(function(ba,ca,da,ea,fa,ga,R,L,S,U,V,O,W,X,ha,Q,F,Y,P,Z,ia,$,ja,ka,la,ma,na,oa,pa,qa,z,ra,sa,ta,ua,va,wa,xa,ya,za,Aa,Ba,Ca,Da,Ea,Fa,Ga,Ha,Ia,Ja,Ka,La,Ma,Na,Oa,Pa,Qa,Ra,k,aa){R("JS");S(null,"JS.ScriptExt",["JU.AU"],function(){c$=V(function(){this.e=this.vwr=null;this.chk=!1;this.st=null;this.slen=0;U(this,arguments)},JS,"ScriptExt");k(c$,"init",function(a){this.e=a;this.vwr=this.e.vwr;return this},"~O");k(c$,"atomExpressionAt",function(a){return this.e.atomExpressionAt(a)},"~N");k(c$,"checkLength",
function(a){this.e.checkLength(a)},"~N");k(c$,"error",function(a){this.e.error(a)},"~N");k(c$,"invArg",function(){this.e.invArg()});k(c$,"invPO",function(){this.error(23)});k(c$,"getShapeProperty",function(a,c){return this.e.getShapeProperty(a,c)},"~N,~S");k(c$,"paramAsStr",function(a){return this.e.paramAsStr(a)},"~N");k(c$,"centerParameter",function(a){return this.e.centerParameter(a,null)},"~N");k(c$,"floatParameter",function(a){return this.e.floatParameter(a)},"~N");k(c$,"getPoint3f",function(a,
c){return this.e.getPoint3f(a,c,!0)},"~N,~B");k(c$,"intParameter",function(a){return this.e.intParameter(a)},"~N");k(c$,"isFloatParameter",function(a){switch(this.e.tokAt(a)){case 2:case 3:return!0}return!1},"~N");k(c$,"setShapeProperty",function(a,c,b){this.e.setShapeProperty(a,c,b)},"~N,~S,~O");k(c$,"showString",function(a){this.e.showString(a)},"~S");k(c$,"stringParameter",function(a){return this.e.stringParameter(a)},"~N");k(c$,"getToken",function(a){return this.e.getToken(a)},"~N");k(c$,"tokAt",
function(a){return this.e.tokAt(a)},"~N");k(c$,"setShapeId",function(a,c,b){b&&this.invArg();c=this.e.setShapeNameParameter(c).toLowerCase();this.setShapeProperty(a,"thisID",c);return c},"~N,~N,~B");k(c$,"getColorTrans",function(a,c,b,e){b=3.4028235E38;1765808134!=a.theTok&&--c;switch(this.tokAt(c+1)){case 603979967:c++;b=this.isFloatParameter(c+1)?a.getTranslucentLevel(++c):this.vwr.getFloat(570425353);break;case 1073742074:c++,b=0}a.isColorParam(c+1)?e[0]=a.getArgbParam(++c):1073742333==this.tokAt(c+
1)?(e[0]=0,a.iToken=c+1):3.4028235E38==b?this.invArg():e[0]=-2147483648;return b},"JS.ScriptEval,~N,~B,~A");k(c$,"finalizeObject",function(a,c,b,e,f,d,g,j){f&&this.setShapeProperty(a,"set",d);-2147483648!=c&&this.e.setShapePropertyBs(a,"color",Integer.$valueOf(c),j);3.4028235E38!=b&&this.e.setShapeTranslucency(a,"","translucent",b,j);0!=e&&this.setShapeProperty(a,"scale",Integer.$valueOf(e));0<g&&(this.e.setMeshDisplayProperty(a,g,0)||this.invArg())},"~N,~N,~N,~N,~B,~O,~N,JU.BS");k(c$,"getIntArray2",
function(a){a=this.e.getToken(a).getList();for(var c=JU.AU.newInt2(a.size()),b=c.length;0<=--b;){var e=a.get(b).getList();null==e&&this.invArg();c[b]=F(e.size(),0);for(var f=c[b].length;0<=--f;)c[b][f]=e.get(f).intValue}return c},"~N");k(c$,"getAllPoints",function(a,c){var b=null,e=null;try{switch(this.e.tokAt(a)){case 7:b=this.e.getPointArray(a,-1,!1);break;case 12290:case 10:case 1073742325:e=this.atomExpressionAt(a)}null==b&&(null==e&&(e=this.vwr.getAllAtoms()),b=this.bsToArray(e))}catch(f){if(!Q(f,
Exception))throw f;}(null==b||b.length<c)&&this.invArg();return b},"~N,~N");k(c$,"bsToArray",function(a){for(var c=Array(a.cardinality()),b=a.nextSetBit(0),e=0;0<=b;b=a.nextSetBit(b+1))c[e++]=this.vwr.ms.at[b];return c},"JU.BS")});R("JS");S(["JS.ScriptExt"],"JS.CmdExt","java.lang.Boolean $.Float $.Long java.util.Hashtable $.Map JU.AU $.BS $.Base64 $.Lst $.M3 $.M4 $.Measure $.P3 $.P4 $.PT $.Quat $.SB $.V3 J.api.Interface J.atomdata.RadiusData J.c.STER $.VDW J.i18n.GT JM.Atom $.AtomCollection $.BondSet $.LabelToken $.Measurement JS.SV $.ScriptCompiler $.ScriptError $.ScriptEval $.ScriptInterruption $.ScriptMathProcessor $.ScriptParam $.T JU.BSUtil $.BoxInfo $.C $.Edge $.Elements $.Escape $.Logger $.Parser $.Point3fi $.SimpleUnitCell JV.FileManager $.StateManager $.Viewer".split(" "),
function(){c$=Z(JS,"CmdExt",JS.ScriptExt);X(c$,function(){$(this,JS.CmdExt,[])});aa(c$,"dispatch",function(a,c,b){this.chk=this.e.chk;this.slen=this.e.slen;this.st=b;switch(a){case 1073741866:b[0].value=this.prepareBinaryOutput(b[0]);break;case 4098:this.assign();break;case 134221829:this.cache();break;case 4102:this.calculate();break;case 4103:this.capture();break;case 4105:this.centerAt();break;case 134221831:this.compare();break;case 528395:this.console();break;case 4106:this.connect(1);break;
case 1094717448:this.configuration();break;case 134221834:this.data();break;case 1613238294:this.connect(0);break;case 4120:this.image();break;case 4122:this.invertSelected();break;case 4124:this.macro();break;case 4125:this.mapProperty();break;case 4126:this.minimize();break;case 603983903:this.modelkit();break;case 1275072532:this.modulation();break;case 4130:this.mutate();break;case 4131:this.navigate();break;case 4133:case 134221850:case 4138:this.plot(b);break;case 134222350:this.show();break;
case 528443:this.stereo();break;case 1814695966:this.unitcell(c?2:1,!1);break;case 134221856:return this.write(c?b:null);case 6:this.measure();break;case 21:this.polyhedra();break;case 20:this.ellipsoid();break;case 4:this.struts()}return null},"~N,~B,~A");k(c$,"macro",function(){if(!this.chk){var a=this.e.optParameterAsString(1);if(0==a.length)this.showString(this.vwr.getMacro(null));else{var c=this.vwr.getMacro(a);null==c?this.showString("macro "+a+" could not be found. Current macros include:\n"+
this.vwr.getMacro(null)):(this.showString("running "+c),this.e.cmdScript(4124,c,null))}}});k(c$,"evalParallel",function(a,c){this.chk=this.e.chk;this.slen=this.e.slen;var b=(new JS.ScriptEval).setViewer(this.vwr);b.historyDisabled=!0;b.compiler=new JS.ScriptCompiler(this.vwr);b.sm=c;try{b.restoreScriptContext(a,!0,!1,!1),b.setAllowJSThreads(!1),b.dispatchCommands(!1,!1,!1)}catch(e){if(Q(e,Exception))return this.e.vwr.setStringProperty("_errormessage",""+e),null==b.thisContext&&(JU.Logger.error("Error evaluating context "+
e),e.printStackTrace()),!1;throw e;}return!0},"JS.ScriptContext,JV.ShapeManager");k(c$,"getBitsetIdent",function(a,c,b,e,f,d){return this.getBitsetIdentFull(a,c,b,e,f,d,null)},"JU.BS,~S,~O,~B,~N,~B");k(c$,"getBitsetIdentFull",function(a,c,b,e,f,d,g){var j=!L(b,JM.BondSet);j&&(null==c?c=this.vwr.getStandardLabelFormat(0):0==c.length&&(c="%[label]"));var h=null==c?-1:c.indexOf("%"),C=2147483647!=f;if(null==a||this.chk||j&&0>h)return null==c&&(c=""),d?z(-1,[c]):c;var h=this.vwr.ms,m=0,q=h.getLabeler();
b=j||!e?null:b.associatedAtoms;e=null==c||0==c.length;var n=j||e?null:JM.LabelToken.getBondLabelValues();c=e?null:j?q.compile(this.vwr,c,"\x00",null):q.compile(this.vwr,c,"\u0001",n);var l=C?1:a.cardinality(),s=null!=g;s||(g=Array(l));var k=new JU.P3;for(f=C?f:a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var x;j?x=e?h.at[f].getInfo():q.formatLabelAtomArray(this.vwr,h.at[f],c,"\x00",b,k):(x=h.bo[f],x=e?x.getIdentity():q.formatLabelBond(this.vwr,x,c,n,b,k));x=JU.PT.formatStringI(x,"#",m+1);g[s?f:m]=x;
m++;if(C)break}return 1==l&&!d?g[0]:g},"JU.BS,~S,~O,~B,~N,~B,~A");k(c$,"getLoadSymmetryParams",function(a,c,b){var e=this.e;this.chk=e.chk;this.slen=e.slen;var f=null,d=this.tokAt(a);if(1073742332==d||8==d)f=e.getFractionalPoint(a),d=this.tokAt(a=e.iToken+1);switch(d){case 1073741938:case 1073742080:case 1094713350:case 1073742163:case 1073742114:case 134217764:case 1814695966:null==f&&(f=JU.P3.new3(555,555,-1)),e.iToken=a-1}d=null;if(null!=f){b.put("lattice",f);a=e.iToken+1;c.append(" "+JU.SimpleUnitCell.escapeMultiplier(f));
a=this.checkPacked(a,b,c);1094713350==this.tokAt(a)&&(b.put("centroid",Boolean.TRUE),c.append(" CENTROID"),a=this.checkPacked(++a,b,c));if(1073742163==this.tokAt(a)){var g;c.append(" SUPERCELL ");if(e.isPoint3f(++a)){g=this.getPoint3f(a,!1);if(g.x!=O(g.x)||g.y!=O(g.y)||g.z!=O(g.z)||1>g.x||1>g.y||1>g.z)e.iToken=a,this.invArg();a=e.iToken}else g=this.stringParameter(a);c.append(JU.Escape.e(g));b.put("supercell",g);a=this.checkPacked(++a,b,c)}g=0;1073742114==this.tokAt(a)&&(a++,g=this.floatParameter(a++),
c.append(" range "+g));b.put("symmetryRange",Float.$valueOf(g));g=null;var j;g=-2147483648;134217764==this.tokAt(a)&&(++a,g=JU.PT.rep(this.paramAsStr(a++),"''",'"'),c.append(" spacegroup "+JU.PT.esc(g)),g.equalsIgnoreCase("ignoreOperators")?g=-999:(0==g.length?(j=this.vwr.getCurrentUnitCell(),null!=j&&(g=j.getSpaceGroupName())):0<=g.indexOf(",")&&9>f.x&&(9>f.y&&0==f.z)&&(g+="#doNormalize=0"),b.put("spaceGroupName",g),g=-2));f=null;if(1814695966==this.tokAt(a)){++a;j=e.optParameterAsString(a);0==j.length?
(j=this.vwr.getCurrentUnitCell(),null!=j&&(f=j.getUnitCellAsArray(!0),d=j.getCartesianOffset())):4==this.tokAt(a)?(f=P(6,0),JU.SimpleUnitCell.setOabc(j,f,null)):f=e.floatParameterSet(a,6,9);(null==f||6!=f.length&&9!=f.length)&&this.invArg();c.append(" unitcell [");for(a=0;a<f.length;a++)c.append((0==a?"":" ")+f[a]);c.append("]");b.put("unitcell",f);-2147483648==g&&(g=-1);a=e.iToken+1}-2147483648!=g&&b.put("spaceGroupIndex",Integer.$valueOf(g))}f=!1;null==d&&1073742066==this.tokAt(a)&&(d=this.getPoint3f(++a,
!0),f=e.coordinatesAreFractional);null!=d&&(f?(d.setT(e.fractionalPoint),b.put("unitCellOffsetFractional",f?Boolean.TRUE:Boolean.FALSE),c.append(" offset {"+d.x+" "+d.y+" "+d.z+"/1}")):c.append(" offset "+JU.Escape.eP(d)),b.put("unitCellOffset",d),a=e.iToken+1);return a},"~N,JU.SB,java.util.Map");k(c$,"checkPacked",function(a,c,b){switch(this.tokAt(a)){case 1073741938:c.put("packed",Boolean.TRUE);var e=null,f=this.tokAt(++a);switch(f){case 1814695966:case 1678381065:break;default:this.e.isArrayParameter(a)?
(e=this.e.getPointArray(a,-1,!1),a=this.e.iToken):this.isFloatParameter(a)?(e=this.floatParameter(a),e=z(-1,[new JU.P3,JU.P3.new3(e,e,e)])):(e=[],--a)}a++;if(this.e.chk)break;switch(f){case 1814695966:e=this.e.optParameterAsString(a++).toLowerCase();if(JU.PT.isOneOf(e,";conventional;primitive;"))return c.put("fillRange",e),b.append(' FILL UNITCELL "'+e+'"'),a;e=this.vwr.getCurrentUnitCell();if(null!=e){e=JU.BoxInfo.toOABC(e.getUnitCellVerticesNoOffset(),e.getCartesianOffset());break}case 1678381065:e=
JU.BoxInfo.toOABC(this.vwr.ms.getBBoxVertices(),null)}switch(e.length){case 2:f=e[1];e=z(-1,[e[0],JU.P3.newP(e[0]),new JU.P3,new JU.P3]);e[1].x=f.x;e[2].y=f.y;e[3].z=f.z;break;case 3:e=z(-1,[new JU.P3,e[0],e[1],e[2]]);break;case 4:break;default:e=z(-1,[new JU.P3,JU.P3.new3(10,0,0),JU.P3.new3(0,10,0),JU.P3.new3(0,0,10)])}c.put("fillRange",e);b.append(" FILL ["+e[0]+e[1]+e[2]+e[3]+"]");break;case 1073742080:e=NaN,this.isFloatParameter(++a)&&(e=this.floatParameter(a++)),this.e.chk||(c.put("packed",Boolean.TRUE),
b.append(" PACKED"),Float.isNaN(e)||(c.put("packingError",Float.$valueOf(e)),b.append(" "+e)))}return a},"~N,java.util.Map,JU.SB");k(c$,"cache",function(){var a=this.tokAt(1),c=null,b=2;switch(a){case 1275069441:case 1073742119:c=this.e.optParameterAsString(b++);case 1073741882:this.checkLength(b);this.chk||("all".equals(c)&&(c=null),c=this.vwr.cacheFileByName(c,1275069441==a),this.showString(0>c?"cache cleared":c+" bytes "+(1275069441==a?" cached":" removed")));break;default:this.invArg()}});k(c$,
"calculate",function(){var a=!1,c=!1,b=null,e=null,f=this.e,d=-2147483648,d=-1;if(2<=(f.iToken=f.slen))switch(f.clearDefinedVariableAtomSets(),this.getToken(1).tok){case 2:if(3!=this.intParameter(1)||!this.paramAsStr(2).equalsIgnoreCase("D"))break;0>this.vwr.am.cmi&&f.errorStr(30,"calculate 3D");b="load append $ filter '2D';select visible;center selected";f.optParameterAsString(3).equalsIgnoreCase("ZAP")&&(b+=";zap modelIndex="+Math.max(this.vwr.am.cmi,0));this.chk||f.runScript(b);return;case 1073741824:this.checkLength(2);
break;case 134217764:f.iToken=1;b=2==this.slen?null:this.atomExpressionAt(2);f.checkLast(f.iToken);this.chk||f.showString(""+this.vwr.findSpaceGroup(b,!0));return;case 1086324752:f.iToken=1;b=2==this.slen?null:this.atomExpressionAt(2);f.checkLast(f.iToken);this.chk||f.showString(this.vwr.calculateChirality(b));return;case 1631586315:this.checkLength(2);if(this.chk)return;d=this.vwr.calculateFormalCharges(null);this.showString(J.i18n.GT.i(J.i18n.GT.$("{0} charges modified"),d));return;case 1075838996:this.checkLength(2);
this.chk||this.vwr.ms.assignAromaticBondsBs(!0,null);return;case 1613238294:2!=f.slen&&(b=(c=1639976963==this.tokAt(++f.iToken))?this.vwr.bsA():this.atomExpressionAt(f.iToken),!c&&1639976963!=this.tokAt(++f.iToken)&&(e=this.atomExpressionAt(f.iToken)));if(this.chk)return;d=this.vwr.autoHbond(b,e,!1);-2147483648!=d&&f.report(J.i18n.GT.i(J.i18n.GT.$("{0} hydrogen bonds"),Math.abs(d)),!1);return;case 1612709900:a=this.tokAt(2);(c=1073742335==a)?f.iToken++:528443==a&&f.iToken++;b=this.slen==f.iToken+
1?null:this.atomExpressionAt(f.iToken+1);null==b&&528443==a&&(b=this.vwr.getAtomBitSet("_C & connected(3) & !connected(double)"));f.checkLast(f.iToken);this.chk||(this.vwr.addHydrogens(b,0),c&&(null==b&&(b=this.vwr.bsA()),this.vwr.makeConnections(0.1,1E8,515,1073742025,b,b,null,!1,!1,0),this.vwr.ms.assignAromaticBondsBs(!0,null)));return;case 1111492619:f.iToken=1;b=2==this.slen?null:this.atomExpressionAt(2);f.checkLast(f.iToken);this.chk||f.getPartialCharges(b);return;case 1088421903:case 134217762:this.chk||
(1275203608==this.tokAt(2)?(a=4==this.tokAt(3)?this.stringParameter(3):null,b=null!=a||3==this.slen?null:this.atomExpressionAt(3),b=z(-1,[a,null,b]),this.showString(f.getShapePropertyData(21,"symmetry",b)?b[1]:"")):this.showString(this.vwr.ms.calculatePointGroup(this.vwr.bsA())));return;case 1111490574:this.checkLength(2);this.chk||(this.vwr.calculateStraightness(),this.vwr.addStateScript("set quaternionFrame '"+this.vwr.getQuaternionFrame()+"'; calculate straightness",!1,!0));return;case 1639976963:b=
4>this.slen||this.isFloatParameter(3)?null:this.atomExpressionAt(2);switch(this.tokAt(++f.iToken)){case 4138:break;case 1111490587:if(this.chk)return;f.showString(this.vwr.getAnnotationParser(!0).calculateDSSRStructure(this.vwr,b));return;case 1073741915:c=!0;d=this.slen==f.iToken+1?-1:O(this.floatParameter(++f.iToken));break;case 0:c=this.vwr.getBoolean(603979826);break;default:this.invArg()}this.chk||this.showString(this.vwr.calculateStructures(b,c,!0,d));return;case 659482:b=f.iToken+1<this.slen?
this.atomExpressionAt(++f.iToken):null;e=f.iToken+1<this.slen?this.atomExpressionAt(++f.iToken):null;this.checkLength(++f.iToken);this.chk||(d=this.vwr.calculateStruts(b,e),0<d&&(this.setShapeProperty(1,"type",Integer.$valueOf(32768)),f.setShapePropertyBs(1,"color",Integer.$valueOf(16777215),null),f.setShapeTranslucency(1,"","translucent",0.5,null),this.setShapeProperty(1,"type",Integer.$valueOf(1023))),this.showString(J.i18n.GT.i(J.i18n.GT.$("{0} struts added"),d)));return;case 2097180:a=!0;case 1111490575:c=
!1;switch(this.tokAt(2)){case 134217759:f.iToken++;break;case 0:c=!a;break;case 1073741952:c=!0;f.iToken++;break;default:c=!0}b=f.iToken+1<this.slen?this.atomExpressionAt(++f.iToken):this.vwr.bsA();this.checkLength(++f.iToken);this.chk||this.vwr.calculateSurface(b,c?3.4028235E38:-1);return}f.errorStr2(53,"CALCULATE","3D? aromatic? hbonds? hydrogen? formalCharge? partialCharge? pointgroup? straightness? structure? struts? surfaceDistance FROM? surfaceDistance WITHIN?")});k(c$,"capture",function(){if(!this.chk&&
!this.vwr.allowCapture())this.showString("Cannot capture on this platform");else{var a=this.vwr.captureParams,c=null==a?"GIF":a.get("type"),b=0,e=0,f=this.e.slen,d="",g=1073742070!=this.vwr.am.animationReplayMode,j=1,h=this.tokAt(j),C=603979967==h;C&&(h=this.tokAt(++j));var m=null;switch(0==h?h=102409:h){case 4:d=this.e.optParameterAsString(j++);if(0==d.length){e=102409;break}c=d.toLowerCase();c.endsWith(".gift")||c.endsWith(".pngt")?(C=!0,d=d.substring(0,d.length-1),c=d.toLowerCase()):!c.endsWith(".gif")&&
!c.contains(".png")&&(d+=".gif");c.endsWith(".png")?(c.endsWith("0.png")||(d=d.substring(0,d.length-4)+"0000.png"),c="PNG"):c="GIF";C&&(c+="T");h=d.indexOf("0000.");h=0>h||h!=d.lastIndexOf(".")-4;e=!1;528411==this.tokAt(j)&&(g=!0,this.tokAt(++j));switch(this.tokAt(j)){case 134222850:m=this.stringParameter(++j);break;case 1073742129:e=!0;case 1611141175:a="y";g=!0;j++;e?(j<f&&2!=this.tokAt(j)&&(a=this.e.optParameterAsString(j++).toLowerCase()),m="rotate Y 10 10;rotate Y -10 -10;rotate Y -10 -10;rotate Y 10 10",
f=j<f?this.intParameter(j++):5,m=0>f?JU.PT.rep(m,"10;",""+-f+";"):JU.PT.rep(m,"10",""+f)):(j<f&&(a=this.e.optParameterAsString(j++).toLowerCase()),m="rotate Y 360 30;");if(this.chk)return;this.vwr.setNavigationMode(!1);if(""===a||0>"xyz".indexOf(a))a="y";m=JU.PT.rep(m,"Y",a);break;case 3:case 2:b=this.floatParameter(j++)}if(this.chk)return;if(null!=m){m="set waitformoveto true;"+m+";set waitformoveto "+this.vwr.g.waitForMoveTo;m="capture "+(C?"transparent ":"")+JU.PT.esc(d)+(g?" LOOP;":";")+m+";capture end;";
this.e.cmdScript(0,null,m);return}e=1073742031;a=new java.util.Hashtable;C=this.vwr.getInt(553648132);h&&(a.put("streaming",Boolean.TRUE),g||this.showString(J.i18n.GT.o(J.i18n.GT.$("Note: Enable looping using the LOOP keyword just after the file name or {0}"),z(-1,["ANIMATION MODE LOOP"]))),this.showString(J.i18n.GT.o(J.i18n.GT.$("Animation delay based on: {0}"),z(-1,["ANIMATION FPS "+C]))));a.put("captureFps",Integer.$valueOf(C));break;case 102409:case 1073741874:null!=a&&a.put("captureSilent",Boolean.TRUE);
case 1073742335:case 1073742334:this.checkLength(-2);e=h;break;default:this.invArg()}this.chk||null==a||(a.put("type",c),c=Integer.$valueOf(this.vwr.getBackgroundArgb()),a.put("backgroundColor",c),a.put("fileName",d),a.put("quality",Integer.$valueOf(-1)),a.put("endTime",Long.$valueOf(0>=b?-1:System.currentTimeMillis()+W(1E3*b))),a.put("captureMode",JS.T.nameOf(e).toLowerCase()),a.put("captureLooping",g?Boolean.TRUE:Boolean.FALSE),b=this.vwr.processWriteOrCapture(a),null==b&&(b="canceled"),JU.Logger.info(b))}});
k(c$,"centerAt",function(){var a=this.getToken(1).tok;switch(a){case 1073741826:case 96:case 1678381065:break;default:this.invArg()}var c=JU.P3.new3(0,0,0);5==this.slen?(c.x=this.floatParameter(2),c.y=this.floatParameter(3),c.z=this.floatParameter(4)):this.e.isCenterParameter(2)?(c=this.centerParameter(2),this.e.checkLast(this.e.iToken)):this.checkLength(2);!this.chk&&!this.vwr.isJmolDataFrame()&&this.vwr.tm.setCenterAt(a,c)});k(c$,"compare",function(){var a=this.e,c=!1,b=!1,e=!1,f=!1,d=!1,g=null,
j=null,h=null,C=null,m=null,q=null;a.iToken=0;var n=this.isFloatParameter(1)?this.floatParameter(++a.iToken):NaN,l=null,s=null,k=null,f=0;if(4115==this.tokAt(1))s=this.vwr.bsA();else if(s=this.atomExpressionAt(1),a.isArrayParameter(++a.iToken))l=a.getPointArray(a.iToken,-1,!1);else if(1140850689!=(f=this.tokAt(a.iToken))&&4115!=f)k=this.atomExpressionAt(a.iToken);var x=null,u=!1,p=!1,r=null,A=JU.BSUtil.copy(s);null!=k&&A.or(k);for(var N=null==l&&null!=k&&A.equals(s),A=N,t=a.iToken+1;t<this.slen;++t)switch(this.getToken(t).tok){case 4115:A=
!0;null==k&&(k=JU.BSUtil.copy(s));break;case 134218757:if(u=!0,f=this.tokAt(t+1),4!=f&&1275203608!=f){r="*";break}case 134218756:r=(p=1275203608==this.tokAt(++t))?"polyhedra":this.stringParameter(t);if(r.equalsIgnoreCase("polyhedra")||r.equalsIgnoreCase("polyhedron"))p=!0;break;case 1677721602:b=d=!0;r=this.paramAsStr(++t);r.equalsIgnoreCase("SMILES")&&(u=!0,1612709900==this.e.tokAt(t+1)?(r="H",t++):r="*");break;case 3:case 2:n=Math.abs(this.floatParameter(t));break;case 268435504:break;case 2109448:x=
this.atomExpressionAt(++t);t=a.iToken;break;case 10:case 1073742325:null!=q&&this.invArg();h=this.atomExpressionAt(a.iToken);f=N?0:this.tokAt(a.iToken+1);C=null==l&&a.isArrayParameter(a.iToken+1)?null:10==f||1073742325==f?this.atomExpressionAt(++a.iToken):JU.BSUtil.copy(h);null!=x&&(h.and(x),null!=C&&C.and(x));null==C?l=a.getPointArray(++a.iToken,-1,!1):null!=k&&C.and(k);null==m&&(m=new JU.Lst);m.addLast(z(-1,[h,C]));t=a.iToken;break;case 1275203608:u=p=!0;break;case 4125:break;case 7:null!=m&&this.invArg();
c=!0;g=a.getQuaternionArray(a.theToken.getList(),1073742001);this.getToken(++t);j=a.getQuaternionArray(a.theToken.getList(),1073742001);null==q&&(q=new JU.Lst);q.addLast(z(-1,[g,j]));break;case 1073742077:c=!0;break;case 134217751:case 1140850689:c=!1;break;case 528432:b=!0;break;case 4160:e=!0;break;default:this.invArg()}if(!this.chk){A&&(n=0);Float.isNaN(n)||0>n?n=1:!b&&!e&&(b=e=!0);f=0!=n;(N=!c&&null==r&&!p||null!=l)&&J.api.Interface.getInterface("JU.Eigen",this.vwr,"script");null==m&&null==q&&
(p&&null==x&&(x=this.vwr.getAtomBitSet("polyhedra")),null==x?(h=N?this.vwr.getAtomBitSet("spine"):new JU.BS,0>h.nextSetBit(0)?(h=s,C=k):(C=JU.BSUtil.copy(h),h.and(s),C.and(k))):(h=JU.BSUtil.copy(s),C=JU.BSUtil.copy(k),h.and(x),h.and(s),null!=C&&(C.and(x),C.and(k))),m=new JU.Lst,m.addLast(z(-1,[h,C])));var B=null;if(A)for(var B=this.vwr.ms.getModelBS(s,!1),x=Array(B.cardinality()),t=0,D=B.nextSetBit(0);0<=D;D=B.nextSetBit(D+1),t++)x[t]=this.vwr.getModelUndeletedAtomsBitSet(D);else B=JU.BSUtil.newAndSetBit(0),
x=z(-1,[s]);for(var E=0,D=B.nextSetBit(0);E<x.length;E++,D=B.nextSetBit(D+1)){var s=x[E],w=P(2,0);if(A&&p&&0==E)k=s;else{for(var v=null,I=new JU.Lst,y=null,M=A?new JU.Lst:m,t=0;t<m.size();++t){var K=m.get(t);A&&M.addLast(K=z(-1,[JU.BSUtil.copy(K[0]),K[1]]));K[0].and(s)}var G=null,F=null;if(N){null!=l&&(M.clear(),M.addLast(z(-1,[h,l])));try{y=this.vwr.getCenterAndPoints(M,!0)}catch(O){if(Q(O,Exception))this.invArg();else throw O;}v=y[0].length-1;for(t=1;t<=v;t++){I=y[0][t];K=y[1][t];if(!L(I,JM.Atom)||
!L(K,JM.Atom))break;A||JU.Logger.info(" atom 1 "+I.getInfo()+"\tatom 2 "+K.getInfo())}v=JU.Measure.calculateQuaternionRotation(y,w);t=Float.isNaN(w[1])?NaN:Math.round(100*w[0])/100;w=Float.isNaN(w[1])?NaN:Math.round(100*w[1])/100;this.showString("RMSD "+t+" --\x3e "+w+" Angstroms")}else if(c){if(null==q)for(t=0;t<M.size();t++){K=M.get(t);g=this.vwr.getAtomGroupQuaternions(K[0],2147483647);j=this.vwr.getAtomGroupQuaternions(K[1],2147483647);for(v=0;v<g.length&&v<j.length;v++)I.addLast(j[v].div(g[v]))}else for(v=
0;v<g.length&&v<j.length;v++)I.addLast(j[v].div(g[v]));w[0]=0;g=I.toArray(Array(I.size()));v=JU.Quat.sphereMean(g,w,1E-4);this.showString("RMSD = "+w[0]+" degrees")}else{t=new JU.M4;G=new JU.P3;if(null!=s&&null!=r&&("H".equals(r)||"*".equals(r)||"".equals(r)))try{r=this.vwr.getSmilesOpt(s,-1,-1,"H".equals(r)?4096:0,null)}catch(T){if(Q(T,Exception))a.evalError(T.getMessage(),null);else throw T;}if(d){var R;if(null==s||null==k||null==(R=a.getSmilesExt().getFlexFitList(s,k,r,!u)))break;this.vwr.setDihedrals(R,
null,1)}p?(w=JU.BS.copy(h),w.and(s),I=JU.BS.copy(C),I.and(k),w=a.getSmilesExt().mapPolyhedra(w.nextSetBit(0),I.nextSetBit(0),u,t)):w=a.getSmilesExt().getSmilesCorrelation(s,k,r,null,null,t,null,!1,null,G,!1,32|(u?1:2));if(Float.isNaN(w)){this.showString("structures do not match from "+s+" to "+k);break}e&&(F=new JU.V3,t.getTranslation(F));b&&(v=new JU.M3,t.getRotationScale(v),v=JU.Quat.newM(v));this.showString("RMSD = "+w+" Angstroms");A&&(t=this.vwr.getV0abc(D,z(-1,[t])),null!=t&&a.setModelCagePts(D,
t,null))}null!=y&&(G=y[0][0]);null==G&&(y=this.vwr.getCenterAndPoints(M,!0),G=y[0][0]);M=new JU.P3;w=NaN;e&&(null==F&&(F=JU.V3.newVsub(y[1][0],G)),w=1E10);if(b&&(null==v&&a.evalError("option not implemented",null),M.add2(G,v.getNormal()),w=v.getTheta(),0==w&&e))if(0.01<F.length())w=1E10;else if(A)continue;else b=e=f=!1;if(!Float.isNaN(w)&&!Float.isNaN(M.x)&&(y=null,b&&(e&&0!=n)&&(y=this.vwr.ms.getAtomPointVector(s),t=JS.ScriptMathProcessor.getMatrix4f(v.getMatrix(),F),y=JU.Measure.transformPoints(y,
t,G)),a.useThreads()||(f=!1),this.vwr.rotateAboutPointsInternal(a,G,M,w/n,w,f,s,F,y,null,null)&&f&&a.isJS))throw new JS.ScriptInterruption(a,"compare",1);}}}});k(c$,"configuration",function(){var a=null,c=this.vwr.bsA();if(1==this.slen){if(this.chk)return;a=this.vwr.ms.setConformation(c);this.vwr.ms.addStateScript("select",null,c,null,"configuration",!0,!1)}else if(this.isFloatParameter(1)){c=this.intParameter(this.e.checkLast(1));if(this.chk)return;a=this.vwr.ms.getConformation(this.vwr.am.cmi,c-
1,!0,null);this.vwr.addStateScript("configuration "+c+";",!0,!1)}else{a=this.atomExpressionAt(1);if(this.chk)return;c=this.intParameter(this.e.checkLast(this.e.iToken+1));this.vwr.addStateScript("configuration "+JU.Escape.eBS(a)+" "+c+";",!0,!1);a=this.vwr.ms.getConformation(this.vwr.am.cmi,c-1,!0,a)}this.setShapeProperty(1,"type",Integer.$valueOf(30720));this.e.setShapeSizeBs(1,0,a);this.vwr.autoHbond(a,a,!0);this.vwr.selectStatus(a,!1,0,this.e.tQuiet,!1)});k(c$,"measure",function(){var a=this.e,
c=null,b=0,e=null;if(2==this.slen)switch(this.tokAt(1)){case 1073742334:this.setShapeProperty(6,"hideAll",Boolean.TRUE);return;case 12291:this.chk||this.vwr.clearAllMeasurements();return}this.vwr.shm.loadShape(6);switch(this.tokAt(1)){case 134218756:var f=this.stringParameter(3==this.slen?2:4);if(this.chk)return;var d=this.vwr.ms.at,c=this.vwr.ms.ac,b=null;try{b=this.vwr.getSmilesMatcher().getCorrelationMaps(f,d,c,this.vwr.bsA(),2)}catch(g){if(Q(g,Exception))a.evalError(g.getMessage(),null);else throw g;
}if(null==b)return;this.setShapeProperty(6,"maps",b);return}switch(this.slen){case 2:switch(this.getToken(1).tok){case 0:case 1073742335:this.vwr.shm.loadShape(6);this.setShapeProperty(6,"hideAll",Boolean.FALSE);return;case 1073742001:this.chk||a.showStringPrint(this.vwr.getMeasurementInfoAsString(),!1);return;case 4:this.setShapeProperty(6,"setFormats",this.stringParameter(1));return}a.errorStr(24,"ON, OFF, DELETE");break;case 3:switch(this.getToken(1).tok){case 12291:if(1073742327==this.getToken(2).tok)this.chk||
this.vwr.clearAllMeasurements();else{var j=this.intParameter(2)-1;this.chk||this.vwr.deleteMeasurement(j)}return}}for(var h=0,C=0,m=-1,q=-1,n=-1,l=F(5,0),k=P(-1,[3.4028235E38,3.4028235E38]),H=!1,x=!1,u=!1,p=!0,r=null,A=null,f=268435538,z=d=null,t=null,B=null,D=new JU.Lst,E=new JU.BS,w=null,v=null,I=0,y=0,M=NaN,K=null,j=1;j<this.slen;++j)switch(this.getToken(j).tok){case 1073741974:1!=j&&this.invArg();c=a.optParameterAsString(++j);continue;case 1073741824:a.errorStr(24,"ALL, ALLCONNECTED, DELETE");
break;default:this.error(15);break;case 268435568:134217736!=this.tokAt(j+1)&&this.invArg();j++;u=!0;break;case 1073741832:K=this.paramAsStr(++j).toLowerCase();break;case 134217736:case 1073741834:case 1073742327:x=1073741834==a.theTok;q=-1;H=!0;x&&u&&this.invArg();break;case 1765808134:b=JU.C.getColix(a.getArgbParam(++j));j=a.iToken;break;case 1073742066:a.isPoint3f(++j)?(e=this.getPoint3f(j,!1),e=P(-1,[1,e.x,e.y,e.z,0,0,0])):e=a.floatParameterSet(j,7,7);j=a.iToken;break;case 1665140738:case 1073741917:y=
O((1665140738==a.theTok?2E3:1E3)*this.floatParameter(++j));null!=c&&0>=y&&(y=-1);break;case 3:null!=r&&this.invArg();p=H=!0;n=(n+1)%2;k[n]=this.floatParameter(j);break;case 12291:268435538!=f&&this.invArg();f=12291;break;case 4114:var G=this.floatParameter(++j),R=this.paramAsStr(++j),S=this.paramAsStr(++j);this.chk||(B=this.vwr.getFont3D(R,S,G));break;case 2:G=this.intParameter(j);if(H)p=!0,n=(n+1)%2,k[n]=G;else{q=this.vwr.ms.getFirstAtomIndexFromAtomNumber(G,this.vwr.getVisibleFramesBitSet());if(!this.chk&&
0>q)return;null!=w&&this.invArg();4<(l[0]=++h)&&a.bad();l[h]=q}break;case 1094713359:m=this.intParameter(++j);break;case 1073742334:268435538!=f&&this.invArg();f=1073742334;break;case 1073742335:268435538!=f&&this.invArg();f=1073742335;break;case 1073742114:p=H=!0;q=-1;break;case 1073741989:case 1073741990:A=Boolean.$valueOf(1073741989==a.theTok);H=!0;u=1073741990==a.theTok;break;case 1648363544:0<=n&&this.invArg();r=a.encodeRadiusParameter(j,!1,!0);if(null==r)return;r.values=k;j=a.iToken;H=u=!0;
A=Boolean.$valueOf(!1);1==I&&(I++,h++,G=JU.BSUtil.copy(E),JU.BSUtil.invertInPlace(G,this.vwr.ms.ac),G.and(this.vwr.ms.getAtomsWithinRadius(5,E,!1,null)),D.addLast(G));break;case 12290:case 10:case 1073742325:I++;case 1073742332:case 8:case 1073742330:0<=q&&this.invArg();h=Array(1);w=a.centerParameter(j,h);if(L(h[0],JU.BS)&&(w=E=h[0],!this.chk&&0==E.length()))return;L(w,JU.P3)&&(j=new JU.Point3fi,j.setT(w),j.mi=m,w=j);4<(h=++C)&&a.bad();j=a.iToken;D.addLast(w);break;case 1715472409:z=this.paramAsStr(j);
break;case 1073742188:M=this.floatParameter(++j);break;case 4:G=this.stringParameter(j);JM.Measurement.isUnits(G)?t=G:d=G;break;case 1073742164:v=a.tickParamAsStr(j,!1,!0,!0),j=a.iToken,f=12290}(null!=r&&(0<=n||2!=h)||2>h&&null==c&&(null==v||1==h))&&a.bad();null!=d&&0!=d.indexOf(h+":")&&(d=h+":"+d);p&&k[1]<k[0]&&(k[1]=k[0],k[0]=3.4028235E38==k[1]?3.4028235E38:-200);if(!this.chk)if(a=null!=c&&null==w&&268435538==f,null!=w||null!=v||a){null==r&&(r=new J.atomdata.RadiusData(k,0,null,null));null!=v&&
(v.id="default");if(a)f=266284;else if(null!=w&&(null!=z||null!=d)&&268435538==f)f=12290;l=null;if(null!=B||null!=K||0!=b||null!=d&&(a||0<=d.indexOf("\n")))l=J.api.Interface.getInterface("JM.Text",this.vwr,"script").newMeasure(this.vwr,B,b);null!=l&&(l.pymolOffset=e,l.setAlignmentLCR(K));this.setShapeProperty(6,"measure",this.vwr.newMeasurementData(c,D).set(f,null,r,z,d,t,v,x,u,A,H,y,b,l,M))}else switch(a=null==c?l:c,f){case 12291:this.setShapeProperty(6,"delete",a);break;case 1073742335:this.setShapeProperty(6,
"show",a);break;case 1073742334:this.setShapeProperty(6,"hide",a);break;default:this.setShapeProperty(6,null==d?"toggle":"toggleOn",a),null!=d&&this.setShapeProperty(6,"setFormats",d)}});k(c$,"connect",function(a){var c=this.e,b=P(2,0),e=Array(2);e[0]=e[1]=this.vwr.bsA();var f=NaN,d=F(-1,[-2147483648]),g=0,j=131071,h=1073742026,C=!1,m=!1,k=!1,n=3.4028235E38,l=!1,s=0,H=0,x=new JU.BS,u=!1,p=0,r=0,A=0,N=!1;if(1==this.slen)this.chk||this.vwr.rebondState(c.$isStateScript);else if(1073877011==this.tokAt(1))this.chk||
this.vwr.connectNBO(this.e.optParameterAsString(2));else{for(;a<this.slen;++a){switch(this.getToken(a).tok){case 1073742335:case 1073742334:this.checkLength(2);this.chk||this.vwr.rebondState(c.$isStateScript);return;case 2:case 3:if(0<s){(m||l)&&c.error(23);j=JU.Edge.getBondOrderFromFloat(this.floatParameter(a));131071==j&&this.invArg();m=!0;break}2<++H&&c.bad();var t=this.floatParameter(a);268435634==this.tokAt(a+1)&&(t=-t/100,a++);b[g++]=t;break;case 12290:case 10:case 1073742325:(2<s||u&&0<s)&&
c.bad();(m||l)&&this.invArg();e[s++]=this.atomExpressionAt(a);u=c.isBondSet;if(2==s){for(var t=c.iToken,B=a;B<t;B++)if(1073741824==this.tokAt(B)&&this.paramAsStr(B).equals("_1")){p=a;break}c.iToken=t}a=c.iToken;break;case 1086324742:N=!0;break;case 1765808134:case 603979967:case 1073742074:l=!0;n=this.getColorTrans(c,a,!1,d);a=c.iToken;break;case 1073742086:d=1073741852==this.tokAt(2);this.checkLength(d?3:2);if(this.chk)return;this.vwr.clearModelDependentObjects();this.vwr.ms.deleteAllBonds();f=new JU.BS;
this.vwr.ms.setPdbConectBonding(0,0,f);if(d){c=c.$isStateScript&&this.vwr.getBoolean(603979872);this.vwr.ms.autoBondBs4(null,null,f,null,this.vwr.getMadBond(),c);this.vwr.addStateScript(c?"set legacyAutoBonding TRUE;connect PDB AUTO;set legacyAutoBonding FALSE;":"connect PDB auto;",!1,!0);return}this.vwr.addStateScript("connect PDB;",!1,!0);return;case 1073741830:case 1073741852:case 1073741904:case 1073742025:case 1073742026:k=!0;++a!=this.slen&&this.invArg();h=c.theTok;1073741852==h&&!(131071==
j||2048==j||515==j)&&this.invArg();break;case 659482:l||(d[0]=16777215,n=0.5,f=this.vwr.getFloat(570425406),l=!0),k||(h=1073742026,k=!0);case 1073741824:if(c.isColorParam(a)){r=-a;break}case 1075838996:case 1613238294:j=this.paramAsStr(a);131071==(j=JS.ScriptParam.getBondOrderFromString(j))&&this.invArg();m&&c.error(18);m=!0;switch(j){case 33:switch(this.tokAt(a+1)){case 3:j=JS.ScriptParam.getPartialBondOrderFromFloatEncodedInt(this.st[++a].intValue);break;case 2:j=this.intParameter(++a)}break;case 2048:2==
this.tokAt(a+1)&&(j=this.intParameter(++a)<<11,A=this.floatParameter(++a));break;case 65537:k||(h=1073742025,k=!0)}break;case 1665140738:f=this.floatParameter(++a);l=!0;break;case 1073742333:case 12291:++a!=this.slen&&this.invArg();h=12291;C=!0;l=!1;break;default:r=a}0<a&&(r==-a||r==a&&c.isColorParam(a)?(l=!0,d[0]=c.getArgbParam(a),a=c.iToken):r==a&&this.invArg())}if(!this.chk){2>g&&(0==g&&(b[0]=1E8),b[1]=b[0],b[0]=0.1);l&&(m||(j=65535),k||(h=1073742025));m=g=0;if(0<p){A=new JU.BS;this.vwr.definedAtomSets.put("_1",
A);N=e[0];for(k=N.nextSetBit(0);0<=k;k=N.nextSetBit(k+1))A.set(k),e=this.vwr.makeConnections(b[0],b[1],j,h,A,this.atomExpressionAt(p),x,u,!1,0),g+=Math.abs(e[0]),m+=e[1],A.clear(k)}else e=this.vwr.makeConnections(b[0],b[1],j,h,e[0],e[1],x,u,N,A),g+=Math.abs(e[0]),m+=e[1];b=c.doReport();C?b&&c.report(J.i18n.GT.i(J.i18n.GT.$("{0} connections deleted"),m),!1):(l&&(this.vwr.selectBonds(x),Float.isNaN(f)||c.setShapeSizeBs(1,Math.round(2E3*f),null),this.finalizeObject(1,d[0],n,0,!1,null,0,x),this.vwr.selectBonds(null)),
b&&c.report(J.i18n.GT.o(J.i18n.GT.$("{0} new bonds; {1} modified"),z(-1,[Integer.$valueOf(g),Integer.$valueOf(m)])),!1))}}},"~N");k(c$,"console",function(){switch(this.getToken(1).tok){case 1073742334:this.chk||this.vwr.showConsole(!1);break;case 1073742335:this.chk||this.vwr.showConsole(!0);break;case 1073741882:this.chk||this.vwr.sm.clearConsole();break;case 134221856:this.showString(this.stringParameter(2));break;default:this.invArg()}});k(c$,"data",function(){var a=this.e,c=null,b=null,e=!1,f;
switch(a.iToken=this.slen){case 5:c=this.paramAsStr(2);case 4:case 2:b=this.paramAsStr(1);if(b.equalsIgnoreCase("clear")){this.chk||this.vwr.setData(null,null,0,0,0,0,0);return}if(0<=(f=b.indexOf("@")))c=""+a.getParameter(b.substring(f+1),4,!0),b=b.substring(0,f).trim();else if(null==c&&0<=(f=b.indexOf(" ")))c=b.substring(f+1).trim(),b=b.substring(0,f).trim(),e=!0;break;default:a.bad()}f=b.substring(0,(b+" ").indexOf(" ")).toLowerCase();if(f.equals("model")||f.equals("append"))a.cmdLoad();else if(!this.chk){var d=
0<=b.toLowerCase().indexOf("(default)");if(f.equals("connect_atoms"))this.vwr.ms.connect(this.parseDataArray(c,!1));else if(0==f.indexOf("ligand_"))this.vwr.setLigandModel(b.substring(7).toUpperCase()+"_data",c.trim());else if(0==f.indexOf("file_"))this.vwr.setLigandModel(b.substring(5)+"_file",c.trim());else if(a=Array(4),f.equals("element_vdw")){a[0]=f;a[1]=c.$replace(";","\n");c=JU.Elements.elementNumberMax;f=F(c+1,0);for(d=1;d<=c;d++)f[d]=d;a[2]=f;a[3]=Integer.$valueOf(0);this.vwr.setData("element_vdw",
a,c,0,0,0,0)}else if(0==f.indexOf("data2d_"))a[0]=b,a[1]=this.parseDataArray(c,!1),a[3]=Integer.$valueOf(2),this.vwr.setData(b,a,0,0,0,0,0);else if(0==f.indexOf("data3d_"))a[0]=b,a[1]=this.parseDataArray(c,!0),a[3]=Integer.$valueOf(3),this.vwr.setData(b,a,0,0,0,0,0);else{var g=JU.PT.getTokens(b);if(0==f.indexOf("property_")&&!(2==g.length&&g[1].equals("set"))){d=this.vwr.bsA();a[0]=f;var j=e?0:this.vwr.getP("propertyAtomNumberField").intValue(),h=e?0:this.vwr.getP("propertyAtomNumberColumnCount").intValue(),
k=e?-2147483648:this.vwr.getP("propertyDataField").intValue(),m=e?0:this.vwr.getP("propertyDataColumnCount").intValue();!e&&0<=b.indexOf(" ")&&(3==g.length&&(j=JU.PT.parseInt(g[1]),k=JU.PT.parseInt(g[2])),5==g.length&&(j=JU.PT.parseInt(g[1]),h=JU.PT.parseInt(g[2]),k=JU.PT.parseInt(g[3]),m=JU.PT.parseInt(g[4])));0>j&&(j=0);0>k&&(k=0);b=this.vwr.ms.ac;e=null;g=JU.BS.newN(b);if(0<j){for(var e=F(b+2,0),q=0;q<=b;q++)e[q]=-1;for(q=d.nextSetBit(0);0<=q;q=d.nextSetBit(q+1)){var n=this.vwr.ms.at[q].getAtomNumber();
n>b+1||(0>n||g.get(n))||(g.set(n),e[n]=q)}a[2]=e}else a[2]=JU.BSUtil.copy(d);a[1]=c;a[3]=Integer.$valueOf(0);this.vwr.setData(f,a,b,j,h,k,m)}else"occupany".equals(f)&&(f="occupancy"),j=JM.AtomCollection.getUserSettableType(f),-1<j?this.vwr.setAtomData(j,f,c,d):(a[0]=b,a[1]=c,a[3]=Integer.$valueOf(0),this.vwr.setData(f,a,0,0,0,0,0))}}});k(c$,"ellipsoid",function(){var a=this.e,c=0,b=1,e=3.4028235E38,f=!1,d=!1;this.setShapeProperty(20,"thisID",null);switch(this.getToken(1).tok){case 1073742335:c=2147483647;
break;case 1073742334:break;case 2:c=this.intParameter(1);break;case 36867:this.e.sm.loadShape(20);this.setShapeProperty(20,"select",this.paramAsStr(2));b=a.iToken;d=f=!0;break;case 1073741974:case 268435633:case 1073741824:this.e.sm.loadShape(20);1073741974==a.theTok&&b++;this.setShapeId(20,b,!1);b=a.iToken;f=!0;break;default:this.invArg()}if(f){for(c=F(-1,[-2147483648]);++b<this.slen;){var f=this.paramAsStr(b),g=null;this.getToken(b);if(!d)switch(a.theTok){case 1073742330:f="points";g=Array(3);
g[0]=a.objectNameParameter(++b);if(this.chk)continue;a.getShapePropertyData(24,"getVertices",g);break;case 1825200146:g=this.e.optParameterAsString(++b);if(0==g.length)continue;break;case 1611272194:var g=Array(3),j=null;switch(this.getToken(b+1).tok){case 11:for(var b=a.theToken.value,h=3;0<=--h;)b.getColumnV(h,g[h]=new JU.V3);break;case 1073742195:b+=2;case 268435520:j=new JU.Lst;for(h=3;0<=--h;){switch(this.tokAt(++b)){case 268435520:break;default:a.isCenterParameter(b)?j.addLast(JS.SV.newV(8,
this.centerParameter(b))):268435520!=this.tokAt(b)&&j.addLast(this.getToken(b))}b=a.iToken}268435521!=this.getToken(++b).tok&&this.invArg();break;case 7:j=a.theToken.getList();switch(j.size()){case 1:j=new JU.Lst;for(h=3;0<=--h;)j.addLast(this.getToken(++b));break;case 3:break;default:this.invArg()}break;default:for(h=0;3>h;h++)g[h]=new JU.V3,g[h].setT(this.centerParameter(++b)),b=a.iToken}if(null!=j)for(b=3;0<=--b;)switch(h=j.get(b),h.tok){case 7:g[b]=JU.V3.new3(JS.SV.fValue(h.getList().get(0)),
JS.SV.fValue(h.getList().get(1)),JS.SV.fValue(h.getList().get(2)));break;case 8:g[b]=JU.V3.newV(h.value)}b=a.iToken;break;case 12289:g=this.centerParameter(++b);b=a.iToken;break;case 1094713359:g=Integer.$valueOf(this.intParameter(++b));break;case 12291:g=Boolean.TRUE,this.checkLength(b+1)}if(null==g)switch(a.theTok){case 1073742335:f="on";g=Boolean.TRUE;break;case 1073742334:f="on";g=Boolean.FALSE;break;case 1073742138:this.isFloatParameter(b+1)?g=Float.$valueOf(this.floatParameter(++b)):a.isCenterParameter(b)?
(b=this.centerParameter(b),g=P(-1,[b.x,b.y,b.z])):g=a.floatParameterSet(++b,3,3);b=a.iToken;break;case 12290:case 10:case 1073742325:f="atoms";g=this.atomExpressionAt(b);b=a.iToken;break;case 1765808134:case 603979967:case 1073742074:e=this.getColorTrans(a,b,!0,c);b=a.iToken;continue;case 1073742075:g=this.paramAsStr(++b)}null==g&&this.invArg();this.setShapeProperty(20,f.toLowerCase(),g)}this.finalizeObject(20,c[0],e,0,!1,null,0,null);this.setShapeProperty(20,"thisID",null)}else a.setShapeSizeBs(20,
c,null)});k(c$,"image",function(){this.chk||this.vwr.getConsole();var a=1,c=null;1073741974==this.tokAt(1)&&(c=this.e.optParameterAsString(++a),a++);var b=this.e.optParameterAsString(a),e=this.e.optParameterAsString(this.slen-1).equalsIgnoreCase("close");if(!e&&(this.slen==a||this.slen==a+2))b=this.slen==a+2?this.intParameter(a++):-1,a=0>b?-1:this.intParameter(a),e=new java.util.Hashtable,e.put("fileName","\u0001\u0001"+c),e.put("backgroundColor",Integer.$valueOf(this.vwr.getBackgroundArgb())),e.put("type",
"png"),e.put("quality",Integer.$valueOf(-1)),e.put("width",Integer.$valueOf(b)),e.put("height",Integer.$valueOf(a)),this.chk||this.vwr.processWriteOrCapture(e);else{if(e)switch(this.slen){case 2:b="closeall";break;case 3:case 4:break;default:this.checkLength(0)}this.chk||this.vwr.fm.loadImage(e?"\u0001close":b,"\u0001"+b+"\u0001"+("".equals(c)||null==c?null:c),!1)}});k(c$,"invertSelected",function(){var a=this.e,c=null,b=null,e=null,f=-2147483648,d=1;switch(this.tokAt(1)){case 0:if(this.chk)return;
e=this.vwr.bsA();c=this.vwr.ms.getAtomSetCenter(e);this.vwr.invertAtomCoord(c,null,e,-1,!1);return;case 528443:case 1140850689:d++;case 10:case 1073742325:case 12290:e=this.atomExpressionAt(d);if(!a.isAtomExpression(a.iToken+1)){a.checkLengthErrorPt(a.iToken+1,a.iToken+1);if(!this.chk)for(a=e.nextSetBit(0);0<=a;a=e.nextSetBit(a+1))this.vwr.invertAtomCoord(null,null,e,a,!1);return}f=e.nextSetBit(0);e=this.atomExpressionAt(a.iToken+1);break;case 134217751:c=a.centerParameter(2,null);break;case 134217750:b=
a.planeParameter(1,!1);break;case 134219265:b=a.hklParameter(2,null)}a.checkLengthErrorPt(a.iToken+1,1);null==b&&(null==c&&-2147483648==f)&&this.invArg();this.chk||-1!=f&&this.vwr.invertSelected(c,b,f,e)});k(c$,"mapProperty",function(){for(var a,c,b,e,f,d=0,g=0,j=0,h=this.e;;){if(1113589787==this.tokAt(1))a=this.vwr.bsA(),c=this.atomExpressionAt(2),b=e="selected";else{a=this.atomExpressionAt(1);if(1073742336!=this.tokAt(++h.iToken)||!JS.T.tokAttr(d=this.tokAt(++h.iToken),1077936128))break;b=this.paramAsStr(h.iToken);
c=this.atomExpressionAt(++h.iToken);if(1073742336!=this.tokAt(++h.iToken)||!JS.T.tokAttr(g=this.tokAt(++h.iToken),2048))break;e=this.paramAsStr(h.iToken)}f=JS.T.tokAttr(j=this.tokAt(h.iToken+1),1077936128)?this.paramAsStr(++h.iToken):JS.T.nameOf(j=1094715393);h.checkLast(h.iToken);if(this.chk)return;var k=null;this.showString("mapping "+b.toUpperCase()+" for "+a.cardinality()+" atoms to "+e.toUpperCase()+" for "+c.cardinality()+" atoms using "+f.toUpperCase());if(JS.T.tokAttrOr(d,1094713344,1111490560)&&
JS.T.tokAttrOr(g,1094713344,1111490560)&&JS.T.tokAttrOr(j,1094713344,1111490560)){var m=this.getBitsetPropertyFloat(a,d|224,null,NaN,NaN),q=this.getBitsetPropertyFloat(a,j|224,null,NaN,NaN),d=this.getBitsetPropertyFloat(c,j|224,null,NaN,NaN),n=1715472409==g,l=P(n?this.vwr.ms.ac:d.length,0),k=new JU.BS;if(m.length==q.length){for(var s=new java.util.Hashtable,j=0;j<m.length;j++)s.put(Float.$valueOf(q[j]),Float.$valueOf(m[j]));m=-1;for(j=q=0;j<d.length;j++){var m=c.nextSetBit(m+1),H=s.get(Float.$valueOf(d[j]));
null!=H&&(k.set(m),l[n?m:q]=H.floatValue(),q++)}n?this.vwr.setData(e,z(-1,[e,l,k,Integer.$valueOf(1),Boolean.TRUE]),this.vwr.ms.ac,0,0,2147483647,0):JS.T.tokAttr(g,2048)?this.vwr.setAtomProperty(k,g,0,0,null,l,null):this.error(56)}}if(null==k){b=this.getBitsetIdent(a,"{"+f+"=%["+f+"]}."+e+" = %["+b+"]",null,!1,2147483647,!1);a=new JU.SB;for(j=0;j<b.length;j++)0>b[j].indexOf("null")&&a.append(b[j]).appendC("\n");JU.Logger.debugging&&JU.Logger.debug(a.toString());b=JU.BSUtil.copy(this.vwr.slm.bsSubset);
this.vwr.slm.setSelectionSubset(c);try{h.runScript(a.toString())}catch(x){if(Q(x,Exception))c=x,this.vwr.slm.setSelectionSubset(b),h.errorStr(-1,"Error: "+c.getMessage());else if(Q(x,Error))c=x,this.vwr.slm.setSelectionSubset(b),h.errorStr(-1,"Error: "+c.toString());else throw x;}this.vwr.slm.setSelectionSubset(b)}this.showString("DONE");return}this.invArg()});k(c$,"minimize",function(){for(var a=null,c=2147483647,b=0,e=!1,f=!1,d=null,g=!1,j=this.vwr.getMinimizer(!1),h=1;h<this.slen;h++)switch(this.getToken(h).tok){case 1073741828:e=
!0;continue;case 1073741874:case 1073742162:this.checkLength(2);if(this.chk||null==j)return;j.setProperty(this.paramAsStr(h),null);return;case 1073741882:this.checkLength(2);if(this.chk||null==j)return;j.setProperty("clear",null);return;case 1073741894:1!=h&&this.invArg();c=a=0;b=F(5,0);if(1073741882==this.tokAt(++h))this.checkLength(3);else{for(;4>a&&!this.isFloatParameter(h);)b[++a]=this.atomExpressionAt(h).nextSetBit(0),h=this.e.iToken+1;b[0]=a;1==a&&this.invArg();c=this.floatParameter(this.e.checkLast(h))}this.chk||
this.vwr.getMinimizer(!0).setProperty("constraint",z(-1,[b,Float.$valueOf(c)]));return;case 1073741905:b=this.floatParameter(++h);continue;case 1073741935:c=0;continue;case 12293:1!=h&&this.invArg();d=this.atomExpressionAt(++h);0>d.nextSetBit(0)&&(d=null);h=this.e.iToken;this.chk||this.vwr.getMinimizer(!0).setProperty("fixed",d);if(h+1==this.slen)return;continue;case 10:case 1073742325:g=!0;case 1275082245:1275082245==this.e.theTok&&h++;a=this.atomExpressionAt(h);h=this.e.iToken;1073742072==this.tokAt(h+
1)&&(h++,g=!0);continue;case 1073742148:f=!0;break;case 266298:c=this.intParameter(++h);continue;default:this.invArg()}if(!this.chk)try{this.vwr.minimize(this.e,c,b,a,d,0,(e?8:0)|(g?16:0)|(f?1:0))}catch(k){if(Q(k,Exception))throw new JS.ScriptInterruption(this.e,"minimize",1);throw k;}});k(c$,"modulation",function(){var a=null,c=this.e,b=!0,e=!1,f=null,d=1;switch(this.getToken(d).tok){case 1073742334:b=!1;case 0:case 1073742335:break;case 12290:case 10:case 1073742325:f=this.atomExpressionAt(1);switch(this.tokAt(c.iToken+
1)){case 1073742334:b=!1;case 1073742335:c.iToken++}c.checkLast(c.iToken);break;case 1073742332:case 8:a=c.getPoint3f(1,!1,!0);e=1073742335==this.tokAt(c.iToken+1);break;default:var g=c.theToken.value.toString();d++;g.equalsIgnoreCase("t")?c.theTok=3:g.equalsIgnoreCase("m")||g.equalsIgnoreCase("q")?c.theTok=2:this.invArg();case 3:case 2:switch(c.theTok){case 3:this.isFloatParameter(d)?(a=this.floatParameter(d),a=JU.P3.new3(a,a,a)):a=c.getPoint3f(d,!1,!0);break;case 2:2==this.tokAt(d)?(e=this.intParameter(d),
a=JU.P3.new3(e,e,e)):a=c.getPoint3f(d,!1,!0),e=!0}break;case 1073742138:b=this.floatParameter(2);this.chk||this.vwr.setFloatProperty("modulationScale",b);return}this.chk||(this.vwr.tm.setVibrationPeriod(0),this.vwr.setModulation(f,b,a,e))});k(c$,"mutate",function(){var a=this.e.iToken,c,b=null,e=null,f=null,d=!1;switch(this.tokAt(++a)){case 1073741904:b="alpha";d=!0;c=null;switch(this.tokAt(++a)){case 0:this.invArg();break;default:switch(e=this.e.paramAsStr(a),a=this.e.iToken,this.tokAt(a+1)){case 0:break;
case 268435520:case 1073742195:case 7:b=null;f=this.e.floatParameterSet(++a,2,2147483647);1==f.length%2&&this.invArg();a=this.e.iToken;break;default:b=this.e.paramAsStr(++a),a=this.e.iToken}}break;case 2:this.st[1]=JS.T.o(4,""+this.st[1].value);default:c=this.atomExpressionAt(a);a=++this.e.iToken;break;case 268435633:c=this.vwr.getFrameAtoms(),a=++this.e.iToken}if(!this.chk&&null!=c){c.and(this.vwr.getFrameAtoms());var g=c.nextSetBit(0);0>g&&this.invArg();g=this.vwr.ms.at[g].mi;if(this.vwr.ms.isTrajectory(g)||
!this.vwr.ms.am[g].isBioModel)return}null==e&&(e=this.e.optParameterAsString(a));this.e.checkLast(a);if(!this.chk){a=e.startsWith("~");if(!a&&!d&&(0<=e.indexOf(".")||0>e.indexOf("-")))d=z(-1,[e]),e=null;else if(e=JU.PT.replaceAllCharacters(e,",; \t\n"," ").trim().toUpperCase(),!a&&0<=e.indexOf("-"))d=JU.PT.split(e,"-");else{if(a||3!=e.length||!this.vwr.getJBR().isKnownPDBGroup(e,20))e=this.vwr.getJBR().toStdAmino3(a?e.substring(1):e);d=JU.PT.getTokens(e)}this.e.iToken=this.e.slen;0<d.length&&!this.vwr.getJBR().getBioModelSet(this.vwr.ms).mutate(c,
e,d,b,f)&&this.invArg()}});k(c$,"navigate",function(){var a=this.e;if(1==this.slen)a.setBooleanProperty("navigationMode",!0);else{var c=JU.V3.new3(0,1,0),b=new JU.Lst,e;if(2==this.slen)switch(this.getToken(1).tok){case 1073742335:case 1073742334:if(this.chk)return;a.setObjectMad10(34,"axes",10);this.setShapeProperty(34,"position",JU.P3.new3(50,50,3.4028235E38));a.setBooleanProperty("navigationMode",!0);this.vwr.tm.setNavOn(1073742335==a.theTok);return;case 1073742162:this.chk||this.vwr.tm.setNavXYZ(0,
0,0);return;case 8:case 1112152078:break;default:this.invArg()}!this.chk&&!this.vwr.getBoolean(603979889)&&a.setBooleanProperty("navigationMode",!0);for(var f=1;f<this.slen;f++){var d=this.isFloatParameter(f)?this.floatParameter(f++):2;0>d&&this.invArg();!this.chk&&0<d&&a.refresh(!1);switch(this.getToken(f).tok){case 8:case 1073742332:e=this.getPoint3f(f,!0);a.iToken++;a.iToken!=this.slen&&this.invArg();this.chk||this.vwr.tm.setNavXYZ(e.x,e.y,e.z);return;case 554176526:e=this.floatParameter(++f);
this.chk||b.addLast(z(-1,[Integer.$valueOf(554176526),Float.$valueOf(d),Float.$valueOf(e)]));continue;case 12289:e=this.centerParameter(++f);f=a.iToken;this.chk||b.addLast(z(-1,[Integer.$valueOf(134217751),Float.$valueOf(d),e]));continue;case 528432:switch(this.getToken(++f).tok){case 1111492629:c.set(1,0,0);f++;break;case 1111492630:c.set(0,1,0);f++;break;case 1111492631:c.set(0,0,1);f++;break;case 8:case 1073742332:c.setT(this.getPoint3f(f,!0));f=a.iToken+1;break;case 1073741824:this.invArg()}e=
this.floatParameter(f);this.chk||b.addLast(z(-1,[Integer.$valueOf(528432),Float.$valueOf(d),c,Float.$valueOf(e)]));continue;case 4160:var g=e=NaN;if(this.isFloatParameter(++f))e=this.floatParameter(f),g=this.floatParameter(++f);else switch(this.tokAt(f)){case 1111492629:e=this.floatParameter(++f);break;case 1111492630:g=this.floatParameter(++f);break;default:e=this.centerParameter(f);f=a.iToken;this.chk||b.addLast(z(-1,[Integer.$valueOf(4160),Float.$valueOf(d),e]));continue}this.chk||b.addLast(z(-1,
[Integer.$valueOf(268435634),Float.$valueOf(d),Float.$valueOf(e),Float.$valueOf(g)]));continue;case 268435632:continue;case 1112152078:e=new JU.Lst;a.isAtomExpression(f+1)?(g=this.atomExpressionAt(++f),f=a.iToken):g=this.vwr.bsA();if(this.chk)return;this.vwr.getPolymerPointsAndVectors(g,e);var j;if(0<(j=e.size())){for(var g=Array(j),h=0;h<j;h++)g[h]=e.get(h);b.addLast(z(-1,[Integer.$valueOf(1112152078),Float.$valueOf(d),g]));continue}break;case 1073742084:if(1073742330==this.getToken(f+1).tok){f++;
e=a.objectNameParameter(++f);if(this.chk)return;this.setShapeProperty(22,"thisID",e);e=this.getShapeProperty(22,"vertices");a.refresh(!1);null==e&&this.invArg();g=O(this.isFloatParameter(f+1)?this.floatParameter(++f):0);j=O(this.isFloatParameter(f+1)?this.floatParameter(++f):2147483647);b.addLast(z(-1,[Integer.$valueOf(1073742084),Float.$valueOf(d),e,null,F(-1,[g,j])]));continue}for(e=new JU.Lst;a.isCenterParameter(f+1);)e.addLast(this.centerParameter(++f)),f=a.iToken;if(0<e.size()){e=e.toArray(Array(e.size()));
this.chk||b.addLast(z(-1,[Integer.$valueOf(1073742084),Float.$valueOf(d),e,null,F(-1,[0,2147483647])]));continue}default:this.invArg()}}!this.chk&&!this.vwr.isJmolDataFrame()&&this.vwr.tm.navigateList(a,b)}});k(c$,"plot",function(a){var c=this.e,b=this.vwr.am.cmi;0>b&&c.errorStr(30,"plot");var b=this.vwr.ms.getJmolDataSourceFrame(b),e=a.length-1,f=a!==this.st,d=!0,g=this.st;f&&(c.st=this.st=a);var j=f?134222350:a[0].tok,h=f||134221850==j||4138==j?0:1,k=null,m=!0,q=!1;switch(j){case 135176:m=!1;q=
!0;break;case 134222350:d=m=!1;break;case 134221856:m=!1,4==JS.CmdExt.tokAtArray(e,a)?k=this.stringParameter(e--):1073742336==JS.CmdExt.tokAtArray(e-1,a)?(k=this.paramAsStr(e-2)+"."+this.paramAsStr(e),e-=3):(c.st=this.st=g,c.iToken=this.st.length,this.error(13)),c.slen=this.slen=e+1}var f="",n=null,l="",s=!1,H=!1,x=!1,u=!1,p=Array(3),r=F(3,0),A=JU.BSUtil.copy(this.vwr.bsA()),N="; select "+JU.Escape.eBS(A)+";\n ",u=c.optParameterAsString(e).toLowerCase(),t=null,B=null,D=null,E=JS.CmdExt.tokAtArray(h,
a);4==E&&(E=JS.T.getTokFromName(a[h].value));switch(E){default:c.iToken=1;this.invArg();break;case 134221834:c.iToken=1;u="data";N="";break;case 1715472409:c.iToken=h+1;for(a=0;3>a;a++){switch(this.tokAt(c.iToken)){case 4:r[a]=JS.T.getTokFromName(c.getToken(c.iToken).value);break;default:r[a]=this.tokAt(c.iToken);break;case 0:0==a&&this.invArg();case 1287653388:case 32:case 64:a=2;continue}1715472409!=r[a]&&!JS.T.tokAttr(r[a],1077936128)&&this.invArg();p[a]=this.getToken(c.iToken).value.toString();
c.iToken++}1287653388==this.tokAt(c.iToken)&&(D=this.stringParameter(++c.iToken),d=!1,c.iToken++);32==this.tokAt(c.iToken)&&(t=this.getPoint3f(++c.iToken,!1),c.iToken++);64==this.tokAt(c.iToken)&&(B=this.getPoint3f(++c.iToken,!1),c.iToken++);u="property "+p[0]+(null==p[1]?"":" "+p[1])+(null==p[2]?"":" "+p[2]);0>A.nextSetBit(0)&&(A=this.vwr.getModelUndeletedAtomsBitSet(b));l="select "+JU.Escape.eBS(A)+";\n ";break;case 4138:u.equalsIgnoreCase("draw")&&(u=c.optParameterAsString(--e).toLowerCase());
u=e>h&&u.startsWith("r");u="ramachandran"+(u?" r":"")+(135176==j?" draw":"");break;case 134221850:case 136314895:f=' "'+this.vwr.getQuaternionFrame()+'"';l="set quaternionFrame"+f+";\n  ";s=!0;u.equalsIgnoreCase("draw")&&(q=!0,u=c.optParameterAsString(--e).toLowerCase());x=(H=u.startsWith("deriv")||u.startsWith("diff"))&&0<u.indexOf("2");H&&e--;if(u.equalsIgnoreCase("helix")||u.equalsIgnoreCase("axis"))H=q=!0,e=-1;u=((e<=h?"":c.optParameterAsString(e))+"w").substring(0,1);if(u.equals("a")||u.equals("r"))H=
!0;JU.PT.isOneOf(u,";w;x;y;z;r;a;")||c.evalError("QUATERNION [w,x,y,z,a,r] [difference][2]",null);u="quaternion "+u+(H?" difference":"")+(x?"2":"")+(q?" draw":"")}this.st=g;if(this.chk)return"";if(m&&(l+="plot "+u,g=this.vwr.ms.getJmolDataFrameIndex(b,l),0<g&&134221856!=j&&134222350!=j))return this.vwr.setCurrentModelIndexClear(g,!0),"";m=e=g=null;h=Array(3);if(1715472409==E){g=this.getBitsetPropertyFloat(A,r[0]|224,1715472409==r[0]?p[0]:null,null==t?NaN:t.x,null==B?NaN:B.x);h[0]=p[0]+" "+JU.Escape.eAF(g);
null!=p[1]&&(e=this.getBitsetPropertyFloat(A,r[1]|224,1715472409==r[1]?p[1]:null,null==t?NaN:t.y,null==B?NaN:B.y),h[1]=p[1]+" "+JU.Escape.eAF(e));null!=p[2]&&(m=this.getBitsetPropertyFloat(A,r[2]|224,1715472409==r[2]?p[2]:null,null==t?NaN:t.z,null==B?NaN:B.z),h[2]=p[2]+" "+JU.Escape.eAF(m));null==t&&(t=JU.P3.new3(this.getPlotMinMax(g,!1,r[0]),this.getPlotMinMax(e,!1,r[1]),this.getPlotMinMax(m,!1,r[2])));null==B&&(B=JU.P3.new3(this.getPlotMinMax(g,!0,r[0]),this.getPlotMinMax(e,!0,r[1]),this.getPlotMinMax(m,
!0,r[2])));JU.Logger.info("plot min/max: "+t+" "+B);q=n=null;if(d){q=JU.P3.new3(1,1,1);n=new JU.P3;n.ave(B,t);q.sub2(B,t);q.set(q.x/200,q.y/200,q.z/200);JS.T.tokAttr(r[0],1094713344)?(q.x=1,n.x=0):0.1<q.x&&10>=q.x&&(q.x=1);JS.T.tokAttr(r[1],1094713344)?(q.y=1,n.y=0):0.1<q.y&&10>=q.y&&(q.y=1);JS.T.tokAttr(r[2],1094713344)?(q.z=1,n.z=0):0.1<q.z&&10>=q.z&&(q.z=1);if(null==p[2]||null==p[1])n.z=t.z=B.z=q.z=0;for(a=0;a<g.length;a++)g[a]=(g[a]-n.x)/q.x;if(null!=p[1])for(a=0;a<e.length;a++)e[a]=(e[a]-n.y)/
q.y;if(null!=p[2])for(a=0;a<m.length;a++)m[a]=(m[a]-n.z)/q.z}n=z(-1,[A,g,e,m,t,B,q,n,D,h])}if(134221856==j)return this.vwr.writeFileData(k,"PLOT_"+u,b,n);d=u.equals("data")?"1 0 H 0 0 0 # Jmol PDB-encoded data":this.vwr.getPdbData(b,u,null,n,null,!0);if(134222350==j)return d;JU.Logger.debugging&&JU.Logger.debug(d);if(135176==j)return c.runScript(d),"";j=this.vwr.fm.getFileInfo();k=this.vwr.getBoolean(603979792);this.vwr.g.appendNew=!0;d=null!=d&&null==this.vwr.openStringInlineParamsAppend(d,null,
!0);this.vwr.g.appendNew=k;this.vwr.fm.setFileInfo(j);if(!d)return"";j=this.vwr.ms.mc;this.vwr.ms.setJmolDataFrame(l,b,j-1);1715472409!=E&&(l+=";\n"+N);l=this.vwr.addStateScript(l,!0,!1);d=150;switch(E){default:b="frame 0.0; frame last; reset;select visible;wireframe only;";d=10;break;case 1715472409:this.vwr.setFrameTitle(j-1,u+" plot for model "+this.vwr.getModelNumberDotted(b));b="frame 0.0; frame last; reset;select visible; spacefill 3.0; wireframe 0;draw plotAxisX"+j+' {100 -100 -100} {-100 -100 -100} "'+
p[0]+'";draw plotAxisY'+j+' {-100 100 -100} {-100 -100 -100} "'+p[1]+'";';null!=p[2]&&(b+="draw plotAxisZ"+j+' {-100 -100 100} {-100 -100 -100} "'+p[2]+'";');break;case 4138:this.vwr.setFrameTitle(j-1,"ramachandran plot for model "+this.vwr.getModelNumberDotted(b));b="frame 0.0; frame last; reset;select visible; color structure; spacefill 3.0; wireframe 0;draw ramaAxisX"+j+' {100 0 0} {-100 0 0} "phi";draw ramaAxisY'+j+' {0 100 0} {0 -100 0} "psi";';break;case 134221850:case 136314895:this.vwr.setFrameTitle(j-
1,u.$replace("w"," ")+f+" for model "+this.vwr.getModelNumberDotted(b)),b=JU.C.getHexCode(this.vwr.cm.colixBackgroundContrast),b="frame 0.0; frame last; reset;select visible; wireframe 0; spacefill 3.0; isosurface quatSphere"+j+" color "+b+" sphere 100.0 mesh nofill frontonly translucent 0.8;draw quatAxis"+j+'X {100 0 0} {-100 0 0} color red "x";draw quatAxis'+j+'Y {0 100 0} {0 -100 0} color green "y";draw quatAxis'+j+'Z {0 0 100} {0 0 -100} color blue "z";color structure;draw quatCenter'+j+"{0 0 0} scale 0.02;"}c.runScript(b+
N);l.setModelIndex(this.vwr.am.cmi);this.vwr.setRotationRadius(d,!0);c.sm.loadShape(31);this.showString("frame "+this.vwr.getModelNumberDotted(j-1)+(0<u.length?" created: "+u+(s?f:""):""));return""},"~A");k(c$,"polyhedra",function(){var a=this.e,c=1==this.slen,b=!1,e=c,f=!1,d=!1,g=!1,j=NaN,h=0;a.sm.loadShape(21);this.setShapeProperty(21,"init",Boolean.TRUE);for(var k=3.4028235E38,m=-1,q=F(-1,[-2147483648]),n=-1,l=null,s=null,H=!1,x=null,u=null,p=1;p<this.slen;++p){var r=null,x=null;switch(this.getToken(p).tok){case 1073742197:j=
NaN;case 1073741872:a=1073742197==this.e.theTok?-1:2==this.tokAt(p+1)?this.intParameter(++p):1;this.chk||J.api.Interface.getInterface("JU.BZone",this.vwr,"script").setViewer(this.vwr).createBZ(a,null,!1,s,j);this.setShapeProperty(21,"init",Boolean.FALSE);return;case 6:r="info";x=this.e.theToken.value;e=!0;break;case 134217751:r="points";x=Float.$valueOf(1073742334==this.tokAt(++p)?0:this.e.floatParameter(p));H=!0;break;case 1073742138:j=this.floatParameter(++p);H=!0;continue;case 1814695966:null!=
s&&this.invArg();r="unitCell";x=Boolean.TRUE;e=!0;break;case 1073742072:this.e.restrictSelected(!1,!1),a.theTok=1073742335;case 1073742335:case 12291:case 1073742334:(p+1!=this.slen||e||1<h)&&this.error(18);r=1073742334==a.theTok?"off":1073742335==a.theTok?"on":"delete";f=!0;break;case 7:(null==s||e)&&this.invArg();e=!0;x=this.getIntArray2(p);u=this.getAllPoints(a.iToken+1,3);p=a.iToken;L(u[0],JM.Atom)&&this.setShapeProperty(21,"model",Integer.$valueOf(u[0].getModelIndex()));r="definedFaces";x=z(-1,
[x,u]);break;case 1073741961:r="full";break;case 2:null!=s&&this.invArg();r="nVertices";x=Integer.$valueOf(this.intParameter(p));e=!0;268435504==this.tokAt(p+1)&&p++;break;case 1677721602:null!=s&&this.invArg();0<h&&this.invPO();e=!0;r="bonds";c=!0;break;case 1073741852:-1!=m&&this.invArg(),m=0,p--;case 1665140738:p++;case 3:null!=s&&this.invArg();0<h&&this.invPO();r=0>=m?"radius":"radius1";x=Float.$valueOf(m=0==m?0:this.floatParameter(p));e=!0;break;case 1073742066:if(!this.isFloatParameter(p+1)){l=
this.e.centerParameter(++p,null);p=a.iToken;H=!0;continue}case 1073741937:this.setShapeProperty(21,"collapsed",null);case 1073742099:case 1073741924:r=JS.T.nameOf(a.theTok);switch(this.tokAt(p+1)){case 268435860:case 268435504:p++}x=Float.$valueOf(this.floatParameter(++p));break;case 1094717454:null==s&&this.invArg();r="model";x=Integer.$valueOf(this.intParameter(++p));break;case 1073742170:(1<h||null!=s&&!b||n==p)&&this.invPO();h=3;a.isAtomExpression(++p)?(r=e||b?"to":"toBitSet",x=this.atomExpressionAt(p)):
a.isArrayParameter(p)?(r="toVertices",x=a.getPointArray(p,-1,!1)):this.error(19);p=a.iToken;e=!0;break;case 12290:case 10:case 1073742325:d&&this.invPO();switch(++h){case 1:null!=s&&this.invArg();r="centers";break;case 2:r="to";e=!0;break;default:a.bad()}x=this.atomExpressionAt(p);p=a.iToken;e=(new Boolean(e|p+1==this.slen)).valueOf();break;case 1765808134:case 603979967:case 1073742074:k=this.getColorTrans(a,p,!0,q);p=a.iToken;continue;case 1073741948:case 1073741886:d&&this.error(18);d=!0;this.isFloatParameter(p+
1)&&this.setShapeProperty(21,"faceCenterOffset",Float.$valueOf(this.floatParameter(++p)));r=1073741886==this.e.theTok?"collapsed":null;break;case 1073742044:case 1073741933:case 1073741956:case 1073741934:g&&this.error(18);H=g=!0;r=JS.T.nameOf(a.theTok);break;case 1073742182:case 1073742060:case 1073741861:case 1073741958:case 1073741964:continue;case 1073741974:case 268435633:case 1073741824:case 4:if(!a.isColorParam(p)){1!=p&&this.invPO();s=1073741974==a.theTok?this.stringParameter(++p):a.optParameterAsString(p);
this.setShapeProperty(21,"thisID",s);this.setShapeProperty(21,"model",Integer.$valueOf(this.vwr.am.cmi));if(!a.isCenterParameter(p+1))continue;r="center";x=this.centerParameter(++p);p=a.iToken;b=!0;break}default:if(a.isColorParam(p)){q[0]=a.getArgbParam(p);a.isCenterParameter(p)&&(n=a.iToken+1);p=a.iToken;continue}this.invArg()}null!=r&&this.setShapeProperty(21,r,x);if(f)return}e?(!d&&c&&this.setShapeProperty(21,"bonds",null),this.setShapeProperty(21,"generate",null)):H||this.error(19);null!=l&&this.setShapeProperty(21,
"offset",l);Float.isNaN(j)||this.setShapeProperty(21,"scale",Float.$valueOf(j));-2147483648!=q[0]&&this.setShapeProperty(21,"colorThis",Integer.$valueOf(q[0]));3.4028235E38!=k&&a.setShapeTranslucency(21,"","translucentThis",k,null);this.setShapeProperty(21,"init",Boolean.FALSE)});k(c$,"write",function(a){var c=this.e,b=1,e=1,f=null,d=null,g=null,j=null,h="SPT",k=!0,m=!1,q=!1;null==a?(a=this.st,m=this.vwr.isApplet&&!this.vwr.isSignedApplet||!this.vwr.haveAccess(JV.Viewer.ACCESS.ALL)||0<this.vwr.fm.getPathForAllFiles().length):
(b=e=0,k=!1,m=!k);var n=JS.CmdExt.tokAtArray(b,a);if(4==n&&!k){var l=JS.T.getTokenFromName(JS.SV.sValue(a[0]).toLowerCase());null!=l&&(n=l.tok)}switch(n){case 0:break;case 134221850:case 4138:case 1715472409:return d=this.plot(a),m?d:this.writeMsg(d);case 134222850:c.isArrayParameter(b+1)&&(f=c.stringParameterSet(++b),j=g=".",e=b=c.iToken+1,n=this.tokAt(b));break;default:h=JS.SV.sValue(this.tokenAt(b,a)).toUpperCase()}var s=this.vwr.getExportDriverList(),l=null,z=k?this.slen:a.length,x="",u=null,
p=!1,r=null,A=0,F=null,t=!1,B=null,D=-1,E=-1,w=!1,v=null,I=-2147483648;0!=n&&(k&&1<this.slen&&1073741848==this.tokAt(this.slen-2))&&(h=this.paramAsStr(this.slen-1).toUpperCase(),e=z,z-=2,n=0);switch(n){case 15:case 6:h="VAR";r=this.tokenAt(b++,a);break;case 1073741984:h="INLINE";l=JS.SV.sValue(this.tokenAt(++b,a));b++;break;case 134217762:h="PGRP";b++;x=JS.SV.sValue(this.tokenAt(b,a)).toLowerCase();x.equals("draw")&&b++;break;case 1073742329:b++;t=!0;break;case 1073742158:case 134222850:for(u=JS.SV.sValue(this.tokenAt(++b,
a)).toLowerCase();u.equals("localpath")||u.equals("remotepath");)u.equals("localpath")?g=JS.SV.sValue(this.tokenAt(++b,a)):j=JS.SV.sValue(this.tokenAt(++b,a)),u=JS.SV.sValue(this.tokenAt(++b,a)).toLowerCase();h="SPT";break;case 1228935687:case 134320141:case 1610616855:case 135180:case 1073742015:case 1073742018:case 1073877011:case 1073877010:case 135188:b++;break;case 1073741991:h="ZIPALL";b++;break;case 36868:h="VAR";b+=2;break;case 1073741929:case 4115:case 4120:case 1073742139:case 4166:case 1073741824:case 4:switch(n){case 4115:b+
1<z&&1073742325==a[++b].tok||10==a[b].tok?(u=c.atomExpression(a,b,0,!0,!1,null,!0),b=c.iToken+1):u=this.vwr.getAllAtoms();this.chk||(B=this.vwr.ms.getModelBS(u,!0));break;case 1073741929:n=4120,p=!0;case 4120:h="IMAGE";b++;break;case 1073742139:u=JS.SV.sValue(this.tokenAt(++b,a)).toUpperCase();JU.PT.isOneOf(u,";PNG;PNGJ;")?(F=u,b++):F="PNG";break;case 4166:A=c.intParameterRange(++b,1,10);if(2147483647==A)return"";this.chk||(this.vwr.tm.setVibrationPeriod(0),c.isJS||c.delayScript(100));b++;break;default:n=
4120}if(4120==n&&b<a.length)if(n=JS.T.getTokenFromName(JS.SV.sValue(a[b]).toLowerCase()),null!=n&&(h=JS.SV.sValue(n).toUpperCase()),JU.PT.isOneOf(h,s.toUpperCase())){b++;h=h.substring(0,1).toUpperCase()+h.substring(1).toLowerCase();w=!0;k&&(v="Jmol."+h.toLowerCase());break}else if(JU.PT.isOneOf(h,";ZIP;ZIPALL;SPT;STATE;")){b++;break}else h="IMAGE";2==JS.CmdExt.tokAtArray(b,a)&&(D=JS.SV.iValue(this.tokenAt(b++,a)),0>=D&&this.invArg(),E=JS.SV.iValue(this.tokenAt(b++,a)),0>=E&&this.invArg())}if(e<z){u=
JS.SV.sValue(this.tokenAt(b,a));if(u.equalsIgnoreCase("clipboard")){if(this.chk)return""}else JU.PT.isOneOf(u.toLowerCase(),";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;")?(2==JS.CmdExt.tokAtArray(b+1,a)&&2==JS.CmdExt.tokAtArray(b+2,a)&&(D=JS.SV.iValue(this.tokenAt(++b,a)),0>=D&&this.invArg(),E=JS.SV.iValue(this.tokenAt(++b,a)),0>=E&&this.invArg()),2==JS.CmdExt.tokAtArray(b+1,a)&&(I=JS.SV.iValue(this.tokenAt(++b,a)))):JU.PT.isOneOf(u.toLowerCase(),";xyz;xyzrn;xyzvib;mol;mol67;sdf;v2000;v3000;json;pdb;pqr;cml;cif;cifp1;pwmat;qcjson;xsf;")&&
(h=u.toUpperCase(),b+1==z&&b++);h.equals("IMAGE")&&JU.PT.isOneOf(u.toLowerCase(),";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;")&&(h=u.toUpperCase(),I=-2147483648,b++)}b+2==z&&JS.SV.sValue(this.tokenAt(++b,a));switch(JS.CmdExt.tokAtArray(b,a)){case 0:m=!0;break;case 1073741884:break;case 805306401:v=h.equals("IMAGE")?"?jmol.png":"?jmol."+h.toLowerCase();break;case 1073741824:case 4:v=JS.SV.sValue(this.tokenAt(b,a));if(v.equalsIgnoreCase("clipboard")||!this.vwr.haveAccess(JV.Viewer.ACCESS.ALL))v=
null;break;default:this.invArg()}if(h.equals("IMAGE")||h.equals("FRAME")||h.equals("VIBRATION"))h=null!=v&&0<=v.indexOf(".")?v.substring(v.lastIndexOf(".")+1).toUpperCase():"JPG";if(h.equals("ISOSURFACE")||h.equals("CONTACT"))q=h.equals("CONTACT"),h=null!=v&&0<=v.indexOf(".")?v.substring(v.lastIndexOf(".")+1).toUpperCase():"JVXL",h.equals("PMESH")?h="ISOMESH":h.equals("PMB")&&(h="ISOMESHBIN");n=JU.PT.isOneOf(h.toLowerCase(),";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;");if(!n&&(h.equals("MNU")?
h="MENU":h.equals("WRL")||h.equals("VRML")?(h="Vrml",w=!0):h.equals("X3D")?(h="X3d",w=!0):h.equals("STL")?(h="Stl",w=!0):h.equals("IDTF")?(h="Idtf",w=!0):h.equals("MA")?(h="Maya",w=!0):h.equals("JS")?(h="Js",w=!0):h.equals("OBJ")?(h="Obj",w=!0):h.equals("JVXL")?h="ISOSURFACE":h.equals("XJVXL")?h="ISOSURFACE":h.equals("JMOL")?h="ZIPALL":h.equals("HIS")&&(h="HISTORY"),h.equals("COORD")||h.equals("COORDS")))h=null!=v&&0<=v.indexOf(".")?v.substring(v.lastIndexOf(".")+1).toUpperCase():"XYZ";null!=f&&(JV.FileManager.isJmolType(h)||
this.invArg(),h.equals("PNG")&&(h="PNGJ"));!n&&(!w&&!JU.PT.isOneOf(h,";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;PMB;ISOMESHBIN;ISOMESH;VAR;FILE;FUNCTION;CFI;CIF;CIFP1;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL67;PDB;PGRP;PQR;PWMAT;QUAT;RAMA;SDF;V2000;V3000;QCJSON;XSF;INLINE;"))&&c.errorStr2(54,"COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION [w,x,y,z] [derivative]|RAMACHANDRAN|SPT|STATE|VAR x|ZIP|ZIPALL  CLIPBOARD","CIF|CIFP1|CML|CFI|GIF|GIFT|JPG|JPG64|JMOL|JVXL|MESH|MOL|PDB|PMESH|PNG|PNGJ|PNGT|PPM|PQR|PWMAT|SDF|CD|JSON|QCJSON|V2000|V3000|SPT|XJVXL|XSF|XYZ|XYZRN|XYZVIB|ZIP"+
s.toUpperCase().$replace(";","|"));if(this.chk)return"";var b=Array(1),y,e=this.vwr.getBoolean(603979934);if(w){e&&JU.Logger.startTimer("export");d=new java.util.Hashtable;d.put("type",h);null!=v&&d.put("fileName",v);(k||null!=v)&&d.put("fullPath",b);d.put("width",Integer.$valueOf(D));d.put("height",Integer.$valueOf(E));l=this.vwr.generateOutputForExport(d);if(null==l||0==l.length)return"";if(m)return l;if(!h.equals("Povray")&&!h.equals("Idtf")||null==b[0])return this.writeMsg(l);d=h.equals("Idtf")?
".tex":".ini";v=b[0]+d;y=new java.util.Hashtable;y.put("fileName",v);y.put("type",d);y.put("text",l);y.put("fullPath",b);d=this.vwr.processWriteOrCapture(y);h.equals("Idtf")&&(l=l.substring(0,l.indexOf("\\begin{comment}")));l="Created "+b[0]+":\n\n"+l;e&&this.showString(JU.Logger.getTimerMsg("export",0));null!=d&&((h=!d.startsWith("OK"))&&c.evalError(d,null),c.report(l,h));return""}w=null;s=!1;if(null==l){z=0;l=h.intern();if("MENU"===l)l=this.vwr.getMenu("");else if("PGRP"===l)l=this.vwr.ms.getPointGroupAsString(this.vwr.bsA(),
null,0,1,null,null,x.equals("draw")?"":null);else if("PDB"===l||"PQR"===l)m?l=this.vwr.getPdbAtomData(null,null,"PQR"===l,t):(s=!0,h="PDB_"+l+"-coord "+t);else if("FILE"===l)"?".equals(v)&&(v="?Jmol."+this.vwr.getP("_fileType")),m?l=this.vwr.getCurrentFileAsString("script"):s=!0;else if(JU.PT.isOneOf(l,";CIF;CIFP1;SDF;MOL;MOL67;V2000;V3000;CD;JSON;XYZ;XYZRN;XYZVIB;CML;QCJSON;PWMAT;XSF;")){a=this.vwr.bsA();d=" ("+a.cardinality()+" atoms)";if(0<=this.vwr.am.cmi&&!a.equals(y=this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi)))d+=
"\nNote! Selected atom set "+a+" is not the same as the current model "+y;l=this.vwr.getModelExtract(a,t,!1,l);l.startsWith("ERROR:")&&(w=l)}else if("CFI"===l)l=this.vwr.getModelFileData("selected","cfi",!1);else if("FUNCTION"===l)l=this.vwr.getFunctionCalls(null),h="TXT";else if("VAR"===l)null==r&&(r=c.getParameter(JS.SV.sValue(this.tokenAt(k?2:1,a)),1073742190,!0)),a=null,15==r.tok?(a=new JU.Lst,a.addLast(r.value.data)):6==r.tok&&(a=null==v?new JU.Lst:this.prepareBinaryOutput(r)),null==a?(l=r.asString(),
h="TXT"):null!=v&&(y=new java.util.Hashtable,y.put("data",a),null==(w=l=this.vwr.createZip(v,1==a.size()||v.endsWith(".png")||v.endsWith(".pngj")?"BINARY":"ZIPDATA",y))&&c.evalError("#CANCELED#",null));else if("SPT"===l)if(t)y=this.vwr.ms.getTaintedAtoms(2),this.vwr.setAtomCoordsRelative(JU.P3.new3(0,0,0),null),l=this.vwr.getStateInfo(),this.vwr.ms.setTaintedAtoms(y,2);else{if(l=this.vwr.getStateInfo(),null!=g||null!=j)l=JV.FileManager.setScriptFileReferences(l,g,j,null)}else"ZIP"===l||"ZIPALL"===
l?null!=v&&(y=new java.util.Hashtable,null!=f&&y.put("data",f),null==(w=l=this.vwr.createZip(v,h,y))&&c.evalError("#CANCELED#",null)):"HISTORY"===l?(l=this.vwr.getSetHistory(2147483647),h="SPT"):"MO"===l||"NBO"===l?(l=this.getMoJvxl(2147483647,"NBO"===l),h="XJVXL"):"PMESH"===l||"PMB"===l?(null==(l=this.getIsosurfaceJvxl(29,l))&&this.error(31),h="XJVXL"):"ISOMESH"===l?(null==(l=this.getIsosurfaceJvxl(24,l))&&this.error(31),h="PMESH"):"ISOMESHBIN"===l?(null==(w=this.getIsosurfaceJvxl(24,"ISOMESHBIN"))&&
this.error(31),h="PMB"):"ISOSURFACE"===l||"MESH"===l?(null==(l=this.getIsosurfaceJvxl(q?25:24,l))&&this.error(31),h=0<=l.indexOf("<?xml")?"XJVXL":"JVXL",m||this.showString(this.getShapeProperty(q?25:24,"jvxlFileInfo"))):(k&&(m&&null==v)&&(m=!1,v="\u0001"),z=-1,null==F&&0>I&&(I=-1));null==l&&(l="");0==z&&(null==w||L(w,String))}if(!k)return l;if(m)return c.showStringPrint(l,!0),"";if(null!=w&&L(w,String))return this.writeMsg(w);if(s)return this.writeMsg(this.vwr.writeFileData(v,h,0,null));if(h.equals("SCENE"))w=
F;else if(null==w&&(!n||null!=v))w=l;e&&JU.Logger.startTimer("write");n&&(c.refresh(!1),0>D&&(D=p?250:this.vwr.getScreenWidth()),0>E&&(E=p?250:this.vwr.getScreenHeight()));y=new java.util.Hashtable;null!=v&&y.put("fileName",v);y.put("backgroundColor",Integer.$valueOf(this.vwr.getBackgroundArgb()));y.put("type",h);if(p){y.put("is2D",Boolean.TRUE);var M,c="smiles could not be generated";try{if(M=this.vwr.getOpenSmiles(null),0<M.length){var K=this.vwr.setLoadFormat("_"+M,"2",!1),K=K+("?width="+D+"&height="+
E+"&format="+h.toLowerCase());this.showString(K);c=this.vwr.fm.getFileAsBytes(K,null)}}catch(G){if(!Q(G,Exception))throw G;}if(L(c,String))return this.showString(c),null;w=c}L(w,String)&&-2147483648==I?y.put("text",w):L(w,Array)&&y.put("bytes",w);null!=f&&y.put("scripts",f);null!=B&&y.put("bsFrames",B);y.put("fullPath",b);y.put("quality",Integer.$valueOf(I));y.put("width",Integer.$valueOf(D));y.put("height",Integer.$valueOf(E));y.put("nVibes",Integer.$valueOf(A));c=this.vwr.processWriteOrCapture(y);
null==c&&(c="canceled");n&&c.startsWith("OK")&&(c+="; width="+D+"; height="+E);e&&this.showString(JU.Logger.getTimerMsg("write",0));return this.writeMsg(c+(null==d?"":d))},"~A");k(c$,"prepareBinaryOutput",function(a){var c=a.getMap();if(null==c||!c.containsKey("$_BINARY_$"))return null;a=new JU.Lst;for(var b,c=c.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var e=b.getKey();if(!e.equals("$_BINARY_$")){var f=b.getValue(),d=15==f.tok?f.value.data:null;null==d&&(f=f.asString(),d=f.startsWith(";base64,")?
JU.Base64.decodeBase64(f):f.getBytes());if(e.equals("_DATA_")){a=new JU.Lst;a.addLast(d);break}else e.equals("_IMAGE_")?(a.add(0,e),a.add(1,null),a.add(2,d)):(a.addLast(e),a.addLast(null),a.addLast(d))}}return a},"JS.SV");k(c$,"writeMsg",function(a){if(this.chk||null==a)return"";var c=!a.startsWith("OK");c&&(this.e.evalError(a,null),alert(a));this.e.report(a,c);return a},"~S");k(c$,"show",function(){var a=this.e,c=null,b=this.paramAsStr(1),e=null,f=0;3<this.slen&&268435632==this.tokAt(this.slen-3)&&
268435568==this.tokAt(this.slen-2)?(e="!/"+this.paramAsStr(this.slen-1),this.slen-=3,f=3):2<this.slen&&268435632==this.tokAt(this.slen-2)?(e="/"+this.paramAsStr(this.slen-1),this.slen-=2,f=2):0==(e=this.paramAsStr(this.slen-1)).lastIndexOf("/")?(this.slen--,f=1):e=null;var d=null,g=null,j=2,h=this.getToken(1),g=L(h,JS.SV)&&1073741824!=h.tok?0:h.tok;4==g&&(h=JS.T.getTokenFromName(b.toLowerCase()),null!=h&&(g=h.tok));1296041986!=g&&(1073742158!=g&&1715472409!=g&&1228935687!=g)&&this.checkLength(-3);
2==this.slen&&0<=b.indexOf("?")&&(d=this.vwr.getAllSettings(b.substring(0,b.indexOf("?"))),g=-1);switch(g){case 0:this.chk||(d=a.theToken.escape());break;case 1073741925:a.checkLength23();j=this.st.length;this.chk||(d=this.vwr.getModelInfo("domains"),d=L(d,JS.SV)?this.vwr.getAnnotationInfo(d,a.optParameterAsString(2),1073741925):"domain information has not been loaded");break;case 1715472409:d=this.plot(this.st);j=this.st.length;break;case 1073742189:a.checkLength23();j=this.st.length;this.chk||(d=
this.vwr.getModelInfo("validation"),d=L(d,JS.SV)?this.vwr.getAnnotationInfo(d,a.optParameterAsString(2),1073742189):"validation information has not been loaded");break;case 134221829:this.chk||(d=JU.Escape.e(this.vwr.fm.cacheList()));break;case 1111490587:a.checkLength23();j=this.st.length;this.chk||(d=this.vwr.getModelInfo("dssr"),d=null==d?"no DSSR information has been read":2<j?JS.SV.getVariable(this.vwr.extractProperty(d,this.stringParameter(2),-1)).asString():""+JS.SV.getVariable(d).asString());
break;case 1073741915:g=2;3==this.slen?g=O(this.floatParameter((j=3)-1)):this.checkLength(2+f);this.chk||(d=this.vwr.calculateStructures(null,!0,!1,g));break;case 545259572:this.checkLength(2+f);this.chk||(d=this.vwr.fm.getPathForAllFiles());break;case 1275203608:if(!this.chk){var k=Array(2);this.vwr.shm.getShapePropertyData(21,"allInfo",k);d=JS.SV.getVariable(k[1]).asString()}break;case 1073742038:this.chk||this.vwr.getNMRPredict(a.optParameterAsString(2));return;case 603983903:!this.chk&&3==this.slen&&
(d=""+this.vwr.getModelkitProperty(a.stringParameter(2)),j=3);break;case 1275068433:case 1073741978:case 1073741929:case 1073741879:case 134218757:this.checkLength((1073741879==g||134218757==g&&1073742335==this.tokAt(2)?j=3:2)+f);if(this.chk)return;var m=a.optParameterAsString(2);1073741879==g&&("mf".equals(m)&&(m="formula"),"formula".equals(m)&&(d=this.vwr.getModelInfo("formula"),null!=d&&(d=JU.PT.rep(d," ",""))));if(null==d){try{switch(g){case 1275068433:d=this.vwr.getInchi(this.vwr.bsA(),null,
null);null==d&&(d="?");break;case 1073741978:d=this.vwr.getInchi(this.vwr.bsA(),null,"key");break;case 134218757:m.equalsIgnoreCase("true")?(d=this.vwr.getBioSmiles(null),e=null):null!=e&&(d=this.vwr.getSmilesOpt(null,-1,-1,1,e+"///"),e=null);break;default:d=this.vwr.ms.getModelDataBaseName(this.vwr.bsA()),d=null!=d&&(d.startsWith("$")||d.startsWith(":"))?d.substring(1):null}null==d&&(k=JU.Logger.getLogLevel(),JU.Logger.setLogLevel(4),d=134218757==g?this.vwr.getSmiles(null):this.vwr.getOpenSmiles(null),
JU.Logger.setLogLevel(k))}catch(q){if(Q(q,Exception))d=q.getMessage(),null==d&&(d=""),q.printStackTrace();else throw q;}switch(g){case 1073741929:if(0<d.length){this.vwr.fm.loadImage(this.vwr.setLoadFormat("_"+d,"2",!1),"\u0001"+d,!1);return}d="Could not show drawing -- Either insufficient atoms are selected or the model is a PDB file.";break;case 1073741879:j=3,0<d.length?(d=this.vwr.getChemicalInfo(d,m,this.vwr.bsA()),0<=d.indexOf("FileNotFound")&&(d="?")):d="Could not show name -- Either insufficient atoms are selected or the model is a PDB file."}}break;
case 134217764:case 1296041986:d="";k=null;if(2==(j=this.slen)){if(this.chk)break;k=this.vwr.getSymTemp().getSpaceGroupInfo(this.vwr.ms,null,-1,!1,null)}else if(134217764==g){k=this.paramAsStr(2);j=3;if(this.chk)break;k=this.vwr.getSymTemp().getSpaceGroupInfo(this.vwr.ms,JU.PT.rep(k,"''",'"'),-1,!1,null)}if(null!=k){d=(134217764==g?""+k.get("spaceGroupInfo")+k.get("spaceGroupNote"):"")+k.get("symmetryInfo");break}var g=2==this.tokAt(2)?this.intParameter(2):0,k=4==this.tokAt(2)||12==this.tokAt(2)?
this.paramAsStr(2):null,h=m=null,n=-1;if(3<this.slen&&4!=this.tokAt(3)){j=z(-1,[null,this.vwr.getFrameAtoms()]);m=a.centerParameter(2+(0==g?0:1),j);if(null!=j[0]&&0==j[0].cardinality()){j=this.slen;break}j[0]=null;h=a.centerParameter(++a.iToken,j);if(null!=j[0]&&0==j[0].cardinality()){j=this.slen;break}0==g&&2==this.tokAt(a.iToken+1)&&(n=a.getToken(++a.iToken).intValue)}var l=1<a.iToken&&4==this.tokAt(a.iToken+1)?this.stringParameter(++a.iToken):null;this.checkLength((j=++a.iToken)+f);this.chk||(d=
this.vwr.getSymmetryInfo(this.vwr.getAllAtoms().nextSetBit(0),k,g,null,m,h,0,l,0,n,0),d=null==d?"":L(d,java.util.Map)?JS.SV.getVariable(d).asString():d.toString());break;case 1648363544:g=null;2<this.slen&&(j=this.slen,g=J.c.VDW.getVdwType(this.paramAsStr(2)),null==g&&this.invArg());this.chk||(d=this.vwr.getDefaultVdwNameOrData(0,g,null));break;case 134320141:a.checkLength23();j=this.slen;g=a.optParameterAsString(2);if(null==e&&0<=(m=g.indexOf("/")))e=g.substring(m+1),g=g.substring(0,m);this.chk||
(d=this.vwr.getFunctionCalls(g));break;case 36867:this.checkLength(2+f);this.chk||(d=this.vwr.getAllSettings(null));break;case 1073742166:d=this.vwr.getFrameTitle();break;case 1073742184:2==this.slen?this.chk||this.vwr.showUrl(a.getFullPathName()):(g=this.paramAsStr(2),this.chk||this.vwr.showUrl(g));return;case 1765808134:b="defaultColorScheme";break;case 1610612740:b="scaleAngstromsPerInch";break;case 134221850:case 4138:if(this.chk)return;0>this.vwr.am.cmi&&a.errorStr(30,"show "+a.theToken.value);
d=this.plot(this.st);j=this.slen;break;case 14:case 1112152078:this.chk||(d=this.getContext(!1));break;case 1073741888:g=a.optParameterAsString(2);0<g.length&&(j=3);this.chk||(c=this.vwr.cm.getColorSchemeList(g));break;case 1073742192:this.chk||(d=this.vwr.getAtomDefs(this.vwr.definedAtomSets)+this.vwr.g.getVariableList()+this.getContext(!0));break;case 536870926:this.chk||(d=this.vwr.getTrajectoryState());break;case 553648144:c=""+JS.ScriptEval.commandHistoryLevelMax;break;case 553648149:c=""+JU.Logger.getLogLevel();
break;case 603979825:c=""+this.vwr.getBoolean(603979825);break;case 553648178:d="set strandCountForStrands "+this.vwr.getStrandCount(12)+"; set strandCountForMeshRibbon "+this.vwr.getStrandCount(13);break;case 536875070:d=this.vwr.showTimeout(2==(j=this.slen)?null:this.paramAsStr(2));break;case 536870918:c=JU.Escape.eP(this.vwr.getDefaultLattice());break;case 4126:this.chk||(d=this.vwr.getMinimizationInfo());break;case 1611272194:switch(this.vwr.g.axesMode){case 603979808:d="set axesUnitcell";break;
case 603979804:d="set axesMolecular";break;default:d="set axesWindow"}break;case 1610612737:d="set bondMode "+(this.vwr.getBoolean(603979812)?"OR":"AND");break;case 1649022989:this.chk||(d="set strandCountForStrands "+this.vwr.getStrandCount(12)+"; set strandCountForMeshRibbon "+this.vwr.getStrandCount(13));break;case 1613238294:d="set hbondsBackbone "+this.vwr.getBoolean(603979852)+";set hbondsSolid "+this.vwr.getBoolean(603979854);break;case 1611141175:this.chk||(d=this.vwr.getSpinState());break;
case 1611141176:d="set ssbondsBackbone "+this.vwr.getBoolean(603979952);break;case 1610625028:case 1611141171:d="selectionHalos "+(this.vwr.getSelectionHalosEnabled()?"ON":"OFF");break;case 1612709894:d="set selectHetero "+this.vwr.getBoolean(1612709894);break;case 1073741828:d=JU.Escape.eAP(this.vwr.getAdditionalHydrogens(null,null,768));break;case 1612709900:d="set selectHydrogens "+this.vwr.getBoolean(1612709900);break;case 553648130:case 553648138:case 536870924:case 553648176:case 553648172:case 1073741995:this.chk||
(d=this.vwr.getLightingState());break;case 1073742136:case 4146:this.chk||(d=this.vwr.stm.listSavedStates());break;case 1814695966:this.chk||(d=this.vwr.getUnitCellInfoText());break;case 1073742329:if(2==(j=this.slen)){this.chk||(d=this.vwr.getCoordinateState(this.vwr.bsA()));break}g=this.paramAsStr(2);this.chk||(d=this.vwr.stm.getSavedCoordinates(g));break;case 1073742158:!this.chk&&(null==a.outputBuffer&&null==e)&&this.vwr.sm.clearConsole();if(2==(j=this.slen)){this.chk||(d=this.vwr.getStateInfo());
break}if(null!=e&&3==this.slen){this.chk||(d=this.vwr.getStateInfo());break}else if(1228935687==this.tokAt(2)&&4==(j=this.slen)){this.chk||(d=this.vwr.fm.getEmbeddedFileState(this.paramAsStr(3),!0,"state.spt"));break}j=3;g=this.paramAsStr(2);this.chk||(d=this.vwr.stm.getSavedState(g));break;case 1639976963:if(2==(j=this.slen)){this.chk||(d=this.vwr.ms.getProteinStructureState(this.vwr.bsA(),134222350));break}g=this.paramAsStr(2);this.chk||(d=this.vwr.stm.getSavedStructure(g));break;case 134221834:g=
3==(j=this.slen)?this.paramAsStr(2):null;this.chk||(d=this.vwr.getDataObj(g,null,-2),d=null==d?"no data":JU.Escape.encapsulateData(d[0],d[1],d[3].intValue()));break;case 1073742330:j=3;d=a.setObjectProperty();break;case 1678381065:this.chk||(d=this.vwr.ms.getBoundBoxCommand(!0));break;case 12289:this.chk||(d="center "+JU.Escape.eP(this.vwr.tm.fixedRotationCenter));break;case 135176:this.chk||(d=this.getShapeProperty(22,"command"));break;case 1228935687:if(2==this.slen){this.chk||(null==e&&this.vwr.sm.clearConsole(),
d=this.vwr.getCurrentFileAsString("script"));null==d&&(d="<unavailable>");break}j=3;c=this.paramAsStr(2);this.chk||(null==e&&this.vwr.sm.clearConsole(),d=this.vwr.getFileAsString3(c,!0,null));break;case 4115:d=1073742327==this.tokAt(2)&&0<(j=3)?this.vwr.getModelFileInfoAll():this.vwr.getModelFileInfo();break;case 1610616855:g=2==(j=this.slen)?2147483647:this.intParameter(2);1>g&&this.invArg();this.chk||(this.vwr.sm.clearConsole(),0==a.scriptLevel&&this.vwr.removeCommand(),d=this.vwr.getSetHistory(g));
break;case 135180:this.chk||(d=this.getShapeProperty(24,"jvxlDataXml"));break;case 1073877011:case 1073877010:a.optParameterAsString(2).equalsIgnoreCase("list")?(this.e.sm.loadShape(27),d=this.chk?"":this.getShapeProperty(27,"list -1"),j=3):(k=2==(j=this.slen)?-2147483648:this.intParameter(2),this.chk||(d=this.getMoJvxl(k,1073877011==g)));break;case 1094717454:this.chk||(d=this.vwr.ms.getModelInfoAsString());break;case 537006096:this.chk||(d=this.vwr.getMeasurementInfoAsString());break;case 1073741864:j=
3;!this.chk&&this.slen==j&&(d=this.paramAsStr(2),d=this.vwr.getOrientation(JS.T.getTokFromName(d.equals("box")?"volume":d.equals("rotation")?"best":d),"best",null).toString());break;case 1073742132:g=this.tokAt(2),0==g?g=1073742132:j=3;case 1073742178:case 4129:this.chk||(d=this.vwr.getOrientation(g,null,null).toString());break;case 1073742077:j=2;if(3<this.slen)break;switch(g=this.tokAt(2)){case 1073742178:case 1073742132:case 4129:case 0:this.chk||(d=this.vwr.getOrientation(g,null,null).toString());
break;default:g=a.optParameterAsString(2),d=this.vwr.getOrientation(1073742034,g,null).toString()}j=this.slen;break;case 1073742088:this.chk||(d=this.vwr.ms.getPDBHeader(this.vwr.am.cmi));break;case 134217762:g=a.optParameterAsString(2);0==g.length&&(g=null);j=this.slen;this.chk||(d=this.vwr.ms.getPointGroupAsString(this.vwr.bsA(),"show:"+g,0,0,null,null,null));break;case 1088421903:this.chk||(d=this.vwr.ms.getSymmetryInfoAsString());break;case 1073742176:this.chk||(d="transform:\n"+this.vwr.tm.matrixRotate.toString());
break;case 4168:d="zoom "+(this.vwr.tm.zoomEnabled?""+this.vwr.tm.getZoomSetting():"off");break;case 1611272202:d=this.vwr.getShowFrank()?"frank ON":"frank OFF";break;case 1665140738:b="solventProbeRadius";break;case 1086324744:if(3==(j=this.slen)&&1073742334==this.tokAt(2))g=1086324743;case 1073741863:case 1086326788:case 1073742120:case 1113589787:case 1086324742:case 1140850689:case 1073741982:this.chk||(d=this.vwr.getChimeInfo(g));break;case 537022465:case 1610612738:case 20482:case 1612709912:c=
"?";break;case 1073742030:g=2==(j=this.slen)?null:this.paramAsStr(2);this.chk||(d=this.vwr.getBindingInfo(g));break;case 1073742015:this.chk||(c=this.vwr.getMenu(""));break;case 1073741824:b.equalsIgnoreCase("fileHeader")&&(this.chk||(d=this.vwr.ms.getPDBHeader(this.vwr.am.cmi)));break;case 1073741992:case 36868:b=this.paramAsStr(j++),k=a.getParameter(b,1073742190,!0),this.chk||(d=1073741992==g?k.toJSON():k.escape())}this.checkLength(j+f);this.chk||(null!=d?this.showString(this.filterShow(d,e)):null!=
c?this.showString(b+" = "+c):null!=b&&(0<=b.indexOf(" ")?this.showString(b):this.showString(b+" = "+a.getParameter(b,1073742190,!0).escape())))});k(c$,"filterShow",function(a,c){if(null==c)return a;var b=c.startsWith("!/");c=c.substring(b?2:1).toLowerCase();for(var e=JU.PT.split(a,"\n"),f=new JU.SB,d=0;d<e.length;d++)0>e[d].toLowerCase().indexOf(c)==b&&f.append(e[d]).appendC("\n");return f.toString()},"~S,~S");k(c$,"stereo",function(){for(var a=J.c.STER.DOUBLE,c=-5,b=!1,e=null,f=0,d=1;d<this.slen;++d)if(this.e.isColorParam(d))1<
f&&this.e.bad(),0==f&&(e=F(2,0)),b||(c=3),e[f]=this.e.getArgbParam(d),0==f++&&(e[1]=~e[0]),d=this.e.iToken;else switch(this.getToken(d).tok){case 1073742335:this.e.checkLast(this.e.iToken=1);this.e.iToken=1;break;case 1073742334:this.e.checkLast(this.e.iToken=1);a=J.c.STER.NONE;break;case 2:case 3:c=this.floatParameter(d);b=!0;break;case 1073741824:if(b||(c=3),a=J.c.STER.getStereoMode(this.paramAsStr(d)),null!=a)break;default:this.invArg()}this.chk||this.vwr.setStereoMode(e,a,c)});k(c$,"struts",function(){var a=
this.e,c=1073742072==this.tokAt(1)||1073742335==this.tokAt(1)||1==this.slen,b=a.getMadParameter();if(2147483647==b)return!1;c&&(b=Math.round(2E3*this.vwr.getFloat(570425406)));this.setShapeProperty(1,"type",Integer.$valueOf(32768));a.setShapeSizeBs(1,b,null);this.setShapeProperty(1,"type",Integer.$valueOf(1023));return!0});k(c$,"unitcell",function(a,c){var b=this.e,e=2147483647,f=2147483647,d=null,g=b.tickParamAsStr(a,!0,!1,!1);a=b.iToken;var j=null,h=null,k=null,m=null,q=f=!1,n=this.tokAt(++a);switch(n){case 4142:case 4141:q=
!0;d=JU.P4.new4(0,0,0,-1);b.iToken++;break;case 4:case 1073741824:m=n=this.paramAsStr(a).toLowerCase();if(0<=n.indexOf(",")||this.chk){k=n;break}f=null;b.setModelCagePts(-1,null,null);k=this.vwr.getModelInfo("unitcell_conventional");if(JU.PT.isOneOf(m,";parent;standard;primitive;")){if(null==k&&null!=this.vwr.getModelInfo("isprimitive")){this.showString("Cannot convert unit cell when file data is primitive and have no lattice information");return}m.equals("primitive")&&4==this.tokAt(a+1)&&(f=this.paramAsStr(++a).toUpperCase())}L(k,
Array)&&(h=k);null==f&&(f=this.vwr.getModelInfo("latticeType"));null!=k&&b.setModelCagePts(-1,this.vwr.getV0abc(-1,k),""+k);if(!m.equals("conventional")){n=this.vwr.getModelInfo("unitcell_"+m);if(null==n){if((n=m.equals("primitive"))||m.equals("reciprocal")){var l=this.slen==a+1?1:2==this.tokAt(a+1)?3.141592653589793*this.intParameter(++a):this.floatParameter(++a),s=this.vwr.getCurrentUnitCell(),m=(null==s?"":s.getSpaceGroupName()+" ")+m,h=null==s?z(-1,[JU.P3.new3(0,0,0),JU.P3.new3(1,0,0),JU.P3.new3(0,
1,0),JU.P3.new3(0,0,1)]):s.getUnitCellVectors();null==f&&(f=this.vwr.getSymmetryInfo(this.vwr.getFrameAtoms().nextSetBit(0),null,0,null,null,null,1073741994,null,0,-1,0));null==s&&(s=this.vwr.getSymTemp());s.toFromPrimitive(!0,0==f.length?"P":f.charAt(0),h,this.vwr.getCurrentModelAuxInfo().get("primitiveToCrystal"));n||JU.SimpleUnitCell.getReciprocal(h,h,l);break}}else m=n,0<=n.indexOf(",")&&(k=n);this.showString(m)}break;case 135180:case 1073742330:j=b.objectNameParameter(++a);break;case 1678381065:h=
JU.P3.newP(this.vwr.getBoundBoxCenter());d=this.vwr.getBoundBoxCornerVector();h.sub(d);h=z(-1,[h,JU.P3.new3(2*d.x,0,0),JU.P3.new3(0,2*d.y,0),JU.P3.new3(0,0,2*d.z)]);d=null;b.iToken=a;break;case 1073742176:12!=this.tokAt(++a)&&this.invArg();k=z(-1,[this.getToken(a).value]);break;case 11:case 12:k=this.getToken(a).value;break;case 12289:switch(this.tokAt(++a)){case 12290:case 10:case 1073742325:d=this.vwr.ms.getAtomSetCenter(this.atomExpressionAt(a));this.vwr.toFractional(d,!0);a=b.iToken;break;default:if(b.isCenterParameter(a)){d=
this.centerParameter(a);a=b.iToken;break}this.invArg()}d.x-=0.5;d.y-=0.5;d.z-=0.5;break;case 12290:case 10:case 1073742325:f=this.atomExpressionAt(a).nextSetBit(0);this.chk||this.vwr.am.setUnitCellAtomIndex(f);if(0>f)return;a=b.iToken;break;case 1073742066:f=!0;case 1073742114:d=b.getFractionalPoint(++a);L(d,JU.P4)?f&&this.invArg():d=!f&&555>d.x?this.getSupercell(d,!0):JU.P4.new4(d.x,d.y,d.z,f?1:0);a=b.iToken;break;case 1073741938:case 1073742163:d=b.getFractionalPoint(++a);d=this.getSupercell(d,
1073741938==n);a=b.iToken;break;case 3:case 2:if(111>this.floatParameter(a)){a--;break}e=this.intParameter(a);break;default:b.isArrayParameter(a)?(h=b.getPointArray(a,4,!1),a=b.iToken):this.slen>a+1?(d=b.getFractionalPoint(a),a=b.iToken):a--}f=b.getSetAxesTypeMad10(++a);b.checkLast(b.iToken);if(!(this.chk||2147483647==f)){2147483647==f&&this.vwr.am.setUnitCellAtomIndex(-1);null==h&&null!=k&&(h=this.vwr.getV0abc(-1,k));if(2147483647!=e)this.vwr.ms.setUnitCellOffset(this.vwr.getCurrentUnitCell(),null,
e);else if(null!=j)this.vwr.setCurrentCage(j);else if(q||null!=h){e=c?this.vwr.getCurrentUnitCell():null;if(null!=e){if(j=null,j=this.vwr.getFrameAtoms(),k=null,n=j.cardinality(),q=0==n,!q){k=Array(n);l=this.vwr.ms.at;for(s=n;0<=--s;)k[s]=JU.P3.newP(l[s]),this.vwr.toFractionalUC(e,k[s],!1);b.setModelCagePts(-1,h,m);e=this.vwr.getCurrentUnitCell();for(s=n;0<=--s;)l[s].setT(k[s]),this.vwr.toCartesianUC(e,l[s],!1);this.vwr.ms.setTaintedAtoms(j,2)}}else q=!0;q&&b.setModelCagePts(-1,h,m)}b.setObjectMad10(33,
"unitCell",f);null!=d&&this.vwr.ms.setUnitCellOffset(this.vwr.getCurrentUnitCell(),d,0);null!=g&&this.setShapeProperty(33,"tickInfo",g)}},"~N,~B");k(c$,"getSupercell",function(a,c){(1>a.x||1>a.y||1>a.z||a.x!=O(a.x)||a.y!=O(a.y)||a.z!=O(a.z))&&this.invArg();return JU.SimpleUnitCell.ptToIJK(a,c?1:0)},"JU.T3,~B");k(c$,"modelkit",function(){var a=0,c=this.tokAt(1);switch(c){case 1073742334:case 0:case 1073742335:this.chk||this.vwr.setBooleanProperty("modelkitmode",1073742334!=c);if(0==this.tokAt(a+1))return;
a=++this.e.iToken;break;case 528432:this.e.cmdRotate(!1,!1);return;case 4145:this.e.cmdRotate(!1,!0);return;case 4098:++this.e.iToken;case 134217764:case 4106:this.assign();return;case 4130:++this.e.iToken;this.mutate();return}for(var b=this.vwr.getModelkit(!1);0!=(c=this.tokAt(++a));){var e=this.paramAsStr(a).toLowerCase(),f=null;switch(c){case 1073742335:case 1073742334:this.chk||this.vwr.setBooleanProperty("modelkitmode",1073742335==c);continue;case 1610625028:case 12294:e="hidden";f=Boolean.$valueOf(1610625028!=
c);break;case 36867:e=this.paramAsStr(++a);f=0==this.tokAt(++a)?"true":this.paramAsStr(a);break;case 1073742024:f=this.paramAsStr(++a).toLowerCase();JU.PT.isOneOf(f,";view;edit;molecular;")||this.invArg();break;case 1814695966:f=this.paramAsStr(++a).toLowerCase();if(!JU.PT.isOneOf(f,";packed;extend;")){this.unitcell(2,!0);return}break;case 1296041986:switch(this.tokAt(++a)){case 4:case 1073742333:f=this.paramAsStr(a);break;case 12:f=this.getToken(a).value;break;case 2:f=Integer.$valueOf(this.getToken(a).intValue);
break;default:this.e.isCenterParameter(a)?(e="center",f=this.e.centerParameter(a,null),a=this.e.iToken):this.invArg()}break;case 1088421903:f=this.paramAsStr(++a).toLowerCase();JU.PT.isOneOf(f,";none;applylocal;retainlocal;applyfull;")||this.invArg();break;case 1073742066:if(f=this.paramAsStr(a+1),f.equals("none")){++a;break}case 134217751:case 12289:f=this.e.atomCenterOrCoordinateParameter(++a,null);a=this.e.iToken;break;default:if(JU.PT.isOneOf(e,";autobond;hidden;showsymopinfo;clicktosetelement;addhydrogen;addhydrogens;")){f=
Boolean.$valueOf(0==(c=this.tokAt(++a))||1073742335==c);break}if(JU.PT.isOneOf(e,";view;edit;molecular;")){f=e;e="mode";break}if(JU.PT.isOneOf(e,";packed;extend;")){f=e;e="unitcell";break}this.invArg()}!this.chk&&(null!=f&&null!=(f=b.setProperty(e,f))&&"hidden"!==e&&!b.isHidden())&&this.vwr.showString("modelkit "+e+" = "+f.toString(),!1)}});k(c$,"assign",function(){var a=1073742335==this.tokAt(this.slen-1),c=++this.e.iToken,b=this.tokAt(c),e=-1,f=-1,d=1140850689==b,g=1677721602==b,j=4106==b,h=134217764==
b;d||g||j||h?c++:b=1140850689;0>this.vwr.am.cmi&&this.invArg();var k=this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi);if(g){if(2==this.tokAt(c))e=this.e.intParameter(c);else if(L(this.getToken(c).value,JM.BondSet))e=this.getToken(c).value.nextSetBit(0);else switch(c=this.expFor(c,k),e=c.nextSetBit(0),c.cardinality()){case 1:c=this.expFor(++this.e.iToken,k),f=c.nextSetBit(0),0>f&&this.invArg(),c.set(e);case 2:c=this.vwr.ms.getBondsForSelectedAtoms(c,!1);0<c.cardinality()?e=c.nextSetBit(0):(j=
!0,b=4106);break;default:this.invArg()}c=++this.e.iToken}else if(!(1140850689==b&&4==this.tokAt(c))&&!h){c=this.expFor(c,k);e=c.nextSetBit(0);if(0>e)return;c=++this.e.iToken}var m=null,g=null;h||(j?0>f&&(c=this.expFor(c,k),f=c.nextSetBit(0),m=this.e.optParameterAsString(++this.e.iToken)):(m=this.e.optParameterAsString(c),d&&(g=++this.e.iToken<(a?this.slen-1:this.slen)?this.centerParameter(this.e.iToken):null)));if(!this.chk)switch(this.vwr.pushState(),b){case 1140850689:this.e.clearDefinedVariableAtomSets();
this.vwr.getModelkit(!1).cmdAssignAtom(e,g,m,this.e.fullCommand,a);break;case 1677721602:this.vwr.getModelkit(!1).cmdAssignBond(e,(m+"-").charAt(0),this.e.fullCommand);break;case 4106:this.vwr.getModelkit(!1).cmdAssignConnect(e,f,(m+"1").charAt(0),this.e.fullCommand);break;case 134217764:this.e.showString(this.vwr.getModelkit(!1).cmdAssignSpaceGroup())}});k(c$,"expFor",function(a,c){var b=JU.BS.copy(this.atomExpressionAt(a));b.and(c);return b},"~N,JU.BS");k(c$,"getContext",function(a){for(var c=new JU.SB,
b=this.e.thisContext;null!=b;)a?null!=b.vars&&(c.append(this.getScriptID(b)),c.append(JV.StateManager.getVariableList(b.vars,80,!0,!1))):c.append(JS.ScriptError.getErrorLineMessage(b.functionName,b.scriptFileName,this.e.getLinenumber(b),b.pc,JS.ScriptEval.statementAsString(this.vwr,b.statement,-9999,this.e.debugHigh))),b=b.parentContext;a?null!=this.e.contextVariables&&(c.append(this.getScriptID(null)),c.append(JV.StateManager.getVariableList(this.e.contextVariables,80,!0,!1))):c.append(this.e.getErrorLineMessage2());
return c.toString()},"~B");k(c$,"getIsosurfaceJvxl",function(a,c){return this.chk?"":this.getShapeProperty(a,"PMESH"===c||"MESH"===c?"jvxlMeshX":"ISOMESH"===c?"pmesh":"ISOMESHBIN"===c||"PMB"===c?"pmeshbin":"jvxlDataXml")},"~N,~S");k(c$,"getMoJvxl",function(a,c){var b=c?28:27;this.e.sm.loadShape(b);var e=this.vwr.am.cmi;0>e&&this.e.errorStr(30,"show/write MO/NBO");var f=this.vwr.ms.getInfo(e,"moData");null==f&&this.error(27);var d=this.getShapeProperty(b,"moNumber");(null==d||0==d.intValue())&&this.setShapeProperty(b,
"init",Integer.$valueOf(e));this.setShapeProperty(b,"moData",f);return this.e.sm.getShapePropertyIndex(b,"showMO",a)},"~N,~B");k(c$,"getScriptID",function(a){return"\n# "+(null==a?this.e.functionName:"function "+a.functionName)+" (file "+(null==a?this.e.scriptFileName:a.scriptFileName)+(null==a?"":" context "+a.id)+")\n"},"JS.ScriptContext");k(c$,"tokenAt",function(a,c){return a<c.length?c[a]:null},"~N,~A");c$.tokAtArray=k(c$,"tokAtArray",function(a,c){return a<c.length&&null!=c[a]?c[a].tok:0},"~N,~A");
k(c$,"getPlotMinMax",function(a,c,b){if(null==a)return 0;switch(b){case 1111490568:case 1111490569:case 1111490570:return c?180:-180;case 1111490565:case 1111490576:return c?360:0;case 1111490574:return c?1:-1}b=c?-1E10:1E10;for(var e=a.length;0<=--e;){var f=a[e];Float.isNaN(f)||c==f>b&&(b=f)}return b},"~A,~B,~N");k(c$,"parseDataArray",function(a,c){a=JU.Parser.fixDataString(a);var b=JU.Parser.markLines(a,"\n"),e=b.length;if(!c){for(var f=JU.AU.newFloat2(e),d=0,g=0;d<e;g=b[d++])g=JU.PT.getTokens(a.substring(g,
b[d])),JU.PT.parseFloatArrayData(g,f[d]=P(g.length,0));return f}g=JU.PT.getTokens(a.substring(0,b[0]));if(3!=g.length)return P(0,0,0,0);var j=JU.PT.parseInt(g[0]),h=JU.PT.parseInt(g[1]),k=JU.PT.parseInt(g[2]);if(1>j||1>h||1>k)return P(1,1,1,0);for(var f=JU.AU.newFloat3(j,h),m=0,q=0,d=1,g=b[0];d<e&&m<j;g=b[d++])g=JU.PT.getTokens(a.substring(g,b[d])),g.length<k||(JU.PT.parseFloatArrayData(g,f[m][q]=P(g.length,0)),++q==h&&(m++,q=0));return m!=j?(System.out.println("Error reading 3D data -- nX = "+j+
", but only "+m+" blocks read"),P(1,1,1,0)):f},"~S,~B");k(c$,"getBitsetPropertyFloat",function(a,c,b,e,f){c=null==b||1111490843==c?this.e.getBitsetProperty(a,null,c,null,null,b,null,!1,2147483647,!1):this.vwr.getDataObj(b,a,1);if(null==c||!JU.AU.isAF(c))return null==a?null:P(a.cardinality(),0);if(!Float.isNaN(e))for(a=0;a<c.length;a++)c[a]<e&&(c[a]=NaN);if(!Float.isNaN(f))for(a=0;a<c.length;a++)c[a]>f&&(c[a]=NaN);return c},"JU.BS,~N,~S,~N,~N");Y(c$,"ERROR_invalidArgument",22)})})(Clazz,Clazz.getClassName,
Clazz.newLongArray,Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,Clazz.floatToLong,Clazz.makeConstructor,Clazz.defineEnumConstant,Clazz.exceptionOf,Clazz.newIntArray,Clazz.defineStatics,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,Clazz.p0p,Clazz.pu$h,Clazz.newShortArray,Clazz.innerTypeInstance,Clazz.isClassDefined,
Clazz.prepareCallback,Clazz.newArray,Clazz.castNullAs,Clazz.floatToShort,Clazz.superCall,Clazz.decorateAsType,Clazz.newBooleanArray,Clazz.newCharArray,Clazz.implementOf,Clazz.newDoubleArray,Clazz.overrideConstructor,Clazz.clone,Clazz.doubleToShort,Clazz.getInheritedLevel,Clazz.getParamsType,Clazz.isAF,Clazz.isAB,Clazz.isAI,Clazz.isAS,Clazz.isASS,Clazz.isAP,Clazz.isAFloat,Clazz.isAII,Clazz.isAFF,Clazz.isAFFF,Clazz.tryToSearchAndExecute,Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,
Clazz.overrideMethod,Clazz.declareAnonymous,Clazz.cloneFinals);
