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a.m20;this.m21=a.m21;this.m22=a.m22},"JU.M34");c(c$,"clear33",function(){this.m00=this.m01=this.m02=this.m10=this.m11=this.m12=this.m20=this.m21=this.m22=0});c(c$,"set33",function(a,b,d){switch(a){case 0:switch(b){case 0:this.m00=d;return;case 1:this.m01=d;return;case 2:this.m02=d;return}break;case 1:switch(b){case 0:this.m10=d;return;case 1:this.m11=d;return;case 2:this.m12=d;return}break;case 2:switch(b){case 0:this.m20=d;return;case 1:this.m21=d;return;case 2:this.m22=d;return}}this.err()},"~N,~N,~N");
c(c$,"get33",function(a,b){switch(a){case 0:switch(b){case 0:return this.m00;case 1:return this.m01;case 2:return this.m02}break;case 1:switch(b){case 0:return this.m10;case 1:return this.m11;case 2:return this.m12}break;case 2:switch(b){case 0:return this.m20;case 1:return this.m21;case 2:return this.m22}}this.err();return 0},"~N,~N");c(c$,"setRow33",function(a,b){switch(a){case 0:this.m00=b[0];this.m01=b[1];this.m02=b[2];break;case 1:this.m10=b[0];this.m11=b[1];this.m12=b[2];break;case 2:this.m20=
b[0];this.m21=b[1];this.m22=b[2];break;default:this.err()}},"~N,~A");c(c$,"getRow33",function(a,b){switch(a){case 0:b[0]=this.m00;b[1]=this.m01;b[2]=this.m02;return;case 1:b[0]=this.m10;b[1]=this.m11;b[2]=this.m12;return;case 2:b[0]=this.m20;b[1]=this.m21;b[2]=this.m22;return}this.err()},"~N,~A");c(c$,"setColumn33",function(a,b){switch(a){case 0:this.m00=b[0];this.m10=b[1];this.m20=b[2];break;case 1:this.m01=b[0];this.m11=b[1];this.m21=b[2];break;case 2:this.m02=b[0];this.m12=b[1];this.m22=b[2];break;
default:this.err()}},"~N,~A");c(c$,"getColumn33",function(a,b){switch(a){case 0:b[0]=this.m00;b[1]=this.m10;b[2]=this.m20;break;case 1:b[0]=this.m01;b[1]=this.m11;b[2]=this.m21;break;case 2:b[0]=this.m02;b[1]=this.m12;b[2]=this.m22;break;default:this.err()}},"~N,~A");c(c$,"add33",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.M34");c(c$,"sub33",function(a){this.m00-=a.m00;this.m01-=a.m01;
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this.m22-this.m20*this.m12)+this.m02*(this.m10*this.m21-this.m20*this.m11)});c(c$,"err",function(){throw new ArrayIndexOutOfBoundsException("matrix column/row out of bounds");})});m("JU");w(["JU.M34"],"JU.M3",["JU.T3"],function(){c$=z(JU,"M3",JU.M34,java.io.Serializable);c$.newA9=c(c$,"newA9",function(a){var b=new JU.M3;b.setA(a);return b},"~A");c$.newM3=c(c$,"newM3",function(a){var b=new JU.M3;if(null==a)return b.setScale(1),b;b.m00=a.m00;b.m01=a.m01;b.m02=a.m02;b.m10=a.m10;b.m11=a.m11;b.m12=a.m12;
b.m20=a.m20;b.m21=a.m21;b.m22=a.m22;return b},"JU.M3");c(c$,"setScale",function(a){this.clear33();this.m00=this.m11=this.m22=a},"~N");c(c$,"setM3",function(a){this.setM33(a)},"JU.M34");c(c$,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m10=a[3];this.m11=a[4];this.m12=a[5];this.m20=a[6];this.m21=a[7];this.m22=a[8]},"~A");c(c$,"setElement",function(a,b,d){this.set33(a,b,d)},"~N,~N,~N");c(c$,"getElement",function(a,b){return this.get33(a,b)},"~N,~N");c(c$,"setRow",function(a,b,d,
e){switch(a){case 0:this.m00=b;this.m01=d;this.m02=e;break;case 1:this.m10=b;this.m11=d;this.m12=e;break;case 2:this.m20=b;this.m21=d;this.m22=e;break;default:this.err()}},"~N,~N,~N,~N");c(c$,"setRowV",function(a,b){switch(a){case 0:this.m00=b.x;this.m01=b.y;this.m02=b.z;break;case 1:this.m10=b.x;this.m11=b.y;this.m12=b.z;break;case 2:this.m20=b.x;this.m21=b.y;this.m22=b.z;break;default:this.err()}},"~N,JU.T3");c(c$,"setRowA",function(a,b){this.setRow33(a,b)},"~N,~A");h(c$,"getRow",function(a,b){this.getRow33(a,
b)},"~N,~A");c(c$,"setColumn3",function(a,b,d,e){switch(a){case 0:this.m00=b;this.m10=d;this.m20=e;break;case 1:this.m01=b;this.m11=d;this.m21=e;break;case 2:this.m02=b;this.m12=d;this.m22=e;break;default:this.err()}},"~N,~N,~N,~N");c(c$,"setColumnV",function(a,b){switch(a){case 0:this.m00=b.x;this.m10=b.y;this.m20=b.z;break;case 1:this.m01=b.x;this.m11=b.y;this.m21=b.z;break;case 2:this.m02=b.x;this.m12=b.y;this.m22=b.z;break;default:this.err()}},"~N,JU.T3");c(c$,"getColumnV",function(a,b){switch(a){case 0:b.x=
this.m00;b.y=this.m10;b.z=this.m20;break;case 1:b.x=this.m01;b.y=this.m11;b.z=this.m21;break;case 2:b.x=this.m02;b.y=this.m12;b.z=this.m22;break;default:this.err()}},"~N,JU.T3");c(c$,"setColumnA",function(a,b){this.setColumn33(a,b)},"~N,~A");c(c$,"getColumn",function(a,b){this.getColumn33(a,b)},"~N,~A");c(c$,"add",function(a){this.add33(a)},"JU.M3");c(c$,"sub",function(a){this.sub33(a)},"JU.M3");c(c$,"transpose",function(){this.transpose33()});c(c$,"transposeM",function(a){this.setM33(a);this.transpose33()},
"JU.M3");c(c$,"invertM",function(a){this.setM33(a);this.invert()},"JU.M3");c(c$,"invert",function(){var a=this.determinant3();0!=a&&(a=1/a,this.set9(this.m11*this.m22-this.m12*this.m21,this.m02*this.m21-this.m01*this.m22,this.m01*this.m12-this.m02*this.m11,this.m12*this.m20-this.m10*this.m22,this.m00*this.m22-this.m02*this.m20,this.m02*this.m10-this.m00*this.m12,this.m10*this.m21-this.m11*this.m20,this.m01*this.m20-this.m00*this.m21,this.m00*this.m11-this.m01*this.m10),this.scale(a))});c(c$,"setAsXRotation",
function(a){this.setXRot(a);return this},"~N");c(c$,"setAsYRotation",function(a){this.setYRot(a);return this},"~N");c(c$,"setAsZRotation",function(a){this.setZRot(a);return this},"~N");c(c$,"scale",function(a){this.mul33(a)},"~N");c(c$,"mul",function(a){this.mul2(this,a)},"JU.M3");c(c$,"mul2",function(a,b){this.set9(a.m00*b.m00+a.m01*b.m10+a.m02*b.m20,a.m00*b.m01+a.m01*b.m11+a.m02*b.m21,a.m00*b.m02+a.m01*b.m12+a.m02*b.m22,a.m10*b.m00+a.m11*b.m10+a.m12*b.m20,a.m10*b.m01+a.m11*b.m11+a.m12*b.m21,a.m10*
b.m02+a.m11*b.m12+a.m12*b.m22,a.m20*b.m00+a.m21*b.m10+a.m22*b.m20,a.m20*b.m01+a.m21*b.m11+a.m22*b.m21,a.m20*b.m02+a.m21*b.m12+a.m22*b.m22)},"JU.M3,JU.M3");h(c$,"equals",function(a){return!n(a,JU.M3)?!1: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},"~O");h(c$,"hashCode",function(){return JU.T3.floatToIntBits0(this.m00)^JU.T3.floatToIntBits0(this.m01)^JU.T3.floatToIntBits0(this.m02)^JU.T3.floatToIntBits0(this.m10)^
JU.T3.floatToIntBits0(this.m11)^JU.T3.floatToIntBits0(this.m12)^JU.T3.floatToIntBits0(this.m20)^JU.T3.floatToIntBits0(this.m21)^JU.T3.floatToIntBits0(this.m22)});c(c$,"setZero",function(){this.clear33()});c(c$,"set9",function(a,b,d,e,c,f,j,k,l){this.m00=a;this.m01=b;this.m02=d;this.m10=e;this.m11=c;this.m12=f;this.m20=j;this.m21=k;this.m22=l},"~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"toString",function(){return"[\n  ["+this.m00+"\t"+this.m01+"\t"+this.m02+"]\n  ["+this.m10+"\t"+this.m11+"\t"+this.m12+"]\n  ["+
this.m20+"\t"+this.m21+"\t"+this.m22+"] ]"});c(c$,"setAA",function(a){this.setAA33(a);return this},"JU.A4");c(c$,"setAsBallRotation",function(a,b,d){var e=Math.sqrt(b*b+d*d),c=e*a;if(0==c)return this.setScale(1),!1;a=Math.cos(c);c=Math.sin(c);d=-d/e;b/=e;e=a-1;this.m00=1+e*d*d;this.m01=this.m10=e*d*b;this.m20=-(this.m02=c*d);this.m11=1+e*b*b;this.m21=-(this.m12=c*b);this.m22=a;return!0},"~N,~N,~N");c(c$,"isRotation",function(){return 0.001>Math.abs(this.determinant3()-1)})});m("JU");w(["JU.M34"],
"JU.M4",["JU.T3"],function(){c$=r(function(){this.m33=this.m32=this.m31=this.m30=this.m23=this.m13=this.m03=0;t(this,arguments)},JU,"M4",JU.M34);c$.newA16=c(c$,"newA16",function(a){var b=new JU.M4;b.m00=a[0];b.m01=a[1];b.m02=a[2];b.m03=a[3];b.m10=a[4];b.m11=a[5];b.m12=a[6];b.m13=a[7];b.m20=a[8];b.m21=a[9];b.m22=a[10];b.m23=a[11];b.m30=a[12];b.m31=a[13];b.m32=a[14];b.m33=a[15];return b},"~A");c$.newM4=c(c$,"newM4",function(a){var b=new JU.M4;if(null==a)return b.setIdentity(),b;b.setToM3(a);b.m03=a.m03;
b.m13=a.m13;b.m23=a.m23;b.m30=a.m30;b.m31=a.m31;b.m32=a.m32;b.m33=a.m33;return b},"JU.M4");c$.newMV=c(c$,"newMV",function(a,b){var d=new JU.M4;d.setMV(a,b);return d},"JU.M3,JU.T3");c(c$,"setZero",function(){this.clear33();this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=this.m33=0});c(c$,"setIdentity",function(){this.setZero();this.m00=this.m11=this.m22=this.m33=1});c(c$,"setM4",function(a){this.setM33(a);this.m03=a.m03;this.m13=a.m13;this.m23=a.m23;this.m30=a.m30;this.m31=a.m31;this.m32=a.m32;
this.m33=a.m33;return this},"JU.M4");c(c$,"setMV",function(a,b){this.setM33(a);this.setTranslation(b);this.m33=1},"JU.M3,JU.T3");c(c$,"setToM3",function(a){this.setM33(a);this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=0;this.m33=1},"JU.M34");c(c$,"setToAA",function(a){this.setIdentity();this.setAA33(a)},"JU.A4");c(c$,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m03=a[3];this.m10=a[4];this.m11=a[5];this.m12=a[6];this.m13=a[7];this.m20=a[8];this.m21=a[9];this.m22=a[10];this.m23=
a[11];this.m30=a[12];this.m31=a[13];this.m32=a[14];this.m33=a[15]},"~A");c(c$,"setTranslation",function(a){this.m03=a.x;this.m13=a.y;this.m23=a.z},"JU.T3");c(c$,"setElement",function(a,b,d){if(3>a&&3>b)this.set33(a,b,d);else{(3<a||3<b)&&this.err();switch(a){case 0:this.m03=d;return;case 1:this.m13=d;return;case 2:this.m23=d;return}switch(b){case 0:this.m30=d;break;case 1:this.m31=d;break;case 2:this.m32=d;break;case 3:this.m33=d}}},"~N,~N,~N");c(c$,"getElement",function(a,b){if(3>a&&3>b)return this.get33(a,
b);if(3<a||3<b)return this.err(),0;switch(a){case 0:return this.m03;case 1:return this.m13;case 2:return this.m23;default:switch(b){case 0:return this.m30;case 1:return this.m31;case 2:return this.m32;default:return this.m33}}},"~N,~N");c(c$,"getTranslation",function(a){a.x=this.m03;a.y=this.m13;a.z=this.m23},"JU.T3");c(c$,"getRotationScale",function(a){a.m00=this.m00;a.m01=this.m01;a.m02=this.m02;a.m10=this.m10;a.m11=this.m11;a.m12=this.m12;a.m20=this.m20;a.m21=this.m21;a.m22=this.m22},"JU.M3");
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$,"getRow",function(a,b){3>a&&this.getRow33(a,b);switch(a){case 0:b[3]=this.m03;
return;case 1:b[3]=this.m13;return;case 2:b[3]=this.m23;return;case 3:b[0]=this.m30;b[1]=this.m31;b[2]=this.m32;b[3]=this.m33;return}this.err()},"~N,~A");c(c$,"setColumn4",function(a,b,d,e,c){0==a?(this.m00=b,this.m10=d,this.m20=e,this.m30=c):1==a?(this.m01=b,this.m11=d,this.m21=e,this.m31=c):2==a?(this.m02=b,this.m12=d,this.m22=e,this.m32=c):3==a?(this.m03=b,this.m13=d,this.m23=e,this.m33=c):this.err()},"~N,~N,~N,~N,~N");c(c$,"setColumnA",function(a,b){3>a&&this.setColumn33(a,b);switch(a){case 0:this.m30=
b[3];break;case 1:this.m31=b[3];break;case 2:this.m32=b[3];break;case 3:this.m03=b[0];this.m13=b[1];this.m23=b[2];this.m33=b[3];break;default:this.err()}},"~N,~A");c(c$,"getColumn",function(a,b){3>a&&this.getColumn33(a,b);switch(a){case 0:b[3]=this.m30;break;case 1:b[3]=this.m31;break;case 2:b[3]=this.m32;break;case 3:b[0]=this.m03;b[1]=this.m13;b[2]=this.m23;b[3]=this.m33;break;default:this.err()}},"~N,~A");c(c$,"sub",function(a){this.sub33(a);this.m03-=a.m03;this.m13-=a.m13;this.m23-=a.m23;this.m30-=
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if(this.doGetModel(++this.modelNumber,null)&&(this.iatom0=this.asc.ac,this.processMolSdHeader(),this.processCtab(a),this.vr=null,this.isLastModel(this.modelNumber)))return this.continuing=!1;null!=this.line&&0>this.line.indexOf("$$$$")&&this.discardLinesUntilStartsWith("$$$$");return!0});h(c$,"finalizeSubclassReader",function(){this.finalizeReaderMR()});c(c$,"finalizeReaderMR",function(){this.is2D&&this.set2D();this.isTrajectory=!1;this.finalizeReaderASCR()});c(c$,"processMolSdHeader",function(){var a,
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e}-2147483648==p&&this.haveAtomSerials&&(p=d+1)}this.addMolAtom(p,h,c,l,f,j,k)}for(d=0;d<b;++d)this.rd(),j=0,c=this.line.substring(0,3).trim(),f=this.line.substring(3,6).trim(),k=this.parseIntRange(this.line,6,9),this.is2D&&(1==k&&12<=this.line.length)&&(j=this.parseIntRange(this.line,9,12)),k=this.fixOrder(k,j),this.haveAtomSerials?this.asc.addNewBondFromNames(c,f,k):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(c)-1,this.iatom0+this.parseIntStr(f)-1,k);for(;null!=this.rd()&&0!=this.line.indexOf("$$$$");)if(this.line.toUpperCase().contains("_PARTIAL_CHARGES"))try{for(var v=
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if(0>=this.desiredVibrationNumber?this.doGetModel(this.modelNumber,null):this.doGetVibration(this.vibrationNumber)){this.rd();this.checkCurrentLineForScript();this.asc.newAtomSet();var b=this.line;this.readAtoms(a);this.applySymmetryAndSetTrajectory();this.asc.setAtomSetName(b);if(this.isLastModel(this.modelNumber))return this.continuing=!1}else this.skipAtomSet(a);this.discardLinesUntilNonBlank();return!1});h(c$,"finalizeSubclassReader",function(){this.isTrajectory=!1;this.finalizeReaderASCR()});
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c(c$,"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"<=
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h(c$,"getAtomSetIndex",function(){return this.atom.atomSetIndex});h(c$,"getSymmetry",function(){return this.atom.bsSymmetry});h(c$,"getAtomSite",function(){return this.atom.atomSite+1});h(c$,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});h(c$,"getElementNumber",function(){return 0<this.atom.elementNumber?this.atom.elementNumber:J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});h(c$,"getAtomName",function(){return this.atom.atomName});h(c$,"getFormalCharge",function(){return this.atom.formalCharge});
h(c$,"getPartialCharge",function(){return this.atom.partialCharge});h(c$,"getTensors",function(){return this.atom.tensors});h(c$,"getRadius",function(){return this.atom.radius});h(c$,"getVib",function(){return null==this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});h(c$,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1095761940!=this.atom.vib.z?0:B(this.atom.vib.x)});h(c$,"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");w(["java.util.Hashtable"],"J.adapter.smarter.AtomSetCollection","java.lang.Boolean $.Float java.util.Collections $.Properties JU.AU $.BS $.Lst $.P3 $.V3 J.adapter.smarter.Atom $.Bond $.SmarterJmolAdapter J.api.Interface JU.Logger".split(" "),function(){c$=r(function(){this.atoms=this.atomSetInfo=this.collectionName=this.fileTypeName=this.bsAtoms=this.reader=null;this.ac=0;this.bonds=null;this.bondCount=0;this.structures=null;this.atomSetCount=
this.structureCount=0;this.iSet=-1;this.errorMessage=this.atomSetAuxiliaryInfo=this.atomSetBondCounts=this.atomSetAtomCounts=this.atomSetAtomIndexes=this.atomSetNumbers=null;this.isTrajectory=this.coordinatesAreFractional=!1;this.trajectoryStepCount=0;this.trajectoryNames=this.vibrationSteps=this.trajectorySteps=null;this.allowMultiple=this.doFixPeriodic=!1;this.bsStructuredModels=this.readerList=null;this.haveAnisou=!1;this.baseSymmetryAtomCount=0;this.checkLatticeOnly=!1;this.xtalSymmetry=null;
this.bondIndex0=0;this.checkSpecial=!0;this.atomSymbolicMap=null;this.haveUnitCell=!1;this.vibScale=0;t(this,arguments)},J.adapter.smarter,"AtomSetCollection");I(c$,function(){this.atomSetInfo=new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=D(16,0);this.atomSetAtomIndexes=D(16,0);this.atomSetAtomCounts=D(16,0);this.atomSetBondCounts=D(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSymbolicMap=new java.util.Hashtable});c(c$,"setCollectionName",
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a;this.reader=b;this.allowMultiple=null==b||0>b.desiredVibrationNumber;a=new java.util.Properties;a.put("PATH_KEY",".PATH");a.put("PATH_SEPARATOR",J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR);this.setInfo("properties",a);if(null!=d){e=0;this.readerList=new JU.Lst;for(a=0;a<d.length;a++)(0<d[a].ac||null!=d[a].reader&&d[a].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(e++,d[a]);1<e&&this.setInfo("isMultiFile",Boolean.TRUE)}else null!=e&&(this.setInfo("isMultiFile",Boolean.TRUE),
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if(0!=a){for(var b=Array(a),d=0<a&&null!=this.atoms[0].vib&&!Float.isNaN(this.atoms[0].vib.z),a=d?Array(a):null,e=0==this.trajectoryStepCount?null:this.trajectorySteps.get(this.trajectoryStepCount-1),c=0,f=0;c<this.ac;c++)if(null==this.bsAtoms||this.bsAtoms.get(c)){var j=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=e&&(j=J.adapter.smarter.AtomSetCollection.fixPeriodic(j,e[c]));b[f]=j;d&&(a[f]=this.atoms[c].vib);f++}if(d){if(null==this.vibrationSteps){this.vibrationSteps=new JU.Lst;for(c=0;c<
this.trajectoryStepCount;c++)this.vibrationSteps.addLast(null)}this.vibrationSteps.addLast(a)}this.trajectorySteps.addLast(b);this.trajectoryStepCount++}});c(c$,"appendAtomSetCollection",function(a,b){null!=b.reader&&b.reader.mustFinalizeModelSet&&this.readerList.addLast(b.reader);var d=this.ac;this.setInfo("loadState",b.atomSetInfo.get("loadState"));if(null!=b.bsAtoms){null==this.bsAtoms&&(this.bsAtoms=new JU.BS);for(var e=b.bsAtoms.nextSetBit(0);0<=e;e=b.bsAtoms.nextSetBit(e+1))this.bsAtoms.set(d+
e)}for(var e=0,c=this.atomSetCount,f=0;f<b.atomSetCount;f++){this.newAtomSet();var j=(this.atomSetAuxiliaryInfo[this.iSet]=b.atomSetAuxiliaryInfo[f]).get("PDB_CONECT_firstAtom_count_max");null!=j&&(j[0]+=d);this.setCurrentModelInfo("title",b.collectionName);this.setAtomSetName(b.getAtomSetName(f));for(j=0;j<b.atomSetAtomCounts[f];j++){try{null!=this.bsAtoms&&this.bsAtoms.set(this.ac),this.newCloneAtom(b.atoms[e])}catch(k){if(y(k,Exception))this.errorMessage="appendAtomCollection error: "+k;else throw k;
}e++}this.atomSetNumbers[this.iSet]=0>a?this.iSet+1:1E6*(a+1)+b.atomSetNumbers[f]}for(e=0;e<b.bondCount;e++)f=b.bonds[e],this.addNewBondWithOrder(f.atomIndex1+d,f.atomIndex2+d,f.order);for(e=J.adapter.smarter.AtomSetCollection.globalBooleans.length;0<=--e;)b.getGlobalBoolean(e)&&this.setGlobalBoolean(e);for(e=0;e<b.structureCount;e++)d=b.structures[e],this.addStructure(d),d.modelStartEnd[0]+=c,d.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(c$,"setNoAutoBond",function(){this.setInfo("noAutoBond",
Boolean.TRUE)});c(c$,"freeze",function(a){1==this.atomSetCount&&null==this.collectionName&&(this.collectionName=this.getAtomSetAuxiliaryInfoValue(0,"name"));a&&this.reverseAtomSets();1<this.trajectoryStepCount&&this.finalizeTrajectory();this.getList(!0);this.getList(!1);for(a=0;a<this.atomSetCount;a++)this.setModelInfoForSet("initialAtomCount",Integer.$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=D(this.ac,0),e=this.ac,a=this.atomSetCount;0<=--a;)for(var c=d[a].size();0<=--c;){var f=this.atoms[--e]=d[a].get(c);b[f.index]=e;f.index=e}for(a=0;a<this.bondCount;a++)this.bonds[a].atomIndex1=b[this.bonds[a].atomIndex1],this.bonds[a].atomIndex2=b[this.bonds[a].atomIndex2];for(a=0;a<this.atomSetCount;a++)d=this.getAtomSetAuxiliaryInfoValue(a,"PDB_CONECT_firstAtom_count_max"),null!=d&&(d[0]=b[d[0]],d[1]=
this.atomSetAtomCounts[a])});c(c$,"reverseSets",function(a,b){for(var d=JU.AU.createArrayOfArrayList(this.atomSetCount),e=0;e<this.atomSetCount;e++)d[e]=new JU.Lst;for(e=0;e<b;e++){if(0>a[e].atomSetIndex)return;d[a[e].atomSetIndex].addLast(a[e])}for(e=this.atomSetCount;0<=--e;)for(var c=d[e].size();0<=--c;)a[--b]=d[e].get(c)},"~A,~N");c(c$,"reverseObject",function(a){for(var b=this.atomSetCount,d=s(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$,"reverseArray",function(a){for(var b=this.atomSetCount,d=s(b/2);0<=--d;)JU.AU.swapInt(a,d,b-1-d)},"~A");c(c$,"getList",function(a){var b;for(b=this.ac;0<=--b&&!(null!=this.atoms[b]&&"\x00"!=(a?this.atoms[b].altLoc:this.atoms[b].insertionCode)););if(!(0>b)){var d=Array(this.atomSetCount);for(b=0;b<this.atomSetCount;b++)d[b]="";var e;for(b=0;b<this.ac;b++)if(null!=this.atoms[b]){var c=a?this.atoms[b].altLoc:this.atoms[b].insertionCode;if("\x00"!=c&&0>d[e=this.atoms[b].atomSetIndex].indexOf(c))d[e]+=
c}a=a?"altLocs":"insertionCodes";for(b=0;b<this.atomSetCount;b++)0<d[b].length&&this.setModelInfoForSet(a,d[b],b)}},"~B");c(c$,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=D(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSetInfo=new java.util.Hashtable;this.atomSetCount=0;this.atomSetNumbers=D(16,0);this.atomSymbolicMap=
new java.util.Hashtable;this.bonds=null;this.iSet=-1;this.xtalSymmetry=this.readerList=null;this.structures=Array(16);this.structureCount=0;this.vibrationSteps=this.trajectorySteps=null});c(c$,"discardPreviousAtoms",function(){for(var a=this.ac;0<=--a;)this.atoms[a]=null;this.ac=0;this.atomSymbolicMap.clear();this.atomSetCount=0;this.iSet=-1;for(a=this.atomSetAuxiliaryInfo.length;0<=--a;)this.atomSetAtomCounts[a]=0,this.atomSetBondCounts[a]=0,this.atomSetAuxiliaryInfo[a]=null});c(c$,"removeAtomSet",
function(a){null==this.bsAtoms&&(this.bsAtoms=new JU.BS,this.bsAtoms.setBits(0,this.ac));var b=this.atomSetAtomIndexes[a],d=b+this.atomSetAtomCounts[a];this.bsAtoms.clearBits(b,d);for(b=d;b<this.ac;b++)this.atoms[b].atomSetIndex--;for(b=a+1;b<this.atomSetCount;b++)this.atomSetAuxiliaryInfo[b-1]=this.atomSetAuxiliaryInfo[b],this.atomSetAtomIndexes[b-1]=this.atomSetAtomIndexes[b],this.atomSetBondCounts[b-1]=this.atomSetBondCounts[b],this.atomSetAtomCounts[b-1]=this.atomSetAtomCounts[b],this.atomSetNumbers[b-
1]=this.atomSetNumbers[b];for(b=d=0;b<this.structureCount;b++){var e=this.structures[b];e.modelStartEnd[0]==a&&e.modelStartEnd[1]==a&&(this.structures[b]=null,d++)}if(0<d){a=Array(this.structureCount-d);for(d=b=0;b<this.structureCount;b++)null!=this.structures[b]&&(a[d++]=this.structures[b]);this.structures=a}for(b=0;b<this.bondCount;b++)this.bonds[b].atomSetIndex=this.atoms[this.bonds[b].atomIndex1].atomSetIndex;this.atomSetAuxiliaryInfo[--this.atomSetCount]=null},"~N");c(c$,"removeCurrentAtomSet",
function(){0>this.iSet||(this.iSet--,this.atomSetCount--)});c(c$,"getHydrogenAtomCount",function(){for(var a=0,b=0;b<this.ac;b++)(1==this.atoms[b].elementNumber||this.atoms[b].elementSymbol.equals("H"))&&a++;return a});c(c$,"newCloneAtom",function(a){a=a.getClone();this.addAtom(a);return a},"J.adapter.smarter.Atom");c(c$,"cloneFirstAtomSet",function(a){if(!this.allowMultiple)return 0;this.newAtomSet();0==a&&(a=this.atomSetAtomCounts[0]);for(var b=0;b<a;++b)this.newCloneAtom(this.atoms[b]);return this.ac},
"~N");c(c$,"cloneAtomSetWithBonds",function(a){var b=this.atomSetBondCounts[a?this.iSet:0];a=a?this.cloneLastAtomSet():this.cloneFirstAtomSet(0);if(0<a)for(var d=0;d<b;d++){var e=this.bonds[this.bondCount-b];this.addNewBondWithOrder(e.atomIndex1+a,e.atomIndex2+a,e.order)}},"~B");c(c$,"cloneLastAtomSet",function(){return this.cloneLastAtomSetFromPoints(0,null)});c(c$,"cloneLastAtomSetFromPoints",function(a,b){if(!this.allowMultiple)return 0;var d=0<a?a:this.getLastAtomSetAtomCount(),e=this.getLastAtomSetAtomIndex();
this.newAtomSet();for(var c=0;c<d;++c){var f=this.newCloneAtom(this.atoms[e++]);null!=b&&f.setT(b[c])}return d},"~N,~A");c(c$,"getLastAtomSetAtomCount",function(){return this.atomSetAtomCounts[this.iSet]});c(c$,"getLastAtomSetAtomIndex",function(){return this.ac-this.atomSetAtomCounts[this.iSet]});c(c$,"addNewAtom",function(){return this.addAtom(new J.adapter.smarter.Atom)});c(c$,"addAtom",function(a){this.ac==this.atoms.length&&(this.atoms=2E5<this.ac?JU.AU.ensureLength(this.atoms,this.ac+5E4):JU.AU.doubleLength(this.atoms));
0==this.atomSetCount&&this.newAtomSet();a.index=this.ac;this.atoms[this.ac++]=a;a.atomSetIndex=this.iSet;a.atomSite=this.atomSetAtomCounts[this.iSet]++;return a},"J.adapter.smarter.Atom");c(c$,"addAtomWithMappedName",function(a){var b=this.addAtom(a).atomName;null!=b&&this.atomSymbolicMap.put(b,a)},"J.adapter.smarter.Atom");c(c$,"addAtomWithMappedSerialNumber",function(a){var b=this.addAtom(a).atomSerial;-2147483648!=b&&this.atomSymbolicMap.put(""+b,a)},"J.adapter.smarter.Atom");c(c$,"getAtomFromName",
function(a){return this.atomSymbolicMap.get(a)},"~S");c(c$,"getAtomIndex",function(a){a=this.atomSymbolicMap.get(a);return null==a?-1:a.index},"~S");c(c$,"addNewBondWithOrder",function(a,b,d){if(0>a||a>=this.ac||0>b||b>=this.ac)return null;a=new J.adapter.smarter.Bond(a,b,d);this.addBond(a);return a},"~N,~N,~N");c(c$,"addNewBondFromNames",function(a,b,d){return this.addNewBondWithOrderA(this.getAtomFromName(a),this.getAtomFromName(b),d)},"~S,~S,~N");c(c$,"addNewBondWithOrderA",function(a,b,d){return null==
a||null==b?null:this.addNewBondWithOrder(a.index,b.index,d)},"J.adapter.smarter.Atom,J.adapter.smarter.Atom,~N");c(c$,"addBond",function(a){0<this.trajectoryStepCount||(0>a.atomIndex1||0>a.atomIndex2||0>a.order||this.atoms[a.atomIndex1].atomSetIndex!=this.atoms[a.atomIndex2].atomSetIndex?JU.Logger.debugging&&JU.Logger.debug(">>>>>>BAD BOND:"+a.atomIndex1+"-"+a.atomIndex2+" order="+a.order):(this.bondCount==this.bonds.length&&(this.bonds=JU.AU.arrayCopyObject(this.bonds,this.bondCount+1024)),this.bonds[this.bondCount++]=
a,this.atomSetBondCounts[this.iSet]++))},"J.adapter.smarter.Bond");c(c$,"finalizeStructures",function(){if(0!=this.structureCount){this.bsStructuredModels=new JU.BS;for(var a=new java.util.Hashtable,b=0;b<this.structureCount;b++){var d=this.structures[b];-1==d.modelStartEnd[0]&&(d.modelStartEnd[0]=0,d.modelStartEnd[1]=this.atomSetCount-1);this.bsStructuredModels.setBits(d.modelStartEnd[0],d.modelStartEnd[1]+1);if(0!=d.strandCount){var d=d.structureID+" "+d.modelStartEnd[0],e=a.get(d),e=(null==e?0:
e.intValue())+1;a.put(d,Integer.$valueOf(e))}}for(b=0;b<this.structureCount;b++)d=this.structures[b],1==d.strandCount&&(d.strandCount=a.get(d.structureID+" "+d.modelStartEnd[0]).intValue())}});c(c$,"addStructure",function(a){this.structureCount==this.structures.length&&(this.structures=JU.AU.arrayCopyObject(this.structures,this.structureCount+32));this.structures[this.structureCount++]=a},"J.adapter.smarter.Structure");c(c$,"addVibrationVectorWithSymmetry",function(a,b,d,e,c){if(c){c=this.atoms[a].atomSite;
for(var f=this.atoms[a].atomSetIndex;a<this.ac&&this.atoms[a].atomSetIndex==f;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,b,d,e)}else this.addVibrationVector(a,b,d,e)},"~N,~N,~N,~N,~B");c(c$,"addVibrationVector",function(a,b,d,e){this.allowMultiple||(a%=this.ac);return this.atoms[a].vib=JU.V3.new3(b,d,e)},"~N,~N,~N,~N");c(c$,"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$,"setU",function(a,b,d){var e=a.anisoBorU;null==e&&this.setAnisoBorU(a,e=L(8,0),8);e[b]=d},"J.adapter.smarter.Atom,~N,~N");c(c$,"getXSymmetry",function(){null==this.xtalSymmetry&&(this.xtalSymmetry=J.api.Interface.getOption("adapter.smarter.XtalSymmetry",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$,"setAtomSetCollectionPartialCharges",function(a){if(!this.atomSetInfo.containsKey(a))return!1;for(var b=this.atomSetInfo.get(a),d=b.size();0<=--d;)this.atoms[d].partialCharge=b.get(d).floatValue();JU.Logger.info("Setting partial charges type "+
a);return!0},"~S");c(c$,"mapPartialCharge",function(a,b){this.getAtomFromName(a).partialCharge=b},"~S,~N");c$.fixPeriodic=c(c$,"fixPeriodic",function(a,b){a.x=J.adapter.smarter.AtomSetCollection.fixPoint(a.x,b.x);a.y=J.adapter.smarter.AtomSetCollection.fixPoint(a.y,b.y);a.z=J.adapter.smarter.AtomSetCollection.fixPoint(a.z,b.z);return a},"JU.P3,JU.P3");c$.fixPoint=c(c$,"fixPoint",function(a,b){for(;0.9<a-b;)a-=1;for(;-0.9>a-b;)a+=1;return a},"~N,~N");c(c$,"finalizeTrajectoryAs",function(a,b){this.trajectorySteps=
a;this.vibrationSteps=b;this.trajectoryStepCount=a.size();this.finalizeTrajectory()},"JU.Lst,JU.Lst");c(c$,"finalizeTrajectory",function(){if(0!=this.trajectoryStepCount){var a=this.trajectorySteps.get(0),b=null==this.vibrationSteps?null:this.vibrationSteps.get(0),d=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(null!=this.vibrationSteps&&null!=b&&b.length<d||a.length<d)this.errorMessage="File cannot be loaded as a trajectory";else{for(var d=new JU.V3,e=0,c=0;e<this.ac;e++)if(null==this.bsAtoms||
this.bsAtoms.get(e))null!=this.vibrationSteps&&(this.atoms[e].vib=null==b?d:b[c]),null!=a[c]&&this.atoms[e].setT(a[c]),c++;this.setInfo("trajectorySteps",this.trajectorySteps);null!=this.vibrationSteps&&this.setInfo("vibrationSteps",this.vibrationSteps)}}});c(c$,"newAtomSet",function(){this.newAtomSetClear(!0)});c(c$,"newAtomSetClear",function(a){!this.allowMultiple&&0<=this.iSet&&this.discardPreviousAtoms();this.bondIndex0=this.bondCount;this.isTrajectory&&this.discardPreviousAtoms();this.iSet=this.atomSetCount++;
this.atomSetCount>this.atomSetNumbers.length&&(this.atomSetAtomIndexes=JU.AU.doubleLengthI(this.atomSetAtomIndexes),this.atomSetAtomCounts=JU.AU.doubleLengthI(this.atomSetAtomCounts),this.atomSetBondCounts=JU.AU.doubleLengthI(this.atomSetBondCounts),this.atomSetAuxiliaryInfo=JU.AU.doubleLength(this.atomSetAuxiliaryInfo));this.atomSetAtomIndexes[this.iSet]=this.ac;this.atomSetCount+this.trajectoryStepCount>this.atomSetNumbers.length&&(this.atomSetNumbers=JU.AU.doubleLengthI(this.atomSetNumbers));this.isTrajectory?
this.atomSetNumbers[this.iSet+this.trajectoryStepCount]=this.atomSetCount+this.trajectoryStepCount:this.atomSetNumbers[this.iSet]=this.atomSetCount;a&&this.atomSymbolicMap.clear();this.setCurrentModelInfo("title",this.collectionName)},"~B");c(c$,"getAtomSetAtomIndex",function(a){return this.atomSetAtomIndexes[a]},"~N");c(c$,"getAtomSetAtomCount",function(a){return this.atomSetAtomCounts[a]},"~N");c(c$,"getAtomSetBondCount",function(a){return this.atomSetBondCounts[a]},"~N");c(c$,"setAtomSetName",
function(a){this.isTrajectory?this.setTrajectoryName(a):(this.setModelInfoForSet("name",a,this.iSet),this.allowMultiple||this.setCollectionName(a))},"~S");c(c$,"setTrajectoryName",function(a){if(0!=this.trajectoryStepCount){null==this.trajectoryNames&&(this.trajectoryNames=new JU.Lst);for(var b=this.trajectoryNames.size();b<this.trajectoryStepCount;b++)this.trajectoryNames.addLast(null);this.trajectoryNames.set(this.trajectoryStepCount-1,a)}},"~S");c(c$,"setAtomSetNames",function(a,b,d){for(var e=
this.iSet;0<=--b&&0<=e;--e)(null==d||!d.get(e))&&this.setModelInfoForSet("name",a,e)},"~S,~N,JU.BS");c(c$,"setCurrentAtomSetNumber",function(a){this.setAtomSetNumber(this.iSet+(this.isTrajectory?this.trajectoryStepCount:0),a)},"~N");c(c$,"setAtomSetNumber",function(a,b){this.atomSetNumbers[a]=b},"~N,~N");c(c$,"setAtomSetModelProperty",function(a,b){this.setAtomSetModelPropertyForSet(a,b,this.iSet)},"~S,~S");c(c$,"setAtomSetModelPropertyForSet",function(a,b,d){var e=this.getAtomSetAuxiliaryInfoValue(d,
"modelProperties");null==e&&this.setModelInfoForSet("modelProperties",e=new java.util.Properties,d);e.put(a,b);a.startsWith(".")&&e.put(a.substring(1),b)},"~S,~S,~N");c(c$,"setAtomProperties",function(a,b,d){n(b,String)&&!b.endsWith("\n")&&(b+="\n");0>d&&(d=this.iSet);var e=this.getAtomSetAuxiliaryInfoValue(d,"atomProperties");null==e&&this.setModelInfoForSet("atomProperties",e=new java.util.Hashtable,d);e.put(a,b)},"~S,~O,~N,~B");c(c$,"setAtomSetPartialCharges",function(a){if(!this.atomSetAuxiliaryInfo[this.iSet].containsKey(a))return!1;
a=this.getAtomSetAuxiliaryInfoValue(this.iSet,a);for(var b=a.size();0<=--b;)this.atoms[b].partialCharge=a.get(b).floatValue();return!0},"~S");c(c$,"getAtomSetAuxiliaryInfoValue",function(a,b){return this.atomSetAuxiliaryInfo[0<=a?a:this.iSet].get(b)},"~N,~S");c(c$,"setCurrentModelInfo",function(a,b){this.setModelInfoForSet(a,b,this.iSet)},"~S,~O");c(c$,"setModelInfoForSet",function(a,b,d){0>d||(null==this.atomSetAuxiliaryInfo[d]&&(this.atomSetAuxiliaryInfo[d]=new java.util.Hashtable),null==b?this.atomSetAuxiliaryInfo[d].remove(a):
this.atomSetAuxiliaryInfo[d].put(a,b))},"~S,~O,~N");c(c$,"setAtomSetPropertyForSets",function(a,b,d){for(var e=this.iSet;0<=--d&&0<=e;--e)this.setAtomSetModelPropertyForSet(a,b,e)},"~S,~S,~N");c(c$,"getAtomSetNumber",function(a){return this.atomSetNumbers[a>=this.atomSetCount?0:a]},"~N");c(c$,"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,e){this.setAtomSetModelProperty("FreqValue",
d);d+=" "+(null==e?"cm^-1":e);e=(null==b?"":b+" ")+d;this.setAtomSetName(e);this.setAtomSetModelProperty("Frequency",d);null!=b&&this.setAtomSetModelProperty("FrequencyLabel",b);this.setAtomSetModelProperty(".PATH",(null==a?"":a+J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR+"Frequencies")+"Frequencies");return e},"~S,~S,~S,~S");c(c$,"getBondList",function(){for(var a=Array(this.bondCount),b=0;b<this.bondCount;b++)a[b]=[this.atoms[this.bonds[b].atomIndex1].atomName,this.atoms[this.bonds[b].atomIndex2].atomName,
""+this.bonds[b].order];return a});c(c$,"centralize",function(){for(var a=new JU.P3,b=0;b<this.atomSetCount;b++){var d=this.atomSetAtomCounts[b],e=this.atomSetAtomIndexes[b];a.set(0,0,0);for(var c=e+d;--c>=e;)a.add(this.atoms[c]);a.scale(1/d);for(c=e+d;--c>=e;)this.atoms[c].sub(a)}});c(c$,"mergeTrajectories",function(a){if(this.isTrajectory&&a.isTrajectory&&null==this.vibrationSteps){for(var b=0;b<a.trajectoryStepCount;b++)this.trajectorySteps.add(this.trajectoryStepCount++,a.trajectorySteps.get(b));
this.setInfo("trajectorySteps",this.trajectorySteps)}},"J.adapter.smarter.AtomSetCollection");C(c$,"globalBooleans","someModelsHaveFractionalCoordinates someModelsHaveSymmetry someModelsHaveUnitcells someModelsHaveCONECT isPDB someModelsHaveDomains someModelsHaveValidations".split(" "),"GLOBAL_FRACTCOORD",0,"GLOBAL_SYMMETRY",1,"GLOBAL_UNITCELLS",2,"GLOBAL_CONECT",3,"GLOBAL_ISPDB",4,"GLOBAL_DOMAINS",5,"GLOBAL_VALIDATIONS",6)});m("J.adapter.smarter");w(["javajs.api.GenericLineReader","JU.SB"],"J.adapter.smarter.AtomSetCollectionReader",
"java.io.BufferedReader java.lang.Boolean $.Float $.NullPointerException javajs.api.GenericBinaryDocument JU.BS $.Lst $.M3 $.P3 $.PT $.Quat $.V3 J.adapter.smarter.Atom $.AtomSetCollection J.api.Interface $.JmolAdapter JU.BSUtil $.Logger $.Parser".split(" "),function(){c$=r(function(){this.isBinary=!1;this.validation=this.domains=this.trajectorySteps=this.htParams=this.readerName=this.binaryDoc=this.reader=this.asc=null;this.isConcatenated=!1;this.addedDataKey=this.addedData=null;this.fixJavaFloat=
!0;this.next=this.prevline=this.line=null;this.ptLine=0;this.latticeCells=null;this.iHaveSymmetryOperators=this.iHaveUnitCell=this.doProcessLines=!1;this.continuing=!0;this.vwr=null;this.isSequential=this.getHeader=this.doCheckUnitCell=this.applySymmetryToBonds=this.isTrajectory=this.ignoreFileSymmetryOperators=this.doApplySymmetry=!1;this.vibrationNumber=this.modelNumber=this.templateAtomCount=0;this.desiredVibrationNumber=-2147483648;this.bsModels=null;this.havePartialChargeFilter=!1;this.calculationType=
"?";this.sgName=null;this.ignoreFileSpaceGroupName=this.ignoreFileUnitCell=!1;this.notionalUnitCell=null;this.desiredModelNumber=-2147483648;this.out=this.symmetry=null;this.doPackUnitCell=this.iHaveFractionalCoordinates=!1;this.ptSupercell=null;this.forcePacked=this.mustFinalizeModelSet=!1;this.packingError=0.02;this.loadNote=null;this.merging=this.fileCoordinatesAreFractional=this.doConvertToFractional=!1;this.symmetryRange=0;this.firstLastStep=null;this.lastModelNumber=2147483647;this.desiredSpaceGroupIndex=
-1;this.unitCellOffset=this.fileOffsetFractional=this.fileOffset=this.fileScaling=null;this.unitCellOffsetFractional=!1;this.fileName=this.filePath=this.moreUnitCellInfo=null;this.stateScriptVersionInt=2147483647;this.baseAtomIndex=0;this.haveModel=this.isFinalized=!1;this.previousUnitCell=this.previousSpaceGroup=null;this.nMatrixElements=0;this.filter=this.bsFilter=this.matUnitCellOrientation=null;this.filterAtomType=this.filterAtomName=this.filterChain=this.filterGroup3=this.filterAltLoc=this.haveAtomFilter=
!1;this.filterAtomTypeStr=null;this.filterAtomNameTerminator=";";this.filterEveryNth=this.filterHetero=this.filterElement=!1;this.filterSymop=null;this.nFiltered=this.filterN=0;this.reverseModels=this.doReadMolecularOrbitals=this.allowPDBFilter=this.useAltNames=this.addVibrations=this.doCentralize=this.doSetOrientation=!1;this.nameRequired=null;this.centroidPacked=this.doCentroidUnitCell=!1;this.ms=this.matRot=this.filter2=this.filter1=this.strSupercell=null;this.vibsFractional=!1;this.siteScript=
this.previousScript=null;t(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);I(c$,function(){this.next=D(1,0);this.loadNote=new JU.SB});c(c$,"setup",function(a,b,d){this.setupASCR(a,b,d)},"~S,java.util.Map,~O");c(c$,"setupASCR",function(a,b,d){null!=a&&(this.htParams=b,this.filePath=a.$replace("\\","/"),a=this.filePath.lastIndexOf("/"),this.fileName=this.filePath.substring(a+1),n(d,java.io.BufferedReader)?this.reader=d:n(d,javajs.api.GenericBinaryDocument)&&
(this.binaryDoc=d))},"~S,java.util.Map,~O");c(c$,"readData",function(){this.initialize();this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);try{this.initializeReader();if(null==this.binaryDoc)for(null==this.line&&this.continuing&&this.rd();null!=this.line&&this.continuing;)this.checkLine()&&this.rd();else this.binaryDoc.setOutputChannel(this.out),this.processBinaryDocument();this.finalizeSubclassReader();this.isFinalized||this.finalizeReaderASCR()}catch(a){JU.Logger.info("Reader error: "+
a),this.vwr.isJS||a.printStackTrace(),this.setError(a)}null!=this.reader&&this.reader.close();null!=this.binaryDoc&&this.binaryDoc.close();return this.finish()});c(c$,"fixBaseIndices",function(){try{var a=this.htParams.get("baseModelIndex").intValue();this.baseAtomIndex+=this.asc.ac;a+=this.asc.atomSetCount;this.htParams.put("baseAtomIndex",Integer.$valueOf(this.baseAtomIndex));this.htParams.put("baseModelIndex",Integer.$valueOf(a))}catch(b){if(!y(b,Exception))throw b;}});c(c$,"readDataObject",function(a){this.initialize();
this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);this.initializeReader();this.processDOM(a);return this.finish()},"~O");c(c$,"processDOM",function(){},"~O");c(c$,"processBinaryDocument",function(){});c(c$,"initializeReader",function(){});c(c$,"checkLine",function(){return!0});c(c$,"checkLastModel",function(){if(this.isLastModel(this.modelNumber)&&this.doProcessLines)return this.continuing=this.doProcessLines=!1;this.doProcessLines=!1;return!0});c(c$,"isLastModel",function(a){return 0<
this.desiredModelNumber||a>=this.lastModelNumber},"~N");c(c$,"appendLoadNote",function(a){null==a?this.loadNote=new JU.SB:(this.loadNote.append(a).append("\n"),JU.Logger.info(a))},"~S");c(c$,"initializeTrajectoryFile",function(){this.asc.addAtom(new J.adapter.smarter.Atom);this.trajectorySteps=this.htParams.get("trajectorySteps");null==this.trajectorySteps&&this.htParams.put("trajectorySteps",this.trajectorySteps=new JU.Lst)});c(c$,"finalizeSubclassReader",function(){});c(c$,"finalizeReaderASCR",
function(){this.isFinalized=!0;if(0<this.asc.atomSetCount){this.applySymmetryAndSetTrajectory();this.asc.finalizeStructures();this.doCentralize&&this.asc.centralize();var a=this.asc.getAtomSetAuxiliaryInfo(0);if(null!=this.domains&&null!=a){this.asc.setGlobalBoolean(5);var b=this.domains.getMapKeys(2,!0),d=b.indexOf("{ ",2);0<=d&&(b=b.substring(d+2));d=b.indexOf("_metadata");0>d&&(d=b.indexOf("metadata"));0<=d&&(b=b.substring(0,d));b=JU.PT.rep(JU.PT.replaceAllCharacters(b,"{}","").trim(),"\n","\n  ")+
"\n\nUse SHOW DOMAINS for details.";this.appendLoadNote("\nDomains loaded:\n   "+b);for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("domains",this.domains)}if(null!=this.validation&&null!=a)for(b=this.asc.atomSetCount;0<=--b;)a=this.asc.getAtomSetAuxiliaryInfo(b),a.put("validation",this.validation)}this.fixJavaFloat||this.asc.setInfo("legacyJavaFloat",Boolean.TRUE);this.setLoadNote()});c(c$,"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));this.htParams.containsKey("bsFilter")&&this.htParams.put("filteredAtomCount",Integer.$valueOf(JU.BSUtil.cardinalityOf(this.htParams.get("bsFilter"))));this.calculationType.equals("?")||this.asc.setInfo("calculationType",this.calculationType);var b=a=this.asc.fileTypeName;
0<=b.indexOf("(")&&(b=b.substring(0,b.indexOf("(")));for(var d=this.asc.atomSetCount;0<=--d;)this.asc.setModelInfoForSet("fileName",this.filePath,d),this.asc.setModelInfoForSet("fileType",b,d);this.asc.freeze(this.reverseModels);if(null!=this.asc.errorMessage)return this.asc.errorMessage+"\nfor file "+this.filePath+"\ntype "+a;if(0==(null==this.asc.bsAtoms?this.asc.ac:this.asc.bsAtoms.cardinality())&&0>b.indexOf("DataOnly")&&null==this.asc.atomSetInfo.get("dataOnly"))return"No atoms found\nfor file "+
this.filePath+"\ntype "+a;this.fixBaseIndices();return this.asc});c(c$,"setError",function(a){var b;b=a.getMessage?a.getMessage():a.toString();this.asc.errorMessage=null==this.line?"Error reading file at end of file \n"+b:"Error reading file at line "+this.ptLine+":\n"+this.line+"\n"+b;this.vwr.isJS||a.printStackTrace()},"Throwable");c(c$,"initialize",function(){this.htParams.containsKey("baseAtomIndex")&&(this.baseAtomIndex=this.htParams.get("baseAtomIndex").intValue());this.initializeSymmetry();
this.vwr=this.htParams.remove("vwr");this.htParams.containsKey("stateScriptVersionInt")&&(this.stateScriptVersionInt=this.htParams.get("stateScriptVersionInt").intValue());var a=this.htParams.get("packingError");null!=a?this.packingError=a.floatValue():null!=this.htParams.get("legacyJavaFloat")&&(this.fixJavaFloat=!1);this.merging=this.htParams.containsKey("merging");this.getHeader=this.htParams.containsKey("getHeader");this.isSequential=this.htParams.containsKey("isSequential");this.readerName=this.htParams.get("readerName");
this.htParams.containsKey("outputChannel")&&(this.out=this.htParams.get("outputChannel"));this.htParams.containsKey("vibrationNumber")?this.desiredVibrationNumber=this.htParams.get("vibrationNumber").intValue():this.htParams.containsKey("modelNumber")&&(this.desiredModelNumber=this.htParams.get("modelNumber").intValue());this.applySymmetryToBonds=this.htParams.containsKey("applySymmetryToBonds");this.bsFilter=this.htParams.get("bsFilter");this.setFilter(null);null!=this.strSupercell&&!this.checkFilterKey("NOPACK")&&
(this.forcePacked=!0);a=this.htParams.get("supercell");n(a,String)?this.strSupercell=a:this.ptSupercell=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),n(a,JU.BS)?this.bsModels=a:this.firstLastStep=a):this.htParams.containsKey("firstLastStep")?this.firstLastStep=this.htParams.get("firstLastStep"):this.htParams.containsKey("bsModels")&&
(this.bsModels=this.htParams.get("bsModels"));this.htParams.containsKey("templateAtomCount")&&(this.templateAtomCount=this.htParams.get("templateAtomCount").intValue());if(null!=this.bsModels||null!=this.firstLastStep)this.desiredModelNumber=-2147483648;if(null==this.bsModels&&null!=this.firstLastStep){0>this.firstLastStep[0]&&(this.firstLastStep[0]=0);if(0==this.firstLastStep[2]||this.firstLastStep[1]<this.firstLastStep[0])this.firstLastStep[1]=-1;1>this.firstLastStep[2]&&(this.firstLastStep[2]=
1);this.bsModels=JU.BSUtil.newAndSetBit(this.firstLastStep[0]);if(this.firstLastStep[1]>this.firstLastStep[0])for(a=this.firstLastStep[0];a<=this.firstLastStep[1];a+=this.firstLastStep[2])this.bsModels.set(a)}if(null!=this.bsModels&&(null==this.firstLastStep||-1!=this.firstLastStep[1]))this.lastModelNumber=this.bsModels.length();this.symmetryRange=this.htParams.containsKey("symmetryRange")?this.htParams.get("symmetryRange").floatValue():0;this.initializeSymmetryOptions();this.htParams.containsKey("spaceGroupIndex")&&
(this.desiredSpaceGroupIndex=this.htParams.get("spaceGroupIndex").intValue(),-2==this.desiredSpaceGroupIndex&&(this.sgName=this.htParams.get("spaceGroupName")),this.ignoreFileSpaceGroupName=-2==this.desiredSpaceGroupIndex||0<=this.desiredSpaceGroupIndex,this.ignoreFileSymmetryOperators=-1!=this.desiredSpaceGroupIndex);this.htParams.containsKey("unitCellOffset")&&(this.fileScaling=JU.P3.new3(1,1,1),this.fileOffset=this.htParams.get("unitCellOffset"),this.fileOffsetFractional=JU.P3.newP(this.fileOffset),
this.unitCellOffsetFractional=this.htParams.containsKey("unitCellOffsetFractional"));this.htParams.containsKey("unitcell")&&(a=this.htParams.get("unitcell"),this.merging&&this.setFractionalCoordinates(!0),9==a.length?(this.addPrimitiveLatticeVector(0,a,0),this.addPrimitiveLatticeVector(1,a,3),this.addPrimitiveLatticeVector(2,a,6)):this.setUnitCell(a[0],a[1],a[2],a[3],a[4],a[5]),this.ignoreFileUnitCell=this.iHaveUnitCell,this.merging&&!this.iHaveUnitCell&&this.setFractionalCoordinates(!1));this.domains=
this.htParams.get("domains");this.validation=this.htParams.get("validation");this.isConcatenated=this.htParams.containsKey("concatenate")});c(c$,"initializeSymmetryOptions",function(){this.latticeCells=D(3,0);this.doApplySymmetry=!1;var a=this.htParams.get("lattice");if(null==a||0==a.length()){if(!this.forcePacked&&null==this.strSupercell)return;a=JU.P3.new3(1,1,1)}this.latticeCells[0]=B(a.x);this.latticeCells[1]=B(a.y);this.latticeCells[2]=B(a.z);if((this.doCentroidUnitCell=this.htParams.containsKey("centroid"))&&
(-1==this.latticeCells[2]||0==this.latticeCells[2]))this.latticeCells[2]=1;a=this.forcePacked||this.htParams.containsKey("packed");this.centroidPacked=this.doCentroidUnitCell&&a;this.doPackUnitCell=!this.doCentroidUnitCell&&(a||0>this.latticeCells[2]);this.doApplySymmetry=0<this.latticeCells[0]&&0<this.latticeCells[1];this.doApplySymmetry||(this.latticeCells=D(3,0))});c(c$,"doGetModel",function(a,b){if(null!=b&&null!=this.nameRequired&&0<this.nameRequired.length&&0>b.toUpperCase().indexOf(this.nameRequired))return!1;
var d=null==this.bsModels?1>this.desiredModelNumber||a==this.desiredModelNumber:a>this.lastModelNumber?!1:0<a&&this.bsModels.get(a-1)||this.haveModel&&null!=this.firstLastStep&&0>this.firstLastStep[1]&&(2>this.firstLastStep[2]||0==(a-1-this.firstLastStep[0])%this.firstLastStep[2]);d&&0==this.desiredModelNumber&&this.asc.discardPreviousAtoms();this.haveModel=(new Boolean(this.haveModel|d)).valueOf();d&&(this.doProcessLines=!0);return d},"~N,~S");c(c$,"initializeSymmetry",function(){this.previousSpaceGroup=
this.sgName;this.previousUnitCell=this.notionalUnitCell;this.iHaveUnitCell=this.ignoreFileUnitCell;if(!this.ignoreFileUnitCell){this.notionalUnitCell=L(25,0);for(var a=25;0<=--a;)this.notionalUnitCell[a]=NaN;this.symmetry=null}this.ignoreFileSpaceGroupName||(this.sgName="unspecified!");this.doCheckUnitCell=!1});c(c$,"newAtomSet",function(a){0<=this.asc.iSet?(this.asc.newAtomSet(),this.asc.setCollectionName("<collection of "+(this.asc.iSet+1)+" models>")):this.asc.setCollectionName(a);this.asc.setModelInfoForSet("name",
a,Math.max(0,this.asc.iSet))},"~S");c(c$,"cloneLastAtomSet",function(a,b){var d=this.asc.getLastAtomSetAtomCount();this.asc.cloneLastAtomSetFromPoints(a,b);this.asc.haveUnitCell&&(this.doCheckUnitCell=this.iHaveUnitCell=!0,this.sgName=this.previousSpaceGroup,this.notionalUnitCell=this.previousUnitCell);return d},"~N,~A");c(c$,"setSpaceGroupName",function(a){this.ignoreFileSpaceGroupName||(this.sgName=a.trim(),JU.Logger.info("Setting space group name to "+this.sgName))},"~S");c(c$,"setSymmetryOperator",
function(a){if(this.ignoreFileSymmetryOperators)return-1;var b=this.asc.getXSymmetry().addSpaceGroupOperation(a,!0);0>b&&JU.Logger.warn("Skippings symmetry operation "+a);this.iHaveSymmetryOperators=!0;return b},"~S");c(c$,"initializeCartesianToFractional",function(){for(var a=0;16>a;a++)if(!Float.isNaN(this.notionalUnitCell[6+a]))return;for(a=0;16>a;a++)this.notionalUnitCell[6+a]=0==a%5?1:0;this.nMatrixElements=0});c(c$,"clearUnitCell",function(){if(!this.ignoreFileUnitCell){for(var a=6;22>a;a++)this.notionalUnitCell[a]=
NaN;this.checkUnitCell(6)}});c(c$,"setUnitCellItem",function(a,b){if(!this.ignoreFileUnitCell&&!(0==a&&1==b||3==a&&0==b))!Float.isNaN(b)&&(6<=a&&Float.isNaN(this.notionalUnitCell[6]))&&this.initializeCartesianToFractional(),this.notionalUnitCell[a]=b,JU.Logger.debugging&&JU.Logger.debug("setunitcellitem "+a+" "+b),6>a||Float.isNaN(b)?this.iHaveUnitCell=this.checkUnitCell(6):12==++this.nMatrixElements&&(this.iHaveUnitCell=this.checkUnitCell(22))},"~N,~N");c(c$,"setUnitCell",function(a,b,d,e,c,f){this.ignoreFileUnitCell||
(this.clearUnitCell(),this.notionalUnitCell[0]=a,this.notionalUnitCell[1]=b,this.notionalUnitCell[2]=d,0!=e&&(this.notionalUnitCell[3]=e),0!=c&&(this.notionalUnitCell[4]=c),0!=f&&(this.notionalUnitCell[5]=f),this.iHaveUnitCell=this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");c(c$,"addPrimitiveLatticeVector",function(a,b,d){if(!this.ignoreFileUnitCell){if(0==a)for(var e=0;6>e;e++)this.notionalUnitCell[e]=0;a=6+3*a;this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a++]=b[d++];this.notionalUnitCell[a]=
b[d];if(Float.isNaN(this.notionalUnitCell[0]))for(a=0;6>a;a++)this.notionalUnitCell[a]=-1;this.iHaveUnitCell=this.checkUnitCell(15)}},"~N,~A,~N");c(c$,"checkUnitCell",function(a){for(var b=0;b<a;b++)if(Float.isNaN(this.notionalUnitCell[b]))return!1;if(22==a&&1==this.notionalUnitCell[0]&&1==this.notionalUnitCell[1]&&1==this.notionalUnitCell[2]&&1==this.notionalUnitCell[6]&&1==this.notionalUnitCell[11]&&1==this.notionalUnitCell[16])return!1;this.doApplySymmetry&&(this.getSymmetry(),this.doConvertToFractional=
!this.fileCoordinatesAreFractional);return!0},"~N");c(c$,"getSymmetry",function(){if(!this.iHaveUnitCell)return null;null==this.symmetry&&(this.getNewSymmetry().setUnitCell(this.notionalUnitCell,!1),this.checkUnitCellOffset());return this.symmetry});c(c$,"checkUnitCellOffset",function(){null==this.fileOffsetFractional||null==this.symmetry||(this.fileOffset.setT(this.fileOffsetFractional),this.unitCellOffsetFractional!=this.fileCoordinatesAreFractional&&(this.unitCellOffsetFractional?this.symmetry.toCartesian(this.fileOffset,
!1):this.symmetry.toFractional(this.fileOffset,!1)))});c(c$,"getNewSymmetry",function(){return this.symmetry=this.getInterface("JS.Symmetry")});c(c$,"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.doReadMolecularOrbitals=!this.checkFilterKey("NOMO");this.useAltNames=this.checkFilterKey("ALTNAME");this.reverseModels=this.checkFilterKey("REVERSEMODELS");if(null!=this.filter&&(this.checkFilterKey("HETATM")&&(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"HETATM","HETATM-Y")),this.checkFilterKey("ATOM")&&
(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"ATOM","HETATM-N")),this.checkFilterKey("CELL=")&&(this.strSupercell=this.filter.substring(this.filter.indexOf("CELL=")+5).toLowerCase()),this.nameRequired=JU.PT.getQuotedAttribute(this.filter,"NAME"),null!=this.nameRequired&&(this.nameRequired.startsWith("'")?this.nameRequired=JU.PT.split(this.nameRequired,"'")[1]:this.nameRequired.startsWith('"')&&(this.nameRequired=JU.PT.split(this.nameRequired,'"')[1]),this.filter=JU.PT.rep(this.filter,this.nameRequired,
""),this.filter=JU.PT.rep(this.filter,"NAME=","")),this.filterAtomName=this.checkFilterKey("*.")||this.checkFilterKey("!."),this.filterElement=this.checkFilterKey("_"),this.filterGroup3=this.checkFilterKey("["),this.filterChain=this.checkFilterKey(":"),this.filterAltLoc=this.checkFilterKey("%"),(this.filterEveryNth=this.checkFilterKey("/="))?this.filterN=this.parseIntAt(this.filter,this.filter.indexOf("/=")+2):this.filterAtomType=this.checkFilterKey("="),-2147483648==this.filterN&&(this.filterEveryNth=
!1),this.haveAtomFilter=this.filterAtomName||this.filterAtomType||this.filterElement||this.filterGroup3||this.filterChain||this.filterAltLoc||this.filterHetero||this.filterEveryNth||this.checkFilterKey("/="),null==this.bsFilter&&(this.bsFilter=new JU.BS,this.htParams.put("bsFilter",this.bsFilter),this.filter=(";"+this.filter+";").$replace(",",";"),a=this.getFilter("SYMOP="),null!=a&&(this.filterSymop=" "+a+" "),JU.Logger.info("filtering with "+this.filter),this.haveAtomFilter&&(this.filter1=this.filter,
0<=(a=this.filter.indexOf("|"))))))this.filter1=this.filter.substring(0,a).trim()+";",this.filter2=";"+this.filter.substring(a).trim()},"~S");c(c$,"getFilter",function(a){var b=null==this.filter?-1:this.filter.indexOf(a);return 0>b?null:this.filter.substring(b+a.length,this.filter.indexOf(";",b))},"~S");c(c$,"checkFilterKey",function(a){return null!=this.filter&&0<=this.filter.indexOf(a)},"~S");c(c$,"filterAtom",function(a,b){if(!this.haveAtomFilter)return!0;var d=this.checkFilter(a,this.filter1);
null!=this.filter2&&(d=(new Boolean(d|this.checkFilter(a,this.filter2))).valueOf());d&&this.filterEveryNth&&(d=0==this.nFiltered++%this.filterN);this.bsFilter.setBitTo(0<=b?b:this.asc.ac,d);return d},"J.adapter.smarter.Atom,~N");c(c$,"checkFilter",function(a,b){return(!this.filterGroup3||null==a.group3||!this.filterReject(b,"[",a.group3.toUpperCase()+"]"))&&(!this.filterAtomName||this.allowAtomName(a.atomName,b))&&(null==this.filterAtomTypeStr||null==a.atomName||0<=a.atomName.toUpperCase().indexOf("\x00"+
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"Alchemy":J.adapter.smarter.Resolver.checkFoldingXyz(b)?"FoldingXyz":J.adapter.smarter.Resolver.checkCube(b)?"Cube":J.adapter.smarter.Resolver.checkWien2k(b)?"Wien2k":J.adapter.smarter.Resolver.checkAims(b)?"Aims":J.adapter.smarter.Resolver.checkGenNBO(b,d)?"GenNBO":null},"~N,~A,~S");c$.checkAims=c(c$,"checkAims",function(a){for(var b=0;b<a.length&&!a[b].startsWith("mol 1");b++){var d=JU.PT.getTokens(a[b]);if(0!=d.length&&(d[0].startsWith("atom")&&4<d.length&&Float.isNaN(JU.PT.parseFloat(d[4]))||
d[0].startsWith("multipole")&&6<=d.length||d[0].startsWith("lattice_vector")&&4<=d.length))return!0}return!1},"~A");c$.checkAlchemy=c(c$,"checkAlchemy",function(a){var b;if(0<=(b=a.indexOf("ATOMS"))&&a.indexOf("BONDS")>b)try{return 0<Integer.parseInt(a.substring(0,b).trim())}catch(d){if(!y(d,NumberFormatException))throw d;}return!1},"~S");c$.checkCube=c(c$,"checkCube",function(a){try{for(var b=2;5>=b;b++){var d=new java.util.StringTokenizer(a[b]),e=d.countTokens();if(!(4==e||2==b&&5==e))return!1;
Integer.parseInt(d.nextToken());for(var c=3;0<=--c;)JU.PT.fVal(d.nextToken());5==e&&Integer.parseInt(d.nextToken())}return!0}catch(f){if(!y(f,NumberFormatException))throw f;}return!1},"~A");c$.checkFoldingXyz=c(c$,"checkFoldingXyz",function(a){var b=new java.util.StringTokenizer(a[0].trim()," \t");if(2>b.countTokens())return!1;try{Integer.parseInt(b.nextToken().trim())}catch(d){if(y(d,NumberFormatException))return!1;throw d;}b=a[1].trim();0==b.length&&(b=a[2].trim());b=new java.util.StringTokenizer(b,
" \t");if(0==b.countTokens())return!1;try{Integer.parseInt(b.nextToken().trim())}catch(e){if(y(e,NumberFormatException))return!1;throw e;}return!0},"~A");c$.checkGenNBO=c(c$,"checkGenNBO",function(a,b){return 0<=b.indexOf("$GENNBO")||a[1].startsWith(" Basis set information needed for plotting orbitals")||0<=a[1].indexOf("s in the AO basis:")||0<=a[2].indexOf(" N A T U R A L   A T O M I C   O R B I T A L")},"~A,~S");c$.checkMol=c(c$,"checkMol",function(a){var b=("X"+a[3]).trim().toUpperCase();if(7>
b.length||0<=b.indexOf("."))return 0;if(b.endsWith("V2000"))return 2E3;if(b.endsWith("V3000"))return 3E3;try{var d=Integer.parseInt(a[3].substring(0,3).trim()),e=Integer.parseInt(a[3].substring(3,6).trim());return 0<d&&0<=e&&0!=a[0].indexOf("@<TRIPOS>")&&0!=a[1].indexOf("@<TRIPOS>")&&0!=a[2].indexOf("@<TRIPOS>")?3:0}catch(c){if(!y(c,NumberFormatException))throw c;}return 0},"~A");c$.checkMopacGraphf=c(c$,"checkMopacGraphf",function(a){return 2<a[0].indexOf("MOPAC-Graphical data")},"~A");c$.checkOdyssey=
c(c$,"checkOdyssey",function(a){var b;for(b=0;b<a.length&&(a[b].startsWith("C ")||0==a[b].length);b++);if(b>=a.length||" "!=a[b].charAt(0)||(b+=2)+1>=a.length)return!1;try{var d=Integer.parseInt(a[b].substring(2).trim()),e=Integer.parseInt(a[b].substring(0,2).trim()),c=Integer.parseInt(a[++b].substring(0,2).trim());if(0>d||5<d||0>=c||5<e)return!1;var f=J.adapter.smarter.AtomSetCollectionReader.getTokensFloat(a[b],null,5);return!Float.isNaN(f[1])&&!Float.isNaN(f[2])&&!Float.isNaN(f[3])&&Float.isNaN(f[4])}catch(j){if(!y(j,
Exception))throw j;}return!1},"~A");c$.checkWien2k=c(c$,"checkWien2k",function(a){return a[2].startsWith("MODE OF CALC=")||a[2].startsWith("             RELA")||a[2].startsWith("             NREL")},"~A");c$.checkXyz=c(c$,"checkXyz",function(a){try{Integer.parseInt(a[0].trim());try{Integer.parseInt(a[2].trim())}catch(b){if(y(b,NumberFormatException))return 1;throw b;}return 2}catch(d){if(y(d,NumberFormatException)){if(0<=a[0].indexOf("Bilbao Crys"))return 2}else throw d;}return 0},"~A");c$.checkLineStarts=
c(c$,"checkLineStarts",function(a){for(var b=0;b<J.adapter.smarter.Resolver.lineStartsWithRecords.length;++b)for(var d=J.adapter.smarter.Resolver.lineStartsWithRecords[b],e=1;e<d.length;++e)for(var c=d[e],f=0;f<a.length;f++)if(a[f].startsWith(c))return d[0];return null},"~A");c$.checkHeaderContains=c(c$,"checkHeaderContains",function(a){for(var b=0;b<J.adapter.smarter.Resolver.headerContainsRecords.length;++b)for(var d=J.adapter.smarter.Resolver.headerContainsRecords[b],e=1;e<d.length;++e)if(!(0>
a.indexOf(d[e])))return b=d[0],!b.equals("Xml")?b:0>a.indexOf("<!DOCTYPE HTML PUBLIC")&&0>a.indexOf("XHTML")&&(0>a.indexOf("xhtml")||0<=a.indexOf("<cml"))?J.adapter.smarter.Resolver.getXmlType(a):null;return null},"~S");c$.getXmlType=c(c$,"getXmlType",function(a){return 0<=a.indexOf("http://www.molpro.net/")?"XmlMolpro":0<=a.indexOf("odyssey")?"XmlOdyssey":0<=a.indexOf("C3XML")?"XmlChem3d":0<=a.indexOf("arguslab")?"XmlArgus":0<=a.indexOf("jvxl")||0<=a.indexOf("http://www.xml-cml.org/schema")||0<=
a.indexOf("cml:")?"XmlCml":0<=a.indexOf("XSD")?"XmlXsd":0<=a.indexOf(">vasp")?"XmlVasp":0<=a.indexOf("<GEOMETRY_INFO>")?"XmlQE":"XmlCml(unidentified)"},"~S");c$.checkSpecial2=c(c$,"checkSpecial2",function(a){return J.adapter.smarter.Resolver.checkGromacs(a)?"Gromacs":J.adapter.smarter.Resolver.checkCrystal(a)?"Crystal":J.adapter.smarter.Resolver.checkCastep(a)?"Castep":J.adapter.smarter.Resolver.checkVasp(a,!0)?"VaspPoscar":J.adapter.smarter.Resolver.checkVasp(a,!1)?"VaspChgcar":null},"~A");c$.checkCrystal=
c(c$,"checkCrystal",function(a){var b=a[1].trim();if(b.equals("SLAB")||b.equals("MOLECULE")||b.equals("CRYSTAL")||b.equals("POLYMER")||(b=a[3]).equals("SLAB")||b.equals("MOLECULE")||b.equals("POLYMER"))return!0;for(b=0;b<a.length;b++)if(a[b].trim().equals("OPTGEOM")||a[b].trim().equals("FREQCALC")||a[b].contains("DOVESI")||a[b].contains("TORINO")||a[b].contains("http://www.crystal.unito.it")||a[b].contains("Pcrystal")||a[b].contains("MPPcrystal")||a[b].contains("crystal executable"))return!0;return!1},
"~A");c$.checkGromacs=c(c$,"checkGromacs",function(a){if(-2147483648==JU.PT.parseInt(a[1]))return!1;for(var b=-1,d=2;16>d&&0!=b;d++)if(69!=(b=a[d].length)&&45!=b&&0!=b)return!1;return!0},"~A");c$.checkCastep=c(c$,"checkCastep",function(a){for(var b=0;b<a.length;b++)if(1==a[b].indexOf("Frequencies in         cm-1")||a[b].contains("CASTEP")||a[b].toUpperCase().startsWith("%BLOCK LATTICE_ABC")||a[b].toUpperCase().startsWith("%BLOCK LATTICE_CART")||a[b].toUpperCase().startsWith("%BLOCK POSITIONS_FRAC")||
a[b].toUpperCase().startsWith("%BLOCK POSITIONS_ABS")||a[b].contains("<-- E"))return!0;return!1},"~A");c$.checkVasp=c(c$,"checkVasp",function(a,b){var d=b?2>a[5].length?8:7:6,e=a[d].toLowerCase();b&&e.contains("selective")&&(e=a[++d].toLowerCase());return e.contains("direct")||e.contains("cartesian")},"~A,~B");C(c$,"classBase","J.adapter.readers.");c$.readerSets=c$.prototype.readerSets="cif. ;Cif;MMCif; molxyz. ;Mol3D;Mol;Xyz; more. ;BinaryDcd;Gromacs;Jcampdx;MdCrd;MdTop;Mol2;TlsDataOnly; quantum. ;Adf;Csf;Dgrid;GamessUK;GamessUS;Gaussian;GaussianFchk;GaussianWfn;Jaguar;Molden;MopacGraphf;GenNBO;NWChem;Odyssey;Psi;Qchem;Spartan;SpartanSmol;WebMO; pdb. ;Pdb;Pqr;P2n; pymol. ;PyMOL; simple. ;Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;JSON;Mopac;MopacArchive;Tinker;Input; xtal. ;Abinit;Aims;Bilbao;Castep;Cgd;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;VaspPoscar;VaspChgcar;Wien2k;Xcrysden; xml. ;XmlArgus;XmlCml;XmlChem3d;XmlMolpro;XmlOdyssey;XmlXsd;XmlVasp;XmlQE;".split(" ");
C(c$,"CML_NAMESPACE_URI","http://www.xml-cml.org/schema","LEADER_CHAR_MAX",64,"sptRecords",["spt","# Jmol state","# Jmol script","JmolManifest"],"m3dStartRecords",["Alchemy","STRUCTURE  1.00     1"],"cubeFileStartRecords",["Cube","JVXL","#JVXL"],"mol2Records",["Mol2","mol2","@<TRIPOS>"],"webmoFileStartRecords",["WebMO","[HEADER]"],"moldenFileStartRecords",["Molden","[Molden"],"dcdFileStartRecords",["BinaryDcd","T\x00\x00\x00CORD","\x00\x00\x00TCORD"],"tlsDataOnlyFileStartRecords",["TlsDataOnly","REFMAC\n\nTL",
"REFMAC\r\n\r\n","REFMAC\r\rTL"],"inputFileStartRecords",["Input","#ZMATRIX","%mem=","AM1"],"magresFileStartRecords",["Magres","#$magres","# magres"],"pymolStartRecords",["PyMOL","}q"],"janaStartRecords",["Jana","Version Jana"],"jsonStartRecords",["JSON",'{"mol":'],"jcampdxStartRecords",["Jcampdx","##TITLE"]);c$.fileStartsWithRecords=c$.prototype.fileStartsWithRecords=[J.adapter.smarter.Resolver.sptRecords,J.adapter.smarter.Resolver.m3dStartRecords,J.adapter.smarter.Resolver.cubeFileStartRecords,
J.adapter.smarter.Resolver.mol2Records,J.adapter.smarter.Resolver.webmoFileStartRecords,J.adapter.smarter.Resolver.moldenFileStartRecords,J.adapter.smarter.Resolver.dcdFileStartRecords,J.adapter.smarter.Resolver.tlsDataOnlyFileStartRecords,J.adapter.smarter.Resolver.inputFileStartRecords,J.adapter.smarter.Resolver.magresFileStartRecords,J.adapter.smarter.Resolver.pymolStartRecords,J.adapter.smarter.Resolver.janaStartRecords,J.adapter.smarter.Resolver.jsonStartRecords,J.adapter.smarter.Resolver.jcampdxStartRecords];
C(c$,"mmcifLineStartRecords","MMCif _entry.id _database_PDB_ _pdbx_ _chem_comp.pdbx_type _audit_author.name".split(" "),"cifLineStartRecords",["Cif","data_","_publ"],"pqrLineStartRecords",["Pqr","REMARK   1 PQR"],"p2nLineStartRecords",["P2n","REMARK   1 P2N"],"pdbLineStartRecords","Pdb;HEADER;OBSLTE;TITLE ;CAVEAT;COMPND;SOURCE;KEYWDS;EXPDTA;AUTHOR;REVDAT;SPRSDE;JRNL  ;REMARK ;DBREF ;SEQADV;SEQRES;MODRES;HELIX ;SHEET ;TURN  ;CRYST1;ORIGX1;ORIGX2;ORIGX3;SCALE1;SCALE2;SCALE3;ATOM  ;HETATM;MODEL ;LINK  ".split(";"),
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["VaspOutcar"," vasp."," INCAR:"]);c$.lineStartsWithRecords=c$.prototype.lineStartsWithRecords=[J.adapter.smarter.Resolver.mmcifLineStartRecords,J.adapter.smarter.Resolver.cifLineStartRecords,J.adapter.smarter.Resolver.pqrLineStartRecords,J.adapter.smarter.Resolver.p2nLineStartRecords,J.adapter.smarter.Resolver.pdbLineStartRecords,J.adapter.smarter.Resolver.cgdLineStartRecords,J.adapter.smarter.Resolver.shelxLineStartRecords,J.adapter.smarter.Resolver.ghemicalMMLineStartRecords,J.adapter.smarter.Resolver.jaguarLineStartRecords,
J.adapter.smarter.Resolver.mdlLineStartRecords,J.adapter.smarter.Resolver.spartanSmolLineStartRecords,J.adapter.smarter.Resolver.csfLineStartRecords,J.adapter.smarter.Resolver.mol2Records,J.adapter.smarter.Resolver.mdTopLineStartRecords,J.adapter.smarter.Resolver.hyperChemLineStartRecords,J.adapter.smarter.Resolver.vaspOutcarLineStartRecords];C(c$,"bilbaoContainsRecords",["Bilbao",">Bilbao Crystallographic Server<"],"xmlContainsRecords",'Xml <?xml <atom <molecule <reaction <cml <bond .dtd" <list> <entry <identifier http://www.xml-cml.org/schema/cml2/core'.split(" "),
"gaussianContainsRecords",["Gaussian","Entering Gaussian System","Entering Link 1","1998 Gaussian, Inc."],"ampacContainsRecords",["Ampac","AMPAC Version"],"mopacContainsRecords","Mopac;MOPAC 93 (c) Fujitsu;MOPAC FOR LINUX (PUBLIC DOMAIN VERSION);MOPAC:  VERSION  6;MOPAC   7;MOPAC2;MOPAC (PUBLIC".split(";"),"qchemContainsRecords",["Qchem","Welcome to Q-Chem","A Quantum Leap Into The Future Of Chemistry"],"gamessUKContainsRecords",["GamessUK","GAMESS-UK","G A M E S S - U K"],"gamessUSContainsRecords",
["GamessUS","GAMESS","$CONTRL"],"spartanBinaryContainsRecords",["SpartanSmol","|PropertyArchive","_spartan","spardir","BEGIN Directory Entry Molecule"],"spartanContainsRecords",["Spartan","Spartan"],"adfContainsRecords",["Adf","Amsterdam Density Functional"],"psiContainsRecords",["Psi","    PSI  3","PSI3:"],"nwchemContainsRecords",["NWChem"," argument  1 = "],"uicrcifContainsRecords",["Cif","Crystallographic Information File"],"dgridContainsRecords",["Dgrid","BASISFILE   created by DGrid"],"crystalContainsRecords",
["Crystal","*                                CRYSTAL","TORINO","DOVESI"],"dmolContainsRecords",["Dmol","DMol^3"],"gulpContainsRecords",["Gulp","GENERAL UTILITY LATTICE PROGRAM"],"espressoContainsRecords",["Espresso","Program PWSCF","Program PHONON"],"siestaContainsRecords",["Siesta","MD.TypeOfRun","SolutionMethod","MeshCutoff","WELCOME TO SIESTA"],"xcrysDenContainsRecords",["Xcrysden","PRIMVEC","CONVVEC","PRIMCOORD","ANIMSTEP"],"mopacArchiveContainsRecords",["MopacArchive","SUMMARY OF PM"],"abinitContainsRecords",
["Abinit","http://www.abinit.org","Catholique","Louvain"],"gaussianFchkContainsRecords",["GaussianFchk","Number of point charges in /Mol/"],"inputContainsRecords","Input; ATOMS cartesian;$molecule;&zmat;geometry={;$DATA;%coords;GEOM=PQS;geometry units angstroms".split(";"));c$.headerContainsRecords=c$.prototype.headerContainsRecords=[J.adapter.smarter.Resolver.sptRecords,J.adapter.smarter.Resolver.bilbaoContainsRecords,J.adapter.smarter.Resolver.xmlContainsRecords,J.adapter.smarter.Resolver.gaussianContainsRecords,
J.adapter.smarter.Resolver.ampacContainsRecords,J.adapter.smarter.Resolver.mopacContainsRecords,J.adapter.smarter.Resolver.qchemContainsRecords,J.adapter.smarter.Resolver.gamessUKContainsRecords,J.adapter.smarter.Resolver.gamessUSContainsRecords,J.adapter.smarter.Resolver.spartanBinaryContainsRecords,J.adapter.smarter.Resolver.spartanContainsRecords,J.adapter.smarter.Resolver.mol2Records,J.adapter.smarter.Resolver.adfContainsRecords,J.adapter.smarter.Resolver.psiContainsRecords,J.adapter.smarter.Resolver.nwchemContainsRecords,
J.adapter.smarter.Resolver.uicrcifContainsRecords,J.adapter.smarter.Resolver.dgridContainsRecords,J.adapter.smarter.Resolver.crystalContainsRecords,J.adapter.smarter.Resolver.dmolContainsRecords,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]});m("J.adapter.smarter");w(["J.api.JmolAdapter"],"J.adapter.smarter.SmarterJmolAdapter","java.io.BufferedReader javajs.api.GenericBinaryDocument JU.Rdr J.adapter.smarter.AtomIterator $.AtomSetCollection $.AtomSetCollectionReader $.BondIterator $.Resolver $.StructureIterator JU.Logger".split(" "),function(){c$=z(J.adapter.smarter,"SmarterJmolAdapter",J.api.JmolAdapter);h(c$,"getFileTypeName",function(a){return n(a,J.adapter.smarter.AtomSetCollection)?
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Exception))throw f;}else c.setup(a,e,d);return c}catch(j){try{J.adapter.smarter.SmarterJmolAdapter.close(d)}catch(k){if(!y(k,Exception))throw k;}JU.Logger.error(""+j);return""+j}},"~S,~S,~O,java.util.Map");c(c$,"getAtomSetCollectionFromReader",function(a,b,d){var e=J.adapter.smarter.Resolver.getAtomCollectionReader(a,null,b,d,-1);return n(e,J.adapter.smarter.AtomSetCollectionReader)?(e.setup(a,d,b),e.readData()):""+e},"~S,~O,java.util.Map");h(c$,"getAtomSetCollection",function(a){return J.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollection(a)},
"~O");c$.staticGetAtomSetCollection=c(c$,"staticGetAtomSetCollection",function(a){var b=null;try{var b=a.reader,d=a.readData();return!n(d,J.adapter.smarter.AtomSetCollection)?d:null!=d.errorMessage?d.errorMessage:d}catch(e){try{JU.Logger.info(e.toString())}catch(c){if(y(c,Exception))JU.Logger.error(e.toString());else throw c;}try{b.close()}catch(f){if(!y(f,Exception))throw f;}JU.Logger.error(""+e);return""+e}},"J.adapter.smarter.AtomSetCollectionReader");h(c$,"getAtomSetCollectionReaders",function(a,
b,d,e,c){var f=e.get("vwr"),j=b.length,k=c?Array(j):null,l=null;if(e.containsKey("concatenate")){for(var l="",h=0;h<j;h++){var p=f.getFileAsString3(b[h],!1,null);if(0<h&&3>=j&&p.startsWith("{")){var v=p.contains("/outliers/")?"validation":"domains",p=f.evaluateExpressionAsVariable(p);null!=p&&null!=p.getMap()&&e.put(v,p)}else 0<=b[h].indexOf("/rna3dhub/")?l+="\n_rna3d \n;"+p+"\n;\n":0<=b[h].indexOf("/dssr/")?l+="\n_dssr \n;"+p+"\n;\n":(l+=p,l.endsWith("\n")||(l+="\n"))}j=1;l=JU.Rdr.getBR(l)}v=c?null:
Array(j);p=null;for(h=0;h<j;h++)try{null!=p&&e.put("vwr",f);null==l&&(l=a.getBufferedReaderOrBinaryDocument(h,!1));if(!n(l,java.io.BufferedReader)&&!n(l,javajs.api.GenericBinaryDocument))return l;var E=J.adapter.smarter.Resolver.getAtomCollectionReader(b[h],null==d?null:d[h],l,e,h);if(!n(E,J.adapter.smarter.AtomSetCollectionReader))return E;p=E;p.setup(null,null,null);p.isBinary?p.setup(b[h],e,a.getBufferedReaderOrBinaryDocument(h,!0)):p.setup(b[h],e,l);l=null;if(c)k[h]=p;else{E=p.readData();if(!n(E,
J.adapter.smarter.AtomSetCollection))return E;v[h]=E;if(null!=v[h].errorMessage)return v[h].errorMessage}}catch(A){return JU.Logger.error(""+A),f.isJS||A.printStackTrace(),""+A}return c?k:this.getAtomSetCollectionFromSet(k,v,e)},"J.api.JmolFilesReaderInterface,~A,~A,java.util.Map,~B");h(c$,"getAtomSetCollectionFromSet",function(a,b,d){var e=null==b?Array(a.length):b;if(null==b)for(b=0;b<a.length;b++)try{var c=a[b].readData();if(!n(c,J.adapter.smarter.AtomSetCollection))return c;e[b]=c;if(null!=e[b].errorMessage)return e[b].errorMessage}catch(f){return JU.Logger.error(""+
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Math.round(j),m=Math.round(k),n=Math.round(l),t=Math.round(h),r=this.g3d,u=r.clipCode3(v-p,E-p,A-p),v=r.clipCode3(v+p,E+p,A+p),E=r.clipCode3(m-p,n-p,t-p),p=r.clipCode3(m+p,n+p,t+p);this.clipped=0!=(u|v|E|p);if(0==(u&p&v&E))if(this.dxBf=k-c,this.dyBf=l-f,this.dzBf=h-j,0==e||1==e)this.line3d.plotLineDelta(r.getColorArgbOrGray(a),r.getColorArgbOrGray(b),B(c),B(f),B(j),B(this.dxBf),B(this.dyBf),B(this.dzBf),this.clipped);else{0<e&&(this.diameter=e,this.xAf=c,this.yAf=f,this.zAf=j);this.drawBackside=this.clipped||
2==d||0==d;this.xA=B(this.xAf);this.yA=B(this.yAf);this.zA=B(this.zAf);this.dxB=B(this.dxBf);this.dyB=B(this.dyBf);this.dzB=B(this.dzBf);this.shadesA=r.getShades(this.colixA=a);this.shadesB=r.getShades(this.colixB=b);this.endcaps=d;this.calcArgbEndcap(!0,!0);k=this.xyzfRaster;0<e&&this.generateBaseEllipsePrecisely(!1);2==d&&this.renderFlatEndcap(!0,!0,k);this.line3d.setLineBits(this.dxBf,this.dyBf);r.setZMargin(5);e=r.pixel;a=r.width;b=r.zbuf;c=k[0];f=k[1];j=k[2];k=k[3];for(l=this.rasterCount;0<=
--l;)h=k[l]>>8,u=h>>1,p=c[l],m=f[l],n=j[l],this.tEndcapOpen&&0!=this.argbEndcap&&(this.clipped?(r.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+p,this.yEndcap+m,this.zEndcap-n-1,a,b,e),r.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-p,this.yEndcap-m,this.zEndcap+n-1,a,b,e)):(r.plotPixelUnclipped(this.argbEndcap,this.xEndcap+p,this.yEndcap+m,this.zEndcap-n-1,a,b,e),r.plotPixelUnclipped(this.argbEndcap,this.xEndcap-p,this.yEndcap-m,this.zEndcap+n-1,a,b,e))),this.line3d.plotLineDeltaBits(this.shadesA,
this.shadesB,h,this.xA+p,this.yA+m,this.zA-n,this.dxB,this.dyB,this.dzB,this.clipped),this.drawBackside&&this.line3d.plotLineDelta(this.shadesA[u],this.shadesB[u],this.xA-p,this.yA-m,this.zA+n,this.dxB,this.dyB,this.dzB,this.clipped);r.setZMargin(0);3==d&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;this.zAf+=this.dzBf}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"renderCone",function(a,b,d,e,c,f,j,k,l,h,p){this.dxBf=j-(this.xAf=e);this.dyBf=k-(this.yAf=c);this.dzBf=l-(this.zAf=
f);this.xA=s(Math.floor(this.xAf));this.yA=s(Math.floor(this.yAf));this.zA=s(Math.floor(this.zAf));this.dxB=s(Math.floor(this.dxBf));this.dyB=s(Math.floor(this.dyBf));this.dzB=s(Math.floor(this.dzBf));this.xTip=j;this.yTip=k;this.zTip=l;this.colixA=a;this.shadesA=this.g3d.getShades(a);var v=this.shader.getShadeIndex(this.dxB,this.dyB,-this.dzB);a=this.g3d;e=a.pixel;c=a.width;f=a.zbuf;a.plotPixelClippedArgb(this.shadesA[v],B(j),B(k),B(l),c,f,e);this.diameter=d;if(1>=d)1==d&&this.line3d.plotLineDelta(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(p);!p&&2==this.endcaps&&this.renderFlatEndcap(!1,!0,this.xyzfRaster);a.setZMargin(5);b=this.xyztRaster[0];d=this.xyztRaster[1];j=this.xyztRaster[2];k=this.xyzfRaster[3];l=this.shadesA;for(var v=this.tEndcapOpen&&0!=this.argbEndcap,E=this.rasterCount;0<=--E;){var A=b[E],m=d[E],n=j[E],r=k[E]>>8,t=this.xAf+A,u=this.yAf+m,w=this.zAf-n,A=this.xAf-
A,m=this.yAf-m,n=this.zAf+n,x=l[0];v&&(a.plotPixelClippedArgb(this.argbEndcap,B(t),B(u),B(w),c,f,e),a.plotPixelClippedArgb(this.argbEndcap,B(A),B(m),B(n),c,f,e));0!=x&&(this.line3d.plotLineDeltaA(l,l,r,B(t),B(u),B(w),s(Math.ceil(this.xTip-t)),s(Math.ceil(this.yTip-u)),s(Math.ceil(this.zTip-w)),!0),h&&(this.line3d.plotLineDeltaA(l,l,r,B(t),B(u)+1,B(w),s(Math.ceil(this.xTip-t)),s(Math.ceil(this.yTip-u))+1,s(Math.ceil(this.zTip-w)),!0),this.line3d.plotLineDeltaA(l,l,r,B(t)+1,B(u),B(w),s(Math.ceil(this.xTip-
t))+1,s(Math.ceil(this.yTip-u)),s(Math.ceil(this.zTip-w)),!0)),!p&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDelta(x,x,B(A),B(m),B(n),s(Math.ceil(this.xTip-A)),s(Math.ceil(this.yTip-m)),s(Math.ceil(this.zTip-n)),!0))}a.setZMargin(0)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B,~B");c(c$,"generateBaseEllipsePrecisely",function(a){this.calcCosSin(this.dxBf,this.dyBf,this.dzBf);this.calcPoints(a?2:3,!0);this.interpolatePrecisely(0,1,this.xyzfRaster,this.xyztRaster);a||this.interpolatePrecisely(1,2,this.xyzfRaster,
this.xyztRaster);for(a=3;0<=--a;)for(var b=this.rasterCount;0<=--b;)this.xyzfRaster[a][b]=s(Math.floor(this.xyztRaster[a][b]))},"~B");c(c$,"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$,"calcCosSin",function(a,b,d){var e=a*a+b*b;if(0==e)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var c=Math.sqrt(e),
e=Math.sqrt(e+d*d);this.cosTheta=d/e;this.cosPhi=a/c;this.sinPhi=b/c}},"~N,~N,~N");c(c$,"calcRotatedPoint",function(a,b,d,e,c){c[3][b]=a;a*=3.141592653589793;var f=Math.sin(a)*this.cosTheta,j=Math.cos(a);a=this.radius*(f*this.cosPhi-j*this.sinPhi);f=this.radius*(f*this.sinPhi+j*this.cosPhi);j=this.radius2-(a*a+f*f);j=0<j?Math.sqrt(j):0;d?(c[0][b]=a,c[1][b]=f,c[2][b]=j):(this.tEvenDiameter?(e[0][b]=s(a-0.5),e[1][b]=s(f-0.5)):(e[0][b]=s(a),e[1][b]=s(f)),e[2][b]=s(j+0.5));e[3][b]=this.shader.getShadeFp8(a,
f,j)},"~N,~N,~B,~A,~A");c(c$,"allocRaster",function(a,b,d){if(this.rasterCount>=b[0].length)for(;this.rasterCount>=b[0].length;){for(var e=4;0<=--e;)b[e]=JU.AU.doubleLengthI(b[e]);d[3]=JU.AU.doubleLengthF(d[3])}if(a)for(;this.rasterCount>=d[0].length;)for(e=3;0<=--e;)d[e]=JU.AU.doubleLengthF(d[e]);return this.rasterCount++},"~B,~A,~A");c(c$,"interpolate",function(a,b,d,e){var c=d[0],f=d[1],c=c[b]-c[a];0>c&&(c=-c);f=f[b]-f[a];0>f&&(f=-f);if(!(1>=c+f)){for(var j=this.allocRaster(!1,d,e),c=d[0],f=d[1],
k=d[3],l=e[3][a],h=e[3][b],p=4;0<=--p;){var v=(l+h)/2;this.calcRotatedPoint(v,j,!1,d,e);if(c[j]==c[a]&&f[j]==f[a])k[a]=k[a]+k[j]>>>1,l=v;else if(c[j]==c[b]&&f[j]==f[b])k[b]=k[b]+k[j]>>>1,h=v;else{this.interpolate(a,j,d,e);this.interpolate(j,b,d,e);return}}c[j]=c[a];f[j]=f[b]}},"~N,~N,~A,~A");c(c$,"interpolatePrecisely",function(a,b,d,e){var c=e[0],f=e[1],j=s(Math.floor(c[b]))-s(Math.floor(c[a]));0>j&&(j=-j);f=s(Math.floor(f[b]))-s(Math.floor(f[a]));0>f&&(f=-f);if(!(1>=j+f)){for(var f=e[3],j=f[a],
k=f[b],l=this.allocRaster(!0,d,e),c=e[0],f=e[1],h=d[3],p=4;0<=--p;){var v=(j+k)/2;this.calcRotatedPoint(v,l,!0,d,e);if(s(Math.floor(c[l]))==s(Math.floor(c[a]))&&s(Math.floor(f[l]))==s(Math.floor(f[a])))h[a]=h[a]+h[l]>>>1,j=v;else if(s(Math.floor(c[l]))==s(Math.floor(c[b]))&&s(Math.floor(f[l]))==s(Math.floor(f[b])))h[b]=h[b]+h[l]>>>1,k=v;else{this.interpolatePrecisely(a,l,d,e);this.interpolatePrecisely(l,b,d,e);return}}c[l]=c[a];f[l]=f[b]}},"~N,~N,~A,~A");c(c$,"renderFlatEndcap",function(a,b,d){var e,
c;if(b){if(0==this.dzBf||!this.g3d.setC(this.colixEndcap))return;b=this.xAf;e=this.yAf;c=this.zAf;a&&0>this.dzBf&&(b+=this.dxBf,e+=this.dyBf,c+=this.dzBf);b=B(b);e=B(e);c=B(c)}else{if(0==this.dzB||!this.g3d.setC(this.colixEndcap))return;b=this.xA;e=this.yA;c=this.zA;if(a&&0>this.dzB){if(4==this.endcaps)return;b+=this.dxB;e+=this.dyB;c+=this.dzB}}var f=d[1][0];a=d[1][0];var j=0,k=0,l=d[0],h=d[1];d=d[2];for(var p=this.rasterCount;0<--p;){var v=h[p];v<f?f=v:v>a?a=v:(v=-v,v<f?f=v:v>a&&(a=v))}for(v=f;v<=
a;++v){for(var f=2147483647,E=-2147483648,p=this.rasterCount;0<=--p;){if(h[p]==v){var A=l[p];A<f&&(f=A,j=d[p]);A>E&&(E=A,k=d[p])}h[p]==-v&&(A=-l[p],A<f&&(f=A,j=-d[p]),A>E&&(E=A,k=-d[p]))}p=E-f+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(p,b+f,e+v,c-j-1,c-k-1,null,null)}},"~B,~B,~A");c(c$,"renderSphericalEndcaps",function(){0!=this.colixA&&this.g3d.setC(this.colixA)&&this.g3d.fillSphereXYZ(this.diameter,this.xA,this.yA,this.zA+1);0!=this.colixB&&this.g3d.setC(this.colixB)&&
this.g3d.fillSphereXYZ(this.diameter,this.xA+this.dxB,this.yA+this.dyB,this.zA+this.dzB+1)});c(c$,"calcArgbEndcap",function(a,b){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;this.tEndcapOpen=!1;var d=b?this.dzBf:this.dzB;if(!(3==this.endcaps||0==d)){this.xEndcap=this.xA;this.yEndcap=this.yA;this.zEndcap=this.zA;var e=b?this.dxBf:this.dxB,c=b?this.dyBf:this.dyB;0<=d||!a?(this.endcapShadeIndex=this.shader.getShadeIndex(-e,-c,d),this.colixEndcap=
this.colixA,d=this.shadesA):(this.endcapShadeIndex=this.shader.getShadeIndex(e,c,-d),this.colixEndcap=this.colixB,d=this.shadesB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB);56<this.endcapShadeIndex&&(this.endcapShadeIndex=56);this.argbEndcap=d[this.endcapShadeIndex];this.tEndcapOpen=1==this.endcaps}},"~B,~B")});m("J.g3d");H(J.g3d,"G3DRenderer");m("J.g3d");w(["J.api.JmolRendererInterface","JU.GData","JU.V3"],"J.g3d.Graphics3D","java.lang.NullPointerException java.util.Arrays javajs.awt.Font JU.AU J.api.Interface J.c.STER J.g3d.CylinderRenderer $.ImageRenderer $.LineRenderer $.Pixelator $.PixelatorShaded $.Platform3D $.SphereRenderer $.TextRenderer $.TextSorter $.TextString JU.C $.Normix".split(" "),
function(){c$=r(function(){this.hermite3d=this.circle3d=this.triangle3d=this.cylinder3d=this.sphere3d=this.line3d=this.platform=null;this.antialias2=this.isFullSceneAntialiasingEnabled=!1;this.strings=null;this.stringCount=0;this.anaglyphChannelBytes=null;this.$haveTranslucentObjects=this.twoPass=!1;this.zbufT=this.zbuf=this.pbufT=this.pbuf=null;this.translucencyMask=0;this.renderLow=!1;this.shadesCurrent=null;this.anaglyphLength=0;this.pixel=null;this.zMargin=0;this.aobuf=null;this.saveDiffuse=this.saveAmbient=
this.translucencyLog=this.lastRawColor=this.currentShadeIndex=0;this.shadeIndexes2Sided=this.shadeIndexes=this.vectorNormal=this.vectorAC=this.vectorAB=null;this.pass2Flag01=0;t(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);I(c$,function(){this.vectorAB=new JU.V3;this.vectorAC=new JU.V3;this.vectorNormal=new JU.V3;this.shadeIndexes=M(JU.GData.normixCount,0);this.shadeIndexes2Sided=M(JU.GData.normixCount,0)});h(c$,"clear",function(){this.stringCount=0;this.strings=null;
J.g3d.TextRenderer.clearFontCache()});h(c$,"destroy",function(){this.releaseBuffers();this.graphicsForMetrics=this.platform=null});c(c$,"setZMargin",function(a){this.zMargin=a},"~N");u(c$,function(){F(this,J.g3d.Graphics3D,[]);for(var a=JU.GData.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3});h(c$,"initialize",function(a,b){this.vwr=a;this.apiPlatform=b;this.platform=new J.g3d.Platform3D(b);this.graphicsForMetrics=this.platform.getGraphicsForMetrics();this.line3d=new J.g3d.LineRenderer(this);
this.sphere3d=new J.g3d.SphereRenderer(this);this.cylinder3d=new J.g3d.CylinderRenderer(this)},"JV.Viewer,javajs.api.GenericPlatform");h(c$,"addRenderer",function(a){switch(a){case 1073741880:null==this.circle3d&&(this.circle3d=this.getRenderer("Circle"));break;case 553648147:null==this.hermite3d&&(this.hermite3d=this.getRenderer("Hermite"));case 1073742182:null==this.triangle3d&&(this.triangle3d=this.getRenderer("Triangle"))}},"~N");c(c$,"getRenderer",function(a){a=J.api.Interface.getOption("g3d."+
a+"Renderer",this.vwr,"render");if(null==a)throw new NullPointerException("Interface");a.set(this,this);return a},"~S");h(c$,"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$,"beginRendering",function(a,b,d,e){this.currentlyRendering&&this.endRendering();this.renderLow=e;if(this.windowWidth!=this.newWindowWidth||
this.windowHeight!=this.newWindowHeight||this.newAntialiasing!=this.isFullSceneAntialiasingEnabled)this.windowWidth=this.newWindowWidth,this.windowHeight=this.newWindowHeight,this.isFullSceneAntialiasingEnabled=this.newAntialiasing,this.releaseBuffers();this.setRotationMatrix(a);this.antialiasEnabled=this.antialiasThisFrame=this.newAntialiasing;this.currentlyRendering=!0;if(null!=this.strings)for(a=Math.min(this.strings.length,this.stringCount);0<=--a;)this.strings[a]=null;this.stringCount=0;this.twoPass=
!0;this.isPass2=!1;this.colixCurrent=this.pass2Flag01=0;this.$haveTranslucentObjects=!1;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.setWidthHeight(this.antialiasThisFrame);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();return!0},"~B");h(c$,"endRendering",function(){if(this.currentlyRendering){if(null!=this.pbuf){if(this.isPass2&&null!=this.pbufT)for(var a=this.pbufT.length;0<=--a;)J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,this.pbufT[a],this.bgcolor);this.antialiasThisFrame&&this.downsampleFullSceneAntialiasing(!1)}this.platform.setBackgroundColor(this.bgcolor);
this.platform.notifyEndOfRendering();this.currentlyRendering=!1}});c$.mergeBufferPixel=c(c$,"mergeBufferPixel",function(a,b,d,e){if(0!=d){var c=a[b];if(c!=d){0==c&&(c=e);e=c&16711935;var c=c&65280,f=d&16711935,j=d&65280;switch(d>>24&15){case 0:e=f;c=j;break;case 1:e=(f<<2)+(f<<1)+f+e>>3&16711935;c=(j<<2)+ +(j<<1)+j+c>>3&65280;break;case 2:e=(f<<1)+f+e>>2&16711935;c=(j<<1)+j+c>>2&65280;break;case 3:e=(f<<2)+f+(e<<1)+e>>3&16711935;c=(j<<2)+j+(c<<1)+c>>3&65280;break;case 4:e=e+f>>1&16711935;c=c+j>>1&
65280;break;case 5:e=(f<<1)+f+(e<<2)+e>>3&16711935;c=(j<<1)+j+(c<<2)+c>>3&65280;break;case 6:e=(e<<1)+e+f>>2&16711935;c=(c<<1)+c+j>>2&65280;break;case 7:e=(e<<2)+(e<<1)+e+f>>3&16711935,c=(c<<2)+(c<<1)+c+j>>3&65280}a[b]=4278190080|e|c}}},"~A,~N,~N,~N");h(c$,"getScreenImage",function(a){var b=this.platform.bufferedImage;a&&this.releaseBuffers();return b},"~B");h(c$,"applyAnaglygh",function(a,b){switch(a){case J.c.STER.REDCYAN:this.applyCyanAnaglyph();break;case J.c.STER.CUSTOM:this.applyCustomAnaglyph(b);
break;case J.c.STER.REDBLUE:this.applyBlueAnaglyph();break;case J.c.STER.REDGREEN:this.applyGreenAnaglyph()}},"J.c.STER,~A");h(c$,"snapshotAnaglyphChannelBytes",function(){if(this.currentlyRendering)throw new NullPointerException;this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=M(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});
c(c$,"applyCustomAnaglyph",function(a){var b=a[0];a=a[1]&16777215;for(var d=this.anaglyphLength;0<=--d;){var e=this.anaglyphChannelBytes[d]&255,e=(e|(e|e<<8)<<8)&a;this.pbuf[d]=this.pbuf[d]&b|e}},"~A");c(c$,"applyGreenAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;)this.pbuf[a]=this.pbuf[a]&4294901760|(this.anaglyphChannelBytes[a]&255)<<8});c(c$,"applyBlueAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;)this.pbuf[a]=this.pbuf[a]&4294901760|this.anaglyphChannelBytes[a]&255});c(c$,
"applyCyanAnaglyph",function(){for(var a=this.anaglyphLength;0<=--a;){var b=this.anaglyphChannelBytes[a]&255;this.pbuf[a]=this.pbuf[a]&4294901760|b<<8|b}});h(c$,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});h(c$,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});c(c$,"setTempZSlab",function(a){this.zSlab=a},"~N");h(c$,"setZShade",function(a,b,d,e){a?(this.setZShade2(b,d,e),this.pixel=new J.g3d.PixelatorShaded(this)):this.pixel=new J.g3d.Pixelator(this)},
"~B,~N,~N,~N");c(c$,"downsampleFullSceneAntialiasing",function(a){var b=this.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,e){var c=b<<1;if(0!=e){e&=16777215;for(var f=a.length;0<=--f;)0==a[f]&&(a[f]=e)}for(var j=(e>>2&1061109567)<<
2,j=j+((j&3233857728)>>6),k=0,l=0,f=d;0<=--f;l+=c)for(d=b;0<=--d;++k){var h=(a[l]>>2&1061109567)+(a[l++ +c]>>2&1061109567)+(a[l]>>2&1061109567)+(a[l++ +c]>>2&1061109567),h=h+((h&3233857728)>>6);h==j&&(h=e);a[k]=h&16777215|4278190080}},"~A,~N,~N,~N");c$.downsample2dZ=c(c$,"downsample2dZ",function(a,b,d,e,c){for(var f=d<<1,j=0,k=0;0<=--e;k+=f)for(var l=d;0<=--l;++j,++k){var h=Math.min(b[k],b[k+f]),h=Math.min(h,b[++k]),h=Math.min(h,b[k+f]);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);if(!this.checkTranslucent(0!=d))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");h(c$,"drawFilledCircle",function(a,b,d,e,c,f){if(!this.isClippedZ(f)){var j=s((d+1)/2),j=e<j||e+j>=this.width||c<j||c+j>=this.height;if(!j||!this.isClippedXY(d,e,c))0!=a&&this.setC(a)&&(j?this.isClippedXY(d,e,c)||this.circle3d.plotCircleCenteredClipped(e,c,f,d):this.circle3d.plotCircleCenteredUnclipped(e,
c,f,d)),0!=b&&this.setC(b)&&(j?this.circle3d.plotFilledCircleCenteredClipped(e,c,f,d):this.circle3d.plotFilledCircleCenteredUnclipped(e,c,f,d))}},"~N,~N,~N,~N,~N,~N");h(c$,"volumeRender4",function(a,b,d,e){if(1==a)this.plotPixelClippedArgb(this.argbCurrent,b,d,e,this.width,this.zbuf,this.pixel);else if(!this.isClippedZ(e)){var c=s((a+1)/2),c=b<c||b+c>=this.width||d<c||d+c>=this.height;if(!c||!this.isClippedXY(a,b,d))c?this.circle3d.plotFilledCircleCenteredClipped(b,d,e,a):this.circle3d.plotFilledCircleCenteredUnclipped(b,
d,e,a)}},"~N,~N,~N,~N");h(c$,"fillSphereXYZ",function(a,b,d,e){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,b,d,e,this.width,this.zbuf,this.pixel);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,a,b,d,e,null,null,null,-1,null)},"~N,~N,~N,~N");h(c$,"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$,"fillSphereI",function(a,b){this.fillSphereXYZ(a,b.x,b.y,b.z)},"~N,JU.P3i");h(c$,"fillSphere",function(a,b){this.fillSphereXYZ(a,Math.round(b.x),Math.round(b.y),Math.round(b.z))},"~N,JU.P3");h(c$,"fillEllipsoid",function(a,b,d,e,c,f,j,k,l,h,p){switch(f){case 1:this.plotPixelClippedArgb(this.argbCurrent,d,e,c,this.width,this.zbuf,this.pixel);return;case 0:return}f<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,
f,d,e,c,j,k,l,h,p)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");h(c$,"drawRect",function(a,b,d,e,c,f){if(!(0!=e&&this.isClippedZ(e))){e=c-1;f-=1;c=a+e;var j=b+f;0<=b&&b<this.height&&this.drawHLine(a,b,d,e);0<=j&&j<this.height&&this.drawHLine(a,j,d,e);0<=a&&a<this.width&&this.drawVLine(a,b,d,f);0<=c&&c<this.width&&this.drawVLine(c,b,d,f)}},"~N,~N,~N,~N,~N,~N");c(c$,"drawHLine",function(a,b,d,e){0>e&&(a+=e,e=-e);0>a&&(e+=a,a=0);a+e>=this.width&&(e=this.width-1-a);var c=this.pixel,f=this.argbCurrent;
a+=this.width*b;for(b=0;b<=e;b++)d<this.zbuf[a]&&c.addPixel(a,d,f),a++},"~N,~N,~N,~N");c(c$,"drawVLine",function(a,b,d,e){0>e&&(b+=e,e=-e);0>b&&(e+=b,b=0);b+e>=this.height&&(e=this.height-1-b);a+=this.width*b;b=this.pixel;for(var c=this.argbCurrent,f=0;f<=e;f++)d<this.zbuf[a]&&b.addPixel(a,d,c),a+=this.width},"~N,~N,~N,~N");h(c$,"fillRect",function(a,b,d,e,c,f){if(!this.isClippedZ(e)){e=this.width;if(0>a){c+=a;if(0>=c)return;a=0}if(a+c>e&&(c=e-a,0>=c))return;if(0>b){f+=b;if(0>=f)return;b=0}b+f>this.height&&
(f=this.height-b);for(var j=this.argbCurrent,k=this.zbuf,l=this.pixel;0<=--f;)this.plotPixelsUnclippedCount(j,c,a,b++,d,e,k,l)}},"~N,~N,~N,~N,~N,~N");h(c$,"drawString",function(a,b,d,e,c,f,j){this.currentShadeIndex=0;null!=a&&(this.isClippedZ(f)||this.drawStringNoSlab(a,b,d,e,c,j))},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");h(c$,"drawStringNoSlab",function(a,b,d,e,c,f){if(null!=a){null==this.strings&&(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));
var j=new J.g3d.TextString;j.setText(a,null==b?this.currentFont:this.currentFont=b,this.argbCurrent,JU.C.isColixTranslucent(f)?this.getColorArgbOrGray(f)&16777215|(f&30720)<<13:0,d,e,c);this.strings[this.stringCount++]=j}},"~S,javajs.awt.Font,~N,~N,~N,~N");h(c$,"renderAllStrings",function(a){if(null!=this.strings){2<=this.stringCount&&(null==J.g3d.Graphics3D.sort&&(J.g3d.Graphics3D.sort=new J.g3d.TextSorter),java.util.Arrays.sort(this.strings,J.g3d.Graphics3D.sort));for(var b=0;b<this.stringCount;b++){var d=
this.strings[b];this.plotText(d.x,d.y,d.z,d.argb,d.bgargb,d.text,d.font,a)}this.strings=null;this.stringCount=0}},"~O");h(c$,"plotText",function(a,b,d,e,c,f,j,k){J.g3d.TextRenderer.plot(a,b,d,e,c,f,j,this,k,this.antialiasThisFrame)},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.api.JmolRendererInterface");h(c$,"drawImage",function(a,b,d,e,c,f,j,k){null==a||(0==j||0==k||this.isClippedZ(c))||this.plotImage(b,d,e,a,null,f,j,k)},"~O,~N,~N,~N,~N,~N,~N,~N");h(c$,"plotImage",function(a,b,d,e,c,f,j,k){this.setC(f);
this.isPass2||(this.translucencyMask=-1);0==f&&(this.argbCurrent=0);J.g3d.ImageRenderer.plotImage(a,b,d,e,this,c,this.antialiasThisFrame,this.argbCurrent,j,k)},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");h(c$,"setFontFid",function(a){this.currentFont=javajs.awt.Font.getFont3D(a)},"~N");h(c$,"setFont",function(a){this.currentFont=a},"javajs.awt.Font");h(c$,"drawPixel",function(a,b,d){this.plotPixelClippedArgb(this.argbCurrent,a,b,d,this.width,this.zbuf,this.pixel)},"~N,~N,~N");h(c$,"drawPoints",
function(a,b,d){if(1<d)for(var e=0.8*d*d,c=-d;c<d;c++)for(var f=-d;f<d;f++)c*c+f*f>e||(this.plotPoints(a,b,c,f),this.plotPoints(a,b,c,f));else this.plotPoints(a,b,0,0)},"~N,~A,~N");h(c$,"drawDashedLine",function(a,b,d,e){this.line3d.plotDashedLine(this.argbCurrent,a,b,d.x,d.y,d.z,e.x,e.y,e.z,!0)},"~N,~N,JU.P3i,JU.P3i");h(c$,"drawDottedLine",function(a,b){this.line3d.plotDashedLine(this.argbCurrent,2,1,a.x,a.y,a.z,b.x,b.y,b.z,!0)},"JU.P3i,JU.P3i");h(c$,"drawLineXYZ",function(a,b,d,e,c,f){this.line3d.plotLine(this.argbCurrent,
this.argbCurrent,a,b,d,e,c,f,!0)},"~N,~N,~N,~N,~N,~N");h(c$,"drawLine",function(a,b,d,e,c,f,j,k){this.setC(a)||(a=0);var l=this.argbCurrent;this.setC(b)||(b=0);(0!=a||0!=b)&&this.line3d.plotLine(l,this.argbCurrent,d,e,c,f,j,k,!0)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"drawLineAB",function(a,b){this.line3d.plotLine(this.argbCurrent,this.argbCurrent,a.x,a.y,a.z,b.x,b.y,b.z,!0)},"JU.P3i,JU.P3i");h(c$,"fillCylinderXYZ",function(a,b,d,e,c,f,j,k,l,h){e>this.ht3||(this.setC(a)||(a=0),this.setC(b)||(b=0),(0!=
a||0!=b)&&this.cylinder3d.render(a,b,d,e,c,f,j,k,l,h))},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen",function(a,b,d,e,c,f,j,k){b<=this.ht3&&this.cylinder3d.render(this.colixCurrent,this.colixCurrent,a,b,d,e,c,f,j,k)},"~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillCylinderScreen3I",function(a,b,d,e){b<=this.ht3&&this.cylinder3d.render(this.colixCurrent,this.colixCurrent,a,b,d.x,d.y,d.z,e.x,e.y,e.z)},"~N,~N,JU.P3i,JU.P3i,JU.P3,JU.P3,~N");h(c$,"fillCylinder",function(a,b,d,e){b<=this.ht3&&this.cylinder3d.render(this.colixCurrent,
this.colixCurrent,a,b,d.x,d.y,d.z,e.x,e.y,e.z)},"~N,~N,JU.P3i,JU.P3i");h(c$,"fillCylinderBits",function(a,b,d,e){b<=this.ht3&&this.cylinder3d.renderBits(this.colixCurrent,this.colixCurrent,a,b,d.x,d.y,d.z,e.x,e.y,e.z)},"~N,~N,JU.P3,JU.P3");h(c$,"fillConeScreen",function(a,b,d,e,c){b<=this.ht3&&this.cylinder3d.renderCone(this.colixCurrent,a,b,d.x,d.y,d.z,e.x,e.y,e.z,!1,c)},"~N,~N,JU.P3i,JU.P3i,~B");h(c$,"fillConeSceen3f",function(a,b,d,e){b<=this.ht3&&this.cylinder3d.renderCone(this.colixCurrent,a,
b,d.x,d.y,d.z,e.x,e.y,e.z,!0,!1)},"~N,~N,JU.P3,JU.P3");h(c$,"drawHermite4",function(a,b,d,e,c){this.hermite3d.renderHermiteRope(!1,a,0,0,0,b,d,e,c)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawHermite7",function(a,b,d,e,c,f,j,k,l,h,p,v,E){if(0==E)this.hermite3d.renderHermiteRibbon(a,b,d,e,c,f,j,k,l,h,p,v,0);else{this.hermite3d.renderHermiteRibbon(a,b,d,e,c,f,j,k,l,h,p,v,1);var A=this.colixCurrent;this.setC(E);this.hermite3d.renderHermiteRibbon(a,b,d,e,c,f,j,k,l,h,p,v,-1);this.setC(A)}},"~B,~B,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,JU.P3i,~N,~N");
h(c$,"fillHermite",function(a,b,d,e,c,f,j,k){this.hermite3d.renderHermiteRope(!0,a,b,d,e,c,f,j,k)},"~N,~N,~N,~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"drawTriangle3C",function(a,b,d,e,c,f,j){1==(j&1)&&this.drawLine(b,e,a.x,a.y,a.z,d.x,d.y,d.z);2==(j&2)&&this.drawLine(e,f,d.x,d.y,d.z,c.x,c.y,c.z);4==(j&4)&&this.drawLine(b,f,a.x,a.y,a.z,c.x,c.y,c.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");h(c$,"fillTriangleTwoSided",function(a,b,d,e,c,f,j,k,l,h){this.setColorNoisy(this.getShadeIndex(a));this.triangle3d.fillTriangleXYZ(b,
d,e,c,f,j,k,l,h,!1)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");h(c$,"fillTriangle3f",function(a,b,d,e){var c=this.getShadeIndexP3(a,b,d);e?this.setColorNoisy(c):this.setColor(this.shadesCurrent[c]);this.triangle3d.fillTriangleP3f(a,b,d,!1)},"JU.P3,JU.P3,JU.P3,~B");h(c$,"fillTriangle3i",function(a,b,d,e,c,f,j){j&&(e=this.vectorAB,e.set(b.x-a.x,b.y-a.y,b.z-a.z),null==d?e=this.shader.getShadeIndex(-e.x,-e.y,e.z):(this.vectorAC.set(d.x-a.x,d.y-a.y,d.z-a.z),e.cross(e,this.vectorAC),e=0<=e.z?this.shader.getShadeIndex(-e.x,
-e.y,e.z):this.shader.getShadeIndex(e.x,e.y,-e.z)),56<e&&(e=56),this.setColorNoisy(e));this.triangle3d.fillTriangleP3i(a,b,d,!1)},"JU.P3i,JU.P3i,JU.P3i,JU.T3,JU.T3,JU.T3,~B");h(c$,"fillTriangle3CN",function(a,b,d,e,c,f,j,k,l){if(!this.isPass2&&d==f&&d==l&&b==c&&b==k){d=this.getShadeIndex(d);if(b!=this.colixCurrent||this.currentShadeIndex!=d)this.currentShadeIndex=-1,this.setC(b),this.setColorNoisy(d);b=!1}else this.setTriangleTranslucency(b,c,k),this.triangle3d.setGouraud(this.getShades(b)[this.getShadeIndex(d)],
this.getShades(c)[this.getShadeIndex(f)],this.getShades(k)[this.getShadeIndex(l)]),b=!0;this.triangle3d.fillTriangleP3i(a,e,j,b)},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");c(c$,"getShadeIndex",function(a){return-1E4==a||9999==a?J.g3d.Graphics3D.nullShadeIndex:0>a?this.shadeIndexes2Sided[~a]:this.shadeIndexes[a]},"~N");c(c$,"setTriangleTranslucency",function(a,b,d){this.isPass2&&(a&=14336,b&=14336,d&=14336,this.translucencyMask=(JU.GData.roundInt(s((a+b+d)/3))&30720)<<13|16777215)},"~N,~N,~N");h(c$,
"drawQuadrilateral",function(a,b,d,e,c){this.setC(a);this.drawLineAB(b,d);this.drawLineAB(d,e);this.drawLineAB(e,c);this.drawLineAB(c,b)},"~N,JU.P3i,JU.P3i,JU.P3i,JU.P3i");h(c$,"fillQuadrilateral",function(a,b,d,e){this.setColorNoisy(this.getShadeIndexP3(a,b,d));this.triangle3d.fillTriangleP3f(a,b,d,!1);this.triangle3d.fillTriangleP3f(a,d,e,!1)},"JU.P3,JU.P3,JU.P3,JU.P3");h(c$,"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,e,c,f,j){this.isClipped3(b,d,e)||(b=d*c+b,e<f[b]&&j.addPixel(b,e,a))},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotPixelUnclipped",function(a,b,d,e,c,f,j){b=d*c+b;e<f[b]&&j.addPixel(b,e,a)},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");h(c$,"plotImagePixel",function(a,b,d,e,c,f,j,k,l,h,p){0>b||(b>=j||0>d||d>=k)||(b=d*j+b,e<l[b]&&(8==c?h.addPixel(b,e,a):(c+=p,7>=c&&this.shadeTextPixel(b,e,a,f,c,l))))},"~N,~N,~N,~N,~N,~N,~N,~N,~A,~O,~N");
c(c$,"plotPixelsClipped",function(a,b,d,e,c,f,j,k,l){if(!(0>e||e>=j||d>=f))if(0>d&&(b+=d,d=0),b+d>f&&(b=f-d),!(0>=b)){d=e*f+d;for(b=d+b;d<b;)c<k[d]&&l.addPixel(d,c,a),d++}},"~N,~N,~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotPixelsClippedRaster",function(a,b,d,e,c,f,j){var k,l;if(!(0>=a||0>d||d>=this.height||b>=this.width||e<(l=this.slab)&&c<l||e>(k=this.depth)&&c>k)){var h=this.zbuf,p=(b<<16)+(d<<1)^858993459,v=(e<<10)+512;e=c-e;c=s(a/2);e=JU.GData.roundInt(s(((e<<10)+(0<=e?c:-c))/a));if(0>b){b=
-b;v+=e*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==f){f=this.argbNoisyDn;c=this.argbNoisyUp;for(var E=this.argbCurrent;0<=--a;){j=v>>10;if(j>=l&&j<=k&&j<h[b]){var p=(p<<16)+(p<<1)+p&2147483647,A=p>>16&7;d.addPixel(b,j,0==A?f:1==A?c:E)}++b;v+=e}}else{p=f.r<<8;c=s((j.r-f.r<<8)/a);E=f.g;A=s((j.g-E)/a);f=f.b;for(var m=s((j.b-f)/a);0<=--a;)j=v>>10,j>=l&&(j<=k&&j<h[b])&&d.addPixel(b,j,4278190080|p&16711680|E&65280|f>>8&255),++b,v+=e,p+=c,E+=A,f+=m}}},
"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsUnclippedRaster",function(a,b,d,e,c,f,j){if(!(0>=a)){var k=((b<<16)+(d<<1)^858993459)&2147483647,l=(e<<10)+512;e=c-e;c=s(a/2);e=JU.GData.roundInt(s(((e<<10)+(0<=e?c:-c))/a));b=d*this.width+b;d=this.zbuf;c=this.pixel;if(null==f){f=this.argbNoisyDn;for(var h=this.argbNoisyUp,p=this.argbCurrent;0<=--a;){j=l>>10;if(j<d[b]){var k=(k<<16)+(k<<1)+k&2147483647,v=k>>16&7;c.addPixel(b,j,0==v?f:1==v?h:p)}++b;l+=e}}else{k=f.r<<8;h=JU.GData.roundInt(s((j.r-f.r<<
8)/a));p=f.g;v=JU.GData.roundInt(s((j.g-p)/a));f=f.b;for(var E=JU.GData.roundInt(s((j.b-f)/a));0<=--a;)j=l>>10,j<d[b]&&c.addPixel(b,j,4278190080|k&16711680|p&65280|f>>8&255),++b,l+=e,k+=h,p+=v,f+=E}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(c$,"plotPixelsUnclippedCount",function(a,b,d,e,c,f,j,k){for(d=e*f+d;0<=--b;)c<j[d]&&k.addPixel(d,c,a),++d},"~N,~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(c$,"plotPoints",function(a,b,d,e){var c=this.pixel,f=this.argbCurrent,j=this.zbuf,k=this.width,l=this.antialiasThisFrame;
for(a*=3;0<a;){var h=b[--a],p=b[--a]+e,v=b[--a]+d;if(!this.isClipped3(v,p,h)){var E=p*k+v++;h<j[E]&&c.addPixel(E,h,f);l&&(E=p*k+v,!this.isClipped3(v,p,h)&&h<j[E]&&c.addPixel(E,h,f),E=++p*k+v,!this.isClipped3(v,p,h)&&h<j[E]&&c.addPixel(E,h,f),E=p*k+--v,!this.isClipped3(v,p,h)&&h<j[E]&&c.addPixel(E,h,f))}}},"~N,~A,~N,~N");c(c$,"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$,"getShadeIndexP3",function(a,b,d){this.vectorAB.sub2(b,a);this.vectorAC.sub2(d,a);a=this.vectorNormal;a.cross(this.vectorAB,this.vectorAC);return 0<=a.z?this.shader.getShadeIndex(-a.x,-a.y,a.z):this.shader.getShadeIndex(a.x,a.y,-a.z)},"JU.P3,JU.P3,JU.P3");h(c$,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");h(c$,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,
a.sY,a.sZ)},"JM.Atom");h(c$,"getExportType",function(){return 0});h(c$,"getExportName",function(){return null});c(c$,"canDoTriangles",function(){return!0});c(c$,"isCartesianExport",function(){return!1});h(c$,"initializeExporter",function(){return null},"JV.Viewer,~N,JU.GData,java.util.Map");h(c$,"finalizeOutput",function(){return null});h(c$,"drawBond",function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");h(c$,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(c$,"getPrivateKey",function(){return 0});
h(c$,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});c(c$,"setRotationMatrix",function(a){for(var b=JU.Normix.getVertexVectors(),d=JU.GData.normixCount;0<=--d;){var e=this.transformedVectors[d];a.rotate2(b[d],e);this.shadeIndexes[d]=this.shader.getShadeB(e.x,-e.y,e.z);this.shadeIndexes2Sided[d]=0<=e.z?this.shadeIndexes[d]:this.shader.getShadeB(-e.x,e.y,-e.z)}},"JU.M3");h(c$,"renderCrossHairs",function(a,b,d,e,c){b=this.isAntialiased();this.setC(0>c?10:100<c?11:23);c=Math.max(Math.min(this.width,
Math.round(e.x)),0);d=Math.max(Math.min(this.height,Math.round(e.y)),0);var f=Math.round(e.z)+1,j=b?8:4,k=b?20:10;b=b?2:1;this.drawRect(c-j,d,f,0,k,b);this.drawRect(c,d-j,f,0,b,k);this.drawRect(c-j,d-j,f,0,k,k);j=k;k>>=1;this.setC(a[1]<e.x?21:11);this.drawRect(c-j,d,f,0,k,b);this.setC(a[0]>e.x?21:11);this.drawRect(c+k,d,f,0,k,b);this.setC(a[3]<e.y?21:11);this.drawRect(c,d-j,f,0,b,k);this.setC(a[2]>e.y?21:11);this.drawRect(c,d+k,f,0,b,k)},"~A,~N,~N,JU.P3,~N");h(c$,"initializeOutput",function(){return!1},
"JV.Viewer,~N,java.util.Map");c(c$,"shadeTextPixel",function(a,b,d,e,c,f){0!=e&&J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,e,this.bgcolor);J.g3d.Graphics3D.mergeBufferPixel(this.pbuf,a,d&16777215|c<<24,this.bgcolor);f[a]=b},"~N,~N,~N,~N,~N,~A");C(c$,"sort",null,"nullShadeIndex",50)});m("J.g3d");c$=z(J.g3d,"ImageRenderer");c$.plotImage=c(c$,"plotImage",function(a,b,d,e,c,f,j,k,l,h){k=(j=-2147483648==a)?c.bgcolor:k;j&&(a=0,d=2147483646,l=c.width,h=c.height);if(!(0>=a+l||a>=c.width||0>=b+h||b>=c.height))if(e=
c.apiPlatform.drawImageToBuffer(null,c.platform.offscreenImage,e,l,h,j?k:0),null!=e){j=c.zbuf;var p=c.width,v=c.pixel,E=c.height,A=c.translucencyLog;if(null!=f||0>a||a+l>p||0>b||b+h>E){null==f&&(f=c);for(var m=c=0;c<h;c++)for(var s=0;s<l;s++)f.plotImagePixel(e[m++],a+s,b+c,d,8,k,p,E,j,v,A)}else{m=c=0;for(a=b*p+a;c<h;c++,a+=p-l)for(s=0;s<l;s++,a++)d<j[a]&&v.addPixel(a,d,e[m++])}}},"~N,~N,~N,~O,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B,~N,~N,~N");m("J.g3d");w(["java.util.Hashtable"],"J.g3d.LineRenderer",
["java.lang.Float","JU.BS"],function(){c$=r(function(){this.lineBits=this.shader=this.g3d=null;this.slope=0;this.lineTypeX=!1;this.nBits=0;this.slopeKey=this.lineCache=null;this.cc2=this.cc1=this.z2t=this.y2t=this.x2t=this.z1t=this.y1t=this.x1t=0;t(this,arguments)},J.g3d,"LineRenderer");I(c$,function(){this.lineCache=new java.util.Hashtable});u(c$,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(c$,"setLineBits",function(a,b){this.slope=0!=a?b/a:0<=b?3.4028235E38:-3.4028235E38;this.nBits=
(this.lineTypeX=1>=this.slope&&-1<=this.slope)?this.g3d.width:this.g3d.height;this.slopeKey=Float.$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,e=a+a,c=b+b,f=0;f<this.nBits;f++)d+=c,d>a&&(this.lineBits.set(f),d-=e);this.lineCache.put(this.slopeKey,this.lineBits)}},"~N,~N");c(c$,"clearLineCache",function(){this.lineCache.clear()});
c(c$,"plotLine",function(a,b,d,e,c,f,j,k,l){this.x1t=d;this.x2t=f;this.y1t=e;this.y2t=j;this.z1t=c;this.z2t=k;if(l)switch(this.getTrimmedLine()){case 0:l=!1;break;case 2:return}this.plotLineClipped(a,b,d,e,c,f-d,j-e,k-c,l,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDelta",function(a,b,d,e,c,f,j,k,l){this.x1t=d;this.x2t=d+f;this.y1t=e;this.y2t=e+j;this.z1t=c;this.z2t=c+k;if(l)switch(this.getTrimmedLine()){case 2:return;case 0:l=!1}this.plotLineClipped(a,b,d,e,c,f,j,k,l,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N,~B");
c(c$,"plotLineDeltaA",function(a,b,d,e,c,f,j,k,l,h){this.x1t=e;this.x2t=e+j;this.y1t=c;this.y2t=c+k;this.z1t=f;this.z2t=f+l;if(h)switch(this.getTrimmedLine()){case 2:return;case 0:h=!1}this.plotLineClippedA(a,b,d,e,c,f,j,k,l,h,0,0)},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"plotLineDeltaBits",function(a,b,d,e,c,f,j,k,l,h){this.x1t=e;this.x2t=e+j;this.y1t=c;this.y2t=c+k;this.z1t=f;this.z2t=f+l;h&&2==this.getTrimmedLine()||this.plotLineClippedBits(a,b,d,e,c,f,j,k,l,0,0)},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~B");
c(c$,"plotDashedLine",function(a,b,d,e,c,f,j,k,l,h){this.x1t=e;this.x2t=j;this.y1t=c;this.y2t=k;this.z1t=f;this.z2t=l;if(h)switch(this.getTrimmedLine()){case 2:return;case 0:h=!1}this.plotLineClipped(a,a,e,c,f,j-e,k-c,l-f,h,b,d)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(c$,"getTrimmedLine",function(){this.cc1=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t);this.cc2=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t);if(0==(this.cc1|this.cc2))return 0;var a=this.g3d.xLast,b=this.g3d.yLast,d=this.g3d.slab,e=this.g3d.depth;
do{if(0!=(this.cc1&this.cc2))return 2;var c=this.x2t-this.x1t,f=this.y2t-this.y1t,j=this.z2t-this.z1t;0!=this.cc1?(0!=(this.cc1&8)?(this.y1t+=B(-this.x1t*f/c),this.z1t+=B(-this.x1t*j/c),this.x1t=0):0!=(this.cc1&4)?(this.y1t+=B((a-this.x1t)*f/c),this.z1t+=B((a-this.x1t)*j/c),this.x1t=a):0!=(this.cc1&2)?(this.x1t+=B(-this.y1t*c/f),this.z1t+=B(-this.y1t*j/f),this.y1t=0):0!=(this.cc1&1)?(this.x1t+=B((b-this.y1t)*c/f),this.z1t+=B((b-this.y1t)*j/f),this.y1t=b):0!=(this.cc1&32)?(this.x1t+=B((d-this.z1t)*
c/j),this.y1t+=B((d-this.z1t)*f/j),this.z1t=d):(this.x1t+=B((e-this.z1t)*c/j),this.y1t+=B((e-this.z1t)*f/j),this.z1t=e),this.cc1=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(this.cc2&8)?(this.y2t+=B(-this.x2t*f/c),this.z2t+=B(-this.x2t*j/c),this.x2t=0):0!=(this.cc2&4)?(this.y2t+=B((a-this.x2t)*f/c),this.z2t+=B((a-this.x2t)*j/c),this.x2t=a):0!=(this.cc2&2)?(this.x2t+=B(-this.y2t*c/f),this.z2t+=B(-this.y2t*j/f),this.y2t=0):0!=(this.cc2&1)?(this.x2t+=B((b-this.y2t)*c/f),this.z2t+=B((b-this.y2t)*
j/f),this.y2t=b):0!=(this.cc2&32)?(this.x2t+=B((d-this.z2t)*c/j),this.y2t+=B((d-this.z2t)*f/j),this.z2t=d):(this.x2t+=B((e-this.z2t)*c/j),this.y2t+=B((e-this.z2t)*f/j),this.z2t=e),this.cc2=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(this.cc1|this.cc2));return 1});c(c$,"plotLineClipped",function(a,b,d,e,c,f,j,k,l,h,p){var v=this.g3d.zbuf,E=this.g3d.width,A=0;0==h&&(p=2147483647,h=1);var m=e*E+d,n=this.g3d.bufferSize,t=this.g3d.pixel;0!=a&&(!l&&0<=m&&m<n&&c<v[m])&&t.addPixel(m,c,a);if(!(0==
f&&0==j)){l=1;var r=E;d+=f;var u=e+j;0>f&&(f=-f,l=-1);0>j&&(j=-j,r=-E);E=f+f;e=j+j;c<<=10;if(j<=f){var w=f-1;0>k&&(w=-w);k=s(((k<<10)+w)/f);j=0;w=Math.abs(d-this.x2t)-1;d=Math.abs(d-this.x1t)-1;for(var u=f-1,x=s(u/2);--u>=w&&!(u==x&&(a=b,0==a));){m+=l;c+=k;j+=e;j>f&&(m+=r,j-=E);if(0!=a&&u<d&&0<=m&&m<n&&A<p){var y=c>>10;y<v[m]&&t.addPixel(m,y,a)}A=(A+1)%h}}else{w=j-1;0>k&&(w=-w);k=s(((k<<10)+w)/j);f=0;w=Math.abs(u-this.y2t)-1;d=Math.abs(u-this.y1t)-1;u=j-1;for(x=s(u/2);--u>=w&&!(u==x&&(a=b,0==a));)m+=
r,c+=k,f+=E,f>j&&(m+=l,f-=e),0!=a&&(u<d&&0<=m&&m<n&&A<p)&&(y=c>>10,y<v[m]&&t.addPixel(m,y,a)),A=(A+1)%h}}},"~N,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedA",function(a,b,d,e,c,f,j,k,l,h,p,v){var E=this.g3d.zbuf,A=this.g3d.width,m=0;0==p&&(v=2147483647,p=1);var n=c*A+e,t=this.g3d.bufferSize,r=63>d?d+1:d,u=0<d?d-1:d,w=a[r],x=a[u],y=b[d],r=b[r];b=b[u];a=a[d];d=this.g3d.pixel;0!=a&&(!h&&0<=n&&n<t&&f<E[n])&&d.addPixel(n,f,a);if(!(0==j&&0==k)){h=1;u=A;e+=j;var z=c+k;0>j&&(j=-j,h=-1);0>k&&(k=-k,
u=-A);A=j+j;c=k+k;f<<=10;if(k<=j){var B=j-1;0>l&&(B=-B);l=s(((l<<10)+B)/j);k=0;B=Math.abs(e-this.x2t)-1;e=Math.abs(e-this.x1t)-1;for(var z=j-1,C=s(z/2);--z>=B;){if(z==C){a=y;if(0==a)break;w=r;x=b}n+=h;f+=l;k+=c;k>j&&(n+=u,k-=A);if(0!=a&&z<e&&0<=n&&n<t&&m<v){var D=f>>10;if(D<E[n]){var F=this.shader.nextRandom8Bit();d.addPixel(n,D,85>F?x:170<F?w:a)}}m=(m+1)%p}}else{B=k-1;0>l&&(B=-B);l=s(((l<<10)+B)/k);j=0;B=Math.abs(z-this.y2t)-1;e=Math.abs(z-this.y1t)-1;z=k-1;for(C=s(z/2);--z>=B;){if(z==C){a=y;if(0==
a)break;w=r;x=b}n+=u;f+=l;j+=A;j>k&&(n+=h,j-=c);0!=a&&(z<e&&0<=n&&n<t&&m<v)&&(D=f>>10,D<E[n]&&(F=this.g3d.shader.nextRandom8Bit(),d.addPixel(n,D,85>F?x:170<F?w:a)));m=(m+1)%p}}}},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N");c(c$,"plotLineClippedBits",function(a,b,d,e,c,f,j,k,l,h,p){var v=this.g3d.zbuf,E=this.g3d.width,A=0;0==h&&(p=2147483647,h=1);var m=63>d?d+1:d,n=0<d?d-1:d,u=a[d],r=a[m],t=a[n];d=b[d];m=b[m];b=b[n];n=c*E+e;a=this.g3d.bufferSize;var w,x,y,z;this.lineTypeX?(w=e,x=this.x1t,y=this.x2t,e+=
s(j/2),z=c=0<=j?1:-1,E=0<=k?E:-E,j=l/Math.abs(j)):(w=c,x=this.y1t,y=this.y2t,e=c+s(k/2),c=0<=k?1:-1,z=0<=k?E:-E,E=0<=j?1:-1,j=l/Math.abs(k));k=!1;l=this.g3d.pixel;for(var C=w;;C+=c,w+=c){C==x&&(k=!0);if(C==e){u=d;if(0==u)break;r=m;t=b}if(0!=u&&(k&&0<=n&&n<a&&A<p)&&f<v[n]){var D=this.shader.nextRandom8Bit();l.addPixel(n,B(f),85>D?t:170<D?r:u)}if(C==y)break;A=(A+1)%h;for(n+=z;0>w;)w+=this.nBits;this.lineBits.get(w%this.nBits)&&(n+=E);f+=j}},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~N,~N");C(c$,"VISIBILITY_UNCLIPPED",
0,"VISIBILITY_CLIPPED",1,"VISIBILITY_OFFSCREEN",2)});m("J.g3d");w(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){c$=r(function(){this.g=null;t(this,arguments)},J.g3d,"Pixelator");u(c$,function(a){this.g=a},"J.g3d.Graphics3D");c(c$,"clearPixel",function(a,b){!this.g.isPass2&&this.g.zbuf[a]>b&&(this.g.zbuf[a]=2147483647)},"~N,~N");c(c$,"addPixel",function(a,b,d){this.addPixel1(a,b,d)},"~N,~N,~N");c(c$,"addPixel1",function(a,b,d){if(this.g.isPass2){var e=this.g.zbufT[a];if(b<e){var c=this.g.pbufT[a];
!this.g.translucentCoverOnly&&(0!=c&&e-b>this.g.zMargin)&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,c,this.g.bgcolor);this.g.zbufT[a]=b;this.g.pbufT[a]=d&this.g.translucencyMask}else b!=e&&!this.g.translucentCoverOnly&&b-e>this.g.zMargin&&J.g3d.Graphics3D.mergeBufferPixel(this.g.pbuf,a,d&this.g.translucencyMask,this.g.bgcolor)}else this.g.zbuf[a]=b,this.g.pbuf[a]=d},"~N,~N,~N")});m("J.g3d");w(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){c$=z(J.g3d,"PixelatorShaded",J.g3d.Pixelator);
h(c$,"addPixel",function(a,b,d){if(!(b>this.g.zDepth)){if(b<=this.g.zDepth&&b>=this.g.zSlab){var e=(d&65280)>>8,c=(d&16711680)>>16,f=d&4278190080,j=(this.g.zDepth-b)/(this.g.zDepth-this.g.zSlab);if(1<this.g.zShadePower)for(var k=0;k<this.g.zShadePower;k++)j*=j;d=this.g.zShadeR+B(j*((d&255)-this.g.zShadeR));e=this.g.zShadeG+B(j*(e-this.g.zShadeG));c=this.g.zShadeB+B(j*(c-this.g.zShadeB));d=c<<16|e<<8|d|f}this.addPixel1(a,b,d)}},"~N,~N,~N")});m("J.g3d");c$=r(function(){this.bufferSizeT=this.bufferSize=
this.bufferHeight=this.bufferWidth=this.windowSize=this.windowHeight=this.windowWidth=0;this.zBufferT=this.zBuffer=this.pBufferT=this.pBuffer=this.bufferedImage=null;this.heightOffscreen=this.widthOffscreen=0;this.apiPlatform=this.graphicsForTextOrImage=this.offscreenImage=null;t(this,arguments)},J.g3d,"Platform3D");u(c$,function(a){this.apiPlatform=a},"javajs.api.GenericPlatform");c(c$,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))});c(c$,
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c(c$,"clearScreenBuffer",function(){for(var a=this.bufferSize;0<=--a;)this.zBuffer[a]=2147483647,this.pBuffer[a]=0});c(c$,"setBackgroundColor",function(a){if(null!=this.pBuffer)for(var b=this.bufferSize;0<=--b;)0==this.pBuffer[b]&&(this.pBuffer[b]=a)},"~N");c(c$,"clearTBuffer",function(){for(var a=this.bufferSizeT;0<=--a;)this.zBufferT[a]=2147483647,this.pBufferT[a]=0});c(c$,"clearBuffer",function(){this.clearScreenBuffer()});c(c$,"clearScreenBufferThreaded",function(){});c(c$,"notifyEndOfRendering",
function(){this.apiPlatform.notifyEndOfRendering()});c(c$,"getGraphicsForTextOrImage",function(a,b){if(a>this.widthOffscreen||b>this.heightOffscreen)null!=this.offscreenImage&&(this.apiPlatform.disposeGraphics(this.graphicsForTextOrImage),this.apiPlatform.flushImage(this.offscreenImage)),a>this.widthOffscreen&&(this.widthOffscreen=a),b>this.heightOffscreen&&(this.heightOffscreen=b),this.offscreenImage=this.allocateOffscreenImage(this.widthOffscreen,this.heightOffscreen),this.graphicsForTextOrImage=
this.apiPlatform.getStaticGraphics(this.offscreenImage,J.g3d.Platform3D.backgroundTransparent);return this.graphicsForTextOrImage},"~N,~N");c(c$,"allocateOffscreenImage",function(a,b){return this.apiPlatform.newOffScreenImage(a,b)},"~N,~N");c(c$,"setBackgroundTransparent",function(a){J.g3d.Platform3D.backgroundTransparent=a},"~B");C(c$,"backgroundTransparent",!1);m("J.g3d");w(["JU.P3"],"J.g3d.SphereRenderer",null,function(){c$=r(function(){this.shader=this.g3d=null;this.diameter=this.z=this.y=this.x=
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c(c$,"render",function(a,b,d,e,c,f,j,k,l,h){if(1!=c&&(49<b&&(b&=-2),!this.g3d.isClippedXY(b,d,e))){this.slab=this.g3d.slab;this.depth=this.g3d.depth;var p=b+1>>1;if(!((this.maxZ=c+p)<this.slab||(this.minZ=c-p)>this.depth)){this.minX=d-p;this.maxX=d+p;this.minY=e-p;this.maxY=e+p;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*e+d;this.x=d;this.y=e;this.z=c;this.diameter=b;this.shades=a;a=this.shader;
this.mat=f;if(null!=f&&(this.coef=j,this.mDeriv=k,this.selectedOctant=l,null==a.ellipsoidShades&&a.createEllipsoidShades(),null!=h)){this.planeShade=-1;for(j=0;3>j;j++)if(p=this.dxyz[j][0]=h[j].x-d,k=this.dxyz[j][1]=h[j].y-e,l=this.dxyz[j][2]=h[j].z-c,this.planeShades[j]=a.getShadeIndex(p,k,-l),0==p&&0==k){this.planeShade=this.planeShades[j];break}}if(null!=f||128<b)this.renderQuadrant(-1,-1),this.renderQuadrant(-1,1),this.renderQuadrant(1,-1),this.renderQuadrant(1,1),null!=f&&(this.mDeriv=this.coef=
this.mat=null);else{var v=a.sphereShapeCache[b-1];if(null==v){v=0;f=0!=(b&1);h=b/2;k=h*h;p=s((b+1)/2);l=f?0:0.5;for(j=0;j<p;++j,++l)for(var E=l*l,A=f?0:0.5,m=0;m<p;++m,++A){var n=A*A,n=k-E-n;0<=n&&++v}var v=D(v,0),u=0;l=f?0:0.5;for(j=0;j<p;++j,++l){E=l*l;A=f?0:0.5;for(m=0;m<p;++m,++A)if(n=A*A,n=k-E-n,0<=n){var r=Math.sqrt(n),n=B(r),t=a.getShadeN(A,l,r,h),w=a.getShadeN(-A,l,r,h),x=a.getShadeN(A,-l,r,h),r=a.getShadeN(-A,-l,r,h),n=n|t<<7|w<<13|x<<19|r<<25;v[u++]=n}v[u-1]|=2147483648}a.sphereShapeCache[b-
1]=v}0>this.minX||this.maxX>=this.width||0>this.minY||this.maxY>=this.height||this.minZ<this.slab||c>this.depth?this.renderSphereClipped(v,d,e,c,b):this.renderSphereUnclipped(v,c,b)}this.zbuf=this.shades=null}}},"~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");c(c$,"renderSphereUnclipped",function(a,b,d){var e=0,c=1-(d&1),f=this.offsetPbufBeginLine,j=f-c*this.width;d=s((d+1)/2);var k=this.shades,l=this.zbuf,h=this.width,p=this.g3d.pixel;do{var v=f,E=f-c,A=j,m=j-c,n;do{n=a[e++];var r=b-(n&127);r<l[v]&&p.addPixel(v,
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do{var H=0<=F&&F<f,K=0<=D&&D<f;C=a[k++];var G;G=C&127;var I;e<r?(I=e+G,G=I>=r):(I=e-G,G=I<r);G&&(I=r);if(I>=r&&I<=u){if(t){if(K&&I<m[x]){var L=G?44+(d>>7&7):C>>7&63;n.addPixel(x,I,A[L])}H&&I<m[y]&&(L=G?44+(d>>13&7):C>>13&63,n.addPixel(y,I,A[L]))}w&&(K&&I<m[z]&&(L=G?44+(d>>19&7):C>>19&63,n.addPixel(z,I,A[L])),H&&I<m[B]&&(L=G?44+(d>>25&7):C>>25&63,n.addPixel(B,I,A[L])))}++x;--y;++z;--B;++D;--F;G&&(d=(d<<16)+(d<<1)+d&2147483647)}while(0<=C);h+=f;p-=f;++v;--E}while(0<--c)},"~A,~N,~N,~N,~N");c(c$,"renderQuadrant",
function(a,b){var d=s(this.diameter/2),e=this.x+d*a,c=(0>this.x?-1:this.x<this.width?0:1)+(0>e?-2:e<this.width?0:2);-3==c||3==c||(e=this.y+d*b,e=(0>this.y?-1:this.y<this.height?0:1)+(0>e?-2:e<this.height?0:2),-3==e||3==e||(null==this.mat&&0==c&&0==e&&this.z-d>=this.slab&&this.z<=this.depth?this.renderQuadrantUnclipped(d,a,b):this.renderQuadrantClipped(d,a,b)))},"~N,~N");c(c$,"renderQuadrantUnclipped",function(a,b,d){for(var e=a*a,c=2*a+1,f=0>d?-this.width:this.width,j=this.offsetPbufBeginLine,k=this.zbuf,
l=this.g3d.pixel,h=this.shader.sphereShadeIndexes,p=this.shades,v=0,E=0;E<=e;E+=v+ ++v,j+=f)for(var A=j,m=e-E,n=this.z-a,r=s((v*d+a<<8)/c),u=0,t=0;t<=m;t+=u+ ++u,A+=b)if(!(k[A]<=n)&&(n=s(Math.sqrt(m-t)),n=this.z-n,!(k[A]<=n))){var w=s((u*b+a<<8)/c);l.addPixel(A,n,p[h[(r<<8)+w]])}},"~N,~N,~N");c(c$,"renderQuadrantClipped",function(a,b,d){for(var e=null!=this.mat,c=0<=this.selectedOctant,f=a*a,j=2*a+1,k=0>d?-this.width:this.width,l=this.offsetPbufBeginLine,h=(this.x<<16)+(this.y<<1)^858993459,p=this.y,
v=0,E=0,A=this.g3d.pixel,m=0,n=this.height,r=this.width,u=this.x,t=this.zbuf,w=this.dxyz,x=this.y,y=this.z,z=this.slab,B=this.depth,C=this.ptTemp,D=this.coef,F=this.zroot,G=this.selectedOctant,H=this.shader,K=this.shades,I=this.planeShades,L=H.sphereShadeIndexes,M=this.planeShade,O=this.mat,S=0,R=0;R<=f;R+=S+ ++S,l+=k,p+=d)if(0>p){if(0>d)break}else if(p>=n){if(0<d)break}else{var T=f-(e?0:R),Z=u;e||(v=s((S*d+a<<8)/j));for(var h=(h<<16)+(h<<1)+h&2147483647,V=-1,P=1,W=l,Y=0,X=0;X<=T;X+=Y+ ++Y,W+=b,Z+=
b)if(0>Z){if(0>b)break}else if(Z>=r){if(0<b)break}else{var N;if(e){N=(D[4]*Z+D[5]*p+D[8])/D[2]/2;var U=N*N-(D[0]*Z*Z+D[1]*p*p+D[3]*Z*p+D[6]*Z+D[7]*p-1)/D[2];if(0>U){if(0<=V)break;continue}U=Math.sqrt(U);F[0]=-N-U;F[1]=-N+U;V=y<z?1:0;if(0==(N=s(F[V])))N=y;P=2;m=N;if(c){C.set(Z-u,p-x,N-y);O.rotate(C);U=0;0>C.x&&(U|=1);0>C.y&&(U|=2);0>C.z&&(U|=4);if(U==G){if(0<=M)E=M;else{P=3;E=3.4028235E38;for(N=0;3>N;N++)if(0!=(U=w[N][2]))U=y+(-w[N][0]*(Z-this.x)-w[N][1]*(p-x))/U,U<E&&(E=U,P=N);3==P&&(P=0,E=y);F[0]=
E;E=I[P]}N=s(F[0]);P=3}if(U=y<z?N>=z:N<z)m=N=z,P=0}if(N<z||N>B||t[W]<=m)continue}else{N=s(Math.sqrt(T-X));N=y+(y<z?N:-N);if(U=y<z?N>=z:N<z)N=z,P=0;if(N<z||N>B||t[W]<=N)continue}switch(P){case 0:E=44+(h>>8&7);h=(h<<16)+(h<<1)+h&2147483647;P=1;break;case 2:E=H.getEllipsoidShade(Z,p,F[V],a,this.mDeriv);break;case 3:A.clearPixel(W,m);break;default:E=s((Y*b+a<<8)/j),E=L[(v<<8)+E]}A.addPixel(W,N,K[E])}h=(h+Z+p|1)&2147483647}},"~N,~N,~N");C(c$,"maxOddSizeSphere",49,"maxSphereDiameter",1E3,"maxSphereDiameter2",
2E3,"SHADE_SLAB_CLIPPED",47)});m("J.g3d");w(["java.util.Hashtable"],"J.g3d.TextRenderer",["JU.CU"],function(){c$=r(function(){this.size=this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=null;this.isInvalid=!1;t(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,e,c,f,j,k,l,h){if(0==f.length)return 0;if(0<=
f.indexOf("<su")||0<=f.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,b,d,e,c,f,j,k,l,h);var p=j.getAscent();b-=p;f=J.g3d.TextRenderer.getPlotText3D(a,b,k,f,j,h);if(f.isInvalid)return f.width;h&&0==(e&12632256)&&(e|=263172);h=f.height;j=f.width;var p=f.tmap,v=k.width,E=k.height,A=k.zbuf,m=k.pixel,n=k.translucencyLog;if(null!=l||(0>a||a+f.width>v||0>b||b+f.height>E)&&null!=(l=k))for(var s=0,r=0;r<h;r++)for(var u=0;u<j;u++){var t=p[s++];0!=t&&l.plotImagePixel(e,a+u,b+r,d,t,c,v,E,A,m,
n)}else{a=b*v+a;for(s=r=0;r<h;r++){for(u=0;u<j;u++)t=p[s++],0!=t&&d<A[a]&&(8==t?m.addPixel(a,d,e):(t+=n,7>=t&&k.shadeTextPixel(a,d,e,c,t,A))),a++;a+=v-j}}return f.width},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");c$.plotByCharacter=c(c$,"plotByCharacter",function(a,b,d,e,c,f,j,k,l,h){for(var p=0,v=f.length,E=Math.round(0.25*j.getHeight()),A=-Math.round(0.3*j.getHeight()),m=0,n=0;n<v;n++){if("<"==f.charAt(n)){if(n+5<v&&f.substring(n,n+6).equals("<color")){var m=
e,s=f.indexOf(">",n);if(0>s)continue;e=JU.CU.getArgbFromString(f.substring(n+7,s).trim());n=s;continue}if(n+7<v&&f.substring(n,n+8).equals("</color>")){n+=7;e=m;continue}if(n+4<v&&f.substring(n,n+5).equals("<sub>")){n+=4;b+=E;continue}if(n+4<v&&f.substring(n,n+5).equals("<sup>")){n+=4;b+=A;continue}if(n+5<v&&f.substring(n,n+6).equals("</sub>")){n+=5;b-=E;continue}if(n+5<v&&f.substring(n,n+6).equals("</sup>")){n+=5;b-=A;continue}}s=J.g3d.TextRenderer.plot(a+p,b,d,e,c,f.substring(n,n+1),j,k,l,h);p+=
s}return p},"~N,~N,~N,~N,~N,~S,javajs.awt.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");u(c$,function(a,b){this.ascent=b.getAscent();this.height=b.getHeight();this.width=b.stringWidth(a);0!=this.width&&(this.mapWidth=this.width,this.size=this.mapWidth*this.height)},"~S,javajs.awt.Font");c$.getPlotText3D=c(c$,"getPlotText3D",function(a,b,d,e,c,f){J.g3d.TextRenderer.working=!0;f=f?J.g3d.TextRenderer.htFont3dAntialias:J.g3d.TextRenderer.htFont3d;var j=f.get(c),k=null,h=!1,q=!1;null!=j?k=j.get(e):
(j=new java.util.Hashtable,h=!0);null==k&&(k=new J.g3d.TextRenderer(e,c),q=!0);k.isInvalid=0==k.width||0>=a+k.width||a>=d.width||0>=b+k.height||b>=d.height;if(k.isInvalid)return k;h&&f.put(c,j);q&&(k.setTranslucency(e,c,d),j.put(e,k));J.g3d.TextRenderer.working=!1;return k},"~N,~N,J.g3d.Graphics3D,~S,javajs.awt.Font,~B");c(c$,"setTranslucency",function(a,b,d){a=d.apiPlatform.getTextPixels(a,b,d.platform.getGraphicsForTextOrImage(this.mapWidth,this.height),d.platform.offscreenImage,this.mapWidth,this.height,
this.ascent);if(null!=a){this.tmap=M(this.size,0);for(b=a.length;0<=--b;)d=a[b]&255,0!=d&&(this.tmap[b]=J.g3d.TextRenderer.translucency[d>>5])}},"~S,javajs.awt.Font,J.g3d.Graphics3D");C(c$,"translucency",[7,6,5,4,3,2,1,8],"working",!1);c$.htFont3d=c$.prototype.htFont3d=new java.util.Hashtable;c$.htFont3dAntialias=c$.prototype.htFont3dAntialias=new java.util.Hashtable});m("J.g3d");c$=z(J.g3d,"TextSorter",null,java.util.Comparator);h(c$,"compare",function(a,b){return null==a||null==b?0:a.z>b.z?-1:a.z<
b.z?1:0},"J.g3d.TextString,J.g3d.TextString");m("J.g3d");w(["JU.P3i"],"J.g3d.TextString",null,function(){c$=r(function(){this.font=this.text=null;this.bgargb=this.argb=0;t(this,arguments)},J.g3d,"TextString",JU.P3i);c(c$,"setText",function(a,b,d,e,c,f,j){this.text=a;this.font=b;this.argb=d;this.bgargb=e;this.x=c;this.y=f;this.z=j},"~S,javajs.awt.Font,~N,~N,~N,~N,~N");c(c$,"toString",function(){return T(this,J.g3d.TextString,"toString",[])+" "+this.text})});m("J.g3d");w(["J.g3d.G3DRenderer","JU.Rgb16"],
"J.g3d.TriangleRenderer",["JU.GData"],function(){c$=r(function(){this.rgb16t2=this.rgb16t1=this.rgb16sGouraud=this.rgb16sE=this.rgb16sW=this.azE=this.axE=this.azW=this.axW=this.az=this.ay=this.ax=this.g3d=null;t(this,arguments)},J.g3d,"TriangleRenderer",null,J.g3d.G3DRenderer);I(c$,function(){this.ax=D(3,0);this.ay=D(3,0);this.az=D(3,0);this.axW=D(64,0);this.azW=D(64,0);this.axE=D(64,0);this.azE=D(64,0);this.rgb16t1=new JU.Rgb16;this.rgb16t2=new JU.Rgb16});u(c$,function(){});h(c$,"set",function(a){try{this.rgb16sW=
Array(64);this.rgb16sE=Array(64);for(var b=64;0<=--b;)this.rgb16sW[b]=new JU.Rgb16,this.rgb16sE[b]=new JU.Rgb16;this.g3d=a;this.rgb16sGouraud=Array(3);for(b=3;0<=--b;)this.rgb16sGouraud[b]=new JU.Rgb16}catch(d){if(!y(d,Exception))throw d;}return this},"J.api.JmolRendererInterface,JU.GData");c(c$,"reallocRgb16s",function(a,b){var d=Array(b);System.arraycopy(a,0,d,0,a.length);for(var e=a.length;e<b;++e)d[e]=new JU.Rgb16;return d},"~A,~N");c(c$,"setGouraud",function(a,b,d){this.rgb16sGouraud[0].setInt(a);
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function(a,b,d,e,c){try{b="J.translation."+b+".",null!=d&&this.addBundle(a,b,d),null!=e&&this.addBundle(a,b,e),null!=c&&this.addBundle(a,b,c)}catch(f){if(y(f,Exception))J.i18n.GT.allowDebug&&JU.Logger.errorEx("Some exception occurred!",f),this.resources=null,this.resourceCount=0;else throw f;}},"JV.Viewer,~S,~S,~S,~S");c(c$,"addBundle",function(a,b,d){a=J.i18n.Resource.getResource(a,b,d);null!=a&&(null==this.resources&&(this.resources=Array(8),this.resourceCount=0),this.resources[this.resourceCount]=
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C(c$,"$ignoreApplicationBundle",!1,"$getTextWrapper",null,"languageList",null,"allowDebug",!1,"vwr",null);c$.htLanguages=c$.prototype.htLanguages=new java.util.Hashtable});m("J.i18n");w(null,"J.i18n.Language",["J.i18n.GT"],function(){c$=r(function(){this.nativeLanguage=this.language=this.code=null;this.display=!1;t(this,arguments)},J.i18n,"Language");c$.getLanguageList=c(c$,"getLanguageList",function(){return[new J.i18n.Language("ar",J.i18n.GT._("Arabic"),"\u0627\u0644\u0639\u0631\u0628\u064a\u0629",
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"\u0395\u03bb\u03bb\u03b7\u03bd\u03b9\u03ba\u03ac",!1),new J.i18n.Language("en_AU",J.i18n.GT._("Australian English"),"Australian English",!1),new J.i18n.Language("en_GB",J.i18n.GT._("British English"),"British English",!0),new J.i18n.Language("en_US",J.i18n.GT._("American English"),"American English",!0),new J.i18n.Language("es",J.i18n.GT._("Spanish"),"Espa\u00f1ol",!0),new J.i18n.Language("et",J.i18n.GT._("Estonian"),"Eesti",!1),new J.i18n.Language("eu",J.i18n.GT._("Basque"),"Euskara",!0),new J.i18n.Language("fi",
J.i18n.GT._("Finnish"),"Suomi",!0),new J.i18n.Language("fo",J.i18n.GT._("Faroese"),"F\u00f8royskt",!1),new J.i18n.Language("fr",J.i18n.GT._("French"),"Fran\u00e7ais",!0),new J.i18n.Language("fy",J.i18n.GT._("Frisian"),"Frysk",!1),new J.i18n.Language("gl",J.i18n.GT._("Galician"),"Galego",!1),new J.i18n.Language("hr",J.i18n.GT._("Croatian"),"Hrvatski",!1),new J.i18n.Language("hu",J.i18n.GT._("Hungarian"),"Magyar",!0),new J.i18n.Language("hy",J.i18n.GT._("Armenian"),"\u0540\u0561\u0575\u0565\u0580\u0565\u0576",
!1),new J.i18n.Language("id",J.i18n.GT._("Indonesian"),"Indonesia",!0),new J.i18n.Language("it",J.i18n.GT._("Italian"),"Italiano",!0),new J.i18n.Language("ja",J.i18n.GT._("Japanese"),"\u65e5\u672c\u8a9e",!0),new J.i18n.Language("jv",J.i18n.GT._("Javanese"),"Basa Jawa",!1),new J.i18n.Language("ko",J.i18n.GT._("Korean"),"\ud55c\uad6d\uc5b4",!0),new J.i18n.Language("ms",J.i18n.GT._("Malay"),"Bahasa Melayu",!0),new J.i18n.Language("nb",J.i18n.GT._("Norwegian Bokmal"),"Norsk Bokm\u00e5l",!1),new J.i18n.Language("nl",
J.i18n.GT._("Dutch"),"Nederlands",!0),new J.i18n.Language("oc",J.i18n.GT._("Occitan"),"Occitan",!1),new J.i18n.Language("pl",J.i18n.GT._("Polish"),"Polski",!1),new J.i18n.Language("pt",J.i18n.GT._("Portuguese"),"Portugu\u00eas",!1),new J.i18n.Language("pt_BR",J.i18n.GT._("Brazilian Portuguese"),"Portugu\u00eas brasileiro",!0),new J.i18n.Language("ru",J.i18n.GT._("Russian"),"\u0420\u0443\u0441\u0441\u043a\u0438\u0439",!1),new J.i18n.Language("sl",J.i18n.GT._("Slovenian"),"Sloven\u0161\u010dina",!1),
new J.i18n.Language("sr",J.i18n.GT._("Serbian"),"\u0441\u0440\u043f\u0441\u043a\u0438 \u0458\u0435\u0437\u0438\u043a",!1),new J.i18n.Language("sv",J.i18n.GT._("Swedish"),"Svenska",!0),new J.i18n.Language("ta",J.i18n.GT._("Tamil"),"\u0ba4\u0bae\u0bbf\u0bb4\u0bcd",!1),new J.i18n.Language("te",J.i18n.GT._("Telugu"),"\u0c24\u0c46\u0c32\u0c41\u0c17\u0c41",!1),new J.i18n.Language("tr",J.i18n.GT._("Turkish"),"T\u00fcrk\u00e7e",!0),new J.i18n.Language("ug",J.i18n.GT._("Uyghur"),"Uy\u01a3urq\u0259",!1),new J.i18n.Language("uk",
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d,e,c);f&&null!=this.tickInfo&&(this.atomA.sX=e.x,this.atomA.sY=e.y,this.atomA.sZ=e.z,this.atomB.sX=c.x,this.atomB.sY=c.y,this.atomB.sZ=c.z,this.drawTicks(this.atomA,this.atomB,d,!0))},"JU.P3,JU.P3,~N,JU.P3i,JU.P3i,~B");c(c$,"drawTicks",function(a,b,d,e){Float.isNaN(this.tickInfo.first)&&(this.tickInfo.first=0);this.drawTicks2(a,b,this.tickInfo.ticks.x,8,d,!e?null:null==this.tickInfo.tickLabelFormats?["%0.2f"]:this.tickInfo.tickLabelFormats);this.drawTicks2(a,b,this.tickInfo.ticks.y,4,d,null);this.drawTicks2(a,
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this.vectorT2.x,0);this.vectorT2.scale(e/this.vectorT2.length());e=this.tickInfo.reference;null==e?(this.pointT3.setT(this.vwr.getBoundBoxCenter()),603979810==this.vwr.g.axesMode&&this.pointT3.add3(1,1,1)):this.pointT3.setT(e);this.tm.transformPtScr(this.pointT3,this.pt2i);e=0.2>Math.abs(this.vectorT2.x/this.vectorT2.y);for(var q=!e,p=!e&&0>this.vectorT2.x,v=null!=f&&0<f.length,E,A,m=Array(1),n=this.draw000?0:-1;k<h;){if(k>=this.tickInfo.first&&(this.pointT2.setT(this.pointT),this.tm.transformPt3f(this.pointT2,
this.pointT2),this.drawLine(s(Math.floor(this.pointT2.x)),s(Math.floor(this.pointT2.y)),B(a),E=s(Math.floor(this.pointT2.x+this.vectorT2.x)),A=s(Math.floor(this.pointT2.y+this.vectorT2.y)),B(a),c),v&&(this.draw000||0!=k))){m[0]=Float.$valueOf(0==k?0:k*j);var r=JU.PT.sprintf(f[n%f.length],"f",m);this.drawString(E,A,B(a),4,p,e,q,s(Math.floor(this.pointT2.y)),r)}this.pointT.add(this.vectorT);k+=d;a+=b;n++}}}},"JU.Point3fi,JU.Point3fi,~N,~N,~N,~A");c(c$,"drawLine",function(a,b,d,e,c,f,j){return this.drawLine2(a,
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f?a-(s(e/2)+2+s(q/2)):a+(s(e/2)+2);c=b;c=j?c+s(p/2):0==k||k<b?c+p:c-s(e/2);b=d-e-2;1>b&&(b=1);this.g3d.drawString(h,this.font3d,a,c,b,b,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");c(c$,"drawDashed",function(a,b,d,e,c,f,j){if(!(null==j||0>this.width)){var k=j[0];e-=a;c-=b;f-=d;var h=0,q=j===J.render.FontLineShapeRenderer.ndots,p=q||j===J.render.FontLineShapeRenderer.sixdots;if(p){var v=(e*e+c*c)/(this.width*this.width);q?(k=Math.sqrt(v)/1.5,h=B(k)+3):8>v?j=J.render.FontLineShapeRenderer.twodots:32>v&&(j=J.render.FontLineShapeRenderer.fourdots)}var v=
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x,y,z)}}}},"~N,~N,~N,~N,~N,~N,~A");c(c$,"fillCylinder",function(a,b,d,e,c,f,j,k,h,q){this.asLineOnly?this.g3d.drawLine(a,b,c,f,j,k,h,q):this.g3d.fillCylinderXYZ(a,b,d,!this.isExport||1==this.mad?e:this.mad,c,f,j,k,h,q)},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");C(c$,"dashes",[12,0,0,2,5,7,10],"hDashes",[10,7,6,1,3,4,6,7,9],"ndots",[0,3,1E3],"sixdots",[12,3,6,1,3,5,7,9,11],"fourdots",[13,3,5,2,5,8,11],"twodots",[12,3,4,3,9])});m("J.render");w(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["JU.C"],function(){c$=
z(J.render,"FrankRenderer",J.render.ShapeRenderer);h(c$,"render",function(){var a=this.shape,b=this.vwr.getBooleanProperty("allowKeyStrokes"),d=this.vwr.getBoolean(603979883);this.colix=d?20:this.vwr.isSignedApplet?b||this.vwr.isJS&&!this.vwr.isWebGL?5:10:b?7:12;if(this.isExport||!this.vwr.getShowFrank())return!1;if(!this.g3d.setC(JU.C.getColixTranslucent3(this.colix,this.g3d.haveTranslucentObjects(),0.5)))return!0;b=this.vwr.getImageFontScaling();a.getFont(b);var b=B(a.frankWidth+4*b),e=a.frankDescent;
this.g3d.drawStringNoSlab(a.frankString,a.font3d,this.vwr.gdata.width-b,this.vwr.gdata.height-e,0,0);d&&this.g3d.fillRect(0,0,0,0,2*e,s(3*b/2));return!1})});m("J.render");w(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["java.lang.NullPointerException","J.api.Interface","JU.Logger","JV.JC"],function(){c$=r(function(){this.bsTranslucent=this.renderers=this.shapeManager=this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;t(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);
I(c$,function(){this.bsTranslucent=JU.BS.newN(37)});u(c$,function(){});h(c$,"set",function(a,b){this.vwr=a;this.shapeManager=b},"JV.Viewer,JV.ShapeManager");h(c$,"isRepaintPending",function(){return this.repaintPending});h(c$,"pushHoldRepaint",function(){++this.holdRepaint},"~S");h(c$,"popHoldRepaint",function(a,b){--this.holdRepaint;0>=this.holdRepaint&&(this.holdRepaint=0,a&&(this.repaintPending=!0,this.repaintNow(b)))},"~B,~S");h(c$,"requestRepaintAndWait",function(){"undefined"!=typeof Jmol&&
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null},"~N");c(c$,"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$,"render",function(a,b,d,e){null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();try{var c=this.vwr.getBoolean(603979934);a.renderBackground(null);if(d){this.bsTranslucent.clearAll();null!=e&&a.renderCrossHairs(e,
this.vwr.getScreenWidth(),this.vwr.getScreenHeight(),this.vwr.tm.getNavigationOffset(),this.vwr.tm.navigationDepthPercent);var f=this.vwr.getRubberBandSelection();null!=f&&a.setC(this.vwr.cm.colixRubberband)&&a.drawRect(f.x,f.y,0,0,f.width,f.height)}e=null;for(f=0;37>f&&a.currentlyRendering;++f){var j=this.shapeManager.getShape(f);null!=j&&(c&&(e="rendering "+JV.JC.getShapeClassName(f,!1),JU.Logger.startTimer(e)),(d||this.bsTranslucent.get(f))&&this.getRenderer(f).renderShape(a,b,j)&&this.bsTranslucent.set(f),
c&&JU.Logger.checkTimer(e,!1))}a.renderAllStrings(null)}catch(k){if(y(k,Exception)){this.vwr.isJS||k.printStackTrace();if(this.vwr.async&&"Interface".equals(k.getMessage()))throw new NullPointerException;JU.Logger.error("rendering error? "+k)}else throw k;}},"JU.GData,JM.ModelSet,~B,~A");c(c$,"getAllRenderers",function(){for(var a=!0,b=0;37>b;++b)null==this.shapeManager.getShape(b)||null!=this.getRenderer(b)||(a=this.repaintPending=!this.vwr.async);if(!a)throw new NullPointerException;});h(c$,"renderExport",
function(a,b,d){this.vwr.finalizeTransformParameters();this.shapeManager.finalizeAtoms(null,null);a=this.vwr.initializeExporter(d);if(null==a)return JU.Logger.error("Cannot export "+d.get("type")),null;null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();d=null;try{var e=this.vwr.getBoolean(603979934);a.renderBackground(a);for(var c=0;37>c;++c){var f=this.shapeManager.getShape(c);null!=f&&(e&&(d="rendering "+JV.JC.getShapeClassName(c,!1),JU.Logger.startTimer(d)),this.getRenderer(c).renderShape(a,
b,f),e&&JU.Logger.checkTimer(d,!1))}a.renderAllStrings(a);d=a.finalizeOutput()}catch(j){if(y(j,Exception))this.vwr.isJS||j.printStackTrace(),JU.Logger.error("rendering error? "+j);else throw j;}return d},"JU.GData,JM.ModelSet,java.util.Map")});m("J.render");w(null,"J.render.ShapeRenderer",["JV.JC"],function(){c$=r(function(){this.shape=this.ms=this.g3d=this.tm=this.vwr=null;this.exportType=this.madEnd=this.madMid=this.madBeg=this.mad=this.colix=this.shapeID=this.myVisibilityFlag=0;this.isExport=!1;
t(this,arguments)},J.render,"ShapeRenderer");c(c$,"initRenderer",function(){});c(c$,"setViewerG3dShapeID",function(a,b){this.vwr=a;this.tm=a.tm;this.shapeID=b;this.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(b);this.initRenderer()},"JV.Viewer,~N");c(c$,"renderShape",function(a,b,d){this.g3d=a;this.ms=b;this.shape=d;this.exportType=a.getExportType();this.isExport=0!=this.exportType;a=this.render();this.exportType=0;this.isExport=!1;return a},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");
c(c$,"isVisibleForMe",function(a){return a.isVisible(this.myVisibilityFlag|9)},"JM.Atom")});m("J.render");w(["J.render.FontLineShapeRenderer","JU.BS","$.P3","$.V3"],"J.render.SticksRenderer",["java.lang.Float","J.c.PAL","JM.Bond","JU.C","$.Edge"],function(){c$=r(function(){this.showMultipleBonds=!1;this.modeMultipleBond=this.multipleBondRadiusFactor=this.multipleBondSpacing=0;this.isCartesianExport=!1;this.endcaps=0;this.hbondsSolid=this.bondsBackbone=this.hbondsBackbone=this.ssbondsBackbone=!1;this.bond=
this.b=this.a=null;this.bondOrder=this.mag2d=this.dy=this.dx=this.zB=this.yB=this.xB=this.zA=this.yA=this.xA=0;this.slabByAtom=this.slabbing=this.isAntialiased=this.wireframeOnly=!1;this.bsForPass2=this.p2=this.p1=this.z=this.y=this.x=null;this.isPass2=!1;this.dyStep=this.dxStep=this.yAxis2=this.xAxis2=this.yAxis1=this.xAxis1=0;t(this,arguments)},J.render,"SticksRenderer",J.render.FontLineShapeRenderer);I(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(603979889)?J.render.FontLineShapeRenderer.sixdots:J.render.FontLineShapeRenderer.dashes;this.isCartesianExport=1==this.exportType;this.getMultipleBondSettings(!1);this.wireframeOnly=!this.vwr.checkMotionRendering(1678770178);
this.ssbondsBackbone=this.vwr.getBoolean(603979952);this.hbondsBackbone=this.vwr.getBoolean(603979852);this.bondsBackbone=(new Boolean(this.hbondsBackbone|this.ssbondsBackbone)).valueOf();this.hbondsSolid=this.vwr.getBoolean(603979854);this.isAntialiased=this.g3d.isAntialiased();var b=!1;if(!this.isExport&&this.isPass2)for(var d=this.bsForPass2.nextSetBit(0);0<=d;d=this.bsForPass2.nextSetBit(d+1))this.bond=a[d],this.renderBond();else for(d=this.ms.bondCount;0<=--d;)this.bond=a[d],0!=(this.bond.shapeVisibilityFlags&
this.myVisibilityFlag)&&this.renderBond()&&(b=!0,this.bsForPass2.set(d));return b});c(c$,"getMultipleBondSettings",function(a){this.multipleBondSpacing=a?0.15:this.vwr.getFloat(570425370);this.multipleBondRadiusFactor=a?0.4:this.vwr.getFloat(570425369);0==this.multipleBondSpacing&&this.isCartesianExport&&(this.multipleBondSpacing=0.2);this.modeMultipleBond=this.vwr.g.modeMultipleBond;this.showMultipleBonds=0!=this.multipleBondSpacing&&0!=this.modeMultipleBond&&this.vwr.getBoolean(603979928)},"~B");
c(c$,"renderBond",function(){var a,b;this.a=a=this.bond.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&&JM.Bond.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))||this.slabbing&&(this.vwr.gdata.isClippedZ(this.a.sZ)&&this.vwr.gdata.isClippedZ(this.b.sZ)||this.slabByAtom&&(this.vwr.gdata.isClippedZ(this.a.sZ)||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.isColixTranslucent(this.colixA);var e=!JU.C.isColixTranslucent(this.colixB);if(!b||!e){if(!b&&!e&&!a)return this.g3d.setC(!b?this.colixA:this.colixB),!0;a=!0}}this.bondOrder=d&-131073;if(0==(this.bondOrder&224)&&(0!=(this.bondOrder&256)&&
(this.bondOrder&=-257),0!=(this.bondOrder&1023)&&(!this.showMultipleBonds||2==this.modeMultipleBond&&500<this.mad||65536==(this.bondOrder&98304))))this.bondOrder=1;b=0;switch(this.bondOrder){case 1:case 2:case 3:case 4:break;case 17:case 513:this.bondOrder=1;b=513==d?0:1;break;case 515:case 514:this.bondOrder=2;b=515==d?this.getAromaticDottedBondMask():0;break;default:0!=(this.bondOrder&224)?(this.bondOrder=JU.Edge.getPartialBondOrder(d),b=JU.Edge.getPartialBondDotted(d)):JM.Bond.isOrderH(this.bondOrder)?
(this.bondOrder=1,this.hbondsSolid||(b=-1)):32768==this.bondOrder?this.bondOrder=1:98304==(this.bondOrder&98304)&&(this.getMultipleBondSettings(!0),this.bondOrder&=3,b=-2)}this.xA=this.a.sX;this.yA=this.a.sY;this.xB=this.b.sX;this.yB=this.b.sY;this.mad=this.bond.mad;0<this.multipleBondRadiusFactor&&1<this.bondOrder&&(this.mad*=this.multipleBondRadiusFactor);this.dx=this.xB-this.xA;this.dy=this.yB-this.yA;this.width=B(this.vwr.tm.scaleToScreen(s((this.zA+this.zB)/2),this.mad));this.wireframeOnly&&
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this.mad,-1);else{var b=0==this.dx&&0==this.dy;if(!b||!this.asLineOnly){var d=1<this.bondOrder&&0<this.multipleBondSpacing,e=d&&(null!=this.vwr.getHybridizationAndAxes(this.a.i,this.z,this.x,"pz")||null!=this.vwr.getHybridizationAndAxes(this.b.i,this.z,this.x,"pz"))&&!Float.isNaN(this.x.x);if(b&&!d){a=s(this.width/8)+3;a=this.width+a;d=this.yA-s((this.bondOrder-1)*a/2);do this.fillCylinder(this.colixA,this.colixA,this.endcaps,this.width,this.xA,d,this.zA,this.xA,d,this.zA),d+=a;while(0<--this.bondOrder)}else if(b=
0!=(a&1),1==this.bondOrder)b?this.drawDashed(this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,this.dashDots):this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.xA,this.yA,this.zA,this.xB,this.yB,this.zB);else if(d){e||this.z.setT(JU.P3.getUnlikely());this.x.sub2(this.b,this.a);this.y.cross(this.x,this.z);this.y.normalize();Float.isNaN(this.y.x)&&(this.z.setT(JU.P3.getUnlikely()),this.y.cross(this.x,this.z),this.y.cross(this.y,this.x),this.y.normalize());this.y.scale(this.multipleBondSpacing);
this.x.setT(this.y);this.x.scale((this.bondOrder-1)/2);this.p1.sub2(this.a,this.x);for(this.p2.sub2(this.b,this.x);;){this.isCartesianExport&&!b?this.g3d.drawBond(this.p1,this.p2,this.colixA,this.colixB,this.endcaps,this.mad,-2):(this.tm.transformPtScr(this.p1,this.s1),this.tm.transformPtScr(this.p2,this.s2),b?this.drawDashed(this.s1.x,this.s1.y,this.s1.z,this.s2.x,this.s2.y,this.s2.z,this.dashDots):this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.s1.x,this.s1.y,this.s1.z,this.s2.x,
this.s2.y,this.s2.z),a>>=1,b=0!=(a&1));if(0>=--this.bondOrder)break;this.p1.add(this.y);this.p2.add(this.y);this.stepAxisCoordinates()}}else{this.mag2d=Math.round(Math.sqrt(this.dx*this.dx+this.dy*this.dy));for(this.resetAxisCoordinates();;){0!=(a&1)?this.drawDashed(this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,this.dashDots):this.fillCylinder(this.colixA,this.colixB,this.endcaps,this.width,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB);a>>=1;if(0>=--this.bondOrder)break;
this.stepAxisCoordinates()}}}}},"~N");c(c$,"resetAxisCoordinates",function(){var a=this.mag2d>>3;-1!=this.multipleBondSpacing&&0>this.multipleBondSpacing&&(a*=-this.multipleBondSpacing);a=this.width+a;this.dxStep=s(a*this.dy/this.mag2d);this.dyStep=s(a*-this.dx/this.mag2d);this.xAxis1=this.xA;this.yAxis1=this.yA;this.xAxis2=this.xB;this.yAxis2=this.yB;a=this.bondOrder-1;this.xAxis1-=s(this.dxStep*a/2);this.yAxis1-=s(this.dyStep*a/2);this.xAxis2-=s(this.dxStep*a/2);this.yAxis2-=s(this.dyStep*a/2)});
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0;h<c;h++)this.atomSymmetry.get(g++)&&(a?b+=","+(h+1)+d[k]:j.set(h+1));if(!a)for(k=j.nextSetBit(0);0<=k;k=j.nextSetBit(k+1))b+=","+k;return 0==b.length?"":b.substring(1)},"~B");h(c$,"getModelIndex",function(){return this.mi});c(c$,"getMoleculeNumber",function(a){return this.group.chain.model.ms.getMoleculeIndex(this.i,a)+1},"~B");c(c$,"getFractionalCoord",function(a,b,d,c){c=this.getFractionalCoordPt(a,d,c);return"X"==b?c.x:"Y"==b?c.y:c.z},"~B,~S,~B,JU.P3");c(c$,"getFractionalCoordPt",function(a,
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c(c$,"setFractionalCoord",function(a,b,d){var c=this.getUnitCell();null!=c&&c.toFractional(this,d);switch(a){case 1112541191:case 1112541188:this.x=b;break;case 1112541192:case 1112541189:this.y=b;break;case 1112541193:case 1112541190: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$,"isCursorOnTopOf",function(a,b,d,c){var g=s(this.sD/2);g<d&&(g=d);d=g*g;g=this.sX-a;g*=g;if(g>d)return!1;var f=this.sY-b;d-=g+f*f;if(0>d)return!1;if(null==c)return!0;var g=this.sZ,f=c.sZ,j=s(c.sD/2);if(g<f-j)return!0;a=c.sX-a;b=c.sY-b;b=j*j-(a*a+b*b);return g-Math.sqrt(d)<f-Math.sqrt(b)},"~N,~N,~N,JM.Atom");c(c$,"getInfo",function(){return this.getIdentity(!0)});c(c$,"getInfoXYZ",function(a,b,d){if(b){b=this.getGroup3(!0);var c=this.getChainID();d=this.getFractionalCoordPt(a,
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!1,b):this;return this.getIdentity(a)+" "+b.x+" "+b.y+" "+b.z},"~B,JU.P3");c(c$,"getIdentity",function(a){var b=new JU.SB,d=this.getGroup3(!0);if(null!=d&&0<d.length&&!d.equals("UNK")){b.append("[");b.append(d);b.append("]");d=this.getSeqcodeString();null!=d&&b.append(d);d=this.getChainID();if(0!=d&&32!=d){b.append(":");var c=this.getChainIDStr();256<=d&&(c=JU.PT.esc(c));b.append(c)}if(!a)return b.toString();b.append(".")}b.append(this.getAtomName());0==b.length()&&(b.append(this.getElementSymbolIso(!1)),
b.append(" "),b.appendI(this.getAtomNumber()));0!=this.altloc.charCodeAt(0)&&(b.append("%"),b.appendC(this.altloc));1<this.group.chain.model.ms.mc&&!this.group.chain.model.isJmolDataFrame&&(b.append("/"),b.append(this.getModelNumberForLabel()));b.append(" #");b.appendI(this.getAtomNumber());return b.toString()},"~B");h(c$,"getGroup3",function(a){var b=this.group.getGroup3();return a||null!=b&&0<b.length?b:"UNK"},"~B");h(c$,"getGroup1",function(a){var b=this.group.getGroup1();return"\x00"!=b?""+b:
"\x00"!=a?""+a:""},"~S");h(c$,"isProtein",function(){return this.group.isProtein()});c(c$,"isCarbohydrate",function(){return this.group.isCarbohydrate()});h(c$,"isNucleic",function(){return this.group.isNucleic()});h(c$,"isDna",function(){return this.group.isDna()});h(c$,"isRna",function(){return this.group.isRna()});h(c$,"isPurine",function(){return this.group.isPurine()});h(c$,"isPyrimidine",function(){return this.group.isPyrimidine()});c(c$,"getSeqcode",function(){return this.group.seqcode});h(c$,
"getResno",function(){return this.group.getResno()});c(c$,"isClickable",function(){return this.checkVisible()&&0!=this.clickabilityFlags&&0!=((this.shapeVisibilityFlags|this.group.shapeVisibilityFlags)&this.clickabilityFlags)});c(c$,"setClickable",function(a){0==a?this.clickabilityFlags=0:(this.clickabilityFlags|=a,1040384!=a&&(this.shapeVisibilityFlags|=a))},"~N");c(c$,"checkVisible",function(){if(this.isVisible(2))return this.isVisible(4);var a=this.isVisible(9);if(a){a=this.shapeVisibilityFlags;
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c(c$,"getSurfaceDistance100",function(){return this.group.chain.model.ms.getSurfaceDistance100(this.i)});c(c$,"getVibrationVector",function(){return this.group.chain.model.ms.getVibration(this.i,!1)});c(c$,"getModulation",function(){return this.group.chain.model.ms.getModulation(this.i)});c(c$,"getVibrationCoord",function(a){return this.group.chain.model.ms.getVibrationCoord(this.i,a)},"~S");c(c$,"getModulationCoord",function(a){return this.group.chain.model.ms.getModulationCoord(this.i,a)},"~S");
c(c$,"getPolymerLength",function(){return this.group.getBioPolymerLength()});c(c$,"getPolymerIndexInModel",function(){return this.group.getBioPolymerIndexInModel()});c(c$,"getMonomerIndex",function(){return this.group.getMonomerIndex()});c(c$,"getSelectedGroupCountWithinChain",function(){return this.group.chain.selectedGroupCount});c(c$,"getSelectedGroupIndexWithinChain",function(){return this.group.getSelectedGroupIndex()});c(c$,"getSelectedMonomerCountWithinPolymer",function(){return this.group.getSelectedMonomerCount()});
c(c$,"getSelectedMonomerIndexWithinPolymer",function(){return this.group.getSelectedMonomerIndex()});c(c$,"getChain",function(){return this.group.chain});c(c$,"getModelNumberForLabel",function(){return this.group.chain.model.ms.getModelNumberForAtomLabel(this.mi)});c(c$,"getModelNumber",function(){return this.group.chain.model.ms.getModelNumber(this.mi)%1E6});h(c$,"getBioStructureTypeName",function(){return this.getProteinStructureType().getBioStructureTypeName(!0)});c(c$,"getProteinStructureType",
function(){return this.group.getProteinStructureType()});c(c$,"getProteinStructureSubType",function(){return this.group.getProteinStructureSubType()});c(c$,"getStrucNo",function(){return this.group.getStrucNo()});c(c$,"getStructureId",function(){return this.group.getStructureId()});c(c$,"getProteinStructureTag",function(){return this.group.getProteinStructureTag()});c(c$,"getGroupID",function(){return this.group.groupID});c(c$,"getSeqcodeString",function(){return this.group.getSeqcodeString()});c(c$,
"getInsertionCode",function(){return this.group.getInsertionCode()});h(c$,"equals",function(a){return this===a},"~O");h(c$,"hashCode",function(){return this.i});c(c$,"findAromaticNeighbor",function(a){if(null==this.bonds)return null;for(var b=this.bonds.length;0<=--b;){var d=this.bonds[b],c=d.getOtherAtom(this);if(d.isAromatic()&&c.i!=a)return c}return null},"~N");c(c$,"atomPropertyInt",function(a){switch(a){case 1095763969:return this.getAtomNumber();case 1095761940:return this.getSeqID();case 1095761922:return this.atomID;
case 1095761943:return Math.max(0,this.altloc.charCodeAt(0)-32);case 1095761923:return this.i;case 1095761924:return this.getCovalentBondCount();case 1095761927:return this.group.chain.index+1;case 1766856708:return this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom);case 1087375365:case 1095763978:return this.getElementNumber();case 1095761929:return this.atomicAndIsotopeNumber;case 1229984263:return this.group.chain.model.fileIndex+1;case 1632634891:return this.getFormalCharge();
case 1095761932:return this.getGroupID();case 1095761933:return this.group.groupIndex;case 1095766030:return this.getModelNumber();case -1095766030:return this.group.chain.model.ms.modelFileNumbers[this.mi];case 1095761935:return this.mi;case 1095761936:return this.getMoleculeNumber(!0);case 1129318401:return this.getOccupancy100();case 1095761937:return this.group.getBioPolymerIndexInModel()+1;case 1095761938:return this.getPolymerLength();case 1666189314:return this.getRasMolRadius();case 1095761939:return this.getResno();
case 1095761941:return this.getAtomSite();case 1641025539:return this.getProteinStructureType().getId();case 1238369286:return this.getProteinStructureSubType().getId();case 1095761942:return this.getStrucNo();case 1297090050:return this.getSymOp();case 1095763991: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 1112539137:return this.getADPMinMax(!0);case 1112539138:return this.getADPMinMax(!1);
case 1112541185:case 1112541205:return this.x;case 1112541186:case 1112541206:return this.y;case 1112541187:case 1112541207:return this.z;case 1115297793:case 1113200642:case 1113198595:case 1113198596:case 1113198597:case 1113200646:case 1113200647:case 1113200649:case 1113200650:case 1113200652:case 1650071565:case 1113200654:return a.shm.getAtomShapeValue(b,this.group,this.i);case 1112541194:return this.getBondingRadius();case 1112539139:return a.getNMRCalculation().getChemicalShift(this);case 1112539140:return JU.Elements.getCovalentRadius(this.atomicAndIsotopeNumber);
case 1112539141:case 1112539152:case 1112539150:return this.getGroupParameter(b);case 1112541188:return this.getFractionalCoord(!a.g.legacyJavaFloat,"X",!0,d);case 1112541189:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!0,d);case 1112541190:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Z",!0,d);case 1112541191:return this.getFractionalCoord(!a.g.legacyJavaFloat,"X",!1,d);case 1112541192:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,d);case 1112541193:return this.getFractionalCoord(!a.g.legacyJavaFloat,
"Z",!1,d);case 1114638362:return this.getHydrophobicity();case 1112539142:return a.getNMRCalculation().getMagneticShielding(this);case 1112539143:return this.getMass();case 1129318401:return this.getOccupancy100()/100;case 1112541195:return this.getPartialCharge();case 1112539145:case 1112539146:case 1112539144:if(this.group.chain.model.isJmolDataFrame&&this.group.chain.model.jmolFrameType.startsWith("plot ramachandran"))switch(b){case 1112539145:return this.getFractionalCoord(!a.g.legacyJavaFloat,
"X",!1,d);case 1112539146:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,d);case 1112539144: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.getGroupParameter(b);case 1666189314:case 1113200651:return this.getRadius();case 1112539147:return this.sX;case 1112539148:return this.group.chain.model.ms.vwr.getScreenHeight()-this.sY;case 1112539149:return this.sZ;
case 1114638363:return a.slm.isAtomSelected(this.i)?1:0;case 1112539151:return this.group.chain.model.ms.getSurfaceDistanceMax(),this.getSurfaceDistance100()/100;case 1112541196:return this.getBfactor100()/100;case 1112539153:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"X",d);case 1112539154:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Y",d);case 1112539155:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Z",d);case 1649412120:return this.getVanderwaalsRadiusFloat(a,
J.c.VDW.AUTO);case 1649410049:return b=this.getVibrationVector(),null==b?0:b.length()*a.getFloat(1649410049);case 1112541202:return this.getVibrationCoord("X");case 1112541203:return this.getVibrationCoord("Y");case 1112541204:return this.getVibrationCoord("Z");case 1112539159:return this.getModulationCoord("X");case 1112539156:return this.getModulationCoord("1");case 1112539157:return this.getModulationCoord("2");case 1112539158:return this.getModulationCoord("3");case 1112539160:return this.getModulationCoord("Y");
case 1112539161:return this.getModulationCoord("Z");case 1112539162:return this.getModulationCoord("O");case 1313866249:return this.getVolume(a,J.c.VDW.AUTO);case 1146095627:case 1146095629:case 1146093582:case 1146095628:case 1146095631:case 1146093584:case 1146095626:return a=this.atomPropertyTuple(a,b,d),null==a?-1:a.length()}return this.atomPropertyInt(b)},"JV.Viewer,~N,JU.P3");c(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 1087373315:return d=this.altloc,"\x00"==d?"":""+d;case 1087375362:return this.getAtomName();case 1087375361:return this.getAtomType();case 1087373316:return this.getChainIDStr();case 1087373320:return this.getGroup1("?");case 1087373319:return this.getGroup1("\x00");case 1087373318:return this.getGroup3(!1);case 1087375365:return this.getElementSymbolIso(!0);case 1087373321:return this.getIdentity(!0);case 1087373322:return d=this.getInsertionCode(),
"\x00"==d?"":""+d;case 1826248716:case 1288701959:return d=a.shm.getShapePropertyIndex(5,"label",this.i),null==d&&(d=""),d;case 1641025539:return this.getProteinStructureType().getBioStructureTypeName(!1);case 1238369286:return this.getProteinStructureSubType().getBioStructureTypeName(!1);case 1087373324:return this.getStructureId();case 1087373323:return a.getHybridizationAndAxes(this.i,null,null,"d");case 1087375373:return this.getElementSymbolIso(!1);case 1089470478:return this.getSymmetryOperatorList(!0)}return""},
"JV.Viewer,~N");c(c$,"atomPropertyTuple",function(a,b,d){switch(b){case 1146095627:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!this.group.chain.model.isJmolDataFrame,d);case 1146095629:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d);case 1146093582:return this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,d):this.getFractionalUnitCoordPt(!a.g.legacyJavaFloat,!1,d);case 1146095628:return JU.P3.new3(this.sX,this.group.chain.model.ms.vwr.getScreenHeight()-
this.sY,this.sZ);case 1146095631:return this.getVibrationVector();case 1146093584:return a=this.getModulation(),null==a?null:a.getV3();case 1146095626:return this;case 1766856708:return JU.CU.colorPtFromInt(this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom),d)}return null},"JV.Viewer,~N,JU.P3");c(c$,"isWithinStructure",function(a){return this.group.isWithinStructure(a)},"J.c.STR");h(c$,"getOffsetResidueAtom",function(a,b){return this.group.getAtomIndex(a,b)},"~S,~N");h(c$,"isCrossLinked",
function(a){return this.group.isCrossLinked(a.group)},"JU.BNode");h(c$,"getCrossLinkLeadAtomIndexes",function(a){return this.group.getCrossLinkLead(a)},"JU.Lst");h(c$,"toString",function(){return this.getInfo()});h(c$,"findAtomsLike",function(a){return this.group.chain.model.ms.vwr.getAtomBitSet(a)},"~S");C(c$,"VIBRATION_VECTOR_FLAG",1,"IS_HETERO_FLAG",2,"FLAG_MASK",3,"RADIUS_MAX",16,"RADIUS_GLOBAL",16.1,"MAD_GLOBAL",32200)});m("JM");w(["JU.V3"],"JM.AtomCollection","java.lang.Character $.Float java.util.Arrays $.Hashtable JU.A4 $.AU $.BS $.Lst $.M3 $.Measure $.P3 $.PT J.api.Interface $.JmolModulationSet J.atomdata.RadiusData J.c.PAL $.STR $.VDW JM.Group JS.T JU.BSUtil $.Elements $.Escape $.Logger $.Parser $.Vibration".split(" "),
function(){c$=r(function(){this.at=this.g3d=this.vwr=null;this.ac=0;this.labeler=this.surfaceDistance100s=this.atomTensors=this.atomTensorList=this.hydrophobicities=this.bondingRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.atomSeqIDs=this.atomSerials=this.atomTypes=this.atomNames=null;this.maxVanderwaalsRadius=this.maxBondingRadius=1.4E-45;this.hasBfactorRange=!1;this.bfactor100Hi=this.bfactor100Lo=0;this.bsSurface=null;this.surfaceDistanceMax=this.nSurfaceAtoms=
0;this.bspf=this.averageAtomPoint=null;this.canSkipLoad=this.preserveState=!0;this.haveStraightness=!1;this.bsModulated=this.bsClickable=this.bsVisible=this.bsHidden=this.tainted=null;this.haveBSClickable=this.haveBSVisible=!1;this.aaRet=null;R("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();t(this,arguments)},JM,"AtomCollection");c(c$,"setupAC",function(){this.bsHidden=new JU.BS;this.bsVisible=new JU.BS;this.bsClickable=new JU.BS;null==JM.AtomCollection.userSettableValues&&
(JM.AtomCollection.userSettableValues="atomName atomType coord element formalCharge hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals vibrationVector atomNo seqID".$plit(" "))});c(c$,"releaseModelSet",function(){this.releaseModelSetAC()});c(c$,"releaseModelSetAC",function(){this.atomTensors=this.bondingRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.atomSeqIDs=this.atomSerials=this.atomTypes=this.atomNames=this.tainted=this.bsSurface=this.surfaceDistance100s=
this.bspf=this.g3d=this.vwr=this.at=null});c(c$,"mergeAtomArrays",function(a){this.tainted=a.tainted;this.atomNames=a.atomNames;this.atomTypes=a.atomTypes;this.atomSerials=a.atomSerials;this.atomSeqIDs=a.atomSeqIDs;this.vibrations=a.vibrations;this.occupancies=a.occupancies;this.bfactor100s=a.bfactor100s;this.bondingRadii=a.bondingRadii;this.partialCharges=a.partialCharges;this.atomTensors=a.atomTensors;this.atomTensorList=a.atomTensorList;this.bsModulated=a.bsModulated;this.haveStraightness=!1;this.surfaceDistance100s=
null},"JM.AtomCollection");c(c$,"getAtomPointVector",function(a){var b=new JU.Lst;if(null!=a)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))b.addLast(this.at[d]);return b},"JU.BS");c(c$,"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$,"getQuaternion",function(a,b){return 0>a?null:this.at[a].group.getQuaternion(b)},"~N,~S");c(c$,"getAtomIndexFromAtomNumber",function(a,b){for(var d=0;d<this.ac;d++){var c=this.at[d];if(c.getAtomNumber()==a&&b.get(c.mi))return d}return-1},"~N,JU.BS");c(c$,"setFormalCharges",function(a,b){if(null!=a)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.at[d].setFormalCharge(b),this.taintAtom(d,4)},"JU.BS,~N");c(c$,"getAtomicCharges",function(){for(var a=L(this.ac,0),b=this.ac;0<=--b;)a[b]=
this.at[b].getElementNumber();return a});c(c$,"getRadiusVdwJmol",function(a){return JU.Elements.getVanderwaalsMar(a.getElementNumber(),J.c.VDW.JMOL)/1E3},"JM.Atom");c(c$,"getMaxVanderwaalsRadius",function(){1.4E-45==this.maxVanderwaalsRadius&&this.findMaxRadii();return this.maxVanderwaalsRadius});c(c$,"findMaxRadii",function(){for(var a,b=this.ac;0<=--b;){var d=this.at[b];if((a=d.getBondingRadius())>this.maxBondingRadius)this.maxBondingRadius=a;if((a=d.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO))>
this.maxVanderwaalsRadius)this.maxVanderwaalsRadius=a}});c(c$,"clearBfactorRange",function(){this.hasBfactorRange=!1});c(c$,"calcBfactorRange",function(a){if(!this.hasBfactorRange){this.bfactor100Lo=2147483647;this.bfactor100Hi=-2147483648;if(null==a)for(var b=0;b<this.ac;b++)this.setBf(b);else for(b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.setBf(b);this.hasBfactorRange=!0}},"JU.BS");c(c$,"setBf",function(a){a=this.at[a].getBfactor100();a<this.bfactor100Lo?this.bfactor100Lo=a:a>this.bfactor100Hi&&
(this.bfactor100Hi=a)},"~N");c(c$,"getBfactor100Lo",function(){this.hasBfactorRange||(this.vwr.g.rangeSelected?this.calcBfactorRange(this.vwr.bsA()):this.calcBfactorRange(null));return this.bfactor100Lo});c(c$,"getBfactor100Hi",function(){this.getBfactor100Lo();return this.bfactor100Hi});c(c$,"getSurfaceDistanceMax",function(){null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistanceMax});c(c$,"calculateVolume",function(a,b){var d=0;if(null!=a)for(var c=a.nextSetBit(0);0<=
c;c=a.nextSetBit(c+1))d+=this.at[c].getVolume(this.vwr,b);return d},"JU.BS,J.c.VDW");c(c$,"getSurfaceDistance100",function(a){if(0==this.nSurfaceAtoms)return-1;null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistance100s[a]},"~N");c(c$,"calcSurfaceDistances",function(){this.calculateSurface(null,-1)});c(c$,"calculateSurface",function(a,b){0>b&&(b=3);var d=J.api.Interface.getOption("geodesic.EnvelopeCalculation",this.vwr,"ms").set(this.vwr,this.ac,null);d.calculate(new J.atomdata.RadiusData(null,
b,J.atomdata.RadiusData.EnumType.ABSOLUTE,null),3.4028235E38,a,JU.BSUtil.copyInvert(a,this.ac),!1,!1,!1,!0);var c=d.getPoints();this.surfaceDistanceMax=0;this.bsSurface=d.getBsSurfaceClone();this.surfaceDistance100s=D(this.ac,0);this.nSurfaceAtoms=JU.BSUtil.cardinalityOf(this.bsSurface);if(0==this.nSurfaceAtoms||null==c||0==c.length)return c;for(var d=3.4028235E38==b?0:b,g=0;g<this.ac;g++)if(this.bsSurface.get(g))this.surfaceDistance100s[g]=0;else{for(var f=3.4028235E38,j=this.at[g],k=c.length;0<=
--k;){var h=Math.abs(c[k].distance(j)-d);0>h&&JU.Logger.debugging&&JU.Logger.debug("draw d"+k+" "+JU.Escape.eP(c[k])+' "'+h+" ? "+j.getInfo()+'"');f=Math.min(h,f)}h=this.surfaceDistance100s[g]=s(Math.floor(100*f));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,h)}return c},"JU.BS,~N");c(c$,"setAtomCoord2",function(a,b,d){var c=null,g=null,f=null,j=0,k=1;if(n(d,JU.P3))c=d;else if(n(d,JU.Lst)){f=d;if(0==(k=f.size()))return;j=1}else if(JU.PT.isAP(d)){g=d;if(0==(k=g.length))return;j=2}else return;
d=0;if(null!=a)for(var h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){switch(j){case 1:if(d>=k)return;c=f.get(d++);break;case 2:if(d>=k)return;c=g[d++]}if(null!=c)switch(b){case 1146095626:this.setAtomCoord(h,c.x,c.y,c.z);break;case 1146095627:this.at[h].setFractionalCoordTo(c,!0);this.taintAtom(h,2);break;case 1146095629:this.at[h].setFractionalCoordTo(c,!1);this.taintAtom(h,2);break;case 1146095631:this.setAtomVibrationVector(h,c)}}},"JU.BS,~N,~O");c(c$,"setAtomVibrationVector",function(a,b){this.setVibrationVector(a,
b);this.taintAtom(a,12)},"~N,JU.T3");c(c$,"setAtomCoord",function(a,b,d,c){if(!(0>a||a>=this.ac)){var g=this.at[a];g.set(b,d,c);this.fixTrajectory(g);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"fixTrajectory",function(a){var b=a.mi;if(this.isTrajectory(b)){var d=null!=this.unitCells&&this.unitCells[b].getCoordinatesAreFractional(),c=this.trajectorySteps.get(b)[a.i-this.am[b].firstAtomIndex];c.set(a.x,a.y,a.z);d&&this.unitCells[b].toFractional(c,!0)}},"JM.Atom");c(c$,"setAtomCoordRelative",function(a,
b,d,c){if(!(0>a||a>=this.ac)){var g=this.at[a];g.add3(b,d,c);this.fixTrajectory(g);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(c$,"setAtomsCoordRelative",function(a,b,d,c){if(null!=a)for(var g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))this.setAtomCoordRelative(g,b,d,c)},"JU.BS,~N,~N,~N");c(c$,"setAPa",function(a,b,d,c,g,f,j){var k=0;if(!(null!=f&&0==f.length||null==a)){for(var h=null!=f&&f.length==this.ac||null!=j&&j.length==this.ac,q=a.nextSetBit(0);0<=q;q=a.nextSetBit(q+1)){h&&(k=q);if(null!=f){if(k>=
f.length)return;c=f[k++];if(Float.isNaN(c))continue;d=B(c)}else if(null!=j){if(k>=j.length)return;g=j[k++]}var p=this.at[q];switch(b){case 1087375362:this.taintAtom(q,0);this.setAtomName(q,g);break;case 1095763969:this.taintAtom(q,13);this.setAtomNumber(q,d);break;case 1095761940:this.taintAtom(q,14);this.setAtomSeqID(q,d);break;case 1087375361:this.taintAtom(q,1);this.setAtomType(q,g);break;case 1112541185:case 1112541205:this.setAtomCoord(q,c,p.y,p.z);break;case 1112541186:case 1112541206:this.setAtomCoord(q,
p.x,c,p.z);break;case 1112541187:case 1112541207:this.setAtomCoord(q,p.x,p.y,c);break;case 1112541202:case 1112541203:case 1112541204:this.setVibrationVector2(q,b,c);break;case 1112541188:case 1112541189:case 1112541190:p.setFractionalCoord(b,c,!0);this.taintAtom(q,2);break;case 1112541191:case 1112541192:case 1112541193:p.setFractionalCoord(b,c,!1);this.taintAtom(q,2);break;case 1095763978:case 1087375365:this.setElement(p,d);break;case 1632634891:p.setFormalCharge(d);this.taintAtom(q,4);break;case 1114638362:this.setHydrophobicity(q,
c)&&this.taintAtom(q,5);break;case 1826248716:case 1288701959:this.vwr.shm.setAtomLabel(g,q);break;case 1129318401:2>c&&0.01<c&&(c*=100);this.setOccupancy(q,c)&&this.taintAtom(q,7);break;case 1112541195:this.setPartialCharge(q,c)&&this.taintAtom(q,8);break;case 1112541194:this.setBondingRadius(q,c)&&this.taintAtom(q,6);break;case 1666189314:case 1113200651:0>c?c=0:16<c&&(c=16.1);p.madAtom=aa(2E3*c);break;case 1114638363:this.vwr.slm.setSelectedAtom(p.i,0!=c);break;case 1112541196:this.setBFactor(q,
c)&&this.taintAtom(q,9);break;case 1095763991:p.setValence(d);this.taintAtom(q,10);break;case 1649412120:p.setRadius(c)?this.taintAtom(q,11):this.untaint(q,11);break;default:JU.Logger.error("unsettable atom property: "+JS.T.nameOf(b))}}switch(b){case 1114638363:this.vwr.slm.setSelectedAtom(-1,!1);break;case 1666189314:case 1113200651:this.vwr.setShapeSize(0,2147483647,a)}}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"setElement",function(a,b){this.taintAtom(a.i,3);a.setAtomicAndIsotopeNumber(b);a.paletteID=
J.c.PAL.CPK.id;a.colixAtom=this.vwr.cm.getColixAtomPalette(a,J.c.PAL.CPK.id)},"JM.Atom,~N");c(c$,"getVibrationCoord",function(a,b){var d=this.getVibration(a,!1);if(null==d)return NaN;switch(b){case "X":return d.x;case "Y":return d.y;default:return d.z}},"~N,~S");c(c$,"getModulationCoord",function(a,b){var d=this.getModulation(a);if(null!=d){var c=d.getVibration(!1);null==c&&(c=d);switch(b){case "X":return c.x;case "Y":return c.y;case "Z":return c.z;case "O":return d.getModulation("O",null).floatValue();
case "1":case "2":case "3":return d=d.getModulation("T",null),d="1"==b?d.x:"2"==b?d.y:d.z,d-Math.floor(d)}}return NaN},"~N,~S");c(c$,"getVibration",function(a,b){var d=null==this.vibrations?null:this.vibrations[a];return n(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);n(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$,"setVibrationVector2",function(a,b,d){var c=this.getVibration(a,!0);if(null!=c){switch(b){case 1112541202:c.x=d;break;case 1112541203:c.y=d;break;case 1112541204:c.z=d}this.setAtomVibrationVector(a,c)}},"~N,~N,~N");
c(c$,"setAtomName",function(a,b){var d=this.am[this.at[a].mi].isBioModel?this.vwr.getJBR().lookupSpecialAtomID(b):0;this.at[a].atomID=d;0<d||(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[a]=b)},"~N,~S");c(c$,"setAtomType",function(a,b){null==this.atomTypes&&(this.atomTypes=Array(this.at.length));this.atomTypes[a]=b},"~N,~S");c(c$,"setAtomNumber",function(a,b){null==this.atomSerials&&(this.atomSerials=D(this.at.length,0));this.atomSerials[a]=b;return!0},"~N,~N");c(c$,
"setAtomSeqID",function(a,b){null==this.atomSeqIDs&&(this.atomSeqIDs=D(this.at.length,0));this.atomSeqIDs[a]=b;return!0},"~N,~N");c(c$,"setOccupancy",function(a,b){if(null==this.occupancies){if(100==b)return!1;this.occupancies=L(this.at.length,0);for(var d=this.at.length;0<=--d;)this.occupancies[d]=100}this.occupancies[a]=b;return!0},"~N,~N");c(c$,"setPartialCharge",function(a,b){if(Float.isNaN(b))return!1;if(null==this.partialCharges){if(0==b)return!1;this.partialCharges=L(this.at.length,0)}this.partialCharges[a]=
b;return!0},"~N,~N");c(c$,"setBondingRadius",function(a,b){if(Float.isNaN(b))return!1;null==this.bondingRadii&&(this.bondingRadii=L(this.at.length,0));this.bondingRadii[a]=b;return!0},"~N,~N");c(c$,"setBFactor",function(a,b){if(Float.isNaN(b))return!1;if(null==this.bfactor100s){if(0==b&&null==this.bfactor100s)return!1;this.bfactor100s=V(this.at.length,0)}this.bfactor100s[a]=na(100*(-327.68>b?-327.68:327.67<b?327.67:b)+(0>b?-0.5:0.5));return!0},"~N,~N");c(c$,"setHydrophobicity",function(a,b){if(Float.isNaN(b))return!1;
if(null==this.hydrophobicities){this.hydrophobicities=L(this.at.length,0);for(var d=0;d<this.at.length;d++)this.hydrophobicities[d]=JU.Elements.getHydrophobicity(this.at[d].getGroupID())}this.hydrophobicities[a]=b;return!0},"~N,~N");c(c$,"setAtomData",function(a,b,d,c){var g=null,f=null;switch(a){case 2:this.loadCoordinates(d,!1,!c);return;case 12:this.loadCoordinates(d,!0,!0);return;case 15:g=L(this.ac,0),f=JU.BS.newN(this.ac)}c=JU.Parser.markLines(d,";");var j=0;try{for(var k=JU.PT.parseInt(d.substring(0,
c[0]-1)),h=1;h<=k;h++){var q=JU.PT.getTokens(JU.PT.parseTrimmed(d.substring(c[h],c[h+1]-1))),p=JU.PT.parseInt(q[0])-1;if(!(0>p||p>=this.ac)){var v=this.at[p];j++;var m=q.length-1,A=JU.PT.parseFloat(q[m]);switch(a){case 15:g[p]=A;f.set(p);continue;case 13:this.setAtomNumber(p,B(A));break;case 14:this.setAtomSeqID(p,B(A));break;case 0:this.setAtomName(p,q[m]);break;case 1:this.setAtomType(p,q[m]);break;case 3:v.setAtomicAndIsotopeNumber(B(A));v.paletteID=J.c.PAL.CPK.id;v.colixAtom=this.vwr.cm.getColixAtomPalette(v,
J.c.PAL.CPK.id);break;case 4:v.setFormalCharge(B(A));break;case 5:this.setHydrophobicity(p,A);break;case 6:this.setBondingRadius(p,A);break;case 8:this.setPartialCharge(p,A);break;case 9:this.setBFactor(p,A);break;case 10:v.setValence(B(A));break;case 11:v.setRadius(A)}this.taintAtom(p,a)}}15==a&&0<j&&this.vwr.setData(b,[b,g,f,Integer.$valueOf(1)],0,0,0,0,0)}catch(n){if(y(n,Exception))JU.Logger.error("AtomCollection.loadData error: "+n);else throw n;}},"~N,~S,~S,~B");c(c$,"loadCoordinates",function(a,
b,d){var c=JU.Parser.markLines(a,";"),g=b?new JU.V3:null;try{for(var f=JU.PT.parseInt(a.substring(0,c[0]-1)),j=1;j<=f;j++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[j],c[j+1]))),h=JU.PT.parseInt(k[0])-1,q=JU.PT.parseFloat(k[3]),p=JU.PT.parseFloat(k[4]),v=JU.PT.parseFloat(k[5]);b?(g.set(q,p,v),this.setAtomVibrationVector(h,g)):(this.setAtomCoord(h,q,p,v),d||this.untaint(h,2))}}catch(m){if(y(m,Exception))JU.Logger.error("Frame.loadCoordinate error: "+m);else throw m;}},"~S,~B,~B");c(c$,
"validateBspf",function(a){null!=this.bspf&&(this.bspf.isValid=a);this.averageAtomPoint=null},"~B");c(c$,"validateBspfForModel",function(a,b){null!=this.bspf&&this.bspf.validateModel(a,b)},"~N,~B");c(c$,"setPreserveState",function(a){this.preserveState=a},"~B");c$.getUserSettableType=c(c$,"getUserSettableType",function(a){var b=0==a.indexOf("property_");a=b?a.substring(9):a;for(var d=0;15>d;d++)if(JM.AtomCollection.userSettableValues[d].equalsIgnoreCase(a))return d;return b?15:-1},"~S");c(c$,"getTaintedAtoms",
function(a){return null==this.tainted?null:this.tainted[a]},"~N");c(c$,"taintAtoms",function(a,b){this.canSkipLoad=!1;if(this.preserveState)for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.taintAtom(d,b)},"JU.BS,~N");c(c$,"taintAtom",function(a,b){this.preserveState&&(null==this.tainted&&(this.tainted=Array(15)),null==this.tainted[b]&&(this.tainted[b]=JU.BS.newN(this.ac)),this.tainted[b].set(a),2==b&&this.validateBspfForModel(this.am[this.at[a].mi].trajectoryBaseIndex,!1))},"~N,~N");c(c$,"untaint",
function(a,b){this.preserveState&&(null==this.tainted||null==this.tainted[b]||this.tainted[b].clear(a))},"~N,~N");c(c$,"setTaintedAtoms",function(a,b){this.preserveState&&(null==a?null!=this.tainted&&(this.tainted[b]=null):(null==this.tainted&&(this.tainted=Array(15)),null==this.tainted[b]&&(this.tainted[b]=JU.BS.newN(this.ac)),JU.BSUtil.copy2(a,this.tainted[b])))},"JU.BS,~N");c(c$,"unTaintAtoms",function(a,b){if(!(null==this.tainted||null==this.tainted[b])){for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+
1))this.tainted[b].clear(d);0>this.tainted[b].nextSetBit(0)&&(this.tainted[b]=null)}},"JU.BS,~N");c(c$,"findNearest2",function(a,b,d,c,g){for(var f=null,j=this.ac;0<=--j;)if(!(null!=c&&c.get(j))){var k=this.at[j];k.isClickable()&&this.isCursorOnTopOf(k,a,b,g,f)&&(f=k)}d[0]=f},"~N,~N,~A,JU.BS,~N");c(c$,"isCursorOnTopOf",function(a,b,d,c,g){return 1<a.sZ&&!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(b,d,c,g)},"JM.Atom,~N,~N,~N,JM.Atom");c(c$,"fillADa",function(a,
b){a.atomXyz=this.at;a.ac=this.ac;a.atomicNumber=D(this.ac,0);var d=0!=(b&2);d&&(a.atomRadius=L(this.ac,0));for(var c=0!=(b&16),g=0;g<this.ac;g++){var f=this.at[g];f.isDeleted()||!c&&0<=a.modelIndex&&f.mi!=a.firstModelIndex?(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(g)):(a.atomicNumber[g]=f.getElementNumber(),a.lastModelIndex=f.mi,d&&(a.atomRadius[g]=this.getWorkingRadius(f,a)))}},"J.atomdata.AtomData,~N");c(c$,"getWorkingRadius",function(a,b){var d=0,c=b.radiusData;switch(c.factorType){case J.atomdata.RadiusData.EnumType.ABSOLUTE:d=
c.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:case J.atomdata.RadiusData.EnumType.OFFSET:switch(c.vdwType){case J.c.VDW.BONDING:d=a.getBondingRadius();break;case J.c.VDW.ADPMAX:d=a.getADPMinMax(!0);break;case J.c.VDW.ADPMIN:d=a.getADPMinMax(!1);break;default:d=a.getVanderwaalsRadiusFloat(this.vwr,b.radiusData.vdwType)}d=c.factorType===J.atomdata.RadiusData.EnumType.FACTOR?d*c.value:d+c.value}return d+c.valueExtended},"JM.Atom,J.atomdata.AtomData");c(c$,"calculateHydrogens",function(a,b,
d,c,g){var f=new JU.V3,j=new JU.V3,k=Array(this.ac),h=this.vwr.slm.bsDeleted,q,p=0;if(null!=a)for(var v=a.nextSetBit(0);0<=v;v=a.nextSetBit(v+1))if(!(null!=h&&h.get(v))){var m=this.at[v],A=m.getElementNumber();if(!(c&&6!=A)){var n=6>=A?1.1:10>=A?1:1.3;switch(A){case 7:case 8:n=1}if(!(d&&0<m.getCovalentHydrogenCount())&&(q=this.getImplicitHydrogenCount(m,!1),0!=q)){var s=this.aaRet[0],r=this.aaRet[2],u=this.aaRet[3];k[v]=Array(q);var t=0;if(0==u)switch(q){case 4:f.set(0.635,0.635,0.635),q=JU.P3.newP(f),
q.add(m),k[v][t++]=q,null!=g&&g.addLast(m);case 3:f.set(-0.635,-0.635,0.635),q=JU.P3.newP(f),q.add(m),k[v][t++]=q,null!=g&&g.addLast(m);case 2:f.set(-0.635,0.635,-0.635),q=JU.P3.newP(f),q.add(m),k[v][t++]=q,null!=g&&g.addLast(m);case 1:f.set(0.635,-0.635,-0.635),q=JU.P3.newP(f),q.add(m),k[v][t++]=q,null!=g&&g.addLast(m)}else switch(q){case 3:this.getHybridizationAndAxes(v,A,f,j,"sp3b",!1,!0);q=new JU.P3;q.scaleAdd2(n,f,m);k[v][t++]=q;null!=g&&g.addLast(m);this.getHybridizationAndAxes(v,A,f,j,"sp3c",
!1,!0);q=new JU.P3;q.scaleAdd2(n,f,m);k[v][t++]=q;null!=g&&g.addLast(m);this.getHybridizationAndAxes(v,A,f,j,"sp3d",!1,!0);q=new JU.P3;q.scaleAdd2(n,f,m);k[v][t++]=q;null!=g&&g.addLast(m);break;case 2:r=2==r||5==A||1==u&&4==s||7==A&&this.isAdjacentSp2(m);this.getHybridizationAndAxes(v,A,f,j,r?"sp2b":3==s?"sp3c":"lpa",!1,!0);q=JU.P3.newP(f);q.scaleAdd2(n,f,m);k[v][t++]=q;null!=g&&g.addLast(m);this.getHybridizationAndAxes(v,A,f,j,r?"sp2c":3==s?"sp3d":"lpb",!1,!0);q=JU.P3.newP(f);q.scaleAdd2(n,f,m);
k[v][t++]=q;null!=g&&g.addLast(m);break;case 1:switch(s-u){case 1:if(8==A&&m===m.group.getCarbonylOxygenAtom()){k[v]=null;continue}null!=this.getHybridizationAndAxes(v,A,f,j,2==r||5==A||7==A&&this.isAdjacentSp2(m)?"sp2c":"sp3d",!0,!1)?(q=JU.P3.newP(f),q.scaleAdd2(n,f,m),k[v][t++]=q,null!=g&&g.addLast(m)):k[v]=[];break;case 2:this.getHybridizationAndAxes(v,A,f,j,4==s?"sp2c":"sp2b",!1,!1);q=JU.P3.newP(f);q.scaleAdd2(n,f,m);k[v][t++]=q;null!=g&&g.addLast(m);break;case 3:this.getHybridizationAndAxes(v,
A,f,j,"spb",!1,!0),q=JU.P3.newP(f),q.scaleAdd2(n,f,m),k[v][t++]=q,null!=g&&g.addLast(m)}}p+=t}}}b[0]=p;return k},"JU.BS,~A,~B,~B,JU.Lst");c(c$,"isAdjacentSp2",function(a){for(var b=a.bonds,d=0;d<b.length;d++)for(var c=b[d].getOtherAtom(a).bonds,g=0;g<c.length;g++)switch(c[g].order){case 515:case 514:case 2:case 3:return!0}return!1},"JM.Atom");c(c$,"getImplicitHydrogenCount",function(a,b){var d=a.getTargetValence();if(0>d)return 0;var c=a.getFormalCharge();null==this.aaRet&&(this.aaRet=D(4,0));this.aaRet[0]=
d;this.aaRet[1]=c;this.aaRet[2]=0;this.aaRet[3]=a.getCovalentBondCount();var g=this.am[a.mi],g=g.isBioModel&&!g.isPdbWithMultipleBonds?a.group.getGroup3():null;null!=g&&0==c&&this.vwr.getJBR().getAminoAcidValenceAndCharge(g,a.getAtomName(),this.aaRet)&&(d=this.aaRet[0],c=this.aaRet[1]);0!=c&&(d+=4==d?-Math.abs(c):c,this.aaRet[0]=d);d-=a.getValence();return 0>d&&!b?0:d},"JM.Atom,~B");c(c$,"fixFormalCharges",function(a){for(var b=0,d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1)){var c=this.at[d],g=this.getImplicitHydrogenCount(c,
!0);if(0!=g){var f=c.getFormalCharge(),g=f-g;c.setFormalCharge(g);this.taintAtom(d,4);JU.Logger.debugging&&JU.Logger.debug("atom "+c+" formal charge "+f+" -> "+g);b++}}return b},"JU.BS");c(c$,"getHybridizationAndAxes",function(a,b,d,c,g,f,j){var k=0<g.length&&"-"==g.charAt(0)?g.substring(1):g;if(0<=g.indexOf("d")&&!g.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,d,c,k);g=this.at[a];0==b&&(b=g.getElementNumber());var h=this.getAttached(g,4,f),q=h.length,p=k.charCodeAt(k.length-1)-97;if(0>
p||6<p)p=0;d.set(0,0,0);c.set(0,0,0);for(var v=Array(4),m=0;m<q;m++)v[m]=JU.V3.newVsub(g,h[m]),v[m].normalize(),d.add(v[m]);0<q&&c.setT(v[0]);m=!1;a=new JU.V3;if(3<=q){2.984513>c.angle(v[1])?a.cross(c,v[1]):a.cross(c,v[2]);a.normalize();var A=new JU.V3;2.984513>v[1].angle(v[2])?A.cross(v[1],v[2]):A.cross(c,v[2]);A.normalize();m=0.95<=Math.abs(A.dot(a))}var n=0==k.indexOf("sp3"),s=!n&&0==k.indexOf("sp2"),r=!n&&!s&&0==k.indexOf("sp"),t=0==k.indexOf("p"),u=0==k.indexOf("lp"),A=null;if(f){if(0==q)return null;
if(n){if(3<p||4<q)return null}else if(s){if(2<p||3<q)return null}else if(r&&(1<p||2<q))return null;switch(q){case 1:if(1==b&&!n)return null;if(n){A="sp3";break}switch(h[0].getCovalentBondCount()){case 1:if(2!=h[0].getValence()){A="sp";break}case 2:A=r?"sp":"sp2";break;case 3:if(!s&&!t)return null;A="sp2"}break;case 2:if(0.1>d.length()){if(0<=k.indexOf("2")||0<=k.indexOf("3"))return null;A="sp";break}A=n?"sp3":"sp2";if(0==k.indexOf("sp"))break;if(u){A="lp";break}A=k;break;default:if(m)A="sp2";else{if(u&&
3==q){A="lp";break}A="sp3"}}if(null==A)return null;if(0==k.indexOf("p")){if("sp3"===A)return null}else if(0>k.indexOf(A))return null}if(p<q&&!k.startsWith("p")&&!k.startsWith("l"))return d.sub2(h[p],g),d.normalize(),A;switch(q){case 0:k.equals("sp3c")||k.equals("sp2d")||k.equals("lpa")?d.set(-0.5,-0.7,1):k.equals("sp3b")||k.equals("lpb")?d.set(0.5,-0.7,-1):k.equals("sp3a")?d.set(0,1,0):d.set(0,0,1);c.set(1,0,0);break;case 1:a.setT(JM.AtomCollection.vRef);c.cross(a,d);if(n){for(m=0;m<h[0].bonds.length;m++)if(h[0].bonds[m].isCovalent()&&
h[0].getBondedAtomIndex(m)!=g.i&&(c.sub2(h[0],h[0].bonds[m].getOtherAtom(h[0])),c.cross(d,c),0!=c.length())){c.cross(c,d);break}c.normalize();Float.isNaN(c.x)&&(c.setT(JM.AtomCollection.vRef),c.cross(c,d));a.cross(d,c);a.normalize();d.normalize();c.scaleAdd2(2.828,c,d);3!=p&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(d.x,d.y,d.z,2.09439507*(2==p?1:-1))).rotate(c));d.setT(c);c.cross(a,d);break}a.cross(c,d);switch(h[0].getCovalentBondCount()){case 1:if(2!=h[0].getValence())break;case 2:j=h[0];c.setT(d);
for(a.setT(JM.AtomCollection.vRef);null!=j&&2==j.getCovalentBondCount();){k=j.bonds;b=null;for(m=0;m<k.length;m++)if(k[m].isCovalent()&&(b=k[m].getOtherAtom(j),b!==g)){a.sub2(b,j);break}a.cross(a,c);if(0.1<a.length()||2!=b.getCovalentBondCount())break;g=j;j=b}0.1<a.length()?(d.cross(a,c),d.normalize(),1==p&&d.scale(-1),d.scale(JM.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,c,d),t&&(a.cross(d,c),d.setT(a),a.setT(c)),c.cross(a,d)):(d.setT(c),c.cross(JM.AtomCollection.vRef,c));break;case 3:this.getHybridizationAndAxes(h[0].i,
0,c,a,"pz",!1,j),a.setT(c),s?(c.cross(c,d),1==p&&c.scale(-1),c.scale(JM.AtomCollection.sqrt3_2),d.scaleAdd2(0.5,d,c)):(a.setT(d),d.setT(c)),c.cross(a,d)}break;case 2:if(0.1>d.length()){if(!k.equals("pz")){b=h[0];(g=3==b.getCovalentBondCount())||(g=3==(b=h[1]).getCovalentBondCount());if(g){this.getHybridizationAndAxes(b.i,0,c,d,"pz",!1,j);k.equals("px")&&c.scale(-1);d.setT(v[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(n||u){a.normalize();d.normalize();k.equals("lp")||(0==p||2==p?d.scaleAdd2(-1.2,a,d):d.scaleAdd2(1.2,a,d));c.cross(d,a);break}c.cross(d,a);d.setT(a);0>d.z&&(d.scale(-1),c.scale(-1));break;default:if(n)break;if(!m){c.cross(d,c);break}d.setT(a);0>d.z&&j&&(d.scale(-1),c.scale(-1))}c.normalize();d.normalize();return A},"~N,~N,JU.V3,JU.V3,~S,~B,~B");c(c$,"getHybridizationAndAxesD",function(a,b,d,c){c.startsWith("sp3d2")&&(c="d2sp3"+(5==c.length?"a":c.substring(5)));c.startsWith("sp3d")&&(c=
"dsp3"+(4==c.length?"a":c.substring(4)));if(c.equals("d2sp3")||c.equals("dsp3"))c+="a";var g=c.startsWith("dsp3"),f=c.charCodeAt(c.length-1)-97;if(null!=b&&(!g&&(5<f||!c.startsWith("d2sp3"))||g&&4<f))return null;a=this.at[a];c=this.getAttached(a,6,!0);if(null==c)return null==b?null:"?";var j=c.length;if(3>j&&null!=b)return null;for(var k=f>=j,h=s(j*(j-1)/2),q=JU.AU.newInt2(h),p=D(3,0),h=D(3,h,0),v=0,m=0,A=0;A<j-1;A++)for(var n=A+1;n<j;n++){var r=JU.Measure.computeAngleABC(c[A],a,c[n],!0),r=105>r?
0:150<=r?2:1;h[r][p[r]]=v;p[r]++;q[v++]=[A,n];0==A&&1==r&&m++}v=100*p[0]+10*p[1]+p[2];if(null==b)switch(v){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==m%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(v){default:return null;case 201:break;case 210:case 330:case 411:case 631:if(!g)return null;break;case 300:case 402:case 501:case 802:case 1203:if(g)return null}if(k)if(g)switch(p[1]){case 0:b.sub2(c[q[h[0][0]][0]],a);d.sub2(c[q[h[0][0]][1]],a);b.cross(b,d);b.normalize();4==f&&b.scale(-1);p=this.findNotAttached(j,q,h[2],p[2]);A=p.nextSetBit(0);d.sub2(c[A],
a);d.normalize();d.scale(0.5);b.scaleAdd2(JM.AtomCollection.sqrt3_2,b,d);f=-1;break;case 1:4==f?(d=q[h[1][0]],b.add2(c[d[0]],c[d[1]]),b.scaleAdd2(-2,a,b),f=-1):(p=this.findNotAttached(j,q,h[1],p[1]),f=p.nextSetBit(0));break;default:p=this.findNotAttached(j,q,h[1],p[1]),f=p.nextSetBit(0)}else{v=!1;if(4==j)switch(p[2]){case 1:p=this.findNotAttached(j,q,h[2],p[2]);A=p.nextSetBit(0);f=4==f?A:p.nextSetBit(A+1);break;default:v=!0}else{p=this.findNotAttached(j,q,h[2],p[2]);A=p.nextSetBit(0);for(n=j;n<f&&
0<=A;n++)A=p.nextSetBit(A+1);-1==A?v=!0:f=A}v&&(b.sub2(c[q[h[0][0]][0]],a),d.sub2(c[q[h[0][0]][1]],a),b.cross(b,d),4==f&&b.scale(-1),f=-1)}0<=f&&b.sub2(c[f],a);k&&b.scale(-1);b.normalize();return g?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(c$,"getAttached",function(a,b,d){var c=a.getCovalentBondCount();if(c>b)return null;b=Array(c);if(0<c){for(var c=a.bonds,g=0,f=0;f<c.length;f++)c[f].isCovalent()&&(b[g++]=c[f].getOtherAtom(a));d&&java.util.Arrays.sort(b,S(JM.AtomCollection.AtomSorter,this,null))}return b},
"JM.Atom,~N,~B");c(c$,"findNotAttached",function(a,b,d,c){var g=JU.BS.newN(a);g.setBits(0,a);for(var f=0;f<a;f++)for(var j=0;j<c;j++){var k=b[d[j]];(k[0]==f||k[1]==f)&&g.clear(f)}return g},"~N,~A,~A,~N");c(c$,"getAtomBitsMDa",function(a,b){var d=new JU.BS,c,g;c=n(b,Integer)?b.intValue():0;var f=0;switch(a){case 1613758488:return this.getWaterAtoms(d);case 1095761939:for(f=this.ac;0<=--f;)this.at[f].getResno()==c&&d.set(f);break;case 1297090050:for(f=this.ac;0<=--f;)this.at[f].getSymOp()==c&&d.set(f);
break;case 1095763969:for(f=this.ac;0<=--f;)this.at[f].getAtomNumber()==c&&d.set(f);break;case 1087375362:c=","+b+",";for(f=this.ac;0<=--f;)g=this.at[f].getAtomName(),0<=c.indexOf(g)&&0<=c.indexOf(","+g+",")&&d.set(f);break;case 1087375361:c=","+b+",";for(f=this.ac;0<=--f;)g=this.at[f].getAtomType(),0<=c.indexOf(g)&&0<=c.indexOf(","+g+",")&&d.set(f);break;case 1048613:for(f=this.ac;0<=--f;)this.at[f].getGroupID()==c&&d.set(f);break;case 1048609:return JU.BSUtil.copy(this.getChainBits(c));case 1048614:return JU.BSUtil.copy(this.getSeqcodeBits(c,
!0));case 1613758470:for(f=this.ac;0<=--f;)this.at[f].isHetero()&&d.set(f);break;case 1613758476:for(f=this.ac;0<=--f;)1==this.at[f].getElementNumber()&&d.set(f);break;case 3145741:for(f=this.ac;0<=--f;)this.at[f].isLeadAtom()&&d.set(f);break;case 3145744:for(f=this.ac;0<=--f;)this.at[f].isProtein()&&d.set(f);break;case 3145764:for(f=this.ac;0<=--f;)this.at[f].isCarbohydrate()&&d.set(f);break;case 137363467:case 3145760:g=137363467==a?J.c.STR.HELIX:J.c.STR.SHEET;for(f=this.ac;0<=--f;)this.at[f].isWithinStructure(g)&&
d.set(f);break;case 3145742:for(f=this.ac;0<=--f;)this.at[f].isNucleic()&&d.set(f);break;case 3145732:for(f=this.ac;0<=--f;)this.at[f].isDna()&&d.set(f);break;case 3145750:for(f=this.ac;0<=--f;)this.at[f].isRna()&&d.set(f);break;case 3145746:for(f=this.ac;0<=--f;)this.at[f].isPurine()&&d.set(f);break;case 3145748:for(f=this.ac;0<=--f;)this.at[f].isPyrimidine()&&d.set(f);break;case 1087375365:c=b;g=new JU.BS;for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))g.set(this.at[f].getElementNumber());for(f=
this.ac;0<=--f;)g.get(this.at[f].getElementNumber())&&d.set(f);break;case 1095761941:c=b;g=new JU.BS;for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))g.set(this.at[f].atomSite);for(f=this.ac;0<=--f;)g.get(this.at[f].atomSite)&&d.set(f);break;case 1073741824:return this.getIdentifierOrNull(b);case 1048608:c=b.toUpperCase();0<=c.indexOf("\\?")&&(c=JU.PT.rep(c,"\\?","\u0001"));(g=c.startsWith("?*"))&&(c=c.substring(1));for(f=this.ac;0<=--f;)this.isAtomNameMatch(this.at[f],c,g,g)&&d.set(f);break;case 1048607:for(f=
this.ac;0<=--f;)this.at[f].isAltLoc(b)&&d.set(f);break;case 1048612:return this.getSpecName(b)}if(0>f)return d;c=b;var j;g=c.nextSetBit(0);if(0>g)return d;f=0;switch(a){case 1087373318:for(f=g;0<=f;f=c.nextSetBit(f+1))g=this.at[f].group.selectAtoms(d),g>f&&(f=g);break;case 1095766030:for(f=g;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.at[f].mi;d.set(f);for(g=f;0<=--g;)if(this.at[g].mi==j)d.set(g);else break;for(;++f<this.ac;)if(this.at[f].mi==j)d.set(f);else break}break;case 1087373316:c=JU.BSUtil.copy(b);
for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))this.at[f].getChain().setAtomBitSet(d),c.andNot(d);break;case 1095761937:for(f=g;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.at[f].getPolymerIndexInModel();d.set(f);for(g=f;0<=--g;)if(this.at[g].getPolymerIndexInModel()==j)d.set(g);else break;for(;++f<this.ac;)if(this.at[f].getPolymerIndexInModel()==j)d.set(f);else break}break;case 1641025539:for(f=g;0<=f;f=c.nextSetBit(f+1))if(!d.get(f)){j=this.at[f].group.getStructure();d.set(f);for(g=f;0<=--g;)if(this.at[g].group.getStructure()===
j)d.set(g);else break;for(;++f<this.ac;)if(this.at[f].group.getStructure()===j)d.set(f);else break}}0==f&&JU.Logger.error("MISSING getAtomBits entry for "+JS.T.nameOf(a));return d},"~N,~O");c(c$,"getWaterAtoms",function(a){for(var b=D(2,0),d,c=this.ac;0<=--c;){var g=this.at[c].getGroupID();if(42<=g&&45>g)a.set(c);else if(8==(d=this.at[c]).getElementNumber()&&2==d.getCovalentBondCount()){for(var g=d.bonds,f=0,j,k=g.length;0<=--k&&3>f;)if(g[k].isCovalent()&&1==(j=g[k].getOtherAtom(d)).getElementNumber())b[f++%
2]=j.i;2==f&&(a.set(b[1]),a.set(b[0]),a.set(c))}}return a},"JU.BS");c(c$,"getIdentifierOrNull",function(a){var b=this.getSpecNameOrNull(a,!1);0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));if(null!=b||0<a.indexOf("?"))return b;if(0<a.indexOf("*"))return this.getSpecNameOrNull(a,!0);for(var d=a.length,c=0;c<d&&JU.PT.isLetter(a.charAt(c));)++c;b=this.getSpecNameOrNull(a.substring(0,c),!1);if(c==d)return b;null==b&&(b=new JU.BS);for(var g=c;c<d&&JU.PT.isDigit(a.charAt(c));)++c;var f=0;try{f=Integer.parseInt(a.substring(g,
c))}catch(j){if(y(j,NumberFormatException))return null;throw j;}g=" ";c<d&&"^"==a.charAt(c)&&++c<d&&(g=a.charAt(c));f=JM.Group.getSeqcodeFor(f,g);f=this.getSeqcodeBits(f,!1);if(null==f){" "!=g&&(f=this.getSeqcodeBits(Character.toUpperCase(a.charAt(c)).charCodeAt(0),!1));if(null==f)return null;c++}b.and(f);if(c>=d)return b;if(c!=d-1)return null;b.and(this.getChainBits(a.charCodeAt(c)));return b},"~S");c(c$,"getSpecName",function(a){var b=this.getSpecNameOrNull(a,!1);if(null!=b)return b;0<a.indexOf("*")&&
(b=this.getSpecNameOrNull(a,!0));return null==b?new JU.BS:b},"~S");c(c$,"getSpecNameOrNull",function(a,b){var d=null;a=a.toUpperCase();0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));var c=a.startsWith("?*");c&&(a=a.substring(1));for(var g=this.ac;0<=--g;){var f=this.at[g].getGroup3(!0);if(null!=f&&0<f.length){if(JU.PT.isMatch(f,a,b,!0)){null==d&&(d=JU.BS.newN(g+1));for(d.set(g);0<=--g&&this.at[g].getGroup3(!0).equals(f);)d.set(g);g++}}else this.isAtomNameMatch(this.at[g],a,b,c)&&(null==d&&(d=
JU.BS.newN(g+1)),d.set(g))}return d},"~S,~B");c(c$,"isAtomNameMatch",function(a,b,d,c){return JU.PT.isMatch(a.getAtomName().toUpperCase(),b,d,c)},"JM.Atom,~S,~B,~B");c(c$,"getSeqcodeBits",function(a,b){var d=new JU.BS,c=JM.Group.getSeqNumberFor(a),g=2147483647!=c,f=!0,j=JM.Group.getInsertionCodeChar(a);switch(j){case "?":for(var k=this.ac;0<=--k;){var h=this.at[k].getSeqcode();if(!g||c==JM.Group.getSeqNumberFor(h)&&0!=JM.Group.getInsertionCodeFor(h))d.set(k),f=!1}break;default:for(k=this.ac;0<=--k;)if(h=
this.at[k].getSeqcode(),a==h||!g&&a==JM.Group.getInsertionCodeFor(h)||"*"==j&&c==JM.Group.getSeqNumberFor(h))d.set(k),f=!1}return!f||b?d:null},"~N,~B");c(c$,"getChainBits",function(a){var b=this.vwr.getBoolean(603979823);0<=a&&(300>a&&!b)&&(a=JM.AtomCollection.chainToUpper(a));for(var d=new JU.BS,c=JU.BS.newN(this.ac),g,f=c.nextClearBit(0);f<this.ac;f=c.nextClearBit(f+1)){var j=this.at[f].getChain();a==(g=j.chainID)||!b&&0<=g&&300>g&&a==JM.AtomCollection.chainToUpper(g)?(j.setAtomBitSet(d),c.or(d)):
j.setAtomBitSet(c)}return d},"~N");c$.chainToUpper=c(c$,"chainToUpper",function(a){return 97<=a&&122>=a?a-32:256<=a&&300>a?a-191:a},"~N");c(c$,"getAtomIndices",function(a){for(var b=0,d=D(this.ac,0),c=a.nextSetBit(0);0<=c&&c<this.ac;c=a.nextSetBit(c+1))d[c]=++b;return d},"JU.BS");c(c$,"getAtomsNearPlane",function(a,b){for(var d=new JU.BS,c=this.ac;0<=--c;){var g=this.at[c],f=JU.Measure.distanceToPlane(b,g);(0<a&&-0.1<=f&&f<=a||0>a&&0.1>=f&&f>=a||0==a&&0.01>Math.abs(f))&&d.set(g.i)}return d},"~N,JU.P4");
c(c$,"getAtomsNearPts",function(a,b,d){var c=new JU.BS;if(0==b.length||null!=d&&0==d.cardinality())return c;null==d&&(d=JU.BSUtil.setAll(b.length));for(var g=this.ac;0<=--g;)for(var f=this.at[g],j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))if(f.distance(b[j])<a){c.set(g);break}return c},"~N,~A,JU.BS");c(c$,"clearVisibleSets",function(){this.haveBSClickable=this.haveBSVisible=!1});c(c$,"getRenderable",function(a){this.clearVisibleSets();a.clearAll();for(var b=this.ac;0<=--b;)this.at[b].isVisible(1)&&
a.set(b)},"JU.BS");c(c$,"getVisibleSet",function(a){if(a)this.vwr.setModelVisibility();else if(this.haveBSVisible)return this.bsVisible;this.bsVisible.clearAll();for(a=this.ac;0<=--a;)this.at[a].checkVisible()&&this.bsVisible.set(a);this.haveBSVisible=!0;return this.bsVisible},"~B");c(c$,"getClickableSet",function(a){if(a)this.vwr.setModelVisibility();else if(this.haveBSClickable)return this.bsClickable;this.bsClickable.clearAll();for(a=this.ac;0<=--a;)this.at[a].isClickable()&&this.bsClickable.set(a);
this.haveBSClickable=!0;return this.bsClickable},"~B");c(c$,"isModulated",function(a){return null!=this.bsModulated&&this.bsModulated.get(a)},"~N");c(c$,"deleteModelAtoms",function(a,b,d){this.at=JU.AU.deleteElements(this.at,a,b);this.ac=this.at.length;for(var c=a;c<this.ac;c++)this.at[c].i=c,this.at[c].mi--;null!=this.bsModulated&&JU.BSUtil.deleteBits(this.bsModulated,d);this.deleteAtomTensors(d);this.atomNames=JU.AU.deleteElements(this.atomNames,a,b);this.atomTypes=JU.AU.deleteElements(this.atomTypes,
a,b);this.atomSerials=JU.AU.deleteElements(this.atomSerials,a,b);this.atomSeqIDs=JU.AU.deleteElements(this.atomSeqIDs,a,b);this.bfactor100s=JU.AU.deleteElements(this.bfactor100s,a,b);this.hasBfactorRange=!1;this.occupancies=JU.AU.deleteElements(this.occupancies,a,b);this.partialCharges=JU.AU.deleteElements(this.partialCharges,a,b);this.atomTensorList=JU.AU.deleteElements(this.atomTensorList,a,b);this.vibrations=JU.AU.deleteElements(this.vibrations,a,b);this.nSurfaceAtoms=0;this.surfaceDistance100s=
this.bsSurface=null;if(null!=this.tainted)for(a=0;15>a;a++)JU.BSUtil.deleteBits(this.tainted[a],d)},"~N,~N,JU.BS");c(c$,"getAtomIdentityInfo",function(a,b,d){b.put("_ipt",Integer.$valueOf(a));b.put("atomIndex",Integer.$valueOf(a));b.put("atomno",Integer.$valueOf(this.at[a].getAtomNumber()));b.put("info",this.getAtomInfo(a,null,d));b.put("sym",this.at[a].getElementSymbol())},"~N,java.util.Map,JU.P3");c(c$,"getAtomTensorList",function(a){return 0>a||null==this.atomTensorList||a>=this.atomTensorList.length?
null:this.atomTensorList[a]},"~N");c(c$,"deleteAtomTensors",function(a){if(null!=this.atomTensors){for(var b=new JU.Lst,d,c=this.atomTensors.keySet().iterator();c.hasNext()&&((d=c.next())||1);){for(var g=this.atomTensors.get(d),f=g.size();0<=--f;){var j=g.get(f);(a.get(j.atomIndex1)||0<=j.atomIndex2&&a.get(j.atomIndex2))&&g.remove(f)}0==g.size()&&b.addLast(d)}for(f=b.size();0<=--f;)this.atomTensors.remove(b.get(f))}},"JU.BS");c(c$,"setAtomTensors",function(a,b){if(!(null==b||0==b.size())){null==this.atomTensors&&
(this.atomTensors=new java.util.Hashtable);null==this.atomTensorList&&(this.atomTensorList=Array(this.at.length));this.atomTensorList=JU.AU.ensureLength(this.atomTensorList,this.at.length);this.atomTensorList[a]=JM.AtomCollection.getTensorList(b);for(var d=b.size();0<=--d;){var c=b.get(d);c.atomIndex1=a;c.atomIndex2=-1;c.modelIndex=this.at[a].mi;this.addTensor(c,c.type);null!=c.altType&&this.addTensor(c,c.altType)}}},"~N,JU.Lst");c$.getTensorList=c(c$,"getTensorList",function(a){for(var b=-1,d=!1,
c=a.size(),g=c;0<=--g;){var f=a.get(g);f.forThermalEllipsoid?b=g:2==f.iType&&(d=!0)}var j=Array((0<=b||!d?0:1)+c);if(0<=b&&(j[0]=a.get(b),1==a.size()))return j;if(d){b=0;for(g=c;0<=--g;)f=a.get(g),f.forThermalEllipsoid||(j[++b]=f)}else for(g=0;g<c;g++)j[g]=a.get(g);return j},"JU.Lst");c(c$,"getAtomTensor",function(a,b){var d=this.getAtomTensorList(a);if(null!=d&&null!=b){b=b.toLowerCase();for(var c=0;c<d.length;c++){var g=d[c];if(null!=g&&(b.equals(g.type)||b.equals(g.altType)))return g}}return null},
"~N,~S");c(c$,"addTensor",function(a,b){b=b.toLowerCase();var d=this.atomTensors.get(b);null==d&&this.atomTensors.put(b,d=new JU.Lst);d.addLast(a)},"JU.Tensor,~S");c(c$,"getAllAtomTensors",function(a){if(null==this.atomTensors)return null;if(null!=a)return this.atomTensors.get(a.toLowerCase());a=new JU.Lst;for(var b,d=this.atomTensors.entrySet().iterator();d.hasNext()&&((b=d.next())||1);)a.addAll(b.getValue());return a},"~S");c(c$,"scaleVectorsToMax",function(a){if(!(null==this.vibrations||0==a)){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(!(0==b||b==a)){b=a/b;a=!1;for(c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1)){var g=this.getVibration(c,!1),f=this.getModulation(c);null!=f?f.scaleVibration(b):g.scale(b);a||(this.taintAtom(c,12),a=!0)}this.tainted[12].or(d)}}},"~N");c$.$AtomCollection$AtomSorter$=function(){G(self.c$);c$=r(function(){P(this,arguments);t(this,arguments)},
JM.AtomCollection,"AtomSorter",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.i>b.i?1:a.i<b.i?-1:0},"JM.Atom,JM.Atom");c$=K()};C(c$,"TAINT_ATOMNAME",0,"TAINT_ATOMTYPE",1,"TAINT_COORD",2,"TAINT_ELEMENT",3,"TAINT_FORMALCHARGE",4,"TAINT_HYDROPHOBICITY",5,"TAINT_BONDINGRADIUS",6,"TAINT_OCCUPANCY",7,"TAINT_PARTIALCHARGE",8,"TAINT_TEMPERATURE",9,"TAINT_VALENCE",10,"TAINT_VANDERWAALS",11,"TAINT_VIBRATION",12,"TAINT_ATOMNO",13,"TAINT_SEQID",14,"TAINT_MAX",15,"userSettableValues",null,"almost180",
2.984513);c$.sqrt3_2=c$.prototype.sqrt3_2=Math.sqrt(3)/2;c$.vRef=c$.prototype.vRef=JU.V3.new3(3.14159,2.71828,1.41421)});m("JM");w(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){c$=r(function(){this.bspf=this.cubeIterator=null;this.isZeroBased=this.hemisphereOnly=this.threadSafe=!1;this.modelIndex=2147483647;this.atomIndex=-1;this.distanceSquared=this.zeroBase=0;this.bsSelected=null;this.checkGreater=this.isGreaterOnly=!1;this.radiusData=null;this.vdw1=
0;this.isVdw=!1;this.vwr=this.atoms=null;this.iNext=0;t(this,arguments)},JM,"AtomIteratorWithinModel",null,J.api.AtomIndexIterator);u(c$,function(){});c(c$,"initialize",function(a,b,d,c,g,f){this.bspf=a;this.bsSelected=b;this.isGreaterOnly=d;this.isZeroBased=c;this.hemisphereOnly=g;this.threadSafe=f;this.cubeIterator=null},"J.bspt.Bspf,JU.BS,~B,~B,~B,~B");h(c$,"setModel",function(a,b,d,c,g,f,j){this.threadSafe&&(b=-1-b);if(b!=this.modelIndex||null==this.cubeIterator)this.cubeIterator=this.bspf.getCubeIterator(b),
this.modelIndex=b;this.zeroBase=this.isZeroBased?d:0;if(-2147483648!=f){this.atomIndex=0>f?-1:c;if(this.isVdw=null!=j)this.radiusData=j,this.atoms=a.at,this.vwr=a.vwr,f=j.factorType===J.atomdata.RadiusData.EnumType.OFFSET?5+j.value:5*j.value,this.vdw1=this.atoms[c].getVanderwaalsRadiusFloat(this.vwr,j.vdwType);this.checkGreater=this.isGreaterOnly&&2147483647!=c;this.setCenter(g,f)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");h(c$,"setCenter",function(a,b){this.setCenter2(a,b)},"JU.T3,~N");
c(c$,"setCenter2",function(a,b){null!=this.cubeIterator&&(this.cubeIterator.initialize(a,b,this.hemisphereOnly),this.distanceSquared=b*b)},"JU.T3,~N");h(c$,"hasNext",function(){return this.hasNext2()});c(c$,"hasNext2",function(){if(0<=this.atomIndex)for(;this.cubeIterator.hasMoreElements();){var a=this.cubeIterator.nextElement();if((this.iNext=a.i)!=this.atomIndex&&(!this.checkGreater||this.iNext>this.atomIndex)&&(null==this.bsSelected||this.bsSelected.get(this.iNext)))return!0}else if(this.cubeIterator.hasMoreElements())return a=
this.cubeIterator.nextElement(),this.iNext=a.i,!0;this.iNext=-1;return!1});h(c$,"next",function(){return this.iNext-this.zeroBase});h(c$,"foundDistance2",function(){return null==this.cubeIterator?-1:this.cubeIterator.foundDistance2()});h(c$,"addAtoms",function(a){for(var b;this.hasNext();)if(0<=(b=this.next())){var d;if(this.isVdw){d=this.atoms[b].getVanderwaalsRadiusFloat(this.vwr,this.radiusData.vdwType)+this.vdw1;switch(this.radiusData.factorType){case J.atomdata.RadiusData.EnumType.OFFSET:d+=
2*this.radiusData.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:d*=this.radiusData.value}d*=d}else d=this.distanceSquared;this.foundDistance2()<=d&&a.set(b)}},"JU.BS");h(c$,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)})});m("JM");w(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){c$=r(function(){this.center=this.bsModels=null;this.distance=0;t(this,arguments)},JM,"AtomIteratorWithinModelSet",JM.AtomIteratorWithinModel);
u(c$,function(a){F(this,JM.AtomIteratorWithinModelSet,[]);this.bsModels=a},"JU.BS");h(c$,"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");w(["JU.Edge",
"JV.JC"],"JM.Bond",["JU.C"],function(){c$=r(function(){this.atom2=this.atom1=null;this.shapeVisibilityFlags=this.colix=this.mad=0;t(this,arguments)},JM,"Bond",JU.Edge);u(c$,function(a,b,d,c,g){this.atom1=a;this.atom2=b;this.colix=g;this.setOrder(d);this.setMad(c)},"JM.Atom,JM.Atom,~N,~N,~N");c(c$,"setMad",function(a){this.mad=a;this.setShapeVisibility(0!=a)},"~N");c(c$,"setShapeVisibility",function(a){0!=(this.shapeVisibilityFlags&JM.Bond.myVisibilityFlag)!=a&&(this.atom1.addDisplayedBond(JM.Bond.myVisibilityFlag,
a),this.atom2.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.shapeVisibilityFlags=a?this.shapeVisibilityFlags|JM.Bond.myVisibilityFlag:this.shapeVisibilityFlags&~JM.Bond.myVisibilityFlag)},"~B");c(c$,"getIdentity",function(){return this.index+1+" "+JU.Edge.getBondOrderNumberFromOrder(this.order)+" "+this.atom1.getInfo()+" -- "+this.atom2.getInfo()+" "+this.atom1.distance(this.atom2)});h(c$,"isCovalent",function(){return 0!=(this.order&1023)});h(c$,"isHydrogen",function(){return JM.Bond.isOrderH(this.order)});
c$.isOrderH=c(c$,"isOrderH",function(a){return 0!=(a&30720)},"~N");c(c$,"isStereo",function(){return 0!=(this.order&1024)});c(c$,"isPartial",function(){return 0!=(this.order&224)});c(c$,"isAromatic",function(){return 0!=(this.order&512)});c(c$,"isPymolStyle",function(){return 98304==(this.order&98304)});c(c$,"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$,"is",function(a){return(this.order&-131073)==a},"~N");h(c$,"getOtherAtomNode",function(a){return this.atom1===a?this.atom2:this.atom2===a?this.atom1:null},"JU.Node");h(c$,"toString",function(){return this.atom1+" - "+this.atom2});c$.myVisibilityFlag=c$.prototype.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(1)});m("JM");w(["JM.AtomCollection"],"JM.BondCollection","JU.AU $.BS JM.Bond $.BondIteratorSelected $.HBond JU.BSUtil $.C $.Edge $.Logger".split(" "),
function(){c$=r(function(){this.bo=null;this.bondCount=0;this.molecules=this.freeBonds=this.numCached=null;this.defaultCovalentMad=this.moleculeCount=0;this.bsAromatic=this.bsAromaticDouble=this.bsAromaticSingle=null;this.haveHiddenBonds=!1;t(this,arguments)},JM,"BondCollection",JM.AtomCollection);c(c$,"setupBC",function(){this.bsAromatic=new JU.BS;this.numCached=D(5,0);this.freeBonds=Array(5);for(var a=5;0<--a;)this.freeBonds[a]=Array(200);this.setupAC()});h(c$,"releaseModelSet",function(){this.releaseModelSetBC()});
c(c$,"releaseModelSetBC",function(){this.freeBonds=this.bo=null;this.releaseModelSetAC()});c(c$,"resetMolecules",function(){this.molecules=null;this.moleculeCount=0});c(c$,"getBondIteratorForType",function(a,b){return new JM.BondIteratorSelected(this.bo,this.bondCount,a,b,this.vwr.getBoolean(603979812))},"~N,JU.BS");c(c$,"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],f=a.get(g.atom1.i),g=a.get(g.atom2.i);((new Boolean(!b&f&g)).valueOf()||(new Boolean(b&(new Boolean(f|g)).valueOf())).valueOf())&&
d.set(c)}return d},"JU.BS,~B");c(c$,"bondAtoms",function(a,b,d,c,g,f,j,k){d=this.getOrAddBond(a,b,d,c,g,f,!0);k&&(d.order|=131072,j&&(a.group=b.group,a.group.addAtoms(a.i)));return d},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B,~B");c(c$,"getOrAddBond",function(a,b,d,c,g,f,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),n(this.bo[a],JM.HBond)&&(this.bo[a].energy=f))):(this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+
250)),a=this.setBond(this.bondCount++,this.bondMutually(a,b,d,c,f)).index);null!=g&&g.set(a);return this.bo[a]},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B");c(c$,"setBond",function(a,b){return this.bo[b.index=a]=b},"~N,JM.Bond");c(c$,"bondMutually",function(a,b,d,c,g){d=JM.Bond.isOrderH(d)?new JM.HBond(a,b,d,c,0,g):new JM.Bond(a,b,d,c,0);this.addBondToAtom(a,d);this.addBondToAtom(b,d);return d},"JM.Atom,JM.Atom,~N,~N,~N");c(c$,"addBondToAtom",function(a,b){null==a.bonds?(a.bonds=Array(1),a.bonds[0]=b):a.bonds=
this.addToBonds(b,a.bonds)},"JM.Atom,JM.Bond");c(c$,"addToBonds",function(a,b){var d;if(null==b)d=0<this.numCached[1]?this.freeBonds[1][--this.numCached[1]]:Array(1),d[0]=a;else{var c=b.length;d=c+1;d=5>d&&0<this.numCached[d]?this.freeBonds[d][--this.numCached[d]]:Array(d);d[c]=a;for(var g=c;0<=--g;)d[g]=b[g];5>c&&200>this.numCached[c]&&(this.freeBonds[c][this.numCached[c]++]=b)}return d},"JM.Bond,~A");c(c$,"addHBond",function(a,b,d,c){this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,
this.bondCount+250));return this.setBond(this.bondCount++,this.bondMutually(a,b,d,1,c)).index},"JM.Atom,JM.Atom,~N,~N");c$.getBondOrderFull=c(c$,"getBondOrderFull",function(a,b,d,c,g){if(0==a||0==b||d<c)return 0;a=a+b+g;return d>a*a?0:1},"~N,~N,~N,~N,~N");c(c$,"deleteAllBonds2",function(){this.vwr.setShapeProperty(1,"reset",null);for(var a=this.bondCount;0<=--a;)this.bo[a].deleteAtomReferences(),this.bo[a]=null;this.bondCount=0});c(c$,"getDefaultMadFromOrder",function(a){return JM.Bond.isOrderH(a)?
1:32768==a?s(Math.floor(2E3*this.vwr.getFloat(570425406))):this.defaultCovalentMad},"~N");c(c$,"deleteConnections",function(a,b,d,c,g,f,j){var k=0>a,h=0>b,q=k||h;a=this.fixD(a,k);b=this.fixD(b,h);var p=new JU.BS,v=0,m=d|=131072;!j&&JM.Bond.isOrderH(d)&&(d=30720);if(f)f=c;else{f=new JU.BS;for(var A=c.nextSetBit(0);0<=A;A=c.nextSetBit(A+1)){var n=this.at[A];if(null!=n.bonds)for(var s=n.bonds.length;0<=--s;)g.get(n.getBondedAtomIndex(s))&&f.set(n.bonds[s].index)}}for(A=f.nextSetBit(0);A<this.bondCount&&
0<=A;A=f.nextSetBit(A+1))if(c=this.bo[A],this.isInRange(c.atom1,c.atom2,a,b,k,h,q)&&(j||m==(c.order&-257|131072)||0!=(d&c.order&30720)))p.set(A),v++;0<v&&this.dBm(p,!1);return[0,v]},"~N,~N,~N,JU.BS,JU.BS,~B,~B");c(c$,"fixD",function(a,b){return b?-a:a*a},"~N,~B");c(c$,"isInRange",function(a,b,d,c,g,f,j){var k=a.distanceSquared(b);return j?(j=Math.sqrt(k),a=a.getBondingRadius()+b.getBondingRadius(),(g?j>=a*d:k>=d)&&(f?j<=a*c:k<=c)):k>=d&&k<=c},"JM.Atom,JM.Atom,~N,~N,~B,~B,~B");c(c$,"dBm",function(a,
b){this.deleteBonds(a,b)},"JU.BS,~B");c(c$,"dBb",function(a,b){var d=a.nextSetBit(0);if(!(0>d)){this.resetMolecules();for(var c=-1,g=a.cardinality(),f=d;f<this.bondCount;++f){var j=this.bo[f];if(0<g&&a.get(f)){g--;if(!b){var k=j.atom1.mi;k!=c&&this.am[c=k].resetBoundCount()}j.deleteAtomReferences()}else this.setBond(d++,j)}for(c=this.bondCount;--c>=d;)this.bo[c]=null;this.bondCount=d;d=this.vwr.getShapeProperty(1,"sets");if(null!=d)for(c=0;c<d.length;c++)JU.BSUtil.deleteBits(d[c],a);JU.BSUtil.deleteBits(this.bsAromatic,
a)}},"JU.BS,~B");c(c$,"resetAromatic",function(){for(var a=this.bondCount;0<=--a;){var b=this.bo[a];b.isAromatic()&&b.setOrder(515)}});c(c$,"assignAromaticBondsBs",function(a,b){a||(this.bsAromatic=new JU.BS);this.bsAromaticSingle=new JU.BS;this.bsAromaticDouble=new JU.BS;for(var d=null==b,c=d?this.bondCount-1:b.nextSetBit(0),g=c;0<=g;g=d?g-1:b.nextSetBit(g+1)){var f=this.bo[g];this.bsAromatic.get(g)&&f.setOrder(515);switch(f.order&-131073){case 515:this.bsAromatic.set(g);break;case 513:this.bsAromaticSingle.set(g);
break;case 514:this.bsAromaticDouble.set(g)}}for(g=c=(d=null==b)?this.bondCount-1:b.nextSetBit(0);0<=g;g=d?g-1:b.nextSetBit(g+1))f=this.bo[g],f.is(515)&&(!this.bsAromaticDouble.get(g)&&!this.bsAromaticSingle.get(g))&&(this.assignAromaticDouble(f)||this.assignAromaticSingle(f));for(g=c;0<=g;g=d?g-1:b.nextSetBit(g+1))if(f=this.bo[g],this.bsAromaticDouble.get(g))f.is(514)||(this.bsAromatic.set(g),f.setOrder(514));else if((this.bsAromaticSingle.get(g)||f.isAromatic())&&!f.is(513))this.bsAromatic.set(g),
f.setOrder(513);this.assignAromaticNandO(b);this.bsAromaticDouble=this.bsAromaticSingle=null},"~B,JU.BS");c(c$,"assignAromaticDouble",function(a){var b=a.index;if(this.bsAromaticSingle.get(b))return!1;if(this.bsAromaticDouble.get(b))return!0;this.bsAromaticDouble.set(b);return!this.assignAromaticSingleForAtom(a.atom1,b)||!this.assignAromaticSingleForAtom(a.atom2,b)?(this.bsAromaticDouble.clear(b),!1):!0},"JM.Bond");c(c$,"assignAromaticSingle",function(a){var b=a.index;if(this.bsAromaticDouble.get(b))return!1;
if(this.bsAromaticSingle.get(b))return!0;this.bsAromaticSingle.set(b);return!this.assignAromaticDoubleForAtom(a.atom1)||!this.assignAromaticDoubleForAtom(a.atom2)?(this.bsAromaticSingle.clear(b),!1):!0},"JM.Bond");c(c$,"assignAromaticSingleForAtom",function(a,b){var d=a.bonds;if(null==d||this.assignAromaticSingleHetero(a))return!1;for(var c=d.length;0<=--c;){var g=d[c],f=g.index;if(!(f==b||!g.isAromatic()||this.bsAromaticSingle.get(f)))if(this.bsAromaticDouble.get(f)||!this.assignAromaticSingle(g))return!1}return!0},
"JM.Atom,~N");c(c$,"assignAromaticDoubleForAtom",function(a){var b=a.bonds;if(null==b)return!1;a=this.assignAromaticSingleHetero(a);for(var d=-1,c=b.length;0<=--c;)this.bsAromaticDouble.get(b[c].index)&&(a=!0),b[c].isAromatic()&&(d=c);for(c=b.length;0<=--c;){var g=b[c],f=g.index;if(g.isAromatic()&&!this.bsAromaticDouble.get(f)&&!this.bsAromaticSingle.get(f))if(!a&&this.assignAromaticDouble(g))a=!0;else if((a||c<d)&&!this.assignAromaticSingle(g))return!1}return a},"JM.Atom");c(c$,"assignAromaticSingleHetero",
function(a){var b=a.getElementNumber();switch(b){case 6:case 7:case 8:case 16:break;default:return!0}var d=a.getValence();switch(b){case 6:return 4==d;case 7:case 8:return d==10-b&&1>a.getFormalCharge();case 16:return d==18-b&&1>a.getFormalCharge()}return!1},"JM.Atom");c(c$,"assignAromaticNandO",function(a){for(var b,d=null==a,c=d?this.bondCount-1:a.nextSetBit(0);0<=c;c=d?c-1:a.nextSetBit(c+1))if(b=this.bo[c],b.is(513)){var g,f=b.atom2,j,k=f.getElementNumber();7==k||8==k?(j=k,g=f,f=b.atom1,k=f.getElementNumber()):
(g=b.atom1,j=g.getElementNumber());if(!(7!=j&&8!=j)){var h=g.getValence();if(!(0>h)){var q=g.getCovalentBondCount();g=g.getFormalCharge();switch(j){case 7:3==h&&(3==q&&1>g&&6==k&&3==f.getValence())&&b.setOrder(514);break;case 8:1==h&&(0==g&&(14==k||16==k))&&b.setOrder(514)}}}}},"JU.BS");c(c$,"getAtomBitsMDb",function(a,b){var d;switch(a){default:return this.getAtomBitsMDa(a,b);case 1678770178:d=new JU.BS;for(var c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))d.set(this.bo[c].atom1.i),d.set(this.bo[c].atom2.i);
return d;case 1048585:d=new JU.BS;for(c=this.bondCount;0<=--c;)this.bo[c].isAromatic()&&(d.set(this.bo[c].atom1.i),d.set(this.bo[c].atom2.i));return d}},"~N,~O");c(c$,"setBondOrder",function(a,b){var d=b.charCodeAt(0)-48,c=this.bo[a];switch(b){case "0":case "1":case "2":case "3":break;case "p":case "m":d=JU.Edge.getBondOrderNumberFromOrder(c.getCovalentOrder()).charCodeAt(0)-48+("p"==b?1:-1);3<d?d=1:0>d&&(d=3);break;default:return null}var g=new JU.BS;try{if(0==d){var f=new JU.BS;f.set(c.index);g.set(c.atom1.i);
g.set(c.atom2.i);this.dBm(f,!1);return g}c.setOrder(d|131072);this.removeUnnecessaryBonds(c.atom1,!1);this.removeUnnecessaryBonds(c.atom2,!1);g.set(c.atom1.i);g.set(c.atom2.i)}catch(j){if(y(j,Exception))JU.Logger.error("Exception in seBondOrder: "+j.toString());else throw j;}return g},"~N,~S");c(c$,"removeUnnecessaryBonds",function(a,b){var d=new JU.BS,c=new JU.BS,g=a.bonds;if(null!=g){for(var f=0;f<g.length;f++)g[f].isCovalent()?1==g[f].getOtherAtom(a).getElementNumber()&&d.set(g[f].getOtherAtom(a).i):
c.set(g[f].index);0<=c.nextSetBit(0)&&this.dBm(c,!1);b&&d.set(a.i);0<=d.nextSetBit(0)&&this.vwr.deleteAtoms(d,!1)}},"JM.Atom,~B");c(c$,"displayBonds",function(a,b){b||(this.haveHiddenBonds=!0);for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))d<this.bondCount&&0!=this.bo[d].mad&&this.bo[d].setShapeVisibility(b)},"JM.BondSet,~B");C(c$,"BOND_GROWTH_INCREMENT",250,"MAX_BONDS_LENGTH_TO_CACHE",5,"MAX_NUM_TO_CACHE",200)});m("JM");H(JM,"BondIterator");m("JM");w(["JM.BondIterator"],"JM.BondIteratorSelected",
null,function(){c$=r(function(){this.bonds=null;this.iBond=this.bondType=this.bondCount=0;this.bsSelected=null;this.bondSelectionModeOr=!1;t(this,arguments)},JM,"BondIteratorSelected",null,JM.BondIterator);u(c$,function(a,b,d,c,g){this.bonds=a;this.bondCount=b;this.bondType=d;this.bsSelected=c;this.bondSelectionModeOr=g},"~A,~N,~N,JU.BS,~B");h(c$,"hasNext",function(){if(131071==this.bondType)return this.iBond=this.bsSelected.nextSetBit(this.iBond),0<=this.iBond&&this.iBond<this.bondCount;for(;this.iBond<
this.bondCount;++this.iBond){var a=this.bonds[this.iBond];if(!(65535!=this.bondType&&0==(a.order&this.bondType))&&!(65535==this.bondType&&32768!=a.order)){var b=this.bsSelected.get(a.atom1.i),a=this.bsSelected.get(a.atom2.i);if(!this.bondSelectionModeOr&&b&&a||this.bondSelectionModeOr&&(b||a))return!0}}return!1});h(c$,"nextIndex",function(){return this.iBond});h(c$,"next",function(){return this.bonds[this.iBond++]})});m("JM");w(["JU.BS"],"JM.BondSet",["JU.BSUtil"],function(){c$=r(function(){this.associatedAtoms=
null;t(this,arguments)},JM,"BondSet",JU.BS);u(c$,function(){F(this,JM.BondSet,[])});c$.newBS=c(c$,"newBS",function(a,b){var d=new JM.BondSet;JU.BSUtil.copy2(a,d);d.associatedAtoms=b;return d},"JU.BS,~A")});m("JM");c$=r(function(){this.model=null;this.index=this.chainID=0;this.isRna=this.isDna=!1;this.groupCount=0;this.groups=null;this.selectedGroupCount=0;t(this,arguments)},JM,"Chain");c(c$,"getAtom",function(a){return this.model.ms.at[a]},"~N");u(c$,function(a,b,d){this.model=a;this.chainID=b;this.index=
d;this.groups=Array(16)},"JM.Model,~N,~N");c(c$,"calcSelectedGroupsCount",function(a){for(var b=this.selectedGroupCount=0;b<this.groupCount;b++)this.groups[b].selectedIndex=this.groups[b].isSelected(a)?this.selectedGroupCount++:-1},"JU.BS");c(c$,"selectSeqcodeRange",function(a,b,d,c){var g,f,j,k=!1;for(f=a;f<this.groupCount&&this.groups[f].seqcode!=b;f++);if(f==this.groupCount){if(0<a)return-1;k=!0;j=2147483647;for(var h=this.groupCount;0<=--h;)if((g=this.groups[h].seqcode)>b&&g-b<j)f=h,j=g-b;if(2147483647==
j)return-1}if(2147483647==d)b=this.groupCount-1,k=!0;else{for(b=f;b<this.groupCount&&this.groups[b].seqcode!=d;b++);if(b==this.groupCount){if(0<a)return-1;k=!0;j=2147483647;for(h=f;h<this.groupCount;h++)if((g=this.groups[h].seqcode)<d&&d-g<j)b=h,j=d-g;if(2147483647==j)return-1}}for(h=f;h<=b;++h)this.groups[h].selectAtoms(c);return k?-1:b+1},"~N,~N,~N,JU.BS");c(c$,"fixIndices",function(a,b){for(var d=0;d<this.groupCount;d++)this.groups[d].fixIndices(a,b)},"~N,JU.BS");c(c$,"setAtomBitSet",function(a){for(var b=
0;b<this.groupCount;b++)this.groups[b].selectAtoms(a)},"JU.BS");c(c$,"getIDStr",function(){return 0==this.chainID?"":256>this.chainID?""+String.fromCharCode(this.chainID):this.model.ms.vwr.chainMap.get(Integer.$valueOf(this.chainID))});m("JM");w(["java.lang.Short","java.util.Hashtable","JV.JC"],"JM.Group","JU.BS $.Quat J.c.STR JU.BSUtil $.Escape $.Logger".split(" "),function(){c$=r(function(){this.groupIndex=0;this.group1="\x00";this.chain=null;this.leadAtomIndex=this.firstAtomIndex=-1;this.shapeVisibilityFlags=
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function(){return 1>this.groupID?"":JM.Group.group3Names[this.groupID]});c(c$,"getGroup1",function(){return"?"});c(c$,"getBioPolymerLength",function(){return 0});c(c$,"getMonomerIndex",function(){return-1});c(c$,"getGroups",function(){return null});c(c$,"getStructure",function(){return null});c(c$,"getStrucNo",function(){return 0});c(c$,"getProteinStructureType",function(){return J.c.STR.NOT});c(c$,"getProteinStructureSubType",function(){return this.getProteinStructureType()});c(c$,"setProteinStructureType",
function(){return-1},"J.c.STR,~N");c(c$,"isProtein",function(){return!1});c(c$,"isNucleic",function(){return!1});c(c$,"isDna",function(){return!1});c(c$,"isRna",function(){return!1});c(c$,"isPurine",function(){return!1});c(c$,"isPyrimidine",function(){return!1});c(c$,"isCarbohydrate",function(){return!1});c(c$,"getResno",function(){return-2147483648==this.seqcode?0:this.seqcode>>8});c$.getSeqNumberFor=c(c$,"getSeqNumberFor",function(a){return JM.Group.haveSequenceNumber(a)?a>>8:2147483647},"~N");
c$.haveSequenceNumber=c(c$,"haveSequenceNumber",function(a){return 0!=(a&128)},"~N");c(c$,"getSeqcodeString",function(){return JM.Group.getSeqcodeStringFor(this.seqcode)});c$.getSeqcodeFor=c(c$,"getSeqcodeFor",function(a,b){if(-2147483648==a)return a;"A"<=b&&"Z">=b||("a"<=b&&"z">=b||"0"<=b&&"9">=b||"?"==b||"*"==b)||(" "!=b&&"\x00"!=b&&JU.Logger.warn("unrecognized insertionCode:"+b),b="\x00");return(2147483647==a?0:a<<8|128)+b.charCodeAt(0)},"~N,~S");c$.getSeqcodeStringFor=c(c$,"getSeqcodeStringFor",
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function(){2==this.count&&this.vwr.slm.isSelected(this.countPlusIndices[1])&&this.vwr.slm.isSelected(this.countPlusIndices[2])&&this.formatMeasurement(null)});c(c$,"formatDistance",function(a){var b=this.getLabelString();if(null==b)return"";if(null==a){var d=this.strFormat.indexOf("//");a=0<=d?this.strFormat.substring(d+2):null;null==a&&(a=this.vwr.g.measureDistanceUnits,this.strFormat+="//"+a)}a=JM.Measurement.fixUnits(a);d=b.indexOf("//");0<=d&&(b=b.substring(0,d),0==b.length&&(b="%VALUE"));d=this.fixValue(a,
0<=b.indexOf("%V"));return this.formatString(d,a,b)},"~S");c$.fixUnits=c(c$,"fixUnits",function(a){return a.equals("nanometers")?"nm":a.equals("picometers")?"pm":a.equals("angstroms")?"\u00c5":a.equals("vanderwaals")||a.equals("vdw")?"%":a},"~S");c(c$,"fixValue",function(a,b){if(2!=this.count)return this.value;var d=this.value;if(null!=a){var c=a.equals("%");if(c||a.endsWith("hz")){var g=this.getAtomIndex(1),f=this.getAtomIndex(2);if(0<=g&&0<=f){var g=this.getAtom(1),f=this.getAtom(2),j=!c&&1==JM.Measurement.nmrType(a);
this.type=c?"percent":j?"dipoleCouplingConstant":"J-CouplingConstant";d=c?d/(g.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO)+f.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO)):j?this.vwr.getNMRCalculation().getDipolarConstantHz(g,f):this.vwr.getNMRCalculation().getIsoOrAnisoHz(!0,g,f,a,null);this.$isValid=!Float.isNaN(d);c&&(a="pm")}}if(a.equals("nm"))return b?Math.round(100*d)/1E3:d/10;if(a.equals("pm"))return b?Math.round(1E3*d)/10:100*d;if(a.equals("au"))return b?Math.round(1E3*(d/0.5291772))/
1E3:d/0.5291772;if(a.endsWith("khz"))return b?Math.round(d/10)/100:d/1E3}return b?Math.round(100*d)/100:d},"~S,~B");c$.nmrType=c(c$,"nmrType",function(a){return 0>a.indexOf("hz")?0:a.startsWith("dc_")||a.equals("khz")?1:2},"~S");c(c$,"formatAngle",function(a){var b=this.getLabelString();0<=b.indexOf("%V")&&(a=Math.round(10*a)/10);return this.formatString(a,"\u00b0",b)},"~N");c(c$,"getLabelString",function(){var a=this.countPlusIndices[0]+":",b=null;if(null!=this.strFormat){if(0==this.strFormat.length)return null;
b=2<this.strFormat.length&&0==this.strFormat.indexOf(a)?this.strFormat:null}null==b&&(this.strFormat=null,b=this.vwr.getDefaultMeasurementLabel(this.countPlusIndices[0]));0==b.indexOf(a)&&(b=b.substring(2));null==this.strFormat&&(this.strFormat=a+b);return b});c(c$,"formatString",function(a,b,d){return JM.LabelToken.formatLabelMeasure(this.vwr,this,d,a,b)},"~N,~S,~S");c(c$,"sameAsPoints",function(a,b){if(this.count!=a[0])return!1;for(var d=!0,c=1;c<=this.count&&d;c++)d=this.countPlusIndices[c]==a[c];
if(d)for(c=0;c<this.count&&d;c++)null!=b[c]&&(d=0.01>this.pts[c].distance(b[c]));if(d)return!0;switch(this.count){default:return!0;case 2:return this.sameAsIJ(a,b,1,2)&&this.sameAsIJ(a,b,2,1);case 3:return this.sameAsIJ(a,b,1,3)&&this.sameAsIJ(a,b,2,2)&&this.sameAsIJ(a,b,3,1);case 4:return this.sameAsIJ(a,b,1,4)&&this.sameAsIJ(a,b,2,3)&&this.sameAsIJ(a,b,3,2)&&this.sameAsIJ(a,b,4,1)}},"~A,~A");c(c$,"sameAsIJ",function(a,b,d,c){d=this.countPlusIndices[d];a=a[c];return 0<=d||0<=a?d==a:0.01>this.pts[-2-
d].distance(b[-2-a])},"~A,~A,~N,~N");c(c$,"sameAs",function(a,b){return this.sameAsIJ(this.countPlusIndices,this.pts,a,b)},"~N,~N");c(c$,"toVector",function(a){for(var b=new JU.Lst,d=1;d<=this.count;d++)b.addLast(this.getLabel(d,a,!1));b.addLast(this.strMeasurement);return b},"~B");c(c$,"getMeasurement",function(a){if(null==this.countPlusIndices||2>this.count)return NaN;for(var b=this.count;0<=--b;)if(-1==this.countPlusIndices[b+1])return NaN;var b=null==a?this.getAtom(1):a[0],d=null==a?this.getAtom(2):
a[1],c;switch(this.count){case 2:return b.distance(d);case 3:return c=null==a?this.getAtom(3):a[2],JU.Measure.computeAngleABC(b,d,c,!0);case 4:return c=null==a?this.getAtom(3):a[2],a=null==a?this.getAtom(4):a[3],JU.Measure.computeTorsion(b,d,c,a,!0);default:return NaN}},"~A");c(c$,"getLabel",function(a,b,d){var c=this.countPlusIndices[a];return 0>c?(d?"modelIndex "+this.getAtom(a).mi+" ":"")+JU.Escape.eP(this.getAtom(a)):b?"(({"+c+"}))":this.vwr.getAtomInfo(c)},"~N,~B,~B");c(c$,"setModelIndex",function(a){if(null!=
this.pts)for(var b=0;b<this.count;b++)null!=this.pts[b]&&(this.pts[b].mi=a)},"~N");c(c$,"isValid",function(){return!(this.sameAs(1,2)||2<this.count&&this.sameAs(1,3)||4==this.count&&this.sameAs(2,4))});c$.find=c(c$,"find",function(a,b){for(var d=b.countPlusIndices,c=b.pts,g=a.size();0<=--g;)if(a.get(g).sameAsPoints(d,c))return g;return-1},"JU.Lst,JM.Measurement");c(c$,"isConnected",function(a,b){for(var d=-1,c=1;c<=b;c++){var g=this.getAtomIndex(c);if(!(0>g)){if(0<=d&&!a[g].isBonded(a[d]))return!1;
d=g}}return!0},"~A,~N");c(c$,"getInfoAsString",function(a){var b=this.fixValue(a,!0);a=new JU.SB;a.append(2==this.count?null==this.type?"distance":this.type:3==this.count?"angle":"dihedral");a.append(" \t").appendF(b);a.append(" \t").append(JU.PT.esc(this.strMeasurement));for(b=1;b<=this.count;b++)a.append(" \t").append(this.getLabel(b,!1,!1));null!=this.thisID&&a.append(" \t").append(this.thisID);return a.toString()},"~S");c(c$,"isInRange",function(a,b){if(a.factorType===J.atomdata.RadiusData.EnumType.FACTOR){var d=
this.getAtom(1),c=this.getAtom(2),d=(d.getVanderwaalsRadiusFloat(this.vwr,a.vdwType)+c.getVanderwaalsRadiusFloat(this.vwr,a.vdwType))*a.value;return b<=d}return 3.4028235E38==a.values[0]||b>=a.values[0]&&b<=a.values[1]},"J.atomdata.RadiusData,~N");c(c$,"isIntramolecular",function(a,b){for(var d=-1,c=1;c<=b;c++){var g=this.getAtomIndex(c);if(!(0>g))if(g=a[g].getMoleculeNumber(!1),0>d)d=g;else if(g!=d)return!1}return!0},"~A,~N");c(c$,"isMin",function(a){var b=this.getAtom(1),d=this.getAtom(2),c=B(100*
d.distanceSquared(b)),b=b.getAtomName(),d=d.getAtomName(),d=0>b.compareTo(d)?b+d:d+b;a=a.get(d);return null!=a&&c==a.intValue()},"java.util.Map");C(c$,"NMR_NOT",0,"NMR_DC",1,"NMR_JC",2)});m("JM");w(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["java.lang.Float","JU.BS","$.Lst","JM.Measurement","JU.BSUtil"],function(){c$=r(function(){this.points=this.measurements=this.measurementStrings=this.client=null;this.mustNotBeConnected=this.mustBeConnected=!1;this.tickInfo=null;this.tokAction=1060866;
this.note=this.strFormat=this.radiusData=null;this.isAll=!1;this.colix=0;this.intramolecular=null;this.mad=0;this.vwr=this.ms=this.minArray=this.units=this.atoms=this.text=this.thisID=null;this.iFirstAtom=0;this.justOneModel=!0;this.htMin=null;t(this,arguments)},JM,"MeasurementData",null,J.api.JmolMeasurementClient);u(c$,function(){});c(c$,"init",function(a,b,d){this.vwr=b;this.points=d;this.thisID=a;return this},"~S,JV.Viewer,JU.Lst");c(c$,"setModelSet",function(a){this.ms=a;return this},"JM.ModelSet");
c(c$,"set",function(a,b,d,c,g,f,j,k,h,q,p,v,m){this.ms=this.vwr.ms;this.tokAction=a;2<=this.points.size()&&(n(this.points.get(0),JU.BS)&&n(this.points.get(1),JU.BS))&&(this.justOneModel=JU.BSUtil.haveCommon(this.vwr.ms.getModelBS(this.points.get(0),!1),this.vwr.ms.getModelBS(this.points.get(1),!1)));this.htMin=b;this.radiusData=d;this.strFormat=c;this.units=g;this.tickInfo=f;this.mustBeConnected=j;this.mustNotBeConnected=k;this.intramolecular=h;this.isAll=q;this.mad=p;this.colix=v;this.text=m;return this},
"~N,java.util.Map,J.atomdata.RadiusData,~S,~S,JM.TickInfo,~B,~B,Boolean,~B,~N,~N,JM.Text");c(c$,"processNextMeasure",function(a){var b=a.getMeasurement(null);if(!(null!=this.htMin&&!a.isMin(this.htMin)||null!=this.radiusData&&!a.isInRange(this.radiusData,b)))if(null==this.measurementStrings&&null==this.measurements){var d=this.minArray[this.iFirstAtom];a.value=b;b=a.fixValue(this.units,!1);this.minArray[this.iFirstAtom]=-Infinity==1/d?b:Math.min(d,b)}else null!=this.measurementStrings?this.measurementStrings.addLast(a.getStringUsing(this.vwr,
this.strFormat,this.units)):this.measurements.addLast(Float.$valueOf(a.getMeasurement(null)))},"JM.Measurement");c(c$,"getMeasurements",function(a,b){if(b){this.minArray=L(this.points.get(0).cardinality(),0);for(var d=0;d<this.minArray.length;d++)this.minArray[d]=-0;this.define(null,this.ms);return this.minArray}if(a)return this.measurements=new JU.Lst,this.define(null,this.ms),this.measurements;this.measurementStrings=new JU.Lst;this.define(null,this.ms);return this.measurementStrings},"~B,~B");
c(c$,"define",function(a,b){this.client=null==a?this:a;this.atoms=b.at;var d=this.points.size();if(!(2>d)){var c=-1,g=Array(4),f=D(5,0),j=(new JM.Measurement).setPoints(b,f,g,null);j.setCount(d);for(var k=-1,h=0;h<d;h++){var q=this.points.get(h);if(n(q,JU.BS)){k=q.cardinality();if(0==k)return;1<k&&(c=0);k=h;0==h&&(this.iFirstAtom=0);f[h+1]=q.nextSetBit(0)}else g[h]=q,f[h+1]=-2-h}this.nextMeasure(0,k,j,c)}},"J.api.JmolMeasurementClient,JM.ModelSet");c(c$,"nextMeasure",function(a,b,d,c){if(a>b)d.isValid()&&
((!this.mustBeConnected||d.isConnected(this.atoms,a))&&(!this.mustNotBeConnected||!d.isConnected(this.atoms,a))&&(null==this.intramolecular||d.isIntramolecular(this.atoms,a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(d);else{var g=this.points.get(a),f=d.countPlusIndices,j=0==a?2147483647:f[a];if(0>j)this.nextMeasure(a+1,b,d,c);else{for(var k=!1,h=g.nextSetBit(0),q=0;0<=h;h=g.nextSetBit(h+1),q++)if(h!=j){var p=this.atoms[h].mi;if(0<=c&&this.justOneModel)if(0==a)c=p;else if(c!=
p)continue;f[a+1]=h;0==a&&(this.iFirstAtom=q);k=!0;this.nextMeasure(a+1,b,d,c)}k||this.nextMeasure(a+1,b,d,c)}}},"~N,~N,JM.Measurement,~N")});m("JM");w(["JM.Measurement"],"JM.MeasurementPending",null,function(){c$=r(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;t(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$,"addPoint",function(a,b,d){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==b){if(0<this.getIndexOf(a))return d&&(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=
this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(b))return d&&(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=!0;this.count=this.numSet+1;this.pts[a]=b;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;d&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);return this.count},"~N,JU.Point3fi,~B")});m("JM");w(["JU.BS","$.SB"],"JM.Model",["java.util.Hashtable",
"JU.AU","JU.BSUtil"],function(){c$=r(function(){this.ms=null;this.hydrogenCount=this.fileIndex=this.modelIndex=0;this.hasRasmolHBonds=this.isPdbWithMultipleBonds=this.isBioModel=!1;this.loadState="";this.loadScript=null;this.isModelKit=!1;this.dataFrames=null;this.dataSourceFrame=-1;this.jmolFrameType=this.jmolData=null;this.ac=this.firstAtomIndex=0;this.bsAtomsDeleted=this.bsAtoms=null;this.trajectoryBaseIndex=0;this.isTrajectory=!1;this.bondCount=this.selectedTrajectory=-1;this.nInsertions=this.nAltLocs=
this.moleculeCount=this.firstMoleculeIndex=0;this.groupCount=-1;this.chainCount=0;this.chains=null;this.biosymmetryCount=0;this.properties=this.auxiliaryInfo=null;this.defaultRotationRadius=0;this.orientation=this.biosymmetry=this.defaultStructure=null;this.isJmolDataFrame=this.structureTainted=!1;this.frameDelay=0;this.dssrCache=this.simpleCage=null;t(this,arguments)},JM,"Model");I(c$,function(){this.loadScript=new JU.SB;this.bsAtoms=new JU.BS;this.bsAtomsDeleted=new JU.BS;this.chains=Array(8)});
c(c$,"getModelSet",function(){return this.ms});c(c$,"isModelkit",function(){return this.isModelKit});c(c$,"getTrueAtomCount",function(){return this.bsAtoms.cardinality()-this.bsAtomsDeleted.cardinality()});c(c$,"resetBoundCount",function(){this.bondCount=-1});c(c$,"getBondCount",function(){if(0<=this.bondCount)return this.bondCount;var a=this.ms.bo;this.bondCount=0;for(var b=this.ms.bondCount;0<=--b;)a[b].atom1.mi==this.modelIndex&&this.bondCount++;return this.bondCount});u(c$,function(){});c(c$,
"set",function(a,b,d,c,g,f){this.ms=a;this.dataSourceFrame=this.modelIndex=b;this.trajectoryBaseIndex=(this.isTrajectory=0<=d)?d:b;null==f&&(f=new java.util.Hashtable);this.auxiliaryInfo=f;f.containsKey("biosymmetryCount")&&(this.biosymmetryCount=f.get("biosymmetryCount").intValue(),this.biosymmetry=f.get("biosymmetry"));this.properties=g;null==c?this.jmolFrameType="modelSet":(this.jmolData=c,this.isJmolDataFrame=!0,f.put("jmolData",c),f.put("title",c),this.jmolFrameType=0<=c.indexOf("ramachandran")?
"ramachandran":0<=c.indexOf("quaternion")?"quaternion":"data");return this},"JM.ModelSet,~N,~N,~S,java.util.Properties,java.util.Map");c(c$,"getChainCount",function(a){if(1<this.chainCount&&!a)for(a=0;a<this.chainCount;a++)if(0==this.chains[a].chainID)return this.chainCount-1;return this.chainCount},"~B");c(c$,"getGroupCountHetero",function(a){for(var b=0,d=this.chainCount;0<=--d;)for(var c=this.chains[d].groupCount;0<=--c;)this.chains[d].groups[c].isHetero()==a&&b++;return b},"~B");c(c$,"calcSelectedGroupsCount",
function(a){for(var b=this.chainCount;0<=--b;)this.chains[b].calcSelectedGroupsCount(a)},"JU.BS");c(c$,"getGroupCount",function(){if(0>this.groupCount){this.groupCount=0;for(var a=this.chainCount;0<=--a;)this.groupCount+=this.chains[a].groupCount}return this.groupCount});c(c$,"getChainAt",function(a){return a<this.chainCount?this.chains[a]:null},"~N");c(c$,"getChain",function(a){for(var b=this.chainCount;0<=--b;){var d=this.chains[b];if(d.chainID==a)return d}return null},"~N");c(c$,"fixIndices",function(a,
b,d){this.fixIndicesM(a,b,d)},"~N,~N,JU.BS");c(c$,"fixIndicesM",function(a,b,d){this.dataSourceFrame>a&&this.dataSourceFrame--;this.trajectoryBaseIndex>a&&this.trajectoryBaseIndex--;this.firstAtomIndex-=b;for(a=0;a<this.chainCount;a++)this.chains[a].fixIndices(b,d);JU.BSUtil.deleteBits(this.bsAtoms,d);JU.BSUtil.deleteBits(this.bsAtomsDeleted,d)},"~N,~N,JU.BS");c(c$,"freeze",function(){this.freezeM()});c(c$,"freezeM",function(){this.chains=JU.AU.arrayCopyObject(this.chains,this.chainCount);this.groupCount=
-1;this.getGroupCount();for(var a=0;a<this.chainCount;++a)this.chains[a].groups=JU.AU.arrayCopyObject(this.chains[a].groups,this.chains[a].groupCount)});c(c$,"getPdbData",function(){},"JV.Viewer,~S,~S,~B,JU.BS,JU.OC,~A,JU.SB,JU.BS");c(c$,"getBioBranches",function(a){return a},"JU.Lst");c(c$,"clearBioPolymers",function(){});c(c$,"getAllPolymerInfo",function(){},"JU.BS,java.util.Map,JU.Lst");c(c$,"getBioPolymerCount",function(){return 0});c(c$,"calculateStructures",function(){return""},"~B,~B,~B,~B,~B");
c(c$,"setStructureList",function(){},"java.util.Map");c(c$,"getChimeInfo",function(a,b){this.getChimeInfoM(a,b)},"JU.SB,~N");c(c$,"getChimeInfoM",function(a,b){a.append("\nNumber of Atoms ..... "+(this.ms.ac-b));0<b&&a.append(" ("+b+")");a.append("\nNumber of Bonds ..... "+this.ms.bondCount);a.append("\nNumber of Models ...... "+this.ms.mc)},"JU.SB,~N");c(c$,"setConformation",function(){},"JU.BS");c(c$,"getPdbConformation",function(){return!1},"JU.BS,~N");c(c$,"getFullPDBHeader",function(){return null});
c(c$,"getSequenceBits",function(){return null},"JM.ModelSet,~S,JU.BS");c(c$,"getBasePairBits",function(){return null},"JM.ModelSet,~S");c(c$,"resetRasmolBonds",function(){},"JM.Model,JU.BS");c(c$,"calcRasmolHydrogenBonds",function(){},"JM.ModelSet,JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS");c(c$,"getFullProteinStructureState",function(){return null},"JM.ModelSet,JU.BS,~B,~B,~N");c(c$,"calculateAllPolymers",function(){},"JM.ModelSet,~A,~N,~N,JU.BS");c(c$,"getGroupsWithinAll",function(){return null},"JM.ModelSet,~N,JU.BS");
c(c$,"getSelectCodeRange",function(){return null},"JM.ModelSet,~A");c(c$,"calculateStruts",function(){return 0},"JM.ModelSet,JU.BS,JU.BS");c(c$,"getPolymerPointsAndVectors",function(){},"JU.BS,JU.Lst,~B,~N");c(c$,"recalculatePoints",function(){},"JM.ModelSet,~N");c(c$,"getDefaultLargePDBRendering",function(){},"JU.SB,~N");c(c$,"calcSelectedMonomersCount",function(){},"JU.BS");c(c$,"getBioPolymerCountInModel",function(){return 0},"JM.ModelSet,~N");c(c$,"calculateStraightnessAll",function(){},"JM.ModelSet")});
m("JM");w(["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 JU.BSUtil $.Elements $.JmolMolecule $.Logger".split(" "),function(){c$=r(function(){this.mergeModelSet=this.ms=this.vwr=null;this.appendNew=this.merging=!1;this.specialAtomIndexes=this.group3Counts=this.group3Lists=this.jmolData=null;this.doAddHydrogens=this.doMinimize=this.isPyMOLsession=this.isTrajectory=
this.is2D=this.someModelsAreModulated=this.someModelsHaveUnitcells=!1;this.groups=this.jbr=this.fileHeader=null;this.groupCount=0;this.firstAtomIndexes=this.seqcodes=this.group3Of=this.chainOf=this.htAtomMap=this.modulationTUV=null;this.iModel=0;this.model=null;this.currentChainID=0;this.isNewChain=!1;this.currentChain=null;this.currentGroupSequenceNumber=0;this.currentGroupInsertionCode="\x00";this.nullGroup=this.currentGroup3=null;this.adapterTrajectoryCount=this.adapterModelCount=this.baseTrajectoryCount=
this.baseGroupIndex=this.baseAtomIndex=this.baseModelCount=this.baseModelIndex=0;this.modulationOn=this.noAutoBond=!1;this.$mergeGroups=this.htGroup1=null;this.iChain=0;this.structuresDefinedInFile=this.vStereo=null;t(this,arguments)},JM,"ModelLoader");I(c$,function(){this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});u(c$,function(a,b,d,c,g,f){this.vwr=a;this.ms=new JM.ModelSet(a,b);var j=a.getModelAdapter();this.mergeModelSet=g;(this.merging=null!=this.mergeModelSet&&
0<this.mergeModelSet.ac)?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);null==f?(this.initializeInfo(b,null),this.createModelSet(null,null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||(this.ms.canSkipLoad=!1),a=j.getAtomSetCollectionAuxiliaryInfo(c),a.put("loadScript",d),this.initializeInfo(j.getFileTypeName(c).toLowerCase().intern(),a),this.createModelSet(j,c,f),null!=this.jbr&&this.jbr.setLoader(null),
this.jbr=null)},"JV.Viewer,~S,JU.SB,~O,JM.ModelSet,JU.BS");c(c$,"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.ms.haveBioModels&&(this.jbr=this.vwr.getJBR().setLoader(this));this.jmolData=this.ms.getInfoM("jmolData");this.fileHeader=this.ms.getInfoM("fileHeader");this.ms.trajectorySteps=this.ms.getInfoM("trajectorySteps");
this.isTrajectory=null!=this.ms.trajectorySteps;this.isPyMOLsession=this.ms.getMSInfoB("isPyMOL");this.doAddHydrogens=null!=this.jbr&&!this.isTrajectory&&!this.isPyMOLsession&&!this.ms.getMSInfoB("pdbNoHydrogens")&&(this.ms.getMSInfoB("pdbAddHydrogens")||this.vwr.getBooleanProperty("pdbAddHydrogens"));null!=b&&(b.remove("pdbNoHydrogens"),b.remove("pdbAddHydrogens"),b.remove("trajectorySteps"),this.isTrajectory&&(this.ms.vibrationSteps=b.remove("vibrationSteps")),b.containsKey("legacyJavaFloat")&&
this.vwr.setBooleanProperty("legacyJavaFloat",!0));this.htGroup1=this.ms.getInfoM("htGroup1");var 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=null==this.ms.trajectorySteps?0:this.ms.trajectorySteps.size();this.ms.someModelsHaveSymmetry=this.ms.getMSInfoB("someModelsHaveSymmetry");
this.someModelsHaveUnitcells=this.ms.getMSInfoB("someModelsHaveUnitcells");this.someModelsAreModulated=this.ms.getMSInfoB("someModelsAreModulated");this.ms.someModelsHaveFractionalCoordinates=this.ms.getMSInfoB("someModelsHaveFractionalCoordinates");this.merging&&(this.ms.haveBioModels=(new Boolean(this.ms.haveBioModels|this.mergeModelSet.haveBioModels)).valueOf(),this.ms.bioModel=this.mergeModelSet.bioModel,this.ms.someModelsHaveSymmetry=(new Boolean(this.ms.someModelsHaveSymmetry|this.mergeModelSet.getMSInfoB("someModelsHaveSymmetry"))).valueOf(),
this.someModelsHaveUnitcells=(new Boolean(this.someModelsHaveUnitcells|this.mergeModelSet.getMSInfoB("someModelsHaveUnitcells"))).valueOf(),this.ms.someModelsHaveFractionalCoordinates=(new Boolean(this.ms.someModelsHaveFractionalCoordinates|this.mergeModelSet.getMSInfoB("someModelsHaveFractionalCoordinates"))).valueOf(),this.ms.someModelsHaveAromaticBonds=(new Boolean(this.ms.someModelsHaveAromaticBonds|this.mergeModelSet.someModelsHaveAromaticBonds)).valueOf(),this.ms.msInfo.put("someModelsHaveSymmetry",
Boolean.$valueOf(this.ms.someModelsHaveSymmetry)),this.ms.msInfo.put("someModelsHaveUnitcells",Boolean.$valueOf(this.someModelsHaveUnitcells)),this.ms.msInfo.put("someModelsHaveFractionalCoordinates",Boolean.$valueOf(this.ms.someModelsHaveFractionalCoordinates)),this.ms.msInfo.put("someModelsHaveAromaticBonds",Boolean.$valueOf(this.ms.someModelsHaveAromaticBonds)))},"~S,java.util.Map");c(c$,"getGroup3",function(a){return a>=this.group3Of.length?null:this.group3Of[a]},"~N");c(c$,"getFirstAtomIndex",
function(a){return this.firstAtomIndexes[a]},"~N");c(c$,"getAtomCount",function(){return this.ms.ac});c(c$,"createModelSet",function(a,b,d){var c=null==a?0:a.getAtomCount(b);0<c&&JU.Logger.info("reading "+c+" atoms");this.adapterModelCount=null==a?1:a.getAtomSetCount(b);this.appendNew=!this.merging||null==a||1<this.adapterModelCount||this.isTrajectory||this.vwr.getBoolean(603979792);this.htAtomMap.clear();this.chainOf=Array(32);this.group3Of=Array(32);this.seqcodes=D(32,0);this.firstAtomIndexes=D(32,
0);this.currentChainID=2147483647;this.currentChain=null;this.currentGroupInsertionCode="\uffff";this.currentGroup3="xxxxx";this.iModel=-1;this.model=null;if(this.merging&&(this.baseModelCount=this.mergeModelSet.mc,this.baseTrajectoryCount=this.mergeModelSet.mergeTrajectories(this.isTrajectory),0<this.baseTrajectoryCount)){if(this.isTrajectory){if(null==this.mergeModelSet.vibrationSteps){this.mergeModelSet.vibrationSteps=new JU.Lst;for(var g=this.mergeModelSet.trajectorySteps.size();0<=--g;)this.mergeModelSet.vibrationSteps.addLast(null)}for(g=
0;g<this.ms.trajectorySteps.size();g++)this.mergeModelSet.trajectorySteps.addLast(this.ms.trajectorySteps.get(g)),this.mergeModelSet.vibrationSteps.addLast(null==this.ms.vibrationSteps?null:this.ms.vibrationSteps.get(g))}this.ms.trajectorySteps=this.mergeModelSet.trajectorySteps;this.ms.vibrationSteps=this.mergeModelSet.vibrationSteps}this.initializeAtomBondModelCounts(c);null!=d&&(this.doMinimize||this.is2D)&&d.setBits(this.baseAtomIndex,this.baseAtomIndex+c);null==a?this.setModelNameNumberProperties(0,
-1,"",1,null,null,null):(0<this.adapterModelCount&&(JU.Logger.info("ModelSet: haveSymmetry:"+this.ms.someModelsHaveSymmetry+" haveUnitcells:"+this.someModelsHaveUnitcells+" haveFractionalCoord:"+this.ms.someModelsHaveFractionalCoordinates),JU.Logger.info(this.adapterModelCount+" model"+(1==this.ms.mc?"":"s")+' in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.')),g=this.ms.getInfoM("defaultOrientationQuaternion"),null!=g&&(JU.Logger.info("defaultOrientationQuaternion = "+
g),JU.Logger.info('Use "set autoLoadOrientation TRUE" before loading or "restore orientation DEFAULT" after loading to view this orientation.')),this.iterateOverAllNewModels(a,b),this.iterateOverAllNewAtoms(a,b),this.iterateOverAllNewBonds(a,b),this.merging&&!this.appendNew&&(g=a.getAtomSetAuxiliaryInfo(b,0),this.ms.setInfo(this.baseModelIndex,"initialAtomCount",g.get("initialAtomCount")),this.ms.setInfo(this.baseModelIndex,"initialBondCount",g.get("initialBondCount"))),this.initializeUnitCellAndSymmetry(),
this.initializeBonding());this.finalizeGroupBuild();this.is2D&&this.doMinimize&&this.applyStereochemistry();this.doAddHydrogens&&this.jbr.finalizeHydrogens();null!=a&&(this.ms.calculatePolymers(this.groups,this.groupCount,this.baseGroupIndex,null),null!=this.jbr&&this.jbr.iterateOverAllNewStructures(a,b));this.setDefaultRendering(this.vwr.getInt(553648170));var f=this.vwr.rd;d=this.ms.ac;c=this.ms.at;for(g=this.baseAtomIndex;g<d;g++)c[g].setMadAtom(this.vwr,f);f=this.ms.am;for(g=f[this.baseModelIndex].firstAtomIndex;g<
d;g++)f[c[g].mi].bsAtoms.set(g);this.freeze();this.finalizeShapes();this.vwr.setModelSet(this.ms);this.setAtomProperties();null!=a&&a.finish(b);null!=this.mergeModelSet&&this.mergeModelSet.releaseModelSet();this.mergeModelSet=null},"J.api.JmolAdapter,~O,JU.BS");c(c$,"setDefaultRendering",function(a){if(!this.isPyMOLsession){for(var b=new JU.SB,d=this.ms.mc,c=this.ms.am,g=this.baseModelIndex;g<d;g++)c[g].isBioModel&&c[g].getDefaultLargePDBRendering(b,a);0!=b.length()&&(b.append("select *;"),a=this.ms.getInfoM("jmolscript"),
null==a&&(a=""),b.append(a),this.ms.msInfo.put("jmolscript",b.toString()))}},"~N");c(c$,"setAtomProperties",function(){for(var a=this.ms.mc,b=this.baseModelIndex;b<a;b++){var d=this.ms.getInfo(b,"atomProperties"),c=this.ms.getInfo(b,"groupPropertyList");if(null!=d)for(var g,d=d.entrySet().iterator();d.hasNext()&&((g=d.next())||1);){var f=g.getKey(),j=g.getValue(),k=this.ms.getModelAtomBitSetIncludingDeleted(b,!0);if(this.doAddHydrogens)var h=null!=c&&JU.PT.isOneOf(f,c),j=this.jbr.fixPropertyValue(k,
j,h);f="property_"+f.toLowerCase();JU.Logger.info("creating "+f+" for model "+this.ms.getModelName(b));this.vwr.setData(f,[f,j,k,Integer.$valueOf(-1),Boolean.FALSE],this.ms.ac,0,0,2147483647,0)}}});c(c$,"initializeAtomBondModelCounts",function(a){var b=this.adapterTrajectoryCount;this.merging?(this.appendNew?(this.baseModelIndex=this.baseModelCount,this.ms.mc=this.baseModelCount+this.adapterModelCount):(this.baseModelIndex=this.vwr.am.cmi,0>this.baseModelIndex&&(this.baseModelIndex=this.baseModelCount-
1),this.ms.mc=this.baseModelCount),this.ms.ac=this.baseAtomIndex=this.mergeModelSet.ac,this.ms.bondCount=this.mergeModelSet.bondCount,this.$mergeGroups=this.mergeModelSet.getGroups(),this.groupCount=this.baseGroupIndex=this.$mergeGroups.length,this.ms.mergeModelArrays(this.mergeModelSet),this.ms.growAtomArrays(this.ms.ac+a)):(this.ms.mc=this.adapterModelCount,this.ms.ac=0,this.ms.bondCount=0,this.ms.at=Array(a),this.ms.bo=Array(250+a));this.doAddHydrogens&&this.jbr.initializeHydrogenAddition();1<
b&&(this.ms.mc+=b-1);this.ms.am=JU.AU.arrayCopyObject(this.ms.am,this.ms.mc);this.ms.modelFileNumbers=JU.AU.arrayCopyI(this.ms.modelFileNumbers,this.ms.mc);this.ms.modelNumbers=JU.AU.arrayCopyI(this.ms.modelNumbers,this.ms.mc);this.ms.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.ms.modelNumbersForAtomLabel,this.ms.mc);this.ms.modelNames=JU.AU.arrayCopyS(this.ms.modelNames,this.ms.mc);this.ms.frameTitles=JU.AU.arrayCopyS(this.ms.frameTitles,this.ms.mc);if(this.merging)for(a=0;a<this.mergeModelSet.mc;a++)(this.ms.am[a]=
this.mergeModelSet.am[a]).ms=this.ms},"~N");c(c$,"mergeGroups",function(){var a=this.mergeModelSet.getAuxiliaryInfo(null),b=a.get("group3Lists"),a=a.get("group3Counts");if(null!=b){for(var d=0;d<this.baseModelCount;d++)this.group3Lists[d+1]=b[d+1],this.group3Counts[d+1]=a[d+1],this.structuresDefinedInFile.set(d);this.group3Lists[0]=b[0];this.group3Counts[0]=a[0]}!this.appendNew&&this.ms.haveBioModels&&this.structuresDefinedInFile.clear(this.baseModelIndex)});c(c$,"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 f=a.getAtomSetNumber(b,g),j=a.getAtomSetName(b,g),k=a.getAtomSetAuxiliaryInfo(b,g);k.containsKey("modelID")&&k.put("modelID0",k.get("modelID"));var h=k.get("modelProperties");this.vwr.setStringProperty("_fileType",k.get("fileType"));
null==j&&(j=null!=this.jmolData&&2<this.jmolData.indexOf(";")?this.jmolData.substring(this.jmolData.indexOf(":")+2,this.jmolData.indexOf(";")):this.appendNew?""+f%1E6:"");this.setModelNameNumberProperties(c,d,j,f,h,k,this.jmolData)&&this.jbr.setGroupLists(c);null!=this.ms.getInfo(c,"periodicOriginXyz")&&(this.ms.someModelsHaveSymmetry=!0)}d=this.ms.am[this.baseModelIndex];this.vwr.setSmilesString(this.ms.msInfo.get("smilesString"));g=this.ms.msInfo.remove("loadState");f=this.ms.msInfo.remove("loadScript");
if(0>f.indexOf("Viewer.AddHydrogens")||!d.isModelKit){j=JU.PT.split(g,"\n");k=new JU.SB;for(g=0;g<j.length;g++)h=d.loadState.indexOf(j[g]),(0>h||h!=d.loadState.lastIndexOf(j[g]))&&k.append(j[g]).appendC("\n");d.loadState+=d.loadScript.toString()+k.toString();d.loadScript=new JU.SB;d.loadScript.append("  ").appendSB(f).append(";\n")}if(this.isTrajectory){g=this.ms.mc-c+1;JU.Logger.info(g+" trajectory steps read");this.ms.setInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(g));d=this.adapterModelCount;
for(g=c;g<this.ms.mc;g++,d++)this.ms.am[g]=this.ms.am[this.baseModelCount],this.ms.modelNumbers[g]=a.getAtomSetNumber(b,d),this.ms.modelNames[g]=a.getAtomSetName(b,d),this.structuresDefinedInFile.set(g)}this.finalizeModels(this.baseModelCount)},"J.api.JmolAdapter,~O");c(c$,"setModelNameNumberProperties",function(a,b,d,c,g,f,j){var k=null!=f&&Boolean.TRUE===f.get("isPDB");this.appendNew?(this.ms.am[a]=k?this.jbr.getBioModel(a,b,j,g,f):(new JM.Model).set(this.ms,a,b,j,g,f),this.ms.modelNumbers[a]=c,
this.ms.modelNames[a]=d):(b=f.get("PDB_CONECT_firstAtom_count_max"),null!=b&&this.ms.setInfo(a,"PDB_CONECT_firstAtom_count_max",b));b=this.ms.am;c=this.ms.at;b[a].bsAtoms.set(c.length+1);b[a].bsAtoms.clear(c.length+1);c=this.ms.getInfo(a,"altLocs");b[a].nAltLocs=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].nInsertions=null==c?0:c.length;d=null!=this.ms.modelSetName&&this.ms.modelSetName.startsWith("Jmol Model Kit")||
d.startsWith("Jmol Model Kit")||"Jme".equals(this.ms.getInfo(a,"fileType"));b[a].isModelKit=d;return k},"~N,~N,~S,~N,java.util.Properties,java.util.Map,~S");c(c$,"finalizeModels",function(a){var b=this.ms.mc;if(b!=a){var d,c=0,g=-1,f=this.ms.modelNumbers,j=this.ms.modelNames;if(this.isTrajectory)for(var k=a;++k<this.ms.mc;)f[k]=f[k-1]+1;if(0<a){if(1E6>f[0])for(k=0;k<a;k++)0==j[k].length&&(j[k]=""+f[k]),f[k]+=1E6,this.ms.modelNumbersForAtomLabel[k]="1."+(k+1);var h=f[a-1],h=h-h%1E6;1E6>f[a]&&(h+=1E6);
for(k=a;k<b;k++)f[k]+=h}for(var q=this.ms.am,k=a;k<b;++k)if(this.ms.setInfo(k,"fileType",this.ms.modelSetTypeName),null!=this.fileHeader&&this.ms.setInfo(k,"fileHeader",this.fileHeader),h=s(f[k]/1E6),h!=g&&(c=0,g=h),c++,0==h?(d=""+this.ms.getModelNumber(k),h=1):d=h+"."+c,this.ms.modelNumbersForAtomLabel[k]=d,q[k].fileIndex=h-1,this.ms.modelFileNumbers[k]=1E6*h+c,null==j[k]||0==j[k].length)j[k]=d;if(this.merging)for(k=0;k<a;k++)q[k].ms=this.ms;for(k=0;k<b;k++)this.ms.setInfo(k,"modelName",j[k]),this.ms.setInfo(k,
"modelNumber",Integer.$valueOf(f[k]%1E6)),this.ms.setInfo(k,"modelFileNumber",Integer.$valueOf(this.ms.modelFileNumbers[k])),this.ms.setInfo(k,"modelNumberDotted",this.ms.getModelNumberDotted(k)),a=this.ms.getInfo(k,"altLocs"),null!=a&&JU.Logger.info("model "+this.ms.getModelNumberDotted(k)+" alternative locations: "+a)}},"~N");c(c$,"iterateOverAllNewAtoms",function(a,b){var d=-1,c=!1,g=!1,f=a.getAtomIterator(b),j=0,k=this.ms.am;0<this.ms.mc&&(this.nullGroup=(new JM.Group).setGroup(new JM.Chain(this.ms.am[this.baseModelIndex],
32,-1),"",0,-1,-1));for(;f.hasNext();){j++;var h=f.getAtomSetIndex()+this.baseModelIndex;h!=d&&(this.iChain=0,this.iModel=h,this.model=k[h],this.currentChainID=2147483647,this.isNewChain=!0,k[h].bsAtoms.clearAll(),c=k[h].isBioModel,d=h,g=c&&this.doAddHydrogens,null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var h=f.getGroup3(),q=f.getChainID();this.checkNewGroup(a,q,h,f.getSequenceNumber(),f.getInsertionCode(),g,!1);q=f.getElementNumber();g&&1==JU.Elements.getElementNumber(q)&&this.jbr.setHaveHsAlready(!0);
var p=f.getAtomName(),v=g?this.getPdbCharge(h,p):f.getFormalCharge();this.addAtom(c,f.getSymmetry(),f.getAtomSite(),f.getUniqueID(),q,p,v,f.getPartialCharge(),f.getTensors(),f.getOccupancy(),f.getBfactor(),f.getXYZ(),f.getIsHetero(),f.getSerial(),f.getSeqID(),h,f.getVib(),f.getAltLoc(),f.getRadius())}0<this.groupCount&&g&&this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain?1:0);d=-1;c=null;g=this.ms.at;for(f=0;f<this.ms.ac;f++)g[f].mi!=d&&(d=g[f].mi,k[d].firstAtomIndex=f,h=this.ms.getDefaultVdwType(d),
h!==c&&(JU.Logger.info("Default Van der Waals type for model set to "+h.getVdwLabel()),c=h));JU.Logger.info(j+" atoms created")},"J.api.JmolAdapter,~O");c(c$,"getPdbCharge",function(a,b){return a.equals("ARG")&&b.equals("NH1")||a.equals("LYS")&&b.equals("NZ")||a.equals("HIS")&&b.equals("ND1")?1:0},"~S,~S");c(c$,"addAtom",function(a,b,d,c,g,f,j,k,h,q,p,v,m,n,s,r,t,u,w){var x=0,y=null;if(null!=f){var z;if(0<=(z=f.indexOf("\x00")))y=f.substring(z+1),f=f.substring(0,z);a&&(0<=f.indexOf("*")&&(f=f.$replace("*",
"'")),x=this.vwr.getJBR().lookupSpecialAtomID(f),2==x&&"CA".equalsIgnoreCase(r)&&(x=0))}a=this.ms.addAtom(this.iModel,this.nullGroup,g,f,y,n,s,d,v,w,t,j,k,q,p,h,m,x,b);a.altloc=u;this.htAtomMap.put(c,a)},"~B,JU.BS,~N,~O,~N,~S,~N,~N,JU.Lst,~N,~N,JU.P3,~B,~N,~N,~S,JU.V3,~S,~N");c(c$,"checkNewGroup",function(a,b,d,c,g,f,j){var k=null==d?null:d.intern();b!=this.currentChainID&&(this.currentChainID=b,this.currentChain=this.getOrAllocateChain(this.model,b),this.currentGroupInsertionCode="\uffff",this.currentGroupSequenceNumber=
-1,this.currentGroup3="xxxx",this.isNewChain=!0);if(c!=this.currentGroupSequenceNumber||g!=this.currentGroupInsertionCode||k!==this.currentGroup3){0<this.groupCount&&f&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!j?1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=c;this.currentGroupInsertionCode=g;for(this.currentGroup3=k;this.groupCount>=this.group3Of.length;)this.chainOf=JU.AU.doubleLength(this.chainOf),this.group3Of=JU.AU.doubleLengthS(this.group3Of),
this.seqcodes=JU.AU.doubleLengthI(this.seqcodes),this.firstAtomIndexes=JU.AU.doubleLengthI(this.firstAtomIndexes);this.firstAtomIndexes[this.groupCount]=this.ms.ac;this.chainOf[this.groupCount]=this.currentChain;this.group3Of[this.groupCount]=d;this.seqcodes[this.groupCount]=JM.Group.getSeqcodeFor(c,g);++this.groupCount}},"J.api.JmolAdapter,~N,~S,~N,~S,~B,~B");c(c$,"getOrAllocateChain",function(a,b){var d=a.getChain(b);if(null!=d)return d;a.chainCount==a.chains.length&&(a.chains=JU.AU.doubleLength(a.chains));
return a.chains[a.chainCount++]=new JM.Chain(a,b,0==b||32==b?-1:this.iChain++)},"JM.Model,~N");c(c$,"iterateOverAllNewBonds",function(a,b){var d=a.getBondIterator(b);if(null!=d){var c=this.vwr.getMadBond();this.ms.defaultCovalentMad=null==this.jmolData?c:0;for(var g=!1;d.hasNext();){var f=d.getEncodedOrder(),j=f,k=this.bondAtoms(d.getAtomUniqueID1(),d.getAtomUniqueID2(),j);null!=k&&(1<j&&(1025!=j&&1041!=j)&&(g=!0),j=d.getRadius(),0<j&&k.setMad(aa(2E3*j)),j=d.getColix(),0<=j&&(k.colix=j),k.order|=
f&98304)}g&&(this.ms.someModelsHaveSymmetry&&!this.vwr.getBoolean(603979794))&&JU.Logger.info('ModelSet: use "set appletSymmetryToBonds TRUE " to apply the file-based multiple bonds to symmetry-generated atoms.');this.ms.defaultCovalentMad=c}},"J.api.JmolAdapter,~O");c(c$,"bondAtoms",function(a,b,d){var c=this.htAtomMap.get(a);if(null==c)return JU.Logger.error("bondAtoms cannot find atomUid1?:"+a),null;a=this.htAtomMap.get(b);if(null==a)return JU.Logger.error("bondAtoms cannot find atomUid2?:"+b),
null;if(c.isBonded(a))return null;1025==d||1041==d?(b=this.ms.bondMutually(c,a,this.is2D?d:1,this.ms.getDefaultMadFromOrder(1),0),null==this.vStereo&&(this.vStereo=new JU.Lst),this.vStereo.addLast(b)):(b=this.ms.bondMutually(c,a,d,this.ms.getDefaultMadFromOrder(d),0),b.isAromatic()&&(this.ms.someModelsHaveAromaticBonds=!0));this.ms.bondCount==this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount+250));this.ms.setBond(this.ms.bondCount++,b);return b},"~O,~O,~N");c(c$,"initializeUnitCellAndSymmetry",
function(){this.someModelsAreModulated&&null==this.ms.bsModulated&&(this.ms.bsModulated=new JU.BS);if(this.someModelsHaveUnitcells){this.ms.unitCells=Array(this.ms.mc);this.ms.haveUnitCells=!0;for(var a=null!=this.mergeModelSet&&null!=this.mergeModelSet.unitCells,b=0,d=0;b<this.ms.mc;b++)if(a&&b<this.baseModelCount)this.ms.unitCells[b]=this.mergeModelSet.unitCells[b];else{this.ms.unitCells[b]=J.api.Interface.getSymmetry(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(1089470478,null);a=this.ms.at;b=this.baseAtomIndex;d=-1;for(c=0;b<this.ms.ac;b++)a[b].mi!=d&&(d=a[b].mi,c=this.baseAtomIndex+this.ms.getInfoI(d,"presymmetryAtomIndex")+this.ms.getInfoI(d,"presymmetryAtomCount")),b>=c&&this.ms.bsSymmetry.set(b)}if(this.appendNew&&this.ms.someModelsHaveFractionalCoordinates){for(var a=this.ms.at,c=-1,
d=null,g=!1,f=!this.vwr.getBoolean(603979875),b=this.baseAtomIndex;b<this.ms.ac;b++)a[b].mi!=c&&(c=a[b].mi,d=this.ms.getUnitCell(c),g=null!=d&&d.getCoordinatesAreFractional()),g&&(d=a[b].getUnitCell(),d.toCartesian(d.toSupercell(a[b]),!1),f&&JU.PT.fixPtFloats(a[b],1E4));for(a=this.baseModelIndex;a<this.ms.mc;a++)if(this.ms.isTrajectory(a)&&(d=this.ms.getUnitCell(a),null!=d&&d.getCoordinatesAreFractional()&&d.isSupercell())){c=this.ms.trajectorySteps.get(a);for(b=c.length;0<=--b;)null!=c[b]&&d.toSupercell(c[b])}}});
c(c$,"initializeBonding",function(){var a=null==this.ms.getInfoM("someModelsHaveCONECT")?null:new JU.BS;null!=a&&this.ms.setPdbConectBonding(this.baseAtomIndex,this.baseModelIndex,a);var b=0,d=this.vwr.getBoolean(603979794),c=this.vwr.getBoolean(603979798),g=this.vwr.getBoolean(603979846),f=null,j=!1,k=this.ms.mc,h=this.ms.am;if(!this.noAutoBond)for(var q=this.baseModelIndex;q<k;q++){var b=h[q].bsAtoms.cardinality(),p=this.ms.getInfoI(q,"initialBondCount"),v=h[q].isBioModel;0>p&&(p=this.ms.bondCount);
var m=this.ms.getInfoB(q,"hasSymmetry");if(g||c&&(0==p||v&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||p<s(b/2))||m&&!d&&!this.ms.getInfoB(q,"hasBonds")))if(j=!0,this.merging||1<k)null==f&&(f=JU.BS.newN(this.ms.ac)),(q==this.baseModelIndex||!this.isTrajectory)&&f.or(h[q].bsAtoms)}this.modulationOn&&this.ms.setModulation(null,!0,this.modulationTUV,!1);j?(this.ms.autoBondBs4(f,f,a,null,this.ms.defaultCovalentMad,this.vwr.getBoolean(603979873)),JU.Logger.info("ModelSet: autobonding; use  autobond=false  to not generate bonds automatically")):
(this.ms.initializeBspf(),JU.Logger.info("ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation"))});c(c$,"finalizeGroupBuild",function(){this.groups=Array(this.groupCount);if(this.merging)for(var a=0;a<this.$mergeGroups.length;a++)(this.groups[a]=this.$mergeGroups[a]).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]);if(null!=this.group3Lists&&null!=this.ms.msInfo){this.ms.msInfo.put("group3Lists",this.group3Lists);this.ms.msInfo.put("group3Counts",this.group3Counts);for(a=0;a<this.group3Counts.length;a++)null==this.group3Counts[a]&&(this.group3Counts[a]=D(0,0))}});c(c$,"distinguishAndPropagateGroup",function(a,b,d,c,g,f){var j=f-1;if(j<g)throw new NullPointerException;var k=this.ms.at[g].mi,h=null==d||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(b,d,c,g,f,
k,this.specialAtomIndexes,this.ms.at);null==h?(h=(new JM.Group).setGroup(b,d,c,g,j),null!=this.jbr&&(h.groupID=this.jbr.getGroupID(d)),c="o>"):c=h.isProtein()?"p>":h.isNucleic()?"n>":h.isCarbohydrate()?"c>":"o>";null!=d&&(this.countGroup(k,c,d),h.isNucleic()&&(d=null==this.htGroup1?null:this.htGroup1.get(d),null!=d&&(h.group1=d.charAt(0))));this.addGroup(b,h);this.groups[a]=h;h.groupIndex=a;for(a=f;--a>=g;)this.ms.at[a].setGroup(h)},"~N,JM.Chain,~S,~N,~N,~N");c(c$,"addGroup",function(a,b){a.groupCount==
a.groups.length&&(a.groups=JU.AU.doubleLength(a.groups));a.groups[a.groupCount++]=b},"JM.Chain,JM.Group");c(c$,"countGroup",function(a,b,d){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var g=(d+"   ").substring(0,3),f=this.group3Lists[c].indexOf(g);0>f&&(this.group3Lists[c]+=",["+g+"]",f=this.group3Lists[c].indexOf(g),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][s(f/6)]++;f=this.group3Lists[c].indexOf(",["+g);
0<=f&&(this.group3Lists[c]=this.group3Lists[c].substring(0,f)+b+this.group3Lists[c].substring(f+2));0<=a&&this.countGroup(-1,b,d)}},"~N,~S,~S");c(c$,"freeze",function(){this.htAtomMap.clear();this.ms.ac<this.ms.at.length&&this.ms.growAtomArrays(this.ms.ac);this.ms.bondCount<this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount));for(var a=5;0<--a;){this.ms.numCached[a]=0;for(var b=this.ms.freeBonds[a],d=b.length;0<=--d;)b[d]=null}this.ms.setAtomNamesAndNumbers(0,this.baseAtomIndex,
this.mergeModelSet);this.findElementsPresent();this.ms.resetMolecules();this.currentChain=this.model=null;!this.ms.haveBioModels||this.isPyMOLsession?this.ms.freezeModels():(a=this.vwr.getBoolean(603979826),a=this.ms.calculateStructuresAllExcept(this.structuresDefinedInFile,a,!1,!0,!0,a),0<a.length&&JU.Logger.info(a))});c(c$,"findElementsPresent",function(){this.ms.elementsPresent=Array(this.ms.mc);for(var a=0;a<this.ms.mc;a++)this.ms.elementsPresent[a]=JU.BS.newN(64);for(a=this.ms.ac;0<=--a;){var b=
this.ms.at[a].getAtomicAndIsotopeNumber();b>=JU.Elements.elementNumberMax&&(b=JU.Elements.elementNumberMax+JU.Elements.altElementIndexFromNumber(b));this.ms.elementsPresent[this.ms.at[a].mi].set(b)}});c(c$,"applyStereochemistry",function(){this.set2dZ(this.baseAtomIndex,this.ms.ac);if(null!=this.vStereo){var a=new JU.BS;a.setBits(this.baseAtomIndex,this.ms.ac);for(var b=this.vStereo.size();0<=--b;){var d=this.vStereo.get(b),c=1025==d.order?3:-3;d.order=1;d.atom2.z!=d.atom1.z&&0>c==d.atom2.z<d.atom1.z&&
(c/=3);var g=JU.JmolMolecule.getBranchBitSet(this.ms.at,d.atom2.i,a,null,d.atom1.i,!1,!0);g.set(d.atom2.i);for(var f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1))this.ms.at[f].z+=c;d.atom2.x=(d.atom1.x+d.atom2.x)/2;d.atom2.y=(d.atom1.y+d.atom2.y)/2}this.vStereo=null}this.is2D=!1});c(c$,"set2dZ",function(a,b){var d=JU.BS.newN(b),c=new JU.BS,g=new JU.V3,f=JU.V3.new3(0,1,0),j=new JU.V3,k=new JU.BS;k.setBits(a,b);for(var h=a;h<b;h++)!d.get(h)&&!c.get(h)&&(c=this.getBranch2dZ(h,-1,k,c,g,f,j),d.or(c))},"~N,~N");
c(c$,"getBranch2dZ",function(a,b,d,c,g,f,j){c=JU.BS.newN(this.ms.ac);if(0>a)return c;var k=new JU.BS;k.or(d);0<=b&&k.clear(b);JM.ModelLoader.setBranch2dZ(this.ms.at[a],c,k,g,f,j);return c},"~N,~N,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setBranch2dZ=c(c$,"setBranch2dZ",function(a,b,d,c,g,f){var j=a.i;if(d.get(j)&&(d.clear(j),b.set(j),null!=a.bonds))for(j=a.bonds.length;0<=--j;){var k=a.bonds[j];k.isHydrogen()||(k=k.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,k,c,g,f),JM.ModelLoader.setBranch2dZ(k,b,d,c,
g,f))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3");c$.setAtom2dZ=c(c$,"setAtom2dZ",function(a,b,d,c,g){d.sub2(b,a);d.z=0;d.normalize();g.cross(c,d);d=Math.acos(d.dot(c));b.z=a.z+0.8*Math.sin(4*d)},"JM.Atom,JM.Atom,JU.V3,JU.V3,JU.V3");c(c$,"finalizeShapes",function(){this.ms.sm=this.vwr.shm;this.ms.sm.setModelSet(this.ms);this.ms.setBsHidden(this.vwr.slm.getHiddenSet());this.merging||this.ms.sm.resetShapes();this.ms.sm.loadDefaultShapes(this.ms);this.ms.someModelsHaveAromaticBonds&&this.vwr.getBoolean(603979944)&&
this.ms.assignAromaticBondsBs(!1,null);this.merging&&1==this.baseModelCount&&this.ms.sm.setShapePropertyBs(6,"clearModelIndex",null,null)});c(c$,"undeleteAtom",function(a){this.ms.at[a].valence=0},"~N");c$.createAtomDataSet=c(c$,"createAtomDataSet",function(a,b,d,c,g){if(null==c)return null;var f=a.getModelAdapter(),j=new JU.P3,k=b.at,h=a.getFloat(570425363);if(null!=b.unitCells)for(var q=g.nextSetBit(0);0<=q;q=g.nextSetBit(q+1))if(null!=k[q].atomSymmetry){h=-h;break}for(var q=-1,p=0,v=JU.BSUtil.cardinalityOf(g)==
a.ms.ac,m=f.getAtomIterator(c);m.hasNext();){var n=m.getXYZ();if(!Float.isNaN(n.x+n.y+n.z))if(1146095626==d){q=g.nextSetBit(q+1);if(0>q)break;p++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+q+": "+k[q]+" --\x3e ("+n.x+","+n.y+","+n.z);b.setAtomCoord(q,n.x,n.y,n.z)}else{j.setT(n);n=JU.BS.newN(b.ac);b.getAtomsWithin(h,j,n,-1);n.and(g);if(v)if(p=JU.BSUtil.cardinalityOf(n),0==p){JU.Logger.warn("createAtomDataSet: no atom found at position "+j);continue}else 1<p&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+
p+" atoms found at position "+j);switch(d){case 1146095631:var s=m.getVib();if(null==s)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+j+" vib: "+s);b.setAtomCoords(n,1146095631,s);break;case 1129318401:b.setAtomProperty(n,d,0,m.getOccupancy(),null,null,null);break;case 1112541195:b.setAtomProperty(n,d,0,m.getPartialCharge(),null,null,null);break;case 1112541196:b.setAtomProperty(n,d,0,m.getBfactor(),null,null,null)}}}switch(d){case 1146095631:b=f.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+
b);a.setStringProperty("_vibrationName",b);break;case 1146095626:if(JU.Logger.info(p+" atom positions read"),b.recalculateLeadMidpointsAndWingVectors(-1),p==b.ac)return"boundbox {*};reset"}return null},"JV.Viewer,JM.ModelSet,~N,~O,JU.BS");C(c$,"defaultGroupCount",32)});m("JM");w(["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 $.Bond $.BondSet $.HBond $.Model $.StateScript JS.SV JU.BSUtil $.BoxInfo $.Elements $.Escape $.JmolMolecule $.Logger $.SimpleUnitCell JV.JC".split(" "),
function(){c$=r(function(){this.am=this.modelSetName=this.bsSymmetry=null;this.mc=0;this.unitCells=this.bioModel=null;this.haveUnitCells=!1;this.elementsPresent=this.frameTitles=this.modelNames=this.modelNumbersForAtomLabel=this.modelFileNumbers=this.modelNumbers=this.closest=null;this.haveBioModels=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=this.trajectorySteps=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.triangulator=this.vOrientations=this.htPeaks=this.symTemp=null;this.echoShapeActive=this.selectionHaloEnabled=!1;this.pointGroup=this.modelSetTypeName=null;this.maxBondWarned=!1;t(this,arguments)},
JM,"ModelSet",JM.BondCollection);u(c$,function(a,b){this.vwr=a;this.modelSetName=b;this.selectedMolecules=new JU.BS;this.stateScripts=new JU.Lst;this.boxInfo=new JU.BoxInfo;this.boxInfo.addBoundBoxPoint(JU.P3.new3(-10,-10,-10));this.boxInfo.addBoundBoxPoint(JU.P3.new3(10,10,10));this.am=Array(1);this.modelNumbers=D(1,0);this.modelFileNumbers=D(1,0);this.modelNumbersForAtomLabel=Array(1);this.modelNames=Array(1);this.frameTitles=Array(1);this.closest=Array(1);this.ptTemp=new JU.P3;this.ptTemp1=new JU.P3;
this.ptTemp2=new JU.P3;this.matTemp=new JU.M3;this.matInv=new JU.M3;this.mat4=new JU.M4;this.mat4t=new JU.M4;this.vTemp=new JU.V3;this.setupBC()},"JV.Viewer,~S");h(c$,"releaseModelSet",function(){this.am=null;this.unitCells=this.bsAll=this.bsSymmetry=this.am=this.closest[0]=null;this.releaseModelSetBC()});c(c$,"setSelectionHaloEnabled",function(a){this.selectionHaloEnabled=a},"~B");c(c$,"getSelectionHaloEnabled",function(){return this.selectionHaloEnabled});c(c$,"getEchoStateActive",function(){return this.echoShapeActive});
c(c$,"setEchoStateActive",function(a){this.echoShapeActive=a},"~B");c(c$,"getModelSetTypeName",function(){return this.modelSetTypeName});c(c$,"getModelNumberIndex",function(a,b,d){if(b){for(b=0;b<this.mc;b++)if(this.modelNumbers[b]==a||1E6>a&&this.modelNumbers[b]==1E6+a)return b;return-1}for(b=0;b<this.mc;b++)if(this.modelFileNumbers[b]==a)return d&&this.isTrajectory(b)&&this.setTrajectory(b),b;return-1},"~N,~B,~B");c(c$,"getBitSetTrajectories",function(){if(null==this.trajectorySteps)return null;
for(var a=new JU.BS,b=this.mc;0<=--b;){var d=this.am[b].selectedTrajectory;0<=d&&(a.set(d),b=this.am[b].trajectoryBaseIndex)}return a});c(c$,"setTrajectoryBs",function(a){for(var b=0;b<this.mc;b++)a.get(b)&&this.setTrajectory(b)},"JU.BS");c(c$,"setTrajectory",function(a){if(!(0>a)&&this.isTrajectory(a)&&this.at[this.am[a].firstAtomIndex].mi!=a){var b=this.am[a].trajectoryBaseIndex;this.am[b].selectedTrajectory=a;this.setAtomPositions(b,a,this.trajectorySteps.get(a),null,0,null==this.vibrationSteps?
null:this.vibrationSteps.get(a),!0);b=this.vwr.am.cmi;0<=b&&(b!=a&&this.am[b].fileIndex==this.am[a].fileIndex)&&this.vwr.setCurrentModelIndexClear(a,!1)}},"~N");c(c$,"morphTrajectories",function(a,b,d){if(!(0>a||0>b||!this.isTrajectory(a)||!this.isTrajectory(b)))if(0==d)this.setTrajectory(a);else if(1==d)this.setTrajectory(b);else{var c=this.am[a].trajectoryBaseIndex;this.am[c].selectedTrajectory=a;this.setAtomPositions(c,a,this.trajectorySteps.get(a),this.trajectorySteps.get(b),d,null==this.vibrationSteps?
null:this.vibrationSteps.get(a),!0);b=this.vwr.am.cmi;0<=b&&(b!=a&&this.am[b].fileIndex==this.am[a].fileIndex)&&this.vwr.setCurrentModelIndexClear(a,!1)}},"~N,~N,~N");c(c$,"setAtomPositions",function(a,b,d,c,g,f,j){var k=new JU.BS,h=new JU.V3,q=this.am[a].firstAtomIndex,p=q+this.getAtomCountInModel(a);if(0==g)for(var v=0;q<p&&v<d.length;q++,v++)this.at[q].mi=b,null!=d[v]&&(j?this.at[q].setFractionalCoordTo(d[v],!0):this.at[q].setT(d[v]),null!=this.vibrationSteps&&(null!=f&&null!=f[v]&&(h=f[v]),this.setVibrationVector(q,
h)),k.set(q));else{f=new JU.P3;h=Math.min(d.length,c.length);for(v=0;q<p&&v<h;q++,v++)this.at[q].mi=b,null==d[v]||null==c[v]||(f.sub2(c[v],d[v]),f.scaleAdd2(g,f,d[v]),j?this.at[q].setFractionalCoordTo(f,!0):this.at[q].setT(f),k.set(q))}this.initializeBspf();this.validateBspfForModel(a,!1);this.recalculateLeadMidpointsAndWingVectors(a);this.sm.refreshShapeTrajectories(a,k,null);this.am[a].hasRasmolHBonds&&this.bioModel.resetRasmolBonds(this.am[a],k)},"~N,~N,~A,~A,~N,~A,~B");c(c$,"getFrameOffsets",
function(a){if(null==a)return null;for(var b=Array(this.mc),d=0;d<this.mc;d++)b[d]=new JU.P3;for(var c=0,g=0,f=b[0],j=null!=this.trajectorySteps&&this.trajectorySteps.size()==this.mc,k=j?this.mc:1,h=0;h<k;h++){j&&this.setTrajectory(h);for(d=0;d<=this.ac;d++){if(d==this.ac||this.at[d].mi!=c){0<g&&(f.scale(-1/g),0!=c&&f.sub(b[0]),g=0);if(d==this.ac)break;c=this.at[d].mi;f=b[c]}a.get(d)&&(f.add(this.at[d]),g++)}}b[0].set(0,0,0);return b},"JU.BS");c(c$,"getAtoms",function(a,b){switch(a){default:return JU.BSUtil.andNot(this.getAtomBitsMaybeDeleted(a,
b),this.vwr.slm.bsDeleted);case 1048610:var d=b.intValue(),c=this.getModelNumberIndex(d,!0,!0);return 0>c&&0<d?new JU.BS:this.vwr.getModelUndeletedAtomsBitSet(c)}},"~N,~O");c(c$,"findNearestAtomIndex",function(a,b,d,c){if(0==this.ac)return-1;this.closest[0]=null;this.g3d.isAntialiased()&&(a<<=1,b<<=1);this.findNearest2(a,b,this.closest,d,c);this.sm.findNearestShapeAtomIndex(a,b,this.closest,d);a=null==this.closest[0]?-1:this.closest[0].i;this.closest[0]=null;return a},"~N,~N,JU.BS,~N");c(c$,"calculatePointGroup",
function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,!1,null,0,0)},"JU.BS");c(c$,"getPointGroupInfo",function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,!0,null,0,0)},"JU.BS");c(c$,"getPointGroupAsString",function(a,b,d,c,g){return this.calculatePointGroupForFirstModel(a,!0,b,!1,d,c,g)},"JU.BS,~B,~S,~N,~N");c(c$,"calculatePointGroupForFirstModel",function(a,b,d,c,g,f,j){var k=this.vwr.am.cmi,h=null==a?-1:a.nextSetBit(0);0>k&&0<=h&&(k=this.at[h].mi);0>k&&(k=this.vwr.getVisibleFramesBitSet().nextSetBit(0),
a=null);var q=this.vwr.getModelUndeletedAtomsBitSet(k);null!=a&&q.and(a);h=q.nextSetBit(0);0>h&&(q=this.vwr.getModelUndeletedAtomsBitSet(k),h=q.nextSetBit(0));a=this.vwr.shm.getShapePropertyIndex(18,"mad",h);a=null!=a&&0!=a.intValue()||this.vwr.tm.vibrationOn;this.pointGroup=J.api.Interface.getSymmetry(this.vwr,"ms").setPointGroup(this.pointGroup,this.at,q,a,this.vwr.getFloat(570425382),this.vwr.getFloat(570425384));if(!b&&!c)return this.pointGroup.getPointGroupName();b=this.pointGroup.getPointGroupInfo(k,
d,c,g,f,j);return c?b:(1<this.mc?"frame "+this.getModelNumberDotted(k)+"; ":"")+b},"JU.BS,~B,~B,~B,~S,~N,~N");c(c$,"modelsOf",function(a,b){for(var d=JU.BS.newN(this.mc),c=null==a,g=c?this.ac-1:a.nextSetBit(0);0<=g;g=c?g-1:a.nextSetBit(g+1)){var f=this.am[this.at[g].mi].trajectoryBaseIndex;this.isJmolDataFrameForModel(f)||(d.set(f),b.set(g))}return d},"JU.BS,JU.BS");c(c$,"getDefaultStructure",function(a,b){for(var d=this.modelsOf(a,b),c=new JU.SB,g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))this.am[g].isBioModel&&
null!=this.am[g].defaultStructure&&c.append(this.am[g].defaultStructure);return c.toString()},"JU.BS,JU.BS");c(c$,"makeConnections",function(a,b,d,c,g,f,j,k,h,q){if(1073741852==c&&2048!=d){var p="connect ";0.1!=a&&(p+=a+" ");1E8!=b&&(p+=b+" ");this.addStateScript(p,k?g:null,k?null:g,k?null:f," auto",!1,!0)}this.moleculeCount=0;return this.makeConnections2(a,b,d,c,g,f,j,k,h,q)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"setPdbConectBonding",function(a,b,d){for(var c=this.vwr.getMadBond();b<this.mc;b++){var g=
this.getInfo(b,"PDB_CONECT_bonds");if(null!=g){var f=g.size();this.setInfo(b,"initialBondCount",Integer.$valueOf(f));for(var j=this.getInfo(b,"PDB_CONECT_firstAtom_count_max"),k=j[0]+a,h=k+j[1],j=j[2],q=D(j+1,0),p=k;p<h;p++)if(0<(k=this.atomSerials[p]))q[k]=p+1;for(h=0;h<f;h++){var k=g.get(h),p=k[0],v=k[1],k=k[2];if(!(0>p||0>v||p>j||v>j))if(p=q[p]-1,v=q[v]-1,!(0>p||0>v)){var m=this.at[p],n=this.at[v];null!=d&&(m.isHetero()&&d.set(p),n.isHetero()&&d.set(v));if(m.altloc==n.altloc||"\x00"==m.altloc||
"\x00"==n.altloc)this.getOrAddBond(m,n,k,2048==k?1:c,null,0,!1)}}}}},"~N,~N,JU.BS");c(c$,"deleteAllBonds",function(){this.moleculeCount=0;for(var a=this.stateScripts.size();0<=--a;)this.stateScripts.get(a).isConnect()&&this.stateScripts.remove(a);this.deleteAllBonds2()});c(c$,"includeAllRelatedFrames",function(a){for(var b,d=0;d<this.mc;d++)if(a.get(d)){if(this.isTrajectory(d)&&!a.get(b=this.am[d].trajectoryBaseIndex)){a.set(b);this.includeAllRelatedFrames(a);break}}else(this.isTrajectory(d)&&a.get(this.am[d].trajectoryBaseIndex)||
this.isJmolDataFrameForModel(d)&&a.get(this.am[d].dataSourceFrame))&&a.set(d)},"JU.BS");c(c$,"deleteModels",function(a){this.moleculeCount=0;this.includeAllRelatedFrames(a);var b=JU.BSUtil.cardinalityOf(a);if(0==b)return null;for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.clearDataFrameReference(d);if(b==this.mc)return b=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.vwr.zap(!0,!1,!1),b;this.validateBspf(!1);for(var c=Array(this.mc-b),g=this.am,b=new JU.BS,f=d=0;d<this.mc;d++)a.get(d)?
(this.getAtomCountInModel(d),b.or(this.getModelAtomBitSetIncludingDeleted(d,!1))):(this.am[d].modelIndex=f,c[f++]=this.am[d]);this.am=c;var j=this.mc,k=this.getBondsForSelectedAtoms(b,!0);this.deleteBonds(k,!0);for(f=d=0;d<j;d++)if(a.get(d)){var h=g[d].ac;if(0!=h){var q=g[d].bsAtoms,p=g[d].firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,q);this.deleteModel(f,p,h,q,k);for(var v=j;--v>d;)g[v].fixIndices(f,h,q);this.vwr.shm.deleteShapeAtoms([c,this.at,[f,p,h]],q);this.mc--}}else f++;this.deleteModel(-1,
0,0,null,null);return b},"JU.BS");c(c$,"setAtomProperty",function(a,b,d,c,g,f,j){switch(b){case 1115297793:case 1113200642:case 1113200647:case 1113200649:case 1113200650:case 1650071565:case 1113200654:if(4<c&&(c=4),null!=f){d=L(this.ac,0);try{var k=a.nextSetBit(0);for(g=0;0<=k;k=a.nextSetBit(k+1))d[k]=f[g++]}catch(h){if(y(h,Exception))return;throw h;}f=d}case 1113200646:case 1113200652:k=null;d=0;null==f?(16<c&&(c=16.1),0>c&&(c=0),d=s(Math.floor(2E3*c))):k=new J.atomdata.RadiusData(f,0,null,null);
this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(b),d,k,a);return}this.setAPm(a,b,d,c,g,f,j)},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"getFileData",function(a){if(0>a)return"";var b=this.getInfo(a,"fileData");if(null!=b)return b;if(!this.getInfoB(a,"isCIF"))return this.getPDBHeader(a);b=this.vwr.getCifData(a);this.setInfo(a,"fileData",b);return b},"~N");c(c$,"addHydrogens",function(a,b){var d=this.mc-1,c=new JU.BS;if(this.isTrajectory(d)||1<this.am[d].getGroupCount())return c;this.growAtomArrays(this.ac+b.length);
var g=this.vwr.rd,f=this.getDefaultMadFromOrder(1);this.am[d].dssrCache=null;for(var j=0,k=this.am[d].ac+1;j<a.size();j++,k++){var h=a.get(j),q=this.addAtom(d,h.group,1,"H"+k,null,k,h.getSeqID(),k,b[j],NaN,null,0,0,100,NaN,null,!1,0,null);q.setMadAtom(this.vwr,g);c.set(q.i);this.bondAtoms(h,q,1,f,null,0,!1,!1)}this.sm.loadDefaultShapes(this);return c},"JU.Lst,~A");c(c$,"mergeModelArrays",function(a){this.at=a.at;this.bo=a.bo;this.stateScripts=a.stateScripts;this.proteinStructureTainted=a.proteinStructureTainted;
this.thisStateModel=-1;this.bsSymmetry=a.bsSymmetry;this.modelFileNumbers=a.modelFileNumbers;this.modelNumbersForAtomLabel=a.modelNumbersForAtomLabel;this.modelNames=a.modelNames;this.modelNumbers=a.modelNumbers;this.frameTitles=a.frameTitles;this.mergeAtomArrays(a)},"JM.ModelSet");c(c$,"getUnitCell",function(a){return!this.haveUnitCells||0>a||a>=this.mc?null:null!=this.am[a].simpleCage?this.am[a].simpleCage:null==this.unitCells||a>=this.unitCells.length||!this.unitCells[a].haveUnitCell()?null:this.unitCells[a]},
"~N");c(c$,"setModelCage",function(a,b){0>a||a>=this.mc||(this.am[a].simpleCage=b,this.haveUnitCells=!0)},"~N,J.api.SymmetryInterface");c(c$,"getPlaneIntersection",function(a,b,d,c,g){var f=null;switch(a){case 1614417948:if(null==g)return null;f=g.getCanonicalCopy(d,!0);break;case 1679429641:f=this.boxInfo.getCanonicalCopy(d)}a=new JU.Lst;a.addLast(f);return this.intersectPlane(b,a,c)},"~N,JU.P4,~N,~N,J.api.SymmetryInterface");c(c$,"getModelName",function(a){return 1>this.mc?"":0<=a?this.modelNames[a]:
this.modelNumbersForAtomLabel[-1-a]},"~N");c(c$,"getModelTitle",function(a){return this.getInfo(a,"title")},"~N");c(c$,"getModelFileName",function(a){return this.getInfo(a,"fileName")},"~N");c(c$,"getModelFileType",function(a){return this.getInfo(a,"fileType")},"~N");c(c$,"setFrameTitle",function(a,b){if(n(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$,"getGroups",function(){for(var a=0,b=0;b<this.mc;b++)a+=this.am[b].getGroupCount();for(var a=Array(a),d=b=0;b<this.mc;b++)for(var c=0;c<this.am[b].chainCount;c++)for(var g=0;g<this.am[b].chains[c].groupCount;g++)a[d]=this.am[b].chains[c].groups[g],a[d].groupIndex=d,d++;return a});c(c$,"getNotionalUnitcell",function(){var a=
this.getUnitCell(0);return null==a?null:a.getNotionalUnitCell()});c(c$,"setCrystallographicDefaults",function(){return!this.haveBioModels&&this.someModelsHaveSymmetry&&this.someModelsHaveFractionalCoordinates});c(c$,"getBoundBoxCenter",function(a){return this.isJmolDataFrameForModel(a)?new JU.P3:this.boxInfo.getBoundBoxCenter()},"~N");c(c$,"getBoundBoxCornerVector",function(){return this.boxInfo.getBoundBoxCornerVector()});c(c$,"getBBoxVertices",function(){return this.boxInfo.getBoundBoxVertices()});
c(c$,"setBoundBox",function(a,b,d,c){this.isBbcageDefault=!1;this.bboxAtoms=this.bboxModels=null;this.boxInfo.setBoundBox(a,b,d,c)},"JU.P3,JU.P3,~B,~N");c(c$,"getBoundBoxCommand",function(a){if(!a&&null!=this.bboxAtoms)return"boundbox "+JU.Escape.eBS(this.bboxAtoms);this.ptTemp.setT(this.boxInfo.getBoundBoxCenter());var b=this.boxInfo.getBoundBoxCornerVector();a=a?"boundbox "+JU.Escape.eP(this.ptTemp)+" "+JU.Escape.eP(b)+"\n#or\n":"";this.ptTemp.sub(b);a+="boundbox corners "+JU.Escape.eP(this.ptTemp)+
" ";this.ptTemp.scaleAdd2(2,b,this.ptTemp);b=Math.abs(8*b.x*b.y*b.z);return a+=JU.Escape.eP(this.ptTemp)+" # volume = "+b},"~B");c(c$,"findAtomsInRectangle",function(a){for(var b=this.vwr.getVisibleFramesBitSet(),d=new JU.BS,c=this.ac;0<=--c;){var g=this.at[c];b.get(g.mi)?g.checkVisible()&&a.contains(g.sX,g.sY)&&d.set(c):c=this.am[g.mi].firstAtomIndex}return d},"JU.Rectangle");c(c$,"getDefaultVdwType",function(a){return!this.am[a].isBioModel?J.c.VDW.AUTO_BABEL:0==this.am[a].hydrogenCount?J.c.VDW.AUTO_JMOL:
J.c.VDW.AUTO_BABEL},"~N");c(c$,"setRotationRadius",function(a,b){return this.isJmolDataFrameForModel(a)?(this.am[a].defaultRotationRadius=b,!1):!0},"~N,~N");c(c$,"calcRotationRadius",function(a,b){if(this.isJmolDataFrameForModel(a)){var d=this.am[a].defaultRotationRadius;return 0==d?10:d}for(var d=0,c=this.ac;0<=--c;)if(this.isJmolDataFrameForAtom(this.at[c]))for(a=this.at[c].mi;0<=c&&this.at[c].mi==a;)c--;else{var g=this.at[c],g=b.distance(g)+this.getRadiusVdwJmol(g);g>d&&(d=g)}return 0==d?10:d},
"~N,JU.P3");c(c$,"calcBoundBoxDimensions",function(a,b){null!=a&&0>a.nextSetBit(0)&&(a=null);null==a&&this.isBbcageDefault||0==this.ac||(this.bboxModels=this.getModelBS(this.bboxAtoms=JU.BSUtil.copy(a),!1),this.calcAtomsMinMax(a,this.boxInfo)==this.ac&&(this.isBbcageDefault=!0),null==a&&null!=this.unitCells&&this.calcUnitCellMinMax(),this.boxInfo.setBbcage(b))},"JU.BS,~N");c(c$,"getBoxInfo",function(a,b){if(null==a)return this.boxInfo;var d=new JU.BoxInfo;this.calcAtomsMinMax(a,d);d.setBbcage(b);
return d},"JU.BS,~N");c(c$,"calcAtomsMinMax",function(a,b){b.reset();for(var d=0,c=null==a,g=c?this.ac-1:a.nextSetBit(0);0<=g;g=c?g-1:a.nextSetBit(g+1))d++,this.isJmolDataFrameForAtom(this.at[g])||b.addBoundBoxPoint(this.at[g]);return d},"JU.BS,JU.BoxInfo");c(c$,"calcUnitCellMinMax",function(){for(var a=0;a<this.mc;a++)if(this.unitCells[a].getCoordinatesAreFractional())for(var b=this.unitCells[a].getUnitCellVertices(),d=0;8>d;d++)this.boxInfo.addBoundBoxPoint(b[d])});c(c$,"calcRotationRadiusBs",function(a){for(var b=
this.getAtomSetCenter(a),d=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var g=this.at[c],g=b.distance(g)+this.getRadiusVdwJmol(g);g>d&&(d=g)}return 0==d?10:d},"JU.BS");c(c$,"getCenterAndPoints",function(a,b){for(var d,c,g=b?1:0,f=a.size();0<=--f;){var j=a.get(f);d=j[0];n(j[1],JU.BS)?(c=j[1],g+=Math.min(d.cardinality(),c.cardinality())):g+=Math.min(d.cardinality(),j[1].length)}var h=O(2,g,null);b&&(h[0][0]=new JU.P3,h[1][0]=new JU.P3);for(f=a.size();0<=--f;)if(j=a.get(f),d=j[0],n(j[1],JU.BS)){c=j[1];
for(var j=d.nextSetBit(0),l=c.nextSetBit(0);0<=j&&0<=l;j=d.nextSetBit(j+1),l=c.nextSetBit(l+1))h[0][--g]=this.at[j],h[1][g]=this.at[l],b&&(h[0][0].add(this.at[j]),h[1][0].add(this.at[l]))}else{c=j[1];j=d.nextSetBit(0);for(l=0;0<=j&&l<c.length;j=d.nextSetBit(j+1),l++)h[0][--g]=this.at[j],h[1][g]=c[l],b&&(h[0][0].add(this.at[j]),h[1][0].add(c[l]))}b&&(h[0][0].scale(1/(h[0].length-1)),h[1][0].scale(1/(h[1].length-1)));return h},"JU.Lst,~B");c(c$,"getAtomSetCenter",function(a){for(var b=new JU.P3,d=0,
c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.isJmolDataFrameForAtom(this.at[c])||(d++,b.add(this.at[c]));0<d&&b.scale(1/d);return b},"JU.BS");c(c$,"getAverageAtomPoint",function(){null==this.averageAtomPoint&&(this.averageAtomPoint=new JU.P3).setT(this.getAtomSetCenter(this.vwr.getAllAtoms()));return this.averageAtomPoint});c(c$,"setAPm",function(a,b,d,c,g,f,j){this.setAPa(a,b,d,c,g,f,j);switch(b){case 1095763991:case 1632634891:this.vwr.getBoolean(603979944)&&this.assignAromaticBondsBs(!0,null)}},
"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"addStateScript",function(a,b,d,c,g,f,j){var h=this.vwr.am.cmi;f?(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$,"calculateStructuresAllExcept",function(a,b,d,c,g,f){this.freezeModels();var j="";a=JU.BSUtil.copyInvert(a,this.mc);g&&this.setDefaultStructure(a);
for(var h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1))j+=this.am[h].calculateStructures(b,d,c,g,f);g&&this.setStructureIndexes();return j},"JU.BS,~B,~B,~B,~B,~B");c(c$,"setDefaultStructure",function(a){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.am[b].isBioModel&&null==this.am[b].defaultStructure&&(this.am[b].defaultStructure=this.getProteinStructureState(this.am[b].bsAtoms,!1,!1,0))},"JU.BS");c(c$,"setProteinType",function(a,b){var d=-1,c=-1,g=this.getModelBS(a,!1);this.setDefaultStructure(g);
for(var f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){c!=f-1&&(d=-1);var d=this.at[f].group.setProteinStructureType(b,d),j=this.at[f].mi;this.proteinStructureTainted=this.am[j].structureTainted=!0;c=f=this.at[f].group.lastAtomIndex}d=D(this.mc,0);for(f=0;f<this.ac;)j=this.at[f].mi,g.get(j)?(c=this.at[f].getStrucNo(),1E3>c&&c>d[j]&&(d[j]=c),f=this.at[f].group.lastAtomIndex+1):f=this.am[j].firstAtomIndex+this.am[j].ac;for(f=0;f<this.ac;)j=this.at[f].mi,g.get(j)?(1E3<this.at[f].getStrucNo()&&this.at[f].group.setStrucNo(++d[j]),
f=this.at[f].group.lastAtomIndex+1):f=this.am[j].firstAtomIndex+this.am[j].ac},"JU.BS,J.c.STR");c(c$,"freezeModels",function(){for(var a=this.mc;0<=--a;)this.am[a].freeze()});c(c$,"getStructureList",function(){return this.vwr.getStructureList()});c(c$,"setStructureList",function(a){for(var b=this.mc;0<=--b;)this.am[b].setStructureList(a)},"java.util.Map");c(c$,"setConformation",function(a){for(var b=this.getModelBS(a,!1),d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.am[d].setConformation(a);return a},
"JU.BS");c(c$,"getConformation",function(a,b,d){for(var c=new JU.BS,g=this.mc;0<=--g;)if(g==a||0>a){var f=this.getAltLocListInModel(g),j=this.getAltLocCountInModel(g);if(!(0<b&&b>=j)){var h=this.vwr.getModelUndeletedAtomsBitSet(g);if(0<=b&&!this.am[g].getPdbConformation(h,b))for(;0<=--j;)j!=b&&h.andNot(this.getAtomBitsMDa(1048607,f.substring(j,j+1)));0<=h.nextSetBit(0)&&(c.or(h),d&&this.am[g].setConformation(h))}}return c},"~N,~N,~B");c(c$,"getHeteroList",function(a){for(var b=new java.util.Hashtable,
d=!1,c=this.mc;0<=--c;)if(0>a||c==a){var g=this.getInfo(c,"hetNames");if(null!=g)for(var d=!0,f,g=g.entrySet().iterator();g.hasNext()&&((f=g.next())||1);){var j=f.getKey();b.put(j,f.getValue())}}return d?b:this.getInfoM("hetNames")},"~N");c(c$,"getInfoM",function(a){return null==this.msInfo?null:this.msInfo.get(a)},"~S");c(c$,"getMSInfoB",function(a){a=this.getInfoM(a);return n(a,Boolean)&&a.booleanValue()},"~S");c(c$,"mergeTrajectories",function(a){if(null==this.trajectorySteps){if(!a)return 0;this.trajectorySteps=
new JU.Lst}for(a=this.trajectorySteps.size();a<this.mc;a++)this.trajectorySteps.addLast(null);return this.mc},"~B");c(c$,"getTrajectoryIndex",function(a){return this.am[a].trajectoryBaseIndex},"~N");c(c$,"isTrajectory",function(a){return this.am[a].isTrajectory},"~N");c(c$,"isTrajectoryMeasurement",function(a){if(null!=a)for(var b=a[0],d,c=1;c<=b;c++)if(0<=(d=a[c])&&this.am[this.at[d].mi].isTrajectory)return!0;return!1},"~A");c(c$,"getModelBS",function(a,b){for(var d=new JU.BS,c=0,g=null==a,c=g?0:
a.nextSetBit(0);0<=c&&c<this.ac;c=g?c+1:a.nextSetBit(c+1)){d.set(c=this.at[c].mi);if(b)for(var f=this.am[c].trajectoryBaseIndex,j=0;j<this.mc;j++)this.am[j].trajectoryBaseIndex==f&&d.set(j);c=this.am[c].firstAtomIndex+this.am[c].ac-1}return d},"JU.BS,~B");c(c$,"getIterativeModels",function(a){for(var b=new JU.BS,d=0;d<this.mc;d++)(a||!this.isJmolDataFrameForModel(d))&&this.am[d].trajectoryBaseIndex==d&&b.set(d);return b},"~B");c(c$,"isTrajectorySubFrame",function(a){return this.am[a].isTrajectory&&
this.am[a].trajectoryBaseIndex!=a},"~N");c(c$,"selectDisplayedTrajectories",function(a){for(var b=0;b<this.mc;b++)this.am[b].isTrajectory&&this.at[this.am[b].firstAtomIndex].mi!=b&&a.clear(b);return a},"JU.BS");c(c$,"fillAtomData",function(a,b){if(0!=(b&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);a.atomMolecule=D(this.ac,0);for(var d,c=0;c<this.molecules.length;c++){d=a.bsMolecules[c]=this.molecules[c].atomList;for(var g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))a.atomMolecule[g]=
c}}0!=(b&8)?(d=D(1,0),a.hAtomRadius=this.vwr.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,d,!1,!0,null),a.hydrogenAtomCount=d[0]):(a.firstAtomIndex=0>a.modelIndex?null==a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.am[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=0==this.ac?0:this.at[a.firstAtomIndex].mi,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,b))},"J.atomdata.AtomData,~N");c(c$,"getModelNumberDotted",function(a){return 1>
this.mc||a>=this.mc||0>a?"":JU.Escape.escapeModelFileNumber(this.modelFileNumbers[a])},"~N");c(c$,"getModelNumber",function(a){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$,"setInfo",function(a,b,d){this.am[a].auxiliaryInfo.put(b,d)},"~N,~O,~O");c(c$,"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$,"getInsertionCountInModel",function(a){return this.am[a].nInsertions},"~N");c$.modelFileNumberFromFloat=c(c$,"modelFileNumberFromFloat",function(a){var b=s(Math.floor(a));for(a=s(Math.floor(1E4*
(a-b+1E-5)));0!=a&&0==a%10;)a/=10;return 1E6*b+a},"~N");c(c$,"getAltLocCountInModel",function(a){return this.am[a].nAltLocs},"~N");c(c$,"getChainCountInModelWater",function(a,b){if(0>a){for(var d=0,c=this.mc;0<=--c;)d+=this.am[c].getChainCount(b);return d}return this.am[a].getChainCount(b)},"~N,~B");c(c$,"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$,"calcSelectedGroupsCount",function(){for(var a=
this.vwr.bsA(),b=this.mc;0<=--b;)this.am[b].calcSelectedGroupsCount(a)});c(c$,"calcSelectedMonomersCount",function(){for(var a=this.vwr.bsA(),b=this.mc;0<=--b;)this.am[b].calcSelectedMonomersCount(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$,"getFileHeader",function(a){if(0>a)return"";if(this.am[a].isBioModel)return this.am[a].getFullPDBHeader();a=this.getInfo(a,"fileHeader");null==a&&(a=this.modelSetName);return null!=a?a:"no header information found"},"~N");c(c$,"getAltLocIndexInModel",function(a,b){if("\x00"==b)return 0;var d=this.getAltLocListInModel(a);return 0==d.length?0:d.indexOf(b)+1},"~N,~S");c(c$,
"getInsertionCodeIndexInModel",function(a,b){if("\x00"==b)return 0;var d=this.getInsertionListInModel(a);return 0==d.length?0:d.indexOf(b)+1},"~N,~S");c(c$,"getAltLocListInModel",function(a){a=this.getInfo(a,"altLocs");return null==a?"":a},"~N");c(c$,"getInsertionListInModel",function(a){a=this.getInfo(a,"insertionCodes");return null==a?"":a},"~N");c(c$,"getModelSymmetryCount",function(a){return 0<this.am[a].biosymmetryCount?this.am[a].biosymmetryCount:null==this.unitCells||null==this.unitCells[a]?
0:this.unitCells[a].getSpaceGroupOperationCount()},"~N");c(c$,"getModelCellRange",function(a){return null==this.unitCells?null:this.unitCells[a].getCellRange()},"~N");c(c$,"getLastVibrationVector",function(a,b){if(null!=this.vibrations)for(var d,c=0>=a?0:this.am[a].firstAtomIndex,g=0>a||a>=this.mc-1?this.ac:this.am[a+1].firstAtomIndex;--g>=c;)if((0>a||this.at[g].mi==a)&&((1276121113==b||0==b)&&null!=(d=this.getModulation(g))||(4166==b||0==b)&&null!=(d=this.getVibration(g,!1)))&&d.isNonzero())return g;
return-1},"~N,~N");c(c$,"getModulationList",function(a,b,d){var c=new JU.Lst;if(null!=this.vibrations)for(var g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))n(this.vibrations[g],J.api.JmolModulationSet)?c.addLast(this.vibrations[g].getModulation(b,d)):c.addLast(Float.$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(null==this.partialCharges||0>a)return null;var c=d=0,g=0,f=
0,j=new JU.V3,h=new JU.V3;null==b&&(b=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var l=b.nextSetBit(0);0<=l;l=b.nextSetBit(l+1))if(!(this.at[l].mi!=a||this.at[l].isDeleted())){var q=this.partialCharges[l];0>q?(c++,f+=q,h.scaleAdd2(q,this.at[l],h)):0<q&&(d++,g+=q,j.scaleAdd2(q,this.at[l],j))}if(0.01<Math.abs(g+f))return JU.Logger.info("Dipole calculation requires balanced charges: "+g+" "+f),null;if(0==c||0==d)return null;j.add(h);j.scale(4.8);return j},"~N,JU.BS");c(c$,"getMoleculeCountInModel",
function(a){var b=0;0==this.moleculeCount&&this.getMolecules();if(0>a)return this.moleculeCount;for(var d=0;d<this.mc;d++)a==d&&(b+=this.am[d].moleculeCount);return b},"~N");c(c$,"calcSelectedMoleculesCount",function(){var a=this.vwr.bsA();0==this.moleculeCount&&this.getMolecules();this.selectedMolecules.xor(this.selectedMolecules);for(var b=new JU.BS,d=0;d<this.moleculeCount;d++)JU.BSUtil.copy2(a,b),b.and(this.molecules[d].atomList),0<b.length()&&this.selectedMolecules.set(d)});c(c$,"setCentroid",
function(a,b){var d=this.getNotInCentroid(a,b);null!=d&&0<=d.nextSetBit(0)&&this.vwr.deleteAtoms(d,!1)},"JU.BS,~A");c(c$,"getNotInCentroid",function(a,b){var d=a.nextSetBit(0);if(0>d)return null;d=this.getUnitCell(this.at[d].mi);return null==d?null:d.notInCentroid(this,a,b)},"JU.BS,~A");c(c$,"getMolecules",function(){if(0<this.moleculeCount)return this.molecules;null==this.molecules&&(this.molecules=Array(4));this.moleculeCount=0;for(var a=null,b=Array(this.mc),d=null,c=0;c<this.mc;c++)b[c]=this.vwr.getModelUndeletedAtomsBitSet(c),
a=this.am[c],a.moleculeCount=0,d=a.getBioBranches(d);this.molecules=JU.JmolMolecule.getMolecules(this.at,b,d,null);for(c=this.moleculeCount=this.molecules.length;0<=--c;)a=this.am[this.molecules[c].modelIndex],a.firstMoleculeIndex=c,a.moleculeCount++;return this.molecules});c(c$,"initializeBspf",function(){if(!(null!=this.bspf&&this.bspf.isValid)){this.showRebondTimes&&JU.Logger.startTimer("build bspf");var a=new J.bspt.Bspf(3);JU.Logger.debugging&&JU.Logger.debug("sequential bspt order");for(var b=
JU.BS.newN(this.mc),d=this.ac;0<=--d;){var c=this.at[d];!c.isDeleted()&&!this.isTrajectorySubFrame(c.mi)&&(a.addTuple(this.am[c.mi].trajectoryBaseIndex,c),b.set(c.mi))}this.showRebondTimes&&(JU.Logger.checkTimer("build bspf",!1),a.stats());for(d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))a.validateModel(d,!0);a.isValid=!0;this.bspf=a}});c(c$,"initializeBspt",function(a){this.initializeBspf();this.bspf.isInitializedIndex(a)||this.bspf.initialize(a,this.at,this.vwr.getModelUndeletedAtomsBitSet(a))},"~N");
c(c$,"setIteratorForPoint",function(a,b,d,c){0>b?a.setCenter(d,c):(this.initializeBspt(b),a.setModel(this,b,this.am[b].firstAtomIndex,2147483647,d,c,null))},"J.api.AtomIndexIterator,~N,JU.T3,~N");c(c$,"setIteratorForAtom",function(a,b,d,c,g){0>b&&(b=this.at[d].mi);b=this.am[b].trajectoryBaseIndex;this.initializeBspt(b);a.setModel(this,b,this.am[b].firstAtomIndex,d,this.at[d],c,g)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");c(c$,"getSelectedAtomIterator",function(a,b,d,c,g){this.initializeBspf();
if(g){g=this.getModelBS(a,!1);for(var f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1))this.initializeBspt(f);g=new JM.AtomIteratorWithinModelSet(g)}else g=new JM.AtomIteratorWithinModel;g.initialize(this.bspf,a,b,d,c,this.vwr.isParallel());return g},"JU.BS,~B,~B,~B,~B");h(c$,"getBondCountInModel",function(a){return 0>a?this.bondCount:this.am[a].getBondCount()},"~N");c(c$,"getAtomCountInModel",function(a){return 0>a?this.ac:this.am[a].ac},"~N");c(c$,"getModelAtomBitSetIncludingDeletedBs",function(a){var b=
new JU.BS;null==a&&null==this.bsAll&&(this.bsAll=JU.BSUtil.setAll(this.ac));if(null==a)b.or(this.bsAll);else for(var d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))b.or(this.getModelAtomBitSetIncludingDeleted(d,!1));return b},"JU.BS");c(c$,"getModelAtomBitSetIncludingDeleted",function(a,b){var d=0>a?this.bsAll:this.am[a].bsAtoms;null==d&&(d=this.bsAll=JU.BSUtil.setAll(this.ac));return b?JU.BSUtil.copy(d):d},"~N,~B");c(c$,"getAtomBitsMaybeDeleted",function(a,b){var d,c;switch(a){default:return this.getAtomBitsMDa(a,
b);case 1073741925:return this.getAnnotationBits("domains",1073741925,b);case 1073742189:return this.getAnnotationBits("validation",1073742189,b);case 1073741916:return this.getAnnotationBits("dssr",1073741916,b);case 1073742128:return this.getAnnotationBits("rna3d",1073742128,b);case 1678770178:case 1048585:return this.getAtomBitsMDb(a,b);case 1073741864:return c=new JU.BS,!this.haveBioModels||0!=b.length%2?c:this.getAtomBitsMDa(1087373318,this.bioModel.getBasePairBits(this,b));case 1679429641:var g=
this.getBoxInfo(b,1);c=this.getAtomsWithin(g.getBoundBoxCornerVector().length()+1E-4,g.getBoundBoxCenter(),null,-1);for(d=c.nextSetBit(0);0<=d;d=c.nextSetBit(d+1))g.isWithin(this.at[d])||c.clear(d);return c;case 1095761925:c=new JU.BS;d=b;this.ptTemp1.set(d[0]/1E3,d[1]/1E3,d[2]/1E3);for(d=this.ac;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,!1)&&c.set(d);return c;case 1095761926:c=JU.BSUtil.newBitSet2(0,this.ac);d=b;g=[s(d[0]/1E3)-1,s(d[1]/1E3)-1,s(d[2]/1E3)-1,s(d[0]/1E3),s(d[1]/1E3),
s(d[2]/1E3),0];for(d=this.mc;0<=--d;){var f=this.getUnitCell(d);null==f?JU.BSUtil.andNot(c,this.am[d].bsAtoms):c.andNot(f.notInCentroid(this,this.am[d].bsAtoms,g))}return c;case 1095761936:return this.getMoleculeBitSet(b);case 1087373320:return this.getSequenceBits(b,null);case 1048615:return this.haveBioModels?this.bioModel.getSelectCodeRange(this,b):new JU.BS;case 3145772:c=JU.BS.newN(this.ac);g=-1;f=0;for(d=this.ac;0<=--d;){var j=this.at[d],h=j.atomSymmetry;if(null!=h){if(j.mi!=g){g=j.mi;if(null==
this.getModelCellRange(g))continue;f=this.getModelSymmetryCount(g)}for(var j=0,l=f;0<=--l;)if(h.get(l)&&1<++j){c.set(d);break}}}return c;case 1089470478:return JU.BSUtil.copy(null==this.bsSymmetry?this.bsSymmetry=JU.BS.newN(this.ac):this.bsSymmetry);case 1614417948:c=new JU.BS;if(null==this.vwr.getCurrentUnitCell())return c;this.ptTemp1.set(1,1,1);for(d=this.ac;0<=--d;)this.isInLatticeCell(d,this.ptTemp1,this.ptTemp2,!1)&&c.set(d);return c}},"~N,~O");c(c$,"getAnnotationBits",function(a,b,d){for(var c=
new JU.BS,g=this.vwr.getAnnotationParser(),f,j=this.mc;0<=--j;)null!=(f=this.getInfo(j,a))&&c.or(g.getAtomBits(this.vwr,d,this.getCachedAnnotationMap(j,a+" V ",f),this.am[j].dssrCache,b,j,this.am[j].bsAtoms));return c},"~S,~N,~S");c(c$,"getCachedAnnotationMap",function(a,b,d){a=null==this.am[a].dssrCache&&null!=d?this.am[a].dssrCache=new java.util.Hashtable:this.am[a].dssrCache;if(null==a)return null;var c=a.get(b);null==c&&null!=d&&(c=n(d,JS.SV)||n(d,java.util.Hashtable)?d:this.vwr.evaluateExpressionAsVariable(d),
a.put(b,c));return n(c,JS.SV)||n(c,java.util.Hashtable)?c:null},"~N,~S,~O");c(c$,"isInLatticeCell",function(a,b,d,c){var g=this.getUnitCell(this.at[a].mi);d.setT(this.at[a]);return null!=g&&g.checkUnitCell(g,b,d,c)},"~N,JU.P3,JU.P3,~B");c(c$,"getAtomsWithinRadius",function(a,b,d,c){var g=new JU.BS,f=this.getIterativeModels(!1);b=JU.BSUtil.andNot(b,this.vwr.slm.bsDeleted);var j=this.getSelectedAtomIterator(null,!1,!1,!1,!1);if(d){d=!this.vwr.g.legacyJavaFloat;for(var h=new JU.P3,l=b.nextSetBit(0);0<=
l;l=b.nextSetBit(l+1))for(var q=this.mc;0<=--q;)f.get(q)&&(0>a?this.getAtomsWithin(a,this.at[l].getFractionalUnitCoordPt(d,!0,h),g,-1):(this.setIteratorForAtom(j,q,l,a,c),j.addAtoms(g)))}else{g.or(b);for(l=b.nextSetBit(0);0<=l;l=b.nextSetBit(l+1))0>a?this.getAtomsWithin(a,this.at[l],g,this.at[l].mi):(this.setIteratorForAtom(j,-1,l,a,c),j.addAtoms(g))}j.release();return g},"~N,JU.BS,~B,J.atomdata.RadiusData");c(c$,"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 f=this.at[g];0<=c&&this.at[g].mi!=c||!d.get(g)&&f.getFractionalUnitDistance(b,this.ptTemp1,this.ptTemp2)<=a&&d.set(f.i)}return d}c=this.getIterativeModels(!0);g=this.getSelectedAtomIterator(null,!1,!1,!1,!1);for(f=this.mc;0<=--f;)c.get(f)&&(this.setIteratorForAtom(g,-1,this.am[f].firstAtomIndex,-1,null),g.setCenter(b,a),g.addAtoms(d));g.release();return d},"~N,JU.P3,JU.BS,~N");c(c$,"deleteBonds",function(a,b){if(!b)for(var d=new JU.BS,c=new JU.BS,g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+
1)){var f=this.bo[g].atom1;this.am[f.mi].isModelKit||(d.clearAll(),c.clearAll(),d.set(f.i),c.set(this.bo[g].getAtomIndex2()),this.addStateScript("connect ",null,d,c,"delete",!1,!0))}this.dBb(a,b)},"JU.BS,~B");c(c$,"makeConnections2",function(a,b,d,c,g,f,j,h,l,q){null==j&&(j=new JU.BS);var p=65535==d,v=131071==d;v&&(d=1);var m=JM.Bond.isOrderH(d),n=!1,s=!1,r=!1,t=!1;switch(c){case 12291:return this.deleteConnections(a,b,d,g,f,h,v);case 603979873:case 1073741852:if(515!=d)return this.autoBond(g,f,j,
h,m,603979873==c);s=t=!0;break;case 1087373321:n=s=!0;break;case 1073742025:s=!0;break;case 1073741904:r=!0}c=!n||p;p=!n&&!p;this.defaultCovalentMad=this.vwr.getMadBond();var v=0>a,u=0>b,w=v||u,x=!h||0.1!=a||1E8!=b;x&&(a=this.fixD(a,v),b=this.fixD(b,u));var z=this.getDefaultMadFromOrder(d),B=0,C=0,D=null,F=null,G=null,H="\x00",K=d|131072;try{for(var I=g.nextSetBit(0);0<=I;I=g.nextSetBit(I+1)){if(h)D=this.bo[I],F=D.atom1,G=D.atom2;else{F=this.at[I];if(F.isDeleted())continue;H=this.isModulated(I)?"\x00":
F.altloc}for(var L=h?0:f.nextSetBit(0);0<=L;L=f.nextSetBit(L+1)){if(h)L=2147483646;else{if(L==I)continue;G=this.at[L];if(F.mi!=G.mi||G.isDeleted())continue;if("\x00"!=H&&H!=G.altloc&&"\x00"!=G.altloc)continue;D=F.getBond(G)}if(!((null==D?s:r)||x&&!this.isInRange(F,G,a,b,v,u,w)))if(null==D)j.set(this.bondAtoms(F,G,d,z,j,q,l,!0).index),B++;else if(p&&(D.setOrder(d),this.bsAromatic.clear(D.index)),c||d==D.order||K==D.order||m&&D.isHydrogen())j.set(D.index),C++}}}catch(M){if(!y(M,Exception))throw M;}t&&
this.assignAromaticBondsBs(!0,j);n||this.sm.setShapeSizeBs(1,-2147483648,null,j);return[B,C]},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(c$,"autoBondBs4",function(a,b,d,c,g,f){if(f)return this.autoBond_Pre_11_9_24(a,b,d,c,g);if(0==this.ac)return 0;0==g&&(g=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();f=this.vwr.getFloat(570425348);var j=this.vwr.getFloat(570425364),j=j*j,h=0;this.showRebondTimes&&JU.Logger.startTimer("autobond");var l=-1,q=null==a,p,v;q?(v=0,p=null):(a.equals(b)?p=a:(p=
JU.BSUtil.copy(a),p.or(b)),v=p.nextSetBit(0));for(var m=this.getSelectedAtomIterator(null,!1,!1,!0,!1),n=!1;0<=v&&v<this.ac;v=q?v+1:p.nextSetBit(v+1)){var s=q||a.get(v),r=q||b.get(v),t=this.at[v];if(!t.isDeleted()){var u=t.mi;if(u!=l){l=u;if(this.isJmolDataFrameForModel(u)){v=this.am[u].firstAtomIndex+this.am[u].ac-1;continue}n=this.getInfoB(u,"autoBondUsingOccupation")}u=t.getBondingRadius();if(0!=u){var w=null!=d&&d.get(v);for(this.setIteratorForAtom(m,-1,v,u+this.maxBondingRadius+f,null);m.hasNext();){var x=
this.at[m.next()];if(!x.isDeleted()){var y=x.i,z=q||a.get(y),B=q||b.get(y);!z&&!B||(!(s&&B||r&&z)||w&&d.get(y)||n&&null!=this.occupancies&&50>this.occupancies[v]!=50>this.occupancies[y])||(y=JM.BondCollection.getBondOrderFull(u,x.getBondingRadius(),m.foundDistance2(),j,f),0<y&&this.autoBondCheck(t,x,y,g,c)&&h++)}}m.release()}}}this.showRebondTimes&&JU.Logger.checkTimer("autoBond",!1);return h},"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B");c(c$,"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 f=a.getFormalCharge();if(0!=f){var j=b.getFormalCharge();if(0>f&&0>j||0<f&&0<j)return!1}if(a.altloc!=b.altloc&&"\x00"!=a.altloc&&"\x00"!=b.altloc&&null==this.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$,"autoBond_Pre_11_9_24",function(a,b,d,c,g){if(0==this.ac)return 0;0==g&&(g=1);1.4E-45==this.maxBondingRadius&&
this.findMaxRadii();var f=this.vwr.getFloat(570425348),j=this.vwr.getFloat(570425364),j=j*j,h=0;this.initializeBspf();for(var l=-1,q=this.ac;0<=--q;){var p=null==a||a.get(q),v=null==b||b.get(q);if(p||v){var m=this.at[q];if(!m.isDeleted()){var n=m.mi;if(n!=l&&(l=n,this.isJmolDataFrameForModel(n))){for(;0<=--q&&this.at[q].mi==n;);q++;continue}var s=m.getBondingRadius();if(0!=s){var r=s+this.maxBondingRadius+f;this.initializeBspt(n);n=this.bspf.getCubeIterator(n);for(n.initialize(m,r,!0);n.hasMoreElements();)if(r=
n.nextElement(),!(r===m||r.isDeleted())){var t=r.i,u=null==a||a.get(t),w=null==b||b.get(t);if(!(!u&&!w||null!=d&&d.get(t)&&d.get(q)))if(p&&w||v&&u)t=JM.BondCollection.getBondOrderFull(s,r.getBondingRadius(),n.foundDistance2(),j,f),0<t&&this.autoBondCheck(m,r,t,g,c)&&h++}n.release()}}}}return h},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(c$,"autoBond",function(a,b,d,c,g,f){if(c){c=a;a=new JU.BS;b=new JU.BS;for(var j=c.nextSetBit(0);0<=j;j=c.nextSetBit(j+1))a.set(this.bo[j].atom1.i),b.set(this.bo[j].atom2.i)}return[g?
this.autoHbond(a,b,!1):this.autoBondBs4(a,b,null,d,this.vwr.getMadBond(),f),0]},"JU.BS,JU.BS,JU.BS,~B,~B,~B");c(c$,"autoHbond",function(a,b,d){if(d){for(var c=this.getModelBS(a,!1),g=c.nextSetBit(0);0<=g&&d;g=c.nextSetBit(g+1))d=!this.am[g].hasRasmolHBonds;if(d)return 0}d=!1;for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))if(1==this.at[g].getElementNumber()){d=!0;break}c=new JU.BS;g=this.vwr.getBoolean(603979853);if(null==b||g&&!d)return JU.Logger.info((null==b?"DSSP/DSSR ":"RasMol")+" pseudo-hbond calculation"),
this.calcRasmolHydrogenBonds(a,b,null,!1,2147483647,!1,c),-JU.BSUtil.cardinalityOf(c);JU.Logger.info(d?"Standard Hbond calculation":"Jmol pseudo-hbond calculation");var f=null;if(!d){f=new JU.BS;for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))switch(this.at[g].atomID){case 64:case 4:case 14:case 15:case 16:case 17:f.set(g)}}var j=this.vwr.getFloat(570425361),h=3.141592653589793*this.vwr.getFloat(570425360)/180,l=j*j,q=JM.ModelSet.hbondMin*JM.ModelSet.hbondMin,p=j>JM.ModelSet.hbondMin?q:l,v=j>JM.ModelSet.hbondMin?
JM.ModelSet.hbondMin:j,m=0,n=0,s=new JU.V3,r=new JU.V3;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var t=null,u=null;b=this.getSelectedAtomIterator(b,!1,!1,!1,!1);for(g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1)){var w=this.at[g],x=w.getElementNumber(),y=1==x;if(!(!y&&(d||7!=x&&8!=x)||y&&!d)){var z,B,C;if(y){x=w.bonds;if(null==x)continue;C=!1;for(z=0;z<x.length&&!C;z++)C=x[z].getOtherAtom(w).getElementNumber(),C=7==C||8==C;if(!C)continue;B=v;x=1;z=p;C=!1}else B=j,x=q,z=
l,C=f.get(g);for(this.setIteratorForAtom(b,-1,w.i,B,null);b.hasNext();){B=this.at[b.next()];var D=B.getElementNumber();if(!(B===w||!y&&7!=D&&8!=D||y&&1==D||(n=b.foundDistance2())<x||n>z||C&&f.get(B.i)||w.isBonded(B))){if(0<h){s.sub2(w,B);if(null==(u=JM.ModelSet.checkMinAttachedAngle(w,h,s,r,d)))continue;s.scale(-1);if(null==(t=JM.ModelSet.checkMinAttachedAngle(B,h,s,r,d)))continue}var D=0,F;y&&!Float.isNaN(t.x)&&!Float.isNaN(u.x)?(F=4096,D=JM.HBond.getEnergy(Math.sqrt(n),t.distance(w),t.distance(u),
B.distance(u))/1E3):F=2048;c.set(this.addHBond(w,B,F,D));m++}}}}b.release();this.sm.setShapeSizeBs(1,-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return d?m:-m},"JU.BS,JU.BS,~B");c$.checkMinAttachedAngle=c(c$,"checkMinAttachedAngle",function(a,b,d,c,g){var f=a.bonds;if(null==f||0==f.length)return JU.P3.new3(NaN,0,0);for(var j=null,h=3.4028235E38,l=f.length;0<=--l;)if(f[l].isCovalent()){var q=f[l].getOtherAtom(a);if(g||1!=q.getElementNumber()){c.sub2(a,q);var p=c.angle(d);
if(p<b)return null;p<h&&(j=q,h=p)}}return j},"JM.Atom,~N,JU.V3,JU.V3,~B");c(c$,"setStructureIndexes",function(){for(var a,b=0,d=-1,c=-1,g=-1,f=0;f<this.ac;f++){if((c=this.at[f].mi)!=g)b=0,g=c,d=-1;if((a=this.at[f].getStrucNo())!=d&&0!=a)this.at[f].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$,"getAtomsConnected",function(a,b,d,c){for(var g=n(c,JM.BondSet),f=g?new JM.BondSet:new JU.BS,j=D(this.ac,0),h,l=30720==d,q=65535==d,p=0;p<this.bondCount;p++){var v=this.bo[p];if(q||v.is(d)||l&&v.isHydrogen())g?f.set(p):(c.get(v.atom1.i)&&(j[h=v.atom2.i]++,f.set(h)),c.get(v.atom2.i)&&(j[h=v.atom1.i]++,f.set(h)))}if(g)return f;d=0==a;for(h=this.ac;0<=--h;)c=j[h],c<a||c>b?f.clear(h):
d&&0==c&&f.set(h);return f},"~N,~N,~N,JU.BS");c(c$,"getSymTemp",function(a){return null==this.symTemp||a?this.symTemp=J.api.Interface.getSymmetry(this.vwr,"ms"):this.symTemp},"~B");c(c$,"createModels",function(a){a=this.mc+a;var b=JU.AU.arrayCopyObject(this.am,a);this.validateBspf(!1);this.modelNumbers=JU.AU.arrayCopyI(this.modelNumbers,a);this.modelFileNumbers=JU.AU.arrayCopyI(this.modelFileNumbers,a);this.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.modelNumbersForAtomLabel,a);this.modelNames=
JU.AU.arrayCopyS(this.modelNames,a);this.frameTitles=JU.AU.arrayCopyS(this.frameTitles,a);for(var d=s(this.modelFileNumbers[this.mc-1]/1E6)+1,c=this.mc,g=0;c<a;c++)this.modelNumbers[c]=c+this.mc,this.modelFileNumbers[c]=1E6*d+ ++g,this.modelNumbersForAtomLabel[c]=this.modelNames[c]=d+"."+g;this.thisStateModel=-1;d=this.getInfoM("group3Lists");null!=d&&(c=this.getInfoM("group3Counts"),d=JU.AU.arrayCopyS(d,a),c=JU.AU.arrayCopyII(c,a),this.msInfo.put("group3Lists",d),this.msInfo.put("group3Counts",c));
this.unitCells=JU.AU.arrayCopyObject(this.unitCells,a);for(c=this.mc;c<a;c++)b[c]=(new JM.Model).set(this,c,-1,null,null,null),b[c].loadState=" model create #"+c+";";this.am=b;this.mc=a},"~N");c(c$,"deleteModel",function(a,b,d,c,g){if(0>a)this.validateBspf(!1),this.bsAll=null,this.resetMolecules(),this.isBbcageDefault=!1,this.calcBoundBoxDimensions(null,1);else{this.modelNumbers=JU.AU.deleteElements(this.modelNumbers,a,1);this.modelFileNumbers=JU.AU.deleteElements(this.modelFileNumbers,a,1);this.modelNumbersForAtomLabel=
JU.AU.deleteElements(this.modelNumbersForAtomLabel,a,1);this.modelNames=JU.AU.deleteElements(this.modelNames,a,1);this.frameTitles=JU.AU.deleteElements(this.frameTitles,a,1);this.thisStateModel=-1;var f=this.getInfoM("group3Lists"),j=this.getInfoM("group3Counts"),h=a+1;if(null!=f&&null!=f[h])for(var l=s(f[h].length/6);0<=--l;)0<j[h][l]&&(j[0][l]-=j[h][l],0==j[0][l]&&(f[0]=f[0].substring(0,6*l)+",["+f[0].substring(6*l+2)));null!=f&&(this.msInfo.put("group3Lists",JU.AU.deleteElements(f,a,1)),this.msInfo.put("group3Counts",
JU.AU.deleteElements(j,a,1)));null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(l=this.stateScripts.size();0<=--l;)this.stateScripts.get(l).deleteAtoms(a,g,c)||this.stateScripts.remove(l);this.deleteModelAtoms(b,d,c);this.vwr.deleteModelAtoms(a,b,d,c)}},"~N,~N,~N,JU.BS,JU.BS");c(c$,"assignAtom",function(a,b,d){null==b&&(b="C");var c=this.at[a],g=new JU.BS,f=1==c.getElementNumber(),g=JU.Elements.elementNumberFromSymbol(b,!0),j=!1;if(0<g)this.setElement(c,g),this.vwr.shm.setShapeSizeBs(0,
0,this.vwr.rd,JU.BSUtil.newAndSetBit(a)),this.setAtomName(a,b+c.getAtomNumber()),this.am[c.mi].isModelKit||this.taintAtom(a,0);else if(b.equals("Pl"))c.setFormalCharge(c.getFormalCharge()+1);else if(b.equals("Mi"))c.setFormalCharge(c.getFormalCharge()-1);else if(b.equals("X"))j=!0;else if(!b.equals("."))return;this.removeUnnecessaryBonds(c,j);b=0;1==c.getCovalentBondCount()&&(f?b=1.5:!f&&1==g&&(b=1));0!=b&&(f=JU.V3.newVsub(c,this.at[c.getBondedAtomIndex(0)]),j=f.length(),f.normalize(),f.scale(b-j),
this.setAtomCoordRelative(a,f.x,f.y,f.z));a=JU.BSUtil.newAndSetBit(a);1!=g&&d&&(this.validateBspf(!1),g=this.getAtomsWithinRadius(1,a,!1,null),g.andNot(a),0<=g.nextSetBit(0)&&this.vwr.deleteAtoms(g,!1),g=this.vwr.getModelUndeletedAtomsBitSet(c.mi),g.andNot(this.getAtomBitsMDa(1613758476,null)),this.makeConnections2(0.1,1.8,1,1073741904,a,g,null,!1,!1,0));this.vwr.addHydrogens(a,!1,!0)},"~N,~S,~B");c(c$,"deleteAtoms",function(a){this.averageAtomPoint=null;if(null!=a){for(var b=new JU.BS,d=a.nextSetBit(0);0<=
d&&d<this.ac;d=a.nextSetBit(d+1))this.at[d].deleteBonds(b);for(d=0;d<this.mc;d++)this.am[d].bsAtomsDeleted.or(a),this.am[d].bsAtomsDeleted.and(this.am[d].bsAtoms),this.am[d].dssrCache=null;this.deleteBonds(b,!1)}},"JU.BS");c(c$,"adjustAtomArrays",function(a,b,d){this.ac=d;for(var c=b;c<d;c++){this.at[c]=this.at[a[c]];this.at[c].i=c;var g=this.am[this.at[c].mi];g.firstAtomIndex==a[c]&&(g.firstAtomIndex=c);g.bsAtoms.set(c)}if(null!=this.vibrations)for(c=b;c<d;c++)this.vibrations[c]=this.vibrations[a[c]];
if(null!=this.occupancies)for(c=b;c<d;c++)this.occupancies[c]=this.occupancies[a[c]];if(null!=this.bfactor100s)for(c=b;c<d;c++)this.bfactor100s[c]=this.bfactor100s[a[c]];if(null!=this.partialCharges)for(c=b;c<d;c++)this.partialCharges[c]=this.partialCharges[a[c]];if(null!=this.atomTensorList)for(c=b;c<d;c++)if(g=this.atomTensorList[c]=this.atomTensorList[a[c]],null!=g)for(var f=g.length;0<=--f;){var j=g[f];null!=j&&(j.atomIndex1=c)}if(null!=this.atomNames)for(c=b;c<d;c++)this.atomNames[c]=this.atomNames[a[c]];
if(null!=this.atomTypes)for(c=b;c<d;c++)this.atomTypes[c]=this.atomTypes[a[c]];if(null!=this.atomSerials)for(c=b;c<d;c++)this.atomSerials[c]=this.atomSerials[a[c]];if(null!=this.atomSeqIDs)for(c=b;c<d;c++)this.atomSeqIDs[c]=this.atomSeqIDs[a[c]]},"~A,~N,~N");c(c$,"growAtomArrays",function(a){this.at=JU.AU.arrayCopyObject(this.at,a);null!=this.vibrations&&(this.vibrations=JU.AU.arrayCopyObject(this.vibrations,a));null!=this.occupancies&&(this.occupancies=JU.AU.arrayCopyF(this.occupancies,a));null!=
this.bfactor100s&&(this.bfactor100s=JU.AU.arrayCopyShort(this.bfactor100s,a));null!=this.partialCharges&&(this.partialCharges=JU.AU.arrayCopyF(this.partialCharges,a));null!=this.atomTensorList&&(this.atomTensorList=JU.AU.arrayCopyObject(this.atomTensorList,a));null!=this.atomNames&&(this.atomNames=JU.AU.arrayCopyS(this.atomNames,a));null!=this.atomTypes&&(this.atomTypes=JU.AU.arrayCopyS(this.atomTypes,a));null!=this.atomSerials&&(this.atomSerials=JU.AU.arrayCopyI(this.atomSerials,a));null!=this.atomSeqIDs&&
(this.atomSeqIDs=JU.AU.arrayCopyI(this.atomSeqIDs,a))},"~N");c(c$,"addAtom",function(a,b,d,c,g,f,j,h,l,q,p,v,m,n,s,r,t,u,w){h=(new JM.Atom).setAtom(a,this.ac,l,q,w,h,d,v,t);this.am[a].ac++;this.am[a].bsAtoms.set(this.ac);JU.Elements.isElement(d,1)&&this.am[a].hydrogenCount++;this.ac>=this.at.length&&this.growAtomArrays(this.ac+100);this.at[this.ac]=h;this.setBFactor(this.ac,s);this.setOccupancy(this.ac,n);this.setPartialCharge(this.ac,m);null!=r&&this.setAtomTensors(this.ac,r);h.group=b;h.colixAtom=
this.vwr.cm.getColixAtomPalette(h,J.c.PAL.CPK.id);null!=c&&(null!=g&&(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[this.ac]=g),h.atomID=u,0==u&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern()));-2147483648!=f&&(null==this.atomSerials&&(this.atomSerials=D(this.at.length,0)),this.atomSerials[this.ac]=f);0!=j&&(null==this.atomSeqIDs&&(this.atomSeqIDs=D(this.at.length,0)),this.atomSeqIDs[this.ac]=j);null!=p&&this.setVibrationVector(this.ac,
p);this.ac++;return h},"~N,JM.Group,~N,~S,~S,~N,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.Lst,~B,~N,JU.BS");c(c$,"getInlineData",function(a){var b=null;if(0<=a)b=this.am[a].loadScript;else for(a=this.mc;0<=--a&&!(0<(b=this.am[a].loadScript).length()););a=b.lastIndexOf('data "');if(0>a)return null;a=b.indexOf2('"',a+7);var d=b.lastIndexOf('end "');return d<a||0>a?null:b.substring2(a+2,d)},"~N");c(c$,"isAtomPDB",function(a){return 0<=a&&this.am[this.at[a].mi].isBioModel},"~N");c(c$,"isAtomAssignable",function(a){return 0<=
a&&this.at[a].mi==this.mc-1},"~N");c(c$,"haveModelKit",function(){for(var a=0;a<this.mc;a++)if(this.am[a].isModelKit)return!0;return!1});c(c$,"getModelKitStateBitset",function(a,b){for(var d=JU.BSUtil.copy(b),c=0;c<this.mc;c++)this.am[c].isModelKit||d.andNot(this.am[c].bsAtoms);return JU.BSUtil.deleteBits(a,d)},"JU.BS,JU.BS");c(c$,"setAtomNamesAndNumbers",function(a,b,d){0>b&&(a=this.am[this.at[a].mi].firstAtomIndex);null==this.atomSerials&&(this.atomSerials=D(this.ac,0));null==this.atomNames&&(this.atomNames=
Array(this.ac));for(var c=this.isXYZ&&this.vwr.getBoolean(603979978),g=2147483647,f=1;a<this.ac;++a){var j=this.at[a];j.mi!=g&&(g=j.mi,f=c?0:1);if(a>=-b){if(0==this.atomSerials[a]||0>b)this.atomSerials[a]=a<b?d.atomSerials[a]:f;if(null==this.atomNames[a]||0>b)this.atomNames[a]=(j.getElementSymbol()+this.atomSerials[a]).intern()}(!this.am[g].isModelKit||0<j.getElementNumber()&&!j.isDeleted())&&f++}},"~N,~N,JM.AtomCollection");c(c$,"setUnitCellOffset",function(a,b,d){null!=a&&(null==b?a.setOffset(d):
a.setOffsetPt(b))},"J.api.SymmetryInterface,JU.T3,~N");c(c$,"connect",function(a){this.resetMolecules();for(var b=new JU.BS,d=0;d<a.length;d++){var c=a[d];if(!(null==c||2>c.length)){var g=B(c[0]),f=0>g;f&&(g=-1-g);var j=B(c[1]);if(!(0>j||g>=this.ac||j>=this.ac)){var h=2<c.length?B(c[2]):1;0>h&&(h&=65535);var l=3<c.length?aa(1E3*a[d][3]):this.getDefaultMadFromOrder(h);0==h||0==l&&32768!=h&&!JM.Bond.isOrderH(h)?(c=this.at[g].getBond(this.at[j]),null!=c&&b.set(c.index)):this.bondAtoms(this.at[g],this.at[j],
h,l,null,4<c.length?c[4]:0,f,!0)}}}0<=b.nextSetBit(0)&&this.deleteBonds(b,!1)},"~A");c(c$,"allowSpecAtom",function(){return 1!=this.mc||this.am[0].isBioModel});c(c$,"setFrameDelayMs",function(a,b){for(var d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))this.am[this.am[d].trajectoryBaseIndex].frameDelay=a},"~N,JU.BS");c(c$,"getFrameDelayMs",function(a){return a<this.am.length&&0<=a?this.am[this.am[a].trajectoryBaseIndex].frameDelay:0},"~N");c(c$,"getModelIndexFromId",function(a){var b=0<=a.indexOf("#"),
d=a.toLowerCase().endsWith(".basemodel");d&&(a=a.substring(0,a.length-10));for(var c=-1,g=null,f=0;f<this.mc;f++){var j=this.getInfo(f,"modelID"),h=a.startsWith("~")?"~"+this.getModelNumberDotted(f):null;if(!(null==h&&null==j&&null==(j=this.getModelTitle(f)))){b&&(g=this.getModelFileName(f),g.endsWith("#molfile")?j=g:(g+="#",j=g+j));if(a.equalsIgnoreCase(j)||a.equalsIgnoreCase(h))return d?this.vwr.getJDXBaseModelIndex(f):f;null!=g&&a.startsWith(g)&&(c=-2)}}return null==g&&!b?-2:c},"~S");c(c$,"getAuxiliaryInfo",
function(a){var b=this.msInfo;if(null==b)return null;for(var d=new JU.Lst,c=0;c<this.mc;++c)(null==a||a.get(c))&&d.addLast(this.getModelAuxiliaryInfo(c));b.put("models",d);return b},"JU.BS");c(c$,"getDihedralMap",function(a){for(var b=new JU.Lst,d=a.length,c=null,g=null,f=null,j=null,h=d-1;0<=--h;)for(var l=d;--l>h;)if(c=this.at[a[h]],g=this.at[a[l]],c.isBonded(g))for(var q=d;0<=--q;)if(q!=h&&q!=l&&(f=this.at[a[q]]).isBonded(c))for(var p=d;0<=--p;)if(p!=h&&p!=l&&p!=q&&(j=this.at[a[p]]).isBonded(g)){var v=
D(4,0);v[0]=f.i;v[1]=c.i;v[2]=g.i;v[3]=j.i;b.addLast(v)}d=b.size();a=JU.AU.newInt2(d);for(h=d;0<=--h;)a[d-h-1]=b.get(h);return a},"~A");c(c$,"setModulation",function(a,b,d,c){if(null==this.bsModulated)if(b)this.bsModulated=new JU.BS;else if(null==a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var g=this.vwr.getFloat(1276121113),f=!1,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){var h=this.getModulation(j);null!=h&&(h.setModTQ(this.at[j],b,d,c,g),null!=this.bsModulated&&this.bsModulated.setBitTo(j,
b),f=!0)}f||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(c$,"getBoundBoxOrientation",function(a,b){var d=b.nextSetBit(0);if(0>d)return"{0 0 0 1}";var c=null==this.vOrientations?0:this.vOrientations.length;if(0==c){for(var g=Array(3375),c=0,f=new JU.P4,j=-7;7>=j;j++)for(var h=-7;7>=h;h++)for(var l=0;14>=l;l++,c++)1<(g[c]=JU.V3.new3(j/7,h/7,l/14)).length()&&--c;this.vOrientations=Array(c);for(j=c;0<=--j;)l=Math.sqrt(1-g[j].lengthSquared()),Float.isNaN(l)&&(l=0),f.set4(g[j].x,g[j].y,g[j].z,l),this.vOrientations[j]=
JU.Quat.newP4(f)}for(var g=new JU.P3,f=3.4028235E38,q=null,p=null,j=0;j<c;j++){var l=this.vOrientations[j],v=new JU.BoxInfo;v.setMargin(0);for(h=d;0<=h;h=b.nextSetBit(h+1))v.addBoundBoxPoint(l.transform2(this.at[h],g));switch(a){default:case 1313866249:case 1073741863:h=(v.bbCorner1.x-v.bbCorner0.x)*(v.bbCorner1.y-v.bbCorner0.y)*(v.bbCorner1.z-v.bbCorner0.z);break;case 1112541205:h=v.bbCorner1.x-v.bbCorner0.x;break;case 1112541206:h=v.bbCorner1.y-v.bbCorner0.y;break;case 1112541207:h=v.bbCorner1.z-
v.bbCorner0.z}h<f&&(q=l,p=v,f=h)}if(1313866249!=a&&1073741863!=a)return q.toString();l=JU.Quat.newQ(q);d=p.bbCorner1.x-p.bbCorner0.x;c=p.bbCorner1.y-p.bbCorner0.y;j=p.bbCorner1.z-p.bbCorner0.z;d<c&&(g.set(0,0,1),l=JU.Quat.newVA(g,90).mulQ(l),h=d,d=c,c=h);c<j&&(j>d&&(g.set(0,1,0),l=JU.Quat.newVA(g,90).mulQ(l),h=d,d=j,j=h),g.set(1,0,0),l=JU.Quat.newVA(g,90).mulQ(l),h=c,c=j,j=h);return 1313866249==a?f+"\t{"+d+" "+c+" "+j+"}":0==l.getTheta()?"{0 0 0 1}":l.toString()},"~N,JU.BS");c(c$,"intersectPlane",
function(a,b,d){return(null==this.triangulator?this.triangulator=J.api.Interface.getUtil("TriangleData",this.vwr,"ms"):this.triangulator).intersectPlane(a,b,d)},"JU.P4,JU.Lst,~N");c(c$,"getUnitCellForAtom",function(a){if(0>a||a>this.ac)return null;if(null!=this.bsModulated){var b=this.getModulation(a),b=null==b?null:b.getSubSystemUnitCell();if(null!=b)return b}return this.getUnitCell(this.at[a].mi)},"~N");c(c$,"clearCache",function(){for(var a=this.mc;0<=--a;)this.am[a].dssrCache=null});c(c$,"getSymMatrices",
function(a){var b=this.getModelSymmetryCount(a);if(0==b)return null;var d=Array(b),c=this.am[a].biosymmetry;null==c&&(c=this.getUnitCell(a));for(a=b;0<=--a;)d[a]=c.getSpaceGroupOperation(a);return d},"~N");c(c$,"getBsBranches",function(a){for(var b=s(a.length/6),d=Array(b),c=new java.util.Hashtable,g=0,f=0;g<b;g++,f+=6)if(!(1>Math.abs(a[f+5]-a[f+4]))){var j=B(a[f+1]),h=B(a[f+2]),l=""+j+"_"+h;if(!c.containsKey(l)){c.put(l,Boolean.TRUE);for(var l=this.vwr.getBranchBitSet(h,j,!0),q=this.at[j].bonds,
j=this.at[j],p=0;p<q.length;p++){var v=q[p];if(v.isCovalent()&&(v=v.getOtherAtom(j).i,v!=h&&l.get(v))){l=null;break}}d[g]=l}}return d},"~A");c(c$,"recalculatePositionDependentQuantities",function(a,b){this.haveStraightness&&this.calculateStraightness();this.recalculateLeadMidpointsAndWingVectors(-1);for(var d=this.getModelBS(a,!1),c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))this.sm.refreshShapeTrajectories(c,a,b);this.averageAtomPoint=null},"JU.BS,JU.M4");c(c$,"moveAtoms",function(a,b,d,c,g,f,j,h){if(null!=
a){for(b=g.nextSetBit(0);0<=b;b=g.nextSetBit(b+1))a.rotTrans(this.at[b]);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(f),this.mat4.setIdentity(),this.mat4.setTranslation(this.vTemp),this.mat4t.setToM3(this.matTemp),this.mat4.mul(this.mat4t),this.mat4t.setIdentity(),this.vTemp.scale(-1),this.mat4t.setTranslation(this.vTemp),
this.mat4.mul(this.mat4t)):this.mat4.setToM3(this.matTemp);for(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);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$,"setDihedrals",function(a,b,d){var c=s(a.length/6);1<d&&(d=1);for(var g=0,f=0;g<c;g++,f+=6){var j=b[g];if(!(null==j||j.isEmpty())){var h=this.at[B(a[f+1])],l=JU.V3.newVsub(this.at[B(a[f+2])],h),l=JU.A4.newVA(l,-((a[f+5]-a[f+4])*d)/57.29577951308232);this.matTemp.setAA(l);this.ptTemp.setT(h);for(h=j.nextSetBit(0);0<=h;h=j.nextSetBit(h+1))this.at[h].sub(this.ptTemp),this.matTemp.rotate(this.at[h]),this.at[h].add(this.ptTemp),this.taintAtom(h,
2)}}},"~A,~A,~N");c(c$,"setAtomCoordsRelative",function(a,b){this.setAtomsCoordRelative(b,a.x,a.y,a.z);this.mat4.setIdentity();this.vTemp.setT(a);this.mat4.setTranslation(this.vTemp);this.recalculatePositionDependentQuantities(b,this.mat4)},"JU.T3,JU.BS");c(c$,"setAtomCoords",function(a,b,d){this.setAtomCoord2(a,b,d);switch(b){case 1112541202:case 1112541203:case 1112541204:case 1146095631:break;default:this.recalculatePositionDependentQuantities(a,null)}},"JU.BS,~N,~O");c(c$,"invertSelected",function(a,
b,d,c,g){if(null!=a)for(var f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1)){d=2*(a.x-this.at[f].x);c=2*(a.y-this.at[f].y);var j=2*(a.z-this.at[f].z);this.setAtomCoordRelative(f,d,c,j)}else if(null!=b){a=JU.V3.new3(b.x,b.y,b.z);a.normalize();for(var h=Math.sqrt(b.x*b.x+b.y*b.y+b.z*b.z),f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1))j=2*-JU.Measure.distanceToPlaneD(b,h,this.at[f]),d=a.x*j,c=a.y*j,j*=a.z,this.setAtomCoordRelative(f,d,c,j)}else if(0<=d&&(b=this.at[d],a=b.bonds,null!=a)){g=new JU.BS;j=new JU.Lst;
h=this.vwr.getModelUndeletedAtomsBitSet(b.mi);for(f=0;f<a.length;f++){var l=a[f].getOtherAtom(b);c.get(l.i)?g.or(JU.JmolMolecule.getBranchBitSet(this.at,l.i,h,null,d,!0,!0)):j.addLast(l)}0!=j.size()&&(a=JU.Measure.getCenterAndPoints(j)[0],f=JU.V3.newVsub(b,a),f=JU.Quat.newVA(f,180),this.moveAtoms(null,null,f.getMatrix(),null,g,b,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS,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){for(var c=0,g=new JU.Lst,f=a.nextSetBit(0);0<=f&&c<b;f=a.nextSetBit(f+1)){var j=this.at[f].group,h=j.getQuaternion(d);if(null==h&&(-2147483648==j.seqcode&&(h=j.getQuaternionFrame(this.at)),null==h))continue;c++;g.addLast(h);f=j.lastAtomIndex}return g.toArray(Array(g.size()))},
"JU.BS,~N,~S");c(c$,"getSequenceBits",function(a,b){return this.haveBioModels&&0<a.length?this.bioModel.getSequenceBits(this,a,b):new JU.BS},"~S,JU.BS");c(c$,"calculatePolymers",function(a,b,d,c){this.haveBioModels&&this.bioModel.calculateAllPolymers(this,a,b,d,c)},"~A,~N,~N,JU.BS");c(c$,"getBioPolymerCountInModel",function(a){return this.haveBioModels?this.bioModel.getBioPolymerCountInModel(this,a):0},"~N");c(c$,"getPolymerPointsAndVectors",function(a,b,d,c){if(this.haveBioModels)for(var g=0;g<this.mc;++g)this.am[g].getPolymerPointsAndVectors(a,
b,d,c)},"JU.BS,JU.Lst,~B,~N");c(c$,"recalculateLeadMidpointsAndWingVectors",function(a){this.haveBioModels&&this.bioModel.recalculatePoints(this,a)},"~N");c(c$,"calcRasmolHydrogenBonds",function(a,b,d,c,g,f,j){this.haveBioModels&&this.bioModel.calcRasmolHydrogenBonds(this,a,b,d,c,g,f,j)},"JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS");c(c$,"calculateStraightness",function(){this.haveBioModels&&!this.haveStraightness&&this.bioModel.calculateStraightnessAll(this)});c(c$,"calculateStruts",function(a,b){return this.haveBioModels?
this.bioModel.calculateStruts(this,a,b):0},"JU.BS,JU.BS");c(c$,"getGroupsWithin",function(a,b){return this.haveBioModels?this.bioModel.getGroupsWithinAll(this,a,b):new JU.BS},"~N,JU.BS");c(c$,"getProteinStructureState",function(a,b,d,c){return this.haveBioModels?this.bioModel.getFullProteinStructureState(this,a,b,d,c):""},"JU.BS,~B,~B,~N");c(c$,"calculateStructures",function(a,b,d,c,g){if(!this.haveBioModels)return"";var f=new JU.BS;a=JU.BSUtil.copyInvert(this.modelsOf(a,f),this.mc);if(!g)return this.calculateStructuresAllExcept(a,
b,d,c,!1,!1);for(g=0;g<this.mc;g++)a.get(g)||this.am[g].clearBioPolymers();this.calculatePolymers(null,0,0,a);b=this.calculateStructuresAllExcept(a,b,d,c,!0,!1);this.vwr.shm.resetBioshapes(f);this.setStructureIndexes();return b},"JU.BS,~B,~B,~B,~B");C(c$,"hbondMin",2.5)});m("JM");w(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){c$=r(function(){this.rotationMatrix=this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=null;this.cameraY=
this.cameraX=this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.vwr=this.pymolView=this.moveToText=null;t(this,arguments)},JM,"Orientation");I(c$,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});u(c$,function(a,b,d){this.vwr=a;null!=d?(this.pymolView=d,this.moveToText="moveTo -1.0 PyMOL "+JU.Escape.eAF(d)):(a.finalizeTransformParameters(),b?(b=a.ms.getInfoM("defaultOrientationMatrix"),null==b?this.rotationMatrix.setScale(1):
this.rotationMatrix.setM3(b)):a.tm.getRotation(this.rotationMatrix),this.xTrans=a.tm.getTranslationXPercent(),this.yTrans=a.tm.getTranslationYPercent(),this.zoom=a.tm.getZoomSetting(),this.center.setT(a.tm.fixedRotationCenter),this.windowCenteredFlag=a.tm.isWindowCentered(),this.rotationRadius=a.getFloat(570425388),this.navigationMode=a.getBoolean(603979887),this.moveToText=a.tm.getMoveToText(-1,!1),this.navigationMode&&(this.xNav=a.tm.getNavigationOffsetPercent("X"),this.yNav=a.tm.getNavigationOffsetPercent("Y"),
this.navDepth=a.tm.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");w(null,"JM.StateScript",["JU.SB","JU.BSUtil","$.Escape"],function(){c$=r(function(){this.modelIndex=0;this.script2=
this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;t(this,arguments)},JM,"StateScript");u(c$,function(a,b,d,c,g,f,j){this.modelIndex=a;this.script1=b;this.bsBonds=JU.BSUtil.copy(d);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(g);this.script2=f;this.inDefinedStateBlock=j},"~N,~S,JU.BS,JU.BS,JU.BS,~S,~B");c(c$,"isValid",function(){return null!=this.script1&&0<this.script1.length&&(null==this.bsBonds||0<=this.bsBonds.nextSetBit(0))&&(null==this.bsAtoms1||
0<=this.bsAtoms1.nextSetBit(0))&&(null==this.bsAtoms2||0<=this.bsAtoms2.nextSetBit(0))});h(c$,"toString",function(){if(!this.isValid())return"";var a=JU.SB.newS(this.script1);null!=this.bsBonds&&a.append(" ").append(JU.Escape.eBond(this.bsBonds));null!=this.bsAtoms1&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms1));null!=this.bsAtoms2&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms2));null!=this.script2&&a.append(" ").append(this.script2);a=a.toString();a.endsWith(";")||(a+=";");return a});c(c$,
"isConnect",function(){return 0<=this.script1.indexOf("connect")});c(c$,"deleteAtoms",function(a,b,d){if(a==this.modelIndex)return!1;if(a>this.modelIndex)return!0;JU.BSUtil.deleteBits(this.bsBonds,b);JU.BSUtil.deleteBits(this.bsAtoms1,d);JU.BSUtil.deleteBits(this.bsAtoms2,d);return this.isValid()},"~N,JU.BS,JU.BS");c(c$,"setModelIndex",function(a){this.modelIndex=a},"~N")});m("JM");c$=r(function(){this.id="";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=0;this.signFactor=
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w(["JU.Int2IntHash"],"JU.C","java.lang.Byte $.Float JU.AU $.CU $.PT $.SB J.c.PAL JU.Escape $.Logger".split(" "),function(){c$=z(JU,"C");u(c$,function(){});c$.getColix=c(c$,"getColix",function(a){if(0==a)return 0;var b=0;-16777216!=(a&4278190080)&&(b=JU.C.getTranslucentFlag(a>>24&255),a|=4278190080);var c=JU.C.colixHash.get(a);3==(c&3)&&(b=0);return(0<c?c:JU.C.allocateColix(a,!1))|b},"~N");c$.allocateColix=c(c$,"allocateColix",function(a,b){var c;if(b)c=2047;else{for(c=JU.C.colixMax;4<=--c;)if((a&
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2047,"TRANSLUCENT_SHIFT",11,"ALPHA_SHIFT",13,"TRANSLUCENT_MASK",30720,"TRANSPARENT",16384,"OPAQUE_MASK",-30721,"BLACK",4,"ORANGE",5,"PINK",6,"BLUE",7,"WHITE",8,"CYAN",9,"RED",10,"GREEN",11,"GRAY",12,"SILVER",13,"LIME",14,"MAROON",15,"NAVY",16,"OLIVE",17,"PURPLE",18,"TEAL",19,"MAGENTA",20,"YELLOW",21,"HOTPINK",22,"GOLD",23);for(var a=[4278190080,4294944E3,4294951115,4278190335,4294967295,4278255615,4294901760,4278222848,4286611584,4290822336,4278255360,4286578688,4278190208,4286611456,4286578816,4278222976,
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c(c$,"makeColorScheme",function(a,b,d){a=JU.ColorEncoder.fixName(a);if(null==b){this.schemes.remove(a);a=this.createColorScheme(a,!1,d);if(d)switch(a){case 2147483647:return 0;case 12:this.paletteFriendly=this.getPaletteAC();break;case 10:this.paletteBW=this.getPaletteBW();break;case 11:this.paletteWB=this.getPaletteWB();break;case 0:case 1:this.argbsRoygb=JV.JC.argbsRoygbScale;break;case 6:case 7:this.argbsRwb=JV.JC.argbsRwbScale;break;case 2:this.argbsCpk=J.c.PAL.argbsCpk;break;case 3:JU.ColorEncoder.getRasmolScale();
break;case 5:this.getAmino();break;case 4:this.getShapely()}return a}this.schemes.put(a,b);this.setThisScheme(a,b);a=this.createColorScheme(a,!1,d);if(d)switch(a){case 10:this.paletteBW=this.thisScale;break;case 11:this.paletteWB=this.thisScale;break;case 0:case 1:this.argbsRoygb=this.thisScale;this.ihalf=s(this.argbsRoygb.length/3);break;case 6:case 7:this.argbsRwb=this.thisScale;break;case 2:this.argbsCpk=this.thisScale;break;case 5:this.argbsAmino=this.thisScale;break;case 4:this.argbsShapely=
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var a=this.getValueLowerCase("emulate","jmol");this.setStringProperty("defaults",a.equals("chime")?"RasMol":"Jmol");this.setStringProperty("backgroundColor",this.getValue("bgcolor",this.getValue("boxbgcolor","black")));this.viewer.setBooleanProperty("frank",!0);this.loading=!0;for(var b,a=0,d=J.c.CBK.values();a<d.length&&((b=d[a])||1);a++)this.setValue(b.name()+"Callback",null);this.loading=!1;this.language=this.getJmolParameter("language");new J.i18n.GT(this.viewer,this.language);null!=this.language&&
System.out.print("requested language="+this.language+"; ");this.doTranslate=!"none".equals(this.language)&&this.getBooleanValue("doTranslate",!0);this.language=J.i18n.GT.getLanguage();System.out.println("language="+this.language);if(null==this.b$.get(J.c.CBK.SCRIPT)&&null==this.b$.get(J.c.CBK.ERROR)&&(null!=this.b$.get(J.c.CBK.MESSAGE)||null!=this.statusForm||null!=this.statusText))this.doTranslate&&null==this.getValue("doTranslate",null)&&(this.doTranslate=!1,JU.Logger.warn("Note -- Presence of message callback disables disable translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet()")),
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h(c$,"script",function(a){this.scriptNoWait(a)},"~S");h(c$,"scriptCheck",function(a){return null==a||0==a.length?"":this.scriptProcessor(a,null,0)},"~S");h(c$,"scriptNoWait",function(a){return null==a||0==a.length?"":this.scriptProcessor(a,null,2)},"~S");c(c$,"scriptWait",function(a){return this.scriptWait(a,null)},"~S");c(c$,"scriptWait",function(a,b){if(null==a||0==a.length)return"";this.outputBuffer=null;return this.scriptProcessor(a,b,1)},"~S,~S");h(c$,"scriptWaitOutput",function(a){if(null==
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c$.findBestFit=c(c$,"findBestFit",function(a,b){for(var d=-1,c=2147483647,g=b.length;0<=--g;){var f=b[g];f>=a&&f<c&&(c=f,d=g)}0<=d&&(b[d]=0);return d},"~N,~A");c$.findShorter=c(c$,"findShorter",function(a,b){for(var d=b.length;0<=--d;)if(0==b[d])return b[d]=a,d;for(var c=0,g=b[0],d=b.length;0<--d;)b[d]<g&&(g=b[d],c=d);return g<a?(b[c]=a,c):-1},"~N,~A");c(c$,"clearTempPoints",function(){for(var a=0;6>a;a++)this.lengthsFreePoints[a]=0,this.freePoints[a]=null});c(c$,"allocTempPoints",function(a){var b;
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b?this.freeEnum[b]:Array(a)},"~N");c(c$,"freeTempEnum",function(a){for(var b=0;b<this.freeEnum.length;b++)if(this.freeEnum[b]===a){this.lengthsFreeEnum[b]=a.length;return}b=JU.TempArray.findShorter(a.length,this.lengthsFreeEnum);0<=b&&(this.freeEnum[b]=a)},"~A");c$.getSlabWithinRange=c(c$,"getSlabWithinRange",function(a,b){return[Integer.$valueOf(1073742114),[Float.$valueOf(a),Float.$valueOf(b)],Boolean.FALSE,null]},"~N,~N");c$.getSlabObjectType=c(c$,"getSlabObjectType",function(a,b,d,c){return[Integer.$valueOf(a),
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-1;this.modScale=NaN;t(this,arguments)},JU,"Vibration",JU.V3);c(c$,"setTempPoint",function(a,b,d){switch(this.modDim){case -2:break;default:a.scaleAdd2(Math.cos(6.283185307179586*b.x)*d,this,a)}},"JU.T3,JU.T3,~N,~N");c(c$,"getInfo",function(a){a.put("vibVector",JU.V3.newV(this));a.put("vibType",-2==this.modDim?"spin":-1==this.modDim?"vib":"mod")},"java.util.Map");h(c$,"clone",function(){var a=new JU.Vibration;a.setT(this);a.modDim=this.modDim;return a});c(c$,"setXYZ",function(a){this.setT(a)},"JU.T3");
c(c$,"setType",function(a){this.modDim=a;return this},"~N");c(c$,"isNonzero",function(){return 0!=this.x||0!=this.y||0!=this.z});C(c$,"twoPI",6.283185307179586,"TYPE_VIBRATION",-1,"TYPE_SPIN",-2)});m("JV");w(["javajs.api.EventManager","J.i18n.GT","JU.Rectangle","JV.MouseState"],["JV.ActionManager","$.Gesture","$.MotionPoint"],"java.lang.Character $.Float JU.P3 $.PT J.api.Interface J.thread.HoverWatcherThread JU.BSUtil $.Escape $.Logger $.Point3fi JV.binding.Binding $.JmolBinding".split(" "),function(){c$=
r(function(){this.vwr=null;this.isMultiTouch=this.haveMultiTouchInput=!1;this.predragBinding=this.rasmolBinding=this.dragBinding=this.pfaatBinding=this.jmolBinding=this.b=null;this.LEFT_DRAGGED=this.LEFT_CLICKED=0;this.dragGesture=this.hoverWatcherThread=null;this.apm=1;this.pickingStyleSelect=this.pickingStyle=this.bondPickingMode=0;this.pickingStyleMeasure=5;this.rootPickingStyle=0;this.pickAtomAssignType="C";this.pickBondAssignType="p";this.isPickAtomAssignCharge=!1;this.xyRange=0;this.mouseDragFactor=
this.gestureSwipeFactor=1;this.mouseWheelFactor=1.15;this.dragged=this.pressed=this.clicked=this.moved=this.current=null;this.clickedCount=this.pressedCount=0;this.dragSelectedMode=this.labelMode=this.drawMode=!1;this.measuresEnabled=!0;this.hoverActive=this.haveSelection=!1;this.mp=null;this.dragAtomIndex=-1;this.rubberbandSelectionMode=!1;this.rectRubber=null;this.isAltKeyReleased=!0;this.isMultiTouchServer=this.isMultiTouchClient=this.keyProcessing=!1;this.clickAction=this.dragAction=this.pressAction=
0;this.measurementQueued=null;this.selectionWorking=!1;t(this,arguments)},JV,"ActionManager",null,javajs.api.EventManager);I(c$,function(){this.current=new JV.MouseState("current");this.moved=new JV.MouseState("moved");this.clicked=new JV.MouseState("clicked");this.pressed=new JV.MouseState("pressed");this.dragged=new JV.MouseState("dragged");this.rectRubber=new JU.Rectangle});c(c$,"setViewer",function(a){this.vwr=a;this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.LEFT_CLICKED=JV.binding.Binding.getMouseAction(1,
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b)}}});c(c$,"processMultitouchEvent",function(){},"~N,~N,~N,~N,JU.P3,~N");c(c$,"bnd",function(a,b){return this.b.isBound(a,b)},"~N,~N");c(c$,"bind",function(a,b){var d=JV.ActionManager.getActionFromName(b),c=JV.binding.Binding.getMouseActionStr(a);0!=c&&(0<=d?this.b.bindAction(c,d):this.b.bindName(c,b))},"~S,~S");c(c$,"clearBindings",function(){this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.rasmolBinding=this.dragBinding=this.pfaatBinding=null});c(c$,"unbindAction",function(a,b){if(null==
a&&null==b)this.clearBindings();else{var d=JV.ActionManager.getActionFromName(b),c=JV.binding.Binding.getMouseActionStr(a);0<=d?this.b.unbindAction(c,d):0!=c&&this.b.unbindName(c,b);null==b&&this.b.unbindUserAction(a)}},"~S,~S");c$.newAction=c(c$,"newAction",function(a,b,d){JV.ActionManager.actionInfo[a]=d;JV.ActionManager.actionNames[a]=b},"~N,~S,~S");c$.getActionName=c(c$,"getActionName",function(a){return a<JV.ActionManager.actionNames.length?JV.ActionManager.actionNames[a]:null},"~N");c$.getActionFromName=
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return-1},"~S");c(c$,"getAtomPickingMode",function(){return this.apm});c(c$,"setPickingMode",function(a){var b=!1;switch(a){case -1:b=!0;this.bondPickingMode=35;a=1;break;case 35:case 34:case 33:this.vwr.setBooleanProperty("bondPicking",!0);this.bondPickingMode=a;return;case 8:this.bondPickingMode=a;if(this.vwr.getBondPicking())return;b=!0}b=(new Boolean(b|this.apm!=a)).valueOf();this.apm=a;b&&this.resetMeasurement()},"~N");c(c$,"setAtomPickingOption",function(a){switch(this.apm){case 32:this.pickAtomAssignType=
a,this.isPickAtomAssignCharge=this.pickAtomAssignType.equals("Pl")||this.pickAtomAssignType.equals("Mi")}},"~S");c(c$,"setBondPickingOption",function(a){switch(this.bondPickingMode){case 33:this.pickBondAssignType=Character.toLowerCase(a.charAt(0))}},"~S");c(c$,"getPickingState",function(){var a=";set modelkitMode "+this.vwr.getBoolean(603979883)+";set picking "+JV.ActionManager.getPickingModeName(this.apm);32==this.apm&&(a+="_"+this.pickAtomAssignType);a+=";";0!=this.bondPickingMode&&(a+="set picking "+
JV.ActionManager.getPickingModeName(this.bondPickingMode));33==this.bondPickingMode&&(a+="_"+this.pickBondAssignType);return a+";"});c(c$,"getPickingStyle",function(){return this.pickingStyle});c(c$,"setPickingStyle",function(a){this.pickingStyle=a;4<=a?(this.pickingStyleMeasure=a,this.resetMeasurement()):(3>a&&(this.rootPickingStyle=a),this.pickingStyleSelect=a);this.rubberbandSelectionMode=!1;switch(this.pickingStyleSelect){case 2:this.b.name.equals("extendedSelect")||this.setBinding(null==this.pfaatBinding?
this.pfaatBinding=JV.binding.Binding.newBinding(this.vwr,"Pfaat"):this.pfaatBinding);break;case 3:this.b.name.equals("drag")||this.setBinding(null==this.dragBinding?this.dragBinding=JV.binding.Binding.newBinding(this.vwr,"Drag"):this.dragBinding);this.rubberbandSelectionMode=!0;break;case 1:this.b.name.equals("selectOrToggle")||this.setBinding(null==this.rasmolBinding?this.rasmolBinding=JV.binding.Binding.newBinding(this.vwr,"Rasmol"):this.rasmolBinding);break;default:this.b!==this.jmolBinding&&this.setBinding(this.jmolBinding)}this.b.name.equals("drag")||
(this.predragBinding=this.b)},"~N");c(c$,"setGestureSwipeFactor",function(a){this.gestureSwipeFactor=a},"~N");c(c$,"setMouseDragFactor",function(a){this.mouseDragFactor=a},"~N");c(c$,"setMouseWheelFactor",function(a){this.mouseWheelFactor=a},"~N");c(c$,"setCurrent",function(a,b,d,c){this.vwr.hoverOff();this.current.set(a,b,d,c)},"~N,~N,~N,~N");c(c$,"getCurrentX",function(){return this.current.x});c(c$,"getCurrentY",function(){return this.current.y});c(c$,"setMouseMode",function(){this.drawMode=this.labelMode=
!1;this.dragSelectedMode=this.vwr.getDragSelected();this.measuresEnabled=!this.dragSelectedMode;if(!this.dragSelectedMode)switch(this.apm){default:return;case 32:this.measuresEnabled=!this.isPickAtomAssignCharge;return;case 4:this.drawMode=!0;this.measuresEnabled=!1;break;case 2:this.labelMode=!0;this.measuresEnabled=!1;break;case 9:this.measuresEnabled=!1;break;case 19:case 22:case 20:case 21:this.measuresEnabled=!1;return}this.exitMeasurementMode(null)});c(c$,"clearMouseInfo",function(){this.pressedCount=
this.clickedCount=0;this.dragGesture.setAction(0,0);this.exitMeasurementMode(null)});c(c$,"isMTClient",function(){return this.isMultiTouchClient});c(c$,"isMTServer",function(){return this.isMultiTouchServer});c(c$,"dispose",function(){this.clear()});c(c$,"clear",function(){this.startHoverWatcher(!1);null!=this.predragBinding&&(this.b=this.predragBinding);this.vwr.setPickingMode(null,1);this.vwr.setPickingStyle(null,this.rootPickingStyle);this.isAltKeyReleased=!0});c(c$,"startHoverWatcher",function(a){if(!this.vwr.isPreviewOnly)try{a?
null==this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread=new J.thread.HoverWatcherThread(this,this.current,this.moved,this.vwr)):null!=this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread.interrupt(),this.hoverWatcherThread=null)}catch(b){if(!y(b,Exception))throw b;}},"~B");c(c$,"setModeMouse",function(a){-1==a&&this.startHoverWatcher(!1)},"~N");h(c$,"keyPressed",function(a,b){if(this.keyProcessing)return!1;this.vwr.hoverOff();this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&
this.isAltKeyReleased&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1);this.isAltKeyReleased=!1;this.moved.modifiers|=8;break;case 16:this.dragged.modifiers|=1;this.moved.modifiers|=1;break;case 17:this.moved.modifiers|=2;break;case 27:this.exitMeasurementMode("escape")}var d=8464|this.moved.modifiers;!this.labelMode&&!this.b.isUserAction(d)&&this.checkMotionRotateZoom(d,this.current.x,0,0,!1);if(this.vwr.getBoolean(603979887))switch(a){case 38:case 40:case 37:case 39:case 32:case 46:this.vwr.navigate(a,
b)}this.keyProcessing=!1;return!0},"~N,~N");h(c$,"keyReleased",function(a){switch(a){case 18:this.dragSelectedMode&&this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1);this.isAltKeyReleased=!0;this.moved.modifiers&=-9;break;case 16:this.moved.modifiers&=-2;break;case 17:this.moved.modifiers&=-3}0==this.moved.modifiers&&this.vwr.setCursor(0);if(this.vwr.getBoolean(603979887))switch(a){case 38:case 40:case 37:case 39:this.vwr.navigate(0,0)}},"~N");h(c$,"mouseEnterExit",
function(a,b,d){this.setCurrent(a,b,d,0)},"~N,~N,~N,~B");c(c$,"setMouseActions",function(a,b,d){this.pressAction=JV.binding.Binding.getMouseAction(a,b,d?5:4);this.dragAction=JV.binding.Binding.getMouseAction(a,b,1);this.clickAction=JV.binding.Binding.getMouseAction(a,b,2)},"~N,~N,~B");h(c$,"mouseAction",function(a,b,d,c,g,f){if(this.vwr.getMouseEnabled())switch(JU.Logger.debuggingHigh&&0!=a&&this.vwr.showString("mouse action: "+a+" "+f+" "+JV.binding.Binding.getMouseActionName(JV.binding.Binding.getMouseAction(g,
f,a),!1),!1),a){case 0:this.setCurrent(b,d,c,f);this.moved.setCurrent(this.current,0);if(null!=this.mp||this.hoverActive){this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,f,0);this.checkClickAction(d,c,b,0);break}if(this.isZoomArea(d)){this.checkMotionRotateZoom(this.LEFT_DRAGGED,0,0,0,!1);break}8==this.vwr.currentCursor&&this.vwr.setCursor(0);break;case 4:this.setMouseMode();this.pressedCount=this.pressed.check(20,d,c,f,b,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.vwr.checkInMotion(1),
this.setCurrent(b,d,c,f));this.pressAction=JV.binding.Binding.getMouseAction(this.pressedCount,f,4);this.vwr.setCursor(12);this.pressed.setCurrent(this.current,1);this.dragged.setCurrent(this.current,1);this.vwr.setFocus();this.dragGesture.setAction(this.dragAction,b);this.checkPressedAction(d,c,b);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,f,!1);a=d-this.dragged.x;g=c-this.dragged.y;this.setCurrent(b,d,c,f);this.dragged.setCurrent(this.current,-1);this.dragGesture.add(this.dragAction,
d,c,b);this.checkDragWheelAction(this.dragAction,d,c,a,g,b,1);break;case 5:this.setMouseActions(this.pressedCount,f,!0);this.setCurrent(b,d,c,f);this.vwr.spinXYBy(0,0,0);f=!this.pressed.check(this.xyRange,d,c,f,b,9223372036854775E3);this.checkReleaseAction(d,c,b,f);break;case 3:if(this.vwr.isApplet&&!this.vwr.hasFocus())break;this.setCurrent(b,this.current.x,this.current.y,f);this.checkDragWheelAction(JV.binding.Binding.getMouseAction(0,f,3),this.current.x,this.current.y,0,c,b,3);break;case 2:this.setMouseMode();
this.clickedCount=1<g?g:this.clicked.check(0,0,0,f,b,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(b,d,c,f);this.setMouseActions(this.clickedCount,f,!1);this.clicked.setCurrent(this.current,this.clickedCount);this.vwr.setFocus();if(9!=this.apm&&this.bnd(JV.binding.Binding.getMouseAction(1,f,4),31))break;this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,f,2);this.checkClickAction(d,c,b,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(c$,"checkPressedAction",function(a,
b,d){var c=JV.binding.Binding.getButtonMods(this.pressAction),g=this.bnd(JV.binding.Binding.getMouseAction(1,c,4),31);if(0!=c){this.pressAction=this.vwr.notifyMouseClicked(a,b,this.pressAction,4);if(0==this.pressAction)return;c=JV.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,c,!1);JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));if(this.drawMode&&(this.bnd(this.dragAction,8)||this.bnd(this.dragAction,9))||this.labelMode&&
this.bnd(this.dragAction,10))this.vwr.checkObjectDragged(-2147483648,0,a,b,this.dragAction);else{this.checkUserAction(this.pressAction,a,b,0,0,d,4);d=!1;switch(this.apm){case 32:d=this.bnd(this.clickAction,0);break;case 28:d=this.bnd(this.dragAction,7)||this.bnd(this.dragAction,14);break;case 26:case 36:case 27:d=this.bnd(this.dragAction,7)||this.bnd(this.dragAction,27)||this.bnd(this.dragAction,14);break;case 29:d=this.bnd(this.dragAction,11)||this.bnd(this.dragAction,14);break;case 30:d=this.bnd(this.dragAction,
12)||this.bnd(this.dragAction,27)||this.bnd(this.dragAction,14)}if(d){if(this.dragAtomIndex=this.vwr.findNearestAtomIndexMovable(a,b,!0),0<=this.dragAtomIndex&&(32==this.apm||31==this.apm)&&this.vwr.ms.isAtomAssignable(this.dragAtomIndex))this.enterMeasurementMode(this.dragAtomIndex),this.mp.addPoint(this.dragAtomIndex,null,!1)}else this.bnd(this.pressAction,23)?(g="j",this.vwr.getBoolean(603979883)&&(g=this.vwr.checkObjectClicked(a,b,this.LEFT_CLICKED),g=null!=g&&"bond".equals(g.get("type"))?"b":
0<=this.vwr.findNearestAtomIndex(a,b)?"a":"m"),this.vwr.popupMenu(a,b,g)):this.dragSelectedMode?(this.haveSelection=!0,g&&(this.haveSelection=0<=this.vwr.findNearestAtomIndexMovable(a,b,!0)),this.haveSelection&&(this.bnd(this.dragAction,13)||this.bnd(this.dragAction,14))&&this.vwr.moveSelected(-2147483648,0,-2147483648,-2147483648,-2147483648,null,!1,!1)):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(c$,"checkDragWheelAction",function(a,b,d,c,g,f,j){var h=JV.binding.Binding.getButtonMods(a);
if(0!=h){h=this.vwr.notifyMouseClicked(b,d,JV.binding.Binding.getMouseAction(this.pressedCount,h,j),j);if(0==h)return;0<h&&(a=h)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.vwr.refresh(3,"rubberBand selection");else if(!this.checkUserAction(a,b,d,c,g,f,j)){if(0<=this.vwr.getRotateBondIndex()){if(this.bnd(a,26)){this.vwr.moveSelected(c,g,-2147483648,b,d,null,!1,!1);return}this.bnd(a,25)||this.vwr.setRotateBondIndex(-1)}f=null;if(0<=this.dragAtomIndex)switch(this.apm){case 26:this.setMotion(13,
!0);this.bnd(a,27)&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(c,!0),this.getDegrees(g,!1),null):this.vwr.moveSelected(c,g,this.bnd(a,14)?-g:-2147483648,-2147483648,-2147483648,null,!0,!1);return;case 36:case 27:case 30:f=this.vwr.ms.getAtoms(3145754,JU.BSUtil.newAndSetBit(this.dragAtomIndex)),36==this.apm&&f.and(this.vwr.getAtomBitSet("ligand"));case 28:case 29:1==this.dragGesture.getPointCount()&&this.vwr.undoMoveActionClear(this.dragAtomIndex,2,!0);this.setMotion(13,
!0);if(this.bnd(a,27))this.vwr.rotateSelected(this.getDegrees(c,!0),this.getDegrees(g,!1),f);else{switch(this.apm){case 36:case 27:case 30:this.vwr.select(f,!1,0,!0)}this.vwr.moveAtomWithHydrogens(this.dragAtomIndex,c,g,this.bnd(a,14)?-g:-2147483648,f)}return}0<=this.dragAtomIndex&&1==j&&this.bnd(this.clickAction,0)&&32==this.apm?(a=this.vwr.findNearestAtomIndexMovable(b,d,!1),0<=a?(null!=this.mp?this.mp.setCount(1):this.measuresEnabled&&this.enterMeasurementMode(a),this.addToMeasurement(a,null,!0),
this.mp.colix=20):null!=this.mp&&(this.mp.setCount(1),this.mp.colix=23),null!=this.mp&&(this.mp.traceX=b,this.mp.traceY=d,this.vwr.refresh(3,"assignNew"))):!this.drawMode&&!this.labelMode&&this.bnd(a,45)?this.vwr.translateXYBy(c,g):this.dragSelectedMode&&this.haveSelection&&(this.bnd(a,13)||this.bnd(a,27))?(b=this.vwr.bsA().nextSetBit(0),0>b||(1==this.dragGesture.getPointCount()?this.vwr.undoMoveActionClear(b,2,!0):this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1),
this.setMotion(13,!0),this.bnd(a,27)&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(c,!0),this.getDegrees(g,!1),null):this.vwr.moveSelected(c,g,-2147483648,-2147483648,-2147483648,null,!0,!1))):this.drawMode&&(this.bnd(a,8)||this.bnd(a,9))||this.labelMode&&this.bnd(a,10)?(this.setMotion(13,!0),this.vwr.checkObjectDragged(this.dragged.x,this.dragged.y,b,d,a)):this.checkMotionRotateZoom(a,b,c,g,!0)?this.vwr.tm.slabEnabled&&this.checkSlideZoom(a)?this.vwr.slabDepthByPixels(g):
this.vwr.zoomBy(g):this.bnd(a,25)?this.vwr.rotateXYBy(this.getDegrees(c,!0),this.getDegrees(g,!1)):this.bnd(a,29)?0==c&&1<Math.abs(g)?(this.setMotion(8,!0),this.vwr.zoomBy(g+(0<g?-1:1))):0==g&&1<Math.abs(c)&&(this.setMotion(13,!0),this.vwr.rotateZBy(-c+(0<c?1:-1),2147483647,2147483647)):this.bnd(a,46)?this.zoomByFactor(g,2147483647,2147483647):this.bnd(a,28)?(this.setMotion(13,!0),this.vwr.rotateZBy(-c,2147483647,2147483647)):this.vwr.tm.slabEnabled&&(this.bnd(a,6)?this.vwr.depthByPixels(g):this.bnd(a,
38)?this.vwr.slabByPixels(g):this.bnd(a,39)&&this.vwr.slabDepthByPixels(g))}},"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkReleaseAction",function(a,b,d,c){JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));this.vwr.checkInMotion(0);this.vwr.setInMotion(!1);this.vwr.setCursor(0);this.dragGesture.add(this.dragAction,a,b,d);c&&this.vwr.setRotateBondIndex(-2147483648);0<=this.dragAtomIndex&&(29==this.apm||30==this.apm)&&this.minimize(!0);if(32==this.apm&&this.bnd(this.clickAction,
0))null==this.mp||0>this.dragAtomIndex||this.assignNew(a,b);else if(this.dragAtomIndex=-1,this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=this.b.name.equals("drag"),this.rectRubber.x=2147483647,c&&this.vwr.notifyMouseClicked(a,b,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.drawMode&&(this.bnd(this.dragAction,8)||this.bnd(this.dragAction,9))||this.labelMode&&this.bnd(this.dragAction,10))this.vwr.checkObjectDragged(2147483647,
0,a,b,this.dragAction);else if(this.dragSelectedMode&&(this.bnd(this.dragAction,13)&&this.haveSelection)&&this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,!1,!1),(!c||!this.checkUserAction(this.pressAction,a,b,0,0,d,5))&&this.vwr.getBoolean(603979780)&&this.bnd(this.dragAction,44))a=this.getExitRate(),0<a&&this.vwr.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.vwr.g.logGestures&&this.vwr.log("$NOW$ swipe "+this.dragGesture+
" "+a)},"~N,~N,~N,~B");c(c$,"checkClickAction",function(a,b,d,c){if(0<c){if(this.checkUserAction(this.clickAction,a,b,0,0,d,32768))return;this.clickAction=this.vwr.notifyMouseClicked(a,b,this.clickAction,32768);if(0==this.clickAction)return}JU.Logger.debugging&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.clickAction,!1));if(this.bnd(this.clickAction,2)){if(this.vwr.frankClicked(a,b)){this.vwr.popupMenu(-a,b,"j");return}if(this.vwr.frankClickedModelKit(a,b)){this.vwr.popupMenu(0,0,"m");
return}}d=null;var g=!1,f=!1,j=null;this.drawMode||(j=this.vwr.checkObjectClicked(a,b,this.clickAction),null!=j&&(g="bond".equals(j.get("type")),f="isosurface".equals(j.get("type")),d=this.getPoint(j)));g&&(c=1);if(!(null!=d&&Float.isNaN(d.x))){var h=this.findNearestAtom(a,b,d,0<c);if(0==c&&32!=this.apm)null!=this.mp&&((null!=d||0==this.mp.getIndexOf(h))&&this.mp.addPoint(h,d,!1),this.mp.haveModified&&this.vwr.setPendingMeasurement(this.mp),this.vwr.refresh(3,"measurementPending"));else if(this.setMouseMode(),
this.bnd(this.clickAction,43)&&this.vwr.tm.stopMotion(),this.vwr.getBoolean(603979887)&&23==this.apm&&this.bnd(this.clickAction,21))this.vwr.navTranslatePercent(100*a/this.vwr.getScreenWidth()-50,100*b/this.vwr.getScreenHeight()-50);else{if(g){if(this.bnd(this.clickAction,34==this.bondPickingMode||33==this.bondPickingMode?0:5)){this.bondPicked(j.get("index").intValue());return}}else{if(f)return;if(32!=this.apm&&null!=this.mp&&this.bnd(this.clickAction,20)){this.atomOrPointPicked(h,d);4==this.addToMeasurement(h,
d,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,37)){null!=this.mp?(this.addToMeasurement(h,d,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(h),this.addToMeasurement(h,d,!0));this.atomOrPointPicked(h,d);return}}this.isSelectAction(this.clickAction)?f||this.atomOrPointPicked(h,d):this.bnd(this.clickAction,24)&&0>h&&this.reset()}}},"~N,~N,~N,~N");c(c$,"checkUserAction",function(a,b,d,c,g,f,
j){if(!this.b.isUserAction(a))return!1;for(var h=!1,l,q=this.b.getBindings(),p=a+"\t",m,n=q.keySet().iterator();n.hasNext()&&((m=n.next())||1);)if(0==m.indexOf(p)&&JU.PT.isAS(l=q.get(m))){var s=l[1],r=null;if(0<=s.indexOf("_ATOM")){var t=this.findNearestAtom(b,d,null,!0),s=JU.PT.rep(s,"_ATOM","({"+(0<=t?""+t:"")+"})");0<=t&&(s=JU.PT.rep(s,"_POINT",JU.Escape.eP(this.vwr.ms.at[t])))}if(!this.drawMode&&(0<=s.indexOf("_POINT")||0<=s.indexOf("_OBJECT")||0<=s.indexOf("_BOND"))){t=this.vwr.checkObjectClicked(b,
d,a);if(null!=t&&null!=(r=t.get("pt")))t.get("type").equals("bond")&&(s=JU.PT.rep(s,"_BOND","[{"+t.get("index")+"}]")),s=JU.PT.rep(s,"_POINT",JU.Escape.eP(r)),s=JU.PT.rep(s,"_OBJECT",JU.Escape.escapeMap(t));s=JU.PT.rep(s,"_BOND","[{}]");s=JU.PT.rep(s,"_OBJECT","{}")}s=JU.PT.rep(s,"_POINT","{}");s=JU.PT.rep(s,"_ACTION",""+a);s=JU.PT.rep(s,"_X",""+b);s=JU.PT.rep(s,"_Y",""+(this.vwr.getScreenHeight()-d));s=JU.PT.rep(s,"_DELTAX",""+c);s=JU.PT.rep(s,"_DELTAY",""+g);s=JU.PT.rep(s,"_TIME",""+f);s=JU.PT.rep(s,
"_MODE",""+j);s.startsWith("+:")&&(h=!0,s=s.substring(2));this.vwr.evalStringQuiet(s)}return!h},"~N,~N,~N,~N,~N,~N,~N");c(c$,"checkMotionRotateZoom",function(a,b,d,c,g){b=this.checkSlideZoom(a);var f=this.bnd(a,25),j=this.bnd(a,29);if(!b&&!f&&!j)return!1;a=(d=j&&(0==d||Math.abs(c)>5*Math.abs(d)))||this.isZoomArea(this.moved.x)||this.bnd(a,46)?8:f||j?13:this.bnd(a,1)?12:0;this.setMotion(a,g);return d||b},"~N,~N,~N,~N,~B");c(c$,"getExitRate",function(){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$,"isRubberBandSelect",function(a){a=a&-8193|32768;return this.rubberbandSelectionMode&&(this.bnd(a,35)||this.bnd(a,34)||this.bnd(a,32))},"~N");c(c$,"getRubberBand",function(){return this.rubberbandSelectionMode&&2147483647!=this.rectRubber.x?this.rectRubber:null});c(c$,"calcRectRubberBand",function(){var a=this.vwr.antialiased?2:1;this.current.x<this.pressed.x?(this.rectRubber.x=
this.current.x*a,this.rectRubber.width=(this.pressed.x-this.current.x)*a):(this.rectRubber.x=this.pressed.x*a,this.rectRubber.width=(this.current.x-this.pressed.x)*a);this.current.y<this.pressed.y?(this.rectRubber.y=this.current.y*a,this.rectRubber.height=(this.pressed.y-this.current.y)*a):(this.rectRubber.y=this.pressed.y*a,this.rectRubber.height=(this.current.y-this.pressed.y)*a)});c(c$,"getDegrees",function(a,b){return 180*(a/Math.min(500,b?this.vwr.getScreenWidth():this.vwr.getScreenHeight()))*
this.mouseDragFactor},"~N,~B");c(c$,"checkSlideZoom",function(a){return this.bnd(a,40)&&this.isZoomArea(this.pressed.x)},"~N");c(c$,"isZoomArea",function(a){return a>98*this.vwr.getScreenWidth()*(this.vwr.isStereoDouble()?2:1)/100},"~N");c(c$,"getPoint",function(a){var b=new JU.Point3fi;b.setT(a.get("pt"));b.mi=a.get("modelIndex").intValue();return b},"java.util.Map");c(c$,"findNearestAtom",function(a,b,d,c){a=this.drawMode||null!=d?-1:this.vwr.findNearestAtomIndexMovable(a,b,!1);return 0<=a&&(c||
null==this.mp)&&!this.vwr.slm.isInSelectionSubset(a)?-1:a},"~N,~N,JU.Point3fi,~B");c(c$,"isSelectAction",function(a){return this.bnd(a,17)||!this.drawMode&&!this.labelMode&&1==this.apm&&this.bnd(a,1)||this.dragSelectedMode&&(this.bnd(this.dragAction,27)||this.bnd(this.dragAction,13))||this.bnd(a,22)||this.bnd(a,35)||this.bnd(a,32)||this.bnd(a,34)||this.bnd(a,36)||this.bnd(a,30)},"~N");c(c$,"enterMeasurementMode",function(a){this.vwr.setPicked(-1);this.vwr.setPicked(a);this.vwr.setCursor(1);this.vwr.setPendingMeasurement(this.mp=
this.getMP());this.measurementQueued=this.mp},"~N");c(c$,"getMP",function(){return J.api.Interface.getInterface("JM.MeasurementPending",this.vwr,"mouse").set(this.vwr.ms)});c(c$,"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$,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),b=this.measurementQueued.getAtomIndex(2);if(!(0>a||0>b))try{var d=this.vwr.getSmilesOpt(null,a,b,!1,!0,!1,!1,!1);this.vwr.setStatusMeasuring("measureSequence",-2,d,0)}catch(c){if(y(c,Exception))JU.Logger.error(c.toString());else throw c;}});c(c$,"minimize",
function(a){var b=this.dragAtomIndex;a&&(this.dragAtomIndex=-1);this.vwr.dragMinimizeAtom(b)},"~B");c(c$,"queueAtom",function(a,b){var d=this.measurementQueued.addPoint(a,b,!0);0<=a&&this.vwr.setStatusAtomPicked(a,"Atom #"+d+":"+this.vwr.getAtomInfo(a),null);return d},"~N,JU.Point3fi");c(c$,"setMotion",function(a,b){switch(this.vwr.currentCursor){case 3:break;default:this.vwr.setCursor(a)}b&&this.vwr.setInMotion(!0)},"~N,~B");c(c$,"zoomByFactor",function(a,b,d){0!=a&&(this.setMotion(8,!0),this.vwr.zoomByFactor(Math.pow(this.mouseWheelFactor,
a),b,d),this.vwr.setInMotion(!1))},"~N,~N,~N");c(c$,"runScript",function(a){this.vwr.script(a)},"~S");c(c$,"atomOrPointPicked",function(a,b){if(0>a){this.resetMeasurement();if(this.bnd(this.clickAction,33)){this.runScript("select none");return}if(5!=this.apm&&6!=this.apm)return}var d=2;switch(this.apm){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var c=8==this.apm,d=25==this.apm;if(!this.bnd(this.clickAction,c?5:3))return;if(null==this.measurementQueued||0==this.measurementQueued.count||
2<this.measurementQueued.count)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);if(2!=this.queueAtom(a,b))return;c=c||this.measurementQueued.isConnected(this.vwr.ms.at,2)?" DELETE":d?"STRUTS":"";this.runScript("connect "+this.measurementQueued.getMeasurementScript(" ",!0)+c);this.resetMeasurement();return;case 21:d++;case 20:d++;case 18:case 19:case 22:if(!this.bnd(this.clickAction,20))return;if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>
d)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);this.queueAtom(a,b);c=this.measurementQueued.count;1==c&&(this.vwr.setPicked(-1),this.vwr.setPicked(a));if(c<d)return;22==this.apm?this.getSequence():(this.vwr.setStatusMeasuring("measurePicked",d,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.apm||4==this.pickingStyleMeasure)&&this.runScript("measure "+this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();
return}c=null!=this.mp&&1!=this.apm?1:this.apm;switch(c){case 3:if(!this.bnd(this.clickAction,17))return;null==b?this.zoomTo(a):this.runScript("zoomTo "+JU.Escape.eP(b));return;case 5:case 6:this.bnd(this.clickAction,17)&&this.checkTwoAtomAction(b,a)}if(null==b){switch(c){case 1:!this.drawMode&&!this.labelMode&&this.bnd(this.clickAction,1)?this.zoomTo(a):this.bnd(this.clickAction,17)&&this.vwr.setStatusAtomPicked(a,null,null);return;case 2:this.bnd(this.clickAction,19)&&(this.runScript("set labeltoggle {atomindex="+
a+"}"),this.vwr.setStatusAtomPicked(a,null,null));return;case 31:if(this.bnd(this.clickAction,0)){var d=this.vwr.getAtomBitSet("connected(atomIndex="+a+") and !within(SMARTS,'[r50,R]')"),g=d.cardinality();switch(g){case 0:case 1:return;case 3:case 4:for(var f=D(g,0),j=D(g,0),h=0,c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1),h++)f[h]=this.vwr.getBranchBitSet(c,a,!0).cardinality(),j[h]=c;for(h=0;h<g-2;h++){for(var l=-2147483648,q=0,c=0;c<g;c++)f[c]>=l&&d.get(j[c])&&(q=j[c],l=f[c]);d.clear(q)}}this.vwr.undoMoveActionClear(a,
2,!0);this.vwr.invertSelected(null,null,a,d);this.vwr.setStatusAtomPicked(a,"inverted: "+JU.Escape.eBS(d),null)}return;case 7:this.bnd(this.clickAction,4)&&(d=JU.BSUtil.newAndSetBit(a),this.vwr.deleteAtoms(d,!1),this.vwr.setStatusAtomPicked(a,"deleted: "+JU.Escape.eBS(d),null));return}c="atomindex="+a;switch(this.apm){default:return;case 9:this.selectAtoms(c);break;case 10:this.selectAtoms("within(group, "+c+")");break;case 11:this.selectAtoms("within(chain, "+c+")");break;case 13:this.selectAtoms("within(polymer, "+
c+")");break;case 14:this.selectAtoms("within(structure, "+c+")");break;case 12:this.selectAtoms("within(molecule, "+c+")");break;case 16:this.selectAtoms("within(model, "+c+")");break;case 17:this.selectAtoms("visible and within(element, "+c+")");break;case 15:this.selectAtoms("visible and within(site, "+c+")")}this.vwr.clearClickCount();this.vwr.setStatusAtomPicked(a,null,null)}},"~N,JU.Point3fi");c(c$,"assignNew",function(a,b){if(2==this.mp.count)this.vwr.undoMoveActionClear(-1,4146,!0),this.runScript("assign connect "+
this.mp.getMeasurementScript(" ",!1));else if(this.pickAtomAssignType.equals("Xx"))this.exitMeasurementMode("bond dropped");else if(this.pressed.inRange(this.xyRange,this.dragged.x,this.dragged.y)){var d="assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'"';this.isPickAtomAssignCharge?(d+=";{atomindex="+this.dragAtomIndex+"}.label='%C'; ",this.vwr.undoMoveActionClear(this.dragAtomIndex,4,!0)):this.vwr.undoMoveActionClear(-1,4146,!0);this.runScript(d)}else this.isPickAtomAssignCharge||
(this.vwr.undoMoveActionClear(-1,4146,!0),d=this.vwr.ms.at[this.dragAtomIndex],1==d.getElementNumber()?this.runScript("assign atom ({"+this.dragAtomIndex+'}) "X"'):(d=JU.P3.new3(a,b,d.sZ),this.vwr.tm.unTransformPoint(d,d),this.runScript("assign atom ({"+this.dragAtomIndex+'}) "'+this.pickAtomAssignType+'" '+JU.Escape.eP(d))));this.exitMeasurementMode(null)},"~N,~N");c(c$,"bondPicked",function(a){33==this.bondPickingMode&&this.vwr.undoMoveActionClear(-1,4146,!0);switch(this.bondPickingMode){case 33:this.runScript("assign bond [{"+
a+'}] "'+this.pickBondAssignType+'"');break;case 34:this.vwr.setRotateBondIndex(a);break;case 8:this.vwr.deleteBonds(JU.BSUtil.newAndSetBit(a))}},"~N");c(c$,"checkTwoAtomAction",function(a,b){var d=5==this.apm;if(this.vwr.tm.spinOn||this.vwr.tm.navOn||null!=this.vwr.getPendingMeasurement())this.resetMeasurement(),this.vwr.tm.spinOn&&this.runScript("spin off");else{2<=this.measurementQueued.count&&this.resetMeasurement();var c=this.measurementQueued.count;if(1==c)if(null==a){if(this.measurementQueued.getAtomIndex(1)==
b)return}else if(0==this.measurementQueued.getAtom(1).distance(a))return;if(0<=b||null!=a)c=this.queueAtom(b,a);2>c?d?this.vwr.scriptStatus(1==c?J.i18n.GT._("pick one more atom in order to spin the model around an axis"):J.i18n.GT._("pick two atoms in order to spin the model around an axis")):this.vwr.scriptStatus(1==c?J.i18n.GT._("pick one more atom in order to display the symmetry relationship"):J.i18n.GT._("pick two atoms in order to display the symmetry relationship between them")):(c=this.measurementQueued.getMeasurementScript(" ",
!1),d?this.runScript("spin"+c+" "+this.vwr.getInt(553648157)):this.runScript("draw symop"+c+";show symop"+c))}},"JU.Point3fi,~N");c(c$,"reset",function(){this.runScript("!reset")});c(c$,"selectAtoms",function(a){if(!(null!=this.mp||this.selectionWorking)){this.selectionWorking=!0;var b=this.rubberbandSelectionMode||this.bnd(this.clickAction,35)?"selected and not ("+a+") or (not selected) and ":this.bnd(this.clickAction,32)?"selected and not ":this.bnd(this.clickAction,34)?"selected or ":0==this.clickAction||
this.bnd(this.clickAction,36)?"selected tog ":this.bnd(this.clickAction,30)?"":null;if(null!=b)try{var d=this.vwr.getAtomBitSetEval(null,b+("("+a+")"));this.vwr.select(d,!1,0,!1);this.vwr.refresh(3,"selections set")}catch(c){if(!y(c,Exception))throw c;}this.selectionWorking=!1}},"~S");c(c$,"selectRb",function(a){var b=this.vwr.ms.findAtomsInRectangle(this.rectRubber);0<b.length()&&(b=JU.Escape.eBS(b),this.bnd(a,34)?this.runScript("selectionHalos on;select selected or "+b):this.bnd(a,32)?this.runScript("selectionHalos on;select selected and not "+
b):this.runScript("selectionHalos on;select selected tog "+b));this.vwr.refresh(3,"mouseReleased")},"~N");c(c$,"toggleMeasurement",function(){if(null!=this.mp){var a=this.mp.count;2<=a&&4>=a&&this.runScript("!measure "+this.mp.getMeasurementScript(" ",!0));this.exitMeasurementMode(null)}});c(c$,"zoomTo",function(a){this.runScript("zoomTo (atomindex="+a+")");this.vwr.setStatusAtomPicked(a,null,null)},"~N");h(c$,"keyTyped",function(){return!1},"~N,~N");C(c$);c$.actionInfo=c$.prototype.actionInfo=Array(47);c$.actionNames=c$.prototype.actionNames=Array(47);JV.ActionManager.newAction(0,"_assignNew",J.i18n.GT.o(J.i18n.GT._("assign/new atom or bond (requires {0})"),"set picking assignAtom_??/assignBond_?"));JV.ActionManager.newAction(1,"_center",J.i18n.GT._("center"));JV.ActionManager.newAction(2,"_clickFrank",J.i18n.GT._("pop up recent context menu (click on Jmol frank)"));JV.ActionManager.newAction(4,"_deleteAtom",
J.i18n.GT.o(J.i18n.GT._("delete atom (requires {0})"),"set picking DELETE ATOM"));JV.ActionManager.newAction(5,"_deleteBond",J.i18n.GT.o(J.i18n.GT._("delete bond (requires {0})"),"set picking DELETE BOND"));JV.ActionManager.newAction(6,"_depth",J.i18n.GT.o(J.i18n.GT._("adjust depth (back plane; requires {0})"),"SLAB ON"));JV.ActionManager.newAction(7,"_dragAtom",J.i18n.GT.o(J.i18n.GT._("move atom (requires {0})"),"set picking DRAGATOM"));JV.ActionManager.newAction(8,"_dragDrawObject",J.i18n.GT.o(J.i18n.GT._("move whole DRAW object (requires {0})"),
"set picking DRAW"));JV.ActionManager.newAction(9,"_dragDrawPoint",J.i18n.GT.o(J.i18n.GT._("move specific DRAW point (requires {0})"),"set picking DRAW"));JV.ActionManager.newAction(10,"_dragLabel",J.i18n.GT.o(J.i18n.GT._("move label (requires {0})"),"set picking LABEL"));JV.ActionManager.newAction(11,"_dragMinimize",J.i18n.GT.o(J.i18n.GT._("move atom and minimize molecule (requires {0})"),"set picking DRAGMINIMIZE"));JV.ActionManager.newAction(12,"_dragMinimizeMolecule",J.i18n.GT.o(J.i18n.GT._("move and minimize molecule (requires {0})"),
"set picking DRAGMINIMIZEMOLECULE"));JV.ActionManager.newAction(13,"_dragSelected",J.i18n.GT.o(J.i18n.GT._("move selected atoms (requires {0})"),"set DRAGSELECTED"));JV.ActionManager.newAction(14,"_dragZ",J.i18n.GT.o(J.i18n.GT._("drag atoms in Z direction (requires {0})"),"set DRAGSELECTED"));JV.ActionManager.newAction(15,"_multiTouchSimulation",J.i18n.GT._("simulate multi-touch using the mouse)"));JV.ActionManager.newAction(16,"_navTranslate",J.i18n.GT.o(J.i18n.GT._("translate navigation point (requires {0} and {1})"),
["set NAVIGATIONMODE","set picking NAVIGATE"]));JV.ActionManager.newAction(17,"_pickAtom",J.i18n.GT._("pick an atom"));JV.ActionManager.newAction(3,"_pickConnect",J.i18n.GT.o(J.i18n.GT._("connect atoms (requires {0})"),"set picking CONNECT"));JV.ActionManager.newAction(18,"_pickIsosurface",J.i18n.GT.o(J.i18n.GT._("pick an ISOSURFACE point (requires {0}"),"set DRAWPICKING"));JV.ActionManager.newAction(19,"_pickLabel",J.i18n.GT.o(J.i18n.GT._("pick a label to toggle it hidden/displayed (requires {0})"),
"set picking LABEL"));JV.ActionManager.newAction(20,"_pickMeasure",J.i18n.GT.o(J.i18n.GT._("pick an atom to include it in a measurement (after starting a measurement or after {0})"),"set picking DISTANCE/ANGLE/TORSION"));JV.ActionManager.newAction(21,"_pickNavigate",J.i18n.GT.o(J.i18n.GT._("pick a point or atom to navigate to (requires {0})"),"set NAVIGATIONMODE"));JV.ActionManager.newAction(22,"_pickPoint",J.i18n.GT.o(J.i18n.GT._("pick a DRAW point (for measurements) (requires {0}"),"set DRAWPICKING"));
JV.ActionManager.newAction(23,"_popupMenu",J.i18n.GT._("pop up the full context menu"));JV.ActionManager.newAction(24,"_reset",J.i18n.GT._("reset (when clicked off the model)"));JV.ActionManager.newAction(25,"_rotate",J.i18n.GT._("rotate"));JV.ActionManager.newAction(26,"_rotateBranch",J.i18n.GT.o(J.i18n.GT._("rotate branch around bond (requires {0})"),"set picking ROTATEBOND"));JV.ActionManager.newAction(27,"_rotateSelected",J.i18n.GT.o(J.i18n.GT._("rotate selected atoms (requires {0})"),"set DRAGSELECTED"));
JV.ActionManager.newAction(28,"_rotateZ",J.i18n.GT._("rotate Z"));JV.ActionManager.newAction(29,"_rotateZorZoom",J.i18n.GT._("rotate Z (horizontal motion of mouse) or zoom (vertical motion of mouse)"));JV.ActionManager.newAction(30,"_select",J.i18n.GT.o(J.i18n.GT._("select an atom (requires {0})"),"set pickingStyle EXTENDEDSELECT"));JV.ActionManager.newAction(31,"_selectAndDrag",J.i18n.GT.o(J.i18n.GT._("select and drag atoms (requires {0})"),"set DRAGSELECTED"));JV.ActionManager.newAction(32,"_selectAndNot",
J.i18n.GT.o(J.i18n.GT._("unselect this group of atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT"));JV.ActionManager.newAction(33,"_selectNone",J.i18n.GT.o(J.i18n.GT._("select NONE (requires {0})"),"set pickingStyle EXTENDEDSELECT"));JV.ActionManager.newAction(34,"_selectOr",J.i18n.GT.o(J.i18n.GT._("add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT"));JV.ActionManager.newAction(35,"_selectToggle",J.i18n.GT.o(J.i18n.GT._("toggle selection (requires {0})"),
"set pickingStyle DRAG/EXTENDEDSELECT/RASMOL"));JV.ActionManager.newAction(36,"_selectToggleOr",J.i18n.GT.o(J.i18n.GT._("if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG"));JV.ActionManager.newAction(37,"_setMeasure",J.i18n.GT._("pick an atom to initiate or conclude a measurement"));JV.ActionManager.newAction(38,"_slab",J.i18n.GT.o(J.i18n.GT._("adjust slab (front plane; requires {0})"),"SLAB ON"));JV.ActionManager.newAction(39,
"_slabAndDepth",J.i18n.GT.o(J.i18n.GT._("move slab/depth window (both planes; requires {0})"),"SLAB ON"));JV.ActionManager.newAction(40,"_slideZoom",J.i18n.GT._("zoom (along right edge of window)"));JV.ActionManager.newAction(41,"_spinDrawObjectCCW",J.i18n.GT.o(J.i18n.GT._("click on two points to spin around axis counterclockwise (requires {0})"),"set picking SPIN"));JV.ActionManager.newAction(42,"_spinDrawObjectCW",J.i18n.GT.o(J.i18n.GT._("click on two points to spin around axis clockwise (requires {0})"),
"set picking SPIN"));JV.ActionManager.newAction(43,"_stopMotion",J.i18n.GT.o(J.i18n.GT._("stop motion (requires {0})"),"set waitForMoveTo FALSE"));JV.ActionManager.newAction(44,"_swipe",J.i18n.GT._("spin model (swipe and release button and stop motion simultaneously)"));JV.ActionManager.newAction(45,"_translate",J.i18n.GT._("translate"));JV.ActionManager.newAction(46,"_wheelZoom",J.i18n.GT._("zoom"));C(c$);JV.ActionManager.pickingModeNames="off identify label center draw spin symmetry deleteatom deletebond atom group chain molecule polymer structure site model element measure distance angle torsion sequence navigate connect struts dragselected dragmolecule dragatom dragminimize dragminimizemolecule invertstereo assignatom assignbond rotatebond identifybond dragligand".$plit(" ");C(c$,"pickingStyleNames",null);JV.ActionManager.pickingStyleNames="toggle selectOrToggle extendedSelect drag measure measureoff".$plit(" ");
C(c$,"MAX_DOUBLE_CLICK_MILLIS",700,"MININUM_GESTURE_DELAY_MILLISECONDS",10,"SLIDE_ZOOM_X_PERCENT",98,"DEFAULT_MOUSE_DRAG_FACTOR",1,"DEFAULT_MOUSE_WHEEL_FACTOR",1.15,"DEFAULT_GESTURE_SWIPE_FACTOR",1);c$=r(function(){this.time=this.y=this.x=this.index=0;t(this,arguments)},JV,"MotionPoint");c(c$,"set",function(a,b,d,c){this.index=a;this.x=b;this.y=d;this.time=c},"~N,~N,~N,~N");h(c$,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});c$=r(function(){this.action=0;this.nodes=
null;this.time0=this.ptNext=0;this.vwr=null;t(this,arguments)},JV,"Gesture");u(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$,"getSpeedPixelsPerMillisecond",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b),g=360*((d.x-c.x)/this.vwr.getScreenWidth()),f=360*((d.y-c.y)/this.vwr.getScreenHeight());return Math.sqrt(g*g+f*f)/(d.time-c.time)},"~N,~N");c(c$,"getDX",function(a,b){a=this.getPointCount2(a,b);
if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b);return d.x-c.x},"~N,~N");c(c$,"getDY",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var d=this.getNode(this.ptNext-1-b),c=this.getNode(this.ptNext-a-b);return d.y-c.y},"~N,~N");c(c$,"getPointCount",function(){return this.ptNext});c(c$,"getPointCount2",function(a,b){a>this.nodes.length-b&&(a=this.nodes.length-b);for(var d=a+1;0<=--d&&!(0<=this.getNode(this.ptNext-d-b).index););return d},"~N,~N");c(c$,"getNode",
function(a){return this.nodes[(a+this.nodes.length+this.nodes.length)%this.nodes.length]},"~N");h(c$,"toString",function(){return 0==this.nodes.length?""+this:JV.binding.Binding.getMouseActionName(this.action,!1)+" nPoints = "+this.ptNext+" "+this.nodes[0]})});m("JV");w(["JU.BS"],"JV.AnimationManager",["J.api.Interface","JU.BSUtil"],function(){c$=r(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;t(this,arguments)},JV,"AnimationManager");I(c$,function(){this.bsVisibleModels=
new JU.BS});u(c$,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,!0)},"~B");c(c$,"setAnimationNext",function(){return this.setAnimationRelative(this.animationDirection)});c(c$,"currentIsLast",function(){return this.isMovie?this.lastFramePainted==this.caf:this.lastModelPainted==this.cmi});c(c$,"currentFrameIs",function(a){var b=this.cmi;return 0==this.morphCount?b==a:0.001>Math.abs(this.currentMorphModel-a)},"~N");c(c$,"clear",function(){this.setMovie(null);this.initializePointers(0);this.setAnimationOn(!1);this.setModel(0,
!0);this.currentDirection=1;this.cai=-1;this.setAnimationDirection(1);this.setAnimationFps(10);this.setAnimationReplayMode(1073742070,0,0);this.initializePointers(0)});c(c$,"getModelSpecial",function(a){switch(a){case -1:a=this.firstFrameIndex;break;case 0:if(0<this.morphCount)return"-"+(1+this.currentMorphModel);a=this.cmi;break;case 1:a=this.lastFrameIndex}return this.vwr.getModelNumberDotted(a)},"~N");c(c$,"setDisplay",function(a){this.bsDisplay=null==a||0==a.cardinality()?null:JU.BSUtil.copy(a)},
"JU.BS");c(c$,"setMorphCount",function(a){this.morphCount=this.isMovie?0:a},"~N");c(c$,"morph",function(a){var b=B(a);0.001>Math.abs(b-a)?a=b:0.999<Math.abs(b-a)&&(a=b+=1);a-=b;b-=1;if(0==a)this.currentMorphModel=b,this.setModel(b,!0);else{var d;this.setModel(b,!0);d=b+1;this.currentMorphModel=b+a;d==b||(0>d||0>b)||this.vwr.ms.morphTrajectories(b,d,a)}},"~N");c(c$,"setModel",function(a,b){0>a&&this.stopThread(!1);var d=this.cmi,c=this.vwr.ms,g=null==c?0:c.mc;if(1==g)this.cmi=a=0;else if(0>a||a>=g)a=
-1;var c=null,f=!1;if(this.cmi!=a){if(0<g){var g=this.vwr.ms,j=g.isJmolDataFrameForModel(a),h=g.isJmolDataFrameForModel(this.cmi);h&&g.setJmolDataFrame(null,-1,this.cmi);-1!=this.cmi&&this.vwr.saveModelOrientation();if(h||j)c=g.getJmolFrameType(a)+" "+a+" <--  "+this.cmi+" "+g.getJmolFrameType(this.cmi),f=g.getJmolDataSourceFrame(a)==g.getJmolDataSourceFrame(this.cmi)}this.cmi=a;null!=c&&(0<=a&&this.vwr.restoreModelOrientation(a),f&&(0<=c.indexOf("quaternion")||0>c.indexOf("plot")&&0>c.indexOf("ramachandran")&&
0>c.indexOf(" property "))&&this.vwr.restoreModelRotation(d))}this.setViewer(b)},"~N,~B");c(c$,"setBackgroundModelIndex",function(a){var b=this.vwr.ms;if(null==b||0>a||a>=b.mc)a=-1;this.backgroundModelIndex=a;0<=a&&this.vwr.ms.setTrajectory(a);this.vwr.setTainted(!0);this.setFrameRangeVisible()},"~N");c(c$,"initializePointers",function(a){this.firstFrameIndex=0;this.lastFrameIndex=(0==a?0:this.getFrameCount())-1;this.frameStep=a;this.vwr.setFrameVariables()},"~N");c(c$,"setAnimationDirection",function(a){this.animationDirection=
a},"~N");c(c$,"setAnimationFps",function(a){1>a&&(a=1);50<a&&(a=50);this.animationFps=a;this.vwr.setFrameVariables()},"~N");c(c$,"setAnimationReplayMode",function(a,b,d){this.firstFrameDelay=0<b?b:0;this.firstFrameDelayMs=B(1E3*this.firstFrameDelay);this.lastFrameDelay=0<d?d:0;this.lastFrameDelayMs=B(1E3*this.lastFrameDelay);this.animationReplayMode=a;this.vwr.setFrameVariables()},"~N,~N,~N");c(c$,"setAnimationRange",function(a,b){var d=this.getFrameCount();0>a&&(a=0);0>b&&(b=d);a>=d&&(a=d-1);b>=
d&&(b=d-1);this.currentMorphModel=this.firstFrameIndex=a;this.lastFrameIndex=b;this.frameStep=b<a?-1:1;this.rewindAnimation()},"~N,~N");c(c$,"pauseAnimation",function(){this.stopThread(!0)});c(c$,"reverseAnimation",function(){this.currentDirection=-this.currentDirection;this.animationOn||this.resumeAnimation()});c(c$,"repaintDone",function(){this.lastModelPainted=this.cmi;this.lastFramePainted=this.caf});c(c$,"resumeAnimation",function(){0>this.cmi&&this.setAnimationRange(this.firstFrameIndex,this.lastFrameIndex);
1>=this.getFrameCount()?this.animation(!1):(this.animation(!0),this.animationPaused=!1,null==this.animationThread&&(this.intAnimThread++,this.animationThread=J.api.Interface.getOption("thread.AnimationThread",this.vwr,"script"),this.animationThread.setManager(this,this.vwr,[this.firstFrameIndex,this.lastFrameIndex,this.intAnimThread]),this.animationThread.start()))});c(c$,"setAnimationLast",function(){this.setFrame(0<this.animationDirection?this.lastFrameIndex:this.firstFrameIndex)});c(c$,"rewindAnimation",
function(){this.setFrame(0<this.animationDirection?this.firstFrameIndex:this.lastFrameIndex);this.currentDirection=1;this.vwr.setFrameVariables()});c(c$,"setAnimationPrevious",function(){return this.setAnimationRelative(-this.animationDirection)});c(c$,"getAnimRunTimeSeconds",function(){var a=this.getFrameCount();if(this.firstFrameIndex==this.lastFrameIndex||0>this.lastFrameIndex||0>this.firstFrameIndex||this.lastFrameIndex>=a||this.firstFrameIndex>=a)return 0;for(var b=Math.min(this.firstFrameIndex,
this.lastFrameIndex),a=Math.max(this.firstFrameIndex,this.lastFrameIndex),d=1*(a-b)/this.animationFps+this.firstFrameDelay+this.lastFrameDelay;b<=a;b++)d+=this.vwr.ms.getFrameDelayMs(this.modelIndexForFrame(b))/1E3;return d});c(c$,"setMovie",function(a){if(this.isMovie=null!=a&&null==a.get("scripts")){this.animationFrames=a.get("frames");if(null==this.animationFrames||0==this.animationFrames.length)this.isMovie=!1;else if(this.caf=a.get("currentFrame").intValue(),0>this.caf||this.caf>=this.animationFrames.length)this.caf=
0;this.setFrame(this.caf)}this.isMovie||(this.animationFrames=null);this.vwr.setBooleanProperty("_ismovie",this.isMovie);this.bsDisplay=null;this.currentMorphModel=this.morphCount=0},"java.util.Map");c(c$,"modelIndexForFrame",function(a){return this.isMovie?this.animationFrames[a]-1:a},"~N");c(c$,"getFrameCount",function(){return this.isMovie?this.animationFrames.length:this.vwr.ms.mc});c(c$,"setFrame",function(a){try{if(this.isMovie){var b=this.modelIndexForFrame(a);this.caf=a;a=b}else this.caf=
a;this.setModel(a,!0)}catch(d){if(!y(d,Exception))throw d;}},"~N");c(c$,"setViewer",function(a){this.vwr.ms.setTrajectory(this.cmi);this.vwr.tm.setFrameOffset(this.cmi);-1==this.cmi&&a&&this.setBackgroundModelIndex(-1);this.vwr.setTainted(!0);this.setFrameRangeVisible();this.vwr.setStatusFrameChanged(!1,!0);null!=this.vwr.ms&&!this.vwr.g.selectAllModels&&this.vwr.slm.setSelectionSubset(this.vwr.getModelUndeletedAtomsBitSet(this.cmi))},"~B");c(c$,"setFrameRangeVisible",function(){this.bsVisibleModels.clearAll();
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0==a&&(this.firstFrameIndex=this.lastFrameIndex),a=0;1==a&&0>this.cmi&&this.setFrame(b)}});c(c$,"animation",function(a){this.animationOn=a;this.vwr.setBooleanProperty("_animating",a)},"~B");c(c$,"setAnimationRelative",function(a){a=this.getFrameStep(a);var b=(this.isMovie?this.caf:this.cmi)+a,d=0,c=0,g;0<this.morphCount?(d=1/(this.morphCount+1),c=this.currentMorphModel+a*d,g=this.isNotInRange(c)):g=this.isNotInRange(b);if(g)switch(this.animationReplayMode){case 1073742070:return!1;case 528410:c=b=
this.animationDirection==this.currentDirection?this.firstFrameIndex:this.lastFrameIndex;break;case 1073742082:this.currentDirection=-this.currentDirection,b-=2*a,c-=2*a*d}if(1>this.morphCount){if(0>b||b>=this.getFrameCount())return!1;this.setFrame(b);return!0}this.morph(c+1);return!0},"~N");c(c$,"isNotInRange",function(a){var b=a-0.001;return b>this.firstFrameIndex&&b>this.lastFrameIndex||(b=a+0.001)<this.firstFrameIndex&&b<this.lastFrameIndex},"~N");c(c$,"getFrameStep",function(a){return this.frameStep*
a*this.currentDirection},"~N");C(c$,"FRAME_FIRST",-1,"FRAME_LAST",1,"MODEL_CURRENT",0)});m("JV.binding");w(["java.util.Hashtable"],"JV.binding.Binding","java.lang.Boolean java.util.Arrays JU.Lst $.PT $.SB J.api.Interface JU.Escape $.Logger".split(" "),function(){c$=r(function(){this.bindings=this.name=null;t(this,arguments)},JV.binding,"Binding");I(c$,function(){this.bindings=new java.util.Hashtable});c$.getMouseAction=c(c$,"getMouseAction",function(a,b,d){2<a&&(a=2);switch(a){case 0:break;case 1:a=
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0<=a.indexOf("ALT")&&(b|=8);0<=a.indexOf("CTRL")&&(b|=2);0<=a.indexOf("SHIFT")&&(b|=1);return b},"~S");c$.getButtonMods=c(c$,"getButtonMods",function(a){return a&63},"~N");c$.getClickCount=c(c$,"getClickCount",function(a){return(a&768)>>8},"~N");c$.getMouseActionName=c(c$,"getMouseActionName",function(a,b){var d=new JU.SB;if(0==a)return"";var c=JV.binding.Binding.includes(a,8)&&!JV.binding.Binding.includes(a,16)&&!JV.binding.Binding.includes(a,4),g="      ".toCharArray();JV.binding.Binding.includes(a,
2)&&(d.append("CTRL+"),g[5]="C");!c&&JV.binding.Binding.includes(a,8)&&(d.append("ALT+"),g[4]="A");JV.binding.Binding.includes(a,1)&&(d.append("SHIFT+"),g[3]="S");JV.binding.Binding.includes(a,16)?(g[2]="L",d.append("LEFT")):JV.binding.Binding.includes(a,4)?(g[2]="R",d.append("RIGHT")):c?(g[2]="M",d.append("MIDDLE")):JV.binding.Binding.includes(a,32)&&(g[2]="W",d.append("WHEEL"));JV.binding.Binding.includes(a,512)&&(d.append("+double"),g[1]="2");JV.binding.Binding.includes(a,4096)?(d.append("+down"),
g[0]="1"):JV.binding.Binding.includes(a,8192)?(d.append("+drag"),g[0]="2"):JV.binding.Binding.includes(a,16384)?(d.append("+up"),g[0]="3"):JV.binding.Binding.includes(a,32768)&&(d.append("+click"),g[0]="4");return b?String.instantialize(g)+":"+d.toString():d.toString()},"~N,~B");c(c$,"getBindings",function(){return this.bindings});u(c$,function(){});c(c$,"bindAction",function(a,b){this.addBinding(a+"\t"+b,[a,b])},"~N,~N");c(c$,"bindName",function(a,b){this.addBinding(a+"\t",Boolean.TRUE);this.addBinding(a+
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JU.Logger.debug("adding binding "+a+"\t==\t"+JU.Escape.e(b));this.bindings.put(a,b)},"~S,~O");c(c$,"removeBinding",function(a,b){JU.Logger.debugging&&JU.Logger.debug("removing binding "+b);null==a?this.bindings.remove(b):a.remove()},"java.util.Iterator,~S");c(c$,"unbindUserAction",function(a){var b=this.bindings.keySet().iterator();for(a="\t"+a;b.hasNext();){var d=b.next();d.endsWith(a)&&this.removeBinding(b,d)}},"~S");c(c$,"unbindMouseAction",function(a){var b=this.bindings.keySet().iterator();for(a+=
"\t";b.hasNext();){var d=b.next();d.startsWith(a)&&this.removeBinding(b,d)}},"~N");c(c$,"isBound",function(a,b){return this.bindings.containsKey(a+"\t"+b)},"~N,~N");c(c$,"isUserAction",function(a){return this.bindings.containsKey(a+"\t")},"~N");c(c$,"getBindingInfo",function(a,b,d){var c=new JU.SB;d=null==d||d.equalsIgnoreCase("all")?null:d.toLowerCase();for(var g=Array(a.length),f=new JU.Lst,j,h=this.bindings.values().iterator();h.hasNext()&&((j=h.next())||1);)if(JU.PT.isAI(j)){var l=j,q=l[1];null==
g[q]&&(g[q]=new JU.Lst);l=JV.binding.Binding.getMouseActionName(l[0],!0);(null==d||0<=(b[q]+";"+a[q]+";"+l).toLowerCase().indexOf(d))&&g[q].addLast(l)}else JU.PT.isAS(j)&&(q=j[0],l=j[1],(null==d||0<=d.indexOf("user")||0<=q.indexOf(d)||0<=l.indexOf(d))&&f.addLast(j));for(q=0;q<a.length;q++){var p;null==g[q]||0==(p=g[q].size())||this.addInfo(c,g[q].toArray(Array(p)),b[q],a[q])}for(q=0;q<f.size();q++)l=f.get(q),this.addInfo(c,["USER:::"+l[0]],"user-defined",l[1]);return c.toString()},"~A,~A,~S");c(c$,
"addInfo",function(a,b,d,c){java.util.Arrays.sort(b);JU.PT.leftJustify(a,"                      ",d);a.append("\t");d="";for(var g=a.length(),f=0;f<b.length;f++)a.append(d).append(b[f].substring(7)),d=", ";g=a.length()-g;20>g&&a.append("                 ".substring(0,20-g));a.append("\t").append(c).appendC("\n")},"JU.SB,~A,~S,~S");c$.includes=c(c$,"includes",function(a,b){return(a&b)==b},"~N,~N");c$.newBinding=c(c$,"newBinding",function(a,b){return J.api.Interface.getInterface("JV.binding."+b+"Binding",
a,"script")},"JV.Viewer,~S");C(c$,"LEFT",16,"MIDDLE",8,"RIGHT",4,"WHEEL",32,"ALT",8,"CTRL",2,"SHIFT",1,"CTRL_ALT",10,"CTRL_SHIFT",3,"MAC_COMMAND",20,"BUTTON_MASK",28,"BUTTON_MODIFIER_MASK",63,"SINGLE",256,"DOUBLE",512,"COUNT_MASK",768,"DOWN",4096,"DRAG",8192,"UP",16384,"CLICK",32768,"MODE_MASK",61440)});m("JV.binding");w(["JV.binding.JmolBinding"],"JV.binding.DragBinding",null,function(){c$=z(JV.binding,"DragBinding",JV.binding.JmolBinding);u(c$,function(){F(this,JV.binding.DragBinding,[]);this.set("drag")});
h(c$,"setSelectBindings",function(){this.bindAction(33040,30);this.bindAction(33041,35);this.bindAction(33048,34);this.bindAction(33049,32);this.bindAction(4368,31);this.bindAction(8464,13);this.bindAction(33040,17)})});m("JV.binding");w(["JV.binding.Binding"],"JV.binding.JmolBinding",null,function(){c$=z(JV.binding,"JmolBinding",JV.binding.Binding);u(c$,function(){F(this,JV.binding.JmolBinding,[]);this.set("toggle")});c(c$,"set",function(a){this.name=a;this.setGeneralBindings();this.setSelectBindings()},
"~S");c(c$,"setSelectBindings",function(){this.bindAction(33296,30);this.bindAction(33040,36)});c(c$,"setGeneralBindings",function(){this.bindAction(8474,45);this.bindAction(8454,45);this.bindAction(8721,45);this.bindAction(8712,45);this.bindAction(8464,25);this.bindAction(8720,25);this.bindAction(8472,28);this.bindAction(8453,28);this.bindAction(8465,29);this.bindAction(8456,29);this.bindAction(288,46);this.bindAction(8464,40);this.bindAction(8464,16);this.bindAction(4370,23);this.bindAction(4356,
23);this.bindAction(33040,2);this.bindAction(8467,38);this.bindAction(8723,6);this.bindAction(8475,39);this.bindAction(8464,44);this.bindAction(8464,41);this.bindAction(8465,42);this.bindAction(8473,13);this.bindAction(8465,14);this.bindAction(8472,27);this.bindAction(8465,26);this.bindAction(8465,10);this.bindAction(8472,9);this.bindAction(8465,8);this.bindAction(33297,24);this.bindAction(33288,24);this.bindAction(33296,43);this.bindAction(8464,7);this.bindAction(8464,11);this.bindAction(8464,12);
this.bindAction(33040,17);this.bindAction(33040,22);this.bindAction(33040,19);this.bindAction(33040,20);this.bindAction(33296,37);this.bindAction(33040,18);this.bindAction(33043,21);this.bindAction(33040,4);this.bindAction(33040,5);this.bindAction(33040,3);this.bindAction(33040,0);this.bindAction(33043,1)})});m("JV");w(null,"JV.ColorManager","java.lang.Float JU.AU J.c.PAL JU.C $.ColorEncoder $.Elements $.Logger JV.JC".split(" "),function(){c$=r(function(){this.colorData=this.altArgbsCpk=this.argbsCpk=
this.g3d=this.vwr=this.ce=null;this.isDefaultColorRasmol=!1;this.colixRubberband=22;this.colixBackgroundContrast=0;t(this,arguments)},JV,"ColorManager");u(c$,function(a,b){this.vwr=a;this.ce=new JU.ColorEncoder(null,a);this.g3d=b;this.argbsCpk=J.c.PAL.argbsCpk;this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1)},"JV.Viewer,JU.GData");c(c$,"setDefaultColors",function(a){a?(this.isDefaultColorRasmol=!0,this.argbsCpk=JU.AU.arrayCopyI(JU.ColorEncoder.getRasmolScale(),-1)):(this.isDefaultColorRasmol=
!1,this.argbsCpk=J.c.PAL.argbsCpk);this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1);this.ce.createColorScheme(a?"Rasmol=":"Jmol=",!0,!0);for(a=J.c.PAL.argbsCpk.length;0<=--a;)this.g3d.changeColixArgb(a,this.argbsCpk[a]);for(a=JV.JC.altArgbsCpk.length;0<=--a;)this.g3d.changeColixArgb(JU.Elements.elementNumberMax+a,this.altArgbsCpk[a])},"~B");c(c$,"setRubberbandArgb",function(a){this.colixRubberband=0==a?0:JU.C.getColix(a)},"~N");c(c$,"setColixBackgroundContrast",function(a){this.colixBackgroundContrast=
JU.C.getBgContrast(a)},"~N");c(c$,"getColixBondPalette",function(a,b){switch(b){case 19:return this.ce.getColorIndexFromPalette(a.getEnergy(),-2.5,-0.5,7,!1)}return 10},"JM.Bond,~N");c(c$,"getColixAtomPalette",function(a,b){var d=0,c;c=this.vwr.ms;switch(b){case 84:return null==this.colorData||a.i>=this.colorData.length?12:this.ce.getColorIndex(this.colorData[a.i]);case 0:case 1:c=a.getAtomicAndIsotopeNumber();if(c<JU.Elements.elementNumberMax)return this.g3d.getChangeableColix(c,this.argbsCpk[c]);
d=c;c=JU.Elements.altElementIndexFromNumber(c);if(0<c)return this.g3d.getChangeableColix(JU.Elements.elementNumberMax+c,this.altArgbsCpk[c]);c=JU.Elements.getElementNumber(d);return this.g3d.getChangeableColix(c,this.argbsCpk[c]);case 2:return c=JU.ColorEncoder.quantize4(a.getPartialCharge(),-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.getGroupParameter(1112539150),-1,1,7,!1);case 70:return d=this.vwr.ms.getSurfaceDistanceMax(),this.ce.getColorIndexFromPalette(a.getSurfaceDistance100(),0,d,7,!1);case 8:return this.ce.getColorIndexFromPalette(a.getGroupID(),0,0,5,!1);case 9:return this.ce.getColorIndexFromPalette(a.getGroupID(),
0,0,4,!1);case 75:return this.ce.getColorIndexFromPalette(a.getSelectedGroupIndexWithinChain(),0,a.getSelectedGroupCountWithinChain()-1,1,!1);case 87:return c=this.vwr.ms.am[a.mi],this.ce.getColorIndexFromPalette(a.getPolymerIndexInModel(),0,c.getBioPolymerCount()-1,1,!1);case 76:return this.ce.getColorIndexFromPalette(a.getSelectedMonomerIndexWithinPolymer(),0,a.getSelectedMonomerCountWithinPolymer()-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.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.getProteinStructureSubType().getColor();
break;case 10:c=a.getChainID(),null==JU.ColorEncoder.argbsChainAtom&&(JU.ColorEncoder.argbsChainAtom=this.getArgbs(1141899265),JU.ColorEncoder.argbsChainHetero=this.getArgbs(1613758470)),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$,"setElementArgb",function(a,b){1073741991==b&&this.argbsCpk===J.c.PAL.argbsCpk||(b=this.getJmolOrRasmolArgb(a,b),this.argbsCpk===J.c.PAL.argbsCpk&&(this.argbsCpk=JU.AU.arrayCopyRangeI(J.c.PAL.argbsCpk,0,-1),this.altArgbsCpk=
JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1)),a<JU.Elements.elementNumberMax?(this.argbsCpk[a]=b,this.g3d.changeColixArgb(a,b)):(a=JU.Elements.altElementIndexFromNumber(a),this.altArgbsCpk[a]=b,this.g3d.changeColixArgb(JU.Elements.elementNumberMax+a,b)))},"~N,~N");c(c$,"getPropertyColorRange",function(){return this.ce.isReversed?[this.ce.hi,this.ce.lo]:[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");w(["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 $.Lst $.OC $.PT $.Rdr $.SB J.api.Interface J.io.FileReader $.JmolBinary JS.SV JU.Logger JV.Viewer".split(" "),function(){c$=r(function(){this.jmb=this.vwr=null;
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c(c$,"clearPngjCache",function(a){this.jmb.clearPngjCache(null==a?null:this.getCanonicalName(JU.Rdr.getZipRoot(a)))},"~S");c(c$,"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$,"setFileInfo",function(a){this.fullPathName=a[0];
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b&&(a=JV.FileManager.setScriptFileRefs(a,b,!0));null!=d&&(a=JV.FileManager.setScriptFileRefs(a,d,!1));a=JU.PT.rep(a,'\u0001"','"');if(null!=c){for(;c.endsWith("/");)c=c.substring(0,c.length-1);for(b=0;b<JV.FileManager.scriptFilePrefixes.length;b++)d=JV.FileManager.scriptFilePrefixes[b],a=JU.PT.rep(a,d+".",d+c)}return a},"~S,~S,~S,~S");c$.setScriptFileRefs=c(c$,"setScriptFileRefs",function(a,b,d){if(null==b)return a;var c=0==b.length,g=new JU.Lst;J.io.JmolBinary.getFileReferences(a,g);for(var f=new JU.Lst,
j=new JU.Lst,h=g.size(),l=0;l<h;l++){var q=g.get(l),p=q;if(d==JU.OC.isLocal(p)){var m=c?-1:p.indexOf("/"+b+"/");0<=m?p=p.substring(m+1):(m=p.lastIndexOf("/"),0>m&&!c&&(p="/"+p),(0>m||c)&&m++,p=b+p.substring(m))}JU.Logger.info("FileManager substituting "+q+" --\x3e "+p);f.addLast('"'+q+'"');j.addLast('\u0001"'+p+'"')}return JU.PT.replaceStrings(a,f,j)},"~S,~S,~B");c$.stripPath=c(c$,"stripPath",function(a){var b=Math.max(a.lastIndexOf("|"),a.lastIndexOf("/"));return a.substring(b+1)},"~S");c$.fixFileNameVariables=
c(c$,"fixFileNameVariables",function(a,b){var d=JU.PT.rep(a,"%FILE",b);if(0>d.indexOf("%LC"))return d;b=b.toLowerCase();d=JU.PT.rep(d,"%LCFILE",b);4==b.length&&(d=JU.PT.rep(d,"%LC13",b.substring(1,3)));return d},"~S,~S");c(c$,"cachePut",function(a,b){a=a.$replace("\\","/");JU.Logger.debugging&&JU.Logger.debug("cachePut "+a);null==b||"".equals(b)?this.cache.remove(a):(this.cache.put(a,b),this.jmb.getCachedPngjBytes(a))},"~S,~O");c(c$,"cacheGet",function(a,b){a=a.$replace("\\","/");var d=a.indexOf("|");
0<=d&&(a=a.substring(0,d));a=this.getFilePath(a,!0,!1);d=null;(d=Jmol.Cache.get(a))||(d=this.cache.get(a));return b&&n(d,String)?null:d},"~S,~B");c(c$,"cacheClear",function(){JU.Logger.info("cache cleared");this.cache.clear();this.clearPngjCache(null)});c(c$,"cacheFileByNameAdd",function(a,b){if(null==a||!b&&a.equalsIgnoreCase(""))return this.cacheClear(),-1;var d;if(b){a=this.vwr.resolveDatabaseFormat(a);d=this.getFileAsBytes(a,null);if(n(d,String))return 0;this.cachePut(a,d)}else{if(a.endsWith("*"))return JU.AU.removeMapKeys(this.cache,
a.substring(0,a.length-1));d=this.cache.remove(a.$replace("\\","/"))}return null==d?0:(n(d,String),d.length)},"~S,~B");c(c$,"cacheList",function(){for(var a=new java.util.Hashtable,b,d=this.cache.entrySet().iterator();d.hasNext()&&((b=d.next())||1);)a.put(b.getKey(),Integer.$valueOf(JU.PT.isAB(b.getValue())?b.getValue().length:b.getValue().toString().length));return a});c(c$,"getCanonicalName",function(a){var b=this.getClassifiedName(a,!0);return null==b?a:b[2]},"~S");h(c$,"postByteArray",function(a,
b){var d=this.getBufferedInputStreamOrErrorMessageFromName(a,null,!1,!1,b,!1,!0);if(n(d,String))return d;try{d=JU.Rdr.getStreamAsBytes(d,null)}catch(c){if(y(c,java.io.IOException))try{d.close()}catch(g){if(!y(g,java.io.IOException))throw g;}else throw c;}return null==d?"":JU.Rdr.fixUTF(d)},"~S,~A");C(c$,"SIMULATION_PROTOCOL","http://SIMULATION/");c$.scriptFilePrefixes=c$.prototype.scriptFilePrefixes=['/*file*/"','FILE0="','FILE1="']});m("JV");w(["java.util.Hashtable","JU.P3","J.c.CBK"],"JV.GlobalSettings",
"java.lang.Boolean $.Float JU.DF $.PT $.SB J.c.STR JS.SV JU.Escape $.Logger JV.JC $.StateManager $.Viewer".split(" "),function(){c$=r(function(){this.databases=this.htUserVariables=this.htPropertyFlagsRemoved=this.htBooleanParameterFlags=this.htNonbooleanParameterValues=this.vwr=null;this.zDepth=0;this.zShadePower=3;this.zSlab=50;this.slabByAtom=this.slabByMolecule=!1;this.appendNew=this.allowEmbeddedScripts=!0;this.appletProxy="";this.applySymmetryToBonds=!1;this.atomTypes="";this.autoBond=!0;this.axesOrientationRasmol=
!1;this.bondRadiusMilliAngstroms=150;this.bondTolerance=0.45;this.defaultDirectory="";this.defaultStructureDSSP=!0;this.ptDefaultLattice=null;this.defaultLoadFilter=this.defaultLoadScript="";this.defaultDropScript="zap; load SYNC \"%FILE\";if (%ALLOWCARTOONS && _loadScript == '' && defaultLoadScript == '' && _filetype == 'Pdb') {if ({(protein or nucleic)&*/1.1} && {*/1.1}[1].groupindex != {*/1.1}[0].groupindex){select protein or nucleic;cartoons only;}if ({visible}){color structure}else{wireframe -0.1};if (!{visible}){spacefill 23%};select *}";
this.forceAutoBond=!1;this.fractionalRelative=!0;this.inlineNewlineChar="|";this.pubChemFormat=this.nihResolverFormat=this.smilesUrlFormat=this.nmrPredictFormat=this.nmrUrlFormat=this.loadLigandFormat=this.loadFormat=null;this.edsUrlFormat="http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";this.edsUrlFormatDiff="http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE_diff.omap";this.edsUrlCutoff="http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat";this.minBondDistance=0.4;this.minPixelSelRadius=
6;this.pdbSequential=this.pdbGetHeader=this.pdbAddHydrogens=!1;this.percentVdwAtom=23;this.smallMoleculeMaxAtoms=4E4;this.smartAromatic=!0;this.solventOn=this.allowMoveAtoms=this.allowRotateSelected=this.legacyJavaFloat=this.legacyHAddition=this.legacyAutoBonding=this.zeroBasedXyzRasmol=!1;this.defaultTorsionLabel=this.defaultDistanceLabel=this.defaultAngleLabel="%VALUE %UNITS";this.measureAllModels=this.justifyMeasurements=!1;this.minimizationSteps=100;this.minimizationRefresh=!0;this.minimizationSilent=
!1;this.minimizationCriterion=0.001;this.antialiasDisplay=!1;this.displayCellParameters=this.antialiasTranslucent=this.imageState=this.antialiasImages=!0;this.dotsSelectedOnly=!1;this.dotSurface=!0;this.dotDensity=3;this.meshScale=this.dotScale=1;this.isosurfaceKey=this.greyscaleRendering=!1;this.isosurfacePropertySmoothing=!0;this.isosurfacePropertySmoothingPower=7;this.platformSpeed=10;this.repaintWaitMs=1E3;this.showHiddenSelectionHalos=!1;this.showMeasurements=this.showKeyStrokes=!0;this.showTiming=
!1;this.zoomLarge=!0;this.zoomHeight=!1;this.backgroundImageFileName=null;this.hbondsBackbone=this.bondModeOr=this.partialDots=!1;this.hbondsAngleMinimum=90;this.hbondsDistanceMaximum=3.25;this.hbondsRasmol=!0;this.hbondsSolid=!1;this.modeMultipleBond=2;this.showMultipleBonds=this.showHydrogens=!0;this.ssbondsBackbone=!1;this.multipleBondSpacing=-1;this.multipleBondRadiusFactor=0;this.chainCaseSensitive=this.cartoonRibose=this.cartoonLadders=this.cartoonFancy=this.backboneSteps=this.cartoonRockets=
this.cartoonBaseEdges=!1;this.hermiteLevel=0;this.rangeSelected=this.highResolutionFlag=!1;this.rasmolHeteroSetting=this.rasmolHydrogenSetting=!0;this.ribbonAspectRatio=16;this.rocketBarrels=this.ribbonBorder=!1;this.sheetSmoothing=1;this.translucent=this.traceAlpha=!0;this.allowGestures=this.twistedSheets=!1;this.allowMultiTouch=this.allowModelkit=!0;this.allowKeyStrokes=!1;this.animationFps=10;this.atomPicking=!0;this.autoFps=!1;this.axesMode=603979810;this.axesScale=2;this.starWidth=0.05;this.bondPicking=
!1;this.dataSeparator="~~~";this.debugScript=!1;this.defaultDrawArrowScale=0.5;this.defaultLabelXYZ="%a";this.defaultLabelPDB="%m%r";this.defaultTranslucent=0.5;this.delayMaximumMs=0;this.dipoleScale=1;this.drawFontSize=14;this.drawPicking=this.drawHover=this.dragSelected=this.disablePopupMenu=!1;this.dsspCalcHydrogen=!0;this.energyUnits="kJ";this.exportScale=1;this.helpPath="http://chemapps.stolaf.edu/jmol/docs/index.htm";this.fontScaling=!1;this.fontCaching=!0;this.forceField="MMFF";this.helixStep=
1;this.hideNameInPopup=!1;this.hoverDelayMs=500;this.loadAtomDataTolerance=0.01;this.logGestures=this.logCommands=!1;this.measureDistanceUnits="nanometers";this.measurementLabels=!0;this.monitorEnergy=this.messageStyleChime=!1;this.modulationScale=1;this.multiProcessor=!0;this.particleRadius=20;this.pickingSpinRate=10;this.pickLabel="";this.pointGroupDistanceTolerance=0.2;this.pointGroupLinearTolerance=8;this.preserveState=!0;this.propertyColorScheme="roygb";this.quaternionFrame="p";this.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.vectorScale=1;this.vectorsCentered=this.vectorSymmetry=!1;this.vibrationScale=this.vibrationPeriod=
1;this.navigationPeriodic=this.navigationMode=this.hideNavigationPoint=this.wireframeRotation=!1;this.navigationSpeed=5;this.showNavigationPointAlways=!1;this.stereoState=null;this.modelKitMode=!1;this.objMad=this.objStateOn=this.objColors=null;this.ellipsoidFill=this.ellipsoidArrows=this.ellipsoidArcs=this.ellipsoidDots=this.ellipsoidAxes=!1;this.ellipsoidBall=!0;this.ellipsoidDotCount=200;this.ellipsoidAxisDiameter=0.02;this.testFlag4=this.testFlag3=this.testFlag2=this.testFlag1=!1;this.structureList=
null;this.haveSetStructureList=!1;this.userDatabases=null;this.bondingVersion=0;t(this,arguments)},JV,"GlobalSettings");I(c$,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.objColors=D(8,0);this.objStateOn=ga(8,!1);this.objMad=D(8,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,[30,90,-15,95]);this.structureList.put(J.c.STR.SHEET,[-180,-10,70,180,-180,-45,-180,-130,140,180,90,180]);this.structureList.put(J.c.STR.HELIX,
[-160,0,-100,45])});u(c$,function(a,b,d){this.vwr=a;this.htNonbooleanParameterValues=new java.util.Hashtable;this.htBooleanParameterFlags=new java.util.Hashtable;this.htPropertyFlagsRemoved=new java.util.Hashtable;null!=b&&(d||(this.htUserVariables=b.htUserVariables),this.debugScript=b.debugScript,this.disablePopupMenu=b.disablePopupMenu,this.messageStyleChime=b.messageStyleChime,this.defaultDirectory=b.defaultDirectory,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.databases=b.databases,this.showTiming=b.showTiming,this.wireframeRotation=b.wireframeRotation,this.testFlag1=b.testFlag1,this.testFlag2=b.testFlag2,this.testFlag3=b.testFlag3,this.testFlag4=b.testFlag4);null==
this.databases&&(this.databases=new java.util.Hashtable,this.getDataBaseList(JV.JC.databases),this.getDataBaseList(this.userDatabases));this.loadFormat=this.databases.get("pdb");this.loadLigandFormat=this.databases.get("ligand");this.nmrUrlFormat=this.databases.get("nmr");this.nmrPredictFormat=this.databases.get("nmrdb");this.smilesUrlFormat=this.databases.get("nci")+"/file?format=sdf&get3d=True";this.nihResolverFormat=this.databases.get("nci");this.pubChemFormat=this.databases.get("pubchem");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.setI("historyLevel",0);this.setF("cameraDepth",3);this.setI("depth",0);this.setF("gestureSwipeFactor",1);this.setB("hideNotSelected",!1);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.setI("stateversion",0);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.setB("axesWindow",!0);
this.setB("axesMolecular",!1);this.setB("axesPosition",!1);this.setB("axesUnitcell",!1);this.setI("backgroundModel",0);this.setB("colorRasmol",!1);this.setO("currentLocalPath","");this.setO("defaultLattice","{0 0 0}");this.setO("defaultColorScheme","Jmol");this.setO("defaultDirectoryLocal","");this.setO("defaults","Jmol");this.setO("defaultVDW","Jmol");this.setO("exportDrivers","Idtf;Maya;Povray;Vrml;X3d;Tachyon;Obj");this.setI("propertyAtomNumberColumnCount",0);this.setI("propertyAtomNumberField",
0);this.setI("propertyDataColumnCount",0);this.setI("propertyDataField",0);this.setB("undo",!0);this.setB("allowEmbeddedScripts",this.allowEmbeddedScripts);this.setB("allowGestures",this.allowGestures);this.setB("allowKeyStrokes",this.allowKeyStrokes);this.setB("allowModelkit",this.allowModelkit);this.setB("allowMultiTouch",this.allowMultiTouch);this.setB("allowRotateSelected",this.allowRotateSelected);this.setB("allowMoveAtoms",this.allowMoveAtoms);this.setI("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.setB("axesOrientationRasmol",this.axesOrientationRasmol);this.setB("backboneSteps",this.backboneSteps);this.setB("bondModeOr",this.bondModeOr);this.setB("bondPicking",this.bondPicking);this.setI("bondRadiusMilliAngstroms",this.bondRadiusMilliAngstroms);this.setF("bondTolerance",this.bondTolerance);this.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.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.setO("edsUrlFormat",
this.edsUrlFormat);this.setO("edsUrlFormatDiff",this.edsUrlFormatDiff);this.setO("edsUrlCutoff",this.edsUrlCutoff);this.setB("ellipsoidArcs",this.ellipsoidArcs);this.setB("ellipsoidArrows",this.ellipsoidArrows);this.setB("ellipsoidAxes",this.ellipsoidAxes);this.setF("ellipsoidAxisDiameter",this.ellipsoidAxisDiameter);this.setB("ellipsoidBall",this.ellipsoidBall);this.setI("ellipsoidDotCount",this.ellipsoidDotCount);this.setB("ellipsoidDots",this.ellipsoidDots);this.setB("ellipsoidFill",this.ellipsoidFill);
this.setO("energyUnits",this.energyUnits);this.setF("exportScale",this.exportScale);this.setB("fontScaling",this.fontScaling);this.setB("fontCaching",this.fontCaching);this.setB("forceAutoBond",this.forceAutoBond);this.setO("forceField",this.forceField);this.setB("fractionalRelative",this.fractionalRelative);this.setF("particleRadius",this.particleRadius);this.setB("greyscaleRendering",this.greyscaleRendering);this.setF("hbondsAngleMinimum",this.hbondsAngleMinimum);this.setF("hbondsDistanceMaximum",
this.hbondsDistanceMaximum);this.setB("hbondsBackbone",this.hbondsBackbone);this.setB("hbondsRasmol",this.hbondsRasmol);this.setB("hbondsSolid",this.hbondsSolid);this.setI("helixStep",this.helixStep);this.setO("helpPath",this.helpPath);this.setI("hermiteLevel",this.hermiteLevel);this.setB("hideNameInPopup",this.hideNameInPopup);this.setB("hideNavigationPoint",this.hideNavigationPoint);this.setB("highResolution",this.highResolutionFlag);this.setF("hoverDelay",this.hoverDelayMs/1E3);this.setB("imageState",
this.imageState);this.setB("isosurfaceKey",this.isosurfaceKey);this.setB("isosurfacePropertySmoothing",this.isosurfacePropertySmoothing);this.setI("isosurfacePropertySmoothingPower",this.isosurfacePropertySmoothingPower);this.setB("justifyMeasurements",this.justifyMeasurements);this.setB("legacyAutoBonding",this.legacyAutoBonding);this.setB("legacyHAddition",this.legacyHAddition);this.setB("legacyJavaFloat",this.legacyJavaFloat);this.setF("loadAtomDataTolerance",this.loadAtomDataTolerance);this.setO("loadFormat",
this.loadFormat);this.setO("loadLigandFormat",this.loadLigandFormat);this.setB("logCommands",this.logCommands);this.setB("logGestures",this.logGestures);this.setB("measureAllModels",this.measureAllModels);this.setB("measurementLabels",this.measurementLabels);this.setO("measurementUnits",this.measureDistanceUnits);this.setI("meshScale",this.meshScale);this.setB("messageStyleChime",this.messageStyleChime);this.setF("minBondDistance",this.minBondDistance);this.setI("minPixelSelRadius",this.minPixelSelRadius);
this.setI("minimizationSteps",this.minimizationSteps);this.setB("minimizationRefresh",this.minimizationRefresh);this.setB("minimizationSilent",this.minimizationSilent);this.setF("minimizationCriterion",this.minimizationCriterion);this.setB("modelKitMode",this.modelKitMode);this.setF("modulationScale",this.modulationScale);this.setB("monitorEnergy",this.monitorEnergy);this.setF("multipleBondRadiusFactor",this.multipleBondRadiusFactor);this.setF("multipleBondSpacing",this.multipleBondSpacing);this.setB("multiProcessor",
this.multiProcessor&&1<JV.Viewer.nProcessors);this.setB("navigationMode",this.navigationMode);this.setB("navigationPeriodic",this.navigationPeriodic);this.setF("navigationSpeed",this.navigationSpeed);this.setO("nmrPredictFormat",this.nmrPredictFormat);this.setO("nmrUrlFormat",this.nmrUrlFormat);this.setB("partialDots",this.partialDots);this.setB("pdbAddHydrogens",this.pdbAddHydrogens);this.setB("pdbGetHeader",this.pdbGetHeader);this.setB("pdbSequential",this.pdbSequential);this.setI("percentVdwAtom",
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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 f,j=null;if(0!=d&&this.vwr.getBondPicking()&&null!=(j=this.shapes[1].checkObjectClicked(a,b,d,c,!1)))return j;for(var h=0;h<JV.ShapeManager.clickableMax;h++)if(null!=(f=this.shapes[JV.ShapeManager.hoverable[h]])&&
null!=(j=f.checkObjectClicked(a,b,d,c,g)))return j;return null},"~N,~N,~N,JU.BS,~B");c(c$,"checkObjectDragged",function(a,b,d,c,g,f,j){for(var h=!1,l=0<j?j+1:37;!h&&j<l;++j)null!=this.shapes[j]&&(h=this.shapes[j].checkObjectDragged(a,b,d,c,g,f));return h},"~N,~N,~N,~N,~N,JU.BS,~N");c(c$,"checkObjectHovered",function(a,b,d,c){var g=this.shapes[1];if(c&&null!=g&&g.checkObjectHovered(a,b,d))return!0;for(c=0;c<JV.ShapeManager.hoverable.length;c++)if(g=this.shapes[JV.ShapeManager.hoverable[c]],null!=g&&
g.checkObjectHovered(a,b,d))return!0;return!1},"~N,~N,JU.BS,~B");c(c$,"deleteShapeAtoms",function(a,b){if(null!=this.shapes)for(var d=0;37>d;d++)null!=this.shapes[d]&&this.setShapePropertyBs(d,"deleteModelAtoms",a,b)},"~A,JU.BS");c(c$,"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$,"getAtomShapeValue",function(a,b,d){a=JV.JC.shapeTokenIndex(a);
if(0>a||null==this.shapes[a])return 0;d=this.shapes[a].getSize(d);if(0==d){if(0==(b.shapeVisibilityFlags&this.shapes[a].vf))return 0;d=this.shapes[a].getSizeG(b)}return d/2E3},"~N,JM.Group,~N");c(c$,"getObjectMap",function(a,b){if(null!=this.shapes)for(var d=Boolean.$valueOf(b),c=16;30>c;++c)this.getShapePropertyData(c,"getNames",[a,d])},"java.util.Map,~B");c(c$,"getProperty",function(a){return a.equals("getShapes")?this.shapes:null},"~O");c(c$,"getShape",function(a){return null==this.shapes?null:
this.shapes[a]},"~N");c(c$,"mergeShapes",function(a){if(null!=a)if(null==this.shapes)this.shapes=a;else for(var b=0;b<a.length;++b)null!=a[b]&&(null==this.shapes[b]&&this.loadShape(b),this.shapes[b].merge(a[b]))},"~A");c(c$,"resetBioshapes",function(a){if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].isBioShape&&(this.shapes[b].setModelSet(this.ms),this.shapes[b].setShapeSizeRD(0,null,a),this.shapes[b].setProperty("color",J.c.PAL.NONE,a))},"JU.BS");c(c$,
"setAtomLabel",function(a,b){null!=this.shapes&&(this.loadShape(5),this.shapes[5].setProperty("label:"+a,Integer.$valueOf(b),null))},"~S,~N");c(c$,"setModelVisibility",function(){var a=this.shapes;if(!(null==a||null==a[0])){for(var b=this.vwr.getVisibleFramesBitSet(),d=8;33>d;d++)null!=a[d]&&a[d].setModelVisibilityFlags(b);for(var c=this.vwr.getBoolean(603979922),g=this.vwr.slm.bsDeleted,f=this.ms.at,d=this.ms.ac;0<=--d;){var j=f[d];j.shapeVisibilityFlags&=-64;if(!(null!=g&&g.get(d)||!c&&1==j.getElementNumber())&&
b.get(j.mi)){var h=1;this.ms.isAtomHidden(d)||(h|=8,0!=j.madAtom&&(h|=16),j.setShapeVisibility(h,!0))}}this.ms.clearVisibleSets();for(d=0;37>d;++d)b=a[d],null!=b&&b.setAtomClickability()}});c(c$,"finalizeAtoms",function(a,b){var d=this.vwr,c=d.tm,g=this.bsRenderableAtoms;if(null!=a){var f=this.ms.getAtomSetCenter(a),j=new JU.P3;c.transformPt3f(f,j);j.add(b);c.unTransformPoint(j,j);j.sub(f);d.setAtomCoordsRelative(j,a);b.set(0,0,0)}this.ms.getRenderable(g);for(var h=this.ms.vibrations,l=null!=h&&c.vibrationOn,
f=this.ms.at,q=g.nextSetBit(0);0<=q;q=g.nextSetBit(q+1)){var j=f[q],p=l&&j.hasVibration()?c.transformPtVib(j,h[q]):c.transformPt(j);j.sX=p.x;j.sY=p.y;j.sZ=p.z;var m=Math.abs(j.madAtom);m==JM.Atom.MAD_GLOBAL&&(m=B(2E3*d.getFloat(1141899265)));j.sD=aa(d.tm.scaleToScreen(p.z,m))}h=d.gdata;if(c.slabEnabled){q=d.getBoolean(603979940);c=d.getBoolean(603979939);l=h.slab;p=h.depth;if(q)for(var m=this.ms.getMolecules(),n=this.ms.getMoleculeCountInModel(-1),q=0;q<n;q++){var r=m[q],t=0,j=r.firstAtomIndex;if(g.get(j)){for(;t<
r.ac&&!h.isClippedZ(f[j].sZ-(f[j].sD>>1));t++,j++);if(t!=r.ac){j=r.firstAtomIndex;for(t=0;t<r.ac;t++)g.clear(j),f[j++].sZ=0}}}for(q=g.nextSetBit(0);0<=q;q=g.nextSetBit(q+1))if(j=f[q],h.isClippedZ(j.sZ-(c?f[q].sD>>1:0)))j.setClickable(0),m=s((c?-1:1)*j.sD/2),(j.sZ+m<l||j.sZ-m>p||!h.isInDisplayRange(j.sX,j.sY))&&g.clear(q)}if(0==this.ms.ac||!d.getShowNavigationPoint())return null;d=2147483647;h=-2147483648;c=2147483647;l=-2147483648;for(q=g.nextSetBit(0);0<=q;q=g.nextSetBit(q+1))j=f[q],j.sX<d&&(d=j.sX),
j.sX>h&&(h=j.sX),j.sY<c&&(c=j.sY),j.sY>l&&(l=j.sY);this.navMinMax[0]=d;this.navMinMax[1]=h;this.navMinMax[2]=c;this.navMinMax[3]=l;return this.navMinMax},"JU.BS,JU.P3");c(c$,"setModelSet",function(a){this.ms=this.vwr.ms=a},"JM.ModelSet");c(c$,"checkInheritedShapes",function(){null!=this.shapes[24]&&this.setShapePropertyBs(24,"remapInherited",null,null)});c(c$,"restrictSelected",function(a,b){var d=this.vwr.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(),f=21;0<=--f;)6!=f&&
null!=this.getShape(f)&&this.setShapeSizeBs(f,0,null,g);null!=this.getShape(21)&&this.setShapePropertyBs(21,"delete",g,null);this.setLabel(null,g);a||this.vwr.setBooleanProperty("bondModeOr",c);this.vwr.select(d,!1,0,!0)},"~B,~B");C(c$,"hoverable",[31,25,24,22,36]);c$.clickableMax=c$.prototype.clickableMax=JV.ShapeManager.hoverable.length-1});m("JV");w(["java.util.Hashtable"],["JV.Connections","$.Connection","$.StateManager","$.Scene"],["java.util.Arrays","JU.BS","$.SB","JM.Orientation","JU.BSUtil"],
function(){c$=r(function(){this.saved=this.vwr=null;this.lastCoordinates=this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=this.lastContext=this.lastOrientation="";t(this,arguments)},JV,"StateManager");I(c$,function(){this.saved=new java.util.Hashtable});c$.getVariableList=c(c$,"getVariableList",function(a,b,d,c){var g=new JU.SB,f=0,j=Array(a.size()),h;for(a=a.entrySet().iterator();a.hasNext()&&((h=a.next())||1);){var l=h.getKey(),q=h.getValue();if((d||!l.startsWith("site_"))&&
(!c||"@"==l.charAt(0)))j[f++]=l+("@"==l.charAt(0)?" "+q.asString():" = "+JV.StateManager.varClip(l,q.escape(),b))}java.util.Arrays.sort(j,0,f);for(b=0;b<f;b++)null!=j[b]&&g.append("  ").append(j[b]).append(";\n");0==f&&!c&&g.append("# --no global user variables defined--;\n");return g.toString()},"java.util.Map,~N,~B,~B");c$.getObjectIdFromName=c(c$,"getObjectIdFromName",function(a){if(null==a)return-1;a="background axis1      axis2      axis3      boundbox   unitcell   frank      ".indexOf(a.toLowerCase());
return 0>a?a:s(a/11)},"~S");c$.getObjectNameFromId=c(c$,"getObjectNameFromId",function(a){return 0>a||8<=a?null:"background axis1      axis2      axis3      boundbox   unitcell   frank      ".substring(11*a,11*a+11).trim()},"~N");u(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"clear",function(a){this.vwr.setShowAxes(!1);this.vwr.setShowBbcage(!1);this.vwr.setShowUnitCell(!1);a.clear()},"JV.GlobalSettings");c(c$,"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$,"getOrientationFor",function(a){return JV.StateManager.getNoCase(this.saved,0<a.length?"Orientation_"+a:this.lastOrientation)},
"~S");c(c$,"saveContext",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Context_"):this.saved.put(this.lastContext="Context_"+a,b)},"~S,~O");c(c$,"getContext",function(a){return this.saved.get(0==a.length?this.lastContext:"Context_"+a)},"~S");c(c$,"saveBonds",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Bonds_");else{var b=new JV.Connections(this.vwr);b.saveName=this.lastConnections="Bonds_"+a;this.saved.put(b.saveName,b)}},"~S");c(c$,"restoreBonds",function(a){this.vwr.clearModelDependentObjects();
a=JV.StateManager.getNoCase(this.saved,0<a.length?"Bonds_"+a:this.lastConnections);return null!=a&&a.restore()},"~S");c$.varClip=c(c$,"varClip",function(a,b,d){0<d&&b.length>d&&(b=b.substring(0,d)+" #...more ("+b.length+" bytes -- use SHOW "+a+" or MESSAGE @"+a+" to view)");return b},"~S,~S,~N");C(c$,"OBJ_BACKGROUND",0,"OBJ_AXIS1",1,"OBJ_AXIS2",2,"OBJ_AXIS3",3,"OBJ_BOUNDBOX",4,"OBJ_UNITCELL",5,"OBJ_FRANK",6,"OBJ_MAX",8,"objectNameList","background axis1      axis2      axis3      boundbox   unitcell   frank      ");
c$=r(function(){this.scene=this.saveName=null;t(this,arguments)},JV,"Scene");u(c$,function(a){this.scene=a},"java.util.Map");c(c$,"restore",function(a,b){var d=this.scene.get("generator");null!=d&&d.generateScene(this.scene);d=this.scene.get("pymolView");return null!=d&&a.tm.moveToPyMOL(a.eval,b,d)},"JV.Viewer,~N");c$=r(function(){this.saveName=null;this.bondCount=0;this.vwr=this.connections=null;t(this,arguments)},JV,"Connections");u(c$,function(a){var b=a.ms;if(null!=b){this.vwr=a;this.bondCount=
b.bondCount;this.connections=Array(this.bondCount+1);a=b.bo;for(b=this.bondCount;0<=--b;){var d=a[b];this.connections[b]=new JV.Connection(d.atom1.i,d.atom2.i,d.mad,d.colix,d.order,d.getEnergy(),d.shapeVisibilityFlags)}}},"JV.Viewer");c(c$,"restore",function(){var a=this.vwr.ms;if(null==a)return!1;a.deleteAllBonds();for(var b=this.bondCount;0<=--b;){var d=this.connections[b],c=a.ac;d.atomIndex1>=c||d.atomIndex2>=c||(c=a.bondAtoms(a.at[d.atomIndex1],a.at[d.atomIndex2],d.order,d.mad,null,d.energy,!1,
!0),c.colix=d.colix,c.shapeVisibilityFlags=d.shapeVisibilityFlags)}for(b=this.bondCount;0<=--b;)a.bo[b].index=b;this.vwr.setShapeProperty(1,"reportAll",null);return!0});c$=r(function(){this.shapeVisibilityFlags=this.energy=this.order=this.colix=this.mad=this.atomIndex2=this.atomIndex1=0;t(this,arguments)},JV,"Connection");u(c$,function(a,b,d,c,g,f,j){this.atomIndex1=a;this.atomIndex2=b;this.mad=d;this.colix=c;this.order=g;this.energy=f;this.shapeVisibilityFlags=j},"~N,~N,~N,~N,~N,~N,~N")});m("JV");
w(["java.util.Hashtable"],"JV.StatusManager","java.lang.Boolean $.Float javajs.awt.Dimension JU.Lst $.PT J.api.Interface J.c.CBK JU.Logger".split(" "),function(){c$=r(function(){this.cbl=this.jsl=this.vwr=null;this.statusList="";this.allowStatusReporting=!1;this.messageQueue=null;this.statusPtr=0;this.jmolScriptCallbacks=null;this.minSyncRepeatMs=100;this.stereoSync=this.syncDisabled=this.isSynced=this.drivingSync=this.syncingMouse=this.syncingScripts=!1;this.qualityPNG=this.qualityJPG=-1;this.imageType=
null;t(this,arguments)},JV,"StatusManager");I(c$,function(){this.messageQueue=new java.util.Hashtable;this.jmolScriptCallbacks=new java.util.Hashtable});u(c$,function(a){this.vwr=a},"JV.Viewer");c(c$,"recordStatus",function(a){return this.allowStatusReporting&&0<this.statusList.length&&(this.statusList.equals("all")||0<=this.statusList.indexOf(a))},"~S");c(c$,"setStatusChanged",function(a,b,d,c){if(this.recordStatus(a)){var g=new JU.Lst;g.addLast(Integer.$valueOf(++this.statusPtr));g.addLast(a);g.addLast(Integer.$valueOf(b));
g.addLast(d);b=c?null:this.messageQueue.get(a);null==b?this.messageQueue.put(a,b=new JU.Lst):b.size()==JV.StatusManager.MAXIMUM_QUEUE_LENGTH&&b.remove(0);b.addLast(g)}},"~S,~N,~O,~B");c(c$,"getStatusChanged",function(a){var b=0<a.length&&"-"==a.charAt(0),d=0<a.length&&"+"==a.charAt(0),c=!1;b?this.statusList=JU.PT.rep(this.statusList,a.substring(1,a.length),""):(a=JU.PT.rep(a,"+",""),this.statusList.equals(a)||d&&0<=this.statusList.indexOf(a)?c=!0:(d||(this.statusList=""),this.statusList+=a,JU.Logger.debugging&&
JU.Logger.debug("StatusManager messageQueue = "+this.statusList)));a=new JU.Lst;if(c)for(var g,c=this.messageQueue.entrySet().iterator();c.hasNext()&&((g=c.next())||1);)a.addLast(g.getValue());this.messageQueue.clear();this.statusPtr=0;return a},"~S");c(c$,"setJmolStatusListener",function(a,b){this.jsl=a;this.cbl=null==b?a:b},"J.api.JmolStatusListener,J.api.JmolCallbackListener");c(c$,"setJmolCallbackListener",function(a){this.cbl=a},"J.api.JmolCallbackListener");c(c$,"jmolScriptCallback",function(a){a=
this.jmolScriptCallbacks.get(a);null!=a&&this.vwr.evalStringQuietSync(a,!0,!1);return a},"J.c.CBK");c(c$,"setCallbackFunction",function(a,b){var d=J.c.CBK.getCallback(a);System.out.println("callback set for "+a+" "+b+" "+d);if(null!=d){var c=null==b?0:7<b.length&&0==b.toLowerCase().indexOf("script:")?7:11<b.length&&0==b.toLowerCase().indexOf("jmolscript:")?11:0;0==c?this.jmolScriptCallbacks.remove(d):this.jmolScriptCallbacks.put(d,b.substring(c).trim())}null!=this.cbl&&this.cbl.setCallbackFunction(a,
b)},"~S,~S");c(c$,"notifyEnabled",function(a){return null!=this.cbl&&this.cbl.notifyEnabled(a)},"J.c.CBK");c(c$,"setStatusAppletReady",function(a,b){var d=b?this.jmolScriptCallback(J.c.CBK.APPLETREADY):null;this.notifyEnabled(J.c.CBK.APPLETREADY)&&this.cbl.notifyCallback(J.c.CBK.APPLETREADY,[d,a,Boolean.$valueOf(b),null])},"~S,~B");c(c$,"setStatusAtomMoved",function(a){var b=this.jmolScriptCallback(J.c.CBK.ATOMMOVED);this.setStatusChanged("atomMoved",-1,a,!1);this.notifyEnabled(J.c.CBK.ATOMMOVED)&&
this.cbl.notifyCallback(J.c.CBK.ATOMMOVED,[b,a])},"JU.BS");c(c$,"setStatusAtomPicked",function(a,b,d){var c=this.jmolScriptCallback(J.c.CBK.PICK);JU.Logger.info("setStatusAtomPicked("+a+","+b+")");this.setStatusChanged("atomPicked",a,b,!1);this.notifyEnabled(J.c.CBK.PICK)&&this.cbl.notifyCallback(J.c.CBK.PICK,[c,b,Integer.$valueOf(a),d])},"~N,~S,java.util.Map");c(c$,"setStatusClicked",function(a,b,d,c,g){var f=this.jmolScriptCallback(J.c.CBK.CLICK);if(!this.notifyEnabled(J.c.CBK.CLICK))return d;g=
[d,g];this.cbl.notifyCallback(J.c.CBK.CLICK,[f,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(d),Integer.$valueOf(c),g]);return g[0]},"~N,~N,~N,~N,~N");c(c$,"setStatusResized",function(a,b){var d=this.jmolScriptCallback(J.c.CBK.RESIZE);this.notifyEnabled(J.c.CBK.RESIZE)&&this.cbl.notifyCallback(J.c.CBK.RESIZE,[d,Integer.$valueOf(a),Integer.$valueOf(b)])},"~N,~N");c(c$,"haveHoverCallback",function(){return this.jmolScriptCallbacks.containsKey(J.c.CBK.HOVER)||this.notifyEnabled(J.c.CBK.HOVER)});
c(c$,"setStatusAtomHovered",function(a,b){var d=this.jmolScriptCallback(J.c.CBK.HOVER);this.notifyEnabled(J.c.CBK.HOVER)&&this.cbl.notifyCallback(J.c.CBK.HOVER,[d,b,Integer.$valueOf(a)])},"~N,~S");c(c$,"setStatusObjectHovered",function(a,b,d){var c=this.jmolScriptCallback(J.c.CBK.HOVER);this.notifyEnabled(J.c.CBK.HOVER)&&this.cbl.notifyCallback(J.c.CBK.HOVER,[c,b,Integer.$valueOf(-1),a,Float.$valueOf(d.x),Float.$valueOf(d.y),Float.$valueOf(d.z)])},"~S,~S,JU.T3");c(c$,"setFileLoadStatus",function(a,
b,d,c,g,f,j){null==a&&"resetUndo".equals(b)&&(b=this.vwr.getProperty("DATA_API","getAppConsole",null),null!=b&&b.zap(),b=this.vwr.getZapName());this.setStatusChanged("fileLoaded",g,a,!1);null!=c&&this.setStatusChanged("fileLoadError",g,c,!1);var h=this.jmolScriptCallback(J.c.CBK.LOADSTRUCT);f&&this.notifyEnabled(J.c.CBK.LOADSTRUCT)&&(f=this.vwr.getP("_smilesString"),0!=f.length&&(b=f),this.cbl.notifyCallback(J.c.CBK.LOADSTRUCT,[h,a,b,d,c,Integer.$valueOf(g),this.vwr.getP("_modelNumber"),this.vwr.getModelNumberDotted(this.vwr.ms.mc-
1),j]))},"~S,~S,~S,~S,~N,~B,Boolean");c(c$,"setStatusFrameChanged",function(a,b,d,c,g,f,j){if(null!=this.vwr.ms){var h=this.vwr.am.animationOn,l=h?-2-g:g;this.setStatusChanged("frameChanged",l,0<=g?this.vwr.getModelNumberDotted(g):"",!1);var q=this.jmolScriptCallback(J.c.CBK.ANIMFRAME);this.notifyEnabled(J.c.CBK.ANIMFRAME)&&this.cbl.notifyCallback(J.c.CBK.ANIMFRAME,[q,[l,a,b,d,c,g],j,Float.$valueOf(f)]);h||this.vwr.checkMenuUpdate()}},"~N,~N,~N,~N,~N,~N,~S");c(c$,"setStatusDragDropped",function(a,
b,d,c){this.setStatusChanged("dragDrop",0,"",!1);var g=this.jmolScriptCallback(J.c.CBK.DRAGDROP);if(!this.notifyEnabled(J.c.CBK.DRAGDROP))return!1;this.cbl.notifyCallback(J.c.CBK.DRAGDROP,[g,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(d),c]);return!0},"~N,~N,~N,~S");c(c$,"setScriptEcho",function(a,b){if(null!=a){this.setStatusChanged("scriptEcho",0,a,!1);var d=this.jmolScriptCallback(J.c.CBK.ECHO);this.notifyEnabled(J.c.CBK.ECHO)&&this.cbl.notifyCallback(J.c.CBK.ECHO,[d,a,Integer.$valueOf(b?
1:0)])}},"~S,~B");c(c$,"setStatusMeasuring",function(a,b,d,c){this.setStatusChanged(a,b,d,!1);var g=null;a.equals("measureCompleted")?(JU.Logger.info("measurement["+b+"] = "+d),g=this.jmolScriptCallback(J.c.CBK.MEASURE)):a.equals("measurePicked")&&(this.setStatusChanged("measurePicked",b,d,!1),JU.Logger.info("measurePicked "+b+" "+d));this.notifyEnabled(J.c.CBK.MEASURE)&&this.cbl.notifyCallback(J.c.CBK.MEASURE,[g,d,Integer.$valueOf(b),a,Float.$valueOf(c)])},"~S,~N,~S,~N");c(c$,"notifyError",function(a,
b,d){var c=this.jmolScriptCallback(J.c.CBK.ERROR);this.notifyEnabled(J.c.CBK.ERROR)&&this.cbl.notifyCallback(J.c.CBK.ERROR,[c,a,b,this.vwr.getShapeErrorState(),d])},"~S,~S,~S");c(c$,"notifyMinimizationStatus",function(a,b,d,c,g){var f=this.jmolScriptCallback(J.c.CBK.MINIMIZATION);this.notifyEnabled(J.c.CBK.MINIMIZATION)&&this.cbl.notifyCallback(J.c.CBK.MINIMIZATION,[f,a,b,d,c,g])},"~S,Integer,Float,Float,~S");c(c$,"setScriptStatus",function(a,b,d,c){if(-1>d){var g=-2-d;this.setStatusChanged("scriptStarted",
g,b,!1);a="script "+g+" started"}else if(null==a)return;var g=0==d?this.jmolScriptCallback(J.c.CBK.SCRIPT):null,f="Script completed"===a;if(this.recordStatus("script")){var j=null!=c;this.setStatusChanged(j?"scriptError":"scriptStatus",0,a,!1);if(j||f)this.setStatusChanged("scriptTerminated",1,"Jmol script terminated"+(j?" unsuccessfully: "+a:" successfully"),!1)}f&&(this.vwr.getBoolean(603979880)&&this.vwr.getBoolean(603979825))&&(a=[null,"script <exiting>",b,Integer.$valueOf(-1),c],this.notifyEnabled(J.c.CBK.SCRIPT)&&
this.cbl.notifyCallback(J.c.CBK.SCRIPT,a),this.processScript(a),a="Jmol script completed.");a=[g,a,b,Integer.$valueOf(f?-1:d),c];this.notifyEnabled(J.c.CBK.SCRIPT)&&this.cbl.notifyCallback(J.c.CBK.SCRIPT,a);this.processScript(a)},"~S,~S,~N,~S");c(c$,"processScript",function(a){var b=a[3].intValue();null!=this.vwr.scriptEditor&&(0<b?this.vwr.scriptEditor.notifyScriptTermination():0>b?-2==b&&this.vwr.scriptEditor.notifyScriptStart():this.vwr.scriptEditor.isVisible()&&0<a[2].length&&this.vwr.scriptEditor.notifyContext(this.vwr.getScriptContext("SE notify"),
a));null!=this.vwr.appConsole&&0==b&&this.vwr.appConsole.sendConsoleMessage(null==a[1]?null:a[1].toString())},"~A");c(c$,"doSync",function(){return this.isSynced&&this.drivingSync&&!this.syncDisabled});c(c$,"setSync",function(a){this.syncingMouse?null!=a&&this.syncSend(a,"*",0):this.syncingScripts||this.syncSend("!"+this.vwr.tm.getMoveToText(this.minSyncRepeatMs/1E3,!1),"*",0)},"~S");c(c$,"setSyncDriver",function(a){this.stereoSync&&4!=a&&(this.syncSend("SET_GRAPHICS_OFF","*",0),this.stereoSync=!1);
switch(a){case 4:if(!this.syncDisabled)return;this.syncDisabled=!1;break;case 3:this.syncDisabled=!0;break;case 5:this.stereoSync=this.isSynced=this.drivingSync=!0;break;case 1:this.isSynced=this.drivingSync=!0;break;case 2:this.drivingSync=!1;this.isSynced=!0;break;default:this.isSynced=this.drivingSync=!1}JU.Logger.debugging&&JU.Logger.debug(this.vwr.appletName+" sync mode="+a+"; synced? "+this.isSynced+"; driving? "+this.drivingSync+"; disabled? "+this.syncDisabled)},"~N");c(c$,"syncSend",function(a,
b,d){(0!=d||this.notifyEnabled(J.c.CBK.SYNC))&&this.cbl.notifyCallback(J.c.CBK.SYNC,[null,a,b,Integer.$valueOf(d)])},"~S,~S,~N");c(c$,"modifySend",function(a,b,d,c){this.notifyEnabled(J.c.CBK.STRUCTUREMODIFIED)&&this.cbl.notifyCallback(J.c.CBK.STRUCTUREMODIFIED,[null,Integer.$valueOf(d),Integer.$valueOf(a),Integer.$valueOf(b),c])},"~N,~N,~N,~S");c(c$,"getSyncMode",function(){return!this.isSynced?0:this.drivingSync?1:2});c(c$,"showUrl",function(a){null!=this.jsl&&this.jsl.showUrl(a)},"~S");c(c$,"clearConsole",
function(){null!=this.vwr.appConsole&&this.vwr.appConsole.sendConsoleMessage(null);null!=this.jsl&&this.cbl.notifyCallback(J.c.CBK.MESSAGE,null)});c(c$,"functionXY",function(a,b,d){return null==this.jsl?L(Math.abs(b),Math.abs(d),0):this.jsl.functionXY(a,b,d)},"~S,~N,~N");c(c$,"functionXYZ",function(a,b,d,c){return null==this.jsl?L(Math.abs(b),Math.abs(d),Math.abs(d),0):this.jsl.functionXYZ(a,b,d,c)},"~S,~N,~N,~N");c(c$,"jsEval",function(a){return null==this.jsl?"":this.jsl.eval(a)},"~S");c(c$,"createImage",
function(a,b,d,c,g){return null==this.jsl?null:this.jsl.createImage(a,b,null==d?c:d,g)},"~S,~S,~S,~A,~N");c(c$,"getRegistryInfo",function(){return null==this.jsl?null:this.jsl.getRegistryInfo()});c(c$,"dialogAsk",function(a,b){var d=a.equals("Save Image"),c=J.api.Interface.getOption("dialog.Dialog",this.vwr,"status");if(null==c)return null;c.setupUI(!1);d&&c.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);var g=c.getFileNameFromDialog(this.vwr,a,b);d&&null!=g&&(this.qualityJPG=c.getQuality("JPG"),
this.qualityPNG=c.getQuality("PNG"),d=c.getType(),null!=d&&(this.imageType=d));return g},"~S,~S");c(c$,"getJspecViewProperties",function(a){return null==this.jsl?null:this.jsl.getJSpecViewProperty(null==a||0==a.length?"":":"+a)},"~S");c(c$,"resizeInnerPanel",function(a,b){return null==this.jsl?new javajs.awt.Dimension(a,b):this.jsl.resizeInnerPanel("preferredWidthHeight "+a+" "+b+";")},"~N,~N");C(c$,"MAXIMUM_QUEUE_LENGTH",16,"SYNC_OFF",0,"SYNC_DRIVER",1,"SYNC_SLAVE",2,"SYNC_DISABLE",3,"SYNC_ENABLE",
4,"SYNC_STEREO",5)});m("JV");w("JU.A4 $.M3 $.M4 $.P3 $.P3i $.V3 J.c.STER JU.Point3fi".split(" "),"JV.TransformManager","java.lang.Boolean $.Float java.util.Hashtable JU.P4 $.Quat $.SB J.api.Interface JU.Escape $.Logger".split(" "),function(){c$=r(function(){this.spinThread=this.vibrationThread=this.movetoThread=this.vwr=null;this.perspectiveModel=11;this.modelRadiusPixels=this.modelRadius=this.modelCenterOffset=this.cameraDistanceFromCenter=this.aperatureAngle=this.referencePlaneOffset=this.cameraScaleFactor=
0;this.navigationShiftXY=this.navigationOffset=this.navigationCenter=null;this.navigationDepthPercent=0;this.vectorTemp=this.matrixTemp=null;this.haveNotifiedNaN=!1;this.spinX=0;this.spinY=30;this.spinZ=0;this.spinFps=30;this.navZ=this.navY=this.navX=0;this.navFps=NaN;this.doTransform4D=this.isSpinSelected=this.isSpinFixed=this.isSpinInternal=!1;this.rotationCenterDefault=this.perspectiveShiftXY=this.perspectiveOffset=this.fixedRotationCenter=this.fixedRotationOffset=null;this.rotationRadiusDefault=
0;this.internalRotationCenter=this.internalTranslation=this.internalRotationAxis=this.fixedRotationAxis=null;this.internalRotationAngle=0;this.rotationAxis=this.pointT2=this.vectorT2=this.vectorT=this.axisangleT=this.matrixTemp4=this.matrixTemp3=this.matrixRotate=null;this.rotationRate=0;this.cameraSetting=this.camera=this.fixedTranslation=null;this.yTranslationFraction=this.xTranslationFraction=0.5;this.previousY=this.previousX=this.prevZoomSetting=0;this.zoomEnabled=!0;this.zmPctSet=this.zmPct=
100;this.zoomRatio=0;this.internalSlab=this.zShadeEnabled=this.slabEnabled=!1;this.depthValue=this.slabValue=this.depthPercentSetting=this.slabPercentSetting=0;this.zSlabPercentSetting=50;this.zDepthPercentSetting=0;this.zSlabPoint=null;this.slabRange=this.zDepthValue=this.zSlabValue=0;this.depthPlane=this.slabPlane=null;this.perspectiveDepth=!0;this.scale3D=!1;this.cameraDepthSetting=this.cameraDepth=3;this.visualRangeAngstroms=0;this.cameraDistance=1E3;this.scale3DAngstromsPerInch=this.scaleDefaultPixelsPerAngstrom=
this.scalePixelsPerAngstrom=this.screenPixelCount=this.height=this.width=0;this.zoomHeight=this.useZoomLarge=this.antialias=!1;this.screenHeight=this.screenWidth=0;this.ptVibTemp=this.point3iScreenTemp=this.point3fScreenTemp=this.matrixTransformInv=this.matrixTransform=null;this.navigating=!1;this.defaultMode=this.mode=0;this.matrixTest=this.aaTest1=this.ptTest3=this.ptTest2=this.ptTest1=this.untransformedPoint=null;this.vibrationOn=this.spinIsGesture=this.navOn=this.spinOn=!1;this.vibrationScale=
this.vibrationPeriodMs=this.vibrationPeriod=0;this.stereoColors=this.stereoMode=this.vibrationT=null;this.stereoDegrees=NaN;this.stereoRadians=0;this.stereoFrame=!1;this.matrixStereo=null;this.windowCentered=!1;this.ptOffset=this.bsSelectedAtoms=this.frameOffset=null;this.navMode=1;this.zoomFactor=3.4028235E38;this.navigationSlabOffset=0;this.nav=null;t(this,arguments)},JV,"TransformManager");I(c$,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=new JU.P3;
this.matrixTemp=new JU.M4;this.vectorTemp=new JU.V3;this.fixedRotationOffset=new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.pointT2=
new JU.P3;this.rotationAxis=new JU.V3;this.fixedTranslation=new JU.P3;this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=new JU.M4;this.point3fScreenTemp=new JU.P3;this.point3iScreenTemp=new JU.P3i;this.ptVibTemp=new JU.Point3fi;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.c.STER.NONE;this.matrixStereo=
new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=new JU.P3});u(c$,function(){});c$.getTransformManager=c(c$,"getTransformManager",function(a,b,d,c){c=c?J.api.Interface.getInterface("JV.TransformManager4D",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,f){null==d?this.matrixRotate.mul2(a,this.matrixRotate):(this.vwr.moveAtoms(f,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$,"rotateAxisAngleAtCenter",function(a,b,d,c,g,f,j){null!=b&&this.moveRotationCenter(b,!0);this.setSpinOff();this.setNavOn(!1);if(this.vwr.headless){if(f&&3.4028235E38==g)return!1;f=!1}if(Float.isNaN(c)||0==c||0==g)return!1;null!=b&&this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(d);this.rotationRate=c;if(f)return this.fixedRotationAxis.setVA(d,0.017453292*c),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=j,this.setSpin(a,!0,g,null,null,j,
!1),3.4028235E38!=g;a=0.017453292*g;this.fixedRotationAxis.setVA(d,g);this.rotateAxisAngleRadiansFixed(a,j);return!0},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAxisAngleRadiansFixed",function(a,b){this.axisangleT.setAA(this.fixedRotationAxis);this.axisangleT.angle=a;this.rotateAxisAngle2(this.axisangleT,b)},"~N,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,d,c,g,f,j,h,l,q,p,m,n){this.setSpinOff();this.setNavOn(!1);if(null==m&&(null==q||0.001>q.length())&&(j?Float.isNaN(c)||
0==c:0==g))return!1;var r=null;null==m&&(r=JU.V3.newVsub(d,b),f&&r.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(r),this.internalTranslation=null==q?null:JU.V3.newV(q));b=null!=h;if(j)return null==m?(0==g&&(g=NaN),Float.isNaN(g)?this.rotationRate=c:(n=s(Math.abs(g)/Math.abs(c)*this.spinFps+0.5),this.rotationRate=g/n*this.spinFps,null!=q&&this.internalTranslation.scale(1/n)),this.internalRotationAxis.setVA(r,0.017453292*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),this.isSpinInternal=
!0,this.isSpinFixed=!1,this.isSpinSelected=b):g=c,this.setSpin(a,!0,g,p,m,h,l),!Float.isNaN(g);a=0.017453292*g;this.internalRotationAxis.setVA(r,a);this.rotateAxisAngleRadiansInternal(a,h,n);return!1},"J.api.JmolScriptEvaluator,JU.T3,JU.T3,~N,~N,~B,~B,JU.BS,~B,JU.V3,JU.Lst,~A,JU.M4");c(c$,"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 s(Math.floor(b/100*this.width));case "y":return s(Math.floor(b/100*this.height));case "z":return s(Math.floor(b/100*this.screenPixelCount))}return 0},"~S,~N");c(c$,"angstromsToPixels",function(a){return s(Math.floor(this.scalePixelsPerAngstrom*a))},"~N");c(c$,"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){switch(a){case 4130:return this.getMoveToText(1,!1);case 1073742132:return JU.Quat.newM(this.vwr.tm.matrixRotate).toString();case 1073742178:return a=new JU.SB,JV.TransformManager.truncate2(a,
this.getTranslationXPercent()),JV.TransformManager.truncate2(a,this.getTranslationYPercent()),a.toString();default:return this.getMoveToText(1,!0)+"\n#OR\n"+this.getRotateZyzText(!0)}},"~N");c(c$,"getOrientationInfo",function(){var a=new java.util.Hashtable;a.put("moveTo",this.getMoveToText(1,!1));a.put("center","center "+this.getCenterText());a.put("centerPt",this.fixedRotationCenter);var b=new JU.A4;b.setM(this.matrixRotate);a.put("axisAngle",b);a.put("quaternion",JU.Quat.newM(this.matrixRotate).toPoint4f());
a.put("rotationMatrix",this.matrixRotate);a.put("rotateZYZ",this.getRotateZyzText(!1));a.put("rotateXYZ",this.getRotateXyzText());a.put("transXPercent",Float.$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$,"setSlabEnabled",function(a){this.slabEnabled=a;this.vwr.g.setB("slabEnabled",a)},"~B");c(c$,"setZShadeEnabled",function(a){this.zShadeEnabled=a;this.vwr.g.setB("zShade",a)},"~B");c(c$,"setZoomEnabled",function(a){this.zoomEnabled=a;this.vwr.g.setB("zoomEnabled",a)},"~B");c(c$,"slabReset",function(){this.slabToPercent(100);this.depthToPercent(0);
this.slabPlane=this.depthPlane=null;this.setSlabEnabled(!1);this.setZShadeEnabled(!1)});c(c$,"getSlabPercentSetting",function(){return this.slabPercentSetting});c(c$,"slabByPercentagePoints",function(a){this.slabPlane=null;this.slabPercentSetting+=a;this.slabDepthChanged();this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1)},"~N");c(c$,"slabDepthChanged",function(){this.vwr.g.setI("slab",this.slabPercentSetting);this.vwr.g.setI("depth",this.depthPercentSetting)});
c(c$,"depthByPercentagePoints",function(a){this.depthPlane=null;this.depthPercentSetting+=a;this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1);this.slabDepthChanged()},"~N");c(c$,"slabDepthByPercentagePoints",function(a){this.depthPlane=this.slabPlane=null;this.slabPercentSetting+=a;this.depthPercentSetting+=a;this.slabDepthChanged()},"~N");c(c$,"slabToPercent",function(a){this.vwr.setFloatProperty("slabRange",0);this.slabPercentSetting=a;this.slabPlane=
null;this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1);this.slabDepthChanged()},"~N");c(c$,"depthToPercent",function(a){this.vwr.g.setI("depth",a);this.depthPercentSetting=a;this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1);this.slabDepthChanged()},"~N");c(c$,"zSlabToPercent",function(a){this.zSlabPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zDepthPercentSetting=
a)},"~N");c(c$,"zDepthToPercent",function(a){this.zDepthPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zSlabPercentSetting=a)},"~N");c(c$,"slabInternal",function(a,b){b?(this.depthPlane=a,this.depthPercentSetting=0):(this.slabPlane=a,this.slabPercentSetting=100)},"JU.P4,~B");c(c$,"setSlabDepthInternal",function(a){this.finalizeTransformParameters();a?this.depthPlane=null:this.slabPlane=null;this.slabInternal(this.getSlabDepthPlane(a),a)},"~B");c(c$,"getSlabDepthPlane",
function(a){if(a){if(null!=this.depthPlane)return this.depthPlane}else if(null!=this.slabPlane)return this.slabPlane;var b=this.matrixTransform;return JU.P4.new4(-b.m20,-b.m21,-b.m22,-b.m23+(a?this.depthValue:this.slabValue))},"~B");c(c$,"getCameraFactors",function(){this.aperatureAngle=360*Math.atan2(this.screenPixelCount/2,this.referencePlaneOffset)/3.141592653589793;this.cameraDistanceFromCenter=this.referencePlaneOffset/this.scalePixelsPerAngstrom;var a=JU.P3.new3(s(this.screenWidth/2),s(this.screenHeight/
2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(s(this.screenWidth/2),s(this.screenHeight/2),0);this.vwr.tm.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);var d=JU.P3.new3(s(this.screenWidth/2),s(this.screenHeight/2),this.cameraDistanceFromCenter*this.scalePixelsPerAngstrom);this.vwr.tm.unTransformPoint(d,d);d.sub(this.fixedRotationCenter);b.add(d);return[a,b,this.fixedRotationCenter,JU.P3.new3(this.cameraDistanceFromCenter,this.aperatureAngle,this.scalePixelsPerAngstrom)]});
c(c$,"setPerspectiveDepth",function(a){this.perspectiveDepth!=a&&(this.perspectiveDepth=a,this.vwr.g.setB("perspectiveDepth",a),this.resetFitToScreen(!1))},"~B");c(c$,"getPerspectiveDepth",function(){return this.perspectiveDepth});c(c$,"setCameraDepthPercent",function(a,b){this.resetNavigationPoint(b);var d=0>a?-a/100:a;0!=d&&(this.cameraDepthSetting=d,this.vwr.g.setF("cameraDepth",this.cameraDepthSetting),this.cameraDepth=NaN)},"~N,~B");c(c$,"getCameraDepth",function(){return this.cameraDepthSetting});
c(c$,"setScreenParameters0",function(a,b,d,c,g,f){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=d,this.width=(this.antialias=c)?2*a:a,this.height=c?2*b:b,this.scaleFitToScreen(!1,d,g,f))},"~N,~N,~B,~B,~B,~B");c(c$,"setAntialias",function(a){var b=this.antialias!=a;this.width=(this.antialias=a)?2*this.screenWidth:this.screenWidth;this.height=this.antialias?2*this.screenHeight:this.screenHeight;b&&this.scaleFitToScreen(!1,this.useZoomLarge,!1,!1)},"~B");c(c$,"defaultScaleToScreen",
function(a){return this.screenPixelCount/2/a},"~N");c(c$,"resetFitToScreen",function(a){this.scaleFitToScreen(a,this.vwr.g.zoomLarge,!0,!0)},"~B");c(c$,"scaleFitToScreen",function(a,b,d,c){0==this.width||0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*(a?0.5:this.xTranslationFraction),this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),c&&this.resetNavigationPoint(d),this.zoomHeight&&(b=this.height>this.width),this.screenPixelCount=
b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");c(c$,"scaleToScreen",function(a,b){if(0==b||2>a)return 0;var d=this.scaleToPerspective(a,b*this.scalePixelsPerAngstrom/1E3);return 0<d?d:1},"~N,~N");c(c$,"unscaleToScreen",function(a,b){var d=b/this.scalePixelsPerAngstrom;return this.perspectiveDepth?d/this.getPerspectiveFactor(a):d},"~N,~N");c(c$,"scaleToPerspective",
function(a,b){return this.perspectiveDepth?b*this.getPerspectiveFactor(a):b},"~N,~N");c(c$,"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):
s(Math.floor(this.modelCenterOffset*this.slabRange/(2*this.modelRadius)*(this.zmPctSet/100)));this.depthValue=this.zValueFromPercent(this.depthPercentSetting);this.zSlabPercentSetting==this.zDepthPercentSetting?(this.zSlabValue=this.slabValue,this.zDepthValue=this.depthValue):(this.zSlabValue=this.zValueFromPercent(this.zSlabPercentSetting),this.zDepthValue=this.zValueFromPercent(this.zDepthPercentSetting));if(null!=this.zSlabPoint)try{this.transformPt3f(this.zSlabPoint,this.pointT2),this.zSlabValue=
B(this.pointT2.z)}catch(a){if(!y(a,Exception))throw a;}this.vwr.g.setO("_slabPlane",JU.Escape.eP4(this.getSlabDepthPlane(!1)));this.vwr.g.setO("_depthPlane",JU.Escape.eP4(this.getSlabDepthPlane(!0)));this.slabEnabled||(this.slabValue=0,this.depthValue=2147483647)});c(c$,"zValueFromPercent",function(a){return s(Math.floor((1-a/50)*this.modelRadiusPixels+this.modelCenterOffset))},"~N");c(c$,"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(y(a,
Exception))System.out.println("ERROR INVERTING matrixTransform!");else throw a;}});c(c$,"rotatePoint",function(a,b){this.matrixRotate.rotate2(a,b);b.y=-b.y},"JU.T3,JU.T3");c(c$,"getScreenTemp",function(a){this.matrixTransform.rotTrans2(a,this.point3fScreenTemp)},"JU.T3");c(c$,"transformPoints",function(a,b,d){for(;0<=--a;)d[a].setT(this.transformPt(b[a]))},"~N,~A,~A");c(c$,"transformPtScr",function(a,b){b.setT(this.transformPt(a))},"JU.T3,JU.P3i");c(c$,"transformPtNoClip",function(a,b){this.applyPerspective(a,
null);b.setT(this.point3fScreenTemp)},"JU.P3,JU.P3");c(c$,"transformPt",function(a){return this.applyPerspective(a,this.internalSlab?a:null)},"JU.T3");c(c$,"transformPtVib",function(a,b){this.ptVibTemp.setT(a);return this.applyPerspective(this.getVibrationPoint(b,this.ptVibTemp,NaN),a)},"JU.P3,JU.Vibration");c(c$,"getVibrationPoint",function(a,b,d){a.setTempPoint(b,this.vibrationT,Float.isNaN(d)?this.vibrationScale:d,this.vwr.g.modulationScale);return b},"JU.Vibration,JU.T3,~N");c(c$,"transformPt3f",
function(a,b){this.applyPerspective(a,a);b.setT(this.point3fScreenTemp)},"JU.T3,JU.P3");c(c$,"transformPt2D",function(a){-3.4028235E38==a.z?(this.point3iScreenTemp.x=s(Math.floor(a.x/100*this.screenWidth)),this.point3iScreenTemp.y=s(Math.floor((1-a.y/100)*this.screenHeight))):(this.point3iScreenTemp.x=B(a.x),this.point3iScreenTemp.y=this.screenHeight-B(a.y));this.antialias&&(this.point3iScreenTemp.x<<=1,this.point3iScreenTemp.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.point3fScreenTemp);
this.point3iScreenTemp.z=B(this.point3fScreenTemp.z);return this.point3iScreenTemp},"JU.T3");c(c$,"applyPerspective",function(a,b){this.getScreenTemp(a);var d=this.point3fScreenTemp.z;Float.isNaN(d)?(!this.haveNotifiedNaN&&JU.Logger.debugging&&JU.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=!0,d=this.point3fScreenTemp.z=1):0>=d&&(d=this.point3fScreenTemp.z=1);switch(this.mode){case 1:this.point3fScreenTemp.x-=this.navigationShiftXY.x;this.point3fScreenTemp.y-=this.navigationShiftXY.y;
break;case 2:this.point3fScreenTemp.x+=this.perspectiveShiftXY.x,this.point3fScreenTemp.y+=this.perspectiveShiftXY.y}this.perspectiveDepth&&(d=this.getPerspectiveFactor(d),this.point3fScreenTemp.x*=d,this.point3fScreenTemp.y*=d);switch(this.mode){case 1:this.point3fScreenTemp.x+=this.navigationOffset.x;this.point3fScreenTemp.y+=this.navigationOffset.y;break;case 2:this.point3fScreenTemp.x-=this.perspectiveShiftXY.x,this.point3fScreenTemp.y-=this.perspectiveShiftXY.y;case 0:this.point3fScreenTemp.x+=
this.fixedRotationOffset.x,this.point3fScreenTemp.y+=this.fixedRotationOffset.y}Float.isNaN(this.point3fScreenTemp.x)&&!this.haveNotifiedNaN&&(JU.Logger.debugging&&JU.Logger.debug("NaN found in transformPoint "),this.haveNotifiedNaN=!0);this.point3iScreenTemp.set(B(this.point3fScreenTemp.x),B(this.point3fScreenTemp.y),B(this.point3fScreenTemp.z));if(null!=b&&(null!=this.slabPlane&&0<b.x*this.slabPlane.x+b.y*this.slabPlane.y+b.z*this.slabPlane.z+this.slabPlane.w||null!=this.depthPlane&&0>b.x*this.depthPlane.x+
b.y*this.depthPlane.y+b.z*this.depthPlane.z+this.depthPlane.w))this.point3iScreenTemp.z=1;return this.point3iScreenTemp},"JU.T3,JU.T3");c(c$,"transformVector",function(a,b){this.matrixTransform.rotate2(a,b)},"JU.V3,JU.V3");c(c$,"move",function(a,b,d,c,g,f,j){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm");this.movetoThread.setManager(this,this.vwr,[b,c,[d,g,f,j]]);0<f&&this.movetoThread.setEval(a);this.movetoThread.run()},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");
c(c$,"isInPosition",function(a,b){if(Float.isNaN(b))return!0;this.aaTest1.setVA(a,b/57.29577951308232);this.ptTest1.set(4.321,1.23456,3.14159);this.getRotation(this.matrixTest);this.matrixTest.rotate2(this.ptTest1,this.ptTest2);this.matrixTest.setAA(this.aaTest1).rotate2(this.ptTest1,this.ptTest3);return 0.1>this.ptTest3.distance(this.ptTest2)},"JU.V3,~N");c(c$,"moveToPyMOL",function(a,b,d){var c=JU.M3.newA9(d);c.invert();var g=d[9],f=-d[10],j=-d[11],h=JU.P3.new3(d[12],d[13],d[14]),l=d[15],q=d[16],
p=d[17];this.setPerspectiveDepth(!(0<=p));var p=Math.abs(p)/2,m=Math.tan(3.141592653589793*p/180),p=j*m,m=0.5/m-0.5,n=50/p;0<l&&(l=50+B((j-l)*n),j=50+B((j-q)*n),this.setSlabEnabled(!0),this.slabToPercent(l),this.depthToPercent(j),21==d.length&&(q=0!=d[18],n=0!=d[19],d=d[20],this.setZShadeEnabled(q),q&&(n?this.vwr.setIntProperty("zSlab",B(Math.min(100,l+d*(j-l)))):this.vwr.setIntProperty("zSlab",B((l+j)/2)),this.vwr.setIntProperty("zDepth",j))));this.moveTo(a,b,h,null,0,c,100,NaN,NaN,p,null,NaN,NaN,
NaN,m,g,f);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(c$,"moveTo",function(a,b,d,c,g,f,j,h,l,q,p,m,n,s,r,t,u){if(null==f)if(f=new JU.M3,c=JU.V3.newV(c),Float.isNaN(g))f.m00=NaN;else if(0.01>g&&-0.01<g)f.setScale(1);else{if(0==c.x&&0==c.y&&0==c.z)return;var w=new JU.A4;w.setVA(c,g/57.29577951308232);f.setAA(w)}t==this.cameraSetting.x&&(t=NaN);u==this.cameraSetting.y&&(u=NaN);r==this.cameraDepth&&(r=NaN);Float.isNaN(t)||(h=50*t/q/this.width*this.screenPixelCount);Float.isNaN(u)||(l=50*u/q/this.height*
this.screenPixelCount);g=null==d?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(q);if(0>=b)this.setAll(d,f,p,j,h,l,q,g,s,m,n,r,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,[d,f,p,[b,j,h,l,q,g,s,m,n,r,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(z){if(!y(z,Exception))throw z;}},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.T3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(c$,"setAll",function(a,b,d,c,g,f,j,h,l,q,p,m,n,s){Float.isNaN(b.m00)||this.setRotation(b);null!=a&&this.moveRotationCenter(a,!this.windowCentered);null!=d&&1==this.mode&&this.navigationCenter.setT(d);Float.isNaN(m)||this.setCameraDepthPercent(m,!1);!Float.isNaN(n)&&!Float.isNaN(s)&&this.setCamera(n,s);Float.isNaN(c)||
this.zoomToPercent(c);Float.isNaN(j)||(this.modelRadius=j);Float.isNaN(h)||(this.scaleDefaultPixelsPerAngstrom=h);!Float.isNaN(g)&&!Float.isNaN(f)&&(this.translateToPercent("x",g),this.translateToPercent("y",f));1==this.mode&&(!Float.isNaN(q)&&!Float.isNaN(p)&&this.navTranslatePercentOrTo(0,q,p),Float.isNaN(l)||this.setNavigationDepthPercent(l))},"JU.P3,JU.M3,JU.P3,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(c$,"stopMotion",function(){this.movetoThread=null});c(c$,"getRotationText",function(){this.axisangleT.setM(this.matrixRotate);
var a=57.29577951308232*this.axisangleT.angle,b=new JU.SB;this.vectorT.set(this.axisangleT.x,this.axisangleT.y,this.axisangleT.z);if(0.01>a)return"{0 0 1 0}";this.vectorT.normalize();this.vectorT.scale(1E3);b.append("{");JV.TransformManager.truncate0(b,this.vectorT.x);JV.TransformManager.truncate0(b,this.vectorT.y);JV.TransformManager.truncate0(b,this.vectorT.z);JV.TransformManager.truncate2(b,a);b.append("}");return b.toString()});c(c$,"getMoveToText",function(a,b){this.finalizeTransformParameters();
var 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$,"setSpin",function(a,b,d,c,g,f,j){this.navOn&&b&&this.setNavOn(!1);this.spinOn!=b&&(this.spinOn=b,this.vwr.g.setB("_spinning",b),b?null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread",this.vwr,"tm"),this.spinThread.setManager(this,this.vwr,[Float.$valueOf(d),c,g,f,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$,"setVibrationPeriod",function(a){if(Float.isNaN(a))a=this.vibrationPeriod;else if(0==a)this.vibrationPeriodMs=this.vibrationPeriod=0;else{this.vibrationPeriod=Math.abs(a);this.vibrationPeriodMs=B(1E3*this.vibrationPeriod);
if(0<a)return;a=-a}this.setVibrationOn(0<a&&0<=this.vwr.ms.getLastVibrationVector(this.vwr.am.cmi,0))},"~N");c(c$,"setVibrationT",function(a){this.vibrationT.x=a;0==this.vibrationScale&&(this.vibrationScale=this.vwr.g.vibrationScale)},"~N");c(c$,"isVibrationOn",function(){return this.vibrationOn});c(c$,"setVibrationOn",function(a){a?1>this.vwr.ms.mc?(this.vibrationOn=!1,this.vibrationT.x=0):(null==this.vibrationThread&&(this.vibrationThread=J.api.Interface.getOption("thread.VibrationThread",this.vwr,
"tm"),this.vibrationThread.setManager(this,this.vwr,null),this.vibrationThread.start()),this.vibrationOn=!0):(null!=this.vibrationThread&&(this.vibrationThread.interrupt(),this.vibrationThread=null),this.vibrationOn=!1,this.vibrationT.x=0)},"~B");c(c$,"clearVibration",function(){this.setVibrationOn(!1);this.vibrationScale=0});c(c$,"setStereoMode2",function(a){this.stereoMode=J.c.STER.CUSTOM;this.stereoColors=a},"~A");c(c$,"setStereoMode",function(a){this.stereoColors=null;this.stereoMode=a},"J.c.STER");
c(c$,"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",
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"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 96:d.add(this.vwr.ms.getAverageAtomPoint());break;case 1679429641:d.add(this.vwr.getBoundBoxCenter());break;case 1073741826:d.setT(this.rotationCenterDefault)}this.setRotationCenterAndRadiusXYZ(d,!0);this.resetFitToScreen(!0)},"~N,JU.P3");c(c$,"setFrameOffset",function(a){null==this.vwr.frameOffsets||0>a||a>=this.vwr.frameOffsets.length?this.frameOffset.set(0,0,0):this.frameOffset.setT(this.vwr.frameOffsets[a])},"~N");c(c$,
"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$,"unTransformPoint",
function(a,b){this.untransformedPoint.setT(a);switch(this.mode){case 1:this.untransformedPoint.x-=this.navigationOffset.x;this.untransformedPoint.y-=this.navigationOffset.y;break;case 2:this.point3fScreenTemp.x+=this.perspectiveShiftXY.x,this.point3fScreenTemp.y+=this.perspectiveShiftXY.y;case 0:this.untransformedPoint.x-=this.fixedRotationOffset.x,this.untransformedPoint.y-=this.fixedRotationOffset.y}if(this.perspectiveDepth){var d=this.getPerspectiveFactor(this.untransformedPoint.z);this.untransformedPoint.x/=
d;this.untransformedPoint.y/=d}switch(this.mode){case 1:this.untransformedPoint.x+=this.navigationShiftXY.x;this.untransformedPoint.y+=this.navigationShiftXY.y;break;case 2:this.untransformedPoint.x-=this.perspectiveShiftXY.x,this.untransformedPoint.y-=this.perspectiveShiftXY.y}this.matrixTransformInv.rotTrans2(this.untransformedPoint,b)},"JU.T3,JU.T3");c(c$,"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$,"setScreenParameters",function(a,b,d,c,g,f){var j=1==this.mode?JU.P3.newP(this.navigationCenter):null,h=JU.P3.newP(this.navigationOffset);h.x/=this.width;h.y/=this.height;this.setScreenParameters0(a,b,d,c,g,f);
null!=j&&(this.navigationCenter.setT(j),this.navTranslatePercentOrTo(-1,h.x*this.width,h.y*this.height),this.setNavigatePt(j))},"~N,~N,~B,~B,~B,~B");c(c$,"navInterrupt",function(){null!=this.nav&&this.nav.interrupt()});c(c$,"getNav",function(){if(null!=this.nav)return!0;this.nav=J.api.Interface.getOption("navigate.Navigator",this.vwr,"tm");if(null==this.nav)return!1;this.nav.set(this,this.vwr);return!0});c(c$,"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$,"getNavigationState",function(){return 1==this.mode&&this.getNav()?this.nav.getNavigationState():""});C(c$,"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");w(["java.lang.Enum","javajs.api.PlatformViewer","J.api.JmolViewer","J.atomdata.AtomDataServer","java.util.Hashtable"],"JV.Viewer","java.io.Reader java.lang.Boolean $.Character $.Float $.NullPointerException javajs.awt.Dimension JU.BS $.CU $.DF $.Lst $.Measure $.P3 $.P3i $.PT $.Rdr $.SB $.V3 J.adapter.smarter.SmarterJmolAdapter J.api.Interface $.JmolAppConsoleInterface J.atomdata.RadiusData J.c.FIL $.STER $.VDW J.i18n.GT JM.ModelSet JS.SV $.T J.thread.TimeoutThread JU.BSUtil $.C $.CommandHistory $.Elements $.Escape $.GData $.JmolMolecule $.Logger $.Parser $.TempArray JV.ActionManager $.AnimationManager $.ColorManager $.FileManager $.GlobalSettings $.JC $.ModelManager $.SelectionManager $.ShapeManager $.StateManager $.StatusManager $.TransformManager JV.binding.Binding".split(" "),
function(){c$=r(function(){this.queueOnHold=this.isSingleThreaded=this.isWebGL=this.isJS=this.haveDisplay=this.autoExit=this.testAsync=!1;this.fullName="";this.fm=this.ms=this.definedAtomSets=this.compiler=null;this.mustRender=this.listCommands=this.isSyntaxCheck=this.isSyntaxAndFileCheck=this.isJNLP=this.isApplet=!1;this.appletName=this.htmlName="";this.tryPt=0;this.insertedCommand="";this.tm=this.sm=this.g=this.rm=this.slm=this.shm=this.dm=this.cm=this.am=this.acm=this.html5Applet=this.gdata=null;
this.logFilePath=this.syncId="";this.useCommandThread=this.noGraphicsAllowed=this.multiTouch=this.isSilent=this.isSignedAppletLocal=this.isSignedApplet=this.isPrintOnly=this.allowScripting=!1;this.tempArray=this.eval=this.scm=this.stm=this.mm=this.commandHistory=this.access=this.modelAdapter=this.display=this.vwrOptions=this.commandOptions=null;this.async=this.allowArrayDotNotation=!1;this.errorMessageUntranslated=this.errorMessage=this.chainList=this.chainMap=this.rd=this.defaultVdw=this.actionStatesRedo=
this.actionStates=this.dimScreen=null;this.privateKey=0;this.headless=this.isPreviewOnly=this.dataOnly=!1;this.frameOffsets=this.bsFrameOffsets=this.lastData=this.jsc=this.smilesMatcher=this.minimizer=this.annotationParser=this.ligandModelSet=this.ligandModels=this.mouse=null;this.motionEventNumber=0;this.inMotion=!1;this.refreshing=!0;this.axesAreTainted=!1;this.maximumSize=2147483647;this.imageFontScaling=1;this.gRight=null;this.isStereoSlave=!1;this.jsParams=this.captureParams=null;this.antialiased=
!1;this.hoverAtomIndex=-1;this.hoverText=null;this.hoverEnabled=!0;this.currentCursor=0;this.ptTemp=null;this.prevFrame=-2147483648;this.prevMorphModel=0;this.haveJDX=!1;this.jsv=null;this.frankOn=!0;this.scriptEditorVisible=!1;this.pm=this.headlessImageParams=this.modelkitPopup=this.jmolpopup=this.scriptEditor=this.appConsole=null;this.isTainted=!0;this.showSelected=this.movingSelected=!1;this.rotatePrev2=this.rotatePrev1=this.rotateBondIndex=-1;this.bsRotateBranch=null;this.creatingImage=!1;this.userVdwMars=
this.userVdws=this.bsUserVdws=this.outputManager=null;this.currentShapeID=-1;this.localFunctions=this.currentShapeState=null;this.$isKiosk=!1;this.executor=null;this.displayLoadErrors=!0;this.$isParallel=!1;this.stateScriptVersionInt=0;this.jbr=this.jzt=this.logFileName=this.nmrCalculation=this.timeouts=this.jsExporter3D=null;t(this,arguments)},JV,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,javajs.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,f,j,h){var l=new java.util.Hashtable;l.put("display",a);l.put("adapter",b);l.put("statusListener",j);l.put("platform",h);l.put("options",f);l.put("fullName",d);l.put("documentBase",
c);l.put("codeBase",g);return new JV.Viewer(l)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,javajs.api.GenericPlatform");u(c$,function(a){F(this,JV.Viewer,[]);this.commandHistory=new JU.CommandHistory;this.dimScreen=new javajs.awt.Dimension(0,0);this.rd=new J.atomdata.RadiusData(null,0,null,null);this.defaultVdw=J.c.VDW.JMOL;this.localFunctions=new java.util.Hashtable;this.privateKey=Math.random();this.actionStates=new JU.Lst;this.actionStatesRedo=new JU.Lst;this.chainMap=
new java.util.Hashtable;this.chainList=new JU.Lst;this.setOptions(a)},"java.util.Map");c(c$,"haveAccess",function(a){return this.access===a},"JV.Viewer.ACCESS");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,!0,!1)},"~S,JU.BS");c(c$,"setOptions",function(a){this.vwrOptions=
a;JU.Logger.debugging&&JU.Logger.debug("Viewer constructor "+this);this.modelAdapter=a.get("adapter");var b=a.get("statusListener");this.fullName=a.get("fullName");null==this.fullName&&(this.fullName="");var 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(n(d,String)){c=d;this.isJS=(this.isWebGL=0<=c.indexOf(".awtjs."))||0<=c.indexOf(".awtjs2d.");this.async=!this.dataOnly&&!this.autoExit&&(this.testAsync||this.isJS&&a.containsKey("async"));
var d=null,g="?";self.Jmol&&(d=Jmol._applets[this.htmlName.split("_object")[0]],g=Jmol._version);null!=g&&(this.html5Applet=d,JV.Viewer.strJavaVersion=g,JV.Viewer.strJavaVendor="Java2Script "+(this.isWebGL?"(WebGL)":"(HTML5)"));d=J.api.Interface.getInterface(c,this,"setOptions")}this.apiPlatform=d;this.display=a.get("display");this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.noGraphicsAllowed=this.checkOption2("noGraphics","-n");this.haveDisplay=this.isWebGL||null!=this.display&&!this.noGraphicsAllowed&&
!this.headless&&!this.dataOnly;this.headless=(this.noGraphicsAllowed=(new Boolean(this.noGraphicsAllowed&null==this.display)).valueOf())||this.apiPlatform.isHeadless();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||!this.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(this.isJS||null!=d&&!d.equals(""))(this.rm=d).set(this,this.shm);this.ms=new JM.ModelSet(this,null);this.initialize(!0);this.fm=new JV.FileManager(this);this.definedAtomSets=new java.util.Hashtable;this.setJmolStatusListener(b);this.isApplet?(JU.Logger.info("vwrOptions: \n"+JU.Escape.escapeMap(this.vwrOptions)),b=this.vwrOptions.get("documentLocation"),!this.isJS&&(null!=b&&b.startsWith("file:/"))&&(b=b.substring(0,b.substring(0,(b+"?").indexOf("?")).lastIndexOf("/")),JU.Logger.info("setting current directory to "+
b),this.cd(b)),b=JV.Viewer.appletDocumentBase,c=b.indexOf("#"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("?"),0<=c&&(b=b.substring(0,c)),c=b.lastIndexOf("/"),0<=c&&(b=b.substring(0,c)),JV.Viewer.jsDocumentBase=b,this.fm.setAppletContext(JV.Viewer.appletDocumentBase),a=a.get("appletProxy"),null!=a&&this.setStringProperty("appletProxy",a),this.isSignedApplet?(this.logFilePath=JU.PT.rep(JV.Viewer.appletCodeBase,"file://",""),this.logFilePath=JU.PT.rep(this.logFilePath,"file:/",""),0<=this.logFilePath.indexOf("//")?
this.logFilePath=null:this.isSignedAppletLocal=!0):this.isJS||(this.logFilePath=null)):(this.gdata.setBackgroundTransparent(this.checkOption2("backgroundTransparent","-b")),(this.isSilent=this.checkOption2("silent","-i"))&&JU.Logger.setLogLevel(3),this.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) 2012 Jmol Development\nJmol Version: "+JV.Viewer.getJmolVersion()+
"\njava.vendor: "+JV.Viewer.strJavaVendor+"\njava.version: "+JV.Viewer.strJavaVersion+"\nos.name: "+JV.Viewer.strOSName+"\nAccess: "+this.access+"\nmemory: "+this.getP("_memory")+"\nprocessors available: "+JV.Viewer.nProcessors+"\nuseCommandThread: "+this.useCommandThread+(!this.isApplet?"":"\nappletId:"+this.htmlName+(this.isSignedApplet?" (signed)":"")));this.allowScripting&&this.getScriptManager();this.zap(!1,!0,!1);this.g.setO("language",J.i18n.GT.getLanguage());this.stm.setJmolDefaults();JU.Elements.covalentVersion=
1;this.allowArrayDotNotation=!0},"java.util.Map");c(c$,"setDisplay",function(a){this.display=a;this.apiPlatform.setViewer(this,a)},"~O");c(c$,"newMeasurementData",function(a,b){return J.api.Interface.getInterface("JM.MeasurementData",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(this.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$,"checkOption2",function(a,b){return this.vwrOptions.containsKey(a)||0<=this.commandOptions.indexOf(b)},"~S,~S");c(c$,"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.modelkitPopup&&this.modelkitPopup.jpiDispose();try{null!=this.appConsole&&(this.appConsole.dispose(),this.appConsole=null),null!=this.scriptEditor&&(this.scriptEditor.dispose(),this.scriptEditor=null)}catch(a){if(!y(a,Exception))throw a;}});c(c$,"reset",function(a){this.ms.calcBoundBoxDimensions(null,1);this.axesAreTainted=!0;this.tm.homePosition(a);
this.ms.setCrystallographicDefaults()?this.stm.setCrystallographicDefaults():this.setAxesMode(603979810);this.prevFrame=-2147483648;this.tm.spinOn||this.setSync()},"~B");h(c$,"homePosition",function(){this.evalString("reset spin")});c(c$,"initialize",function(a){this.g=new JV.GlobalSettings(this,this.g,a);this.setStartupBooleans();this.g.setI("_width",this.dimScreen.width);this.g.setI("_height",this.dimScreen.height);this.haveDisplay&&(this.g.setB("_is2D",this.isJS&&!this.isWebGL),this.g.setB("_multiTouchClient",
this.acm.isMTClient()),this.g.setB("_multiTouchServer",this.acm.isMTServer()));this.cm.setDefaultColors(!1);this.setObjectColor("background","black");this.setObjectColor("axis1","red");this.setObjectColor("axis2","green");this.setObjectColor("axis3","blue");this.am.setAnimationOn(!1);this.am.setAnimationFps(this.g.animationFps);this.sm.allowStatusReporting=this.g.statusReporting;this.setBooleanProperty("antialiasDisplay",this.g.antialiasDisplay);this.stm.resetLighting();this.tm.setDefaultPerspective()},
"~B");c(c$,"saveModelOrientation",function(){this.ms.saveModelOrientation(this.am.cmi,this.stm.getOrientation())});c(c$,"restoreModelOrientation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!0)},"~N");c(c$,"restoreModelRotation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!1)},"~N");c(c$,"getGLmolView",function(){var a=this.tm;return{center:a.fixedRotationCenter,quaternion:a.getRotationQuaternion(),xtrans:a.xTranslationFraction,ytrans:a.yTranslationFraction,
scale:a.scalePixelsPerAngstrom,zoom:a.zoomPercent,cameraDistance:a.cameraDistance,pixelCount:a.screenPixelCount,perspective:a.perspectiveDepth,width:a.width,height:a.height}});c(c$,"setRotationRadius",function(a,b){b&&(a=this.tm.setRotationRadius(a,!1));this.ms.setRotationRadius(this.am.cmi,a)&&this.g.setF("rotationRadius",a)},"~N,~B");c(c$,"setCenterBitSet",function(a,b){this.isJmolDataFrame()||this.tm.setNewRotationCenter(0<JU.BSUtil.cardinalityOf(a)?this.ms.getAtomSetCenter(a):null,b)},"JU.BS,~B");
c(c$,"setNewRotationCenter",function(a){this.isJmolDataFrame()||this.tm.setNewRotationCenter(a,!0)},"JU.P3");c(c$,"navigate",function(a,b){this.isJmolDataFrame()||(this.tm.navigateKey(a,b),!this.tm.vibrationOn&&0!=a&&this.refresh(1,"Viewer:navigate()"))},"~N,~N");c(c$,"move",function(a,b,d,c,g,f,j){this.tm.move(a,b,d,c,g,f,j);this.moveUpdate(f)},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(c$,"moveTo",function(a,b,d,c,g,f,j,h,l,q,p,m,n,s,r,t,u){this.haveDisplay||(b=0);this.setTainted(!0);
this.tm.moveTo(a,b,d,c,g,f,j,h,l,q,p,m,n,s,r,t,u)},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.V3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(c$,"moveUpdate",function(a){0<a?this.requestRepaintAndWait("moveUpdate"):0==a&&this.setSync()},"~N");c(c$,"navigatePt",function(a){this.tm.setNavigatePt(a);this.setSync()},"JU.P3");c(c$,"navigateAxis",function(a,b){this.tm.navigateAxis(a,b);this.setSync()},"JU.V3,~N");c(c$,"navTranslatePercent",function(a,b){this.isJmolDataFrame()||(this.tm.navTranslatePercentOrTo(0,
a,b),this.setSync())},"~N,~N");c(c$,"zoomBy",function(a){this.tm.zoomBy(a);this.refresh(2,this.sm.syncingMouse?"Mouse: zoomBy "+a:"")},"~N");c(c$,"zoomByFactor",function(a,b,d){this.tm.zoomByFactor(a,b,d);this.refresh(2,!this.sm.syncingMouse?"":"Mouse: zoomByFactor "+a+(2147483647==b?"":" "+b+" "+d))},"~N,~N,~N");c(c$,"rotateXYBy",function(a,b){this.tm.rotateXYBy(a,b,null);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateXYBy "+a+" "+b:"")},"~N,~N");c(c$,"spinXYBy",function(a,b,d){this.tm.spinXYBy(a,
b,d);0==a&&0==b||this.refresh(2,this.sm.syncingMouse?"Mouse: spinXYBy "+a+" "+b+" "+d:"")},"~N,~N,~N");c(c$,"rotateZBy",function(a,b,d){this.tm.rotateZBy(a,b,d);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateZBy "+a+(2147483647==b?"":" "+b+" "+d):"")},"~N,~N,~N");c(c$,"rotateSelected",function(a,b,d){this.isJmolDataFrame()||(this.tm.rotateXYBy(a,b,this.setMovableBitSet(d,!1)),this.refreshMeasures(!0),this.refresh(2,this.sm.syncingMouse?"Mouse: rotateMolecule "+a+" "+b:""))},"~N,~N,JU.BS");c(c$,
"setMovableBitSet",function(a,b){null==a&&(a=this.bsA());a=JU.BSUtil.copy(a);JU.BSUtil.andNot(a,this.getMotionFixedAtoms());b&&!this.g.allowMoveAtoms&&(a=this.ms.getMoleculeBitSet(a));return a},"JU.BS,~B");c(c$,"translateXYBy",function(a,b){this.tm.translateXYBy(a,b);this.refresh(2,this.sm.syncingMouse?"Mouse: translateXYBy "+a+" "+b:"")},"~N,~N");h(c$,"rotateFront",function(){this.tm.resetRotation();this.refresh(1,"Viewer:rotateFront()")});c(c$,"translate",function(a,b,d,c){var g="\x00"==d?B(b):
"%"==d?this.tm.percentToPixels(a,b):this.tm.angstromsToPixels(b*("n"==d?10:1));if(null!=c){if(0==g)return;this.tm.setSelectedTranslation(c,a,g)}else switch(a){case "X":case "x":"\x00"==d?this.tm.translateToPercent("x",b):this.tm.translateXYBy(g,0);break;case "Y":case "y":"\x00"==d?this.tm.translateToPercent("y",b):this.tm.translateXYBy(0,g);break;case "Z":case "z":"\x00"==d?this.tm.translateToPercent("z",b):this.tm.translateZBy(g)}this.refresh(1,"Viewer:translate()")},"~S,~N,~S,JU.BS");c(c$,"slabByPixels",
function(a){this.tm.slabByPercentagePoints(a);this.refresh(3,"slabByPixels")},"~N");c(c$,"depthByPixels",function(a){this.tm.depthByPercentagePoints(a);this.refresh(3,"depthByPixels")},"~N");c(c$,"slabDepthByPixels",function(a){this.tm.slabDepthByPercentagePoints(a);this.refresh(3,"slabDepthByPixels")},"~N");c(c$,"finalizeTransformParameters",function(){this.tm.finalizeTransformParameters();this.gdata.setSlab(this.tm.slabValue);this.gdata.setDepth(this.tm.depthValue);this.gdata.setZShade(this.tm.zShadeEnabled,
this.tm.zSlabValue,this.tm.zDepthValue,this.g.zShadePower)});c(c$,"getScalePixelsPerAngstrom",function(a){return this.tm.scalePixelsPerAngstrom*(a||!this.antialiased?1:0.5)},"~B");c(c$,"setSpin",function(a,b){if(JU.PT.isOneOf(a,";x;y;z;fps;X;Y;Z;FPS;")){var d="x;y;z;fps;X;Y;Z;FPS".indexOf(a);switch(d){case 0:this.tm.setSpinXYZ(b,NaN,NaN);break;case 2:this.tm.setSpinXYZ(NaN,b,NaN);break;case 4:this.tm.setSpinXYZ(NaN,NaN,b);break;default:this.tm.setSpinFps(b);break;case 10:this.tm.setNavXYZ(b,NaN,NaN);
break;case 12:this.tm.setNavXYZ(NaN,b,NaN);break;case 14:this.tm.setNavXYZ(NaN,NaN,b);break;case 16:this.tm.setNavFps(b)}this.g.setI((10>d?"spin":"nav")+a,b)}},"~S,~N");c(c$,"getSpinState",function(){return this.getStateCreator().getSpinState(!1)});c(c$,"getOrientationText",function(a,b){switch(a){case 1313866249:case 1073741863:case 1112541205:case 1112541206:case 1112541207:case 135270418:return this.ms.getBoundBoxOrientation(a,this.bsA());case 1073742035:return this.stm.getSavedOrientationText(b);
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if(a.equalsIgnoreCase("spinOn"))return this.tm.spinOn;if(a.equalsIgnoreCase("isNavigating"))return this.tm.isNavigating();if(a.equalsIgnoreCase("showSelections"))return this.ms.getSelectionHaloEnabled();if(this.g.htUserVariables.containsKey(a)){b=this.g.getUserVariable(a);if(1048589==b.tok)return!0;if(1048588==b.tok)return!1}JU.Logger.error("vwr.getBooleanProperty("+a+") - unrecognized");return!1},"~S");h(c$,"getInt",function(a){switch(a){case 553648132:return this.am.animationFps;case 553648143:return this.g.dotDensity;
case 553648144:return this.g.dotScale;case 553648146:return this.g.helixStep;case 553648151:return this.g.meshScale;case 553648153:return this.g.minPixelSelRadius;case 553648154:return this.g.percentVdwAtom;case 553648157:return this.g.pickingSpinRate;case 553648166:return this.g.ribbonAspectRatio;case 536870922:return this.g.scriptDelay;case 553648170:return this.g.smallMoleculeMaxAtoms;case 553648184:return this.g.strutSpacing}JU.Logger.error("viewer.getInt("+JS.T.nameOf(a)+") - not listed");return 0},
"~N");c(c$,"getDelayMaximumMs",function(){return this.haveDisplay?this.g.delayMaximumMs:1});c(c$,"getHermiteLevel",function(){return this.tm.spinOn?0:this.g.hermiteLevel});c(c$,"getHoverDelay",function(){return this.g.modelKitMode?20:this.g.hoverDelayMs});h(c$,"getBoolean",function(a){switch(a){case 1074790662:return this.ms.getMSInfoB("isPDB");case 603979780:return this.g.allowGestures;case 603979784:return this.g.allowMultiTouch;case 603979785:return this.g.allowRotateSelected;case 603979792:return this.g.appendNew;
case 603979794:return this.g.applySymmetryToBonds;case 603979796:return this.g.atomPicking;case 603979798:return this.g.autoBond;case 603979800:return this.g.autoFps;case 603979806:return this.g.axesOrientationRasmol;case 603979811:return this.g.backboneSteps;case 603979812:return this.g.bondModeOr;case 603979816:return this.g.cartoonBaseEdges;case 603979817:return this.g.cartoonFancy;case 603979818:return this.g.cartoonLadders;case 603979819:return this.g.cartoonRibose;case 603979820:return this.g.cartoonRockets;
case 603979823:return this.g.chainCaseSensitive||0<this.chainList.size();case 603979825:return this.g.debugScript;case 603979826:return this.g.defaultStructureDSSP;case 603979827:return this.g.disablePopupMenu;case 603979828:return this.g.displayCellParameters;case 603979830:return this.g.dotSurface;case 603979829:return this.g.dotsSelectedOnly;case 603979833:return this.g.drawPicking;case 603979844:return this.g.fontCaching;case 603979845:return this.g.fontScaling;case 603979846:return this.g.forceAutoBond;
case 603979848:return!1;case 603979850:return this.g.greyscaleRendering;case 603979852:return this.g.hbondsBackbone;case 603979853:return this.g.hbondsRasmol;case 603979854:return this.g.hbondsSolid;case 1613758470:return this.g.rasmolHeteroSetting;case 603979858:return this.g.hideNameInPopup;case 603979864:return this.g.highResolutionFlag;case 1613758476:return this.g.rasmolHydrogenSetting;case 603979869:return this.g.isosurfaceKey;case 603979871:return this.g.justifyMeasurements;case 603979873:return this.g.legacyAutoBonding;
case 603979874:return this.g.legacyHAddition;case 603979875:return this.g.legacyJavaFloat;case 603979877:return this.g.logGestures;case 603979878:return this.g.measureAllModels;case 603979879:return this.g.measurementLabels;case 603979880:return this.g.messageStyleChime;case 603979883:return this.g.modelKitMode;case 603979887:return this.g.navigationMode;case 603979888:return this.g.navigationPeriodic;case 603979889:return this.g.partialDots;case 603979892:return this.g.pdbSequential;case 603979894:return this.g.preserveState;
case 603979898:return this.g.ribbonBorder;case 603979900:return this.g.rocketBarrels;case 603979906:return this.g.selectAllModels;case 603979920:return this.g.showHiddenSelectionHalos;case 603979922:return this.g.showHydrogens;case 603979926:return this.g.showMeasurements;case 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 1613758488:return this.g.solventOn;case 603979952:return this.g.ssbondsBackbone;case 603979955:return this.g.strutsMultiple;case 603979966:return this.g.traceAlpha;case 603979967:return this.g.translucent;case 603979968:return this.g.twistedSheets;case 603979972:return this.g.vectorsCentered;case 603979973:return this.g.vectorSymmetry;case 603979974:return this.g.waitForMoveTo;case 603979978:return this.g.zeroBasedXyzRasmol}JU.Logger.error("viewer.getBoolean("+
JS.T.nameOf(a)+") - not listed");return!1},"~N");c(c$,"allowEmbeddedScripts",function(){return this.g.allowEmbeddedScripts&&!this.isPreviewOnly});c(c$,"getDragSelected",function(){return this.g.dragSelected&&!this.g.modelKitMode});c(c$,"getBondPicking",function(){return this.g.bondPicking||this.g.modelKitMode});c(c$,"useMinimizationThread",function(){return this.g.useMinimizationThread&&!this.autoExit});h(c$,"getFloat",function(a){switch(a){case 1141899265:return this.g.particleRadius;case 570425346:return this.g.axesScale;
case 570425348:return this.g.bondTolerance;case 570425354:return this.g.defaultTranslucent;case 570425352:return this.g.defaultDrawArrowScale;case 570425355:return this.g.dipoleScale;case 570425356:return this.g.drawFontSize;case 570425358:return this.g.exportScale;case 570425360:return this.g.hbondsAngleMinimum;case 570425361:return this.g.hbondsDistanceMaximum;case 570425363:return this.g.loadAtomDataTolerance;case 570425364:return this.g.minBondDistance;case 1276121113:return this.g.modulationScale;
case 570425370:return this.g.multipleBondSpacing;case 570425369:return this.g.multipleBondRadiusFactor;case 570425374:return this.g.navigationSpeed;case 570425382:return this.g.pointGroupDistanceTolerance;case 570425384:return this.g.pointGroupLinearTolerance;case 570425388:return this.tm.modelRadius;case 570425392:return this.g.sheetSmoothing;case 570425394:return this.g.solventProbeRadius;case 570425403:return this.g.starWidth;case 570425406:return this.g.strutDefaultRadius;case 570425408:return this.g.strutLengthMaximum;
case 1649410049:return this.g.vectorScale;case 570425412:return this.g.vibrationPeriod}JU.Logger.error("viewer.getFloat("+JS.T.nameOf(a)+") - not listed");return 0},"~N");h(c$,"setStringProperty",function(a,b){if(null!=b)if("_"==a.charAt(0))this.g.setO(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 603979776:this.setBooleanPropertyTok(a,d,JS.SV.newV(4,b).asBoolean());break;case 553648128:this.setIntPropertyTok(a,d,JS.SV.newV(4,b).asInt());break;case 570425344:this.setFloatPropertyTok(a,
d,JU.PT.parseFloat(b));break;default:this.setStringPropertyTok(a,d,b)}}},"~S,~S");c(c$,"setStringPropertyTok",function(a,b,d){switch(b){case 545259556:this.g.edsUrlCutoff=d;break;case 545259557:this.g.edsUrlFormat=d;break;case 545259558:this.g.edsUrlFormatDiff=d;break;case 545259521:this.setAnimationMode(d);return;case 545259569:this.g.nmrPredictFormat=d;break;case 545259548:this.g.defaultDropScript=d;break;case 545259571:d=this.fm.setPathForAllFiles(d);break;case 545259559:this.setUnits(d,!1);return;
case 545259561:this.g.forceField=d="UFF".equalsIgnoreCase(d)?"UFF":"MMFF";this.minimizer=null;break;case 545259570:this.g.nmrUrlFormat=d;break;case 545259568:this.setUnits(d,!0);return;case 545259566:this.g.loadLigandFormat=d;break;case 545259543:this.g.defaultLabelPDB=d;break;case 545259544:this.g.defaultLabelXYZ=d;break;case 545259549:this.g.defaultLoadFilter=d;break;case 545259567:d=this.getOutputManager().setLogFile(d);if(null==d)return;break;case 545259560: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 545259564:new J.i18n.GT(this,d);b=J.i18n.GT.getLanguage();this.modelkitPopup=null;null!=this.jmolpopup&&(this.jmolpopup.jpiDispose(),this.jmolpopup=
null,this.getPopupMenu());this.sm.setCallbackFunction("language",b);d=J.i18n.GT.getLanguage();break;case 545259565:this.g.loadFormat=d;break;case 545259534:this.setObjectColor("background",d);return;case 545259528:this.setObjectColor("axis1",d);return;case 545259530:this.setObjectColor("axis2",d);return;case 545259532:this.setObjectColor("axis3",d);return;case 545259536:this.setObjectColor("boundbox",d);return;case 545259586:this.setObjectColor("unitcell",d);return;case 545259578:this.setPropertyColorScheme(d,
!1,!1);break;case 545259563: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 545259562:this.g.helpPath=d;break;case 545259552:!d.equalsIgnoreCase("RasMol")&&
!d.equalsIgnoreCase("PyMOL")&&(d="Jmol");this.setDefaultsType(d);break;case 545259545:this.setDefaultColors(d.equalsIgnoreCase("rasmol"));return;case 545259572:this.setPickingMode(d,0);return;case 545259574:this.setPickingStyle(d,0);return;case 545259540:break;default:if(a.toLowerCase().endsWith("callback")){this.sm.setCallbackFunction(a,0==d.length||d.equalsIgnoreCase("none")?null:d);break}if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(4,
d));return}}this.g.setO(a,d)},"~S,~N,~S");h(c$,"setFloatProperty",function(a,b){if(!Float.isNaN(b))if("_"==a.charAt(0))this.g.setF(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,d,""+b);break;case 603979776:this.setBooleanPropertyTok(a,d,0!=b);break;case 553648128:this.setIntPropertyTok(a,d,B(b));break;default:this.setFloatPropertyTok(a,d,b)}}},"~S,~N");c(c$,"setFloatPropertyTok",function(a,b,d){switch(b){case 570425366:this.ms.setModulation(null,
!1,null,!1);this.g.modulationScale=d=Math.max(0.1,d);this.ms.setModulation(null,!0,null,!1);break;case 570425381:this.g.particleRadius=Math.abs(d);break;case 570425356:this.g.drawFontSize=d;break;case 570425358:this.g.exportScale=d;break;case 570425403:this.g.starWidth=d;break;case 570425369:this.g.multipleBondRadiusFactor=d;break;case 570425370:this.g.multipleBondSpacing=d;break;case 570425393:this.tm.setSlabRange(d);break;case 570425365:this.g.minimizationCriterion=d;break;case 570425359:this.haveDisplay&&
this.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",B(d));break;case 570425378:this.setSpin("Y",B(d));break;case 570425380:this.setSpin("Z",B(d));break;case 570425371:if(Float.isNaN(d))return;this.setSpin("FPS",B(d));break;case 570425363:this.g.loadAtomDataTolerance=
d;break;case 570425360:this.g.hbondsAngleMinimum=d;break;case 570425361:this.g.hbondsDistanceMaximum=d;break;case 570425382:this.g.pointGroupDistanceTolerance=d;break;case 570425384:this.g.pointGroupLinearTolerance=d;break;case 570425357:this.g.ellipsoidAxisDiameter=d;break;case 570425398:this.setSpin("x",B(d));break;case 570425400:this.setSpin("y",B(d));break;case 570425402:this.setSpin("z",B(d));break;case 570425396:this.setSpin("fps",B(d));break;case 570425352:this.g.defaultDrawArrowScale=d;break;
case 570425354:this.g.defaultTranslucent=d;break;case 570425346:this.setAxesScale(d);break;case 570425416:this.tm.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=
B(1E3*d);break;case 570425392:this.g.sheetSmoothing=d;break;case 570425355:d=JV.Viewer.checkFloatRange(d,-10,10);this.g.dipoleScale=d;break;case 570425404:this.tm.setStereoDegrees(d);break;case 1649410049:this.setVectorScale(d);return;case 570425412:this.setVibrationPeriod(d);return;case 570425414:this.setVibrationScale(d);return;case 570425348:this.setBondTolerance(d);return;case 570425364:this.setMinBondDistance(d);return;case 570425390:this.tm.setScaleAngstromsPerInch(d);break;case 570425394:d=
JV.Viewer.checkFloatRange(d,0,10);this.g.solventProbeRadius=d;break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(3,Float.$valueOf(d)));return}}this.g.setF(a,d)},"~S,~N,~N");h(c$,"setIntProperty",function(a,b){if(-2147483648!=b)if("_"==a.charAt(0))this.g.setI(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,d,""+b);break;case 603979776:this.setBooleanPropertyTok(a,d,0!=
b);break;case 570425344:this.setFloatPropertyTok(a,d,b);break;default:this.setIntPropertyTok(a,d,b)}}},"~S,~N");c(c$,"setIntPropertyTok",function(a,b,d){switch(b){case 553648138:d=0==d?0:1;this.g.bondingVersion=JU.Elements.bondingVersion=d;break;case 553648137:this.gdata.setCelPower(d);break;case 553648129:this.gdata.setAmbientOcclusion(d);break;case 553648158:this.g.platformSpeed=Math.min(Math.max(d,0),10);break;case 553648151:this.g.meshScale=d;break;case 553648153:this.g.minPixelSelRadius=d;break;
case 553648149:this.g.isosurfacePropertySmoothingPower=d;break;case 553648165:this.g.repaintWaitMs=d;break;case 553648170:this.g.smallMoleculeMaxAtoms=d;break;case 553648152:this.g.minimizationSteps=d;break;case 553648184:this.g.strutSpacing=d;break;case 553648156:d=JV.Viewer.checkIntRange(d,0,1E3);this.gdata.setPhongExponent(d);break;case 553648146:this.g.helixStep=d;this.ms.haveStraightness=!1;break;case 553648144:this.g.dotScale=d;break;case 553648143:this.g.dotDensity=d;break;case 553648140:this.g.delayMaximumMs=
d;break;case 553648150:JU.Logger.setLogLevel(d);JU.Logger.info("logging level set to "+d);this.g.setI("logLevel",d);null!=this.eval&&this.eval.setDebugging();return;case 553648134:this.setAxesMode(2==d?603979808:1==d?603979804:603979810);return;case 553648178:this.setStrandCount(0,d);return;case 553648182:this.setStrandCount(12,d);return;case 553648180:this.setStrandCount(13,d);return;case 553648155:return;case 536870922:this.g.scriptDelay=d;break;case 553648176:d=0>d?JV.Viewer.checkIntRange(d,-10,
-1):JV.Viewer.checkIntRange(d,0,100);this.gdata.setSpecularPower(d);break;case 553648172:d=JV.Viewer.checkIntRange(-d,-10,-1);this.gdata.setSpecularPower(d);break;case 553648136:this.setMarBond(d);return;case 536870924:this.setBooleanPropertyTok(a,b,1==d);return;case 553648174:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setSpecularPercent(d);break;case 553648142:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setDiffusePercent(d);break;case 553648130:d=JV.Viewer.checkIntRange(d,0,100);this.gdata.setAmbientPercent(d);
break;case 553648186:this.tm.zDepthToPercent(d);break;case 553648188:this.tm.zSlabToPercent(d);break;case 554176526:this.tm.depthToPercent(d);break;case 554176565:this.tm.slabToPercent(d);break;case 553648190:this.g.zShadePower=Math.max(d,1);break;case 553648166:this.g.ribbonAspectRatio=d;break;case 553648157:this.g.pickingSpinRate=1>d?1:d;break;case 553648132:this.setAnimationFps(d);return;case 553648154:this.setPercentVdwAtom(d);break;case 553648147:this.g.hermiteLevel=d;break;case 553648145:case 553648148:case 553648160:case 553648159:case 553648162:case 553648164:break;
default:if(!this.g.htNonbooleanParameterValues.containsKey(a)){this.g.setUserVariable(a,JS.SV.newI(d));return}}this.g.setI(a,d)},"~S,~N,~N");c$.checkIntRange=c(c$,"checkIntRange",function(a,b,d){return a<b?b:a>d?d:a},"~N,~N,~N");c$.checkFloatRange=c(c$,"checkFloatRange",function(a,b,d){return a<b?b:a>d?d:a},"~N,~N,~N");h(c$,"setBooleanProperty",function(a,b){if("_"==a.charAt(0))this.g.setB(a,b);else{var d=JS.T.getTokFromName(a);switch(JS.T.getParamType(d)){case 545259520:this.setStringPropertyTok(a,
d,"");break;case 553648128:this.setIntPropertyTok(a,d,b?1:0);break;case 570425344:this.setFloatPropertyTok(a,d,b?1:0);break;default:this.setBooleanPropertyTok(a,d,b)}}},"~S,~B");c(c$,"setBooleanPropertyTok",function(a,b,d){var c=!0;switch(b){case 603979875:this.g.legacyJavaFloat=d;break;case 603979927:this.g.showModVecs=d;break;case 603979937:this.g.showUnitCellDetails=d;break;case 603979848:c=!1;break;case 603979972:this.g.vectorsCentered=d;break;case 603979811:this.g.backboneSteps=d;break;case 603979819:(this.g.cartoonRibose=
d)&&this.getBoolean(603979816)&&this.setBooleanPropertyTok("cartoonBaseEdges",603979816,!1);break;case 603979837:this.g.ellipsoidArrows=d;break;case 603979967:this.g.translucent=d;break;case 603979818:this.g.cartoonLadders=d;break;case 603979968:b=this.g.twistedSheets;this.g.twistedSheets=d;b!=d&&this.checkCoordinatesChanged();break;case 603979822:this.gdata.setCel(d);break;case 603979817:this.g.cartoonFancy=d;break;case 603979934:this.g.showTiming=d;break;case 603979973:this.g.vectorSymmetry=d;break;
case 603979869:this.g.isosurfaceKey=d;break;case 603979889:this.g.partialDots=d;break;case 603979873:this.g.legacyAutoBonding=d;break;case 603979826:this.g.defaultStructureDSSP=d;break;case 603979834:this.g.dsspCalcHydrogen=d;break;case 603979782:(this.g.allowModelkit=d)||this.setModelKitMode(!1);break;case 603979883:this.setModelKitMode(d);break;case 603979885:this.g.multiProcessor=d&&1<JV.Viewer.nProcessors;break;case 603979884:this.g.monitorEnergy=d;break;case 603979853:this.g.hbondsRasmol=d;break;
case 603979881:this.g.minimizationRefresh=d;break;case 603979882:this.g.minimizationSilent=d;break;case 603979868:d&&(this.$isKiosk=!0,this.g.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));break;case 603979974:this.g.waitForMoveTo=d;break;case 603979876:this.g.logCommands=!0;break;case 603979877:this.g.logGestures=!0;break;case 603979784:this.g.allowMultiTouch=d;break;case 603979894:this.g.preserveState=d;this.ms.setPreserveState(d);this.undoClear();break;
case 603979955:this.g.strutsMultiple=d;break;case 603979842:break;case 603979939:this.g.slabByAtom=d;break;case 603979940:this.g.slabByMolecule=d;break;case 603979902:this.g.saveProteinStructureState=d;break;case 603979780:this.g.allowGestures=d;break;case 603979867:this.g.imageState=d;break;case 603979970:this.g.useMinimizationThread=d;break;case 603979781:this.g.disablePopupMenu&&(d=!1);this.g.allowKeyStrokes=d;break;case 603979831:this.g.dragSelected=d;this.showSelected=!1;break;case 603979924:this.g.showKeyStrokes=
d;break;case 603979844:this.g.fontCaching=d;break;case 603979796:this.g.atomPicking=d;break;case 603979814:this.highlight(null);this.g.bondPicking=d;break;case 603979906:this.g.selectAllModels=d;break;case 603979880:this.g.messageStyleChime=d;break;case 603979892:this.g.pdbSequential=d;break;case 603979890:this.g.pdbAddHydrogens=d;break;case 603979891:this.g.pdbGetHeader=d;break;case 603979838:this.g.ellipsoidAxes=d;break;case 603979836:this.g.ellipsoidArcs=d;break;case 603979839:this.g.ellipsoidBall=
d;break;case 603979840:this.g.ellipsoidDots=d;break;case 603979841:this.g.ellipsoidFill=d;break;case 603979845:this.g.fontScaling=d;break;case 603979956:this.setSyncTarget(0,d);break;case 603979958:this.setSyncTarget(1,d);break;case 603979976:this.g.wireframeRotation=d;break;case 603979870:this.g.isosurfacePropertySmoothing=d;break;case 603979833:this.g.drawPicking=d;break;case 603979786:case 603979790:case 603979788:this.setAntialias(b,d);break;case 603979944:this.g.smartAromatic=d;break;case 603979794:this.setApplySymmetryToBonds(d);
break;case 603979792:this.g.appendNew=d;break;case 603979800:this.g.autoFps=d;break;case 603979971:JU.DF.setUseNumberLocalization(this.g.useNumberLocalization=d);break;case 603979918:case 1611272202:a="showFrank";this.setFrankOn(d);break;case 1613758488:a="solventProbe";this.g.solventOn=d;break;case 603979948:this.g.solventOn=d;break;case 603979785:this.g.allowRotateSelected=d;break;case 603979783:this.g.allowMoveAtoms=d;this.g.allowRotateSelected=d;this.g.dragSelected=d;this.showSelected=!1;break;
case 536870922:this.setIntPropertyTok("showScript",b,d?1:0);return;case 603979778:this.g.allowEmbeddedScripts=d;break;case 603979888:this.g.navigationPeriodic=d;break;case 603979984:this.tm.setZShadeEnabled(d);return;case 603979832:this.haveDisplay&&(this.g.drawHover=d);break;case 603979887:this.setNavigationMode(d);break;case 603979886:return;case 603979860:this.g.hideNavigationPoint=d;break;case 603979930:this.g.showNavigationPointAlways=d;break;case 603979896:this.setRefreshing(d);break;case 603979871: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 603979872:J.i18n.GT.setDoTranslate(d);break;case 603979862:this.slm.setHideNotSelected(d);break;case 603979904:this.setScriptQueue(d);break;case 603979830:this.g.dotSurface=d;break;case 603979829:this.g.dotsSelectedOnly=d;break;case 1611141171:this.setSelectionHalos(d);break;case 603979910:this.g.rasmolHydrogenSetting=d;break;case 603979908:this.g.rasmolHeteroSetting=d;break;case 603979928:this.g.showMultipleBonds=d;break;case 603979920:this.g.showHiddenSelectionHalos=
d;break;case 603979975:this.tm.setWindowCentered(d);break;case 603979828:this.g.displayCellParameters=d;break;case 603979960:this.g.testFlag1=d;break;case 603979962:this.g.testFlag2=d;break;case 603979964:this.g.testFlag3=d;break;case 603979965:this.jmolTest();this.g.testFlag4=d;break;case 603979898:this.g.ribbonBorder=d;break;case 603979816:(this.g.cartoonBaseEdges=d)&&this.getBoolean(603979819)&&this.setBooleanPropertyTok("cartoonRibose",603979819,!1);break;case 603979820:this.g.cartoonRockets=
d;break;case 603979900:this.g.rocketBarrels=d;break;case 603979850:this.gdata.setGreyscaleMode(this.g.greyscaleRendering=d);break;case 603979879:this.g.measurementLabels=d;break;case 603979810: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 603979893:this.setPerspectiveDepth(d);return;case 603979798:this.setAutoBond(d);
return;case 603979914:this.setShowAxes(d);return;case 603979916:this.setShowBbcage(d);return;case 603979922:this.setShowHydrogens(d);return;case 603979926:this.setShowMeasurements(d);return;case 603979936:this.setShowUnitCell(d);return;case 603979812:c=!1;this.g.bondModeOr=d;break;case 603979978:c=!1;this.g.zeroBasedXyzRasmol=d;this.reset(!0);break;case 603979895:c=!1;this.g.rangeSelected=d;break;case 603979878:c=!1;this.g.measureAllModels=d;break;case 603979954:c=!1;this.sm.allowStatusReporting=
d;break;case 603979823:c=!1;this.g.chainCaseSensitive=d;break;case 603979858:c=!1;this.g.hideNameInPopup=d;break;case 603979827:c=!1;this.g.disablePopupMenu=d;break;case 603979846:c=!1;this.g.forceAutoBond=d;break;default:if(!this.g.htBooleanParameterFlags.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.getBoolean(d));return}}this.g.setB(a,d);c&&this.setTainted(!0)},"~S,~N,~B");c(c$,"setModelKitMode",function(a){if(null!=this.acm&&this.allowScripting){if(a||this.g.modelKitMode)this.setPickingMode(null,
a?33:1),this.setPickingMode(null,a?32:1);var b=this.g.modelKitMode!=a;this.g.modelKitMode=a;this.highlight(null);a?(this.setNavigationMode(!1),this.selectAll(),this.setAtomPickingOption("C"),this.setBondPickingOption("p"),this.isApplet||this.popupMenu(0,0,"m"),b&&this.sm.setCallbackFunction("modelkit","ON"),this.g.modelKitMode=!0,0==this.ms.ac&&this.zap(!1,!0,!0)):(this.acm.setPickingMode(-1),this.setStringProperty("pickingStyle","toggle"),this.setBooleanProperty("bondPicking",!1),b&&this.sm.setCallbackFunction("modelkit",
"OFF"))}},"~B");c(c$,"setSmilesString",function(a){null==a?this.g.removeParam("_smilesString"):this.g.setO("_smilesString",a)},"~S");c(c$,"removeUserVariable",function(a){this.g.removeUserVariable(a);a.endsWith("callback")&&this.sm.setCallbackFunction(a,null)},"~S");c(c$,"jmolTest",function(){});c(c$,"showParameter",function(a,b,d){d=""+this.g.getParameterEscaped(a,d);(b||0>d.indexOf("<not defined>"))&&this.showString(a+" = "+d,!1)},"~S,~B,~N");c(c$,"showString",function(a,b){!this.isJS&&(this.isScriptQueued()&&
(!this.isSilent||b))&&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$,"getShowNavigationPoint",function(){return!this.g.navigationMode?!1:this.tm.isNavigating()&&!this.g.hideNavigationPoint||this.g.showNavigationPointAlways||this.getInMotion(!0)});c(c$,"getCurrentSolventProbeRadius",function(){return this.g.solventOn?this.g.solventProbeRadius:0});c(c$,"getTestFlag",function(a){switch(a){case 1:return this.g.testFlag1;case 2:return this.g.testFlag2;case 3:return this.g.testFlag3;case 4:return this.g.testFlag4}return!1},"~N");h(c$,"setPerspectiveDepth",function(a){this.tm.setPerspectiveDepth(a)},
"~B");h(c$,"setAxesOrientationRasmol",function(a){this.g.setB("axesOrientationRasmol",a);this.g.axesOrientationRasmol=a;this.reset(!0)},"~B");c(c$,"setAxesScale",function(a){a=JV.Viewer.checkFloatRange(a,-100,100);this.g.axesScale=a;this.axesAreTainted=!0},"~N");c(c$,"getAxisPoints",function(){this.shm.loadShape(34);return 0==this.getObjectMad(1)||603979808!=this.g.axesMode||this.getShapeProperty(34,"axesTypeXY").booleanValue()||null!=this.getShapeProperty(34,"origin")?null:this.getShapeProperty(34,
"axisPoints")});c(c$,"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 603979810:this.g.removeParam("axesunitcell"),this.g.removeParam("axesmolecular"),this.g.setB("axesWindow",!0),a=0}this.g.setI("axesMode",a)},"~N");c(c$,
"setSelectionHalos",function(a){a!=this.ms.getSelectionHaloEnabled()&&(this.g.setB("selectionHalos",a),this.shm.loadShape(8),this.ms.setSelectionHaloEnabled(a))},"~B");c(c$,"getSelectionHaloEnabled",function(a){var b=this.ms.getSelectionHaloEnabled()||a&&this.showSelected;a&&(this.showSelected=!1);return b},"~B");c(c$,"setStrandCount",function(a,b){b=JV.Viewer.checkIntRange(b,0,20);switch(a){case 12:this.g.strandCountForStrands=b;break;case 13:this.g.strandCountForMeshRibbon=b;break;default:this.g.strandCountForStrands=
b,this.g.strandCountForMeshRibbon=b}this.g.setI("strandCount",b);this.g.setI("strandCountForStrands",this.g.strandCountForStrands);this.g.setI("strandCountForMeshRibbon",this.g.strandCountForMeshRibbon)},"~N,~N");c(c$,"getStrandCount",function(a){return 12==a?this.g.strandCountForStrands:this.g.strandCountForMeshRibbon},"~N");c(c$,"setNavigationMode",function(a){this.g.navigationMode=a;this.tm.setNavigationMode(a)},"~B");h(c$,"setAutoBond",function(a){this.g.setB("autobond",a);this.g.autoBond=a},
"~B");c(c$,"makeConnections",function(a,b,d,c,g,f,j,h,l,q){this.clearModelDependentObjects();this.clearMinimization();return this.ms.makeConnections(a,b,d,c,g,f,j,h,l,q)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");h(c$,"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$,"setShowBbcage",function(a){this.setObjectMad(32,"boundbox",
a?-4:0);this.g.setB("showBoundBox",a)},"~B");c(c$,"getShowBbcage",function(){return 0!=this.getObjectMad(4)});c(c$,"setShowUnitCell",function(a){this.setObjectMad(33,"unitcell",a?-2:0);this.g.setB("showUnitCell",a)},"~B");c(c$,"getShowUnitCell",function(){return 0!=this.getObjectMad(5)});c(c$,"setShowAxes",function(a){this.setObjectMad(34,"axes",a?-2:0);this.g.setB("showAxes",a)},"~B");c(c$,"getShowAxes",function(){return 0!=this.getObjectMad(1)});h(c$,"setFrankOn",function(a){this.isPreviewOnly&&
(a=!1);this.frankOn=a;this.setObjectMad(36,"frank",a?1:0)},"~B");c(c$,"getShowFrank",function(){return this.isPreviewOnly||this.isApplet&&this.creatingImage?!1:this.isSignedApplet&&!this.isSignedAppletLocal&&!this.isJS||this.frankOn});h(c$,"setShowMeasurements",function(a){this.g.setB("showMeasurements",a);this.g.showMeasurements=a},"~B");c(c$,"setUnits",function(a,b){this.g.setUnits(a);b&&(this.g.setUnits(a),this.setShapeProperty(6,"reformatDistances",null))},"~S,~B");h(c$,"setRasmolDefaults",function(){this.setDefaultsType("RasMol")});
h(c$,"setJmolDefaults",function(){this.setDefaultsType("Jmol")});c(c$,"setDefaultsType",function(a){a.equalsIgnoreCase("RasMol")?this.stm.setRasMolDefaults():a.equalsIgnoreCase("PyMOL")?this.stm.setPyMOLDefaults():(this.stm.setJmolDefaults(),this.setIntProperty("bondingVersion",0),this.shm.setShapeSizeBs(0,0,this.rd,this.getAllAtoms()))},"~S");c(c$,"setAntialias",function(a,b){switch(a){case 603979786:this.g.antialiasDisplay=b;break;case 603979790:this.g.antialiasTranslucent=b;break;case 603979788:this.g.antialiasImages=
b;return}this.resizeImage(0,0,!1,!1,!0)},"~N,~B");c(c$,"allocTempPoints",function(a){return this.tempArray.allocTempPoints(a)},"~N");c(c$,"freeTempPoints",function(a){this.tempArray.freeTempPoints(a)},"~A");c(c$,"allocTempScreens",function(a){return this.tempArray.allocTempScreens(a)},"~N");c(c$,"freeTempScreens",function(a){this.tempArray.freeTempScreens(a)},"~A");c(c$,"allocTempEnum",function(a){return this.tempArray.allocTempEnum(a)},"~N");c(c$,"freeTempEnum",function(a){this.tempArray.freeTempEnum(a)},
"~A");c(c$,"getFont3D",function(a,b,d){return this.gdata.getFont3DFSS(a,b,d)},"~S,~S,~N");c(c$,"getAtomGroupQuaternions",function(a,b){return this.ms.getAtomGroupQuaternions(a,b,this.getQuaternionFrame())},"JU.BS,~N");c(c$,"setStereoMode",function(a,b,d){this.setFloatProperty("stereoDegrees",d);this.setBooleanProperty("greyscaleRendering",b.isBiColor());null!=a?this.tm.setStereoMode2(a):this.tm.setStereoMode(b)},"~A,J.c.STER,~N");c(c$,"isStereoDouble",function(){return this.tm.stereoMode===J.c.STER.DOUBLE});
c(c$,"getChimeInfo",function(a){return this.getPropertyManager().getChimeInfo(a,this.bsA())},"~N");c(c$,"getModelFileInfo",function(){return this.getPropertyManager().getModelFileInfo(this.getVisibleFramesBitSet())});c(c$,"getModelFileInfoAll",function(){return this.getPropertyManager().getModelFileInfo(null)});h(c$,"getProperty",function(a,b,d){if(!"DATA_API".equals(a))return this.getPropertyManager().getProperty(a,b,d);switch("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........".indexOf(b)){case 0:return this.scriptCheckRet(d,
!0);case 20:return null==this.appConsole?"":this.appConsole.getText();case 40:return this.showEditor(d),null;case 60:return this.scriptEditorVisible=d.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:n(d,J.api.JmolAppConsoleInterface)?this.appConsole=d:null!=d&&!d.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=d&&d.booleanValue())&&(this.isJS&&(this.appConsole=J.api.Interface.getOption("consolejs.AppletConsole",this,"script")),null!=this.appConsole&&this.appConsole.start(this)),
this.scriptEditor=this.isJS||null==this.appConsole?null:this.appConsole.getScriptEditor(),this.appConsole;case 100:return null==this.appConsole&&(null!=d&&d.booleanValue())&&(this.getProperty("DATA_API","getAppConsole",Boolean.TRUE),this.scriptEditor=null==this.appConsole?null:this.appConsole.getScriptEditor()),this.scriptEditor;case 120:return null!=this.jmolpopup&&this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.menuStructure=d;case 140:return this.ms.getSymTemp(!0).getSpaceGroupInfo(this.ms,
null);case 160:return this.g.disablePopupMenu=!0,null;case 180:return this.g.defaultDirectory;case 200:return n(d,String)?this.getMenu(d):this.getPopupMenu();case 220:return this.shm.getProperty(d)}JU.Logger.error("ERROR in getProperty DATA_API: "+b);return null},"~S,~S,~O");c(c$,"showEditor",function(a){var b=this.getProperty("DATA_API","getScriptEditor",Boolean.TRUE);null!=b&&b.show(a)},"~A");c(c$,"getPropertyManager",function(){null==this.pm&&(this.pm=J.api.Interface.getInterface("JV.PropertyManager",
this,"prop")).setViewer(this);return this.pm});c(c$,"getModelExtract",function(a,b,d,c){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),b,d,c)},"~O,~B,~B,~S");c(c$,"setTainted",function(a){this.isTainted=this.axesAreTainted=a&&(this.refreshing||this.creatingImage)},"~B");c(c$,"notifyMouseClicked",function(a,b,d,c){var g=JV.binding.Binding.getButtonMods(d),f=JV.binding.Binding.getClickCount(d);this.g.setI("_mouseX",a);this.g.setI("_mouseY",this.dimScreen.height-b);this.g.setI("_mouseAction",
d);this.g.setI("_mouseModifiers",g);this.g.setI("_clickCount",f);return this.sm.setStatusClicked(a,this.dimScreen.height-b,d,f,c)},"~N,~N,~N,~N");c(c$,"checkObjectClicked",function(a,b,d){return this.shm.checkObjectClicked(a,b,d,this.getVisibleFramesBitSet(),this.g.drawPicking)},"~N,~N,~N");c(c$,"checkObjectHovered",function(a,b){return 0<=a&&null!=this.shm&&this.shm.checkObjectHovered(a,b,this.getVisibleFramesBitSet(),this.getBondPicking())},"~N,~N");c(c$,"checkObjectDragged",function(a,b,d,c,g){var f=
0;switch(this.getPickingMode()){case 2:f=5;break;case 4:f=22}this.shm.checkObjectDragged(a,b,d,c,g,this.getVisibleFramesBitSet(),f)&&(this.refresh(1,"checkObjectDragged"),22==f&&this.scriptEcho(this.getShapeProperty(22,"command")))},"~N,~N,~N,~N,~N");c(c$,"rotateAxisAngleAtCenter",function(a,b,d,c,g,f,j){(a=this.tm.rotateAxisAngleAtCenter(a,b,d,c,g,f,j))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(c$,"rotateAboutPointsInternal",function(a,b,d,c,g,f,j,h,l,q,
p){if(this.headless){if(f&&3.4028235E38==g)return!1;f=!1}(a=this.tm.rotateAboutPointsInternal(a,b,d,c,g,!1,f,j,!1,h,l,q,p))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.Lst,~A,JU.M4");c(c$,"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){return this.ms.calculateMolecularDipole(this.am.cmi,a)},"JU.BS");c(c$,"setDefaultLattice",function(a){Float.isNaN(a.x+a.y+a.z)||this.g.ptDefaultLattice.setT(a);this.g.setO("defaultLattice",JU.Escape.eP(a))},"JU.P3");c(c$,"getDefaultLattice",function(){return this.g.ptDefaultLattice});c(c$,"getData",function(a,b){var d="";if(b.equalsIgnoreCase("MOL")||b.equalsIgnoreCase("SDF")||b.equalsIgnoreCase("V2000")||b.equalsIgnoreCase("V3000")||b.equalsIgnoreCase("XYZVIB")||
b.equalsIgnoreCase("CD")||b.equalsIgnoreCase("JSON"))return this.getModelExtract(a,!1,!1,b);if(0==b.toLowerCase().indexOf("property_"))d='{selected}.label("%{'+b+'}")';else{if(b.equalsIgnoreCase("CML"))return this.getModelCml(this.getAtomBitSet(a),2147483647,!0);d=b.equalsIgnoreCase("PDB")?'{selected and not hetero}.label("ATOM  %5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  ").lines+{selected and hetero}.label("HETATM%5i %-4a%1A%3.3n %1c%4R%1E   %8.3x%8.3y%8.3z%6.2Q%6.2b          %2e  ").lines':
b.equalsIgnoreCase("XYZRN")?'"" + {selected}.size + "\n\n"+{selected}.label("%-2e %8.3x %8.3y %8.3z %4.2[vdw] 1 [%n]%r.%a#%i").lines':b.startsWith("USER:")?'{selected}.label("'+b.substring(5)+'").lines':'"" + {selected}.size + "\n\n"+{selected}.label("%-2e %10.5x %10.5y %10.5z").lines'}a.equals("selected")||(d=JU.PT.rep(d,"selected",a));return this.evaluateExpression(d)},"~S,~S");c(c$,"getModelCml",function(a,b,d){return this.getPropertyManager().getModelCml(a,b,d)},"JU.BS,~N,~B");c(c$,"getPdbAtomData",
function(a,b){return this.getPropertyManager().getPdbAtomData(null==a?this.bsA():a,b)},"JU.BS,JU.OC");c(c$,"isJmolDataFrame",function(){return this.ms.isJmolDataFrameForModel(this.am.cmi)});c(c$,"setFrameTitle",function(a,b){this.ms.setFrameTitle(JU.BSUtil.newAndSetBit(a),b)},"~N,~S");c(c$,"setFrameTitleObj",function(a){this.shm.loadShape(31);this.ms.setFrameTitle(this.getVisibleFramesBitSet(),a)},"~O");c(c$,"getFrameTitle",function(){return this.ms.getFrameTitle(this.am.cmi)});c(c$,"setAtomProperty",
function(a,b,d,c,g,f,j){1649412120==b&&this.shm.deleteVdwDependentShapes(a);this.clearMinimization();this.ms.setAtomProperty(a,b,d,c,g,f,j);switch(b){case 1112541185:case 1112541186:case 1112541187:case 1112541188:case 1112541189:case 1112541190:case 1112539153:case 1112539154:case 1112539155:case 1087375365:this.refreshMeasures(!0)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(c$,"checkCoordinatesChanged",function(){this.ms.recalculatePositionDependentQuantities(null,null);this.refreshMeasures(!0)});c(c$,"setAtomCoords",
function(a,b,d){0!=a.cardinality()&&(this.ms.setAtomCoords(a,b,d),this.checkMinimization(),this.sm.setStatusAtomMoved(a))},"JU.BS,~N,~O");c(c$,"setAtomCoordsRelative",function(a,b){null==b&&(b=this.bsA());0!=b.cardinality()&&(this.ms.setAtomCoordsRelative(a,b),this.checkMinimization(),this.sm.setStatusAtomMoved(b))},"JU.T3,JU.BS");c(c$,"invertAtomCoordPt",function(a,b){this.ms.invertSelected(a,null,-1,null,b);this.checkMinimization();this.sm.setStatusAtomMoved(b)},"JU.P3,JU.BS");c(c$,"invertAtomCoordPlane",
function(a,b){this.ms.invertSelected(null,a,-1,null,b);this.checkMinimization();this.sm.setStatusAtomMoved(b)},"JU.P4,JU.BS");c(c$,"invertSelected",function(a,b,d,c){var g=this.bsA();0!=g.cardinality()&&(this.ms.invertSelected(a,b,d,c,g),this.checkMinimization(),this.sm.setStatusAtomMoved(g))},"JU.P3,JU.P4,~N,JU.BS");c(c$,"moveAtoms",function(a,b,d,c,g,f,j,h){0!=j.cardinality()&&(this.ms.moveAtoms(a,b,d,c,j,g,f,h),this.checkMinimization(),this.sm.setStatusAtomMoved(j))},"JU.M4,JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B");
c(c$,"moveSelected",function(a,b,d,c,g,f,j,h){0!=d&&(-2147483648==c&&(this.rotateBondIndex=-1),this.isJmolDataFrame()||(-2147483648==a?(this.showSelected=!0,this.shm.loadShape(8),this.refresh(6,"moveSelected")):2147483647==a?this.showSelected&&(this.showSelected=!1,this.refresh(6,"moveSelected")):this.movingSelected||(this.movingSelected=!0,this.stopMinimization(),0<=this.rotateBondIndex&&-2147483648!=c?this.actionRotateBond(a,b,c,g):(f=this.setMovableBitSet(f,!h),0!=f.cardinality()&&(j?(c=this.ms.getAtomSetCenter(f),
this.tm.finalizeTransformParameters(),g=this.g.antialiasDisplay?2:1,j=this.tm.transformPt(c),a=-2147483648!=d?JU.P3.new3(j.x,j.y,j.z+d+0.5):JU.P3.new3(j.x+a*g+0.5,j.y+b*g+0.5,j.z),b=new JU.P3,this.tm.unTransformPoint(a,b),b.sub(c),this.setAtomCoordsRelative(b,f)):this.tm.rotateXYBy(a,b,f))),this.refresh(2,""),this.movingSelected=!1)))},"~N,~N,~N,~N,~N,JU.BS,~B,~B");c(c$,"highlightBond",function(a,b){if(!b||this.hoverEnabled){var d=null;if(0<=a){var c=this.ms.bo[a],d=c.atom2.i;if(!this.ms.isAtomAssignable(d))return;
d=JU.BSUtil.newAndSetBit(d);d.set(c.atom1.i)}this.highlight(d);this.refresh(3,"highlightBond")}},"~N,~B");c(c$,"highlight",function(a){null!=a&&this.shm.loadShape(8);this.setShapeProperty(8,"highlight",a)},"JU.BS");c(c$,"setRotateBondIndex",function(a){if(0<=this.rotateBondIndex||!(0>a))this.rotatePrev1=-1,this.bsRotateBranch=null,-2147483648!=a&&(this.rotateBondIndex=a,this.highlightBond(a,!1))},"~N");c(c$,"getRotateBondIndex",function(){return this.rotateBondIndex});c(c$,"actionRotateBond",function(a,
b,d,c){if(!(0>this.rotateBondIndex)){var g=this.bsRotateBranch,f,j;if(null==g){j=this.ms.bo[this.rotateBondIndex];f=j.atom1;j=j.atom2;this.undoMoveActionClear(f.i,2,!0);d=JU.P3.new3(d,c,s((f.sZ+j.sZ)/2));this.tm.unTransformPoint(d,d);if(1==j.getCovalentBondCount()||d.distance(f)<d.distance(j)&&1!=f.getCovalentBondCount())c=f,f=j,j=c;if(90<JU.Measure.computeAngleABC(d,f,j,!0)||90<JU.Measure.computeAngleABC(d,j,f,!0))g=this.getBranchBitSet(j.i,f.i,!0);if(null!=g){d=0;for(c=f.bonds.length;0<=--c;)if(g.get(f.getBondedAtomIndex(c))&&
2==++d){g=null;break}}null==g&&(g=this.ms.getMoleculeBitSetForAtom(f.i));this.bsRotateBranch=g;this.rotatePrev1=f.i;this.rotatePrev2=j.i}else f=this.ms.at[this.rotatePrev1],j=this.ms.at[this.rotatePrev2];d=JU.V3.new3(j.sX-f.sX,j.sY-f.sY,0);a=JU.V3.new3(a,b,0);d.cross(d,a);a=(0<d.z?1:-1)*a.length();g=JU.BSUtil.copy(g);g.andNot(this.slm.getMotionFixedAtoms());this.rotateAboutPointsInternal(this.eval,f,j,0,a,!1,g,null,null,null,null)}},"~N,~N,~N,~N");c(c$,"refreshMeasures",function(a){this.setShapeProperty(6,
"refresh",null);a&&this.stopMinimization()},"~B");c(c$,"functionXY",function(a,b,d){var c=null;if(0==a.indexOf("file:"))c=this.getFileAsString3(a.substring(5),!1,null);else if(0!=a.indexOf("data2d_"))return this.sm.functionXY(a,b,d);b=Math.abs(b);d=Math.abs(d);if(null==c){a=this.getDataFloat2D(a);if(null!=a)return a;c=""}a=L(b,d,0);var g=L(b*d,0);JU.Parser.parseStringInfestedFloatArray(c,null,g);for(var f=c=0;c<b;c++)for(var j=0;j<d;j++)a[c][j]=g[f++];return a},"~S,~N,~N");c(c$,"functionXYZ",function(a,
b,d,c){var g=null;if(0==a.indexOf("file:"))g=this.getFileAsString3(a.substring(5),!1,null);else if(0!=a.indexOf("data3d_"))return this.sm.functionXYZ(a,b,d,c);b=Math.abs(b);d=Math.abs(d);c=Math.abs(c);if(null==g){a=this.getDataFloat3D(a);if(null!=a)return a;g=""}a=L(b,d,c,0);var f=L(b*d*c,0);JU.Parser.parseStringInfestedFloatArray(g,null,f);for(var j=g=0;g<b;g++)for(var h=0;h<d;h++)for(var l=0;l<c;l++)a[g][h][l]=f[j++];return a},"~S,~N,~N,~N");h(c$,"extractMolData",function(a){if(null==a){a=this.am.cmi;
if(0>a)return null;a=this.getModelNumberDotted(a)}return this.getModelExtract(a,!0,!1,"V2000")},"~S");c(c$,"getNMRPredict",function(a){var b=this.getModelExtract("selected",!0,!1,"V2000"),d=b.indexOf("\n"),b="Jmol "+JV.Viewer.version_date+b.substring(d);return a?(this.isApplet?this.showUrl(this.g.nmrUrlFormat+b):(this.syncScript("true","*",0),this.syncScript("H1Simulate:",".",0)),null):this.getFileAsString3(this.g.nmrPredictFormat+b,!1,null)},"~B");c(c$,"getHelp",function(a){0>this.g.helpPath.indexOf("?")?
(0<a.length&&0!=a.indexOf("?")&&(a="?search="+JU.PT.rep(a," ","%20")),a+=(0==a.length?"?ver=":"&ver=")+JV.JC.version):a="&"+a;this.showUrl(this.g.helpPath+a)},"~S");c(c$,"show2D",function(a){this.showUrl(this.setLoadFormat("_"+a,"2",!1))},"~S");c(c$,"getChemicalInfo",function(a,b){var d=null,c="/";switch(null==b?1073742035:b.tok){case 1073741977:c="I";break;case 1073741978:c="K";break;case 1073742159:c="T";break;case 1073742160:c="S";break;case 1073742035:c="N";break;default:d=JS.SV.sValue(b)}var g=
this.setLoadFormat("_"+a,c,!1);"/"==c&&(g+=JU.PT.rep(d," ","%20"));return this.getFileAsString4(g,-1,!1,!1,!1,"file")},"~S,JS.T");c(c$,"addCommand",function(a){!this.autoExit&&(this.haveDisplay&&this.getPreserveState())&&this.commandHistory.addCommand(JU.PT.replaceAllCharacters(a,"\r\n\t"," "))},"~S");c(c$,"removeCommand",function(){return this.commandHistory.removeCommand()});h(c$,"getSetHistory",function(a){return this.commandHistory.getSetHistory(a)},"~N");c(c$,"historyFind",function(a,b){return this.commandHistory.find(a,
b)},"~S,~N");c(c$,"setHistory",function(a){this.commandHistory.getSetHistory(-2147483648);this.commandHistory.addCommand(this.getFileAsString4(a,-1,!1,!1,!0,null))},"~S");c(c$,"getOutputChannel",function(a,b){return this.getOutputManager().getOutputChannel(a,b)},"~S,~A");h(c$,"writeTextFile",function(a,b){var d=new java.util.Hashtable;d.put("fileName",a);d.put("type","txt");d.put("text",b);this.outputToFile(d)},"~S,~S");h(c$,"clipImageOrPasteText",function(a){return!this.haveAccess(JV.Viewer.ACCESS.ALL)?
"no":this.getOutputManager().clipImageOrPasteText(a)},"~S");h(c$,"getClipboardText",function(){if(!this.haveAccess(JV.Viewer.ACCESS.ALL))return"no";try{return this.getOutputManager().getClipboardText()}catch(a){if(y(a,Error))return J.i18n.GT._("clipboard is not accessible -- use signed applet");throw a;}});c(c$,"processWriteOrCapture",function(a){return this.getOutputManager().processWriteOrCapture(a)},"java.util.Map");c(c$,"createZip",function(a,b,d){var c=new java.util.Hashtable;c.put("fileName",
a);c.put("type",b);c.put("text",this.getStateInfo());n(d,Array)?c.put("scripts",d):n(d,JU.Lst)&&c.put("imageData",d);return this.getOutputManager().outputToFile(c)},"~S,~S,~O");h(c$,"outputToFile",function(a){return this.getOutputManager().outputToFile(a)},"java.util.Map");c(c$,"getOutputManager",function(){return null!=this.outputManager?this.outputManager:(this.outputManager=J.api.Interface.getInterface("JV.OutputManager"+(this.isJS?"JS":"Awt"),this,"file")).setViewer(this,this.privateKey)});c(c$,
"setSyncTarget",function(a,b){switch(a){case 0:this.sm.syncingMouse=b;break;case 1:this.sm.syncingScripts=b;break;case 2:this.sm.syncSend(b?"GET_GRAPHICS":"SET_GRAPHICS_OFF","*",0);Float.isNaN(this.tm.stereoDegrees)&&this.setFloatProperty("stereoDegrees",-5);b&&(this.setBooleanProperty("_syncMouse",!1),this.setBooleanProperty("_syncScript",!1));return}!this.sm.syncingScripts&&!this.sm.syncingMouse&&this.setSync()},"~N,~B");h(c$,"syncScript",function(a,b,d){this.getStateCreator().syncScript(a,b,d)},
"~S,~S,~N");h(c$,"getModelIndexFromId",function(a){return this.ms.getModelIndexFromId(a)},"~S");c(c$,"setSyncDriver",function(a){this.sm.setSyncDriver(a)},"~N");c(c$,"getPartialCharges",function(){return this.ms.getPartialCharges()});c(c$,"setProteinType",function(a,b){this.ms.setProteinType(null==b?this.bsA():b,a)},"J.c.STR,JU.BS");c(c$,"getVanderwaalsMar",function(a){return this.defaultVdw===J.c.VDW.USER?this.userVdwMars[a]:JU.Elements.getVanderwaalsMar(a,this.defaultVdw)},"~N");c(c$,"getVanderwaalsMarType",
function(a,b){if(null==b)b=this.defaultVdw;else switch(b){case J.c.VDW.AUTO:case J.c.VDW.AUTO_BABEL:case J.c.VDW.AUTO_JMOL:case J.c.VDW.AUTO_RASMOL:this.defaultVdw!==J.c.VDW.AUTO&&(b=this.defaultVdw)}b===J.c.VDW.USER&&null==this.bsUserVdws&&(b=J.c.VDW.JMOL);return b===J.c.VDW.USER?this.userVdwMars[a&127]:JU.Elements.getVanderwaalsMar(a,b)},"~N,J.c.VDW");c(c$,"setVdwStr",function(a){a=J.c.VDW.getVdwType(a);null==a&&(a=J.c.VDW.AUTO);switch(a){case J.c.VDW.JMOL:case J.c.VDW.BABEL:case J.c.VDW.RASMOL:case J.c.VDW.AUTO:case J.c.VDW.USER:break;
default:a=J.c.VDW.JMOL}a!==this.defaultVdw&&(a===J.c.VDW.USER&&null==this.bsUserVdws)&&this.setUserVdw(this.defaultVdw);this.defaultVdw=a;this.g.setO("defaultVDW",a.getVdwLabel())},"~S");c(c$,"setUserVdw",function(a){this.userVdwMars=D(JU.Elements.elementNumberMax,0);this.userVdws=L(JU.Elements.elementNumberMax,0);this.bsUserVdws=new JU.BS;a===J.c.VDW.USER&&(a=J.c.VDW.JMOL);for(var b=1;b<JU.Elements.elementNumberMax;b++)this.userVdwMars[b]=JU.Elements.getVanderwaalsMar(b,a),this.userVdws[b]=this.userVdwMars[b]/
1E3},"J.c.VDW");c(c$,"getDefaultVdwNameOrData",function(a,b,d){switch(a){case -2147483648:return this.defaultVdw.getVdwLabel();case 2147483647:if(null==(d=this.bsUserVdws))return"";b=J.c.VDW.USER}if(null==b||b===J.c.VDW.AUTO)b=this.defaultVdw;b===J.c.VDW.USER&&null==this.bsUserVdws&&this.setUserVdw(this.defaultVdw);return this.getDataManager().getDefaultVdwNameOrData(b,d)},"~N,J.c.VDW,JU.BS");c(c$,"deleteAtoms",function(a,b){var d=null==a?-1:a.nextSetBit(0);if(0>d)return 0;this.clearModelDependentObjects();
if(!b){this.sm.modifySend(d,this.ms.at[d].mi,4,"deleting atom "+this.ms.at[d].getAtomName());this.ms.deleteAtoms(a);var c=this.slm.deleteAtoms(a);this.setTainted(!0);this.sm.modifySend(d,this.ms.at[d].mi,-4,"OK");return c}return this.deleteModels(this.ms.at[d].mi,a)},"JU.BS,~B");c(c$,"deleteModels",function(a,b){this.clearModelDependentObjects();this.sm.modifySend(-1,a,5,"deleting model "+this.getModelNumberDotted(a));this.setCurrentModelIndexClear(0,!1);this.am.setAnimationOn(!1);var d=JU.BSUtil.copy(this.slm.bsDeleted),
c=null==b?JU.BSUtil.newAndSetBit(a):this.ms.getModelBS(b,!1),c=this.ms.deleteModels(c);this.slm.processDeletedModelAtoms(c);null!=this.eval&&this.eval.deleteAtomsInVariables(c);this.setAnimationRange(0,0);this.clearRepaintManager(-1);this.am.clear();this.am.initializePointers(1);this.setCurrentModelIndexClear(1<this.ms.mc?-1:0,1<this.ms.mc);this.hoverAtomIndex=-1;this.setFileLoadStatus(J.c.FIL.DELETED,null,null,null,null,null);this.refreshMeasures(!0);null!=d&&c.andNot(d);this.sm.modifySend(-1,a,
-5,"OK");return JU.BSUtil.cardinalityOf(c)},"~N,JU.BS");c(c$,"deleteBonds",function(a){var b=this.ms.bo[a.nextSetBit(0)].atom1.mi;this.sm.modifySend(-1,b,2,"delete bonds "+JU.Escape.eBond(a));this.ms.deleteBonds(a,!1);this.sm.modifySend(-1,b,-2,"OK")},"JU.BS");c(c$,"deleteModelAtoms",function(a,b,d,c){this.sm.modifySend(-1,a,1,"delete atoms "+JU.Escape.eBS(c));JU.BSUtil.deleteBits(this.bsFrameOffsets,c);this.getDataManager().deleteModelAtoms(b,d,c);this.sm.modifySend(-1,a,-1,"OK")},"~N,~N,~N,JU.BS");
c(c$,"getQuaternionFrame",function(){return this.g.quaternionFrame.charAt(2==this.g.quaternionFrame.length?1:0)});c(c$,"loadImageData",function(a,b,d,c){null==a&&this.scriptEcho(b);null==d?this.setBackgroundImage(null==a?null:b,a):(this.shm.loadShape(31),this.setShapeProperty(31,"text",b),null!=a&&this.setShapeProperty(31,"image",a));this.isJS&&null!=c&&(c.mustResumeEval=!0,this.eval.resumeEval(c))},"~O,~S,~S,JS.ScriptContext");c(c$,"cd",function(a){null==a?a=".":0==a.length&&(this.setStringProperty("defaultDirectory",
""),a=".");a=this.fm.getDefaultDirectory(a+(a.equals("=")?"":a.endsWith("/")?"X.spt":"/X.spt"));0<a.length&&this.setStringProperty("defaultDirectory",a);this.fm.getFilePath(a+"/",!0,!1).startsWith("file:/")&&JV.FileManager.setLocalPath(this,a,!1);return a},"~S");c(c$,"setErrorMessage",function(a,b){this.errorMessageUntranslated=b;null!=a&&this.eval.stopScriptThreads();return this.errorMessage=a},"~S,~S");h(c$,"getErrorMessage",function(){return this.errorMessage});h(c$,"getErrorMessageUn",function(){return null==
this.errorMessageUntranslated?this.errorMessage:this.errorMessageUntranslated});c(c$,"setShapeErrorState",function(a,b){this.currentShapeID=a;this.currentShapeState=b},"~N,~S");c(c$,"getShapeErrorState",function(){if(0>this.currentShapeID)return"";this.shm.releaseShape(this.currentShapeID);this.clearRepaintManager(this.currentShapeID);return JV.JC.getShapeClassName(this.currentShapeID,!1)+" "+this.currentShapeState});c(c$,"handleError",function(a,b){try{b&&this.zapMsg(""+a),this.undoClear(),0==JU.Logger.getLogLevel()&&
JU.Logger.setLogLevel(4),this.setCursor(0),this.setBooleanProperty("refreshing",!0),this.fm.setPathForAllFiles(""),JU.Logger.error("vwr handling error condition: "+a+"  "),this.isJS||a.printStackTrace(),this.notifyError("Error","doClear="+b+"; "+a,""+a)}catch(d){try{JU.Logger.error("Could not notify error "+a+": due to "+d)}catch(c){}}},"Error,~B");c(c$,"getFunctions",function(a){return a?JV.Viewer.staticFunctions:this.localFunctions},"~B");c(c$,"removeFunction",function(a){a=a.toLowerCase();null!=
this.getFunction(a)&&(JV.Viewer.staticFunctions.remove(a),this.localFunctions.remove(a))},"~S");c(c$,"getFunction",function(a){if(null==a)return null;a=(JV.Viewer.isStaticFunction(a)?JV.Viewer.staticFunctions:this.localFunctions).get(a);return null==a||null==a.geTokens()?null:a},"~S");c$.isStaticFunction=c(c$,"isStaticFunction",function(a){return a.startsWith("static_")},"~S");c(c$,"isFunction",function(a){return(JV.Viewer.isStaticFunction(a)?JV.Viewer.staticFunctions:this.localFunctions).containsKey(a)},
"~S");c(c$,"clearFunctions",function(){JV.Viewer.staticFunctions.clear();this.localFunctions.clear()});c(c$,"addFunction",function(a){var b=a.getName();(JV.Viewer.isStaticFunction(b)?JV.Viewer.staticFunctions:this.localFunctions).put(b,a)},"J.api.JmolScriptFunction");c(c$,"getFunctionCalls",function(a){return this.getStateCreator().getFunctionCalls(a)},"~S");c(c$,"warn",function(a){this.isPrintOnly||JU.Logger.warn(a)},"~S");c(c$,"checkPrivateKey",function(a){return a==this.privateKey},"~N");c(c$,
"bindAction",function(a,b){this.haveDisplay&&this.acm.bind(a,b)},"~S,~S");c(c$,"unBindAction",function(a,b){this.haveDisplay&&this.acm.unbindAction(a,b)},"~S,~S");c(c$,"getPlaneIntersection",function(a,b,d,c){return this.ms.getPlaneIntersection(a,b,d,c,1614417948==a?this.getCurrentUnitCell():null)},"~N,JU.P4,~N,~N");c(c$,"calculateStruts",function(a,b){return this.ms.calculateStruts(null==a?this.bsA():a,null==b?this.bsA():b)},"JU.BS,JU.BS");c(c$,"getPreserveState",function(){return this.g.preserveState&&
null!=this.scm});c(c$,"isKiosk",function(){return this.$isKiosk});c(c$,"hasFocus",function(){return this.haveDisplay&&(this.$isKiosk||this.apiPlatform.hasFocus(this.display))});c(c$,"setFocus",function(){this.haveDisplay&&!this.apiPlatform.hasFocus(this.display)&&this.apiPlatform.requestFocusInWindow(this.display)});c(c$,"stopMinimization",function(){null!=this.minimizer&&this.minimizer.setProperty("stop",null)});c(c$,"clearMinimization",function(){null!=this.minimizer&&this.minimizer.setProperty("clear",
null)});c(c$,"getMinimizationInfo",function(){return null==this.minimizer?"":this.minimizer.getProperty("log",0)});c(c$,"checkMinimization",function(){this.refreshMeasures(!0);if(this.g.monitorEnergy){try{this.minimize(null,0,0,this.getAllAtoms(),null,0,!1,!1,!0,!1)}catch(a){if(!y(a,Exception))throw a;}this.echoMessage(this.getP("_minimizationForceField")+" Energy = "+this.getP("_minimizationEnergy"))}});c(c$,"minimize",function(a,b,d,c,g,f,j,h,l,q){var p=this.g.forceField,m=this.getModelUndeletedAtomsBitSetBs(this.getVisibleFramesBitSet());
null==c?c=this.getModelUndeletedAtomsBitSet(this.getVisibleFramesBitSet().length()-1):c.and(m);0>=f&&(f=5);g=JU.BSUtil.copy(null==g?this.slm.getMotionFixedAtoms():g);var n=0<g.cardinality();n&&c.andNot(g);f=h?new JU.BS:this.ms.getAtomsWithinRadius(f,c,!0,null);f.andNot(c);n?g.and(f):g=f;g.and(m);j&&c.or(this.addHydrogens(c,q,l));if(200<c.cardinality())JU.Logger.error("Too many atoms for minimization (>200)");else try{l||JU.Logger.info("Minimizing "+c.cardinality()+" atoms"),this.getMinimizer(!0).minimize(b,
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m("JSV.common");w(["java.lang.Enum","JSV.common.Coordinate"],"JSV.common.Annotation",["java.lang.Double","JU.CU"],function(){c$=r(function(){this.text="";this.is2D=this.$isPixels=!1;this.offsetY=this.offsetX=0;this.spec=null;t(this,arguments)},JSV.common,"Annotation",JSV.common.Coordinate);c(c$,"setA",function(a,b,d,c,g,f,j,h){this.set(a,b);this.spec=d;this.text=c;this.$isPixels=g;this.is2D=f;this.offsetX=j;this.offsetY=h;return this},"~N,~N,JSV.common.Spectrum,~S,~B,~B,~N,~N");c(c$,"setSpec",function(a){this.spec=
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n,b,r,s,!1,!1,0,0)}catch(t){if(y(t,Exception))return null;throw t;}},"J.api.GenericGraphics,JSV.common.Spectrum,JU.Lst,JSV.common.Annotation");G(self.c$);c$=z(JSV.common.Annotation,"AType",Enum);x(c$,"Integration",0,[]);x(c$,"PeakList",1,[]);x(c$,"Measurements",2,[]);x(c$,"OverlayLegend",3,[]);x(c$,"Views",4,[]);x(c$,"NONE",5,[]);c$=K()});m("JSV.common");w(["JSV.common.Annotation"],"JSV.common.ColoredAnnotation",null,function(){c$=r(function(){this.color=null;t(this,arguments)},JSV.common,"ColoredAnnotation",
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this.getColor3(255,255,255);this.elementColors=new java.util.Hashtable;this.setColor(JSV.common.ScriptToken.TITLECOLOR,JSV.common.ColorParameters.BLACK);this.setColor(JSV.common.ScriptToken.UNITSCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.SCALECOLOR,JSV.common.ColorParameters.BLACK);this.setColor(JSV.common.ScriptToken.COORDINATESCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.GRIDCOLOR,JSV.common.ColorParameters.LIGHT_GRAY);this.setColor(JSV.common.ScriptToken.PLOTCOLOR,
JSV.common.ColorParameters.BLUE);this.setColor(JSV.common.ScriptToken.PLOTAREACOLOR,JSV.common.ColorParameters.WHITE);this.setColor(JSV.common.ScriptToken.BACKGROUNDCOLOR,this.getColor3(192,192,192));this.setColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.PEAKTABCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR,JSV.common.ColorParameters.DARK_GRAY);for(var a=0;8>a;a++)JSV.common.ColorParameters.defaultPlotColors[a]=
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this.setColorFromString(b,d);break;case JSV.common.ScriptToken.TITLEFONTNAME:case JSV.common.ScriptToken.DISPLAYFONTNAME:c=this.getFontName(b,d)}null!=a&&null!=c&&a.setColorOrFont(this,b)},"JSV.common.PanelData,JSV.common.ScriptToken,~S");c(c$,"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)});
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this.displayFontName=b:this.displayFontName}return null},"JSV.common.ScriptToken,~S");C(c$,"BLACK",null,"RED",null,"LIGHT_GRAY",null,"DARK_GRAY",null,"BLUE",null,"WHITE",null);c$.defaultPlotColors=c$.prototype.defaultPlotColors=Array(8);c$.defaultPlotColorNames=c$.prototype.defaultPlotColorNames="black darkGreen darkred orange magenta cyan maroon darkGray".split(" ")});m("JSV.common");c$=z(JSV.common,"CoordComparator",null,java.util.Comparator);h(c$,"compare",function(a,b){return a.getXVal()>b.getXVal()?
1:a.getXVal()<b.getXVal()?-1:0},"JSV.common.Coordinate,JSV.common.Coordinate");m("JSV.common");w(["JSV.common.CoordComparator"],"JSV.common.Coordinate",["java.lang.Double","java.util.Arrays","$.StringTokenizer","JU.DF","$.Lst"],function(){c$=r(function(){this.yVal=this.xVal=0;t(this,arguments)},JSV.common,"Coordinate");u(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});
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c$.getMinX=c(c$,"getMinX",function(a,b,d){for(var c=1.7976931348623157E308;b<d;b++){var g=a[b].getXVal();g<c&&(c=g)}return c},"~A,~N,~N");c$.getMinX=c(c$,"getMinX",function(a,b){for(var d=1.7976931348623157E308,c=0;c<a.size();c++){var g=a.get(c).getXYCoords(),g=JSV.common.Coordinate.getMinX(g,b.getStartingPointIndex(c),b.getEndingPointIndex(c));g<d&&(d=g)}return d},"JU.Lst,JSV.common.ViewData");c$.getMaxX=c(c$,"getMaxX",function(a,b,d){for(var c=-1.7976931348623157E308;b<d;b++){var g=a[b].getXVal();
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c=0;c<a.size();c++){var g=a.get(c).getUserYFactor(),f=a.get(c).getYRef(),j=a.get(c).getXYCoords(),g=(JSV.common.Coordinate.getMinY(j,b.getStartingPointIndex(c),b.getEndingPointIndex(c))-f)*g+f;g<d&&(d=g)}return d},"JU.Lst,JSV.common.ViewData");c$.getMaxY=c(c$,"getMaxY",function(a,b,d){for(var c=-1.7976931348623157E308;b<d;b++){var g=a[b].getYVal();g>c&&(c=g)}return c},"~A,~N,~N");c$.getMaxYUser=c(c$,"getMaxYUser",function(a,b){for(var d=-1.7976931348623157E308,c=0;c<a.size();c++){var g=a.get(c).getUserYFactor(),
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JSV.common.Coordinate.parabolicInterpolation(a,b)},"~A,~N,~B");c$.parabolicInterpolation=c(c$,"parabolicInterpolation",function(a,b){var d=a[b-1].yVal,c=a[b+1].yVal;return a[b].xVal+(d-c)/2/(d-2*a[b].yVal+c)*(a[b+1].xVal-a[b].xVal)},"~A,~N");c$.getPickedCoordinates=c(c$,"getPickedCoordinates",function(a,b,d,c){if(null==b)return!1;var g=b.getXVal();d.setXVal(g);d.setYVal(b.getYVal());if(null==c)return!0;b=JSV.common.Coordinate.getNearestIndexForX(a,g);c.setXVal(a[b].getXVal());c.setYVal(a[b].getYVal());
return!0},"~A,JSV.common.Coordinate,JSV.common.Coordinate,JSV.common.Coordinate");c$.shiftX=c(c$,"shiftX",function(a,b){for(var d=a.length;0<=--d;)a[d].xVal+=b},"~A,~N");c$.getNearestXWithYAbove=c(c$,"getNearestXWithYAbove",function(a,b,d,c,g){b=JSV.common.Coordinate.getNearestIndexForX(a,b);var f=c?-1:1;if(g)for(;b<a.length&&0>f*(a[b].yVal-d);)b++;else for(;0<=b&&0>f*(a[b].yVal-d);)b--;return-1==b||b==a.length?NaN:JSV.common.Coordinate.findXForPeakNearest(a,a[b].getXVal(),c)},"~A,~N,~N,~B,~B");c$.c=
c$.prototype.c=new JSV.common.CoordComparator});m("JSV.common");w(["java.lang.Enum"],"JSV.common.ExportType",null,function(){c$=z(JSV.common,"ExportType",Enum);c$.getType=c(c$,"getType",function(a){a=a.toUpperCase();if(a.equalsIgnoreCase("Original..."))return JSV.common.ExportType.SOURCE;if(a.startsWith("XML"))return JSV.common.ExportType.AML;for(var b,d=0,c=JSV.common.ExportType.values();d<c.length&&((b=c[d])||1);d++)if(b.name().equals(a))return b;return JSV.common.ExportType.UNK},"~S");c$.isExportMode=
c(c$,"isExportMode",function(a){return JSV.common.ExportType.getType(a)!==JSV.common.ExportType.UNK},"~S");x(c$,"UNK",0,[]);x(c$,"SOURCE",1,[]);x(c$,"DIF",2,[]);x(c$,"FIX",3,[]);x(c$,"SQZ",4,[]);x(c$,"PAC",5,[]);x(c$,"XY",6,[]);x(c$,"DIFDUP",7,[]);x(c$,"PNG",8,[]);x(c$,"JPG",9,[]);x(c$,"SVG",10,[]);x(c$,"SVGI",11,[]);x(c$,"CML",12,[]);x(c$,"AML",13,[]);x(c$,"PDF",14,[])});m("JSV.common");w("JSV.common.XYScaleConverter java.util.Hashtable JU.BS $.Lst JSV.common.Coordinate JSV.dialog.JSVDialog".split(" "),
"JSV.common.GraphSet","java.lang.Boolean $.Double $.Float JU.DF $.PT JSV.common.Annotation $.ColorParameters $.ColoredAnnotation $.ImageView $.Integral $.IntegralData $.Measurement $.MeasurementData $.PanelData $.Parameters $.PeakData $.PeakPickEvent $.PlotWidget $.ScaleData $.ScriptToken $.Spectrum $.ViewData JU.Logger".split(" "),function(){c$=r(function(){this.gs2dLinkedY=this.gs2dLinkedX=null;this.cur1D2Locked=!1;this.spectra=this.highlights=null;this.allowStacking=this.isSplittable=!0;this.widgets=
this.graphsTemp=this.pendingIntegral=this.pendingMeasurement=this.lastAnnotation=this.selectedSpectrumIntegrals=this.selectedSpectrumMeasurements=this.annotations=null;this.haveSingleYScale=this.isLinked=!1;this.iSpectrumClicked=this.iSpectrumMovedTo=0;this.iSpectrumSelected=-1;this.stackSelected=!1;this.viewData=this.bsSelected=null;this.reversePlot=!1;this.nSplit=1;this.yStackOffsetPercent=0;this.showAllStacked=!0;this.pd=this.imageView=this.viewList=null;this.sticky2Dcursor=!1;this.nSpectra=0;
this.fracY=this.fracX=1;this.fY0=this.fX0=0;this.cur2Dy=this.cur1D2x2=this.cur1D2x1=this.cur2Dx1=this.cur2Dx0=this.pin2Dy01=this.pin2Dx01=this.pin2Dy1=this.pin2Dy0=this.pin2Dx1=this.pin2Dx0=this.pin1Dy01=this.pin1Dx01=this.pin1Dy1=this.pin1Dy0=this.pin1Dx1=this.pin1Dx0=this.zoomBox2D=this.zoomBox1D=null;this.xPixels0=this.xPixel10=this.yPixels=this.xPixels=this.yPixel000=this.yPixel11=this.xPixel11=this.yPixel00=this.xPixel00=this.yHArrows=this.xHArrows=this.xVArrows=this.yPixel1=this.xPixel1=this.yPixel0=
this.xPixel0=0;this.allowStackedYScale=!0;this.drawXAxisLeftToRight=!1;this.xAxisLeftToRight=!0;this.iPreviousSpectrumClicked=-1;this.zoomEnabled=this.$haveSelectedSpectrum=!1;this.currentZoomIndex=0;this.lastClickX=NaN;this.lastPixelX=2147483647;this.bottom=this.left=this.top=this.right=this.width=this.height=0;this.coordTemp=this.piMouseOver=null;this.FONT_PLAIN=0;this.FONT_BOLD=1;this.FONT_ITALIC=2;this.is2DSpectrum=!1;this.selectedIntegral=this.selectedMeasurement=null;this.lastXMax=NaN;this.lastSpecClicked=
-1;this.inPlotMove=!1;this.xPixelMovedTo2=this.xPixelMovedTo=-1;this.xValueMovedTo=this.yValueMovedTo=0;this.haveLeftRightArrows=!1;this.yPixelPlot1=this.yPixelPlot0=this.xPixelPlot0=this.xPixelPlot1=0;this.nextClickForSetPeak=!1;this.mapX=null;R("JSV.common.GraphSet.Highlight")||JSV.common.GraphSet.$GraphSet$Highlight$();this.triggered=!0;this.gMain=this.g2d=this.plotColors=this.image2D=this.jsvp=this.aIntegrationRatios=this.dialogs=null;t(this,arguments)},JSV.common,"GraphSet",null,JSV.common.XYScaleConverter);
I(c$,function(){this.highlights=new JU.Lst;this.spectra=new JU.Lst;this.graphsTemp=new JU.Lst;this.bsSelected=new JU.BS;this.coordTemp=new JSV.common.Coordinate;this.mapX=new java.util.Hashtable});u(c$,function(a){this.pd=a;this.jsvp=a.jsvp;this.g2d=a.g2d},"JSV.common.PanelData");c(c$,"setSpectrumMovedTo",function(a){return this.iSpectrumMovedTo=a},"~N");c(c$,"setSpectrumClicked",function(a){this.stackSelected=this.showAllStacked;if(0>a||this.iSpectrumClicked!=a)this.lastClickX=NaN,this.lastPixelX=
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"JSV.common.Annotation.AType");c(c$,"dispose",function(){this.widgets=this.graphsTemp=this.imageView=this.pendingMeasurement=this.lastAnnotation=this.annotations=this.viewList=this.viewData=this.spectra=null;this.disposeImage();if(null!=this.dialogs)for(var a,b=this.dialogs.entrySet().iterator();b.hasNext()&&((a=b.next())||1);){var d=a.getValue();n(d,JSV.dialog.JSVDialog)&&d.dispose()}this.dialogs=null});c(c$,"isDrawNoSpectra",function(){return-2147483648==this.iSpectrumSelected});c(c$,"getFixedSelectedSpectrumIndex",
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s(this.top/2);this.yPixel1=this.yPixel11-s(this.bottom/2);this.yPixels=this.yPixel1-this.yPixel0+1;null!=this.imageView&&this.is2DSpectrum&&(this.setImageWindow(),this.pd.display1D?(this.xPixels=s(Math.floor(0.8*(this.pd.display1D?1*(this.xPixels0-this.imageView.xPixels)/this.xPixels0:1)*this.xPixels0)),this.xPixel1=this.xPixel0+this.xPixels-1):(this.xPixels=0,this.xPixel1=this.imageView.xPixel0-30))},"~N");c(c$,"hasPoint",function(a,b){return a>=this.xPixel00&&a<=this.xPixel11&&b>=this.yPixel000&&
b<=this.yPixel11*this.nSplit},"~N,~N");c(c$,"isInPlotRegion",function(a,b){return a>=this.xPixel0&&a<=this.xPixel1&&b>=this.yPixel0&&b<=this.yPixel1},"~N,~N");c(c$,"getSplitPoint",function(a){return Math.max(0,Math.min(s((a-this.yPixel000)/(this.yPixel11-this.yPixel00)),this.nSplit-1))},"~N");c(c$,"isSplitWidget",function(a,b){return this.isSplittable&&a>=this.xPixel11-20&&b>=this.yPixel00+1&&a<=this.xPixel11-10&&b<=this.yPixel00+11},"~N,~N");c(c$,"initGraphSet",function(a,b){null==JSV.common.GraphSet.veryLightGrey&&
(JSV.common.GraphSet.veryLightGrey=this.g2d.getColor3(200,200,200));this.setPlotColors(JSV.common.ColorParameters.defaultPlotColors);this.xAxisLeftToRight=this.getSpectrumAt(0).shouldDisplayXAxisIncreasing();this.setDrawXAxis();var d=D(this.nSpectra,0),c=D(this.nSpectra,0);this.bsSelected.setBits(0,this.nSpectra);this.allowStackedYScale=!0;0>=b&&(b=2147483647);this.isSplittable=1<this.nSpectra;this.showAllStacked=(this.allowStacking=this.spectra.get(0).isStackable())&&1<this.nSpectra;for(var g=0;g<
this.nSpectra;g++){var f=this.spectra.get(g).getXYCoords().length-1;d[g]=JSV.common.Coordinate.intoRange(a,0,f);c[g]=JSV.common.Coordinate.intoRange(b,0,f);this.allowStackedYScale=(new Boolean(this.allowStackedYScale&(this.spectra.get(g).getYUnits().equals(this.spectra.get(0).getYUnits())&&this.spectra.get(g).getUserYFactor()==this.spectra.get(0).getUserYFactor()))).valueOf()}this.getView(0,0,0,0,d,c,null,null);this.viewList=new JU.Lst;this.viewList.addLast(this.viewData)},"~N,~N");c(c$,"getView",
function(a,b,d,c,g,f,j,h){var l=0==this.graphsTemp.size()?this.spectra:this.graphsTemp,q=this.getSpectrumAt(0).getSubSpectra(),m=null==q||2==q.size()&&q.get(1).isImaginary(),n=!this.getSpectrumAt(0).is1D();m&&d==c?l=this.spectra:d==c&&(this.viewData=new JSV.common.ViewData(q,d,c,this.getSpectrum().isContinuous()),l=null);null!=l&&(this.viewData=new JSV.common.ViewData(l,d,c,g,f,this.getSpectrumAt(0).isContinuous(),n),a!=b&&this.getScale().setXRange(a,b));null!=j&&(JSV.common.ScaleData.copyScaleFactors(j,
this.viewData.getScaleData()),null!=h&&JSV.common.ScaleData.copyYScales(h,this.viewData.getScaleData()),this.getCurrentView())},"~N,~N,~N,~N,~A,~A,~A,~A");c(c$,"isNearby",function(a,b,d,c){var g=a.getXVal(),f=d.toPixelX(g);a=this.toPixelY(a.getYVal());g=b.getXVal();d=d.toPixelX(g);b=this.toPixelY(b.getYVal());return Math.abs(f-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$,"toPixelX0",
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"getXPixels",function(){return this.xPixels});h(c$,"getYPixels",function(){return this.yPixels});c(c$,"getScale",function(){return this.viewData.getScale()});c(c$,"toPixelYint",function(a){return this.yPixel1-s(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.remove(c);0<a.text.length&&(!d||!b)&&this.annotations.addLast(a)},"JSV.common.Annotation,~B");c(c$,"setImageWindow",function(){this.imageView.setPixelWidthHeight(s((this.pd.display1D?0.6:1)*this.xPixels0),this.yPixels);this.imageView.setXY0(this.getSpectrumAt(0),s(Math.floor(this.xPixel10-this.imageView.xPixels)),
this.yPixel0)});c(c$,"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)){var c=this.toX(a),g=this.toY(b),f=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(f,g);this.pd.repaint();break;
case 1:case -2:case -3:for(f=null!=this.pendingMeasurement&&this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,-1));f;){this.setScale(this.getSpectrumIndex(this.pendingMeasurement.spec));if(3!=d){if(!this.findNearestMaxMin()){f=!1;break}a=this.xPixelMovedTo}c=this.toX(a);g=this.toY(b);this.pendingMeasurement.setPt2(c,g);if(0==this.pendingMeasurement.text.length){f=!1;break}this.setMeasurement(this.pendingMeasurement);if(1!=d){f=!1;break}this.setSpectrumClicked(this.getSpectrumIndex(this.pendingMeasurement.spec));
this.pendingMeasurement=(new JSV.common.Measurement).setM1(c,g,this.pendingMeasurement.spec);break}f||(this.pendingMeasurement=null);this.pd.repaint();break;case 5:this.findNearestMaxMin()?(a=this.getFixedSelectedSpectrumIndex(),Double.isNaN(this.lastXMax)||this.lastSpecClicked!=a||null==this.pendingMeasurement?(this.lastXMax=this.xValueMovedTo,this.lastSpecClicked=a,this.pendingMeasurement=(new JSV.common.Measurement).setM1(this.xValueMovedTo,this.yValueMovedTo,this.spectra.get(a))):(this.pendingMeasurement.setPt2(this.xValueMovedTo,
this.yValueMovedTo),0<this.pendingMeasurement.text.length&&this.setMeasurement(this.pendingMeasurement),this.pendingMeasurement=null,this.lastXMax=NaN)):this.lastXMax=NaN}}else this.pendingMeasurement=null},"~N,~N,~N");c(c$,"checkIntegralNormalizationClick",function(a,b){if(null==this.selectedSpectrumIntegrals)return!1;var c=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5);if(null==c)return!1;this.selectedIntegral=c;this.pd.normalizeIntegral();this.updateDialog(JSV.common.Annotation.AType.Integration,
-1);this.setSpectrumClicked(this.getSpectrumIndex(c.spec));return!0},"~N,~N");c(c$,"getNearestPeak",function(a,b,c){var e=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),b,c,a.isInverted(),!1);a=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),b,c,a.isInverted(),!0);return Double.isNaN(e)?a:Double.isNaN(a)?e:Math.abs(e-b)<Math.abs(a-b)?e:a},"JSV.common.Spectrum,~N,~N");c(c$,"findMeasurement",function(a,b,c,e){if(null==a||0==a.size())return null;if(0==e){var g=this.findMeasurement(a,
b,c,-1);return null!=g||n(a.get(0),JSV.common.Integral)?g:this.findMeasurement(a,b,c,-2)}for(var f=a.size();0<=--f;){var g=a.get(f),j,h,l,q;n(g,JSV.common.Integral)?(j=h=this.toPixelX(g.getXVal2()),l=this.toPixelYint(g.getYVal()),q=this.toPixelYint(g.getYVal2())):(j=this.toPixelX(g.getXVal()),h=this.toPixelX(g.getXVal2()),l=q=-2==e?this.yPixel1-2:this.toPixelY(g.getYVal()));switch(e){case 1:if(4>Math.abs(b-j)+Math.abs(c-l))return g;break;case 2:if(4>Math.abs(b-h)+Math.abs(c-q))return g;break;case -5:l=
q=s((l+q)/2),h=j+20;default:if(JSV.common.GraphSet.isOnLine(b,c,j,l,h,q))return g}}return null},"JSV.common.MeasurementData,~N,~N,~N");c(c$,"setMeasurement",function(a){var b=this.getSpectrumIndex(a.spec),c=this.getDialog(JSV.common.Annotation.AType.Measurements,b);null==c&&this.addDialog(b,JSV.common.Annotation.AType.Measurements,c=new JSV.common.MeasurementData(JSV.common.Annotation.AType.Measurements,a.spec));c.getData().addLast(a.copyM());this.updateDialog(JSV.common.Annotation.AType.Measurements,
-1)},"JSV.common.Measurement");c(c$,"checkArrowUpDownClick",function(a,b){var c=!1,e=this.isArrowClick(a,b,3)?JSV.common.GraphSet.RT2:this.isArrowClick(a,b,4)?1/JSV.common.GraphSet.RT2:0;if(0!=e){1<this.nSplit&&this.setSpectrumSelected(this.iSpectrumMovedTo);if((1==this.nSpectra||0<=this.iSpectrumSelected)&&this.spectra.get(this.getFixedSelectedSpectrumIndex()).isTransmittance())e=1/e;this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,e);c=!0}else this.isArrowClick(a,b,-1)&&
(this.resetViewCompletely(),c=!0);c&&(null!=this.imageView&&(this.update2dImage(!1),this.resetPinsFromView()),this.pd.taintedAll=!0);return c},"~N,~N");c(c$,"resetViewCompletely",function(){this.clearViews();this.showAllStacked&&!this.stackSelected&&this.closeDialogsExcept(JSV.common.Annotation.AType.NONE);this.viewData.resetScaleFactors();this.updateDialogs()});c(c$,"checkArrowLeftRightClick",function(a,b){if(this.haveLeftRightArrows){var c=this.isArrowClick(a,b,1)?-1:this.isArrowClick(a,b,2)?1:
0;if(0!=c)return this.setSpectrumClicked((this.iSpectrumSelected+c)%this.nSpectra),!0;if(this.isArrowClick(a,b,0)){if(this.showAllStacked)return this.showAllStacked=!1,this.setSpectrumClicked(this.getFixedSelectedSpectrumIndex()),!0;this.showAllStacked=this.allowStacking;this.setSpectrumSelected(-1);this.stackSelected=!1}}return!1},"~N,~N");c(c$,"isArrowClick",function(a,b,c){switch(c){case 3:case 4:case -1:return c=s((this.yPixel00+this.yPixel11)/2)+15*(3==c?-1:4==c?1:0),10>Math.abs(this.xVArrows-
a)&&10>Math.abs(c-b);case 1:case 2:case 0:return c=this.xHArrows+15*(1==c?-1:2==c?1:0),10>Math.abs(c-a)&&10>Math.abs(this.yHArrows-b)}return!1},"~N,~N,~N");c(c$,"setWidgetValueByUser",function(a){var b;b=a===this.cur2Dy?""+this.imageView.toSubspectrumIndex(a.yPixel0):a===this.pin1Dx01?""+Math.min(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal())+" - "+Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()):a===this.pin1Dy01?""+Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal())+" - "+Math.max(this.pin1Dy0.getYVal(),
this.pin1Dy1.getYVal()):a===this.pin2Dx01?""+Math.min(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal())+" - "+Math.max(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal()):a===this.pin2Dy01?""+s(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+s(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):""+a.getValue();b=this.pd.getInput("New value?","Set Slider",b);if(null!=b){b=b.trim();try{if(a===this.pin1Dx01||a===this.pin1Dy01||a===this.pin2Dx01||a===this.pin2Dy01){var c=b.indexOf("-",1);
if(!(0>c)){var e=Double.$valueOf(b.substring(0,c)).doubleValue(),g=Double.$valueOf(b.substring(c+1)).doubleValue();a===this.pin1Dx01?this.doZoom(e,this.pin1Dy0.getYVal(),g,this.pin1Dy1.getYVal(),!0,!1,!1,!0,!0):a===this.pin1Dy01?this.doZoom(this.pin1Dx0.getXVal(),e,this.pin1Dx1.getXVal(),g,null==this.imageView,null==this.imageView,!1,!1,!0):a===this.pin2Dx01?(this.imageView.setView0(this.imageView.toPixelX0(e),this.pin2Dy0.yPixel0,this.imageView.toPixelX0(g),this.pin2Dy1.yPixel0),this.doZoom(e,this.pin1Dy0.getYVal(),
g,this.pin1Dy1.getYVal(),!1,!1,!1,!0,!0)):a===this.pin2Dy01&&(this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.toPixelY0(e),this.pin2Dx1.xPixel0,this.imageView.toPixelY0(g)),this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!1,!0))}}else{var f=Double.$valueOf(b).doubleValue();a.isXtype?(g=a===this.pin1Dx0||a===this.cur2Dx0||a===this.pin2Dx0?this.pin1Dx1.getXVal():
this.pin1Dx0.getXVal(),this.doZoom(f,0,g,0,!a.is2D,!1,!1,!0,!0)):a===this.cur2Dy?this.setCurrentSubSpectrum(s(f)):a===this.pin2Dy0||a===this.pin2Dy1?(g=a===this.pin2Dy0?this.pin2Dy1.yPixel0:this.pin2Dy0.yPixel0,this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.subIndexToPixelY(s(f)),this.pin2Dx1.xPixel0,g)):(g=a===this.pin1Dy0?this.pin1Dy1.getYVal():this.pin1Dy0.getYVal(),this.doZoom(this.pin1Dx0.getXVal(),f,this.pin1Dx1.getXVal(),g,null==this.imageView,null==this.imageView,!1,!1,!0))}}catch(j){if(!y(j,
Exception))throw j;}}},"JSV.common.PlotWidget");c(c$,"removeAllHighlights",function(a){if(null==a)this.highlights.clear();else for(var b=this.highlights.size();0<=--b;)this.highlights.get(b).spectrum===a&&this.highlights.remove(b)},"JSV.common.Spectrum");c(c$,"setCoordClicked",function(a,b,c){0==c&&(this.nextClickForSetPeak=!1);if(Double.isNaN(b))return this.pd.coordClicked=null,this.pd.coordsClicked=null;this.pd.coordClicked=(new JSV.common.Coordinate).set(this.lastClickX=b,c);this.pd.coordsClicked=
this.getSpectrum().getXYCoords();this.pd.xPixelClicked=this.lastPixelX=a;return this.pd.coordClicked},"~N,~N,~N");c(c$,"setWidgets",function(a,b,c){if(a||null==this.pin1Dx0)null==this.zoomBox1D?this.newPins():this.resetPinPositions();this.setDerivedPins(b);this.setPinSliderPositions(c)},"~B,~N,~B");c(c$,"newPins",function(){this.zoomBox1D=new JSV.common.PlotWidget("zoomBox1D");this.pin1Dx0=new JSV.common.PlotWidget("pin1Dx0");this.pin1Dx1=new JSV.common.PlotWidget("pin1Dx1");this.pin1Dy0=new JSV.common.PlotWidget("pin1Dy0");
this.pin1Dy1=new JSV.common.PlotWidget("pin1Dy1");this.pin1Dx01=new JSV.common.PlotWidget("pin1Dx01");this.pin1Dy01=new JSV.common.PlotWidget("pin1Dy01");this.cur1D2x1=new JSV.common.PlotWidget("cur1D2x1");this.cur1D2x1.color=JSV.common.ScriptToken.PEAKTABCOLOR;this.cur1D2x2=new JSV.common.PlotWidget("cur1D2x2");this.cur1D2x2.color=JSV.common.ScriptToken.PEAKTABCOLOR;if(null!=this.imageView){this.zoomBox2D=new JSV.common.PlotWidget("zoomBox2D");this.pin2Dx0=new JSV.common.PlotWidget("pin2Dx0");this.pin2Dx1=
new JSV.common.PlotWidget("pin2Dx1");this.pin2Dy0=new JSV.common.PlotWidget("pin2Dy0");this.pin2Dy1=new JSV.common.PlotWidget("pin2Dy1");this.pin2Dx01=new JSV.common.PlotWidget("pin2Dx01");this.pin2Dy01=new JSV.common.PlotWidget("pin2Dy01");this.cur2Dx0=new JSV.common.PlotWidget("cur2Dx0");this.cur2Dx1=new JSV.common.PlotWidget("cur2Dx1");this.cur2Dy=new JSV.common.PlotWidget("cur2Dy");this.pin2Dy0.setY(0,this.imageView.toPixelY0(0));var a=this.getSpectrumAt(0).getSubSpectra().size();this.pin2Dy1.setY(a,
this.imageView.toPixelY0(a))}this.setWidgetX(this.pin1Dx0,this.getScale().minX);this.setWidgetX(this.pin1Dx1,this.getScale().maxX);this.setWidgetY(this.pin1Dy0,this.getScale().minY);this.setWidgetY(this.pin1Dy1,this.getScale().maxY);this.widgets=[this.zoomBox1D,this.zoomBox2D,this.pin1Dx0,this.pin1Dx01,this.pin1Dx1,this.pin1Dy0,this.pin1Dy01,this.pin1Dy1,this.pin2Dx0,this.pin2Dx01,this.pin2Dx1,this.pin2Dy0,this.pin2Dy01,this.pin2Dy1,this.cur2Dx0,this.cur2Dx1,this.cur2Dy,this.cur1D2x1,this.cur1D2x2]});
c(c$,"setWidgetX",function(a,b){a.setX(b,this.toPixelX0(b))},"JSV.common.PlotWidget,~N");c(c$,"setWidgetY",function(a,b){a.setY(b,this.toPixelY0(b))},"JSV.common.PlotWidget,~N");c(c$,"resetPinsFromView",function(){null!=this.pin1Dx0&&(this.setWidgetX(this.pin1Dx0,this.getScale().minXOnScale),this.setWidgetX(this.pin1Dx1,this.getScale().maxXOnScale),this.setWidgetY(this.pin1Dy0,this.getScale().minYOnScale),this.setWidgetY(this.pin1Dy1,this.getScale().maxYOnScale))});c(c$,"resetPinPositions",function(){this.resetX(this.pin1Dx0);
this.resetY(this.pin1Dy0);this.resetY(this.pin1Dy1);null==this.imageView?(null!=this.gs2dLinkedX&&this.resetX(this.cur1D2x1),null!=this.gs2dLinkedY&&this.resetX(this.cur1D2x2)):(this.pin2Dy0.setY(this.pin2Dy0.getYVal(),this.imageView.toPixelY0(this.pin2Dy0.getYVal())),this.pin2Dy1.setY(this.pin2Dy1.getYVal(),this.imageView.toPixelY0(this.pin2Dy1.getYVal())))});c(c$,"resetX",function(a){this.setWidgetX(a,a.getXVal())},"JSV.common.PlotWidget");c(c$,"resetY",function(a){this.setWidgetY(a,a.getYVal())},
"JSV.common.PlotWidget");c(c$,"setPinSliderPositions",function(a){this.pin1Dx0.yPixel0=this.pin1Dx1.yPixel0=this.pin1Dx01.yPixel0=this.yPixel0-5;this.pin1Dx0.yPixel1=this.pin1Dx1.yPixel1=this.pin1Dx01.yPixel1=this.yPixel0;this.cur1D2x1.yPixel1=this.cur1D2x2.yPixel1=this.yPixel0-5;this.cur1D2x1.yPixel0=this.cur1D2x2.yPixel0=this.yPixel1+6;null==this.imageView?(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=this.pin1Dy01.xPixel0=this.xPixel1+5,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=
this.xPixel1):(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=this.pin1Dy01.xPixel0=this.imageView.xPixel1+15,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=this.imageView.xPixel1+10,this.pin2Dx0.yPixel0=this.pin2Dx1.yPixel0=this.pin2Dx01.yPixel0=this.yPixel0-5,this.pin2Dx0.yPixel1=this.pin2Dx1.yPixel1=this.pin2Dx01.yPixel1=this.yPixel0,this.pin2Dy0.xPixel0=this.pin2Dy1.xPixel0=this.pin2Dy01.xPixel0=this.imageView.xPixel1+5,this.pin2Dy0.xPixel1=this.pin2Dy1.xPixel1=this.pin2Dy01.xPixel1=
this.imageView.xPixel1,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=this.yPixel1+6,this.cur2Dx0.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=this.yPixel1+6,this.cur2Dx1.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dy.xPixel0=a?s((this.xPixel1+this.imageView.xPixel0)/2):this.imageView.xPixel0-6,this.cur2Dy.xPixel1=this.imageView.xPixel1+5)},"~B");c(c$,"setDerivedPins",function(a){this.triggered=!0;null!=this.gs2dLinkedX&&this.cur1D2x1.setX(this.cur1D2x1.getXVal(),
this.toPixelX(this.cur1D2x1.getXVal()));null!=this.gs2dLinkedY&&this.cur1D2x2.setX(this.cur1D2x2.getXVal(),this.toPixelX(this.cur1D2x2.getXVal()));this.pin1Dx01.setX(0,s((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2));this.pin1Dy01.setY(0,s((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,s((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,s((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2));this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=this.imageView.subIndexToPixelY(a);
this.pin2Dx01.setEnabled(Math.min(this.pin2Dx0.xPixel0,this.pin2Dx1.xPixel0)!=this.imageView.xPixel0||Math.max(this.pin2Dx0.xPixel0,this.pin2Dx1.xPixel1)!=this.imageView.xPixel1);this.pin2Dy01.setEnabled(Math.min(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel0)!=this.yPixel0||Math.max(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel1)!=this.yPixel1)}},"~N");c(c$,"doZoom",function(a,b,c,e,g,f,j,h,l){a==c?(a=this.getScale().minXOnScale,c=this.getScale().maxXOnScale):this.isLinked&&h&&this.pd.doZoomLinked(this,a,
c,l,j,g);a>c&&(h=a,a=c,c=h);b>e&&(h=b,b=e,e=h);h=!g&&null!=this.imageView&&(this.imageView.minZ!=b||this.imageView.maxZ!=e);if(this.zoomEnabled||h){if(j){if(!this.getScale().isInRangeX(a)&&!this.getScale().isInRangeX(c))return;this.getScale().isInRangeX(a)?this.getScale().isInRangeX(c)||(c=this.getScale().maxX):a=this.getScale().minX}this.pd.taintedAll=!0;j=this.viewData.getScaleData();var q=D(this.nSpectra,0),m=D(this.nSpectra,0);this.graphsTemp.clear();var n=this.getSpectrumAt(0).getSubSpectra(),
n=null==n||2==n.size();if(this.getSpectrumAt(0).is1D()&&!n){if(this.graphsTemp.addLast(this.getSpectrum()),!JSV.common.ScaleData.setDataPointIndices(this.graphsTemp,a,c,3,q,m))return}else if(!JSV.common.ScaleData.setDataPointIndices(this.spectra,a,c,3,q,m))return;if(n=b==e)g=!h&&g?g=this.getScale().spectrumScaleFactor:1,1E-4>Math.abs(g-1)&&(b=this.getScale().minYOnScale,e=this.getScale().maxYOnScale);g=null;if(n||f)this.getCurrentView(),g=this.viewData.getNewScales(this.iSpectrumSelected,n,b,e);this.getView(a,
c,b,e,q,m,j,g);this.setXPixelMovedTo(1E10,1.7976931348623157E308,0,0);this.setWidgetX(this.pin1Dx0,a);this.setWidgetX(this.pin1Dx1,c);this.setWidgetY(this.pin1Dy0,b);this.setWidgetY(this.pin1Dy1,e);null==this.imageView?this.updateDialogs():(a=this.getSpectrumAt(0).getSubIndex(),c=this.imageView.fixSubIndex(a),c!=a&&this.setCurrentSubSpectrum(c),h&&this.update2dImage(!1));l&&this.addCurrentZoom()}},"~N,~N,~N,~N,~B,~B,~B,~B,~B");c(c$,"updateDialogs",function(){this.updateDialog(JSV.common.Annotation.AType.PeakList,
-1);this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)});c(c$,"setCurrentSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.setCurrentSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(c$,"addCurrentZoom",function(){if(this.viewList.size()>this.currentZoomIndex+1)for(var a=this.viewList.size()-1;a>this.currentZoomIndex;a--)this.viewList.remove(a);this.viewList.addLast(this.viewData);
this.currentZoomIndex++});c(c$,"setZoomTo",function(a){this.currentZoomIndex=a;this.viewData=this.viewList.get(a);this.resetPinsFromView()},"~N");c(c$,"clearViews",function(){this.isLinked&&this.pd.clearLinkViews(this);this.setZoom(0,0,0,0);for(var a=this.viewList.size();1<=--a;)this.viewList.remove(a)});c(c$,"drawAll",function(a,b,c,e,g,f){this.g2d=this.pd.g2d;this.gMain=a;var h=this.getSpectrumAt(0).getSubIndex();this.is2DSpectrum=!this.getSpectrumAt(0).is1D()&&(this.isLinked||this.pd.getBoolean(JSV.common.ScriptToken.DISPLAY2D))&&
(null!=this.imageView||this.get2DImage());null!=this.imageView&&f&&(this.pd.isPrinting&&this.g2d!==this.pd.g2d0&&this.g2d.newGrayScaleImage(a,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,this.imageView.getBuffer()),this.is2DSpectrum&&this.setPositionForFrame(e),this.draw2DImage());var k=this.stackSelected||!this.showAllStacked?this.iSpectrumSelected:-1,l=!this.showAllStacked||1==this.nSpectra||0<=k,m=null==this.imageView||this.pd.display1D,p=0<=k?1:0,n=this.getFixedSelectedSpectrumIndex();
if(m&&f&&(this.fillBox(a,this.xPixel0,this.yPixel0,this.xPixel1,this.yPixel1,JSV.common.ScriptToken.PLOTAREACOLOR),0>k)){l=!0;for(k=0;k<this.nSpectra;k++)this.doPlot(k,e)&&0!=p++&&(l=(new Boolean(l&this.viewData.areYScalesSame(k-1,k))).valueOf())}var s=1==this.nSpectra?0:!this.showAllStacked?this.iSpectrumMovedTo:this.iSpectrumSelected;c=c===a?b:c;if(f){var k=!this.isLinked&&this.isSplittable&&(1==this.nSplit||this.pd.currentSplitPoint==e),r=this.zoomEnabled&&!this.isDrawNoSpectra()&&this.pd.isCurrentGraphSet(this)&&
this.spectra.get(0).isScalable()&&(k||1==this.nSpectra)&&(1==this.nSplit||this.pd.currentSplitPoint==this.iSpectrumMovedTo);this.drawFrame(a,s,k,this.isSplittable,r)}if(this.pd.isCurrentGraphSet(this)&&e==this.pd.currentSplitPoint&&(2>p||0<=this.iSpectrumSelected))this.$haveSelectedSpectrum=!0;this.haveSingleYScale=this.showAllStacked&&1<this.nSpectra?this.allowStackedYScale&&l:!0;if(m){l=B(this.yPixels*(this.yStackOffsetPercent/100));this.haveLeftRightArrows=!1;for(r=k=0;k<this.nSpectra;k++)if(this.doPlot(k,
e)){var s=this.stackSelected&&0<=this.iSpectrumSelected&&this.iSpectrumSelected!=k,t=!this.reversePlot&&this.getShowAnnotation(JSV.common.Annotation.AType.Integration,k)&&(!this.showAllStacked||this.iSpectrumSelected==k)?this.getDialog(JSV.common.Annotation.AType.Integration,k).getData():null;this.setScale(k);var u=this.spectra.get(k);1<this.nSplit&&(n=k);var w=!s&&(1==this.nSplit||this.showAllStacked||this.iSpectrumSelected==e),x=w&&this.$haveSelectedSpectrum&&k==n;w&&(this.resetPinsFromView(),this.drawWidgets(b,
c,h,g,m,x,!1));this.haveSingleYScale&&(k==n&&f)&&(this.drawGrid(a),this.pd.isPrinting&&1<this.nSplit&&this.drawSpectrumSource(a,k));w&&this.drawWidgets(b,c,h,!1,m,x,!0);!this.isDrawNoSpectra()&&((1==this.nSpectra||0<=this.iSpectrumSelected)&&(this.haveSingleYScale&&k==n||this.showAllStacked&&this.stackSelected&&k==this.iSpectrumSelected))&&this.drawHighlightsAndPeakTabs(b,c,k);if(f){if((1==p&&0>this.iSpectrumSelected||this.iSpectrumSelected==k&&this.pd.isCurrentGraphSet(this))&&this.pd.titleOn&&!this.pd.titleDrawn)this.pd.drawTitle(a,
this.height,this.width,this.pd.getDrawTitle(this.pd.isPrinting)),this.pd.titleDrawn=!0;this.haveSingleYScale&&k==n&&(this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.YUNITSON)&&this.drawYUnits(a))}w=u.isContinuous();x=(1<this.nSplit?k==this.iSpectrumMovedTo:this.isLinked||k==n)&&!this.pd.isPrinting&&u.isContinuous();f&&this.drawSpectrum(a,k,r,s,t,w,x);this.drawMeasurements(b,k);null!=this.pendingMeasurement&&this.pendingMeasurement.spec===
u&&this.drawMeasurement(b,this.pendingMeasurement);x&&0<=this.xPixelMovedTo&&this.drawSpectrumPointer(b,u,r,t);1<this.nSpectra&&(1==this.nSplit&&this.pd.isCurrentGraphSet(this)&&f)&&(this.haveLeftRightArrows=!0,this.pd.isPrinting||(this.setScale(0),s=this.iSpectrumSelected,2!=this.nSpectra&&(this.setPlotColor(a,(s+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<=s&&(this.setPlotColor(a,
s),this.fillCircle(a,this.xHArrows,this.yHArrows,!0)),this.setCurrentBoxColor(a),this.fillCircle(a,this.xHArrows,this.yHArrows,!1),this.setPlotColor(a,(s+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)));r-=l}f&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&this.drawXScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.XUNITSON)&&this.drawXUnits(a))}else f&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&
this.drawXScale(a,this.imageView),this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this.imageView),0<=h&&this.draw2DUnits(a)),this.drawWidgets(b,c,h,g,m,!0,!1),this.drawWidgets(b,c,h,g,m,!0,!0);null!=this.annotations&&this.drawAnnotations(b,this.annotations,null)},"~O,~O,~O,~N,~B,~B");c(c$,"drawSpectrumSource",function(a,b){this.pd.printFilePath(a,this.pd.thisWidth-this.pd.right,this.yPixel0,this.spectra.get(b).getFilePath())},"~O,~N");c(c$,"doPlot",function(a,b){var c=this.stackSelected&&
0<=this.iSpectrumSelected&&this.iSpectrumSelected!=a,e=this.showAllStacked||-1==this.iSpectrumSelected||this.iSpectrumSelected==a;return 1<this.nSplit?a==b:e&&(!this.pd.isPrinting||!c)},"~N,~N");c(c$,"drawSpectrumPointer",function(a,b,c,e){this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);var g=this.pd.integralShiftMode;null!=e&&((!this.pd.ctrlPressed||this.pd.isIntegralDrag)&&!this.isOnSpectrum(this.pd.mouseX,this.pd.mouseY,-1)?e=null:0==g&&(g=this.getShiftMode(this.pd.mouseX,this.pd.mouseY)));
var f=this.yValueMovedTo;this.yValueMovedTo=null==e?b.getYValueAt(this.xValueMovedTo):e.getPercentYValueAt(this.xValueMovedTo);this.setCoordStr(this.xValueMovedTo,this.yValueMovedTo);0!=g?(this.setPlotColor(a,0),b=0>g?this.yPixelPlot0:this.yPixelPlot1,this.drawHandle(a,0>g?this.xPixelPlot1:this.xPixelPlot0,b,!1)):(null!=e&&this.g2d.setStrokeBold(a,!0),Double.isNaN(f)||null!=this.pendingMeasurement?(this.g2d.drawLine(a,this.xPixelMovedTo,this.yPixel0,this.xPixelMovedTo,this.yPixel1),0<=this.xPixelMovedTo2&&
this.g2d.drawLine(a,this.xPixelMovedTo2,this.yPixel0,this.xPixelMovedTo2,this.yPixel1),this.yValueMovedTo=NaN):(b=null==e?c+this.toPixelY(this.yValueMovedTo):this.toPixelYint(this.yValueMovedTo/100),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixelMovedTo,b-10,this.xPixelMovedTo,b+10)),null!=e&&this.g2d.setStrokeBold(a,!1))},"~O,JSV.common.Spectrum,~N,JSV.common.IntegralData");c(c$,"setScale",function(a){this.viewData.setScale(a,this.xPixels,this.yPixels,this.spectra.get(a).isInverted())},"~N");c(c$,
"draw2DUnits",function(a){var b=this.getSpectrumAt(0).nucleusX,c=this.getSpectrumAt(0).nucleusY;this.setColorFromToken(a,JSV.common.ScriptToken.PLOTCOLOR);this.drawUnits(a,b,this.imageView.xPixel1+5*this.pd.scalingFactor,this.yPixel1,1,1);this.drawUnits(a,c,this.imageView.xPixel0-5*this.pd.scalingFactor,this.yPixel0,1,0)},"~O");c(c$,"drawPeakTabs",function(a,b,c){var e=1==this.nSpectra||0<=this.iSpectrumSelected?c.getPeakList():null;if(null!=e&&0<e.size()){null!=this.piMouseOver&&this.piMouseOver.spectrum===
c&&this.pd.isMouseUp()?(this.g2d.setGraphicsColor(b,this.g2d.getColor4(240,240,240,140)),this.drawPeak(b,this.piMouseOver,0),c.setHighlightedPeak(this.piMouseOver)):c.setHighlightedPeak(null);this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);for(b=e.size();0<=--b;){var g=e.get(b);this.drawPeak(a,g,g===c.getSelectedPeak()?14:7)}}},"~O,~O,JSV.common.Spectrum");c(c$,"drawPeak",function(a,b,c){if(!this.pd.isPrinting){var e=b.getXMin(),g=b.getXMax();e!=g&&this.drawBar(a,b,e,g,null,c)}},"~O,JSV.common.PeakInfo,~N");
c(c$,"drawWidgets",function(a,b,c,e,g,f,h){this.setWidgets(e,c,g);if(!this.pd.isPrinting||!(null==this.imageView?!this.cur1D2Locked:this.sticky2Dcursor)){!this.pd.isPrinting&&!h&&(g?(this.fillBox(a,this.xPixel0,this.pin1Dx0.yPixel1,this.xPixel1,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin1Dx0.xPixel0,this.pin1Dx0.yPixel1,this.pin1Dx1.xPixel0,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.PLOTCOLOR)):(this.fillBox(a,this.imageView.xPixel0,this.pin2Dx0.yPixel1,this.imageView.xPixel1,
this.pin2Dx0.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dx0.xPixel0,this.pin2Dx0.yPixel1,this.pin2Dx1.xPixel0,this.pin2Dx1.yPixel1+2,JSV.common.ScriptToken.PLOTCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,this.yPixel1,this.pin2Dy1.xPixel1+2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,this.pin2Dy0.yPixel1,this.pin2Dy1.xPixel1+2,this.pin2Dy1.yPixel0,JSV.common.ScriptToken.PLOTCOLOR)),this.fillBox(a,this.pin1Dy0.xPixel1,this.yPixel1,this.pin1Dy1.xPixel1+
2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),f&&this.fillBox(a,this.pin1Dy0.xPixel1,this.pin1Dy0.yPixel1,this.pin1Dy1.xPixel1+2,this.pin1Dy1.yPixel0,JSV.common.ScriptToken.PLOTCOLOR));for(c=0;c<this.widgets.length;c++)if(e=this.widgets[c],!(null==e||!e.isPinOrCursor&&!this.zoomEnabled)){var k=e===this.cur1D2x1||e===this.cur1D2x2||e===this.cur2Dx0||e===this.cur2Dx1||e===this.cur2Dy;if((e.isPin||!e.isPinOrCursor)!=h){if(e.is2D){if(e===this.cur2Dx0&&!g)continue}else{var l=e===this.pin1Dy0||e===this.pin1Dy1||
e===this.pin1Dy01;if(null!=this.imageView&&g==l||l&&!f||e===this.cur1D2x1&&null==this.gs2dLinkedX||e===this.cur1D2x2&&null==this.gs2dLinkedY||e===this.zoomBox1D&&(this.pd.isIntegralDrag||0!=this.pd.integralShiftMode))if(!this.isLinked||null!=this.imageView)continue}if(!this.pd.isPrinting||k)e.isPinOrCursor?(this.setColorFromToken(a,e.color),this.g2d.drawLine(a,e.xPixel0,e.yPixel0,e.xPixel1,e.yPixel1),e.isVisible=!0,e.isPin&&this.drawHandle(a,e.xPixel0,e.yPixel0,!e.isEnabled)):e.xPixel1!=e.xPixel0&&
this.fillBox(b,e.xPixel0,e.yPixel0,e.xPixel1,e.yPixel1,e===this.zoomBox1D&&this.pd.shiftPressed?JSV.common.ScriptToken.ZOOMBOXCOLOR2:JSV.common.ScriptToken.ZOOMBOXCOLOR)}}}},"~O,~O,~N,~B,~B,~B,~B");c(c$,"drawBar",function(a,b,c,e,g,f){var h=e+c,k=Math.abs(e-c),l=Math.abs(this.toX(this.xPixel1)-this.toX(this.xPixel0));0<f&&k>l/20&&(k=l/20,c=h/2-k,e=h/2+k);c=this.toPixelX(c);e=this.toPixelX(e);c>e&&(h=c,c=e,e=h);c=this.fixX(c);e=this.fixX(e);3>e-c&&(c-=2,e+=2);null!=b&&b.setPixelRange(c,e);0==f?this.fillBox(a,
c,this.yPixel0,e,this.yPixel0+this.yPixels,g):(this.fillBox(a,c,this.yPixel0,e,this.yPixel0+3,g),null!=b&&(c=s((c+e)/2),this.fillBox(a,c-1,this.yPixel0,c+1,this.yPixel0+f,g)))},"~O,JSV.common.PeakInfo,~N,~N,JSV.common.ScriptToken,~N");c(c$,"drawSpectrum",function(a,b,c,e,g,f,h){var k=this.spectra.get(b);this.drawPlot(a,b,k,f,c,e,null,h);null!=g&&(this.haveIntegralDisplayed(b)&&this.drawPlot(a,b,k,!0,c,!1,g,!0),this.drawIntegralValues(a,b,c));null!=this.getIntegrationRatios(b)&&this.drawAnnotations(a,
this.getIntegrationRatios(b),JSV.common.ScriptToken.INTEGRALPLOTCOLOR)},"~O,~N,~N,~B,JSV.common.IntegralData,~B,~B");c(c$,"getMeasurements",function(a,b){var c=this.getDialog(a,b);return null==c||0==c.getData().size()||!c.getState()?null:c.getData()},"JSV.common.Annotation.AType,~N");c(c$,"drawPlot",function(a,b,c,e,g,f,h,k){var l=null==h?c.getXYCoords():this.getIntegrationGraph(b).getXYCoords(),m=null!=h;h=m?h.getBitSet():null;var p=!m&&!f&&null!=this.pendingIntegral&&this.pendingIntegral.spec===
this.spectra.get(b);k=p||null!=c.fillColor&&k;f=f?-2:m?-1:!this.allowStacking?0:b;this.setPlotColor(a,f);var n=!0,s=this.toPixelY(0);m?k=(new Boolean(k&s==this.fixY(s))).valueOf():s=this.fixY(s);var r=m||k?this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR):null;c=null==r||null==c.fillColor?r:c.fillColor;r=this.viewData.getStartingPointIndex(b);b=this.viewData.getEndingPointIndex(b);if(e){b--;var t=(m||null!=this.pendingIntegral)&&this.g2d.canDoLineTo();t&&this.g2d.doStroke(a,!0);var u=!1;
for(e=r;e<=b;e++){var w=l[e],x=l[e+1],y=m?this.toPixelYint(w.getYVal()):this.toPixelY(w.getYVal());if(-2147483648!=y){var z=m?this.toPixelYint(x.getYVal()):this.toPixelY(x.getYVal());if(-2147483648!=z){var w=w.getXVal(),x=x.getXVal(),B=this.toPixelX(w),C=this.toPixelX(x),y=this.fixY(g+y),z=this.fixY(g+z);m&&(e==r&&(this.xPixelPlot1=B,this.yPixelPlot0=y),this.xPixelPlot0=C,this.yPixelPlot1=z);if(!(C==B&&y==z))if(k&&p&&this.pendingIntegral.overlaps(w,x))null!=c&&(this.g2d.doStroke(a,!1),this.g2d.setGraphicsColor(a,
c)),this.g2d.fillRect(a,Math.min(B,C),Math.min(s,y),Math.max(1,Math.abs(C-B)),Math.abs(s-y)),null!=c&&(this.g2d.doStroke(a,!1),this.g2d.doStroke(a,!0),u=!1,this.setPlotColor(a,f));else if(!(y==z&&y==this.yPixel0)&&(null!=h&&h.get(e)!=n&&(n=h.get(e),t&&u&&(this.g2d.doStroke(a,!1),this.g2d.doStroke(a,!0),u=!1),!this.pd.isPrinting&&0!=this.pd.integralShiftMode?this.setPlotColor(a,0):n?this.setColorFromToken(a,JSV.common.ScriptToken.INTEGRALPLOTCOLOR):this.setPlotColor(a,-3)),!this.pd.isPrinting||n))u?
this.g2d.lineTo(a,C,z):(this.g2d.drawLine(a,B,y,C,z),u=t)}}}t&&this.g2d.doStroke(a,!1)}else{for(e=r;e<=b;e++)m=l[e],z=this.toPixelY(m.getYVal()),-2147483648!=z&&(B=this.toPixelX(m.getXVal()),y=this.toPixelY(Math.max(this.getScale().minYOnScale,0)),y=this.fixY(g+y),z=this.fixY(g+z),y==z&&(y==this.yPixel0||y==this.yPixel1)||this.g2d.drawLine(a,B,y,B,z));this.getScale().isYZeroOnScale()&&(g+=this.toPixelY(this.getScale().spectrumYRef),g==this.fixY(g)&&this.g2d.drawLine(a,this.xPixel1,g,this.xPixel0,
g))}},"~O,~N,JSV.common.Spectrum,~B,~N,~B,JSV.common.IntegralData,~B");c(c$,"drawFrame",function(a,b,c,e,g){if(!this.pd.gridOn||this.pd.isPrinting)if(this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR),this.g2d.drawRect(a,this.xPixel0,this.yPixel0,this.xPixels,this.yPixels),this.pd.isPrinting)return;this.setCurrentBoxColor(a);g&&(0<=b&&(this.setPlotColor(a,b),this.fillArrow(a,3,this.xVArrows,s((this.yPixel00+this.yPixel11)/2)-9,!0),this.fillArrow(a,4,this.xVArrows,s((this.yPixel00+this.yPixel11)/
2)+9,!0),this.setCurrentBoxColor(a)),this.fillArrow(a,3,this.xVArrows,s((this.yPixel00+this.yPixel11)/2)-9,!1),this.fillCircle(a,this.xVArrows,s((this.yPixel00+this.yPixel11)/2),!1),this.fillArrow(a,4,this.xVArrows,s((this.yPixel00+this.yPixel11)/2)+9,!1));if(null==this.imageView&&c){b=this.xPixel00+10;c=this.xPixel11-10;g=this.yPixel00+1;var f=this.yPixel11-2;this.g2d.drawLine(a,b,g,c,g);this.g2d.drawLine(a,c,g,c,f);this.g2d.drawLine(a,b,f,c,f);e&&this.fillBox(a,c-10,g,c,g+10,null)}},"~O,~N,~B,~B,~B");
c(c$,"drawGrid",function(a){if(this.pd.gridOn&&null==this.imageView){this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR);var b;if(Double.isNaN(this.getScale().firstX)){b=this.getScale().maxXOnScale+this.getScale().steps[0]/2;for(var c=this.getScale().minXOnScale;c<b;c+=this.getScale().steps[0]){var e=this.toPixelX(c);this.g2d.drawLine(a,e,this.yPixel0,e,this.yPixel1)}}else{b=1.0001*this.getScale().maxXOnScale;for(c=this.getScale().firstX;c<=b;c+=this.getScale().steps[0])e=this.toPixelX(c),
this.g2d.drawLine(a,e,this.yPixel0,e,this.yPixel1)}for(c=this.getScale().firstY;c<this.getScale().maxYOnScale+this.getScale().steps[1]/2;c+=this.getScale().steps[1])b=this.toPixelY(c),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixel0,b,this.xPixel1,b)}},"~O");c(c$,"drawXScale",function(a,b){this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);this.pd.isPrinting&&this.g2d.drawLine(a,b.getXPixel0(),this.yPixel1,b.getXPixel0()+b.getXPixels()-1,this.yPixel1);for(var c=this.getScale().precision[0],
e=this.pd.setFont(a,b.getXPixels(),0,this.pd.isPrinting?10:12,!1),g=this.yPixel1,f=this.yPixel1+4*this.pd.scalingFactor,h=this.yPixel1+2*this.pd.scalingFactor,e=e.getHeight(),k=b.toPixelX(this.getScale().steps[0])-b.toPixelX(0),l=Math.abs(0.95*k),m=this.getScale().firstX-this.getScale().steps[0],p=1.0001*(this.getScale().maxXOnScale+this.getScale().steps[0]),n=0;2>n;n++){1==n&&JSV.common.ScaleData.fixScale(this.mapX);for(var r=1E10,t=m;t<=p;t+=this.getScale().steps[0]){var k=b.toPixelX(t),u=Double.$valueOf(t),
w;switch(n){case 0:w=JU.DF.formatDecimalDbl(t,c);this.mapX.put(u,w);this.drawTick(a,k,g,f,b);k=Math.abs(r-t);r=this.getScale().minorTickCounts[0];if(0!=r){k/=r;for(w=1;w<r;w++)this.drawTick(a,b.toPixelX(t-w*k),g,h,b)}r=t;continue;case 1:w=this.mapX.get(u);if(null==w||k!=b.fixX(k))continue;var u=this.pd.getStringWidth(w),x=k+s(u/2)==b.fixX(k+s(u/2))?2:0;0<x&&this.g2d.drawString(a,w,k-s(u/x),f+e);t+=Math.floor(u/l)*this.getScale().steps[0]}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(c$,
"drawTick",function(a,b,c,e,g){b==g.fixX(b)&&this.g2d.drawLine(a,b,c,b,e)},"~O,~N,~N,~N,JSV.common.XYScaleConverter");c(c$,"drawYScale",function(a,b){var c=b.getScale(),e=c.precision[1],g=this.pd.setFont(a,b.getXPixels(),0,this.pd.isPrinting?10:12,!1).getHeight(),f=c.maxYOnScale+c.steps[1]/2,h=-2147483648;this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);for(var k=0;2>k;k++){1==k&&JSV.common.ScaleData.fixScale(this.mapX);for(var l=c.firstY;l<f;l+=c.steps[1]){var m=Double.$valueOf(l),p=b.getXPixel0(),
n=b.toPixelY(l);if(n==b.fixY(n)){var r;0==k&&this.g2d.drawLine(a,p,n,p-3*this.pd.scalingFactor,n);if(!(Math.abs(n-h)<=g))switch(h=n,k){case 0:r=JU.DF.formatDecimalDbl(l,e);this.mapX.put(m,r);break;case 1:r=this.mapX.get(m);if(null==r)continue;r.startsWith("0")&&r.contains("E")&&(r="0");this.g2d.drawString(a,r,p-4*this.pd.scalingFactor-this.pd.getStringWidth(r),n+s(g/3))}}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(c$,"drawXUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!0);
null!=b&&this.drawUnits(a,b,this.xPixel1+25*this.pd.scalingFactor,this.yPixel1+5*this.pd.scalingFactor,1,1)},"~O");c(c$,"drawUnits",function(a,b,c,e,g,f){this.setColorFromToken(a,JSV.common.ScriptToken.UNITSCOLOR);this.pd.setFont(a,(null==this.imageView?this:this.imageView).getXPixels(),2,10,!1);this.g2d.drawString(a,b,s(c-this.pd.getStringWidth(b)*g),s(e+this.pd.getFontHeight()*f))},"~O,~S,~N,~N,~N,~N");c(c$,"drawYUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!1);null!=b&&this.drawUnits(a,
b,(this.pd.isPrinting?30:5)*this.pd.scalingFactor,this.yPixel0+(this.pd.isPrinting?0:5)*this.pd.scalingFactor,0,-1)},"~O");c(c$,"drawHighlightsAndPeakTabs",function(a,b,c){var e=this.getMeasurements(JSV.common.Annotation.AType.PeakList,c),g=this.spectra.get(c);if(this.pd.isPrinting)null!=e&&(this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR),this.printPeakList(a,g,e));else{if(null==e){for(var f=0;f<this.highlights.size();f++){var h=this.highlights.get(f);h.spectrum===g&&(this.pd.setHighlightColor(h.color),
this.drawBar(b,null,h.x1,h.x2,JSV.common.ScriptToken.HIGHLIGHTCOLOR,0))}this.drawPeakTabs(a,b,g)}if(null!=e){b=g.isInverted()?this.yPixel1-10*this.pd.scalingFactor:this.yPixel0;this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);for(f=e.size();0<=--f;)g=e.get(f),g=this.toPixelX(g.getXVal()),this.g2d.drawLine(a,g,b,g,b+10*this.pd.scalingFactor);this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,c))&&(b=this.toPixelY(e.getThresh()),b==this.fixY(b)&&!this.pd.isPrinting&&this.g2d.drawLine(a,
this.xPixel0,b,this.xPixel1,b))}}},"~O,~O,~N");c(c$,"printPeakList",function(a,b,c){var e=c.getMeasurementListArray(null);if(0!=e.length){this.pd.setFont(a,this.xPixels,0,8,!1);for(var g=this.pd.getFontHeight(),f=D(c.size(),0),h=D(c.size(),0),k=0,l=5*this.pd.scalingFactor,m=10*this.pd.scalingFactor,p=15*this.pd.scalingFactor,n=25*this.pd.scalingFactor,r=0;r<e.length;r++)h[r]=this.toPixelX(Double.parseDouble(e[r][1])),0==r?f[r]=h[r]:(f[r]=Math.max(f[r-1]+g,h[r]+g),k+=f[r]-h[r]);k/=2*e.length;f[0]-
k<this.xPixel0+n&&(k=f[0]-(this.xPixel0+n));for(r=0;r<e.length;r++)f[r]-=k;r=b.isInverted();b=this.pd.getStringWidth("99.9999");for(var k=6<=e[0].length?this.pd.getStringWidth("99.99"):0,n=r?-1:1,t=(r?this.yPixel1:this.yPixel0)+n*(k+b+p),r=0;r<e.length;r++)this.g2d.drawLine(a,f[r],t,f[r],t+l*n),this.g2d.drawLine(a,f[r],t+l*n,h[r],t+m*n),this.g2d.drawLine(a,h[r],t+m*n,h[r],t+p*n),0<k&&0<e[r][4].length&&this.g2d.drawLine(a,s((f[r]+f[r-1])/2),t-b+l,s((f[r]+f[r-1])/2),t-b-l);t-=2*n*this.pd.scalingFactor;
0<k&&(this.drawStringRotated(a,-90,f[0]-p,t,"  ppm"),this.drawStringRotated(a,-90,f[0]-p,t-b-l," Hz"));for(r=c.size();0<=--r;)this.drawStringRotated(a,-90*n,f[r]+s(n*g/3),t,e[r][1]),0<k&&0<e[r][4].length&&(c=s((f[r]+f[r-1])/2)+s(g/3),this.drawStringRotated(a,-90,c,t-b-l,e[r][4]))}},"~O,JSV.common.Spectrum,JSV.common.PeakData");c(c$,"drawStringRotated",function(a,b,c,e,g){this.g2d.drawStringRotated(a,g,c,e,b)},"~O,~N,~N,~N,~S");c(c$,"drawAnnotations",function(a,b,c){this.pd.setFont(a,this.xPixels,
1,12,!1);for(var e=b.size();0<=--e;){var g=b.get(e);this.setAnnotationColor(a,g,c);var f=(g.is2D?this.imageView:this).toPixelX(g.getXVal()),h=g.isPixels()?s(this.yPixel0+10*this.pd.scalingFactor-g.getYVal()):g.is2D?this.imageView.subIndexToPixelY(s(g.getYVal())):this.toPixelY(g.getYVal());this.g2d.drawString(a,g.text,f+g.offsetX*this.pd.scalingFactor,h-g.offsetY*this.pd.scalingFactor)}},"~O,JU.Lst,JSV.common.ScriptToken");c(c$,"drawIntegralValues",function(a,b,c){var e=this.getMeasurements(JSV.common.Annotation.AType.Integration,
b);if(null!=e){this.pd.isPrinting?this.pd.setFont(a,this.xPixels,0,8,!1):this.pd.setFont(a,this.xPixels,1,12,!1);this.setColorFromToken(a,JSV.common.ScriptToken.INTEGRALPLOTCOLOR);var g=this.pd.getFontHeight();this.g2d.setStrokeBold(a,!0);for(var f=e.size();0<=--f;){var h=e.get(f);if(0!=h.getValue()){var k=this.toPixelX(h.getXVal2()),l=c*this.pd.scalingFactor+this.toPixelYint(h.getYVal()),m=c*this.pd.scalingFactor+this.toPixelYint(h.getYVal2());k!=this.fixX(k)||(l!=this.fixY(l)||m!=this.fixY(m))||
(this.pd.isPrinting||this.g2d.drawLine(a,k,l,k,m),this.g2d.drawString(a,"  "+h.text,k,s((l+m)/2)+s(g/3)))}}this.g2d.setStrokeBold(a,!1)}b==this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumIntegrals=e)},"~O,~N,~N");c(c$,"drawMeasurements",function(a,b){var c=this.getMeasurements(JSV.common.Annotation.AType.Measurements,b);if(null!=c)for(var e=c.size();0<=--e;)this.drawMeasurement(a,c.get(e));b==this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumMeasurements=c)},"~O,~N");c(c$,"drawMeasurement",
function(a,b){if(!(0==b.text.length&&b!==this.pendingMeasurement)){this.pd.setFont(a,this.xPixels,1,12,!1);this.g2d.setGraphicsColor(a,b===this.pendingMeasurement?this.pd.getColor(JSV.common.ScriptToken.PEAKTABCOLOR):this.pd.BLACK);var c=this.toPixelX(b.getXVal()),e=this.toPixelY(b.getYVal()),g=this.toPixelX(b.getXVal2());if(!Double.isNaN(b.getXVal())&&!(c!=this.fixX(c)||g!=this.fixX(g))){var f=2<=Math.abs(c-g),h=this.getScale().isYZeroOnScale()&&b.spec.isHNMR(),k=s((c+g)/2);this.g2d.setStrokeBold(a,
!0);f&&this.g2d.drawLine(a,c,e,g,e);h&&this.g2d.drawLine(a,c+1,this.yPixel1-1,g,this.yPixel1-1);this.g2d.setStrokeBold(a,!1);f&&this.g2d.drawString(a,b.text,k+b.offsetX,e-b.offsetY);h&&(this.g2d.drawLine(a,c,this.yPixel1,c,this.yPixel1-6*this.pd.scalingFactor),this.g2d.drawLine(a,g,this.yPixel1,g,this.yPixel1-6*this.pd.scalingFactor))}}},"~O,JSV.common.Measurement");c(c$,"getPinSelected",function(a,b){if(null!=this.widgets)for(var c=0;c<this.widgets.length;c++)if(null!=this.widgets[c]&&this.widgets[c].isPinOrCursor&&
this.widgets[c].selected(a,b))return this.widgets[c];return null},"~N,~N");c(c$,"set2DCrossHairs",function(a,b){var c;if(a==this.imageView.fixX(a)&&b==this.fixY(b)&&(this.pin1Dx1.setX(c=this.imageView.toX(a),this.toPixelX(c)),this.cur2Dx1.setX(c,a),this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b)),this.isLinked)){var e=this.imageView.toY(b);this.pd.set2DCrossHairsLinked(this,c,e,!this.sticky2Dcursor)}},"~N,~N");c(c$,"reset2D",function(a){a?(this.imageView.setView0(this.imageView.xPixel0,
this.pin2Dy0.yPixel0,this.imageView.xPixel1,this.pin2Dy1.yPixel0),this.doZoom(0,this.getScale().minY,0,this.getScale().maxY,!0,!1,!1,!1,!0)):this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.yPixel0,this.pin2Dx1.xPixel0,this.imageView.yPixel1)},"~B");c(c$,"setAnnotationText",function(a){var b=this.pd.getInput("New text?","Set Label",a.text);if(null==b)return!1;0==b.length?this.annotations.removeObj(a):a.text=b;return!0},"JSV.common.Annotation");c(c$,"checkIntegral",function(a,b,c){var e=
this.getDialog(JSV.common.Annotation.AType.Integration,-1);null!=e&&(a=e.getData().addIntegralRegion(a,b),c&&n(e,JSV.dialog.JSVDialog)&&e.update(null,0,0),this.selectedSpectrumIntegrals=null,this.pendingIntegral=c?null:a)},"~N,~N,~B");c(c$,"setToolTipForPixels",function(a,b){var c=this.getPinSelected(a,b),e=this.getScale().precision[0],g=this.getScale().precision[1];if(null!=c)this.setStartupPinTip()||(c===this.pin1Dx01||c===this.pin2Dx01?e=JU.DF.formatDecimalDbl(Math.min(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),
e)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),e):c===this.pin1Dy01?e=JU.DF.formatDecimalDbl(Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()),g)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()),g):c===this.cur2Dy?(c=this.imageView.toSubspectrumIndex(c.yPixel0),e=this.get2DYLabel(c,e)):e=c===this.pin2Dy01?""+s(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+s(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):
c.isXtype?JU.DF.formatDecimalDbl(c.getXVal(),e):c.is2D?""+s(c.getYVal()):JU.DF.formatDecimalDbl(c.getYVal(),g),this.pd.setToolTipText(e));else{if(null!=this.imageView){if(this.imageView.fixX(a)==a&&this.fixY(b)==b){c=this.imageView.toSubspectrumIndex(b);e=JU.DF.formatDecimalDbl(this.imageView.toX(a),e)+" "+this.getSpectrum().getAxisLabel(!0)+",  "+this.get2DYLabel(c,e);this.pd.setToolTipText(this.pd.display1D?e:"");this.pd.coordStr=e;return}if(!this.pd.display1D){this.pd.setToolTipText("");this.pd.coordStr=
"";return}}var c=this.toX(this.fixX(a)),e=null!=this.imageView&&this.imageView.isXWithinRange(a)?this.imageView.toSubspectrumIndex(this.fixY(b)):this.toY(this.fixY(b)),g=this.setCoordStr(c,e),f=this.getFixedSelectedSpectrumIndex();this.isInPlotRegion(a,b)?1!=this.nSpectra&&this.haveIntegralDisplayed(f)&&(e=this.getIntegrationGraph(f).getPercentYValueAt(c),g+=", "+JU.DF.formatDecimalDbl(e,1)):e=NaN;this.pd.setToolTipText(null!=this.pendingMeasurement||null!=this.selectedMeasurement||null!=this.selectedIntegral?
this.pd.hasFocus()?"Press ESC to delete "+(null!=this.selectedIntegral?"integral, DEL to delete all visible, or N to normalize":null==this.pendingMeasurement?'"'+this.selectedMeasurement.text+'" or DEL to delete all visible':"measurement"):"":Double.isNaN(e)?null:g)}},"~N,~N");c(c$,"setCoordStr",function(a,b){var c=JU.DF.formatDecimalDbl(a,this.getScale().precision[0]);this.pd.coordStr="("+c+(this.haveSingleYScale||0<=this.iSpectrumSelected?", "+JU.DF.formatDecimalDbl(b,this.getScale().precision[1]):
"")+")";return c},"~N,~N");c(c$,"setStartupPinTip",function(){if(null==this.pd.startupPinTip)return!1;this.pd.setToolTipText(this.pd.startupPinTip);this.pd.startupPinTip=null;return!0});c(c$,"get2DYLabel",function(a,b){var c=this.getSpectrumAt(0).getSubSpectra().get(a);return JU.DF.formatDecimalDbl(c.getY2D(),b)+(c.y2DUnits.equals("HZ")?" HZ ("+JU.DF.formatDecimalDbl(c.getY2DPPM(),b)+" PPM)":"")},"~N,~N");c(c$,"isOnSpectrum",function(a,b,c){var e=null,g=!0,f=0>c;if(f){e=this.getDialog(JSV.common.Annotation.AType.Integration,
-1);if(null==e)return!1;e=e.getData().getXYCoords();c=this.getFixedSelectedSpectrumIndex()}else{this.setScale(c);var h=this.spectra.get(c),e=h.xyCoords,g=h.isContinuous()}var h=c*B(this.yPixels*(this.yStackOffsetPercent/100)),k=this.viewData.getStartingPointIndex(c);c=this.viewData.getEndingPointIndex(c);if(g)for(g=k;g<c;g++){var l=e[g],m=e[g+1],k=this.toPixelX(l.getXVal()),p=this.toPixelX(m.getXVal()),l=f?this.toPixelYint(l.getYVal()):this.toPixelY(l.getYVal()),m=f?this.toPixelYint(m.getYVal()):
this.toPixelY(m.getYVal());if(!(-2147483648==l||-2147483648==m))if(l=this.fixY(l)-h,m=this.fixY(m)-h,JSV.common.GraphSet.isOnLine(a,b,k,l,p,m))return!0}else for(g=k;g<=c;g++)if(f=e[g],m=this.toPixelY(f.getYVal()),-2147483648!=m&&(k=this.toPixelX(f.getXVal()),l=this.toPixelY(Math.max(this.getScale().minYOnScale,0)),l=this.fixY(l),m=this.fixY(m),!(l==m&&(l==this.yPixel0||l==this.yPixel1))&&JSV.common.GraphSet.isOnLine(a,b,k,l,k,m)))return!0;return!1},"~N,~N,~N");c$.distance=c(c$,"distance",function(a,
b){return Math.sqrt(a*a+b*b)},"~N,~N");c$.findCompatibleGraphSet=c(c$,"findCompatibleGraphSet",function(a,b){for(var c=0;c<a.size();c++)if(JSV.common.Spectrum.areXScalesCompatible(b,a.get(c).getSpectrum(),!1,!1))return a.get(c);return null},"JU.Lst,JSV.common.Spectrum");c$.isGoodEvent=c(c$,"isGoodEvent",function(a,b,c){return null==b?5<Math.abs(a.xPixel1-a.xPixel0)&&5<Math.abs(a.yPixel1-a.yPixel0):c?5<Math.abs(a.xPixel0-b.xPixel0):5<Math.abs(a.yPixel0-b.yPixel0)},"JSV.common.PlotWidget,JSV.common.PlotWidget,~B");
c$.isOnLine=c(c$,"isOnLine",function(a,b,c,e,g,f){var h=Math.abs(c-a);if(2>h&&2>Math.abs(e-b))return!0;var k=g-a;if(2>Math.abs(k)&&2>Math.abs(f-b))return!0;var l=e-f;if(2<Math.abs(l)&&e<b==f<b)return!1;var m=c-g;return 2<Math.abs(m)&&c<a==g<a?!1:JSV.common.GraphSet.distance(h,e-b)+JSV.common.GraphSet.distance(k,b-f)<JSV.common.GraphSet.distance(m,l)+2},"~N,~N,~N,~N,~N,~N");c$.setFractionalPositions=c(c$,"setFractionalPositions",function(a,b,c){var e=b.size(),g=0,f=0;a.isLinked=c!==JSV.common.PanelData.LinkMode.NONE;
if(c===JSV.common.PanelData.LinkMode.NONE){for(var h=0;h<e;h++)c=b.get(h),g+=(c.getSpectrumAt(0).is1D(),1)*c.nSplit;g=1/g;for(h=0;h<e;h++)c=b.get(h),c.isLinked=!1,a=c.getSpectrumAt(0).is1D()?g:1*g,c.fX0=0,c.fY0=f,c.fracX=1,c.fracY=a,f+=a*c.nSplit}else{var g=null,k=-1;if(2==e||3==e)for(h=0;h<e;h++)if(c=b.get(h),!c.getSpectrum().is1D()){g=c;0<=k&&(h=-2);k=h;break}if(-2==k||-1==k&&2!=e)JSV.common.GraphSet.setFractionalPositions(a,b,JSV.common.PanelData.LinkMode.NONE);else for(h=0;h<e;h++)c=b.get(h),
c.isLinked=!0,a=c.getSpectrumAt(0),a.is1D()?(null!=g&&(k=g.getSpectrumAt(0),JSV.common.Spectrum.areLinkableX(a,k)&&(c.gs2dLinkedX=g),JSV.common.Spectrum.areLinkableY(a,k)&&(c.gs2dLinkedY=g)),c.fX0=0,c.fY0=f,c.fracX=null==g?1:0.5,c.fracY=3==e||null==g?0.5:1,f+=0.5):(c.fX0=0.5,c.fY0=0,c.fracX=0.5,c.fracY=1)}},"JSV.common.PanelData,JU.Lst,JSV.common.PanelData.LinkMode");c(c$,"addAnnotation",function(a,b){if(0==a.size()||1==a.size()&&a.get(0).equalsIgnoreCase("none"))return this.lastAnnotation=this.annotations=
null;4>a.size()&&null==this.lastAnnotation&&(this.lastAnnotation=this.getAnnotation((this.getScale().maxXOnScale+this.getScale().minXOnScale)/2,(this.getScale().maxYOnScale+this.getScale().minYOnScale)/2,b,!1,!1,0,0));var c=this.getAnnotation(a,this.lastAnnotation);if(null==c)return null;if(null==this.annotations&&1==a.size()&&'"'==a.get(0).charAt(0))return c=c.text,this.getSpectrum().setTitle(c),c;this.lastAnnotation=c;this.addAnnotation(c,!1);return null},"JU.Lst,~S");c(c$,"addHighlight",function(a,
b,c,e){null==c&&(c=this.getSpectrumAt(0));a=S(JSV.common.GraphSet.Highlight,this,null,a,b,c,null==e?this.pd.getColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR):e);this.highlights.contains(a)||this.highlights.addLast(a)},"~N,~N,JSV.common.Spectrum,javajs.api.GenericColor");c(c$,"addPeakHighlight",function(a){for(var b=this.spectra.size();0<=--b;){var c=this.spectra.get(b);this.removeAllHighlights(c);if(!(null==a||a.isClearAll()||c!==a.spectrum)){var e=a.toString();if(null!=e){var g=JU.PT.getQuotedAttribute(e,
"xMin"),e=JU.PT.getQuotedAttribute(e,"xMax");if(null==g||null==e)break;g=JU.PT.parseFloat(g);e=JU.PT.parseFloat(e);if(Float.isNaN(g)||Float.isNaN(e))break;this.pd.addHighlight(this,g,e,c,200,140,140,100);c.setSelectedPeak(a);!this.getScale().isInRangeX(g)&&!(this.getScale().isInRangeX(e)||g<this.getScale().minX&&this.getScale().maxX<e)&&this.setZoomTo(0)}}}},"JSV.common.PeakInfo");c(c$,"advanceSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.advanceSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());
this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(c$,"checkSpectrumClickedEvent",function(a,b,c){if(this.nextClickForSetPeak)return!1;if(0<c&&this.checkArrowLeftRightClick(a,b))return!0;if(1<c||(null!=this.pendingMeasurement||!this.isInPlotRegion(a,b))||0==c&&(c=this.isOnSpectrum(a,b,-1),this.pd.integralShiftMode=c?this.getShiftMode(a,b):0,this.pd.isIntegralDrag=0==this.pd.integralShiftMode&&(c||this.haveIntegralDisplayed(-1)&&null!=this.findMeasurement(this.getIntegrationGraph(-1),a,
b,0)),0!=this.pd.integralShiftMode)||!this.showAllStacked)return!1;this.stackSelected=!1;for(c=0;c<this.nSpectra;c++)if(this.isOnSpectrum(a,b,c))return this.setSpectrumClicked(this.iPreviousSpectrumClicked=c),!1;if(this.isDialogOpen())return!1;this.setSpectrumClicked(-1);return this.stackSelected=!1},"~N,~N,~N");c(c$,"getShiftMode",function(a,b){return this.isStartEndIntegral(a,!1)?b:this.isStartEndIntegral(a,!0)?-b:0},"~N,~N");c(c$,"isDialogOpen",function(){return this.isVisible(this.getDialog(JSV.common.Annotation.AType.Integration,
-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,-1))});c(c$,"isStartEndIntegral",function(a,b){return b?20>this.xPixelPlot1-a:20>a-this.xPixelPlot0},"~N,~B");c(c$,"checkWidgetEvent",function(a,b,c){if(this.zoomEnabled&&this.triggered)if(this.triggered=!1,c)2==this.pd.clickCount&&null==this.pendingMeasurement?(-1==this.iSpectrumClicked&&0<=this.iPreviousSpectrumClicked&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),
this.processPendingMeasurement(a,b,2)):null==this.pendingMeasurement&&(c=this.getPinSelected(a,b),null==c&&(b=this.fixY(b),a<this.xPixel1?(this.pd.shiftPressed&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),a=this.fixX(a),this.zoomBox1D.setX(this.toX(a),a),this.zoomBox1D.yPixel0=b,c=this.zoomBox1D):null!=this.imageView&&a<this.imageView.xPixel1&&(this.zoomBox2D.setX(this.imageView.toX(a),this.imageView.fixX(a)),this.zoomBox2D.yPixel0=b,c=this.zoomBox2D)),this.pd.thisWidget=c);else if(this.nextClickForSetPeak=
!1,c=this.pd.thisWidget,null!=c)if(c===this.zoomBox1D)this.zoomBox1D.xPixel1=this.fixX(a),this.zoomBox1D.yPixel1=this.fixY(b),this.pd.isIntegralDrag&&this.zoomBox1D.xPixel0!=this.zoomBox1D.xPixel1&&this.checkIntegral(this.zoomBox1D.getXVal(),this.toX(this.zoomBox1D.xPixel1),!1);else if(c===this.zoomBox2D)this.zoomBox2D.xPixel1=this.imageView.fixX(a),this.zoomBox2D.yPixel1=this.fixY(b);else if(c===this.cur2Dy)b=this.fixY(b),this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=b,this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b));
else if(!(c===this.cur2Dx0||c===this.cur2Dx1))if(c===this.pin1Dx0||c===this.pin1Dx1||c===this.pin1Dx01){a=this.fixX(a);c.setX(this.toX0(a),a);if(c===this.pin1Dx01){c=a-s((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2);a=this.pin1Dx0.xPixel0+c;b=this.pin1Dx1.xPixel0+c;if(0==c||this.fixX(a)!=a||this.fixX(b)!=b)return;this.pin1Dx0.setX(this.toX0(a),a);this.pin1Dx1.setX(this.toX0(b),b)}this.doZoom(this.pin1Dx0.getXVal(),0,this.pin1Dx1.getXVal(),0,!0,!1,!1,!0,!1)}else if(c===this.pin1Dy0||c===this.pin1Dy1||
c===this.pin1Dy01){b=this.fixY(b);c.setY(this.toY0(b),b);if(c===this.pin1Dy01){c=b-s((this.pin1Dy0.yPixel0+this.pin1Dy1.yPixel0)/2)+1;b=this.pin1Dy0.yPixel0+c;a=this.pin1Dy1.yPixel0+c;c=this.toY0(b);var e=this.toY0(a);if(Math.min(c,e)==this.getScale().minY||Math.max(c,e)==this.getScale().maxY)return;this.pin1Dy0.setY(c,b);this.pin1Dy1.setY(e,a)}this.doZoom(0,this.pin1Dy0.getYVal(),0,this.pin1Dy1.getYVal(),null==this.imageView,null==this.imageView,!1,!1,!1)}else if(c===this.pin2Dx0||c===this.pin2Dx1||
c===this.pin2Dx01){a=this.imageView.fixX(a);c.setX(this.imageView.toX0(a),a);if(c===this.pin2Dx01){c=a-s((this.pin2Dx0.xPixel0+this.pin2Dx1.xPixel0)/2)+1;a=this.pin2Dx0.xPixel0+c;b=this.pin2Dx1.xPixel0+c;if(this.imageView.fixX(a)!=a||this.imageView.fixX(b)!=b)return;this.pin2Dx0.setX(this.imageView.toX0(a),a);this.pin2Dx1.setX(this.imageView.toX0(b),b)}JSV.common.GraphSet.isGoodEvent(this.pin2Dx0,this.pin2Dx1,!0)?(this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,this.pin2Dx1.xPixel0,
this.pin2Dy1.yPixel0),this.doZoom(this.pin2Dx0.getXVal(),this.getScale().minY,this.pin2Dx1.getXVal(),this.getScale().maxY,!1,!1,!1,!0,!1)):this.reset2D(!0)}else if(c===this.pin2Dy0||c===this.pin2Dy1||c===this.pin2Dy01){b=this.fixY(b);c.setY(this.imageView.toSubspectrumIndex(b),b);if(c===this.pin2Dy01){c=b-s((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2)+1;b=this.pin2Dy0.yPixel0+c;a=this.pin2Dy1.yPixel0+c;if(b!=this.fixY(b)||a!=this.fixY(a))return;this.pin2Dy0.setY(this.imageView.toSubspectrumIndex(b),
b);this.pin2Dy1.setY(this.imageView.toSubspectrumIndex(a),a)}JSV.common.GraphSet.isGoodEvent(this.pin2Dy0,this.pin2Dy1,!1)?this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,this.pin2Dx1.xPixel1,this.pin2Dy1.yPixel1):this.reset2D(!1)}},"~N,~N,~B");c(c$,"clearIntegrals",function(){this.checkIntegral(NaN,0,!1)});c(c$,"clearMeasurements",function(){this.removeDialog(this.getFixedSelectedSpectrumIndex(),JSV.common.Annotation.AType.Measurements)});c$.createGraphSetsAndSetLinkMode=c(c$,"createGraphSetsAndSetLinkMode",
function(a,b,c,e,g,f){for(var h=new JU.Lst,k=0;k<c.size();k++){var l=c.get(k),m=f===JSV.common.PanelData.LinkMode.NONE?JSV.common.GraphSet.findCompatibleGraphSet(h,l):null;null==m&&h.addLast(m=new JSV.common.GraphSet(b.getPanelData()));m.addSpec(l)}JSV.common.GraphSet.setFractionalPositions(a,h,f);for(k=h.size();0<=--k;)h.get(k).initGraphSet(e,g),JU.Logger.info("JSVGraphSet "+(k+1)+" nSpectra = "+h.get(k).nSpectra);return h},"JSV.common.PanelData,JSV.api.JSVPanel,JU.Lst,~N,~N,JSV.common.PanelData.LinkMode");
c(c$,"drawGraphSet",function(a,b,c,e,g,f,h,k,l,m,p){this.zoomEnabled=this.pd.getBoolean(JSV.common.ScriptToken.ENABLEZOOM);this.height=g*this.pd.scalingFactor;this.width=e*this.pd.scalingFactor;this.left=f*this.pd.scalingFactor;this.right=h*this.pd.scalingFactor;this.top=k*this.pd.scalingFactor;this.bottom=l*this.pd.scalingFactor;this.$haveSelectedSpectrum=!1;this.selectedSpectrumMeasurements=this.selectedSpectrumIntegrals=null;if(!this.pd.isPrinting&&null!=this.widgets)for(e=0;e<this.widgets.length;e++)null!=
this.widgets[e]&&(this.widgets[e].isVisible=!1);for(e=0;e<this.nSplit;e++)this.setPositionForFrame(e),this.drawAll(a,b,c,e,m||1<this.nSplit,p);this.setPositionForFrame(1<this.nSplit?this.pd.currentSplitPoint:0)},"~O,~O,~O,~N,~N,~N,~N,~N,~N,~B,~B");c(c$,"escapeKeyPressed",function(a){null!=this.zoomBox1D&&(this.zoomBox1D.xPixel0=this.zoomBox1D.xPixel1=0);null!=this.zoomBox2D&&(this.zoomBox2D.xPixel0=this.zoomBox2D.xPixel1=0);this.inPlotMove&&(null!=this.pendingMeasurement?this.pendingMeasurement=null:
(this.pendingMeasurement=this.pd.thisWidget=null,null!=this.selectedSpectrumMeasurements&&null!=this.selectedMeasurement&&(a?this.selectedSpectrumMeasurements.clear(this.getScale().minXOnScale,this.getScale().maxXOnScale):this.selectedSpectrumMeasurements.removeObj(this.selectedMeasurement),this.selectedMeasurement=null,this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)),null!=this.selectedSpectrumIntegrals&&null!=this.selectedIntegral&&(a?this.selectedSpectrumIntegrals.clear(this.getScale().minXOnScale,
this.getScale().maxXOnScale):this.selectedSpectrumIntegrals.removeObj(this.selectedIntegral),this.selectedIntegral=null,this.updateDialog(JSV.common.Annotation.AType.Integration,-1))))},"~B");c$.findGraphSet=c(c$,"findGraphSet",function(a,b,c){for(var e=a.size();0<=--e;)if(a.get(e).hasPoint(b,c))return a.get(e);return null},"JU.Lst,~N,~N");c(c$,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.spectra.size()&&null==(b=this.spectra.get(c).findMatchingPeakInfo(a));c++);return b},"JSV.common.PeakInfo");
c(c$,"getCurrentSpectrumIndex",function(){return 1==this.nSpectra?0:this.iSpectrumSelected});c(c$,"getSelectedIntegral",function(){return this.selectedIntegral});c(c$,"getShowAnnotation",function(a,b){var c=this.getDialog(a,b);return null!=c&&c.getState()},"JSV.common.Annotation.AType,~N");c(c$,"hasFileLoaded",function(a){for(var b=this.spectra.size();0<=--b;)if(this.spectra.get(b).getFilePathForwardSlash().equals(a))return!0;return!1},"~S");c(c$,"haveSelectedSpectrum",function(){return this.$haveSelectedSpectrum});
c(c$,"mouseClickedEvent",function(a,b,c,e){this.selectedIntegral=this.selectedMeasurement=null;var g=this.nextClickForSetPeak;this.nextClickForSetPeak=!1;if(!this.checkArrowUpDownClick(a,b))if(this.lastClickX=NaN,this.lastPixelX=2147483647,this.isSplitWidget(a,b))this.splitStack(this.pd.graphSets,1==this.nSplit);else{var f=this.getPinSelected(a,b);if(null!=f)this.setWidgetValueByUser(f);else if(f=null!=this.imageView&&a==this.imageView.fixX(a)&&b==this.fixY(b),2==c&&(-1==this.iSpectrumClicked&&0<=
this.iPreviousSpectrumClicked)&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),!f&&e)this.setSpectrumClicked(this.iPreviousSpectrumClicked),null!=this.pendingMeasurement?this.processPendingMeasurement(a,b,-3):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,b,3);else if(this.lastXMax=NaN,2==c)f?(this.sticky2Dcursor&&this.addAnnotation(this.getAnnotation(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b),this.pd.coordStr,!1,!0,5,5),!0),this.sticky2Dcursor=!this.sticky2Dcursor,
this.set2DCrossHairs(a,b)):this.isInTopBar(a,b)?this.doZoom(this.toX0(this.xPixel0),0,this.toX0(this.xPixel1),0,!0,!1,!1,!0,!0):this.isInRightBar(a,b)?this.doZoom(this.getScale().minXOnScale,this.viewList.get(0).getScale().minYOnScale,this.getScale().maxXOnScale,this.viewList.get(0).getScale().maxYOnScale,!0,!0,!1,!1,!1):this.isInTopBar2D(a,b)?this.reset2D(!0):this.isInRightBar2D(a,b)?this.reset2D(!1):null!=this.pendingMeasurement?this.processPendingMeasurement(a,b,-2):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,
b,2);else if(f){if(null!=this.annotations&&(c=(new JSV.common.Coordinate).set(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b)),c=this.findAnnotation2D(c),null!=c&&this.setAnnotationText(c)))return;this.sticky2Dcursor=!1;this.set2DCrossHairs(a,b)}else{if(this.isInPlotRegion(a,b)){if(null!=this.selectedSpectrumIntegrals&&this.checkIntegralNormalizationClick(a,b))return;if(null!=this.pendingMeasurement){this.processPendingMeasurement(a,b,1);return}this.setCoordClicked(a,this.toX(a),this.toY(b));
this.updateDialog(JSV.common.Annotation.AType.PeakList,-1);if(g){this.shiftSpectrum(NaN,NaN);return}}else this.setCoordClicked(0,NaN,0);this.pd.notifyPeakPickedListeners(null)}}},"~N,~N,~N,~B");c(c$,"updateDialog",function(a,b){var c=this.getDialog(a,b);if(null!=c&&this.isVisible(c)){var e=this.toX(this.xPixel1)-this.toX(this.xPixel0),g=this.getSpectrum().isInverted()?this.yPixel1-this.pd.mouseY:this.pd.mouseY-this.yPixel0;c.update(this.pd.coordClicked,e,g)}},"JSV.common.Annotation.AType,~N");c(c$,
"isVisible",function(a){return n(a,JSV.dialog.JSVDialog)&&a.isVisible()},"JSV.api.AnnotationData");c(c$,"mouseReleasedEvent",function(a,b){if(null!=this.pendingMeasurement)2>Math.abs(this.toPixelX(this.pendingMeasurement.getXVal())-a)&&(this.pendingMeasurement=null),this.processPendingMeasurement(a,b,-2),this.setToolTipForPixels(a,b);else if(0!=this.pd.integralShiftMode)this.pd.integralShiftMode=0,this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0;else{0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo);
var c=this.pd.thisWidget;if(this.pd.isIntegralDrag)JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,null,!0)&&this.checkIntegral(this.toX(this.zoomBox1D.xPixel0),this.toX(this.zoomBox1D.xPixel1),!0),this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0=0,this.pendingIntegral=null,this.pd.isIntegralDrag=!1;else if(c===this.zoomBox2D)JSV.common.GraphSet.isGoodEvent(this.zoomBox2D,null,!0)&&(this.imageView.setZoom(this.zoomBox2D.xPixel0,this.zoomBox2D.yPixel0,this.zoomBox2D.xPixel1,this.zoomBox2D.yPixel1),this.zoomBox2D.xPixel1=
this.zoomBox2D.xPixel0,this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!0,!0));else if(c===this.zoomBox1D){if(JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,null,!0)){var c=this.zoomBox1D.xPixel1,e=this.pd.shiftPressed;this.doZoom(this.toX(this.zoomBox1D.xPixel0),e?this.toY(this.zoomBox1D.yPixel0):0,this.toX(c),e?this.toY(this.zoomBox1D.yPixel1):0,!0,e,!0,!0,!0);this.zoomBox1D.xPixel1=
this.zoomBox1D.xPixel0}}else(c===this.pin1Dx0||c===this.pin1Dx1||c===this.cur2Dx0||c===this.cur2Dx1)&&this.addCurrentZoom()}},"~N,~N");c(c$,"mouseMovedEvent",function(a,b){if(1<this.nSpectra){var c=this.getSplitPoint(b);this.setPositionForFrame(c);this.setSpectrumMovedTo(1<this.nSplit?c:this.iSpectrumSelected);0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo)}this.inPlotMove=this.isInPlotRegion(a,b);this.setXPixelMovedTo(1.7976931348623157E308,1.7976931348623157E308,this.inPlotMove?a:
-1,-1);this.inPlotMove&&(this.xValueMovedTo=this.toX(this.xPixelMovedTo),this.yValueMovedTo=this.getSpectrum().getYValueAt(this.xValueMovedTo));if(0!=this.pd.integralShiftMode){var c=this.getDialog(JSV.common.Annotation.AType.Integration,-1),e=c.getData().getXYCoords(),e=e[0<this.pd.integralShiftMode?e.length-1:0].getYVal();c.getData().shiftY(this.pd.integralShiftMode,this.toPixelYint(e)+b-(0<this.pd.integralShiftMode?this.yPixelPlot1:this.yPixelPlot0),this.yPixel0,this.yPixels)}else this.pd.isIntegralDrag||
(null!=this.pendingMeasurement?(this.processPendingMeasurement(a,b,0),this.setToolTipForPixels(a,b)):(this.selectedMeasurement=this.inPlotMove&&null!=this.selectedSpectrumMeasurements?this.findMeasurement(this.selectedSpectrumMeasurements,a,b,0):null,this.selectedIntegral=null,this.inPlotMove&&(null!=this.selectedSpectrumIntegrals&&null==this.selectedMeasurement)&&(this.selectedIntegral=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,0),null==this.selectedIntegral&&(this.selectedIntegral=
this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5))),this.setToolTipForPixels(a,b),null==this.imageView?(this.piMouseOver=null,c=1<this.nSplit?this.iSpectrumMovedTo:this.iSpectrumClicked,!this.isDrawNoSpectra()&&0<=c&&(c=this.spectra.get(c),null!=c.getPeakList()&&(this.coordTemp.setXVal(this.toX(a)),this.coordTemp.setYVal(this.toY(b)),this.piMouseOver=c.findPeakByCoord(a,this.coordTemp)))):!this.pd.display1D&&this.sticky2Dcursor&&this.set2DCrossHairs(a,b)))},"~N,~N");c(c$,"nextView",function(){this.currentZoomIndex+
1<this.viewList.size()&&this.setZoomTo(this.currentZoomIndex+1)});c(c$,"previousView",function(){0<this.currentZoomIndex&&this.setZoomTo(this.currentZoomIndex-1)});c(c$,"resetView",function(){this.setZoomTo(0)});c(c$,"removeAllHighlights",function(){this.removeAllHighlights(null)});c(c$,"removeHighlight",function(a){this.highlights.remove(a)},"~N");c(c$,"removeHighlight",function(a,b){for(var c=this.highlights.size();0<=--c;){var e=this.highlights.get(c);e.x1==a&&e.x2==b&&this.highlights.remove(c)}},
"~N,~N");c(c$,"scaleYBy",function(a){if(null!=this.imageView||this.zoomEnabled)this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,a),null!=this.imageView&&(this.update2dImage(!1),this.resetPinsFromView()),this.pd.refresh()},"~N");c(c$,"selectSpectrum",function(a,b,c){for(var e=!1,g=this.spectra.size();0<=--g;)if((null==a||this.getSpectrumAt(g).getFilePathForwardSlash().equals(a))&&this.getSpectrumAt(g).matchesPeakTypeModel(b,c))this.setSpectrumSelected(g),1<this.nSplit&&this.splitStack(this.pd.graphSets,
!0),e=!0;1<this.nSpectra&&(!e&&0<=this.iSpectrumSelected&&!this.pd.isCurrentGraphSet(this))&&this.setSpectrumSelected(-2147483648);return e},"~S,~S,~S");c(c$,"selectPeakByFileIndex",function(a,b,c){for(var e,g=this.spectra.size();0<=--g;)if(null!=(e=this.getSpectrumAt(g).selectPeakByFileIndex(a,b,c)))return e;return null},"~S,~S,~S");c(c$,"setSelected",function(a){0>a?(this.bsSelected.clearAll(),this.setSpectrumClicked(-1)):(this.bsSelected.set(a),this.setSpectrumClicked(1==this.bsSelected.cardinality()?
a:-1),1<this.nSplit&&0<=a&&(this.pd.currentSplitPoint=a))},"~N");c(c$,"setSelectedIntegral",function(a){var b=this.selectedIntegral.getSpectrum();this.getIntegrationGraph(this.getSpectrumIndex(b)).setSelectedIntegral(this.selectedIntegral,a)},"~N");c(c$,"setShowAnnotation",function(a,b){var c=this.getDialog(a,-1);if(null==c)null!=b&&b!==Boolean.TRUE||(a===JSV.common.Annotation.AType.PeakList||a===JSV.common.Annotation.AType.Integration||a===JSV.common.Annotation.AType.Measurements)&&this.pd.showDialog(a);
else if(null==b)n(c,JSV.dialog.JSVDialog)?c.setVisible(!1):c.setState(!c.getState());else{var e=b.booleanValue();c.setState(e);(e||n(c,JSV.dialog.JSVDialog))&&this.pd.showDialog(a)}},"JSV.common.Annotation.AType,Boolean");c(c$,"checkIntegral",function(a,b){if(!this.getSpectrum().canIntegrate()||this.reversePlot)return!1;var c=this.getFixedSelectedSpectrumIndex(),e=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==b)return!0;switch(JSV.common.IntegralData.IntMode.getMode(b.toUpperCase())){case JSV.common.IntegralData.IntMode.ON:this.integrate(c,
a);break;case JSV.common.IntegralData.IntMode.OFF:this.integrate(c,null);break;case JSV.common.IntegralData.IntMode.TOGGLE:this.integrate(c,null==e?a:null);break;case JSV.common.IntegralData.IntMode.AUTO:null==e&&(this.checkIntegral(a,"ON"),e=this.getDialog(JSV.common.Annotation.AType.Integration,-1));null!=e&&e.getData().autoIntegrate();break;case JSV.common.IntegralData.IntMode.LIST:this.pd.showDialog(JSV.common.Annotation.AType.Integration);break;case JSV.common.IntegralData.IntMode.MARK:null==
e&&(this.checkIntegral(a,"ON"),e=this.getDialog(JSV.common.Annotation.AType.Integration,-1));null!=e&&e.getData().addMarks(b.substring(4).trim());break;case JSV.common.IntegralData.IntMode.MIN:if(null!=e)try{var g=Double.parseDouble(JSV.common.ScriptToken.getTokens(b).get(1));e.getData().setMinimumIntegral(g)}catch(f){if(!y(f,Exception))throw f;}break;case JSV.common.IntegralData.IntMode.UPDATE:null!=e&&e.getData().update(a)}this.updateDialog(JSV.common.Annotation.AType.Integration,-1);return!0},
"JSV.common.Parameters,~S");c(c$,"setSpectrum",function(a,b){b&&1<this.nSplit?1<this.nSplit&&this.setSpectrumClicked(a):(this.setSpectrumClicked(a),this.showAllStacked=this.stackSelected=!1);0<=a&&this.dialogsToFront(this.getSpectrum())},"~N,~B");c(c$,"setSpectrumJDX",function(a){var b=this.getFixedSelectedSpectrumIndex();this.spectra.remove(b);this.spectra.add(b,a);this.pendingMeasurement=null;this.clearViews();this.viewData.newSpectrum(this.spectra)},"JSV.common.Spectrum");c(c$,"setZoom",function(a,
b,c,e){this.setZoomTo(0);0==a&&0==c&&0==b&&0==e?(this.newPins(),this.imageView=null,this.getScale(),this.getScale()):this.doZoom(a,b,c,e,!0,b!=e,!1,!0,!0)},"~N,~N,~N,~N");c(c$,"shiftSpectrum",function(a,b){var c=this.getSpectrum();if(!c.isNMR()||!c.is1D())return!1;if(1.7976931348623157E308==b||1.7976931348623157E308==a)a=-c.addSpecShift(0);else{if(4.9E-324==b)return this.nextClickForSetPeak=!0,this.jsvp.showMessage("Click on or beside a peak to set its chemical shift.","Set Reference"),!1;if(Double.isNaN(a)||
4.9E-324==a){var e=4.9E-324==a?this.lastClickX:this.getNearestPeak(c,this.lastClickX,this.toY(this.pd.mouseY));if(Double.isNaN(e))return!1;if(Double.isNaN(b))try{var g=this.pd.getInput("New chemical shift (set blank to reset)","Set Reference",""+e).trim();b=0==g.length?e-c.addSpecShift(0):Double.parseDouble(g)}catch(f){if(y(f,Exception))return!1;throw f;}a=b-e}}if(0==a)return!1;c.addSpecShift(a);if(null!=this.annotations)for(e=this.annotations.size();0<=--e;)this.annotations.get(e).spec===c&&this.annotations.get(e).addSpecShift(a);
if(null!=this.dialogs)for(var h,e=this.dialogs.entrySet().iterator();e.hasNext()&&((h=e.next())||1);)h.getValue().getSpectrum()===c&&h.getValue().setSpecShift(a);this.getScale().addSpecShift(a);Double.isNaN(this.lastClickX)||(this.lastClickX+=a);this.updateDialogs();this.doZoom(0,this.getScale().minYOnScale,0,this.getScale().maxYOnScale,!0,!0,!1,!0,!1);this.pd.repaint();return!0},"~N,~N");c(c$,"toPeak",function(a){a*=this.drawXAxisLeftToRight?1:-1;Double.isNaN(this.lastClickX)&&(this.lastClickX=this.lastPixelX=
0);var b=this.getSpectrum(),c=this.setCoordClicked(this.lastPixelX,this.lastClickX,0);a=b.setNextPeak(c,a);0>a||(a=b.getPeakList().get(a),b.setSelectedPeak(a),this.setCoordClicked(a.getXPixel(),a.getX(),0),this.pd.notifyPeakPickedListeners(new JSV.common.PeakPickEvent(this.jsvp,this.pd.coordClicked,a)))},"~N");c(c$,"scaleSelectedBy",function(a){for(var b=this.bsSelected.nextSetBit(0);0<=b;b=this.bsSelected.nextSetBit(b+1))this.viewData.scaleSpectrum(b,a)},"~N");h(c$,"toString",function(){return"gs: "+
this.nSpectra+" "+this.spectra+" "+this.spectra.get(0).getFilePath()});c(c$,"setXPointer",function(a,b){null!=a&&this.setSpectrumClicked(this.getSpectrumIndex(a));this.xValueMovedTo=this.lastClickX=b;this.lastPixelX=this.toPixelX(b);this.setXPixelMovedTo(b,1.7976931348623157E308,0,0);this.yValueMovedTo=NaN},"JSV.common.Spectrum,~N");c(c$,"setXPointer2",function(a,b){null!=a&&this.setSpectrumClicked(this.getSpectrumIndex(a));this.setXPixelMovedTo(1.7976931348623157E308,b,0,0)},"JSV.common.Spectrum,~N");
c(c$,"hasCurrentMeasurement",function(a){return null!=(a===JSV.common.Annotation.AType.Integration?this.selectedSpectrumIntegrals:this.selectedSpectrumMeasurements)},"JSV.common.Annotation.AType");c(c$,"getDialog",function(a,b){-1==b&&(b=this.getCurrentSpectrumIndex());return null==this.dialogs||0>b?null:this.dialogs.get(a+"_"+b)},"JSV.common.Annotation.AType,~N");c(c$,"removeDialog",function(a,b){null!=this.dialogs&&0<=a&&this.dialogs.remove(b+"_"+a)},"~N,JSV.common.Annotation.AType");c(c$,"addDialog",
function(a,b,c){null==this.dialogs&&(this.dialogs=new java.util.Hashtable);a=b+"_"+a;c.setGraphSetKey(a);this.dialogs.put(a,c);return c},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");c(c$,"removeDialog",function(a){var b=a.getGraphSetKey();this.dialogs.remove(b);a=a.getData();null!=a&&this.dialogs.put(b,a)},"JSV.dialog.JSVDialog");c(c$,"getPeakListing",function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;var e=this.getDialog(JSV.common.Annotation.AType.PeakList,-1);
if(null==e){if(!c)return null;this.addDialog(a,JSV.common.Annotation.AType.PeakList,e=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,this.getSpectrum()))}e.getData().setPeakList(b,-2147483648,this.viewData.getScale());n(e,JSV.dialog.JSVDialog)&&e.setFields();return e.getData()},"~N,JSV.common.Parameters,~B");c(c$,"setPeakListing",function(a){var b=this.getDialog(JSV.common.Annotation.AType.PeakList,-1),c=n(b,JSV.dialog.JSVDialog)?b:null;(null==a?null==c||!c.isVisible():a.booleanValue())?
this.pd.showDialog(JSV.common.Annotation.AType.PeakList):n(b,JSV.dialog.JSVDialog)&&b.setVisible(!1)},"Boolean");c(c$,"haveIntegralDisplayed",function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null!=a&&a.getState()},"~N");c(c$,"getIntegrationGraph",function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null==a?null:a.getData()},"~N");c(c$,"setIntegrationRatios",function(a){var b=this.getFixedSelectedSpectrumIndex();null==this.aIntegrationRatios&&
(this.aIntegrationRatios=Array(this.nSpectra));this.aIntegrationRatios[b]=JSV.common.IntegralData.getIntegrationRatiosFromString(this.getSpectrum(),a)},"~S");c(c$,"getIntegrationRatios",function(a){return null==this.aIntegrationRatios?null:this.aIntegrationRatios[a]},"~N");c(c$,"integrate",function(a,b){var c=this.getSpectrumAt(a);if(null==b||!c.canIntegrate())return this.removeDialog(a,JSV.common.Annotation.AType.Integration),!1;this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(c,
b));return!0},"~N,JSV.common.Parameters");c(c$,"getIntegration",function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;var e=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==e){if(!c)return null;e=this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(this.getSpectrum(),b))}return e.getData()},"~N,JSV.common.Parameters,~B");c(c$,"getMeasurementInfo",function(a,b){var c;switch(a){case JSV.common.Annotation.AType.PeakList:c=this.getPeakListing(b,
null,!1);break;case JSV.common.Annotation.AType.Integration:c=this.getIntegration(b,null,!1);break;default:return null}if(null==c)return null;var e=new java.util.Hashtable;c.getInfo(e);return e},"JSV.common.Annotation.AType,~N");c(c$,"getInfo",function(a,b){var c=new java.util.Hashtable;if("viewInfo".equalsIgnoreCase(a))return this.getScale().getInfo(c);var e=new JU.Lst;c.put("spectra",e);for(var g=0;g<this.nSpectra;g++)if(!(0<=b&&g!=b)){var f=this.spectra.get(g),h=f.getInfo(a);if(0<=b&&null!=a&&
(2==h.size()||a.equalsIgnoreCase("id")))return 2==h.size()&&h.remove("id"),h;JSV.common.Parameters.putInfo(a,h,"type",f.getDataType());JSV.common.Parameters.putInfo(a,h,"titleLabel",f.getTitleLabel());JSV.common.Parameters.putInfo(a,h,"filePath",f.getFilePath().$replace("\\","/"));JSV.common.Parameters.putInfo(a,h,"PeakList",JSV.common.Parameters.isMatch(a,"PeakList")?this.getMeasurementInfo(JSV.common.Annotation.AType.PeakList,g):null);JSV.common.Parameters.putInfo(a,h,"Integration",JSV.common.Parameters.isMatch(a,
"Integration")?this.getMeasurementInfo(JSV.common.Annotation.AType.Integration,g):null);if(0<=b)return h;e.addLast(h)}return c},"~S,~N");c(c$,"getTitle",function(a){return 1==this.nSpectra||0<=this.iSpectrumSelected&&(!a||1==this.nSplit)?this.getSpectrum().getTitle():null},"~B");c(c$,"getCurrentView",function(){this.setScale(this.getFixedSelectedSpectrumIndex());return this.viewData.getScale()});c(c$,"set2DXY",function(a,b,c){var e;null!=this.gs2dLinkedX&&(e=this.toPixelX(a),e!=this.fixX(e)&&(e=-2147483648,
a=1.7976931348623157E308),this.cur1D2x1.setX(a,e));null!=this.gs2dLinkedY&&(e=this.toPixelX(b),e!=this.fixX(e)&&(e=-2147483648,b=1.7976931348623157E308),this.cur1D2x2.setX(b,e));this.cur1D2Locked=c},"~N,~N,~B");c(c$,"dialogsToFront",function(a){if(null!=this.dialogs){null==a&&(a=this.getSpectrum());for(var b,c=this.dialogs.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var e=b.getValue();this.isVisible(e)&&(null==a?e.setVisible(!0):e.setFocus(e.getSpectrum()===a))}}},"JSV.common.Spectrum");
c(c$,"setPlotColors",function(a){var b=a;if(b.length>this.nSpectra)a=Array(this.nSpectra),System.arraycopy(b,0,a,0,this.nSpectra),b=a;else if(this.nSpectra>b.length){a=Array(this.nSpectra);var c=this.nSpectra-b.length;System.arraycopy(b,0,a,0,b.length);for(var e=0,b=b.length;e<c;e++,b++)a[b]=this.generateRandomColor();b=a}this.plotColors=b},"~O");c(c$,"disposeImage",function(){null!=this.image2D&&this.image2D.parentNode.removeChild(this.image2D);this.plotColors=this.highlights=this.pd=this.jsvp=this.image2D=
null});c(c$,"generateRandomColor",function(){for(;;){var a=s(255*Math.random()),b=s(255*Math.random()),c=s(255*Math.random()),a=this.g2d.getColor3(a,b,c);if(0!=a.getRGB())return a}});c(c$,"setPlotColor0",function(a){this.plotColors[0]=a},"~O");c(c$,"getPlotColor",function(a){return a>=this.plotColors.length?null:this.plotColors[a]},"~N");c(c$,"setColorFromToken",function(a,b){null!=b&&this.g2d.setGraphicsColor(a,b===JSV.common.ScriptToken.PLOTCOLOR?this.plotColors[0]:this.pd.getColor(b))},"~O,JSV.common.ScriptToken");
c(c$,"setPlotColor",function(a,b){var c;switch(b){case -3:c=JSV.common.GraphSet.veryLightGrey;break;case -2:c=this.pd.BLACK;break;case -1:c=this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR);break;default:c=this.plotColors[b]}this.g2d.setGraphicsColor(a,c)},"~O,~N");c(c$,"draw2DImage",function(){null!=this.imageView&&this.g2d.drawGrayScaleImage(this.gMain,this.image2D,this.imageView.xPixel0,this.imageView.yPixel0,this.imageView.xPixel0+this.imageView.xPixels-1,this.imageView.yPixel0+this.imageView.yPixels-
1,this.imageView.xView1,this.imageView.yView1,this.imageView.xView2,this.imageView.yView2)});c(c$,"get2DImage",function(){this.imageView=new JSV.common.ImageView;this.imageView.set(this.viewList.get(0).getScale());if(!this.update2dImage(!0))return!1;this.imageView.resetZoom();return this.sticky2Dcursor=!0});c(c$,"update2dImage",function(a){this.imageView.set(this.viewData.getScale());var b=this.getSpectrumAt(0),c=this.imageView.get2dBuffer(b,!a);if(null==c)return this.imageView=this.image2D=null,
!1;a&&(c=this.imageView.adjustView(b,this.viewData),this.imageView.resetView());this.image2D=this.g2d.newGrayScaleImage(this.gMain,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,c);this.setImageWindow();return!0},"~B");c(c$,"getAnnotation",function(a,b,c,e,g,f,h){return(new JSV.common.ColoredAnnotation).setCA(a,b,this.getSpectrum(),c,this.pd.BLACK,e,g,f,h)},"~N,~N,~S,~B,~B,~N,~N");c(c$,"getAnnotation",function(a,b){return JSV.common.Annotation.getColoredAnnotation(this.g2d,this.getSpectrum(),
a,b)},"JU.Lst,JSV.common.Annotation");c(c$,"fillBox",function(a,b,c,e,g,f){this.setColorFromToken(a,f);this.g2d.fillRect(a,Math.min(b,e),Math.min(c,g),Math.abs(b-e),Math.abs(c-g))},"~O,~N,~N,~N,~N,JSV.common.ScriptToken");c(c$,"drawHandle",function(a,b,c,e){e?this.g2d.drawRect(a,b-2,c-2,4,4):this.g2d.fillRect(a,b-2,c-2,5,5)},"~O,~N,~N,~B");c(c$,"setCurrentBoxColor",function(a){this.g2d.setGraphicsColor(a,this.pd.BLACK)},"~O");c(c$,"fillArrow",function(a,b,c,e,g){var f=1;switch(b){case 1:case 3:f=
-1}c=[c-5,c-5,c+5,c+5,c+8,c,c-8];e=[e+5*f,e-f,e-f,e+5*f,e+5*f,e+10*f,e+5*f];switch(b){case 1:case 2:g?this.g2d.fillPolygon(a,e,c,7):this.g2d.drawPolygon(a,e,c,7);break;case 3:case 4:g?this.g2d.fillPolygon(a,c,e,7):this.g2d.drawPolygon(a,c,e,7)}},"~O,~N,~N,~N,~B");c(c$,"fillCircle",function(a,b,c,e){e?this.g2d.fillCircle(a,b-4,c-4,8):this.g2d.drawCircle(a,b-4,c-4,8)},"~O,~N,~N,~B");c(c$,"setAnnotationColor",function(a,b,c){null!=c?this.setColorFromToken(a,c):(c=null,n(b,JSV.common.ColoredAnnotation)&&
(c=b.getColor()),null==c&&(c=this.pd.BLACK),this.g2d.setGraphicsColor(a,c))},"~O,JSV.common.Annotation,JSV.common.ScriptToken");c(c$,"setSolutionColor",function(a,b,c){for(var e=0;e<this.nSpectra;e++){var g=this.spectra.get(e),f=b||!g.canShowSolutionColor()?-1:a.getColour(g,c);g.setFillColor(-1==f?null:this.pd.vwr.parameters.getColor1(f))}},"JSV.api.VisibleInterface,~B,~B");c(c$,"setIRMode",function(a,b){for(var c=0;c<this.nSpectra;c++){var e=this.spectra.get(c);if(e.dataType.equals(b)){var g=JSV.common.Spectrum.taConvert(e,
a);g!==e&&this.pd.setSpecForIRMode(g)}}},"JSV.common.Spectrum.IRMode,~S");c$.$GraphSet$Highlight$=function(){G(self.c$);c$=r(function(){P(this,arguments);this.x2=this.x1=0;this.spectrum=this.color=null;t(this,arguments)},JSV.common.GraphSet,"Highlight");h(c$,"toString",function(){return"highlight "+this.x1+" "+this.x2+" "+this.spectrum});u(c$,function(a,b,c,e){this.x1=a;this.x2=b;this.color=e;this.spectrum=c},"~N,~N,JSV.common.Spectrum,javajs.api.GenericColor");h(c$,"equals",function(a){return!n(a,
JSV.common.GraphSet.Highlight)?!1:a.x1==this.x1&&a.x2==this.x2},"~O");c$=K()};C(c$,"ARROW_RESET",-1,"ARROW_HOME",0,"ARROW_LEFT",1,"ARROW_RIGHT",2,"ARROW_UP",3,"ARROW_DOWN",4);c$.RT2=c$.prototype.RT2=Math.sqrt(2);C(c$,"veryLightGrey",null,"minNumOfPointsForZoom",3,"MIN_DRAG_PIXELS",5,"ONLINE_CUTOFF",2)});m("JSV.common");w(["JSV.common.XYScaleConverter"],"JSV.common.ImageView",["java.lang.Double","JSV.common.Coordinate","$.ScaleData"],function(){c$=r(function(){this.buf2d=null;this.yView2=this.xView2=
this.yView1=this.xView1=this.yPixelZoom2=this.xPixelZoom2=this.yPixelZoom1=this.xPixelZoom1=this.yPixels=this.xPixels=this.imageHeight=this.imageWidth=this.yPixel1=this.xPixel1=this.yPixel0=this.xPixel0=this.averageGray=this.grayFactorLast=0;this.minX=NaN;this.maxZ=this.minZ=this.maxY=this.minY=this.maxX=0;this.scaleData=null;t(this,arguments)},JSV.common,"ImageView",null,JSV.common.XYScaleConverter);c(c$,"set",function(a){Double.isNaN(this.minX)&&(this.minX=a.minX,this.maxX=a.maxX);this.minZ=a.minY;
this.maxZ=a.maxY;this.scaleData=new JSV.common.ScaleData},"JSV.common.ScaleData");c(c$,"setZoom",function(a,b,c,e){this.xPixelZoom1=Math.min(a,c);this.yPixelZoom1=Math.min(b,e);this.xPixelZoom2=Math.max(a,c);this.yPixelZoom2=Math.max(b,e);this.setView()},"~N,~N,~N,~N");c(c$,"setXY0",function(a,b,c){this.xPixel0=b;this.yPixel0=c;this.xPixel1=this.xPixel0+this.xPixels-1;this.yPixel1=this.yPixel0+this.yPixels-1;this.setMinMaxY(a)},"JSV.common.Spectrum,~N,~N");c(c$,"setPixelWidthHeight",function(a,b){this.xPixels=
a;this.yPixels=b},"~N,~N");c(c$,"resetView",function(){this.yView1=this.xView1=0;this.xView2=this.imageWidth-1;this.yView2=this.imageHeight-1});c(c$,"setView",function(){0==this.xPixelZoom1&&this.resetZoom();var a=this.toImageX(this.xPixelZoom1),b=this.toImageY(this.yPixelZoom1),c=this.toImageX(this.xPixelZoom2),e=this.toImageY(this.yPixelZoom2);this.xView1=Math.min(a,c);this.yView1=Math.min(b,e);this.xView2=Math.max(a,c);this.yView2=Math.max(b,e);this.setScaleData();this.resetZoom()});c(c$,"resetZoom",
function(){this.xPixelZoom1=this.xPixel0;this.yPixelZoom1=this.yPixel0;this.xPixelZoom2=this.xPixel1;this.yPixelZoom2=this.yPixel1});c(c$,"toImageX",function(a){return this.xView1+s(Math.floor((a-this.xPixel0)/(this.xPixels-1)*(this.xView2-this.xView1)))},"~N");c(c$,"toImageY",function(a){return this.yView1+s(Math.floor((a-this.yPixel0)/(this.yPixels-1)*(this.yView2-this.yView1)))},"~N");c(c$,"toImageX0",function(a){return JSV.common.Coordinate.intoRange(s((1*a-this.xPixel0)/(this.xPixels-1)*(this.imageWidth-
1)),0,this.imageWidth-1)},"~N");c(c$,"toImageY0",function(a){return JSV.common.Coordinate.intoRange(s((1*a-this.yPixel0)/(this.yPixels-1)*(this.imageHeight-1)),0,this.imageHeight-1)},"~N");c(c$,"isXWithinRange",function(a){return a>=this.xPixel0-5&&a<this.xPixel0+this.xPixels+5},"~N");c(c$,"toSubspectrumIndex",function(a){return JSV.common.Coordinate.intoRange(this.imageHeight-1-this.toImageY(a),0,this.imageHeight-1)},"~N");c(c$,"toX0",function(a){return this.maxX+(this.minX-this.maxX)*(this.fixX(a)-
this.xPixel0)/(this.xPixels-1)},"~N");c(c$,"toPixelX0",function(a){return this.xPixel1-s((a-this.minX)/(this.maxX-this.minX)*(this.xPixels-1))},"~N");c(c$,"toPixelY0",function(a){return this.yPixel1-s(a/(this.imageHeight-1)*(this.yPixels-1))},"~N");c(c$,"subIndexToPixelY",function(a){return this.yPixel0+s(1*(this.imageHeight-1-a-this.yView1)/(this.yView2-this.yView1)*(this.yPixels-1))},"~N");c(c$,"fixSubIndex",function(a){return JSV.common.Coordinate.intoRange(a,this.imageHeight-1-this.yView2,this.imageHeight-
1-this.yView1)},"~N");c(c$,"setView0",function(a,b,c,e){a=this.toImageX0(a);b=this.toImageY0(b);c=this.toImageX0(c);e=this.toImageY0(e);this.xView1=Math.min(a,c);this.yView1=Math.min(b,e);this.xView2=Math.max(a,c);this.yView2=Math.max(b,e);this.resetZoom()},"~N,~N,~N,~N");c(c$,"get2dBuffer",function(a,b){var c=a.getSubSpectra();if(null==c||!c.get(0).isContinuous())return null;var e=a.getXYCoords(),g=c.size();this.imageWidth=e.length;this.imageHeight=g;var f=255/(this.maxZ-this.minZ);if(!b&&null!=
this.buf2d&&f==this.grayFactorLast)return this.buf2d;this.grayFactorLast=f;for(var h=this.imageWidth*this.imageHeight,k=D(h,0),l=0,m=0;m<g;m++){var p=c.get(m).xyCoords;if(p.length!=e.length)return null;for(var n=c.get(m).getUserYFactor(),r=0;r<e.length;r++){var t=p[r].getYVal(),t=255-JSV.common.Coordinate.intoRange(s((t*n-this.minZ)*f),0,255);k[--h]=t;l+=t}}this.averageGray=1-l/(this.imageWidth*this.imageHeight)/255;System.out.println("Average gray = "+this.averageGray);return this.buf2d=k},"JSV.common.Spectrum,~B");
c(c$,"adjustView",function(a,b){for(var c=0,e=!1;((e=0.05>this.averageGray)||0.3<this.averageGray)&&10>c++;)b.scaleSpectrum(-2,e?2:0.5),this.set(b.getScale()),this.get2dBuffer(a,!1);return this.buf2d},"JSV.common.Spectrum,JSV.common.ViewData");c(c$,"getBuffer",function(){return this.buf2d});c(c$,"setMinMaxY",function(a){a=a.getSubSpectra();var b=a.get(0);this.maxY=b.getY2D();this.minY=a.get(a.size()-1).getY2D();b.y2DUnits.equalsIgnoreCase("Hz")&&(this.maxY/=b.freq2dY,this.minY/=b.freq2dY);this.setScaleData()},
"JSV.common.Spectrum");c(c$,"setScaleData",function(){this.scaleData.minY=this.minY;this.scaleData.maxY=this.maxY;this.scaleData.setYScale(this.toY(this.yPixel0),this.toY(this.yPixel1),!1,!1)});h(c$,"fixX",function(a){return a<this.xPixel0?this.xPixel0:a>this.xPixel1?this.xPixel1:a},"~N");h(c$,"fixY",function(a){return JSV.common.Coordinate.intoRange(a,this.yPixel0,this.yPixel1)},"~N");h(c$,"getScale",function(){return this.scaleData});h(c$,"toX",function(a){return this.maxX+(this.minX-this.maxX)*
this.toImageX(this.fixX(a))/(this.imageWidth-1)},"~N");h(c$,"toY",function(a){a=this.toSubspectrumIndex(a);return this.maxY+(this.minY-this.maxY)*a/(this.imageWidth-1)},"~N");h(c$,"toPixelX",function(a){var b=this.toX(this.xPixel0),c=this.toX(this.xPixel1);return this.xPixel0+s((a-b)/(c-b)*(this.xPixels-1))},"~N");h(c$,"toPixelY",function(a){return s(this.yPixel0+(a-this.scaleData.minYOnScale)/(this.scaleData.maxYOnScale-this.scaleData.minYOnScale)*this.yPixels)},"~N");h(c$,"getXPixels",function(){return this.xPixels});
h(c$,"getYPixels",function(){return this.yPixels});h(c$,"getXPixel0",function(){return this.xPixel0});C(c$,"DEFAULT_MIN_GRAY",0.05,"DEFAULT_MAX_GRAY",0.3)});m("JSV.common");w(["JSV.common.Measurement"],"JSV.common.Integral",null,function(){c$=z(JSV.common,"Integral",JSV.common.Measurement);c(c$,"setInt",function(a,b,c,e,g,f){this.setA(a,b,c,"",!1,!1,0,6);this.setPt2(g,f);this.setValue(e);return this},"~N,~N,JSV.common.Spectrum,~N,~N,~N")});m("JSV.common");c$=z(JSV.common,"IntegralComparator",null,
java.util.Comparator);h(c$,"compare",function(a,b){return a.getXVal()<b.getXVal()?-1:a.getXVal()>b.getXVal()?1:0},"JSV.common.Measurement,JSV.common.Measurement");m("JSV.common");w(["java.lang.Enum","JSV.common.MeasurementData","$.IntegralComparator"],"JSV.common.IntegralData","java.lang.Double java.util.Collections $.StringTokenizer JU.AU $.BS $.DF $.Lst $.PT JSV.common.Annotation $.Coordinate $.Integral $.ScriptToken".split(" "),function(){c$=r(function(){this.intRange=this.percentOffset=this.percentMinY=
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this.percentRange=Math.max(10,this.percentRange)});c$.getIntegrationRatiosFromString=c(c$,"getIntegrationRatiosFromString",function(a,b){for(var c=new JU.Lst,e=new java.util.StringTokenizer(b,",");e.hasMoreTokens();){var g=e.nextToken(),g=new java.util.StringTokenizer(g,":"),g=(new JSV.common.Annotation).setA(Double.parseDouble(g.nextToken()),0,a,g.nextToken(),!0,!1,0,0);c.addLast(g)}return c},"JSV.common.Spectrum,~S");c(c$,"getXYCoords",function(){return this.xyCoords});c(c$,"getPercentYValueAt",
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!1)}});c(c$,"getInfo",function(a){a.put("offset",Double.$valueOf(this.myParams.integralOffset));a.put("range",Double.$valueOf(this.myParams.integralRange));a.put("normalizationFactor",Double.$valueOf(this.normalizationFactor));a.put("integralTotal",Double.$valueOf(this.integralTotal));T(this,JSV.common.IntegralData,"getInfo",[a])},"java.util.Map");c(c$,"setMinimumIntegral",function(a){for(var b=this.size();0<=--b;)this.get(b).getValue()<a&&this.remove(b)},"~N");G(self.c$);c$=z(JSV.common.IntegralData,
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c$.toT=c(c$,"toT",function(a){if(!a.isAbsorbance())return null;var b=a.getXYCoords(),c=Array(b.length);JSV.common.Coordinate.isYInRange(b,0,4)||(b=JSV.common.Coordinate.normalise(b,0,4));for(var e=0;e<b.length;e++)c[e]=(new JSV.common.Coordinate).set(b[e].getXVal(),JSV.common.Spectrum.toTransmittance(b[e].getYVal()));return JSV.common.Spectrum.newSpectrum(a,c,"TRANSMITTANCE")},"JSV.common.Spectrum");c$.toA=c(c$,"toA",function(a){if(!a.isTransmittance())return null;for(var b=a.getXYCoords(),c=Array(b.length),
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c$.toAbsorbance=c(c$,"toAbsorbance",function(a,b){return Math.min(4,b?2-JSV.common.Spectrum.log10(a):-JSV.common.Spectrum.log10(a))},"~N,~B");c$.toTransmittance=c(c$,"toTransmittance",function(a){return 0>=a?1:Math.pow(10,-a)},"~N");c$.log10=c(c$,"log10",function(a){return Math.log(a)/Math.log(10)},"~N");c$.process=c(c$,"process",function(a,b){if(b===JSV.common.Spectrum.IRMode.TO_ABS||b===JSV.common.Spectrum.IRMode.TO_TRANS)for(var c=0;c<a.size();c++)a.set(c,JSV.common.Spectrum.taConvert(a.get(c),
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c(c$,"getInfo",function(a){var b=new java.util.Hashtable;if("id".equalsIgnoreCase(a))return b.put(a,this.id),b;b.put("id",this.id);JSV.common.Parameters.putInfo(a,b,"specShift",Double.$valueOf(this.specShift));var c="header".equals(a);if(!c&&null!=a)for(var e=this.headerTable.size();0<=--e;){var g=this.headerTable.get(e);if(g[0].equalsIgnoreCase(a)||g[2].equalsIgnoreCase(a))return b.put(a,g[1]),b}for(var g=new java.util.Hashtable,f=this.getHeaderRowDataAsArray(),e=0;e<f.length;e++){var h=JSV.source.JDXSourceStreamTokenizer.cleanLabel(f[e][0]);
if(!(null!=a&&!c&&!h.equals(a))){var k=JSV.common.Spectrum.fixInfoValue(f[e][1]);if(null==a){var l=new java.util.Hashtable;l.put("value",k);l.put("index",Integer.$valueOf(e+1));b.put(h,l)}else b.put(h,k)}}0<g.size()&&b.put("header",g);c||(JSV.common.Parameters.putInfo(a,b,"titleLabel",this.getTitleLabel()),JSV.common.Parameters.putInfo(a,b,"type",this.getDataType()),JSV.common.Parameters.putInfo(a,b,"isHZToPPM",Boolean.$valueOf(this.$isHZtoPPM)),JSV.common.Parameters.putInfo(a,b,"subSpectrumCount",
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"JSV.common.PeakInfo");c(c$,"getBasePeakInfo",function(){return 0==this.peakList.size()?new JSV.common.PeakInfo:new JSV.common.PeakInfo(' baseModel="" '+this.peakList.get(0))});c(c$,"getAxisLabel",function(a){var b=a?this.piUnitsX:this.piUnitsY;null==b&&(b=a?this.xLabel:this.yLabel);null==b&&(b=a?this.xUnits:this.yUnits);return null==b?"":b.equalsIgnoreCase("WAVENUMBERS")?"1/cm":b.equalsIgnoreCase("nanometers")?"nm":b},"~B");c(c$,"findXForPeakNearest",function(a){return JSV.common.Coordinate.findXForPeakNearest(this.xyCoords,
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f);break;case JSV.common.ScriptToken.DEFAULTLOADSCRIPT:f=JU.PT.rep(f,"''",'"');this.defaultLoadScript=0<f.length?f:null;break;case JSV.common.ScriptToken.DEFAULTNMRNORMALIZATION:this.nmrMaxY=JU.PT.parseFloat(f);break;case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(f);break;case JSV.common.ScriptToken.CLOSE:this.execClose(f);break;case JSV.common.ScriptToken.DEBUG:JU.Logger.setLogLevel(f.toLowerCase().equals("high")?6:JSV.common.Parameters.isTrue(f)?5:4);break;
case JSV.common.ScriptToken.GETPROPERTY:var l=null==this.selectedPanel?null:this.getPropertyAsJavaObject(f);null!=l&&this.selectedPanel.showMessage(JU.PT.toJSON(null,l),f);break;case JSV.common.ScriptToken.HIDDEN:this.si.siExecHidden(JSV.common.Parameters.isTrue(f));break;case JSV.common.ScriptToken.INTEGRATIONRATIOS:this.integrationRatios=f;this.execIntegrate(null);break;case JSV.common.ScriptToken.INTERFACE:this.interfaceOverlaid=this.checkOvelayInterface(f);break;case JSV.common.ScriptToken.INTEGRALOFFSET:case JSV.common.ScriptToken.INTEGRALRANGE:this.execSetIntegralParameter(k,
Double.parseDouble(f));break;case JSV.common.ScriptToken.JMOL:this.si.syncToJmol(f);break;case JSV.common.ScriptToken.JSV:this.syncScript(JU.PT.trimQuotes(f));break;case JSV.common.ScriptToken.LOAD:if(0==f.length){null!=this.defaultLoadScript&&this.runScriptNow(this.defaultLoadScript);break}this.load(f,(null==this.defaultLoadScript?"":this.defaultLoadScript+";")+a.getRemainingScript());e=null==this.selectedPanel?null:this.si.siLoaded(f);a=null;break;case JSV.common.ScriptToken.LOADIMAGINARY:this.loadImaginary=
JSV.common.Parameters.isTrue(f);break;case JSV.common.ScriptToken.PEAK:this.execPeak(f);break;case JSV.common.ScriptToken.PEAKLIST:this.execPeakList(f);break;case JSV.common.ScriptToken.SCALEBY:this.scaleSelectedBy(this.panelNodes,f);break;case JSV.common.ScriptToken.SCRIPT:if(f.equals("")||f.toLowerCase().startsWith("inline"))this.execScriptInline(f);else{var m=JSV.common.JSVFileManager.getFileAsString(f);null!=m&&100>this.scriptLevelCount&&this.runScriptNow(m)}break;case JSV.common.ScriptToken.SELECT:this.execSelect(f);
break;case JSV.common.ScriptToken.SPECTRUM:case JSV.common.ScriptToken.SPECTRUMNUMBER:this.setSpectrum(f)||(b=!1);break;case JSV.common.ScriptToken.STACKOFFSETY:this.execOverlayOffsetY(JU.PT.parseInt(""+JU.PT.parseFloat(f)));break;case JSV.common.ScriptToken.TEST:this.si.siExecTest(f);break;case JSV.common.ScriptToken.OVERLAY:case JSV.common.ScriptToken.VIEW:this.execView(f,!0);break;case JSV.common.ScriptToken.HIGHLIGHT:b=this.highlight(g);break;case JSV.common.ScriptToken.FINDX:case JSV.common.ScriptToken.GETSOLUTIONCOLOR:case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:case JSV.common.ScriptToken.IRMODE:case JSV.common.ScriptToken.LABEL:case JSV.common.ScriptToken.LINK:case JSV.common.ScriptToken.OVERLAYSTACKED:case JSV.common.ScriptToken.PRINT:case JSV.common.ScriptToken.SETPEAK:case JSV.common.ScriptToken.SETX:case JSV.common.ScriptToken.SHIFTX:case JSV.common.ScriptToken.SHOWERRORS:case JSV.common.ScriptToken.SHOWMEASUREMENTS:case JSV.common.ScriptToken.SHOWMENU:case JSV.common.ScriptToken.SHOWKEY:case JSV.common.ScriptToken.SHOWPEAKLIST:case JSV.common.ScriptToken.SHOWINTEGRATION:case JSV.common.ScriptToken.SHOWPROPERTIES:case JSV.common.ScriptToken.SHOWSOURCE:case JSV.common.ScriptToken.YSCALE:case JSV.common.ScriptToken.WRITE:case JSV.common.ScriptToken.ZOOM:if(this.isClosed()){b=
!1;break}switch(k){case JSV.common.ScriptToken.FINDX:this.pd().findX(null,Double.parseDouble(f));break;case JSV.common.ScriptToken.GETSOLUTIONCOLOR:this.show("solutioncolor"+f.toLowerCase());break;case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:this.execIntegrate(f);break;case JSV.common.ScriptToken.IRMODE:this.execIRMode(f);break;case JSV.common.ScriptToken.LABEL:this.pd().addAnnotation(JSV.common.ScriptToken.getTokens(f));break;case JSV.common.ScriptToken.LINK:this.pd().linkSpectra(JSV.common.PanelData.LinkMode.getMode(f));
break;case JSV.common.ScriptToken.OVERLAYSTACKED:this.pd().splitStack(!JSV.common.Parameters.isTrue(f));break;case JSV.common.ScriptToken.PRINT:e=this.execWrite(null);break;case JSV.common.ScriptToken.SETPEAK:this.pd().shiftSpectrum(NaN,f.equalsIgnoreCase("NONE")?1.7976931348623157E308:f.equalsIgnoreCase("?")?4.9E-324:Double.parseDouble(f));break;case JSV.common.ScriptToken.SETX:this.pd().shiftSpectrum(4.9E-324,Double.parseDouble(f));break;case JSV.common.ScriptToken.SHIFTX:this.pd().shiftSpectrum(f.equalsIgnoreCase("NONE")?
1.7976931348623157E308:Double.parseDouble(f),NaN);break;case JSV.common.ScriptToken.SHOWERRORS:this.show("errors");break;case JSV.common.ScriptToken.SHOWINTEGRATION:this.pd().showAnnotation(JSV.common.Annotation.AType.Integration,JSV.common.Parameters.getTFToggle(f));break;case JSV.common.ScriptToken.SHOWKEY:this.setOverlayLegendVisibility(JSV.common.Parameters.getTFToggle(f),!0);break;case JSV.common.ScriptToken.SHOWMEASUREMENTS:this.pd().showAnnotation(JSV.common.Annotation.AType.Measurements,JSV.common.Parameters.getTFToggle(f));
break;case JSV.common.ScriptToken.SHOWMENU:this.showMenu(-2147483648,0);break;case JSV.common.ScriptToken.SHOWPEAKLIST:this.pd().showAnnotation(JSV.common.Annotation.AType.PeakList,JSV.common.Parameters.getTFToggle(f));break;case JSV.common.ScriptToken.SHOWPROPERTIES:this.show("properties");break;case JSV.common.ScriptToken.SHOWSOURCE:this.show("source");break;case JSV.common.ScriptToken.YSCALE:this.setYScale(f);break;case JSV.common.ScriptToken.WINDOW:this.si.siNewWindow(JSV.common.Parameters.isTrue(f),
!1);break;case JSV.common.ScriptToken.WRITE:e=this.execWrite(f);break;case JSV.common.ScriptToken.ZOOM:b=this.execZoom(f)}}}catch(p){if(y(p,Exception))e=p.toString(),JU.Logger.error(p.toString()),b=!1,--c;else throw p;}}}this.scriptLevelCount--;this.si.siExecScriptComplete(e,!0);return b},"~S");c(c$,"execClose",function(a){var b=!a.startsWith("!");b||(a=a.substring(1));this.close(JU.PT.trimQuotes(a));(!b||0==this.panelNodes.size())&&this.si.siValidateAndRepaint(!0)},"~S");c(c$,"checkOvelayInterface",
function(a){return a.equalsIgnoreCase("single")||a.equalsIgnoreCase("overlay")},"~S");c(c$,"execPeak",function(a){try{var b=JSV.common.ScriptToken.getTokens(a);a=' type="'+b.get(0).toUpperCase()+'" _match="'+JU.PT.trimQuotes(b.get(1).toUpperCase())+'"';2<b.size()&&b.get(2).equalsIgnoreCase("all")&&(a+=' title="ALL"');this.processPeakPickEvent(new JSV.common.PeakInfo(a),!1)}catch(c){if(!y(c,Exception))throw c;}},"~S");c(c$,"execPeakList",function(a){var b=this.parameters,c=JSV.common.Parameters.getTFToggle(a);
if(0>a.indexOf("="))this.isClosed()||this.pd().getPeakListing(null,c);else for(var c=JSV.common.ScriptToken.getTokens(a),e=c.size();0<=--e;){a=c.get(e);var g=a.indexOf("=");if(!(0>=g)){var f=a.substring(0,g);a=a.substring(g+1);try{f.startsWith("thr")?b.peakListThreshold=Double.$valueOf(a).doubleValue():f.startsWith("int")&&(b.peakListInterpolation=a.equalsIgnoreCase("none")?"NONE":"parabolic"),this.isClosed()||this.pd().getPeakListing(b,Boolean.TRUE)}catch(h){if(!y(h,Exception))throw h;}}}},"~S");
c(c$,"highlight",function(a){var b=JSV.common.ScriptToken.getTokens(a),c=b.size();switch(c){case 3:case 5:case 6:case 7:break;case 2:case 4:if(b.get(c-1).equalsIgnoreCase("OFF"))break;default:return!1}if(!this.isClosed()){a=JU.PT.parseFloat(1<c?b.get(1):"");var e=JU.PT.parseFloat(2<c?b.get(2):""),g=this.getRGB(3<c?b.get(3):"100"),f=this.getRGB(4<c?b.get(4):"100"),h=this.getRGB(5<c?b.get(5):"100"),b=this.getRGB(6<c?b.get(6):"100");Float.isNaN(a)||Float.isNaN(e)?this.pd().removeAllHighlights():(this.pd().removeHighlight(a,
e),0>b&&(b=150),0<=g&&(0<=f&&0<=h)&&this.pd().addHighlight(null,a,e,null,g,f,h,b));this.repaint(!0)}return!0},"~S");c(c$,"getRGB",function(a){a=JU.PT.parseFloat(a);return B(Float.isNaN(a)?-1:1<a?a:255*a)},"~S");c(c$,"execZoom",function(a){var b=0,c=0,e=0,g=0;a=JU.PT.rep(a," - "," ").$replace(","," ");a=JSV.common.ScriptToken.getTokens(a);switch(a.size()){default:return!1;case 0:return b=this.pd().getCurrentGraphSet().getCurrentView(),a=Math.round(100*b.minXOnScale)/100+","+Math.round(100*b.maxXOnScale)/
100,a=this.selectedPanel.getInput("Enter zoom range x1 x2","Zoom",a),null==a||this.execZoom(a);case 1:return a=a.get(0),a.equalsIgnoreCase("next")?this.pd().nextView():a.toLowerCase().startsWith("prev")?this.pd().previousView():a.equalsIgnoreCase("out")?this.pd().resetView():a.equalsIgnoreCase("clear")&&this.pd().clearAllView(),!0;case 2:b=Double.parseDouble(a.get(0));c=Double.parseDouble(a.get(1));break;case 4:b=Double.parseDouble(a.get(0)),e=Double.parseDouble(a.get(1)),c=Double.parseDouble(a.get(2)),
g=Double.parseDouble(a.get(3))}this.pd().setZoom(b,e,c,g);return!0},"~S");c(c$,"scaleSelectedBy",function(a,b){try{for(var c=Double.parseDouble(b),e=a.size();0<=--e;)a.get(e).pd().scaleSelectedBy(c)}catch(g){if(!y(g,Exception))throw g;}},"JU.Lst,~S");c(c$,"pd",function(){return null==this.selectedPanel?null:this.selectedPanel.getPanelData()});c(c$,"isClosed",function(){return null==this.pd()});c(c$,"execSelect",function(a){if(a.startsWith("ID ")){if(!this.isClosed())try{this.pd().selectSpectrum(null,
"ID",JU.PT.trimQuotes(a.substring(3)),!0)}catch(b){if(!y(b,Exception))throw b;}}else{for(var c=this.panelNodes,e=c.size();0<=--e;)c.get(e).pd().selectFromEntireSet(-2147483648);c=new JU.Lst;this.fillSpecList(a,c,!1)}},"~S");c(c$,"execView",function(a,b){if(a.equals(""))this.checkOverlay();else{var c=new JU.Lst,e=this.fillSpecList(a,c,!0);0<c.size()&&this.si.siOpenDataOrFile(null,e,c,e,-1,-1,!1,null,null);b||this.si.siValidateAndRepaint(!1)}},"~S,~B");c(c$,"execIRMode",function(a){for(var b=JSV.common.Spectrum.IRMode.getMode(a),
c=this.pd().getSpectrum().dataType,e=this.panelNodes.size();0<=--e;)this.panelNodes.get(e).pd().setIRMode(b,c);this.setIRmode(a)},"~S");c(c$,"execIntegrate",function(a){this.isClosed()||(this.pd().checkIntegral(this.parameters,a),null!=this.integrationRatios&&this.pd().setIntegrationRatios(this.integrationRatios),this.integrationRatios=null,this.repaint(!0))},"~S");c(c$,"repaint",function(a){this.selectedPanel.doRepaint(a)},"~B");c(c$,"execSetIntegralParameter",function(a,b){var c=this.parameters;
switch(a){case JSV.common.ScriptToken.INTEGRALRANGE:c.integralRange=b;break;case JSV.common.ScriptToken.INTEGRALOFFSET:c.integralOffset=b}this.isClosed()||this.pd().checkIntegral(this.parameters,"update")},"JSV.common.ScriptToken,~N");c(c$,"setYScale",function(a){var b=JSV.common.ScriptToken.getTokens(a),c=0,e=!1;1<b.size()&&b.get(0).equalsIgnoreCase("ALL")&&(e=!0,c++);a=Double.parseDouble(b.get(c++));b=Double.parseDouble(b.get(c));if(e){e=this.pd().getSpectrum();for(c=this.panelNodes.size();0<=--c;){var g=
this.panelNodes.get(c);g.source===this.currentSource&&JSV.common.Spectrum.areXScalesCompatible(e,g.getSpectrum(),!1,!1)&&g.pd().setZoom(0,a,0,b)}}else this.pd().setZoom(0,a,0,b)},"~S");c(c$,"setOverlayLegendVisibility",function(a,b){b&&(this.overlayLegendVisible=null==a?!this.overlayLegendVisible:a===Boolean.TRUE);for(var c=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes),e=this.panelNodes.size();0<=--e;)this.showOverlayLegend(this.panelNodes.get(e),this.panelNodes.get(e)===c&&this.overlayLegendVisible)},
"Boolean,~B");c(c$,"showOverlayLegend",function(a,b){var c=a.legend;null==c&&b&&(c=a.setLegend(1<a.pd().getNumberOfSpectraInCurrentSet()&&1==a.pd().getNumberOfGraphSets()?this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null):null));null!=c&&c.setVisible(b)},"JSV.common.PanelNode,~B");c(c$,"syncScript",function(a){a.equals("TEST")&&(a=JSV.common.JSViewer.testScript);JU.Logger.info("JSViewer.syncScript Jmol>JSV "+a);if(0>a.indexOf("<PeakData"))a.startsWith("JSVSTR:")?this.si.syncToJmol(a):
(this.runScriptNow(a),0<=a.indexOf("#SYNC_PEAKS")&&this.syncPeaksAfterSyncScript());else{JU.Logger.info(">>toJSV>> "+a);var b=JU.PT.getQuotedAttribute(a,"sourceID"),c,e,g,f;if(null==b){e=JU.PT.getQuotedAttribute(a,"file");g=JU.PT.getQuotedAttribute(a,"index");if(null==e||null==g)return;e=JU.PT.rep(e,"#molfile","");c=JU.PT.getQuotedAttribute(a,"model");b=JU.PT.getQuotedAttribute(a,"src");f=null!=b&&b.startsWith("Jmol")?null:this.returnFromJmolModel;if(null!=c&&null!=f&&!c.equals(f)){JU.Logger.info("JSV ignoring model "+
c+"; should be "+f);return}this.returnFromJmolModel=null;if(0==this.panelNodes.size()||!this.checkFileAlreadyLoaded(e))JU.Logger.info("file "+e+" not found -- JSViewer closing all and reopening"),this.si.siSyncLoad(e);a=JU.PT.getQuotedAttribute(a,"type");f=null}else e=null,g=c=b,f=","+JU.PT.getQuotedAttribute(a,"atom")+",",a="ID";g=this.selectPanelByPeak(e,g,f);f=this.pd();f.selectSpectrum(e,a,c,!0);this.si.siSendPanelChange();f.addPeakHighlight(g);this.repaint(!0);(null==b||null!=g&&null!=g.getAtoms())&&
this.si.syncToJmol(this.jmolSelect(g))}},"~S");c(c$,"syncPeaksAfterSyncScript",function(){var a=this.currentSource;if(null!=a)try{var b="file="+JU.PT.esc(a.getFilePath()),c=a.getSpectra().get(0).getPeakList(),e=new JU.SB;e.append("[");for(var g=c.size(),a=0;a<g;a++){var f=c.get(a).toString(),f=f+" "+b;e.append(JU.PT.esc(f));0<a&&e.append(",")}e.append("]");this.si.syncToJmol("Peaks: "+e)}catch(h){if(!y(h,Exception))throw h;}});c(c$,"checkFileAlreadyLoaded",function(a){if(this.isClosed())return!1;
if(this.pd().hasFileLoaded(a))return!0;for(var b=this.panelNodes.size();0<=--b;)if(this.panelNodes.get(b).pd().hasFileLoaded(a))return this.si.siSetSelectedPanel(this.panelNodes.get(b).jsvp),!0;return!1},"~S");c(c$,"selectPanelByPeak",function(a,b,c){if(null==this.panelNodes)return null;for(var e=null,g=this.panelNodes.size();0<=--g;)this.panelNodes.get(g).pd().addPeakHighlight(null);e=this.pd().selectPeakByFileIndex(a,b,c);if(null!=e)this.setNode(JSV.common.PanelNode.findNode(this.selectedPanel,
this.panelNodes));else for(g=this.panelNodes.size();0<=--g;){var f=this.panelNodes.get(g);if(null!=(e=f.pd().selectPeakByFileIndex(a,b,c))){this.setNode(f);break}}return e},"~S,~S,~S");c(c$,"processPeakPickEvent",function(a){if(n(a,JSV.common.PeakInfo)){var b=this.pd().findMatchingPeakInfo(a);if(null==b){if(!"ALL".equals(a.getTitle()))return;for(var c=null,e=0;e<this.panelNodes.size();e++)if(null!=(b=this.panelNodes.get(e).pd().findMatchingPeakInfo(a))){c=this.panelNodes.get(e);break}if(null==c)return;
this.setNode(c)}a=b}else this.si.siSetSelectedPanel(a.getSource()),a=a.getPeakInfo();this.pd().addPeakHighlight(a);this.syncToJmol(a);a.isClearAll()?this.repaint(!1):this.pd().selectSpectrum(a.getFilePath(),a.getType(),a.getModel(),!0);this.si.siCheckCallbacks(a.getTitle())},"~O,~B");c(c$,"newStructToJmol",function(a){JU.Logger.info("sending new structure to Jmol:\n"+a);this.si.syncToJmol("struct:"+a)},"~S");c(c$,"syncToJmol",function(a){this.repaint(!0);this.returnFromJmolModel=a.getModel();this.si.syncToJmol(this.jmolSelect(a))},
"JSV.common.PeakInfo");c(c$,"sendPanelChange",function(){var a=this.pd(),b=a.getSpectrum(),c=b.getSelectedPeak();null==c&&(c=b.getModelPeakInfoForAutoSelectOnLoad());null==c&&(c=b.getBasePeakInfo());a.addPeakHighlight(c);JU.Logger.info(Thread.currentThread()+"JSViewer sendFrameChange "+this.selectedPanel);this.syncToJmol(c)});c(c$,"jmolSelect",function(a){var b="IR".equals(a.getType())||"RAMAN".equals(a.getType())?"vibration ON; selectionHalos OFF;":"vibration OFF; selectionhalos "+(null==a.getAtoms()?
"OFF":"ON");return"Select: "+a+' script="'+b+' " sourceID="'+this.pd().getSpectrum().sourceID+'"'},"JSV.common.PeakInfo");c(c$,"getPropertyAsJavaObject",function(a){var b=new java.util.Hashtable;if("SOURCEID".equalsIgnoreCase(a))return b.put(a,null==this.pd()?"":this.pd().getSpectrum().sourceID),b;if(null!=a&&a.startsWith("DATA_"))return b.put(a,""+JSV.common.JSVFileManager.htCorrelationCache.get(a.substring(5))),b;var c=!1;if(null!=a&&a.toUpperCase().startsWith("ALL ")||"all".equalsIgnoreCase(a))a=
a.substring(3).trim(),c=!0;"".equals(a)&&(a=null);var e=this.pd().getInfo(!0,a);if(!c&&null!=e)return e;null!=e&&b.put("current",e);c=new JU.Lst;for(e=0;e<this.panelNodes.size();e++)null!=this.panelNodes.get(e).jsvp&&c.addLast(this.panelNodes.get(e).getInfo(a));b.put("items",c);return b},"~S");c(c$,"getCoordinate",function(){if(!this.isClosed()){var a=this.pd().getClickedCoordinate();if(null!=a)return a.getXVal()+" "+a.getYVal()}return""});c(c$,"fillSpecList",function(a,b,c){var e,g=null,f=a.equalsIgnoreCase("NONE");
if(f||a.equalsIgnoreCase("all"))a="*";if(0>a.indexOf("*")){e=a.$plit(" ");a=new JU.SB;for(var h=0;h<e.length;h++){var k=e[h].indexOf(".");k!=e[h].lastIndexOf(".")&&(e[h]=e[h].substring(0,k+1)+e[h].substring(k+1).$replace(".","_"));a.append(e[h]).append(" ")}a=a.toString().trim()}if(a.equals("*"))e=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes));else if(a.startsWith('"')||a.startsWith("'"))e=JSV.common.ScriptToken.getTokens(a);else if(a=JU.PT.rep(a,"_",
" _ "),a=JU.PT.rep(a,"-"," - "),e=JSV.common.ScriptToken.getTokens(a),g=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes)),0==g.size())return null;var l=this.isClosed()?"1.":JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes).id,l=l.substring(0,l.indexOf(".")+1);a=new JU.SB;for(var m=e.size(),p=null,h=0;h<m;h++){var n=e.get(h),k=NaN,r=-1;h+1<m&&e.get(h+1).equals("*")?(h+=2,k=Double.parseDouble(e.get(h))):h+1<m&&e.get(h+1).equals("_")&&(h+=
2,r=Integer.parseInt(e.get(h)));if(n.equals("-")){null==p&&(p=g.get(0));n=h+1==m?g.get(g.size()-1):e.get(++h);n.contains(".")||(n=l+n);for(k=0;k<g.size()&&!g.get(k).equals(p);)k++;for(k++;k<g.size()&&!p.equals(n);){var s=JSV.common.PanelNode.findNodeById(p=g.get(k++),this.panelNodes);b.addLast(s.pd().getSpectrumAt(0));a.append(",").append(p)}}else if(n.startsWith("'")&&n.endsWith("'")&&(n='"'+JU.PT.trim(n,"'")+'"'),n.startsWith('"'))for(var n=JU.PT.trim(n,'"'),r=this.panelNodes.size(),t=0;t<r;t++){if(s=
this.panelNodes.get(t),null!=s.fileName&&s.fileName.startsWith(n)||null!=s.frameTitle&&s.frameTitle.startsWith(n))this.addSpecToList(s.pd(),k,-1,b,c),a.append(",").append(s.id)}else n.contains(".")||(n=l+n),s=JSV.common.PanelNode.findNodeById(n,this.panelNodes),null!=s&&(p=n,this.addSpecToList(s.pd(),k,r,b,c),a.append(",").append(n),0<r&&a.append(".").appendI(r))}c&&0<b.size()&&(s=JSV.common.PanelNode.findNodeById(a.substring(1),this.panelNodes),null!=s&&(this.setNode(s),b.clear()));return f?"NONE":
0<a.length()?a.toString().substring(1):null},"~S,JU.Lst,~B");c(c$,"addSpecToList",function(a,b,c,e,g){g?(a.getSpectrumAt(0).setUserYFactor(Double.isNaN(b)?1:b),a.addToList(c-1,e)):a.selectFromEntireSet(c-1)},"JSV.common.PanelData,~N,~N,JU.Lst,~B");c(c$,"getSolutionColor",function(a){var b=this.pd().getSpectrum(),c=b.canShowSolutionColor()?JSV.common.JSViewer.getInterface("JSV.common.Visible"):null;return null==c?-1:c.getColour(b,a)},"~B");c(c$,"openDataOrFile",function(a,b,c,e,g,f,h,k){if("NONE".equals(b))return this.close("View*"),
0;this.si.writeStatus("");var l=null,m=null,p=null,n=!1;null!=e&&e.startsWith("cache://")&&(a=Jmol.Cache.get(b=e));if(null!=a)try{p=b,m=l=JSV.common.JSVFileManager.getFullPathName(b)}catch(r){if(!y(r,JSV.exception.JSVException))throw r;}else if(null!=c)n=!0,m=p=l="View"+ ++this.nViews;else if(null!=e)try{this.recentURL=l=(new java.net.URL(JSV.common.JSVFileManager.appletDocumentBase,e,null)).toString(),p=JSV.common.JSVFileManager.getTagName(l)}catch(s){if(y(s,java.net.MalformedURLException))l=this.apiPlatform.newFile(e),
p=l.getName(),m=l=l.getFullPath(),this.recentURL=null;else throw s;}b=-1;if(0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,l))||0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,e)))return n?(--this.nViews,this.setNode(this.panelNodes.get(b))):this.si.writeStatus(l+" is already open"),-1;!h&&!n&&this.close("all");this.si.setCursor(3);try{this.si.siSetCurrentSource(n?JSV.source.JDXSource.createView(c):JSV.source.JDXReader.createJDXSource(JSV.common.JSVFileManager.getBufferedReaderForData(a),l,this.obscureTitleFromUser===
Boolean.TRUE,this.loadImaginary,g,f,this.nmrMaxY))}catch(t){if(y(t,Exception))return alert(t.toString()),this.si.setCursor(0),this.isApplet&&this.selectedPanel.showMessage(t.toString(),"Error Opening File"),-3;throw t;}this.si.setCursor(0);System.gc();null==m?(m=this.currentSource.getFilePath(),null!=m&&(p=m.substring(m.lastIndexOf("/")+1))):this.currentSource.setFilePath(m);null==k&&!n&&(k=m);null!=k&&this.currentSource.setID(k);this.si.siSetLoaded(p,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();n||c&&this.currentSource.isCompoundSource?this.combineSpectra(n?e:null):this.splitSpectra();this.pd().taintedAll=!0;n||this.si.siUpdateRecentMenus(l);return 0},"~O,~S,JU.Lst,~S,~N,~N,~B,~S");c(c$,"close",function(a){var b=0,c=null==a?-2:a.indexOf(">");0<c&&(b=JU.PT.parseInt(a.substring(c+1).trim()),a=a.substring(0,c).trim());"*".equals(a)&&(a="all");var e=
"all"===a;if(null==a||0==b&&a.equalsIgnoreCase("all"))this.closeSource(null);else{var g=a.equalsIgnoreCase("views"),c=new JU.Lst;a=a.$replace("\\","/");var f=this.panelNodes.size(),b=f-b;if(a.endsWith("*"))for(a=a.substring(0,a.length-1);0<=--f;)this.panelNodes.get(f).fileName.startsWith(a)&&c.addLast(this.panelNodes.get(f).source);else if(a.equalsIgnoreCase("selected"))for(a=null;0<=--f;)e=this.panelNodes.get(f).source,this.panelNodes.get(f).isSelected&&(null==a||a!==e)&&c.addLast(e),a=e;else if(e||
g||a.equalsIgnoreCase("simulations"))for(a=0;0<=--f&&a<b;){if(e||(g?this.panelNodes.get(f).isView:this.panelNodes.get(f).isSimulation))c.addLast(this.panelNodes.get(f).source),a++}else e=0==a.length?this.currentSource:JSV.common.PanelNode.findSourceByNameOrId(a,this.panelNodes),null!=e&&c.addLast(e);for(f=c.size();0<=--f;)this.closeSource(c.get(f));null==this.selectedPanel&&0<this.panelNodes.size()&&this.si.siSetSelectedPanel(JSV.common.PanelNode.getLastFileFirstNode(this.panelNodes))}},"~S");c(c$,
"load",function(a,b){var c=JSV.common.ScriptToken.getTokens(a),e=c.get(0),g=null,f=0;e.equalsIgnoreCase("ID")&&(g=JU.PT.trimQuotes(c.get(1)),e=c.get(2),f=2);var h=e.equalsIgnoreCase("APPEND"),k=e.equalsIgnoreCase("CHECK");(h||k)&&f++;0<f&&(e=c.get(f));null==b&&(b=this.defaultLoadScript);e.equals("?")?this.openFileFromDialog(h,!1,!1,b):e.equals("http://?")?this.openFileFromDialog(h,!0,!1,null):e.equals("$?")?this.openFileFromDialog(h,!0,!0,null):(e.equalsIgnoreCase("MOL")&&(e="http://SIMULATION/MOL="+
JU.PT.trimQuotes(c.get(++f))),!k&&!h&&(e.equals('""')&&null!=this.currentSource&&(e=this.currentSource.getFilePath()),this.close("all")),e=JU.PT.trimQuotes(e),e.startsWith("$")&&(e="http://SIMULATION/"+e.substring(1)),k=f+1<c.size()?Integer.$valueOf(c.get(++f)).intValue():-1,c=f+1<c.size()?Integer.$valueOf(c.get(++f)).intValue():k,this.si.siOpenDataOrFile(null,null,null,e,k,c,h,b,g))},"~S,~S");c(c$,"combineSpectra",function(a){var b=this.currentSource,c=b.getSpectra(),c=this.si.siGetNewJSVPanel2(c);
c.setTitle(b.getTitle());c.getTitle().equals("")&&(c.getPanelData().setViewTitle(b.getFilePath()),c.setTitle(a));this.si.siSetPropertiesFromPreferences(c,!0);this.spectraTree.createTree(++this.fileCount,b,[c]).getPanelNode().isView=!0;b=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);b.setFrameTitle(a);b.isView=!0;this.autoShowLegend&&1==this.pd().getNumberOfGraphSets()&&b.setLegend(this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null));this.si.siSetMenuEnables(b,!1)},"~S");
c(c$,"closeSource",function(a){for(var b=this.spectraTree.getRootNode(),c=null==a?null:a.getFilePath(),e=new JU.Lst,b=b.children();b.hasMoreElements();){var g=b.nextElement();if(null==c||g.getPanelNode().source.getFilePath().equals(c)){for(var f=g.children();f.hasMoreElements();){var h=f.nextElement();e.addLast(h);this.panelNodes.removeObj(h.getPanelNode())}e.addLast(g);if(null!=c)break}}this.spectraTree.deleteNodes(e);null==a&&(null!=this.currentSource&&this.currentSource.dispose(),this.currentSource=
null,null!=this.selectedPanel&&this.selectedPanel.dispose());this.currentSource===a&&(this.si.siSetSelectedPanel(null),this.si.siSetCurrentSource(null));for(e=c=0;e<this.panelNodes.size();e++)b=JU.PT.parseFloat(this.panelNodes.get(e).id),b>=c+1&&(c=s(Math.floor(b)));this.fileCount=c;System.gc();JU.Logger.checkMemory();this.si.siSourceClosed(a)},"JSV.source.JDXSource");c(c$,"setFrameAndTreeNode",function(a){null==this.panelNodes||(0>a||a>=this.panelNodes.size())||this.setNode(this.panelNodes.get(a))},
"~N");c(c$,"selectFrameNode",function(a){a=JSV.common.PanelNode.findNode(a,this.panelNodes);if(null==a)return null;this.spectraTree.setPath(this.spectraTree.newTreePath(a.treeNode.getPath()));this.setOverlayLegendVisibility(null,!1);return a},"JSV.api.JSVPanel");c(c$,"setSpectrum",function(a){if(0<=a.indexOf(".")){a=JSV.common.PanelNode.findNodeById(a,this.panelNodes);if(null==a)return!1;this.setNode(a)}else{a=JU.PT.parseInt(a);if(0>=a)return this.checkOverlay(),!1;this.setFrameAndTreeNode(a-1)}return!0},
"~S");c(c$,"splitSpectra",function(){for(var a=this.currentSource,b=a.getSpectra(),c=Array(b.size()),e=null,g=0;g<b.size();g++)e=b.get(g),e=this.si.siGetNewJSVPanel(e),this.si.siSetPropertiesFromPreferences(e,!0),c[g]=e;this.spectraTree.createTree(++this.fileCount,a,c);this.si.siGetNewJSVPanel(null);a=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);this.si.siSetMenuEnables(a,!0)});c(c$,"selectedTreeNode",function(a){null!=a&&(a.isLeaf()?this.setNode(a.getPanelNode()):System.out.println("not a leaf"),
this.si.siSetCurrentSource(a.getPanelNode().source))},"JSV.api.JSVTreeNode");c(c$,"dispose",function(){this.fileHelper=null;null!=this.viewDialog&&this.viewDialog.dispose();this.viewDialog=null;null!=this.overlayLegendDialog&&this.overlayLegendDialog.dispose();this.overlayLegendDialog=null;null!=this.jsvpPopupMenu&&(this.jsvpPopupMenu.jpiDispose(),this.jsvpPopupMenu=null);if(null!=this.panelNodes)for(var a=this.panelNodes.size();0<=--a;)this.panelNodes.get(a).dispose(),this.panelNodes.remove(a)});
c(c$,"runScript",function(a){null==this.scriptQueue?this.si.siProcessCommand(a):this.scriptQueue.addLast(a)},"~S");c(c$,"requestRepaint",function(){null!=this.selectedPanel&&this.repaintManager.refresh()});c(c$,"repaintDone",function(){this.repaintManager.repaintDone()});c(c$,"checkOverlay",function(){null!=this.mainPanel&&this.markSelectedPanels(this.panelNodes,this.mainPanel.getCurrentPanelIndex());this.viewDialog=this.getDialog(JSV.common.Annotation.AType.Views,null)});c(c$,"markSelectedPanels",
function(a,b){for(var c=a.size();0<=--c;)a.get(c).isSelected=b==c},"JU.Lst,~N");c(c$,"execOverlayOffsetY",function(a){if(-2147483648==a){if(null==this.selectedPanel)return;a=this.selectedPanel.getInput("Enter a vertical offset in percent for stacked plots","Overlay",""+this.recentStackPercent);a=JU.PT.parseFloat(a);if(Float.isNaN(a))return;a=B(a)}this.recentStackPercent=a;this.parameters.viewOffset=a;this.isClosed()&&this.pd().setYStackOffsetPercent(a)},"~N");c(c$,"execScriptInline",function(a){0<
a.length&&(a=a.substring(6).trim());0==a.length&&(a=this.selectedPanel.getInput("Enter a JSpecView script","Script",this.recentScript));null!=a&&(this.recentScript=a,this.runScriptNow(a))},"~S");c(c$,"setDisplay",function(a){this.apiPlatform.setViewer(this,this.display=a);var b=D(2,0);this.apiPlatform.getFullScreenDimensions(a,b);this.setScreenDimension(b[0],b[1])},"~O");c(c$,"setScreenDimension",function(a,b){b=Math.min(b,this.maximumSize);a=Math.min(a,this.maximumSize);this.dimScreen.width==a&&
this.dimScreen.height==b||this.resizeImage(a,b)},"~N,~N");c(c$,"resizeImage",function(a,b){0<a?(this.dimScreen.width=a,this.dimScreen.height=b):(a=0==this.dimScreen.width?this.dimScreen.width=500:this.dimScreen.width,b=0==this.dimScreen.height?this.dimScreen.height=500:this.dimScreen.height);this.g2d.setWindowParameters(a,b)},"~N,~N");c(c$,"updateJS",function(){null!=this.selectedPanel&&this.selectedPanel.paintComponent(this.apiPlatform.getGraphics(null))});c(c$,"processMouseEvent",function(a,b,c,
e,g){return null!=this.selectedPanel&&this.selectedPanel.processMouseEvent(a,b,c,e,g)},"~N,~N,~N,~N,~N");c(c$,"processTwoPointGesture",function(a){this.isClosed()||this.selectedPanel.processTwoPointGesture(a)},"~A");c(c$,"getApplet",function(){return this.html5Applet});c(c$,"openFileAsyncSpecial",function(a){var b=null==this.currentSource?"NO":this.getDialogManager().getDialogInput(this,"Do you want to append this file? (Answer NO to replace.)","Drag/Drop Action",3,null,null,"YES");null!=b&&(b=b.toLowerCase().startsWith("y")?
"append":"",this.runScript("load "+b+' "'+a+'"'))},"~S,~N");c(c$,"getHeight",function(){return this.dimScreen.height});c(c$,"getWidth",function(){return this.dimScreen.width});c(c$,"getPlatformInterface",function(a){return JSV.common.JSViewer.getInterface("JSV."+(this.isJS?"js2d.Js":"java.Awt")+a)},"~S");c(c$,"getDialogManager",function(){if(null!=this.dialogManager)return this.dialogManager;this.dialogManager=this.getPlatformInterface("DialogManager");return this.dialogManager.set(this)});c(c$,"getDialog",
function(a,b){switch(a){case JSV.common.Annotation.AType.Integration:return JSV.common.JSViewer.getInterface("JSV.dialog.IntegrationDialog").setParams("Integration for "+b,this,b);case JSV.common.Annotation.AType.Measurements:return JSV.common.JSViewer.getInterface("JSV.dialog.MeasurementsDialog").setParams("Measurements for "+b,this,b);case JSV.common.Annotation.AType.PeakList:return JSV.common.JSViewer.getInterface("JSV.dialog.PeakListDialog").setParams("Peak List for "+b,this,b);case JSV.common.Annotation.AType.OverlayLegend:return this.overlayLegendDialog=
JSV.common.JSViewer.getInterface("JSV.dialog.OverlayLegendDialog").setParams(this.pd().getViewTitle(),this,null);case JSV.common.Annotation.AType.Views:return this.viewDialog=JSV.common.JSViewer.getInterface("JSV.dialog.ViewsDialog").setParams("View/Combine/Close Spectra",this,null);default:return null}},"JSV.common.Annotation.AType,JSV.common.Spectrum");c(c$,"show",function(a){this.getDialogManager();if(a.equals("properties"))this.dialogManager.showProperties(null,this.pd().getSpectrum());else if(a.equals("errors"))this.dialogManager.showSourceErrors(null,
this.currentSource);else if(a.equals("source"))null==this.currentSource?0<this.panelNodes.size()&&this.dialogManager.showMessageDialog(null,"Please Select a Spectrum","Select Spectrum",0):this.dialogManager.showSource(this,this.pd().getSpectrum().getFilePath());else if(a.startsWith("solutioncolorfill"))if(0<=a.indexOf("all"))for(var b=this.panelNodes.size();0<=--b;)this.panelNodes.get(b).pd().setSolutionColor(a);else this.pd().setSolutionColor(a);else a.startsWith("solutioncolor")&&(a=this.getSolutionColorStr(0>
a.indexOf("false")),a="background-color:rgb("+a+")'><br />Predicted Solution Colour- RGB("+a+")<br /><br />",this.isJS?this.dialogManager.showMessage(this,"<div style='width:100%;height:100%;"+a+"</div>","Predicted Colour"):this.selectedPanel.showMessage("<html><body style='"+a+"</body></html>","Predicted Colour"))},"~S");c(c$,"getDialogPrint",function(a){if(!this.isJS)try{var b=this.getPlatformInterface("PrintDialog").set(this.offWindowFrame,this.lastPrintLayout,a).getPrintLayout();null!=b&&(this.lastPrintLayout=
b);return b}catch(c){if(!y(c,Exception))throw c;}return new JSV.common.PrintLayout},"~B");c(c$,"setIRmode",function(a){this.irMode=a.equals("AtoT")?JSV.common.Spectrum.IRMode.TO_TRANS:a.equals("TtoA")?JSV.common.Spectrum.IRMode.TO_ABS:JSV.common.Spectrum.IRMode.getMode(a)},"~S");c(c$,"getOptionFromDialog",function(a,b,c){return this.getDialogManager().getOptionFromDialog(null,a,this.selectedPanel,b,c)},"~A,~S,~S");c(c$,"print",function(a){return this.execWrite('PDF "'+a+'"')},"~S");c(c$,"execWrite",
function(a){this.isJS&&null==a&&(a="PDF");a=JSV.common.JSViewer.getInterface("JSV.export.Exporter").write(this,null==a?null:JSV.common.ScriptToken.getTokens(a),!1);this.si.writeStatus(a);return a},"~S");c(c$,"$export",function(a,b){null==a&&(a="XY");var c=this.pd(),e=c.getNumberOfSpectraInCurrentSet();if(-1>b||b>=e)return"Maximum spectrum index (0-based) is "+(e-1)+".";c=0>b?c.getSpectrum():c.getSpectrumAt(b);try{return JSV.common.JSViewer.getInterface("JSV.export.Exporter").exportTheSpectrum(this,
JSV.common.ExportType.getType(a),null,c,0,c.getXYCoords().length-1,null,!1)}catch(g){if(y(g,Exception))return JU.Logger.error(g.toString()),null;throw g;}},"~S,~N");h(c$,"postByteArray",function(a,b){return JSV.common.JSVFileManager.postByteArray(a,b)},"~S,~A");c(c$,"getOutputChannel",function(a,b){for(;a.startsWith("/");)a=a.substring(1);return(new JU.OC).setParams(this,a,!b,null)},"~S,~B");c$.getInterface=c(c$,"getInterface",function(a){try{var b=ba._4Name(a);return null==b?null:b.newInstance()}catch(c){if(y(c,
Exception))return JU.Logger.error("Interface.java Error creating instance for "+a+": \n"+c),null;throw c;}},"~S");c(c$,"showMessage",function(a){null!=this.selectedPanel&&null!=a&&this.selectedPanel.showMessage(a,null)},"~S");c(c$,"openFileFromDialog",function(a,b,c,e){var g=null;c?(g=this.fileHelper.getUrlFromDialog("Enter the name or identifier of a compound",this.recentSimulation),null!=g&&(this.recentSimulation=g,this.load((a?"APPEND ":"")+'"$'+g+'"',e))):b?(g=this.fileHelper.getUrlFromDialog("Enter the URL of a JCAMP-DX File",
null==this.recentURL?this.recentOpenURL:this.recentURL),null!=g&&(this.recentOpenURL=g,this.load((a?"APPEND ":"")+'"'+g+'"',e))):(b=[Boolean.$valueOf(a),e],b=this.fileHelper.showFileOpenDialog(this.mainPanel,b),null!=b&&this.openFile(b.getFullPath(),!a))},"~B,~B,~B,~S");c(c$,"openFile",function(a,b){if(b&&null!=this.panelNodes){var c=JSV.common.PanelNode.findSourceByNameOrId((new java.io.File(a)).getAbsolutePath(),this.panelNodes);null!=c&&this.closeSource(c)}this.si.siOpenDataOrFile(null,null,null,
a,-1,-1,!0,this.defaultLoadScript,null)},"~S,~B");c(c$,"selectPanel",function(a,b){var c=-1;if(null!=b){for(var e=b.size();0<=--e;){var g=b.get(e).jsvp;g===a?c=e:(g.setEnabled(!1),g.setFocusable(!1),g.getPanelData().closeAllDialogsExcept(JSV.common.Annotation.AType.NONE))}this.markSelectedPanels(b,c)}return c},"JSV.api.JSVPanel,JU.Lst");c(c$,"checkAutoIntegrate",function(){this.autoIntegrate&&this.pd().integrateAll(this.parameters)});c(c$,"parseInitScript",function(a){null==a&&(a="");a=new JSV.common.ScriptTokenizer(a,
!0);for(JU.Logger.debugging&&JU.Logger.info("Running in DEBUG mode");a.hasMoreTokens();){var b=a.nextToken(),c=new JSV.common.ScriptTokenizer(b,!1),e=c.nextToken();e.equalsIgnoreCase("SET")&&(e=c.nextToken());var e=e.toUpperCase(),g=JSV.common.ScriptToken.getScriptToken(e),b=JSV.common.ScriptToken.getValue(g,c,b);JU.Logger.info("KEY-> "+e+" VALUE-> "+b+" : "+g);try{switch(g){default:this.parameters.set(null,g,b);break;case JSV.common.ScriptToken.UNKNOWN:break;case JSV.common.ScriptToken.APPLETID:this.fullName=
this.appletName+"__"+(this.appletName=b)+"__";e=null;"undefined"!=typeof Jmol&&(e=Jmol._applets[b]);this.html5Applet=e;break;case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(b);break;case JSV.common.ScriptToken.COMPOUNDMENUON:this.allowCompoundMenu=Boolean.parseBoolean(b);break;case JSV.common.ScriptToken.APPLETREADYCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:this.si.siExecSetCallback(g,
b);break;case JSV.common.ScriptToken.ENDINDEX:this.initialEndIndex=Integer.parseInt(b);break;case JSV.common.ScriptToken.INTERFACE:this.checkOvelayInterface(b);break;case JSV.common.ScriptToken.IRMODE:this.setIRmode(b);break;case JSV.common.ScriptToken.MENUON:this.allowMenu=Boolean.parseBoolean(b);break;case JSV.common.ScriptToken.OBSCURE:null==this.obscureTitleFromUser&&(this.obscureTitleFromUser=Boolean.$valueOf(b));break;case JSV.common.ScriptToken.STARTINDEX:this.initialStartIndex=Integer.parseInt(b);
break;case JSV.common.ScriptToken.SYNCID:this.fullName=this.appletName+"__"+(this.syncID=b)+"__"}}catch(f){if(!y(f,Exception))throw f;}}},"~S");c(c$,"getSolutionColorStr",function(a){a=JU.CU.colorPtFromInt(this.getSolutionColor(a),null);return B(a.x)+","+B(a.y)+","+B(a.z)},"~B");C(c$,"sourceLabel","Original...","FILE_OPEN_OK",0,"FILE_OPEN_ALREADY",-1,"FILE_OPEN_ERROR",-3,"FILE_OPEN_NO_DATA",-4,"OVERLAY_DIALOG",-1,"OVERLAY_OFFSET",99,"PORTRAIT",1,"PAGE_EXISTS",0,"NO_SUCH_PAGE",1,"testScript",'<PeakData  index="1" title="" model="~1.1" type="1HNMR" xMin="3.2915" xMax="3.2965" atoms="15,16,17,18,19,20" multiplicity="" integral="1"> src="JPECVIEW" file="http://SIMULATION/$caffeine"',
"NLEVEL_MAX",100)});m("JSV.common");w(["JSV.common.Annotation","$.Coordinate"],"JSV.common.Measurement",null,function(){c$=r(function(){this.pt2=null;this.value=0;t(this,arguments)},JSV.common,"Measurement",JSV.common.Annotation);I(c$,function(){this.pt2=new JSV.common.Coordinate});c(c$,"setM1",function(a,b,c){this.setA(a,b,c,"",!1,!1,0,6);this.setPt2(this.getXVal(),this.getYVal());return this},"~N,~N,JSV.common.Spectrum");c(c$,"copyM",function(){var a=new JSV.common.Measurement;a.setA(this.getXVal(),
this.getYVal(),this.spec,this.text,!1,!1,this.offsetX,this.offsetY);a.setPt2(this.pt2.getXVal(),this.pt2.getYVal());return a});c(c$,"setPt2",function(a,b){this.spec=a;b&&this.setPt2(this.getXVal(),this.getYVal());return this},"JSV.common.Spectrum,~B");c(c$,"setPt2",function(a,b){this.pt2.setXVal(a);this.pt2.setYVal(b);this.value=Math.abs(a-this.getXVal());this.text=this.spec.setMeasurementText(this)},"~N,~N");c(c$,"getSpectrum",function(){return this.spec});c(c$,"setValue",function(a){this.value=
a;this.text=this.spec.setMeasurementText(this)},"~N");c(c$,"getValue",function(){return this.value});c(c$,"getXVal2",function(){return this.pt2.getXVal()});c(c$,"getYVal2",function(){return this.pt2.getYVal()});h(c$,"addSpecShift",function(a){this.setXVal(this.getXVal()+a);this.pt2.setXVal(this.pt2.getXVal()+a)},"~N");c(c$,"setYVal2",function(a){this.pt2.setYVal(a)},"~N");c(c$,"overlaps",function(a,b){return Math.min(this.getXVal(),this.getXVal2())<Math.max(a,b)&&Math.max(this.getXVal(),this.getXVal2())>
Math.min(a,b)},"~N,~N");h(c$,"toString",function(){return"["+this.getXVal()+","+this.pt2.getXVal()+"]"})});m("JSV.common");w(["JU.Lst","JSV.api.AnnotationData"],"JSV.common.MeasurementData",["JU.AU","$.DF","JSV.common.Annotation","$.Parameters"],function(){c$=r(function(){this.units=this.spec=this.type=null;this.precision=0;this.myParams=null;this.isON=!0;this.key=null;t(this,arguments)},JSV.common,"MeasurementData",JU.Lst,JSV.api.AnnotationData);u(c$,function(a,b){F(this,JSV.common.MeasurementData,
[]);this.type=a;this.spec=b;this.myParams=(new JSV.common.Parameters).setName("MeasurementData")},"JSV.common.Annotation.AType,JSV.common.Spectrum");c(c$,"getMeasurements",function(){return this});h(c$,"getAType",function(){return this.type});h(c$,"getState",function(){return this.isON});h(c$,"setState",function(a){this.isON=a},"~B");c(c$,"setMeasurements",function(){},"JU.Lst");h(c$,"getParameters",function(){return this.myParams});c(c$,"getDataHeader",function(){return JSV.common.MeasurementData.HEADER});
c(c$,"getMeasurementListArray",function(a){this.units=a;var b=this.getMeasurementListArrayReal(a),c=this.spec.isNMR()?4:2;a=this.spec.isHNMR()&&a.equals("ppm")?4:2;for(var e=Array(this.size()),g=this.size();0<=--g;)e[g]=[""+(g+1),JU.DF.formatDecimalDbl(b[g][0],c),JU.DF.formatDecimalDbl(b[g][1],c),JU.DF.formatDecimalDbl(b[g][2],a)];return e},"~S");c(c$,"getMeasurementListArrayReal",function(a){a=this.spec.isNMR()&&a.equalsIgnoreCase("HZ");for(var b=JU.AU.newDouble2(this.size()),c=0,e=this.size();0<=
--e;){var g=this.get(e).getValue();a&&(g*=this.spec.observedFreq);b[c++]=[this.get(e).getXVal(),this.get(e).getXVal2(),g]}return b},"~S");c$.checkParameters=c(c$,"checkParameters",function(a,b){if(0==a.size())return!1;var c=a.getParameters();switch(a.getAType()){case JSV.common.Annotation.AType.PeakList:return b.peakListInterpolation.equals(c.peakListInterpolation)&&b.peakListThreshold==c.peakListThreshold}return!1},"JSV.common.MeasurementData,JSV.common.ColorParameters");h(c$,"getSpectrum",function(){return this.spec});
h(c$,"getData",function(){return this});c(c$,"clear",function(a,b){for(var c=this.size();0<=--c;){var e=this.get(c);(0==e.text.length||e.overlaps(a,b))&&this.remove(c)}},"~N,~N");h(c$,"setSpecShift",function(a){for(var b=this.size();0<=--b;){var c=this.get(b),e=c.getXVal()+a;c.setXVal(e);c.setValue(e);c.text=JU.DF.formatDecimalDbl(e,this.precision)}},"~N");h(c$,"getGraphSetKey",function(){return this.key});h(c$,"setGraphSetKey",function(a){this.key=a},"~S");h(c$,"isVisible",function(){return!0});
c(c$,"getInfo",function(a){a.put("header",this.getDataHeader());a.put("table",this.getMeasurementListArrayReal("ppm"));null!=this.units&&a.put("units",this.units)},"java.util.Map");c$.HEADER=c$.prototype.HEADER=["","start","end","value"]});m("JSV.common");w(["java.lang.Enum","javajs.api.EventManager","java.util.Hashtable","JU.Lst"],"JSV.common.PanelData","java.lang.Boolean $.Double javajs.awt.Font JU.CU JSV.common.Annotation $.Coordinate $.GraphSet $.JSVFileManager $.JSVersion $.JSViewer $.MeasurementData $.Parameters $.PeakPickEvent $.ScriptToken $.Spectrum $.SubSpecChangeEvent $.ZoomEvent JSV.dialog.JSVDialog J.api.GenericGraphics JU.Logger".split(" "),
function(){c$=r(function(){this.graphSets=this.jsvp=this.options=this.currentGraphSet=this.listeners=this.vwr=this.g2d0=this.g2d=null;this.currentSplitPoint=0;this.coordsClicked=this.coordClicked=this.thisWidget=null;this.isIntegralDrag=this.drawXAxisLeftToRight=this.shiftPressed=this.ctrlPressed=!1;this.xAxisLeftToRight=!0;this.scalingFactor=1;this.integralShiftMode=0;this.left=60;this.right=50;this.coordStr="";this.startupPinTip="Click to set.";this.title=null;this.endIndex=this.startIndex=this.thisHeight=
this.thisWidth=this.nSpectra=this.clickCount=0;this.titleFontName=this.displayFontName=this.viewTitle=this.commonFilePath=null;this.isPrinting=!1;this.doReset=!0;this.printingFontName=null;this.printGraphPosition="default";this.isLinked=this.display1D=this.titleDrawn=!1;this.spectra=this.printJobTitle=null;this.taintedAll=!0;this.mouseState=this.currentFont=null;this.titleOn=this.gridOn=!1;this.mouseY=this.mouseX=0;this.linking=!1;this.xPixelClicked=0;this.gMain=this.optionsSaved=this.bgcolor=this.BLACK=
this.zoomBoxColor2=this.zoomBoxColor=this.highlightColor=this.unitsColor=this.titleColor=this.scaleColor=this.plotAreaColor=this.peakTabColor=this.integralPlotColor=this.gridColor=this.coordinatesColor=null;t(this,arguments)},JSV.common,"PanelData",null,javajs.api.EventManager);I(c$,function(){this.listeners=new JU.Lst;this.options=new java.util.Hashtable});u(c$,function(a,b){this.vwr=b;this.jsvp=a;this.g2d=this.g2d0=b.g2d;this.BLACK=this.g2d.getColor1(0);this.highlightColor=this.g2d.getColor4(255,
0,0,200);this.zoomBoxColor=this.g2d.getColor4(150,150,100,130);this.zoomBoxColor2=this.g2d.getColor4(150,100,100,130)},"JSV.api.JSVPanel,JSV.common.JSViewer");c(c$,"addListener",function(a){this.listeners.contains(a)||this.listeners.addLast(a)},"JSV.api.PanelListener");c(c$,"getCurrentGraphSet",function(){return this.currentGraphSet});c(c$,"dispose",function(){this.jsvp=null;for(var a=0;a<this.graphSets.size();a++)this.graphSets.get(a).dispose();this.listeners=this.options=this.thisWidget=this.coordsClicked=
this.coordClicked=this.currentGraphSet=this.currentFont=this.graphSets=null});c(c$,"setViewTitle",function(a){this.viewTitle=a},"~S");c(c$,"getViewTitle",function(){return null==this.viewTitle?this.getTitle():this.viewTitle});c(c$,"getInfo",function(a,b){var c=new java.util.Hashtable,e=null;if(a)return this.currentGraphSet.getInfo(b,this.getCurrentSpectrumIndex());for(var g,e=this.options.entrySet().iterator();e.hasNext()&&((g=e.next())||1);)JSV.common.Parameters.putInfo(b,c,g.getKey().name(),g.getValue());
JSV.common.Parameters.putInfo(b,c,"type",this.getSpectrumAt(0).getDataType());JSV.common.Parameters.putInfo(b,c,"title",this.title);JSV.common.Parameters.putInfo(b,c,"nSets",Integer.$valueOf(this.graphSets.size()));e=new JU.Lst;for(g=this.graphSets.size();0<=--g;)e.addLast(this.graphSets.get(g).getInfo(b,-1));c.put("sets",e);return c},"~B,~S");c(c$,"setBooleans",function(a,b){if(null==b)for(var c,e=a.getBooleans().entrySet().iterator();e.hasNext()&&((c=e.next())||1);)this.setBooleans(a,c.getKey());
else this.setBoolean(b,a.getBoolean(b))},"JSV.common.Parameters,JSV.common.ScriptToken");c(c$,"setBoolean",function(a,b){this.taintedAll=!0;if(a===JSV.common.ScriptToken.REVERSEPLOT)this.currentGraphSet.setReversePlot(b);else switch(this.options.put(a,Boolean.$valueOf(b)),a){case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:this.doReset=!0}},"JSV.common.ScriptToken,~B");c(c$,"getBoolean",function(a){if(a===JSV.common.ScriptToken.REVERSEPLOT)return this.currentGraphSet.reversePlot;
if(null==this.options)return!1;a=this.options.get(a);return null!=a&&n(a,Boolean)&&a===Boolean.TRUE},"JSV.common.ScriptToken");c(c$,"setFontName",function(a,b){switch(a){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.displayFontName=b;break;case JSV.common.ScriptToken.TITLEFONTNAME:this.titleFontName=b}null!=b&&this.options.put(a,b)},"JSV.common.ScriptToken,~S");c(c$,"getDisplay1D",function(){return this.display1D});c(c$,"initOne",function(a){this.spectra=new JU.Lst;this.spectra.addLast(a);this.initMany(this.spectra,
0,0)},"JSV.common.Spectrum");c(c$,"initMany",function(a,b,c){this.startIndex=b;this.endIndex=c;this.nSpectra=a.size();this.spectra=a;this.commonFilePath=a.get(0).getFilePath();for(b=0;b<this.nSpectra;b++)if(!this.commonFilePath.equalsIgnoreCase(a.get(b).getFilePath())){this.commonFilePath=null;break}this.setGraphSets(JSV.common.PanelData.LinkMode.NONE)},"JU.Lst,~N,~N");c(c$,"setGraphSets",function(a){this.graphSets=JSV.common.GraphSet.createGraphSetsAndSetLinkMode(this,this.jsvp,this.spectra,this.startIndex,
this.endIndex,a);this.currentGraphSet=this.graphSets.get(0);this.title=this.getSpectrum().getTitleLabel()},"JSV.common.PanelData.LinkMode");c(c$,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.graphSets.size()&&null==(b=this.graphSets.get(c).findMatchingPeakInfo(a));c++);return b},"JSV.common.PeakInfo");c(c$,"integrateAll",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).integrate(-1,a)},"JSV.common.ColorParameters");c(c$,"getNumberOfGraphSets",function(){return this.graphSets.size()});
c(c$,"getTitle",function(){return this.title});c(c$,"refresh",function(){this.doReset=!0});c(c$,"addAnnotation",function(a){a=this.currentGraphSet.addAnnotation(a,this.getTitle());null!=a&&(this.title=a)},"JU.Lst");c(c$,"addPeakHighlight",function(a){for(var b=0;b<this.graphSets.size();b++)this.graphSets.get(b).addPeakHighlight(a)},"JSV.common.PeakInfo");c(c$,"selectPeakByFileIndex",function(a,b,c){var e=this.currentGraphSet.selectPeakByFileIndex(a,b,c);if(null==e)for(var g=this.graphSets.size();0<=
--g&&!(this.graphSets.get(g)!==this.currentGraphSet&&null!=(e=this.graphSets.get(g).selectPeakByFileIndex(a,b,c))););return e},"~S,~S,~S");c(c$,"setPlotColors",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).setPlotColors(a)},"~A");c(c$,"selectSpectrum",function(a,b,c,e){e&&this.currentGraphSet.selectSpectrum(a,b,c);if("ID".equals(b))this.jumpToSpectrumIndex(this.getCurrentSpectrumIndex(),!0);else for(e=0;e<this.graphSets.size();e++)this.graphSets.get(e)!==this.currentGraphSet&&
this.graphSets.get(e).selectSpectrum(a,b,c)},"~S,~S,~S,~B");c(c$,"hasFileLoaded",function(a){for(var b=this.graphSets.size();0<=--b;)if(this.graphSets.get(b).hasFileLoaded(a))return!0;return!1},"~S");c(c$,"clearAllView",function(){for(var a=this.graphSets.size();0<=--a;)this.graphSets.get(a).resetViewCompletely()});c(c$,"drawGraph",function(a,b,c,e,g,f){var h;this.gMain=a;this.display1D=!this.isLinked&&this.getBoolean(JSV.common.ScriptToken.DISPLAY1D);var k=40,l=50,m=this.isPrinting||this.doReset||
this.thisWidth!=e||this.thisHeight!=g;m&&(this.taintedAll=!0);this.taintedAll&&this.g2d.fillBackground(c,this.bgcolor);b!==a&&(this.g2d.fillBackground(b,null),a!==c&&this.g2d.fillBackground(a,null),this.g2d.setStrokeBold(a,!1));this.isPrinting?(k*=3,l*=3,this.scalingFactor=10,h=!1):(this.scalingFactor=1,h=this.getBoolean(JSV.common.ScriptToken.COORDINATESON),this.titleOn=this.getBoolean(JSV.common.ScriptToken.TITLEON),this.gridOn=this.getBoolean(JSV.common.ScriptToken.GRIDON));this.titleDrawn=this.doReset=
!1;this.thisWidth=e;this.thisHeight=g;for(var p=this.graphSets.size();0<=--p;)this.graphSets.get(p).drawGraphSet(a,b,c,e,g,this.left,this.right,k,l,m,this.taintedAll);this.titleOn&&(!this.titleDrawn&&this.taintedAll)&&this.drawTitle(a,g*this.scalingFactor,e*this.scalingFactor,this.getDrawTitle(this.isPrinting));h&&null!=this.coordStr&&this.drawCoordinates(b,k,this.thisWidth-this.right,k-20);f&&this.taintedAll&&(c=null!=this.commonFilePath?this.commonFilePath:1==this.graphSets.size()&&null!=this.currentGraphSet.getTitle(!0)?
this.getSpectrum().getFilePath():null,null!=c&&this.printFilePath(a,this.left,g,c));this.isPrinting&&this.printVersion(a,g);this.taintedAll=this.isPrinting||a===b},"~O,~O,~O,~N,~N,~B");c(c$,"drawCoordinates",function(a,b,c,e){this.g2d.setGraphicsColor(a,this.coordinatesColor);b=this.setFont(a,this.jsvp.getWidth(),0,12,!0);this.g2d.drawString(a,this.coordStr,c-b.stringWidth(this.coordStr),e)},"~O,~N,~N,~N");c(c$,"setFont",function(a,b,c,e,g){return this.g2d.setFont(a,this.getFont(a,b,c,e,g))},"~O,~N,~N,~N,~B");
c(c$,"printFilePath",function(a,b,c,e){b*=this.scalingFactor;c*=this.scalingFactor;0<e.indexOf("?")&&(e=e.substring(e.indexOf("?")+1));e=e.substring(e.lastIndexOf("/")+1);e=e.substring(e.lastIndexOf("\\")+1);this.g2d.setGraphicsColor(a,this.BLACK);var g=this.setFont(a,1E3,0,9,!0);b!=this.left*this.scalingFactor&&(b-=g.stringWidth(e));this.g2d.drawString(a,e,b,c-g.getHeight())},"~O,~N,~N,~S");c(c$,"printVersion",function(a,b){this.g2d.setGraphicsColor(a,this.BLACK);var c=this.setFont(a,100,0,12,!0),
e=this.jsvp.getApiPlatform().getDateFormat(null)+" JSpecView "+JSV.common.JSVersion.VERSION_SHORT,g=c.stringWidth(e);this.g2d.drawString(a,e,(this.thisWidth-this.right)*this.scalingFactor-g,b*this.scalingFactor-3*c.getHeight())},"~O,~N");c(c$,"drawTitle",function(a,b,c,e){e=e.$replace("\n"," ");var g=this.getFont(a,c,this.isPrinting||this.getBoolean(JSV.common.ScriptToken.TITLEBOLDON)?1:0,14,!0),f=g.stringWidth(e);f>c&&(g=s(14*c/f),10>g&&(g=10),g=this.getFont(a,c,this.isPrinting||this.getBoolean(JSV.common.ScriptToken.TITLEBOLDON)?
1:0,g,!0));this.g2d.setGraphicsColor(a,this.titleColor);this.setCurrentFont(this.g2d.setFont(a,g));this.g2d.drawString(a,e,this.isPrinting?this.left*this.scalingFactor:5,b-s(g.getHeight()*(this.isPrinting?2:0.5)))},"~O,~N,~N,~S");c(c$,"setCurrentFont",function(a){this.currentFont=a},"javajs.awt.Font");c(c$,"getFontHeight",function(){return this.currentFont.getAscent()});c(c$,"getStringWidth",function(a){return this.currentFont.stringWidth(a)},"~S");c(c$,"selectFromEntireSet",function(a){for(var b=
0,c=0;b<this.graphSets.size();b++)if(-2147483648==a)this.graphSets.get(b).setSelected(-1);else for(var e=this.graphSets.get(b).spectra,g=0;g<e.size();g++,c++)(0>a||a==c)&&this.graphSets.get(b).setSelected(g)},"~N");c(c$,"addToList",function(a,b){for(var c=0;c<this.spectra.size();c++)(0>a||c==a)&&b.addLast(this.spectra.get(c))},"~N,JU.Lst");c(c$,"scaleSelectedBy",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).scaleSelectedBy(a)},"~N");c(c$,"setCurrentGraphSet",function(a,
b,c){b=1<a.nSplit?a.getSplitPoint(b):a.getCurrentSpectrumIndex();var e=this.currentGraphSet!==a,g=e||this.currentSplitPoint!=b;this.currentGraphSet=a;this.currentSplitPoint=b;(e||1<a.nSplit&&g)&&this.setSpectrum(b,!0);if(!e){e=a.checkSpectrumClickedEvent(this.mouseX,this.mouseY,c);if(!e)return;this.currentSplitPoint=b=a.getCurrentSpectrumIndex();this.setSpectrum(b,!0)}this.jumpToSpectrumIndex(b,e||1<a.nSplit&&g)},"JSV.common.GraphSet,~N,~N");c(c$,"jumpToSpectrum",function(a){a=this.currentGraphSet.getSpectrumIndex(a);
this.jumpToSpectrumIndex(a,!0)},"JSV.common.Spectrum");c(c$,"jumpToSpectrumIndex",function(a,b){if(!(0>a||a>=this.currentGraphSet.nSpectra)){this.currentSplitPoint=a;b&&this.setSpectrum(this.currentSplitPoint,1<this.currentGraphSet.nSplit);var c=this.getSpectrum();this.notifySubSpectrumChange(c.getSubIndex(),c)}},"~N,~B");c(c$,"splitStack",function(a){this.currentGraphSet.splitStack(this.graphSets,a)},"~B");c(c$,"getNumberOfSpectraInCurrentSet",function(){return this.currentGraphSet.nSpectra});c(c$,
"getSourceID",function(){return this.getSpectrumAt(0).sourceID});c(c$,"getStartingPointIndex",function(a){return this.currentGraphSet.viewData.getStartingPointIndex(a)},"~N");c(c$,"getEndingPointIndex",function(a){return this.currentGraphSet.viewData.getEndingPointIndex(a)},"~N");c(c$,"haveSelectedSpectrum",function(){return this.currentGraphSet.haveSelectedSpectrum()});c(c$,"getShowAnnotation",function(a){return this.currentGraphSet.getShowAnnotation(a,-1)},"JSV.common.Annotation.AType");c(c$,"showAnnotation",
function(a,b){this.currentGraphSet.setShowAnnotation(a,b)},"JSV.common.Annotation.AType,Boolean");c(c$,"setYStackOffsetPercent",function(a){this.currentGraphSet.yStackOffsetPercent=a},"~N");c(c$,"setSpectrum",function(a,b){this.currentGraphSet.setSpectrum(a,b)},"~N,~B");c(c$,"getSpectrum",function(){return this.currentGraphSet.getSpectrum()});c(c$,"setSpecForIRMode",function(a){this.taintedAll=!0;var b=this.currentGraphSet.getSpectrum();this.currentGraphSet.setSpectrumJDX(a);for(var c=0;c<this.spectra.size();c++)this.spectra.get(c)===
b&&this.spectra.set(c,a)},"JSV.common.Spectrum");c(c$,"isShowAllStacked",function(){return this.currentGraphSet.showAllStacked});c(c$,"getCurrentSpectrumIndex",function(){return this.currentGraphSet.getCurrentSpectrumIndex()});c(c$,"getSpectrumAt",function(a){return null==this.currentGraphSet?null:this.currentGraphSet.getSpectrumAt(a)},"~N");c(c$,"addHighlight",function(a,b,c,e,g,f,h,k){(null==a?this.currentGraphSet:a).addHighlight(b,c,e,this.g2d.getColor4(g,f,h,k))},"JSV.common.GraphSet,~N,~N,JSV.common.Spectrum,~N,~N,~N,~N");
c(c$,"removeHighlight",function(a,b){this.currentGraphSet.removeHighlight(a,b)},"~N,~N");c(c$,"removeAllHighlights",function(){this.currentGraphSet.removeAllHighlights()});c(c$,"setZoom",function(a,b,c,e){this.currentGraphSet.setZoom(a,b,c,e);this.taintedAll=this.doReset=!0;this.notifyListeners(new JSV.common.ZoomEvent)},"~N,~N,~N,~N");c(c$,"resetView",function(){this.currentGraphSet.resetView()});c(c$,"previousView",function(){this.currentGraphSet.previousView()});c(c$,"nextView",function(){this.currentGraphSet.nextView()});
c(c$,"getSelectedIntegral",function(){return this.currentGraphSet.getSelectedIntegral()});c(c$,"advanceSubSpectrum",function(a){this.currentGraphSet.advanceSubSpectrum(a)},"~N");c(c$,"setSelectedIntegral",function(a){this.currentGraphSet.setSelectedIntegral(a)},"~N");c(c$,"scaleYBy",function(a){this.currentGraphSet.scaleYBy(a)},"~N");c(c$,"toPeak",function(a){this.currentGraphSet.toPeak(a)},"~N");c(c$,"getClickedCoordinate",function(){return this.coordClicked});c(c$,"getPickedCoordinates",function(a,
b){return JSV.common.Coordinate.getPickedCoordinates(this.coordsClicked,this.coordClicked,a,b)},"JSV.common.Coordinate,JSV.common.Coordinate");c(c$,"shiftSpectrum",function(a,b){return this.currentGraphSet.shiftSpectrum(a,b)},"~N,~N");c(c$,"findX",function(a,b){this.currentGraphSet.setXPointer(a,b)},"JSV.common.Spectrum,~N");c(c$,"setXPointers",function(a,b,c,e){this.currentGraphSet.setXPointer(a,b);this.currentGraphSet.setXPointer2(c,e)},"JSV.common.Spectrum,~N,JSV.common.Spectrum,~N");c(c$,"isCurrentGraphSet",
function(a){return a===this.currentGraphSet},"JSV.common.GraphSet");c(c$,"repaint",function(){this.jsvp.doRepaint(!1)});c(c$,"setToolTipText",function(a){this.jsvp.setToolTipText(a)},"~S");c(c$,"setHighlightColor",function(a){this.setColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR,a)},"javajs.api.GenericColor");c(c$,"getInput",function(a,b,c){return this.jsvp.getInput(a,b,c)},"~S,~S,~S");c(c$,"getFont",function(a,b,c,e,g){e*=this.scalingFactor;g?400>b&&(e=b*e/400):250>b&&(e=b*e/250);b=this.jsvp.getFontFaceID(this.isPrinting?
this.printingFontName:this.displayFontName);return this.currentFont=javajs.awt.Font.createFont3D(b,c,e,e,this.jsvp.getApiPlatform(),a)},"~O,~N,~N,~N,~B");c(c$,"notifySubSpectrumChange",function(a,b){this.notifyListeners(new JSV.common.SubSpecChangeEvent(a,null==b?null:b.getTitleLabel()))},"~N,JSV.common.Spectrum");c(c$,"notifyPeakPickedListeners",function(a){null==a&&(a=new JSV.common.PeakPickEvent(this.jsvp,this.coordClicked,this.getSpectrum().getAssociatedPeakInfo(this.xPixelClicked,this.coordClicked)));
this.notifyListeners(a)},"JSV.common.PeakPickEvent");c(c$,"notifyListeners",function(a){for(var b=0;b<this.listeners.size();b++)null!=this.listeners.get(b)&&this.listeners.get(b).panelEvent(a)},"~O");c(c$,"escapeKeyPressed",function(a){this.currentGraphSet.escapeKeyPressed(a)},"~B");c(c$,"hasFocus",function(){return this.jsvp.hasFocus()});c(c$,"isMouseUp",function(){return this.mouseState===JSV.common.PanelData.Mouse.UP});c(c$,"doMouseMoved",function(a,b){this.mouseX=a;this.mouseY=b;this.mouseState=
JSV.common.PanelData.Mouse.UP;this.clickCount=0;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&c.mouseMovedEvent(a,b)},"~N,~N");c(c$,"doMousePressed",function(a,b){this.mouseState=JSV.common.PanelData.Mouse.DOWN;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&(this.setCurrentGraphSet(c,b,0),this.clickCount=++this.clickCount%3,c.checkWidgetEvent(a,b,!0))},"~N,~N");c(c$,"doMouseDragged",function(a,b){this.isIntegralDrag=(new Boolean(this.isIntegralDrag|this.ctrlPressed)).valueOf();
this.mouseState=JSV.common.PanelData.Mouse.DOWN;JSV.common.GraphSet.findGraphSet(this.graphSets,a,b)===this.currentGraphSet&&(this.currentGraphSet.checkWidgetEvent(a,b,!1),this.currentGraphSet.mouseMovedEvent(a,b))},"~N,~N");c(c$,"doMouseReleased",function(a,b,c){this.mouseState=JSV.common.PanelData.Mouse.UP;!(null==this.thisWidget&&null==this.currentGraphSet.pendingMeasurement)&&c&&(this.currentGraphSet.mouseReleasedEvent(a,b),this.thisWidget=null,this.isIntegralDrag=!1,this.integralShiftMode=0)},
"~N,~N,~B");c(c$,"doMouseClicked",function(a,b,c){var e=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=e&&(this.setCurrentGraphSet(e,b,this.clickCount),e.mouseClickedEvent(a,b,this.clickCount,c),this.repaint())},"~N,~N,~B");c(c$,"hasCurrentMeasurements",function(a){return this.currentGraphSet.hasCurrentMeasurement(a)},"JSV.common.Annotation.AType");c(c$,"getDialog",function(a){return this.currentGraphSet.getDialog(a,-1)},"JSV.common.Annotation.AType");c(c$,"addDialog",function(a,b,c){this.currentGraphSet.addDialog(a,
b,c)},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");c(c$,"getPeakListing",function(a,b){null!=a&&this.currentGraphSet.getPeakListing(-1,a,!0);this.currentGraphSet.setPeakListing(b)},"JSV.common.Parameters,Boolean");c(c$,"checkIntegral",function(a,b){this.currentGraphSet.checkIntegral(a,b)},"JSV.common.Parameters,~S");c(c$,"setIntegrationRatios",function(a){this.currentGraphSet.setIntegrationRatios(a)},"~S");c(c$,"getView",function(){return this.currentGraphSet.getCurrentView()});c(c$,"closeAllDialogsExcept",
function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).closeDialogsExcept(a)},"JSV.common.Annotation.AType");c(c$,"removeDialog",function(a){this.currentGraphSet.removeDialog(a)},"JSV.dialog.JSVDialog");c(c$,"normalizeIntegral",function(){var a=this.getSelectedIntegral();if(null!=a){var b=a.text;0==b.length&&(b=""+a.getValue());a=this.getInput("Enter a new value for this integral","Normalize Integral",b);try{this.setSelectedIntegral(Double.parseDouble(a))}catch(c){if(!y(c,Exception))throw c;
}}});c(c$,"getDrawTitle",function(a){var b=null;a?b=this.printJobTitle:1==this.nSpectra?b=this.getSpectrum().getPeakTitle():null!=this.viewTitle?(null!=this.currentGraphSet.getTitle(!1)&&(b=this.getSpectrum().getPeakTitle()),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();0<=b.indexOf("\n")&&(b=b.substring(0,b.indexOf("\n")).trim());return b},"~B");c(c$,"getPrintJobTitle",function(a){var b=null;1==this.nSpectra?b=this.getSpectrum().getTitle():null!=this.viewTitle?(1==this.graphSets.size()&&
(b=this.currentGraphSet.getTitle(a)),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();0<=b.indexOf("\n")?b=b.substring(0,b.indexOf("\n")).trim():b.startsWith("$")&&(b=b.substring(1));return b},"~B");c(c$,"linkSpectra",function(a){a===JSV.common.PanelData.LinkMode.ALL&&(a=2==this.nSpectra?JSV.common.PanelData.LinkMode.AB:3==this.nSpectra?JSV.common.PanelData.LinkMode.ABC:JSV.common.PanelData.LinkMode.NONE);a!==JSV.common.PanelData.LinkMode.NONE&&a.toString().length!=this.nSpectra||this.setGraphSets(a)},
"JSV.common.PanelData.LinkMode");c(c$,"doZoomLinked",function(a,b,c,e,g,f){if(!this.linking){this.linking=!0;for(var h=a.getSpectrumAt(0),k=this.graphSets.size();0<=--k;){var l=this.graphSets.get(k);l!==a&&JSV.common.Spectrum.areXScalesCompatible(h,this.graphSets.get(k).getSpectrumAt(0),!1,!0)&&l.doZoom(b,0,c,0,f,!1,g,!1,e)}this.linking=!1}},"JSV.common.GraphSet,~N,~N,~B,~B,~B");c(c$,"clearLinkViews",function(a){if(!this.linking){this.linking=!0;for(var b=a.getSpectrum(),c=this.graphSets.size();0<=
--c;){var e=this.graphSets.get(c);e!==a&&JSV.common.Spectrum.areXScalesCompatible(b,this.graphSets.get(c).getSpectrum(),!1,!0)&&e.clearViews()}this.linking=!1}},"JSV.common.GraphSet");c(c$,"setlinkedXMove",function(a,b,c){if(!this.linking){this.linking=!0;for(var e=a.getSpectrum(),g=this.graphSets.size();0<=--g;){var f=this.graphSets.get(g);f!==a&&JSV.common.Spectrum.areXScalesCompatible(e,this.graphSets.get(g).getSpectrum(),!1,!0)&&null==f.imageView&&(c?f.setXPixelMovedTo(1.7976931348623157E308,
b,0,0):f.setXPixelMovedTo(b,1.7976931348623157E308,0,0))}this.linking=!1}},"JSV.common.GraphSet,~N,~B");c(c$,"set2DCrossHairsLinked",function(a,b,c,e){for(var g=this.graphSets.size();0<=--g;){var f=this.graphSets.get(g);f!==a&&f.set2DXY(b,c,e)}},"JSV.common.GraphSet,~N,~N,~B");c(c$,"dialogsToFront",function(a){this.currentGraphSet.dialogsToFront(a)},"JSV.common.Spectrum");c(c$,"setColor",function(a,b){null!=b&&this.options.put(a,JU.CU.toRGBHexString(b));switch(a){case JSV.common.ScriptToken.BACKGROUNDCOLOR:this.jsvp.setBackgroundColor(this.bgcolor=
b);this.taintedAll=!0;break;case JSV.common.ScriptToken.COORDINATESCOLOR:this.coordinatesColor=b;break;case JSV.common.ScriptToken.GRIDCOLOR:this.gridColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:this.highlightColor=b;255==this.highlightColor.getOpacity255()&&this.highlightColor.setOpacity255(150);break;case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:this.integralPlotColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.PEAKTABCOLOR:this.peakTabColor=b;this.taintedAll=
!0;break;case JSV.common.ScriptToken.PLOTCOLOR:for(var c=this.graphSets.size();0<=--c;)this.graphSets.get(c).setPlotColor0(b);this.taintedAll=!0;break;case JSV.common.ScriptToken.PLOTAREACOLOR:this.plotAreaColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.SCALECOLOR:this.scaleColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.TITLECOLOR:this.titleColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.UNITSCOLOR:this.unitsColor=b;this.taintedAll=!0;break;case JSV.common.ScriptToken.ZOOMBOXCOLOR:this.zoomBoxColor=
b;break;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:this.zoomBoxColor2=b;break;default:JU.Logger.warn("AwtPanel --- unrecognized color: "+a)}},"JSV.common.ScriptToken,javajs.api.GenericColor");c(c$,"getColor",function(a){switch(a){default:return JU.Logger.error("awtgraphset missing color "+a),this.BLACK;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:return this.zoomBoxColor2;case JSV.common.ScriptToken.ZOOMBOXCOLOR:return this.zoomBoxColor;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:return this.highlightColor;
case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:return this.integralPlotColor;case JSV.common.ScriptToken.GRIDCOLOR:return this.gridColor;case JSV.common.ScriptToken.PEAKTABCOLOR:return this.peakTabColor;case JSV.common.ScriptToken.PLOTAREACOLOR:return this.plotAreaColor;case JSV.common.ScriptToken.SCALECOLOR:return this.scaleColor;case JSV.common.ScriptToken.TITLECOLOR:return this.titleColor;case JSV.common.ScriptToken.UNITSCOLOR:return this.unitsColor}},"JSV.common.ScriptToken");c(c$,"getOverlayLegendData",
function(){for(var a=this.currentGraphSet.nSpectra,b=Array(a),c=this.getSpectrumAt(0).getFilePath(),e=this.getSpectrumAt(a-1).getFilePath(),c=!c.equals(e),e=0;e<a;e++){var g=Array(3),f=this.getSpectrumAt(e);this.title=f.getTitle();c&&(this.title=JSV.common.JSVFileManager.getTagName(f.getFilePath())+" - "+this.title);f=this.getCurrentPlotColor(e);g[0]=new Integer(e+1);g[1]=f;g[2]=" "+this.title;b[e]=g}return b});c(c$,"setColorOrFont",function(a,b){if(null==b){for(var c,e=a.elementColors.entrySet().iterator();e.hasNext()&&
((c=e.next())||1);)this.setColorOrFont(a,c.getKey());this.setColorOrFont(a,JSV.common.ScriptToken.DISPLAYFONTNAME);this.setColorOrFont(a,JSV.common.ScriptToken.TITLEFONTNAME)}else{switch(b){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.setFontName(b,a.displayFontName);return;case JSV.common.ScriptToken.TITLEFONTNAME:this.setFontName(b,a.titleFontName);return}this.setColor(b,a.getElementColor(b))}},"JSV.common.ColorParameters,JSV.common.ScriptToken");c(c$,"getCurrentPlotColor",function(a){return this.currentGraphSet.getPlotColor(a)},
"~N");c(c$,"setPrint",function(a,b){null==a?(this.options.putAll(this.optionsSaved),this.optionsSaved=null):(this.printJobTitle=a.title,this.printingFontName=b,this.printGraphPosition=a.position,this.optionsSaved=new java.util.Hashtable,this.optionsSaved.putAll(this.options),this.gridOn=a.showGrid,this.titleOn=a.showTitle,this.setBoolean(JSV.common.ScriptToken.XSCALEON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.XUNITSON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.YSCALEON,a.showYScale),
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e));null!=b&&g.setData(b);this.addDialog(c,a,g);g.reEnable();return g},"JSV.common.Annotation.AType");c(c$,"printPdf",function(a,b){var c=!b.layout.equals("landscape");this.print(a,c?b.imageableHeight:b.imageableWidth,c?b.imageableWidth:b.imageableHeight,b.imageableX,b.imageableY,b.paperHeight,b.paperWidth,c,0)},"J.api.GenericGraphics,JSV.common.PrintLayout");c(c$,"print",function(a,b,c,e,g,f,h,k,l){this.g2d=this.g2d0;if(0==l)return this.isPrinting=!0,l=!1,n(a,J.api.GenericGraphics)&&(this.g2d=a,
a=this.gMain),this.printGraphPosition.equals("default")?k?(b=450,c=280):(b=280,c=450):this.printGraphPosition.equals("fit to page")?l=!0:k?(b=450,c=280,e=s(s(h-c)/2),g=s(s(f-b)/2)):(b=280,c=450,g=s(s(h-280)/2),e=s(s(f-450)/2)),this.g2d.translateScale(a,e,g,0.1),this.taintedAll=!0,this.drawGraph(a,a,a,s(c),s(b),l),this.isPrinting=!1,0;this.isPrinting=!1;return 1},"~O,~N,~N,~N,~N,~N,~N,~B,~N");h(c$,"keyPressed",function(a,b){if(this.isPrinting)return!1;this.checkKeyControl(a,!0);switch(a){case 27:case 127:case 8:return this.escapeKeyPressed(27!=
a),this.isIntegralDrag=!1,this.repaint(),!0}var c=0,e=!1;if(0==b)switch(a){case 37:case 39:this.doMouseMoved(39==a?++this.mouseX:--this.mouseX,this.mouseY);this.repaint();e=!0;break;case 33:case 34:c=33==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;e=!0;break;case 40:case 38:e=40==a?-1:1,null==this.getSpectrumAt(0).getSubSpectra()?this.notifySubSpectrumChange(e,null):(this.advanceSubSpectrum(e),this.repaint()),e=!0}else if(this.checkMod(a,2))switch(a){case 40:case 38:case 45:case 61:c=61==
a||38==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;e=!0;break;case 37:case 39:this.toPeak(39==a?1:-1),e=!0}0!=c&&(this.scaleYBy(c),this.repaint());return e},"~N,~N");h(c$,"keyReleased",function(a){this.isPrinting||this.checkKeyControl(a,!1)},"~N");h(c$,"keyTyped",function(a,b){if(this.isPrinting)return!1;switch(a){case "n":if(0!=b)break;this.normalizeIntegral();return!0;case 26:if(2!=b)break;this.previousView();this.repaint();return!0;case 25:if(2!=b)break;this.nextView();this.repaint();return!0}return!1},
"~N,~N");h(c$,"mouseAction",function(a,b,c,e,g,f){if(!this.isPrinting)switch(a){case 4:if(!this.checkMod(f,16))break;this.doMousePressed(c,e);break;case 5:this.doMouseReleased(c,e,this.checkMod(f,16));this.repaint();break;case 1:this.doMouseDragged(c,e);this.repaint();break;case 0:this.jsvp.getFocusNow(!1);if(0!=(f&28)){this.doMouseDragged(c,e);this.repaint();break}this.doMouseMoved(c,e);null!=this.coordStr&&this.repaint();break;case 2:if(this.checkMod(f,4)){this.jsvp.showMenu(c,e);break}this.ctrlPressed=
!1;this.doMouseClicked(c,e,this.updateControlPressed(f))}},"~N,~N,~N,~N,~N,~N");c(c$,"checkMod",function(a,b){return(a&b)==b},"~N,~N");c(c$,"checkKeyControl",function(a,b){switch(a){case 17:case 157:this.ctrlPressed=b;break;case 16:this.shiftPressed=b}},"~N,~B");c(c$,"updateControlPressed",function(a){return this.ctrlPressed=(new Boolean(this.ctrlPressed|(this.checkMod(a,2)||this.checkMod(a,20)))).valueOf()},"~N");h(c$,"mouseEnterExit",function(a,b,c,e){if(e)this.thisWidget=null,this.isIntegralDrag=
!1,this.integralShiftMode=0;else try{this.jsvp.getFocusNow(!1)}catch(g){if(y(g,Exception))System.out.println("pd "+this+" cannot focus");else throw g;}},"~N,~N,~N,~B");c(c$,"setSolutionColor",function(a){var b=0<=a.indexOf("none"),c=0>a.indexOf("false");if(0>a.indexOf("all"))b=b?-1:this.vwr.getSolutionColor(c),this.getSpectrum().setFillColor(-1==b?null:this.vwr.parameters.getColor1(b));else{a=JSV.common.JSViewer.getInterface("JSV.common.Visible");for(var e=this.graphSets.size();0<=--e;)this.graphSets.get(e).setSolutionColor(a,
b,c)}},"~S");c(c$,"setIRMode",function(a,b){for(var c=this.graphSets.size();0<=--c;)this.graphSets.get(c).setIRMode(a,b)},"JSV.common.Spectrum.IRMode,~S");G(self.c$);c$=z(JSV.common.PanelData,"LinkMode",Enum);c$.getMode=c(c$,"getMode",function(a){if(a.equals("*"))return JSV.common.PanelData.LinkMode.ALL;for(var b,c=0,e=JSV.common.PanelData.LinkMode.values();c<e.length&&((b=e[c])||1);c++)if(b.name().equalsIgnoreCase(a))return b;return JSV.common.PanelData.LinkMode.NONE},"~S");x(c$,"ALL",0,[]);x(c$,
"NONE",1,[]);x(c$,"AB",2,[]);x(c$,"ABC",3,[]);c$=K();G(self.c$);c$=z(JSV.common.PanelData,"Mouse",Enum);x(c$,"UP",0,[]);x(c$,"DOWN",1,[]);c$=K();C(c$,"defaultPrintHeight",450,"defaultPrintWidth",280,"topMargin",40,"bottomMargin",50,"leftMargin",60,"rightMargin",50)});m("JSV.common");w(null,"JSV.common.PanelNode",["JU.SB","JSV.common.Parameters"],function(){c$=r(function(){this.legend=this.id=this.jsvp=this.fileName=this.source=this.treeNode=null;this.isSimulation=this.isView=this.isSelected=!1;this.frameTitle=
null;t(this,arguments)},JSV.common,"PanelNode");u(c$,function(a,b,c,e){this.id=a;this.source=c;this.fileName=b;this.isSimulation=0<=c.getFilePath().indexOf("http://SIMULATION/");this.jsvp=e;null!=e&&(this.pd().getSpectrumAt(0).setId(a),this.frameTitle=e.getTitle())},"~S,~S,JSV.source.JDXSource,JSV.api.JSVPanel");c(c$,"setTreeNode",function(a){this.treeNode=a},"JSV.api.JSVTreeNode");c(c$,"getTreeNode",function(){return this.treeNode});c(c$,"dispose",function(){this.source.dispose();null!=this.jsvp&&
this.jsvp.dispose();this.legend=this.jsvp=this.source=null});c(c$,"pd",function(){return this.jsvp.getPanelData()});c(c$,"getSpectrum",function(){return this.pd().getSpectrum()});c(c$,"setLegend",function(a){null!=this.legend&&this.legend.dispose();return this.legend=a},"JSV.dialog.JSVDialog");h(c$,"toString",function(){return(null==this.id?"":this.id+": ")+(null==this.frameTitle?this.fileName:this.frameTitle)});c$.findSourceByNameOrId=c(c$,"findSourceByNameOrId",function(a,b){for(var c=b.size();0<=
--c;){var e=b.get(c);if(a.equals(e.id)||a.equalsIgnoreCase(e.source.getFilePath()))return e.source}for(c=b.size();0<=--c;)if(e=b.get(c),a.equals(e.fileName))return e.source;return null},"~S,JU.Lst");c$.findNodeById=c(c$,"findNodeById",function(a,b){if(null!=a)for(var c=b.size();0<=--c;)if(a.equals(b.get(c).id)||a.equals(b.get(c).frameTitle))return b.get(c);return null},"~S,JU.Lst");c$.findNode=c(c$,"findNode",function(a,b){for(var c=b.size();0<=--c;)if(b.get(c).jsvp===a)return b.get(c);return null},
"JSV.api.JSVPanel,JU.Lst");c$.getSpectrumListAsString=c(c$,"getSpectrumListAsString",function(a){for(var b=new JU.SB,c=0;c<a.size();c++){var e=a.get(c);e.isView||b.append(" ").append(e.id)}return b.toString().trim()},"JU.Lst");c$.isOpen=c(c$,"isOpen",function(a,b){if(null!=b)for(var c=a.size();0<=--c&&!b.equals(a.get(c).source.getFilePath())&&!b.equals(a.get(c).frameTitle););return-1},"JU.Lst,~S");c(c$,"setFrameTitle",function(a){this.frameTitle=a},"~S");c$.getLastFileFirstNode=c(c$,"getLastFileFirstNode",
function(a){for(var b=a.size(),c=0==b?null:a.get(b-1),b=b-1;0<=--b&&a.get(b).source===c.source;)c=a.get(b);return null==c?null:c.jsvp},"JU.Lst");c(c$,"getInfo",function(a){var b=this.pd().getInfo(!1,a);JSV.common.Parameters.putInfo(a,b,"panelId",this.id);JSV.common.Parameters.putInfo(a,b,"panelFileName",this.fileName);JSV.common.Parameters.putInfo(a,b,"panelSource",this.source.getFilePath());return b},"~S")});m("JSV.common");w(null,"JSV.common.Parameters",["java.lang.Boolean","java.util.Hashtable",
"JSV.common.ScriptToken"],function(){c$=r(function(){this.name=null;this.integralMinY=0.1;this.integralRange=50;this.integralOffset=30;this.integralDrawAll=!1;this.viewOffset=0;this.peakListThreshold=NaN;this.peakListInterpolation="parabolic";this.precision=2;this.htBooleans=null;t(this,arguments)},JSV.common,"Parameters");u(c$,function(){this.htBooleans=new java.util.Hashtable;this.setBoolean(JSV.common.ScriptToken.TITLEON,!0);this.setBoolean(JSV.common.ScriptToken.ENABLEZOOM,!0);this.setBoolean(JSV.common.ScriptToken.DISPLAY2D,
!0);this.setBoolean(JSV.common.ScriptToken.COORDINATESON,!0);this.setBoolean(JSV.common.ScriptToken.GRIDON,!0);this.setBoolean(JSV.common.ScriptToken.XSCALEON,!0);this.setBoolean(JSV.common.ScriptToken.YSCALEON,!0);this.setBoolean(JSV.common.ScriptToken.XUNITSON,!0);this.setBoolean(JSV.common.ScriptToken.YUNITSON,!0)});c(c$,"setName",function(a){this.name=a;return this},"~S");c(c$,"getBooleans",function(){return this.htBooleans});c(c$,"setBoolean",function(a,b){this.htBooleans.put(a,Boolean.$valueOf(b));
return b},"JSV.common.ScriptToken,~B");c(c$,"getBoolean",function(a){return Boolean.TRUE===this.htBooleans.get(a)},"JSV.common.ScriptToken");c$.isTrue=c(c$,"isTrue",function(a){return 0==a.length||Boolean.parseBoolean(a)},"~S");c$.getTFToggle=c(c$,"getTFToggle",function(a){return a.equalsIgnoreCase("TOGGLE")?null:JSV.common.Parameters.isTrue(a)?Boolean.TRUE:Boolean.FALSE},"~S");c(c$,"setP",function(a,b,c){switch(b){default:return;case JSV.common.ScriptToken.COORDINATESON:case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:case JSV.common.ScriptToken.ENABLEZOOM:case JSV.common.ScriptToken.GRIDON:case JSV.common.ScriptToken.REVERSEPLOT:case JSV.common.ScriptToken.TITLEON:case JSV.common.ScriptToken.TITLEBOLDON:case JSV.common.ScriptToken.XSCALEON:case JSV.common.ScriptToken.XUNITSON:case JSV.common.ScriptToken.YSCALEON:case JSV.common.ScriptToken.YUNITSON:c=
JSV.common.Parameters.getTFToggle(c);if(null!=c){this.setBoolean(b,c.booleanValue());break}if(null==a)return;c=!a.getBoolean(b);switch(b){case JSV.common.ScriptToken.XSCALEON:this.setBoolean(JSV.common.ScriptToken.XUNITSON,c);a.setBoolean(JSV.common.ScriptToken.XUNITSON,c);break;case JSV.common.ScriptToken.YSCALEON:this.setBoolean(JSV.common.ScriptToken.YUNITSON,c),a.setBoolean(JSV.common.ScriptToken.YUNITSON,c)}this.setBoolean(b,c)}null!=a&&a.setBooleans(this,b)},"JSV.common.PanelData,JSV.common.ScriptToken,~S");
c$.isMatch=c(c$,"isMatch",function(a,b){return null==a||b.equalsIgnoreCase(a)},"~S,~S");c$.putInfo=c(c$,"putInfo",function(a,b,c,e){null!=e&&JSV.common.Parameters.isMatch(a,c)&&b.put(null==a?c:a,e)},"~S,java.util.Map,~S,~O")});m("JSV.common");w(["JSV.common.MeasurementData"],"JSV.common.PeakData",["java.lang.Double","JU.DF","JSV.common.Coordinate","$.PeakPick"],function(){c$=r(function(){this.maxY=this.minY=this.thresh=0;t(this,arguments)},JSV.common,"PeakData",JSV.common.MeasurementData);c(c$,"getThresh",
function(){return this.thresh});h(c$,"getDataHeader",function(){return this.spec.isHNMR()?JSV.common.PeakData.HNMR_HEADER:["peak",this.spec.getXUnits(),this.spec.getYUnits()]});h(c$,"getMeasurementListArray",function(){for(var a=Array(this.size()),b=[-1E100,1E100,1E100],c,e=0,g=this.size();0<=--g;e++)c=this.spec.getPeakListArray(this.get(g),b,this.maxY),a[e]=2==c.length?[""+(e+1),JU.DF.formatDecimalDbl(c[0],2),JU.DF.formatDecimalDbl(c[1],4)]:[""+(e+1),JU.DF.formatDecimalDbl(c[0],4),JU.DF.formatDecimalDbl(c[1],
4),JU.DF.formatDecimalDbl(c[2],2),0==c[3]?"":JU.DF.formatDecimalDbl(c[3],2),0==c[4]?"":JU.DF.formatDecimalDbl(c[4],2),0==c[5]?"":JU.DF.formatDecimalDbl(c[5],2)];return a},"~S");h(c$,"getMeasurementListArrayReal",function(){for(var a=$(this.size(),0),b=[-1E100,1E100,1E100],c=0,e=this.size();0<=--e;c++)a[c]=this.spec.getPeakListArray(this.get(e),b,this.maxY);return a},"~S");c(c$,"getInfo",function(a){a.put("interpolation",this.myParams.peakListInterpolation);a.put("threshold",Double.$valueOf(this.myParams.peakListThreshold));
T(this,JSV.common.PeakData,"getInfo",[a])},"java.util.Map");c(c$,"setPeakList",function(a,b,c){this.precision=-2147483648==b?this.spec.getDefaultUnitPrecision():b;var e=this.spec.getXYCoords();if(!(3>e.length)){this.clear();null!=a&&(this.myParams.peakListInterpolation=a.peakListInterpolation,this.myParams.peakListThreshold=a.peakListThreshold);a=this.myParams.peakListInterpolation.equals("parabolic");var g=this.spec.isInverted();this.minY=c.minYOnScale;this.maxY=c.maxYOnScale;var f=c.minXOnScale;
c=c.maxXOnScale;this.thresh=this.myParams.peakListThreshold;Double.isNaN(this.thresh)&&(this.thresh=this.myParams.peakListThreshold=(this.minY+this.maxY)/2);var h=0,k=[e[0].getYVal(),h=e[1].getYVal(),0],l=0;if(g)for(g=2;g<e.length;g++){var m=k[g%3]=e[g].getYVal();if(h<this.thresh&&(k[(g-2)%3]>h&&h<m)&&(h=a?JSV.common.Coordinate.parabolicInterpolation(e,g-1):e[g-1].getXVal(),h>=f||h<=c))if(h=(new JSV.common.PeakPick).setValue(h,m,this.spec,null,0),this.addLast(h),100==++l)break;h=m}else for(g=2;g<
e.length;g++){m=k[g%3]=e[g].getYVal();if(h>this.thresh&&(k[(g-2)%3]<h&&h>m)&&(h=a?JSV.common.Coordinate.parabolicInterpolation(e,g-1):e[g-1].getXVal(),h>=f&&h<=c&&(h=(new JSV.common.PeakPick).setValue(h,m,this.spec,JU.DF.formatDecimalDbl(h,b),h),this.addLast(h),100==++l)))break;h=m}}},"JSV.common.Parameters,~N,JSV.common.ScaleData");c$.HNMR_HEADER=c$.prototype.HNMR_HEADER="peak shift/ppm intens shift/hz diff/hz 2-diff 3-diff".split(" ")});m("JSV.common");w(null,"JSV.common.PeakInfo",["JU.PT"],function(){c$=
r(function(){this.px1=this.px0=this.yMax=this.yMin=this.xMax=this.xMin=0;this.atomKey=this._match=this.spectrum=this.id=this.atoms=this.model=this.title=this.filePathForwardSlash=this.file=this.index=this.type2=this.type=this.stringInfo=null;t(this,arguments)},JSV.common,"PeakInfo");u(c$,function(){});u(c$,function(a){this.stringInfo=a;this.type=JU.PT.getQuotedAttribute(a,"type");null==this.type&&(this.type="");this.type=this.type.toUpperCase();var b=this.type.indexOf("/");this.type2=0>b?"":JSV.common.PeakInfo.fixType(this.type.substring(this.type.indexOf("/")+
1));this.type=0<=b?JSV.common.PeakInfo.fixType(this.type.substring(0,b))+"/"+this.type2:JSV.common.PeakInfo.fixType(this.type);this.id=JU.PT.getQuotedAttribute(a,"id");this.index=JU.PT.getQuotedAttribute(a,"index");this.file=JU.PT.getQuotedAttribute(a,"file");System.out.println("pi file="+this.file);this.filePathForwardSlash=null==this.file?null:this.file.$replace("\\","/");this.model=JU.PT.getQuotedAttribute(a,"model");a.contains('baseModel=""')||(this.atoms=JU.PT.getQuotedAttribute(a,"atoms"));
this.atomKey=","+this.atoms+",";this.title=JU.PT.getQuotedAttribute(a,"title");this._match=JU.PT.getQuotedAttribute(a,"_match");this.xMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMax"));this.xMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMin"));this.yMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMax"));this.yMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMin"))},"~S");c(c$,"isClearAll",function(){return null==this.spectrum});c(c$,"getType",function(){return this.type});c(c$,"getAtoms",
function(){return this.atoms});c(c$,"getXMax",function(){return this.xMax});c(c$,"getXMin",function(){return this.xMin});c(c$,"getYMin",function(){return this.yMin});c(c$,"getYMax",function(){return this.yMax});c(c$,"getX",function(){return(this.xMax+this.xMin)/2});c(c$,"getMatch",function(){return this._match});c$.fixType=c(c$,"fixType",function(a){return a.equals("HNMR")?"1HNMR":a.equals("CNMR")?"13CNMR":a},"~S");h(c$,"toString",function(){return this.stringInfo});c(c$,"getIndex",function(){return this.index});
c(c$,"getTitle",function(){return this.title});c(c$,"checkFileIndex",function(a,b,c){return null!=c?0<=this.atomKey.indexOf(c):b.equals(this.index)&&(a.equals(this.file)||a.equals(this.filePathForwardSlash))},"~S,~S,~S");c(c$,"checkFileTypeModel",function(a,b,c){return a.equals(this.file)&&this.checkModel(c)&&this.type.endsWith(b)},"~S,~S,~S");c(c$,"checkTypeModel",function(a,b){return this.checkType(a)&&this.checkModel(b)},"~S,~S");c(c$,"checkModel",function(a){return null!=a&&a.equals(this.model)},
"~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$,"checkId",function(a){return null!=this.id&&null!=a&&a.toUpperCase().startsWith("ID=")&&((a=a.substring(3)).equals(this.id)||a.startsWith("#")&&a.equals("#"+this.index))},"~S");c(c$,"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$,"getXPixel",function(){return s((this.px0+this.px1)/2)});c$.nullPeakInfo=c$.prototype.nullPeakInfo=new JSV.common.PeakInfo});m("JSV.common");w(["JSV.common.Measurement"],"JSV.common.PeakPick",
null,function(){c$=z(JSV.common,"PeakPick",JSV.common.Measurement);c(c$,"setValue",function(a,b,c,e,g){null==e?(this.set(a,b),this.setPt2(c,!1)):(this.setA(a,b,c,e,!1,!1,0,6),this.value=g,this.setPt2(this.getXVal(),this.getYVal()));return this},"~N,~N,JSV.common.Spectrum,~S,~N")});m("JSV.common");w(["java.util.EventObject"],"JSV.common.PeakPickEvent",null,function(){c$=r(function(){this.peakInfo=this.coord=null;t(this,arguments)},JSV.common,"PeakPickEvent",java.util.EventObject);u(c$,function(a,b,
c){F(this,JSV.common.PeakPickEvent,[a]);this.coord=b;this.peakInfo=null==c?null:c},"~O,JSV.common.Coordinate,JSV.common.PeakInfo");c(c$,"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");w(["JSV.common.Coordinate","$.ScriptToken"],"JSV.common.PlotWidget",null,function(){c$=r(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;t(this,arguments)},JSV.common,"PlotWidget",JSV.common.Coordinate);I(c$,function(){this.color=JSV.common.ScriptToken.PLOTCOLOR});h(c$,"toString",function(){return this.name+(!this.isPinOrCursor?""+this.xPixel0+" "+this.yPixel0+" / "+this.xPixel1+" "+this.yPixel1:" x="+this.getXVal()+"/"+this.xPixel0+" y="+this.getYVal()+"/"+this.yPixel0)});u(c$,function(a){F(this,JSV.common.PlotWidget,
[]);this.name=a;this.isPin="p"==a.charAt(0);this.isPinOrCursor="z"!=a.charAt(0);this.isXtype=0<=a.indexOf("x");this.is2Donly=(this.is2D=0<=a.indexOf("2D"))&&"p"==a.charAt(0)},"~S");c(c$,"selected",function(a,b){return this.isVisible&&5>Math.abs(a-this.xPixel0)&&5>Math.abs(b-this.yPixel0)},"~N,~N");c(c$,"setX",function(a,b){this.setXVal(a);this.xPixel0=this.xPixel1=b},"~N,~N");c(c$,"setY",function(a,b){this.setYVal(a);this.yPixel0=this.yPixel1=b},"~N,~N");c(c$,"getValue",function(){return this.isXtype?
this.getXVal():this.getYVal()});c(c$,"setEnabled",function(a){this.isEnabled=a},"~B")});m("JSV.common");c$=r(function(){this.imageableWidth=this.imageableHeight=this.paperWidth=this.paperHeight=this.imageableY=this.imageableX=0;this.layout="landscape";this.position="fit to page";this.showTitle=this.showYScale=this.showXScale=this.showGrid=!0;this.font="Helvetica";this.paper=null;this.asPDF=!0;this.date=this.title=null;t(this,arguments)},JSV.common,"PrintLayout");I(c$,function(){this.paperHeight=B(72*
Math.min(11,11.69));this.paperWidth=B(72*Math.min(8.5,8.27));this.imageableHeight=this.paperHeight;this.imageableWidth=this.paperWidth});m("JSV.common");c$=r(function(){this.repaintPending=!1;this.vwr=null;t(this,arguments)},JSV.common,"RepaintManager");u(c$,function(a){this.vwr=a},"JSV.common.JSViewer");c(c$,"refresh",function(){if(this.repaintPending)return!1;this.repaintPending=!0;this.vwr.pd().taintedAll=!0;var a=this.vwr.html5Applet;"undefined"!=typeof Jmol&&(Jmol._repaint&&a)&&Jmol._repaint(a,
!1);this.repaintDone();return!0});c(c$,"repaintDone",function(){this.repaintPending=!1;this.notify()});m("JSV.common");w(null,"JSV.common.ScaleData",["java.lang.Double","JSV.common.Coordinate"],function(){c$=r(function(){this.maxX=this.minX=this.pointCount=this.endDataPointIndex=this.startDataPointIndex=this.initMaxY=this.initMinY=this.initMaxYOnScale=this.initMinYOnScale=0;this.firstX=NaN;this.specShift=this.maxXOnScale=this.minXOnScale=0;this.minorTickCounts=this.steps=this.exportPrecision=this.precision=
null;this.maxY=this.minY=this.maxYOnScale=this.minYOnScale=0;this.isShiftZoomedY=!1;this.spectrumScaleFactor=1;this.spectrumYRef=0;this.userYFactor=1;this.yFactorForScale=this.xFactorForScale=this.maxY2D=this.minY2D=this.firstY=0;t(this,arguments)},JSV.common,"ScaleData");I(c$,function(){this.precision=D(2,0);this.exportPrecision=D(2,0);this.steps=$(2,0);this.minorTickCounts=D(2,0)});u(c$,function(){});u(c$,function(a,b){this.startDataPointIndex=a;this.endDataPointIndex=b;this.pointCount=this.endDataPointIndex-
this.startDataPointIndex+1},"~N,~N");u(c$,function(a,b,c,e,g){this.minX=JSV.common.Coordinate.getMinX(a,b,c);this.maxX=JSV.common.Coordinate.getMaxX(a,b,c);this.minY=JSV.common.Coordinate.getMinY(a,b,c);0<this.minY&&!e&&(this.minY=0);this.maxY=JSV.common.Coordinate.getMaxY(a,b,c);this.setScale(e,g)},"~A,~N,~N,~B,~B");c(c$,"setScale",function(a,b){this.setXScale();a||(this.maxXOnScale+=this.steps[0]/2);this.setYScale(this.minY,this.maxY,!0,b)},"~B,~B");c(c$,"setXScale",function(){var a=this.setScaleParams(this.minX,
this.maxX,0);this.firstX=Math.floor(this.minX/a)*a;1E-4<Math.abs((this.minX-this.firstX)/a)&&(this.firstX+=a);this.minXOnScale=this.minX;this.maxXOnScale=this.maxX});c(c$,"isYZeroOnScale",function(){return this.minYOnScale<this.spectrumYRef&&this.maxYOnScale>this.spectrumYRef});c(c$,"setYScale",function(a,b,c,e){0==a&&0==b&&(b=1);this.isShiftZoomedY&&(a=this.minYOnScale,b=this.maxYOnScale);var g=this.setScaleParams(a,b,1),f=e?g/2:g/4;e=e?g/4:g/2;this.isShiftZoomedY||(this.minYOnScale=0==a?0:c?f*Math.floor(a/
f):a,this.maxYOnScale=c?e*Math.ceil(1.05*b/e):b);this.firstY=0==a?0:Math.floor(a/f)*f;if(0>this.minYOnScale&&0<this.maxYOnScale)for(this.firstY=0;this.firstY-g>this.minYOnScale;)this.firstY-=g;else 0!=this.minYOnScale&&1E-4<Math.abs((a-this.firstY)/f)&&(this.firstY+=f);c&&(this.initMinYOnScale=this.minYOnScale,this.initMaxYOnScale=this.maxYOnScale,this.initMinY=a,this.initMaxY=b)},"~N,~N,~B,~B");c(c$,"scale2D",function(a){var b=this.maxY-this.minY;1==a?(this.maxY=this.initMaxY,this.minY=this.initMinY):
this.maxY=this.minY+b/a},"~N");c(c$,"setXRange",function(a,b){this.minX=a;this.maxX=b;this.setXScale()},"~N,~N");c$.getXRange=c(c$,"getXRange",function(a,b,c,e,g,f,h,k){for(var l=0,m=0,l=g;l<=f;l++)if(g=b[l].getXVal(),g>=c){h[a]=l;break}for(;l<=f&&!(g=b[l].getXVal(),m++,g>=e);l++);k[a]=l-1;return m},"~N,~A,~N,~N,~N,~N,~A,~A");c(c$,"setScaleParams",function(a,b,c){a=b==a?1:Math.abs(b-a)/14;var e=Math.log10(Math.abs(a));b=s(Math.floor(e));this.exportPrecision[c]=b;this.precision[c]=0>=b?Math.min(8,
1-b):3<b?-2:0;a=0;for(e=Math.pow(10,e-b);e>JSV.common.ScaleData.NTICKS[a];)a++;this.steps[c]=Math.pow(10,b)*JSV.common.ScaleData.NTICKS[a];e=Math.log10(Math.abs(100010*this.steps[c]));b=e-Math.floor(e);for(a=e=0;a<JSV.common.ScaleData.NTICKS.length;a++)if(0.001>Math.abs(b-JSV.common.ScaleData.LOGTICKS[a])){e=JSV.common.ScaleData.NTICKS[a];break}this.minorTickCounts[c]=e;return this.steps[c]},"~N,~N,~N");c(c$,"isInRangeX",function(a){return a>=this.minX&&a<=this.maxX},"~N");c(c$,"addSpecShift",function(a){this.specShift+=
a;this.minX+=a;this.maxX+=a;this.minXOnScale+=a;this.maxXOnScale+=a;this.firstX+=a},"~N");c(c$,"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,e){this.minX=a;this.maxX=b;this.minY=c;this.maxY=e},"~N,~N,~N,~N");c(c$,"toX",function(a,b,c){return this.toXScaled(a,b,c,this.xFactorForScale)},"~N,~N,~B");c(c$,"toX0",function(a,b,c,e){return this.toXScaled(a,c,e,(this.maxXOnScale-this.minXOnScale)/(c-b))},"~N,~N,~N,~B");c(c$,"toXScaled",function(a,
b,c,e){return c?this.maxXOnScale-(b-a)*e:this.minXOnScale+(b-a)*e},"~N,~N,~B,~N");c(c$,"toPixelX",function(a,b,c,e){return this.toPixelXScaled(a,b,c,e,this.xFactorForScale)},"~N,~N,~N,~B");c(c$,"toPixelX0",function(a,b,c,e){return this.toPixelXScaled(a,b,c,e,(this.maxXOnScale-this.minXOnScale)/(c-b))},"~N,~N,~N,~B");c(c$,"toPixelXScaled",function(a,b,c,e,g){a=s((a-this.minXOnScale)/g);return e?b+a:c-a},"~N,~N,~N,~B,~N");c(c$,"toY",function(a,b){return this.maxYOnScale+(b-a)*this.yFactorForScale},
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a.setYLabel(this.yLabel);a.setXYCoords(this.xyCoords);a.setContinuous(this.continuous);a.setIncreasing(this.xIncreases);a.observedFreq=this.observedFreq;a.observedNucl=this.observedNucl;a.offset=this.offset;a.dataPointNum=this.dataPointNum;a.shiftRefType=this.shiftRefType;a.$isHZtoPPM=this.$isHZtoPPM;a.numDim=this.numDim;a.nucleusX=this.nucleusX;a.nucleusY=this.nucleusY;a.freq2dX=this.freq2dX;a.freq2dY=this.freq2dY;a.setFilePath(this.filePath);a.nH=this.nH},"JSV.source.JDXDataObject");c(c$,"getTypeLabel",
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c(c$,"getPeakListArray",function(a,b,c){var e=a.getXVal();a=a.getYVal();this.isNMR()&&(a/=c);c=Math.abs(e-b[0]);b[0]=e;var g=c+b[1];b[1]=c;var f=g+b[2];b[2]=g;return this.isNMR()?[e,a,e*this.observedFreq,20<c*this.observedFreq?0:c*this.observedFreq,20<g*this.observedFreq?0:g*this.observedFreq,20<f*this.observedFreq?0:f*this.observedFreq]:[e,a]},"JSV.common.Measurement,~A,~N");C(c$,"ERROR",1.7976931348623157E308,"SCALE_NONE",0,"SCALE_TOP",1,"SCALE_BOTTOM",2,"SCALE_TOP_BOTTOM",3,"gyroData",[1,42.5774806,
2,6.53590131,3,45.4148,3,32.436,6,6.2661,7,16.5483,9,5.9842,10,4.5752,11,13.663,13,10.70839657,14,3.07770646,15,4.3172657,17,5.7742,19,40.07757016,21,3.3631,23,11.26952167,25,2.6083,27,11.1031,29,8.4655,31,17.2514409,33,3.2717,35,4.1765,37,3.4765,37,5.819,39,3.46,39,1.9893,40,2.4737,41,1.0919,43,2.8688,45,10.3591,47,2.4041,49,2.4048,50,4.2505,51,11.2133,53,2.4115,55,10.5763,57,1.3816,59,10.077,61,3.8114,63,11.2982,65,12.103,67,2.6694,69,10.2478,71,13.0208,73,1.4897,75,7.315,77,8.1571,79,10.7042,81,
11.5384,83,1.6442,85,4.1254,87,13.9811,87,1.8525,89,2.0949,91,3.9748,93,10.4523,95,2.7874,97,2.8463,99,9.6294,99,1.9553,101,2.1916,103,1.3477,105,1.957,107,1.7331,109,1.9924,111,9.0692,113,9.4871,113,9.3655,115,9.3856,115,14.0077,117,15.261,119,15.966,121,10.2551,123,5.5532,123,11.2349,125,13.5454,127,8.5778,129,11.8604,131,3.5159,133,5.6234,135,4.2582,137,4.7634,138,5.6615,139,6.0612,137,4.88,139,5.39,141,2.37,141,13.0359,143,2.319,145,1.429,143,11.59,147,5.62,147,1.7748,149,14631,151,10.5856,153,
4.6745,155,1.312,157,1.72,159,10.23,161,1.4654,163,2.0508,165,9.0883,167,1.2281,169,3.531,171,7.5261,173,2.073,175,4.8626,176,3.451,177,1.7282,179,1.0856,180,4.087,181,5.1627,183,1.7957,185,9.7176,187,9.817,187,0.9856,189,3.3536,191,0.7658,191,0.8319,195,9.2922,197,0.7406,199,7.7123,201,2.8469,203,24.7316,205,24.9749,207,9.034,209,6.963,209,11.7,211,9.16,223,5.95,223,1.3746,225,11.187,227,5.6,229,1.4,231,10.2,235,0.83,237,9.57,239,3.09,243,4.6,1E100])});m("JSV.source");w(null,"JSV.source.JDXDecompressor",
["java.lang.Double","JSV.common.Coordinate","JU.Logger"],function(){c$=r(function(){this.lineNumber=this.ich=this.nPoints=this.deltaX=this.yFactor=this.xFactor=0;this.t=null;this.dx=this.firstX=0;this.maxY=4.9E-324;this.minY=1.7976931348623157E308;this.debugging=!1;this.xyCoords=null;this.ipt=0;this.lastLine=this.line=null;this.lineLen=0;this.errorLog=null;this.lastDif=this.difVal=-2147483648;this.yval=this.xval=this.dupCount=0;this.firstLastX=null;t(this,arguments)},JSV.source,"JDXDecompressor");
c(c$,"getMinY",function(){return this.minY});c(c$,"getMaxY",function(){return this.maxY});u(c$,function(a,b,c,e,g,f){this.t=a;this.firstX=b;this.xFactor=c;this.yFactor=e;this.deltaX=g;this.nPoints=f;this.lineNumber=a.labelLineNo;this.debugging=JU.Logger.isActiveLevel(6)},"JSV.source.JDXSourceStreamTokenizer,~N,~N,~N,~N,~N");c(c$,"addPoint",function(a){if(this.ipt==this.xyCoords.length){var b=Array(2*this.ipt);System.arraycopy(this.xyCoords,0,b,0,this.ipt);this.xyCoords=b}b=a.getYVal();b>this.maxY?
this.maxY=b:b<this.minY&&(this.minY=b);this.debugging&&this.logError("Coord: "+this.ipt+a);this.xyCoords[this.ipt++]=a;this.firstLastX[1]=a.getXVal()},"JSV.common.Coordinate");c(c$,"decompressData",function(a,b){this.errorLog=a;this.firstLastX=b;this.debugging&&this.logError("firstX="+this.firstX+" xFactor="+this.xFactor+" yFactor="+this.yFactor+" deltaX="+this.deltaX+" nPoints="+this.nPoints);this.testAlgorithm();this.xyCoords=Array(this.nPoints);var c=Math.abs(0.35*this.deltaX),e=Math.abs(1.4*this.deltaX),
g=Math.abs(0.6*this.deltaX);try{for(;null!=(this.line=this.t.readLineTrimmed())&&0>this.line.indexOf("##");)if(this.lineNumber++,this.debugging&&this.logError(this.lineNumber+"\t"+this.line),0!=(this.lineLen=this.line.length)){this.ich=0;var f=-2147483648!=this.lastDif;this.xval=this.getValueDelim()*this.xFactor;0==this.ipt&&(b[0]=this.xval,this.dx=this.firstX-this.xval);this.xval+=this.dx;var h=(new JSV.common.Coordinate).set(this.xval,(this.yval=this.getYValue())*this.yFactor);if(0==this.ipt)this.addPoint(h);
else{var k=this.xyCoords[this.ipt-1],l=Math.abs(k.getXVal()-h.getXVal());if(f&&l<c){this.xyCoords[this.ipt-1]=h;var m=k.getYVal(),p=h.getYVal();p!=m&&this.logError(this.lastLine+"\n"+this.line+"\nY-value Checkpoint Error! Line "+this.lineNumber+" for y1="+p+" y0="+m)}else this.addPoint(h),(l<g||l>e)&&this.logError(this.lastLine+"\n"+this.line+"\nX-sequence Checkpoint Error! Line "+this.lineNumber+" |x1-x0|="+l+" instead of "+Math.abs(this.deltaX)+" for x1="+h.getXVal()+" x0="+k.getXVal())}for(;this.ich<
this.lineLen||-2147483648!=this.difVal||0<this.dupCount;)this.xval+=this.deltaX,Double.isNaN(this.yval=this.getYValue())||this.addPoint((new JSV.common.Coordinate).set(this.xval,this.yval*this.yFactor));this.lastLine=this.line}}catch(n){if(!y(n,java.io.IOException))throw n;}this.nPoints!=this.ipt&&(this.logError("Decompressor did not find "+this.nPoints+" points -- instead "+this.ipt),c=Array(this.ipt),System.arraycopy(this.xyCoords,0,c,0,this.ipt),this.xyCoords=c);return 0<this.deltaX?this.xyCoords:
JSV.common.Coordinate.reverse(this.xyCoords)},"JU.SB,~A");c(c$,"logError",function(a){this.debugging&&JU.Logger.debug(a);this.errorLog.append(a).appendC("\n")},"~S");c(c$,"getYValue",function(){if(0<this.dupCount)return--this.dupCount,this.yval=-2147483648==this.lastDif?this.yval:this.yval+this.lastDif;if(-2147483648!=this.difVal)return this.yval+=this.difVal,this.lastDif=this.difVal,this.difVal=-2147483648,this.yval;if(this.ich==this.lineLen)return NaN;var a=this.line.charAt(this.ich);this.debugging&&
JU.Logger.info(""+a);switch(a){case "%":this.difVal=0;break;case "J":case "K":case "L":case "M":case "N":case "O":case "P":case "Q":case "R":this.difVal=a.charCodeAt(0)-73;break;case "j":case "k":case "l":case "m":case "n":case "o":case "p":case "q":case "r":this.difVal=105-a.charCodeAt(0);break;case "S":case "T":case "U":case "V":case "W":case "X":case "Y":case "Z":this.dupCount=a.charCodeAt(0)-82;break;case "s":this.dupCount=9;break;case "+":case "-":case ".":case "0":case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":case "@":case "A":case "B":case "C":case "D":case "E":case "F":case "G":case "H":case "I":case "a":case "b":case "c":case "d":case "e":case "f":case "g":case "h":case "i":return this.lastDif=
-2147483648,this.getValue();case "?":return this.lastDif=-2147483648,NaN;default:return this.ich++,this.lastDif=-2147483648,this.getYValue()}this.ich++;-2147483648!=this.difVal?this.difVal=this.getDifDup(this.difVal):this.dupCount=this.getDifDup(this.dupCount)-1;return this.getYValue()});c(c$,"getDifDup",function(a){var b=this.ich;this.next();var c=a+this.line.substring(b,this.ich);return b==this.ich?a:Integer.$valueOf(c).intValue()},"~N");c(c$,"getValue",function(){var a=this.ich;if(this.ich==this.lineLen)return NaN;
var a=this.line.charAt(this.ich),b=0;switch(a){case "+":case "-":case ".":case "0":case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":return this.getValueDelim();case "@":case "A":case "B":case "C":case "D":case "E":case "F":case "G":case "H":case "I":b=a.charCodeAt(0)-64;a=++this.ich;break;case "a":case "b":case "c":case "d":case "e":case "f":case "g":case "h":case "i":b=96-a.charCodeAt(0);a=++this.ich;break;default:return this.ich++,this.getValue()}this.next();return Double.$valueOf(b+
this.line.substring(a,this.ich)).doubleValue()});c(c$,"getValueDelim",function(){for(var a=this.ich,b="\x00";this.ich<this.lineLen&&0<=" ,\t\n".indexOf(b=this.line.charAt(this.ich));)this.ich++;var c=1;switch(b){case "-":c=-1;case "+":a=++this.ich}b=this.next();if("E"==b&&this.ich+3<this.lineLen)switch(this.line.charAt(this.ich+1)){case "-":case "+":this.ich+=4,this.ich<this.lineLen&&("0"<=(b=this.line.charAt(this.ich))&&"9">=b)&&this.ich++}return c*Double.$valueOf(this.line.substring(a,this.ich)).doubleValue()});
c(c$,"next",function(){for(;this.ich<this.lineLen&&0>"+-%@ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrs? ,\t\n".indexOf(this.line.charAt(this.ich));)this.ich++;return this.ich==this.lineLen?"\x00":this.line.charAt(this.ich)});c(c$,"testAlgorithm",function(){});C(c$,"allDelim","+-%@ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrs? ,\t\n","WHITE_SPACE"," ,\t\n")});m("JSV.source");w(["JU.Lst"],"JSV.source.JDXHeader",null,function(){c$=r(function(){this.title="";this.jcampdx="5.01";this.origin=this.dataClass=
this.dataType="";this.owner="PUBLIC DOMAIN";this.time=this.date=this.longDate="";this.headerTable=this.qualifiedType=null;t(this,arguments)},JSV.source,"JDXHeader");I(c$,function(){this.headerTable=new JU.Lst});c(c$,"setTitle",function(a){this.title=a},"~S");c(c$,"setJcampdx",function(a){this.jcampdx=a},"~S");c(c$,"setDataType",function(a){this.dataType=a},"~S");c(c$,"setDataClass",function(a){this.dataClass=a},"~S");c(c$,"setOrigin",function(a){this.origin=a},"~S");c(c$,"setOwner",function(a){this.owner=
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this.qualifiedType=JSV.source.JDXHeader.getTypeName(this.dataType):this.qualifiedType});c(c$,"getJcampdx",function(){return this.jcampdx});c(c$,"getDataType",function(){return this.dataType});c(c$,"getOrigin",function(){return this.origin});c(c$,"getOwner",function(){return this.owner});c(c$,"getLongDate",function(){return this.longDate});c(c$,"getDate",function(){return this.date});c(c$,"getTime",function(){return this.time});c(c$,"getDataClass",function(){return this.dataClass});c(c$,"setHeaderTable",
function(a){this.headerTable=a},"JU.Lst");c(c$,"getHeaderTable",function(){return this.headerTable});c(c$,"getHeaderRowDataAsArray",function(a,b){var c=Array((a?6:5)+this.headerTable.size()+b),e=0;c[e++]=["##TITLE",this.title];c[e++]=["##JCAMP-DX",this.jcampdx];c[e++]=["##DATA TYPE",this.dataType];a&&(c[e++]=["##DATA CLASS",this.dataClass]);c[e++]=["##ORIGIN",this.origin];c[e++]=["##OWNER",this.owner];for(var g=0;g<this.headerTable.size();g++)c[e++]=this.getRow(g);return c},"~B,~N");c(c$,"getRow",
function(a){a=this.headerTable.get(a);return[a[0],JU.PT.rep(a[1],"<","&lt;")]},"~N");C(c$,"typeNames","ND NMR SPECTRUM   NMR;NMR SPECTRUM      NMR;INFRARED SPECTRUM IR;MASS SPECTRUM     MS;RAMAN SPECTRUM    RAMAN;GAS CHROMATOGRAM  GC;UV/VIS SPECTRUM   UV/VIS".split(";"))});m("JSV.source");w(["J.api.JmolJDXMOLReader"],"JSV.source.JDXReader","java.io.BufferedReader $.StringReader java.lang.Double $.Float java.util.Hashtable $.StringTokenizer JU.Lst $.PT $.SB JSV.api.JSVZipReader JSV.common.Coordinate $.JSVFileManager $.JSViewer $.PeakInfo $.Spectrum JSV.exception.JSVException JSV.source.JDXDecompressor $.JDXSource $.JDXSourceStreamTokenizer JU.Logger".split(" "),
function(){c$=r(function(){this.nmrMaxY=NaN;this.errorLog=this.t=this.source=null;this.isZipFile=this.done=this.obscure=!1;this.filePath=null;this.loadImaginary=!0;this.isTabularData=this.isSimulation=!1;this.blockID=this.nSpec=this.lastSpec=this.firstSpec=0;this.peakData=this.acdMolFile=this.acdAssignments=this.modelSpectrum=this.reader=this.mpr=null;t(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);
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"stream",b,c,-1,-1,e)},"java.io.InputStream,~B,~B,~N");c$.createJDXSource=c(c$,"createJDXSource",function(a,b,c,e,g,f,h){var k=null;try{null==a&&(a=JSV.common.JSVFileManager.getBufferedReaderFromName(b,"##TITLE"));a.mark(400);var l=ca(400,"\x00");a.read(l,0,400);a.reset();var k=String.instantialize(l),m=k.indexOf("#"),p=k.indexOf("<");if(0>m||0<=p&&p<m){var n=k.toLowerCase(),n=n.contains("<animl")||n.contains("<!doctype technique")?"AnIML":n.contains("xml-cml")?"CML":null;c=null;null!=n&&(c=JSV.common.JSViewer.getInterface("JSV.source."+
n+"Reader").getSource(b,a));a.close();if(null==c)throw JU.Logger.error(k+"..."),new JSV.exception.JSVException("File type not recognized");return c}return(new JSV.source.JDXReader(b,c,e,g,f,h)).getJDXSource(a)}catch(r){if(y(r,Exception))throw null!=a&&a.close(),null!=k&&JU.Logger.error(k+"..."),a=r.getMessage(),new JSV.exception.JSVException("Error reading data: "+a);throw r;}},"java.io.BufferedReader,~S,~B,~B,~N,~N,~N");c(c$,"getJDXSource",function(a){this.source=new JSV.source.JDXSource(0,this.filePath);
this.isZipFile=n(a,JSV.api.JSVZipReader);this.t=new JSV.source.JDXSourceStreamTokenizer(a);this.errorLog=new JU.SB;for(var b=a=null,c=!1;!this.done&&"##TITLE".equals(this.t.peakLabel());){c=!0;null!=a&&!this.isZipFile&&this.errorLog.append("Warning - file is a concatenation without LINK record -- does not conform to IUPAC standards!\n");for(var e=new JSV.common.Spectrum,g=new JU.Lst;!this.done&&null!=(a=this.t.getLabel())&&null!=(b=this.getValue(a));)if(this.isTabularData){this.setTabularDataType(e,
a);if(!this.processTabularData(e,g))throw new JSV.exception.JSVException("Unable to read JDX file");this.addSpectrum(e,!1);e=null}else a.equals("##DATATYPE")&&b.toUpperCase().equals("LINK")?(this.getBlockSpectra(g),e=null):a.equals("##NTUPLES")||a.equals("##VARNAME")?(this.getNTupleSpectra(g,e,a),e=null):(null==e&&(e=new JSV.common.Spectrum),this.readDataLabel(e,a,b,this.errorLog,this.obscure)||(JSV.source.JDXReader.addHeader(g,this.t.rawLabel,b),this.checkCustomTags(e,a,b)))}if(!c)throw new JSV.exception.JSVException("##TITLE record not found");
this.source.setErrorLog(this.errorLog.toString());return this.source},"~O");c(c$,"getValue",function(a){var b=this.isTabularDataLabel(a)?"":this.t.getValue();return"##END".equals(a)?null:b},"~S");c(c$,"isTabularDataLabel",function(a){return this.isTabularData=0<="##DATATABLE##PEAKTABLE##XYDATA##XYPOINTS#".indexOf(a+"#")},"~S");c(c$,"addSpectrum",function(a,b){if(!this.loadImaginary&&a.isImaginary())return JU.Logger.info("FileReader skipping imaginary spectrum -- use LOADIMAGINARY TRUE to load this spectrum."),
!0;if(null!=this.acdAssignments){if(!a.dataType.equals("MASS SPECTRUM")&&!a.isContinuous())return JU.Logger.info("Skipping ACD Labs line spectrum for "+a),!0;if(0<this.acdAssignments.size())try{this.mpr.setACDAssignments(a.title,a.getTypeLabel(),this.source.peakCount,this.acdAssignments,this.acdMolFile)}catch(c){if(y(c,Exception))JU.Logger.info("Failed to create peak data: "+c);else throw c;}null!=this.acdMolFile&&JSV.common.JSVFileManager.htCorrelationCache.put("mol",this.acdMolFile)}Float.isNaN(this.nmrMaxY)?
1E4<=a.getMaxY()&&a.doNormalize(1E3):a.doNormalize(this.nmrMaxY);this.isSimulation&&a.setSimulated(this.filePath);this.nSpec++;if(0<this.firstSpec&&this.nSpec<this.firstSpec)return!0;if(0<this.lastSpec&&this.nSpec>this.lastSpec)return!(this.done=!0);a.setBlockID(this.blockID);this.source.addJDXSpectrum(null,a,b);return!0},"JSV.common.Spectrum,~B");c(c$,"getBlockSpectra",function(a){JU.Logger.debug("--JDX block start--");for(var b="",c=null,e=0==this.source.type,g=!1;null!=(b=this.t.getLabel())&&!b.equals("##TITLE");)c=
this.getValue(b),e&&!JSV.source.JDXReader.readHeaderLabel(this.source,b,c,this.errorLog,this.obscure)&&JSV.source.JDXReader.addHeader(a,this.t.rawLabel,c),b.equals("##BLOCKS")&&100<JU.PT.parseInt(c)&&0>=this.firstSpec&&(g=!0);c=this.getValue(b);if(!"##TITLE".equals(b))throw new JSV.exception.JSVException("Unable to read block source");e&&this.source.setHeaderTable(a);this.source.type=1;this.source.isCompoundSource=!0;e=new JSV.common.Spectrum;a=new JU.Lst;this.readDataLabel(e,b,c,this.errorLog,this.obscure);
try{for(var f;null!=(f=this.t.getLabel());){if(null==(c=this.getValue(f))&&"##END".equals(b)){JU.Logger.debug("##END= "+this.t.getValue());break}b=f;if(this.isTabularData){if(this.setTabularDataType(e,b),!this.processTabularData(e,a))throw new JSV.exception.JSVException("Unable to read Block Source");}else{if(b.equals("##DATATYPE")&&c.toUpperCase().equals("LINK"))this.getBlockSpectra(a),b=e=null;else if(b.equals("##NTUPLES")||b.equals("##VARNAME"))this.getNTupleSpectra(a,e,b),e=null,b="";if(this.done)break;
if(null==e){e=new JSV.common.Spectrum;a=new JU.Lst;if(""===b)continue;if(null==b){b="##END";continue}}if(null==c){if(0<e.getXYCoords().length&&!this.addSpectrum(e,g))return this.source;e=new JSV.common.Spectrum;a=new JU.Lst}else this.readDataLabel(e,b,c,this.errorLog,this.obscure)||(JSV.source.JDXReader.addHeader(a,this.t.rawLabel,c),this.checkCustomTags(e,b,c))}}}catch(h){if(y(h,Exception))throw new JSV.exception.JSVException(h.getMessage());throw h;}this.addErrorLogSeparator();this.source.setErrorLog(this.errorLog.toString());
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break}if(c.equals("##PAGE"))k=this.t.getValue();else{if(null==l&&(l=new JSV.common.Spectrum,b.copyTo(l),l.setTitle(b.getTitle()),!l.is1D())){var n=k.indexOf("=");if(0<=n)try{l.setY2D(Double.parseDouble(k.substring(n+1).trim()));var r=k.substring(0,n).trim(),s=g.indexOf(r);0<=s&&l.setY2DUnits(f.get("##UNITS").get(s))}catch(t){if(!y(t,Exception))throw t;}}n=new JU.Lst;for(l.setHeaderTable(n);!c.equals("##DATATABLE");)JSV.source.JDXReader.addHeader(n,this.t.rawLabel,this.t.getValue()),c=this.t.getLabel();
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e+"\n"),this.errorLog.append("Number of points in Header "+a.nPointsFile+" Found "+k.length+"\n"));JU.Logger.debugging&&System.err.println(this.errorLog.toString())},"JSV.source.JDXDataObject,~A");c$.addHeader=c(c$,"addHeader",function(a,b,c){for(var e,g=0;g<a.size();g++)if((e=a.get(g))[0].equals(b)){e[1]=c;return}a.addLast([b,c,JSV.source.JDXSourceStreamTokenizer.cleanLabel(b)])},"JU.Lst,~S,~S");c(c$,"checkCustomTags",function(a,b,c){10<b.length&&(b=b.substring(0,10));null==a?System.out.println(b):
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this.mpr.readACDAssignments(a.nPointsFile,40==b);break}}catch(e){if(y(e,Exception))throw new JSV.exception.JSVException(e.getMessage());throw e;}finally{this.reader=null}return!0},"JSV.common.Spectrum,~S,~S");c(c$,"getMpr",function(){return null==this.mpr?this.mpr=JSV.common.JSViewer.getInterface("J.jsv.JDXMOLParser"):this.mpr});h(c$,"rd",function(){return this.reader.readLine()});h(c$,"setSpectrumPeaks",function(a,b,c){this.modelSpectrum.setPeakList(this.peakData,b,c);this.modelSpectrum.isNMR()&&
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c(c$,"dispose",function(){this.jdxSpectra=this.headerTable=null});u(c$,function(a,b){F(this,JSV.source.JDXSource,[]);this.type=a;this.setFilePath(b);this.headerTable=new JU.Lst;this.jdxSpectra=new JU.Lst;this.isCompoundSource=0!=a},"~N,~S");c(c$,"getJDXSpectrum",function(a){return this.jdxSpectra.size()<=a?null:this.jdxSpectra.get(a)},"~N");c(c$,"addJDXSpectrum",function(a,b,c){null==a&&(a=this.filePath);b.setFilePath(a);a=this.jdxSpectra.size();(0==a||!this.jdxSpectra.get(a-1).addSubSpectrum(b,c))&&
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c(c$,"getLastSelectedPathComponent",function(){return null==this.selectedPath?null:this.selectedPath.getLastPathComponent()});h(c$,"setSelectedPanel",function(a,b){if(null!=b){var c=JSV.common.PanelNode.findNode(b,this.vwr.panelNodes).treeNode;this.setSelectionPath(this.vwr.spectraTree.newTreePath(c.getPath()))}},"JSV.api.ScriptInterface,JSV.api.JSVPanel");c(c$,"setSelectionPath",function(a){this.selectedPath=a;this.valueChanged()},"JSV.api.JSVTreePath");h(c$,"createTree",function(a,b,c){var e=this.vwr.spectraTree,
g=e.getRootNode(),f=this.vwr.panelNodes,h=JSV.common.JSVFileManager.getTagName(b.getFilePath()),k=new JSV.common.PanelNode(null,h,b,null),l=new JSV.tree.SimpleTreeNode(h,k);k.setTreeNode(l);e.spectraTreeModel.insertNodeInto(l,g,g.getChildCount());for(g=0;g<c.length;g++){var k=new JSV.common.PanelNode(a+"."+(g+1),h,b,c[g]),m=new JSV.tree.SimpleTreeNode(k.toString(),k);k.setTreeNode(m);f.addLast(k);e.spectraTreeModel.insertNodeInto(m,l,l.getChildCount())}this.vwr.selectFrameNode(c[0]);return l},"~N,JSV.source.JDXSource,~A");
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