c-n;if(!(c+n<this.slab||q>this.depth)){var z=d-n,A=d+n,H=f-n,E=f+n;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*f+d;var m=this.shader;this.mat=e;if(null!=e&&(this.coef=j,this.mDeriv=l,this.selectedOctant=k,null==m.ellipsoidShades&&m.createEllipsoidShades(),null!=h)){this.planeShade=-1;for(j=0;3>j;j++)if(n=this.dxyz[j][0]=h[j].x-d,l=this.dxyz[j][1]=h[j].y-f,k=this.dxyz[j][2]=h[j].z-c,this.planeShades[j]=m.getShadeIndex(n,l,-k),0==n&&0==l){this.planeShade=this.planeShades[j];break}}if(null!=e||128<b)this.renderQuadrant(-1,-1,d,f,c,b,a),this.renderQuadrant(-1,
1,d,f,c,b,a),this.renderQuadrant(1,-1,d,f,c,b,a),this.renderQuadrant(1,1,d,f,c,b,a),null!=e&&(this.mDeriv=this.coef=this.mat=null);else{var p=m.sphereShapeCache[b-1];if(null==p){p=0;e=0!=(b&1);h=b/2;l=h*h;n=u((b+1)/2);k=e?0:0.5;for(j=0;j<n;++j,++k)for(var t=k*k,s=e?0:0.5,w=0;w<n;++w,++s){var v=s*s,v=l-t-v;0<=v&&++p}var p=B(p,0),x=0;k=e?0:0.5;for(j=0;j<n;++j,++k){t=k*k;s=e?0:0.5;for(w=0;w<n;++w,++s)if(v=s*s,v=l-t-v,0<=v){var y=Math.sqrt(v),v=C(y),D=m.getShadeN(s,k,y,h),F=m.getShadeN(-s,k,y,h),G=m.getShadeN(s,
-k,y,h),y=m.getShadeN(-s,-k,y,h),v=v|D<<7|F<<13|G<<19|y<<25;p[x++]=v}p[x-1]|=2147483648}m.sphereShapeCache[b-1]=p}0>z||A>=this.width||0>H||E>=this.height||q<this.slab||c>this.depth?this.renderSphereClipped(p,d,f,c,b,a):this.renderSphereUnclipped(p,c,b,a)}this.zbuf=null}}},"~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");c(c$,"renderSphereUnclipped",function(a,b,d,f){var c=0,e=1-(d&1),j=this.offsetPbufBeginLine,l=j-e*this.width;d=u((d+1)/2);var k=this.zbuf,h=this.width,n=this.g3d.pixel;do{var q=j,z=j-e,A=l,
H=l-e,E;do{E=a[c++];var m=b-(E&127);m<k[q]&&n.addPixel(q,m,f[E>>7&63]);m<k[z]&&n.addPixel(z,m,f[E>>13&63]);m<k[A]&&n.addPixel(A,m,f[E>>19&63]);m<k[H]&&n.addPixel(H,m,f[E>>25&63]);++q;--z;++A;--H}while(0<=E);j+=h;l-=h}while(0<--d)},"~A,~N,~N,~A");c(c$,"renderSphereClipped",function(a,b,d,f,c,e){var j=this.width,l=this.height,k=0,h=1-(c&1),n=this.offsetPbufBeginLine,q=n-h*j;c=u((c+1)/2);var z=d,A=d-h;d=(b<<16)+(d<<1)^858993459;var H=this.zbuf,m=this.g3d.pixel,p=this.slab,s=this.depth;do{var t=0<=z&&
z<l,v=0<=A&&A<l,w=n,x=n-h,y=q,B=q-h,C,D=b,F=b-h;do{var G=0<=F&&F<j,I=0<=D&&D<j;C=a[k++];var L;L=C&127;var K;f<p?(K=f+L,L=K>=p):(K=f-L,L=K<p);L&&(K=p);if(K>=p&&K<=s){if(t){if(I&&K<H[w]){var M=L?44+(d>>7&7):C>>7&63;m.addPixel(w,K,e[M])}G&&K<H[x]&&(M=L?44+(d>>13&7):C>>13&63,m.addPixel(x,K,e[M]))}v&&(I&&K<H[y]&&(M=L?44+(d>>19&7):C>>19&63,m.addPixel(y,K,e[M])),G&&K<H[B]&&(M=L?44+(d>>25&7):C>>25&63,m.addPixel(B,K,e[M])))}++w;--x;++y;--B;++D;--F;L&&(d=(d<<16)+(d<<1)+d&2147483647)}while(0<=C);n+=j;q-=j;++z;
--A}while(0<--c)},"~A,~N,~N,~N,~N,~A");c(c$,"renderQuadrant",function(a,b,d,f,c,e,j){e=u(e/2);var l=d+e*a,k=(0>d?-1:d<this.width?0:1)+(0>l?-2:l<this.width?0:2);-3==k||3==k||(l=f+e*b,l=(0>f?-1:f<this.height?0:1)+(0>l?-2:l<this.height?0:2),-3==l||3==l||(null==this.mat&&0==k&&0==l&&c-e>=this.slab&&c<=this.depth?this.renderQuadrantUnclipped(e,a,b,c,j):this.renderQuadrantClipped(e,a,b,d,f,c,j)))},"~N,~N,~N,~N,~N,~N,~A");c(c$,"renderQuadrantUnclipped",function(a,b,d,f,c){for(var e=a*a,j=2*a+1,l=0>d?-this.width:
this.width,k=this.offsetPbufBeginLine,h=this.zbuf,n=this.g3d.pixel,q=this.shader.sphereShadeIndexes,z=0,A=0;A<=e;A+=z+ ++z,k+=l)for(var m=k,E=e-A,p=f-a,s=u((z*d+a<<8)/j),t=0,w=0;w<=E;w+=t+ ++t,m+=b)if(!(h[m]<=p)&&(p=u(Math.sqrt(E-w)),p=f-p,!(h[m]<=p))){var v=u((t*b+a<<8)/j);n.addPixel(m,p,c[q[(s<<8)+v]])}},"~N,~N,~N,~N,~A");c(c$,"renderQuadrantClipped",function(a,b,d,f,c,e,j){for(var l=null!=this.mat,k=0<=this.selectedOctant,h=a*a,n=2*a+1,q=0>d?-this.width:this.width,z=this.offsetPbufBeginLine,A=
(f<<16)+(c<<1)^858993459,m=0,E=0,p=this.g3d.pixel,s=0,t=this.height,w=this.width,v=this.zbuf,x=this.dxyz,y=this.slab,B=this.depth,C=this.ptTemp,D=this.coef,F=this.zroot,G=this.selectedOctant,I=this.shader,K=this.planeShades,L=I.sphereShadeIndexes,M=this.planeShade,N=this.mat,O=0,P=0,Q=c;P<=h;P+=O+ ++O,z+=q,Q+=d)if(0>Q){if(0>d)break}else if(Q>=t){if(0<d)break}else{var U=h-(l?0:P);l||(m=u((O*d+a<<8)/n));for(var A=(A<<16)+(A<<1)+A&2147483647,R=f,X=0,V=0,W=-1,T=1,Z=z;V<=U;V+=X+ ++X,Z+=b,R+=b)if(0>R){if(0>
b)break}else if(R>=w){if(0<b)break}else{var S;if(l){S=(D[4]*R+D[5]*Q+D[8])/D[2]/2;var Y=S*S-(D[0]*R*R+D[1]*Q*Q+D[3]*R*Q+D[6]*R+D[7]*Q-1)/D[2];if(0>Y){if(0<=W)break;continue}Y=Math.sqrt(Y);F[0]=-S-Y;F[1]=-S+Y;W=e<y?1:0;if(0==(S=u(F[W])))S=e;T=2;s=S;if(k){C.set(R-f,Q-c,S-e);N.rotate(C);Y=0;0>C.x&&(Y|=1);0>C.y&&(Y|=2);0>C.z&&(Y|=4);if(Y==G){if(0<=M)E=M;else{T=3;E=3.4028235E38;for(S=0;3>S;S++)if(0!=(Y=x[S][2]))Y=e+(-x[S][0]*(R-f)-x[S][1]*(Q-c))/Y,Y<E&&(E=Y,T=S);3==T&&(T=0,E=e);F[0]=E;E=K[T]}S=u(F[0]);
T=3}if(Y=e<y?S>=y:S<y)s=S=y,T=0}if(S<y||S>B||v[Z]<=s)continue}else{S=u(Math.sqrt(U-V));S=e+(e<y?S:-S);if(Y=e<y?S>=y:S<y)S=y,T=0;if(S<y||S>B||v[Z]<=S)continue}switch(T){case 0:E=44+(A>>8&7);A=(A<<16)+(A<<1)+A&2147483647;T=1;break;case 2:E=I.getEllipsoidShade(R,Q,F[W],a,this.mDeriv);break;case 3:p.clearPixel(Z,s);break;default:E=u((X*b+a<<8)/n),E=L[(m<<8)+E]}p.addPixel(Z,S,j[E])}A=(A+R+Q|1)&2147483647}},"~N,~N,~N,~N,~N,~N,~A");G(c$,"maxOddSizeSphere",49,"maxSphereDiameter",1E3,"maxSphereDiameter2",
2E3,"SHADE_SLAB_CLIPPED",47)});m("J.g3d");x(["java.util.Hashtable"],"J.g3d.TextRenderer",["JU.CU"],function(){c$=w(function(){this.size=this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=null;this.isInvalid=!1;s(this,arguments)},J.g3d,"TextRenderer");c$.clearFontCache=c(c$,"clearFontCache",function(){J.g3d.TextRenderer.working||(J.g3d.TextRenderer.htFont3d.clear(),J.g3d.TextRenderer.htFont3dAntialias.clear())});c$.plot=c(c$,"plot",function(a,b,d,f,c,e,j,l,k,h){if(0==e.length)return 0;if(0<=
e.indexOf("<su")||0<=e.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,b,d,f,c,e,j,l,k,h);var n=j.getAscent();b-=n;e=J.g3d.TextRenderer.getPlotText3D(a,b,l,e,j,h);if(e.isInvalid)return e.width;h&&0==(f&12632256)&&(f|=263172);h=e.height;j=e.width;var n=e.tmap,q=l.width,z=l.height,A=l.zbuf,m=l.pixel,E=l.translucencyLog;if(null!=k||(0>a||a+e.width>q||0>b||b+e.height>z)&&null!=(k=l))for(var p=l=0;p<h;p++)for(var s=0;s<j;s++){var t=n[l++];0!=t&&k.plotImagePixel(f,a+s,b+p,d,t,c,q,z,A,m,E)}else{l=
p=0;for(a=b*q+a;p<h;p++,a+=q-j)for(s=0;s<j;s++)m.addImagePixel(n[l++],E,a++,d,f,c)}return e.width},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");c$.plotByCharacter=c(c$,"plotByCharacter",function(a,b,d,f,c,e,j,l,k,h){for(var n=0,q=e.length,z=Math.round(0.25*j.getHeight()),A=-Math.round(0.3*j.getHeight()),m=0,E=0;E<q;E++){if("<"==e.charAt(E)){if(E+5<q&&e.substring(E,E+6).equals("<color")){var m=f,p=e.indexOf(">",E);if(0>p)continue;f=JU.CU.getArgbFromString(e.substring(E+
7,p).trim());E=p;continue}if(E+7<q&&e.substring(E,E+8).equals("</color>")){E+=7;f=m;continue}if(E+4<q&&e.substring(E,E+5).equals("<sub>")){E+=4;b+=z;continue}if(E+4<q&&e.substring(E,E+5).equals("<sup>")){E+=4;b+=A;continue}if(E+5<q&&e.substring(E,E+6).equals("</sub>")){E+=5;b-=z;continue}if(E+5<q&&e.substring(E,E+6).equals("</sup>")){E+=5;b-=A;continue}}p=J.g3d.TextRenderer.plot(a+n,b,d,f,c,e.substring(E,E+1),j,l,k,h);n+=p}return n},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");
p(c$,function(a,b){this.ascent=b.getAscent();this.height=b.getHeight();this.width=b.stringWidth(a);0!=this.width&&(this.mapWidth=this.width,this.size=this.mapWidth*this.height)},"~S,JU.Font");c$.getPlotText3D=c(c$,"getPlotText3D",function(a,b,d,f,c,e){J.g3d.TextRenderer.working=!0;e=e?J.g3d.TextRenderer.htFont3dAntialias:J.g3d.TextRenderer.htFont3d;var j=e.get(c),l=null,k=!1,h=!1;null!=j?l=j.get(f):(j=new java.util.Hashtable,k=!0);null==l&&(l=new J.g3d.TextRenderer(f,c),h=!0);l.isInvalid=0==l.width||
0>=a+l.width||a>=d.width||0>=b+l.height||b>=d.height;if(l.isInvalid)return l;k&&e.put(c,j);h&&(l.setTranslucency(f,c,d),j.put(f,l));J.g3d.TextRenderer.working=!1;return l},"~N,~N,J.g3d.Graphics3D,~S,JU.Font,~B");c(c$,"setTranslucency",function(a,b,d){a=d.apiPlatform.getTextPixels(a,b,d.platform.getGraphicsForTextOrImage(this.mapWidth,this.height),d.platform.offscreenImage,this.mapWidth,this.height,this.ascent);if(null!=a){this.tmap=P(this.size,0);for(b=a.length;0<=--b;)d=a[b]&255,0!=d&&(this.tmap[b]=
J.g3d.TextRenderer.translucency[d>>5])}},"~S,JU.Font,J.g3d.Graphics3D");G(c$,"translucency",P(-1,[7,6,5,4,3,2,1,8]),"working",!1);c$.htFont3d=c$.prototype.htFont3d=new java.util.Hashtable;c$.htFont3dAntialias=c$.prototype.htFont3dAntialias=new java.util.Hashtable});m("J.g3d");x(["JU.P3i"],"J.g3d.TextString",null,function(){c$=w(function(){this.font=this.text=null;this.bgargb=this.argb=0;s(this,arguments)},J.g3d,"TextString",JU.P3i,java.util.Comparator);c(c$,"setText",function(a,b,d,f,c,e,j){this.text=
a;this.font=b;this.argb=d;this.bgargb=f;this.x=c;this.y=e;this.z=j},"~S,JU.Font,~N,~N,~N,~N,~N");h(c$,"compare",function(a,b){return null==a||null==b?0:a.z>b.z?-1:a.z<b.z?1:0},"J.g3d.TextString,J.g3d.TextString");c(c$,"toString",function(){return T(this,J.g3d.TextString,"toString",[])+" "+this.text})});m("J.g3d");x(["J.g3d.G3DRenderer","$.PrecisionRenderer","JU.Rgb16"],"J.g3d.TriangleRenderer",["JU.GData"],function(){c$=w(function(){this.rgb16t2=this.rgb16t1=this.rgb16sGouraud=this.rgb16sE=this.rgb16sW=
this.azE=this.axE=this.azW=this.axW=this.bb=this.aa=this.az=this.ay=this.ax=this.g3d=null;s(this,arguments)},J.g3d,"TriangleRenderer",J.g3d.PrecisionRenderer,J.g3d.G3DRenderer);O(c$,function(){this.ax=B(3,0);this.ay=B(3,0);this.az=B(3,0);this.aa=L(64,0);this.bb=L(64,0);this.axW=B(64,0);this.azW=B(64,0);this.axE=B(64,0);this.azE=B(64,0);this.rgb16t1=new JU.Rgb16;this.rgb16t2=new JU.Rgb16});p(c$,function(){I(this,J.g3d.TriangleRenderer,[])});h(c$,"set",function(a){try{this.rgb16sW=Array(64);this.rgb16sE=
Array(64);for(var b=64;0<=--b;)this.rgb16sW[b]=new JU.Rgb16,this.rgb16sE[b]=new JU.Rgb16;this.g3d=a;this.rgb16sGouraud=Array(3);for(b=3;0<=--b;)this.rgb16sGouraud[b]=new JU.Rgb16}catch(d){if(!D(d,Exception))throw d;}return this},"J.api.JmolRendererInterface,JU.GData");c(c$,"reallocRgb16s",function(a,b){var d=Array(b);Zystem.arraycopy(a,0,d,0,a.length);for(var f=a.length;f<b;++f)d[f]=new JU.Rgb16;return d},"~A,~N");c(c$,"setGouraud",function(a,b,d){this.rgb16sGouraud[0].setInt(a);this.rgb16sGouraud[1].setInt(b);
this.rgb16sGouraud[2].setInt(d)},"~N,~N,~N");c(c$,"fillTriangle",function(a,b,d,f){this.ax[0]=a.x;this.ax[1]=b.x;this.ax[2]=d.x;this.ay[0]=a.y;this.ay[1]=b.y;this.ay[2]=d.y;this.az[0]=a.z;this.az[1]=b.z;this.az[2]=d.z;if(!(1>=this.az[0]||1>=this.az[1]||1>=this.az[2])){b=this.g3d.clipCode3(this.ax[0],this.ay[0],this.az[0]);d=this.g3d.clipCode3(this.ax[1],this.ay[1],this.az[1]);var c=this.g3d.clipCode3(this.ax[2],this.ay[2],this.az[2]),e=b|d|c;a=0!=e;if(!a||!(-1==e||0!=(b&d&c))){c=0;this.ay[1]<this.ay[c]&&
(c=1);this.ay[2]<this.ay[c]&&(c=2);var e=(c+1)%3,j=(c+2)%3;if(this.ay[e]>this.ay[j])var l=e,e=j,j=l;b=this.ay[c];var k=this.ay[e],h=this.ay[j];d=h-b+1;if(!(d>3*this.g3d.height)){if(d>this.axW.length){var n=d+31&-32;this.axW=B(n,0);this.azW=B(n,0);this.axE=B(n,0);this.azE=B(n,0);this.aa=L(n,0);this.bb=L(n,0);this.rgb16sW=this.reallocRgb16s(this.rgb16sW,n);this.rgb16sE=this.reallocRgb16s(this.rgb16sE,n)}var q;f?(n=this.rgb16sW,q=this.rgb16sE):n=q=null;l=k-b;0==l?(this.ax[e]<this.ax[c]&&(l=e,e=c,c=l),
this.generateRaster(d,c,j,this.axW,this.azW,0,n),this.generateRaster(d,e,j,this.axE,this.azE,0,q)):k==h?(this.ax[j]<this.ax[e]&&(l=e,e=j,j=l),this.generateRaster(d,c,e,this.axW,this.azW,0,n),this.generateRaster(d,c,j,this.axE,this.azE,0,q)):(k=this.ax[j]-this.ax[c],h=JU.GData.roundInt(u(d/2)),0>k&&(h=-h),this.ax[c]+u((k*l+h)/d)<this.ax[e]?(this.generateRaster(d,c,j,this.axW,this.azW,0,n),this.generateRaster(l+1,c,e,this.axE,this.azE,0,q),this.generateRaster(d-l,e,j,this.axE,this.azE,l,q)):(this.generateRaster(l+
1,c,e,this.axW,this.azW,0,n),this.generateRaster(d-l,e,j,this.axW,this.azW,l,n),this.generateRaster(d,c,j,this.axE,this.azE,0,q)));this.g3d.setZMargin(5);c=this.g3d.pass2Flag01;e=1-c;j=0;0>b&&(d+=b,j-=b,b=0);b+d>this.g3d.height&&(d=this.g3d.height-b);if(f)if(a)for(;--d>=c;++b,++j)a=this.axE[j]-(f=this.axW[j])+e,0<a&&this.g3d.plotPixelsClippedRaster(a,f,b,this.azW[j],this.azE[j],this.rgb16sW[j],this.rgb16sE[j]);else for(;--d>=c;++b,++j)a=this.axE[j]-(f=this.axW[j])+e,1==c&&0>a&&(a=1,f--),0<a&&this.g3d.plotPixelsUnclippedRaster(a,
f,b,this.azW[j],this.azE[j],this.rgb16sW[j],this.rgb16sE[j]);else if(a)for(;--d>=c;++b,++j)a=this.axE[j]-(f=this.axW[j])+e,0<a&&this.g3d.plotPixelsClippedRasterBits(a,f,b,this.azW[j],this.azE[j],null,null,this.aa[j],this.bb[j]);else for(;--d>=c;++b,++j)a=this.axE[j]-(f=this.axW[j])+e,1==c&&0>a&&(a=1,f--),0<a&&this.g3d.plotPixelsUnclippedRasterBits(a,f,b,null,null,this.aa[j],this.bb[j]);this.g3d.setZMargin(0)}}}},"JU.P3i,JU.P3i,JU.P3i,~B");c(c$,"generateRaster",function(a,b,d,f,c,e,j){var l=this.ax[b],
k=this.ax[d]-l,h,n,q;0<=k?(h=1,n=k,q=0):(h=-1,n=-k,q=1-a);var z;n<=a?z=0:(z=JU.GData.roundInt(u(k/a)),n%=a);this.setRastAB(this.ay[b],this.az[b],this.ay[d],this.az[d]);for(var A=this.a,m=this.b,E=f===this.axE,p=0,s=this.ay[b],t=a-1,k=e;p<=t;++k,++p,++s){if(0==k||k>e)f[k]=p==t?this.ax[d]:l,c[k]=this.getZCurrent(A,m,s),E&&(this.setRastAB(this.axW[k],this.azW[k],f[k],c[k]),this.aa[k]=this.a,this.bb[k]=this.b);l+=z;q+=n;0<q&&(l+=h,q-=a)}if(null!=j){f=this.rgb16t1;f.setRgb(this.rgb16sGouraud[b]);b=this.rgb16t2;
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2*b/10)));break;default:d?d=C(this.vwr.tm.scaleToScreen(a,u(b/10))):(this.g3d.isAntialiased()&&(b+=b),d=b)}return d},"~N,~N");c(c$,"renderLine",function(a,b,d,f){0>d?this.g3d.drawDashedLineBits(8,4,a,b):this.g3d.fillCylinderBits(this.endcap,d,a,b);f&&null!=this.tickInfo&&(this.checkTickTemps(),this.tickAs.setT(a),this.tickBs.setT(b),this.drawTicks(d,!0))},"JU.P3,JU.P3,~N,~B");c(c$,"checkTickTemps",function(){null==this.tickA&&(this.tickA=new JU.P3,this.tickB=new JU.P3,this.tickAs=new JU.P3,this.tickBs=
new JU.P3)});c(c$,"drawTicks",function(a,b){Float.isNaN(this.tickInfo.first)&&(this.tickInfo.first=0);this.drawTicks2(this.tickInfo.ticks.x,8,a,!b?null:null==this.tickInfo.tickLabelFormats?v(-1,["%0.2f"]):this.tickInfo.tickLabelFormats);this.drawTicks2(this.tickInfo.ticks.y,4,a,null);this.drawTicks2(this.tickInfo.ticks.z,2,a,null)},"~N,~B");c(c$,"drawTicks2",function(a,b,d,f){if(0!=a&&(this.g3d.isAntialiased()&&(b*=2),this.vectorT2.set(this.tickBs.x,this.tickBs.y,0),this.vectorT.set(this.tickAs.x,
this.tickAs.y,0),this.vectorT2.sub(this.vectorT),!(50>this.vectorT2.length()))){var c=this.tickInfo.signFactor;this.vectorT.sub2(this.tickB,this.tickA);var e=this.vectorT.length();if(null!=this.tickInfo.scale)if(Float.isNaN(this.tickInfo.scale.x)){var j=this.vwr.getUnitCellInfo(0);Float.isNaN(j)||this.vectorT.set(this.vectorT.x/j,this.vectorT.y/this.vwr.getUnitCellInfo(1),this.vectorT.z/this.vwr.getUnitCellInfo(2))}else this.vectorT.set(this.vectorT.x*this.tickInfo.scale.x,this.vectorT.y*this.tickInfo.scale.y,
this.vectorT.z*this.tickInfo.scale.z);j=this.vectorT.length()+1E-4*a;if(!(j<a)){this.vectorT.scale(a/j*e/j);var e=(this.tickBs.z-this.tickAs.z)/(j/a),j=j+this.tickInfo.first,l=u(Math.floor(this.tickInfo.first/a))*a-this.tickInfo.first;this.pointT.scaleAdd2(l/a,this.vectorT,this.tickA);var l=l+this.tickInfo.first,k=this.tickAs.z;0>d&&(d=1);this.vectorT2.set(-this.vectorT2.y,this.vectorT2.x,0);this.vectorT2.scale(b/this.vectorT2.length());b=this.tickInfo.reference;null==b?(this.pointT3.setT(this.vwr.getBoundBoxCenter()),
603979809==this.vwr.g.axesMode&&this.pointT3.add3(1,1,1)):this.pointT3.setT(b);this.tm.transformPtScr(this.pointT3,this.pt2i);b=0.2>Math.abs(this.vectorT2.x/this.vectorT2.y);for(var h=!b,n=!b&&0>this.vectorT2.x,q=null!=f&&0<f.length,z,A,m=Array(1),E=this.draw000?0:-1;l<j;){if(l>=this.tickInfo.first&&(this.pointT2.setT(this.pointT),this.tm.transformPt3f(this.pointT2,this.pointT2),this.drawLine(u(Math.floor(this.pointT2.x)),u(Math.floor(this.pointT2.y)),C(k),z=u(Math.floor(this.pointT2.x+this.vectorT2.x)),
A=u(Math.floor(this.pointT2.y+this.vectorT2.y)),C(k),d),q&&(this.draw000||0!=l))){m[0]=Float.$valueOf(0==l?0:l*c);var p=JU.PT.sprintf(f[E%f.length],"f",m);this.drawString(z,A,C(k),4,n,b,h,u(Math.floor(this.pointT2.y)),p)}this.pointT.add(this.vectorT);l+=a;k+=e;E++}}}},"~N,~N,~N,~A");c(c$,"drawLine",function(a,b,d,f,c,e,j){return this.drawLine2(a,b,d,f,c,e,j)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawLine2",function(a,b,d,f,c,e,j){this.pt0.set(a,b,d);this.pt1.set(f,c,e);if(this.dotsOrDashes)null!=this.dashDots&&
this.drawDashed(a,b,d,f,c,e,this.dashDots);else{if(0>j)return this.g3d.drawDashedLineBits(8,4,this.pt0,this.pt1),1;this.g3d.fillCylinderBits(2,j,this.pt0,this.pt1)}return u((j+1)/2)},"~N,~N,~N,~N,~N,~N,~N");c(c$,"drawString",function(a,b,d,f,c,e,j,l,k){if(null!=k){var h=this.font3d.stringWidth(k),n=this.font3d.getAscent();a=c?a-(u(f/2)+2+h):e?a-(u(f/2)+2+u(h/2)):a+(u(f/2)+2);c=b;c=j?c+u(n/2):0==l||l<b?c+n:c-u(f/2);b=d-f-2;1>b&&(b=1);this.g3d.drawString(k,this.font3d,a,c,b,b,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");
c(c$,"drawDashed",function(a,b,d,f,c,e,j){if(!(null==j||0>this.width)){var l=j[0];f-=a;c-=b;e-=d;var k=0,h=j===J.render.FontLineShapeRenderer.ndots,n=h||j===J.render.FontLineShapeRenderer.sixdots;if(n){var q=(f*f+c*c)/(this.width*this.width);h?(l=Math.sqrt(q)/1.5,k=C(l)+2):8>q?j=J.render.FontLineShapeRenderer.twodots:32>q&&(j=J.render.FontLineShapeRenderer.fourdots)}var q=j[1],z=j[2],A=this.colixA,m=0==z?this.colixB:this.colixA;0==k&&(k=j.length);for(var E=0,p=3;p<k;p++){var E=h?E+1:j[p],s=u(Math.floor(a+
f*E/l)),t=u(Math.floor(b+c*E/l)),w=u(Math.floor(d+e*E/l));if(n)this.s1.set(s,t,w),p==q?this.g3d.setC(this.colixA):p==z&&this.g3d.setC(this.colixB),this.g3d.fillSphereI(this.width,this.s1);else{p==q&&(A=this.colixB);E=j[++p];p==z&&(m=this.colixB);var v=u(Math.floor(a+f*E/l)),x=u(Math.floor(b+c*E/l)),y=u(Math.floor(d+e*E/l));this.fillCylinder(A,m,2,this.width,s,t,w,v,x,y)}}}},"~N,~N,~N,~N,~N,~N,~A");c(c$,"fillCylinder",function(a,b,d,f,c,e,j,l,k,h){this.asLineOnly?this.g3d.drawLine(a,b,c,e,j,l,k,h):
this.g3d.fillCylinderXYZ(a,b,d,!this.isExport||1==this.mad?f:this.mad,c,e,j,l,k,h)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");G(c$,"dashes",B(-1,[12,0,0,2,5,7,10]),"hDashes",B(-1,[10,7,6,1,3,4,6,7,9]),"ndots",B(-1,[0,3,1E3]),"sixdots",B(-1,[12,3,6,1,3,5,7,9,11]),"fourdots",B(-1,[13,3,5,2,5,8,11]),"twodots",B(-1,[12,3,4,3,9]))});m("J.render");x(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["JV.Viewer"],function(){c$=F(J.render,"FrankRenderer",J.render.ShapeRenderer);h(c$,"render",function(){var a=this.shape,
b=this.vwr.getBooleanProperty("allowKeyStrokes"),d=this.vwr.getBoolean(603983903);this.colix=d?20:this.vwr.isSignedApplet?b||(JV.Viewer.isJS||JV.Viewer.isSwingJS)&&!this.vwr.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);b=C(a.frankWidth+4*b);this.g3d.drawStringNoSlab(a.frankString,a.font3d,this.vwr.gdata.width-
b,this.vwr.gdata.height-a.frankDescent,0,0);a=d?this.vwr.getModelkit(!1):null;d&&!a.isHidden()&&(this.g3d.setC(12),this.g3d.fillTextRect(0,0,1,0,10,104),d=a.getActiveMenu(),null!=d&&("atomMenu".equals(d)?(this.g3d.setC(21),this.g3d.fillTextRect(0,0,0,0,10,26)):"bondMenu".equals(d)?(this.g3d.setC(7),this.g3d.fillTextRect(0,26,0,0,10,26)):"xtalMenu".equals(d)&&(this.g3d.setC(8),this.g3d.fillTextRect(0,52,0,0,10,26))));return!1})});m("J.render");x(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",
"java.lang.NullPointerException $.Thread J.api.Interface JU.Logger JV.JC $.Viewer".split(" "),function(){c$=w(function(){this.bsTranslucent=this.renderers=this.shapeManager=this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;s(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);O(c$,function(){this.bsTranslucent=JU.BS.newN(37)});p(c$,function(){});h(c$,"set",function(a,b){this.vwr=a;this.shapeManager=b},"JV.Viewer,JV.ShapeManager");h(c$,"isRepaintPending",function(){return this.repaintPending});
h(c$,"pushHoldRepaint",function(){++this.holdRepaint},"~S");h(c$,"popHoldRepaint",function(a,b){--this.holdRepaint;0>=this.holdRepaint&&(this.holdRepaint=0,a&&(this.repaintPending=!0,this.repaintNow(b)))},"~B,~S");h(c$,"requestRepaintAndWait",function(a){var b=null;JV.Viewer.isJS&&!JV.Viewer.isSwingJS&&(b=self.Jmol&&Jmol.repaint?Jmol:null);if(null==b)try{this.repaintNow(a),JV.Viewer.isJS||this.wait(this.vwr.g.repaintWaitMs),this.repaintPending&&(JU.Logger.error("repaintManager requestRepaintAndWait timeout"),
this.repaintDone())}catch(d){if(D(d,InterruptedException))Zystem.out.println("repaintManager requestRepaintAndWait interrupted thread="+Thread.currentThread().getName());else throw d;}else b.repaint(this.vwr.html5Applet,!1),this.repaintDone()},"~S");h(c$,"repaintIfReady",function(a){if(this.repaintPending)return!1;this.repaintPending=!0;0==this.holdRepaint&&this.repaintNow(a);return!0},"~S");c(c$,"repaintNow",function(){this.vwr.haveDisplay&&this.vwr.apiPlatform.repaint(this.vwr.display)},"~S");h(c$,
"repaintDone",function(){this.repaintPending=!1});h(c$,"clear",function(a){if(null!=this.renderers)if(0<=a)this.renderers[a]=null;else for(a=0;37>a;++a)this.renderers[a]=null},"~N");c(c$,"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");h(c$,"render",function(a,b,d,f){null==this.renderers&&
(this.renderers=Array(37));this.getAllRenderers();try{var c=this.vwr.getBoolean(603979934);a.renderBackground(null);if(d){this.bsTranslucent.clearAll();null!=f&&a.renderCrossHairs(f,this.vwr.getScreenWidth(),this.vwr.getScreenHeight(),this.vwr.tm.getNavigationOffset(),this.vwr.tm.navigationDepthPercent);var e=this.vwr.getRubberBandSelection();null!=e&&a.setC(this.vwr.cm.colixRubberband)&&a.drawRect(e.x,e.y,0,0,e.width,e.height);this.vwr.noFrankEcho=!0}f=null;for(e=0;37>e&&a.currentlyRendering;++e){var j=
this.shapeManager.getShape(e);null!=j&&(c&&(f="rendering "+JV.JC.getShapeClassName(e,!1),JU.Logger.startTimer(f)),(d||this.bsTranslucent.get(e))&&this.getRenderer(e).renderShape(a,b,j)&&this.bsTranslucent.set(e),c&&JU.Logger.checkTimer(f,!1))}a.renderAllStrings(null)}catch(l){if(D(l,Exception)){l.printStackTrace();if(this.vwr.async&&"Interface".equals(l.getMessage()))throw new NullPointerException;JU.Logger.error("rendering error? "+l)}else throw l;}},"JU.GData,JM.ModelSet,~B,~A");c(c$,"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;});h(c$,"renderExport",function(a,b,d){this.shapeManager.finalizeAtoms(null,!0);a=this.vwr.initializeExporter(d);if(null==a)return JU.Logger.error("Cannot export "+d.get("type")),null;null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();d=null;try{var f=this.vwr.getBoolean(603979934);a.renderBackground(a);
for(var c=0;37>c;++c){var e=this.shapeManager.getShape(c);null!=e&&(f&&(d="rendering "+JV.JC.getShapeClassName(c,!1),JU.Logger.startTimer(d)),this.getRenderer(c).renderShape(a,b,e),f&&JU.Logger.checkTimer(d,!1))}a.renderAllStrings(a);d=a.finalizeOutput()}catch(j){if(D(j,Exception))j.printStackTrace(),JU.Logger.error("rendering error? "+j);else throw j;}return d},"JU.GData,JM.ModelSet,java.util.Map")});m("J.render");x(null,"J.render.ShapeRenderer",["JV.JC"],function(){c$=w(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;s(this,arguments)},J.render,"ShapeRenderer");c(c$,"initRenderer",function(){});c(c$,"setViewerG3dShapeID",function(a,b){this.vwr=a;this.tm=a.tm;this.shapeID=b;this.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(b);this.initRenderer()},"JV.Viewer,~N");c(c$,"renderShape",function(a,b,d){this.setup(a,b,d);a=this.render();this.exportType=0;this.isExport=!1;return a},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");
c(c$,"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$,"isVisibleForMe",function(a){return a.isVisible(this.myVisibilityFlag|9)},"JM.Atom")});m("J.render");x(["J.render.FontLineShapeRenderer","JU.BS","$.P3","$.V3"],"J.render.SticksRenderer","java.lang.Float JU.A4 $.M3 J.c.PAL JU.C $.Edge".split(" "),function(){c$=w(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;s(this,arguments)},J.render,"SticksRenderer",J.render.FontLineShapeRenderer);O(c$,function(){this.x=new JU.V3;this.y=new JU.V3;this.z=new JU.V3;this.p1=new JU.P3;this.p2=new JU.P3;this.bsForPass2=JU.BS.newN(64)});h(c$,"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 f=this.vwr.gdata.isClippedZ(this.a.sZ);if(f&&this.vwr.gdata.isClippedZ(this.b.sZ)||this.slabByAtom&&(f||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),f=!JU.C.renderPass2(this.colixB),!b||!f)){if(!b&&!f&&!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=C(this.vwr.tm.scaleToScreen(u((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=u(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=u(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*=
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c(c$,"isHetero",function(){return 0!=(this.formalChargeAndFlags&2)});c(c$,"hasVibration",function(){return 0!=(this.formalChargeAndFlags&1)});c(c$,"setFormalCharge",function(a){this.formalChargeAndFlags=this.formalChargeAndFlags&15|(-2147483648==a?0:7<a?7:-3>a?-3:a)<<24},"~N");c(c$,"setVibrationVector",function(){this.formalChargeAndFlags|=1});h(c$,"getFormalCharge",function(){return this.formalChargeAndFlags>>24});c(c$,"getOccupancy100",function(){var a=this.group.chain.model.ms.occupancies;return null==
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null));return b.distance(d)},"JU.T3,JU.T3,JU.T3");c(c$,"setFractionalCoord",function(a,b,d){var c=this.getUnitCell();null!=c&&c.toFractional(this,d);switch(a){case 1111492615:case 1111492612:this.x=b;break;case 1111492616:case 1111492613:this.y=b;break;case 1111492617:case 1111492614:this.z=b}null!=c&&c.toCartesian(this,d)},"~N,~N,~B");c(c$,"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=u(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,j=u(c.sD/2);if(g<e-j)return!0;a=c.sX-a;b=c.sY-b;b=j*j-(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?
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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});h(c$,"getBioStructureTypeName",function(){return this.group.getProteinStructureType().getBioStructureTypeName(!0)});
h(c$,"equals",function(a){return this===a},"~O");h(c$,"hashCode",function(){return this.i});c(c$,"findAromaticNeighbor",function(a){if(null==this.bonds)return null;for(var b=this.bonds.length;0<=--b;){var d=this.bonds[b],c=d.getOtherAtom(this);if(d.isAromatic()&&c.i!=a)return c}return null},"~N");c(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?u(this.sX/2):this.sX;case 1111490572:return a.getScreenHeight()-(a.antialiased?
u(this.sY/2):this.sY);case 1111490573:return a.antialiased?u(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$,"getNominalMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getNaturalIsotope(this.getElementNumber())});
h(c$,"getMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getAtomicMass(this.getElementNumber())});c(c$,"atomPropertyString",function(a,b){var d;switch(b){case 1086324739:return d=this.altloc,"\x00"==d?"":""+d;case 1086326786:return this.getAtomName();case 1086326785:return this.getAtomType();case 1086326788:return this.getChainIDStr();case 1086324752:return this.getCIPChirality(!0);case 1086324753:return this.getCIPChiralityRule();case 1086324744:return this.getGroup1("?");
case 1086324747:return d=this.group.getSeqcodeString(),null==d?"":d;case 1086324743:return this.getGroup1("\x00");case 1086324742:return this.getGroup3(!1);case 1086326789:return this.getElementSymbolIso(!0);case 1086324745:return this.getIdentity(!0);case 1086324746:return d=this.group.getInsertionCode(),"\x00"==d?"":""+d;case 1825200146:case 1287653388:return d=a.shm.getShapePropertyIndex(5,"label",this.i),null==d&&(d=""),d;case 1639976963:return this.group.getProteinStructureType().getBioStructureTypeName(!1);
case 1237320707:return this.group.getProteinStructureSubType().getBioStructureTypeName(!1);case 1086324749:return this.group.getStructureId();case 1086324748:return a.getHybridizationAndAxes(this.i,null,null,"d");case 1086326798:return this.getElementSymbolIso(!1);case 1088421903:return this.getSymmetryOperatorList(!0)}return""},"JV.Viewer,~N");h(c$,"getCIPChirality",function(a){var b=(this.formalChargeAndFlags&496)>>4;0==b&&(1<this.atomicAndIsotopeNumber&&a)&&(b=this.group.chain.model.ms.getAtomCIPChiralityCode(this),
this.formalChargeAndFlags|=(0==b?3:b)<<4);return JV.JC.getCIPChiralityName(b)},"~B");c(c$,"getCIPChiralityRule",function(){var a=0==this.getCIPChirality(!0).length?-1:(this.formalChargeAndFlags&3584)>>9;return JV.JC.getCIPRuleName(a+1)});h(c$,"setCIPChirality",function(a){this.formalChargeAndFlags=this.formalChargeAndFlags&-4081|a<<4},"~N");h(c$,"getCIPChiralityCode",function(){return(this.formalChargeAndFlags&496)>>4});h(c$,"getInsertionCode",function(){return this.group.getInsertionCode()});c(c$,
"atomPropertyTuple",function(a,b,d){switch(b){case 1073742329:return JU.P3.newP(this);case 1145047051:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d);case 1145047053:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d);case 1145045006:return this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d):this.getFractionalUnitCoordPt(!a.g.legacyJavaFloat,!1,d);case 1145047052:return JU.P3.new3(a.antialiased?u(this.sX/2):this.sX,a.getScreenHeight()-(a.antialiased?
u(this.sY/2):this.sY),a.antialiased?u(this.sZ/2):this.sZ);case 1145047055:return this.getVibrationVector();case 1145045008:return a=this.getModulation(),null==a?null:a.getV3();case 1145047050:return this;case 1765808134:return JU.CU.colorPtFromInt(this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom),d)}return null},"JV.Viewer,~N,JU.P3");h(c$,"getOffsetResidueAtom",function(a,b){return this.group.getAtomIndex(a,b)},"~S,~N");h(c$,"isCrossLinked",function(a){return this.group.isCrossLinked(a.group)},
"JU.Node");h(c$,"getCrossLinkVector",function(a,b,d){return this.group.getCrossLinkVector(a,b,d)},"JU.Lst,~B,~B");h(c$,"toString",function(){return this.getInfo()});h(c$,"findAtomsLike",function(a){return this.group.chain.model.ms.vwr.getAtomBitSet(a)},"~S");c(c$,"getUnitID",function(a){var b=this.group.chain.model;return b.isBioModel?b.getUnitID(this,a):""},"~N");h(c$,"getFloatProperty",function(a){a=this.group.chain.model.ms.vwr.getDataObj(a,null,1);var b=NaN;if(null!=a)try{b=a[this.i]}catch(d){if(!D(d,
Exception))throw d;}return b},"~S");h(c$,"modelIsRawPDB",function(){var a=this.group.chain.model;return a.isBioModel&&!a.isPdbWithMultipleBonds&&0==a.hydrogenCount});G(c$,"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)});m("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 $.Logger $.Parser $.Vibration".split(" "),function(){c$=w(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.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;X("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();this.atomCapacity=0;s(this,arguments)},JM,"AtomCollection");c(c$,"getAtom",function(a){return 0<=a&&a<this.at.length?this.at[a]:null},"~N");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(null!=c&&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=L(this.ac,0),b=this.ac;0<=--b;)a[b]=null==this.at[b]?0: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$,"findMaxRadii",function(){for(var a,b=this.ac;0<=--b;){var d=this.at[b];if(null!=d){if((a=d.getBondingRadius())>this.maxBondingRadius)this.maxBondingRadius=a;if((a=d.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO))>this.maxVanderwaalsRadius)this.maxVanderwaalsRadius=a}}});c(c$,"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){null!=this.at[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$,"calculateSurface",function(a,b){0>b&&(b=3);var d=J.api.Interface.getOption("geodesic.EnvelopeCalculation",this.vwr,"ms").set(this.vwr,this.ac,null);d.calculate(new J.atomdata.RadiusData(null,b,J.atomdata.RadiusData.EnumType.ABSOLUTE,null),3.4028235E38,a,JU.BSUtil.copyInvert(a,this.ac),!1,!1,!1,!0);var c=d.getPoints();this.surfaceDistanceMax=0;this.bsSurface=d.getBsSurfaceClone();
this.surfaceDistance100s=B(this.ac,0);this.nSurfaceAtoms=JU.BSUtil.cardinalityOf(this.bsSurface);if(0==this.nSurfaceAtoms||null==c||0==c.length)return c;for(var d=3.4028235E38==b?0:b,g=0;g<this.ac;g++)if(this.bsSurface.get(g)||null==this.at[g])this.surfaceDistance100s[g]=0;else{for(var e=3.4028235E38,j=this.at[g],l=c.length;0<=--l;)e=Math.min(Math.abs(c[l].distance(j)-d),e);e=this.surfaceDistance100s[g]=u(Math.floor(100*e));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,e)}return c},"JU.BS,~N");
c(c$,"setAtomCoord2",function(a,b,d){var c=null,g=null,e=null,j=0,l=1;if(t(d,JU.P3))c=d;else if(t(d,JU.Lst)){e=d;if(0==(l=e.size()))return;j=1}else if(JU.AU.isAP(d)){g=d;if(0==(l=g.length))return;j=2}else return;d=0;if(null!=a)for(var h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){switch(j){case 1:if(d>=l)return;c=e.get(d++);break;case 2:if(d>=l)return;c=g[d++]}if(null!=c)switch(b){case 1145047050:this.setAtomCoord(h,c.x,c.y,c.z);break;case 1145047051:this.at[h].setFractionalCoordTo(c,!0);this.taintAtom(h,
2);break;case 1145047053:this.at[h].setFractionalCoordTo(c,!1);this.taintAtom(h,2);break;case 1145047055:this.setAtomVibrationVector(h,c)}}},"JU.BS,~N,~O");c(c$,"setAtomVibrationVector",function(a,b){this.setVibrationVector(a,b);this.taintAtom(a,12)},"~N,JU.T3");c(c$,"setAtomCoord",function(a,b,d,c){if(!(0>a||a>=this.ac)){var g=this.at[a];g.set(b,d,c);this.fixTrajectory(g);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"fixTrajectory",function(a){this.isTrajectory(a.mi)&&this.trajectory.fixAtom(a)},"JM.Atom");
c(c$,"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,j){var l=0;if(!(null!=e&&0==e.length||null==a)){for(var h=null!=e&&e.length==this.ac||null!=j&&j.length==this.ac,r=a.nextSetBit(0);0<=r;r=a.nextSetBit(r+
1)){h&&(l=r);if(null!=e){if(l>=e.length)return;c=e[l++];if(Float.isNaN(c))continue;d=C(c)}else if(null!=j){if(l>=j.length)return;g=j[l++]}var n=this.at[r],q;switch(b){case 1086326786:this.setAtomName(r,g,!0);break;case 1086326785:this.setAtomType(r,g);break;case 1086326788:this.setChainID(r,g);break;case 1094715393:this.setAtomNumber(r,d,!0);break;case 1094713365:this.setAtomSeqID(r,d);break;case 1111492609:case 1111492629:this.setAtomCoord(r,c,n.y,n.z);break;case 1111492610:case 1111492630:this.setAtomCoord(r,
n.x,c,n.z);break;case 1111492611:case 1111492631:this.setAtomCoord(r,n.x,n.y,c);break;case 1111492626:case 1111492627:case 1111492628:this.setVibrationVector2(r,b,c);break;case 1111492612:case 1111492613:case 1111492614:n.setFractionalCoord(b,c,!0);this.taintAtom(r,2);break;case 1111492615:case 1111492616:case 1111492617:n.setFractionalCoord(b,c,!1);this.taintAtom(r,2);break;case 1094715402:case 1086326789:this.setElement(n,d,!0);break;case 1631586315:this.resetPartialCharges();n.setFormalCharge(d);
this.taintAtom(r,4);break;case 1113589786:this.setHydrophobicity(r,c);break;case 1128269825:q=2>c&&0.01<=c?100*c:c;this.setOccupancy(r,q,!0);break;case 1111492619:this.setPartialCharge(r,c,!0);break;case 1111492618:this.setBondingRadius(r,c);break;case 1111492620:this.setBFactor(r,c,!0);break;case 1094715412:this.setAtomResno(r,d);break;case 1825200146:case 1287653388:this.vwr.shm.setAtomLabel(g,r);break;case 1665140738:case 1112152075:q=c;0>q?q=0:16<q&&(q=16.1);n.madAtom=ea(2E3*q);break;case 1113589787:this.vwr.slm.setSelectedAtom(n.i,
0!=c);break;case 1094715417:n.setValence(d);this.taintAtom(r,10);break;case 1648363544:n.setRadius(c)?this.taintAtom(r,11):this.untaint(r,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 t(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);t(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$,"setAtomNumber",
function(a,b,d){d&&b==this.at[a].getAtomNumber()||(null==this.atomSerials&&(this.atomSerials=B(this.at.length,0)),this.atomSerials[a]=b,d&&this.taintAtom(a,13))},"~N,~N,~B");c(c$,"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=B(this.at.length,0)),this.atomResnos[a]=b,this.taintAtom(a,15))},"~N,~N");c(c$,"setAtomSeqID",function(a,b){b!=this.at[a].getSeqID()&&(null==this.atomSeqIDs&&(this.atomSeqIDs=B(this.at.length,0)),this.atomSeqIDs[a]=b,this.taintAtom(a,14))},"~N,~N");c(c$,"setOccupancy",function(a,b,d){if(!(d&&b==this.at[a].getOccupancy100())){if(null==this.occupancies){if(100==b)return;
this.occupancies=L(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$,"setPartialCharge",function(a,b,d){if(!Float.isNaN(b)){if(null==this.partialCharges){this.bsPartialCharges=new JU.BS;if(0==b)return;this.partialCharges=L(this.at.length,0)}this.bsPartialCharges.set(a);this.partialCharges[a]=b;d&&this.taintAtom(a,8)}},"~N,~N,~B");c(c$,"setBondingRadius",function(a,b){Float.isNaN(b)||b==this.at[a].getBondingRadius()||
(null==this.bondingRadii?this.bondingRadii=L(this.at.length,0):this.bondingRadii.length<this.at.length&&(this.bondingRadii=JU.AU.ensureLength(this.bondingRadii,this.at.length)),this.bondingRadii[a]=b,this.taintAtom(a,6))},"~N,~N");c(c$,"setBFactor",function(a,b,d){if(!(Float.isNaN(b)||d&&b==this.at[a].getBfactor100())){if(null==this.bfactor100s){if(0==b)return;this.bfactor100s=W(this.at.length,0)}this.bfactor100s[a]=za(100*(-327.68>b?-327.68:327.67<b?327.67:b)+(0>b?-0.5:0.5));d&&this.taintAtom(a,
9)}},"~N,~N,~B");c(c$,"setHydrophobicity",function(a,b){if(!(Float.isNaN(b)||b==this.at[a].getHydrophobicity())){if(null==this.hydrophobicities){this.hydrophobicities=L(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$,"setAtomData",function(a,b,d,c){var g=null,e=null;switch(a){case 2:this.loadCoordinates(d,!1,!c);return;case 12:this.loadCoordinates(d,!0,
!0);return;case 17:g=L(this.ac,0),e=JU.BS.newN(this.ac)}c=JU.Parser.markLines(d,";");var j=0;try{for(var l=JU.PT.parseInt(d.substring(0,c[0]-1)),h=1;h<=l;h++){var r=JU.PT.getTokens(JU.PT.parseTrimmed(d.substring(c[h],c[h+1]-1))),n=JU.PT.parseInt(r[0])-1;if(!(0>n||n>=this.ac)){var q=this.at[n];j++;var z=r.length-1,A=JU.PT.parseFloat(r[z]);switch(a){case 17:g[n]=A;e.set(n);continue;case 0:this.setAtomName(n,r[z],!0);break;case 13:this.setAtomNumber(n,C(A),!0);break;case 15:this.setAtomResno(n,C(A));
break;case 14:this.setAtomSeqID(n,C(A));break;case 1:this.setAtomType(n,r[z]);break;case 16:this.setChainID(n,r[z]);break;case 3:q.setAtomicAndIsotopeNumber(C(A));q.paletteID=J.c.PAL.CPK.id;q.colixAtom=this.vwr.cm.getColixAtomPalette(q,J.c.PAL.CPK.id);break;case 4:q.setFormalCharge(C(A));break;case 5:this.setHydrophobicity(n,A);break;case 6:this.setBondingRadius(n,A);break;case 8:this.setPartialCharge(n,A,!0);break;case 9:this.setBFactor(n,A,!0);break;case 10:q.setValence(C(A));break;case 11:q.setRadius(A)}this.taintAtom(n,
a)}}17==a&&0<j&&this.vwr.setData(b,v(-1,[b,g,e,Integer.$valueOf(1)]),0,0,0,0,0)}catch(m){if(D(m,Exception))JU.Logger.error("AtomCollection.loadData error: "+m);else throw m;}},"~N,~S,~S,~B");c(c$,"loadCoordinates",function(a,b,d){var c=JU.Parser.markLines(a,";"),g=b?new JU.V3:null;try{for(var e=JU.PT.parseInt(a.substring(0,c[0]-1)),j=1;j<=e;j++){var l=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[j],c[j+1]))),h=JU.PT.parseInt(l[0])-1,r=l[3].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(l[3]),
n=l[4].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(l[4]),q=JU.PT.parseFloat(l[5]);b?(g.set(r,n,q),this.setAtomVibrationVector(h,g)):(this.setAtomCoord(h,r,n,q),d||this.untaint(h,2))}}catch(z){if(D(z,Exception))JU.Logger.error("Frame.loadCoordinate error: "+z);else throw z;}},"~S,~B,~B");c(c$,"validateBspf",function(a){null!=this.bspf&&(this.bspf.isValid=a)},"~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,j,l=this.ac;0<=--l;)if(!(null!=c&&c.get(l)||null==(j=this.at[l])))j.isClickable()&&this.isCursorOnTopOf(j,a,b,g,e)&&(e=j);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=B(this.ac,0);var d=0!=(b&2);d&&(a.atomRadius=L(this.ac,0));for(var c=0!=(b&16),g=0;g<this.ac;g++){var e=this.at[g];null==e||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){var g=256==(c&256),e=512==(c&512),j=4==(c&4),l=2048==(c&2048);c=4096==(c&4096);var h=new JU.V3,r=new JU.V3,n=Array(this.ac),q=this.vwr.slm.bsDeleted,z,A=0;if(null!=a)for(var m=a.nextSetBit(0);0<=m;m=a.nextSetBit(m+1))if(!(null!=q&&q.get(m))){var p=this.at[m],s=p.getElementNumber();if(!(e&&6!=s)){var t=6>=s?1.1:10>=s?1:1.3;switch(s){case 7:case 8:t=1}z=g||l||c?p.getCovalentHydrogenCount():0;if(!(g&&0<z||l&&0==z)){var u=this.getMissingHydrogenCount(p,!1);if(!(g&&0==u)){l||(z=u);var u=this.aaRet[0],
w=this.aaRet[2],v=this.aaRet[3]-(l?z:0);if(!(0==v&&p.isHetero())){n[m]=Array(z);var x=0;if(0==v)switch(z){case 4:h.set(0.635,0.635,0.635),z=JU.P3.newP(h),z.add(p),n[m][x++]=z,null!=d&&d.addLast(p);case 3:h.set(-0.635,-0.635,0.635),z=JU.P3.newP(h),z.add(p),n[m][x++]=z,null!=d&&d.addLast(p);case 2:h.set(-0.635,0.635,-0.635),z=JU.P3.newP(h),z.add(p),n[m][x++]=z,null!=d&&d.addLast(p);case 1:h.set(0.635,-0.635,-0.635),z=JU.P3.newP(h),z.add(p),n[m][x++]=z,null!=d&&d.addLast(p)}else switch(z){case 3:this.getHybridizationAndAxes(m,
s,h,r,"sp3b",!1,!0,j);z=new JU.P3;z.scaleAdd2(t,h,p);n[m][x++]=z;null!=d&&d.addLast(p);this.getHybridizationAndAxes(m,s,h,r,"sp3c",!1,!0,j);z=new JU.P3;z.scaleAdd2(t,h,p);n[m][x++]=z;null!=d&&d.addLast(p);this.getHybridizationAndAxes(m,s,h,r,"sp3d",!1,!0,j);z=new JU.P3;z.scaleAdd2(t,h,p);n[m][x++]=z;null!=d&&d.addLast(p);break;case 2:w=2==w||5==s||1==v&&4==u||7==s&&this.isAdjacentSp2(p);this.getHybridizationAndAxes(m,s,h,r,w?"sp2b":3==u?"sp3c":"lpa",!1,!0,j);z=JU.P3.newP(h);z.scaleAdd2(t,h,p);n[m][x++]=
z;null!=d&&d.addLast(p);this.getHybridizationAndAxes(m,s,h,r,w?"sp2c":3==u?"sp3d":"lpb",!1,!0,j);z=JU.P3.newP(h);z.scaleAdd2(t,h,p);n[m][x++]=z;null!=d&&d.addLast(p);break;case 1:switch(u-v){case 1:if(8==s&&p===p.group.getCarbonylOxygenAtom()){n[m]=null;continue}null!=this.getHybridizationAndAxes(m,s,h,r,2==w||5==s||6==s&&1==this.aaRet[1]||7==s&&(new Boolean((new Boolean(p.group.getNitrogenAtom()===p&0==p.getFormalCharge())).valueOf()||this.isAdjacentSp2(p))).valueOf()?"sp2c":"sp3d",!0,!1,j)?(z=JU.P3.newP(h),
z.scaleAdd2(t,h,p),n[m][x++]=z,null!=d&&d.addLast(p)):n[m]=[];break;case 2:this.getHybridizationAndAxes(m,s,h,r,4==u?"sp2c":"sp2b",!1,!1,j);z=JU.P3.newP(h);z.scaleAdd2(t,h,p);n[m][x++]=z;null!=d&&d.addLast(p);break;case 3:this.getHybridizationAndAxes(m,s,h,r,"spb",!1,!0,j),z=JU.P3.newP(h),z.scaleAdd2(t,h,p),n[m][x++]=z,null!=d&&d.addLast(p)}}A+=x}}}}}b[0]=A;return n},"JU.BS,~A,JU.Lst,~N");c(c$,"isAdjacentSp2",function(a){for(var b=a.bonds,d=0;d<b.length;d++)for(var c=b[d].getOtherAtom(a).bonds,g=
0;g<c.length;g++)switch(c[g].getCovalentOrder()){case 2:case 3:return!0}return!1},"JM.Atom");c(c$,"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=B(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,j,l){var h=0<g.length&&"-"==g.charAt(0)?g.substring(1):g;if(0<=g.indexOf("d")&&!g.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,d,c,h);g=this.at[a];0==b&&(b=g.getElementNumber());var r=this.getAttached(g,4,e,l),n=r.length,q=h.charCodeAt(h.length-1)-97;if(0>q||6<q)q=0;d.set(0,0,0);c.set(0,0,0);for(var z=Array(4),A=0;A<n;A++){var m=r[A];if(null==m){n=A;break}z[A]=JU.V3.newVsub(g,m);z[A].normalize();d.add(z[A])}0<n&&c.setT(z[0]);m=!1;a=new JU.V3;if(3<=n){2.984513>c.angle(z[1])?
a.cross(c,z[1]):a.cross(c,z[2]);a.normalize();var p=new JU.V3;2.984513>z[1].angle(z[2])?p.cross(z[1],z[2]):p.cross(c,z[2]);p.normalize();m=0.95<=Math.abs(p.dot(a))}var A=0==h.indexOf("sp3"),s=!A&&0==h.indexOf("sp2"),t=!A&&!s&&0==h.indexOf("sp"),u=0==h.indexOf("p"),w=0==h.indexOf("lp"),p=null;if(e){if(0==n)return null;if(A){if(3<q||4<n)return null}else if(s){if(2<q||3<n)return null}else if(t&&(1<q||2<n))return null;switch(n){case 1:if(1==b&&!A)return null;if(A){p="sp3";break}switch(r[0].getCovalentBondCount()){case 1:if(2!=
r[0].getValence()){p="sp";break}case 2:p=t?"sp":"sp2";break;case 3:if(!s&&!u)return null;p="sp2"}break;case 2:if(0.1>d.length()){if(0<=h.indexOf("2")||0<=h.indexOf("3"))return null;p="sp";break}p=A?"sp3":"sp2";if(0==h.indexOf("sp"))break;if(w){p="lp";break}p=h;break;default:if(m&&!l)p="sp2";else{m&&d.setT(a);if(w&&3==n){p="lp";break}p="sp3"}}if(null==p)return null;if(0==h.indexOf("p")){if("sp3"===p)return null}else if(0>h.indexOf(p))return null}if(q<n&&!h.startsWith("p")&&!h.startsWith("l"))return d.sub2(r[q],
g),d.normalize(),p;switch(n){case 0:h.equals("sp3c")||h.equals("sp2d")||h.equals("lpa")?d.set(-0.5,-0.7,1):h.equals("sp3b")||h.equals("lpb")?d.set(0.5,-0.7,-1):h.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(A){for(A=r[0].getBondCount();0<=--A;)if(r[0].bonds[A].isCovalent()&&r[0].getBondedAtomIndex(A)!=g.i&&(c.sub2(r[0],r[0].bonds[A].getOtherAtom(r[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!=q&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(d.x,d.y,d.z,2.09439507*(2==q?1:-1))).rotate(c));d.setT(c);c.cross(a,d);break}a.cross(c,d);switch(r[0].getCovalentBondCount()){case 1:if(2!=r[0].getValence())break;case 2:j=r[0];c.setT(d);for(a.setT(JM.AtomCollection.vRef);null!=j&&2==j.getCovalentBondCount();){l=j.bonds;m=null;for(A=0;A<l.length;A++)if(l[A].isCovalent()&&(m=l[A].getOtherAtom(j),
m!==g)){a.sub2(m,j);break}a.cross(a,c);if(0.1<a.length()||2!=m.getCovalentBondCount())break;g=j;j=m}t||(0.1<a.length()?(d.cross(a,c),d.normalize(),1==q&&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(r[0].i,0,c,a,"pz",!1,j,l),a.setT(c),s?(c.cross(c,d),1==q&&c.scale(-1),c.scale(JM.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,d,c)):t||(a.setT(d),
d.setT(c)),c.cross(a,d)}break;case 2:if(0.1>d.length()){if(!h.equals("pz")){m=r[0];(b=3==m.getCovalentBondCount())||(b=3==(m=r[1]).getCovalentBondCount());if(b){this.getHybridizationAndAxes(m.i,0,c,d,"pz",!1,j,l);h.equals("px")&&c.scale(-1);d.setT(z[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(s){c.cross(d,a);break}if(A||w){a.normalize();d.normalize();h.equals("lp")||(0==q||2==q?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(A)break;if(!m){c.cross(d,c);break}d.setT(a);0>d.z&&j&&(d.scale(-1),c.scale(-1))}c.normalize();d.normalize();return p},"~N,~N,JU.V3,JU.V3,~S,~B,~B,~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,!1);if(null==c)return null==b?null:"?";var j=c.length;if(3>j&&null!=b)return null;for(var l=e>=j,h=u(j*(j-1)/2),r=JU.AU.newInt2(h),n=B(3,0),h=B(3,h,0),q=0,z=0,A=0;A<j-1;A++)for(var m=A+1;m<j;m++){var p=JU.Measure.computeAngleABC(c[A],a,c[m],!0),p=105>p?0:150<=p?2:1;h[p][n[p]]=q;n[p]++;r[q++]=B(-1,[A,m]);0==A&&1==p&&z++}q=100*n[0]+10*n[1]+n[2];if(null==b)switch(q){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==z%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(q){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(l)if(g)switch(n[1]){case 0:b.sub2(c[r[h[0][0]][0]],a);d.sub2(c[r[h[0][0]][1]],a);b.cross(b,d);b.normalize();4==e&&b.scale(-1);n=this.findNotAttached(j,r,h[2],n[2]);A=n.nextSetBit(0);d.sub2(c[A],a);d.normalize();d.scale(0.5);b.scaleAdd2(JM.AtomCollection.sqrt3_2,b,d);e=-1;break;case 1:4==e?(d=r[h[1][0]],b.add2(c[d[0]],c[d[1]]),b.scaleAdd2(-2,a,b),e=-1):(n=this.findNotAttached(j,
r,h[1],n[1]),e=n.nextSetBit(0));break;default:n=this.findNotAttached(j,r,h[1],n[1]),e=n.nextSetBit(0)}else{q=!1;if(4==j)switch(n[2]){case 1:n=this.findNotAttached(j,r,h[2],n[2]);A=n.nextSetBit(0);e=4==e?A:n.nextSetBit(A+1);break;default:q=!0}else{n=this.findNotAttached(j,r,h[2],n[2]);A=n.nextSetBit(0);for(m=j;m<e&&0<=A;m++)A=n.nextSetBit(A+1);-1==A?q=!0:e=A}q&&(b.sub2(c[r[h[0][0]][0]],a),d.sub2(c[r[h[0][0]][1]],a),b.cross(b,d),4==e&&b.scale(-1),e=-1)}0<=e&&b.sub2(c[e],a);l&&b.scale(-1);b.normalize();
return g?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(c$,"getAttached",function(a,b,d,c){var g=a.getCovalentBondCount();if(g>b)return null;b=Array(g);if(0<g){for(var g=a.bonds,e=0,j=0;j<g.length;j++)if(g[j].isCovalent()){var l=g[j].getOtherAtom(a);if(!c||1!=l.getAtomicAndIsotopeNumber())b[e++]=l}d&&!c&&java.util.Arrays.sort(b,R(JM.AtomCollection.AtomSorter,this,null))}return b},"JM.Atom,~N,~B,~B");c(c$,"findNotAttached",function(a,b,d,c){var g=JU.BS.newN(a);g.setBits(0,a);for(var e=0;e<a;e++)for(var j=
0;j<c;j++){var l=b[d[j]];(l[0]==e||l[1]==e)&&g.clear(e)}return g},"~N,~A,~A,~N");c(c$,"getAtomBitsMDa",function(a,b,d){var c=t(b,Integer)?b.intValue():0;switch(a){case 1086326786:case 1086326785:var g=1086326785==a,e=","+b+",";for(a=this.ac;0<=--a;)null!=this.at[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;)null!=this.at[a]&&this.at[a].getAtomNumber()==c&&d.set(a);return d;case 2097155:for(a=this.ac;0<=
--a;)null!=this.at[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;)null!=this.at[a]&&this.at[a].getElementNumber()==c&&d.set(a);return d;case 1612709894:for(a=this.ac;0<=--a;)null!=this.at[a]&&this.at[a].isHetero()&&d.set(a);return d;case 1073741824:return this.getIdentifierOrNull(b);
case 2097165:for(a=this.ac;0<=--a;)null!=this.at[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;)null!=this.at[a]&&this.at[a].getResno()==c&&d.set(a);return d;case 1612709912:b=B(2,0);for(a=this.ac;0<=--a;)if(null!=this.at[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,
j=0,l=c.length;0<=--l&&3>j;)if(c[l].isCovalent()&&1==(e=c[l].getOtherAtom(g)).getElementNumber())b[j++%2]=e.i;2==j&&(d.set(b[1]),d.set(b[0]),d.set(a))}return d;case 1073742355:for(a=this.ac;0<=--a;)null!=this.at[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;)null!=this.at[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;)null!=this.at[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;)null!=this.at[a]&&this.at[a].group.getInsCode()==c&&d.set(a);return d;case 1296041986:for(a=this.ac;0<=--a;)null!=this.at[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;)null!=this.at[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;)null!=this.at[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$,"getChainBits",function(a){var b=this.vwr.getBoolean(603979822);b?97<=a&&122>=a&&(a+=159):0<=a&&300>a&&(a=this.chainToUpper(a));for(var d=new JU.BS,c=JU.BS.newN(this.ac),g,e=c.nextClearBit(0);e<this.ac;e=c.nextClearBit(e+
1))if(null!=this.at[e]){var j=this.at[e].group.chain;a==(g=j.chainID)||!b&&0<=g&&300>g&&a==this.chainToUpper(g)?(j.setAtomBits(d),c.or(d)):j.setAtomBits(c)}return d},"~N");c(c$,"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,j=JM.Group.getInsertionCodeChar(a);switch(j){case "?":for(var l=this.ac;0<=--l;)if(null!=this.at[l]){var h=this.at[l].group.seqcode;if((!g||c==JM.Group.getSeqNumberFor(h))&&0!=JM.Group.getInsertionCodeFor(h))d.set(l),e=!1}break;default:for(l=this.ac;0<=--l;)if(null!=this.at[l]&&(h=this.at[l].group.seqcode,a==h||!g&&a==JM.Group.getInsertionCodeFor(h)||"*"==j&&c==JM.Group.getSeqNumberFor(h)))d.set(l),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$,"getSpecNameOrNull",function(a,b){var d=null;a=a.toUpperCase();0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));
var c=a.startsWith("?*");c&&(a=a.substring(1));for(var g=this.ac;0<=--g;)if(null!=this.at[g]){var e=this.at[g].getGroup3(!0);if(null!=e&&0<e.length){if(JU.PT.isMatch(e,a,b,!0)){null==d&&(d=JU.BS.newN(g+1));for(d.set(g);0<=--g&&this.at[g].getGroup3(!0).equals(e);)d.set(g);g++}}else this.isAtomNameMatch(this.at[g],a,b,c)&&(null==d&&(d=JU.BS.newN(g+1)),d.set(g))}return d},"~S,~B");c(c$,"isAtomNameMatch",function(a,b,d,c){return JU.PT.isMatch(a.getAtomName().toUpperCase(),b,d,c)},"JM.Atom,~S,~B,~B");
c(c$,"getAtomIndices",function(a){for(var b=0,d=B(this.ac,0),c=a.nextSetBit(0);0<=c&&c<this.ac;c=a.nextSetBit(c+1))d[c]=++b;return d},"JU.BS");c(c$,"getAtomsNearPlane",function(a,b){for(var d=new JU.BS,c=this.ac;0<=--c;){var g=this.at[c];if(null!=g){var 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;)null!=this.at[b]&&this.at[b].isVisible(1)&&a.set(b)},"JU.BS");c(c$,"getVisibleSet",function(a){if(a)this.vwr.setModelVisibility(),this.vwr.shm.finalizeAtoms(null,!0);else if(this.haveBSVisible)return this.bsVisible;this.bsVisible.clearAll();for(a=this.ac;0<=--a;)null!=this.at[a]&&this.at[a].checkVisible()&&this.bsVisible.set(a);null!=this.vwr.shm.bsSlabbedInternal&&this.bsVisible.andNot(this.vwr.shm.bsSlabbedInternal);this.haveBSVisible=!0;return this.bsVisible},
"~B");c(c$,"getClickableSet",function(a){if(a)this.vwr.setModelVisibility();else if(this.haveBSClickable)return this.bsClickable;this.bsClickable.clearAll();for(a=this.ac;0<=--a;)null!=this.at[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 j=g.get(e);(a.get(j.atomIndex1)||0<=j.atomIndex2&&a.get(j.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$,"getTensorList",function(a){for(var b=
-1,d=!1,c=a.size(),g=c;0<=--g;){var e=a.get(g);e.forThermalEllipsoid?b=g:2==e.iType&&(d=!0)}var j=Array((0<=b||!d?0:1)+c);if(0<=b&&(j[0]=a.get(b),1==a.size()))return j;if(d){b=0;for(g=c;0<=--g;)e=a.get(g),e.forThermalEllipsoid||(j[++b]=e)}else for(g=0;g<c;g++)j[g]=a.get(g);return j},"JU.Lst");c(c$,"getAtomTensor",function(a,b){var d=this.getAtomTensorList(a);if(null!=d&&null!=b){b=b.toLowerCase();for(var c=0;c<d.length;c++){var g=d[c];if(null!=g&&(b.equals(g.type)||b.equals(g.altType)))return g}}return null},
"~N,~S");c(c$,"getAllAtomTensors",function(a){if(null==this.atomTensors)return null;if(null!=a)return this.atomTensors.get(a.toLowerCase());a=new JU.Lst;for(var b,d=this.atomTensors.entrySet().iterator();d.hasNext()&&((b=d.next())||1);)a.addAll(b.getValue());return a},"~S");c(c$,"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(){N(self.c$);c$=w(function(){$(this,arguments);s(this,arguments)},JM.AtomCollection,"AtomSorter",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.i>b.i?1:a.i<b.i?-1:0},"JM.Atom,JM.Atom");c$=M()};G(c$,"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);G(c$,"userSettableValues",null,"TAINT_ATOMNAME",0,"TAINT_ATOMTYPE",1,"TAINT_COORD",2,"TAINT_ELEMENT",3,"TAINT_FORMALCHARGE",4,"TAINT_HYDROPHOBICITY",5,"TAINT_BONDINGRADIUS",6,"TAINT_OCCUPANCY",7,"TAINT_PARTIALCHARGE",8,"TAINT_TEMPERATURE",9,"TAINT_VALENCE",10,"TAINT_VANDERWAALS",11,"TAINT_VIBRATION",12,"TAINT_ATOMNO",13,"TAINT_SEQID",14,"TAINT_RESNO",15,"TAINT_CHAIN",16,"TAINT_MAX",17,"CALC_H_DOALL",256,"CALC_H_JUSTC",512,"CALC_H_HAVEH",1024,"CALC_H_QUICK",4,"CALC_H_IGNORE_H",
2048,"CALC_H_ALLOW_H",4096)});m("JM");x(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){c$=w(function(){this.bspf=this.cubeIterator=null;this.isZeroBased=this.hemisphereOnly=this.threadSafe=!1;this.modelIndex=2147483647;this.atomIndex=-1;this.distanceSquared=this.zeroBase=0;this.bsSelected=null;this.checkGreater=this.isGreaterOnly=!1;this.radiusData=null;this.vdw1=0;this.isVdw=!1;this.vwr=this.atoms=null;this.iNext=0;s(this,arguments)},JM,"AtomIteratorWithinModel",
null,J.api.AtomIndexIterator);p(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");h(c$,"setModel",function(a,b,d,c,g,e,j){this.threadSafe&&(b=-1-b);if(b!=this.modelIndex||null==this.cubeIterator)this.cubeIterator=this.bspf.getCubeIterator(b),this.modelIndex=b;this.zeroBase=this.isZeroBased?d:0;if(-2147483648!=e){this.atomIndex=
0>e?-1:c;if(this.isVdw=null!=j)this.radiusData=j,this.atoms=a.at,this.vwr=a.vwr,e=j.factorType===J.atomdata.RadiusData.EnumType.OFFSET?5+j.value:5*j.value,this.vdw1=this.atoms[c].getVanderwaalsRadiusFloat(this.vwr,j.vdwType);this.checkGreater=this.isGreaterOnly&&2147483647!=c;this.setCenter(g,e)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");h(c$,"setCenter",function(a,b){this.setCenter2(a,b)},"JU.T3,~N");c(c$,"setCenter2",function(a,b){null!=this.cubeIterator&&(this.cubeIterator.initialize(a,
b,this.hemisphereOnly),this.distanceSquared=b*b)},"JU.T3,~N");h(c$,"hasNext",function(){return this.hasNext2()});c(c$,"hasNext2",function(){if(0<=this.atomIndex)for(;this.cubeIterator.hasMoreElements();){var a=this.cubeIterator.nextElement();if((this.iNext=a.i)!=this.atomIndex&&(!this.checkGreater||this.iNext>this.atomIndex)&&(null==this.bsSelected||this.bsSelected.get(this.iNext)))return!0}else if(this.cubeIterator.hasMoreElements())return a=this.cubeIterator.nextElement(),this.iNext=a.i,!0;this.iNext=
-1;return!1});h(c$,"next",function(){return this.iNext-this.zeroBase});h(c$,"foundDistance2",function(){return null==this.cubeIterator?-1:this.cubeIterator.foundDistance2()});h(c$,"addAtoms",function(a){for(var b;this.hasNext();)if(0<=(b=this.next())){var d;if(this.isVdw){d=this.atoms[b].getVanderwaalsRadiusFloat(this.vwr,this.radiusData.vdwType)+this.vdw1;switch(this.radiusData.factorType){case J.atomdata.RadiusData.EnumType.OFFSET:d+=2*this.radiusData.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:d*=
this.radiusData.value}d*=d}else d=this.distanceSquared;this.foundDistance2()<=d&&a.set(b)}},"JU.BS");h(c$,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)});h(c$,"getPosition",function(){return null})});m("JM");x(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){c$=w(function(){this.center=this.bsModels=null;this.distance=0;s(this,arguments)},JM,"AtomIteratorWithinModelSet",JM.AtomIteratorWithinModel);p(c$,function(a){I(this,
JM.AtomIteratorWithinModelSet,[]);this.bsModels=a},"JU.BS");h(c$,"setCenter",function(a,b){this.center=a;this.distance=b;this.set(0)},"JU.T3,~N");c(c$,"set",function(a){if(0>(this.modelIndex=this.bsModels.nextSetBit(a))||null==(this.cubeIterator=this.bspf.getCubeIterator(this.modelIndex)))return!1;this.setCenter2(this.center,this.distance);return!0},"~N");h(c$,"hasNext",function(){return this.hasNext2()?!0:!this.set(this.modelIndex+1)?!1:this.hasNext()})});m("JM");x(["JU.Edge","JV.JC"],"JM.Bond",
["JU.C"],function(){c$=w(function(){this.atom2=this.atom1=null;this.shapeVisibilityFlags=this.colix=this.mad=0;s(this,arguments)},JM,"Bond",JU.Edge);p(c$,function(a,b,d,c,g){I(this,JM.Bond,[]);this.atom1=a;this.atom2=b;this.colix=g;this.setOrder(d);this.setMad(c)},"JM.Atom,JM.Atom,~N,~N,~N");c(c$,"setMad",function(a){this.mad=a;this.setShapeVisibility(0!=a)},"~N");c(c$,"setShapeVisibility",function(a){0!=(this.shapeVisibilityFlags&JM.Bond.myVisibilityFlag)!=a&&(this.atom1.addDisplayedBond(JM.Bond.myVisibilityFlag,
a),this.atom2.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.shapeVisibilityFlags=a?this.shapeVisibilityFlags|JM.Bond.myVisibilityFlag:this.shapeVisibilityFlags&~JM.Bond.myVisibilityFlag)},"~B");c(c$,"getIdentity",function(){return this.index+1+" "+JU.Edge.getBondOrderNumberFromOrder(this.order)+" "+this.atom1.getInfo()+" -- "+this.atom2.getInfo()+" "+this.atom1.distance(this.atom2)});h(c$,"isCovalent",function(){return 0!=(this.order&1023)});h(c$,"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");h(c$,"getAtomIndex1",function(){return this.atom1.i});h(c$,"getAtomIndex2",function(){return this.atom2.i});h(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$,"is",function(a){return(this.order&-131073)==a},"~N");h(c$,"getOtherNode",function(a){return this.atom1===a?this.atom2:this.atom2===a||null==a?this.atom1:null},"JU.SimpleNode");c(c$,"setAtropisomerOptions",function(a,b){b.get(this.atom1.i);var d,c=2147483647,g=this.atom1.bonds;for(d=0;d<g.length;d++){var e=g[d].getOtherAtom(this.atom1);if(e!==this.atom2)break}if(d<g.length){g=this.atom2.bonds;for(c=0;c<g.length&&!(e=g[c].getOtherAtom(this.atom2),e!==this.atom1);c++);}this.order=
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function(){c$=w(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.haveAtropicBonds=this.haveHiddenBonds=!1;s(this,arguments)},JM,"BondCollection",JM.AtomCollection);c(c$,"setupBC",function(){this.bsAromatic=new JU.BS;this.numCached=B(5,0);this.freeBonds=Array(5);for(var a=5;0<--a;)this.freeBonds[a]=Array(200);this.setupAC()});c(c$,"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$,"bondAtoms",function(a,b,d,c,g,e,j,l){d=this.getOrAddBond(a,b,d,c,g,e,!0);l&&(d.order|=131072,j&&(a.group=b.group,a.group.addAtoms(a.i)));return d},
"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B,~B");c(c$,"getOrAddBond",function(a,b,d,c,g,e,j){if(131071==d||65535==d)d=1;a.isBonded(b)?(a=a.getBond(b).index,j&&(this.bo[a].setOrder(d),this.bo[a].setMad(c),t(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$,"addHBond",function(a,b,d,c){this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+250));return this.setBond(this.bondCount++,this.bondMutually(a,b,d,1,c)).index},"JM.Atom,JM.Atom,~N,~N");c(c$,"deleteAllBonds2",function(){this.vwr.setShapeProperty(1,
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A;A=c.nextSetBit(A+1)){var m=this.at[A];if(null!=m.bonds)for(var p=m.bonds.length;0<=--p;)g.get(m.getBondedAtomIndex(p))&&e.set(m.bonds[p].index)}}for(A=e.nextSetBit(0);A<this.bondCount&&0<=A;A=e.nextSetBit(A+1))if(c=this.bo[A],this.isInRange(c.atom1,c.atom2,a,b,l,h,r)&&(j||z==(c.order&-257|131072)||0!=(d&c.order&30720)))n.set(A),q++;0<q&&this.deleteBonds(n,!1);return B(-1,[0,q])},"~N,~N,~N,JU.BS,JU.BS,~B,~B");c(c$,"fixD",function(a,b){return b?-a:a*a},"~N,~B");c(c$,"isInRange",function(a,b,d,c,g,
e,j){var l=a.distanceSquared(b);return j?(j=Math.sqrt(l),a=a.getBondingRadius()+b.getBondingRadius(),(g?j>=a*d:l>=d)&&(e?j<=a*c:l<=c)):l>=d&&l<=c},"JM.Atom,JM.Atom,~N,~N,~B,~B,~B");c(c$,"dBb",function(a,b){var d=a.nextSetBit(0);if(!(0>d)){this.resetMolecules();for(var c=-1,g=a.cardinality(),e=d;e<this.bondCount;++e){var j=this.bo[e];if(0<g&&a.get(e)){g--;if(!b){var l=j.atom1.mi;l!=c&&this.am[c=l].resetBoundCount()}j.deleteAtomReferences()}else this.setBond(d++,j)}for(c=this.bondCount;--c>=d;)this.bo[c]=
null;this.bondCount=d;d=this.vwr.getShapeProperty(1,"sets");if(null!=d)for(c=0;c<d.length;c++)JU.BSUtil.deleteBits(d[c],a);JU.BSUtil.deleteBits(this.bsAromatic,a)}},"JU.BS,~B");c(c$,"resetAromatic",function(){for(var a=this.bondCount;0<=--a;){var b=this.bo[a];b.isAromatic()&&b.setOrder(515)}});c(c$,"assignAromaticBondsBs",function(a,b){a||(this.bsAromatic=new JU.BS);this.bsAromaticSingle=new JU.BS;this.bsAromaticDouble=new JU.BS;for(var d=null==b,c=d?this.bondCount-1:b.nextSetBit(0),g=c;0<=g;g=d?
g-1:b.nextSetBit(g+1)){var e=this.bo[g];this.bsAromatic.get(g)&&e.setOrder(515);switch(e.order&-131073){case 515:if(!this.assignAromaticMustBeSingle(e.atom1)&&!this.assignAromaticMustBeSingle(e.atom2)){this.bsAromatic.set(g);break}e.order=513;case 513:this.bsAromaticSingle.set(g);break;case 514:this.bsAromaticDouble.set(g)}}for(var c=(d=null==b)?this.bondCount-1:b.nextSetBit(0),j=new JU.BS,g=c;0<=g;g=d?g-1:b.nextSetBit(g+1))e=this.bo[g],e.is(515)&&(!this.bsAromaticDouble.get(g)&&!this.bsAromaticSingle.get(g))&&
(j.set(g),8==e.atom1.getElementNumber()||8==e.atom2.getElementNumber()?this.assignAromaticDouble(e)||this.assignAromaticSingle(e):j.set(g));for(g=j.nextSetBit(0);0<=g;g=j.nextSetBit(g+1))this.assignAromaticDouble(e=this.bo[g])||this.assignAromaticSingle(e);j=new JU.BS;for(g=c;0<=g;g=d?g-1:b.nextSetBit(g+1))if(e=this.bo[g],this.bsAromaticDouble.get(g))e.is(514)||(this.bsAromatic.set(g),j.set(e.atom1.mi),e.setOrder(514));else if((this.bsAromaticSingle.get(g)||e.isAromatic())&&!e.is(513))this.bsAromatic.set(g),
e.setOrder(513);d=this.am;for(g=j.nextSetBit(0);0<=g;g=j.nextSetBit(g+1))d[g].isBioModel&&(d[g].isPdbWithMultipleBonds=!0);this.assignAromaticNandO(b);this.bsAromaticDouble=this.bsAromaticSingle=null},"~B,JU.BS");c(c$,"assignAromaticDouble",function(a){var b=a.index;if(this.bsAromaticSingle.get(b))return!1;if(this.bsAromaticDouble.get(b))return!0;this.bsAromaticDouble.set(b);return!this.assignAromaticSingleForAtom(a.atom1,b)||!this.assignAromaticSingleForAtom(a.atom2,b)?(this.bsAromaticDouble.clear(b),
!1):!0},"JM.Bond");c(c$,"assignAromaticSingle",function(a){var b=a.index;if(this.bsAromaticDouble.get(b))return!1;if(this.bsAromaticSingle.get(b))return!0;this.bsAromaticSingle.set(b);return!this.assignAromaticDoubleForAtom(a.atom1)||!this.assignAromaticDoubleForAtom(a.atom2)?(this.bsAromaticSingle.clear(b),!1):!0},"JM.Bond");c(c$,"assignAromaticSingleForAtom",function(a,b){var d=a.bonds;if(null==d)return!1;for(var c=d.length;0<=--c;){var g=d[c],e=g.index;if(!(e==b||!g.isAromatic()||this.bsAromaticSingle.get(e)))if(this.bsAromaticDouble.get(e)||
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function(a){if(this.assignAromaticMustBeSingle(a.atom1)||this.assignAromaticMustBeSingle(a.atom2))return!1;switch(a.getCovalentOrder()){case 1:case 2:return 3>=a.atom1.getCovalentBondCount()&&3>=a.atom2.getCovalentBondCount();default:return!1}},"JM.Bond");c(c$,"assignAromaticMustBeSingle",function(a){var b=a.getElementNumber();switch(b){case 6:case 7:case 8:case 16:break;default:return!0}var d=a.getValence();switch(b){case 6:return 4==d;case 7:return a.group.getNitrogenAtom()===a||3==d&&1>a.getFormalCharge();
case 8:return a.group.getCarbonylOxygenAtom()!==a&&2==d&&1>a.getFormalCharge();case 16:return 5==a.group.groupID||2==d&&1>a.getFormalCharge()}return!1},"JM.Atom");c(c$,"assignAromaticNandO",function(a){for(var b,d=null==a,c=d?this.bondCount-1:a.nextSetBit(0);0<=c;c=d?c-1:a.nextSetBit(c+1))if(b=this.bo[c],b.is(513)){var g,e=b.atom2,j,l=e.getElementNumber();7==l||8==l?(j=l,g=e,e=b.atom1,l=e.getElementNumber()):(g=b.atom1,j=g.getElementNumber());if(!(7!=j&&8!=j)){var h=g.getValence();if(!(0>h)){var r=
g.getCovalentBondCount();g=g.getFormalCharge();switch(j){case 7:3==h&&(3==r&&1>g&&6==l&&3==e.getValence())&&b.setOrder(514);break;case 8:1==h&&(0==g&&(14==l||16==l))&&b.setOrder(514)}}}}},"JU.BS");c(c$,"getAtomBitsMDb",function(a,b){var d=new JU.BS;switch(a){default:return this.getAtomBitsMDa(a,b,d);case 1677721602:for(var c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))d.set(this.bo[c].atom1.i),d.set(this.bo[c].atom2.i);return d;case 1073742331:for(c=this.bondCount;0<=--c;)this.bo[c].isAromatic()&&(d.set(this.bo[c].atom1.i),
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c(c$,"refresh",function(a){this.value=this.getMeasurement(a);this.isTrajectory=this.ms.isTrajectoryMeasurement(this.countPlusIndices);this.formatMeasurement(null)},"~A");c(c$,"getMeasurementScript",function(a,b){for(var d=new JU.SB,c=a.equals(" "),g=1;g<=this.count;g++)d.append(1<g?a:" ").append(this.getLabel(g,c,b));return d.toString()},"~S,~B");c(c$,"formatMeasurementAs",function(a,b,d){null!=a&&0==a.length&&(a=null);if(d||!(null!=a&&0!=a.indexOf(this.countPlusIndices[0]+":")))this.strFormat=a,
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a.equals("%");if(null==this.property&&(c||a.endsWith("hz"))){var g=this.getAtomIndex(1),e=this.getAtomIndex(2);if(0<=g&&0<=e){var g=this.getAtom(1),e=this.getAtom(2),j=JM.Measurement.nmrType(a),l=!c&&1==j;this.type=c?"percent":l?"dipoleCouplingConstant":3==j?"NOE or 3JHH":"J-CouplingConstant";3==j?(g=this.vwr.getNMRCalculation().getNOEorJHH(v(-1,[g,null,null,e]),11),null==g?(d=NaN,this.newUnits=a=""):(d=g[1],a=this.newUnits=2==g.length?"noe":"hz")):d=c?d/(g.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO)+
e.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO)):l?this.vwr.getNMRCalculation().getDipolarConstantHz(g,e):this.vwr.getNMRCalculation().getIsoOrAnisoHz(!0,g,e,a,null);this.$isValid=!Float.isNaN(d);c&&(a="pm")}}if(Float.isNaN(d))return NaN;if(a.equals("hz"))return b?Math.round(10*d)/10:d;if(a.equals("noe"))return b?Math.round(100*d)/100:d;if(a.equals("nm"))return b?Math.round(100*d)/1E3:d/10;if(a.equals("pm"))return b?Math.round(1E3*d)/10:100*d;if(a.equals("au"))return b?Math.round(1E3*(d/0.5291772))/
1E3:d/0.5291772;if(a.endsWith("khz"))return b?Math.round(d/10)/100:d/1E3}return b?Math.round(100*d)/100:d},"~S,~B");c(c$,"checkJ",function(a){null!=this.property||(null!=a||null!=this.units)||(a=this.vwr.g.measureDistanceUnits,"+hz".equals(a)&&(this.property="property_J",this.units=a))},"~S");c$.nmrType=c(c$,"nmrType",function(a){return 0>a.indexOf("hz")?0:a.equals("noe_hz")?3: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$,"getPropMeasurement",function(a){if(null==this.countPlusIndices||2!=this.count)return NaN;for(var b=this.count;0<=--b;)if(0>this.countPlusIndices[b+1])return NaN;try{var d=
null==a?this.getAtom(1):a[0],c=null==a?this.getAtom(2):a[1],g=this.vwr.getDataObj(this.property,null,2),e=d.i,j=c.i;return null==g||j>=g.length||e>=g.length?NaN:g[e][j]}catch(l){return NaN}},"~A");c(c$,"getMeasurement",function(a){this.checkJ(null);if(!Float.isNaN(this.fixedValue))return this.fixedValue;if(null!=this.property)return this.getPropMeasurement(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);
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"~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$,"isMin",function(a){var b=this.getAtom(1),d=this.getAtom(2),c=C(100*d.distanceSquared(b)),b=b.getAtomName(),d=d.getAtomName(),d=0>b.compareTo(d)?b+d:d+b;a=a.get(d);return null!=a&&c==a.intValue()},"java.util.Map");c$.isUnits=c(c$,"isUnits",function(a){return JU.PT.isOneOf((a.startsWith("+")?a.substring(1):a).toLowerCase(),";nm;nanometers;pm;picometers;angstroms;angstroms;ang;\u00c5;au;vanderwaals;vdw;%;noe;")||0>a.indexOf(" ")&&a.endsWith("hz")},"~S");G(c$,"NMR_NOT",
0,"NMR_DC",1,"NMR_JC",2,"NMR_NOE_OR_J",3)});m("JM");x(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["java.lang.Float","JU.BS","$.Lst","JM.Measurement","JU.BSUtil"],function(){c$=w(function(){this.points=this.measurements=this.measurementStrings=this.client=null;this.mustNotBeConnected=this.mustBeConnected=!1;this.tickInfo=null;this.tokAction=12290;this.note=this.property=this.strFormat=this.radiusData=null;this.isAll=!1;this.colix=0;this.intramolecular=null;this.mad=0;this.units=this.text=
this.thisID=null;this.fixedValue=0;this.ms=this.minArray=this.atoms=null;this.allowSelf=!1;this.vwr=null;this.iFirstAtom=0;this.justOneModel=!0;this.htMin=null;s(this,arguments)},JM,"MeasurementData",null,J.api.JmolMeasurementClient);p(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,j,l,h,r,n,q,z,A,m){this.ms=this.vwr.ms;this.tokAction=
a;2<=this.points.size()&&(t(this.points.get(0),JU.BS)&&t(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.property=c;this.strFormat=g;this.units=e;this.tickInfo=j;this.mustBeConnected=l;this.mustNotBeConnected=h;this.intramolecular=r;this.isAll=n;this.mad=q;this.colix=z;this.text=A;this.fixedValue=m;return this},"~N,java.util.Map,J.atomdata.RadiusData,~S,~S,~S,JM.TickInfo,~B,~B,Boolean,~B,~N,~N,JM.Text,~N");
c(c$,"processNextMeasure",function(a){var b=a.getMeasurement(null);if(!(null!=this.htMin&&!a.isMin(this.htMin)||null!=this.radiusData&&!a.isInRange(this.radiusData,b)))if(null==this.measurementStrings&&null==this.measurements){var d=this.minArray[this.iFirstAtom];a.value=b;b=a.fixValue(this.units,!1);this.minArray[this.iFirstAtom]=-Infinity==1/d?b:Math.min(d,b)}else null!=this.measurementStrings?this.measurementStrings.addLast(a.getStringUsing(this.vwr,this.strFormat,this.units)):this.measurements.addLast(Float.$valueOf(a.getMeasurement(null)))},
"JM.Measurement");c(c$,"getMeasurements",function(a,b){if(b){this.minArray=L(this.points.get(0).cardinality(),0);for(var d=0;d<this.minArray.length;d++)this.minArray[d]=-0;this.define(null,this.ms);return this.minArray}if(a)return this.allowSelf=!0,this.measurements=new JU.Lst,this.define(null,this.ms),this.measurements;this.measurementStrings=new JU.Lst;this.define(null,this.ms);return this.measurementStrings},"~B,~B");c(c$,"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=B(5,0),j=(new JM.Measurement).setPoints(b,e,g,null);j.setCount(d);j.property=this.property;j.strFormat=this.strFormat;j.units=this.units;j.fixedValue=this.fixedValue;for(var l=-1,h=0;h<d;h++){var r=this.points.get(h);if(t(r,JU.BS)){l=r.cardinality();if(0==l)return;1<l&&(c=0);l=h;0==h&&(this.iFirstAtom=0);e[h+1]=r.nextSetBit(0)}else g[h]=r,e[h+1]=-2-h}this.nextMeasure(0,l,j,c)}},"J.api.JmolMeasurementClient,JM.ModelSet");c(c$,"nextMeasure",function(a,
b,d,c){if(a>b)(this.allowSelf&&!this.mustBeConnected&&!this.mustNotBeConnected||d.isValid())&&((!this.mustBeConnected||d.isConnected(this.atoms,a))&&(!this.mustNotBeConnected||!d.isConnected(this.atoms,a))&&(null==this.intramolecular||d.isIntramolecular(this.atoms,a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(d);else{var g=this.points.get(a),e=d.countPlusIndices,j=0==a?2147483647:e[a];if(0>j)this.nextMeasure(a+1,b,d,c);else{for(var l=!1,h=g.nextSetBit(0),r=0;0<=h;h=g.nextSetBit(h+
1),r++)if(h!=j||this.allowSelf){var n=this.atoms[h].mi;if(0<=c&&this.justOneModel)if(0==a)c=n;else if(c!=n)continue;e[a+1]=h;0==a&&(this.iFirstAtom=r);l=!0;this.nextMeasure(a+1,b,d,c)}l||this.nextMeasure(a+1,b,d,c)}}},"~N,~N,JM.Measurement,~N")});m("JM");x(["JM.Measurement"],"JM.MeasurementPending",null,function(){c$=w(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;s(this,arguments)},JM,"MeasurementPending",JM.Measurement);c(c$,"set",function(a){return this.setM(a,
null,NaN,0,null,0)},"JM.ModelSet");c(c$,"checkPoint",function(a){for(var b=1;b<=this.numSet;b++)if(this.countPlusIndices[b]==-1-b&&0.01>this.pts[b-1].distance(a))return!1;return!0},"JU.Point3fi");c(c$,"getIndexOf",function(a){for(var b=1;b<=this.numSet;b++)if(this.countPlusIndices[b]==a)return b;return 0},"~N");h(c$,"setCount",function(a){this.setCountM(a);this.numSet=a},"~N");c(c$,"addPoint",function(a,b,d){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==b){if(0<this.getIndexOf(a))return d&&
(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(b))return d&&(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=!0;this.count=this.numSet+1;this.pts[a]=b;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;d&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);
return this.count},"~N,JU.Point3fi,~B")});m("JM");x(["JU.BS","$.SB"],"JM.Model",["java.util.Hashtable","JU.AU","JU.BSUtil","JV.FileManager"],function(){c$=w(function(){this.mat4=this.ms=null;this.fileIndex=this.modelIndex=0;this.isModelKit=this.isPdbWithMultipleBonds=this.isBioModel=!1;this.translation=this.dataFrames=this.biosymmetry=this.properties=this.auxiliaryInfo=this.orientation=this.dssrCache=this.simpleCage=this.chains=null;this.dataSourceFrame=-1;this.loadState="";this.loadScript=null;this.isTrajectory=
this.isJmolDataFrame=this.structureTainted=this.hasRasmolHBonds=!1;this.act=this.insertionCount=this.altLocCount=this.trajectoryBaseIndex=0;this.bondCount=-1;this.chainCount=0;this.groupCount=-1;this.firstMoleculeIndex=this.firstAtomIndex=this.biosymmetryCount=this.moleculeCount=this.hydrogenCount=0;this.bsAtomsDeleted=this.bsAtoms=null;this.frameDelay=this.defaultRotationRadius=0;this.selectedTrajectory=-1;this.bsCheck=this.pdbID=this.jmolFrameType=this.jmolData=null;this.hasChirality=!1;this.isOrderly=
!0;s(this,arguments)},JM,"Model");O(c$,function(){this.chains=Array(8);this.loadScript=new JU.SB;this.bsAtoms=new JU.BS;this.bsAtomsDeleted=new JU.BS});p(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;a=e.get("biosymmetryCount");null!=a&&(this.biosymmetryCount=a.intValue(),this.biosymmetry=e.get("biosymmetry"));a=e.get("fileName");null!=
a&&e.put("fileName",JV.FileManager.stripTypePrefix(a));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$,"getTrueAtomCount",function(){return JU.BSUtil.andNot(this.bsAtoms,this.bsAtomsDeleted).cardinality()});c(c$,"isContainedIn",
function(a){null==this.bsCheck&&(this.bsCheck=new JU.BS);this.bsCheck.clearAll();this.bsCheck.or(a);a=JU.BSUtil.andNot(this.bsAtoms,this.bsAtomsDeleted);this.bsCheck.and(a);return this.bsCheck.equals(a)},"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)})});m("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 $.Logger JV.JC".split(" "),function(){c$=w(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.isMOL2D=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.$mergeGroups=this.appendToModelIndex=this.htGroup1=null;this.iChain=0;this.vStereo=null;this.lastModel=-1;this.structuresDefinedInFile=null;this.stereodir=1;s(this,arguments)},JM,"ModelLoader");O(c$,function(){this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});p(c$,function(a,
b,d,c,g,e){this.vwr=a;this.ms=new JM.ModelSet(a,b);var j=a.getModelAdapter();this.modelSet0=g;(this.merging=null!=g&&0<g.ac)?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);null==e?(this.initializeInfo(b,null),this.createModelSet(null,null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||(this.ms.canSkipLoad=!1),a=j.getAtomSetCollectionAuxiliaryInfo(c),a.put("loadScript",d),this.initializeInfo(j.getFileTypeName(c).toLowerCase().intern(),
a),this.createModelSet(j,c,e),null!=this.jbr&&this.jbr.setLoader(null),this.jbr=null)},"JV.Viewer,~S,JU.SB,~O,JM.ModelSet,JU.BS");c(c$,"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.getBoolean(603979894));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.appendToModelIndex=null==this.ms.msInfo?null:this.ms.msInfo.get("appendToModelIndex");this.appendNew=!this.isMutate&&(!this.merging||null==a||1<this.adapterModelCount||this.isTrajectory||this.vwr.getBoolean(603979792)&&null==this.appendToModelIndex);this.htAtomMap.clear();this.chainOf=Array(32);this.group3Of=Array(32);this.seqcodes=B(32,0);this.firstAtomIndexes=B(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++)null!=c[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(),j=g.getValue(),l=this.ms.getModelAtomBitSetIncludingDeleted(b,!0);if(this.doAddHydrogens)var h=null!=c&&JU.PT.isOneOf(e,c),j=this.jbr.fixPropertyValue(l,j,h);e="property_"+e.toLowerCase();JU.Logger.info("creating "+e+" for model "+this.ms.getModelName(b));this.vwr.setData(e,v(-1,[e,j,l,Integer.$valueOf(-1),Boolean.FALSE]),this.ms.ac,0,0,2147483647,0)}}});c(c$,"initializeAtomBondModelCounts",function(a){var b=
this.adapterTrajectoryCount;if(this.merging){if(this.appendNew)this.baseModelIndex=this.baseModelCount,this.ms.mc=this.baseModelCount+this.adapterModelCount;else{this.baseModelIndex=null==this.appendToModelIndex?this.vwr.am.cmi:this.appendToModelIndex.intValue();if(0>this.baseModelIndex||this.baseModelIndex>=this.baseModelCount)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)}else 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),j=a.getAtomSetName(b,g),l=a.getAtomSetAuxiliaryInfo(b,g);l.containsKey("modelID")&&l.put("modelID0",l.get("modelID"));var h=l.get("modelProperties");this.vwr.setStringProperty("_fileType",l.get("fileType"));null==j&&(j=null!=this.jmolData&&2<this.jmolData.indexOf(";")?this.jmolData.substring(this.jmolData.indexOf(":")+2,this.jmolData.indexOf(";")):this.appendNew?
""+e%1E6:"");this.setModelNameNumberProperties(c,d,j,e,h,l,this.jmolData)}d=this.ms.am[null==this.appendToModelIndex?this.baseModelIndex:this.ms.mc-1];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){j=JU.PT.split(g,"\n");l=new JU.SB;for(g=0;g<j.length;g++)h=d.loadState.indexOf(j[g]),(0>h||h!=d.loadState.lastIndexOf(j[g]))&&l.append(j[g]).appendC("\n");d.loadState+=
d.loadScript.toString()+l.toString();d.loadScript=new JU.SB;if(0<=e.indexOf("load append ")||0<=e.indexOf('data "append '))e.insert(0,";var anew = appendNew;"),e.append(";set appendNew anew");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,j){if(this.appendNew){var l=null!=e&&Boolean.TRUE===e.get("isPDB");this.ms.am[a]=l?this.jbr.getBioModel(a,b,j,g,e):(new JM.Model).set(this.ms,a,b,j,g,e);this.ms.modelNumbers[a]=c;this.ms.modelNames[a]=d;l&&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$,"finalizeModels",function(a){var b=this.ms.mc;if(b!=a){var d,c=0,g=-1,e=this.ms.modelNumbers,j=this.ms.modelNames;if(this.isTrajectory)for(var l=a;++l<this.ms.mc;)e[l]=e[l-1]+1;if(0<a){if(1E6>e[0])for(l=0;l<a;l++)0==j[l].length&&(j[l]=""+e[l]),e[l]+=1E6,this.ms.modelNumbersForAtomLabel[l]="1."+(l+1);var h=e[a-1],h=h-h%1E6;1E6>e[a]&&(h+=1E6);for(l=a;l<b;l++)e[l]+=h}for(var r=this.ms.am,
l=a;l<b;++l)if(this.ms.setInfo(l,"fileType",this.ms.modelSetTypeName),null!=this.fileHeader&&this.ms.setInfo(l,"fileHeader",this.fileHeader),h=u(e[l]/1E6),h!=g&&(c=0,g=h),c++,0==h?(d=""+this.ms.getModelNumber(l),h=1):d=h+"."+c,this.ms.modelNumbersForAtomLabel[l]=d,r[l].fileIndex=h-1,this.ms.modelFileNumbers[l]=1E6*h+c,null==j[l]||0==j[l].length)j[l]=d;if(this.merging)for(l=0;l<a;l++)r[l].ms=this.ms;for(l=0;l<b;l++)this.ms.setInfo(l,"modelName",j[l]),this.ms.setInfo(l,"modelNumber",Integer.$valueOf(e[l]%
1E6)),this.ms.setInfo(l,"modelFileNumber",Integer.$valueOf(this.ms.modelFileNumbers[l])),this.ms.setInfo(l,"modelNumberDotted",this.ms.getModelNumberDotted(l)),a=this.ms.getInfo(l,"altLocs"),null!=a&&JU.Logger.info("model "+this.ms.getModelNumberDotted(l)+" alternative locations: "+a)}},"~N");c(c$,"iterateOverAllNewAtoms",function(a,b){var d=-1,c=!1,g=!1,e=a.getAtomIterator(b);this.ms.setCapacity(a.getAtomCount(b));var j=0,l=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();){j++;var h=e.getAtomSetIndex()+this.baseModelIndex;h!=d&&(this.iChain=0,this.iModel=h,this.model=l[h],this.currentChainID=2147483647,this.isNewChain=!0,this.model.bsAtoms.clearAll(),this.model.isOrderly=null==this.appendToModelIndex,c=this.model.isBioModel,d=h,g=c&&this.doAddHydrogens,null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var h=e.getGroup3(),r=e.getChainID();this.checkNewGroup(a,r,h,e.getSequenceNumber(),e.getInsertionCode(),g,!1);r=e.getElementNumber();
g&&1==JU.Elements.getElementNumber(r)&&this.jbr.setHaveHsAlready(!0);var n=e.getAtomName(),q=g?this.getPdbCharge(h,n):e.getFormalCharge();this.addAtom(c,e.getSymmetry(),e.getAtomSite(),e.getUniqueID(),r,n,q,e.getPartialCharge(),e.getTensors(),e.getOccupancy(),e.getBfactor(),e.getXYZ(),e.getIsHetero(),e.getSerial(),e.getSeqID(),h,e.getVib(),e.getAltLoc(),e.getRadius(),e.getBondRadius())}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=l[0].firstAtomIndex=0;e<this.ms.ac;e++)null!=g[e]&&g[e].mi>d&&(d=g[e].mi,h=l[d],h.firstAtomIndex=e,h.isOrderly=h.act==h.bsAtoms.length(),h=this.ms.getDefaultVdwType(d),h!==c&&(JU.Logger.info("Default Van der Waals type for model set to "+h.getVdwLabel()),c=h));JU.Logger.info(j+" atoms created")},"J.api.JmolAdapter,~O");c(c$,"addJmolDataProperties",function(a,b){if(null!=b)for(var d=a.bsAtoms,c=d.cardinality(),g,e=b.entrySet().iterator();e.hasNext()&&((g=e.next())||1);){var j=g.getKey(),l=g.getValue();
if(l.length!=c)break;var h=j.startsWith("property_")?1715472409:JS.T.getTokFromName(j);switch(h){default:if(JS.T.tokAttr(h,2048)){this.vwr.setAtomProperty(d,h,0,0,null,l,null);break}case 1111492629:case 1111492630:case 1111492631:j="property_"+j;case 1715472409:this.vwr.setData(j,v(-1,[j,l,d,Integer.$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,j,l,h,r,n,q,z,A,m,p,s,t,u,w){var v=0,x=null;if(null!=e){var y;if(0<=(y=e.indexOf("\x00")))x=e.substring(y+1),e=e.substring(0,y);a&&(0<=e.indexOf("*")&&(e=e.$replace("*","'")),v=this.vwr.getJBR().lookupSpecialAtomID(e),2==v&&"CA".equalsIgnoreCase(p)&&(v=0))}a=this.ms.addAtom(this.iModel,this.nullGroup,g,e,x,A,m,d,q,u,s,j,l,r,n,h,z,v,b,w);a.altloc=t;this.htAtomMap.put(c,a)},"~B,JU.BS,~N,~O,~N,~S,~N,~N,JU.Lst,~N,~N,JU.P3,~B,~N,~N,~S,JU.V3,~S,~N,~N");c(c$,
"checkNewGroup",function(a,b,d,c,g,e,j){var l=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||l!==this.currentGroup3){0<this.groupCount&&e&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!j?1:0),this.jbr.setHaveHsAlready(!1));
this.currentGroupSequenceNumber=c;this.currentGroupInsertionCode=g;for(this.currentGroup3=l;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(),g=this.isMutate&&!this.vwr.getBoolean(603979894);this.ms.defaultCovalentMad=
null==this.jmolData?c:0;for(var e=!1;d.hasNext();){var j=d.getEncodedOrder(),l=g?1:j,h=this.bondAtoms(d.getAtomUniqueID1(),d.getAtomUniqueID2(),l);null!=h&&(1<l&&(1025!=l&&1041!=l)&&(e=!0),l=d.getRadius(),0<l&&h.setMad(ea(2E3*l)),l=d.getColix(),0<=l&&(h.colix=l),h.order|=j&98304)}e&&(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$,"bondAtoms",function(a,b,d){var c=this.htAtomMap.get(a);if(null==c)return JU.Logger.error("bondAtoms cannot find atomUid1?:"+a),null;a=this.htAtomMap.get(b);if(null==a)return JU.Logger.error("bondAtoms cannot find atomUid2?:"+b),null;if(c.isBonded(a))return null;1025==d||1041==d?(b=c.getModelIndex(),b!=this.lastModel&&(this.lastModel=b,b=this.ms.getModelAuxiliaryInfo(b),this.isMOL2D=null!=b&&"2D".equals(b.get("dimension"))),d=this.ms.bondMutually(c,a,this.isMOL2D?
d:1,this.ms.getDefaultMadFromOrder(1),0),null==this.vStereo&&(this.vStereo=new JU.Lst),this.vStereo.addLast(d)):(d=this.ms.bondMutually(c,a,d,this.ms.getDefaultMadFromOrder(d),0),d.isAromatic()&&(this.ms.someModelsHaveAromaticBonds=!0));this.ms.bondCount==this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount+250));this.ms.setBond(this.ms.bondCount++,d);return d},"~O,~O,~N");c(c$,"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$,"initializeBonding",function(){var a=this.ms.mc,b=this.ms.am,d=0,c=this.ms.getInfoM("bsExcludeBonding");null==c&&(c=null==this.ms.getInfoM("someModelsHaveCONECT")?null:new JU.BS,null!=c&&this.ms.setPdbConectBonding(this.baseAtomIndex,
this.baseModelIndex,c));var g=this.vwr.getBoolean(603979794),e=this.vwr.getBoolean(603979798),j=this.vwr.getBoolean(603979846),l=null,h=!1;if(!this.noAutoBond)for(var r=this.baseModelIndex;r<a;r++){var d=b[r].bsAtoms.cardinality(),n=this.ms.getInfoI(r,"initialBondCount"),q=b[r].isBioModel;0>n&&(n=this.ms.bondCount);if(j||e&&(0==n||q&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||n<u(d/2))||this.ms.getInfoB(r,"hasSymmetry")&&!g&&!this.ms.getInfoB(r,"hasBonds")))if(h=!0,this.merging||
1<a)null==l&&(l=JU.BS.newN(this.ms.ac)),(r==this.baseModelIndex||!this.isTrajectory)&&l.or(b[r].bsAtoms)}this.modulationOn&&this.ms.setModulation(null,!0,this.modulationTUV,!1);h?(this.ms.autoBondBs4(l,l,c,null,this.ms.defaultCovalentMad,this.vwr.getBoolean(603979872)),JU.Logger.info("ModelSet: autobonding; use  autobond=false  to not generate bonds automatically")):JU.Logger.info("ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation")});c(c$,"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]=B(0,0))}});c(c$,"distinguishAndPropagateGroup",function(a,b,d,c,g,e){if(e<g)throw new NullPointerException;var j=null==d||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(b,d,c,g,e,this.specialAtomIndexes,this.ms.at);null==j?(j=(new JM.Group).setGroup(b,d,c,g,e),null!=this.jbr&&(j.groupID=this.jbr.getGroupID(d)),c="o>"):c=j.isProtein()?"p>":j.isNucleic()?"n>":j.isCarbohydrate()?"c>":"o>";null!=d&&(this.countGroup(this.ms.at[g].mi,
c,d),j.isNucleic()&&(d=null==this.htGroup1?null:this.htGroup1.get(d),null!=d&&(j.group1=d.charAt(0))));this.addGroup(b,j);this.groups[a]=j;j.groupIndex=a;for(a=e+1;--a>=g;)this.ms.at[a].group=j},"~N,JM.Chain,~S,~N,~N,~N");c(c$,"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$,"countGroup",function(a,b,d){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var g=(d+"   ").substring(0,
3),e=this.group3Lists[c].indexOf(g);0>e&&(this.group3Lists[c]+=",["+g+"]",e=this.group3Lists[c].indexOf(g),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][u(e/6)]++;e=this.group3Lists[c].indexOf(",["+g);0<=e&&(this.group3Lists[c]=this.group3Lists[c].substring(0,e)+b+this.group3Lists[c].substring(e+2));0<=a&&this.countGroup(-1,b,d)}},"~N,~S,~S");c(c$,"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$,"findElementsPresent",function(){this.ms.elementsPresent=Array(this.ms.mc);for(var a=0;a<this.ms.mc;a++)this.ms.elementsPresent[a]=JU.BS.newN(64);for(a=this.ms.ac;0<=--a;){var b=this.ms.at[a];if(null!=b){var d=b.getAtomicAndIsotopeNumber();d>=JU.Elements.elementNumberMax&&(d=JU.Elements.elementNumberMax+JU.Elements.altElementIndexFromNumber(d));this.ms.elementsPresent[b.mi].set(d)}}});
c(c$,"applyStereochemistry",function(){this.set2DLengths(this.baseAtomIndex,this.ms.ac);var a=new JU.V3;if(null!=this.vStereo){var b=this.vStereo.size();a:for(;0<=--b;)for(var d=this.vStereo.get(b),c=d.atom1,g=c.bonds,e=c.getBondCount();0<=--e;){var j=g[e];if(j!==d&&(j=j.getOtherAtom(c),a.sub2(j,c),0.1>Math.abs(a.x))){1025==d.order==0>a.y&&(this.stereodir=-1);break a}}}this.set2dZ(this.baseAtomIndex,this.ms.ac,a);if(null!=this.vStereo){a=new JU.BS;a.setBits(this.baseAtomIndex,this.ms.ac);for(b=this.vStereo.size();0<=
--b;){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);g=JU.JmolMolecule.getBranchBitSet(this.ms.at,d.atom2.i,a,null,d.atom1.i,!1,!0);g.set(d.atom2.i);for(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$,"set2DLengths",function(a,b){for(var d=0,c=0,g=a;g<b;g++){var e=this.ms.at[g],j=e.bonds;if(null!=j)for(var l=j.length;0<=
--l;)if(null!=j[l]){var h=j[l].getOtherAtom(e);1!=h.getAtomNumber()&&h.getIndex()>g&&(d+=h.distance(e),c++)}}if(0!=c){d=1.45/(d/c);for(g=a;g<b;g++)this.ms.at[g].scale(d)}},"~N,~N");c(c$,"set2dZ",function(a,b,d){var c=JU.BS.newN(b),g=new JU.BS,e=JU.V3.new3(0,1,0),j=new JU.V3,l=new JU.BS;for(l.setBits(a,b);a<b;a++)!c.get(a)&&!g.get(a)&&(g=this.getBranch2dZ(a,-1,l,g,d,e,j,this.stereodir),c.or(g))},"~N,~N,JU.V3");c(c$,"getBranch2dZ",function(a,b,d,c,g,e,j,l){c=JU.BS.newN(this.ms.ac);if(0>a)return c;var h=
new JU.BS;h.or(d);0<=b&&h.clear(b);JM.ModelLoader.setBranch2dZ(this.ms.at[a],c,h,g,e,j,l);return c},"~N,~N,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3,~N");c$.setBranch2dZ=c(c$,"setBranch2dZ",function(a,b,d,c,g,e,j){var l=a.i;if(d.get(l)&&(d.clear(l),b.set(l),null!=a.bonds))for(l=a.bonds.length;0<=--l;){var h=a.bonds[l];h.isHydrogen()||(h=h.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,h,c,g,e,j),JM.ModelLoader.setBranch2dZ(h,b,d,c,g,e,j))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3,~N");c$.setAtom2dZ=c(c$,"setAtom2dZ",
function(a,b,d,c,g,e){d.sub2(b,a);d.z=0;d.normalize();g.cross(c,d);d=Math.acos(d.dot(c));e=0.4*-e*Math.sin(4*d);b.z=a.z+e},"JM.Atom,JM.Atom,JU.V3,JU.V3,JU.V3,~N");c(c$,"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$,"createAtomDataSet",function(a,b,d,c,g){if(null==c)return null;var e=a.getModelAdapter(),j=new JU.P3,l=b.at,h=a.getFloat(570425363);if(null!=b.unitCells)for(var r=g.nextSetBit(0);0<=r;r=g.nextSetBit(r+1))if(null!=l[r].atomSymmetry){h=-h;break}for(var r=-1,n=0,q=JU.BSUtil.cardinalityOf(g)==a.ms.ac,z=e.getAtomIterator(c);z.hasNext();){var A=
z.getXYZ();if(!Float.isNaN(A.x+A.y+A.z))if(1145047050==d){r=g.nextSetBit(r+1);if(0>r)break;n++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+r+": "+l[r]+" --\x3e ("+A.x+","+A.y+","+A.z);b.setAtomCoord(r,A.x,A.y,A.z)}else{j.setT(A);A=JU.BS.newN(b.ac);b.getAtomsWithin(h,j,A,-1);A.and(g);if(q)if(n=JU.BSUtil.cardinalityOf(A),0==n){JU.Logger.warn("createAtomDataSet: no atom found at position "+j);continue}else 1<n&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+n+" atoms found at position "+
j);switch(d){case 1145047055:var m=z.getVib();if(null==m)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+j+" vib: "+m);b.setAtomCoords(A,1145047055,m);break;case 1128269825:b.setAtomProperty(A,d,0,z.getOccupancy(),null,null,null);break;case 1111492619:b.setAtomProperty(A,d,0,z.getPartialCharge(),null,null,null);break;case 1111492620:b.setAtomProperty(A,d,0,z.getBfactor(),null,null,null)}}}switch(d){case 1145047055:b=e.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+b);a.setStringProperty("_vibrationName",
b);break;case 1145047050:if(JU.Logger.info(n+" atom positions read"),b.recalculateLeadMidpointsAndWingVectors(-1),n==b.ac)return"boundbox {*};reset"}return null},"JV.Viewer,JM.ModelSet,~N,~O,JU.BS");G(c$,"defaultGroupCount",32)});m("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 $.SimpleUnitCell JV.JC".split(" "),
function(){c$=w(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;s(this,arguments)},JM,"ModelSet",JM.BondCollection);c(c$,"getBoxInfo",function(){return this.boxInfo});
p(c$,function(a,b){I(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=B(1,0);this.modelFileNumbers=B(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$,"getFrameOffsets",function(a,b){if(null==a){if(b)for(var d=this.mc;0<=--d;){var c=this.am[d];!c.isJmolDataFrame&&!c.isTrajectory&&this.translateModel(c.modelIndex,null)}return null}if(0>a.nextSetBit(0))return null;if(b){for(var g=JU.BSUtil.copy(a),e=null,j=new JU.P3,d=0;d<this.mc;d++){c=this.am[d];if(!c.isJmolDataFrame&&!c.isTrajectory){var l=g.nextSetBit(0);c.bsAtoms.get(l)&&(null==e?e=JU.P3.newP(this.at[l]):(j.sub2(e,this.at[l]),this.translateModel(d,j)))}g.andNot(c.bsAtoms)}return null}g=
Array(this.mc);for(d=this.mc;0<=--d;)g[d]=new JU.P3;var j=e=0,l=g[0],h=null!=this.trajectory&&this.trajectory.steps.size()==this.mc,r=h?this.mc:1;g[0].set(0,0,0);for(c=0;c<r;c++){h&&this.setTrajectory(c);for(d=0;d<=this.ac;d++){if(d==this.ac||this.at[d].mi!=e){0<j&&(l.scale(-1/j),0!=e&&l.sub(g[0]),j=0);if(d==this.ac)break;e=this.at[d].mi;l=g[e]}a.get(d)&&(l.add(this.at[d]),j++)}}return g},"JU.BS,~B");c(c$,"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,j){return this.calculatePointGroupForFirstModel(a,!0,!1,b,d,c,g,e,j)},"JU.BS,~S,~N,~N,~A,JU.P3,~S");
c(c$,"calculatePointGroupForFirstModel",function(a,b,d,c,g,e,j,l,h){var r=this.pointGroup,n=J.api.Interface.getSymmetry(this.vwr,"ms"),q=null,z=!1,A=!1,m=!1,p=null!=j,s=this.vwr.am.cmi;if(!p)if(j=null==a?-1:a.nextSetBit(0),0>s&&0<=j&&(s=this.at[j].mi),0>s&&(s=this.vwr.getVisibleFramesBitSet().nextSetBit(0),a=null),q=this.vwr.getModelUndeletedAtomsBitSet(s),m=null!=a&&q.cardinality()!=a.cardinality(),null!=a&&q.and(a),j=q.nextSetBit(0),0>j&&(q=this.vwr.getModelUndeletedAtomsBitSet(s),j=q.nextSetBit(0)),
A=this.vwr.shm.getShapePropertyIndex(18,"mad",j),z=null!=A&&0!=A.intValue()||this.vwr.tm.vibrationOn,A=null!=c&&0<=c.toUpperCase().indexOf(":POLY")){r=v(-1,[Integer.$valueOf(j),null]);this.vwr.shm.getShapePropertyData(21,"points",r);j=r[1];if(null==j)return null;q=null;z=!1;r=null}else j=this.at;var t;if(null!=c&&0<=(t=c.indexOf(":")))c=c.substring(0,t);if(null!=c&&0<=(t=c.indexOf(".")))g=JU.PT.parseInt(c.substring(t+1)),0>g&&(g=0),c=c.substring(0,t);r=n.setPointGroup(r,l,j,q,z,p?0:this.vwr.getFloat(570425382),
this.vwr.getFloat(570425384),m);!A&&!p&&(this.pointGroup=r);if(!b&&!d)return r.getPointGroupName();b=r.getPointGroupInfo(s,h,d,c,g,e);return d?b:(1<this.mc?"frame "+this.getModelNumberDotted(s)+"; ":"")+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$,"makeConnections",function(a,b,d,c,g,e,j,l,h,r){if(1073741852==c&&2048!=d){var n="connect ";0.1!=a&&(n+=a+" ");1E8!=b&&(n+=b+" ");this.addStateScript(n,l?g:null,l?null:g,l?null:e," auto",!1,!0)}this.moleculeCount=0;return this.makeConnections2(a,b,d,c,g,e,j,l,h,r)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"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.$valueOf(e));for(var j=this.getInfo(b,"PDB_CONECT_firstAtom_count_max"),l=j[0]+a,h=l+j[1],j=j[2],r=B(j+1,0),n=l;n<h;n++)if(0<(l=this.atomSerials[n]))r[l]=n+1;for(h=0;h<e;h++){var l=g.get(h),n=l[0],q=l[1],l=l[2];if(!(0>n||0>q||n>j||q>j))if(n=r[n]-1,q=r[q]-1,!(0>n||0>q)){var z=this.at[n],A=this.at[q];null!=d&&(z.isHetero()&&d.set(n),A.isHetero()&&d.set(q));if(z.altloc==A.altloc||"\x00"==z.altloc||"\x00"==A.altloc)this.getOrAddBond(z,A,l,2048==l?1:c,null,0,!1)}}}}},
"~N,~N,JU.BS");c(c$,"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);var c;if(b==this.mc)return c=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.vwr.zap(!0,!1,!1),c;this.validateBspf(!1);c=new JU.BS;for(var g=!0,e=!1,j=new JU.BS,d=0;d<this.mc;d++){var l=this.am[d],g=(new Boolean(g&l.isOrderly)).valueOf();
a.get(d)?(0<=l.fileIndex&&j.set(l.fileIndex),c.or(this.getModelAtomBitSetIncludingDeleted(d,!1))):0<=l.fileIndex&&j.get(l.fileIndex)&&(e=!0)}if(!g||e)return this.vwr.deleteAtoms(c,!1),null;b=Array(this.mc-b);g=this.am;for(e=d=0;d<this.mc;d++)a.get(d)||(l=this.am[d],l.modelIndex=e,b[e++]=l);this.am=b;l=this.mc;j=this.getBondsForSelectedAtoms(c,!0);this.deleteBonds(j,!0);for(e=d=0;d<l;d++)if(a.get(d)){var h=g[d],r=h.act;if(0!=r){var n=h.bsAtoms,h=h.firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,
n);this.deleteModel(e,n,j);this.deleteModelAtoms(h,r,n);this.vwr.deleteModelAtoms(e,h,r,n);for(var q=l;--q>d;)g[q].fixIndices(e,r,n);this.vwr.shm.deleteShapeAtoms(v(-1,[b,this.at,B(-1,[e,h,r])]),n);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 c},"JU.BS");c(c$,"resetMolecules",
function(){this.molecules=this.bsAll=null;this.moleculeCount=0;this.resetChirality()});c(c$,"resetChirality",function(){if(this.haveChirality)for(var a=-1,b=this.ac;0<=--b;){var d=this.at[b];null!=d&&(d.setCIPChirality(0),d.mi!=a&&d.mi<this.am.length&&(this.am[a=d.mi].hasChirality=!1))}});c(c$,"deleteModel",function(a,b,d){if(!(0>a)){this.modelNumbers=JU.AU.deleteElements(this.modelNumbers,a,1);this.modelFileNumbers=JU.AU.deleteElements(this.modelFileNumbers,a,1);this.modelNumbersForAtomLabel=JU.AU.deleteElements(this.modelNumbersForAtomLabel,
a,1);this.modelNames=JU.AU.deleteElements(this.modelNames,a,1);this.frameTitles=JU.AU.deleteElements(this.frameTitles,a,1);this.thisStateModel=-1;var c=this.getInfoM("group3Lists"),g=this.getInfoM("group3Counts"),e=a+1;if(null!=c&&null!=c[e])for(var j=u(c[e].length/6);0<=--j;)0<g[e][j]&&(g[0][j]-=g[e][j],0==g[0][j]&&(c[0]=c[0].substring(0,6*j)+",["+c[0].substring(6*j+2)));null!=c&&(this.msInfo.put("group3Lists",JU.AU.deleteElements(c,a,1)),this.msInfo.put("group3Counts",JU.AU.deleteElements(g,a,1)));
null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(j=this.stateScripts.size();0<=--j;)this.stateScripts.get(j).deleteAtoms(a,d,b)||this.stateScripts.removeItemAt(j)}},"~N,JU.BS,JU.BS");c(c$,"setAtomProperty",function(a,b,d,c,g,e,j){switch(b){case 1114249217:case 1112152066:case 1112152071:case 1112152073:case 1112152074:case 1649022989:case 1112152078:if(4<c&&(c=4),null!=e){d=L(this.ac,0);try{var h=a.nextSetBit(0);for(g=0;0<=h;h=a.nextSetBit(h+1))d[h]=e[g++]}catch(k){if(D(k,
Exception))return;throw k;}e=d}case 1112152070:case 1112152076:h=null;d=0;null==e?(16<c&&(c=16.1),0>c&&(c=0),d=u(Math.floor(2E3*c))):h=new J.atomdata.RadiusData(e,0,null,null);this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(b),d,h,a);return}this.setAPm(a,b,d,c,g,e,j)},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"getFileData",function(a){if(0>a)return"";var b=this.getInfo(a,"fileData");if(null!=b)return b;if(!this.getInfoB(a,"isCIF"))return this.getPDBHeader(a);b=this.vwr.getCifData(a);this.setInfo(a,"fileData",
b);return b},"~N");c(c$,"addHydrogens",function(a,b){var d=this.mc-1,c=new JU.BS;if(this.isTrajectory(d)||1<this.am[d].getGroupCount())return c;this.growAtomArrays(this.ac+b.length);var g=this.vwr.rd,e=this.getDefaultMadFromOrder(1);this.am[d].resetDSSR(!1);for(var j=0,h=this.am[d].act+1;j<a.size();j++,h++){var k=a.get(j),r=this.addAtom(d,k.group,1,"H"+h,null,h,k.getSeqID(),h,b[j],NaN,null,0,0,100,NaN,null,!1,0,null,NaN);r.setMadAtom(this.vwr,g);c.set(r.i);this.bondAtoms(k,r,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(t(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$,"findAtomsInRectangle",function(a){for(var b=this.vwr.getVisibleFramesBitSet(),d=new JU.BS,c=this.ac;0<=--c;){var g=this.at[c];null!=g&&(b.get(g.mi)?g.checkVisible()&&a.contains(g.sX,g.sY)&&d.set(c):c=this.am[g.mi].firstAtomIndex)}return d},
"JU.Rectangle");c(c$,"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(a=this.at[c],null!=a)if(this.isJmolDataFrameForAtom(a))for(a=a.mi;0<=c&&null!=this.at[c]&&this.at[c].mi==a;)c--;else a=this.at[c],null!=a&&(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++;var e=this.at[g];null!=e&&!this.isJmolDataFrameForAtom(e)&&b.addBoundBoxPoint(e)}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$,"getCenterAndPoints",function(a,b){for(var d,c,g=b?1:0,e=a.size();0<=--e;){var j=a.get(e);d=j[0];t(j[1],JU.BS)?(c=j[1],g+=Math.min(d.cardinality(),
c.cardinality())):g+=Math.min(d.cardinality(),j[1].length)}var h=v(2,g,null);b&&(h[0][0]=new JU.P3,h[1][0]=new JU.P3);for(e=a.size();0<=--e;)if(j=a.get(e),d=j[0],t(j[1],JU.BS)){c=j[1];for(var j=d.nextSetBit(0),k=c.nextSetBit(0);0<=j&&0<=k;j=d.nextSetBit(j+1),k=c.nextSetBit(k+1))h[0][--g]=this.at[j],h[1][g]=this.at[k],b&&(h[0][0].add(this.at[j]),h[1][0].add(this.at[k]))}else{c=j[1];j=d.nextSetBit(0);for(k=0;0<=j&&k<c.length;j=d.nextSetBit(j+1),k++)h[0][--g]=this.at[j],h[1][g]=c[k],b&&(h[0][0].add(this.at[j]),
h[1][0].add(c[k]))}b&&(h[0][0].scale(1/(h[0].length-1)),h[1][0].scale(1/(h[1].length-1)));return h},"JU.Lst,~B");c(c$,"getAtomSetCenter",function(a){for(var b=new JU.P3,d=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.isJmolDataFrameForAtom(this.at[c])||(d++,b.add(this.at[c]));1<d&&b.scale(1/d);return b},"JU.BS");c(c$,"getAverageAtomPoint",function(){return this.getAtomSetCenter(this.vwr.bsA())});c(c$,"setAPm",function(a,b,d,c,g,e,j){this.setAPa(a,b,d,c,g,e,j);switch(b){case 1094715417:case 1631586315:this.vwr.getBoolean(603979944)&&
this.assignAromaticBondsBs(!0,null)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"addStateScript",function(a,b,d,c,g,e,j){var h=this.vwr.am.cmi;e?(this.thisStateModel!=h&&(a="frame "+(0>h?"all #"+h:this.getModelNumberDotted(h))+";\n  "+a),this.thisStateModel=h):this.thisStateModel=-1;a=new JM.StateScript(this.thisStateModel,a,b,d,c,g,j);a.isValid()&&this.stateScripts.addLast(a);return a},"~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");c(c$,"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$,"getMSInfoB",function(a){a=this.getInfoM(a);return t(a,Boolean)&&a.booleanValue()},"~S");c(c$,"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$,"getModelBS",function(a,b){var d=new JU.BS,c=0,g=null==a;b=(new Boolean(b&null!=this.trajectory)).valueOf();for(var e=g?0:a.nextSetBit(0);0<=e&&e<this.ac;e=g?e+1:a.nextSetBit(e+1))null!=this.at[e]&&(d.set(c=this.at[e].mi),b&&this.trajectory.getModelBS(c,d),c=this.am[c],c.isOrderly&&(e=c.firstAtomIndex+c.act-1));return d},"JU.BS,~B");c(c$,"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$,"fillAtomData",function(a,b){if(0!=(b&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);a.atomMolecule=B(this.ac,0);for(var d,c=0;c<this.molecules.length;c++){d=a.bsMolecules[c]=this.molecules[c].atomList;for(var g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))a.atomMolecule[g]=c}}0!=(b&8)?(d=B(1,0),a.hAtomRadius=this.vwr.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,d,
null,512),a.hydrogenAtomCount=d[0]):(a.firstAtomIndex=0>a.modelIndex?null==a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.am[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=0==this.ac?0:this.at[a.firstAtomIndex].mi,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,b))},"J.atomdata.AtomData,~N");c(c$,"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=u(Math.floor(a));for(a=u(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$,"getModulationList",function(a,b,d){var c=new JU.Lst;if(null!=this.vibrations)for(var g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))t(this.vibrations[g],J.api.JmolModulationSet)?
c.addLast(this.vibrations[g].getModulation(b,d)):c.addLast(Float.$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,j=new JU.V3,h=new JU.V3;null==b&&(b=this.getModelAtomBitSetIncludingDeleted(-1,!1));this.vwr.getOrCalcPartialCharges(this.am[a].bsAtoms,null);for(var k=b.nextSetBit(0);0<=k;k=b.nextSetBit(k+1))if(!(this.at[k].mi!=a||this.at[k].isDeleted())){var r=
this.partialCharges[k];0>r?(c++,e+=r,h.scaleAdd2(r,this.at[k],h)):0<r&&(d++,g+=r,j.scaleAdd2(r,this.at[k],j))}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;j.add(h);j.scale(4.8);return j},"~N,JU.BS");c(c$,"getMoleculeCountInModel",function(a){var b=0;0==this.moleculeCount&&this.getMolecules();if(0>a)return this.moleculeCount;for(var d=0;d<this.mc;d++)a==d&&(b+=this.am[d].moleculeCount);return b},"~N");c(c$,"calcSelectedMoleculesCount",
function(){var a=this.vwr.bsA();0==this.moleculeCount&&this.getMolecules();this.selectedMolecules.xor(this.selectedMolecules);for(var b=new JU.BS,d=0;d<this.moleculeCount;d++)JU.BSUtil.copy2(a,b),b.and(this.molecules[d].atomList),0<b.length()&&this.selectedMolecules.set(d)});c(c$,"setCentroid",function(a,b){var d=this.getNotInCentroid(a,b);null!=d&&0<=d.nextSetBit(0)&&this.vwr.deleteAtoms(d,!1)},"JU.BS,~A");c(c$,"getNotInCentroid",function(a,b){var d=a.nextSetBit(0);if(0>d)return null;d=this.getUnitCell(this.at[d].mi);
return null==d?null:d.notInCentroid(this,a,b)},"JU.BS,~A");c(c$,"getMolecules",function(){if(0<this.moleculeCount)return this.molecules;null==this.molecules&&(this.molecules=Array(4));this.moleculeCount=0;for(var a=null,b=Array(this.mc),d=null,c=0;c<this.mc;c++)b[c]=this.vwr.getModelUndeletedAtomsBitSet(c),a=this.am[c],a.moleculeCount=0,d=a.isBioModel?a.getBioBranches(d):null;this.molecules=JU.JmolMolecule.getMolecules(this.at,b,d,null);for(c=this.moleculeCount=this.molecules.length;0<=--c;)a=this.am[this.molecules[c].modelIndex],
a.firstMoleculeIndex=c,a.moleculeCount++;return this.molecules});c(c$,"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];null!=c&&(!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");h(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$,"getAtomBitsMaybeDeleted",function(a,b){var d;switch(a){default:return this.getAtomBitsMDa(a,b,new JU.BS);case 1073741925:case 1073742189:case 1111490587:case 1073742128:case 1073741863:case 1086324744:return d=new JU.BS,this.haveBioModels?this.bioModelset.getAtomBitsStr(a,b,d):d;case 1677721602:case 1073742331:return this.getAtomBitsMDb(a,
b);case 1678381065:var c=this.getBoxInfo(b,1);d=this.getAtomsWithin(c.getBoundBoxCornerVector().length()+1E-4,c.getBoundBoxCenter(),null,-1);for(var g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))c.isWithin(this.at[g])||d.clear(g);return d;case 1094713349:d=new JU.BS;for(g=this.ac;0<=--g;)null!=this.at[g]&&this.isInLatticeCell(g,b,this.ptTemp2,!1)&&d.set(g);return d;case 1094713350:d=JU.BSUtil.newBitSet2(0,this.ac);c=B(-1,[C(b.x)-1,C(b.y)-1,C(b.z)-1,C(b.x),C(b.y),C(b.z),0]);for(g=this.mc;0<=--g;){var e=
this.getUnitCell(g);null==e?JU.BSUtil.andNot(d,this.am[g].bsAtoms):d.andNot(e.notInCentroid(this,this.am[g].bsAtoms,c))}return d;case 1094713360:return this.getMoleculeBitSet(b);case 1073742363:return this.getSelectCodeRange(b);case 2097196:d=JU.BS.newN(this.ac);c=-1;e=0;for(g=this.ac;0<=--g;){var j=this.at[g];if(null!=j){var h=j.atomSymmetry;if(null!=h){if(j.mi!=c){c=j.mi;if(null==this.getModelCellRange(c))continue;e=this.getModelSymmetryCount(c)}for(var j=0,k=e;0<=--k;)if(h.get(k)&&1<++j){d.set(g);
break}}}}return d;case 1088421903:return JU.BSUtil.copy(null==this.bsSymmetry?this.bsSymmetry=JU.BS.newN(this.ac):this.bsSymmetry);case 1814695966:d=new JU.BS;if(null==this.vwr.getCurrentUnitCell())return d;this.ptTemp1.set(1,1,1);for(g=this.ac;0<=--g;)null!=this.at[g]&&this.isInLatticeCell(g,this.ptTemp1,this.ptTemp2,!1)&&d.set(g);return d}},"~N,~O");c(c$,"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 j=this.am[e],h,k=j.chainCount;0<=--k;){var r=j.chains[k];if(-1==a||a==(h=r.chainID)||!g&&0<h&&300>h&&a==this.chainToUpper(h))for(var n=r.groups,r=r.groupCount,q=0;0<=q;)q=JM.ModelSet.selectSeqcodeRange(n,r,q,d,c,b)}return b},"~A");c$.selectSeqcodeRange=c(c$,"selectSeqcodeRange",function(a,b,d,c,g,e){var j,h,k,r=!1;for(h=d;h<b&&a[h].seqcode!=c;h++);if(h==b){if(0<d)return-1;r=!0;k=2147483647;for(var n=b;0<=--n;)if((j=a[n].seqcode)>c&&j-c<k)h=
n,k=j-c;if(2147483647==k)return-1}if(2147483647==g)c=b-1,r=!0;else{for(c=h;c<b&&a[c].seqcode!=g;c++);if(c==b){if(0<d)return-1;r=!0;k=2147483647;for(n=h;n<b;n++)if((j=a[n].seqcode)<g&&g-j<k)c=n,k=g-j;if(2147483647==k)return-1}}for(n=h;n<=c;++n)a[n].setAtomBits(e);return r?-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 j=this.getSelectedAtomIterator(null,!1,!1,!1,!1);if(d){d=!this.vwr.g.legacyJavaFloat;for(var h=new JU.P3,k=b.nextSetBit(0);0<=k;k=b.nextSetBit(k+1))for(var r=this.mc;0<=--r;)e.get(r)&&(0>a?this.getAtomsWithin(a,this.at[k].getFractionalUnitCoordPt(d,!0,h),g,-1):(this.setIteratorForAtom(j,r,k,a,c),j.addAtoms(g)))}else{g.or(b);for(k=b.nextSetBit(0);0<=k;k=b.nextSetBit(k+1))0>a?this.getAtomsWithin(a,
this.at[k],g,this.at[k].mi):(this.setIteratorForAtom(j,-1,k,a,c),j.addAtoms(g))}j.release();return g},"~N,JU.BS,~B,J.atomdata.RadiusData");c(c$,"getAtomsWithin",function(a,b,d,c){null==d&&(d=new JU.BS);if(0>a){a=-a;for(var g=this.ac;0<=--g;){var e=this.at[g];null==e||0<=c&&e.mi!=c||!d.get(g)&&e.getFractionalUnitDistance(b,this.ptTemp1,this.ptTemp2)<=a&&d.set(e.i)}return d}c=this.getIterativeModels(!0);g=this.getSelectedAtomIterator(null,!1,!1,!1,!1);for(e=this.mc;0<=--e;)c.get(e)&&!this.am[e].bsAtoms.isEmpty()&&
(this.setIteratorForAtom(g,-1,this.am[e].firstAtomIndex,-1,null),g.setCenter(b,a),g.addAtoms(d));g.release();return d},"~N,JU.T3,JU.BS,~N");c(c$,"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$,"makeConnections2",function(a,b,d,c,
g,e,j,h,k,r){null==j&&(j=new JU.BS);var n=65535==d,q=131071==d,z=65537==d;q&&(d=1);var A=JU.Edge.isOrderH(d),m=!1,p=!1,s=!1,t=!1;switch(c){case 12291:return this.deleteConnections(a,b,d,g,e,h,q);case 603979872:case 1073741852:if(515!=d){if(h){a=g;g=new JU.BS;e=new JU.BS;for(var u=a.nextSetBit(0);0<=u;u=a.nextSetBit(u+1))g.set(this.bo[u].atom1.i),e.set(this.bo[u].atom2.i)}return B(-1,[A?this.autoHbond(g,e,!1):this.autoBondBs4(g,e,null,j,this.vwr.getMadBond(),603979872==c),0])}p=t=!0;break;case 1086324745:m=
p=!0;break;case 1073742025:p=!0;break;case 1073741904:s=!0}c=!m||n;n=!m&&!n;this.defaultCovalentMad=this.vwr.getMadBond();var q=0>a,w=0>b,v=q||w,x=!h||0.1!=a||1E8!=b;x&&(a=this.fixD(a,q),b=this.fixD(b,w));var y=this.getDefaultMadFromOrder(d),C=0,F=0,G=null,I=null,K=null,L="\x00",M=d|131072,N=0!=(d&512);try{for(u=g.nextSetBit(0);0<=u;u=g.nextSetBit(u+1)){if(h)G=this.bo[u],I=G.atom1,K=G.atom2;else{I=this.at[u];if(I.isDeleted())continue;L=this.isModulated(u)?"\x00":I.altloc}for(var O=h?0:e.nextSetBit(0);0<=
O;O=e.nextSetBit(O+1)){if(h)O=2147483646;else{if(O==u)continue;K=this.at[O];if(null==K||I.mi!=K.mi||K.isDeleted())continue;if("\x00"!=L&&L!=K.altloc&&"\x00"!=K.altloc)continue;G=I.getBond(K)}if(!(null==G?p:s)&&!(x&&!this.isInRange(I,K,a,b,q,w,v)||N&&!this.allowAromaticBond(G)))if(null==G)j.set(this.bondAtoms(I,K,d,y,j,r,k,!0).index),C++;else if(n&&(G.setOrder(d),z&&(this.haveAtropicBonds=!0,G.setAtropisomerOptions(g,e)),this.bsAromatic.clear(G.index)),c||d==G.order||M==G.order||A&&G.isHydrogen())j.set(G.index),
F++}}}catch(P){if(!D(P,Exception))throw P;}t&&this.assignAromaticBondsBs(!0,j);m||this.sm.setShapeSizeBs(1,-2147483648,null,j);return B(-1,[C,F])},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"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 j=this.vwr.getFloat(570425364),j=j*j,h=0;this.showRebondTimes&&JU.Logger.startTimer("autobond");var k=
-1,r=null==a,n,q;r?(q=0,n=null):(a.equals(b)?n=a:(n=JU.BSUtil.copy(a),n.or(b)),q=n.nextSetBit(0));for(var z=this.getSelectedAtomIterator(null,!1,!1,!0,!1),m=!1;0<=q&&q<this.ac;q=r?q+1:n.nextSetBit(q+1)){var p=r||a.get(q),s=r||b.get(q),t=this.at[q];if(!(null==t||t.isDeleted())){var u=t.mi;if(u!=k){k=u;if(this.isJmolDataFrameForModel(u)){q=this.am[u].firstAtomIndex+this.am[u].act-1;continue}m=this.getInfoB(u,"autoBondUsingOccupation")}u=t.getBondingRadius();if(0!=u){var w=t.getFormalCharge(),v=0!=w;
v&&(w=Math.signum(w));var x=null!=d&&d.get(q);for(this.setIteratorForAtom(z,-1,q,u+this.maxBondingRadius+e,null);z.hasNext();){var y=this.at[z.next()];if(!y.isDeleted()){var B=y.i,C=r||a.get(B),D=r||b.get(B);!C&&!D||(!(p&&D||s&&C)||x&&d.get(B)||m&&null!=this.occupancies&&50>this.occupancies[q]!=50>this.occupancies[B]||v&&Math.signum(y.getFormalCharge())==w)||(B=this.isBondable(u,y.getBondingRadius(),z.foundDistance2(),j,e)?1:0,0<B&&this.autoBondCheck(t,y,B,g,c)&&h++)}}z.release()}}}this.showRebondTimes&&
JU.Logger.checkTimer("autoBond",!1);return h},"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 j=b.getFormalCharge();if(0>e&&0>j||0<e&&0<j)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$,"autoBond_Pre_11_9_24",function(a,b,d,c,g){if(0==this.ac)return 0;0==g&&(g=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var e=this.vwr.getFloat(570425348),j=this.vwr.getFloat(570425364),j=j*j,h=0;this.initializeBspf();for(var k=-1,r=this.ac;0<=--r;){var n=this.at[r];if(null!=n){var q=null==a||a.get(r),z=null==b||b.get(r);if((q||z)&&!n.isDeleted()){var m=
n.mi;if(m!=k&&(k=m,this.isJmolDataFrameForModel(m))){for(;0<=--r&&!(null==this.at[r]||this.at[r].mi!=m););r++;continue}var p=n.getBondingRadius();if(0!=p){var s=p+this.maxBondingRadius+e;this.initializeBspt(m);m=this.bspf.getCubeIterator(m);for(m.initialize(n,s,!0);m.hasMoreElements();)if(s=m.nextElement(),!(s===n||s.isDeleted())){var t=s.i,u=null==a||a.get(t),w=null==b||b.get(t);if(!(!u&&!w||null!=d&&d.get(t)&&d.get(r)))if(q&&w||z&&u)t=this.isBondable(p,s.getBondingRadius(),m.foundDistance2(),j,
e)?1:0,0<t&&this.autoBondCheck(n,s,t,g,c)&&h++}m.release()}}}}return h},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(c$,"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 j,h;d?(j=this.vwr.getFloat(570425361),h=1):(j=this.vwr.getFloat(570425360),h=JM.ModelSet.hbondMinRasmol*JM.ModelSet.hbondMinRasmol);var k=j*j,r=3.141592653589793*this.vwr.getFloat(570425359)/
180,n=0,q=0,m=new JU.V3,A=new JU.V3;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var p=null,s=null;b=this.getSelectedAtomIterator(b,!1,!1,!1,!1);for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1)){var t=this.at[g],u=t.getElementNumber(),w=1==u;if(!(w?!d:d||7!=u&&8!=u)){if(w){var u=!1,v=t.bonds;if(null==v)continue;for(var x=!1,y=0;!x&&y<v.length;y++)x=v[y].getOtherAtom(t).getElementNumber(),x=7==x||8==x;if(!x)continue}else u=e.get(g);for(this.setIteratorForAtom(b,-1,t.i,j,null);b.hasNext();)if(v=
this.at[b.next()],y=v.getElementNumber(),!(v===t||(w?1==y:7!=y&&8!=y)||(q=b.foundDistance2())<h||q>k||u&&e.get(v.i)||t.isBonded(v))){if(0<r){m.sub2(t,v);if(null==(s=JM.ModelSet.checkMinAttachedAngle(t,r,m,A,d)))continue;m.scale(-1);if(null==(p=JM.ModelSet.checkMinAttachedAngle(v,r,m,A,d)))continue}y=0;w&&!Float.isNaN(p.x)&&!Float.isNaN(s.x)?(x=4096,y=JM.HBond.getEnergy(Math.sqrt(q),p.distance(t),p.distance(s),v.distance(s))/1E3):x=2048;c.set(this.addHBond(t,v,x,y));n++}}}b.release();this.sm.setShapeSizeBs(1,
-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return d?n:-n},"JU.BS,JU.BS,~B");c$.checkMinAttachedAngle=c(c$,"checkMinAttachedAngle",function(a,b,d,c,g){var e=a.bonds,j=!0,h=null;if(null!=e&&0<e.length)for(var k=3.4028235E38,r=e.length;0<=--r;)if(e[r].isCovalent()){var j=!1,n=e[r].getOtherAtom(a);if(g||1!=n.getElementNumber()){c.sub2(a,n);var q=c.angle(d);if(q<b)return null;q<k&&(h=n,k=q)}}return j?JU.P3.new3(NaN,0,0):h},"JM.Atom,~N,JU.V3,JU.V3,~B");c(c$,"setStructureIndexes",
function(){for(var a,b=0,d=-1,c=-1,g=-1,e=0;e<this.ac;e++)if(null!=this.at[e]){if((c=this.at[e].mi)!=g)b=0,g=c,d=-1;if((a=this.at[e].group.getStrucNo())!=d&&0!=a)this.at[e].group.setStrucNo(++b),d=b}});c(c$,"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=u(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$,"deleteAtoms",function(a){if(null!=a){for(var b=new JU.BS,d=a.nextSetBit(0);0<=d&&d<this.ac;d=a.nextSetBit(d+1))this.at[d].$delete(b);
for(d=0;d<this.mc;d++){var c=this.am[d];c.resetDSSR(!1);c.bsAtomsDeleted.or(a);c.bsAtomsDeleted.and(c.bsAtoms);a=JU.BSUtil.andNot(c.bsAtoms,c.bsAtomsDeleted);c.firstAtomIndex=a.nextSetBit(0);c.act=a.cardinality();c.isOrderly=c.act==c.bsAtoms.length()}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 j=g[e];null!=j&&(j.atomIndex1=c)}if(null!=this.atomNames)for(c=b;c<d;c++)this.atomNames[c]=this.atomNames[a[c]];if(null!=this.atomTypes)for(c=b;c<d;c++)this.atomTypes[c]=this.atomTypes[a[c]];
if(null!=this.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,j,h,k,r,n,q,m,A,p,s,t,u,w,v){h=(new JM.Atom).setAtom(a,this.ac,k,r,w,h,d,
q,t);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]=h;this.setBFactor(this.ac,p,!1);this.setOccupancy(this.ac,A,!1);this.setPartialCharge(this.ac,m,!1);null!=s&&this.setAtomTensors(this.ac,s);h.group=b;h.colixAtom=this.vwr.cm.getColixAtomPalette(h,J.c.PAL.CPK.id);null!=c&&(null!=g&&(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[this.ac]=
g),h.atomID=u,0==u&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern()));-2147483648!=e&&(null==this.atomSerials&&(this.atomSerials=B(this.at.length,0)),this.atomSerials[this.ac]=e);0!=j&&(null==this.atomSeqIDs&&(this.atomSeqIDs=B(this.at.length,0)),this.atomSeqIDs[this.ac]=j);null!=n&&this.setVibrationVector(this.ac,n);Float.isNaN(v)||this.setBondingRadius(this.ac,v);this.ac++;return h},"~N,JM.Group,~N,~S,~S,~N,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.Lst,~B,~N,JU.BS,~N");
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$,"isAtomInLastModel",function(a){return 0<=
a&&this.at[a].mi==this.mc-1},"~N");c(c$,"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=B(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 j=this.at[a];if(null!=j){j.mi!=g&&(g=j.mi,e=c?0:1);var h=this.atomSerials[a];if(a>=-b){if(0==h||0>b)this.atomSerials[a]=a<b?d.atomSerials[a]:e;if(null==this.atomNames[a]||0>b)this.atomNames[a]=(j.getElementSymbol()+this.atomSerials[a]).intern()}else h>e&&(e=h);(!this.am[g].isModelKit||0<j.getElementNumber()&&!j.isDeleted())&&e++}}},"~N,~N,JM.AtomCollection");c(c$,"setUnitCellOffset",function(a,
b,d){null!=a&&(null==b?a.setOffset(d):a.setOffsetPt(b))},"J.api.SymmetryInterface,JU.T3,~N");c(c$,"connect",function(a){this.resetMolecules();for(var b=new JU.BS,d=0;d<a.length;d++){var c=a[d];if(!(null==c||2>c.length)){var g=C(c[0]),e=0>g;e&&(g=-1-g);var j=C(c[1]);if(!(0>j||g>=this.ac||j>=this.ac)){var h=2<c.length?C(c[2]):1;0>h&&(h&=65535);var k=3<c.length?ea(1E3*a[d][3]):this.getDefaultMadFromOrder(h);0==h||0==k&&32768!=h&&!JU.Edge.isOrderH(h)?(c=this.at[g].getBond(this.at[j]),null!=c&&b.set(c.index)):
this.bondAtoms(this.at[g],this.at[j],h,k,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$,"getModelIndexFromId",function(a){var b=0<=a.indexOf("#"),d=a.toLowerCase().endsWith(".basemodel");
d&&(a=a.substring(0,a.length-10));for(var c=-1,g=null,e=0;e<this.mc;e++){var j=this.getInfo(e,"modelID"),h=a.startsWith("~")?"~"+this.getModelNumberDotted(e):null;if(!(null==h&&null==j&&null==(j=this.getModelTitle(e)))){b&&(g=this.getModelFileName(e),g.endsWith("#molfile")?j=g:(g+="#",j=g+j));if(a.equalsIgnoreCase(j)||a.equalsIgnoreCase(h))return d?this.vwr.getJDXBaseModelIndex(e):e;null!=g&&a.startsWith(g)&&(c=-2)}}return null==g&&!b?-2:c},"~S");c(c$,"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,j=null,h=d-1;0<=--h;)for(var k=d;--k>h;)if(c=this.at[a[h]],g=this.at[a[k]],c.isBonded(g))for(var r=d;0<=--r;)if(r!=h&&r!=k&&(e=this.at[a[r]]).isBonded(c))for(var n=
d;0<=--n;)if(n!=h&&n!=k&&n!=r&&(j=this.at[a[n]]).isBonded(g)){var q=B(4,0);q[0]=e.i;q[1]=c.i;q[2]=g.i;q[3]=j.i;b.addLast(q)}d=b.size();a=JU.AU.newInt2(d);for(h=d;0<=--h;)a[d-h-1]=b.get(h);return a},"~A");c(c$,"setModulation",function(a,b,d,c){if(null==this.bsModulated)if(b)this.bsModulated=new JU.BS;else if(null==a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var g=this.vwr.getFloat(1275072532),e=!1,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){var h=this.getModulation(j);
null!=h&&(h.setModTQ(this.at[j],b,d,c,g),null!=this.bsModulated&&this.bsModulated.setBitTo(j,b),e=!0)}e||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(c$,"getBoundBoxOrientation",function(a,b){var d=0,c=0,g=0,e=null,j=null,h=b.nextSetBit(0),k=0;if(0<=h){c=null==this.vOrientations?0:this.vOrientations.length;if(0==c){e=Array(3375);c=0;k=new JU.P4;for(d=-7;7>=d;d++)for(g=-7;7>=g;g++)for(var r=0;14>=r;r++,c++)1<(e[c]=JU.V3.new3(d/7,g/7,r/14)).length()&&--c;this.vOrientations=Array(c);for(d=c;0<=--d;)r=
Math.sqrt(1-e[d].lengthSquared()),Float.isNaN(r)&&(r=0),k.set4(e[d].x,e[d].y,e[d].z,r),this.vOrientations[d]=JU.Quat.newP4(k)}var r=new JU.P3,k=3.4028235E38,n=null,q=new JU.BoxInfo;q.setMargin(1312817669==a?0:0.1);for(d=0;d<c;d++){e=this.vOrientations[d];q.reset();for(g=h;0<=g;g=b.nextSetBit(g+1))q.addBoundBoxPoint(e.transform2(this.at[g],r));switch(a){default:case 1312817669:case 1073741864:case 1814695966:g=(q.bbCorner1.x-q.bbCorner0.x)*(q.bbCorner1.y-q.bbCorner0.y)*(q.bbCorner1.z-q.bbCorner0.z);
break;case 1111492629:g=q.bbCorner1.x-q.bbCorner0.x;break;case 1111492630:g=q.bbCorner1.y-q.bbCorner0.y;break;case 1111492631:g=q.bbCorner1.z-q.bbCorner0.z}g<k&&(j=e,n=q,q=new JU.BoxInfo,q.setMargin(0.1),k=g)}switch(a){default:return j;case 1814695966:h=n.getBoundBoxVertices();h=v(-1,[h[0],h[4],h[2],h[1]]);j=j.inv();for(d=0;4>d;d++)j.transform2(h[d],h[d]),0<d&&h[d].sub(h[0]);return h;case 1312817669:case 1073741864:e=JU.Quat.newQ(j),d=n.bbCorner1.x-n.bbCorner0.x,c=n.bbCorner1.y-n.bbCorner0.y,g=n.bbCorner1.z-
n.bbCorner0.z,d<c&&(r.set(0,0,1),e=JU.Quat.newVA(r,90).mulQ(e),j=d,d=c,c=j),c<g&&(g>d&&(r.set(0,1,0),e=JU.Quat.newVA(r,90).mulQ(e),j=d,d=g,g=j),r.set(1,0,0),e=JU.Quat.newVA(r,90).mulQ(e),j=c,c=g,g=j)}}return 1312817669==a?k+"\t{"+d+" "+c+" "+g+"}\t"+b:1814695966==a?null:null==e||0==e.getTheta()?new JU.Quat:e},"~N,JU.BS");c(c$,"getUnitCellForAtom",function(a){if(0>a||a>this.ac)return null;if(null!=this.bsModulated){var b=this.getModulation(a),b=null==b?null:b.getSubZystemUnitCell();if(null!=b)return b}return this.getUnitCell(this.at[a].mi)},
"~N");c(c$,"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=u(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 j=C(a[e+1]),h=C(a[e+2]),k=""+j+"_"+
h;if(!c.containsKey(k)){c.put(k,Boolean.TRUE);for(var k=this.vwr.getBranchBitSet(h,j,!0),r=this.at[j].bonds,j=this.at[j],n=0;n<r.length;n++){var q=r[n];if(q.isCovalent()&&(q=q.getOtherAtom(j).i,q!=h&&k.get(q))){k=null;break}}d[g]=k}}return d},"~A");c(c$,"recalculatePositionDependentQuantities",function(a,b){null!=this.vwr.shm.getShape(21)&&this.vwr.shm.getShapePropertyData(21,"move",v(-1,[a,b]));this.haveStraightness&&this.calculateStraightnessAll();this.recalculateLeadMidpointsAndWingVectors(-1);
for(var d=this.getModelBS(a,!1),c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))if(this.sm.notifyAtomPositionsChanged(c,a,b),null!=b){var g=this.am[c];g.isContainedIn(a)&&(null==g.mat4&&(g.mat4=JU.M4.newM4(null)),g.mat4.mul2(b,g.mat4))}},"JU.BS,JU.M4");c(c$,"moveAtoms",function(a,b,d,c,g,e,j,h){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(!h){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));j?(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))j?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);j||(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);h||(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$,"setDihedrals",function(a,b,d){var c=u(a.length/6);1<d&&(d=1);for(var g=
0,e=0;g<c;g++,e+=6){var j=b[g];if(!(null==j||j.isEmpty())){var h=this.at[C(a[e+1])],k=JU.V3.newVsub(this.at[C(a[e+2])],h),k=JU.A4.newVA(k,-((a[e+5]-a[e+4])*d)/57.29577951308232);this.matTemp.setAA(k);this.ptTemp.setT(h);for(h=j.nextSetBit(0);0<=h;h=j.nextSetBit(h+1))this.at[h].sub(this.ptTemp),this.matTemp.rotate(this.at[h]),this.at[h].add(this.ptTemp),this.taintAtom(h,2)}}},"~A,~A,~N");c(c$,"setAtomCoordsRelative",function(a,b){this.setAtomsCoordRelative(b,a.x,a.y,a.z);this.mat4.setIdentity();this.vTemp.setT(a);
this.mat4.setTranslation(this.vTemp);this.recalculatePositionDependentQuantities(b,this.mat4)},"JU.T3,JU.BS");c(c$,"setAtomCoords",function(a,b,d){this.setAtomCoord2(a,b,d);switch(b){case 1111492626:case 1111492627:case 1111492628:case 1145047055:break;default:this.recalculatePositionDependentQuantities(a,null)}},"JU.BS,~N,~O");c(c$,"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 j=2*(a.z-this.at[g].z);this.setAtomCoordRelative(g,e,d,j)}else if(null!=b){a=JU.V3.new3(b.x,b.y,b.z);a.normalize();for(var h=Math.sqrt(b.x*b.x+b.y*b.y+b.z*b.z),g=c.nextSetBit(0);0<=g;g=c.nextSetBit(g+1))j=2*-JU.Measure.distanceToPlaneD(b,h,this.at[g]),e=a.x*j,d=a.y*j,j*=a.z,this.setAtomCoordRelative(g,e,d,j)}else if(0<=d&&(b=this.at[d],a=b.bonds,null!=a)){e=new JU.BS;j=new JU.Lst;h=this.vwr.getModelUndeletedAtomsBitSet(b.mi);for(g=0;g<a.length;g++){var k=a[g].getOtherAtom(b);c.get(k.i)?e.or(JU.JmolMolecule.getBranchBitSet(this.at,
k.i,h,null,d,!0,!0)):j.addLast(k)}0!=j.size()&&(a=JU.Measure.getCenterAndPoints(j)[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$,"getCellWeights",function(a){var b=null,d=a.nextSetBit(0),c=-1;if(0<=d&&null!=this.getUnitCell(c=this.at[d].mi)){var g=new JU.P3;this.getModelAtomBitSetIncludingDeleted(c,!0).and(a);b=L(a.cardinality(),0);for(c=0;0<=d;d=a.nextSetBit(d+1))b[c++]=JU.SimpleUnitCell.getCellWeight(this.at[d].getFractionalUnitCoordPt(!0,
!1,g))}return b},"JU.BS");c(c$,"getAtomGroupQuaternions",function(a,b,d){var c=0,g=new JU.Lst;a=JU.BSUtil.copy(a);for(var e=new JU.BS,j=a.nextSetBit(0);0<=j&&c<b;j=a.nextSetBit(j+1)){var h=this.at[j].group;h.setAtomBits(e);a.andNot(e);var k=h.getQuaternion(d);if(null==k&&(this.am[this.at[j].mi].isBioModel||(k=h.getQuaternionFrame(this.at)),null==k))continue;c++;g.addLast(k)}return g.toArray(Array(g.size()))},"JU.BS,~N,~S");c(c$,"getConformation",function(a,b,d,c){var g=new JU.BS;if(0<=b)for(var e=
this.mc;0<=--e;)if(!(e!=a&&0<=a)){var j=this.am[e],h=this.vwr.getModelUndeletedAtomsBitSet(a);null!=c&&h.and(c);if(!(0>h.nextSetBit(0)))if(b>=j.altLocCount)0==b&&g.or(h);else if(!this.am[e].isBioModel||!this.am[e].getConformation(b,d,h,g)){for(var k=this.getAltLocCountInModel(e),j=this.getAltLocListInModel(e),r=new JU.BS;0<=--k;)k!=b&&h.andNot(this.getAtomBitsMDa(1073742355,j.substring(k,k+1),r));0<=h.nextSetBit(0)&&g.or(h)}}return g},"~N,~N,~B,JU.BS");c(c$,"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,j){this.haveBioModels&&this.bioModelset.calcAllRasmolHydrogenBonds(a,b,d,c,g,e,j,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,j){this.freezeModels();return this.haveBioModels?this.bioModelset.calculateAllStructuresExcept(a,b,d,c,g,e,j):""},"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,j=null;c&&(e=new java.util.Hashtable,j=new JU.Lst,e.put("atoms",j),e.put("points",g));var h=null==b?-1:b.nextSetBit(0);b=this.vwr.getModelUndeletedAtomsBitSet(0>
h?this.vwr.am.cmi:this.at[h].mi);0>h&&(h=b.nextSetBit(0));if(0<=h){var k=this.getUnitCellForAtom(h);if(null!=k){b=k.getIterator(this.vwr,this.at[h],this.at,b,a);for(null!=d&&b.setCenter(d,a);b.hasNext();)h=b.next(),d=b.getPosition(),g.addLast(d),c&&j.addLast(Integer.$valueOf(h))}}return c?e:g},"~N,JU.BS,JU.P3,~B");c(c$,"calculateDssrProperty",function(a){if(null!=a){if(null==this.dssrData||this.dssrData.length<this.ac)this.dssrData=L(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$,"calculateChiralityForAtoms",function(a,b){this.haveChirality=!0;for(var d=a.nextSetBit(0);0<=
d;d=a.nextSetBit(d+1))this.at[d].setCIPChirality(0);J.api.Interface.getSymmetry(this.vwr,"ms").calculateCIPChiralityForAtoms(this.vwr,a);if(!b)return null;for(var c="",d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))c+=this.at[d].getCIPChirality(!1);return c},"JU.BS,~B");G(c$,"hbondMinRasmol",2.5)});m("JM");x(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){c$=w(function(){this.rotationMatrix=this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=
null;this.cameraY=this.cameraX=this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.vwr=this.pymolView=this.moveToText=null;s(this,arguments)},JM,"Orientation");O(c$,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});p(c$,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")});m("JM");x(null,"JM.StateScript",["JU.SB","JU.BSUtil",
"$.Escape"],function(){c$=w(function(){this.modelIndex=0;this.script2=this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;s(this,arguments)},JM,"StateScript");p(c$,function(a,b,d,c,g,e,j){this.modelIndex=a;this.script1=b;this.bsBonds=JU.BSUtil.copy(d);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(g);this.script2=e;this.inDefinedStateBlock=j},"~N,~S,JU.BS,JU.BS,JU.BS,~S,~B");c(c$,"isValid",function(){return null!=this.script1&&0<this.script1.length&&
(null==this.bsBonds||0<=this.bsBonds.nextSetBit(0))&&(null==this.bsAtoms1||0<=this.bsAtoms1.nextSetBit(0))&&(null==this.bsAtoms2||0<=this.bsAtoms2.nextSetBit(0))});h(c$,"toString",function(){if(!this.isValid())return"";var a=JU.SB.newS(this.script1);null!=this.bsBonds&&a.append(" ").append(JU.Escape.eBond(this.bsBonds));null!=this.bsAtoms1&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms1));null!=this.bsAtoms2&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms2));null!=this.script2&&a.append(" ").append(this.script2);
a=a.toString();a.endsWith(";")||(a+=";");return a});c(c$,"isConnect",function(){return 0<=this.script1.indexOf("connect")});c(c$,"deleteAtoms",function(a,b,d){if(a==this.modelIndex)return!1;if(a>this.modelIndex)return!0;JU.BSUtil.deleteBits(this.bsBonds,b);JU.BSUtil.deleteBits(this.bsAtoms1,d);JU.BSUtil.deleteBits(this.bsAtoms2,d);return this.isValid()},"~N,JU.BS,JU.BS");c(c$,"setModelIndex",function(a){this.modelIndex=a},"~N")});m("JM");K(JM,"Structure");m("JM");c$=w(function(){this.id="";this.type=
" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=0;this.signFactor=1;this.reference=null;s(this,arguments)},JM,"TickInfo");p(c$,function(a){this.ticks=a},"JU.P3");m("JU");x(["JU.P3","$.V3"],"JU.BoxInfo",["JU.Point3fi"],function(){c$=w(function(){this.bbVertices=this.bbVector=this.bbCenter=this.bbCorner1=this.bbCorner0=null;this.isScaleSet=!1;this.margin=0;s(this,arguments)},JU,"BoxInfo");O(c$,function(){this.bbCorner0=new JU.P3;this.bbCorner1=new JU.P3;this.bbCenter=new JU.P3;this.bbVector=
new JU.V3;this.bbVertices=Array(8);for(var a=0;8>a;a++)JU.BoxInfo.unitBboxPoints[a]=JU.P3.new3(-1,-1,-1),JU.BoxInfo.unitBboxPoints[a].scaleAdd2(2,JU.BoxInfo.unitCubePoints[a],JU.BoxInfo.unitBboxPoints[a])});p(c$,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$,"getVerticesFromOABC",function(a){for(var b=Array(8),d=0;7>=d;d++)b[d]=JU.P3.newP(a[0]),4==(d&4)&&b[d].add(a[1]),2==(d&2)&&b[d].add(a[2]),1==(d&1)&&b[d].add(a[3]);return b},"~A");c$.getCanonicalCopy=c(c$,"getCanonicalCopy",function(a,b){for(var d=Array(8),c=0;8>c;c++)d[JU.BoxInfo.toCanonical[c]]=JU.P3.newP(a[c]);JU.BoxInfo.scaleBox(d,
b);return d},"~A,~N");c$.toOABC=c(c$,"toOABC",function(a,b){var d=JU.P3.newP(a[0]),c=JU.P3.newP(a[4]),g=JU.P3.newP(a[2]),e=JU.P3.newP(a[1]);c.sub(d);g.sub(d);e.sub(d);null!=b&&d.add(b);return v(-1,[d,c,g,e])},"~A,JU.T3");c(c$,"getBoundBoxCenter",function(){this.isScaleSet||this.setBbcage(1);return this.bbCenter});c(c$,"getBoundBoxCornerVector",function(){this.isScaleSet||this.setBbcage(1);return this.bbVector});c(c$,"getBoundBoxPoints",function(a){this.isScaleSet||this.setBbcage(1);return a?v(-1,
[this.bbCenter,JU.P3.newP(this.bbVector),this.bbCorner0,this.bbCorner1]):v(-1,[this.bbCorner0,this.bbCorner1])},"~B");c(c$,"getBoundBoxVertices",function(){this.isScaleSet||this.setBbcage(1);return this.bbVertices});c(c$,"setBoundBoxFromOABC",function(a){for(var b=JU.P3.newP(a[0]),d=new JU.P3,c=0;4>c;c++)d.add(a[c]);this.setBoundBox(b,d,!0,1)},"~A");c(c$,"setBoundBox",function(a,b,d,c){if(null!=a){if(0==c)return;if(d){if(0==a.distance(b))return;this.bbCorner0.set(Math.min(a.x,b.x),Math.min(a.y,b.y),
Math.min(a.z,b.z));this.bbCorner1.set(Math.max(a.x,b.x),Math.max(a.y,b.y),Math.max(a.z,b.z))}else{if(0==b.x||0==b.y&&0==b.z)return;this.bbCorner0.set(a.x-b.x,a.y-b.y,a.z-b.z);this.bbCorner1.set(a.x+b.x,a.y+b.y,a.z+b.z)}}this.setBbcage(c)},"JU.T3,JU.T3,~B,~N");c(c$,"setMargin",function(a){this.margin=a},"~N");c(c$,"addBoundBoxPoint",function(a){this.isScaleSet=!1;JU.BoxInfo.addPoint(a,this.bbCorner0,this.bbCorner1,this.margin)},"JU.T3");c$.addPoint=c(c$,"addPoint",function(a,b,d,c){a.x-c<b.x&&(b.x=
a.x-c);a.x+c>d.x&&(d.x=a.x+c);a.y-c<b.y&&(b.y=a.y-c);a.y+c>d.y&&(d.y=a.y+c);a.z-c<b.z&&(b.z=a.z-c);a.z+c>d.z&&(d.z=a.z+c)},"JU.T3,JU.T3,JU.T3,~N");c$.addPointXYZ=c(c$,"addPointXYZ",function(a,b,d,c,g,e){a-e<c.x&&(c.x=a-e);a+e>g.x&&(g.x=a+e);b-e<c.y&&(c.y=b-e);b+e>g.y&&(g.y=b+e);d-e<c.z&&(c.z=d-e);d+e>g.z&&(g.z=d+e)},"~N,~N,~N,JU.P3,JU.P3,~N");c(c$,"setBbcage",function(a){this.isScaleSet=!0;this.bbCenter.add2(this.bbCorner0,this.bbCorner1);this.bbCenter.scale(0.5);this.bbVector.sub2(this.bbCorner1,
this.bbCenter);0<a?this.bbVector.scale(a):(this.bbVector.x-=a/2,this.bbVector.y-=a/2,this.bbVector.z-=a/2);for(a=8;0<=--a;){var b=this.bbVertices[a];b.setT(JU.BoxInfo.unitBboxPoints[a]);b.x*=this.bbVector.x;b.y*=this.bbVector.y;b.z*=this.bbVector.z;b.add(this.bbCenter)}this.bbCorner0.setT(this.bbVertices[0]);this.bbCorner1.setT(this.bbVertices[7])},"~N");c(c$,"isWithin",function(a){this.isScaleSet||this.setBbcage(1);return a.x>=this.bbCorner0.x&&a.x<=this.bbCorner1.x&&a.y>=this.bbCorner0.y&&a.y<=
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JV.ActionManager.newAction(25,"_rotate",J.i18n.GT.$("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$,"isDrawOrLabelAction",function(a){return this.drawMode&&this.bnd(a,[8,9])||this.labelMode&&this.bnd(a,[10])},"~N");c(c$,"getBondPickingMode",function(){return this.bondPickingMode});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;this.vwr.setStringProperty("pickingStyle","toggle");this.vwr.setBooleanProperty("bondPicking",!1);break;case 35:case 34:case 33:case 8:this.vwr.setBooleanProperty("bondPicking",!0);this.bondPickingMode=a;this.resetMeasurement();return}b=(new Boolean(b|this.apm!=
a)).valueOf();this.apm=a;b&&this.resetMeasurement()},"~N");c(c$,"getPickingState",function(){var a=";set modelkitMode "+this.vwr.getBoolean(603983903)+";set picking "+JV.ActionManager.getPickingModeName(this.apm);32==this.apm&&(a+="_"+this.vwr.getModelkitProperty("atomType"));a+=";";0!=this.bondPickingMode&&(a+="set picking "+JV.ActionManager.getPickingModeName(this.bondPickingMode));33==this.bondPickingMode&&(a+="_"+this.vwr.getModelkitProperty("bondType"));return a+";"});c(c$,"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$,"isDraggedIsShiftDown",function(){return 0!=(this.dragged.modifiers&1)});c(c$,"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$,"setMouseMode",function(){this.drawMode=this.labelMode=!1;this.dragSelectedMode=
this.vwr.getDragSelected();this.measuresEnabled=!this.dragSelectedMode;if(!this.dragSelectedMode)switch(this.apm){default:return;case 32:this.measuresEnabled=!this.vwr.getModelkit(!1).isPickAtomAssignCharge();return;case 4:this.drawMode=!0;this.measuresEnabled=!1;break;case 2:this.labelMode=!0;this.measuresEnabled=!1;break;case 9:this.measuresEnabled=!1;break;case 19:case 22:case 20:case 21:this.measuresEnabled=!1;return}this.exitMeasurementMode(null)});c(c$,"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(!D(b,Exception))throw b;}},"~B");c(c$,"setModeMouse",
function(a){-1==a&&this.startHoverWatcher(!1)},"~N");h(c$,"keyPressed",function(a,b){if(this.keyProcessing)return!1;this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&this.isAltKeyReleased&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1,b);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.vwr.hoverOff();this.exitMeasurementMode("escape");
break;default:this.vwr.hoverOff()}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");h(c$,"keyTyped",function(){return!1},"~N,~N");h(c$,"keyReleased",function(a){switch(a){case 18:this.moved.modifiers&=-9;this.dragSelectedMode&&this.vwr.moveSelected(2147483647,0,-2147483648,
-2147483648,-2147483648,null,!1,!1,this.moved.modifiers);this.isAltKeyReleased=!0;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");h(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");h(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(10,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(10,0,0,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 37: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){this.dragAtomIndex=this.vwr.findNearestAtomIndexMovable(a,b,!0);if(0<=this.dragAtomIndex&&
(32==this.apm||31==this.apm))34==this.bondPickingMode&&this.vwr.setModelkitProperty("bondAtomIndex",Integer.$valueOf(this.dragAtomIndex)),this.enterMeasurementMode(this.dragAtomIndex),this.mp.addPoint(this.dragAtomIndex,null,!1);a=this.vwr.getModelkitProperty("screenXY");this.mkBondPressed=null!=a&&this.pressed.inRange(10,a[0],a[1])}else this.bnd(this.pressAction,[23])?this.vwr.popupMenu(a,b,this.vwr.getBoolean(603983903)?"m":"j"):this.dragSelectedMode?(this.haveSelection=!g||0<=this.vwr.findNearestAtomIndexMovable(a,
b,!0))&&this.bnd(this.dragAction,[13,14])&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1,c):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(c$,"checkDragWheelAction",function(a,b,d,c,g,e,j){var h=JV.binding.Binding.getButtonMods(a);if(0!=h){var k=this.vwr.notifyMouseClicked(b,d,JV.binding.Binding.getMouseAction(this.pressedCount,h,j),j);if(0==k)return;0<k&&(a=k)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.vwr.refresh(3,"rubberBand selection");
else if(!this.checkUserAction(a,b,d,c,g,e,j))if(e=this.vwr.g.modelKitMode?this.vwr.getModelkit(!1).getRotateBondIndex():-1,0<=e&&(0<=this.dragAtomIndex||this.mkBondPressed||this.bnd(a,[26])))0<=this.dragAtomIndex&&(null==this.measurementQueued||0==this.measurementQueued.numSet?this.vwr.setPendingMeasurement(this.vwr.getModelkit(!1).setBondMeasure(e,this.measurementQueued=this.mp=this.getMP())):this.measurementQueued.refresh(null)),this.vwr.moveSelected(c,g,-2147483648,b,d,null,!1,!1,0<=this.dragAtomIndex?
0:16);else{e=null;if(0<=this.dragAtomIndex&&2!=this.apm)switch(this.apm){case 26:this.dragSelected(a,c,g,!0);return;case 36:case 37:case 27:case 30:e=this.vwr.ms.getAtoms(37==this.apm?1094717454:1094713360,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 37: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==j&&this.bnd(this.clickAction,[0])&&32==this.apm)a=this.vwr.findNearestAtomIndexMovable(b,d,!1),0<=a?(null!=this.mp?this.mp.setCount(1):this.measuresEnabled&&this.enterMeasurementMode(a),this.addToMeasurement(a,null,!0),this.mp.colix=20):null!=this.mp&&(this.mp.setCount(1),this.mp.colix=23),
null!=this.mp&&(this.vwr.antialiased&&(b<<=1,d<<=1),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,h),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$,"dragSelected",function(a,b,d,c){this.setMotion(13,!0);this.bnd(a,[27])&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(b,
!0),this.getDegrees(d,!1),null):this.vwr.moveSelected(b,d,c&&this.bnd(a,[14])?-d:-2147483648,-2147483648,-2147483648,null,!0,!1,this.dragged.modifiers)},"~N,~N,~N,~B");c(c$,"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);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.exitMeasurementMode(null):34==this.bondPickingMode?(this.vwr.setModelkitProperty("bondAtomIndex",Integer.$valueOf(this.dragAtomIndex)),this.exitMeasurementMode(null)):this.assignNew();else if(this.dragAtomIndex=-1,this.mkBondPressed=!1,this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=this.b.name.equals("drag"),this.rectRubber.x=
2147483647,c&&this.vwr.notifyMouseClicked(a,b,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.isDrawOrLabelAction(this.dragAction))this.vwr.checkObjectDragged(2147483647,0,a,b,this.dragAction);else if(this.haveSelection&&(this.dragSelectedMode&&this.bnd(this.dragAction,[13]))&&this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1,this.dragged.modifiers),(!c||!this.checkUserAction(this.pressAction,a,b,0,0,d,5))&&this.vwr.getBoolean(603979780)&&this.bnd(this.dragAction,
[44]))a=this.getExitRate(),0<a&&this.vwr.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.vwr.g.logGestures&&this.vwr.log("$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(10,0,"m");return}}d=null;var g=!1,e=!1,j=null;if(!this.drawMode&&(j=this.vwr.checkObjectClicked(a,b,this.clickAction),null!=j)){if(this.labelMode){this.pickLabel(j.get("atomIndex").intValue());return}g="bond".equals(j.get("type"));e="isosurface".equals(j.get("type"));
d=this.getPoint(j)}g&&(c=1);if(!(null!=d&&Float.isNaN(d.x))){var h=this.findNearestAtom(a,b,d,0<c);if(0==c&&32!=this.apm)null!=this.mp&&((null!=d||0==this.mp.getIndexOf(h))&&this.mp.addPoint(h,d,!1),this.mp.haveModified&&this.vwr.setPendingMeasurement(this.mp),this.vwr.refresh(3,"measurementPending"));else if(this.setMouseMode(),this.bnd(this.clickAction,[43])&&this.vwr.tm.stopMotion(),this.vwr.getBoolean(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(j.get("index").intValue());return}}else{if(e)return;if(32!=this.apm&&null!=this.mp&&this.bnd(this.clickAction,[20])){this.atomOrPointPicked(h,d);4==this.addToMeasurement(h,d,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,[37])){null!=this.mp?(this.addToMeasurement(h,d,!0),this.toggleMeasurement()):!this.drawMode&&
(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(h),this.addToMeasurement(h,d,!0));this.atomOrPointPicked(h,d);return}}this.isSelectAction(this.clickAction)?e||this.atomOrPointPicked(h,d):this.bnd(this.clickAction,[24])&&0>h&&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$,"checkUserAction",function(a,b,d,c,g,e,j){if(!this.b.isUserAction(a))return!1;for(var h=!1,k,r=this.b.getBindings(),n=a+"\t",q,m=r.keySet().iterator();m.hasNext()&&((q=m.next())||1);)if(0==q.indexOf(n)&&JU.AU.isAS(k=r.get(q))){var p=k[1],s=null;if(0<=p.indexOf("_ATOM")){var t=this.findNearestAtom(b,d,null,!0),p=JU.PT.rep(p,"_ATOM","({"+(0<=t?""+t:"")+"})");0<=t&&
(p=JU.PT.rep(p,"_POINT",JU.Escape.eP(this.vwr.ms.at[t])))}if(!this.drawMode&&(0<=p.indexOf("_POINT")||0<=p.indexOf("_OBJECT")||0<=p.indexOf("_BOND"))){t=this.vwr.checkObjectClicked(b,d,a);if(null!=t&&null!=(s=t.get("pt")))t.get("type").equals("bond")&&(p=JU.PT.rep(p,"_BOND","[{"+t.get("index")+"}]")),p=JU.PT.rep(p,"_POINT",JU.Escape.eP(s)),p=JU.PT.rep(p,"_OBJECT",JU.Escape.escapeMap(t));p=JU.PT.rep(p,"_BOND","[{}]");p=JU.PT.rep(p,"_OBJECT","{}")}p=JU.PT.rep(p,"_POINT","{}");p=JU.PT.rep(p,"_ACTION",
""+a);p=JU.PT.rep(p,"_X",""+b);p=JU.PT.rep(p,"_Y",""+(this.vwr.getScreenHeight()-d));p=JU.PT.rep(p,"_DELTAX",""+c);p=JU.PT.rep(p,"_DELTAY",""+g);p=JU.PT.rep(p,"_TIME",""+e);p=JU.PT.rep(p,"_MODE",""+j);p.startsWith("+:")&&(h=!0,p=p.substring(2));this.vwr.evalStringQuiet(p)}return!h},"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkMotionRotateZoom",function(a,b,d,c,g){b=this.bnd(a,[40])&&this.isZoomArea(this.pressed.x);var e=this.bnd(a,[25]),j=this.bnd(a,[29]);if(!b&&!e&&!j)return!1;a=(d=j&&(0==d||Math.abs(c)>5*
Math.abs(d)))||this.isZoomArea(this.moved.x)||this.bnd(a,[46])?8:e||j?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$,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),b=this.measurementQueued.getAtomIndex(2);if(!(0>a||0>b))try{var d=this.vwr.getSmilesOpt(null,a,b,1048576,null);this.vwr.setStatusMeasuring("measureSequence",-2,d,0)}catch(c){if(D(c,Exception))JU.Logger.error(c.toString());else throw c;}});c(c$,"minimize",
function(a){var b=this.dragAtomIndex;a&&(this.dragAtomIndex=-1,this.mkBondPressed=!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(){this.vwr.getModelkit(!1).handleAssignNew(this.pressed,this.dragged,this.mp,this.dragAtomIndex)||this.exitMeasurementMode("bond dropped");this.exitMeasurementMode(null)});c(c$,"bondPicked",function(a){33==this.bondPickingMode&&this.vwr.undoMoveActionClear(-1,4146,!0);switch(this.bondPickingMode){case 33:this.vwr.setModelkitProperty("scriptAssignBond",Integer.$valueOf(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$,"selectAtoms",function(a){if(!(null!=this.mp||this.selectionWorking)){this.selectionWorking=!0;var b=this.rubberbandSelectionMode||this.bnd(this.clickAction,[35])?"selected and not ("+a+") or (not selected) and ":this.bnd(this.clickAction,[32])?"selected and not ":this.bnd(this.clickAction,[34])?"selected or ":0==this.clickAction||this.bnd(this.clickAction,
[36])?"selected tog ":this.bnd(this.clickAction,[30])?"":null;if(null!=b)try{var d=this.vwr.getAtomBitSetEval(null,b+("("+a+")"));this.setAtomsPicked(d,"selected: "+JU.Escape.eBS(d));this.vwr.refresh(3,"selections set")}catch(c){if(!D(c,Exception))throw c;}this.selectionWorking=!1}},"~S");c(c$,"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$,"zoomTo",function(a){this.runScript("zoomTo (atomindex="+
a+")");this.vwr.setStatusAtomPicked(a,null,null,!1)},"~N");c(c$,"userActionEnabled",function(a){return this.vwr.isFunction(JV.ActionManager.getActionName(a).toLowerCase())},"~N");c(c$,"userAction",function(a,b){if(!this.userActionEnabled(a))return!1;var d=JS.ScriptEval.runUserAction(JV.ActionManager.getActionName(a),b,this.vwr);return!JS.SV.vF.equals(d)},"~N,~A");G(c$);c$.actionInfo=c$.prototype.actionInfo=
Array(47);c$.actionNames=c$.prototype.actionNames=Array(47);G(c$);JV.ActionManager.pickingModeNames="off identify label center draw spin symmetry deleteatom deletebond atom group chain molecule polymer structure site model element measure distance angle torsion sequence navigate connect struts dragselected dragmolecule dragatom dragminimize dragminimizemolecule invertstereo assignatom assignbond rotatebond identifybond dragligand dragmodel".$plit(" ");
G(c$,"pickingStyleNames",null);JV.ActionManager.pickingStyleNames="toggle selectOrToggle extendedSelect drag measure measureoff".$plit(" ");G(c$,"MAX_DOUBLE_CLICK_MILLIS",700,"MININUM_GESTURE_DELAY_MILLISECONDS",10,"SLIDE_ZOOM_X_PERCENT",98,"DEFAULT_MOUSE_DRAG_FACTOR",1,"DEFAULT_MOUSE_WHEEL_FACTOR",1.15,"DEFAULT_GESTURE_SWIPE_FACTOR",1,"XY_RANGE",10);c$=w(function(){this.time=this.y=this.x=this.index=0;s(this,arguments)},JV,"MotionPoint");c(c$,"set",function(a,b,d,c){this.index=a;this.x=b;this.y=
d;this.time=c},"~N,~N,~N,~N");h(c$,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});c$=w(function(){this.action=0;this.nodes=null;this.time0=this.ptNext=0;this.vwr=null;s(this,arguments)},JV,"Gesture");p(c$,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$,"getNode",function(a){return this.nodes[(a+this.nodes.length+this.nodes.length)%this.nodes.length]},"~N");h(c$,"toString",function(){return 0==this.nodes.length?""+this:JV.binding.Binding.getMouseActionName(this.action,!1)+" nPoints = "+this.ptNext+" "+this.nodes[0]})});m("JV");x(["JU.BS"],"JV.AnimationManager",["J.api.Interface","JU.BSUtil"],function(){c$=w(function(){this.vwr=
this.animationThread=null;this.animationOn=!1;this.lastFrameDelayMs=this.firstFrameDelayMs=this.animationFps=0;this.bsVisibleModels=null;this.animationReplayMode=1073742070;this.animationFrames=this.bsDisplay=null;this.animationPaused=this.isMovie=!1;this.morphCount=this.caf=this.cmi=0;this.currentDirection=this.animationDirection=1;this.frameStep=this.lastFrameIndex=this.firstFrameIndex=0;this.backgroundModelIndex=-1;this.firstFrameDelay=this.currentMorphModel=0;this.lastFrameDelay=1;this.intAnimThread=
this.lastModelPainted=this.lastFramePainted=0;this.cai=-1;s(this,arguments)},JV,"AnimationManager");O(c$,function(){this.bsVisibleModels=new JU.BS});p(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"setAnimationOn",function(a){a!=this.animationOn&&(!a||this.vwr.headless?this.stopThread(!1):(this.vwr.tm.spinOn||this.vwr.refresh(3,"Anim:setAnimationOn"),this.setAnimationRange(-1,-1),this.resumeAnimation()))},"~B");c(c$,"stopThread",function(a){var b=!1;null!=this.animationThread&&(this.animationThread.interrupt(),
this.animationThread=null,b=!0);this.animationPaused=a;b&&!this.vwr.tm.spinOn&&this.vwr.refresh(3,"Viewer:setAnimationOff");this.animation(!1);this.vwr.setStatusFrameChanged(!1,!1)},"~B");c(c$,"setAnimationNext",function(){return this.setAnimationRelative(this.animationDirection)});c(c$,"currentIsLast",function(){return this.isMovie?this.lastFramePainted==this.caf:this.lastModelPainted==this.cmi});c(c$,"currentFrameIs",function(a){var b=this.cmi;return 0==this.morphCount?b==a:0.001>Math.abs(this.currentMorphModel-
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1)})});m("JV");x(null,"JV.ColorManager","java.lang.Character $.Float JU.AU J.c.PAL JU.C $.ColorEncoder $.Elements $.Logger JV.JC".split(" "),function(){c$=w(function(){this.colorData=this.altArgbsCpk=this.argbsCpk=this.g3d=this.vwr=this.ce=null;this.isDefaultColorRasmol=!1;this.colixRubberband=22;this.colixBackgroundContrast=0;s(this,arguments)},JV,"ColorManager");p(c$,function(a,b){this.vwr=a;this.ce=new JU.ColorEncoder(null,a);this.g3d=b;this.argbsCpk=J.c.PAL.argbsCpk;this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,
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-1,1,JV.JC.PARTIAL_CHARGE_RANGE_SIZE),this.g3d.getChangeableColix(JV.JC.PARTIAL_CHARGE_COLIX_RED+c,JV.JC.argbsRwbScale[c]);case 3:return c=a.getFormalCharge()- -4,this.g3d.getChangeableColix(JV.JC.FORMAL_CHARGE_COLIX_RED+c,JV.JC.argbsFormalCharge[c]);case 68:case 5:return 68==b?(c=this.vwr.ms.getBfactor100Lo(),d=this.vwr.ms.getBfactor100Hi()):(c=0,d=1E4),this.ce.getColorIndexFromPalette(a.getBfactor100(),c,d,7,!1);case 86:return this.ce.getColorIndexFromPalette(a.group.getGroupParameter(1111490574),
-1,1,7,!1);case 70:return d=this.vwr.ms.getSurfaceDistanceMax(),this.ce.getColorIndexFromPalette(a.getSurfaceDistance100(),0,d,7,!1);case 24:return c=a.group.groupID,42<=c&&(c=24+"PGCATU".indexOf(Character.toUpperCase(a.group.group1))-1),this.ce.getColorIndexFromPalette(c,0,0,17,!1);case 8:return this.ce.getColorIndexFromPalette(a.group.groupID,0,0,5,!1);case 9:return this.ce.getColorIndexFromPalette(a.group.groupID,0,0,4,!1);case 75:return this.ce.getColorIndexFromPalette(a.group.selectedIndex,0,
a.group.chain.selectedGroupCount-1,1,!1);case 87:return c=this.vwr.ms.am[a.mi],this.ce.getColorIndexFromPalette(a.group.getBioPolymerIndexInModel(),0,(c.isBioModel?c.getBioPolymerCount():0)-1,1,!1);case 76:return this.ce.getColorIndexFromPalette(a.group.getSelectedMonomerIndex(),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,1073741991);break;case 17:c=a.getAtomicAndIsotopeNumber();d=this.getJmolOrRasmolArgb(c,1073742116);break;case 7:d=a.group.getProteinStructureSubType().getColor();break;case 10:c=a.getChainID(),null==JU.ColorEncoder.argbsChainAtom&&(JU.ColorEncoder.argbsChainAtom=
this.getArgbs(1140850689),JU.ColorEncoder.argbsChainHetero=this.getArgbs(1612709894)),c=((0>c?0:256<=c?c-256:c)&31)%JU.ColorEncoder.argbsChainAtom.length,d=(a.isHetero()?JU.ColorEncoder.argbsChainHetero:JU.ColorEncoder.argbsChainAtom)[c]}return 0==d?22:JU.C.getColix(d)},"JM.Atom,~N");c(c$,"getArgbs",function(a){return this.vwr.getJBR().getArgbs(a)},"~N");c(c$,"getJmolOrRasmolArgb",function(a,b){switch(b){case 1073741991:if(a>=JU.Elements.elementNumberMax)break;return this.ce.getArgbFromPalette(a,
0,0,2);case 1073742116:if(a>=JU.Elements.elementNumberMax)break;return this.ce.getArgbFromPalette(a,0,0,3);default:return b}return JV.JC.altArgbsCpk[JU.Elements.altElementIndexFromNumber(a)]},"~N,~N");c(c$,"setElementArgb",function(a,b){if(1073741991==b&&this.argbsCpk===J.c.PAL.argbsCpk)return 0;b=this.getJmolOrRasmolArgb(a,b);this.argbsCpk===J.c.PAL.argbsCpk&&(this.argbsCpk=JU.AU.arrayCopyRangeI(J.c.PAL.argbsCpk,0,-1),this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1));if(a<JU.Elements.elementNumberMax){if(2147483647==
b)return JU.C.getColix(this.argbsCpk[a]);this.argbsCpk[a]=b;this.g3d.changeColixArgb(a,b);return 0}a=JU.Elements.altElementIndexFromNumber(a);this.altArgbsCpk[a]=b;this.g3d.changeColixArgb(JU.Elements.elementNumberMax+a,b);return 0},"~N,~N");c(c$,"getPropertyColorRange",function(){return this.ce.isReversed?L(-1,[this.ce.hi,this.ce.lo]):L(-1,[this.ce.lo,this.ce.hi])});c(c$,"setPropertyColorRangeData",function(a,b){this.colorData=a;this.ce.currentPalette=this.ce.createColorScheme(this.vwr.g.propertyColorScheme,
!0,!1);this.ce.hi=-3.4028235E38;this.ce.lo=3.4028235E38;if(null!=a){for(var d=null==b,c,g=d?a.length-1:b.nextSetBit(0);0<=g;g=d?g-1:b.nextSetBit(g+1))if(!Float.isNaN(c=a[g]))this.ce.hi=Math.max(this.ce.hi,c),this.ce.lo=Math.min(this.ce.lo,c);this.setPropertyColorRange(this.ce.lo,this.ce.hi)}},"~A,JU.BS");c(c$,"setPropertyColorRange",function(a,b){this.ce.setRange(a,b,a>b);JU.Logger.debugging&&JU.Logger.debug('ColorManager: color "'+this.ce.getCurrentColorSchemeName()+'" range '+a+" "+b)},"~N,~N");
c(c$,"setPropertyColorScheme",function(a,b,d){var c=0==a.length;c&&(a="=");var g=this.getPropertyColorRange();this.ce.currentPalette=this.ce.createColorScheme(a,!0,d);c||this.setPropertyColorRange(g[0],g[1]);this.ce.isTranslucent=b},"~S,~B,~B");c(c$,"getColorSchemeList",function(a){a=null==a||0==a.length?this.ce.currentPalette:this.ce.createColorScheme(a,!0,!1);return JU.ColorEncoder.getColorSchemeList(this.ce.getColorSchemeArray(a))},"~S");c(c$,"getColorEncoder",function(a){if(null==a||0==a.length)return this.ce;
var b=new JU.ColorEncoder(this.ce,this.vwr);b.currentPalette=b.createColorScheme(a,!1,!0);return 2147483647==b.currentPalette?null:b},"~S")});m("JV");x(["javajs.api.BytePoster","java.util.Hashtable"],"JV.FileManager","java.io.BufferedInputStream $.BufferedReader java.lang.Boolean java.net.URL $.URLEncoder java.util.Map JU.AU $.BArray $.Base64 $.LimitedLineReader $.Lst $.OC $.PT $.Rdr $.SB J.api.Interface J.io.FileReader JS.SV JU.Escape $.Logger JV.JC $.JmolAsyncException $.Viewer".split(" "),function(){c$=
w(function(){this.jzu=this.spartanDoc=this.vwr=null;this.pathForAllFiles="";this.nameAsGiven="zapped";this.lastFullPathName=this.fullPathName=null;this.lastNameAsGiven="zapped";this.spardirCache=this.pngjCache=this.cache=this.appletProxy=this.appletDocumentBaseURL=this.fileName=null;s(this,arguments)},JV,"FileManager",null,javajs.api.BytePoster);O(c$,function(){this.cache=new java.util.Hashtable});p(c$,function(a){this.vwr=a;this.clear()},"JV.Viewer");c(c$,"spartanUtil",function(){return null==this.spartanDoc?
this.spartanDoc=J.api.Interface.getInterface("J.adapter.readers.spartan.SpartanUtil",this.vwr,"fm getSpartanUtil()").set(this):this.spartanDoc});c(c$,"getJzu",function(){return null==this.jzu?this.jzu=J.api.Interface.getOption("io.JmolUtil",this.vwr,"file"):this.jzu});c(c$,"clear",function(){this.setFileInfo(v(-1,[this.vwr.getZapName()]));this.spardirCache=null});c(c$,"setLoadState",function(a){this.vwr.getPreserveState()&&a.put("loadState",this.vwr.g.getLoadState(a))},"java.util.Map");c(c$,"getPathForAllFiles",
function(){return this.pathForAllFiles});c(c$,"setPathForAllFiles",function(a){0<a.length&&(!a.endsWith("/")&&!a.endsWith("|"))&&(a+="/");return this.pathForAllFiles=a},"~S");c(c$,"setFileInfo",function(a){null==a?(this.fullPathName=this.lastFullPathName,this.nameAsGiven=this.lastNameAsGiven):(this.fullPathName=a[0],this.fileName=a[Math.min(1,a.length-1)],this.nameAsGiven=a[Math.min(2,a.length-1)],this.nameAsGiven.equals("zapped")||(this.lastNameAsGiven=this.nameAsGiven,this.lastFullPathName=this.fullPathName))},
"~A");c(c$,"getFileInfo",function(){return v(-1,[this.fullPathName,this.fileName,this.nameAsGiven])});c(c$,"getFullPathName",function(a){var b=null!=this.fullPathName?this.fullPathName:this.nameAsGiven;return!a||!b.equals("zapped")?b:null!=this.lastFullPathName?this.lastFullPathName:this.lastNameAsGiven},"~B");c(c$,"getFileName",function(){return null!=this.fileName?this.fileName:this.nameAsGiven});c(c$,"getAppletDocumentBase",function(){return null==this.appletDocumentBaseURL?"":this.appletDocumentBaseURL.toString()});
c(c$,"setAppletContext",function(a){try{Zystem.out.println('setting document base to "'+a+'"'),this.appletDocumentBaseURL=0==a.length?null:new java.net.URL(ba("java.net.URL"),a,null)}catch(b){if(D(b,java.net.MalformedURLException))Zystem.out.println("error setting document base to "+a);else throw b;}},"~S");c(c$,"setAppletProxy",function(a){this.appletProxy=null==a||0==a.length?null:a},"~S");c(c$,"createAtomSetCollectionFromFile",function(a,b,d){null==b.get("atomDataOnly")&&this.setLoadState(b);var c=
a;a=this.vwr.resolveDatabaseFormat(a);!c.equals(a)&&(0>c.indexOf("/")&&JV.Viewer.hasDatabasePrefix(c))&&b.put("dbName",c);a.endsWith("%2D%")&&(c=b.get("filter"),b.put("filter",(null==c?"":c)+"2D"),a=a.substring(0,a.length-4));var g=a.indexOf("::"),c=0<=g?a.substring(g+2):a,g=0<=g?a.substring(0,g):null;JU.Logger.info("\nFileManager.getAtomSetCollectionFromFile("+c+")"+(a.equals(c)?"":" //"+a));var e=this.getClassifiedName(c,!0);if(1==e.length)return e[0];a=e[0];e=e[1];b.put("fullPathName",(null==g?
"":g+"::")+JV.FileManager.fixDOSName(a));this.vwr.getBoolean(603979879)&&this.vwr.getBoolean(603979825)&&this.vwr.getChimeMessenger().update(a);b=new J.io.FileReader(this.vwr,e,a,c,g,null,b,d);b.run();return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(c$,"createAtomSetCollectionFromFiles",function(a,b,d){this.setLoadState(b);for(var c=Array(a.length),g=Array(a.length),e=Array(a.length),j=0;j<a.length;j++){var h=a[j].indexOf("::"),k=0<=h?a[j].substring(h+2):a[j],h=0<=h?a[j].substring(0,h):null,
r=this.getClassifiedName(k,!0);if(1==r.length)return r[0];c[j]=r[0];a[j]=JV.FileManager.fixDOSName(r[0]);e[j]=h;g[j]=k}b.put("fullPathNames",c);b.put("fileTypes",e);a=this.newFilesReader(c,g,e,null,b,d);a.run();return a.getAtomSetCollection()},"~A,java.util.Map,~B");c(c$,"createAtomSetCollectionFromString",function(a,b,d){this.setLoadState(b);var c=0<=a.indexOf("Viewer.AddHydrogens")?this.getFileInfo():null;b=new J.io.FileReader(this.vwr,"string",null,null,null,JU.Rdr.getBR(a),b,d);b.run();null!=
c&&this.setFileInfo(c);!d&&!t(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$,"createAtomSeCollectionFromStrings",function(a,b,d,c){if(!d.containsKey("isData")){var g='"'+this.vwr.getDataSeparator()+'"',e='"'+(c?"append":"model")+' inline"',j=new JU.SB;j.append('set dataSeparator "~~~next file~~~";\ndata ').append(e);
for(var h=0;h<a.length;h++)0<h&&j.append("~~~next file~~~"),j.append(a[h]);j.append("end ").append(e).append(";set dataSeparator ").append(g);b.appendSB(j)}this.setLoadState(d);JU.Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");b=Array(a.length);g=Array(a.length);for(h=0;h<a.length;h++)b[h]="string["+h+"]",g[h]=JV.FileManager.newDataReader(this.vwr,a[h]);a=this.newFilesReader(b,b,null,g,d,c);a.run();return a.getAtomSetCollection()},"~A,JU.SB,java.util.Map,~B");c(c$,"createAtomSeCollectionFromArrayData",
function(a,b,d){JU.Logger.info("FileManager.getAtomSetCollectionFromArrayData(Vector)");for(var c=a.size(),g=Array(c),e=Array(c),j=0;j<c;j++)g[j]="String["+j+"]",e[j]=JV.FileManager.newDataReader(this.vwr,a.get(j));a=this.newFilesReader(g,g,null,e,b,d);a.run();return a.getAtomSetCollection()},"JU.Lst,java.util.Map,~B");c$.newDataReader=c(c$,"newDataReader",function(a,b){var d=t(b,String)?"String":JU.AU.isAS(b)?"Array":t(b,JU.Lst)?"List":null;return null==d?null:J.api.Interface.getInterface("JU."+
d+"DataReader",a,"file").setData(b)},"JV.Viewer,~O");c(c$,"newFilesReader",function(a,b,d,c,g,e){var j=J.api.Interface.getOption("io.FilesReader",this.vwr,"file");j.set(this,this.vwr,a,b,d,c,g,e);return j},"~A,~A,~A,~A,java.util.Map,~B");c(c$,"createAtomSetCollectionFromDOM",function(a,b){var d=J.api.Interface.getOption("io.DOMReader",this.vwr,"file");d.set(this,this.vwr,a,b);d.run();return d.getAtomSetCollection()},"~O,java.util.Map");c(c$,"createAtomSetCollectionFromReader",function(a,b,d,c){a=
new J.io.FileReader(this.vwr,b,a,null,null,d,c,!1);a.run();return a.getAtomSetCollection()},"~S,~S,~O,java.util.Map");c(c$,"getBufferedInputStream",function(a){a=this.getBufferedReaderOrErrorMessageFromName(a,Array(2),!0,!0);return t(a,java.io.BufferedInputStream)?a:null},"~S");c(c$,"getBufferedInputStreamOrErrorMessageFromName",function(a,b,d,c,g,e,j){var h=null,k=null;b=j&&null==g?b=this.getPngjOrDroppedBytes(b,a):null;try{j&&(0<=a.indexOf(".png")&&null==this.pngjCache&&!this.vwr.getBoolean(603979960))&&
(this.pngjCache=new java.util.Hashtable);if(null==b){var r=0<=a.indexOf("?POST?_PNGJBIN_"),n=r||0<=a.indexOf("?POST?_PNGJ_");if(0<a.indexOf("?POST?_PNG_")||n){var q=Array(1),m=this.vwr.getImageAsBytes(n?"PNGJ":"PNG",0,0,-1,q);if(null!=q[0])return q[0];r?(g=m,a=JU.PT.rep(a,"?_","=_")):a=(new JU.SB).append(a).append("=").appendSB(JU.Base64.getBase64(m)).toString()}var p=JU.OC.urlTypeIndex(a),r=0<=p,n=null;if(r&&0<=(p=a.indexOf("?POST?")))n=a.substring(p+6),a=a.substring(0,p);var s=null!=this.appletDocumentBaseURL;
if(s||r){s&&(r&&null!=this.appletProxy)&&(a=this.appletProxy+"?url="+this.urlEncode(a));var u=s?new java.net.URL(this.appletDocumentBaseURL,a,null):new java.net.URL(ba("java.net.URL"),a,null);if(c)return null;a=u.toString();d&&0>a.toLowerCase().indexOf("password")&&JU.Logger.info("FileManager opening url "+a);k=this.vwr.apiPlatform.getURLContents(u,g,n,!1);m=null;if(t(k,JU.SB)){a=k;if(e&&!JU.Rdr.isBase64(a))return JU.Rdr.getBR(a.toString());m=JU.Rdr.getBytesFromSB(a)}else JU.AU.isAB(k)&&(m=k);null!=
m&&(k=JU.Rdr.getBIS(m))}else if(!j||null==(b=this.cacheGet(a,!0)))d&&JU.Logger.info("FileManager opening file "+a),k=this.vwr.apiPlatform.getBufferedFileInputStream(a);if(t(k,String))return k}h=null==b?k:JU.Rdr.getBIS(b);c&&(h.close(),h=null);return h}catch(v){if(D(v,Exception))try{null!=h&&h.close()}catch(w){if(!D(w,java.io.IOException))throw w;}else throw v;}return""+v},"~S,~S,~B,~B,~A,~B,~B");c$.getBufferedReaderForResource=c(c$,"getBufferedReaderForResource",function(a,b,d,c){c=a.vwrOptions.get("codePath")+
d+c;if(a.async){a=a.fm.cacheGet(c,!1);if(null==a)throw new JV.JmolAsyncException(c);return JU.Rdr.getBufferedReader(JU.Rdr.getBIS(a),null)}return a.fm.getBufferedReaderOrErrorMessageFromName(c,v(-1,[null,null]),!1,!0)},"JV.Viewer,~O,~S,~S");c(c$,"urlEncode",function(a){try{return java.net.URLEncoder.encode(a,"utf-8")}catch(b){if(D(b,java.io.UnsupportedEncodingException))return a;throw b;}},"~S");c(c$,"getFullPathNameOrError",function(a,b,d){var c=this.getClassifiedName(JV.JC.fixProtocol(a),!0);if(null==
c||null==c[0]||2>c.length)return v(-1,[null,"cannot read file name: "+a]);a=c[0];c=JV.FileManager.fixDOSName(c[0]);a=JU.Rdr.getZipRoot(a);b=this.getBufferedInputStreamOrErrorMessageFromName(a,c,!1,!b,null,!1,!b);d[0]=c;t(b,String)&&(d[1]=b);return b},"~S,~B,~A");c(c$,"getBufferedReaderOrErrorMessageFromName",function(a,b,d,c){a=JV.JC.fixProtocol(a);var g=this.cacheGet(a,!1),e=JU.AU.isAB(g),j=e?g:null;if(a.startsWith("cache://")){if(null==g)return"cannot read "+a;if(e)j=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],j,!1,d,!1,c,null)},"~S,~A,~B,~B");c(c$,"getUnzippedReaderOrStreamFromName",function(a,b,d,c,g,e,j){if(e&&null==b){var h=a.endsWith(".spt")?v(-1,[null,null,null]):0>a.indexOf(".spardir")?null:this.spartanUtil().getFileList(a,g);if(null!=h)return h}a=JV.JC.fixProtocol(a);null==b&&(null!=(b=this.getCachedPngjBytes(a))&&null!=j)&&
j.put("sourcePNGJ",Boolean.TRUE);e=a=a.$replace("#_DOCACHE_","");g=null;0<=a.indexOf("|")&&(g=JU.PT.split(a.$replace("\\","/"),"|"),null==b&&JU.Logger.info("FileManager opening zip "+a),a=g[0]);a=null==b?this.getBufferedInputStreamOrErrorMessageFromName(a,e,!0,!1,null,!c,!0):JU.AU.isAB(b)?JU.Rdr.getBIS(b):b;try{if(t(a,String)||t(a,java.io.BufferedReader))return a;JU.Rdr.isGzipS(a)?a=JU.Rdr.getUnzippedInputStream(this.vwr.getJzt(),a):JU.Rdr.isBZip2S(a)&&(a=JU.Rdr.getUnzippedInputStreamBZip2(this.vwr.getJzt(),
a));if(JU.Rdr.isTar(a))return h=this.vwr.getJzt().getZipFileDirectory(a,g,1,c),t(h,String)?JU.Rdr.getBR(h):h;if(c&&null==g)return a;if(JU.Rdr.isCompoundDocumentS(a)){var k=J.api.Interface.getInterface("JU.CompoundDocument",this.vwr,"file");k.setDocStream(this.vwr.getJzt(),a);var r=k.getAllDataFiles("Molecule","Input").toString();return c?JU.Rdr.getBIS(r.getBytes()):JU.Rdr.getBR(r)}if(JU.Rdr.isMessagePackS(a)||JU.Rdr.isPickleS(a))return a;a=JU.Rdr.getPngZipStream(a,!0);if(JU.Rdr.isZipS(a)){if(d)return this.vwr.getJzt().newZipInputStream(a);
h=this.vwr.getJzt().getZipFileDirectory(a,g,1,c);return t(h,String)?JU.Rdr.getBR(h):h}return c?a:JU.Rdr.getBufferedReader(a,null)}catch(n){if(D(n,Exception))return n.toString();throw n;}},"~S,~O,~B,~B,~B,~B,java.util.Map");c(c$,"getZipDirectory",function(a,b,d){a=this.getBufferedInputStreamOrErrorMessageFromName(a,a,!1,!1,null,!1,d);return this.vwr.getJzt().getZipDirectoryAndClose(a,b?"JmolManifest":null)},"~S,~B,~B");c(c$,"getFileAsBytes",function(a,b){if(null==a)return null;var d=a,c=null;0<=a.indexOf("|")&&
(c=JU.PT.split(a,"|"),a=c[0]);var g=null!=c?null:this.getPngjOrDroppedBytes(d,a);if(null==g){d=this.getBufferedInputStreamOrErrorMessageFromName(a,d,!1,!1,null,!1,!0);if(t(d,String))return"Error:"+d;try{g=null!=b||null==c||1>=c.length||!JU.Rdr.isZipS(d)&&!JU.Rdr.isPngZipStream(d)&&!JU.Rdr.isTar(d)?JU.Rdr.getStreamAsBytes(d,b):this.vwr.getJzt().getZipFileContentsAsBytes(d,c,1),d.close()}catch(e){if(D(e,Exception))return e.toString();throw e;}}if(null==b||!JU.AU.isAB(g))return g;b.write(g,0,-1);return g.length+
" bytes"},"~S,JU.OC");c(c$,"getFileAsMap",function(a,b){var d=new java.util.Hashtable,c;if(null==a){c=Array(1);var g=this.vwr.getImageAsBytes(b,-1,-1,-1,c);if(null!=c[0])return d.put("_ERROR_",c[0]),d;c=JU.Rdr.getBIS(g)}else{g=Array(2);c=this.getFullPathNameOrError(a,!0,g);if(t(c,String))return d.put("_ERROR_",c),d;if(!this.checkSecurity(g[0]))return d.put("_ERROR_","java.io. Security exception: cannot read file "+g[0]),d}try{this.vwr.getJzt().readFileAsMap(c,d,a)}catch(e){if(D(e,Exception))d.clear(),
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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;s(this,arguments)},JV,"GlobalSettings");O(c$,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.objColors=B(7,0);this.objStateOn=ja(7,!1);this.objMad10=B(7,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,
L(-1,[30,90,-15,95]));this.structureList.put(J.c.STR.SHEET,L(-1,[-180,-10,70,180,-180,-45,-180,-130,140,180,90,180]));this.structureList.put(J.c.STR.HELIX,L(-1,[-160,0,-100,45]))});p(c$,function(a,b,d){this.vwr=a;this.htNonbooleanParameterValues=new java.util.Hashtable;this.htBooleanParameterFlags=new java.util.Hashtable;this.htPropertyFlagsRemoved=new java.util.Hashtable;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.pubChemFormat=JV.JC.databases.get("pubchem");this.resolverResolver=JV.JC.databases.get("resolverresolver");this.macroDirectory="https://chemapps.stolaf.edu/jmol/macros";null!=b&&(d||(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.nihResolverFormat=b.nihResolverFormat);null==this.nihResolverFormat&&(this.nihResolverFormat=JV.JC.databases.get("nci"));this.setCIR(this.nihResolverFormat);var c;d=0;for(var g=J.c.CBK.values();d<g.length&&((c=g[d])||1);d++)this.resetValue(c.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("hbondHXDistanceMaximum",this.hbondHXDistanceMaximum);this.setF("hbondsDistanceMaximum",this.hbondNODistanceMaximum);
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("minimizationMaxAtoms",this.minimizationMaxAtoms);this.setI("smallMoleculeMaxAtoms",this.smallMoleculeMaxAtoms);this.setO("smilesUrlFormat",this.smilesUrlFormat);this.setO("macroDirectory",this.macroDirectory);
this.setO("nihResolverFormat",this.nihResolverFormat);this.setO("pubChemFormat",this.pubChemFormat);this.setB("showUnitCellDetails",this.showUnitCellDetails);this.setB("solventProbe",this.dotSolvent);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,d=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)?d.equalsIgnoreCase(this.energyUnits)||
this.setO("energyUnits",this.energyUnits):this.setO("measurementUnits",this.measureDistanceUnits)},"~S");c(c$,"isJmolVariable",function(a){return"_"==a.charAt(0)||this.htNonbooleanParameterValues.containsKey(a=a.toLowerCase())||this.htBooleanParameterFlags.containsKey(a)||0<=JV.GlobalSettings.unreportedProperties.indexOf(";"+a+";")},"~S");c(c$,"resetValue",function(a,b){this.setO(a,null==b?"":b.getParameter(a,!0))},"~S,JV.GlobalSettings");c(c$,"setB",function(a,b){a=a.toLowerCase();this.htNonbooleanParameterValues.containsKey(a)||
this.htBooleanParameterFlags.put(a,b?Boolean.TRUE:Boolean.FALSE)},"~S,~B");c(c$,"setI",function(a,b){2147483647!=b&&this.setO(a,Integer.$valueOf(b))},"~S,~N");c(c$,"setF",function(a,b){Float.isNaN(b)||this.setO(a,Float.$valueOf(b))},"~S,~N");c(c$,"setO",function(a,b){a=a.toLowerCase();null==b||this.htBooleanParameterFlags.containsKey(a)||this.htNonbooleanParameterValues.put(a,b)},"~S,~O");c(c$,"removeParam",function(a){a=a.toLowerCase();this.htBooleanParameterFlags.containsKey(a)?(this.htBooleanParameterFlags.remove(a),
this.htPropertyFlagsRemoved.containsKey(a)||this.htPropertyFlagsRemoved.put(a,Boolean.FALSE)):this.htNonbooleanParameterValues.containsKey(a)&&this.htNonbooleanParameterValues.remove(a)},"~S");c(c$,"setUserVariable",function(a,b){null!=b&&(a=a.toLowerCase(),this.htUserVariables.put(a,b.setName(a)));return b},"~S,JS.SV");c(c$,"unsetUserVariable",function(a){a.equals("all")||a.equals("variables")?(this.htUserVariables.clear(),JU.Logger.info("all user-defined variables deleted")):this.htUserVariables.containsKey(a)&&
(JU.Logger.info("variable "+a+" deleted"),this.htUserVariables.remove(a))},"~S");c(c$,"removeUserVariable",function(a){this.htUserVariables.remove(a)},"~S");c(c$,"getUserVariable",function(a){if(null==a)return null;a=a.toLowerCase();return this.htUserVariables.get(a)},"~S");c(c$,"getParameterEscaped",function(a,b){a=a.toLowerCase();if(this.htNonbooleanParameterValues.containsKey(a)){var d=this.htNonbooleanParameterValues.get(a);return JV.StateManager.varClip(a,JU.Escape.e(d),b)}return this.htBooleanParameterFlags.containsKey(a)?
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--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});G(c$,"TRUE",1,"FALSE",0,"UNKNOWN",-1)});m("JV");x(null,"JV.ShapeManager","java.lang.Boolean JU.BS $.P3 J.api.Interface J.c.PAL $.VDW JM.Atom JU.BSUtil JV.JC".split(" "),
function(){c$=w(function(){this.navMinMax=this.bsSlabbedInternal=this.bsRenderableAtoms=this.vwr=this.shapes=this.ms=null;s(this,arguments)},JV,"ShapeManager");O(c$,function(){this.navMinMax=B(4,0)});p(c$,function(a){this.vwr=a;this.bsRenderableAtoms=new JU.BS;this.bsSlabbedInternal=new JU.BS},"JV.Viewer");c(c$,"findNearestShapeAtomIndex",function(a,b,d,c){if(null!=this.shapes)for(var g=0;g<this.shapes.length&&null==d[0];++g)null!=this.shapes[g]&&this.shapes[g].findNearestAtomIndex(a,b,d,c)},"~N,~N,~A,JU.BS");
c(c$,"getShapePropertyIndex",function(a,b,d){if(null==this.shapes||null==this.shapes[a])return null;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getProperty(b,d);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~N");c(c$,"getShapePropertyData",function(a,b,d){if(null==this.shapes||null==this.shapes[a])return!1;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getPropertyData(b,d);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~A");c(c$,"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 null!=this.shapes[6]&&0<=this.shapes[6].getIndexFromName(a)?6:-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$,"notifyAtomPositionsChanged",function(a,b,d){var c=Integer.$valueOf(a);a=this.vwr.getModelUndeletedAtomsBitSet(a);for(var g=0;37>g;g++)null!=this.shapes[g]&&this.setShapePropertyBs(g,"refreshTrajectories",v(-1,
[c,b,d]),a)},"~N,JU.BS,JU.M4");c(c$,"releaseShape",function(a){null!=this.shapes&&(this.shapes[a]=null)},"~N");c(c$,"resetShapes",function(){this.shapes=Array(37)});c(c$,"setShapeSizeBs",function(a,b,d,c){if(null!=this.shapes){if(null==c&&(1!=a||2147483647!=b))c=this.vwr.bsA();null!=d&&(0!=d.value&&d.vdwType===J.c.VDW.TEMP)&&this.ms.getBfactor100Lo();this.vwr.setShapeErrorState(a,"set size");(null==d?0!=b:0!=d.value)&&this.loadShape(a);null!=this.shapes[a]&&this.shapes[a].setShapeSizeRD(b,d,c);this.vwr.setShapeErrorState(-1,
null)}},"~N,~N,J.atomdata.RadiusData,JU.BS");c(c$,"setLabel",function(a,b){if(null==a){if(null==this.shapes[5])return}else this.loadShape(5),this.setShapeSizeBs(5,0,null,b);this.setShapePropertyBs(5,"label",a,b)},"~O,JU.BS");c(c$,"setShapePropertyBs",function(a,b,d,c){null==this.shapes||null==this.shapes[a]||(null==c&&(c=this.vwr.bsA()),this.vwr.setShapeErrorState(a,"set "+b),this.shapes[a].setProperty(b.intern(),d,c),this.vwr.setShapeErrorState(-1,null))},"~N,~S,~O,JU.BS");c(c$,"checkFrankclicked",
function(a,b){var d=this.shapes[36];return null!=d&&d.wasClicked(a,b)},"~N,~N");c(c$,"checkObjectClicked",function(a,b,d,c,g){var e,j=null;if(2==this.vwr.getPickingMode())return this.shapes[5].checkObjectClicked(a,b,d,c,!1);if(0!=d&&this.vwr.getBondsPickable()&&null!=(j=this.shapes[1].checkObjectClicked(a,b,d,c,!1)))return j;for(var h=0;h<JV.ShapeManager.clickableMax;h++)if(null!=(e=this.shapes[JV.ShapeManager.hoverable[h]])&&null!=(j=e.checkObjectClicked(a,b,d,c,g)))return j;return null},"~N,~N,~N,JU.BS,~B");
c(c$,"checkObjectDragged",function(a,b,d,c,g,e,j){for(var h=!1,k=0<j?j+1:37;!h&&j<k;++j)null!=this.shapes[j]&&(h=this.shapes[j].checkObjectDragged(a,b,d,c,g,e));return h},"~N,~N,~N,~N,~N,JU.BS,~N");c(c$,"checkObjectHovered",function(a,b,d,c){var g=this.shapes[1];if(c&&null!=g&&g.checkObjectHovered(a,b,d))return!0;for(c=0;c<JV.ShapeManager.hoverable.length;c++)if(g=this.shapes[JV.ShapeManager.hoverable[c]],null!=g&&g.checkObjectHovered(a,b,d))return!0;return!1},"~N,~N,JU.BS,~B");c(c$,"deleteShapeAtoms",
function(a,b){if(null!=this.shapes)for(var d=0;37>d;d++)null!=this.shapes[d]&&this.setShapePropertyBs(d,"deleteModelAtoms",a,b)},"~A,JU.BS");c(c$,"deleteVdwDependentShapes",function(a){null==a&&(a=this.vwr.bsA());null!=this.shapes[24]&&this.shapes[24].setProperty("deleteVdw",null,a);null!=this.shapes[25]&&this.shapes[25].setProperty("deleteVdw",null,a)},"JU.BS");c(c$,"getAtomShapeValue",function(a,b,d){a=JV.JC.shapeTokenIndex(a);if(0>a||null==this.shapes[a])return 0;d=this.shapes[a].getSize(d);if(0==
d){if(0==(b.shapeVisibilityFlags&this.shapes[a].vf))return 0;d=this.shapes[a].getSizeG(b)}return d/2E3},"~N,JM.Group,~N");c(c$,"replaceGroup",function(a,b){if(null!=this.shapes)for(var d=9;16>d;d++)null!=this.shapes[d]&&this.shapes[d].replaceGroup(a,b)},"JM.Group,JM.Group");c(c$,"getObjectMap",function(a,b){if(null!=this.shapes)for(var d=Boolean.$valueOf(b),c=16;30>c;++c)this.getShapePropertyData(c,"getNames",v(-1,[a,d]))},"java.util.Map,~B");c(c$,"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$,"setModelVisibility",function(){var a=this.shapes;if(!(null==a||null==a[0])){for(var b=this.vwr.getVisibleFramesBitSet(),d=8;33>d;d++)null!=a[d]&&a[d].setModelVisibilityFlags(b);var a=this.vwr.getBoolean(603979922),c=this.vwr.slm.bsDeleted,g=this.ms.at;this.ms.clearVisibleSets();if(0<g.length)for(d=this.ms.ac;0<=--d;){var e=g[d];null!=e&&(e.shapeVisibilityFlags&=-64);if(!(null!=c&&c.get(d))&&b.get(e.mi)){var j=1;if(!this.ms.isAtomHidden(d)&&(a||1!=e.getElementNumber()))j|=8,0!=e.madAtom&&
(j|=16),e.setShapeVisibility(j,!0)}}this.setShapeVis()}});c(c$,"setShapeVis",function(){for(var a=0;37>a;++a){var b=this.shapes[a];null!=b&&b.setAtomClickability()}});c(c$,"finalizeAtoms",function(a,b){var d=this.vwr,c=d.tm;b&&d.finalizeTransformParameters();if(null!=a){var g=this.ms.getAtomSetCenter(a),e=new JU.P3;c.transformPt3f(g,e);e.add(c.ptOffset);c.unTransformPoint(e,e);e.sub(g);d.setAtomCoordsRelative(e,a);c.ptOffset.set(0,0,0);c.bsSelectedAtoms=null}g=this.bsRenderableAtoms;this.ms.getAtomsInFrame(g);
var j=this.ms.vibrations,h=null!=j&&c.vibrationOn,k=null!=this.ms.bsModulated&&null!=this.ms.occupancies,r=this.ms.at,n,q=!1,m=this.bsSlabbedInternal;m.clearAll();for(var p=g.nextSetBit(0);0<=p;p=g.nextSetBit(p+1)){var e=r[p],s=h&&e.hasVibration()?c.transformPtVib(e,j[p]):c.transformPt(e);1==s.z&&(c.internalSlab&&c.xyzIsSlabbedInternal(e))&&m.set(p);e.sX=s.x;e.sY=s.y;e.sZ=s.z;var t=Math.abs(e.madAtom);t==JM.Atom.MAD_GLOBAL&&(t=C(2E3*d.getFloat(1140850689)));e.sD=ea(d.tm.scaleToScreen(s.z,t));if(k&&
null!=j[p]&&-2147483648!=(n=j[p].getOccupancy100(h)))q=!0,e.setShapeVisibility(2,!1),0<=n&&50>n?e.setShapeVisibility(24,!1):e.setShapeVisibility(8|(0<e.madAtom?16:0),!0),this.ms.occupancies[e.i]=Math.abs(n)}q&&this.setShapeVis();n=d.gdata;if(c.slabEnabled){p=d.getBoolean(603979940);c=d.getBoolean(603979939);j=n.slab;h=n.depth;if(p){k=this.ms.getMolecules();q=this.ms.getMoleculeCountInModel(-1);for(p=0;p<q;p++)if(m=k[p],s=0,e=m.firstAtomIndex,g.get(e)){for(;s<m.ac&&!n.isClippedZ(r[e].sZ-(r[e].sD>>
1));s++,e++);if(s!=m.ac){e=m.firstAtomIndex;for(s=0;s<m.ac;s++)g.clear(e),r[e++].sZ=0}}}for(p=g.nextSetBit(0);0<=p;p=g.nextSetBit(p+1))if(e=r[p],n.isClippedZ(e.sZ-(c?r[p].sD>>1:0)))e.setClickable(0),k=u((c?-1:1)*e.sD/2),(e.sZ+k<j||e.sZ-k>h||!n.isInDisplayRange(e.sX,e.sY))&&g.clear(p)}if(0==this.ms.ac||!d.getShowNavigationPoint())return null;d=2147483647;n=-2147483648;c=2147483647;j=-2147483648;for(p=g.nextSetBit(0);0<=p;p=g.nextSetBit(p+1))e=r[p],e.sX<d&&(d=e.sX),e.sX>n&&(n=e.sX),e.sY<c&&(c=e.sY),
e.sY>j&&(j=e.sY);this.navMinMax[0]=d;this.navMinMax[1]=n;this.navMinMax[2]=c;this.navMinMax[3]=j;return this.navMinMax},"JU.BS,~B");c(c$,"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 d=this.vwr.slm.getSelectedAtomsNoSubset();if(b){this.vwr.slm.invertSelection();var c=this.vwr.slm.bsSubset;null!=c&&(d=this.vwr.slm.getSelectedAtomsNoSubset(),
d.and(c),this.vwr.select(d,!1,0,!0),JU.BSUtil.invertInPlace(d,this.vwr.ms.ac),d.and(c))}JU.BSUtil.andNot(d,this.vwr.slm.bsDeleted);c=this.vwr.getBoolean(603979812);a||this.vwr.setBooleanProperty("bondModeOr",!0);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(32768),null);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(1023),null);for(var g=this.vwr.bsA(),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",c);this.vwr.select(d,!1,0,!0)},"~B,~B");G(c$,"hoverable",B(-1,[31,20,25,24,22,36]));c$.clickableMax=c$.prototype.clickableMax=JV.ShapeManager.hoverable.length-1});m("JV");x(["java.util.Hashtable"],["JV.Connection","$.Scene","$.StateManager","$.Connections"],["java.util.Arrays","JU.BS","$.SB","JM.Orientation","JU.BSUtil"],function(){c$=w(function(){this.saved=this.vwr=
null;this.lastCoordinates=this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=this.lastContext=this.lastOrientation="";s(this,arguments)},JV,"StateManager");O(c$,function(){this.saved=new java.util.Hashtable});c$.getVariableList=c(c$,"getVariableList",function(a,b,d,c){var g=new JU.SB,e=0,j=Array(a.size()),h;for(a=a.entrySet().iterator();a.hasNext()&&((h=a.next())||1);){var k=h.getKey(),r=h.getValue();if((d||!k.startsWith("site_"))&&(!c||"@"==k.charAt(0)))j[e++]=k+
("@"==k.charAt(0)?" "+r.asString():" = "+JV.StateManager.varClip(k,r.escape(),b))}java.util.Arrays.sort(j,0,e);for(b=0;b<e;b++)null!=j[b]&&g.append("  ").append(j[b]).append(";\n");0==e&&!c&&g.append("# --no global user variables defined--;\n");return g.toString()},"java.util.Map,~N,~B,~B");c$.getObjectIdFromName=c(c$,"getObjectIdFromName",function(a){if(null==a)return-1;a="background axis1      axis2      axis3      boundbox   unitcell   frank      ".indexOf(a.toLowerCase());return 0>a?a:u(a/11)},
"~S");c$.getObjectNameFromId=c(c$,"getObjectNameFromId",function(a){return 0>a||7<=a?null:"background axis1      axis2      axis3      boundbox   unitcell   frank      ".substring(11*a,11*a+11).trim()},"~N");p(c$,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$,"getNoCase",function(a,b){for(var d,c=a.entrySet().iterator();c.hasNext()&&((d=c.next())||1);)if(d.getKey().equalsIgnoreCase(b))return d.getValue();return null},"java.util.Map,~S");c(c$,"listSavedStates",function(){for(var a="",b,
d=this.saved.keySet().iterator();d.hasNext()&&((b=d.next())||1);)a+="\n"+b;return a});c(c$,"deleteSavedType",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();)b.next().startsWith(a)&&b.remove()},"~S");c(c$,"deleteSaved",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();){var d=b.next();(d.startsWith(a)||d.endsWith("_"+a)&&d.indexOf("_")==d.lastIndexOf("_"+a))&&b.remove()}},"~S");c(c$,"saveSelection",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Selected_"):
(a=this.lastSelected="Selected_"+a,this.saved.put(a,JU.BSUtil.copy(b)))},"~S,JU.BS");c(c$,"restoreSelection",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Selected_"+a:this.lastSelected);if(null==a)return this.vwr.select(new JU.BS,!1,0,!1),!1;this.vwr.select(a,!1,0,!1);return!0},"~S");c(c$,"saveState",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("State_"):(a=this.lastState="State_"+a,this.saved.put(a,this.vwr.getStateInfo()))},"~S");c(c$,"getSavedState",function(a){a=
JV.StateManager.getNoCase(this.saved,0<a.length?"State_"+a:this.lastState);return null==a?"":a},"~S");c(c$,"saveStructure",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Shape_"):(a=this.lastShape="Shape_"+a,this.saved.put(a,this.vwr.getStructureState()))},"~S");c(c$,"getSavedStructure",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Shape_"+a:this.lastShape);return null==a?"":a},"~S");c(c$,"saveCoordinates",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Coordinates_"):
(a=this.lastCoordinates="Coordinates_"+a,this.saved.put(a,this.vwr.getCoordinateState(b)))},"~S,JU.BS");c(c$,"getSavedCoordinates",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Coordinates_"+a:this.lastCoordinates);return null==a?"":a},"~S");c(c$,"getOrientation",function(){return new JM.Orientation(this.vwr,!1,null)});c(c$,"getSavedOrientationText",function(a){var b;if(null!=a)return b=this.getOrientationFor(a),null==b?"":b.getMoveToText(!0);a=new JU.SB;for(var d=this.saved.entrySet().iterator();d.hasNext()&&
((b=d.next())||1);)b.getKey().startsWith("Orientation_")&&a.append(b.getValue().getMoveToText(!0));return a.toString()},"~S");c(c$,"saveScene",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Scene_");else{var d=new JV.Scene(b);d.saveName=this.lastScene="Scene_"+a;this.saved.put(d.saveName,d)}},"~S,java.util.Map");c(c$,"restoreScene",function(a,b){var d=JV.StateManager.getNoCase(this.saved,0<a.length?"Scene_"+a:this.lastScene);return null!=d&&d.restore(this.vwr,b)},"~S,~N");c(c$,
"saveOrientation",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Orientation_");else{var d=new JM.Orientation(this.vwr,a.equalsIgnoreCase("default"),b);d.saveName=this.lastOrientation="Orientation_"+a;this.saved.put(d.saveName,d)}},"~S,~A");c(c$,"restoreOrientation",function(a,b,d){a=this.getOrientationFor(a);return null!=a&&a.restore(b,d)},"~S,~N,~B");c(c$,"getOrientationFor",function(a){return JV.StateManager.getNoCase(this.saved,0<a.length?"Orientation_"+a:this.lastOrientation)},
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c(c$,"dialogAsk",function(a,b,d){var c=a.equals("Save Image"),g=J.api.Interface.getOption("dialog.Dialog",this.vwr,"status");if(null==g)return null;g.setupUI(!1);c&&g.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);a=g.getFileNameFromDialog(this.vwr,a,b);c&&null!=a&&(this.qualityJPG=g.getQuality("JPG"),this.qualityPNG=g.getQuality("PNG"),c=g.getType(),null!=d&&(d.put("qualityJPG",Integer.$valueOf(this.qualityJPG)),d.put("qualityPNG",Integer.$valueOf(this.qualityPNG)),null!=c&&d.put("dialogImageType",
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c(c$,"registerAudio",function(a,b){this.stopAudio(a);null==this.audios&&(this.audios=new java.util.Hashtable);null==b?this.audios.remove(a):this.audios.put(a,b.get("audioPlayer"))},"~S,java.util.Map");c(c$,"stopAudio",function(a){null!=this.audios&&(a=this.audios.get(a),null!=a&&a.action("kill"))},"~S");c(c$,"playAudio",function(a){if(this.vwr.getBoolean(603979797))try{var b=null==a?"close":a.get("action"),d=null==a?null:a.get("id");if(null!=b&&0<b.length){if(null==d||0==d.length){if(null==this.audios||
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!1);else{"=".equals(b)&&(b="~",this.setSyncDriver(2));var c="~".equals(b);if(0<d||!c&&!".".equals(b))if(this.syncSend(a,b,d),!"*".equals(b)||a.startsWith("{"))return;if(a.equalsIgnoreCase("on")||a.equalsIgnoreCase("true"))this.setSyncDriver(1);else if(a.equalsIgnoreCase("off")||a.equalsIgnoreCase("false"))this.setSyncDriver(0);else if(a.equalsIgnoreCase("slave"))this.setSyncDriver(2);else if(b=this.getSyncMode(),0!=b)if(1!=b&&(c=!1),JU.Logger.debugging&&JU.Logger.debug(this.vwr.htmlName+" syncing with script: "+
a),c&&this.setSyncDriver(3),0!=a.indexOf("Mouse: ")){b=JV.JC.getServiceCommand(a);switch(b){case 70:case 42:case 49:case 56:case 63:this.syncSend(a,".",d);return;case 0:case 77:case 28:case 35:if(c)return;case 21:case 7:case 14:if(null==(a=this.vwr.getJSV().processSync(a,b)))return}this.vwr.evalStringQuietSync(a,!0,!1)}else this.mouseScript(a),c&&this.vwr.setSyncDriver(4)}},"~S,~S,~N");c(c$,"mouseScript",function(a){var b=JU.PT.getTokens(a),d=b[1];try{switch(d=(d.toLowerCase()+"...............").substring(0,
15),"zoombyfactor...zoomby.........rotatezby......rotatexyby.....translatexyby..rotatemolecule.spinxyby.......rotatearcball..".indexOf(d)){case 0:switch(b.length){case 3:this.vwr.zoomByFactor(JU.PT.parseFloat(b[2]),2147483647,2147483647);return;case 5:this.vwr.zoomByFactor(JU.PT.parseFloat(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseInt(b[4]));return}break;case 15:switch(b.length){case 3:this.vwr.zoomBy(JU.PT.parseInt(b[2]));return}break;case 30:switch(b.length){case 3:this.vwr.rotateZBy(JU.PT.parseInt(b[2]),
2147483647,2147483647);return;case 5:this.vwr.rotateZBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseInt(b[4]))}break;case 45:this.vwr.rotateXYBy(JU.PT.parseFloat(b[2]),JU.PT.parseFloat(b[3]));return;case 60:this.vwr.translateXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]));return;case 75:this.vwr.rotateSelected(JU.PT.parseFloat(b[2]),JU.PT.parseFloat(b[3]),null);return;case 90:this.vwr.spinXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseFloat(b[4]));return;case 105:this.vwr.rotateXYBy(JU.PT.parseInt(b[2]),
JU.PT.parseInt(b[3]));return}}catch(c){if(!D(c,Exception))throw c;}this.vwr.showString("error reading SYNC command: "+a,!1)},"~S");G(c$,"MAXIMUM_QUEUE_LENGTH",16,"SYNC_OFF",0,"SYNC_DRIVER",1,"SYNC_SLAVE",2,"SYNC_DISABLE",3,"SYNC_ENABLE",4,"SYNC_STEREO",5)});m("JV");x("JU.A4 $.M3 $.M4 $.P3 $.P3i $.V3 J.c.STER JU.Point3fi".split(" "),"JV.TransformManager","java.lang.Boolean $.Float java.util.Hashtable JU.P4 $.Quat $.SB J.api.Interface JU.Escape $.Logger".split(" "),function(){c$=w(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;s(this,arguments)},JV,"TransformManager");O(c$,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=new JU.P3;this.matrixTemp=new JU.M4;this.vectorTemp=new JU.V3;this.fixedRotationOffset=new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=
new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.pointT2=new JU.P3;this.rotationAxis=new JU.V3;this.fixedTranslation=new JU.P3;this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=
new JU.M4;this.fScrPt=new JU.P3;this.iScrPt=new JU.P3i;this.ptVibTemp=new JU.Point3fi;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.c.STER.NONE;this.matrixStereo=new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=new JU.P3});p(c$,function(){});c$.getTransformManager=c(c$,"getTransformManager",function(a,b,d,c){c=c?J.api.Interface.getInterface("JV.TransformManager4D",
a,"tm"):new JV.TransformManager;c.vwr=a;c.setScreenParameters(b,d,!0,!1,!0,!0);return c},"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$,"spinXYBy",function(a,b,d){if(0==a&&0==b)null!=this.spinThread&&this.spinIsGesture&&this.clearSpin();else{this.clearSpin();var c=JU.P3.newP(this.fixedRotationCenter),g=new JU.P3;this.transformPt3f(c,g);a=JU.P3.new3(-b,a,0);a.add(g);this.unTransformPoint(a,a);this.vwr.setInMotion(!1);this.rotateAboutPointsInternal(null,
a,c,10*d,NaN,!1,!0,null,!0,null,null,null,null)}},"~N,~N,~N");c(c$,"rotateXYBy",function(a,b,d){this.rotate3DBall(a,b,d)},"~N,~N,JU.BS");c(c$,"rotateZBy",function(a,b,d){2147483647!=b&&2147483647!=d&&this.resetXYCenter(b,d);this.rotateZRadians(a/57.29577951308232)},"~N,~N,~N");c(c$,"applyRotation",function(a,b,d,c,g,e){null==d?this.matrixRotate.mul2(a,this.matrixRotate):(this.vwr.moveAtoms(e,a,this.matrixRotate,c,this.internalRotationCenter,b,d,g),null!=c&&this.internalRotationCenter.add(c))},"JU.M3,~B,JU.BS,JU.V3,~B,JU.M4");
c(c$,"rotate3DBall",function(a,b,d){this.matrixTemp3.setAsBallRotation(0.017453292,-b,-a)&&this.applyRotation(this.matrixTemp3,!1,d,null,!1,null)},"~N,~N,JU.BS");c(c$,"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$,"rotateAxisAngleAtCenter",function(a,b,d,c,g,e,j){null!=b&&this.moveRotationCenter(b,!0);e&&this.setSpinOff();this.setNavOn(!1);if(this.vwr.headless){if(e&&3.4028235E38==g)return!1;e=!1}if(Float.isNaN(c)||0==c||0==g)return!1;null!=b&&this.setRotationPointXY(b);
this.setFixedRotationCenter(b);this.rotationAxis.setT(d);this.rotationRate=c;if(e)return this.fixedRotationAxis.setVA(d,0.017453292*c),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=j,this.setSpin(a,!0,g,null,null,j,!1),3.4028235E38!=g;a=0.017453292*g;this.fixedRotationAxis.setVA(d,g);this.rotateAxisAngleRadiansFixed(a,j);return!0},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAxisAngleRadiansFixed",function(a,b){this.axisangleT.setAA(this.fixedRotationAxis);
this.axisangleT.angle=a;this.rotateAxisAngle2(this.axisangleT,b)},"~N,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,d,c,g,e,j,h,k,r,n,q,p){j&&this.setSpinOff();this.setNavOn(!1);if(null==q&&(null==r||0.001>r.length())&&(j?Float.isNaN(c)||0==c:0==g))return!1;var m=null;null==q&&(m=JU.V3.newVsub(d,b),e&&m.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(m),this.internalTranslation=null==r?null:JU.V3.newV(r));b=null!=h;if(j)return null==q?(0==g&&(g=NaN),Float.isNaN(g)?this.rotationRate=
c:(p=u(Math.abs(g)/Math.abs(c)*this.spinFps+0.5),this.rotationRate=g/p*this.spinFps,null!=r&&this.internalTranslation.scale(1/p)),this.internalRotationAxis.setVA(m,0.017453292*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),this.isSpinInternal=!0,this.isSpinFixed=!1,this.isSpinSelected=b):g=c,this.setSpin(a,!0,g,n,q,h,k),!Float.isNaN(g);a=0.017453292*g;this.internalRotationAxis.setVA(m,a);this.rotateAxisAngleRadiansInternal(a,h,p);return!1},"J.api.JmolScriptEvaluator,JU.T3,JU.T3,~N,~N,~B,~B,JU.BS,~B,JU.V3,JU.Lst,~A,JU.M4");
c(c$,"rotateAxisAngleRadiansInternal",function(a,b,d){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,d);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$,"centerAt",function(a,
b,d){null==d?this.translateXYBy(a,b):(this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1),this.fixedTranslation.x=a,this.fixedTranslation.y=b,this.setFixedRotationCenter(d))},"~N,~N,JU.P3");c(c$,"percentToPixels",function(a,b){switch(a){case "x":return u(Math.floor(b/100*this.width));case "y":return u(Math.floor(b/100*this.height));case "z":return u(Math.floor(b/100*this.screenPixelCount))}return 0},"~S,~N");c(c$,"angstromsToPixels",function(a){return u(Math.floor(this.scalePixelsPerAngstrom*
a))},"~N");c(c$,"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 d=this.getRotationQ();b&&(d=d.inv());return d.toString();case 1073742178:var d=new JU.SB,c=this.getTranslationXPercent();JV.TransformManager.truncate2(d,b?-c:c);c=this.getTranslationYPercent();JV.TransformManager.truncate2(d,b?-c:c);return d.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$,"zoomByFactor",function(a,b,d){!(0>=a)&&this.zoomEnabled&&(1!=this.mode?(this.zoomRatio=a,this.zmPctSet*=a,this.resetXYCenter(b,d)):this.getNav()&&this.nav.zoomByFactor(a,
b,d))},"~N,~N,~N");c(c$,"zoomToPercent",function(a){this.zmPctSet=a;this.zoomRatio=0},"~N");c(c$,"translateZBy",function(a){a>=this.screenPixelCount||(a=this.scalePixelsPerAngstrom/(1-1*a/this.screenPixelCount),a>=this.screenPixelCount||(a=100*(a/this.scaleDefaultPixelsPerAngstrom),this.zoomRatio=a/this.zmPctSet,this.zmPctSet=a))},"~N");c(c$,"resetXYCenter",function(a,b){if(!(2147483647==a||2147483647==b)){this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1);var d=new JU.P3;this.transformPt3f(this.fixedRotationCenter,
d);d.set(a,b,d.z);this.unTransformPoint(d,d);this.fixedTranslation.set(a,b,0);this.setFixedRotationCenter(d)}},"~N,~N");c(c$,"zoomByPercent",function(a){var b=a*this.zmPctSet/100;0==b&&(b=0>a?-1:1);this.zoomRatio=(b+this.zmPctSet)/this.zmPctSet;this.zmPctSet+=b},"~N");c(c$,"setScaleAngstromsPerInch",function(a){if(this.scale3D=0<a)this.scale3DAngstromsPerInch=a;this.perspectiveDepth=!this.scale3D},"~N");c(c$,"setSlabRange",function(a){this.slabRange=a},"~N");c(c$,"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(u(this.screenWidth/2),u(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(u(this.screenWidth/2),u(this.screenHeight/2),0);this.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);var d=JU.P3.new3(u(this.screenWidth/2),u(this.screenHeight/2),this.cameraDistanceFromCenter*this.scalePixelsPerAngstrom);
this.unTransformPoint(d,d);d.sub(this.fixedRotationCenter);b.add(d);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$,"setCameraDepthPercent",function(a,b){this.resetNavigationPoint(b);
var d=0>a?-a/100:a;0!=d&&(this.cameraDepthSetting=d,this.vwr.g.setF("cameraDepth",this.cameraDepthSetting),this.cameraDepth=NaN)},"~N,~B");c(c$,"getCameraDepth",function(){return this.cameraDepthSetting});c(c$,"setScreenParameters0",function(a,b,d,c,g,e){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=d,this.width=(this.antialias=c)?2*a:a,this.height=c?2*b:b,this.scaleFitToScreen(!1,d,g,e))},"~N,~N,~B,~B,~B,~B");c(c$,"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$,"scaleFitToScreen",function(a,b,d,c){0==this.width||0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*(a?0.5:this.xTranslationFraction),
this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),c&&this.resetNavigationPoint(d),this.zoomHeight&&(b=this.height>this.width),this.screenPixelCount=b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");c(c$,"scaleToScreen",function(a,b){if(0==b||2>a)return 0;var d=this.scaleToPerspective(a,b*this.scalePixelsPerAngstrom/
1E3);return 0<d?d:1},"~N,~N");c(c$,"unscaleToScreen",function(a,b){var d=b/this.scalePixelsPerAngstrom;return this.perspectiveDepth?d/this.getPerspectiveFactor(a):d},"~N,~N");c(c$,"scaleToPerspective",function(a,b){return this.perspectiveDepth?b*this.getPerspectiveFactor(a):b},"~N,~N");c(c$,"setNavigationMode",function(a){this.mode=a?1:this.defaultMode;this.resetNavigationPoint(!0)},"~B");c(c$,"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$,"calcSlabAndDepthValues",function(){this.slabValue=1>this.slabRange?this.zValueFromPercent(this.slabPercentSetting):u(Math.floor(this.modelCenterOffset*this.slabRange/(2*this.modelRadius)*(this.zmPctSet/100)));this.depthValue=this.zValueFromPercent(this.depthPercentSetting);this.zSlabPercentSetting==this.zDepthPercentSetting?(this.zSlabValue=this.slabValue,this.zDepthValue=this.depthValue):(this.zSlabValue=this.zValueFromPercent(this.zSlabPercentSetting),
this.zDepthValue=this.zValueFromPercent(this.zDepthPercentSetting));if(null!=this.zSlabPoint)try{this.transformPt3f(this.zSlabPoint,this.pointT2),this.zSlabValue=C(this.pointT2.z)}catch(a){if(!D(a,Exception))throw a;}this.vwr.g.setO("_slabPlane",JU.Escape.eP4(this.getSlabDepthPlane(!1)));this.vwr.g.setO("_depthPlane",JU.Escape.eP4(this.getSlabDepthPlane(!0)));this.slabEnabled||(this.slabValue=0,this.depthValue=2147483647)});c(c$,"zValueFromPercent",function(a){return u(Math.floor((1-a/50)*this.modelRadiusPixels+
this.modelCenterOffset))},"~N");c(c$,"calcTransformMatrix",function(){this.matrixTransform.setIdentity();this.vectorTemp.sub2(this.frameOffset,this.fixedRotationCenter);this.matrixTransform.setTranslation(this.vectorTemp);this.matrixTemp.setToM3(this.stereoFrame?this.matrixStereo:this.matrixRotate);this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTemp.setIdentity();this.matrixTemp.m00=this.matrixTemp.m11=this.matrixTemp.m22=this.scalePixelsPerAngstrom;this.matrixTemp.m11=
this.matrixTemp.m22=-this.scalePixelsPerAngstrom;this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTransform.m23+=this.modelCenterOffset;try{this.matrixTransformInv.setM4(this.matrixTransform).invert()}catch(a){if(D(a,Exception))Zystem.out.println("ERROR INVERTING matrixTransform!");else throw a;}});c(c$,"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,d){return a.setCalcPoint(b,this.vibrationT,Float.isNaN(d)?this.vibrationScale:d,this.vwr.g.modulationScale)},"JU.Vibration,JU.T3,~N");c(c$,"transformPt2D",function(a){-3.4028235E38==a.z?(this.iScrPt.x=u(Math.floor(a.x/100*this.screenWidth)),this.iScrPt.y=u(Math.floor((1-a.y/100)*this.screenHeight))):(this.iScrPt.x=C(a.x),this.iScrPt.y=
this.screenHeight-C(a.y));this.antialias&&(this.iScrPt.x<<=1,this.iScrPt.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.fScrPt);this.iScrPt.z=C(this.fScrPt.z);return this.iScrPt},"JU.T3");c(c$,"applyPerspective",function(a,b){this.getScreenTemp(a);var d=this.fScrPt.z;Float.isNaN(d)?(!this.haveNotifiedNaN&&JU.Logger.debugging&&JU.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=!0,d=this.fScrPt.z=1):0>=d&&(d=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&&(d=this.getPerspectiveFactor(d),this.fScrPt.x*=d,this.fScrPt.y*=d);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(C(this.fScrPt.x),C(this.fScrPt.y),C(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,d,c,g,e,j){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm");this.movetoThread.setManager(this,this.vwr,v(-1,[b,c,L(-1,[d,g,e,j])]));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,d){var c=JU.M3.newA9(d);c.invert();var g=d[9],e=-d[10],j=-d[11],h=JU.P3.new3(d[12],d[13],d[14]),k=d[15],r=d[16],n=d[17];this.setPerspectiveDepth(!(0<=n));var n=Math.abs(n)/2,q=Math.tan(3.141592653589793*n/180),n=j*
q,q=0.5/q-0.5,p=50/n;0<k&&(k=50+C((j-k)*p),j=50+C((j-r)*p),this.setSlabEnabled(!0),this.slabToPercent(k),this.depthToPercent(j),21==d.length&&(r=0!=d[18],p=0!=d[19],d=d[20],this.setZShadeEnabled(r),r&&(p?this.vwr.setIntProperty("zSlab",C(Math.min(100,k+d*(j-k)))):this.vwr.setIntProperty("zSlab",C((k+j)/2)),this.vwr.setIntProperty("zDepth",j))));this.moveTo(a,b,h,null,0,c,100,NaN,NaN,n,null,NaN,NaN,NaN,q,g,e);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(c$,"moveTo",function(a,b,d,c,g,e,j,h,k,r,n,
q,p,m,s,t,u){if(null==e)if(e=new JU.M3,c=JU.V3.newV(c),Float.isNaN(g))e.m00=NaN;else if(0.01>g&&-0.01<g)e.setScale(1);else{if(0==c.x&&0==c.y&&0==c.z)return;var w=new JU.A4;w.setVA(c,g/57.29577951308232);e.setAA(w)}t==this.cameraSetting.x&&(t=NaN);u==this.cameraSetting.y&&(u=NaN);s==this.cameraDepth&&(s=NaN);Float.isNaN(t)||(h=50*t/r/this.width*this.screenPixelCount);Float.isNaN(u)||(k=50*u/r/this.height*this.screenPixelCount);g=null==d?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(r);
if(0>=b)this.setAll(d,e,n,j,h,k,r,g,m,q,p,s,t,u),this.vwr.moveUpdate(b),this.vwr.finalizeTransformParameters();else try{null==this.movetoThread&&(this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm"));var x=this.movetoThread.setManager(this,this.vwr,v(-1,[d,e,n,L(-1,[b,j,h,k,r,g,m,q,p,s,t,u])]));0>=x||this.vwr.g.waitForMoveTo?(0<x&&this.movetoThread.setEval(a),this.movetoThread.run(),this.vwr.isSingleThreaded||(this.movetoThread=null)):this.movetoThread.start()}catch(y){if(!D(y,
Exception))throw y;}},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.T3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(c$,"setAll",function(a,b,d,c,g,e,j,h,k,r,n,q,p,m){Float.isNaN(b.m00)||this.setRotation(b);null!=a&&this.moveRotationCenter(a,!this.windowCentered);null!=d&&1==this.mode&&this.navigationCenter.setT(d);Float.isNaN(q)||this.setCameraDepthPercent(q,!1);!Float.isNaN(p)&&!Float.isNaN(m)&&this.setCamera(p,m);Float.isNaN(c)||this.zoomToPercent(c);Float.isNaN(j)||(this.modelRadius=j);Float.isNaN(h)||
(this.scaleDefaultPixelsPerAngstrom=h);!Float.isNaN(g)&&!Float.isNaN(e)&&(this.translateToPercent("x",g),this.translateToPercent("y",e));1==this.mode&&(!Float.isNaN(r)&&!Float.isNaN(n)&&this.navTranslatePercentOrTo(0,r,n),Float.isNaN(k)||this.setNavigationDepthPercent(k))},"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$,"getMoveToText",function(a,b){this.finalizeTransformParameters();var d=new JU.SB;d.append("moveto ");b&&d.append("/* time, axisAngle */ ");
d.appendF(a);d.append(" ").append(this.getRotationText());b&&d.append(" /* zoom, translation */ ");JV.TransformManager.truncate2(d,this.zmPctSet);JV.TransformManager.truncate2(d,this.getTranslationXPercent());JV.TransformManager.truncate2(d,this.getTranslationYPercent());d.append(" ");b&&d.append(" /* center, rotationRadius */ ");d.append(this.getCenterText());d.append(" ").appendF(this.modelRadius);d.append(this.getNavigationText(b));b&&d.append(" /* cameraDepth, cameraX, cameraY */ ");JV.TransformManager.truncate2(d,
this.cameraDepth);JV.TransformManager.truncate2(d,this.cameraSetting.x);JV.TransformManager.truncate2(d,this.cameraSetting.y);d.append(";");return d.toString()},"~N,~B");c(c$,"getCenterText",function(){return JU.Escape.eP(this.fixedRotationCenter)});c(c$,"getRotateXyzText",function(){var a=new JU.SB,b=this.matrixRotate.m20,d=-(57.29577951308232*Math.asin(b)),c;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,this.matrixRotate.m11)),c=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,
this.matrixRotate.m22),c=57.29577951308232*Math.atan2(this.matrixRotate.m10,this.matrixRotate.m00));a.append("reset");a.append(";center ").append(this.getCenterText());0!=b&&(a.append("; rotate x"),JV.TransformManager.truncate2(a,b));0!=d&&(a.append("; rotate y"),JV.TransformManager.truncate2(a,d));0!=c&&(a.append("; rotate z"),JV.TransformManager.truncate2(a,c));a.append(";");this.addZoomTranslationNavigationText(a);return a.toString()});c(c$,"addZoomTranslationNavigationText",function(a){100!=this.zmPct&&
(a.append(" zoom"),JV.TransformManager.truncate2(a,this.zmPct),a.append(";"));var b=this.getTranslationXPercent();0!=b&&(a.append(" translate x"),JV.TransformManager.truncate2(a,b),a.append(";"));b=this.getTranslationYPercent();0!=b&&(a.append(" translate y"),JV.TransformManager.truncate2(a,b),a.append(";"));if(this.modelRadius!=this.rotationRadiusDefault||10==this.modelRadius)a.append(" set rotationRadius"),JV.TransformManager.truncate2(a,this.modelRadius),a.append(";");1==this.mode&&(a.append("navigate 0 center ").append(JU.Escape.eP(this.navigationCenter)),
a.append(";navigate 0 translate"),JV.TransformManager.truncate2(a,this.getNavigationOffsetPercent("X")),JV.TransformManager.truncate2(a,this.getNavigationOffsetPercent("Y")),a.append(";navigate 0 depth "),JV.TransformManager.truncate2(a,this.navigationDepthPercent),a.append(";"))},"JU.SB");c(c$,"getRotateZyzText",function(a){var b=new JU.SB,d=this.vwr.ms.getInfoM("defaultOrientationMatrix");null==d?d=this.matrixRotate:(d=JU.M3.newM3(d),d.invert(),d.mul2(this.matrixRotate,d));var c=d.m22,g=57.29577951308232*
Math.acos(c);0.999<c||-0.999>c?(c=57.29577951308232*Math.atan2(d.m10,d.m11),d=0):(c=57.29577951308232*Math.atan2(d.m21,-d.m20),d=57.29577951308232*Math.atan2(d.m12,d.m02));0!=c&&(0!=g&&0!=d&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");b.append("reset");b.append(";center ").append(this.getCenterText());0!=c&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,c));0!=g&&(b.append("; rotate y"),JV.TransformManager.truncate2(b,g));0!=d&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,
d));b.append(";");this.addZoomTranslationNavigationText(b);return b.toString()},"~B");c$.truncate0=c(c$,"truncate0",function(a,b){a.appendC(" ");a.appendI(Math.round(b))},"JU.SB,~N");c$.truncate2=c(c$,"truncate2",function(a,b){a.appendC(" ");a.appendF(Math.round(100*b)/100)},"JU.SB,~N");c(c$,"setSpinXYZ",function(a,b,d){Float.isNaN(a)||(this.spinX=a);Float.isNaN(b)||(this.spinY=b);Float.isNaN(d)||(this.spinZ=d);(this.isSpinInternal||this.isSpinFixed)&&this.clearSpin()},"~N,~N,~N");c(c$,"setSpinFps",
function(a){0>=a?a=1:50<a&&(a=50);this.spinFps=a},"~N");c(c$,"setNavXYZ",function(a,b,d){Float.isNaN(a)||(this.navX=a);Float.isNaN(b)||(this.navY=b);Float.isNaN(d)||(this.navZ=d)},"~N,~N,~N");c(c$,"clearSpin",function(){this.setSpinOff();this.setNavOn(!1);this.isSpinFixed=this.isSpinInternal=!1});c(c$,"setSpinOn",function(){this.setSpin(null,!0,3.4028235E38,null,null,null,!1)});c(c$,"setSpinOff",function(){this.setSpin(null,!1,3.4028235E38,null,null,null,!1)});c(c$,"setSpin",function(a,b,d,c,g,e,
j){this.navOn&&b&&this.setNavOn(!1);this.spinOn!=b&&(this.spinOn=b,this.vwr.g.setB("_spinning",b),b?null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread",this.vwr,"tm"),this.spinThread.setManager(this,this.vwr,v(-1,[Float.$valueOf(d),c,g,e,j?Boolean.TRUE:null])),this.spinIsGesture=j,Float.isNaN(d)||3.4028235E38==d||!this.vwr.g.waitForMoveTo?this.spinThread.start():(this.spinThread.setEval(a),this.spinThread.run())):null!=this.spinThread&&(this.spinThread.reset(),this.spinThread=
null))},"J.api.JmolScriptEvaluator,~B,~N,JU.Lst,~A,JU.BS,~B");c(c$,"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=C(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",function(a,b){this.setRotationCenterAndRadiusXYZ(a,!1);b&&this.setRotationPointXY(this.fixedRotationCenter)},"JU.P3,~B");c(c$,"setCenter",function(){this.setRotationCenterAndRadiusXYZ(this.fixedRotationCenter,
!0)});c(c$,"setCenterAt",function(a,b){var d=JU.P3.newP(b);switch(a){case 1073741826:break;case 96:d.add(this.vwr.ms.getAverageAtomPoint());break;case 1678381065:d.add(this.vwr.getBoundBoxCenter());break;default:d.setT(this.rotationCenterDefault)}this.setRotationCenterAndRadiusXYZ(d,!0);this.resetFitToScreen(!0)},"~N,JU.P3");c(c$,"setFrameOffset",function(a){null==this.frameOffsets||0>a||a>=this.frameOffsets.length?this.frameOffset.set(0,0,0):this.frameOffset.setT(this.frameOffsets[a])},"~N");c(c$,
"setSelectedTranslation",function(a,b,d){this.bsSelectedAtoms=a;switch(b){case "X":case "x":this.ptOffset.x+=d;break;case "Y":case "y":this.ptOffset.y+=d;break;case "Z":case "z":this.ptOffset.z+=d}},"JU.BS,~S,~N");c(c$,"setNavFps",function(a){this.navFps=a},"~N");c(c$,"calcCameraFactors",function(){Float.isNaN(this.cameraDepth)&&(this.cameraDepth=this.cameraDepthSetting,this.zoomFactor=3.4028235E38);this.cameraDistance=this.cameraDepth*this.screenPixelCount;this.referencePlaneOffset=this.cameraDistance+
this.screenPixelCount/2;this.scalePixelsPerAngstrom=this.scale3D&&!this.perspectiveDepth&&1!=this.mode?72/this.scale3DAngstromsPerInch*(this.antialias?2:1):this.screenPixelCount/this.visualRangeAngstroms;1!=this.mode&&(this.mode=0==this.camera.z?0:2);this.perspectiveShiftXY.set(0==this.camera.z?0:100*(this.camera.x*this.scalePixelsPerAngstrom/this.screenWidth),0==this.camera.z?0:100*(this.camera.y*this.scalePixelsPerAngstrom/this.screenHeight),0);this.modelRadiusPixels=this.modelRadius*this.scalePixelsPerAngstrom;
var a=2*this.modelRadius/this.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$,"unTransformPoint",
function(a,b){this.untransformedPoint.setT(a);switch(this.mode){case 1:this.untransformedPoint.x-=this.navigationOffset.x;this.untransformedPoint.y-=this.navigationOffset.y;break;case 2:this.fScrPt.x+=this.perspectiveShiftXY.x,this.fScrPt.y+=this.perspectiveShiftXY.y;case 0:this.untransformedPoint.x-=this.fixedRotationOffset.x,this.untransformedPoint.y-=this.fixedRotationOffset.y}if(this.perspectiveDepth){var d=this.getPerspectiveFactor(this.untransformedPoint.z);this.untransformedPoint.x/=d;this.untransformedPoint.y/=
d}switch(this.mode){case 1:this.untransformedPoint.x+=this.navigationShiftXY.x;this.untransformedPoint.y+=this.navigationShiftXY.y;break;case 2:this.untransformedPoint.x-=this.perspectiveShiftXY.x,this.untransformedPoint.y-=this.perspectiveShiftXY.y}this.matrixTransformInv.rotTrans2(this.untransformedPoint,b)},"JU.T3,JU.T3");c(c$,"resetNavigationPoint",function(a){5>this.zmPct&&1!=this.mode?(this.perspectiveDepth=!0,this.mode=1):(1==this.mode?(this.navMode=1,this.slabPercentSetting=0,this.perspectiveDepth=
!0):a&&(this.slabPercentSetting=100),this.vwr.setFloatProperty("slabRange",0),a&&this.setSlabEnabled(1==this.mode),this.zoomFactor=3.4028235E38,this.zmPctSet=this.zmPct)},"~B");c(c$,"setNavigatePt",function(a){this.navigationCenter.setT(a);this.navMode=3;this.navigating=!0;this.finalizeTransformParameters();this.navigating=!1},"JU.P3");c(c$,"setNavigationSlabOffsetPercent",function(a){this.vwr.g.setF("navigationSlab",a);this.calcCameraFactors();this.navigationSlabOffset=a/50*this.modelRadiusPixels},
"~N");c(c$,"getNavigationOffset",function(){this.transformPt3f(this.navigationCenter,this.navigationOffset);return this.navigationOffset});c(c$,"getNavPtHeight",function(){return this.height/2});c(c$,"getNavigationOffsetPercent",function(a){this.getNavigationOffset();return 0==this.width||0==this.height?0:"X"==a?100*(this.navigationOffset.x-this.width/2)/this.width:100*(this.navigationOffset.y-this.getNavPtHeight())/this.height},"~S");c(c$,"getNavigationText",function(a){a=a?" /* navigation center, translation, depth */ ":
" ";if(1!=this.mode)return a+"{0 0 0} 0 0 0";this.getNavigationOffset();return a+JU.Escape.eP(this.navigationCenter)+" "+this.getNavigationOffsetPercent("X")+" "+this.getNavigationOffsetPercent("Y")+" "+this.navigationDepthPercent},"~B");c(c$,"setScreenParameters",function(a,b,d,c,g,e){var j=1==this.mode?JU.P3.newP(this.navigationCenter):null,h=JU.P3.newP(this.navigationOffset);h.x/=this.width;h.y/=this.height;this.setScreenParameters0(a,b,d,c,g,e);null!=j&&(this.navigationCenter.setT(j),this.navTranslatePercentOrTo(-1,
h.x*this.width,h.y*this.height),this.setNavigatePt(j))},"~N,~N,~B,~B,~B,~B");c(c$,"navInterrupt",function(){null!=this.nav&&this.nav.interrupt()});c(c$,"getNav",function(){if(null!=this.nav)return!0;this.nav=J.api.Interface.getOption("navigate.Navigator",this.vwr,"tm");if(null==this.nav)return!1;this.nav.set(this,this.vwr);return!0});c(c$,"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$,"navTranslatePercentOrTo",function(a,b,d){this.getNav()&&this.nav.navTranslatePercentOrTo(a,b,d)},"~N,~N,~N");c(c$,"calcNavigationPoint",function(){this.getNav()&&this.nav.calcNavigationPoint()});
c(c$,"getNavigationState",function(){return 1==this.mode&&this.getNav()?this.nav.getNavigationState():""});G(c$,"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)});m("JV");x(["java.lang.Enum","J.api.JmolViewer","$.PlatformViewer","J.atomdata.AtomDataServer","java.util.Hashtable"],"JV.Viewer","java.io.BufferedInputStream $.BufferedReader $.Reader java.lang.Boolean $.Character $.Float $.NullPointerException java.util.Arrays JU.AU $.BS $.CU $.DF $.Lst $.P3 $.P3i $.PT $.Quat $.Rdr $.SB 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 $.TransformManager JV.binding.Binding".split(" "),
function(){c$=w(function(){this.queueOnHold=this.isSingleThreaded=this.isWebGL=this.isJSNoAWT=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.executor=null;this.screenHeight=this.screenWidth=0;this.errorMessageUntranslated=this.errorMessage=this.chainList=
this.chainMap=this.rd=this.defaultVdw=this.actionStatesRedo=this.actionStates=null;this.privateKey=0;this.dataOnly=!1;this.maximumSize=2147483647;this.gRight=null;this.isStereoSlave=!1;this.imageFontScaling=1;this.antialiased=!1;this.prevFrame=-2147483648;this.prevMorphModel=0;this.haveJDX=!1;this.jzt=this.outputManager=this.jsv=null;this.headless=this.isPreviewOnly=!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.jsParams=this.captureParams=null;this.cirChecked=!1;this.hoverAtomIndex=-1;this.hoverText=null;this.hoverLabel="%U";this.hoverEnabled=!0;this.currentCursor=0;this.ptTemp=null;this.selectionHalosEnabled=!1;this.noFrankEcho=this.frankOn=!0;this.scriptEditorVisible=!1;this.pm=this.headlessImageParams=this.modelkit=this.jmolpopup=this.scriptEditor=this.appConsole=null;this.isTainted=
!0;this.showSelected=this.movingSelected=!1;this.atomHighlighted=-1;this.creatingImage=!1;this.userVdwMars=this.userVdws=this.bsUserVdws=null;this.currentShapeID=-1;this.localFunctions=this.currentShapeState=null;this.$isKiosk=!1;this.displayLoadErrors=!0;this.$isParallel=!1;this.stateScriptVersionInt=2147483647;this.timeouts=this.jsExporter3D=null;this.chainCaseSpecified=!1;this.macros=this.nboParser=this.triangulator=this.jsonParser=this.jcm=this.jbr=this.logFileName=this.nmrCalculation=null;this.consoleFontScale=
1;s(this,arguments)},JV,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,J.api.PlatformViewer]);c(c$,"finalize",function(){JU.Logger.debugging&&JU.Logger.debug("vwr finalize "+this);T(this,JV.Viewer,"finalize",[])});c(c$,"setInsertedCommand",function(a){this.insertedCommand=a},"~S");c$.getJmolVersion=h(c$,"getJmolVersion",function(){return null==JV.Viewer.version_date?JV.Viewer.version_date=JV.JC.version+"  "+JV.JC.date:JV.Viewer.version_date});c$.allocateViewer=c(c$,"allocateViewer",function(a,
b,d,c,g,e,j,h){var k=new java.util.Hashtable;k.put("display",a);k.put("adapter",b);k.put("statusListener",j);k.put("platform",h);k.put("options",e);k.put("fullName",d);k.put("documentBase",c);k.put("codeBase",g);return new JV.Viewer(k)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,J.api.GenericPlatform");p(c$,function(a){I(this,JV.Viewer,[]);this.commandHistory=new JU.CommandHistory;this.rd=new J.atomdata.RadiusData(null,0,null,null);this.defaultVdw=J.c.VDW.JMOL;
this.localFunctions=new java.util.Hashtable;this.privateKey=Math.random();this.actionStates=new JU.Lst;this.actionStatesRedo=new JU.Lst;this.chainMap=new java.util.Hashtable;this.chainList=new JU.Lst;this.setOptions(a)},"java.util.Map");c(c$,"haveAccess",function(a){return this.access===a},"JV.Viewer.ACCESS");h(c$,"getModelAdapter",function(){return null==this.modelAdapter?this.modelAdapter=new J.adapter.smarter.SmarterJmolAdapter:this.modelAdapter});h(c$,"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,d){null==b&&(b=this.bsA());0==d&&(d=2);return this.getSmilesMatcher().getCorrelationMaps(a,this.ms.at,this.ms.ac,b,d)},"~S,JU.BS,~N");c(c$,"setOptions",function(a){this.vwrOptions=a;JU.Logger.debugging&&JU.Logger.debug("Viewer constructor "+
this);this.modelAdapter=a.get("adapter");var b=a.get("statusListener");this.fullName=a.get("fullName");null==this.fullName&&(this.fullName="");var d=a.get("codePath");null==d&&(d="../java/");JV.Viewer.appletCodeBase=d.toString();JV.Viewer.appletIdiomaBase=JV.Viewer.appletCodeBase.substring(0,JV.Viewer.appletCodeBase.lastIndexOf("/",JV.Viewer.appletCodeBase.length-2)+1)+"idioma";d=a.get("documentBase");JV.Viewer.appletDocumentBase=null==d?"":d.toString();d=a.get("options");this.commandOptions=null==
d?"":d.toString();(a.containsKey("debug")||0<=this.commandOptions.indexOf("-debug"))&&JU.Logger.setLogLevel(5);this.isApplet&&a.containsKey("maximumSize")&&this.setMaximumSize(a.get("maximumSize").intValue());(this.isJNLP=this.checkOption2("isJNLP","-jnlp"))&&JU.Logger.info("setting JNLP mode TRUE");this.isApplet=(this.isSignedApplet=this.isJNLP||this.checkOption2("signedApplet","-signed"))||this.checkOption2("applet","-applet");this.allowScripting=!this.checkOption2("noscripting","-noscripting");
var c=this.fullName.indexOf("__");this.htmlName=0>c?this.fullName:this.fullName.substring(0,c);this.appletName=JU.PT.split(this.htmlName+"_","_")[0];this.syncId=0>c?"":this.fullName.substring(c+2,this.fullName.length-2);this.access=this.checkOption2("access:READSPT","-r")?JV.Viewer.ACCESS.READSPT:this.checkOption2("access:NONE","-R")?JV.Viewer.ACCESS.NONE:JV.Viewer.ACCESS.ALL;(this.isPreviewOnly=a.containsKey("previewOnly"))&&a.remove("previewOnly");this.isPrintOnly=this.checkOption2("printOnly",
"-p");this.dataOnly=this.checkOption2("isDataOnly","\x00");this.autoExit=this.checkOption2("exit","-x");d=a.get("platform");c="unknown";null==d&&(d=this.commandOptions.contains("platform=")?this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");if(t(d,String)){c=d;this.isWebGL=0<=c.indexOf(".awtjs.");JV.Viewer.isJS=this.isJSNoAWT=this.isWebGL||0<=c.indexOf(".awtjs2d.");this.async=!this.dataOnly&&!this.autoExit&&(this.testAsync||JV.Viewer.isJS&&a.containsKey("async"));
var g=d=null,e="?";self.Jmol&&(g=Jmol,d=Jmol._applets[this.htmlName.split("_object")[0]],e=Jmol._version);null!=e&&(this.html5Applet=d,JV.Viewer.jmolObject=g,JV.Viewer.strJavaVersion=e,JV.Viewer.strJavaVendor="Java2Script "+(this.isWebGL?"(WebGL)":"(HTML5)"));d=J.api.Interface.getInterface(c,this,"setOptions")}this.apiPlatform=d;this.display=a.get("display");this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.noGraphicsAllowed=this.checkOption2("noDisplay","-n");this.headless=this.apiPlatform.isHeadless();
this.haveDisplay=this.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);
d=a.get("graphicsAdapter");null==d&&!this.isWebGL&&(d=J.api.Interface.getOption("g3d.Graphics3D",this,"setOptions"));this.gdata=null==d&&(this.isWebGL||!JV.Viewer.isJS)?new JU.GData:d;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);c=a.containsKey("4DMouse");this.tm=JV.TransformManager.getTransformManager(this,2147483647,0,c);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);
d=a.get("repaintManager");null==d&&(d=J.api.Interface.getOption("render.RepaintManager",this,"setOptions"));if(JV.Viewer.isJS||null!=d&&!d.equals(""))(this.rm=d).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,c=b.indexOf("#"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("?"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("/"),0<=c&&(b=b.substring(0,c)),JV.Viewer.jsDocumentBase=b,this.fm.setAppletContext(JV.Viewer.appletDocumentBase),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"),d=a.get("headlistMaxTimeMs"),null==d&&(d=Integer.$valueOf(6E4)),this.setTimeout(""+Math.random(),d.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.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;this.allowScripting&&this.getScriptManager()},"java.util.Map");c(c$,"setMaximumSize",function(a){this.maximumSize=Math.max(a,100)},"~N");c(c$,"setStereo",function(a,b){this.isStereoSlave=a;this.gRight=
b},"~B,~O");c(c$,"getMenu",function(a){this.getPopupMenu();return a.equals("\x00")?(this.popupMenu(this.screenWidth-120,0,"j"),"OK"):null==this.jmolpopup?"":this.jmolpopup.jpiGetMenuAsString("Jmol version "+JV.Viewer.getJmolVersion()+"|_GET_MENU|"+a)},"~S");h(c$,"resizeInnerPanel",function(a,b){if(!this.autoExit&&this.haveDisplay)return this.sm.resizeInnerPanel(a,b);this.setScreenDimension(a,b);return B(-1,[this.screenWidth,this.screenHeight])},"~N,~N");h(c$,"setScreenDimension",function(a,b){b=Math.min(b,
this.maximumSize);a=Math.min(a,this.maximumSize);this.tm.stereoDoubleFull&&(a=u((a+1)/2));this.screenWidth==a&&this.screenHeight==b||this.resizeImage(a,b,!1,!1,!0)},"~N,~N");c(c$,"resizeImage",function(a,b,d,c,g){if(d||!this.creatingImage){var e=this.antialiased;this.antialiased=g?this.g.antialiasDisplay&&this.checkMotionRendering(603979786):d&&!c?this.g.antialiasImages:!1;!c&&(!d&&(0<a||e!=this.antialiased))&&this.setShapeProperty(5,"clearBoxes",null);this.imageFontScaling=(this.antialiased?2:1)*
(g||this.tm.scale3D||0>=a?1:1*(this.g.zoomLarge==b>a?b:a)/this.getScreenDim());0<a?(this.screenWidth=a,this.screenHeight=b,d||(this.g.setI("_width",a),this.g.setI("_height",b))):(a=0==this.screenWidth?this.screenWidth=500:this.screenWidth,b=0==this.screenHeight?this.screenHeight=500:this.screenHeight);this.tm.setScreenParameters(a,b,d||g?this.g.zoomLarge:!1,this.antialiased,!1,!1);this.gdata.setWindowParameters(a,b,this.antialiased);0<a&&!d&&this.setStatusResized(a,b)}},"~N,~N,~B,~B,~B");h(c$,"getScreenWidth",
function(){return this.screenWidth});h(c$,"getScreenHeight",function(){return this.screenHeight});c(c$,"getScreenDim",function(){return this.g.zoomLarge==this.screenHeight>this.screenWidth?this.screenHeight:this.screenWidth});c(c$,"setWidthHeightVar",function(){this.g.setI("_width",this.screenWidth);this.g.setI("_height",this.screenHeight)});c(c$,"getBoundBoxCenterX",function(){return u(this.screenWidth/2)});c(c$,"getBoundBoxCenterY",function(){return u(this.screenHeight/2)});c(c$,"updateWindow",
function(a,b){if(!this.refreshing||this.creatingImage)return this.refreshing?!1:!JV.Viewer.isJS;(this.isTainted||this.tm.slabEnabled)&&this.setModelVisibility();this.isTainted=!1;null!=this.rm&&0!=a&&this.setScreenDimension(a,b);return!0},"~N,~N");c(c$,"getImage",function(a,b){var d=null;try{this.beginRendering(a,b),this.render(),this.gdata.endRendering(),d=this.gdata.getScreenImage(b)}catch(c){if(D(c,Error))this.gdata.getScreenImage(b),this.handleError(c,!1),this.setErrorMessage("Error during rendering: "+
c,null);else if(D(c,Exception))Zystem.out.println("render error"+c);else throw c;}return d},"~B,~B");c(c$,"beginRendering",function(a,b){this.gdata.beginRendering(this.tm.getStereoRotationMatrix(a),this.g.translucent,b,!this.checkMotionRendering(603979967))},"~B,~B");c(c$,"render",function(){if(!(null==this.mm.modelSet||!this.mustRender||!this.refreshing&&!this.creatingImage||null==this.rm)){var a=this.antialiased&&this.g.antialiasTranslucent,b=this.shm.finalizeAtoms(this.tm.bsSelectedAtoms,!0);this.isWebGL?
(this.rm.renderExport(this.gdata,this.ms,this.jsParams),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$,"drawImage",function(a,b,d,c,g){null!=a&&null!=b&&this.apiPlatform.drawImage(a,b,d,c,this.screenWidth,this.screenHeight,g);this.gdata.releaseScreenImage()},"~O,~O,~N,~N,~B");c(c$,"getScreenImage",function(){return this.getScreenImageBuffer(null,
!0)});h(c$,"getScreenImageBuffer",function(a,b){if(this.isWebGL)return b?this.apiPlatform.allocateRgbImage(0,0,null,0,!1,!0):null;var d=this.tm.stereoDoubleFull||this.tm.stereoDoubleDTI,c=this.tm.stereoMode.isBiColor(),g=null==a&&d;c?(this.beginRendering(!0,b),this.render(),this.gdata.endRendering(),this.gdata.snapshotAnaglyphChannelBytes(),this.beginRendering(!1,b),this.render(),this.gdata.endRendering(),this.gdata.applyAnaglygh(this.tm.stereoMode,this.tm.stereoColors),c=this.gdata.getScreenImage(b)):
c=this.getImage(d,b);var e=null;g&&(e=this.apiPlatform.newBufferedImage(c,this.tm.stereoDoubleDTI?this.screenWidth:this.screenWidth<<1,this.screenHeight),a=this.apiPlatform.getGraphics(e));null!=a&&(d&&(this.tm.stereoMode===J.c.STER.DTI?(this.drawImage(a,c,this.screenWidth>>1,0,!0),c=this.getImage(!1,!1),this.drawImage(a,c,0,0,!0),a=null):(this.drawImage(a,c,this.screenWidth,0,!1),c=this.getImage(!1,!1))),null!=a&&this.drawImage(a,c,0,0,!1));return g?e:c},"~O,~B");c(c$,"evalStringWaitStatusQueued",
function(a,b,d,c,g){return 0==b.indexOf("JSCONSOLE")?(this.html5Applet._showInfo(0>b.indexOf("CLOSE")),0<=b.indexOf("CLEAR")&&this.html5Applet._clearConsole(),null):null==this.getScriptManager()?null:this.scm.evalStringWaitStatusQueued(a,b,d,c,g)},"~S,~S,~S,~B,~B");c(c$,"popupMenu",function(a,b,d){if(this.haveDisplay&&this.refreshing&&!this.isPreviewOnly&&!this.g.disablePopupMenu)switch(d){case "j":try{this.getPopupMenu(),this.jmolpopup.jpiShow(a,b)}catch(c){JU.Logger.info(c.toString()),this.g.disablePopupMenu=
!0}break;case "a":case "b":case "m":if(null==this.getModelkit(!0))break;this.modelkit.showMenu(a,b)}},"~N,~N,~S");c(c$,"getModelkit",function(a){null==this.modelkit?(this.modelkit=J.api.Interface.getInterface("J.modelkit.ModelKit",this,"script")).setMenu(this.apiPlatform.getMenuPopup(null,"m")):a&&this.modelkit.updateMenu();return this.modelkit},"~B");c(c$,"getPopupMenu",function(){if(this.g.disablePopupMenu)return null;if(null==this.jmolpopup&&(this.jmolpopup=this.allowScripting?this.apiPlatform.getMenuPopup(this.menuStructure,
"j"):null,null==this.jmolpopup))return this.async||(this.g.disablePopupMenu=!0),null;this.isJSNoAWT&&this.checkMenuUpdate();return this.jmolpopup.jpiGetMenuAsObject()});h(c$,"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$,"setStatusFrameChanged",function(a){a&&(this.prevFrame=-2147483648);
this.tm.setVibrationPeriod(NaN);var b=this.am.firstFrameIndex,d=this.am.lastFrameIndex,c=this.am.isMovie;a=this.am.cmi;b==d&&!c&&(a=b);var g=this.getModelFileNumber(a),e=this.am.cmi,j=g,h=g%1E6,k=c?b:this.getModelFileNumber(b),r=c?d:this.getModelFileNumber(d),n;c?n=""+(e+1):0==j?(n=this.getModelNumberDotted(b),b!=d&&(n+=" - "+this.getModelNumberDotted(d)),u(k/1E6)==u(r/1E6)&&(j=k)):n=this.getModelNumberDotted(a);0!=j&&(j=1E6>j?1:u(j/1E6));c||(this.g.setI("_currentFileNumber",j),this.g.setI("_currentModelNumberInFile",
h));b=this.am.currentMorphModel;this.g.setI("_currentFrame",e);this.g.setI("_morphCount",this.am.morphCount);this.g.setF("_currentMorphFrame",b);this.g.setI("_frameID",g);this.g.setI("_modelIndex",a);this.g.setO("_modelNumber",n);this.g.setO("_modelName",0>a?"":this.getModelName(a));g=0>a?"":this.ms.getModelTitle(a);this.g.setO("_modelTitle",null==g?"":g);this.g.setO("_modelFile",0>a?"":this.ms.getModelFileName(a));this.g.setO("_modelType",0>a?"":this.ms.getModelFileType(a));e==this.prevFrame&&b==
this.prevMorphModel||(this.prevFrame=e,this.prevMorphModel=b,g=this.getModelName(e),c?g=""+(""===g?e+1:this.am.caf+1)+": "+g:(c=""+this.getModelNumberDotted(e),g.equals(c)||(g=c+": "+g)),this.sm.setStatusFrameChanged(j,h,0>this.am.animationDirection?-k:k,0>this.am.currentDirection?-r:r,e,b,g),this.doHaveJDX()&&this.getJSV().setModel(a),JV.Viewer.isJS&&this.updateJSView(a,-1))},"~B,~B");c(c$,"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)&&(JV.Viewer.isJS&&Zystem.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$,"notifyError",function(a,b,d){this.g.setO("_errormessage",d);this.sm.notifyError(a,b,d)},"~S,~S,~S");c(c$,"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,d,c,g,e){this.setErrorMessage(g,
null);this.g.setI("_loadPoint",a.getCode());var j=a!==J.c.FIL.CREATING_MODELSET;j&&this.setStatusFrameChanged(!1,!1);this.sm.setFileLoadStatus(b,d,c,g,a.getCode(),j,e);j&&(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,d,c){this.sm.setStatusMeasuring(a,b,d,c)},"~S,~N,~S,~N");c(c$,"notifyMinimizationStatus",
function(){var a=this.getP("_minimizationStep"),b=this.getP("_minimizationForceField");this.sm.notifyMinimizationStatus(this.getP("_minimizationStatus"),t(a,String)?Integer.$valueOf(0):a,this.getP("_minimizationEnergy"),a.toString().equals("0")?Float.$valueOf(0):this.getP("_minimizationEnergyDiff"),b)});c(c$,"setStatusAtomPicked",function(a,b,d,c){c&&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&&(c=this.getPendingMeasurement(),null!=c&&(b=b.substring(0,b.length-1)+',"'+c.getString()+'"]'));this.g.setO("_pickinfo",b);this.sm.setStatusAtomPicked(a,b,d);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");h(c$,"getProperty",function(a,b,d){if(!"DATA_API".equals(a))return this.getPropertyManager().getProperty(a,b,d);switch("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........getPreference.......".indexOf(b)){case 0:return this.scriptCheckRet(d,
!0);case 20:return null==this.appConsole?"":this.appConsole.getText();case 40:return this.showEditor(d),null;case 60:return this.scriptEditorVisible=d.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:t(d,J.api.JmolAppConsoleInterface)?this.appConsole=d:null!=d&&!d.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=d&&d.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!=d&&d.booleanValue())&&(this.getProperty("DATA_API","getAppConsole",Boolean.TRUE),this.scriptEditor=null==this.appConsole?null:this.appConsole.getScriptEditor()),this.scriptEditor;case 120:return null!=this.jmolpopup&&this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.menuStructure=d;case 140:return this.getSymTemp().getSpaceGroupInfo(this.ms,
null,-1,!1,null);case 160:return this.g.disablePopupMenu=!0,null;case 180:return this.g.defaultDirectory;case 200:return t(d,String)?this.getMenu(d):this.getPopupMenu();case 220:return this.shm.getProperty(d);case 240:return this.sm.syncSend("getPreference",d,1)}JU.Logger.error("ERROR in getProperty DATA_API: "+b);return null},"~S,~S,~O");c(c$,"notifyMouseClicked",function(a,b,d,c){var g=JV.binding.Binding.getButtonMods(d),e=JV.binding.Binding.getClickCount(d);this.g.setI("_mouseX",a);this.g.setI("_mouseY",
this.screenHeight-b);this.g.setI("_mouseAction",d);this.g.setI("_mouseModifiers",g);this.g.setI("_clickCount",e);return this.sm.setStatusClicked(a,this.screenHeight-b,d,e,c)},"~N,~N,~N,~N");c(c$,"getOutputManager",function(){return null!=this.outputManager?this.outputManager:(this.outputManager=J.api.Interface.getInterface("JV.OutputManager"+(JV.Viewer.isJS?"JS":"Awt"),this,"file")).setViewer(this,this.privateKey)});c(c$,"getJzt",function(){return null==this.jzt?this.jzt=J.api.Interface.getInterface("JU.ZipTools",
this,"zip"):this.jzt});c(c$,"readFileAsMap",function(a,b,d){this.getJzt().readFileAsMap(a,b,d)},"java.io.BufferedInputStream,java.util.Map,~S");c(c$,"getZipDirectoryAsString",function(a){a=this.fm.getBufferedInputStreamOrErrorMessageFromName(a,a,!1,!1,null,!1,!0);return this.getJzt().getZipDirectoryAsStringAndClose(a)},"~S");h(c$,"getImageAsBytes",function(a,b,d,c,g){return this.getOutputManager().getImageAsBytes(a,b,d,c,g)},"~S,~N,~N,~N,~A");h(c$,"releaseScreenImage",function(){this.gdata.releaseScreenImage()});
c(c$,"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,b){return this.vwrOptions.containsKey(a)&&!this.vwrOptions.get(a).toString().equals("false")||0<=this.commandOptions.indexOf(b)},"~S,~S");c(c$,"setStartupBooleans",function(){this.setBooleanProperty("_applet",this.isApplet);
this.setBooleanProperty("_jspecview",!1);this.setBooleanProperty("_signedApplet",this.isSignedApplet);this.setBooleanProperty("_headless",this.headless);this.setStringProperty("_restrict",'"'+this.access+'"');this.setBooleanProperty("_useCommandThread",this.useCommandThread)});c(c$,"getExportDriverList",function(){return this.haveAccess(JV.Viewer.ACCESS.ALL)?this.g.getParameter("exportDrivers",!0):""});h(c$,"dispose",function(){this.gRight=null;null!=this.mouse&&(this.acm.dispose(),this.mouse.dispose(),
this.mouse=null);this.clearScriptQueue();this.clearThreads();this.haltScriptExecution();null!=this.scm&&this.scm.clear(!0);this.gdata.destroy();null!=this.jmolpopup&&this.jmolpopup.jpiDispose();null!=this.modelkit&&this.modelkit.dispose();try{null!=this.appConsole&&(this.appConsole.dispose(),this.appConsole=null),null!=this.scriptEditor&&(this.scriptEditor.dispose(),this.scriptEditor=null)}catch(a){if(!D(a,Exception))throw a;}});c(c$,"reset",function(a){this.ms.calcBoundBoxDimensions(null,1);this.axesAreTainted=
!0;this.tm.homePosition(a);this.ms.setCrystallographicDefaults()?this.stm.setCrystallographicDefaults():this.setAxesMode(603979809);this.prevFrame=-2147483648;this.tm.spinOn||this.setSync()},"~B");h(c$,"homePosition",function(){this.evalString("reset spin")});c(c$,"initialize",function(a,b){this.g=new JV.GlobalSettings(this,this.g,a);this.setStartupBooleans();this.setWidthHeightVar();this.haveDisplay&&(this.g.setB("_is2D",JV.Viewer.isJS&&!this.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=this.g.statusReporting;this.setBooleanProperty("antialiasDisplay",b?!0:this.g.antialiasDisplay);this.stm.resetLighting();this.tm.setDefaultPerspective()},
"~B,~B");c(c$,"saveModelOrientation",function(){this.ms.saveModelOrientation(this.am.cmi,this.stm.getOrientation())});c(c$,"restoreModelOrientation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!0)},"~N");c(c$,"restoreModelRotation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!1)},"~N");c(c$,"getGLmolView",function(){var a=this.tm,b=a.fixedRotationCenter,d=a.getRotationQ();return{center:b,quaternion:d,xtrans:a.xTranslationFraction,ytrans:a.yTranslationFraction,
scale:a.scalePixelsPerAngstrom,zoom:a.zmPctSet,cameraDistance:a.cameraDistance,pixelCount:a.screenPixelCount,perspective:a.perspectiveDepth,width:a.width,height:a.height}});c(c$,"setRotationRadius",function(a,b){b&&(a=this.tm.setRotationRadius(a,!1));this.ms.setRotationRadius(this.am.cmi,a)&&this.g.setF("rotationRadius",a)},"~N,~B");c(c$,"setCenterBitSet",function(a,b){this.isJmolDataFrame()||this.tm.setNewRotationCenter(0<JU.BSUtil.cardinalityOf(a)?this.ms.getAtomSetCenter(a):null,b)},"JU.BS,~B");
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NaN,NaN);break;case 12:this.tm.setNavXYZ(NaN,b,NaN);break;case 14:this.tm.setNavXYZ(NaN,NaN,b);break;case 16:this.tm.setNavFps(b)}this.g.setI((10>d?"spin":"nav")+a,b)}},"~S,~N");c(c$,"getSpinState",function(){return this.getStateCreator().getSpinState(!1)});c(c$,"getOrientationText",function(a,b,d){switch(a){case 1312817669:case 1814695966:case 1073741864:case 1111492629:case 1111492630:case 1111492631:case 134221850:null==d&&(d=this.bsA());if(d.isEmpty())return 1312817669==a?"0":1814695966==a?null:
new JU.Quat;d=this.ms.getBoundBoxOrientation(a,d);return"best"===b&&1312817669!=a?d.div(this.tm.getRotationQ()):d;case 1073742034:return this.stm.getSavedOrientationText(b);default:return this.tm.getOrientationText(a,"best"===b)}},"~N,~S,JU.BS");c(c$,"getCurrentColorRange",function(){return this.cm.getPropertyColorRange()});c(c$,"setDefaultColors",function(a){this.cm.setDefaultColors(a);this.g.setB("colorRasmol",a);this.g.setO("defaultColorScheme",a?"rasmol":"jmol")},"~B");c(c$,"setElementArgb",function(a,
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g));if(0!=k)return this.fm.setFileInfo(n),this.loadAtomDataAndReturnError(h,k);if(e.containsKey("isData"))return h;null!=j&&!t(h,String)&&(b=e.get("fullPathName"),null==b&&(b=""),e.containsKey("loadScript")&&(j=e.get("loadScript")),e.put("loadScript",j=(new JU.SB).append(JU.PT.rep(j.toString(),"$FILENAME$",JU.PT.esc(JV.FileManager.fixDOSName(b))))));return this.createModelSetAndReturnError(h,g,j,e)},"~S,~S,~A,~O,~B,java.util.Map,JU.SB,JU.SB,~N,~S");c(c$,"setLigandModel",function(a,b){null==this.ligandModels&&
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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$,"getConsole",function(){this.getProperty("DATA_API","getAppConsole",Boolean.TRUE);return this.appConsole});h(c$,"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$,"unsetProperty",function(a){a=a.toLowerCase();(a.equals("all")||a.equals("variables"))&&this.fm.setPathForAllFiles("");this.g.unsetUserVariable(a)},"~S");h(c$,"notifyStatusReady",function(a){Zystem.out.println("Jmol applet "+this.fullName+(a?" ready":" destroyed"));a||this.dispose();this.sm.setStatusAppletReady(this.fullName,
a)},"~B");h(c$,"getBooleanProperty",function(a){a=a.toLowerCase();if(this.g.htBooleanParameterFlags.containsKey(a))return this.g.htBooleanParameterFlags.get(a).booleanValue();if(a.endsWith("p!")){if(null==this.acm)return!1;var b=this.acm.getPickingState().toLowerCase();a=a.substring(0,a.length-2)+";";return 0<=b.indexOf(a)}if(a.equalsIgnoreCase("executionPaused"))return null!=this.eval&&this.eval.isPaused();if(a.equalsIgnoreCase("executionStepping"))return null!=this.eval&&this.eval.isStepping();
if(a.equalsIgnoreCase("haveBFactors"))return null!=this.ms.getBFactors();if(a.equalsIgnoreCase("colorRasmol"))return this.cm.isDefaultColorRasmol;if(a.equalsIgnoreCase("frank"))return this.getShowFrank();if(a.equalsIgnoreCase("spinOn"))return this.tm.spinOn;if(a.equalsIgnoreCase("isNavigating"))return this.tm.isNavigating();if(a.equalsIgnoreCase("showSelections"))return this.selectionHalosEnabled;if(this.g.htUserVariables.containsKey(a)){b=this.g.getUserVariable(a);if(1073742335==b.tok)return!0;if(1073742334==
b.tok)return!1}JU.Logger.error("vwr.getBooleanProperty("+a+") - unrecognized");return!1},"~S");h(c$,"getInt",function(a){switch(a){case 553648132:return this.am.animationFps;case 553648141:return this.g.dotDensity;case 553648142:return this.g.dotScale;case 553648144:return this.g.helixStep;case 553648147:return this.g.infoFontSize;case 553648150: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 553648152:return this.g.minimizationMaxAtoms;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$,"getHoverDelay",function(){return this.g.modelKitMode?20:this.g.hoverDelayMs});h(c$,"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 603979821:return this.g.checkCIR;case 603979812:return this.g.bondModeOr;case 603979815:return this.g.cartoonBaseEdges;case 603979816:return this.g.cartoonFancy;
case 603979817:return this.g.cartoonLadders;case 603979818:return this.g.cartoonRibose;case 603979819: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 603979870:return this.g.justifyMeasurements;case 603979872:return this.g.legacyAutoBonding;case 603979873:return this.g.legacyHAddition;case 603979874:return this.g.legacyJavaFloat;case 603979876:return this.g.logGestures;case 603979877:return this.g.measureAllModels;case 603979878:return this.g.measurementLabels;case 603979879:return this.g.messageStyleChime;
case 603983903: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 603979894:return this.g.pdbAddHydrogens;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 603979948:return this.g.dotSolvent;
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$,"getBondsPickable",function(){return this.g.bondPicking||this.g.modelKitMode&&this.getModelkitProperty("isMolecular")===Boolean.TRUE});c(c$,"useMinimizationThread",function(){return this.g.useMinimizationThread&&
!this.autoExit});h(c$,"getFloat",function(a){switch(a){case 1140850689:return this.g.particleRadius;case 570425345:return this.g.axesOffset;case 570425346:return this.g.axesScale;case 570425348:return this.g.bondTolerance;case 570425353:return this.g.defaultTranslucent;case 570425352:return this.g.defaultDrawArrowScale;case 570425354:return this.g.dipoleScale;case 570425355:return this.g.drawFontSize;case 570425357:return this.g.exportScale;case 570425359:return this.g.hbondsAngleMinimum;case 570425361:return this.g.hbondHXDistanceMaximum;
case 570425360:return this.g.hbondNODistanceMaximum;case 570425363:return this.g.loadAtomDataTolerance;case 570425364:return this.g.minBondDistance;case 1275072532:return this.g.modulationScale;case 570425370:return this.g.multipleBondSpacing;case 570425369:return this.g.multipleBondRadiusFactor;case 570425374:return this.g.navigationSpeed;case 570425382:return this.g.pointGroupDistanceTolerance;case 570425384:return this.g.pointGroupLinearTolerance;case 570425388:return this.tm.modelRadius;case 570425392:return this.g.sheetSmoothing;
case 570425394:return this.g.solventProbeRadius;case 570425403:return this.g.starWidth;case 570425406:return this.g.strutDefaultRadius;case 570425408:return this.g.strutLengthMaximum;case 1648361473:return this.g.vectorScale;case 570425412:return this.g.vibrationPeriod;case 570425347:return this.g.cartoonBlockHeight}JU.Logger.error("viewer.getFloat("+JS.T.nameOf(a)+") - not listed");return 0},"~N");h(c$,"setStringProperty",function(a,b){if(!(null==b||null==a||0==a.length))if("_"==a.charAt(0))this.g.setO(a,
b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 603979776:this.setBooleanPropertyTok(a,d,JS.SV.newV(4,b).asBoolean());break;case 553648128:this.setIntPropertyTok(a,d,JS.SV.newV(4,b).asInt());break;case 570425344:this.setFloatPropertyTok(a,d,JU.PT.parseFloat(b));break;default:this.setStringPropertyTok(a,d,b)}}},"~S,~S");c(c$,"setStringPropertyTok",function(a,b,d){switch(b){case 545259567:this.g.macroDirectory=d=null==d||0==d.length?"https://chemapps.stolaf.edu/jmol/macros":d;
this.macros=null;break;case 545259570:this.g.nihResolverFormat=d;break;case 545259521:this.setAnimationMode(d);return;case 545259569:this.g.nmrPredictFormat=d;break;case 545259548:this.g.defaultDropScript=d;break;case 545259572:d=this.fm.setPathForAllFiles(d);break;case 545259558:this.setUnits(d,!1);return;case 545259560:this.g.forceField=d="UFF".equalsIgnoreCase(d)?"UFF":"UFF2D".equalsIgnoreCase(d)?"UFF2D":"MMFF2D".equalsIgnoreCase(d)?"MMFF2D":"MMFF";this.minimizer=null;break;case 545259571:this.g.nmrUrlFormat=
d;break;case 545259568:this.setUnits(d,!0);return;case 545259565:this.g.pdbLoadLigandFormat=d;break;case 545259543:this.g.defaultLabelPDB=d;break;case 545259544:this.g.defaultLabelXYZ=d;break;case 545259549:this.g.defaultLoadFilter=d;break;case 545259566:d=this.getOutputManager().setLogFile(d);if(null==d)return;break;case 545259559:break;case 545259524:this.g.atomTypes=d;break;case 545259538:break;case 545259576:this.g.pickLabel=d;break;case 545259580:this.g.quaternionFrame=2==d.length&&d.startsWith("R")?
d.substring(0,2):""+(d.toLowerCase()+"p").charAt(0);JU.PT.isOneOf(this.g.quaternionFrame,"RC;RP;a;b;c;n;p;q;x;")||(this.g.quaternionFrame="p");this.ms.haveStraightness=!1;break;case 545259555:this.setVdwStr(d);return;case 545259563:new J.i18n.GT(this,d);b=J.i18n.GT.getLanguage();this.modelkit=null;null!=this.jmolpopup&&(this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.getPopupMenu());this.sm.setCallbackFunction("language",b);d=J.i18n.GT.getLanguage();break;case 545259564:this.g.loadFormat=d;break;
case 545259534:this.setObjectColor("background",d);return;case 545259528:this.setObjectColor("axis1",d);return;case 545259530:this.setObjectColor("axis2",d);return;case 545259532:this.setObjectColor("axis3",d);return;case 545259536:this.setObjectColor("boundbox",d);return;case 545259586:this.setObjectColor("unitcell",d);return;case 545259578:this.setPropertyColorScheme(d,!1,!1);break;case 545259562:this.shm.loadShape(35);this.setShapeProperty(35,"atomLabel",d);break;case 545259547:this.g.defaultDistanceLabel=
d;break;case 545259542:this.g.defaultAngleLabel=d;break;case 545259554:this.g.defaultTorsionLabel=d;break;case 545259550:this.g.defaultLoadScript=d;break;case 545259522:this.fm.setAppletProxy(d);break;case 545259546:null==d&&(d="");d=d.$replace("\\","/");this.g.defaultDirectory=d;break;case 545259561:this.g.helpPath=d;break;case 545259552:!d.equalsIgnoreCase("RasMol")&&!d.equalsIgnoreCase("PyMOL")&&(d="Jmol");this.setDefaultsType(d);break;case 545259545:this.setDefaultColors(d.equalsIgnoreCase("rasmol"));
return;case 545259573:this.setPickingMode(d,0);return;case 545259574:this.setPickingStyle(d,0);return;case 545259540:break;default:if(a.toLowerCase().endsWith("callback")){this.sm.setCallbackFunction(a,0==d.length||d.equalsIgnoreCase("none")?null:d);break}if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(4,d));return}}this.g.setO(a,d)},"~S,~N,~S");h(c$,"setFloatProperty",function(a,b){if(!Float.isNaN(b)&&!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setF(a,
b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,d,""+b);break;case 603979776:this.setBooleanPropertyTok(a,d,0!=b);break;case 553648128:this.setIntPropertyTok(a,d,C(b));break;default:this.setFloatPropertyTok(a,d,b)}}},"~S,~N");c(c$,"setFloatPropertyTok",function(a,b,d){switch(b){case 570425347:this.g.cartoonBlockHeight=d;break;case 570425366:this.ms.setModulation(null,!1,null,!1);this.g.modulationScale=d=Math.max(0.1,d);this.ms.setModulation(null,
!0,null,!1);break;case 570425381:this.g.particleRadius=Math.abs(d);break;case 570425355:this.g.drawFontSize=d;break;case 570425357:this.g.exportScale=d;break;case 570425403:this.g.starWidth=d;break;case 570425369:this.g.multipleBondRadiusFactor=d;break;case 570425370:this.g.multipleBondSpacing=d;break;case 570425393:this.tm.setSlabRange(d);break;case 570425365:this.g.minimizationCriterion=d;break;case 570425358:this.haveDisplay&&this.acm.setGestureSwipeFactor(d);break;case 570425367:this.haveDisplay&&
this.acm.setMouseDragFactor(d);break;case 570425368:this.haveDisplay&&this.acm.setMouseWheelFactor(d);break;case 570425408:this.g.strutLengthMaximum=d;break;case 570425406:this.g.strutDefaultRadius=d;break;case 570425376:this.setSpin("X",C(d));break;case 570425378:this.setSpin("Y",C(d));break;case 570425380:this.setSpin("Z",C(d));break;case 570425371:if(Float.isNaN(d))return;this.setSpin("FPS",C(d));break;case 570425363:this.g.loadAtomDataTolerance=d;break;case 570425359:this.g.hbondsAngleMinimum=
d;break;case 570425361:this.g.hbondHXDistanceMaximum=d;break;case 570425360:this.g.hbondNODistanceMaximum=d;break;case 570425382:this.g.pointGroupDistanceTolerance=d;break;case 570425384:this.g.pointGroupLinearTolerance=d;break;case 570425356:this.g.ellipsoidAxisDiameter=d;break;case 570425398:this.setSpin("x",C(d));break;case 570425400:this.setSpin("y",C(d));break;case 570425402:this.setSpin("z",C(d));break;case 570425396:this.setSpin("fps",C(d));break;case 570425352:this.g.defaultDrawArrowScale=
d;break;case 570425353:this.g.defaultTranslucent=d;break;case 570425345:this.setAxesScale(b,d);break;case 570425346:this.setAxesScale(b,d);break;case 570425416:this.tm.visualRangeAngstroms=d;this.refresh(1,"set visualRange");break;case 570425372:this.setNavigationDepthPercent(d);break;case 570425374:this.g.navigationSpeed=d;break;case 570425373:this.tm.setNavigationSlabOffsetPercent(d);break;case 570425350:this.tm.setCameraDepthPercent(d,!1);this.refresh(1,"set cameraDepth");return;case 570425388:this.setRotationRadius(d,
!0);return;case 570425362:this.g.hoverDelayMs=C(1E3*d);break;case 570425392:this.g.sheetSmoothing=d;break;case 570425354:d=JV.Viewer.checkFloatRange(d,-10,10);this.g.dipoleScale=d;break;case 570425404:this.tm.setStereoDegrees(d);break;case 1648361473:this.setVectorScale(d);return;case 570425412:this.setVibrationPeriod(d);return;case 570425414:this.setVibrationScale(d);return;case 570425348:this.setBondTolerance(d);return;case 570425364:this.setMinBondDistance(d);return;case 570425390:this.tm.setScaleAngstromsPerInch(d);
break;case 570425394:d=JV.Viewer.checkFloatRange(d,0,10);this.g.solventProbeRadius=d;break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newF(d));return}}this.g.setF(a,d)},"~S,~N,~N");h(c$,"setIntProperty",function(a,b){if(!(-2147483648==b||null==a||0==a.length))if("_"==a.charAt(0))this.g.setI(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,d,""+b);break;case 603979776:this.setBooleanPropertyTok(a,
d,0!=b);break;case 570425344:this.setFloatPropertyTok(a,d,b);break;default:this.setIntPropertyTok(a,d,b)}}},"~S,~N");c(c$,"setIntPropertyTok",function(a,b,d){switch(b){case 553648152:this.g.minimizationMaxAtoms=d;break;case 553648147:this.g.infoFontSize=Math.max(0,d);break;case 553648167:case 553648146:case 553648168:d=this.eval.setStatic(b,d);break;case 553648185:this.g.vectorTrail=d;break;case 553648138:d=0==d?0:1;this.g.bondingVersion=JU.Elements.bondingVersion=d;break;case 553648137:this.gdata.setCelPower(d);
break;case 553648129:this.gdata.setAmbientOcclusion(d);break;case 553648158:this.g.platformSpeed=Math.min(Math.max(d,0),10);break;case 553648150:this.g.meshScale=d;break;case 553648153:this.g.minPixelSelRadius=d;break;case 553648148:this.g.isosurfacePropertySmoothingPower=d;break;case 553648165:this.g.repaintWaitMs=d;break;case 553648170:this.g.smallMoleculeMaxAtoms=d;break;case 553648151:this.g.minimizationSteps=d;break;case 553648184:this.g.strutSpacing=d;break;case 553648156:d=JV.Viewer.checkIntRange(d,
0,1E3);this.gdata.setPhongExponent(d);break;case 553648144:this.g.helixStep=d;this.ms.haveStraightness=!1;break;case 553648142:this.g.dotScale=d;break;case 553648141:this.g.dotDensity=d;break;case 553648139:this.g.delayMaximumMs=d;break;case 553648149:JU.Logger.setLogLevel(d);JU.Logger.info("logging level set to "+d);this.g.setI("logLevel",d);null!=this.eval&&this.eval.setDebugging();return;case 553648134:this.setAxesMode(2==d?603979808:1==d?603979804:603979809);return;case 553648178:this.setStrandCount(0,
d);return;case 553648182:this.setStrandCount(12,d);return;case 553648180:this.setStrandCount(13,d);return;case 553648155:return;case 536870922:this.g.scriptDelay=d;break;case 553648176:d=0>d?JV.Viewer.checkIntRange(d,-10,-1):JV.Viewer.checkIntRange(d,0,100);this.gdata.setSpecularPower(d);break;case 553648172:d=JV.Viewer.checkIntRange(-d,-10,-1);this.gdata.setSpecularPower(d);break;case 553648136:this.setMarBond(d);return;case 536870924:this.setBooleanPropertyTok(a,b,1==d);return;case 553648174:d=
JV.Viewer.checkIntRange(d,0,100);this.gdata.setSpecularPercent(d);break;case 553648140:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setDiffusePercent(d);break;case 553648130:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setAmbientPercent(d);break;case 553648186:this.tm.zDepthToPercent(d);break;case 553648188:this.tm.zSlabToPercent(d);break;case 554176526:this.tm.depthToPercent(d);break;case 554176565:this.tm.slabToPercent(d);break;case 553648190:this.g.zShadePower=d=Math.max(d,0);break;case 553648166:this.g.ribbonAspectRatio=
d;break;case 553648157:this.g.pickingSpinRate=1>d?1:d;break;case 553648132:this.setAnimationFps(d);return;case 553648154:this.setPercentVdwAtom(d);break;case 553648145:this.g.hermiteLevel=d;break;case 553648143:case 553648160:case 553648159:case 553648162:case 553648164:break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a)){this.g.setUserVariable(a,JS.SV.newI(d));return}}this.g.setI(a,d)},"~S,~N,~N");c$.checkIntRange=c(c$,"checkIntRange",function(a,b,d){return a<b?b:a>d?d:a},"~N,~N,~N");
c$.checkFloatRange=c(c$,"checkFloatRange",function(a,b,d){return a<b?b:a>d?d:a},"~N,~N,~N");h(c$,"setBooleanProperty",function(a,b){if(!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setB(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,d,"");break;case 553648128:this.setIntPropertyTok(a,d,b?1:0);break;case 570425344:this.setFloatPropertyTok(a,d,b?1:0);break;default:this.setBooleanPropertyTok(a,d,b)}}},"~S,~B");c(c$,"setBooleanPropertyTok",
function(a,b,d){var c=!0;switch(b){case 603979821:(this.g.checkCIR=d)&&this.checkCIR(!0);break;case 603979823:this.g.cipRule6Full=d;break;case 603979802:this.g.autoplayMovie=d;break;case 603979797:d=!1;this.g.allowAudio=d;break;case 603979892:this.g.noDelay=d;break;case 603979891:this.g.nboCharges=d;break;case 603979856:this.g.hiddenLinesDashed=d;break;case 603979886:this.g.multipleBondBananas=d;break;case 603979884:this.g.modulateOccupancy=d;break;case 603979874:this.g.legacyJavaFloat=d;break;case 603979927:this.g.showModVecs=
d;break;case 603979937:this.g.showUnitCellDetails=d;break;case 603979848:c=!1;break;case 603979972:this.g.vectorsCentered=d;break;case 603979810:this.g.cartoonBlocks=d;break;case 603979811:this.g.cartoonSteps=d;break;case 603979818:this.g.cartoonRibose=d;break;case 603979837:this.g.ellipsoidArrows=d;break;case 603979967:this.g.translucent=d;break;case 603979817:this.g.cartoonLadders=d;break;case 603979968:b=this.g.twistedSheets;this.g.twistedSheets=d;b!=d&&this.checkCoordinatesChanged();break;case 603979820:this.gdata.setCel(d);
break;case 603979816:this.g.cartoonFancy=d;break;case 603979934:this.g.showTiming=d;break;case 603979973:this.g.vectorSymmetry=d;break;case 603979867:this.g.isosurfaceKey=d;break;case 603979893:this.g.partialDots=d;break;case 603979872:this.g.legacyAutoBonding=d;break;case 603979826:this.g.defaultStructureDSSP=d;break;case 603979834:this.g.dsspCalcHydrogen=d;break;case 603979782:(this.g.allowModelkit=d)||this.setModelKitMode(!1);break;case 603983903:this.setModelKitMode(d);break;case 603979887:this.g.multiProcessor=
d&&1<JV.Viewer.nProcessors;break;case 603979885:this.g.monitorEnergy=d;break;case 603979853:this.g.hbondsRasmol=d;break;case 603979880:this.g.minimizationRefresh=d;break;case 603979881:this.g.minimizationSilent=d;break;case 603979866:d&&(this.$isKiosk=!0,this.g.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));break;case 603979975:this.g.waitForMoveTo=d;break;case 603979875:this.g.logCommands=!0;break;case 603979876:this.g.logGestures=!0;break;case 603979784:this.g.allowMultiTouch=
d;break;case 603979898:this.g.preserveState=d;this.ms.setPreserveState(d);this.undoClear();break;case 603979955:this.g.strutsMultiple=d;break;case 603979842:break;case 603979939:this.g.slabByAtom=d;break;case 603979940:this.g.slabByMolecule=d;break;case 603979903:this.g.saveProteinStructureState=d;break;case 603979780:this.g.allowGestures=d;break;case 603979865:this.g.imageState=d;break;case 603979970:this.g.useMinimizationThread=d;break;case 603979781:this.g.allowKeyStrokes=d;break;case 603979831:this.g.dragSelected=
d;this.showSelected=!1;break;case 603979924:this.g.showKeyStrokes=d;break;case 603979844:this.g.fontCaching=d;break;case 603979796:this.g.atomPicking=d;break;case 603979814:this.highlight(null);this.g.bondPicking=d;break;case 603979906:(this.g.selectAllModels=d)?this.slm.setSelectionSubset(null):this.am.setSelectAllSubset(!1);break;case 603979879:this.g.messageStyleChime=d;break;case 603979896:this.g.pdbSequential=d;break;case 603979894:this.g.pdbAddHydrogens=d;break;case 603979895:this.g.pdbGetHeader=
d;break;case 603979838:this.g.ellipsoidAxes=d;break;case 603979836:this.g.ellipsoidArcs=d;break;case 603979839:this.g.ellipsoidBall=d;break;case 603979840:this.g.ellipsoidDots=d;break;case 603979841:this.g.ellipsoidFill=d;break;case 603979845:this.g.fontScaling=d;break;case 603979956:this.setSyncTarget(0,d);break;case 603979958:this.setSyncTarget(1,d);break;case 603979977:this.g.wireframeRotation=d;break;case 603979868:this.g.isosurfacePropertySmoothing=d;break;case 603979833:this.g.drawPicking=d;
break;case 603979786:case 603979790:case 603979788:this.setAntialias(b,d);break;case 603979944:this.g.smartAromatic=d;break;case 603979794:this.setApplySymmetryToBonds(d);break;case 603979792:this.g.appendNew=d;break;case 603979800:this.g.autoFps=d;break;case 603979971:JU.DF.setUseNumberLocalization(this.g.useNumberLocalization=d);break;case 603979918:case 1611272202:a="showFrank";this.setFrankOn(d);break;case 1612709912:a="solventProbe";this.g.dotSolvent=d;break;case 603979948:this.g.dotSolvent=
d;break;case 603979785:this.g.allowRotateSelected=d;break;case 603979783:this.g.allowMoveAtoms=d;this.showSelected=!1;break;case 536870922:this.setIntPropertyTok("showScript",b,d?1:0);return;case 603979778:this.g.allowEmbeddedScripts=d;break;case 603979890:this.g.navigationPeriodic=d;break;case 603979984:this.tm.setZShadeEnabled(d);return;case 603979832:this.haveDisplay&&(this.g.drawHover=d);break;case 603979889:this.setNavigationMode(d);break;case 603979888:return;case 603979860:this.g.hideNavigationPoint=
d;break;case 603979930:this.g.showNavigationPointAlways=d;break;case 603979900:this.setRefreshing(d);break;case 603979869:this.g.jmolInJSpecView=d;break;case 603979870:this.g.justifyMeasurements=d;break;case 603979952:this.g.ssbondsBackbone=d;break;case 603979852:this.g.hbondsBackbone=d;break;case 603979854:this.g.hbondsSolid=d;break;case 536870924:this.gdata.setSpecular(d);break;case 603979942:this.tm.setSlabEnabled(d);return;case 603979980:this.tm.setZoomEnabled(d);return;case 603979864:this.g.highResolutionFlag=
d;break;case 603979966:this.g.traceAlpha=d;break;case 603979983:this.g.zoomLarge=d;this.tm.setZoomHeight(this.g.zoomHeight,d);break;case 603979982:this.g.zoomHeight=d;this.tm.setZoomHeight(d,this.g.zoomLarge);break;case 603979871:J.i18n.GT.setDoTranslate(d);break;case 603979862:this.slm.setHideNotSelected(d);break;case 603979904:this.setScriptQueue(d);break;case 603979830:this.g.dotSurface=d;break;case 603979829:this.g.dotsSelectedOnly=d;break;case 1611141171:this.setSelectionHalosEnabled(d);break;
case 603979910:this.g.rasmolHydrogenSetting=d;break;case 603979908:this.g.rasmolHeteroSetting=d;break;case 603979928:this.g.showMultipleBonds=d;break;case 603979920:this.g.showHiddenSelectionHalos=d;break;case 603979976:this.tm.setWindowCentered(d);break;case 603979828:this.g.displayCellParameters=d;break;case 603979960:this.g.testFlag1=d;break;case 603979962:this.g.testFlag2=d;break;case 603979964:this.g.testFlag3=d;break;case 603979965:this.jmolTest();this.g.testFlag4=d;break;case 603979901:this.g.ribbonBorder=
d;break;case 603979815:this.g.cartoonBaseEdges=d;break;case 603979819:this.g.cartoonRockets=d;break;case 603979902:this.g.rocketBarrels=d;break;case 603979850:this.gdata.setGreyscaleMode(this.g.greyscaleRendering=d);break;case 603979878:this.g.measurementLabels=d;break;case 603979809:case 603979804:case 603979808:this.setAxesMode(b);return;case 603979806:this.setAxesOrientationRasmol(d);return;case 603979824:this.setStringPropertyTok("defaultcolorscheme",545259545,d?"rasmol":"jmol");return;case 603979825:this.setDebugScript(d);
return;case 603979897:this.setPerspectiveDepth(d);return;case 603979798:this.setAutoBond(d);return;case 603979914:this.setShowAxes(d);return;case 603979916:this.setShowBbcage(d);return;case 603979922:this.setShowHydrogens(d);return;case 603979926:this.setShowMeasurements(d);return;case 603979936:this.setShowUnitCell(d);return;case 603979812:c=!1;this.g.bondModeOr=d;break;case 603979978:c=!1;this.g.zeroBasedXyzRasmol=d;this.reset(!0);break;case 603979899:c=!1;this.g.rangeSelected=d;break;case 603979877:c=
!1;this.g.measureAllModels=d;break;case 603979954:c=!1;this.sm.allowStatusReporting=d;break;case 603979822:c=!1;this.g.chainCaseSensitive=d;break;case 603979858:c=!1;this.g.hideNameInPopup=d;break;case 603979827:c=!1;this.g.disablePopupMenu=d;break;case 603979846:c=!1;this.g.forceAutoBond=d;break;default:if(!this.g.htBooleanParameterFlags.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.getBoolean(d));return}}this.g.setB(a,d);c&&this.setTainted(!0)},"~S,~N,~B");c(c$,"setModelKitMode",
function(a){if(null!=this.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.g.setB("modelkitmode",a);this.highlight(null);a?(this.setNavigationMode(!1),this.selectAll(),this.setStringProperty("picking","assignAtom_C"),this.setStringProperty("picking","assignBond_p"),this.isApplet||this.popupMenu(10,0,"m"),b&&this.sm.setStatusModelKit(1),this.g.modelKitMode=!0,0==this.ms.ac?this.zap(!1,
!0,!0):0<=this.am.cmi&&this.getModelUndeletedAtomsBitSet(this.am.cmi).isEmpty()&&(a=new java.util.Hashtable,a.put("appendToModelIndex",Integer.$valueOf(this.am.cmi)),this.loadDefaultModelKitModel(a))):(this.acm.setPickingMode(-1),this.setStringProperty("pickingStyle","toggle"),this.setBooleanProperty("bondPicking",!1),b&&this.sm.setStatusModelKit(0))}},"~B");c(c$,"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$,"showParameter",function(a,b,d){d=""+this.g.getParameterEscaped(a,d);(b||0>d.indexOf("<not defined>"))&&this.showString(a+" = "+d,!1)},"~S,~B,~N");c(c$,"showString",function(a,b){!JV.Viewer.isJS&&(this.isScriptQueued()&&(!this.isSilent||b)&&!"\x00".equals(a))&&JU.Logger.warn(a);this.scriptEcho(a)},"~S,~B");c(c$,"getAllSettings",function(a){return this.getStateCreator().getAllSettings(a)},
"~S");c(c$,"getBindingInfo",function(a){return this.haveDisplay?this.acm.getBindingInfo(a):""},"~S");c(c$,"getIsosurfacePropertySmoothing",function(a){return a?this.g.isosurfacePropertySmoothingPower:this.g.isosurfacePropertySmoothing?1:0},"~B");c(c$,"setNavigationDepthPercent",function(a){this.tm.setNavigationDepthPercent(a);this.refresh(1,"set navigationDepth")},"~N");c(c$,"getShowNavigationPoint",function(){return!this.g.navigationMode?!1:this.tm.isNavigating()&&!this.g.hideNavigationPoint||this.g.showNavigationPointAlways||
this.getInMotion(!0)});h(c$,"setPerspectiveDepth",function(a){this.tm.setPerspectiveDepth(a)},"~B");h(c$,"setAxesOrientationRasmol",function(a){this.g.setB("axesOrientationRasmol",a);this.g.axesOrientationRasmol=a;this.reset(!0)},"~B");c(c$,"setAxesScale",function(a,b){b=JV.Viewer.checkFloatRange(b,-100,100);570425345==a?this.g.axesOffset=b:this.g.axesScale=b;this.axesAreTainted=!0},"~N,~N");c(c$,"setAxesMode",function(a){this.g.axesMode=a;this.axesAreTainted=!0;switch(a){case 603979808:this.g.removeParam("axesmolecular");
this.g.removeParam("axeswindow");this.g.setB("axesUnitcell",!0);a=2;break;case 603979804:this.g.removeParam("axesunitcell");this.g.removeParam("axeswindow");this.g.setB("axesMolecular",!0);a=1;break;case 603979809:this.g.removeParam("axesunitcell"),this.g.removeParam("axesmolecular"),this.g.setB("axesWindow",!0),a=0}this.g.setI("axesMode",a)},"~N");c(c$,"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=this.showSelected;this.showSelected=!1;return a});c(c$,"setStrandCount",function(a,b){b=JV.Viewer.checkIntRange(b,0,20);switch(a){case 12:this.g.strandCountForStrands=b;break;case 13:this.g.strandCountForMeshRibbon=b;break;default:this.g.strandCountForStrands=b,this.g.strandCountForMeshRibbon=b}this.g.setI("strandCount",b);this.g.setI("strandCountForStrands",this.g.strandCountForStrands);
this.g.setI("strandCountForMeshRibbon",this.g.strandCountForMeshRibbon)},"~N,~N");c(c$,"getStrandCount",function(a){return 12==a?this.g.strandCountForStrands:this.g.strandCountForMeshRibbon},"~N");c(c$,"setNavigationMode",function(a){this.g.navigationMode=a;this.tm.setNavigationMode(a)},"~B");h(c$,"setAutoBond",function(a){this.g.setB("autobond",a);this.g.autoBond=a},"~B");c(c$,"makeConnections",function(a,b,d,c,g,e,j,h,k,r){this.clearModelDependentObjects();this.clearMinimization();return this.ms.makeConnections(a,
b,d,c,g,e,j,h,k,r)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");h(c$,"rebond",function(){this.rebondState(!1)});c(c$,"rebondState",function(a){this.clearModelDependentObjects();this.ms.deleteAllBonds();a=a&&this.g.legacyAutoBonding;this.ms.autoBondBs4(null,null,null,null,this.getMadBond(),a);this.addStateScript(a?"set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;":"connect;",!1,!0)},"~B");h(c$,"setPercentVdwAtom",function(a){this.g.setI("percentVdwAtom",a);this.g.percentVdwAtom=a;this.rd.value=
a/100;this.rd.factorType=J.atomdata.RadiusData.EnumType.FACTOR;this.rd.vdwType=J.c.VDW.AUTO;this.shm.setShapeSizeBs(0,0,this.rd,null)},"~N");h(c$,"getMadBond",function(){return 2*this.g.bondRadiusMilliAngstroms});h(c$,"setShowHydrogens",function(a){this.g.setB("showHydrogens",a);this.g.showHydrogens=a},"~B");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)});h(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});h(c$,"setShowMeasurements",function(a){this.g.setB("showMeasurements",a);this.g.showMeasurements=a},"~B");c(c$,"setUnits",function(a,b){this.g.setUnits(a);b&&(this.g.setUnits(a),this.setShapeProperty(6,"reformatDistances",null))},"~S,~B");h(c$,"setRasmolDefaults",function(){this.setDefaultsType("RasMol")});h(c$,"setJmolDefaults",function(){this.setDefaultsType("Jmol")});c(c$,"setDefaultsType",
function(a){a.equalsIgnoreCase("RasMol")?this.stm.setRasMolDefaults():a.equalsIgnoreCase("PyMOL")?this.stm.setPyMOLDefaults():(this.stm.setJmolDefaults(),this.setIntProperty("bondingVersion",0),this.shm.setShapeSizeBs(0,0,this.rd,this.getAllAtoms()))},"~S");c(c$,"setAntialias",function(a,b){var d=!1;switch(a){case 603979786:d=this.g.antialiasDisplay!=b;this.g.antialiasDisplay=b;break;case 603979790:d=this.g.antialiasTranslucent!=b;this.g.antialiasTranslucent=b;break;case 603979788:this.g.antialiasImages=
b;return}d&&(this.resizeImage(0,0,!1,!1,!0),this.refresh(3,"Viewer:setAntialias()"))},"~N,~B");c(c$,"allocTempPoints",function(a){return this.tempArray.allocTempPoints(a)},"~N");c(c$,"freeTempPoints",function(a){this.tempArray.freeTempPoints(a)},"~A");c(c$,"allocTempScreens",function(a){return this.tempArray.allocTempScreens(a)},"~N");c(c$,"freeTempScreens",function(a){this.tempArray.freeTempScreens(a)},"~A");c(c$,"allocTempEnum",function(a){return this.tempArray.allocTempEnum(a)},"~N");c(c$,"freeTempEnum",
function(a){this.tempArray.freeTempEnum(a)},"~A");c(c$,"getFont3D",function(a,b,d){return this.gdata.getFont3DFSS(a,b,d)},"~S,~S,~N");c(c$,"getAtomGroupQuaternions",function(a,b){return this.ms.getAtomGroupQuaternions(a,b,this.getQuaternionFrame())},"JU.BS,~N");c(c$,"setStereoMode",function(a,b,d){this.setFloatProperty("stereoDegrees",d);this.setBooleanProperty("greyscaleRendering",b.isBiColor());null!=a?this.tm.setStereoMode2(a):this.tm.setStereoMode(b)},"~A,J.c.STER,~N");c(c$,"getChimeInfo",function(a){return this.getPropertyManager().getChimeInfo(a,
this.bsA())},"~N");c(c$,"getModelFileInfo",function(){return this.getPropertyManager().getModelFileInfo(this.getVisibleFramesBitSet())});c(c$,"getModelFileInfoAll",function(){return this.getPropertyManager().getModelFileInfo(null)});c(c$,"showEditor",function(a){var b=this.getProperty("DATA_API","getScriptEditor",Boolean.TRUE);null!=b&&b.show(a)},"~A");c(c$,"getPropertyManager",function(){null==this.pm&&(this.pm=J.api.Interface.getInterface("JV.PropertyManager",this,"prop")).setViewer(this);return this.pm});
c(c$,"setTainted",function(a){this.isTainted=this.axesAreTainted=a&&(this.refreshing||this.creatingImage)},"~B");c(c$,"checkObjectClicked",function(a,b,d){return this.shm.checkObjectClicked(a,b,d,this.getVisibleFramesBitSet(),this.g.drawPicking)},"~N,~N,~N");c(c$,"checkObjectHovered",function(a,b){return 0<=a&&null!=this.shm&&this.shm.checkObjectHovered(a,b,this.getVisibleFramesBitSet(),this.getBondsPickable())},"~N,~N");c(c$,"checkObjectDragged",function(a,b,d,c,g){var e=0;switch(this.getPickingMode()){case 2:e=
5;break;case 4:e=22}return this.shm.checkObjectDragged(a,b,d,c,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$,"rotateAxisAngleAtCenter",function(a,b,d,c,g,e,j){(a=this.tm.rotateAxisAngleAtCenter(a,b,d,c,g,e,j))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,d,c,g,e,j,h,k,r,n){null==a&&(a=this.eval);if(this.headless){if(e&&
3.4028235E38==g)return!1;e=!1}(a=this.tm.rotateAboutPointsInternal(a,b,d,c,g,!1,e,j,!1,h,k,r,n))&&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$,"startSpinningAxis",function(a,b,d){this.tm.spinOn||this.tm.navOn?(this.tm.setSpinOff(),this.tm.setNavOn(!1)):this.tm.rotateAboutPointsInternal(null,a,b,this.g.pickingSpinRate,3.4028235E38,d,!0,null,!1,null,null,null,null)},"JU.T3,JU.T3,~B");c(c$,"getModelDipole",function(){return this.ms.getModelDipole(this.am.cmi)});
c(c$,"calculateMolecularDipole",function(a){try{return this.ms.calculateMolecularDipole(this.am.cmi,a)}catch(b){if(D(b,JV.JmolAsyncException))return null!=this.eval&&this.eval.loadFileResourceAsync(b.getFileName()),null;throw b;}},"JU.BS");c(c$,"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,d,c){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),
b,d,c,!1)},"~O,~B,~B,~S");h(c$,"getData",function(a,b){return this.getModelFileData(a,b,!0)},"~S,~S");c(c$,"getModelFileData",function(a,b,d){return this.getPropertyManager().getAtomData(a,b,d)},"~S,~S,~B");c(c$,"getModelCml",function(a,b,d,c){return this.getPropertyManager().getModelCml(a,b,d,c,!1)},"JU.BS,~N,~B,~B");c(c$,"getPdbAtomData",function(a,b,d,c){return this.getPropertyManager().getPdbAtomData(null==a?this.bsA():a,b,d,c,!1)},"JU.BS,JU.OC,~B,~B");c(c$,"isJmolDataFrame",function(){return this.ms.isJmolDataFrameForModel(this.am.cmi)});
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this.setColorFromString(b,d);break;case JSV.common.ScriptToken.TITLEFONTNAME:case JSV.common.ScriptToken.DISPLAYFONTNAME:c=this.getFontName(b,d)}null!=a&&null!=c&&a.setColorOrFont(this,b)},"JSV.common.PanelData,JSV.common.ScriptToken,~S");c(c$,"getElementColor",function(a){return this.elementColors.get(a)},"JSV.common.ScriptToken");c(c$,"setColor",function(a,b){null!=b&&this.elementColors.put(a,b);return b},"JSV.common.ScriptToken,javajs.api.GenericColor");c(c$,"copy",function(){return this.copy(this.name)});
c(c$,"setElementColors",function(a){this.displayFontName=a.displayFontName;var b;for(a=a.elementColors.entrySet().iterator();a.hasNext()&&((b=a.next())||1);)this.setColor(b.getKey(),b.getValue());return this},"JSV.common.ColorParameters");c(c$,"getColorFromString",function(a){return this.getColor1(JU.CU.getArgbFromString(a))},"~S");c(c$,"getPlotColors",function(a){if(null==a)return this.plotColors[0]=this.getElementColor(JSV.common.ScriptToken.PLOTCOLOR),this.plotColors;a=new java.util.StringTokenizer(a,
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this.displayFontName=b:this.displayFontName}return null},"JSV.common.ScriptToken,~S");G(c$,"BLACK",null,"RED",null,"LIGHT_GRAY",null,"DARK_GRAY",null,"BLUE",null,"WHITE",null);c$.defaultPlotColors=c$.prototype.defaultPlotColors=Array(8);c$.defaultPlotColorNames=c$.prototype.defaultPlotColorNames=v(-1,"black darkGreen darkred orange magenta cyan maroon darkGray".split(" "))});m("JSV.common");c$=F(JSV.common,"CoordComparator",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.getXVal()>
b.getXVal()?1:a.getXVal()<b.getXVal()?-1:0},"JSV.common.Coordinate,JSV.common.Coordinate");m("JSV.common");x(["JSV.common.CoordComparator"],"JSV.common.Coordinate",["java.lang.Double","java.util.Arrays","$.StringTokenizer","JU.Lst"],function(){c$=w(function(){this.yVal=this.xVal=0;s(this,arguments)},JSV.common,"Coordinate");p(c$,function(){});c(c$,"set",function(a,b){this.xVal=a;this.yVal=b;return this},"~N,~N");c(c$,"getXVal",function(){return this.xVal});c(c$,"getYVal",function(){return this.yVal});
c(c$,"setXVal",function(a){this.xVal=a},"~N");c(c$,"setYVal",function(a){this.yVal=a},"~N");c(c$,"copy",function(){return(new JSV.common.Coordinate).set(this.xVal,this.yVal)});c(c$,"equals",function(a){return a.xVal==this.xVal&&a.yVal==this.yVal},"JSV.common.Coordinate");h(c$,"toString",function(){return"["+this.xVal+", "+this.yVal+"]"});c$.isYInRange=c(c$,"isYInRange",function(a,b,d){return JSV.common.Coordinate.getMinY(a,0,a.length-1)>=b&&JSV.common.Coordinate.getMaxY(a,0,a.length-1)>=d},"~A,~N,~N");
c$.normalise=c(c$,"normalise",function(a,b,d){var c=Array(a.length),g=JSV.common.Coordinate.getMinY(a,0,a.length-1);d=(JSV.common.Coordinate.getMaxY(a,0,a.length-1)-g)/(d-b);for(var e=0;e<a.length;e++)c[e]=(new JSV.common.Coordinate).set(a[e].getXVal(),(a[e].getYVal()-g)/d-b);return c},"~A,~N,~N");c$.reverse=c(c$,"reverse",function(a){for(var b=a.length,d=0;d<b;d++){var c=a[d];a[d]=a[--b];a[b]=c}return a},"~A");c$.parseDSV=c(c$,"parseDSV",function(a,b,d){var c,g=c=0,e=new JU.Lst;for(a=new java.util.StringTokenizer(a,
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this.fracY=this.fracX=1;this.fY0=this.fX0=0;this.cur2Dy=this.cur1D2x2=this.cur1D2x1=this.cur2Dx1=this.cur2Dx0=this.pin2Dy01=this.pin2Dx01=this.pin2Dy1=this.pin2Dy0=this.pin2Dx1=this.pin2Dx0=this.pin1Dy01=this.pin1Dx01=this.pin1Dy1=this.pin1Dy0=this.pin1Dx1=this.pin1Dx0=this.zoomBox2D=this.zoomBox1D=null;this.xPixels0=this.xPixel10=this.yPixels=this.xPixels=this.yPixel000=this.yPixel11=this.xPixel11=this.yPixel00=this.xPixel00=this.yHArrows=this.xHArrows=this.xVArrows=this.yPixel1=this.xPixel1=this.yPixel0=
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!0;0>=b&&(b=2147483647);this.isSplittable=1<this.nSpectra;this.showAllStacked=(this.allowStacking=this.spectra.get(0).isStackable())&&1<this.nSpectra;for(var g=0;g<this.nSpectra;g++){var e=this.spectra.get(g).getXYCoords().length-1;d[g]=JSV.common.Coordinate.intoRange(a,0,e);c[g]=JSV.common.Coordinate.intoRange(b,0,e);this.allowStackedYScale=(new Boolean(this.allowStackedYScale&(this.spectra.get(g).getYUnits().equals(this.spectra.get(0).getYUnits())&&this.spectra.get(g).getUserYFactor()==this.spectra.get(0).getUserYFactor()))).valueOf()}this.getView(0,
0,0,0,d,c,null,null);this.viewList=new JU.Lst;this.viewList.addLast(this.viewData)},"~N,~N");c(c$,"getView",function(a,b,d,c,g,e,j,h){var k=0==this.graphsTemp.size()?this.spectra:this.graphsTemp,r=this.getSpectrumAt(0).getSubSpectra(),n=null==r||2==r.size()&&r.get(1).isImaginary(),q=!this.getSpectrumAt(0).is1D();n&&d==c?k=this.spectra:d==c&&(this.viewData=new JSV.common.ViewData(r,d,c,this.getSpectrum().isContinuous()),k=null);null!=k&&(this.viewData=new JSV.common.ViewData(k,d,c,g,e,this.getSpectrumAt(0).isContinuous(),
q),a!=b&&this.getScale().setXRange(a,b));null!=j&&(JSV.common.ScaleData.copyScaleFactors(j,this.viewData.getScaleData()),null!=h&&JSV.common.ScaleData.copyYScales(h,this.viewData.getScaleData()),this.getCurrentView())},"~N,~N,~N,~N,~A,~A,~A,~A");c(c$,"isNearby",function(a,b,d,c){var g=a.getXVal(),e=d.toPixelX(g);a=this.toPixelY(a.getYVal());g=b.getXVal();d=d.toPixelX(g);b=this.toPixelY(b.getYVal());return Math.abs(e-d)+Math.abs(a-b)<c},"JSV.common.Coordinate,JSV.common.Coordinate,JSV.common.XYScaleConverter,~N");
c(c$,"setReversePlot",function(a){(this.reversePlot=a)&&this.closeDialogsExcept(JSV.common.Annotation.AType.NONE);this.setDrawXAxis()},"~B");c(c$,"setDrawXAxis",function(){this.drawXAxisLeftToRight=(new Boolean(this.xAxisLeftToRight^this.reversePlot)).valueOf();for(var a=0;a<this.spectra.size();a++)this.spectra.get(a).setExportXAxisDirection(this.drawXAxisLeftToRight)});c(c$,"isInTopBar",function(a,b){return a==this.fixX(a)&&b>this.pin1Dx0.yPixel0-2&&b<this.pin1Dx0.yPixel1},"~N,~N");c(c$,"isInTopBar2D",
function(a,b){return null!=this.imageView&&a==this.imageView.fixX(a)&&b>this.pin2Dx0.yPixel0-2&&b<this.pin2Dx0.yPixel1},"~N,~N");c(c$,"isInRightBar",function(a,b){return b==this.fixY(b)&&a>this.pin1Dy0.xPixel1&&a<this.pin1Dy0.xPixel0+2},"~N,~N");c(c$,"isInRightBar2D",function(a,b){return null!=this.imageView&&b==this.fixY(b)&&a>this.pin2Dy0.xPixel1&&a<this.pin2Dy0.xPixel0+2},"~N,~N");c(c$,"toX0",function(a){return this.viewList.get(0).getScale().toX0(this.fixX(a),this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},
"~N");c(c$,"toY0",function(a){return this.viewList.get(0).getScale().toY0(this.fixY(a),this.yPixel0,this.yPixel1)},"~N");h(c$,"toX",function(a){return null!=this.imageView&&this.imageView.isXWithinRange(a)?this.imageView.toX(a):this.getScale().toX(this.fixX(a),this.xPixel1,this.drawXAxisLeftToRight)},"~N");h(c$,"toY",function(a){return this.getScale().toY(a,this.yPixel0)},"~N");c(c$,"toPixelX",function(a){return this.getScale().toPixelX(a,this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");
c(c$,"toPixelY",function(a){return this.getScale().toPixelY(a,this.yPixel1)},"~N");c(c$,"toPixelX0",function(a){return this.viewList.get(0).getScale().toPixelX0(a,this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");c(c$,"toPixelY0",function(a){return this.fixY(this.viewList.get(0).getScale().toPixelY0(a,this.yPixel0,this.yPixel1))},"~N");c(c$,"fixX",function(a){return JSV.common.Coordinate.intoRange(a,this.xPixel0,this.xPixel1)},"~N");c(c$,"fixY",function(a){return JSV.common.Coordinate.intoRange(a,
this.yPixel0,this.yPixel1)},"~N");c(c$,"getXPixel0",function(){return this.xPixel0});c(c$,"getXPixels",function(){return this.xPixels});h(c$,"getYPixels",function(){return this.yPixels});c(c$,"getScale",function(){return this.viewData.getScale()});c(c$,"toPixelYint",function(a){return this.yPixel1-u(Double.isNaN(a)?-2147483648:this.yPixels*a)},"~N");c(c$,"findAnnotation2D",function(a){for(var b=this.annotations.size();0<=--b;){var d=this.annotations.get(b);if(this.isNearby(d,a,this.imageView,10))return d}return null},
"JSV.common.Coordinate");c(c$,"addAnnotation",function(a,b){null==this.annotations&&(this.annotations=new JU.Lst);for(var d=!1,c=this.annotations.size();0<=--c;)if(a.is2D?this.isNearby(this.annotations.get(c),a,this.imageView,10):a.equals(this.annotations.get(c)))d=!0,this.annotations.removeItemAt(c);0<a.text.length&&(!d||!b)&&this.annotations.addLast(a)},"JSV.common.Annotation,~B");c(c$,"setImageWindow",function(){this.imageView.setPixelWidthHeight(u((this.pd.display1D?0.6:1)*this.xPixels0),this.yPixels);
this.imageView.setXY0(this.getSpectrumAt(0),u(Math.floor(this.xPixel10-this.imageView.xPixels)),this.yPixel0)});c(c$,"findNearestMaxMin",function(){if(1<this.nSpectra&&0>this.iSpectrumClicked)return!1;this.xValueMovedTo=this.getSpectrum().findXForPeakNearest(this.xValueMovedTo);this.setXPixelMovedTo(this.xValueMovedTo,1.7976931348623157E308,0,0);return!Double.isNaN(this.xValueMovedTo)});c(c$,"setXPixelMovedTo",function(a,b,d,c){1.7976931348623157E308==a&&1.7976931348623157E308==b?(this.xPixelMovedTo=
d,this.xPixelMovedTo2=c,this.isLinked&&this.sticky2Dcursor&&this.pd.setlinkedXMove(this,this.toX(this.xPixelMovedTo),!1)):(1.7976931348623157E308!=a&&(this.xPixelMovedTo=this.toPixelX(a),this.fixX(this.xPixelMovedTo)!=this.xPixelMovedTo&&(this.xPixelMovedTo=-1),this.xPixelMovedTo2=-1,1E10!=a&&this.setSpectrumClicked(this.getFixedSelectedSpectrumIndex())),1.7976931348623157E308!=b&&(this.xPixelMovedTo2=this.toPixelX(b)))},"~N,~N,~N,~N");c(c$,"processPendingMeasurement",function(a,b,d){if(!this.isInPlotRegion(a,
b)||this.is2dClick(a,b))this.pendingMeasurement=null;else{var c=this.toX(a),g=this.toY(b),e=c;switch(d){case 0:this.pendingMeasurement.setPt2(this.toX(a),this.toY(b));break;case 3:case 2:if(0>this.iSpectrumClicked)break;var j=this.spectra.get(this.iSpectrumClicked);this.setScale(this.iSpectrumClicked);3!=d&&(d=this.findMeasurement(this.selectedSpectrumMeasurements,a,b,1),null!=d?(c=d.getXVal(),g=d.getYVal()):null!=(d=this.findMeasurement(this.selectedSpectrumMeasurements,a,b,2))?(c=d.getXVal2(),g=
d.getYVal2()):c=this.getNearestPeak(j,c,g));this.pendingMeasurement=(new JSV.common.Measurement).setM1(c,g,j);this.pendingMeasurement.setPt2(e,g);this.pd.setTaintedAll();this.pd.repaint();break;case 1:case -2:case -3:for(e=null!=this.pendingMeasurement&&this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,-1));e;){this.setScale(this.getSpectrumIndex(this.pendingMeasurement.spec));if(3!=d){if(!this.findNearestMaxMin()){e=!1;break}a=this.xPixelMovedTo}c=this.toX(a);g=this.toY(b);this.pendingMeasurement.setPt2(c,
g);if(0==this.pendingMeasurement.text.length){e=!1;break}this.setMeasurement(this.pendingMeasurement);if(1!=d){e=!1;break}this.setSpectrumClicked(this.getSpectrumIndex(this.pendingMeasurement.spec));this.pendingMeasurement=(new JSV.common.Measurement).setM1(c,g,this.pendingMeasurement.spec);break}e||(this.pendingMeasurement=null);this.pd.setTaintedAll();this.pd.repaint();break;case 5:this.findNearestMaxMin()?(a=this.getFixedSelectedSpectrumIndex(),Double.isNaN(this.lastXMax)||this.lastSpecClicked!=
a||null==this.pendingMeasurement?(this.lastXMax=this.xValueMovedTo,this.lastSpecClicked=a,this.pendingMeasurement=(new JSV.common.Measurement).setM1(this.xValueMovedTo,this.yValueMovedTo,this.spectra.get(a))):(this.pendingMeasurement.setPt2(this.xValueMovedTo,this.yValueMovedTo),0<this.pendingMeasurement.text.length&&this.setMeasurement(this.pendingMeasurement),this.pendingMeasurement=null,this.lastXMax=NaN)):this.lastXMax=NaN}}},"~N,~N,~N");c(c$,"checkIntegralNormalizationClick",function(a,b){if(null==
this.selectedSpectrumIntegrals)return!1;var d=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5);if(null==d)return!1;this.selectedIntegral=d;this.pd.normalizeIntegral();this.updateDialog(JSV.common.Annotation.AType.Integration,-1);this.setSpectrumClicked(this.getSpectrumIndex(d.spec));return!0},"~N,~N");c(c$,"getNearestPeak",function(a,b,d){var c=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),b,d,a.isInverted(),!1);a=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),
b,d,a.isInverted(),!0);return Double.isNaN(c)?a:Double.isNaN(a)?c:Math.abs(c-b)<Math.abs(a-b)?c:a},"JSV.common.Spectrum,~N,~N");c(c$,"findMeasurement",function(a,b,d,c){if(null==a||0==a.size())return null;if(0==c){var g=this.findMeasurement(a,b,d,-1);return null!=g||t(a.get(0),JSV.common.Integral)?g:this.findMeasurement(a,b,d,-2)}for(var e=a.size();0<=--e;){var g=a.get(e),j,h,k,r;t(g,JSV.common.Integral)?(j=h=this.toPixelX(g.getXVal2()),k=this.toPixelYint(g.getYVal()),r=this.toPixelYint(g.getYVal2())):
(j=this.toPixelX(g.getXVal()),h=this.toPixelX(g.getXVal2()),k=r=-2==c?this.yPixel1-2:this.toPixelY(g.getYVal()));switch(c){case 1:if(4>Math.abs(b-j)+Math.abs(d-k))return g;break;case 2:if(4>Math.abs(b-h)+Math.abs(d-r))return g;break;case -5:k=r=u((k+r)/2),h=j+20;default:case -1:case -2:if(JSV.common.GraphSet.isOnLine(b,d,j,k,h,r))return g}}return null},"JSV.common.MeasurementData,~N,~N,~N");c(c$,"setMeasurement",function(a){var b=this.getSpectrumIndex(a.spec),d=this.getDialog(JSV.common.Annotation.AType.Measurements,
b);null==d&&this.addDialog(b,JSV.common.Annotation.AType.Measurements,d=new JSV.common.MeasurementData(JSV.common.Annotation.AType.Measurements,a.spec));d.getData().addLast(a.copyM());this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)},"JSV.common.Measurement");c(c$,"checkArrowUpDownClick",function(a,b){var d=!1,c=this.isArrowClick(a,b,3)?JSV.common.GraphSet.RT2:this.isArrowClick(a,b,4)?1/JSV.common.GraphSet.RT2:0;if(0!=c){1<this.nSplit&&this.setSpectrumSelected(this.iSpectrumMovedTo);
if((1==this.nSpectra||0<=this.iSpectrumSelected)&&this.spectra.get(this.getFixedSelectedSpectrumIndex()).isTransmittance())c=1/c;this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,c);d=!0}else this.isArrowClick(a,b,-1)&&(this.resetViewCompletely(),d=!0);d&&(null!=this.imageView&&(this.update2dImage(!1),this.resetPinsFromView()),this.pd.setTaintedAll());return d},"~N,~N");c(c$,"resetViewCompletely",function(){this.clearViews();this.showAllStacked&&!this.stackSelected&&this.closeDialogsExcept(JSV.common.Annotation.AType.NONE);
this.viewData.resetScaleFactors();this.updateDialogs()});c(c$,"checkArrowLeftRightClick",function(a,b){if(this.haveLeftRightArrows){var d=this.isArrowClick(a,b,1)?-1:this.isArrowClick(a,b,2)?1:0;if(0!=d)return d=this.iSpectrumSelected+d,0>d&&(d=this.nSpectra-1),this.setSpectrumClicked(d%this.nSpectra),!0;if(this.isArrowClick(a,b,0)){if(this.showAllStacked)return this.showAllStacked=!1,this.setSpectrumClicked(this.getFixedSelectedSpectrumIndex()),!0;this.showAllStacked=this.allowStacking;this.setSpectrumSelected(-1);
this.stackSelected=!1}}return!1},"~N,~N");c(c$,"isArrowClick",function(a,b,d){switch(d){case 3:case 4:case -1:return d=u((this.yPixel00+this.yPixel11)/2)+15*(3==d?-1:4==d?1:0),10>Math.abs(this.xVArrows-a)&&10>Math.abs(d-b);case 1:case 2:case 0:return d=this.xHArrows+15*(1==d?-1:2==d?1:0),10>Math.abs(d-a)&&10>Math.abs(this.yHArrows-b)}return!1},"~N,~N,~N");c(c$,"setWidgetValueByUser",function(a){var b;b=a===this.cur2Dy?""+this.imageView.toSubspectrumIndex(a.yPixel0):a===this.pin1Dx01?""+Math.min(this.pin1Dx0.getXVal(),
this.pin1Dx1.getXVal())+" - "+Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()):a===this.pin1Dy01?""+Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal())+" - "+Math.max(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()):a===this.pin2Dx01?""+Math.min(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal())+" - "+Math.max(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal()):a===this.pin2Dy01?""+u(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+u(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):
""+a.getValue();b=this.pd.getInput("New value?","Set Slider",b);if(null!=b){b=b.trim();try{if(a===this.pin1Dx01||a===this.pin1Dy01||a===this.pin2Dx01||a===this.pin2Dy01){var d=b.indexOf("-",1);if(!(0>d)){var c=Double.$valueOf(b.substring(0,d)).doubleValue(),g=Double.$valueOf(b.substring(d+1)).doubleValue();a===this.pin1Dx01?this.doZoom(c,this.pin1Dy0.getYVal(),g,this.pin1Dy1.getYVal(),!0,!1,!1,!0,!0):a===this.pin1Dy01?this.doZoom(this.pin1Dx0.getXVal(),c,this.pin1Dx1.getXVal(),g,null==this.imageView,
null==this.imageView,!1,!1,!0):a===this.pin2Dx01?(this.imageView.setView0(this.imageView.toPixelX0(c),this.pin2Dy0.yPixel0,this.imageView.toPixelX0(g),this.pin2Dy1.yPixel0),this.doZoom(c,this.pin1Dy0.getYVal(),g,this.pin1Dy1.getYVal(),!1,!1,!1,!0,!0)):a===this.pin2Dy01&&(this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.toPixelY0(c),this.pin2Dx1.xPixel0,this.imageView.toPixelY0(g)),this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+
this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!1,!0))}}else{var e=Double.$valueOf(b).doubleValue();a.isXtype?(g=a===this.pin1Dx0||a===this.cur2Dx0||a===this.pin2Dx0?this.pin1Dx1.getXVal():this.pin1Dx0.getXVal(),this.doZoom(e,0,g,0,!a.is2D,!1,!1,!0,!0)):a===this.cur2Dy?this.setCurrentSubSpectrum(u(e)):a===this.pin2Dy0||a===this.pin2Dy1?(g=a===this.pin2Dy0?this.pin2Dy1.yPixel0:this.pin2Dy0.yPixel0,this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.subIndexToPixelY(u(e)),this.pin2Dx1.xPixel0,
g)):(g=a===this.pin1Dy0?this.pin1Dy1.getYVal():this.pin1Dy0.getYVal(),this.doZoom(this.pin1Dx0.getXVal(),e,this.pin1Dx1.getXVal(),g,null==this.imageView,null==this.imageView,!1,!1,!0))}}catch(j){if(!D(j,Exception))throw j;}}},"JSV.common.PlotWidget");c(c$,"removeAllHighlights",function(a){if(null==a)this.highlights.clear();else for(var b=this.highlights.size();0<=--b;)this.highlights.get(b).spectrum===a&&this.highlights.removeItemAt(b)},"JSV.common.Spectrum");c(c$,"setCoordClicked",function(a,b,d){0==
d&&(this.nextClickForSetPeak=null);if(Double.isNaN(b))return this.pd.coordClicked=null,this.pd.coordsClicked=null;this.pd.coordClicked=(new JSV.common.Coordinate).set(this.lastClickX=b,d);this.pd.coordsClicked=this.getSpectrum().getXYCoords();this.pd.xPixelClicked=this.lastPixelX=a;return this.pd.coordClicked},"~N,~N,~N");c(c$,"setWidgets",function(a,b,d){if(a||null==this.pin1Dx0)null==this.zoomBox1D?this.newPins():this.resetPinPositions();this.setDerivedPins(b);this.setPinSliderPositions(d)},"~B,~N,~B");
c(c$,"newPins",function(){this.zoomBox1D=new JSV.common.PlotWidget("zoomBox1D");this.pin1Dx0=new JSV.common.PlotWidget("pin1Dx0");this.pin1Dx1=new JSV.common.PlotWidget("pin1Dx1");this.pin1Dy0=new JSV.common.PlotWidget("pin1Dy0");this.pin1Dy1=new JSV.common.PlotWidget("pin1Dy1");this.pin1Dx01=new JSV.common.PlotWidget("pin1Dx01");this.pin1Dy01=new JSV.common.PlotWidget("pin1Dy01");this.cur1D2x1=new JSV.common.PlotWidget("cur1D2x1");this.cur1D2x1.color=JSV.common.ScriptToken.PEAKTABCOLOR;this.cur1D2x2=
new JSV.common.PlotWidget("cur1D2x2");this.cur1D2x2.color=JSV.common.ScriptToken.PEAKTABCOLOR;if(null!=this.imageView){this.zoomBox2D=new JSV.common.PlotWidget("zoomBox2D");this.pin2Dx0=new JSV.common.PlotWidget("pin2Dx0");this.pin2Dx1=new JSV.common.PlotWidget("pin2Dx1");this.pin2Dy0=new JSV.common.PlotWidget("pin2Dy0");this.pin2Dy1=new JSV.common.PlotWidget("pin2Dy1");this.pin2Dx01=new JSV.common.PlotWidget("pin2Dx01");this.pin2Dy01=new JSV.common.PlotWidget("pin2Dy01");this.cur2Dx0=new JSV.common.PlotWidget("cur2Dx0");
this.cur2Dx1=new JSV.common.PlotWidget("cur2Dx1");this.cur2Dy=new JSV.common.PlotWidget("cur2Dy");this.pin2Dy0.setY(0,this.imageView.toPixelY0(0));var a=this.getSpectrumAt(0).getSubSpectra().size();this.pin2Dy1.setY(a,this.imageView.toPixelY0(a))}this.setWidgetX(this.pin1Dx0,this.getScale().minX);this.setWidgetX(this.pin1Dx1,this.getScale().maxX);this.setWidgetY(this.pin1Dy0,this.getScale().minY);this.setWidgetY(this.pin1Dy1,this.getScale().maxY);this.widgets=v(-1,[this.zoomBox1D,this.zoomBox2D,this.pin1Dx0,
this.pin1Dx01,this.pin1Dx1,this.pin1Dy0,this.pin1Dy01,this.pin1Dy1,this.pin2Dx0,this.pin2Dx01,this.pin2Dx1,this.pin2Dy0,this.pin2Dy01,this.pin2Dy1,this.cur2Dx0,this.cur2Dx1,this.cur2Dy,this.cur1D2x1,this.cur1D2x2])});c(c$,"setWidgetX",function(a,b){a.setX(b,this.toPixelX0(b))},"JSV.common.PlotWidget,~N");c(c$,"setWidgetY",function(a,b){a.setY(b,this.toPixelY0(b))},"JSV.common.PlotWidget,~N");c(c$,"resetPinsFromView",function(){null!=this.pin1Dx0&&(this.setWidgetX(this.pin1Dx0,this.getScale().minXOnScale),
this.setWidgetX(this.pin1Dx1,this.getScale().maxXOnScale),this.setWidgetY(this.pin1Dy0,this.getScale().minYOnScale),this.setWidgetY(this.pin1Dy1,this.getScale().maxYOnScale))});c(c$,"resetPinPositions",function(){this.resetX(this.pin1Dx0);this.resetY(this.pin1Dy0);this.resetY(this.pin1Dy1);null==this.imageView?(null!=this.gs2dLinkedX&&this.resetX(this.cur1D2x1),null!=this.gs2dLinkedY&&this.resetX(this.cur1D2x2)):(this.pin2Dy0.setY(this.pin2Dy0.getYVal(),this.imageView.toPixelY0(this.pin2Dy0.getYVal())),
this.pin2Dy1.setY(this.pin2Dy1.getYVal(),this.imageView.toPixelY0(this.pin2Dy1.getYVal())))});c(c$,"resetX",function(a){this.setWidgetX(a,a.getXVal())},"JSV.common.PlotWidget");c(c$,"resetY",function(a){this.setWidgetY(a,a.getYVal())},"JSV.common.PlotWidget");c(c$,"setPinSliderPositions",function(a){this.pin1Dx0.yPixel0=this.pin1Dx1.yPixel0=this.pin1Dx01.yPixel0=this.yPixel0-5;this.pin1Dx0.yPixel1=this.pin1Dx1.yPixel1=this.pin1Dx01.yPixel1=this.yPixel0;this.cur1D2x1.yPixel1=this.cur1D2x2.yPixel1=
this.yPixel0-5;this.cur1D2x1.yPixel0=this.cur1D2x2.yPixel0=this.yPixel1+6;null==this.imageView?(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=this.pin1Dy01.xPixel0=this.xPixel1+5,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=this.xPixel1):(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=this.pin1Dy01.xPixel0=this.imageView.xPixel1+15,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=this.imageView.xPixel1+10,this.pin2Dx0.yPixel0=this.pin2Dx1.yPixel0=this.pin2Dx01.yPixel0=this.yPixel0-
5,this.pin2Dx0.yPixel1=this.pin2Dx1.yPixel1=this.pin2Dx01.yPixel1=this.yPixel0,this.pin2Dy0.xPixel0=this.pin2Dy1.xPixel0=this.pin2Dy01.xPixel0=this.imageView.xPixel1+5,this.pin2Dy0.xPixel1=this.pin2Dy1.xPixel1=this.pin2Dy01.xPixel1=this.imageView.xPixel1,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=this.yPixel1+6,this.cur2Dx0.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=this.yPixel1+6,this.cur2Dx1.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dy.xPixel0=
a?u((this.xPixel1+this.imageView.xPixel0)/2):this.imageView.xPixel0-6,this.cur2Dy.xPixel1=this.imageView.xPixel1+5)},"~B");c(c$,"setDerivedPins",function(a){this.widgetsAreSet=!0;null!=this.gs2dLinkedX&&this.cur1D2x1.setX(this.cur1D2x1.getXVal(),this.toPixelX(this.cur1D2x1.getXVal()));null!=this.gs2dLinkedY&&this.cur1D2x2.setX(this.cur1D2x2.getXVal(),this.toPixelX(this.cur1D2x2.getXVal()));this.pin1Dx01.setX(0,u((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2));this.pin1Dy01.setY(0,u((this.pin1Dy0.yPixel0+
this.pin1Dy1.yPixel0)/2));this.pin1Dx01.setEnabled(Math.min(this.pin1Dx0.xPixel0,this.pin1Dx1.xPixel0)>this.xPixel0||Math.max(this.pin1Dx0.xPixel0,this.pin1Dx1.xPixel0)<this.xPixel1);this.pin1Dy01.setEnabled(Math.min(this.pin1Dy0.yPixel0,this.pin1Dy1.yPixel0)>Math.min(this.toPixelY(this.getScale().minY),this.toPixelY(this.getScale().maxY))||Math.max(this.pin1Dy0.yPixel0,this.pin1Dy1.yPixel0)<Math.max(this.toPixelY(this.getScale().minY),this.toPixelY(this.getScale().maxY)));if(null!=this.imageView){var b=
this.pin1Dx0.getXVal();this.cur2Dx0.setX(b,this.imageView.toPixelX(b));b=this.pin1Dx1.getXVal();this.cur2Dx1.setX(b,this.imageView.toPixelX(b));b=this.imageView.toX(this.imageView.xPixel0);this.pin2Dx0.setX(b,this.imageView.toPixelX0(b));b=this.imageView.toX(this.imageView.xPixel1);this.pin2Dx1.setX(b,this.imageView.toPixelX0(b));this.pin2Dx01.setX(0,u((this.pin2Dx0.xPixel0+this.pin2Dx1.xPixel0)/2));b=this.imageView.imageHeight-1-this.imageView.yView1;this.pin2Dy0.setY(b,this.imageView.toPixelY0(b));
b=this.imageView.imageHeight-1-this.imageView.yView2;this.pin2Dy1.setY(b,this.imageView.toPixelY0(b));this.pin2Dy01.setY(0,u((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2));this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=this.imageView.subIndexToPixelY(a);this.pin2Dx01.setEnabled(Math.min(this.pin2Dx0.xPixel0,this.pin2Dx1.xPixel0)!=this.imageView.xPixel0||Math.max(this.pin2Dx0.xPixel0,this.pin2Dx1.xPixel1)!=this.imageView.xPixel1);this.pin2Dy01.setEnabled(Math.min(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel0)!=
this.yPixel0||Math.max(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel1)!=this.yPixel1)}},"~N");c(c$,"doZoom",function(a,b,d,c,g,e,j,h,k){a==d?(a=this.getScale().minXOnScale,d=this.getScale().maxXOnScale):this.isLinked&&h&&this.pd.doZoomLinked(this,a,d,k,j,g);a>d&&(h=a,a=d,d=h);b>c&&(h=b,b=c,c=h);h=!g&&null!=this.imageView&&(this.imageView.minZ!=b||this.imageView.maxZ!=c);if(this.zoomEnabled||h){if(j){if(!this.getScale().isInRangeX(a)&&!this.getScale().isInRangeX(d))return;this.getScale().isInRangeX(a)?
this.getScale().isInRangeX(d)||(d=this.getScale().maxX):a=this.getScale().minX}this.pd.setTaintedAll();j=this.viewData.getScaleData();var r=B(this.nSpectra,0),n=B(this.nSpectra,0);this.graphsTemp.clear();var q=this.getSpectrumAt(0).getSubSpectra(),q=null==q||2==q.size();if(this.getSpectrumAt(0).is1D()&&!q){if(this.graphsTemp.addLast(this.getSpectrum()),!JSV.common.ScaleData.setDataPointIndices(this.graphsTemp,a,d,3,r,n))return}else if(!JSV.common.ScaleData.setDataPointIndices(this.spectra,a,d,3,r,
n))return;if(q=b==c)g=!h&&g?g=this.getScale().spectrumScaleFactor:1,1E-4>Math.abs(g-1)&&(b=this.getScale().minYOnScale,c=this.getScale().maxYOnScale);g=null;if(q||e)this.getCurrentView(),g=this.viewData.getNewScales(this.iSpectrumSelected,q,b,c);this.getView(a,d,b,c,r,n,j,g);this.setXPixelMovedTo(1E10,1.7976931348623157E308,0,0);this.setWidgetX(this.pin1Dx0,a);this.setWidgetX(this.pin1Dx1,d);this.setWidgetY(this.pin1Dy0,b);this.setWidgetY(this.pin1Dy1,c);null==this.imageView?this.updateDialogs():
(a=this.getSpectrumAt(0).getSubIndex(),d=this.imageView.fixSubIndex(a),d!=a&&this.setCurrentSubSpectrum(d),h&&this.update2dImage(!1));k&&this.addCurrentZoom()}},"~N,~N,~N,~N,~B,~B,~B,~B,~B");c(c$,"updateDialogs",function(){this.updateDialog(JSV.common.Annotation.AType.PeakList,-1);this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)});c(c$,"setCurrentSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.setCurrentSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());
this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(c$,"addCurrentZoom",function(){if(this.viewList.size()>this.currentZoomIndex+1)for(var a=this.viewList.size()-1;a>this.currentZoomIndex;a--)this.viewList.removeItemAt(a);this.viewList.addLast(this.viewData);this.currentZoomIndex++});c(c$,"setZoomTo",function(a){this.currentZoomIndex=a;this.viewData=this.viewList.get(a);this.resetPinsFromView()},"~N");c(c$,"clearViews",function(){this.isLinked&&this.pd.clearLinkViews(this);this.setZoom(0,
0,0,0);for(var a=this.viewList.size();1<=--a;)this.viewList.removeItemAt(a)});c(c$,"drawAll",function(a,b,d,c,g,e,j){this.g2d=this.pd.g2d;this.gMain=a;var h=this.getSpectrumAt(0),k=h.getSubIndex();this.is2DSpectrum=!h.is1D()&&(this.isLinked||this.pd.getBoolean(JSV.common.ScriptToken.DISPLAY2D))&&(null!=this.imageView||this.get2DImage(h));null!=this.imageView&&e&&(this.pd.isPrinting&&this.g2d!==this.pd.g2d0&&this.g2d.newGrayScaleImage(a,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,
this.imageView.getBuffer()),this.is2DSpectrum&&this.setPositionForFrame(c),this.draw2DImage());var r=this.stackSelected||!this.showAllStacked?this.iSpectrumSelected:-1,n=!this.showAllStacked||1==this.nSpectra||0<=r,h=null==this.imageView||this.pd.display1D,q=0<=r?1:0,p=this.getFixedSelectedSpectrumIndex();if(h&&e&&(this.fillBox(a,this.xPixel0,this.yPixel0,this.xPixel1,this.yPixel1,JSV.common.ScriptToken.PLOTAREACOLOR),0>r)){n=!0;for(r=0;r<this.nSpectra;r++)this.doPlot(r,c)&&0!=q++&&(n=(new Boolean(n&
this.viewData.areYScalesSame(r-1,r))).valueOf())}var m=1==this.nSpectra?0:!this.showAllStacked?this.iSpectrumMovedTo:this.iSpectrumSelected;d=d===a?b:d;if(e){var r=this.pd.getCurrentGraphSet()===this&&!this.isLinked&&(!this.isSplittable||1==this.nSplit||this.pd.currentSplitPoint==c),s=this.zoomEnabled&&!this.isDrawNoSpectra()&&this.pd.isCurrentGraphSet(this)&&this.spectra.get(0).isScalable()&&(r||1==this.nSpectra)&&(1==this.nSplit||this.pd.currentSplitPoint==this.iSpectrumMovedTo);this.drawFrame(a,
m,r,this.isSplittable,s)}if(this.pd.isCurrentGraphSet(this)&&c==this.pd.currentSplitPoint&&(2>q||0<=this.iSpectrumSelected))this.$haveSelectedSpectrum=!0;this.haveSingleYScale=this.showAllStacked&&1<this.nSpectra?this.allowStackedYScale&&n:!0;if(h){n=C(this.yPixels*(this.yStackOffsetPercent/100));this.haveLeftRightArrows=!1;for(s=r=0;r<this.nSpectra;r++)if(this.doPlot(r,c)){var m=this.stackSelected&&0<=this.iSpectrumSelected&&this.iSpectrumSelected!=r,t=!this.reversePlot&&this.getShowAnnotation(JSV.common.Annotation.AType.Integration,
r)&&(!this.showAllStacked||this.iSpectrumSelected==r)?this.getDialog(JSV.common.Annotation.AType.Integration,r).getData():null;this.setScale(r);var u=this.spectra.get(r);1<this.nSplit&&(p=r);var v=!m&&(1==this.nSplit||this.showAllStacked||this.iSpectrumSelected==c),w=v&&this.$haveSelectedSpectrum&&r==p;v&&(this.resetPinsFromView(),this.drawWidgets(b,d,k,g,h,w,!1));this.haveSingleYScale&&(r==p&&e)&&(this.drawGrid(a),this.pd.isPrinting&&1<this.nSplit&&this.drawSpectrumSource(a,r));v&&this.drawWidgets(b,
d,k,!1,h,w,!0);!this.isDrawNoSpectra()&&((1==this.nSpectra||0<=this.iSpectrumSelected)&&(this.haveSingleYScale&&r==p||this.showAllStacked&&this.stackSelected&&r==this.iSpectrumSelected))&&this.drawHighlightsAndPeakTabs(b,d,r);if(e){if((1==q&&0>this.iSpectrumSelected||this.iSpectrumSelected==r&&this.pd.isCurrentGraphSet(this))&&this.pd.titleOn&&!this.pd.titleDrawn)this.pd.drawTitle(a,this.height,this.width,this.pd.getDrawTitle(this.pd.isPrinting)),this.pd.titleDrawn=!0;this.haveSingleYScale&&r==p&&
(this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.YUNITSON)&&this.drawYUnits(a))}var v=u.isContinuous(),w=(1<this.nSplit?r==this.iSpectrumMovedTo:this.isLinked||r==p)&&!this.pd.isPrinting&&v,x=!m&&null!=this.pendingIntegral&&u===this.pendingIntegral.spec;if(e||x)this.drawPlot(x&&!e?b:a,r,u,v,s,m,null,w,x,j);this.drawIntegration(b,r,s,m,t,v,w);this.drawMeasurements(b,r);null!=this.pendingMeasurement&&this.pendingMeasurement.spec===
u&&this.drawMeasurement(b,this.pendingMeasurement);w&&0<=this.xPixelMovedTo&&this.drawSpectrumPointer(b,u,s,t);1<this.nSpectra&&(1==this.nSplit&&this.pd.isCurrentGraphSet(this)&&e)&&(this.haveLeftRightArrows=!0,this.pd.isPrinting||(this.setScale(0),m=this.iSpectrumSelected,2!=this.nSpectra&&(this.setPlotColor(a,(m+this.nSpectra-1)%this.nSpectra),this.fillArrow(a,1,this.yHArrows,this.xHArrows-9,!0),this.setCurrentBoxColor(a),this.fillArrow(a,1,this.yHArrows,this.xHArrows-9,!1)),0<=m&&(this.setPlotColor(a,
m),this.fillCircle(a,this.xHArrows,this.yHArrows,!0)),this.setCurrentBoxColor(a),this.fillCircle(a,this.xHArrows,this.yHArrows,!1),this.setPlotColor(a,(m+1)%this.nSpectra),this.fillArrow(a,2,this.yHArrows,this.xHArrows+9,!0),this.setCurrentBoxColor(a),this.fillArrow(a,2,this.yHArrows,this.xHArrows+9,!1)));s-=n}e&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&this.drawXScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.XUNITSON)&&this.drawXUnits(a))}else e&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&
this.drawXScale(a,this.imageView),this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this.imageView),0<=k&&this.draw2DUnits(a)),this.drawWidgets(b,d,k,g,h,!0,!1),this.drawWidgets(b,d,k,g,h,!0,!0),this.widgetsAreSet=!0;null!=this.annotations&&this.drawAnnotations(b,this.annotations,null)},"~O,~O,~O,~N,~B,~B,~B");c(c$,"drawSpectrumSource",function(a,b){this.pd.printFilePath(a,this.pd.thisWidth-this.pd.right,this.yPixel0,this.spectra.get(b).getFilePath())},"~O,~N");c(c$,"doPlot",
function(a,b){var d=this.stackSelected&&0<=this.iSpectrumSelected&&this.iSpectrumSelected!=a,c=this.showAllStacked||-1==this.iSpectrumSelected||this.iSpectrumSelected==a;return 1<this.nSplit?a==b:c&&(!this.pd.isPrinting||!d)},"~N,~N");c(c$,"drawSpectrumPointer",function(a,b,d,c){this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);var g=this.pd.integralShiftMode;null!=c&&((!this.pd.ctrlPressed||this.pd.isIntegralDrag)&&!this.isOnSpectrum(this.pd.mouseX,this.pd.mouseY,-1)?c=null:0==g&&(g=
this.getShiftMode(this.pd.mouseX,this.pd.mouseY),0==g&&(g=2147483647)));var e=this.yValueMovedTo;this.yValueMovedTo=null==c?b.getYValueAt(this.xValueMovedTo):c.getPercentYValueAt(this.xValueMovedTo);this.setCoordStr(this.xValueMovedTo,this.yValueMovedTo);if(0!=g&&(this.setPlotColor(a,2147483647==g?-1:0),(0>g||2147483647==g)&&this.drawHandle(a,this.xPixelPlot1,this.yPixelPlot0,3,!1),0<g&&this.drawHandle(a,this.xPixelPlot0,this.yPixelPlot1,3,!1),2147483647!=g))return;null!=c&&this.g2d.setStrokeBold(a,
!0);Double.isNaN(e)||null!=this.pendingMeasurement?(this.g2d.drawLine(a,this.xPixelMovedTo,this.yPixel0,this.xPixelMovedTo,this.yPixel1),0<=this.xPixelMovedTo2&&this.g2d.drawLine(a,this.xPixelMovedTo2,this.yPixel0,this.xPixelMovedTo2,this.yPixel1),this.yValueMovedTo=NaN):(b=null==c?d+this.toPixelY(this.yValueMovedTo):this.toPixelYint(this.yValueMovedTo/100),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixelMovedTo,b-10,this.xPixelMovedTo,b+10));null!=c&&this.g2d.setStrokeBold(a,!1)},"~O,JSV.common.Spectrum,~N,JSV.common.IntegralData");
c(c$,"setScale",function(a){this.viewData.setScale(a,this.xPixels,this.yPixels,this.spectra.get(a).isInverted())},"~N");c(c$,"draw2DUnits",function(a){var b=this.getSpectrumAt(0).nucleusX,d=this.getSpectrumAt(0).nucleusY;this.setColorFromToken(a,JSV.common.ScriptToken.PLOTCOLOR);this.drawUnits(a,b,this.imageView.xPixel1+5*this.pd.scalingFactor,this.yPixel1,1,1);this.drawUnits(a,d,this.imageView.xPixel0-5*this.pd.scalingFactor,this.yPixel0,1,0)},"~O");c(c$,"drawPeakTabs",function(a,b,d){var c=1==this.nSpectra||
0<=this.iSpectrumSelected?d.getPeakList():null;if(null!=c&&0<c.size()){null!=this.piMouseOver&&this.piMouseOver.spectrum===d&&this.pd.isMouseUp()?(this.g2d.setGraphicsColor(b,this.g2d.getColor4(240,240,240,140)),this.drawPeak(b,this.piMouseOver,0),d.setHighlightedPeak(this.piMouseOver)):d.setHighlightedPeak(null);this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);for(b=c.size();0<=--b;){var g=c.get(b);this.drawPeak(a,g,g===d.getSelectedPeak()?14:7)}}},"~O,~O,JSV.common.Spectrum");c(c$,
"drawPeak",function(a,b,d){if(!this.pd.isPrinting){var c=b.getXMin(),g=b.getXMax();c!=g&&this.drawBar(a,b,c,g,null,d)}},"~O,JSV.common.PeakInfo,~N");c(c$,"drawWidgets",function(a,b,d,c,g,e,h){this.setWidgets(c,d,g);if(!this.pd.isPrinting||!(null==this.imageView?!this.cur1D2Locked:this.sticky2Dcursor)){!this.pd.isPrinting&&!h&&(g?(this.fillBox(a,this.xPixel0,this.pin1Dx0.yPixel1,this.xPixel1,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin1Dx0.xPixel0,this.pin1Dx0.yPixel1,
this.pin1Dx1.xPixel0,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.PLOTCOLOR)):(this.fillBox(a,this.imageView.xPixel0,this.pin2Dx0.yPixel1,this.imageView.xPixel1,this.pin2Dx0.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dx0.xPixel0,this.pin2Dx0.yPixel1,this.pin2Dx1.xPixel0,this.pin2Dx1.yPixel1+2,JSV.common.ScriptToken.PLOTCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,this.yPixel1,this.pin2Dy1.xPixel1+2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,
this.pin2Dy0.yPixel1,this.pin2Dy1.xPixel1+2,this.pin2Dy1.yPixel0,JSV.common.ScriptToken.PLOTCOLOR)),this.fillBox(a,this.pin1Dy0.xPixel1,this.yPixel1,this.pin1Dy1.xPixel1+2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),e&&this.fillBox(a,this.pin1Dy0.xPixel1,this.pin1Dy0.yPixel1,this.pin1Dy1.xPixel1+2,this.pin1Dy1.yPixel0,JSV.common.ScriptToken.PLOTCOLOR));for(d=0;d<this.widgets.length;d++)if(c=this.widgets[d],!(null==c||!c.isPinOrCursor&&!this.zoomEnabled)){var l=c===this.cur1D2x1||c===this.cur1D2x2||
c===this.cur2Dx0||c===this.cur2Dx1||c===this.cur2Dy;if((c.isPin||!c.isPinOrCursor)!=h){if(c.is2D){if(c===this.cur2Dx0&&!g)continue}else{var k=c===this.pin1Dy0||c===this.pin1Dy1||c===this.pin1Dy01;if(null!=this.imageView&&g==k||k&&!e||c===this.cur1D2x1&&null==this.gs2dLinkedX||c===this.cur1D2x2&&null==this.gs2dLinkedY||c===this.zoomBox1D&&(this.pd.isIntegralDrag||0!=this.pd.integralShiftMode))if(!this.isLinked||null!=this.imageView)continue}if(!this.pd.isPrinting||l)c.isPinOrCursor?(this.setColorFromToken(a,
c.color),this.g2d.drawLine(a,c.xPixel0,c.yPixel0,c.xPixel1,c.yPixel1),c.isVisible=!0,c.isPin&&this.drawHandle(a,c.xPixel0,c.yPixel0,2,!c.isEnabled)):c.xPixel1!=c.xPixel0&&this.fillBox(b,c.xPixel0,c.yPixel0,c.xPixel1,c.yPixel1,c===this.zoomBox1D&&this.pd.shiftPressed?JSV.common.ScriptToken.ZOOMBOXCOLOR2:JSV.common.ScriptToken.ZOOMBOXCOLOR)}}}},"~O,~O,~N,~B,~B,~B,~B");c(c$,"drawBar",function(a,b,d,c,g,e){Math.abs(c-d);Math.abs(this.toX(this.xPixel1)-this.toX(this.xPixel0));d=this.toPixelX(d);c=this.toPixelX(c);
if(d>c){var h=d;d=c;c=h}d=this.fixX(d);c=this.fixX(c);3>c-d&&(d-=2,c+=2);null!=b&&b.setPixelRange(d,c);0==e?this.fillBox(a,d,this.yPixel0,c,this.yPixel0+this.yPixels,g):(this.fillBox(a,d,this.yPixel0+2,c,this.yPixel0+5,g),null!=b&&(d=u((d+c)/2),this.fillBox(a,d-1,this.yPixel0+2,d+1,this.yPixel0+2+e,g)))},"~O,JSV.common.PeakInfo,~N,~N,JSV.common.ScriptToken,~N");c(c$,"drawIntegration",function(a,b,d,c,g){null!=g&&(this.haveIntegralDisplayed(b)&&this.drawPlot(a,b,this.spectra.get(b),!0,d,!1,g,!0,!1,
!1),this.drawIntegralValues(a,b,d));b=this.getIntegrationRatios(b);null!=b&&this.drawAnnotations(a,b,JSV.common.ScriptToken.INTEGRALPLOTCOLOR)},"~O,~N,~N,~B,JSV.common.IntegralData,~B,~B");c(c$,"getMeasurements",function(a,b){var d=this.getDialog(a,b);return null==d||0==d.getData().size()||!d.getState()?null:d.getData()},"JSV.common.Annotation.AType,~N");c(c$,"drawPlot",function(a,b,d,c,g,e,h,l,k,r){var n=null==h?d.getXYCoords():this.getIntegrationGraph(b).getXYCoords(),q=null!=h;h=q?h.getBitSet():
null;l=k||null!=d.fillColor&&l;e=e?-2:q?-1:!this.allowStacking?0:b;this.setPlotColor(a,e);var p=!0,m=this.toPixelY(0);q?l=(new Boolean(l&m==this.fixY(m))).valueOf():m=this.fixY(m);var s=q||l?this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR):null;d=null==s||null==d.fillColor?s:d.fillColor;s=this.viewData.getStartingPointIndex(b);b=this.viewData.getEndingPointIndex(b);if(c&&!r){b--;(r=(q||null!=this.pendingIntegral)&&this.g2d.canDoLineTo())&&this.g2d.doStroke(a,!0);var t=!1;for(c=s;c<=b;c++){var u=
n[c],v=n[c+1],w=q?this.toPixelYint(u.getYVal()):this.toPixelY(u.getYVal());if(-2147483648!=w){var x=q?this.toPixelYint(v.getYVal()):this.toPixelY(v.getYVal());if(-2147483648!=x){var u=u.getXVal(),y=v.getXVal(),v=this.toPixelX(u),B=this.toPixelX(y),w=this.fixY(g+w),x=this.fixY(g+x);q&&(c==s&&(this.xPixelPlot1=v,this.yPixelPlot0=w),this.xPixelPlot0=B,this.yPixelPlot1=x);if(!(B==v&&w==x))if(l&&k&&this.pendingIntegral.overlaps(u,y))null!=d&&(this.g2d.doStroke(a,!1),this.g2d.setGraphicsColor(a,d)),this.g2d.fillRect(a,
Math.min(v,B),Math.min(m,w),Math.max(1,Math.abs(B-v)),Math.abs(m-w)),null!=d&&(this.g2d.doStroke(a,!1),this.g2d.doStroke(a,!0),t=!1,this.setPlotColor(a,e));else if(!(w==x&&w==this.yPixel0)&&(null!=h&&h.get(c)!=p&&(p=h.get(c),r&&t&&(this.g2d.doStroke(a,!1),this.g2d.doStroke(a,!0),t=!1),!this.pd.isPrinting&&0!=this.pd.integralShiftMode?this.setPlotColor(a,0):p?this.setColorFromToken(a,JSV.common.ScriptToken.INTEGRALPLOTCOLOR):this.setPlotColor(a,-3)),!this.pd.isPrinting||p))t?this.g2d.lineTo(a,B,x):
(this.g2d.drawLine(a,v,w,B,x),t=r)}}}r&&this.g2d.doStroke(a,!1)}else{for(c=s;c<=b;c++)k=n[c],x=this.toPixelY(k.getYVal()),-2147483648!=x&&(v=this.toPixelX(k.getXVal()),w=this.toPixelY(Math.max(this.getScale().minYOnScale,0)),w=this.fixY(g+w),x=this.fixY(g+x),w==x&&(w==this.yPixel0||w==this.yPixel1)||(r?this.g2d.fillRect(a,v-1,x-1,3,3):this.g2d.drawLine(a,v,w,v,x)));!r&&this.getScale().isYZeroOnScale()&&(g+=this.toPixelY(this.getScale().spectrumYRef),g==this.fixY(g)&&this.g2d.drawLine(a,this.xPixel1,
g,this.xPixel0,g))}},"~O,~N,JSV.common.Spectrum,~B,~N,~B,JSV.common.IntegralData,~B,~B,~B");c(c$,"drawFrame",function(a,b,d,c,g){if(!this.pd.gridOn||this.pd.isPrinting)if(this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR),this.g2d.drawRect(a,this.xPixel0,this.yPixel0,this.xPixels,this.yPixels),this.pd.isPrinting)return;this.setCurrentBoxColor(a);g&&(0<=b&&(this.setPlotColor(a,b),this.fillArrow(a,3,this.xVArrows,u((this.yPixel00+this.yPixel11)/2)-9,!0),this.fillArrow(a,4,this.xVArrows,u((this.yPixel00+
this.yPixel11)/2)+9,!0),this.setCurrentBoxColor(a)),this.fillArrow(a,3,this.xVArrows,u((this.yPixel00+this.yPixel11)/2)-9,!1),this.fillCircle(a,this.xVArrows,u((this.yPixel00+this.yPixel11)/2),!1),this.fillArrow(a,4,this.xVArrows,u((this.yPixel00+this.yPixel11)/2)+9,!1));if(null==this.imageView&&d){b=this.xPixel00+10;d=this.xPixel11-10;g=this.yPixel00+1;var e=this.yPixel11-2;this.g2d.drawLine(a,b,g,d,g);this.g2d.drawLine(a,d,g,d,e);this.g2d.drawLine(a,b,e,d,e);this.splitterX=this.closerX=-2147483648;
this.drawBox(a,d-10,g,d,g+10,null);this.g2d.drawLine(a,d-10,g+10,d,g);this.g2d.drawLine(a,d,g+10,d-10,g);this.closerX=d-10;this.closerY=g;c&&(d-=10,this.fillBox(a,d-10,g,d,g+10,null),this.splitterX=d-10,this.splitterY=g)}},"~O,~N,~B,~B,~B");c(c$,"drawGrid",function(a){if(this.pd.gridOn&&null==this.imageView){this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR);var b;if(Double.isNaN(this.getScale().firstX)){b=this.getScale().maxXOnScale+this.getScale().steps[0]/2;for(var d=this.getScale().minXOnScale;d<
b;d+=this.getScale().steps[0]){var c=this.toPixelX(d);this.g2d.drawLine(a,c,this.yPixel0,c,this.yPixel1)}}else{b=1.0001*this.getScale().maxXOnScale;for(d=this.getScale().firstX;d<=b;d+=this.getScale().steps[0])c=this.toPixelX(d),this.g2d.drawLine(a,c,this.yPixel0,c,this.yPixel1)}for(d=this.getScale().firstY;d<this.getScale().maxYOnScale+this.getScale().steps[1]/2;d+=this.getScale().steps[1])b=this.toPixelY(d),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixel0,b,this.xPixel1,b)}},"~O");c(c$,"drawXScale",
function(a,b){this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);this.pd.isPrinting&&this.g2d.drawLine(a,b.getXPixel0(),this.yPixel1,b.getXPixel0()+b.getXPixels()-1,this.yPixel1);for(var d=this.getScale().precision[0],c=this.pd.setFont(a,b.getXPixels(),0,this.pd.isPrinting?10:12,!1),g=this.yPixel1,e=this.yPixel1+4*this.pd.scalingFactor,h=this.yPixel1+2*this.pd.scalingFactor,c=c.getHeight(),l=b.toPixelX(this.getScale().steps[0])-b.toPixelX(0),k=Math.abs(0.95*l),r=this.getScale().firstX-this.getScale().steps[0],
n=1.0001*(this.getScale().maxXOnScale+this.getScale().steps[0]),q=0;2>q;q++){1==q&&JSV.common.ScaleData.fixScale(this.mapX);for(var p=1E10,m=r;m<=n;m+=this.getScale().steps[0]){var l=b.toPixelX(m),s=Double.$valueOf(m),t;switch(q){case 0:t=JU.DF.formatDecimalDbl(m,d);this.mapX.put(s,t);this.drawTick(a,l,g,e,b);l=Math.abs(p-m);p=this.getScale().minorTickCounts[0];if(0!=p){l/=p;for(t=1;t<p;t++)this.drawTick(a,b.toPixelX(m-t*l),g,h,b)}p=m;continue;case 1:t=this.mapX.get(s);if(null==t||l!=b.fixX(l))continue;
var s=this.pd.getStringWidth(t),v=l+u(s/2)==b.fixX(l+u(s/2))?2:0;0<v&&this.g2d.drawString(a,t,l-u(s/v),e+c);m+=Math.floor(s/k)*this.getScale().steps[0]}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(c$,"drawTick",function(a,b,d,c,g){b==g.fixX(b)&&this.g2d.drawLine(a,b,d,b,c)},"~O,~N,~N,~N,JSV.common.XYScaleConverter");c(c$,"drawYScale",function(a,b){var d=b.getScale(),c=d.precision[1],g=this.pd.setFont(a,b.getXPixels(),0,this.pd.isPrinting?10:12,!1).getHeight(),e=d.maxYOnScale+d.steps[1]/
2,h=-2147483648;this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);for(var l=0;2>l;l++){1==l&&JSV.common.ScaleData.fixScale(this.mapX);for(var k=d.firstY;k<e;k+=d.steps[1]){var r=Double.$valueOf(k),n=b.getXPixel0(),q=b.toPixelY(k);if(q==b.fixY(q)){var m;0==l&&this.g2d.drawLine(a,n,q,n-3*this.pd.scalingFactor,q);if(!(Math.abs(q-h)<=g))switch(h=q,l){case 0:m=JU.DF.formatDecimalDbl(k,c);this.mapX.put(r,m);break;case 1:m=this.mapX.get(r);if(null==m)continue;m.startsWith("0")&&m.contains("E")&&
(m="0");this.g2d.drawString(a,m,n-4*this.pd.scalingFactor-this.pd.getStringWidth(m),q+u(g/3))}}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(c$,"drawXUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!0);null!=b&&this.drawUnits(a,b,this.xPixel1+25*this.pd.scalingFactor,this.yPixel1+5*this.pd.scalingFactor,1,1)},"~O");c(c$,"drawUnits",function(a,b,d,c,g,e){this.setColorFromToken(a,JSV.common.ScriptToken.UNITSCOLOR);this.pd.setFont(a,(null==this.imageView?this:this.imageView).getXPixels(),
3,10,!1);this.g2d.drawString(a,b,u(d-this.pd.getStringWidth(b)*g),u(c+this.pd.getFontHeight()*e))},"~O,~S,~N,~N,~N,~N");c(c$,"drawYUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!1);null!=b&&this.drawUnits(a,b,(this.pd.isPrinting?30:5)*this.pd.scalingFactor,this.yPixel0+(this.pd.isPrinting?0:5)*this.pd.scalingFactor,0,-1)},"~O");c(c$,"drawHighlightsAndPeakTabs",function(a,b,d){var c=this.getMeasurements(JSV.common.Annotation.AType.PeakList,d),g=this.spectra.get(d);if(this.pd.isPrinting)null!=
c&&(this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR),this.printPeakList(a,g,c));else{if(null==c){for(var e=0;e<this.highlights.size();e++){var h=this.highlights.get(e);h.spectrum===g&&(this.pd.setHighlightColor(h.color),this.drawBar(b,null,h.x1,h.x2,JSV.common.ScriptToken.HIGHLIGHTCOLOR,0))}this.pd.peakTabsOn&&this.drawPeakTabs(a,b,g)}if(null!=c){b=g.isInverted()?this.yPixel1-10*this.pd.scalingFactor:this.yPixel0;this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);for(e=c.size();0<=
--e;)g=c.get(e),g=this.toPixelX(g.getXVal()),this.g2d.drawLine(a,g,b,g,b+10*this.pd.scalingFactor);this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,d))&&(b=this.toPixelY(c.getThresh()),b==this.fixY(b)&&!this.pd.isPrinting&&this.g2d.drawLine(a,this.xPixel0,b,this.xPixel1,b))}}},"~O,~O,~N");c(c$,"printPeakList",function(a,b,d){var c=d.getMeasurementListArray(null);if(0!=c.length){this.pd.setFont(a,this.xPixels,0,8,!1);for(var g=this.pd.getFontHeight(),e=B(d.size(),0),h=B(d.size(),
0),l=0,k=5*this.pd.scalingFactor,r=10*this.pd.scalingFactor,n=15*this.pd.scalingFactor,q=25*this.pd.scalingFactor,m=0;m<c.length;m++)h[m]=this.toPixelX(Double.parseDouble(c[m][1])),0==m?e[m]=h[m]:(e[m]=Math.max(e[m-1]+g,h[m]+g),l+=e[m]-h[m]);l/=2*c.length;e[0]-l<this.xPixel0+q&&(l=e[0]-(this.xPixel0+q));for(m=0;m<c.length;m++)e[m]-=l;m=b.isInverted();b=this.pd.getStringWidth("99.9999");for(var l=6<=c[0].length?this.pd.getStringWidth("99.99"):0,q=m?-1:1,p=(m?this.yPixel1:this.yPixel0)+q*(l+b+n),m=
0;m<c.length;m++)this.g2d.drawLine(a,e[m],p,e[m],p+k*q),this.g2d.drawLine(a,e[m],p+k*q,h[m],p+r*q),this.g2d.drawLine(a,h[m],p+r*q,h[m],p+n*q),0<l&&0<c[m][4].length&&this.g2d.drawLine(a,u((e[m]+e[m-1])/2),p-b+k,u((e[m]+e[m-1])/2),p-b-k);p-=2*q*this.pd.scalingFactor;0<l&&(this.drawStringRotated(a,-90,e[0]-n,p,"  ppm"),this.drawStringRotated(a,-90,e[0]-n,p-b-k," Hz"));for(m=d.size();0<=--m;)this.drawStringRotated(a,-90*q,e[m]+u(q*g/3),p,c[m][1]),0<l&&0<c[m][4].length&&(d=u((e[m]+e[m-1])/2)+u(g/3),this.drawStringRotated(a,
-90,d,p-b-k,c[m][4]))}},"~O,JSV.common.Spectrum,JSV.common.PeakData");c(c$,"drawStringRotated",function(a,b,d,c,g){this.g2d.drawStringRotated(a,g,d,c,b)},"~O,~N,~N,~N,~S");c(c$,"drawAnnotations",function(a,b,d){this.pd.setFont(a,this.xPixels,1,18,!1);for(var c=b.size();0<=--c;){var g=b.get(c);this.setAnnotationColor(a,g,d);var e=(g.is2D?this.imageView:this).toPixelX(g.getXVal()),h=g.isPixels()?u(this.yPixel0+10+10*this.pd.scalingFactor-g.getYVal()):g.is2D?this.imageView.subIndexToPixelY(u(g.getYVal())):
this.toPixelY(g.getYVal());this.g2d.drawString(a,g.text,e+g.offsetX*this.pd.scalingFactor,h-g.offsetY*this.pd.scalingFactor)}},"~O,JU.Lst,JSV.common.ScriptToken");c(c$,"drawIntegralValues",function(a,b,d){var c=this.getMeasurements(JSV.common.Annotation.AType.Integration,b);if(null!=c){this.pd.isPrinting?this.pd.setFont(a,this.xPixels,0,8,!1):this.pd.setFont(a,this.xPixels,1,12,!1);this.setColorFromToken(a,JSV.common.ScriptToken.INTEGRALPLOTCOLOR);var g=this.pd.getFontHeight();this.g2d.setStrokeBold(a,
!0);for(var e=c.size();0<=--e;){var h=c.get(e);if(0!=h.getValue()){var l=this.toPixelX(h.getXVal2()),k=d*this.pd.scalingFactor+this.toPixelYint(h.getYVal()),m=d*this.pd.scalingFactor+this.toPixelYint(h.getYVal2());l!=this.fixX(l)||(k!=this.fixY(k)||m!=this.fixY(m))||(this.pd.isPrinting||this.g2d.drawLine(a,l,k,l,m),this.g2d.drawString(a,"  "+h.text,l,u((k+m)/2)+u(g/3)))}}this.g2d.setStrokeBold(a,!1)}b==this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumIntegrals=c)},"~O,~N,~N");c(c$,"drawMeasurements",
function(a,b){var d=this.getMeasurements(JSV.common.Annotation.AType.Measurements,b);if(null!=d)for(var c=d.size();0<=--c;)this.drawMeasurement(a,d.get(c));b==this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumMeasurements=d)},"~O,~N");c(c$,"drawMeasurement",function(a,b){if(!(0==b.text.length&&b!==this.pendingMeasurement)){this.pd.setFont(a,this.xPixels,1,12,!1);this.g2d.setGraphicsColor(a,b===this.pendingMeasurement?this.pd.getColor(JSV.common.ScriptToken.PEAKTABCOLOR):this.pd.BLACK);var d=
this.toPixelX(b.getXVal()),c=this.toPixelY(b.getYVal()),g=this.toPixelX(b.getXVal2());if(!Double.isNaN(b.getXVal())&&!(d!=this.fixX(d)||g!=this.fixX(g))){var e=2<=Math.abs(d-g),h=this.getScale().isYZeroOnScale()&&b.spec.isHNMR(),l=u((d+g)/2);this.g2d.setStrokeBold(a,!0);e&&this.g2d.drawLine(a,d,c,g,c);h&&this.g2d.drawLine(a,d+1,this.yPixel1-1,g,this.yPixel1-1);this.g2d.setStrokeBold(a,!1);e&&this.g2d.drawString(a,b.text,l+b.offsetX,c-b.offsetY);h&&(this.g2d.drawLine(a,d,this.yPixel1,d,this.yPixel1-
6*this.pd.scalingFactor),this.g2d.drawLine(a,g,this.yPixel1,g,this.yPixel1-6*this.pd.scalingFactor))}}},"~O,JSV.common.Measurement");c(c$,"getPinSelected",function(a,b){if(null!=this.widgets)for(var d=0;d<this.widgets.length;d++)if(null!=this.widgets[d]&&this.widgets[d].isPinOrCursor&&this.widgets[d].selected(a,b))return this.widgets[d];return null},"~N,~N");c(c$,"set2DCrossHairs",function(a,b){var d;if(a==this.imageView.fixX(a)&&b==this.fixY(b)&&(this.pin1Dx1.setX(d=this.imageView.toX(a),this.toPixelX(d)),
this.cur2Dx1.setX(d,a),this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b)),this.isLinked)){var c=this.imageView.toY(b);this.pd.set2DCrossHairsLinked(this,d,c,!this.sticky2Dcursor)}},"~N,~N");c(c$,"reset2D",function(a){a?(this.imageView.setView0(this.imageView.xPixel0,this.pin2Dy0.yPixel0,this.imageView.xPixel1,this.pin2Dy1.yPixel0),this.doZoom(0,this.getScale().minY,0,this.getScale().maxY,!0,!1,!1,!1,!0)):this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.yPixel0,this.pin2Dx1.xPixel0,
this.imageView.yPixel1)},"~B");c(c$,"setAnnotationText",function(a){var b=this.pd.getInput("New text?","Set Label",a.text);if(null==b)return!1;0==b.length?this.annotations.removeObj(a):a.text=b;return!0},"JSV.common.Annotation");c(c$,"checkIntegral",function(a,b,d){var c=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==c)return!1;a=c.getData().addIntegralRegion(a,b);d&&c.isDialog()&&c.update(null,0,0);if(Double.isNaN(b))return!1;this.pendingIntegral=d?null:a;this.pd.isIntegralDrag=
!d;this.selectedSpectrumIntegrals=null;return!0},"~N,~N,~B");c(c$,"setToolTipForPixels",function(a,b){if(this.iSpectrumMovedTo!=this.iSpectrumClicked||this.pd.getCurrentGraphSet()!==this)this.pd.setToolTipText("click spectrum to activate");else if(this.isSplitWidget(a,b))this.pd.setToolTipText("click to "+(1<this.nSplit?"combine":"split"));else if(this.isCloserWidget(a,b))this.pd.setToolTipText("click to close");else{var d=this.getPinSelected(a,b),c=this.getScale().precision[0],g=this.getScale().precision[1];
if(null!=d)this.setStartupPinTip()||(d===this.pin1Dx01||d===this.pin2Dx01?c=JU.DF.formatDecimalDbl(Math.min(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),c)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),c):d===this.pin1Dy01?c=JU.DF.formatDecimalDbl(Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()),g)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()),g):d===this.cur2Dy?(d=this.imageView.toSubspectrumIndex(d.yPixel0),c=
this.get2DYLabel(d,c)):c=d===this.pin2Dy01?""+u(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+u(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):d.isXtype?JU.DF.formatDecimalDbl(d.getXVal(),c):d.is2D?""+u(d.getYVal()):JU.DF.formatDecimalDbl(d.getYVal(),g),this.pd.setToolTipText(c));else{if(null!=this.imageView){if(this.imageView.fixX(a)==a&&this.fixY(b)==b){d=this.imageView.toSubspectrumIndex(b);c="y="+this.get2DYLabel(d,c)+" / x="+JU.DF.formatDecimalDbl(this.imageView.toX(a),
c)+" "+this.getSpectrum().getAxisLabel(!0);this.pd.setToolTipText(c);this.pd.coordStr=c;return}if(!this.pd.display1D){this.pd.setToolTipText("");this.pd.coordStr="";return}}var d=this.toX(this.fixX(a)),c=null!=this.imageView&&this.imageView.isXWithinRange(a)?this.imageView.toSubspectrumIndex(this.fixY(b)):this.toY(this.fixY(b)),g=this.setCoordStr(d,c),e=this.getFixedSelectedSpectrumIndex();this.isInPlotRegion(a,b)?1!=this.nSpectra&&this.haveIntegralDisplayed(e)&&(c=this.getIntegrationGraph(e).getPercentYValueAt(d),
g+=", "+JU.DF.formatDecimalDbl(c,1)):c=NaN;this.pd.setToolTipText(null!=this.selectedIntegral?"click to set value":null!=this.pendingMeasurement||null!=this.selectedMeasurement?this.pd.hasFocus()?"Press ESC to delete "+(null!=this.selectedIntegral?"integral, DEL to delete all visible, or N to normalize":null==this.pendingMeasurement?'"'+this.selectedMeasurement.text+'" or DEL to delete all visible':"measurement"):"":Double.isNaN(c)?null:g)}}},"~N,~N");c(c$,"isFrameBox",function(a,b,d,c){return 5>
Math.abs(a-(d+5))&&5>Math.abs(b-(c+5))},"~N,~N,~N,~N");c(c$,"setCoordStr",function(a,b){var d=JU.DF.formatDecimalDbl(a,this.getScale().precision[0]);this.pd.coordStr="("+d+(this.haveSingleYScale||0<=this.iSpectrumSelected?", "+JU.DF.formatDecimalDbl(b,this.getScale().precision[1]):"")+")";return d},"~N,~N");c(c$,"setStartupPinTip",function(){if(null==this.pd.startupPinTip)return!1;this.pd.setToolTipText(this.pd.startupPinTip);this.pd.startupPinTip=null;return!0});c(c$,"get2DYLabel",function(a,b){var d=
this.getSpectrumAt(0).getSubSpectra().get(a);return JU.DF.formatDecimalDbl(d.getY2DPPM(),b)+" PPM"+(d.y2DUnits.equals("HZ")?" ("+JU.DF.formatDecimalDbl(d.getY2D(),b)+" HZ) ":"")},"~N,~N");c(c$,"isOnSpectrum",function(a,b,d){var c=null,g=!0,e=0>d;if(e){c=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==c)return!1;c=c.getData().getXYCoords();d=this.getFixedSelectedSpectrumIndex()}else{this.setScale(d);var h=this.spectra.get(d),c=h.xyCoords,g=h.isContinuous()}var h=d*C(this.yPixels*
(this.yStackOffsetPercent/100)),l=this.viewData.getStartingPointIndex(d);d=this.viewData.getEndingPointIndex(d);if(g)for(g=l;g<d;g++){var k=c[g],m=c[g+1],l=this.toPixelX(k.getXVal()),n=this.toPixelX(m.getXVal()),k=e?this.toPixelYint(k.getYVal()):this.toPixelY(k.getYVal()),m=e?this.toPixelYint(m.getYVal()):this.toPixelY(m.getYVal());if(!(-2147483648==k||-2147483648==m))if(k=this.fixY(k)-h,m=this.fixY(m)-h,JSV.common.GraphSet.isOnLine(a,b,l,k,n,m))return!0}else for(g=l;g<=d;g++)if(e=c[g],m=this.toPixelY(e.getYVal()),
-2147483648!=m&&(l=this.toPixelX(e.getXVal()),k=this.toPixelY(Math.max(this.getScale().minYOnScale,0)),k=this.fixY(k),m=this.fixY(m),!(k==m&&(k==this.yPixel0||k==this.yPixel1))&&JSV.common.GraphSet.isOnLine(a,b,l,k,l,m)))return!0;return!1},"~N,~N,~N");c$.distance=c(c$,"distance",function(a,b){return Math.sqrt(a*a+b*b)},"~N,~N");c$.findCompatibleGraphSet=c(c$,"findCompatibleGraphSet",function(a,b){for(var d=0;d<a.size();d++)if(JSV.common.Spectrum.areXScalesCompatible(b,a.get(d).getSpectrum(),!1,!1))return a.get(d);
return null},"JU.Lst,JSV.common.Spectrum");c$.isGoodEvent=c(c$,"isGoodEvent",function(a,b,d){return null==b?5<Math.abs(a.xPixel1-a.xPixel0)&&5<Math.abs(a.yPixel1-a.yPixel0):d?5<Math.abs(a.xPixel0-b.xPixel0):5<Math.abs(a.yPixel0-b.yPixel0)},"JSV.common.PlotWidget,JSV.common.PlotWidget,~B");c$.isOnLine=c(c$,"isOnLine",function(a,b,d,c,g,e){var h=Math.abs(d-a);if(2>h&&2>Math.abs(c-b))return!0;var l=g-a;if(2>Math.abs(l)&&2>Math.abs(e-b))return!0;var k=c-e;if(2<Math.abs(k)&&c<b==e<b)return!1;var m=d-g;
return 2<Math.abs(m)&&d<a==g<a?!1:JSV.common.GraphSet.distance(h,c-b)+JSV.common.GraphSet.distance(l,b-e)<JSV.common.GraphSet.distance(m,k)+2},"~N,~N,~N,~N,~N,~N");c$.setFractionalPositions=c(c$,"setFractionalPositions",function(a,b,d){var c=b.size(),g=0,e=0;a.isLinked=d!==JSV.common.PanelData.LinkMode.NONE;if(d===JSV.common.PanelData.LinkMode.NONE){for(var h=0;h<c;h++)d=b.get(h),g+=(d.getSpectrumAt(0).is1D(),1)*d.nSplit;g=1/g;for(h=0;h<c;h++)d=b.get(h),d.isLinked=!1,a=d.getSpectrumAt(0).is1D()?g:
1*g,d.fX0=0,d.fY0=e,d.fracX=1,d.fracY=a,e+=a*d.nSplit}else{var g=null,l=-1;if(2==c||3==c)for(h=0;h<c;h++)if(d=b.get(h),!d.getSpectrum().is1D()){g=d;0<=l&&(h=-2);l=h;break}if(-2==l||-1==l&&2!=c)JSV.common.GraphSet.setFractionalPositions(a,b,JSV.common.PanelData.LinkMode.NONE);else for(h=0;h<c;h++)d=b.get(h),d.isLinked=!0,a=d.getSpectrumAt(0),a.is1D()?(null!=g&&(l=g.getSpectrumAt(0),JSV.common.Spectrum.areLinkableX(a,l)&&(d.gs2dLinkedX=g),JSV.common.Spectrum.areLinkableY(a,l)&&(d.gs2dLinkedY=g)),d.fX0=
0,d.fY0=e,d.fracX=null==g?1:0.5,d.fracY=3==c||null==g?0.5:1,e+=0.5):(d.fX0=0.5,d.fY0=0,d.fracX=0.5,d.fracY=1)}},"JSV.common.PanelData,JU.Lst,JSV.common.PanelData.LinkMode");c(c$,"addAnnotation",function(a,b){if(0==a.size()||1==a.size()&&a.get(0).equalsIgnoreCase("none"))return this.lastAnnotation=this.annotations=null;4>a.size()&&null==this.lastAnnotation&&(this.lastAnnotation=this.getAnnotation((this.getScale().maxXOnScale+this.getScale().minXOnScale)/2,(this.getScale().maxYOnScale+this.getScale().minYOnScale)/
2,b,!1,!1,0,0));var d=this.getAnnotation(a,this.lastAnnotation);if(null==d)return null;if(null==this.annotations&&1==a.size()&&'"'==a.get(0).charAt(0))return d=d.text,this.getSpectrum().setTitle(d),d;this.lastAnnotation=d;this.addAnnotation(d,!1);return null},"JU.Lst,~S");c(c$,"addHighlight",function(a,b,d,c){null==d&&(d=this.getSpectrumAt(0));a=R(JSV.common.GraphSet.Highlight,this,null,a,b,d,null==c?this.pd.getColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR):c);this.highlights.contains(a)||this.highlights.addLast(a)},
"~N,~N,JSV.common.Spectrum,javajs.api.GenericColor");c(c$,"addPeakHighlight",function(a){for(var b=this.spectra.size();0<=--b;){var c=this.spectra.get(b);this.removeAllHighlights(c);if(!(null==a||a.isClearAll()||c!==a.spectrum)){var f=a.toString();if(null!=f){var g=JU.PT.getQuotedAttribute(f,"xMin"),f=JU.PT.getQuotedAttribute(f,"xMax");if(null==g||null==f)break;g=JU.PT.parseFloat(g);f=JU.PT.parseFloat(f);if(Float.isNaN(g)||Float.isNaN(f))break;this.pd.addHighlight(this,g,f,c,200,140,140,100);c.setSelectedPeak(a);
!this.getScale().isInRangeX(g)&&!(this.getScale().isInRangeX(f)||g<this.getScale().minX&&this.getScale().maxX<f)&&this.setZoomTo(0)}}}},"JSV.common.PeakInfo");c(c$,"advanceSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.advanceSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(c$,"checkSpectrumClickedEvent",function(a,b,c){if(null!=this.nextClickForSetPeak||(1<c||null!=this.pendingMeasurement||
!this.isInPlotRegion(a,b))||0==c&&(c=this.isOnSpectrum(a,b,-1),this.pd.integralShiftMode=c?this.getShiftMode(a,b):0,this.pd.isIntegralDrag=0==this.pd.integralShiftMode&&(c||this.haveIntegralDisplayed(-1)&&null!=this.findMeasurement(this.getIntegrationGraph(-1),a,b,0)),0!=this.pd.integralShiftMode)||!this.showAllStacked)return!1;this.stackSelected=!1;for(c=0;c<this.nSpectra;c++)if(this.isOnSpectrum(a,b,c))return this.setSpectrumClicked(this.iPreviousSpectrumClicked=c),!1;if(this.isDialogOpen())return!1;
this.setSpectrumClicked(-1);return this.stackSelected=!1},"~N,~N,~N");c(c$,"getShiftMode",function(a,b){return this.isStartEndIntegral(a,!1)?b:this.isStartEndIntegral(a,!0)?-b:0},"~N,~N");c(c$,"isDialogOpen",function(){return this.isVisible(this.getDialog(JSV.common.Annotation.AType.Integration,-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,-1))});c(c$,"isStartEndIntegral",function(a,b){return b?
20>this.xPixelPlot1-a:20>a-this.xPixelPlot0},"~N,~B");c(c$,"checkWidgetEvent",function(a,b,c){if(!this.widgetsAreSet)return!1;this.widgetsAreSet=!1;if(c){if(2==this.pd.clickCount&&this.lastIntDragX!=a&&!this.is2dClick(a,b)){if(null==this.pendingMeasurement)return-1==this.iSpectrumClicked&&0<=this.iPreviousSpectrumClicked&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),this.processPendingMeasurement(a,b,2),!0}else if(!this.is2dClick(a,b)&&(this.isOnSpectrum(a,b,-1)&&this.checkIntegral(this.toX(a),
NaN,!1),this.lastIntDragX==a&&(this.pd.isIntegralDrag=!0,!this.checkIntegral(this.toX(a),this.toX(a),!1))))return!1;if(null!=this.pendingMeasurement)return!0;c=this.getPinSelected(a,b);null==c&&(b=this.fixY(b),a<this.xPixel1?(this.pd.shiftPressed&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),a=this.fixX(a),null==this.zoomBox1D&&this.newPins(),this.zoomBox1D.setX(this.toX(a),a),this.zoomBox1D.yPixel0=b,c=this.zoomBox1D):null!=this.imageView&&a<this.imageView.xPixel1&&(this.zoomBox2D.setX(this.imageView.toX(a),
this.imageView.fixX(a)),this.zoomBox2D.yPixel0=b,c=this.zoomBox2D));this.pd.thisWidget=c;return!1}this.nextClickForSetPeak=null;c=this.pd.thisWidget;if(null==c)return!1;if(c===this.zoomBox1D)return this.zoomBox1D.xPixel1=this.fixX(a),this.zoomBox1D.yPixel1=this.fixY(b),this.pd.isIntegralDrag&&this.zoomBox1D.xPixel0!=this.zoomBox1D.xPixel1&&(this.lastIntDragX<=a!=this.zoomBox1D.xPixel0<=a&&(this.zoomBox1D.xPixel0=this.lastIntDragX,this.zoomBox1D.xPixel1=a,this.zoomBox1D.setXVal(this.toX(this.zoomBox1D.xPixel0))),
this.lastIntDragX=a,this.checkIntegral(this.zoomBox1D.getXVal(),this.toX(this.zoomBox1D.xPixel1),!1)),!1;if(!this.zoomEnabled)return!1;if(c===this.zoomBox2D)return this.zoomBox2D.xPixel1=this.imageView.fixX(a),this.zoomBox2D.yPixel1=this.fixY(b),!0;if(c===this.cur2Dy)return b=this.fixY(b),this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=b,this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b)),!0;if(c===this.cur2Dx0||c===this.cur2Dx1)return!1;if(c===this.pin1Dx0||c===this.pin1Dx1||c===this.pin1Dx01){a=
this.fixX(a);c.setX(this.toX0(a),a);if(c===this.pin1Dx01){c=a-u((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2);a=this.pin1Dx0.xPixel0+c;b=this.pin1Dx1.xPixel0+c;if(0==c||this.fixX(a)!=a||this.fixX(b)!=b)return!0;this.pin1Dx0.setX(this.toX0(a),a);this.pin1Dx1.setX(this.toX0(b),b)}this.doZoom(this.pin1Dx0.getXVal(),0,this.pin1Dx1.getXVal(),0,!0,!1,!1,!0,!1);return!0}if(c===this.pin1Dy0||c===this.pin1Dy1||c===this.pin1Dy01){b=this.fixY(b);c.setY(this.toY0(b),b);if(c===this.pin1Dy01){c=b-u((this.pin1Dy0.yPixel0+
this.pin1Dy1.yPixel0)/2)+1;b=this.pin1Dy0.yPixel0+c;a=this.pin1Dy1.yPixel0+c;c=this.toY0(b);var f=this.toY0(a);if(Math.min(c,f)==this.getScale().minY||Math.max(c,f)==this.getScale().maxY)return!0;this.pin1Dy0.setY(c,b);this.pin1Dy1.setY(f,a)}this.doZoom(0,this.pin1Dy0.getYVal(),0,this.pin1Dy1.getYVal(),null==this.imageView,null==this.imageView,!1,!1,!1);return!0}if(c===this.pin2Dx0||c===this.pin2Dx1||c===this.pin2Dx01){a=this.imageView.fixX(a);c.setX(this.imageView.toX0(a),a);if(c===this.pin2Dx01){c=
a-u((this.pin2Dx0.xPixel0+this.pin2Dx1.xPixel0)/2)+1;a=this.pin2Dx0.xPixel0+c;b=this.pin2Dx1.xPixel0+c;if(this.imageView.fixX(a)!=a||this.imageView.fixX(b)!=b)return!0;this.pin2Dx0.setX(this.imageView.toX0(a),a);this.pin2Dx1.setX(this.imageView.toX0(b),b)}if(!JSV.common.GraphSet.isGoodEvent(this.pin2Dx0,this.pin2Dx1,!0))return this.reset2D(!0),!0;this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,this.pin2Dx1.xPixel0,this.pin2Dy1.yPixel0);this.doZoom(this.pin2Dx0.getXVal(),this.getScale().minY,
this.pin2Dx1.getXVal(),this.getScale().maxY,!1,!1,!1,!0,!1);return!0}if(c===this.pin2Dy0||c===this.pin2Dy1||c===this.pin2Dy01){b=this.fixY(b);c.setY(this.imageView.toSubspectrumIndex(b),b);if(c===this.pin2Dy01){c=b-u((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2)+1;b=this.pin2Dy0.yPixel0+c;a=this.pin2Dy1.yPixel0+c;if(b!=this.fixY(b)||a!=this.fixY(a))return!0;this.pin2Dy0.setY(this.imageView.toSubspectrumIndex(b),b);this.pin2Dy1.setY(this.imageView.toSubspectrumIndex(a),a)}if(!JSV.common.GraphSet.isGoodEvent(this.pin2Dy0,
this.pin2Dy1,!1))return this.reset2D(!1),!0;this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,this.pin2Dx1.xPixel1,this.pin2Dy1.yPixel1);return!0}return!1},"~N,~N,~B");c(c$,"clearIntegrals",function(){this.checkIntegral(NaN,0,!1)});c(c$,"clearMeasurements",function(){this.removeDialog(this.getFixedSelectedSpectrumIndex(),JSV.common.Annotation.AType.Measurements)});c$.createGraphSetsAndSetLinkMode=c(c$,"createGraphSetsAndSetLinkMode",function(a,b,c,f,g,e){for(var h=new JU.Lst,l=0;l<
c.size();l++){var k=c.get(l),m=e===JSV.common.PanelData.LinkMode.NONE?JSV.common.GraphSet.findCompatibleGraphSet(h,k):null;null==m&&h.addLast(m=new JSV.common.GraphSet(b.getPanelData()));m.addSpec(k)}JSV.common.GraphSet.setFractionalPositions(a,h,e);for(l=h.size();0<=--l;)h.get(l).initGraphSet(f,g),JU.Logger.info("JSVGraphSet "+(l+1)+" nSpectra = "+h.get(l).nSpectra);return h},"JSV.common.PanelData,JSV.api.JSVPanel,JU.Lst,~N,~N,JSV.common.PanelData.LinkMode");c(c$,"drawGraphSet",function(a,b,c,f,
g,e,h,l,k,m,n,q){this.zoomEnabled=this.pd.getBoolean(JSV.common.ScriptToken.ENABLEZOOM);this.height=g*this.pd.scalingFactor;this.width=f*this.pd.scalingFactor;this.left=e*this.pd.scalingFactor;this.right=h*this.pd.scalingFactor;this.top=l*this.pd.scalingFactor;this.bottom=k*this.pd.scalingFactor;this.$haveSelectedSpectrum=!1;this.selectedSpectrumMeasurements=this.selectedSpectrumIntegrals=null;if(!this.pd.isPrinting&&null!=this.widgets)for(f=0;f<this.widgets.length;f++)null!=this.widgets[f]&&(this.widgets[f].isVisible=
!1);for(f=0;f<this.nSplit;f++)this.setPositionForFrame(f),this.drawAll(a,b,c,f,m||1<this.nSplit,n,q);this.setPositionForFrame(1<this.nSplit?this.pd.currentSplitPoint:0)},"~O,~O,~O,~N,~N,~N,~N,~N,~N,~B,~B,~B");c(c$,"escapeKeyPressed",function(a){null!=this.zoomBox1D&&(this.zoomBox1D.xPixel0=this.zoomBox1D.xPixel1=0);null!=this.zoomBox2D&&(this.zoomBox2D.xPixel0=this.zoomBox2D.xPixel1=0);this.inPlotMove&&(null!=this.pendingMeasurement?this.pendingMeasurement=null:(this.pendingMeasurement=this.pd.thisWidget=
null,null!=this.selectedSpectrumMeasurements&&null!=this.selectedMeasurement&&(a?this.selectedSpectrumMeasurements.clear(this.getScale().minXOnScale,this.getScale().maxXOnScale):this.selectedSpectrumMeasurements.removeObj(this.selectedMeasurement),this.selectedMeasurement=null,this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)),null!=this.selectedSpectrumIntegrals&&null!=this.selectedIntegral&&(a?this.selectedSpectrumIntegrals.clear(this.getScale().minXOnScale,this.getScale().maxXOnScale):
this.selectedSpectrumIntegrals.removeObj(this.selectedIntegral),this.selectedIntegral=null,this.updateDialog(JSV.common.Annotation.AType.Integration,-1))))},"~B");c$.findGraphSet=c(c$,"findGraphSet",function(a,b,c){for(var f=a.size();0<=--f;)if(a.get(f).hasPoint(b,c))return a.get(f);return null},"JU.Lst,~N,~N");c(c$,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.spectra.size()&&null==(b=this.spectra.get(c).findMatchingPeakInfo(a));c++);return b},"JSV.common.PeakInfo");c(c$,"getCurrentSpectrumIndex",
function(){return 1==this.nSpectra?0:this.iSpectrumSelected});c(c$,"getSelectedIntegral",function(){return this.selectedIntegral});c(c$,"getShowAnnotation",function(a,b){var c=this.getDialog(a,b);return null!=c&&c.getState()},"JSV.common.Annotation.AType,~N");c(c$,"hasFileLoaded",function(a){for(var b=this.spectra.size();0<=--b;)if(this.spectra.get(b).getFilePathForwardSlash().equals(a))return!0;return!1},"~S");c(c$,"haveSelectedSpectrum",function(){return this.$haveSelectedSpectrum});c(c$,"mouseClickedEvent",
function(a,b,c,f){this.selectedIntegral=this.selectedMeasurement=null;var g=this.nextClickForSetPeak;this.nextClickForSetPeak=null;if(!this.checkArrowUpDownClick(a,b)&&!this.checkArrowLeftRightClick(a,b))if(this.lastClickX=NaN,this.lastPixelX=2147483647,this.isSplitWidget(a,b))this.splitStack(1==this.nSplit);else if(this.isCloserWidget(a,b))this.pd.closeSpectrum();else{var e=this.getPinSelected(a,b);if(null!=e)this.setWidgetValueByUser(e);else if(e=this.is2dClick(a,b),2==c&&(-1==this.iSpectrumClicked&&
0<=this.iPreviousSpectrumClicked)&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),!e&&f)this.setSpectrumClicked(this.iPreviousSpectrumClicked),null!=this.pendingMeasurement?this.processPendingMeasurement(a,b,-3):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,b,3);else if(this.lastXMax=NaN,2==c)e?(this.sticky2Dcursor&&this.addAnnotation(this.getAnnotation(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b),this.pd.coordStr,!1,!0,5,5),!0),this.sticky2Dcursor=!0,this.set2DCrossHairs(a,
b)):this.isInTopBar(a,b)?this.doZoom(this.toX0(this.xPixel0),0,this.toX0(this.xPixel1),0,!0,!1,!1,!0,!0):this.isInRightBar(a,b)?this.doZoom(this.getScale().minXOnScale,this.viewList.get(0).getScale().minYOnScale,this.getScale().maxXOnScale,this.viewList.get(0).getScale().maxYOnScale,!0,!0,!1,!1,!1):this.isInTopBar2D(a,b)?this.reset2D(!0):this.isInRightBar2D(a,b)?this.reset2D(!1):null!=this.pendingMeasurement?this.processPendingMeasurement(a,b,-2):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,
b,2);else if(e){if(null!=this.annotations&&(f=(new JSV.common.Coordinate).set(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b)),f=this.findAnnotation2D(f),null!=f&&this.setAnnotationText(f)))return;1==c&&(this.sticky2Dcursor=!1);this.set2DCrossHairs(a,b)}else{if(this.isInPlotRegion(a,b)){if(null!=this.selectedSpectrumIntegrals&&this.checkIntegralNormalizationClick(a,b))return;if(null!=this.pendingMeasurement){this.processPendingMeasurement(a,b,1);return}this.setCoordClicked(a,this.toX(a),
this.toY(b));this.updateDialog(JSV.common.Annotation.AType.PeakList,-1);if(null!=g){this.nextClickForSetPeak=g;this.shiftSpectrum(4,NaN,NaN);this.nextClickForSetPeak=null;return}}else this.setCoordClicked(0,NaN,0);this.pd.notifyPeakPickedListeners(null)}}},"~N,~N,~N,~B");c(c$,"is2dClick",function(a,b){return null!=this.imageView&&a==this.imageView.fixX(a)&&b==this.fixY(b)},"~N,~N");c(c$,"updateDialog",function(a,b){var c=this.getDialog(a,b);if(null!=c&&this.isVisible(c)){var f=this.toX(this.xPixel1)-
this.toX(this.xPixel0),g=this.getSpectrum().isInverted()?this.yPixel1-this.pd.mouseY:this.pd.mouseY-this.yPixel0;c.update(this.pd.coordClicked,f,g)}},"JSV.common.Annotation.AType,~N");c(c$,"isVisible",function(a){return null!=a&&a.isDialog()&&a.isVisible()},"JSV.api.AnnotationData");c(c$,"mousePressedEvent",function(a,b){this.checkWidgetEvent(a,b,!0)},"~N,~N,~N");c(c$,"mouseReleasedEvent",function(a,b){if(null!=this.pendingMeasurement)2>Math.abs(this.toPixelX(this.pendingMeasurement.getXVal())-a)&&
(this.pendingMeasurement=null),this.processPendingMeasurement(a,b,-2),this.setToolTipForPixels(a,b);else if(0!=this.pd.integralShiftMode)this.pd.integralShiftMode=0,this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0;else{0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo);var c=this.pd.thisWidget;if(this.pd.isIntegralDrag)JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,null,!0)&&this.checkIntegral(this.toX(this.zoomBox1D.xPixel0),this.toX(this.zoomBox1D.xPixel1),!0),this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0=
0,this.pendingIntegral=null,this.pd.isIntegralDrag=!1;else if(c===this.zoomBox2D)JSV.common.GraphSet.isGoodEvent(this.zoomBox2D,null,!0)&&(this.imageView.setZoom(this.zoomBox2D.xPixel0,this.zoomBox2D.yPixel0,this.zoomBox2D.xPixel1,this.zoomBox2D.yPixel1),this.zoomBox2D.xPixel1=this.zoomBox2D.xPixel0,this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!0,!0));else if(c===this.zoomBox1D){if(JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,
null,!0)){var c=this.zoomBox1D.xPixel1,f=this.pd.shiftPressed;this.doZoom(this.toX(this.zoomBox1D.xPixel0),f?this.toY(this.zoomBox1D.yPixel0):0,this.toX(c),f?this.toY(this.zoomBox1D.yPixel1):0,!0,f,!0,!0,!0);this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0}}else(c===this.pin1Dx0||c===this.pin1Dx1||c===this.cur2Dx0||c===this.cur2Dx1)&&this.addCurrentZoom()}},"~N,~N");c(c$,"mouseMovedEvent",function(a,b){if(1<this.nSpectra){var c=this.getSplitPoint(b);this.setPositionForFrame(c);this.setSpectrumMovedTo(1<
this.nSplit?c:this.iSpectrumSelected);0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo)}this.inPlotMove=this.isInPlotRegion(a,b);this.setXPixelMovedTo(1.7976931348623157E308,1.7976931348623157E308,this.inPlotMove?a:-1,-1);this.inPlotMove&&(this.xValueMovedTo=this.toX(this.xPixelMovedTo),this.yValueMovedTo=this.getSpectrum().getYValueAt(this.xValueMovedTo));if(0!=this.pd.integralShiftMode){var c=this.getDialog(JSV.common.Annotation.AType.Integration,-1),f=c.getData().getXYCoords(),f=f[0<
this.pd.integralShiftMode?f.length-1:0].getYVal();c.getData().shiftY(this.pd.integralShiftMode,this.toPixelYint(f)+b-(0<this.pd.integralShiftMode?this.yPixelPlot1:this.yPixelPlot0),this.yPixel0,this.yPixels)}else this.pd.isIntegralDrag||(null!=this.pendingMeasurement?(this.processPendingMeasurement(a,b,0),this.setToolTipForPixels(a,b)):(this.selectedMeasurement=this.inPlotMove&&null!=this.selectedSpectrumMeasurements?this.findMeasurement(this.selectedSpectrumMeasurements,a,b,0):null,this.selectedIntegral=
null,this.inPlotMove&&(null!=this.selectedSpectrumIntegrals&&null==this.selectedMeasurement)&&(this.selectedIntegral=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,0),null==this.selectedIntegral&&(this.selectedIntegral=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5))),this.setToolTipForPixels(a,b),null==this.imageView?(this.piMouseOver=null,c=1<this.nSplit?this.iSpectrumMovedTo:this.iSpectrumClicked,!this.isDrawNoSpectra()&&0<=c&&(c=this.spectra.get(c),null!=c.getPeakList()&&
(this.coordTemp.setXVal(this.toX(a)),this.coordTemp.setYVal(this.toY(b)),this.piMouseOver=c.findPeakByCoord(a,this.coordTemp)))):!this.pd.display1D&&this.sticky2Dcursor&&this.set2DCrossHairs(a,b)))},"~N,~N");c(c$,"nextView",function(){this.currentZoomIndex+1<this.viewList.size()&&this.setZoomTo(this.currentZoomIndex+1)});c(c$,"previousView",function(){0<this.currentZoomIndex&&this.setZoomTo(this.currentZoomIndex-1)});c(c$,"resetView",function(){this.setZoomTo(0)});c(c$,"removeAllHighlights",function(){this.removeAllHighlights(null)});
c(c$,"removeHighlight",function(a){this.highlights.removeItemAt(a)},"~N");c(c$,"removeHighlight",function(a,b){for(var c=this.highlights.size();0<=--c;){var f=this.highlights.get(c);f.x1==a&&f.x2==b&&this.highlights.removeItemAt(c)}},"~N,~N");c(c$,"scaleYBy",function(a){if(null!=this.imageView||this.zoomEnabled)this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,a),null!=this.imageView&&(this.update2dImage(!1),this.resetPinsFromView()),this.pd.refresh()},"~N");c(c$,"selectSpectrum",
function(a,b,c){for(var f=!1,g=this.spectra.size();0<=--g;)if((null==a||this.getSpectrumAt(g).getFilePathForwardSlash().equals(a))&&this.getSpectrumAt(g).matchesPeakTypeModel(b,c))this.setSpectrumSelected(g),1<this.nSplit&&this.splitStack(!0),f=!0;1<this.nSpectra&&(!f&&0<=this.iSpectrumSelected&&!this.pd.isCurrentGraphSet(this))&&this.setSpectrumSelected(-2147483648);return f},"~S,~S,~S");c(c$,"selectPeakByFileIndex",function(a,b,c){for(var f,g=this.spectra.size();0<=--g;)if(null!=(f=this.getSpectrumAt(g).selectPeakByFileIndex(a,
b,c)))return f;return null},"~S,~S,~S");c(c$,"setSelected",function(a){0>a?(this.bsSelected.clearAll(),this.setSpectrumClicked(-1)):(this.bsSelected.set(a),this.setSpectrumClicked(1==this.bsSelected.cardinality()?a:-1),1<this.nSplit&&0<=a&&(this.pd.currentSplitPoint=a))},"~N");c(c$,"setSelectedIntegral",function(a){var b=this.selectedIntegral.getSpectrum();this.getIntegrationGraph(this.getSpectrumIndex(b)).setSelectedIntegral(this.selectedIntegral,a)},"~N");c(c$,"setShowAnnotation",function(a,b){var c=
this.getDialog(a,-1);if(null==c)null!=b&&b!==Boolean.TRUE||(a===JSV.common.Annotation.AType.PeakList||a===JSV.common.Annotation.AType.Integration||a===JSV.common.Annotation.AType.Measurements)&&this.pd.showDialog(a);else if(null==b)c.isDialog()?c.setVisible(!c.isVisible()):this.pd.showDialog(a);else{var f=b.booleanValue();f&&c.setState(f);(f||c.isDialog())&&this.pd.showDialog(a);!f&&c.isDialog()&&c.setVisible(!1)}},"JSV.common.Annotation.AType,Boolean");c(c$,"checkIntegralParams",function(a,b){if(!this.getSpectrum().canIntegrate()||
this.reversePlot)return!1;var c=this.getFixedSelectedSpectrumIndex(),f=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==b)return!0;switch(JSV.common.IntegralData.IntMode.getMode(b.toUpperCase())){case JSV.common.IntegralData.IntMode.NA:return!1;case JSV.common.IntegralData.IntMode.CLEAR:this.integrate(c,null);this.integrate(c,a);break;case JSV.common.IntegralData.IntMode.ON:null==f?this.integrate(c,a):f.setState(!0);break;case JSV.common.IntegralData.IntMode.OFF:null!=f&&f.setState(!1);
break;case JSV.common.IntegralData.IntMode.TOGGLE:null==f?this.integrate(c,a):f.setState(!f.getState());break;case JSV.common.IntegralData.IntMode.AUTO:null==f&&(this.checkIntegralParams(a,"ON"),f=this.getDialog(JSV.common.Annotation.AType.Integration,-1));null!=f&&f.getData().autoIntegrate();break;case JSV.common.IntegralData.IntMode.LIST:this.pd.showDialog(JSV.common.Annotation.AType.Integration);break;case JSV.common.IntegralData.IntMode.MARK:null==f&&(this.checkIntegralParams(a,"ON"),f=this.getDialog(JSV.common.Annotation.AType.Integration,
-1));null!=f&&f.getData().addMarks(b.substring(4).trim());break;case JSV.common.IntegralData.IntMode.MIN:if(null!=f)try{var g=Double.parseDouble(JSV.common.ScriptToken.getTokens(b).get(1));f.getData().setMinimumIntegral(g)}catch(e){if(!D(e,Exception))throw e;}break;case JSV.common.IntegralData.IntMode.UPDATE:null!=f&&f.getData().update(a)}this.updateDialog(JSV.common.Annotation.AType.Integration,-1);return!0},"JSV.common.Parameters,~S");c(c$,"setSpectrum",function(a,b){b&&1<this.nSplit?1<this.nSplit&&
this.setSpectrumClicked(a):(this.setSpectrumClicked(a),this.showAllStacked=this.stackSelected=!1);0<=a&&this.dialogsToFront(this.getSpectrum())},"~N,~B");c(c$,"setSpectrumJDX",function(a){var b=this.getFixedSelectedSpectrumIndex();this.spectra.removeItemAt(b);this.spectra.add(b,a);this.pendingMeasurement=null;this.clearViews();this.viewData.newSpectrum(this.spectra)},"JSV.common.Spectrum");c(c$,"setZoom",function(a,b,c,f){this.setZoomTo(0);0==a&&0==c&&0==b&&0==f?(this.newPins(),this.imageView=null,
this.getScale(),this.getScale()):this.doZoom(a,b,c,f,!0,b!=f,!1,!0,!0)},"~N,~N,~N,~N");c(c$,"shiftSpectrum",function(a,b,c){var f=this.getSpectrum();if(!f.isNMR()||!f.is1D())return!1;var g=null,g=0;if(1.7976931348623157E308==c)g=-f.addSpecShift(0);else switch(a){case 3:g=c;break;case 1:case 2:this.nextClickMode=a;if(Double.isNaN(b))return g=this.pd.getInput("Click on "+(1==a?"or beside a peak to set its chemical shift":"the spectrum set the chemical shift at that point")+(-2147483648==c?"":" to "+
c)+".","Set Reference "+(1==a?"for Peak":"at Point"),"OK"),this.nextClickForSetPeak="OK".equals(g)?Double.$valueOf(c):null,!1;this.nextClickForSetPeak=null;case 4:null!=this.nextClickForSetPeak&&(c=this.nextClickForSetPeak.doubleValue(),this.nextClickForSetPeak=null);Double.isNaN(b)&&(b=this.lastClickX);1==this.nextClickMode&&(b=this.getNearestPeak(f,b,this.toY(this.pd.mouseY)));if(Double.isNaN(c))try{var e=this.pd.getInput("New chemical shift (set blank to reset)","Set Reference",JU.DF.formatDecimalDbl(b,
this.getScale().precision[0])).trim();c=0==e.length?b-f.addSpecShift(0):Double.parseDouble(e)}catch(h){if(D(h,Exception))return!1;throw h;}g=c-b}if(0==g)return!1;f.addSpecShift(g);if(null!=this.annotations)for(a=this.annotations.size();0<=--a;)this.annotations.get(a).spec===f&&this.annotations.get(a).addSpecShift(g);if(null!=this.dialogs){var l;for(a=this.dialogs.entrySet().iterator();a.hasNext()&&((l=a.next())||1);)l.getValue().getSpectrum()===f&&l.getValue().setSpecShift(g)}this.getScale().addSpecShift(g);
Double.isNaN(this.lastClickX)||(this.lastClickX+=g);this.updateDialogs();this.doZoom(0,this.getScale().minYOnScale,0,this.getScale().maxYOnScale,!0,!0,!1,!0,!1);this.pd.setTaintedAll();this.pd.repaint();return!0},"~N,~N,~N");c(c$,"toPeak",function(a){a*=this.drawXAxisLeftToRight?1:-1;Double.isNaN(this.lastClickX)&&(this.lastClickX=this.lastPixelX=0);var b=this.getSpectrum(),c=this.setCoordClicked(this.lastPixelX,this.lastClickX,0);a=b.setNextPeak(c,a);0>a||(a=b.getPeakList().get(a),b.setSelectedPeak(a),
this.setCoordClicked(a.getXPixel(),a.getX(),0),this.pd.notifyPeakPickedListeners(new JSV.common.PeakPickEvent(this.jsvp,this.pd.coordClicked,a)))},"~N");c(c$,"scaleSelectedBy",function(a){for(var b=this.bsSelected.nextSetBit(0);0<=b;b=this.bsSelected.nextSetBit(b+1))this.viewData.scaleSpectrum(b,a)},"~N");h(c$,"toString",function(){return"gs: "+this.nSpectra+" "+this.spectra+" "+this.spectra.get(0).getFilePath()});c(c$,"setXPointer",function(a,b){null!=a&&this.setSpectrumClicked(this.getSpectrumIndex(a));
this.xValueMovedTo=this.lastClickX=b;this.lastPixelX=this.toPixelX(b);this.setXPixelMovedTo(b,1.7976931348623157E308,0,0);this.yValueMovedTo=NaN},"JSV.common.Spectrum,~N");c(c$,"setXPointer2",function(a,b){null!=a&&this.setSpectrumClicked(this.getSpectrumIndex(a));this.setXPixelMovedTo(1.7976931348623157E308,b,0,0)},"JSV.common.Spectrum,~N");c(c$,"hasCurrentMeasurement",function(a){return null!=(a===JSV.common.Annotation.AType.Integration?this.selectedSpectrumIntegrals:this.selectedSpectrumMeasurements)},
"JSV.common.Annotation.AType");c(c$,"getDialog",function(a,b){-1==b&&(b=this.getCurrentSpectrumIndex());return null==this.dialogs||0>b?null:this.dialogs.get(a+"_"+b)},"JSV.common.Annotation.AType,~N");c(c$,"removeDialog",function(a,b){null!=this.dialogs&&0<=a&&this.dialogs.remove(b+"_"+a)},"~N,JSV.common.Annotation.AType");c(c$,"addDialog",function(a,b,c){null==this.dialogs&&(this.dialogs=new java.util.Hashtable);a=b+"_"+a;c.setGraphSetKey(a);this.dialogs.put(a,c);return c},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");
c(c$,"removeDialog",function(a){var b=a.getGraphSetKey();this.dialogs.remove(b);a=a.getData();null!=a&&this.dialogs.put(b,a)},"JSV.dialog.JSVDialog");c(c$,"getPeakListing",function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;var f=this.getDialog(JSV.common.Annotation.AType.PeakList,-1);if(null==f){if(!c)return null;this.addDialog(a,JSV.common.Annotation.AType.PeakList,f=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,this.getSpectrum()))}f.getData().setPeakList(b,
-2147483648,this.viewData.getScale());f.isDialog()&&f.setFields();return f.getData()},"~N,JSV.common.Parameters,~B");c(c$,"setPeakListing",function(a){var b=this.getDialog(JSV.common.Annotation.AType.PeakList,-1),c=null!=b&&b.isDialog()?b:null;(null==a?null==c||!c.isVisible():a.booleanValue())?this.pd.showDialog(JSV.common.Annotation.AType.PeakList):b.isDialog()&&b.setVisible(!1)},"Boolean");c(c$,"haveIntegralDisplayed",function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null!=
a&&a.getState()},"~N");c(c$,"getIntegrationGraph",function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null==a?null:a.getData()},"~N");c(c$,"setIntegrationRatios",function(a){var b=this.getFixedSelectedSpectrumIndex();null==this.aIntegrationRatios&&(this.aIntegrationRatios=Array(this.nSpectra));this.aIntegrationRatios[b]=JSV.common.IntegralData.getIntegrationRatiosFromString(this.getSpectrum(),a)},"~S");c(c$,"getIntegrationRatios",function(a){return null==this.aIntegrationRatios?
null:this.aIntegrationRatios[a]},"~N");c(c$,"integrate",function(a,b){var c=this.getSpectrumAt(a);if(null==b||!c.canIntegrate())return this.removeDialog(a,JSV.common.Annotation.AType.Integration),!1;this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(c,b));return!0},"~N,JSV.common.Parameters");c(c$,"getIntegration",function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;var f=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==f){if(!c)return null;
f=this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(this.getSpectrum(),b))}return f.getData()},"~N,JSV.common.Parameters,~B");c(c$,"getMeasurementInfo",function(a,b){var c;switch(a){case JSV.common.Annotation.AType.PeakList:c=this.getPeakListing(b,null,!1);break;case JSV.common.Annotation.AType.Integration:c=this.getIntegration(b,null,!1);break;default:return null}if(null==c)return null;var f=new java.util.Hashtable;c.getInfo(f);return f},"JSV.common.Annotation.AType,~N");
c(c$,"getInfo",function(a,b){var c=new java.util.Hashtable;if("".equals(a))c.put("KEYS","viewInfo spectra");else if("viewInfo".equalsIgnoreCase(a))return this.getScale().getInfo(c);var f=new JU.Lst;c.put("spectra",f);for(var g=0;g<this.nSpectra;g++)if(!(0<=b&&g!=b)){var e=this.spectra.get(g),h=e.getInfo(a);if(0<=b&&null!=a&&(2==h.size()||a.equalsIgnoreCase("id")))return 2==h.size()&&h.remove("id"),h;JSV.common.Parameters.putInfo(a,h,"type",e.getDataType());JSV.common.Parameters.putInfo(a,h,"titleLabel",
e.getTitleLabel());JSV.common.Parameters.putInfo(a,h,"filePath",e.getFilePath().$replace("\\","/"));JSV.common.Parameters.putInfo(a,h,"PeakList",JSV.common.Parameters.isMatch(a,"PeakList")?this.getMeasurementInfo(JSV.common.Annotation.AType.PeakList,g):null);JSV.common.Parameters.putInfo(a,h,"Integration",JSV.common.Parameters.isMatch(a,"Integration")?this.getMeasurementInfo(JSV.common.Annotation.AType.Integration,g):null);if(0<=b)return h;f.addLast(h)}return c},"~S,~N");c(c$,"getTitle",function(a){return 1==
this.nSpectra||0<=this.iSpectrumSelected&&(!a||1==this.nSplit)?this.getSpectrum().getTitle():null},"~B");c(c$,"getCurrentView",function(){this.setScale(this.getFixedSelectedSpectrumIndex());return this.viewData.getScale()});c(c$,"set2DXY",function(a,b,c){var f;null!=this.gs2dLinkedX&&(f=this.toPixelX(a),f!=this.fixX(f)&&(f=-2147483648,a=1.7976931348623157E308),this.cur1D2x1.setX(a,f));null!=this.gs2dLinkedY&&(f=this.toPixelX(b),f!=this.fixX(f)&&(f=-2147483648,b=1.7976931348623157E308),this.cur1D2x2.setX(b,
f));this.cur1D2Locked=c},"~N,~N,~B");c(c$,"dialogsToFront",function(a){if(null!=this.dialogs){null==a&&(a=this.getSpectrum());for(var b,c=this.dialogs.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var f=b.getValue();this.isVisible(f)&&(null==a?f.setVisible(!0):f.setFocus(f.getSpectrum()===a))}}},"JSV.common.Spectrum");c(c$,"setPlotColors",function(a){var b=a;if(b.length>this.nSpectra)a=Array(this.nSpectra),Zystem.arraycopy(b,0,a,0,this.nSpectra),b=a;else if(this.nSpectra>b.length){a=Array(this.nSpectra);
var c=this.nSpectra-b.length;Zystem.arraycopy(b,0,a,0,b.length);for(var f=0,b=b.length;f<c;f++,b++)a[b]=this.generateRandomColor();b=a}this.plotColors=b},"~O");c(c$,"disposeImage",function(){null!=this.image2D&&this.image2D.parentNode.removeChild(this.image2D);this.plotColors=this.highlights=this.pd=this.jsvp=this.image2D=null});c(c$,"generateRandomColor",function(){for(;;){var a=u(255*Math.random()),b=u(255*Math.random()),c=u(255*Math.random()),a=this.g2d.getColor3(a,b,c);if(0!=a.getRGB())return a}});
c(c$,"setPlotColor0",function(a){this.plotColors[0]=a},"~O");c(c$,"getPlotColor",function(a){return a>=this.plotColors.length?null:this.plotColors[a]},"~N");c(c$,"setColorFromToken",function(a,b){null!=b&&this.g2d.setGraphicsColor(a,b===JSV.common.ScriptToken.PLOTCOLOR?this.plotColors[0]:this.pd.getColor(b))},"~O,JSV.common.ScriptToken");c(c$,"setPlotColor",function(a,b){var c;switch(b){case -3:c=JSV.common.GraphSet.veryLightGrey;break;case -2:c=this.pd.BLACK;break;case -1:c=this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR);
break;default:c=this.plotColors[b]}this.g2d.setGraphicsColor(a,c)},"~O,~N");c(c$,"draw2DImage",function(){null!=this.imageView&&this.g2d.drawGrayScaleImage(this.gMain,this.image2D,this.imageView.xPixel0,this.imageView.yPixel0,this.imageView.xPixel0+this.imageView.xPixels-1,this.imageView.yPixel0+this.imageView.yPixels-1,this.imageView.xView1,this.imageView.yView1,this.imageView.xView2,this.imageView.yView2)});c(c$,"get2DImage",function(){this.imageView=new JSV.common.ImageView;this.imageView.set(this.viewList.get(0).getScale());
if(!this.update2dImage(!0))return!1;this.imageView.resetZoom();return this.sticky2Dcursor=!0},"JSV.common.Spectrum");c(c$,"update2dImage",function(a){this.imageView.set(this.viewData.getScale());var b=this.getSpectrumAt(0),c=this.imageView.get2dBuffer(b,!a);if(null==c)return this.imageView=this.image2D=null,!1;a&&(c=this.imageView.adjustView(b,this.viewData),this.imageView.resetView());this.image2D=this.g2d.newGrayScaleImage(this.gMain,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,
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x(["java.lang.Enum","JSV.common.MeasurementData","$.IntegralComparator"],"JSV.common.IntegralData","java.lang.Double java.util.Collections $.StringTokenizer JU.AU $.BS $.DF $.Lst $.PT JSV.common.Annotation $.Coordinate $.Integral $.ScriptToken".split(" "),function(){c$=w(function(){this.intRange=this.percentOffset=this.percentMinY=0;this.normalizationFactor=1;this.integralTotal=this.offset=this.percentRange=0;this.haveRegions=!1;this.xyCoords=null;s(this,arguments)},JSV.common,"IntegralData",JSV.common.MeasurementData);
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c$.cacheGet=c(c$,"cacheGet",function(a){var b=JSV.common.JSVFileManager.htCorrelationCache.get(a);JU.Logger.debugging&&JU.Logger.info("JSVFileManager cacheGet "+b+" for "+a);return b},"~S");c$.getSimulationReader=c(c$,"getSimulationReader",function(a){var b=JSV.common.JSVFileManager.cacheGet(a);null==b&&JSV.common.JSVFileManager.cachePut(a,b=JSV.common.JSVFileManager.getNMRSimulationJCampDX(a.substring(18)));return JSV.common.JSVFileManager.getBufferedReaderForStringOrBytes(b)},"~S");c$.isAB=c(c$,
"isAB",function(a){return JU.AU.isAB(a)},"~O");c$.isZipFile=c(c$,"isZipFile",function(a){try{var b=P(4,0);a.mark(5);var c=a.read(b,0,4);a.reset();return 4==c&&80==b[0]&&75==b[1]&&3==b[2]&&4==b[3]}catch(f){if(D(f,Exception))throw new JSV.exception.JSVException(f.toString());throw f;}},"java.io.InputStream");c$.isGzip=c(c$,"isGzip",function(a){try{var b=P(4,0);a.mark(5);var c=a.read(b,0,4);a.reset();return 4==c&&31==b[0]&&139==b[1]}catch(f){if(D(f,Exception))throw new JSV.exception.JSVException(f.toString());
throw f;}},"java.io.InputStream");c$.getStreamAsBytes=c(c$,"getStreamAsBytes",function(a,b){try{for(var c=P(1024,0),f=null==b?P(4096,0):null,g=0,e=0;0<(g=a.read(c,0,1024));)e+=g,null==b?(e>=f.length&&(f=JU.AU.ensureLengthByte(f,2*e)),Zystem.arraycopy(c,0,f,e-g,g)):b.write(c,0,g);a.close();return null==b?JU.AU.arrayCopyByte(f,e):e+" bytes"}catch(h){if(D(h,Exception))throw new JSV.exception.JSVException(h.toString());throw h;}},"java.io.BufferedInputStream,JU.OC");c$.postByteArray=c(c$,"postByteArray",
function(a,b){var c=null;try{c=JSV.common.JSVFileManager.getInputStream(a,!1,b)}catch(f){if(D(f,Exception))c=f.toString();else throw f;}if(t(c,String))return c;try{c=JSV.common.JSVFileManager.getStreamAsBytes(c,null)}catch(g){if(D(g,JSV.exception.JSVException))try{c.close()}catch(e){if(!D(e,Exception))throw e;}else throw g;}return null==c?"":JSV.common.JSVFileManager.fixUTF(c)},"~S,~A");c$.getUTFEncoding=c(c$,"getUTFEncoding",function(a){return 3<=a.length&&239==a[0]&&187==a[1]&&191==a[2]?JU.Encoding.UTF8:
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c.substring(1)}return c}catch(f){if(D(f,java.io.IOException))JU.Logger.error("fixUTF error "+f);else throw f;}return String.instantialize(a)},"~A");c$.getInputStream=c(c$,"getInputStream",function(a,b,c){var f=JSV.common.JSVFileManager.isURL(a),g=null!=JSV.common.JSVFileManager.appletDocumentBase,e=null,e=null,h;if(f&&0<=(h=a.indexOf("?POST?")))e=a.substring(h+6),a=a.substring(0,h);if(g||f){var l;try{l=new java.net.URL(JSV.common.JSVFileManager.appletDocumentBase,a,null)}catch(k){if(D(k,Exception))throw new JSV.exception.JSVException("Cannot read "+
a);throw k;}JU.Logger.info("JSVFileManager opening URL "+l+(null==e?"":" with POST of "+e.length+" bytes"));e=JSV.common.JSVFileManager.viewer.apiPlatform.getURLContents(l,c,e,!1)}else b&&JU.Logger.info("JSVFileManager opening file "+a),e=JSV.common.JSVFileManager.viewer.apiPlatform.getBufferedFileInputStream(a);if(t(e,String))throw new JSV.exception.JSVException(e);return e},"~S,~B,~A");c$.getNMRSimulationJCampDX=c(c$,"getNMRSimulationJCampDX",function(a){var b=0,c=null,f=JSV.common.JSVFileManager.getSimulationType(a);
a.startsWith(f)&&(a=a.substring(f.length+1));var g=a.startsWith("MOL=");g&&(a=a.substring(4),b=a.indexOf("/n__Jmol"),0<b&&(a=a.substring(0,b)+JU.PT.rep(a.substring(b),"/n","\n")),c=a=JU.PT.rep(a,"\\n","\n"));var e=""+JSV.common.JSVFileManager.getSimulationHash(a,f);JU.Logger.debugging&&JU.Logger.info("JSVFileManager type="+f+" key="+e+" name="+a);var h=JSV.common.JSVFileManager.cacheGet(e);if(null!=h)return h;var l=g?null:JU.PT.rep(JSV.common.JSVFileManager.nciResolver,"%FILE",JU.PT.escapeUrl(a));
if(!g&&null==(c=JSV.common.JSVFileManager.getFileAsString(l))||0<=c.indexOf("<html"))return JU.Logger.error("no MOL data returned by NCI"),null;var h=f.equals("C13"),k=JSV.common.JSVFileManager.getFileAsString((h?JSV.common.JSVFileManager.nmrdbServerC13:JSV.common.JSVFileManager.nmrdbServerH1)+c),b=(new JU.JSJSONParser).parseMap(k,!0);JSV.common.JSVFileManager.cachePut("json",k);h&&(b=b.get("result"));k=b.get("molfile");null==k?(Zystem.out.println("JSVFileManager: no MOL file returned from EPFL"),
k=c):Zystem.out.println("JSVFileManager: MOL file hash="+k.hashCode());k=JSV.common.JSVFileManager.getAtomMap(k,c);JSV.common.JSVFileManager.cachePut("mol",c);g||Jmol.Cache.put("http://SIMULATION/"+f+"/"+a+"#molfile",c.getBytes());var m="<Signals src="+JU.PT.esc(JU.PT.rep(h?JSV.common.JSVFileManager.nmrdbServerC13:JSV.common.JSVFileManager.nmrdbServerH1,"?POST?molfile=",""))+">\n";if(h){for(var b=b.get("spectrum13C"),h=b.get("jcamp").get("value"),n=b.get("predCSNuc"),q=new JU.SB,p=n.size();0<=--p;)b=
n.get(p),q.append("<Signal "),JSV.common.JSVFileManager.setAttr(q,"type","nucleus",b),null==k?JSV.common.JSVFileManager.setAttr(q,"atoms","assignment",b):q.append('atoms="').appendI(k[JU.PT.parseInt(b.get("assignment"))]).append('" '),JSV.common.JSVFileManager.setAttr(q,"multiplicity","multiplicity",b),b=b.get("integralData"),JSV.common.JSVFileManager.setAttr(q,"xMin","from",b),JSV.common.JSVFileManager.setAttr(q,"xMax","to",b),JSV.common.JSVFileManager.setAttr(q,"integral","value",b),q.append("></Signal>\n");
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f:a)+"\n"+h.substring(h.indexOf("\n##")+1);b=c.indexOf("\n");b=c.indexOf("\n",b+1);0<b&&b==c.indexOf("\n \n")&&(c=c.substring(0,b+1)+"Created "+JSV.common.JSVFileManager.viewer.apiPlatform.getDateFormat("8824")+" by JSpecView "+JSV.common.JSVersion.VERSION+c.substring(b+1));b=h.indexOf("##.");a=JSV.common.JSVFileManager.getAbbreviatedSimulationName(a,f,!1);f=a.indexOf("id='");g&&0<f&&(a=a.substring(f+4,(a+"'").indexOf("'",f+4)));h=h.substring(0,b)+"##$MODELS=\n<Models>\n<ModelData id="+JU.PT.esc(a)+
' type="MOL" src='+JU.PT.esc(l)+">\n"+c+"</ModelData>\n</Models>\n##$SIGNALS=\n"+m+"\n"+h.substring(b);JSV.common.JSVFileManager.cachePut("jcamp",h);JSV.common.JSVFileManager.cachePut(e,h);return h},"~S");c$.getAtomMap=c(c$,"getAtomMap",function(a,b){var c=JSV.common.JSVFileManager.getCoord(a),f=JSV.common.JSVFileManager.getCoord(b),g=c.length;if(g!=f.length)return null;var e=B(g,0),h=new JU.BS;h.setBits(0,g);for(var l=!1,k=0;k<g;k++)for(var m=c[k],n=h.nextSetBit(0);0<=n;n=h.nextSetBit(n+1))if(0.1>
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function(a,b,c){var f=null;try{if(null==(f=a.getClass().getResource(b)))c[0]="Couldn't find file: "+b}catch(g){if(D(g,Exception))c[0]="Exception "+g+" in getResource "+b;else throw g;}return f},"~O,~S,~A");c$.getResourceString=c(c$,"getResourceString",function(a,b,c){a=JSV.common.JSVFileManager.getResource(a,b,c);if(null==a)return c[0]="Error loading resource "+b,null;if(t(a,String))return JSV.common.JSVFileManager.getFileAsString(a);b=new JU.SB;try{for(var f=new java.io.BufferedReader(new java.io.InputStreamReader(a.getContent(),
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if(JSV.common.JSVFileManager.isURL(a))try{if(a.startsWith("http://SIMULATION/"))return JSV.common.JSVFileManager.getAbbrSimulationFileName(a);var b=(new java.net.URL(ba("java.net.URL"),a,null)).getFile();return b.substring(b.lastIndexOf("/")+1)}catch(c){if(D(c,java.io.IOException))return null;throw c;}return JSV.common.JSVFileManager.viewer.apiPlatform.newFile(a).getName()},"~S");c$.setDocumentBase=c(c$,"setDocumentBase",function(a,b){JSV.common.JSVFileManager.viewer=a;JSV.common.JSVFileManager.appletDocumentBase=
b},"JSV.common.JSViewer,java.net.URL");c$.getSimulationType=c(c$,"getSimulationType",function(a){return 0<=a.indexOf("C13/")?"C13":"H1"},"~S");G(c$,"SIMULATION_PROTOCOL","http://SIMULATION/","appletDocumentBase",null,"viewer",null,"jsDocumentBase","");c$.urlPrefixes=c$.prototype.urlPrefixes=v(-1,["http:","https:","ftp:","http://SIMULATION/","file:"]);G(c$,"URL_LOCAL",4);c$.htCorrelationCache=c$.prototype.htCorrelationCache=new java.util.Hashtable;G(c$,"nciResolver","https://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True",
"nmrdbServerH1","https://www.nmrdb.org/tools/jmol/predict.php?POST?molfile=","nmrdbServerC13","https://www.nmrdb.org/service/jsmol13c?POST?molfile=","stringCount",0)});m("JSV.common");x(["javajs.api.BytePoster","J.api.PlatformViewer","JSV.common.Spectrum"],"JSV.common.JSViewer","java.io.File java.lang.Boolean $.Character $.Double $.Float $.Thread java.net.URL java.util.Arrays $.Hashtable JU.CU $.Lst $.OC $.PT $.SB JSV.common.Annotation $.ExportType $.JSVFileManager $.PanelData $.PanelNode $.Parameters $.PeakInfo $.PrintLayout $.RepaintManager $.ScriptToken $.ScriptTokenizer JSV.source.JDXReader $.JDXSource JSV.tree.SimpleTree JU.Logger".split(" "),
function(){c$=w(function(){this.irMode=this.overlayLegendDialog=this.viewDialog=this.dialogManager=this.jsvpPopupMenu=this.fileHelper=this.scriptQueue=this.properties=this.mainPanel=this.selectedPanel=this.repaintManager=this.parameters=this.panelNodes=this.currentSource=this.spectraTree=this.g2d=this.si=null;this.autoShowLegend=this.autoIntegrate=this.interfaceOverlaid=this.loadImaginary=!1;this.obscureTitleFromUser=null;this.allowMenu=!0;this.initialEndIndex=this.initialStartIndex=-1;this.isSigned=
this.isApplet=this.isSingleThreaded=!1;this.recentScript="";this.display=this.html5Applet=this.syncID=this.fullName=this.appletName=null;this.maximumSize=2147483647;this.scriptLevelCount=this.nViews=this.fileCount=this.screenWidth=this.screenHeight=0;this.apiPlatform=this.integrationRatios=this.returnFromJmolModel=null;this.popupZoomEnabled=this.popupAllowMenu=!0;this.defaultLoadScript=null;this.nmrMaxY=NaN;this.overlayLegendVisible=!1;this.recentStackPercent=5;this.offWindowFrame=this.lastPrintLayout=
null;this.recentOpenURL="http://";this.recentURL=null;this.recentSimulation="tylenol";s(this,arguments)},JSV.common,"JSViewer",null,[J.api.PlatformViewer,javajs.api.BytePoster]);O(c$,function(){this.irMode=JSV.common.Spectrum.IRMode.NO_CONVERT});c(c$,"setProperty",function(a,b){null!=this.properties&&this.properties.setProperty(a,b)},"~S,~S");c(c$,"setNode",function(a){a.jsvp!==this.selectedPanel&&this.si.siSetSelectedPanel(a.jsvp);this.si.siSendPanelChange();this.si.siNodeSet(a)},"JSV.common.PanelNode");
p(c$,function(a,b,c){this.si=a;this.isApplet=b;JSV.common.JSViewer.isJS=b&&c;c=null;self.Jmol&&(c=Jmol);JSV.common.JSViewer.jmolObject=c;this.isSigned=a.isSigned();this.apiPlatform=this.getPlatformInterface("Platform");this.apiPlatform.setViewer(this,this.display);this.g2d=this.getPlatformInterface("G2D");this.spectraTree=new JSV.tree.SimpleTree(this);this.parameters=this.getPlatformInterface("Parameters");this.parameters.setName("applet");this.fileHelper=this.getPlatformInterface("FileHelper").set(this);
this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.panelNodes=new JU.Lst;this.repaintManager=new JSV.common.RepaintManager(this);b||this.setPopupMenu(!0,!0)},"JSV.api.ScriptInterface,~B,~B");c(c$,"setPopupMenu",function(a,b){this.popupAllowMenu=a;this.popupZoomEnabled=b},"~B,~B");c(c$,"showMenu",function(a,b){if(this.popupAllowMenu){if(null==this.jsvpPopupMenu)try{this.jsvpPopupMenu=this.getPlatformInterface("Popup"),this.jsvpPopupMenu.jpiInitialize(this,this.isApplet?"appletMenu":"appMenu"),
this.jsvpPopupMenu.setEnabled(this.popupAllowMenu,this.popupZoomEnabled)}catch(c){if(D(c,Exception)){JU.Logger.error(c+" initializing popup menu");return}throw c;}this.jsvpPopupMenu.jpiShow(a,b)}},"~N,~N");c(c$,"runScriptNow",function(a){Zystem.out.println(this.checkScript(a));this.scriptLevelCount++;null==a&&(a="");a=a.trim();if(a.startsWith("!"))a=a.substring(1).trim();else if(a.startsWith(">"))return JU.Logger.error(a),!0;if(0<=a.indexOf("<PeakData"))return this.syncScript(a),!0;JU.Logger.info("RUNSCRIPT "+
a);var b=!0,c=10;a=new JSV.common.ScriptTokenizer(a,!0);for(var f=null;null!=a&&a.hasMoreTokens()&&0<c&&b;){var g=a.nextToken(),e=new JSV.common.ScriptTokenizer(g,!1),h=JSV.common.ScriptToken.getKey(e);if(null!=h){var l=JSV.common.ScriptToken.getScriptToken(h),e=JSV.common.ScriptToken.getValue(l,e,g);try{switch(l){case JSV.common.ScriptToken.UNKNOWN:JU.Logger.info("Unrecognized parameter: "+h);--c;break;default:if(null==this.selectedPanel)break;this.parameters.set(this.pd(),l,e);this.si.siUpdateBoolean(l,
JSV.common.Parameters.isTrue(e));break;case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:this.si.siExecSetCallback(l,e);break;case JSV.common.ScriptToken.DEFAULTLOADSCRIPT:e=JU.PT.rep(e,"''",'"');this.defaultLoadScript=0<e.length?e:null;break;case JSV.common.ScriptToken.DEFAULTNMRNORMALIZATION:this.nmrMaxY=JU.PT.parseFloat(e);break;
case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(e);break;case JSV.common.ScriptToken.CLOSE:this.execClose(e);break;case JSV.common.ScriptToken.DEBUG:JU.Logger.setLogLevel(e.toLowerCase().equals("high")?6:JSV.common.Parameters.isTrue(e)?5:4);break;case JSV.common.ScriptToken.GETPROPERTY:var k=null==this.selectedPanel?null:this.getPropertyAsJavaObject(e);null!=k&&this.selectedPanel.showMessage(JU.PT.toJSON(null,k),e);break;case JSV.common.ScriptToken.HELP:this.execHelp(e);
break;case JSV.common.ScriptToken.HIDDEN:this.si.siExecHidden(JSV.common.Parameters.isTrue(e));break;case JSV.common.ScriptToken.INTEGRATIONRATIOS:this.integrationRatios=e;this.execIntegrate(null);break;case JSV.common.ScriptToken.INTERFACE:this.interfaceOverlaid=this.checkOvelayInterface(e);break;case JSV.common.ScriptToken.INTEGRALOFFSET:case JSV.common.ScriptToken.INTEGRALRANGE:this.execSetIntegralParameter(l,Double.parseDouble(e));break;case JSV.common.ScriptToken.INVERTY:this.execZoom("invertY");
break;case JSV.common.ScriptToken.JMOL:this.si.syncToJmol(e);break;case JSV.common.ScriptToken.JSV:this.syncScript(JU.PT.trimQuotes(e));break;case JSV.common.ScriptToken.LOAD:if(0==e.length){null!=this.defaultLoadScript&&this.runScriptNow(this.defaultLoadScript);break}this.execLoad(e,(null==this.defaultLoadScript?"":this.defaultLoadScript+";")+a.getRemainingScript());f=null==this.selectedPanel?null:this.si.siLoaded(e);a=null;break;case JSV.common.ScriptToken.LOADIMAGINARY:this.loadImaginary=JSV.common.Parameters.isTrue(e);
break;case JSV.common.ScriptToken.PEAK:this.execPeak(e);break;case JSV.common.ScriptToken.PEAKLIST:this.execPeakList(e);break;case JSV.common.ScriptToken.SCALEBY:this.scaleSelectedBy(this.panelNodes,e);break;case JSV.common.ScriptToken.SCRIPT:if(e.equals("")||e.toLowerCase().startsWith("inline"))this.execScriptInline(e);else{var m=JSV.common.JSVFileManager.getFileAsString(e);null!=m&&100>this.scriptLevelCount&&this.runScriptNow(m)}break;case JSV.common.ScriptToken.SELECT:this.execSelect(e);break;
case JSV.common.ScriptToken.SPECTRUM:case JSV.common.ScriptToken.SPECTRUMNUMBER:this.setSpectrum(e)||(b=!1);break;case JSV.common.ScriptToken.STACKOFFSETY:this.execOverlayOffsetY(JU.PT.parseInt(""+JU.PT.parseFloat(e)));break;case JSV.common.ScriptToken.TEST:this.si.siExecTest(e);break;case JSV.common.ScriptToken.OVERLAY:case JSV.common.ScriptToken.VIEW:this.execView(e,!0);break;case JSV.common.ScriptToken.HIGHLIGHT:b=this.highlight(g);break;case JSV.common.ScriptToken.FINDX:case JSV.common.ScriptToken.GETSOLUTIONCOLOR:case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:case JSV.common.ScriptToken.IRMODE:case JSV.common.ScriptToken.LABEL:case JSV.common.ScriptToken.LINK:case JSV.common.ScriptToken.OVERLAYSTACKED:case JSV.common.ScriptToken.PRINT:case JSV.common.ScriptToken.SETPEAK:case JSV.common.ScriptToken.SETX:case JSV.common.ScriptToken.SHIFTX:case JSV.common.ScriptToken.SHOWERRORS:case JSV.common.ScriptToken.SHOWMEASUREMENTS:case JSV.common.ScriptToken.SHOWMENU:case JSV.common.ScriptToken.SHOWKEY:case JSV.common.ScriptToken.SHOWPEAKLIST:case JSV.common.ScriptToken.SHOWINTEGRATION:case JSV.common.ScriptToken.SHOWPROPERTIES:case JSV.common.ScriptToken.SHOWSOURCE:case JSV.common.ScriptToken.YSCALE:case JSV.common.ScriptToken.WRITE:case JSV.common.ScriptToken.ZOOM:if(this.isClosed()){b=
!1;break}switch(l){case JSV.common.ScriptToken.FINDX:this.pd().findX(null,Double.parseDouble(e));break;case JSV.common.ScriptToken.GETSOLUTIONCOLOR:this.show("solutioncolor"+e.toLowerCase());break;case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:this.execIntegrate(e);break;case JSV.common.ScriptToken.IRMODE:this.execIRMode(e);break;case JSV.common.ScriptToken.LABEL:this.pd().addAnnotation(JSV.common.ScriptToken.getTokens(e));break;case JSV.common.ScriptToken.LINK:this.pd().linkSpectra(JSV.common.PanelData.LinkMode.getMode(e));
break;case JSV.common.ScriptToken.OVERLAYSTACKED:this.pd().splitStack(!JSV.common.Parameters.isTrue(e));break;case JSV.common.ScriptToken.PRINT:f=this.execWrite(null);break;case JSV.common.ScriptToken.SETPEAK:case JSV.common.ScriptToken.SETX:case JSV.common.ScriptToken.SHIFTX:this.execShiftSpectrum(l,g);break;case JSV.common.ScriptToken.SHOWERRORS:this.show("errors");break;case JSV.common.ScriptToken.SHOWINTEGRATION:this.pd().showAnnotation(JSV.common.Annotation.AType.Integration,JSV.common.Parameters.getTFToggle(e));
break;case JSV.common.ScriptToken.SHOWKEY:this.setOverlayLegendVisibility(JSV.common.Parameters.getTFToggle(e),!0);break;case JSV.common.ScriptToken.SHOWMEASUREMENTS:this.pd().showAnnotation(JSV.common.Annotation.AType.Measurements,JSV.common.Parameters.getTFToggle(e));break;case JSV.common.ScriptToken.SHOWMENU:this.showMenu(-2147483648,0);break;case JSV.common.ScriptToken.SHOWPEAKLIST:this.pd().showAnnotation(JSV.common.Annotation.AType.PeakList,JSV.common.Parameters.getTFToggle(e));break;case JSV.common.ScriptToken.SHOWPROPERTIES:this.show("properties");
break;case JSV.common.ScriptToken.SHOWSOURCE:this.show("source");break;case JSV.common.ScriptToken.YSCALE:this.setYScale(e);break;case JSV.common.ScriptToken.WINDOW:this.si.siNewWindow(JSV.common.Parameters.isTrue(e),!1);break;case JSV.common.ScriptToken.WRITE:f=this.execWrite(e);break;case JSV.common.ScriptToken.ZOOM:b=this.execZoom(e)}}}catch(n){if(D(n,Exception))f=n.toString(),JU.Logger.error(n.toString()),b=!1,--c;else throw n;}}}this.scriptLevelCount--;this.si.siExecScriptComplete(f,!0);return b},
"~S");c(c$,"execShiftSpectrum",function(a,b){var c=JSV.common.ScriptToken.getTokens(b),f=NaN,g=NaN;switch(c.size()){case 2:g=c.get(1);g.equals("")&&(g="?");g=g.equalsIgnoreCase("NONE")?1.7976931348623157E308:g.equalsIgnoreCase("?")?NaN:Double.parseDouble(g);break;case 3:f=Double.parseDouble(c.get(1));g=Double.parseDouble(c.get(2));break;default:Double.parseDouble("")}c=0;switch(a){case JSV.common.ScriptToken.SETPEAK:c=1;break;case JSV.common.ScriptToken.SETX:c=2;break;case JSV.common.ScriptToken.SHIFTX:c=
3;Double.isNaN(g)&&Double.parseDouble("");break;default:return}this.pd().shiftSpectrum(c,f,g)},"JSV.common.ScriptToken,~S");c(c$,"execClose",function(a){var b=!a.startsWith("!");b||(a=a.substring(1));this.close(JU.PT.trimQuotes(a));(!b||0==this.panelNodes.size())&&this.si.siValidateAndRepaint(!0)},"~S");c(c$,"checkOvelayInterface",function(a){return a.equalsIgnoreCase("single")||a.equalsIgnoreCase("overlay")},"~S");c(c$,"execPeak",function(a){try{var b=JSV.common.ScriptToken.getTokens(JU.PT.rep(a,
"#","INDEX="));a=' type="'+b.get(0).toUpperCase()+'" _match="'+JU.PT.trimQuotes(b.get(1).toUpperCase())+'"';2<b.size()&&b.get(2).equalsIgnoreCase("all")&&(a+=' title="ALL"');this.processPeakPickEvent(new JSV.common.PeakInfo(a),!1)}catch(c){if(!D(c,Exception))throw c;}},"~S");c(c$,"execPeakList",function(a){var b=this.parameters,c=JSV.common.Parameters.getTFToggle(a);if(0>a.indexOf("="))this.isClosed()||this.pd().getPeakListing(null,c);else{var c=JSV.common.ScriptToken.getTokens(a),f=b.peakListThreshold,
g=b.peakListInterpolation;try{for(var e=c.size();0<=--e;){var h=c.get(e),l=h.indexOf("=");if(!(0>=l)){var k=h.substring(0,l);a=h.substring(l+1);k.startsWith("thr")?f=Double.$valueOf(a).doubleValue():k.startsWith("int")&&(g=a.equalsIgnoreCase("none")?"NONE":"parabolic")}}b.peakListThreshold=f;b.peakListInterpolation=g;this.isClosed()||this.pd().getPeakListing(b,Boolean.TRUE)}catch(m){if(!D(m,Exception))throw m;}}},"~S");c(c$,"highlight",function(a){var b=JSV.common.ScriptToken.getTokens(a),c=b.size();
switch(c){case 3:case 5:case 6:case 7:break;case 2:case 4:if(b.get(c-1).equalsIgnoreCase("OFF"))break;default:return!1}if(!this.isClosed()){a=JU.PT.parseFloat(1<c?b.get(1):"");var f=JU.PT.parseFloat(2<c?b.get(2):""),g=this.getRGB(3<c?b.get(3):"100"),e=this.getRGB(4<c?b.get(4):"100"),h=this.getRGB(5<c?b.get(5):"100"),b=this.getRGB(6<c?b.get(6):"100");Float.isNaN(a)||Float.isNaN(f)?this.pd().removeAllHighlights():(this.pd().removeHighlight(a,f),0>b&&(b=150),0<=g&&(0<=e&&0<=h)&&this.pd().addHighlight(null,
a,f,null,g,e,h,b));this.repaint(!0)}return!0},"~S");c(c$,"getRGB",function(a){a=JU.PT.parseFloat(a);return C(Float.isNaN(a)?-1:1<a?a:255*a)},"~S");c(c$,"execZoom",function(a){var b=0,c=0,f=0,g=0;a=JU.PT.rep(a," - "," ").$replace(","," ");a=JSV.common.ScriptToken.getTokens(a);switch(a.size()){default:return!1;case 0:return b=this.pd().getCurrentGraphSet().getCurrentView(),a=Math.round(100*b.minXOnScale)/100+","+Math.round(100*b.maxXOnScale)/100,a=this.selectedPanel.getInput("Enter zoom range x1 x2",
"Zoom",a),null==a||this.execZoom(a);case 1:return a=a.get(0),a.equalsIgnoreCase("next")?this.pd().nextView():a.toLowerCase().startsWith("prev")?this.pd().previousView():a.equalsIgnoreCase("out")?this.pd().resetView():a.equalsIgnoreCase("clear")?this.pd().clearAllView():a.equalsIgnoreCase("invertY")&&this.pd().getCurrentGraphSet().invertYAxis(),!0;case 2:b=Double.parseDouble(a.get(0));c=Double.parseDouble(a.get(1));break;case 3:var e=a.get(0);e.equalsIgnoreCase("X")?(b=Double.parseDouble(a.get(1)),
c=Double.parseDouble(a.get(2))):e.equalsIgnoreCase("Y")&&(f=Double.parseDouble(a.get(1)),g=Double.parseDouble(a.get(2)));break;case 4:b=Double.parseDouble(a.get(0)),f=Double.parseDouble(a.get(1)),c=Double.parseDouble(a.get(2)),g=Double.parseDouble(a.get(3))}this.pd().setZoom(b,f,c,g);return!0},"~S");c(c$,"scaleSelectedBy",function(a,b){try{for(var c=Double.parseDouble(b),f=a.size();0<=--f;)a.get(f).pd().scaleSelectedBy(c)}catch(g){if(!D(g,Exception))throw g;}},"JU.Lst,~S");c(c$,"pd",function(){return null==
this.selectedPanel?null:this.selectedPanel.getPanelData()});c(c$,"isClosed",function(){return null==this.pd()});c(c$,"execSelect",function(a){if(a.startsWith("ID ")){if(!this.isClosed())try{this.pd().selectSpectrum(null,"ID",JU.PT.trimQuotes(a.substring(3)),!0)}catch(b){if(!D(b,Exception))throw b;}}else{for(var c=this.panelNodes,f=c.size();0<=--f;)c.get(f).pd().selectFromEntireSet(-2147483648);c=new JU.Lst;this.fillSpecList(a,c,!1)}},"~S");c(c$,"execView",function(a,b){if(a.equals(""))this.checkOverlay();
else{var c=new JU.Lst,f=this.fillSpecList(a,c,!0);0<c.size()&&this.si.siOpenDataOrFile(null,f,c,f,-1,-1,!1,null,null);b||this.si.siValidateAndRepaint(!1)}},"~S,~B");c(c$,"execIRMode",function(a){for(var b=JSV.common.Spectrum.IRMode.getMode(a),c=this.pd().getSpectrum().dataType,f=this.panelNodes.size();0<=--f;)this.panelNodes.get(f).pd().setIRMode(b,c);this.setIRmode(a)},"~S");c(c$,"execIntegrate",function(a){this.isClosed()||(this.pd().checkIntegral(this.parameters,a),null!=this.integrationRatios&&
this.pd().setIntegrationRatios(this.integrationRatios),this.integrationRatios=null,this.repaint(!0))},"~S");c(c$,"repaint",function(a){this.selectedPanel.doRepaint(a)},"~B");c(c$,"execSetIntegralParameter",function(a,b){var c=this.parameters;switch(a){case JSV.common.ScriptToken.INTEGRALRANGE:c.integralRange=b;break;case JSV.common.ScriptToken.INTEGRALOFFSET:c.integralOffset=b}this.isClosed()||this.pd().checkIntegral(this.parameters,"update")},"JSV.common.ScriptToken,~N");c(c$,"setYScale",function(a){var b=
JSV.common.ScriptToken.getTokens(a),c=0,f=!1;1<b.size()&&b.get(0).equalsIgnoreCase("ALL")&&(f=!0,c++);a=Double.parseDouble(b.get(c++));b=Double.parseDouble(b.get(c));if(f){f=this.pd().getSpectrum();for(c=this.panelNodes.size();0<=--c;){var g=this.panelNodes.get(c);g.source===this.currentSource&&JSV.common.Spectrum.areXScalesCompatible(f,g.getSpectrum(),!1,!1)&&g.pd().setZoom(0,a,0,b)}}else this.pd().setZoom(0,a,0,b)},"~S");c(c$,"setOverlayLegendVisibility",function(a,b){b&&(this.overlayLegendVisible=
null==a?!this.overlayLegendVisible:a===Boolean.TRUE);for(var c=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes),f=this.panelNodes.size();0<=--f;)this.showOverlayLegend(this.panelNodes.get(f),this.panelNodes.get(f)===c&&this.overlayLegendVisible)},"Boolean,~B");c(c$,"showOverlayLegend",function(a,b){var c=a.legend;null==c&&b&&(c=a.setLegend(1<a.pd().getNumberOfSpectraInCurrentSet()&&1==a.pd().getNumberOfGraphSets()?this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null):null));
null!=c&&c.setVisible(b)},"JSV.common.PanelNode,~B");c(c$,"syncScript",function(a){a.equals("TEST")&&(a=JSV.common.JSViewer.testScript);JU.Logger.info("JSViewer.syncScript Jmol>JSV "+a);if(0>a.indexOf("<PeakData"))a.startsWith("JSVSTR:")?this.si.syncToJmol(a):(this.runScriptNow(a),0<=a.indexOf("#SYNC_PEAKS")&&this.syncPeaksAfterSyncScript());else{JU.Logger.info(">>toJSV>> "+a);var b=JU.PT.getQuotedAttribute(a,"sourceID"),c,f,g,e;if(null==b){f=JU.PT.getQuotedAttribute(a,"file");g=JU.PT.getQuotedAttribute(a,
"index");if(null==f||null==g)return;f=JU.PT.rep(f,"#molfile","");c=JU.PT.getQuotedAttribute(a,"model");b=JU.PT.getQuotedAttribute(a,"src");e=null!=b&&b.startsWith("Jmol")?null:this.returnFromJmolModel;if(null!=c&&null!=e&&!c.equals(e)){JU.Logger.info("JSV ignoring model "+c+"; should be "+e);return}this.returnFromJmolModel=null;if(0==this.panelNodes.size()||!this.checkFileAlreadyLoaded(f))JU.Logger.info("file "+f+" not found -- JSViewer closing all and reopening"),this.si.siSyncLoad(f);a=JU.PT.getQuotedAttribute(a,
"type");e=null}else f=null,g=c=b,e=","+JU.PT.getQuotedAttribute(a,"atom")+",",a="ID";g=this.selectPanelByPeak(f,g,e);e=this.pd();e.selectSpectrum(f,a,c,!0);this.si.siSendPanelChange();e.addPeakHighlight(g);this.repaint(!0);(null==b||null!=g&&null!=g.getAtoms())&&this.si.syncToJmol(this.jmolSelect(g))}},"~S");c(c$,"syncPeaksAfterSyncScript",function(){var a=this.currentSource;if(null!=a)try{var b="file="+JU.PT.esc(a.getFilePath()),c=a.getSpectra().get(0).getPeakList(),f=new JU.SB;f.append("[");for(var g=
c.size(),a=0;a<g;a++){var e=c.get(a).toString(),e=e+" "+b;f.append(JU.PT.esc(e));0<a&&f.append(",")}f.append("]");this.si.syncToJmol("Peaks: "+f)}catch(h){if(!D(h,Exception))throw h;}});c(c$,"checkFileAlreadyLoaded",function(a){if(this.isClosed())return!1;if(this.pd().hasFileLoaded(a))return!0;for(var b=this.panelNodes.size();0<=--b;)if(this.panelNodes.get(b).pd().hasFileLoaded(a))return this.si.siSetSelectedPanel(this.panelNodes.get(b).jsvp),!0;return!1},"~S");c(c$,"selectPanelByPeak",function(a,
b,c){if(null==this.panelNodes)return null;for(var f=null,g=this.panelNodes.size();0<=--g;)this.panelNodes.get(g).pd().addPeakHighlight(null);f=this.pd().selectPeakByFileIndex(a,b,c);if(null!=f)this.setNode(JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes));else for(g=this.panelNodes.size();0<=--g;){var e=this.panelNodes.get(g);if(null!=(f=e.pd().selectPeakByFileIndex(a,b,c))){this.setNode(e);break}}return f},"~S,~S,~S");c(c$,"processPeakPickEvent",function(a){if(t(a,JSV.common.PeakInfo)){var b=
this.pd().findMatchingPeakInfo(a);if(null==b){if(!"ALL".equals(a.getTitle()))return;for(var c=null,f=0;f<this.panelNodes.size();f++)if(null!=(b=this.panelNodes.get(f).pd().findMatchingPeakInfo(a))){c=this.panelNodes.get(f);break}if(null==c)return;this.setNode(c)}a=b}else this.si.siSetSelectedPanel(a.getSource()),a=a.getPeakInfo();this.pd().addPeakHighlight(a);this.syncToJmol(a);a.isClearAll()?this.repaint(!1):this.pd().selectSpectrum(a.getFilePath(),a.getType(),a.getModel(),!0);this.si.siCheckCallbacks(a.getTitle())},
"~O,~B");c(c$,"newStructToJmol",function(a){JU.Logger.info("sending new structure to Jmol:\n"+a);this.si.syncToJmol("struct:"+a)},"~S");c(c$,"syncToJmol",function(a){this.repaint(!0);this.returnFromJmolModel=a.getModel();this.si.syncToJmol(this.jmolSelect(a))},"JSV.common.PeakInfo");c(c$,"sendPanelChange",function(){var a=this.pd(),b=a.getSpectrum(),c=b.getSelectedPeak();null==c&&(c=b.getModelPeakInfoForAutoSelectOnLoad());null==c&&(c=b.getBasePeakInfo());a.addPeakHighlight(c);JU.Logger.info(Thread.currentThread()+
"JSViewer sendFrameChange "+this.selectedPanel);this.syncToJmol(c)});c(c$,"jmolSelect",function(a){var b="IR".equals(a.getType())||"RAMAN".equals(a.getType())?"vibration ON; selectionHalos OFF;":"vibration OFF; selectionhalos "+(null==a.getAtoms()?"OFF":"ON");return"Select: "+a+' script="'+b+' " sourceID="'+this.pd().getSpectrum().sourceID+'"'},"JSV.common.PeakInfo");c(c$,"getPropertyAsJavaObject",function(a){var b=new java.util.Hashtable;if("SOURCEID".equalsIgnoreCase(a))return b.put(a,null==this.pd()?
"":this.pd().getSpectrum().sourceID),b;if(null!=a&&a.startsWith("DATA_"))return b.put(a,""+JSV.common.JSVFileManager.cacheGet(a.substring(5))),b;var c=!1;if(null!=a&&a.toUpperCase().startsWith("ALL ")||"all".equalsIgnoreCase(a))a=a.substring(3).trim(),c=!0;"".equals(a)&&(a=null);if("NAMES".equalsIgnoreCase(a)||"KEYS".equalsIgnoreCase(a))a="";var f=this.pd().getInfo(!0,a);if(!c&&null!=f)return f;null!=f&&b.put("current",f);c=new JU.Lst;for(f=0;f<this.panelNodes.size();f++)null!=this.panelNodes.get(f).jsvp&&
c.addLast(this.panelNodes.get(f).getInfo(a));b.put("items",c);return b},"~S");c(c$,"getCoordinate",function(){if(!this.isClosed()){var a=this.pd().getClickedCoordinate();if(null!=a)return a.getXVal()+" "+a.getYVal()}return""});c(c$,"fillSpecList",function(a,b,c){var f,g=null,e=a.equalsIgnoreCase("NONE");if(e||a.equalsIgnoreCase("all"))a="*";if(0>a.indexOf("*")){f=a.$plit(" ");a=new JU.SB;for(var h=0;h<f.length;h++){var l=f[h].indexOf(".");l!=f[h].lastIndexOf(".")&&(f[h]=f[h].substring(0,l+1)+f[h].substring(l+
1).$replace(".","_"));a.append(f[h]).append(" ")}a=a.toString().trim()}if(a.equals("*"))f=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes));else if(a.startsWith('"')||a.startsWith("'"))f=JSV.common.ScriptToken.getTokens(a);else if(a=JU.PT.rep(a,"_"," _ "),a=JU.PT.rep(a,"-"," - "),f=JSV.common.ScriptToken.getTokens(a),g=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes)),0==g.size())return null;var k=this.isClosed()?
"1.":JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes).id,k=k.substring(0,k.indexOf(".")+1);a=new JU.SB;for(var m=f.size(),n=null,h=0;h<m;h++){var p=f.get(h),l=NaN,s=-1;h+1<m&&f.get(h+1).equals("*")?(h+=2,l=Double.parseDouble(f.get(h))):h+1<m&&f.get(h+1).equals("_")&&(h+=2,s=Integer.parseInt(f.get(h)));if(p.equals("-")){null==n&&(n=g.get(0));p=h+1==m?g.get(g.size()-1):f.get(++h);p.contains(".")||(p=k+p);for(l=0;l<g.size()&&!g.get(l).equals(n);)l++;for(l++;l<g.size()&&!n.equals(p);){var t=
JSV.common.PanelNode.findNodeById(n=g.get(l++),this.panelNodes);b.addLast(t.pd().getSpectrumAt(0));a.append(",").append(n)}}else if(p.startsWith("'")&&p.endsWith("'")&&(p='"'+JU.PT.trim(p,"'")+'"'),p.startsWith('"'))for(var p=JU.PT.trim(p,'"'),s=this.panelNodes.size(),u=0;u<s;u++){if(t=this.panelNodes.get(u),null!=t.fileName&&t.fileName.startsWith(p)||null!=t.frameTitle&&t.frameTitle.startsWith(p))this.addSpecToList(t.pd(),l,-1,b,c),a.append(",").append(t.id)}else p.contains(".")||(p=k+p),t=JSV.common.PanelNode.findNodeById(p,
this.panelNodes),null!=t&&(n=p,this.addSpecToList(t.pd(),l,s,b,c),a.append(",").append(p),0<s&&a.append(".").appendI(s))}c&&0<b.size()&&(t=JSV.common.PanelNode.findNodeById(a.substring(1),this.panelNodes),null!=t&&(this.setNode(t),b.clear()));return e?"NONE":0<a.length()?a.toString().substring(1):null},"~S,JU.Lst,~B");c(c$,"addSpecToList",function(a,b,c,f,g){g?(a.getSpectrumAt(0).setUserYFactor(Double.isNaN(b)?1:b),a.addToList(c-1,f)):a.selectFromEntireSet(c-1)},"JSV.common.PanelData,~N,~N,JU.Lst,~B");
c(c$,"getSolutionColor",function(a){var b=this.pd().getSpectrum(),c=b.canShowSolutionColor()?JSV.common.JSViewer.getInterface("JSV.common.Visible"):null;return null==c?-1:c.getColour(b,a)},"~B");c(c$,"openDataOrFile",function(a,b,c,f,g,e,h,l){if("NONE".equals(b))return this.close("View*"),0;this.si.writeStatus("");var k=null,m=null,n=null,p=!1;null!=f&&f.startsWith("cache://")&&(a=Jmol.Cache.get(b=f));var s=null;if(null!=a)try{n=b,m=k=JSV.common.JSVFileManager.getFullPathName(b)}catch(t){if(!D(t,
JSV.exception.JSVException))throw t;}else if(null!=c)p=!0,m=n=k="View"+ ++this.nViews;else if(null!=f)try{s=this.apiPlatform.newFile(f),this.recentURL=k=(new java.net.URL(JSV.common.JSVFileManager.appletDocumentBase,f,null)).toString(),n=JSV.common.JSVFileManager.getTagName(k)}catch(u){if(D(u,java.net.MalformedURLException))n=s.getName(),m=k=s.getFullPath(),this.recentURL=null;else throw u;}b=-1;if(0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,k))||0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,
f)))return p?(--this.nViews,this.setNode(this.panelNodes.get(b))):this.si.writeStatus(k+" is already open"),-1;!h&&!p&&this.close("all");this.si.setCursor(3);try{this.si.siSetCurrentSource(p?JSV.source.JDXSource.createView(c):JSV.source.JDXReader.createJDXSource(s,a,k,this.obscureTitleFromUser===Boolean.TRUE,this.loadImaginary,g,e,this.nmrMaxY))}catch(v){if(D(v,Exception))return alert(v.toString()),this.si.setCursor(0),this.isApplet&&this.selectedPanel.showMessage(v.toString(),"Error Opening File"),
-3;throw v;}this.si.setCursor(0);Zystem.gc();null==m?(m=this.currentSource.getFilePath(),null!=m&&(n=m.substring(m.lastIndexOf("/")+1))):this.currentSource.setFilePath(m);null==l&&!p&&(l=m);null!=l&&this.currentSource.setID(l);this.si.siSetLoaded(n,m);a=this.currentSource.getJDXSpectrum(0);if(null==a)return-4;c=this.currentSource.getSpectra();JSV.common.Spectrum.process(c,this.irMode);c=this.interfaceOverlaid||a.isAutoOverlayFromJmolClick();p||c&&this.currentSource.isCompoundSource?this.combineSpectra(p?
f:null):this.splitSpectra();this.pd().setTaintedAll();p||this.si.siUpdateRecentMenus(k);return 0},"~O,~S,JU.Lst,~S,~N,~N,~B,~S");c(c$,"close",function(a){var b=0,c=null==a?-2:a.indexOf(">");0<c&&(b=JU.PT.parseInt(a.substring(c+1).trim()),a=a.substring(0,c).trim());"*".equals(a)&&(a="all");var f="all"===a;if(null==a||0==b&&a.equalsIgnoreCase("all"))this.closeSource(null);else{var g=a.equalsIgnoreCase("views"),c=new JU.Lst;a=a.$replace("\\","/");var e=this.panelNodes.size(),b=e-b;if(a.endsWith("*"))for(a=
a.substring(0,a.length-1);0<=--e;)this.panelNodes.get(e).fileName.startsWith(a)&&c.addLast(this.panelNodes.get(e).source);else if(a.equalsIgnoreCase("selected"))for(a=null;0<=--e;)f=this.panelNodes.get(e).source,this.panelNodes.get(e).isSelected&&(null==a||a!==f)&&c.addLast(f),a=f;else if(f||g||a.equalsIgnoreCase("simulations"))for(a=0;0<=--e&&a<b;){if(f||(g?this.panelNodes.get(e).isView:this.panelNodes.get(e).isSimulation))c.addLast(this.panelNodes.get(e).source),a++}else f=0==a.length?this.currentSource:
JSV.common.PanelNode.findSourceByNameOrId(a,this.panelNodes),null!=f&&c.addLast(f);for(e=c.size();0<=--e;)this.closeSource(c.get(e));null==this.selectedPanel&&0<this.panelNodes.size()&&this.si.siSetSelectedPanel(JSV.common.PanelNode.getLastFileFirstNode(this.panelNodes))}},"~S");c(c$,"execLoad",function(a,b){var c=JSV.common.ScriptToken.getTokens(a),f=c.get(0),g=null,e=0;f.equalsIgnoreCase("ID")&&(g=JU.PT.trimQuotes(c.get(1)),f=c.get(2),e=2);var h=f.equalsIgnoreCase("APPEND"),l=f.equalsIgnoreCase("CHECK");
(h||l)&&e++;0<e&&(f=c.get(e));null==b&&(b=this.defaultLoadScript);if(f.equals("?"))this.openFileFromDialog(h,!1,null,b);else if(f.equals("http://?"))this.openFileFromDialog(h,!0,null,null);else if(f.equals("$?")||f.equals("$H1?"))this.openFileFromDialog(h,!0,"H1",null);else if(f.equals("$C13?"))this.openFileFromDialog(h,!0,"C13",null);else{var k=f.equalsIgnoreCase("MOL")||f.equalsIgnoreCase("H1"),m=f.equalsIgnoreCase("C13");if(k||m)f="http://SIMULATION/"+(k?"H1/":"C13/")+"MOL="+JU.PT.trimQuotes(c.get(++e));
!l&&!h&&(f.equals('""')&&null!=this.currentSource&&(f=this.currentSource.getFilePath()),this.close("all"));f=JU.PT.trimQuotes(f);if(l=f.startsWith("$"))!f.startsWith("$H1")&&!f.startsWith("$C13")&&(f="$H1/"+f.substring(1)),f="http://SIMULATION/"+f.substring(1);k=e+1<c.size()?Integer.$valueOf(c.get(++e)).intValue():-1;c=e+1<c.size()?Integer.$valueOf(c.get(++e)).intValue():k;this.si.siOpenDataOrFile(null,null,null,f,k,c,h,b,g);l&&(this.close("views"),this.execView("*",!0))}},"~S,~S");c(c$,"combineSpectra",
function(a){for(var b=this.currentSource,c=b.getSpectra(),f=!1,g=c.size();0<=--g;)if(c.get(g).isSimulation){f=!0;break}c=this.si.siGetNewJSVPanel2(c);c.setTitle(b.getTitle());c.getTitle().equals("")&&(c.getPanelData().setViewTitle(b.getFilePath()),c.setTitle(a));this.si.siSetPropertiesFromPreferences(c,!0);this.spectraTree.createTree(++this.fileCount,b,v(-1,[c])).getPanelNode().isView=!0;b=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);b.setFrameTitle(a);b.isView=!0;this.autoShowLegend&&
1==this.pd().getNumberOfGraphSets()&&b.setLegend(this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null));this.si.siSetMenuEnables(b,!1);f&&this.pd().splitStack(!0)},"~S");c(c$,"closeSource",function(a){for(var b=this.spectraTree.getRootNode(),c=null==a?null:a.getFilePath(),f=new JU.Lst,b=b.children();b.hasMoreElements();){var g=b.nextElement();if(null==c||g.getPanelNode().source.matchesFilePath(c)){JU.Logger.info("Closing "+g.getPanelNode().source.getFilePath());for(var e=g.children();e.hasMoreElements();){var h=
e.nextElement();f.addLast(h);this.panelNodes.removeObj(h.getPanelNode())}f.addLast(g);if(null!=c)break}}this.spectraTree.deleteNodes(f);null==a&&(null!=this.currentSource&&this.currentSource.dispose(),this.currentSource=null,null!=this.selectedPanel&&this.selectedPanel.dispose());this.currentSource===a&&(this.si.siSetSelectedPanel(null),this.si.siSetCurrentSource(null));for(f=c=0;f<this.panelNodes.size();f++)b=JU.PT.parseFloat(this.panelNodes.get(f).id),b>=c+1&&(c=u(Math.floor(b)));this.fileCount=
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c(c$,"setSpectrum",function(a){if(0<=a.indexOf(".")){a=JSV.common.PanelNode.findNodeById(a,this.panelNodes);if(null==a)return!1;this.setNode(a)}else{a=JU.PT.parseInt(a);if(0>=a)return this.checkOverlay(),!1;this.setFrameAndTreeNode(a-1)}return!0},"~S");c(c$,"splitSpectra",function(){for(var a=this.currentSource,b=a.getSpectra(),c=Array(b.size()),f=null,g=0;g<b.size();g++)f=b.get(g),f=this.si.siGetNewJSVPanel(f),this.si.siSetPropertiesFromPreferences(f,!0),c[g]=f;this.spectraTree.createTree(++this.fileCount,
a,c);this.si.siGetNewJSVPanel(null);a=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);this.si.siSetMenuEnables(a,!0)});c(c$,"selectedTreeNode",function(a){null!=a&&(a.isLeaf()?this.setNode(a.getPanelNode()):Zystem.out.println("not a leaf"),this.si.siSetCurrentSource(a.getPanelNode().source))},"JSV.api.JSVTreeNode");c(c$,"dispose",function(){this.fileHelper=null;null!=this.viewDialog&&this.viewDialog.dispose();this.viewDialog=null;null!=this.overlayLegendDialog&&this.overlayLegendDialog.dispose();
this.overlayLegendDialog=null;null!=this.jsvpPopupMenu&&(this.jsvpPopupMenu.jpiDispose(),this.jsvpPopupMenu=null);if(null!=this.panelNodes)for(var a=this.panelNodes.size();0<=--a;)this.panelNodes.get(a).dispose(),this.panelNodes.removeItemAt(a)});c(c$,"runScript",function(a){null==this.scriptQueue?this.si.siProcessCommand(a):this.scriptQueue.addLast(a)},"~S");c(c$,"requestRepaint",function(){null!=this.selectedPanel&&this.repaintManager.refresh()});c(c$,"repaintDone",function(){this.repaintManager.repaintDone()});
c(c$,"checkOverlay",function(){null!=this.mainPanel&&this.markSelectedPanels(this.panelNodes,this.mainPanel.getCurrentPanelIndex());this.viewDialog=this.getDialog(JSV.common.Annotation.AType.Views,null)});c(c$,"markSelectedPanels",function(a,b){for(var c=a.size();0<=--c;)a.get(c).isSelected=b==c},"JU.Lst,~N");c(c$,"execOverlayOffsetY",function(a){if(-2147483648==a){if(null==this.selectedPanel)return;a=this.selectedPanel.getInput("Enter a vertical offset in percent for stacked plots","Overlay",""+
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b,this,b);case JSV.common.Annotation.AType.PeakList:return JSV.common.JSViewer.getInterface("JSV.dialog.PeakListDialog").setParams("Peak List for "+b,this,b);case JSV.common.Annotation.AType.OverlayLegend:return this.overlayLegendDialog=JSV.common.JSViewer.getInterface("JSV.dialog.OverlayLegendDialog").setParams(this.pd().getViewTitle(),this,null);case JSV.common.Annotation.AType.Views:return this.viewDialog=JSV.common.JSViewer.getInterface("JSV.dialog.ViewsDialog").setParams("View/Combine/Close Spectra",
this,null);default:return null}},"JSV.common.Annotation.AType,JSV.common.Spectrum");c(c$,"show",function(a){this.getDialogManager();if(a.equals("properties"))this.dialogManager.showProperties(null,this.pd().getSpectrum());else if(a.equals("errors"))this.dialogManager.showSourceErrors(null,this.currentSource);else if(a.equals("source"))null==this.currentSource?0<this.panelNodes.size()&&this.dialogManager.showMessageDialog(null,"Please Select a Spectrum","Select Spectrum",0):this.dialogManager.showSource(this,
this.pd().getSpectrum());else if(a.startsWith("solutioncolorfill"))if(0<=a.indexOf("all"))for(var b=this.panelNodes.size();0<=--b;)this.panelNodes.get(b).pd().setSolutionColor(a);else this.pd().setSolutionColor(a);else a.startsWith("solutioncolor")&&(a=this.getSolutionColorStr(0>a.indexOf("false")),a="background-color:rgb("+a+")'><br />Predicted Solution Colour- RGB("+a+")<br /><br />",JSV.common.JSViewer.isJS?this.dialogManager.showMessage(this,"<div style='width:100%;height:100%;"+a+"</div>","Predicted Colour"):
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return a},"~S");c(c$,"$export",function(a,b){null==a&&(a="XY");var c=this.pd(),f=c.getNumberOfSpectraInCurrentSet();if(-1>b||b>=f)return"Maximum spectrum index (0-based) is "+(f-1)+".";c=0>b?c.getSpectrum():c.getSpectrumAt(b);try{return JSV.common.JSViewer.getInterface("JSV.export.Exporter").exportTheSpectrum(this,JSV.common.ExportType.getType(a),null,c,0,c.getXYCoords().length-1,null,a.equalsIgnoreCase("PDF"))}catch(g){if(D(g,Exception))return JU.Logger.error(g.toString()),null;throw g;}},"~S,~N");
h(c$,"postByteArray",function(a,b){return JSV.common.JSVFileManager.postByteArray(a,b)},"~S,~A");c(c$,"getOutputChannel",function(a,b){for(;a.startsWith("/");)a=a.substring(1);return(new JU.OC).setParams(this,a,!b,null)},"~S,~B");c$.getInterface=c(c$,"getInterface",function(a){try{var b=fa._4Name(a);return null==b?null:b.newInstance()}catch(c){if(D(c,Exception))return JU.Logger.error("Interface.java Error creating instance for "+a+": \n"+c),null;throw c;}},"~S");c(c$,"showMessage",function(a){null!=
this.selectedPanel&&null!=a&&this.selectedPanel.showMessage(a,null)},"~S");c(c$,"openFileFromDialog",function(a,b,c,f){var g=null;if(null!=c){g=this.fileHelper.getUrlFromDialog("Enter the name or identifier of a compound",this.recentSimulation);if(null==g)return;this.recentSimulation=g;g="$"+c+"/"+g}else if(b){g=this.fileHelper.getUrlFromDialog("Enter the URL of a JCAMP-DX File",null==this.recentURL?this.recentOpenURL:this.recentURL);if(null==g)return;this.recentOpenURL=g}else b=v(-1,[Boolean.$valueOf(a),
f]),b=this.fileHelper.showFileOpenDialog(this.mainPanel,b),null!=b&&(g=b.getFullPath());null!=g&&this.runScriptNow("load "+(a?"APPEND ":"")+'"'+g+'"'+(null==f?"":";"+f))},"~B,~B,~S,~S");c(c$,"openFile",function(a,b){if(b&&null!=this.panelNodes){var c=JSV.common.PanelNode.findSourceByNameOrId((new java.io.File(a)).getAbsolutePath(),this.panelNodes);null!=c&&this.closeSource(c)}this.si.siOpenDataOrFile(null,null,null,a,-1,-1,!0,this.defaultLoadScript,null)},"~S,~B");c(c$,"selectPanel",function(a,b){var c=
-1;if(null!=b){for(var f=b.size();0<=--f;){var g=b.get(f).jsvp;g===a?c=f:(g.setEnabled(!1),g.setFocusable(!1),g.getPanelData().closeAllDialogsExcept(JSV.common.Annotation.AType.NONE))}this.markSelectedPanels(b,c)}return c},"JSV.api.JSVPanel,JU.Lst");c(c$,"checkAutoIntegrate",function(){this.autoIntegrate&&this.pd().integrateAll(this.parameters)});c(c$,"parseInitScript",function(a){null==a&&(a="");a=new JSV.common.ScriptTokenizer(a,!0);for(JU.Logger.debugging&&JU.Logger.info("Running in DEBUG mode");a.hasMoreTokens();){var b=
a.nextToken(),c=new JSV.common.ScriptTokenizer(b,!1),f=c.nextToken();f.equalsIgnoreCase("SET")&&(f=c.nextToken());var f=f.toUpperCase(),g=JSV.common.ScriptToken.getScriptToken(f),b=JSV.common.ScriptToken.getValue(g,c,b);JU.Logger.info("KEY-> "+f+" VALUE-> "+b+" : "+g);try{switch(g){default:this.parameters.set(null,g,b);break;case JSV.common.ScriptToken.UNKNOWN:break;case JSV.common.ScriptToken.APPLETID:this.fullName=this.appletName+"__"+(this.appletName=b)+"__";f=null;self.Jmol&&(f=Jmol._applets[b]);
this.html5Applet=f;break;case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(b);break;case JSV.common.ScriptToken.COMPOUNDMENUON:break;case JSV.common.ScriptToken.APPLETREADYCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:this.si.siExecSetCallback(g,b);break;case JSV.common.ScriptToken.ENDINDEX:this.initialEndIndex=
Integer.parseInt(b);break;case JSV.common.ScriptToken.INTERFACE:this.checkOvelayInterface(b);break;case JSV.common.ScriptToken.IRMODE:this.setIRmode(b);break;case JSV.common.ScriptToken.MENUON:this.allowMenu=Boolean.parseBoolean(b);break;case JSV.common.ScriptToken.OBSCURE:null==this.obscureTitleFromUser&&(this.obscureTitleFromUser=Boolean.$valueOf(b));break;case JSV.common.ScriptToken.STARTINDEX:this.initialStartIndex=Integer.parseInt(b);break;case JSV.common.ScriptToken.SYNCID:this.fullName=this.appletName+
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a||b||!c){g=f.name()+" "+f.getTip()+g+" "+f.getDescription();"\t"==a&&(e=f.name()+" ");break}g=f.name()+" "+g;break;default:g=JSV.common.ScriptToken.getNameList(g)}}c?this.si.writeStatus(g):e=g;return e},"~S,~S,~B");c(c$,"checkScript",function(a){return this.checkCommandLineForTip("\x00",a,!1)},"~S");c(c$,"execHelp",function(a){var b=this.checkCommandLineForTip("\u0001",a,!1);if(0>b.indexOf(" ")&&0<b.indexOf(",")){var c=JU.PT.split(b,",");java.util.Arrays.sort(c);for(var b="",f=0;f<c.length;f++)var g=
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a;this.text=this.spec.setMeasurementText(this)},"~N");c(c$,"getValue",function(){return this.value});c(c$,"getXVal2",function(){return this.pt2.getXVal()});c(c$,"getYVal2",function(){return this.pt2.getYVal()});h(c$,"addSpecShift",function(a){this.setXVal(this.getXVal()+a);this.pt2.setXVal(this.pt2.getXVal()+a)},"~N");c(c$,"setYVal2",function(a){this.pt2.setYVal(a)},"~N");c(c$,"overlaps",function(a,b){return Math.min(this.getXVal(),this.getXVal2())<Math.max(a,b)&&Math.max(this.getXVal(),this.getXVal2())>
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c(c$,"getDataHeader",function(){return JSV.common.MeasurementData.HEADER});c(c$,"getMeasurementListArray",function(a){this.units=a;var b=this.getMeasurementListArrayReal(a),c=this.spec.isNMR()?4:2;a=this.spec.isHNMR()&&a.equals("ppm")?4:2;for(var f=Array(this.size()),g=this.size();0<=--g;)f[g]=v(-1,[""+(g+1),JU.DF.formatDecimalDbl(b[g][0],c),JU.DF.formatDecimalDbl(b[g][1],c),JU.DF.formatDecimalDbl(b[g][2],a)]);return f},"~S");c(c$,"getMeasurementListArrayReal",function(a){a=this.spec.isNMR()&&a.equalsIgnoreCase("HZ");
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h(c$,"getSpectrum",function(){return this.spec});h(c$,"getData",function(){return this});c(c$,"clear",function(a,b){for(var c=this.size();0<=--c;){var f=this.get(c);(0==f.text.length||f.overlaps(a,b))&&this.removeItemAt(c)}},"~N,~N");c(c$,"find",function(a){for(var b=this.size();0<=--b;)if(this.get(b).overlaps(a,a))return b;return-1},"~N");h(c$,"setSpecShift",function(a){for(var b=this.size();0<=--b;){var c=this.get(b),f=c.getXVal()+a;c.setXVal(f);c.setValue(f);c.text=JU.DF.formatDecimalDbl(f,this.precision)}},
"~N");h(c$,"getGraphSetKey",function(){return this.key});h(c$,"setGraphSetKey",function(a){this.key=a},"~S");h(c$,"isVisible",function(){return!0});c(c$,"getInfo",function(a){a.put("header",this.getDataHeader());a.put("table",this.getMeasurementListArrayReal("ppm"));null!=this.units&&a.put("units",this.units)},"java.util.Map");h(c$,"isDialog",function(){return!1});c$.HEADER=c$.prototype.HEADER=v(-1,["","start","end","value"])});m("JSV.common");x(["java.lang.Enum","J.api.EventManager","java.util.Hashtable",
"JU.Lst"],"JSV.common.PanelData","java.lang.Boolean $.Double JU.CU JSV.common.Annotation $.Coordinate $.GraphSet $.JSVFileManager $.JSVersion $.JSViewer $.MeasurementData $.Parameters $.PeakPickEvent $.ScriptToken $.Spectrum $.SubSpecChangeEvent $.ZoomEvent JSV.dialog.JSVDialog J.api.GenericGraphics JU.Font $.Logger".split(" "),function(){c$=w(function(){this.graphSets=this.jsvp=this.options=this.currentGraphSet=this.listeners=this.vwr=this.g2d0=this.g2d=null;this.currentSplitPoint=0;this.coordsClicked=
this.coordClicked=this.thisWidget=null;this.isIntegralDrag=this.drawXAxisLeftToRight=this.shiftPressed=this.ctrlPressed=!1;this.xAxisLeftToRight=!0;this.scalingFactor=1;this.integralShiftMode=0;this.left=60;this.right=50;this.coordStr="";this.startupPinTip="Click to set.";this.title=null;this.endIndex=this.startIndex=this.thisHeight=this.thisWidth=this.nSpectra=this.clickCount=0;this.titleFontName=this.displayFontName=this.viewTitle=this.commonFilePath=null;this.isPrinting=!1;this.doReset=!0;this.printingFontName=
null;this.printGraphPosition="default";this.isLinked=this.display1D=this.titleDrawn=!1;this.spectra=this.printJobTitle=null;this.taintedAll=!0;this.testingJavaScript=!1;this.mouseState=this.currentFont=null;this.peakTabsOn=this.titleOn=this.gridOn=!1;this.mouseY=this.mouseX=0;this.linking=!1;this.xPixelClicked=0;this.gMain=this.optionsSaved=this.bgcolor=this.BLACK=this.zoomBoxColor2=this.zoomBoxColor=this.highlightColor=this.unitsColor=this.titleColor=this.scaleColor=this.plotAreaColor=this.peakTabColor=
this.integralPlotColor=this.gridColor=this.coordinatesColor=null;s(this,arguments)},JSV.common,"PanelData",null,J.api.EventManager);O(c$,function(){this.listeners=new JU.Lst;this.options=new java.util.Hashtable});p(c$,function(a,b){this.vwr=b;this.jsvp=a;this.g2d=this.g2d0=b.g2d;this.BLACK=this.g2d.getColor1(0);this.highlightColor=this.g2d.getColor4(255,0,0,200);this.zoomBoxColor=this.g2d.getColor4(150,150,100,130);this.zoomBoxColor2=this.g2d.getColor4(150,100,100,130)},"JSV.api.JSVPanel,JSV.common.JSViewer");
c(c$,"addListener",function(a){this.listeners.contains(a)||this.listeners.addLast(a)},"JSV.api.PanelListener");c(c$,"getCurrentGraphSet",function(){return this.currentGraphSet});c(c$,"dispose",function(){this.jsvp=null;for(var a=0;a<this.graphSets.size();a++)this.graphSets.get(a).dispose();this.listeners=this.options=this.thisWidget=this.coordsClicked=this.coordClicked=this.currentGraphSet=this.currentFont=this.graphSets=null});c(c$,"setViewTitle",function(a){this.viewTitle=a},"~S");c(c$,"getViewTitle",
function(){return null==this.viewTitle?this.getTitle():this.viewTitle});c(c$,"getInfo",function(a,b){var c=new java.util.Hashtable,f=null;if(a)return this.currentGraphSet.getInfo(b,this.getCurrentSpectrumIndex());var g=this.options.entrySet();if("".equals(b)){for(var f="type title nSets ",e,g=g.iterator();g.hasNext()&&((e=g.next())||1);)f+=e.getKey().name()+" ";c.put("KEYS",f)}else{for(g=g.iterator();g.hasNext()&&((e=g.next())||1);)JSV.common.Parameters.putInfo(b,c,e.getKey().name(),e.getValue());
JSV.common.Parameters.putInfo(b,c,"type",this.getSpectrumAt(0).getDataType());JSV.common.Parameters.putInfo(b,c,"title",this.title);JSV.common.Parameters.putInfo(b,c,"nSets",Integer.$valueOf(this.graphSets.size()))}f=new JU.Lst;for(e=this.graphSets.size();0<=--e;)f.addLast(this.graphSets.get(e).getInfo(b,-1));c.put("sets",f);return c},"~B,~S");c(c$,"setBooleans",function(a,b){if(null==b)for(var c,f=a.getBooleans().entrySet().iterator();f.hasNext()&&((c=f.next())||1);)this.setBooleans(a,c.getKey());
else this.setBoolean(b,a.getBoolean(b))},"JSV.common.Parameters,JSV.common.ScriptToken");c(c$,"setBoolean",function(a,b){this.setTaintedAll();if(a===JSV.common.ScriptToken.REVERSEPLOT)this.currentGraphSet.setReversePlot(b);else switch(this.options.put(a,Boolean.$valueOf(b)),a){case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:this.doReset=!0}},"JSV.common.ScriptToken,~B");c(c$,"getBoolean",function(a){if(a===JSV.common.ScriptToken.REVERSEPLOT)return this.currentGraphSet.reversePlot;
if(null==this.options)return!1;a=this.options.get(a);return null!=a&&t(a,Boolean)&&a===Boolean.TRUE},"JSV.common.ScriptToken");c(c$,"setFontName",function(a,b){switch(a){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.displayFontName=b;break;case JSV.common.ScriptToken.TITLEFONTNAME:this.titleFontName=b}null!=b&&this.options.put(a,b)},"JSV.common.ScriptToken,~S");c(c$,"getDisplay1D",function(){return this.display1D});c(c$,"setTaintedAll",function(){this.taintedAll=!0});c(c$,"initOne",function(a){this.spectra=
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this.jsvp,this.spectra,this.startIndex,this.endIndex,a);this.currentGraphSet=this.graphSets.get(0);this.title=this.getSpectrum().getTitleLabel()},"JSV.common.PanelData.LinkMode");c(c$,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.graphSets.size()&&null==(b=this.graphSets.get(c).findMatchingPeakInfo(a));c++);return b},"JSV.common.PeakInfo");c(c$,"integrateAll",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).integrate(-1,a)},"JSV.common.ColorParameters");c(c$,
"getNumberOfGraphSets",function(){return this.graphSets.size()});c(c$,"getTitle",function(){return this.title});c(c$,"refresh",function(){this.doReset=!0});c(c$,"addAnnotation",function(a){a=this.currentGraphSet.addAnnotation(a,this.getTitle());null!=a&&(this.title=a)},"JU.Lst");c(c$,"addPeakHighlight",function(a){for(var b=0;b<this.graphSets.size();b++)this.graphSets.get(b).addPeakHighlight(a)},"JSV.common.PeakInfo");c(c$,"selectPeakByFileIndex",function(a,b,c){var f=this.currentGraphSet.selectPeakByFileIndex(a,
b,c);if(null==f)for(var g=this.graphSets.size();0<=--g&&!(this.graphSets.get(g)!==this.currentGraphSet&&null!=(f=this.graphSets.get(g).selectPeakByFileIndex(a,b,c))););return f},"~S,~S,~S");c(c$,"setPlotColors",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).setPlotColors(a)},"~A");c(c$,"selectSpectrum",function(a,b,c,f){f&&this.currentGraphSet.selectSpectrum(a,b,c);if("ID".equals(b))this.jumpToSpectrumIndex(this.getCurrentSpectrumIndex(),!0);else for(f=0;f<this.graphSets.size();f++)this.graphSets.get(f)!==
this.currentGraphSet&&this.graphSets.get(f).selectSpectrum(a,b,c)},"~S,~S,~S,~B");c(c$,"hasFileLoaded",function(a){for(var b=this.graphSets.size();0<=--b;)if(this.graphSets.get(b).hasFileLoaded(a))return!0;return!1},"~S");c(c$,"clearAllView",function(){for(var a=this.graphSets.size();0<=--a;)this.graphSets.get(a).resetViewCompletely()});c(c$,"drawGraph",function(a,b,c,f,g,e){var h;this.gMain=a;this.display1D=!this.isLinked&&this.getBoolean(JSV.common.ScriptToken.DISPLAY1D);var l=40,k=50,m=this.isPrinting||
this.doReset||this.thisWidth!=f||this.thisHeight!=g;m&&this.setTaintedAll();this.taintedAll&&this.g2d.fillBackground(c,this.bgcolor);b!==a&&(this.g2d.fillBackground(b,null),a!==c&&this.g2d.fillBackground(a,null),this.g2d.setStrokeBold(a,!1));this.isPrinting?(l*=3,k*=3,this.scalingFactor=10,h=!1):(this.scalingFactor=1,h=this.getBoolean(JSV.common.ScriptToken.COORDINATESON),this.titleOn=this.getBoolean(JSV.common.ScriptToken.TITLEON),this.gridOn=this.getBoolean(JSV.common.ScriptToken.GRIDON),this.peakTabsOn=
this.getBoolean(JSV.common.ScriptToken.PEAKTABSON));var n=this.getBoolean(JSV.common.ScriptToken.POINTSONLY);this.titleDrawn=this.doReset=!1;this.thisWidth=f;this.thisHeight=g;for(var p=this.graphSets.size();0<=--p;)this.graphSets.get(p).drawGraphSet(a,b,c,f,g,this.left,this.right,l,k,m,this.taintedAll,n);this.titleOn&&(!this.titleDrawn&&this.taintedAll)&&this.drawTitle(a,g*this.scalingFactor,f*this.scalingFactor,this.getDrawTitle(this.isPrinting));h&&null!=this.coordStr&&this.drawCoordinates(b,l,
this.thisWidth-this.right,l-20);e&&this.taintedAll&&this.printFilePath(a,this.left,g,null!=this.commonFilePath?this.commonFilePath:1==this.graphSets.size()&&null!=this.currentGraphSet.getTitle(!0)?this.getSpectrum().getFilePath():null);this.isPrinting&&this.printVersion(a,g);!this.testingJavaScript&&(this.isPrinting||a===b)?this.setTaintedAll():this.taintedAll=!1},"~O,~O,~O,~N,~N,~B");c(c$,"drawCoordinates",function(a,b,c,f){this.g2d.setGraphicsColor(a,this.coordinatesColor);b=this.setFont(a,this.jsvp.getWidth(),
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this.scalingFactor&&(b-=g.stringWidth(f));this.g2d.drawString(a,f,b,c-g.getHeight())}},"~O,~N,~N,~S");c(c$,"printVersion",function(a,b){this.g2d.setGraphicsColor(a,this.BLACK);var c=this.setFont(a,100,0,12,!0),f=this.jsvp.getApiPlatform().getDateFormat(null)+" JSpecView "+JSV.common.JSVersion.VERSION_SHORT,g=c.stringWidth(f);this.g2d.drawString(a,f,(this.thisWidth-this.right)*this.scalingFactor-g,b*this.scalingFactor-3*c.getHeight())},"~O,~N");c(c$,"drawTitle",function(a,b,c,f){f=f.$replace("\n",
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a},"JU.Font");c(c$,"getFontHeight",function(){return this.currentFont.getAscent()});c(c$,"getStringWidth",function(a){return this.currentFont.stringWidth(a)},"~S");c(c$,"selectFromEntireSet",function(a){for(var b=0,c=0;b<this.graphSets.size();b++)if(-2147483648==a)this.graphSets.get(b).setSelected(-1);else for(var f=this.graphSets.get(b).spectra,g=0;g<f.size();g++,c++)(0>a||a==c)&&this.graphSets.get(b).setSelected(g)},"~N");c(c$,"addToList",function(a,b){for(var c=0;c<this.spectra.size();c++)(0>a||
c==a)&&b.addLast(this.spectra.get(c))},"~N,JU.Lst");c(c$,"scaleSelectedBy",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).scaleSelectedBy(a)},"~N");c(c$,"setCurrentGraphSet",function(a,b){var c=1<a.nSplit?a.getSplitPoint(b):a.getCurrentSpectrumIndex(),f=this.currentGraphSet!==a,g=f||this.currentSplitPoint!=c;this.currentGraphSet=a;this.currentSplitPoint=c;(f||1<a.nSplit&&g)&&this.setSpectrum(c,!0);if(!f){f=a.checkSpectrumClickedEvent(this.mouseX,this.mouseY,this.clickCount);
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"~N,~B");c(c$,"getSpectrum",function(){return this.currentGraphSet.getSpectrum()});c(c$,"setSpecForIRMode",function(a){this.setTaintedAll();var b=this.currentGraphSet.getSpectrum();this.currentGraphSet.setSpectrumJDX(a);for(var c=0;c<this.spectra.size();c++)this.spectra.get(c)===b&&this.spectra.set(c,a)},"JSV.common.Spectrum");c(c$,"isShowAllStacked",function(){return this.currentGraphSet.showAllStacked});c(c$,"getCurrentSpectrumIndex",function(){return this.currentGraphSet.getCurrentSpectrumIndex()});
c(c$,"getSpectrumAt",function(a){return null==this.currentGraphSet?null:this.currentGraphSet.getSpectrumAt(a)},"~N");c(c$,"addHighlight",function(a,b,c,f,g,e,h,l){(null==a?this.currentGraphSet:a).addHighlight(b,c,f,this.g2d.getColor4(g,e,h,l))},"JSV.common.GraphSet,~N,~N,JSV.common.Spectrum,~N,~N,~N,~N");c(c$,"removeHighlight",function(a,b){this.currentGraphSet.removeHighlight(a,b)},"~N,~N");c(c$,"removeAllHighlights",function(){this.currentGraphSet.removeAllHighlights()});c(c$,"setZoom",function(a,
b,c,f){this.currentGraphSet.setZoom(a,b,c,f);this.doReset=!0;this.setTaintedAll();this.notifyListeners(new JSV.common.ZoomEvent)},"~N,~N,~N,~N");c(c$,"resetView",function(){this.currentGraphSet.resetView()});c(c$,"previousView",function(){this.currentGraphSet.previousView()});c(c$,"nextView",function(){this.currentGraphSet.nextView()});c(c$,"getSelectedIntegral",function(){return this.currentGraphSet.getSelectedIntegral()});c(c$,"advanceSubSpectrum",function(a){this.currentGraphSet.advanceSubSpectrum(a)},
"~N");c(c$,"setSelectedIntegral",function(a){this.currentGraphSet.setSelectedIntegral(a)},"~N");c(c$,"scaleYBy",function(a){this.currentGraphSet.scaleYBy(a)},"~N");c(c$,"toPeak",function(a){this.currentGraphSet.toPeak(a)},"~N");c(c$,"getClickedCoordinate",function(){return this.coordClicked});c(c$,"getPickedCoordinates",function(a,b){return JSV.common.Coordinate.getPickedCoordinates(this.coordsClicked,this.coordClicked,a,b)},"JSV.common.Coordinate,JSV.common.Coordinate");c(c$,"shiftSpectrum",function(a,
b,c){return this.currentGraphSet.shiftSpectrum(a,b,c)},"~N,~N,~N");c(c$,"findX",function(a,b){this.currentGraphSet.setXPointer(a,b)},"JSV.common.Spectrum,~N");c(c$,"setXPointers",function(a,b,c,f){this.currentGraphSet.setXPointer(a,b);this.currentGraphSet.setXPointer2(c,f)},"JSV.common.Spectrum,~N,JSV.common.Spectrum,~N");c(c$,"isCurrentGraphSet",function(a){return a===this.currentGraphSet},"JSV.common.GraphSet");c(c$,"repaint",function(){this.jsvp.doRepaint(!1)});c(c$,"setToolTipText",function(a){this.jsvp.setToolTipText(a)},
"~S");c(c$,"setHighlightColor",function(a){this.setColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR,a)},"javajs.api.GenericColor");c(c$,"getInput",function(a,b,c){return this.jsvp.getInput(a,b,c)},"~S,~S,~S");c(c$,"getFont",function(a,b,c,f,g){f*=this.scalingFactor;g?400>b&&(f=b*f/400):250>b&&(f=b*f/250);b=this.jsvp.getFontFaceID(this.isPrinting?this.printingFontName:this.displayFontName);return this.currentFont=JU.Font.createFont3D(b,c,f,f,this.jsvp.getApiPlatform(),a)},"~O,~N,~N,~N,~B");c(c$,"notifySubSpectrumChange",
function(a,b){this.notifyListeners(new JSV.common.SubSpecChangeEvent(a,null==b?null:b.getTitleLabel()))},"~N,JSV.common.Spectrum");c(c$,"notifyPeakPickedListeners",function(a){null==a&&(a=new JSV.common.PeakPickEvent(this.jsvp,this.coordClicked,this.getSpectrum().getAssociatedPeakInfo(this.xPixelClicked,this.coordClicked)));this.notifyListeners(a)},"JSV.common.PeakPickEvent");c(c$,"notifyListeners",function(a){for(var b=0;b<this.listeners.size();b++)null!=this.listeners.get(b)&&this.listeners.get(b).panelEvent(a)},
"~O");c(c$,"escapeKeyPressed",function(a){this.currentGraphSet.escapeKeyPressed(a)},"~B");c(c$,"hasFocus",function(){return this.jsvp.hasFocus()});c(c$,"isMouseUp",function(){return this.mouseState===JSV.common.PanelData.Mouse.UP});c(c$,"doMouseMoved",function(a,b){this.mouseX=a;this.mouseY=b;this.mouseState=JSV.common.PanelData.Mouse.UP;this.clickCount=0;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&c.mouseMovedEvent(a,b)},"~N,~N");c(c$,"doMousePressed",function(a,b){this.mouseState=
JSV.common.PanelData.Mouse.DOWN;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&(this.setCurrentGraphSet(c,b),this.clickCount=++this.clickCount%3,this.currentGraphSet.mousePressedEvent(a,b,this.clickCount))},"~N,~N");c(c$,"doMouseDragged",function(a,b){this.isIntegralDrag=(new Boolean(this.isIntegralDrag|this.ctrlPressed)).valueOf();this.mouseState=JSV.common.PanelData.Mouse.DOWN;JSV.common.GraphSet.findGraphSet(this.graphSets,a,b)===this.currentGraphSet&&(this.currentGraphSet.checkWidgetEvent(a,
b,!1)&&this.setTaintedAll(),this.currentGraphSet.mouseMovedEvent(a,b))},"~N,~N");c(c$,"doMouseReleased",function(a,b,c){this.mouseState=JSV.common.PanelData.Mouse.UP;!(null==this.thisWidget&&null==this.currentGraphSet.pendingMeasurement)&&c&&(this.currentGraphSet.mouseReleasedEvent(a,b),this.thisWidget=null,this.isIntegralDrag=!1,this.integralShiftMode=0)},"~N,~N,~B");c(c$,"doMouseClicked",function(a,b,c){var f=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=f&&(this.setCurrentGraphSet(f,
b),f.mouseClickedEvent(a,b,this.clickCount,c),this.setTaintedAll(),this.repaint())},"~N,~N,~B");c(c$,"hasCurrentMeasurements",function(a){return this.currentGraphSet.hasCurrentMeasurement(a)},"JSV.common.Annotation.AType");c(c$,"getDialog",function(a){return this.currentGraphSet.getDialog(a,-1)},"JSV.common.Annotation.AType");c(c$,"addDialog",function(a,b,c){this.currentGraphSet.addDialog(a,b,c)},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");c(c$,"getPeakListing",function(a,b){null!=a&&
this.currentGraphSet.getPeakListing(-1,a,!0);this.currentGraphSet.setPeakListing(b)},"JSV.common.Parameters,Boolean");c(c$,"checkIntegral",function(a,b){this.currentGraphSet.checkIntegralParams(a,b)},"JSV.common.Parameters,~S");c(c$,"setIntegrationRatios",function(a){this.currentGraphSet.setIntegrationRatios(a)},"~S");c(c$,"getView",function(){return this.currentGraphSet.getCurrentView()});c(c$,"closeAllDialogsExcept",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).closeDialogsExcept(a)},
"JSV.common.Annotation.AType");c(c$,"removeDialog",function(a){this.currentGraphSet.removeDialog(a)},"JSV.dialog.JSVDialog");c(c$,"normalizeIntegral",function(){var a=this.getSelectedIntegral();if(null!=a){var b=a.text;0==b.length&&(b=""+a.getValue());a=this.getInput("Enter a new value for this integral","Normalize Integral",b);try{this.setSelectedIntegral(Double.parseDouble(a))}catch(c){if(!D(c,Exception))throw c;}}});c(c$,"getDrawTitle",function(a){var b=null;a?b=this.printJobTitle:1==this.nSpectra?
b=this.getSpectrum().getPeakTitle():null!=this.viewTitle?(null!=this.currentGraphSet.getTitle(!1)&&(b=this.getSpectrum().getPeakTitle()),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();0<=b.indexOf("\n")&&(b=b.substring(0,b.indexOf("\n")).trim());return b},"~B");c(c$,"getPrintJobTitle",function(a){var b=null;1==this.nSpectra?b=this.getSpectrum().getTitle():null!=this.viewTitle?(1==this.graphSets.size()&&(b=this.currentGraphSet.getTitle(a)),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();
0<=b.indexOf("\n")?b=b.substring(0,b.indexOf("\n")).trim():b.startsWith("$")&&(b=b.substring(1));return b},"~B");c(c$,"linkSpectra",function(a){a===JSV.common.PanelData.LinkMode.ALL&&(a=2==this.nSpectra?JSV.common.PanelData.LinkMode.AB:3==this.nSpectra?JSV.common.PanelData.LinkMode.ABC:JSV.common.PanelData.LinkMode.NONE);a!==JSV.common.PanelData.LinkMode.NONE&&a.toString().length!=this.nSpectra||this.setGraphSets(a)},"JSV.common.PanelData.LinkMode");c(c$,"doZoomLinked",function(a,b,c,f,g,e){if(!this.linking){this.linking=
!0;for(var h=a.getSpectrumAt(0),l=this.graphSets.size();0<=--l;){var k=this.graphSets.get(l);k!==a&&JSV.common.Spectrum.areXScalesCompatible(h,this.graphSets.get(l).getSpectrumAt(0),!1,!0)&&k.doZoom(b,0,c,0,e,!1,g,!1,f)}this.linking=!1}},"JSV.common.GraphSet,~N,~N,~B,~B,~B");c(c$,"clearLinkViews",function(a){if(!this.linking){this.linking=!0;for(var b=a.getSpectrum(),c=this.graphSets.size();0<=--c;){var f=this.graphSets.get(c);f!==a&&JSV.common.Spectrum.areXScalesCompatible(b,this.graphSets.get(c).getSpectrum(),
!1,!0)&&f.clearViews()}this.linking=!1}},"JSV.common.GraphSet");c(c$,"setlinkedXMove",function(a,b,c){if(!this.linking){this.linking=!0;for(var f=a.getSpectrum(),g=this.graphSets.size();0<=--g;){var e=this.graphSets.get(g);e!==a&&JSV.common.Spectrum.areXScalesCompatible(f,this.graphSets.get(g).getSpectrum(),!1,!0)&&null==e.imageView&&(c?e.setXPixelMovedTo(1.7976931348623157E308,b,0,0):e.setXPixelMovedTo(b,1.7976931348623157E308,0,0))}this.linking=!1}},"JSV.common.GraphSet,~N,~B");c(c$,"set2DCrossHairsLinked",
function(a,b,c,f){for(var g=this.graphSets.size();0<=--g;){var e=this.graphSets.get(g);e!==a&&e.set2DXY(b,c,f)}},"JSV.common.GraphSet,~N,~N,~B");c(c$,"dialogsToFront",function(a){this.currentGraphSet.dialogsToFront(a)},"JSV.common.Spectrum");c(c$,"setColor",function(a,b){null!=b&&this.options.put(a,JU.CU.toRGBHexString(b));switch(a){case JSV.common.ScriptToken.COORDINATESCOLOR:this.coordinatesColor=b;return;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:this.highlightColor=b;255==this.highlightColor.getOpacity255()&&
this.highlightColor.setOpacity255(150);return;case JSV.common.ScriptToken.ZOOMBOXCOLOR:this.zoomBoxColor=b;return;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:this.zoomBoxColor2=b;return;case JSV.common.ScriptToken.BACKGROUNDCOLOR:this.jsvp.setBackgroundColor(this.bgcolor=b);break;case JSV.common.ScriptToken.GRIDCOLOR:this.gridColor=b;break;case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:this.integralPlotColor=b;break;case JSV.common.ScriptToken.PEAKTABCOLOR:this.peakTabColor=b;break;case JSV.common.ScriptToken.PLOTCOLOR:for(var c=
this.graphSets.size();0<=--c;)this.graphSets.get(c).setPlotColor0(b);break;case JSV.common.ScriptToken.PLOTAREACOLOR:this.plotAreaColor=b;break;case JSV.common.ScriptToken.SCALECOLOR:this.scaleColor=b;break;case JSV.common.ScriptToken.TITLECOLOR:this.titleColor=b;break;case JSV.common.ScriptToken.UNITSCOLOR:this.unitsColor=b;break;default:JU.Logger.warn("AwtPanel --- unrecognized color: "+a);return}this.taintedAll=!0},"JSV.common.ScriptToken,javajs.api.GenericColor");c(c$,"getColor",function(a){switch(a){default:return JU.Logger.error("awtgraphset missing color "+
a),this.BLACK;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:return this.zoomBoxColor2;case JSV.common.ScriptToken.ZOOMBOXCOLOR:return this.zoomBoxColor;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:return this.highlightColor;case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:return this.integralPlotColor;case JSV.common.ScriptToken.GRIDCOLOR:return this.gridColor;case JSV.common.ScriptToken.PEAKTABCOLOR:return this.peakTabColor;case JSV.common.ScriptToken.PLOTAREACOLOR:return this.plotAreaColor;case JSV.common.ScriptToken.SCALECOLOR:return this.scaleColor;
case JSV.common.ScriptToken.TITLECOLOR:return this.titleColor;case JSV.common.ScriptToken.UNITSCOLOR:return this.unitsColor}},"JSV.common.ScriptToken");c(c$,"getOverlayLegendData",function(){for(var a=this.currentGraphSet.nSpectra,b=Array(a),c=this.getSpectrumAt(0).getFilePath(),f=this.getSpectrumAt(a-1).getFilePath(),c=null!=c&&null!=f&&!c.equals(f),f=0;f<a;f++){var g=Array(3),e=this.getSpectrumAt(f);this.title=e.getTitle();c&&(this.title=JSV.common.JSVFileManager.getTagName(e.getFilePath())+" - "+
this.title);e=this.getCurrentPlotColor(f);g[0]=new Integer(f+1);g[1]=e;g[2]=" "+this.title;b[f]=g}return b});c(c$,"setColorOrFont",function(a,b){if(null==b){for(var c,f=a.elementColors.entrySet().iterator();f.hasNext()&&((c=f.next())||1);)this.setColorOrFont(a,c.getKey());this.setColorOrFont(a,JSV.common.ScriptToken.DISPLAYFONTNAME);this.setColorOrFont(a,JSV.common.ScriptToken.TITLEFONTNAME)}else{switch(b){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.setFontName(b,a.displayFontName);return;case JSV.common.ScriptToken.TITLEFONTNAME:this.setFontName(b,
a.titleFontName);return}this.setColor(b,a.getElementColor(b))}},"JSV.common.ColorParameters,JSV.common.ScriptToken");c(c$,"getCurrentPlotColor",function(a){return this.currentGraphSet.getPlotColor(a)},"~N");c(c$,"setPrint",function(a,b){null==a?(this.options.putAll(this.optionsSaved),this.optionsSaved=null):(this.printJobTitle=a.title,this.printingFontName=b,this.printGraphPosition=a.position,this.optionsSaved=new java.util.Hashtable,this.optionsSaved.putAll(this.options),this.gridOn=a.showGrid,this.titleOn=
a.showTitle,this.setBoolean(JSV.common.ScriptToken.XSCALEON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.XUNITSON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.YSCALEON,a.showYScale),this.setBoolean(JSV.common.ScriptToken.YUNITSON,a.showYScale))},"JSV.common.PrintLayout,~S");c(c$,"setDefaultPrintOptions",function(a){a.showGrid=this.gridOn;a.showXScale=this.getBoolean(JSV.common.ScriptToken.XSCALEON);a.showYScale=this.getBoolean(JSV.common.ScriptToken.YSCALEON);a.showTitle=this.titleOn},
"JSV.common.PrintLayout");c(c$,"showDialog",function(a){var b=this.getDialog(a);this.closeAllDialogsExcept(a);if(null!=b&&t(b,JSV.dialog.JSVDialog))return b.reEnable();var c=this.getCurrentSpectrumIndex();if(0>c)return this.jsvp.showMessage("To enable "+a+" first select a spectrum by clicking on it.",""+a),null;var f=this.getSpectrum(),g=this.vwr.getDialog(a,f);null==b&&a===JSV.common.Annotation.AType.Measurements&&(b=new JSV.common.MeasurementData(JSV.common.Annotation.AType.Measurements,f));null!=
b&&g.setData(b);this.addDialog(c,a,g);g.reEnable();return g},"JSV.common.Annotation.AType");c(c$,"printPdf",function(a,b){var c=!b.layout.equals("landscape");this.print(a,c?b.imageableHeight:b.imageableWidth,c?b.imageableWidth:b.imageableHeight,b.imageableX,b.imageableY,b.paperHeight,b.paperWidth,c,0)},"J.api.GenericGraphics,JSV.common.PrintLayout");c(c$,"print",function(a,b,c,f,g,e,h,l,k){this.g2d=this.g2d0;if(0==k)return this.isPrinting=!0,k=!1,t(a,J.api.GenericGraphics)&&(this.g2d=a,a=this.gMain),
this.printGraphPosition.equals("default")?l?(b=450,c=280):(b=280,c=450):this.printGraphPosition.equals("fit to page")?k=!0:l?(b=450,c=280,f=u(u(h-c)/2),g=u(u(e-b)/2)):(b=280,c=450,g=u(u(h-280)/2),f=u(u(e-450)/2)),this.g2d.translateScale(a,f,g,0.1),this.setTaintedAll(),this.drawGraph(a,a,a,u(c),u(b),k),this.isPrinting=!1,0;this.isPrinting=!1;return 1},"~O,~N,~N,~N,~N,~N,~N,~B,~N");h(c$,"keyPressed",function(a,b){if(this.isPrinting)return!1;this.checkKeyControl(a,!0);switch(a){case 27:case 127:case 8:return this.escapeKeyPressed(27!=
a),this.isIntegralDrag=!1,this.setTaintedAll(),this.repaint(),!0}var c=0,f=!1;if(0==b)switch(a){case 37:case 39:this.doMouseMoved(39==a?++this.mouseX:--this.mouseX,this.mouseY);this.repaint();f=!0;break;case 33:case 34:c=33==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;f=!0;break;case 40:case 38:f=40==a?-1:1,null==this.getSpectrumAt(0).getSubSpectra()?this.notifySubSpectrumChange(f,null):(this.advanceSubSpectrum(f),this.setTaintedAll(),this.repaint()),f=!0}else if(this.checkMod(a,2))switch(a){case 40:case 38:case 45:case 61:c=
61==a||38==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;f=!0;break;case 37:case 39:this.toPeak(39==a?1:-1),f=!0}0!=c&&(this.scaleYBy(c),this.setTaintedAll(),this.repaint());return f},"~N,~N");h(c$,"keyReleased",function(a){this.isPrinting||this.checkKeyControl(a,!1)},"~N");h(c$,"keyTyped",function(a,b){if(this.isPrinting)return!1;switch(a){case "n":if(0!=b)break;this.normalizeIntegral();return!0;case 26:if(2!=b)break;this.previousView();this.setTaintedAll();this.repaint();return!0;case 25:if(2!=
b)break;this.nextView();this.setTaintedAll();this.repaint();return!0}return!1},"~N,~N");h(c$,"mouseAction",function(a,b,c,f,g,e){if(!this.isPrinting)switch(a){case 4:if(!this.checkMod(e,16))break;this.doMousePressed(c,f);break;case 5:this.doMouseReleased(c,f,this.checkMod(e,16));this.setTaintedAll();this.repaint();break;case 1:this.doMouseDragged(c,f);this.repaint();break;case 0:this.jsvp.getFocusNow(!1);if(0!=(e&28)){this.doMouseDragged(c,f);this.repaint();break}this.doMouseMoved(c,f);null!=this.coordStr&&
this.repaint();break;case 2:if(this.checkMod(e,4)){this.jsvp.showMenu(c,f);break}this.ctrlPressed=!1;this.doMouseClicked(c,f,this.updateControlPressed(e))}},"~N,~N,~N,~N,~N,~N");c(c$,"checkMod",function(a,b){return(a&b)==b},"~N,~N");c(c$,"checkKeyControl",function(a,b){switch(a){case 17:case 157:this.ctrlPressed=b;break;case 16:this.shiftPressed=b}},"~N,~B");c(c$,"updateControlPressed",function(a){return this.ctrlPressed=(new Boolean(this.ctrlPressed|(this.checkMod(a,2)||this.checkMod(a,20)))).valueOf()},
"~N");h(c$,"mouseEnterExit",function(a,b,c,f){if(f)this.thisWidget=null,this.isIntegralDrag=!1,this.integralShiftMode=0;else try{this.jsvp.getFocusNow(!1)}catch(g){if(D(g,Exception))Zystem.out.println("pd "+this+" cannot focus");else throw g;}},"~N,~N,~N,~B");c(c$,"setSolutionColor",function(a){var b=0<=a.indexOf("none"),c=0>a.indexOf("false");if(0>a.indexOf("all"))b=b?-1:this.vwr.getSolutionColor(c),this.getSpectrum().setFillColor(-1==b?null:this.vwr.parameters.getColor1(b));else{a=JSV.common.JSViewer.getInterface("JSV.common.Visible");
for(var f=this.graphSets.size();0<=--f;)this.graphSets.get(f).setSolutionColor(a,b,c)}},"~S");c(c$,"setIRMode",function(a,b){for(var c=this.graphSets.size();0<=--c;)this.graphSets.get(c).setIRMode(a,b)},"JSV.common.Spectrum.IRMode,~S");c(c$,"closeSpectrum",function(){this.vwr.close("views");this.vwr.close(this.getSourceID());this.vwr.execView("*",!0)});N(self.c$);c$=F(JSV.common.PanelData,"LinkMode",Enum);c$.getMode=c(c$,"getMode",function(a){if(a.equals("*"))return JSV.common.PanelData.LinkMode.ALL;
for(var b,c=0,f=JSV.common.PanelData.LinkMode.values();c<f.length&&((b=f[c])||1);c++)if(b.name().equalsIgnoreCase(a))return b;return JSV.common.PanelData.LinkMode.NONE},"~S");y(c$,"ALL",0,[]);y(c$,"NONE",1,[]);y(c$,"AB",2,[]);y(c$,"ABC",3,[]);c$=M();N(self.c$);c$=F(JSV.common.PanelData,"Mouse",Enum);y(c$,"UP",0,[]);y(c$,"DOWN",1,[]);c$=M();G(c$,"defaultPrintHeight",450,"defaultPrintWidth",280,"topMargin",40,"bottomMargin",50,"leftMargin",60,"rightMargin",50)});m("JSV.common");x(null,"JSV.common.PanelNode",
["JU.SB","JSV.common.Parameters"],function(){c$=w(function(){this.legend=this.id=this.jsvp=this.fileName=this.source=this.treeNode=null;this.isSimulation=this.isView=this.isSelected=!1;this.frameTitle=null;s(this,arguments)},JSV.common,"PanelNode");p(c$,function(a,b,c,f){this.id=a;this.source=c;this.fileName=b;this.isSimulation=0<=c.getFilePath().indexOf("http://SIMULATION/");this.jsvp=f;null!=f&&(this.pd().getSpectrumAt(0).setId(a),this.frameTitle=f.getTitle())},"~S,~S,JSV.source.JDXSource,JSV.api.JSVPanel");
c(c$,"setTreeNode",function(a){this.treeNode=a},"JSV.api.JSVTreeNode");c(c$,"getTreeNode",function(){return this.treeNode});c(c$,"dispose",function(){this.source.dispose();null!=this.jsvp&&this.jsvp.dispose();this.legend=this.jsvp=this.source=null});c(c$,"pd",function(){return this.jsvp.getPanelData()});c(c$,"getSpectrum",function(){return this.pd().getSpectrum()});c(c$,"setLegend",function(a){null!=this.legend&&this.legend.dispose();return this.legend=a},"JSV.dialog.JSVDialog");h(c$,"toString",function(){return(null==
this.id?"":this.id+": ")+(null==this.frameTitle?this.fileName:this.frameTitle)});c$.findSourceByNameOrId=c(c$,"findSourceByNameOrId",function(a,b){for(var c=b.size();0<=--c;){var f=b.get(c);if(a.equals(f.id)||a.equals(f.source.getSpectra().get(0).sourceID)||f.source.matchesFilePath(a))return f.source}for(c=b.size();0<=--c;)if(f=b.get(c),a.equals(f.fileName))return f.source;return null},"~S,JU.Lst");c$.findNodeById=c(c$,"findNodeById",function(a,b){if(null!=a)for(var c=b.size();0<=--c;)if(a.equals(b.get(c).id)||
a.equals(b.get(c).frameTitle))return b.get(c);return null},"~S,JU.Lst");c$.findNode=c(c$,"findNode",function(a,b){for(var c=b.size();0<=--c;)if(b.get(c).jsvp===a)return b.get(c);return null},"JSV.api.JSVPanel,JU.Lst");c$.getSpectrumListAsString=c(c$,"getSpectrumListAsString",function(a){for(var b=new JU.SB,c=0;c<a.size();c++){var f=a.get(c);f.isView||b.append(" ").append(f.id)}return b.toString().trim()},"JU.Lst");c$.isOpen=c(c$,"isOpen",function(a,b){if(null!=b)for(var c=a.size();0<=--c&&!a.get(c).source.matchesFilePath(b)&&
!b.equals(a.get(c).frameTitle););return-1},"JU.Lst,~S");c(c$,"setFrameTitle",function(a){this.frameTitle=a},"~S");c$.getLastFileFirstNode=c(c$,"getLastFileFirstNode",function(a){for(var b=a.size(),c=0==b?null:a.get(b-1),b=b-1;0<=--b&&a.get(b).source===c.source;)c=a.get(b);return null==c?null:c.jsvp},"JU.Lst");c(c$,"getInfo",function(a){var b=this.pd().getInfo(!1,a);JSV.common.Parameters.putInfo(a,b,"panelId",this.id);JSV.common.Parameters.putInfo(a,b,"panelFileName",this.fileName);JSV.common.Parameters.putInfo(a,
b,"panelSource",this.source.getFilePath());return b},"~S")});m("JSV.common");x(null,"JSV.common.Parameters",["java.lang.Boolean","java.util.Hashtable","JSV.common.ScriptToken"],function(){c$=w(function(){this.name=null;this.integralMinY=0.1;this.integralRange=50;this.integralOffset=30;this.integralDrawAll=!1;this.viewOffset=0;this.peakListThreshold=NaN;this.peakListInterpolation="parabolic";this.precision=2;this.htBooleans=null;s(this,arguments)},JSV.common,"Parameters");p(c$,function(){this.htBooleans=
new java.util.Hashtable;this.setBoolean(JSV.common.ScriptToken.TITLEON,!0);this.setBoolean(JSV.common.ScriptToken.ENABLEZOOM,!0);this.setBoolean(JSV.common.ScriptToken.DISPLAY2D,!0);this.setBoolean(JSV.common.ScriptToken.COORDINATESON,!0);this.setBoolean(JSV.common.ScriptToken.PEAKTABSON,!0);this.setBoolean(JSV.common.ScriptToken.POINTSONLY,!1);this.setBoolean(JSV.common.ScriptToken.GRIDON,!0);this.setBoolean(JSV.common.ScriptToken.XSCALEON,!0);this.setBoolean(JSV.common.ScriptToken.YSCALEON,!0);
this.setBoolean(JSV.common.ScriptToken.XUNITSON,!0);this.setBoolean(JSV.common.ScriptToken.YUNITSON,!0)});c(c$,"setName",function(a){this.name=a;return this},"~S");c(c$,"getBooleans",function(){return this.htBooleans});c(c$,"setBoolean",function(a,b){this.htBooleans.put(a,Boolean.$valueOf(b));return b},"JSV.common.ScriptToken,~B");c(c$,"getBoolean",function(a){return Boolean.TRUE===this.htBooleans.get(a)},"JSV.common.ScriptToken");c$.isTrue=c(c$,"isTrue",function(a){return 0==a.length||Boolean.parseBoolean(a)},
"~S");c$.getTFToggle=c(c$,"getTFToggle",function(a){return a.equalsIgnoreCase("TOGGLE")?null:JSV.common.Parameters.isTrue(a)?Boolean.TRUE:Boolean.FALSE},"~S");c(c$,"setP",function(a,b,c){switch(b){default:return;case JSV.common.ScriptToken.COORDINATESON:case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:case JSV.common.ScriptToken.ENABLEZOOM:case JSV.common.ScriptToken.GRIDON:case JSV.common.ScriptToken.POINTSONLY:case JSV.common.ScriptToken.PEAKTABSON:case JSV.common.ScriptToken.REVERSEPLOT:case JSV.common.ScriptToken.TITLEON:case JSV.common.ScriptToken.TITLEBOLDON:case JSV.common.ScriptToken.XSCALEON:case JSV.common.ScriptToken.XUNITSON:case JSV.common.ScriptToken.YSCALEON:case JSV.common.ScriptToken.YUNITSON:c=
JSV.common.Parameters.getTFToggle(c);if(null!=c){this.setBoolean(b,c.booleanValue());break}if(null==a)return;c=!a.getBoolean(b);switch(b){case JSV.common.ScriptToken.XSCALEON:this.setBoolean(JSV.common.ScriptToken.XUNITSON,c);a.setBoolean(JSV.common.ScriptToken.XUNITSON,c);break;case JSV.common.ScriptToken.YSCALEON:this.setBoolean(JSV.common.ScriptToken.YUNITSON,c),a.setBoolean(JSV.common.ScriptToken.YUNITSON,c)}this.setBoolean(b,c)}null!=a&&a.setBooleans(this,b)},"JSV.common.PanelData,JSV.common.ScriptToken,~S");
c$.isMatch=c(c$,"isMatch",function(a,b){return null==a||b.equalsIgnoreCase(a)},"~S,~S");c$.putInfo=c(c$,"putInfo",function(a,b,c,f){null!=f&&JSV.common.Parameters.isMatch(a,c)&&b.put(null==a?c:a,f)},"~S,java.util.Map,~S,~O")});m("JSV.common");x(["JSV.common.MeasurementData"],"JSV.common.PeakData",["java.lang.Double","JU.DF","JSV.common.Coordinate","$.PeakPick"],function(){c$=w(function(){this.maxY=this.minY=this.thresh=0;s(this,arguments)},JSV.common,"PeakData",JSV.common.MeasurementData);c(c$,"getThresh",
function(){return this.thresh});h(c$,"getDataHeader",function(){return this.spec.isHNMR()?JSV.common.PeakData.HNMR_HEADER:v(-1,["peak",this.spec.getXUnits(),this.spec.getYUnits()])});h(c$,"getMeasurementListArray",function(){for(var a=Array(this.size()),b=Q(-1,[-1E100,1E100,1E100]),c,f=0,g=this.size();0<=--g;f++)c=this.spec.getPeakListArray(this.get(g),b,this.maxY),a[f]=2==c.length?v(-1,[""+(f+1),JU.DF.formatDecimalDbl(c[0],2),JU.DF.formatDecimalDbl(c[1],4)]):v(-1,[""+(f+1),JU.DF.formatDecimalDbl(c[0],
4),JU.DF.formatDecimalDbl(c[1],4),JU.DF.formatDecimalDbl(c[2],2),0==c[3]?"":JU.DF.formatDecimalDbl(c[3],2),0==c[4]?"":JU.DF.formatDecimalDbl(c[4],2),0==c[5]?"":JU.DF.formatDecimalDbl(c[5],2)]);return a},"~S");h(c$,"getMeasurementListArrayReal",function(){for(var a=Q(this.size(),0),b=Q(-1,[-1E100,1E100,1E100]),c=0,f=this.size();0<=--f;c++)a[c]=this.spec.getPeakListArray(this.get(f),b,this.maxY);return a},"~S");c(c$,"getInfo",function(a){a.put("interpolation",this.myParams.peakListInterpolation);a.put("threshold",
Double.$valueOf(this.myParams.peakListThreshold));T(this,JSV.common.PeakData,"getInfo",[a])},"java.util.Map");c(c$,"setPeakList",function(a,b,c){this.precision=-2147483648==b?this.spec.getDefaultUnitPrecision():b;var f=this.spec.getXYCoords();if(!(3>f.length)){this.clear();null!=a&&(this.myParams.peakListInterpolation=a.peakListInterpolation,this.myParams.peakListThreshold=a.peakListThreshold);a=this.myParams.peakListInterpolation.equals("parabolic");var g=this.spec.isInverted();this.minY=c.minYOnScale;
this.maxY=c.maxYOnScale;var e=c.minXOnScale;c=c.maxXOnScale;this.thresh=this.myParams.peakListThreshold;Double.isNaN(this.thresh)&&(this.thresh=this.myParams.peakListThreshold=(this.minY+this.maxY)/2);var h=0,l=Q(-1,[f[0].getYVal(),h=f[1].getYVal(),0]),k=0;if(g)for(g=2;g<f.length;g++){var m=l[g%3]=f[g].getYVal();if(h<this.thresh&&(l[(g-2)%3]>h&&h<m)&&(h=a?JSV.common.Coordinate.parabolicInterpolation(f,g-1):f[g-1].getXVal(),h>=e||h<=c))if(h=(new JSV.common.PeakPick).setValue(h,m,this.spec,null,0),
this.addLast(h),100==++k)break;h=m}else for(g=2;g<f.length;g++){m=l[g%3]=f[g].getYVal();if(h>this.thresh&&(l[(g-2)%3]<h&&h>m)&&(h=a?JSV.common.Coordinate.parabolicInterpolation(f,g-1):f[g-1].getXVal(),h>=e&&h<=c&&(h=(new JSV.common.PeakPick).setValue(h,m,this.spec,JU.DF.formatDecimalDbl(h,b),h),this.addLast(h),100==++k)))break;h=m}}},"JSV.common.Parameters,~N,JSV.common.ScaleData");c$.HNMR_HEADER=c$.prototype.HNMR_HEADER=v(-1,"peak shift/ppm intens shift/hz diff/hz 2-diff 3-diff".split(" "))});m("JSV.common");
x(null,"JSV.common.PeakInfo",["JU.PT"],function(){c$=w(function(){this.px1=this.px0=this.yMax=this.yMin=this.xMax=this.xMin=0;this.atomKey=this._match=this.spectrum=this.id=this.atoms=this.model=this.title=this.filePathForwardSlash=this.file=this.index=this.type2=this.type=this.stringInfo=null;s(this,arguments)},JSV.common,"PeakInfo");p(c$,function(){});p(c$,function(a){this.stringInfo=a;this.type=JU.PT.getQuotedAttribute(a,"type");null==this.type&&(this.type="");this.type=this.type.toUpperCase();
var b=this.type.indexOf("/");this.type2=0>b?"":JSV.common.PeakInfo.fixType(this.type.substring(this.type.indexOf("/")+1));this.type=0<=b?JSV.common.PeakInfo.fixType(this.type.substring(0,b))+"/"+this.type2:JSV.common.PeakInfo.fixType(this.type);this.id=JU.PT.getQuotedAttribute(a,"id");this.index=JU.PT.getQuotedAttribute(a,"index");this.file=JU.PT.getQuotedAttribute(a,"file");Zystem.out.println("pi file="+this.file);this.filePathForwardSlash=null==this.file?null:this.file.$replace("\\","/");this.model=
JU.PT.getQuotedAttribute(a,"model");a.contains('baseModel=""')||(this.atoms=JU.PT.getQuotedAttribute(a,"atoms"));this.atomKey=","+this.atoms+",";this.title=JU.PT.getQuotedAttribute(a,"title");this._match=JU.PT.getQuotedAttribute(a,"_match");this.xMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMax"));this.xMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMin"));this.yMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMax"));this.yMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMin"))},"~S");c(c$,
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"13CNMR":a},"~S");h(c$,"toString",function(){return this.stringInfo});c(c$,"getIndex",function(){return this.index});c(c$,"getTitle",function(){return this.title});c(c$,"checkFileIndex",function(a,b,c){return null!=c?0<=this.atomKey.indexOf(c):b.equals(this.index)&&(a.equals(this.file)||a.equals(this.filePathForwardSlash))},"~S,~S,~S");c(c$,"checkFileTypeModel",function(a,b,c){return a.equals(this.file)&&this.checkModel(c)&&this.type.endsWith(b)},"~S,~S,~S");c(c$,"checkTypeModel",function(a,b){return this.checkType(a)&&
this.checkModel(b)},"~S,~S");c(c$,"checkModel",function(a){return null!=a&&a.equals(this.model)},"~S");c(c$,"checkType",function(a){return a.endsWith(this.type)},"~S");c(c$,"checkTypeMatch",function(a){return this.checkType(a.type)&&(this.checkId(a._match)||this.checkModel(a._match)||0<=this.title.toUpperCase().indexOf(a._match))},"JSV.common.PeakInfo");c(c$,"checkId",function(a){return null==a?!1:null!=this.id&&a.toUpperCase().startsWith("ID=")&&a.substring(3).equals(this.id)||(a=a.toUpperCase()).startsWith("INDEX=")&&
a.equals("INDEX="+this.index)||a.startsWith("#=")&&a.equals("#="+this.index)},"~S");c(c$,"getModel",function(){return this.model});c(c$,"getFilePath",function(){return this.file});c(c$,"autoSelectOnLoad",function(){return this.type.startsWith("GC")});c(c$,"setPixelRange",function(a,b){this.px0=a;this.px1=b},"~N,~N");c(c$,"checkRange",function(a,b){return(2147483647!=a?this.px0<=a&&this.px1>=a:b>=this.xMin&&b<=this.xMax)?Math.abs(b-this.getX()):1E100},"~N,~N");c(c$,"getXPixel",function(){return u((this.px0+
this.px1)/2)});c$.nullPeakInfo=c$.prototype.nullPeakInfo=new JSV.common.PeakInfo});m("JSV.common");x(["JSV.common.Measurement"],"JSV.common.PeakPick",null,function(){c$=F(JSV.common,"PeakPick",JSV.common.Measurement);c(c$,"setValue",function(a,b,c,f,g){null==f?(this.set(a,b),this.setPt2(c,!1)):(this.setA(a,b,c,f,!1,!1,0,6),this.value=g,this.setPt2(this.getXVal(),this.getYVal()));return this},"~N,~N,JSV.common.Spectrum,~S,~N")});m("JSV.common");x(["java.util.EventObject"],"JSV.common.PeakPickEvent",
null,function(){c$=w(function(){this.peakInfo=this.coord=null;s(this,arguments)},JSV.common,"PeakPickEvent",java.util.EventObject);p(c$,function(a,b,c){I(this,JSV.common.PeakPickEvent,[a]);this.coord=b;this.peakInfo=null==c?null:c},"~O,JSV.common.Coordinate,JSV.common.PeakInfo");c(c$,"getCoord",function(){return this.coord});c(c$,"getPeakInfo",function(){return this.peakInfo});h(c$,"toString",function(){return null==this.peakInfo?null:this.peakInfo.toString()})});m("JSV.common");x(["JSV.common.Coordinate",
"$.ScriptToken"],"JSV.common.PlotWidget",null,function(){c$=w(function(){this.yPixel1=this.xPixel1=this.yPixel0=this.xPixel0=0;this.is2Donly=this.is2D=this.isXtype=this.isPinOrCursor=this.isPin=!1;this.isEnabled=!0;this.isVisible=!1;this.color=this.name=null;s(this,arguments)},JSV.common,"PlotWidget",JSV.common.Coordinate);O(c$,function(){this.color=JSV.common.ScriptToken.PLOTCOLOR});h(c$,"toString",function(){return this.name+(!this.isPinOrCursor?""+this.xPixel0+" "+this.yPixel0+" / "+this.xPixel1+
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null;s(this,arguments)},JSV.common,"RepaintManager");p(c$,function(a){this.vwr=a},"JSV.common.JSViewer");c(c$,"refresh",function(){if(this.repaintPending)return!1;this.repaintPending=!0;var a=this.vwr.html5Applet,b=JSV.common.JSViewer.isJS&&!JSV.common.JSViewer.isSwingJS?JSV.common.JSViewer.jmolObject:null;null==b?this.vwr.selectedPanel.repaint():(b.repaint(a,!1),this.repaintDone());return!0});c(c$,"repaintDone",function(){this.repaintPending=!1;this.notify()})});m("JSV.common");x(null,"JSV.common.ScaleData",
["java.lang.Double","JSV.common.Coordinate"],function(){c$=w(function(){this.maxX=this.minX=this.pointCount=this.endDataPointIndex=this.startDataPointIndex=this.initMaxY=this.initMinY=this.initMaxYOnScale=this.initMinYOnScale=0;this.firstX=NaN;this.specShift=this.maxXOnScale=this.minXOnScale=0;this.minorTickCounts=this.steps=this.exportPrecision=this.precision=null;this.maxY=this.minY=this.maxYOnScale=this.minYOnScale=0;this.isShiftZoomedY=!1;this.spectrumScaleFactor=1;this.spectrumYRef=0;this.userYFactor=
1;this.yFactorForScale=this.xFactorForScale=this.maxY2D=this.minY2D=this.firstY=0;s(this,arguments)},JSV.common,"ScaleData");O(c$,function(){this.precision=B(2,0);this.exportPrecision=B(2,0);this.steps=Q(2,0);this.minorTickCounts=B(2,0)});p(c$,function(){});p(c$,function(a,b){this.startDataPointIndex=a;this.endDataPointIndex=b;this.pointCount=this.endDataPointIndex-this.startDataPointIndex+1},"~N,~N");p(c$,function(a,b,c,f,g){this.minX=JSV.common.Coordinate.getMinX(a,b,c);this.maxX=JSV.common.Coordinate.getMaxX(a,
b,c);this.minY=JSV.common.Coordinate.getMinY(a,b,c);0<this.minY&&!f&&(this.minY=0);this.maxY=JSV.common.Coordinate.getMaxY(a,b,c);this.setScale(f,g)},"~A,~N,~N,~B,~B");c(c$,"setScale",function(a,b){this.setXScale();a||(this.maxXOnScale+=this.steps[0]/2);this.setYScale(this.minY,this.maxY,!0,b)},"~B,~B");c(c$,"setXScale",function(){var a=this.setScaleParams(this.minX,this.maxX,0);this.firstX=Math.floor(this.minX/a)*a;1E-4<Math.abs((this.minX-this.firstX)/a)&&(this.firstX+=a);this.minXOnScale=this.minX;
this.maxXOnScale=this.maxX});c(c$,"isYZeroOnScale",function(){return this.minYOnScale<this.spectrumYRef&&this.maxYOnScale>this.spectrumYRef});c(c$,"setYScale",function(a,b,c,f){0==a&&0==b&&(b=1);this.isShiftZoomedY&&(a=this.minYOnScale,b=this.maxYOnScale);var g=this.setScaleParams(a,b,1),e=f?g/2:g/4;f=f?g/4:g/2;this.isShiftZoomedY||(this.minYOnScale=0==a?0:c?e*Math.floor(a/e):a,this.maxYOnScale=c?f*Math.ceil(1.05*b/f):b);this.firstY=0==a?0:Math.floor(a/e)*e;if(0>this.minYOnScale&&0<this.maxYOnScale)for(this.firstY=
0;this.firstY-g>this.minYOnScale;)this.firstY-=g;else 0!=this.minYOnScale&&1E-4<Math.abs((a-this.firstY)/e)&&(this.firstY+=e);c&&(this.initMinYOnScale=this.minYOnScale,this.initMaxYOnScale=this.maxYOnScale,this.initMinY=a,this.initMaxY=b)},"~N,~N,~B,~B");c(c$,"scale2D",function(a){var b=this.maxY-this.minY;1==a?(this.maxY=this.initMaxY,this.minY=this.initMinY):this.maxY=this.minY+b/a},"~N");c(c$,"setXRange",function(a,b){this.minX=a;this.maxX=b;this.setXScale()},"~N,~N");c$.getXRange=c(c$,"getXRange",
function(a,b,c,f,g,e,h,l){for(var k=0,m=0,k=g;k<=e;k++)if(b[k].getXVal()>=c){h[a]=k;m=1;break}for(;++k<=e&&b[k].getXVal()<=f;)m++;l[a]=h[a]+m-1;return m},"~N,~A,~N,~N,~N,~N,~A,~A");c(c$,"setScaleParams",function(a,b,c){a=b==a?1:Math.abs(b-a)/14;var f=Math.log10(Math.abs(a));b=u(Math.floor(f));this.exportPrecision[c]=b;this.precision[c]=0>=b?Math.min(8,1-b):3<b?-2:0;a=0;for(f=Math.pow(10,f-b);f>JSV.common.ScaleData.NTICKS[a];)a++;this.steps[c]=Math.pow(10,b)*JSV.common.ScaleData.NTICKS[a];f=Math.log10(Math.abs(100010*
this.steps[c]));b=f-Math.floor(f);for(a=f=0;a<JSV.common.ScaleData.NTICKS.length;a++)if(0.001>Math.abs(b-JSV.common.ScaleData.LOGTICKS[a])){f=JSV.common.ScaleData.NTICKS[a];break}this.minorTickCounts[c]=f;return this.steps[c]},"~N,~N,~N");c(c$,"isInRangeX",function(a){return a>=this.minX&&a<=this.maxX},"~N");c(c$,"addSpecShift",function(a){this.specShift+=a;this.minX+=a;this.maxX+=a;this.minXOnScale+=a;this.maxXOnScale+=a;this.firstX+=a},"~N");c(c$,"getInfo",function(a){a.put("specShift",Double.$valueOf(this.specShift));
a.put("minX",Double.$valueOf(this.minX));a.put("maxX",Double.$valueOf(this.maxX));a.put("minXOnScale",Double.$valueOf(this.minXOnScale));a.put("maxXOnScale",Double.$valueOf(this.maxXOnScale));a.put("minY",Double.$valueOf(this.minY));a.put("maxY",Double.$valueOf(this.maxY));a.put("minYOnScale",Double.$valueOf(this.minYOnScale));a.put("maxYOnScale",Double.$valueOf(this.maxYOnScale));a.put("minorTickCountX",Integer.$valueOf(this.minorTickCounts[0]));a.put("xStep",Double.$valueOf(this.steps[0]));return a},
"java.util.Map");c(c$,"setMinMax",function(a,b,c,f){this.minX=a;this.maxX=b;this.minY=c;this.maxY=f},"~N,~N,~N,~N");c(c$,"toX",function(a,b,c){return this.toXScaled(a,b,c,this.xFactorForScale)},"~N,~N,~B");c(c$,"toX0",function(a,b,c,f){return this.toXScaled(a,c,f,(this.maxXOnScale-this.minXOnScale)/(c-b))},"~N,~N,~N,~B");c(c$,"toXScaled",function(a,b,c,f){return c?this.maxXOnScale-(b-a)*f:this.minXOnScale+(b-a)*f},"~N,~N,~B,~N");c(c$,"toPixelX",function(a,b,c,f){return this.toPixelXScaled(a,b,c,f,
this.xFactorForScale)},"~N,~N,~N,~B");c(c$,"toPixelX0",function(a,b,c,f){return this.toPixelXScaled(a,b,c,f,(this.maxXOnScale-this.minXOnScale)/(c-b))},"~N,~N,~N,~B");c(c$,"toPixelXScaled",function(a,b,c,f,g){a=u((a-this.minXOnScale)/g);return f?b+a:c-a},"~N,~N,~N,~B,~N");c(c$,"toY",function(a,b){return this.maxYOnScale+(b-a)*this.yFactorForScale},"~N,~N");c(c$,"toY0",function(a,b,c){return Math.max(this.minYOnScale,Math.min(this.maxYOnScale+(b-a)*((this.maxYOnScale-this.minYOnScale)/(c-b)),this.maxYOnScale))},
"~N,~N,~N");c(c$,"toPixelY",function(a,b){return Double.isNaN(a)?-2147483648:b-u(((a-this.spectrumYRef)*this.userYFactor+this.spectrumYRef-this.minYOnScale)/this.yFactorForScale)},"~N,~N");c(c$,"toPixelY0",function(a,b,c){return u(b+(this.maxYOnScale-a)/((this.maxYOnScale-this.minYOnScale)/(c-b)))},"~N,~N,~N");c(c$,"setXYScale",function(a,b,c){var f=this.spectrumYRef,g=this.spectrumScaleFactor,e=1!=g||this.isShiftZoomedY,h=e?this.initMinYOnScale:this.minY,l=e?this.initMaxYOnScale:this.maxY;e&&f<h&&
(f=h);e&&f>l&&(f=l);this.setYScale((h-f)/g+f,(l-f)/g+f,1==g,c);this.xFactorForScale=(this.maxXOnScale-this.minXOnScale)/(a-1);this.yFactorForScale=(this.maxYOnScale-this.minYOnScale)/(b-1)},"~N,~N,~B");c$.copyScaleFactors=c(c$,"copyScaleFactors",function(a,b){for(var c=0;c<a.length;c++)b[c].spectrumScaleFactor=a[c].spectrumScaleFactor,b[c].spectrumYRef=a[c].spectrumYRef,b[c].userYFactor=a[c].userYFactor,b[c].specShift=a[c].specShift,b[c].isShiftZoomedY=a[c].isShiftZoomedY},"~A,~A");c$.copyYScales=
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y(c$,"INTEGRALOFFSET",27,["percent","sets the integral offset from baseline"]);y(c$,"INTEGRALRANGE",28,["percent","sets the height of the total integration"]);y(c$,"INTEGRATE",29,["","see INTEGRATION"]);y(c$,"INTEGRATION",30,["ON/OFF/TOGGLE/AUTO/CLEAR/MIN value/MARK ppm1-ppm2:norm,ppm3-ppm4,...","show/hide integration or set integrals (1D 1H NMR only)"]);y(c$,"INTEGRALPLOTCOLOR",31,["C","color of the integration line"]);y(c$,"INTEGRATIONRATIOS",32,["'x:value,x:value,..'","annotate the spectrum with numbers or text at specific x values"]);
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y(c$,"VERSION",85,[]);y(c$,"VIEW",86,['spectrumID, spectrumID, ... Example: VIEW 3.1, 3.2  or  VIEW "acetophenone"',"creates a view of one or more spectra"]);y(c$,"XSCALEON",87,["T","set FALSE to turn off the x-axis scale"]);y(c$,"XUNITSON",88,["T","set FALSE to turn off the x-axis units"]);y(c$,"YSCALE",89,["[ALL] lowValue highValue"]);y(c$,"YSCALEON",90,["T","set FALSE to turn off the y-axis scale"]);y(c$,"YUNITSON",91,["T","set FALSE to turn off the y-axis units"]);y(c$,"WINDOW",92,[]);y(c$,"WRITE",
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this.addUniqueControls();this.isNumeric&&(this.getUnitOptions(),this.addCombo1&&(this.combo1=this.dialog.addSelectOption("cmbUnits","Units",this.unitOptions,this.unitPtr.intValue(),this.addUnits)),this.addApplyBtn&&this.dialog.addButton("btnApply","Apply"),this.showHideButton=this.dialog.addButton("btnShow","Show"),this.addClearBtn&&this.dialog.addButton("btnClear","Clear"));this.dialog.endLayout();this.checkEnables();this.dialog.setVisible(this.defaultVisible)});c(c$,"callbackAD",function(a,b){if(a.equals("FOCUS"))this.eventFocus();
else if(a.equals("tableSelect"))this.tableSelect(b);else if(a.equals("btnClear"))this.clear();else if(a.equals("btnApply"))this.eventApply();else if(a.equals("btnShow")){var c=this.dialog.getText(this.showHideButton);this.eventShowHide(c.equals("Show"))}else if(a.equals("cmbUnits"))this.setPrecision(this.dialog.getSelectedIndex(this.combo1));else if(a.startsWith("txt"))this.eventApply();else if(a.equals("windowClosing"))return this.done(),!0;null!=this.jsvp&&this.jsvp.doRepaint(!0);return!0},"~S,~S");
c(c$,"addUniqueControls",function(){},"JSV.dialog.DialogManager");h(c$,"getAType",function(){return this.type});h(c$,"getGraphSetKey",function(){return this.graphSetKey});h(c$,"setGraphSetKey",function(a){this.graphSetKey=a},"~S");h(c$,"getSpectrum",function(){return this.$spec});h(c$,"getState",function(){return this.isON});h(c$,"setState",function(a){this.isON=a},"~B");c(c$,"checkEnables",function(){var a=this.checkVisible();this.dialog.setText(this.showHideButton,a?"Hide":"Show")});c(c$,"createTable",
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c(c$,"applyFromFields",function(){this.apply(null)});c(c$,"reEnable",function(){this.paramsReEnable();return this});c(c$,"dispose",function(){this.dialog.dispose()});c(c$,"setVisible",function(a){this.dialog.setVisible(a)},"~B");h(c$,"isVisible",function(){return this.dialog.isVisible()});c(c$,"selectTableRow",function(a){this.dialog.selectTableRow(a)},"~N");c(c$,"repaint",function(){this.dialog.repaint()});c(c$,"setFields",function(){switch(this.type){case JSV.common.Annotation.AType.PeakList:this.myParams=
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c&&this.applyFromFields();if(null==this.xyData||null==a||20<c)break;c=0;var f=1E100;a=a.getXVal();var g=this.xyData;b=Math.abs(b/20);for(var e=g.size();0<=--e;){var h=Math.abs(a-g.get(e).getXVal());h<f&&(f=h,c=e)}f<b&&(this.selectTableRow(g.size()-2-c),this.repaint())}},"JSV.common.Coordinate,~N,~N");c(c$,"getPeakData",function(){var a=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,this.$spec);a.setPeakList(this.myParams,this.precision,this.jsvp.getPanelData().getView());this.xyData=
a;return null});h(c$,"getData",function(){null==this.xyData&&this.createData();return this.xyData});c(c$,"setData",function(a){this.myParams=a.getParameters();this.xyData=a},"JSV.api.AnnotationData");h(c$,"setSpecShift",function(a){null!=this.xyData&&this.xyData.setSpecShift(a)},"~N");c(c$,"setType",function(a){this.type=a;switch(a){case JSV.common.Annotation.AType.Measurements:this.addUnits=!0}},"JSV.common.Annotation.AType");c(c$,"apply",function(a){try{switch(this.type){case JSV.common.Annotation.AType.Integration:var b=
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Exception))throw f;}},"~A");c(c$,"done",function(){null!=this.jsvp&&null!=this.$spec&&this.jsvp.getPanelData().removeDialog(this);null!=this.xyData&&this.xyData.setState(this.isON);this.saveDialogPosition(this.getPosXY());this.dispose();this.jsvp.doRepaint(!0)});c(c$,"restoreDialogPosition",function(a,b){if(null!=a){-2147483648==b[0]&&(b[0]=0,b[1]=-20);var c=this.manager.getLocationOnScreen(a),f=a.getHeight();this.loc=B(-1,[Math.max(0,c[0]+b[0]),Math.max(0,c[1]+f+b[1])]);this.dialog.setIntLocation(this.loc)}},
"JSV.api.JSVPanel,~A");c(c$,"saveDialogPosition",function(a){try{var b=this.manager.getLocationOnScreen(this.dialog);a[0]+=b[0]-this.loc[0];a[1]+=b[1]-this.loc[1]}catch(c){if(!D(c,Exception))throw c;}},"~A");c(c$,"getThreasholdText",function(a){if(Double.isNaN(a)){a=this.jsvp.getPanelData();var b=a.getSpectrum().isInverted()?0.1:0.9,c=a.getClickedCoordinate();a=null==c?(a.getView().minYOnScale*b+a.getView().maxYOnScale)*(1-b):c.getYVal()}return" "+JU.DF.formatDecimalDbl(a,1E3>a?2:-2)},"~N");c(c$,
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-1));break;case JSV.common.Annotation.AType.PeakList:this.createData(),this.skipCreate=!0}});c(c$,"eventApply",function(){switch(this.type){case JSV.common.Annotation.AType.PeakList:this.createData(),this.skipCreate=!0}this.applyFromFields()});c(c$,"eventShowHide",function(a){(this.isON=a)&&this.eventApply();this.jsvp.doRepaint(!0);this.checkEnables()},"~B");c(c$,"clear",function(){this.setState(!0);null!=this.xyData&&(this.xyData.clear(),this.applyFromFields())});c(c$,"paramsReEnable",function(){switch(this.type){case JSV.common.Annotation.AType.PeakList:this.skipCreate=
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c.toString());this.checkEnables();break;case JSV.common.Annotation.AType.PeakList:try{switch(b){case 6:case 5:case 4:var g=Double.parseDouble(c),e=Double.parseDouble(this.tableData[a+3-b][1]);this.jsvp.getPanelData().setXPointers(this.$spec,g,this.$spec,e);break;default:this.jsvp.getPanelData().findX(this.$spec,Double.parseDouble(c))}}catch(h){if(D(h,Exception))this.jsvp.getPanelData().findX(this.$spec,1E100);else throw h;}this.jsvp.doRepaint(!1);break;case JSV.common.Annotation.AType.OverlayLegend:this.jsvp.getPanelData().setSpectrum(a,
!1)}}catch(l){if(!D(l,Exception))throw l;}}},"~N,~N");c(c$,"loadData",function(){var a,b,c;switch(this.type){case JSV.common.Annotation.AType.Integration:null==this.xyData&&this.createData();this.iSelected=-1;a=this.xyData.getMeasurementListArray(null);b=this.xyData.getDataHeader();c=B(-1,[40,65,65,50]);this.createTable(a,b,c);break;case JSV.common.Annotation.AType.Measurements:if(null==this.xyData)break;a=this.xyData.getMeasurementListArray(this.dialog.getSelectedItem(this.combo1).toString());b=
this.xyData.getDataHeader();c=B(-1,[40,65,65,50]);this.createTable(a,b,c);break;case JSV.common.Annotation.AType.PeakList:null==this.xyData&&this.createData();a=this.xyData.getMeasurementListArray(null);b=this.xyData.getDataHeader();c=B(-1,[40,65,50,50,50,50,50]);this.createTable(a,b,c);this.setTableSelectionEnabled(!0);break;case JSV.common.Annotation.AType.OverlayLegend:b=v(-1,["No.","Plot Color","Title"]),a=this.vwr.selectedPanel.getPanelData().getOverlayLegendData(),c=B(-1,[30,60,250]),this.createTable(a,
b,c),this.setTableSelectionEnabled(!0)}});c(c$,"createData",function(){switch(this.type){case JSV.common.Annotation.AType.Integration:this.xyData=new JSV.common.IntegralData(this.$spec,this.myParams);this.iSelected=-1;break;case JSV.common.Annotation.AType.PeakList:try{var a=Double.parseDouble(this.dialog.getText(this.txt1));this.myParams.peakListThreshold=a;this.myParams.peakListInterpolation=this.dialog.getSelectedItem(this.combo1).toString();this.myParams.precision=this.precision;var b=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,
this.$spec);b.setPeakList(this.myParams,this.precision,this.jsvp.getPanelData().getView());this.xyData=b;this.loadData()}catch(c){if(!D(c,Exception))throw c;}}});c(c$,"setPrecision",function(a){this.precision=this.formatOptions[a]},"~N");c(c$,"tableSelect",function(a){if("true".equals(this.getField(a,"adjusting")))this.iColSelected=this.iRowSelected=-1,Zystem.out.println("adjusting"+a);else{var b=JU.PT.parseInt(this.getField(a,"index"));switch("ROW COL ROWCOL".indexOf(this.getField(a,"selector"))){case 8:this.iColSelected=
JU.PT.parseInt(this.getField(a,"index2"));case 0:this.iRowSelected=b;Zystem.out.println("r set to "+b);break;case 4:this.iColSelected=b,Zystem.out.println("c set to "+b)}0<=this.iColSelected&&0<=this.iRowSelected&&this.tableCellSelect(this.iRowSelected,this.iColSelected)}},"~S");c(c$,"getField",function(a,b){a+="&";var c="&"+b+"=",f=a.indexOf(c);return 0>f?null:a.substring(f+c.length,a.indexOf("&",f+1))},"~S,~S")});m("JSV.exception");x(["java.lang.Exception"],"JSV.exception.JSVException",null,function(){c$=
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"#000000";c.fillRect(0,0,f,g);c.fillStyle="#FFFFFF";c.font=b.font;c.fillText(a,0,e);return JSV.js2d.Image.grabPixels(c,f,g)},"~S,JU.Font,~O,~N,~N,~N");c$.allocateRgbImage=c(c$,"allocateRgbImage",function(a,b,c,f,g,e){null==e&&(e={width:a,height:b});e.buf32=c},"~N,~N,~A,~N,~B,~O");c$.getStaticGraphics=c(c$,"getStaticGraphics",function(a){return JSV.js2d.Image.getGraphics(a)},"~O,~B");c$.getGraphics=c(c$,"getGraphics",function(a){return a.getContext("2d")},"~O");c$.drawImage=c(c$,"drawImage",function(a,
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c$.getURLContents=c(c$,"getURLContents",function(a,b,c){try{var f=a.openConnection();null!=b?f.outputBytes(b):null!=c&&f.outputString(c);return f.getContents()}catch(g){if(D(g,Exception))return g.toString();throw g;}},"java.net.URL,~A,~S")});m("JSV.js2d");x(["JSV.api.JSVFileHelper"],"JSV.js2d.JsFileHelper",["JU.PT","JSV.common.JSViewer","JSV.js2d.JsFile"],function(){c$=w(function(){this.vwr=null;s(this,arguments)},JSV.js2d,"JsFileHelper",null,JSV.api.JSVFileHelper);p(c$,function(){});h(c$,"set",function(a){this.vwr=
a;return this},"JSV.common.JSViewer");h(c$,"getFile",function(a){var b=null;a=JU.PT.rep(a,"=","_");b=prompt("Enter a file name:",a);return null==b?null:new JSV.js2d.JsFile(b)},"~S,~O,~B");h(c$,"setDirLastExported",function(a){return a},"~S");h(c$,"setFileChooser",function(){},"JSV.common.ExportType");h(c$,"showFileOpenDialog",function(a,b){JSV.common.JSViewer.jmolObject.loadFileAsynchronously(this,this.vwr.html5Applet,"?",b);return null},"~O,~A");c(c$,"setData",function(a,b,c){if(null!=a)if(null==
b)this.vwr.selectedPanel.showMessage(a,"File Open Error");else{var f=null==c?null:"",g=!1,g=c[0],f=c[1];this.vwr.si.siOpenDataOrFile(String.instantialize(b),"cache://"+a,null,null,-1,-1,g,null,null);null!=f&&this.vwr.runScript(f)}},"~S,~O,~A");h(c$,"getUrlFromDialog",function(a,b){return prompt(a,b)},"~S,~S")});m("JSV.js2d");c$=F(JSV.js2d,"JsFont");c$.newFont=c(c$,"newFont",function(a,b,c,f,g){a=a.equals("Monospaced")?"Courier":a.startsWith("Sans")?"Sans-Serif":"Serif";return(b?"bold ":"")+(c?"italic ":
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1].getYVal()});c(c$,"getMinX",function(){return Double.isNaN(this.minX)?this.minX=JSV.common.Coordinate.getMinX(this.xyCoords,0,this.xyCoords.length-1):this.minX});c(c$,"getMinY",function(){return Double.isNaN(this.minY)?this.minY=JSV.common.Coordinate.getMinY(this.xyCoords,0,this.xyCoords.length-1):this.minY});c(c$,"getMaxX",function(){return Double.isNaN(this.maxX)?this.maxX=JSV.common.Coordinate.getMaxX(this.xyCoords,0,this.xyCoords.length-1):this.maxX});c(c$,"getMaxY",function(){return Double.isNaN(this.maxY)?
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1E100]));c$.gyroMap=c$.prototype.gyroMap=new java.util.Hashtable;for(var a=0,b=JSV.source.JDXDataObject.gyroData.length-1;a<b;a+=2)JSV.source.JDXDataObject.gyroMap.put(""+u(JSV.source.JDXDataObject.gyroData[a]),Double.$valueOf(JSV.source.JDXDataObject.gyroData[a+1]))});m("JSV.source");x(["java.util.Iterator"],"JSV.source.JDXDecompressor",["java.lang.Double","JSV.common.Coordinate","JU.Logger"],function(){c$=w(function(){this.ich=this.nPoints=this.yFactor=this.xFactor=0;this.t=null;this.lastX=this.firstX=
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this.getRow(g);return c},"~B,~N");c(c$,"getRow",function(a){a=this.headerTable.get(a);return[a[0],JU.PT.rep(a[1],"<","&lt;")]},"~N");G(c$,"typeNames",v(-1,"ND NMR SPECTRUM   NMR;NMR SPECTRUM      NMR;INFRARED SPECTRUM IR;MASS SPECTRUM     MS;RAMAN SPECTRUM    RAMAN;GAS CHROMATOGRAM  GC;UV/VIS SPECTRUM   UV/VIS".split(";")))});m("JSV.source");x(["J.api.JmolJDXMOLReader"],"JSV.source.JDXReader","java.io.BufferedReader $.InputStream $.StringReader java.lang.Double $.Float java.util.Hashtable $.LinkedHashMap $.StringTokenizer javajs.api.Interface JU.AU $.Lst $.PT $.Rdr $.SB JSV.api.JSVZipReader JSV.common.Coordinate $.JSVFileManager $.JSViewer $.PeakInfo $.Spectrum JSV.exception.JSVException JSV.source.JDXDecompressor $.JDXSource $.JDXSourceStreamTokenizer JU.Logger".split(" "),
function(){c$=w(function(){this.nmrMaxY=NaN;this.errorLog=this.t=this.source=null;this.isZipFile=this.done=this.obscure=!1;this.filePath=null;this.loadImaginary=!0;this.ignorePeakTables=this.ignoreShiftReference=this.isSimulation=!1;this.lastErrPath=null;this.isTabularData=!1;this.blockID=this.nSpec=this.lastSpec=this.firstSpec=0;this.peakData=this.acdMolFile=this.acdAssignments=this.modelSpectrum=this.reader=this.mpr=null;s(this,arguments)},JSV.source,"JDXReader",null,J.api.JmolJDXMOLReader);c$.getVarList=
c(c$,"getVarList",function(a){a=JSV.source.JDXReader.VAR_LIST_TABLE[0].indexOf(a);return JSV.source.JDXReader.VAR_LIST_TABLE[1].substring(a+1,a+12).trim()},"~S");p(c$,function(a,b,c,f,g,e){a=JU.PT.trimQuotes(a);if(this.isSimulation=null!=a&&a.startsWith("http://SIMULATION/"))this.nmrMaxY=Float.isNaN(e)?1E4:e;this.filePath=a;this.obscure=b;this.firstSpec=f;this.lastSpec=g;this.loadImaginary=c},"~S,~B,~B,~N,~N,~N");c$.createJDXSourceFromStream=c(c$,"createJDXSourceFromStream",function(a,b,c,f){return JSV.source.JDXReader.createJDXSource(null,
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c$.createJDXSource=c(c$,"createJDXSource",function(a,b,c,f,g,e,h,l){var k=h<e,m=null,n=null;if(JU.AU.isAB(b)&&(n=b,JU.Rdr.isZipB(n)))return JSV.source.JDXReader.readBrukerFileZip(n,null==a?c:a.getFullPath());t(b,String)||null!=n?(t(b,String)&&(m=b),b=JSV.common.JSVFileManager.getBufferedReaderForStringOrBytes(b)):b=t(b,java.io.InputStream)?JSV.common.JSVFileManager.getBufferedReaderForInputStream(b):b;var p=n=null;try{if(null==b){if(null!=a&&a.isDirectory())return JSV.source.JDXReader.readBrukerFileDir(a.getFullPath());
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if(0>u||0<=v&&v<u){var w=n.toLowerCase(),w=w.contains("<animl")||w.contains("<!doctype technique")?"AnIML":w.contains("xml-cml")?"CML":null;if(null==w)return JSV.source.JDXReader.readBrukerFileDir(a.getFullPath());p=JSV.common.JSViewer.getInterface("JSV.source."+w+"Reader").getSource(c,b);b.close();if(null==p)throw JU.Logger.error(n+"..."),new JSV.exception.JSVException("File type not recognized");}}null==p&&(p=(new JSV.source.JDXReader(c,f,g,e,h,l)).getJDXSource(b,k));null!=m&&p.setInlineData(m);
return p}catch(x){if(D(x,Exception))throw JSV.common.JSViewer.isJS||x.printStackTrace(),null!=b&&b.close(),null!=n&&JU.Logger.error(n+"..."),a=x.getMessage(),new JSV.exception.JSVException("Error reading data: "+a);throw x;}},"J.api.GenericFileInterface,~O,~S,~B,~B,~N,~N,~N");c$.readBrukerFileDir=c(c$,"readBrukerFileDir",function(a){return javajs.api.Interface.getInterface("JSV.source.BrukerReader").readBrukerDir(a)},"~S");c$.readBrukerFileZip=c(c$,"readBrukerFileZip",function(a,b){return javajs.api.Interface.getInterface("JSV.source.BrukerReader").readBrukerZip(a,
b)},"~A,~S");c(c$,"getJDXSource",function(a,b){this.source=new JSV.source.JDXSource(0,this.filePath);this.isZipFile=t(a,JSV.api.JSVZipReader);this.t=new JSV.source.JDXSourceStreamTokenizer(a);this.errorLog=new JU.SB;for(var c=null,f=null,g=!1;!this.done&&"##TITLE".equals(this.t.peakLabel());){g=!0;null!=c&&!this.isZipFile&&this.logError("Warning - file is a concatenation without LINK record -- does not conform to JCAMP-DX standard 6.1.3!");var e=new JSV.common.Spectrum,h=new JU.Lst;for(b&&e.setHeaderTable(h);!this.done&&
null!=(c=this.t.getLabel())&&null!=(f=this.getValue(c));)if(this.isTabularData){if(this.processTabularData(e,h,c,b),this.addSpectrum(e,!1),this.isSimulation&&e.getXUnits().equals("PPM")&&e.setHZtoPPM(!0),e=null,b){JSV.source.JDXReader.addHeader(h,this.t.rawLabel,"<data>");break}}else{if(!b){if(c.equals("##DATATYPE")&&f.toUpperCase().equals("LINK")){this.getBlockSpectra(h);e=null;continue}if(c.equals("##NTUPLES")||c.equals("##VARNAME")){this.getNTupleSpectra(h,e,c);e=null;continue}}c.equals("##JCAMPDX")&&
this.setVenderSpecificValues(this.t.rawLine);null==e&&(e=new JSV.common.Spectrum);this.processLabel(e,h,c,f,b)}b&&null!=e&&this.addSpectrum(e,!1)}if(!g)throw new JSV.exception.JSVException("##TITLE record not found");this.source.setErrorLog(this.errorLog.toString());return this.source},"~O,~B");c(c$,"processLabel",function(a,b,c,f,g){if(this.readDataLabel(a,c,f,this.errorLog,this.obscure,g)||g)JSV.source.JDXReader.addHeader(b,this.t.rawLabel,f),g||this.checkCustomTags(a,c,f)},"JSV.common.Spectrum,JU.Lst,~S,~S,~B");
c(c$,"logError",function(a){this.errorLog.append(null==this.filePath||this.filePath.equals(this.lastErrPath)?"":this.filePath).append("\n").append(a).append("\n");this.lastErrPath=this.filePath},"~S");c(c$,"setVenderSpecificValues",function(a){0<=a.indexOf("JEOL")&&(Zystem.out.println("Skipping ##SHIFTREFERENCE for JEOL "+a),this.ignoreShiftReference=!0);0<=a.indexOf("MestReNova")&&(this.ignorePeakTables=!0)},"~S");c(c$,"getValue",function(a){var b=this.isTabularDataLabel(a)?"":this.t.getValue();
return"##END".equals(a)?null:b},"~S");c(c$,"isTabularDataLabel",function(a){return this.isTabularData=0<="##DATATABLE##PEAKTABLE##XYDATA##XYPOINTS#".indexOf(a+"#")},"~S");c(c$,"addSpectrum",function(a,b){if(!this.loadImaginary&&a.isImaginary())return JU.Logger.info("FileReader skipping imaginary spectrum -- use LOADIMAGINARY TRUE to load this spectrum."),!0;if(null!=this.acdAssignments){if(!a.dataType.equals("MASS SPECTRUM")&&!a.isContinuous())return JU.Logger.info("Skipping ACD Labs line spectrum for "+
a),!0;if(0<this.acdAssignments.size())try{this.mpr.setACDAssignments(a.title,a.getTypeLabel(),this.source.peakCount,this.acdAssignments,this.acdMolFile)}catch(c){if(D(c,Exception))JU.Logger.info("Failed to create peak data: "+c);else throw c;}null!=this.acdMolFile&&JSV.common.JSVFileManager.cachePut("mol",this.acdMolFile)}Float.isNaN(this.nmrMaxY)?1E4<=a.getMaxY()&&a.normalizeSimulation(1E3):a.normalizeSimulation(this.nmrMaxY);this.isSimulation&&a.setSimulated(this.filePath);this.nSpec++;if(0<this.firstSpec&&
this.nSpec<this.firstSpec)return!0;if(0<this.lastSpec&&this.nSpec>this.lastSpec)return!(this.done=!0);a.setBlockID(this.blockID);this.source.addJDXSpectrum(null,a,b);return!0},"JSV.common.Spectrum,~B");c(c$,"getBlockSpectra",function(a){JU.Logger.debug("--JDX block start--");for(var b="",c=null,f=0==this.source.type,g=!1;null!=(b=this.t.getLabel())&&!b.equals("##TITLE");)c=this.getValue(b),f&&!JSV.source.JDXReader.readHeaderLabel(this.source,b,c,this.errorLog,this.obscure)&&JSV.source.JDXReader.addHeader(a,
this.t.rawLabel,c),b.equals("##BLOCKS")&&100<JU.PT.parseInt(c)&&0>=this.firstSpec&&(g=!0);c=this.getValue(b);if(!"##TITLE".equals(b))throw new JSV.exception.JSVException("Unable to read block source");f&&this.source.setHeaderTable(a);this.source.type=1;this.source.isCompoundSource=!0;f=new JSV.common.Spectrum;a=new JU.Lst;this.readDataLabel(f,b,c,this.errorLog,this.obscure,!1);try{for(var e;null!=(e=this.t.getLabel());){if(null==(c=this.getValue(e))&&"##END".equals(b)){JU.Logger.debug("##END= "+this.t.getValue());
break}b=e;if(this.isTabularData)this.processTabularData(f,a,b,!1);else{if(b.equals("##DATATYPE"))if(c.toUpperCase().equals("LINK"))this.getBlockSpectra(a),b=f=null;else{if(c.toUpperCase().startsWith("NMR PEAK")&&this.ignorePeakTables)return this.done=!0,this.source}else if(b.equals("##NTUPLES")||b.equals("##VARNAME"))this.getNTupleSpectra(a,f,b),f=null,b="";if(this.done)break;if(null==f){f=new JSV.common.Spectrum;a=new JU.Lst;if(""===b)continue;if(null==b){b="##END";continue}}if(null==c){if(0<f.getXYCoords().length&&
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this.errorLog.length()-22&&this.logError("=====================\n")});c(c$,"getNTupleSpectra",function(a,b,c){var f=Q(-1,[1.7976931348623157E308,4.9E-324]);this.blockID=Math.random();0<this.firstSpec&&b.setNumDim(1);var g=c.equals("##VARNAME");g||(c="");var e=new java.util.Hashtable,h=Array(2);0==this.source.type&&(this.source.type=2,this.source.isCompoundSource=!0,this.source.setHeaderTable(a));for(;!(c=g?c:this.t.getLabel()).equals("##PAGE");){for(var g=!1,l=new java.util.StringTokenizer(this.t.getValue(),
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!u.equals("##NTUPLES"))&&n.addLast(c);this.addSpectrum(k,!m);m=!1;k=null}}this.addErrorLogSeparator();this.source.setErrorLog(this.errorLog.toString());JU.Logger.info("NTUPLE MIN/MAX Y = "+f[0]+" "+f[1]);return this.source},"JU.Lst,JSV.source.JDXDataObject,~S");c(c$,"readDataLabel",function(a,b,c,f,g){if(!JSV.source.JDXReader.readHeaderLabel(a,b,c,f,g))return!1;b+=" ";if(0<="##MINX ##MINY ##MAXX ##MAXY ##FIRSTY ##DELTAX ##DATACLASS ".indexOf(b))return!1;switch("##FIRSTX  ##LASTX   ##NPOINTS ##XFACTOR ##YFACTOR ##XUNITS  ##YUNITS  ##XLABEL  ##YLABEL  ##NUMDIM  ##OFFSET  ".indexOf(b)){case 0:return a.fileFirstX=
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b.length)return!0;if(b.equals("##.OBSERVEFREQUENCY "))return a.setObservedFreq(this.parseAFFN(b,c)),!1;if(b.equals("##.OBSERVENUCLEUS "))return a.setObservedNucleus(c),!1;if(b.equals("##$REFERENCEPOINT ")&&!a.isShiftTypeSpecified()){var e=c.indexOf(" ");0<e&&(c=c.substring(0,e));a.setShiftReference(this.parseAFFN(b,c),1,2);return!1}if(b.equals("##.SHIFTREFERENCE ")){if(this.ignoreShiftReference||!a.dataType.toUpperCase().contains("SPECTRUM"))return!1;c=JU.PT.replaceAllCharacters(c,")(","");c=new java.util.StringTokenizer(c,
",");if(4!=c.countTokens())return!1;try{c.nextToken();c.nextToken();var e=Integer.parseInt(c.nextToken().trim()),h=this.parseAFFN(b,c.nextToken().trim());a.setShiftReference(h,e,0)}catch(l){if(!D(l,Exception))throw l;}return!1}return!0}},"JSV.source.JDXDataObject,~S,~S,JU.SB,~B,~B");c$.readHeaderLabel=c(c$,"readHeaderLabel",function(a,b,c,f,g){switch("##TITLE#####JCAMPDX###ORIGIN####OWNER#####DATATYPE##LONGDATE##DATE######TIME####".indexOf(b+"#")){case 0:return a.setTitle(g||null==c||c.equals("")?
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try{this.t.readLineTrimmed()}catch(g){if(!D(g,java.io.IOException))throw g;}1.7976931348623157E308!=a.xFactor&&1.7976931348623157E308!=a.yFactor?(b=this.t.getValue(),b=JSV.common.Coordinate.parseDSV(b,a.xFactor,a.yFactor)):b=JSV.common.Coordinate.parseDSV(this.t.getValue(),1,1);a.setXYCoords(b);b=JSV.common.Coordinate.deltaX(b[b.length-1].getXVal(),b[0].getXVal(),b.length);a.setIncreasing(0<b)}else throw new JSV.exception.JSVException("Unable to read JDX file tabular data for line "+this.t.labelLineNo);
},"JSV.source.JDXDataObject,JU.Lst,~S,~B");c(c$,"readNTUPLECoords",function(a,b,c,f){var g;if(a.dataClass.equals("XYDATA")){g=b.get("##SYMBOL");var e=g.indexOf(c[0]),h=g.indexOf(c[1]);g=b.get("##VARNAME");a.setVarName(g.get(h).toUpperCase());g=b.get(c="##FACTOR");a.setXFactor(this.parseAFFN(c,g.get(e)));a.setYFactor(this.parseAFFN(c,g.get(h)));g=b.get(c="##LAST");a.fileLastX=this.parseAFFN(c,g.get(e));g=b.get(c="##FIRST");a.fileFirstX=this.parseAFFN(c,g.get(e));g=b.get("##VARDIM");a.fileNPoints=Integer.parseInt(g.get(e));
g=b.get("##UNITS");a.setXUnits(g.get(e));a.setYUnits(g.get(h));null==a.nucleusX&&null!=(g=b.get("##.NUCLEUS"))?(a.setNucleusAndFreq(g.get(0),!1),a.setNucleusAndFreq(g.get(e),!0)):null==a.nucleusX&&(a.nucleusX="?");this.decompressData(a,f);return!0}return a.dataClass.equals("PEAKTABLE")||a.dataClass.equals("XYPOINTS")?(a.setContinuous(a.dataClass.equals("XYPOINTS")),g=b.get("##SYMBOL"),e=g.indexOf(c[0]),h=g.indexOf(c[1]),g=b.get("##UNITS"),a.setXUnits(g.get(e)),a.setYUnits(g.get(h)),a.setXYCoords(JSV.common.Coordinate.parseDSV(this.t.getValue(),
a.xFactor,a.yFactor)),!0):!1},"JSV.source.JDXDataObject,java.util.Map,~A,~A");c(c$,"parseAFFN",function(a,b){var c=b.indexOf("E");if(0<c){var f;switch(b.length-c){case 2:case 3:this.logError("Warning - "+a+" value "+b+" is not of the format xxxE[+/-]nn or xxxE[+/-]nnn (spec. 4.5.3) -- warning only; accepted");break;case 4:case 5:if("+"==(f=b.charAt(c+1))||"-"==f)break;default:this.logError("Error - "+a+" value "+b+" is not of the format xxxE[+/-]nn or xxxE[+/-]nnn (spec. 4.5.3) -- "+b.substring(c)+
" ignored!"),b=b.substring(0,c)}}return Double.parseDouble(b)},"~S,~S");c(c$,"decompressData",function(a,b){var c=this.errorLog.length();a.setIncreasing(a.fileLastX>a.fileFirstX);a.setContinuous(!0);var f=new JSV.source.JDXDecompressor(this.t,a.fileFirstX,a.fileLastX,a.xFactor,a.yFactor,a.fileNPoints),g=Zystem.currentTimeMillis(),e=f.decompressData(this.errorLog);JU.Logger.debugging&&JU.Logger.debug("decompression time = "+(Zystem.currentTimeMillis()-g)+" ms");a.setXYCoords(e);g=f.getMinY();null!=
b&&(g<b[0]&&(b[0]=g),g=f.getMaxY(),g>b[1]&&(b[1]=g));a.finalizeCoordinates();this.errorLog.length()!=c&&(c=JSV.common.Coordinate.deltaX(a.fileLastX,a.fileFirstX,a.fileNPoints),this.logError(a.getTitle()),this.logError("firstX from Header "+a.fileFirstX),this.logError("lastX from Header "+a.fileLastX+" Found "+f.lastX),this.logError("deltaX from Header "+c),this.logError("Number of points in Header "+a.fileNPoints+" Found "+f.getNPointsFound()));JU.Logger.debugging&&Zystem.err.println(this.errorLog.toString())},
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