(function(Clazz
,Clazz_newLongArray
,Clazz_doubleToByte
,Clazz_doubleToInt
,Clazz_doubleToLong
,Clazz_declarePackage
,Clazz_instanceOf
,Clazz_load
,Clazz_instantialize
,Clazz_decorateAsClass
,Clazz_floatToInt
,Clazz_makeConstructor
,Clazz_defineEnumConstant
,Clazz_exceptionOf
,Clazz_newIntArray
,Clazz_defineStatics
,Clazz_newFloatArray
,Clazz_declareType
,Clazz_prepareFields
,Clazz_superConstructor
,Clazz_newByteArray
,Clazz_declareInterface
,Clazz_p0p
,Clazz_pu$h
,Clazz_newShortArray
,Clazz_innerTypeInstance
,Clazz_isClassDefined
,Clazz_prepareCallback
,Clazz_newArray
,Clazz_castNullAs
,Clazz_floatToShort
,Clazz_superCall
,Clazz_decorateAsType
,Clazz_newBooleanArray
,Clazz_newCharArray
,Clazz_implementOf
,Clazz_newDoubleArray
,Clazz_overrideConstructor
,Clazz_clone
,Clazz_doubleToShort
,Clazz_getInheritedLevel
,Clazz_getParamsType
,Clazz_isAF
,Clazz_isAI
,Clazz_isAS
,Clazz_isASS
,Clazz_isAP
,Clazz_isAFloat
,Clazz_isAII
,Clazz_isAFF
,Clazz_isAFFF
,Clazz_tryToSearchAndExecute
,Clazz_getStackTrace
,Clazz_inheritArgs
,Clazz_alert
,Clazz_defineMethod
,Clazz_overrideMethod
,Clazz_declareAnonymous
//,Clazz_checkPrivateMethod
,Clazz_cloneFinals
){
var $t$;
//var c$;
Clazz_declarePackage ("JS");
Clazz_load (["JS.JmolCmdExtension"], "JS.CmdExt", ["java.lang.Boolean", "$.Float", "$.Long", "$.Short", "java.util.Hashtable", "JU.AU", "$.BS", "$.Base64", "$.Lst", "$.M3", "$.M4", "$.Measure", "$.P3", "$.PT", "$.Quat", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.c.AXES", "$.STER", "$.VDW", "J.i18n.GT", "JM.Atom", "$.AtomCollection", "$.BondSet", "$.LabelToken", "JS.SV", "$.ScriptCompiler", "$.ScriptError", "$.ScriptEval", "$.ScriptInterruption", "$.ScriptMathProcessor", "$.ScriptParam", "$.T", "JU.BSUtil", "$.BoxInfo", "$.C", "$.Edge", "$.Elements", "$.Escape", "$.Logger", "$.Parser", "$.Point3fi", "$.TempArray", "$.Txt", "JV.FileManager", "$.JC", "$.StateManager", "$.Viewer"], function () {
c$ = Clazz_decorateAsClass (function () {
this.vwr = null;
this.e = null;
this.sm = null;
this.chk = false;
this.fullCommand = null;
this.thisCommand = null;
this.st = null;
this.slen = 0;
this.lastData = null;
Clazz_instantialize (this, arguments);
}, JS, "CmdExt", null, JS.JmolCmdExtension);
Clazz_makeConstructor (c$, 
function () {
});
Clazz_overrideMethod (c$, "init", 
function (se) {
this.e = se;
this.vwr = this.e.vwr;
this.sm = this.e.sm;
return this;
}, "~O");
Clazz_overrideMethod (c$, "dispatch", 
function (iTok, b, st) {
this.chk = this.e.chk;
this.fullCommand = this.e.fullCommand;
this.thisCommand = this.e.thisCommand;
this.slen = this.e.slen;
this.st = st;
switch (iTok) {
case 4098:
this.assign ();
break;
case 135270423:
this.cache ();
break;
case 4102:
this.calculate ();
break;
case 4103:
this.capture ();
break;
case 4105:
this.centerAt ();
break;
case 135270405:
this.compare ();
break;
case 528395:
this.console ();
break;
case 4106:
this.connect (1);
break;
case 1095766024:
this.configuration ();
break;
case 135270408:
this.data ();
break;
case 1612189718:
this.connect (0);
break;
case 1052700:
this.mapProperty ();
break;
case 4126:
this.minimize ();
break;
case 1276121113:
this.modulation ();
break;
case 4131:
this.navigate ();
break;
case 4133:
case 135270418:
case 1052714:
this.plot (st);
break;
case 135270926:
this.show ();
break;
case 528443:
this.stereo ();
break;
case 135270422:
this.write (null);
break;
case 23:
return this.cgo ();
case 25:
return this.contact ();
case 17:
return this.dipole ();
case 22:
return this.draw ();
case 24:
case 29:
case 28:
return this.isosurface (iTok);
case 26:
return this.lcaoCartoon ();
case 6:
this.measure ();
return true;
case 27:
return this.mo (b);
case 21:
return this.polyhedra ();
case 20:
this.ellipsoid ();
break;
case 4:
return this.struts ();
}
return false;
}, "~N,~B,~A");
Clazz_defineMethod (c$, "atomExpressionAt", 
 function (i) {
return this.e.atomExpressionAt (i);
}, "~N");
Clazz_defineMethod (c$, "checkLength", 
 function (i) {
this.e.checkLength (i);
}, "~N");
Clazz_defineMethod (c$, "error", 
 function (err) {
this.e.error (err);
}, "~N");
Clazz_defineMethod (c$, "invArg", 
 function () {
this.e.invArg ();
});
Clazz_defineMethod (c$, "invPO", 
 function () {
this.error (23);
});
Clazz_defineMethod (c$, "getShapeProperty", 
 function (shapeType, propertyName) {
return this.e.getShapeProperty (shapeType, propertyName);
}, "~N,~S");
Clazz_defineMethod (c$, "paramAsStr", 
 function (i) {
return this.e.paramAsStr (i);
}, "~N");
Clazz_defineMethod (c$, "centerParameter", 
 function (i) {
return this.e.centerParameter (i);
}, "~N");
Clazz_defineMethod (c$, "floatParameter", 
 function (i) {
return this.e.floatParameter (i);
}, "~N");
Clazz_defineMethod (c$, "getPoint3f", 
 function (i, allowFractional) {
return this.e.getPoint3f (i, allowFractional);
}, "~N,~B");
Clazz_defineMethod (c$, "getPoint4f", 
 function (i) {
return this.e.getPoint4f (i);
}, "~N");
Clazz_defineMethod (c$, "intParameter", 
 function (index) {
return this.e.intParameter (index);
}, "~N");
Clazz_defineMethod (c$, "isFloatParameter", 
 function (index) {
return this.e.isFloatParameter (index);
}, "~N");
Clazz_defineMethod (c$, "setShapeProperty", 
 function (shapeType, propertyName, propertyValue) {
this.e.setShapeProperty (shapeType, propertyName, propertyValue);
}, "~N,~S,~O");
Clazz_defineMethod (c$, "showString", 
 function (s) {
this.e.showString (s);
}, "~S");
Clazz_defineMethod (c$, "stringParameter", 
 function (index) {
return this.e.stringParameter (index);
}, "~N");
Clazz_defineMethod (c$, "getToken", 
 function (i) {
return this.e.getToken (i);
}, "~N");
Clazz_defineMethod (c$, "tokAt", 
 function (i) {
return this.e.tokAt (i);
}, "~N");
Clazz_defineMethod (c$, "cache", 
 function () {
var tok = this.tokAt (1);
var fileName = null;
var n = 2;
switch (tok) {
case 1276118017:
case 1073742119:
fileName = this.e.optParameterAsString (n++);
case 1073741882:
this.checkLength (n);
if (!this.chk) {
if ("all".equals (fileName)) fileName = null;
var nBytes = this.vwr.cacheFileByName (fileName, tok == 1276118017);
this.showString (nBytes < 0 ? "cache cleared" : nBytes + " bytes " + (tok == 1276118017 ? " cached" : " removed"));
}break;
default:
this.invArg ();
}
});
Clazz_defineMethod (c$, "calculate", 
 function () {
var isSurface = false;
var asDSSP = false;
var bs1 = null;
var bs2 = null;
var n = -2147483648;
if ((this.e.iToken = this.e.slen) >= 2) {
this.e.clearDefinedVariableAtomSets ();
switch (this.getToken (1).tok) {
case 1073741824:
this.checkLength (2);
break;
case 1632634891:
this.checkLength (2);
if (this.chk) return;
n = this.vwr.calculateFormalCharges (null);
this.showString (J.i18n.GT.i (J.i18n.GT._ ("{0} charges modified"), n));
return;
case 1076887572:
this.checkLength (2);
if (!this.chk) this.vwr.ms.assignAromaticBonds ();
return;
case 1612189718:
if (this.e.slen != 2) {
asDSSP = (this.tokAt (++this.e.iToken) == 1641025539);
if (asDSSP) bs1 = this.vwr.bsA ();
 else bs1 = this.atomExpressionAt (this.e.iToken);
if (!asDSSP && !(asDSSP = (this.tokAt (++this.e.iToken) == 1641025539))) bs2 = this.atomExpressionAt (this.e.iToken);
}if (this.chk) return;
n = this.vwr.autoHbond (bs1, bs2, false);
if (n != -2147483648) this.e.report (J.i18n.GT.i (J.i18n.GT._ ("{0} hydrogen bonds"), Math.abs (n)));
return;
case 1613758476:
bs1 = (this.slen == 2 ? null : this.atomExpressionAt (2));
this.e.checkLast (this.e.iToken);
if (!this.chk) this.vwr.addHydrogens (bs1, false, false);
return;
case 1112541196:
this.e.iToken = 1;
bs1 = (this.slen == 2 ? null : this.atomExpressionAt (2));
this.e.checkLast (this.e.iToken);
if (!this.chk) this.vwr.calculatePartialCharges (bs1);
return;
case 1073742102:
if (!this.chk) this.showString (this.vwr.calculatePointGroup ());
return;
case 1112539150:
this.checkLength (2);
if (!this.chk) {
this.vwr.calculateStraightness ();
this.vwr.addStateScript ("set quaternionFrame '" + this.vwr.getQuaternionFrame () + "'; calculate straightness", false, true);
}return;
case 1641025539:
bs1 = (this.slen < 4 ? null : this.atomExpressionAt (2));
switch (this.tokAt (++this.e.iToken)) {
case 1052714:
break;
case 1073741916:
if (this.chk) return;
this.e.showString (this.vwr.getAnnotationParser ().calculateDSSRStructure (this.vwr, bs1));
return;
case 1073741915:
asDSSP = true;
break;
case 0:
asDSSP = this.vwr.getBoolean (603979826);
break;
default:
this.invArg ();
}
if (!this.chk) this.showString (this.vwr.calculateStructures (bs1, asDSSP, true));
return;
case 1708058:
bs1 = (this.e.iToken + 1 < this.slen ? this.atomExpressionAt (++this.e.iToken) : null);
bs2 = (this.e.iToken + 1 < this.slen ? this.atomExpressionAt (++this.e.iToken) : null);
this.checkLength (++this.e.iToken);
if (!this.chk) {
n = this.vwr.calculateStruts (bs1, bs2);
if (n > 0) {
this.setShapeProperty (1, "type", Integer.$valueOf (32768));
this.e.setShapePropertyBs (1, "color", Integer.$valueOf (0x0FFFFFF), null);
this.e.setShapeTranslucency (1, "", "translucent", 0.5, null);
this.setShapeProperty (1, "type", Integer.$valueOf (1023));
}this.showString (J.i18n.GT.i (J.i18n.GT._ ("{0} struts added"), n));
}return;
case 3145756:
isSurface = true;
case 1112539151:
var isFrom = false;
switch (this.tokAt (2)) {
case 135266325:
this.e.iToken++;
break;
case 0:
isFrom = !isSurface;
break;
case 1073741952:
isFrom = true;
this.e.iToken++;
break;
default:
isFrom = true;
}
bs1 = (this.e.iToken + 1 < this.slen ? this.atomExpressionAt (++this.e.iToken) : this.vwr.bsA ());
this.checkLength (++this.e.iToken);
if (!this.chk) this.vwr.calculateSurface (bs1, (isFrom ? 3.4028235E38 : -1));
return;
}
}this.e.errorStr2 (53, "CALCULATE", "aromatic? hbonds? hydrogen? formalCharge? partialCharge? pointgroup? straightness? structure? struts? surfaceDistance FROM? surfaceDistance WITHIN?");
});
Clazz_defineMethod (c$, "capture", 
 function () {
if (!this.chk && !this.vwr.allowCapture ()) {
this.showString ("Cannot capture on this platform");
return;
}var fps = this.vwr.getInt (553648132);
var endTime = 10;
var mode = 0;
var fileName = "";
var params = this.vwr.captureParams;
var looping = !this.vwr.am.animationReplayMode.name ().equals ("ONCE");
var tok = this.tokAt (1);
var sfps = "";
switch (tok) {
case 0:
mode = 1150985;
break;
case 4:
fileName = this.e.optParameterAsString (1);
if (fileName.length == 0) {
mode = 1150985;
break;
}if (!fileName.endsWith (".gif")) fileName += ".gif";
var s = null;
var axis = "y";
var i = 2;
switch (this.tokAt (i)) {
case 1073742129:
looping = true;
i = 3;
axis = (this.tokAt (3) == 2 ? "y" : this.e.optParameterAsString (i++).toLowerCase ());
var n = (this.tokAt (i) == 0 ? 5 : this.intParameter (i++));
s = "; rotate Y 10 10;delay 2.0; rotate Y -10 -10; delay 2.0;rotate Y -10 -10; delay 2.0;rotate Y 10 10;delay 2.0";
s = JU.PT.rep (s, "10", "" + n);
break;
case 1611141175:
looping = true;
i = 3;
axis = this.e.optParameterAsString (i).toLowerCase ();
if (axis.length > 0) i++;
s = "; rotate Y 360 30;delay 15.0;";
if (this.tokAt (i) == 2) sfps = " " + (fps = this.intParameter (i++));
break;
case 3:
endTime = this.floatParameter (2);
break;
case 2:
fps = this.intParameter (2);
break;
}
if (s != null) {
if (!this.chk) this.vwr.setNavigationMode (false);
if (axis === "" || "xyz".indexOf (axis) < 0) axis = "y";
s = JU.PT.rep (s, "Y", axis);
s = "capture " + JU.PT.esc (fileName) + sfps + s + ";capture;";
this.e.cmdScript (0, null, s);
return;
}if (params != null) params =  new java.util.Hashtable ();
mode = 1073742032;
params =  new java.util.Hashtable ();
if (!looping) this.showString (J.i18n.GT.o (J.i18n.GT._ ("Note: Enable looping using {0}"), ["ANIMATION MODE LOOP"]));
this.showString (J.i18n.GT.o (J.i18n.GT._ ("Animation delay based on: {0}"), ["ANIMATION FPS " + fps]));
params.put ("captureFps", Integer.$valueOf (fps));
break;
case 1073741874:
case 1048589:
case 1048588:
this.checkLength (2);
mode = tok;
break;
default:
this.invArg ();
}
if (this.chk || params == null) return;
params.put ("type", "GIF");
params.put ("fileName", fileName);
params.put ("quality", Integer.$valueOf (-1));
params.put ("endTime", Long.$valueOf (System.currentTimeMillis () + Clazz_floatToLong (endTime * 1000)));
params.put ("captureMode", JS.T.nameOf (mode).toLowerCase ());
params.put ("captureLooping", looping ? Boolean.TRUE : Boolean.FALSE);
var msg = this.vwr.processWriteOrCapture (params);
JU.Logger.info (msg);
});
Clazz_defineMethod (c$, "centerAt", 
 function () {
var tok = this.getToken (1).tok;
switch (tok) {
case 1073741826:
case 96:
case 1679429641:
break;
default:
this.invArg ();
}
var pt = JU.P3.new3 (0, 0, 0);
if (this.slen == 5) {
pt.x = this.floatParameter (2);
pt.y = this.floatParameter (3);
pt.z = this.floatParameter (4);
} else if (this.e.isCenterParameter (2)) {
pt = this.centerParameter (2);
this.e.checkLast (this.e.iToken);
} else {
this.checkLength (2);
}if (!this.chk && !this.vwr.isJmolDataFrame ()) this.vwr.tm.setCenterAt (tok, pt);
});
Clazz_defineMethod (c$, "cgo", 
 function () {
var eval = this.e;
this.sm.loadShape (23);
if (this.tokAt (1) == 1073742001 && this.listIsosurface (23)) return false;
var iptDisplayProperty = 0;
var thisId = this.initIsosurface (23);
var idSeen = (thisId != null);
var isWild = (idSeen && this.getShapeProperty (23, "ID") == null);
var isInitialized = false;
var data = null;
var translucentLevel = 3.4028235E38;
var colorArgb = [-2147483648];
var intScale = 0;
for (var i = eval.iToken; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
switch (this.getToken (i).tok) {
case 7:
case 269484096:
case 1073742195:
if (data != null || isWild) this.invArg ();
data = eval.listParameter (i, 2, 2147483647);
i = eval.iToken;
continue;
case 1073742138:
if (++i >= this.slen) this.error (34);
switch (this.getToken (i).tok) {
case 2:
intScale = this.intParameter (i);
continue;
case 3:
intScale = Math.round (this.floatParameter (i) * 100);
continue;
}
this.error (34);
break;
case 1766856708:
case 603979967:
case 1073742074:
translucentLevel = this.getColorTrans (eval, i, false, colorArgb);
i = eval.iToken;
idSeen = true;
continue;
case 1074790550:
thisId = this.setShapeId (23, ++i, idSeen);
isWild = (this.getShapeProperty (23, "ID") == null);
i = eval.iToken;
break;
default:
if (!eval.setMeshDisplayProperty (23, 0, eval.theTok)) {
if (eval.theTok == 269484209 || JS.T.tokAttr (eval.theTok, 1073741824)) {
thisId = this.setShapeId (23, i, idSeen);
i = eval.iToken;
break;
}this.invArg ();
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = eval.iToken;
continue;
}
idSeen = (eval.theTok != 12291);
if (data != null && !isInitialized) {
propertyName = "points";
propertyValue = Integer.$valueOf (intScale);
isInitialized = true;
intScale = 0;
}if (propertyName != null) this.setShapeProperty (23, propertyName, propertyValue);
}
this.finalizeObject (23, colorArgb[0], translucentLevel, intScale, data != null, data, iptDisplayProperty, null);
return true;
});
Clazz_defineMethod (c$, "compare", 
 function () {
var isQuaternion = false;
var doRotate = false;
var doTranslate = false;
var doAnimate = false;
var isFlexFit = false;
var data1 = null;
var data2 = null;
var bsAtoms1 = null;
var bsAtoms2 = null;
var vAtomSets = null;
var vQuatSets = null;
this.e.iToken = 0;
var nSeconds = (this.isFloatParameter (1) ? this.floatParameter (++this.e.iToken) : NaN);
var bsFrom = this.atomExpressionAt (++this.e.iToken);
var coordTo = null;
var bsTo = null;
if (this.e.isArrayParameter (++this.e.iToken)) {
coordTo = this.e.getPointArray (this.e.iToken, -1);
} else if (this.tokAt (this.e.iToken) != 1141899265) {
bsTo = this.atomExpressionAt (this.e.iToken);
}var bsSubset = null;
var isSmiles = false;
var strSmiles = null;
var bs = JU.BSUtil.copy (bsFrom);
if (bsTo != null) bs.or (bsTo);
var isToSubsetOfFrom = (coordTo == null && bsTo != null && bs.equals (bsFrom));
var isFrames = isToSubsetOfFrom;
for (var i = this.e.iToken + 1; i < this.slen; ++i) {
switch (this.getToken (i).tok) {
case 4115:
isFrames = true;
break;
case 135267336:
isSmiles = true;
if (this.tokAt (i + 1) != 4) {
strSmiles = "*";
break;
}case 135267335:
strSmiles = this.stringParameter (++i);
break;
case 1678770178:
isFlexFit = true;
doRotate = true;
strSmiles = this.paramAsStr (++i);
if (strSmiles.equalsIgnoreCase ("SMILES")) {
isSmiles = true;
strSmiles = "*";
}break;
case 3:
case 2:
nSeconds = Math.abs (this.floatParameter (i));
if (nSeconds > 0) doAnimate = true;
break;
case 269484080:
break;
case 3158024:
bsSubset = this.atomExpressionAt (++i);
i = this.e.iToken;
break;
case 10:
case 1048577:
if (vQuatSets != null) this.invArg ();
bsAtoms1 = this.atomExpressionAt (this.e.iToken);
var tok = (isToSubsetOfFrom ? 0 : this.tokAt (this.e.iToken + 1));
bsAtoms2 = (coordTo == null && this.e.isArrayParameter (this.e.iToken + 1) ? null : (tok == 10 || tok == 1048577 ? this.atomExpressionAt (++this.e.iToken) : JU.BSUtil.copy (bsAtoms1)));
if (bsSubset != null) {
bsAtoms1.and (bsSubset);
if (bsAtoms2 != null) bsAtoms2.and (bsSubset);
}if (bsAtoms2 == null) coordTo = this.e.getPointArray (++this.e.iToken, -1);
 else bsAtoms2.and (bsTo);
if (vAtomSets == null) vAtomSets =  new JU.Lst ();
vAtomSets.addLast ([bsAtoms1, bsAtoms2]);
i = this.e.iToken;
break;
case 7:
if (vAtomSets != null) this.invArg ();
isQuaternion = true;
data1 = this.e.getQuaternionArray ((this.e.theToken).getList (), 1073742001);
this.getToken (++i);
data2 = this.e.getQuaternionArray ((this.e.theToken).getList (), 1073742001);
if (vQuatSets == null) vQuatSets =  new JU.Lst ();
vQuatSets.addLast ([data1, data2]);
break;
case 1073742077:
isQuaternion = true;
break;
case 135266320:
case 1141899265:
isQuaternion = false;
break;
case 528432:
doRotate = true;
break;
case 4160:
doTranslate = true;
break;
default:
this.invArg ();
}
}
if (this.chk) return;
if (isFrames) nSeconds = 0;
if (Float.isNaN (nSeconds) || nSeconds < 0) nSeconds = 1;
 else if (!doRotate && !doTranslate) doRotate = doTranslate = true;
doAnimate = (nSeconds != 0);
var isAtoms = (!isQuaternion && strSmiles == null || coordTo != null);
if (vAtomSets == null && vQuatSets == null) {
if (bsSubset == null) {
bsAtoms1 = (isAtoms ? this.vwr.getAtomBitSet ("spine") :  new JU.BS ());
if (bsAtoms1.nextSetBit (0) < 0) {
bsAtoms1 = bsFrom;
bsAtoms2 = bsTo;
} else {
bsAtoms2 = JU.BSUtil.copy (bsAtoms1);
bsAtoms1.and (bsFrom);
bsAtoms2.and (bsTo);
}} else {
bsAtoms1 = JU.BSUtil.copy (bsFrom);
bsAtoms2 = JU.BSUtil.copy (bsTo);
bsAtoms1.and (bsSubset);
bsAtoms2.and (bsSubset);
bsAtoms1.and (bsFrom);
bsAtoms2.and (bsTo);
}vAtomSets =  new JU.Lst ();
vAtomSets.addLast ([bsAtoms1, bsAtoms2]);
}var bsFrames;
if (isFrames) {
var bsModels = this.vwr.ms.getModelBS (bsFrom, false);
bsFrames =  new Array (bsModels.cardinality ());
for (var i = 0, iModel = bsModels.nextSetBit (0); iModel >= 0; iModel = bsModels.nextSetBit (iModel + 1), i++) bsFrames[i] = this.vwr.getModelUndeletedAtomsBitSet (iModel);

} else {
bsFrames = [bsFrom];
}for (var iFrame = 0; iFrame < bsFrames.length; iFrame++) {
bsFrom = bsFrames[iFrame];
var retStddev =  Clazz_newFloatArray (2, 0);
var q = null;
var vQ =  new JU.Lst ();
var centerAndPoints = null;
var vAtomSets2 = (isFrames ?  new JU.Lst () : vAtomSets);
for (var i = 0; i < vAtomSets.size (); ++i) {
var bss = vAtomSets.get (i);
if (isFrames) vAtomSets2.addLast (bss = [JU.BSUtil.copy (bss[0]), bss[1]]);
bss[0].and (bsFrom);
}
var center = null;
var translation = null;
if (isAtoms) {
if (coordTo != null) {
vAtomSets2.clear ();
vAtomSets2.addLast ([bsAtoms1, coordTo]);
}try {
centerAndPoints = this.vwr.getCenterAndPoints (vAtomSets2, true);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.invArg ();
} else {
throw ex;
}
}
var n = centerAndPoints[0].length - 1;
for (var i = 1; i <= n; i++) {
var aij = centerAndPoints[0][i];
var bij = centerAndPoints[1][i];
if (!(Clazz_instanceOf (aij, JM.Atom)) || !(Clazz_instanceOf (bij, JM.Atom))) break;
JU.Logger.info (" atom 1 " + (aij).getInfo () + "\tatom 2 " + (bij).getInfo ());
}
q = JU.Measure.calculateQuaternionRotation (centerAndPoints, retStddev);
var r0 = (Float.isNaN (retStddev[1]) ? NaN : Math.round (retStddev[0] * 100) / 100);
var r1 = (Float.isNaN (retStddev[1]) ? NaN : Math.round (retStddev[1] * 100) / 100);
this.showString ("RMSD " + r0 + " --> " + r1 + " Angstroms");
} else if (isQuaternion) {
if (vQuatSets == null) {
for (var i = 0; i < vAtomSets2.size (); i++) {
var bss = vAtomSets2.get (i);
data1 = this.vwr.getAtomGroupQuaternions (bss[0], 2147483647);
data2 = this.vwr.getAtomGroupQuaternions (bss[1], 2147483647);
for (var j = 0; j < data1.length && j < data2.length; j++) {
vQ.addLast (data2[j].div (data1[j]));
}
}
} else {
for (var j = 0; j < data1.length && j < data2.length; j++) {
vQ.addLast (data2[j].div (data1[j]));
}
}retStddev[0] = 0;
data1 = vQ.toArray ( new Array (vQ.size ()));
q = JU.Quat.sphereMean (data1, retStddev, 0.0001);
this.showString ("RMSD = " + retStddev[0] + " degrees");
} else {
var m4 =  new JU.M4 ();
center =  new JU.P3 ();
if (("*".equals (strSmiles) || "".equals (strSmiles)) && bsFrom != null) try {
strSmiles = this.vwr.getSmiles (bsFrom);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.e.evalError (ex.getMessage (), null);
} else {
throw ex;
}
}
if (isFlexFit) {
var list;
if (bsFrom == null || bsTo == null || (list = this.e.getSmilesExt ().getFlexFitList (bsFrom, bsTo, strSmiles, !isSmiles)) == null) return;
this.vwr.setDihedrals (list, null, 1);
}var stddev = this.e.getSmilesExt ().getSmilesCorrelation (bsFrom, bsTo, strSmiles, null, null, m4, null, !isSmiles, false, null, center, false, false);
if (Float.isNaN (stddev)) {
this.showString ("structures do not match");
return;
}if (doTranslate) {
translation =  new JU.V3 ();
m4.getTranslation (translation);
}if (doRotate) {
var m3 =  new JU.M3 ();
m4.getRotationScale (m3);
q = JU.Quat.newM (m3);
}this.showString ("RMSD = " + stddev + " Angstroms");
}if (centerAndPoints != null) center = centerAndPoints[0][0];
if (center == null) {
centerAndPoints = this.vwr.getCenterAndPoints (vAtomSets2, true);
center = centerAndPoints[0][0];
}var pt1 =  new JU.P3 ();
var endDegrees = NaN;
if (doTranslate) {
if (translation == null) translation = JU.V3.newVsub (centerAndPoints[1][0], center);
endDegrees = 1e10;
}if (doRotate) {
if (q == null) this.e.evalError ("option not implemented", null);
pt1.add2 (center, q.getNormal ());
endDegrees = q.getTheta ();
if (endDegrees == 0 && doTranslate) {
if (translation.length () > 0.01) endDegrees = 1e10;
 else doRotate = doTranslate = doAnimate = false;
}}if (Float.isNaN (endDegrees) || Float.isNaN (pt1.x)) continue;
var ptsB = null;
if (doRotate && doTranslate && nSeconds != 0) {
var ptsA = this.vwr.ms.getAtomPointVector (bsFrom);
var m4 = JS.ScriptMathProcessor.getMatrix4f (q.getMatrix (), translation);
ptsB = JU.Measure.transformPoints (ptsA, m4, center);
}if (!this.e.useThreads ()) doAnimate = false;
if (this.vwr.rotateAboutPointsInternal (this.e, center, pt1, endDegrees / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB, null) && doAnimate && this.e.isJS) throw  new JS.ScriptInterruption (this.e, "compare", 1);
}
});
Clazz_defineMethod (c$, "configuration", 
 function () {
var bsAtoms;
var bsSelected = this.vwr.bsA ();
if (this.slen == 1) {
bsAtoms = this.vwr.ms.setConformation (bsSelected);
this.vwr.ms.addStateScript ("select", null, bsSelected, null, "configuration", true, false);
} else {
var n = this.intParameter (this.e.checkLast (1));
if (this.chk) return;
bsAtoms = this.vwr.getConformation (this.vwr.am.cmi, n - 1, true);
this.vwr.addStateScript ("configuration " + n + ";", true, false);
}if (this.chk) return;
this.setShapeProperty (1, "type", Integer.$valueOf (30720));
this.e.setShapeSizeBs (1, 0, bsAtoms);
this.vwr.autoHbond (bsAtoms, bsAtoms, true);
this.vwr.select (bsAtoms, false, 0, this.e.tQuiet);
});
Clazz_defineMethod (c$, "measure", 
 function () {
var eval = this.e;
var id = null;
var pt = 1;
var colix = 0;
var offset = null;
if (this.slen == 2) switch (this.tokAt (1)) {
case 1048588:
this.setShapeProperty (6, "hideAll", Boolean.TRUE);
return;
case 12291:
if (!this.chk) this.vwr.clearAllMeasurements ();
return;
}
this.vwr.shm.loadShape (6);
switch (this.tokAt (1)) {
case 135267335:
var smarts = this.stringParameter (this.slen == 3 ? 2 : 4);
if (this.chk) return;
var atoms = this.vwr.ms.at;
var ac = this.vwr.getAtomCount ();
var maps = null;
try {
maps = this.vwr.getSmilesMatcher ().getCorrelationMaps (smarts, atoms, ac, this.vwr.bsA (), true, false);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
eval.evalError (ex.getMessage (), null);
} else {
throw ex;
}
}
if (maps == null) return;
this.setShapeProperty (6, "maps", maps);
return;
}
switch (this.slen) {
case 2:
switch (this.getToken (pt).tok) {
case 0:
case 1048589:
this.vwr.shm.loadShape (6);
this.setShapeProperty (6, "hideAll", Boolean.FALSE);
return;
case 1073742001:
if (!this.chk) eval.showStringPrint (this.vwr.getMeasurementInfoAsString (), false);
return;
case 4:
this.setShapeProperty (6, "setFormats", this.stringParameter (1));
return;
}
eval.errorStr (24, "ON, OFF, DELETE");
break;
case 3:
switch (this.getToken (1).tok) {
case 12291:
if (this.getToken (2).tok == 1048579) {
if (!this.chk) this.vwr.clearAllMeasurements ();
} else {
var i = this.intParameter (2) - 1;
if (!this.chk) this.vwr.deleteMeasurement (i);
}return;
}
}
var nAtoms = 0;
var expressionCount = 0;
var modelIndex = -1;
var atomIndex = -1;
var ptFloat = -1;
var countPlusIndexes =  Clazz_newIntArray (5, 0);
var rangeMinMax = [3.4028235E38, 3.4028235E38];
var isAll = false;
var isAllConnected = false;
var isNotConnected = false;
var isRange = true;
var rd = null;
var intramolecular = null;
var tokAction = 269484114;
var strFormat = null;
var font = null;
var points =  new JU.Lst ();
var bs =  new JU.BS ();
var value = null;
var tickInfo = null;
var nBitSets = 0;
var mad = 0;
for (var i = 1; i < this.slen; ++i) {
switch (this.getToken (i).tok) {
case 1074790550:
if (i != 1) this.invArg ();
id = eval.optParameterAsString (++i);
continue;
case 1073741824:
eval.errorStr (24, "ALL, ALLCONNECTED, DELETE");
break;
default:
this.error (15);
break;
case 269484144:
if (this.tokAt (i + 1) != 135266310) this.invArg ();
i++;
isNotConnected = true;
break;
case 135266310:
case 1073741834:
case 1048579:
isAllConnected = (eval.theTok == 1073741834);
atomIndex = -1;
isAll = true;
if (isAllConnected && isNotConnected) this.invArg ();
break;
case 1766856708:
colix = JU.C.getColix (eval.getArgbParam (++i));
i = eval.iToken;
break;
case 1073742066:
if (eval.isPoint3f (++i)) {
var p = this.getPoint3f (i, false);
offset = [1, p.x, p.y, p.z, 0, 0, 0];
} else {
offset = eval.floatParameterSet (i, 7, 7);
}i = eval.iToken;
break;
case 1666189314:
case 1073741917:
mad = Clazz_floatToInt ((eval.theTok == 1666189314 ? 2000 : 1000) * this.floatParameter (++i));
if (id != null && mad <= 0) mad = -1;
break;
case 3:
if (rd != null) this.invArg ();
isAll = true;
isRange = true;
ptFloat = (ptFloat + 1) % 2;
rangeMinMax[ptFloat] = this.floatParameter (i);
break;
case 12291:
if (tokAction != 269484114) this.invArg ();
tokAction = 12291;
break;
case 4114:
var fontsize = this.floatParameter (++i);
var fontface = this.paramAsStr (++i);
var fontstyle = this.paramAsStr (++i);
if (!this.chk) font = this.vwr.getFont3D (fontface, fontstyle, fontsize);
break;
case 2:
var iParam = this.intParameter (i);
if (isAll) {
isRange = true;
ptFloat = (ptFloat + 1) % 2;
rangeMinMax[ptFloat] = iParam;
} else {
atomIndex = this.vwr.getAtomIndexFromAtomNumber (iParam);
if (!this.chk && atomIndex < 0) return;
if (value != null) this.invArg ();
if ((countPlusIndexes[0] = ++nAtoms) > 4) eval.bad ();
countPlusIndexes[nAtoms] = atomIndex;
}break;
case 1095761935:
modelIndex = this.intParameter (++i);
break;
case 1048588:
if (tokAction != 269484114) this.invArg ();
tokAction = 1048588;
break;
case 1048589:
if (tokAction != 269484114) this.invArg ();
tokAction = 1048589;
break;
case 1073742114:
isAll = true;
isRange = true;
atomIndex = -1;
break;
case 1073741989:
case 1073741990:
intramolecular = Boolean.$valueOf (eval.theTok == 1073741989);
isAll = true;
isNotConnected = (eval.theTok == 1073741990);
break;
case 1649412120:
if (ptFloat >= 0) this.invArg ();
rd = eval.encodeRadiusParameter (i, false, true);
if (rd == null) return;
rd.values = rangeMinMax;
i = eval.iToken;
isNotConnected = true;
isAll = true;
intramolecular = Boolean.$valueOf (false);
if (nBitSets == 1) {
nBitSets++;
nAtoms++;
var bs2 = JU.BSUtil.copy (bs);
JU.BSUtil.invertInPlace (bs2, this.vwr.getAtomCount ());
bs2.and (this.vwr.ms.getAtomsWithinRadius (5, bs, false, null));
points.addLast (bs2);
}break;
case 10:
case 1048577:
case 1048586:
case 8:
case 1048582:
if (eval.theTok == 10 || eval.theTok == 1048577) nBitSets++;
if (atomIndex >= 0) this.invArg ();
eval.expressionResult = Boolean.FALSE;
value = this.centerParameter (i);
if (Clazz_instanceOf (eval.expressionResult, JU.BS)) {
value = bs = eval.expressionResult;
if (!this.chk && bs.length () == 0) return;
}if (Clazz_instanceOf (value, JU.P3)) {
var v =  new JU.Point3fi ();
v.setT (value);
v.mi = modelIndex;
value = v;
}if ((nAtoms = ++expressionCount) > 4) eval.bad ();
i = eval.iToken;
points.addLast (value);
break;
case 4:
strFormat = this.stringParameter (i);
break;
case 1073742164:
tickInfo = eval.tickParamAsStr (i, false, true, true);
i = eval.iToken;
tokAction = 1060866;
break;
}
}
if (rd != null && (ptFloat >= 0 || nAtoms != 2) || nAtoms < 2 && id == null && (tickInfo == null || nAtoms == 1)) eval.bad ();
if (strFormat != null && strFormat.indexOf (nAtoms + ":") != 0) strFormat = nAtoms + ":" + strFormat;
if (isRange) {
if (rangeMinMax[1] < rangeMinMax[0]) {
rangeMinMax[1] = rangeMinMax[0];
rangeMinMax[0] = (rangeMinMax[1] == 3.4028235E38 ? 3.4028235E38 : -200);
}}if (this.chk) return;
if (value != null || tickInfo != null) {
if (rd == null) rd =  new J.atomdata.RadiusData (rangeMinMax, 0, null, null);
if (value == null) tickInfo.id = "default";
if (value != null && strFormat != null && tokAction == 269484114) tokAction = 1060866;
var text = null;
if (font != null) text = (J.api.Interface.getInterface ("JM.Text")).newLabel (this.vwr.gdata, font, "", colix, 0, 0, 0, null);
if (text != null) text.pymolOffset = offset;
this.setShapeProperty (6, "measure", this.vwr.newMeasurementData (id, points).set (tokAction, null, rd, strFormat, null, tickInfo, isAllConnected, isNotConnected, intramolecular, isAll, mad, colix, text));
return;
}var propertyValue = (id == null ? countPlusIndexes : id);
switch (tokAction) {
case 12291:
this.setShapeProperty (6, "delete", propertyValue);
break;
case 1048589:
this.setShapeProperty (6, "show", propertyValue);
break;
case 1048588:
this.setShapeProperty (6, "hide", propertyValue);
break;
default:
this.setShapeProperty (6, (strFormat == null ? "toggle" : "toggleOn"), propertyValue);
if (strFormat != null) this.setShapeProperty (6, "setFormats", strFormat);
}
});
Clazz_defineMethod (c$, "connect", 
 function (index) {
var eval = this.e;
var distances =  Clazz_newFloatArray (2, 0);
var atomSets =  new Array (2);
atomSets[0] = atomSets[1] = this.vwr.bsA ();
var radius = NaN;
var colorArgb = [-2147483648];
var distanceCount = 0;
var bondOrder = 131071;
var bo;
var operation = 1073742026;
var isDelete = false;
var haveType = false;
var haveOperation = false;
var translucentLevel = 3.4028235E38;
var isColorOrRadius = false;
var nAtomSets = 0;
var nDistances = 0;
var bsBonds =  new JU.BS ();
var isBonds = false;
var expression2 = 0;
var ptColor = 0;
var energy = 0;
var addGroup = false;
if (this.slen == 1) {
if (!this.chk) this.vwr.rebondState (eval.$isStateScript);
return;
}for (var i = index; i < this.slen; ++i) {
switch (this.getToken (i).tok) {
case 1048589:
case 1048588:
this.checkLength (2);
if (!this.chk) this.vwr.rebondState (eval.$isStateScript);
return;
case 2:
case 3:
if (nAtomSets > 0) {
if (haveType || isColorOrRadius) eval.error (23);
bo = JU.Edge.getBondOrderFromFloat (this.floatParameter (i));
if (bo == 131071) this.invArg ();
bondOrder = bo;
haveType = true;
break;
}if (++nDistances > 2) eval.bad ();
var dist = this.floatParameter (i);
if (this.tokAt (i + 1) == 269484210) {
dist = -dist / 100;
i++;
}distances[distanceCount++] = dist;
break;
case 10:
case 1048577:
if (nAtomSets > 2 || isBonds && nAtomSets > 0) eval.bad ();
if (haveType || isColorOrRadius) this.invArg ();
atomSets[nAtomSets++] = this.atomExpressionAt (i);
isBonds = eval.isBondSet;
if (nAtomSets == 2) {
var pt = eval.iToken;
for (var j = i; j < pt; j++) if (this.tokAt (j) == 1073741824 && this.paramAsStr (j).equals ("_1")) {
expression2 = i;
break;
}
eval.iToken = pt;
}i = eval.iToken;
break;
case 1087373318:
addGroup = true;
break;
case 1766856708:
case 603979967:
case 1073742074:
isColorOrRadius = true;
translucentLevel = this.getColorTrans (eval, i, false, colorArgb);
i = eval.iToken;
break;
case 1074790662:
var isAuto = (this.tokAt (2) == 1073741852);
this.checkLength (isAuto ? 3 : 2);
if (this.chk) return;
this.vwr.clearModelDependentObjects ();
this.vwr.ms.deleteAllBonds ();
var bsExclude =  new JU.BS ();
this.vwr.ms.setPdbConectBonding (0, 0, bsExclude);
if (isAuto) {
var isLegacy = eval.$isStateScript && this.vwr.g.legacyAutoBonding;
this.vwr.ms.autoBondBs4 (null, null, bsExclude, null, this.vwr.getMadBond (), isLegacy);
this.vwr.addStateScript ((isLegacy ? "set legacyAutoBonding TRUE;connect PDB AUTO;set legacyAutoBonding FALSE;" : "connect PDB auto;"), false, true);
return;
}this.vwr.addStateScript ("connect PDB;", false, true);
return;
case 1073741830:
case 1073741852:
case 1073741904:
case 1073742025:
case 1073742026:
haveOperation = true;
if (++i != this.slen) this.invArg ();
operation = eval.theTok;
if (operation == 1073741852 && !(bondOrder == 131071 || bondOrder == 2048 || bondOrder == 515)) this.invArg ();
break;
case 1708058:
if (!isColorOrRadius) {
colorArgb[0] = 0xFFFFFF;
translucentLevel = 0.5;
radius = this.vwr.getFloat (570425406);
isColorOrRadius = true;
}if (!haveOperation) operation = 1073742026;
haveOperation = true;
case 1073741824:
if (eval.isColorParam (i)) {
ptColor = -i;
break;
}case 1076887572:
case 1612189718:
var cmd = this.paramAsStr (i);
if ((bo = JS.ScriptParam.getBondOrderFromString (cmd)) == 131071) {
this.invArg ();
}if (haveType) eval.error (18);
haveType = true;
switch (bo) {
case 33:
switch (this.tokAt (i + 1)) {
case 3:
bo = JS.ScriptParam.getPartialBondOrderFromFloatEncodedInt (this.st[++i].intValue);
break;
case 2:
bo = this.intParameter (++i);
break;
}
break;
case 2048:
if (this.tokAt (i + 1) == 2) {
bo = (this.intParameter (++i) << 11);
energy = this.floatParameter (++i);
}break;
}
bondOrder = bo;
break;
case 1666189314:
radius = this.floatParameter (++i);
isColorOrRadius = true;
break;
case 1048587:
case 12291:
if (++i != this.slen) this.invArg ();
operation = 12291;
isDelete = true;
isColorOrRadius = false;
break;
default:
ptColor = i;
break;
}
if (i > 0) {
if (ptColor == -i || ptColor == i && eval.isColorParam (i)) {
isColorOrRadius = true;
colorArgb[0] = eval.getArgbParam (i);
i = eval.iToken;
} else if (ptColor == i) {
this.invArg ();
}}}
if (this.chk) return;
if (distanceCount < 2) {
if (distanceCount == 0) distances[0] = 1.0E8;
distances[1] = distances[0];
distances[0] = 0.1;
}if (isColorOrRadius) {
if (!haveType) bondOrder = 65535;
if (!haveOperation) operation = 1073742025;
}var nNew = 0;
var nModified = 0;
var result;
if (expression2 > 0) {
var bs =  new JU.BS ();
eval.definedAtomSets.put ("_1", bs);
var bs0 = atomSets[0];
for (var atom1 = bs0.nextSetBit (0); atom1 >= 0; atom1 = bs0.nextSetBit (atom1 + 1)) {
bs.set (atom1);
result = this.vwr.makeConnections (distances[0], distances[1], bondOrder, operation, bs, this.atomExpressionAt (expression2), bsBonds, isBonds, false, 0);
nNew += Math.abs (result[0]);
nModified += result[1];
bs.clear (atom1);
}
} else {
result = this.vwr.makeConnections (distances[0], distances[1], bondOrder, operation, atomSets[0], atomSets[1], bsBonds, isBonds, addGroup, energy);
nNew += Math.abs (result[0]);
nModified += result[1];
}var report = eval.doReport ();
if (isDelete) {
if (report) eval.report (J.i18n.GT.i (J.i18n.GT._ ("{0} connections deleted"), nModified));
return;
}if (isColorOrRadius) {
this.vwr.selectBonds (bsBonds);
if (!Float.isNaN (radius)) eval.setShapeSizeBs (1, Math.round (radius * 2000), null);
this.finalizeObject (1, colorArgb[0], translucentLevel, 0, false, null, 0, bsBonds);
this.vwr.selectBonds (null);
}if (report) eval.report (J.i18n.GT.o (J.i18n.GT._ ("{0} new bonds; {1} modified"), [Integer.$valueOf (nNew), Integer.$valueOf (nModified)]));
}, "~N");
Clazz_defineMethod (c$, "console", 
 function () {
switch (this.getToken (1).tok) {
case 1048588:
if (!this.chk) this.vwr.showConsole (false);
break;
case 1048589:
if (!this.chk) this.vwr.showConsole (true);
break;
case 1073741882:
if (!this.chk) this.vwr.sm.clearConsole ();
break;
case 135270422:
this.showString (this.stringParameter (2));
break;
default:
this.invArg ();
}
});
Clazz_defineMethod (c$, "contact", 
 function () {
var eval = this.e;
this.sm.loadShape (25);
if (this.tokAt (1) == 1073742001 && this.listIsosurface (25)) return false;
var iptDisplayProperty = 0;
eval.iToken = 1;
var thisId = this.initIsosurface (25);
var idSeen = (thisId != null);
var isWild = (idSeen && this.getShapeProperty (25, "ID") == null);
var bsA = null;
var bsB = null;
var bs = null;
var rd = null;
var params = null;
var colorDensity = false;
var sbCommand =  new JU.SB ();
var minSet = 2147483647;
var displayType = 135266319;
var contactType = 0;
var distance = NaN;
var saProbeRadius = NaN;
var localOnly = true;
var intramolecular = null;
var userSlabObject = null;
var colorpt = 0;
var colorByType = false;
var tok;
var okNoAtoms = (eval.iToken > 1);
for (var i = eval.iToken; i < this.slen; ++i) {
switch (tok = this.getToken (i).tok) {
default:
okNoAtoms = true;
if (!eval.setMeshDisplayProperty (25, 0, eval.theTok)) {
if (eval.theTok != 269484209 && !JS.T.tokAttr (eval.theTok, 1073741824)) this.invArg ();
thisId = this.setShapeId (25, i, idSeen);
i = eval.iToken;
break;
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = eval.iToken;
continue;
case 1074790550:
okNoAtoms = true;
this.setShapeId (25, ++i, idSeen);
isWild = (this.getShapeProperty (25, "ID") == null);
i = eval.iToken;
break;
case 1766856708:
switch (this.tokAt (i + 1)) {
case 1073741914:
tok = 0;
colorDensity = true;
sbCommand.append (" color density");
i++;
break;
case 1141899272:
tok = 0;
colorByType = true;
sbCommand.append (" color type");
i++;
break;
}
if (tok == 0) break;
case 603979967:
case 1073742074:
okNoAtoms = true;
if (colorpt == 0) colorpt = i;
eval.setMeshDisplayProperty (25, i, eval.theTok);
i = eval.iToken;
break;
case 554176565:
okNoAtoms = true;
userSlabObject = this.getCapSlabObject (i, false);
this.setShapeProperty (25, "slab", userSlabObject);
i = eval.iToken;
break;
case 1073741914:
colorDensity = true;
sbCommand.append (" density");
if (this.isFloatParameter (i + 1)) {
if (params == null) params =  Clazz_newFloatArray (1, 0);
params[0] = -Math.abs (this.floatParameter (++i));
sbCommand.append (" " + -params[0]);
}break;
case 1073742122:
var resolution = this.floatParameter (++i);
if (resolution > 0) {
sbCommand.append (" resolution ").appendF (resolution);
this.setShapeProperty (25, "resolution", Float.$valueOf (resolution));
}break;
case 135266325:
case 1276118018:
distance = this.floatParameter (++i);
sbCommand.append (" within ").appendF (distance);
break;
case 269484193:
case 2:
case 3:
rd = eval.encodeRadiusParameter (i, false, false);
if (rd == null) return false;
sbCommand.append (" ").appendO (rd);
i = eval.iToken;
break;
case 1073741990:
case 1073741989:
intramolecular = (tok == 1073741989 ? Boolean.TRUE : Boolean.FALSE);
sbCommand.append (" ").appendO (eval.theToken.value);
break;
case 1073742020:
minSet = this.intParameter (++i);
break;
case 1612189718:
case 1073741881:
case 1649412120:
contactType = tok;
sbCommand.append (" ").appendO (eval.theToken.value);
break;
case 1073742135:
if (this.isFloatParameter (i + 1)) saProbeRadius = this.floatParameter (++i);
case 1074790451:
case 1073742036:
case 3145756:
localOnly = false;
case 1276117512:
case 1073741961:
case 135266319:
case 4106:
displayType = tok;
sbCommand.append (" ").appendO (eval.theToken.value);
if (tok == 1073742135) sbCommand.append (" ").appendF (saProbeRadius);
break;
case 1073742083:
params = eval.floatParameterSet (++i, 1, 10);
i = eval.iToken;
break;
case 10:
case 1048577:
if (isWild || bsB != null) this.invArg ();
bs = JU.BSUtil.copy (this.atomExpressionAt (i));
i = eval.iToken;
if (bsA == null) bsA = bs;
 else bsB = bs;
sbCommand.append (" ").append (JU.Escape.eBS (bs));
break;
}
idSeen = (eval.theTok != 12291);
}
if (!okNoAtoms && bsA == null) this.error (13);
if (this.chk) return false;
if (bsA != null) {
if (contactType == 1649412120 && rd == null) rd =  new J.atomdata.RadiusData (null, 0, J.atomdata.RadiusData.EnumType.OFFSET, J.c.VDW.AUTO);
var rd1 = (rd == null ?  new J.atomdata.RadiusData (null, 0.26, J.atomdata.RadiusData.EnumType.OFFSET, J.c.VDW.AUTO) : rd);
if (displayType == 1073742036 && bsB == null && intramolecular != null && intramolecular.booleanValue ()) bsB = bsA;
 else bsB = eval.getMathExt ().setContactBitSets (bsA, bsB, localOnly, distance, rd1, true);
switch (displayType) {
case 1074790451:
case 1073742135:
var bsSolvent = eval.lookupIdentifierValue ("solvent");
bsA.andNot (bsSolvent);
bsB.andNot (bsSolvent);
bsB.andNot (bsA);
break;
case 3145756:
bsB.andNot (bsA);
break;
case 1073742036:
if (minSet == 2147483647) minSet = 100;
this.setShapeProperty (25, "minset", Integer.$valueOf (minSet));
sbCommand.append (" minSet ").appendI (minSet);
if (params == null) params = [0.5, 2];
}
if (intramolecular != null) {
params = (params == null ?  Clazz_newFloatArray (2, 0) : JU.AU.ensureLengthA (params, 2));
params[1] = (intramolecular.booleanValue () ? 1 : 2);
}if (params != null) sbCommand.append (" parameters ").append (JU.Escape.eAF (params));
this.setShapeProperty (25, "set", [Integer.$valueOf (contactType), Integer.$valueOf (displayType), Boolean.$valueOf (colorDensity), Boolean.$valueOf (colorByType), bsA, bsB, rd, Float.$valueOf (saProbeRadius), params, sbCommand.toString ()]);
if (colorpt > 0) eval.setMeshDisplayProperty (25, colorpt, 0);
}if (iptDisplayProperty > 0) {
if (!eval.setMeshDisplayProperty (25, iptDisplayProperty, 0)) this.invArg ();
}if (userSlabObject != null && bsA != null) this.setShapeProperty (25, "slab", userSlabObject);
if (bsA != null && (displayType == 1073742036 || localOnly)) {
var volume = this.getShapeProperty (25, "volume");
if (JU.PT.isAD (volume)) {
var vs = volume;
var v = 0;
for (var i = 0; i < vs.length; i++) v += Math.abs (vs[i]);

volume = Float.$valueOf (v);
}var nsets = (this.getShapeProperty (25, "nSets")).intValue ();
if (colorDensity || displayType != 1276117512) {
this.showString ((nsets == 0 ? "" : nsets + " contacts with ") + "net volume " + volume + " A^3");
}}return true;
});
Clazz_defineMethod (c$, "dipole", 
 function () {
var eval = this.e;
var propertyName = null;
var propertyValue = null;
var iHaveAtoms = false;
var iHaveCoord = false;
var idSeen = false;
this.sm.loadShape (17);
if (this.tokAt (1) == 1073742001 && this.listIsosurface (17)) return false;
this.setShapeProperty (17, "init", null);
if (this.slen == 1) {
this.setShapeProperty (17, "thisID", null);
return false;
}for (var i = 1; i < this.slen; ++i) {
propertyName = null;
propertyValue = null;
switch (this.getToken (i).tok) {
case 1048579:
propertyName = "all";
break;
case 1048589:
propertyName = "on";
break;
case 1048588:
propertyName = "off";
break;
case 12291:
propertyName = "delete";
break;
case 2:
case 3:
propertyName = "value";
propertyValue = Float.$valueOf (this.floatParameter (i));
break;
case 10:
if (this.tokAt (i + 1) == 10) {
this.setShapeProperty (17, "startSet", this.atomExpressionAt (i++));
} else {
propertyName = "atomBitset";
}case 1048577:
if (propertyName == null) propertyName = (iHaveAtoms || iHaveCoord ? "endSet" : "startSet");
propertyValue = this.atomExpressionAt (i);
i = eval.iToken;
if (this.tokAt (i + 1) == 0 && propertyName === "startSet") propertyName = "atomBitset";
iHaveAtoms = true;
break;
case 1048586:
case 8:
var pt = this.getPoint3f (i, true);
i = eval.iToken;
propertyName = (iHaveAtoms || iHaveCoord ? "endCoord" : "startCoord");
propertyValue = pt;
iHaveCoord = true;
break;
case 1678770178:
propertyName = "bonds";
break;
case 4102:
propertyName = "calculate";
if (this.tokAt (i + 1) == 10 || this.tokAt (i + 1) == 1048577) {
propertyValue = this.atomExpressionAt (++i);
i = eval.iToken;
}break;
case 1074790550:
this.setShapeId (17, ++i, idSeen);
i = eval.iToken;
break;
case 135267329:
propertyName = "cross";
propertyValue = Boolean.TRUE;
break;
case 1073742040:
propertyName = "cross";
propertyValue = Boolean.FALSE;
break;
case 1073742066:
if (this.isFloatParameter (i + 1)) {
var v = this.floatParameter (++i);
if (eval.theTok == 2) {
propertyName = "offsetPercent";
propertyValue = Integer.$valueOf (Clazz_floatToInt (v));
} else {
propertyName = "offset";
propertyValue = Float.$valueOf (v);
}} else {
propertyName = "offsetPt";
propertyValue = this.centerParameter (++i);
i = eval.iToken;
}break;
case 1073742068:
propertyName = "offsetSide";
propertyValue = Float.$valueOf (this.floatParameter (++i));
break;
case 1073742188:
propertyName = "value";
propertyValue = Float.$valueOf (this.floatParameter (++i));
break;
case 1073742196:
propertyName = "width";
propertyValue = Float.$valueOf (this.floatParameter (++i));
break;
default:
if (eval.theTok == 269484209 || JS.T.tokAttr (eval.theTok, 1073741824)) {
this.setShapeId (17, i, idSeen);
i = eval.iToken;
break;
}this.invArg ();
}
idSeen = (eval.theTok != 12291 && eval.theTok != 4102);
if (propertyName != null) this.setShapeProperty (17, propertyName, propertyValue);
}
if (iHaveCoord || iHaveAtoms) this.setShapeProperty (17, "set", null);
return true;
});
Clazz_defineMethod (c$, "draw", 
 function () {
var eval = this.e;
this.sm.loadShape (22);
switch (this.tokAt (1)) {
case 1073742001:
if (this.listIsosurface (22)) return false;
break;
case 1073742102:
var pt = 2;
var type = (this.tokAt (pt) == 1073742138 ? "" : this.e.optParameterAsString (pt));
if (type.equals ("chemicalShift")) type = "cs";
var scale = 1;
var index = 0;
if (type.length > 0) {
if (this.isFloatParameter (++pt)) index = this.intParameter (pt++);
}if (this.tokAt (pt) == 1073742138) scale = this.floatParameter (++pt);
if (!this.chk) this.e.runScript (this.vwr.getPointGroupAsString (true, type, index, scale));
return false;
case 137363467:
case 135270418:
case 1052714:
this.plot (this.st);
return false;
}
var havePoints = false;
var isInitialized = false;
var isSavedState = false;
var isIntersect = false;
var isFrame = false;
var plane;
var tokIntersect = 0;
var translucentLevel = 3.4028235E38;
var colorArgb = [-2147483648];
var intScale = 0;
var swidth = "";
var iptDisplayProperty = 0;
var center = null;
var thisId = this.initIsosurface (22);
var idSeen = (thisId != null);
var isWild = (idSeen && this.getShapeProperty (22, "ID") == null);
var connections = null;
var iConnect = 0;
for (var i = eval.iToken; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
switch (this.getToken (i).tok) {
case 1614417948:
case 1679429641:
if (this.chk) break;
var vp = this.vwr.getPlaneIntersection (eval.theTok, null, intScale / 100, 0);
intScale = 0;
propertyName = "polygon";
propertyValue = vp;
havePoints = true;
break;
case 4106:
connections =  Clazz_newIntArray (4, 0);
iConnect = 4;
var farray = eval.floatParameterSet (++i, 4, 4);
i = eval.iToken;
for (var j = 0; j < 4; j++) connections[j] = Clazz_floatToInt (farray[j]);

havePoints = true;
break;
case 1678770178:
case 1141899265:
if (connections == null || iConnect > (eval.theTok == 1095761924 ? 2 : 3)) {
iConnect = 0;
connections = [-1, -1, -1, -1];
}connections[iConnect++] = this.atomExpressionAt (++i).nextSetBit (0);
i = eval.iToken;
connections[iConnect++] = (eval.theTok == 1678770178 ? this.atomExpressionAt (++i).nextSetBit (0) : -1);
i = eval.iToken;
havePoints = true;
break;
case 554176565:
switch (this.getToken (++i).tok) {
case 1048582:
propertyName = "slab";
propertyValue = eval.objectNameParameter (++i);
i = eval.iToken;
havePoints = true;
break;
default:
this.invArg ();
}
break;
case 135267842:
switch (this.getToken (++i).tok) {
case 1614417948:
case 1679429641:
tokIntersect = eval.theTok;
isIntersect = true;
continue;
case 1048582:
propertyName = "intersect";
propertyValue = eval.objectNameParameter (++i);
i = eval.iToken;
isIntersect = true;
havePoints = true;
break;
default:
this.invArg ();
}
break;
case 1073742106:
propertyName = "polygon";
havePoints = true;
var v =  new JU.Lst ();
var nVertices = 0;
var nTriangles = 0;
var points = null;
var vpolygons = null;
if (eval.isArrayParameter (++i)) {
points = eval.getPointArray (i, -1);
nVertices = points.length;
} else {
nVertices = Math.max (0, this.intParameter (i));
points =  new Array (nVertices);
for (var j = 0; j < nVertices; j++) points[j] = this.centerParameter (++eval.iToken);

}switch (this.getToken (++eval.iToken).tok) {
case 11:
case 12:
var sv = JS.SV.newT (eval.theToken);
sv.toArray ();
vpolygons = sv.getList ();
nTriangles = vpolygons.size ();
break;
case 7:
vpolygons = (eval.theToken).getList ();
nTriangles = vpolygons.size ();
break;
default:
nTriangles = Math.max (0, this.intParameter (eval.iToken));
}
var polygons = JU.AU.newInt2 (nTriangles);
for (var j = 0; j < nTriangles; j++) {
var f = (vpolygons == null ? eval.floatParameterSet (++eval.iToken, 3, 4) : JS.SV.flistValue (vpolygons.get (j), 0));
if (f.length < 3 || f.length > 4) this.invArg ();
polygons[j] = [Clazz_floatToInt (f[0]), Clazz_floatToInt (f[1]), Clazz_floatToInt (f[2]), (f.length == 3 ? 7 : Clazz_floatToInt (f[3]))];
}
if (nVertices > 0) {
v.addLast (points);
v.addLast (polygons);
} else {
v = null;
}propertyValue = v;
i = eval.iToken;
break;
case 1297090050:
var xyz = null;
var iSym = 0;
plane = null;
var target = null;
switch (this.tokAt (++i)) {
case 4:
xyz = this.stringParameter (i);
break;
case 12:
xyz = JS.SV.sValue (this.getToken (i));
break;
case 2:
default:
if (!eval.isCenterParameter (i)) iSym = this.intParameter (i++);
if (eval.isCenterParameter (i)) center = this.centerParameter (i);
if (eval.isCenterParameter (eval.iToken + 1)) target = this.centerParameter (++eval.iToken);
if (this.chk) return false;
i = eval.iToken;
}
var bsAtoms = null;
if (center == null && i + 1 < this.slen) {
center = this.centerParameter (++i);
bsAtoms = (this.tokAt (i) == 10 || this.tokAt (i) == 1048577 ? this.atomExpressionAt (i) : null);
i = eval.iToken + 1;
}eval.checkLast (eval.iToken);
if (!this.chk) {
var s = this.vwr.getSymmetryInfo (bsAtoms, xyz, iSym, center, target, thisId, 135176);
eval.runScript (s.length > 0 ? s : "draw ID \"sym_" + thisId + "*\" delete");
}return false;
case 4115:
isFrame = true;
continue;
case 1048586:
case 9:
case 8:
if (eval.theTok == 9 || !eval.isPoint3f (i)) {
propertyValue = this.getPoint4f (i);
if (isFrame) {
eval.checkLast (eval.iToken);
if (!this.chk) eval.runScript (JU.Escape.drawQuat (JU.Quat.newP4 (propertyValue), (thisId == null ? "frame" : thisId), " " + swidth, (center == null ?  new JU.P3 () : center), intScale / 100));
return false;
}propertyName = "planedef";
} else {
propertyValue = center = this.getPoint3f (i, true);
propertyName = "coord";
}i = eval.iToken;
havePoints = true;
break;
case 135267841:
case 135266319:
if (!havePoints && !isIntersect && tokIntersect == 0 && eval.theTok != 135267841) {
propertyName = "plane";
break;
}if (eval.theTok == 135266319) {
plane = eval.planeParameter (i);
} else {
plane = eval.hklParameter (++i);
}i = eval.iToken;
if (tokIntersect != 0) {
if (this.chk) break;
var vpc = this.vwr.getPlaneIntersection (tokIntersect, plane, intScale / 100, 0);
intScale = 0;
propertyName = "polygon";
propertyValue = vpc;
} else {
propertyValue = plane;
propertyName = "planedef";
}havePoints = true;
break;
case 1073742000:
propertyName = "lineData";
propertyValue = eval.floatParameterSet (++i, 0, 2147483647);
i = eval.iToken;
havePoints = true;
break;
case 10:
case 1048577:
propertyName = "atomSet";
propertyValue = this.atomExpressionAt (i);
if (isFrame) center = this.centerParameter (i);
i = eval.iToken;
havePoints = true;
break;
case 7:
propertyName = "modelBasedPoints";
propertyValue = JS.SV.strListValue (eval.theToken);
havePoints = true;
break;
case 1073742195:
case 269484080:
break;
case 269484096:
propertyValue = eval.xypParameter (i);
if (propertyValue != null) {
i = eval.iToken;
propertyName = "coord";
havePoints = true;
break;
}if (isSavedState) this.invArg ();
isSavedState = true;
break;
case 269484097:
if (!isSavedState) this.invArg ();
isSavedState = false;
break;
case 1141899269:
propertyName = "reverse";
break;
case 4:
propertyValue = this.stringParameter (i);
propertyName = "title";
break;
case 135198:
propertyName = "vector";
break;
case 1141899267:
propertyValue = Float.$valueOf (this.floatParameter (++i));
propertyName = "length";
break;
case 3:
propertyValue = Float.$valueOf (this.floatParameter (i));
propertyName = "length";
break;
case 1095761935:
propertyName = "modelIndex";
propertyValue = Integer.$valueOf (this.intParameter (++i));
break;
case 2:
if (isSavedState) {
propertyName = "modelIndex";
propertyValue = Integer.$valueOf (this.intParameter (i));
} else {
intScale = this.intParameter (i);
}break;
case 1073742138:
if (++i >= this.slen) this.error (34);
switch (this.getToken (i).tok) {
case 2:
intScale = this.intParameter (i);
continue;
case 3:
intScale = Math.round (this.floatParameter (i) * 100);
continue;
}
this.error (34);
break;
case 1074790550:
thisId = this.setShapeId (22, ++i, idSeen);
isWild = (this.getShapeProperty (22, "ID") == null);
i = eval.iToken;
break;
case 1073742027:
propertyName = "fixed";
propertyValue = Boolean.FALSE;
break;
case 1060869:
propertyName = "fixed";
propertyValue = Boolean.TRUE;
break;
case 1073742066:
var pt = this.getPoint3f (++i, true);
i = eval.iToken;
propertyName = "offset";
propertyValue = pt;
break;
case 1073741906:
propertyName = "crossed";
break;
case 1073742196:
propertyValue = Float.$valueOf (this.floatParameter (++i));
propertyName = "width";
swidth = propertyName + " " + propertyValue;
break;
case 1073741998:
propertyName = "line";
propertyValue = Boolean.TRUE;
break;
case 1073741908:
propertyName = "curve";
break;
case 1074790416:
propertyName = "arc";
break;
case 1073741846:
propertyName = "arrow";
break;
case 1073741880:
propertyName = "circle";
break;
case 1073741912:
propertyName = "cylinder";
break;
case 1073742194:
propertyName = "vertices";
break;
case 1073742048:
propertyName = "nohead";
break;
case 1073741861:
propertyName = "isbarb";
break;
case 1073742130:
propertyName = "rotate45";
break;
case 1073742092:
propertyName = "perp";
break;
case 1666189314:
case 1073741917:
var isRadius = (eval.theTok == 1666189314);
var f = this.floatParameter (++i);
if (isRadius) f *= 2;
propertyValue = Float.$valueOf (f);
propertyName = (isRadius || this.tokAt (i) == 3 ? "width" : "diameter");
swidth = propertyName + (this.tokAt (i) == 3 ? " " + f : " " + (Clazz_floatToInt (f)));
break;
case 1048582:
if ((this.tokAt (i + 2) == 269484096 || isFrame)) {
var pto = center = this.centerParameter (i);
i = eval.iToken;
propertyName = "coord";
propertyValue = pto;
havePoints = true;
break;
}propertyValue = eval.objectNameParameter (++i);
propertyName = "identifier";
havePoints = true;
break;
case 1766856708:
case 603979967:
case 1073742074:
idSeen = true;
translucentLevel = this.getColorTrans (eval, i, false, colorArgb);
i = eval.iToken;
continue;
default:
if (!eval.setMeshDisplayProperty (22, 0, eval.theTok)) {
if (eval.theTok == 269484209 || JS.T.tokAttr (eval.theTok, 1073741824)) {
thisId = this.setShapeId (22, i, idSeen);
i = eval.iToken;
break;
}this.invArg ();
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = eval.iToken;
continue;
}
idSeen = (eval.theTok != 12291);
if (havePoints && !isInitialized && !isFrame) {
this.setShapeProperty (22, "points", Integer.$valueOf (intScale));
isInitialized = true;
intScale = 0;
}if (havePoints && isWild) this.invArg ();
if (propertyName != null) this.setShapeProperty (22, propertyName, propertyValue);
}
this.finalizeObject (22, colorArgb[0], translucentLevel, intScale, havePoints, connections, iptDisplayProperty, null);
return true;
});
Clazz_defineMethod (c$, "data", 
function () {
var eval = this.e;
var dataString = null;
var dataLabel = null;
var isOneValue = false;
var i;
switch (eval.iToken = this.slen) {
case 5:
dataString = this.paramAsStr (2);
case 4:
case 2:
dataLabel = this.paramAsStr (1);
if (dataLabel.equalsIgnoreCase ("clear")) {
if (!this.chk) this.vwr.setData (null, null, 0, 0, 0, 0, 0);
return;
}if ((i = dataLabel.indexOf ("@")) >= 0) {
dataString = "" + eval.getParameter (dataLabel.substring (i + 1), 4, true);
dataLabel = dataLabel.substring (0, i).trim ();
} else if (dataString == null && (i = dataLabel.indexOf (" ")) >= 0) {
dataString = dataLabel.substring (i + 1).trim ();
dataLabel = dataLabel.substring (0, i).trim ();
isOneValue = true;
}break;
default:
eval.bad ();
}
var dataType = dataLabel + " ";
dataType = dataType.substring (0, dataType.indexOf (" ")).toLowerCase ();
if (dataType.equals ("model") || dataType.equals ("append")) {
eval.cmdLoad ();
return;
}if (this.chk) return;
var isDefault = (dataLabel.toLowerCase ().indexOf ("(default)") >= 0);
if (dataType.equals ("connect_atoms")) {
this.vwr.connect (this.parseDataArray (dataString, false));
return;
}if (dataType.indexOf ("ligand_") == 0) {
this.vwr.setLigandModel (dataLabel.substring (7).toUpperCase () + "_data", dataString.trim ());
return;
}if (dataType.indexOf ("file_") == 0) {
this.vwr.setLigandModel (dataLabel.substring (5) + "_file", dataString.trim ());
return;
}var d = this.lastData =  new Array (4);
if (dataType.equals ("element_vdw")) {
d[0] = dataType;
d[1] = dataString.$replace (';', '\n');
var n = JU.Elements.elementNumberMax;
var eArray =  Clazz_newIntArray (n + 1, 0);
for (var ie = 1; ie <= n; ie++) eArray[ie] = ie;

d[2] = eArray;
d[3] = Integer.$valueOf (0);
this.vwr.setData ("element_vdw", d, n, 0, 0, 0, 0);
return;
}if (dataType.indexOf ("data2d_") == 0) {
d[0] = dataLabel;
d[1] = this.parseDataArray (dataString, false);
d[3] = Integer.$valueOf (2);
this.vwr.setData (dataLabel, d, 0, 0, 0, 0, 0);
return;
}if (dataType.indexOf ("data3d_") == 0) {
d[0] = dataLabel;
d[1] = this.parseDataArray (dataString, true);
d[3] = Integer.$valueOf (3);
this.vwr.setData (dataLabel, d, 0, 0, 0, 0, 0);
return;
}var tokens = JU.PT.getTokens (dataLabel);
if (dataType.indexOf ("property_") == 0 && !(tokens.length == 2 && tokens[1].equals ("set"))) {
var bs = this.vwr.bsA ();
d[0] = dataType;
var atomNumberField = (isOneValue ? 0 : (this.vwr.getP ("propertyAtomNumberField")).intValue ());
var atomNumberFieldColumnCount = (isOneValue ? 0 : (this.vwr.getP ("propertyAtomNumberColumnCount")).intValue ());
var propertyField = (isOneValue ? -2147483648 : (this.vwr.getP ("propertyDataField")).intValue ());
var propertyFieldColumnCount = (isOneValue ? 0 : (this.vwr.getP ("propertyDataColumnCount")).intValue ());
if (!isOneValue && dataLabel.indexOf (" ") >= 0) {
if (tokens.length == 3) {
dataLabel = tokens[0];
atomNumberField = JU.PT.parseInt (tokens[1]);
propertyField = JU.PT.parseInt (tokens[2]);
}if (tokens.length == 5) {
dataLabel = tokens[0];
atomNumberField = JU.PT.parseInt (tokens[1]);
atomNumberFieldColumnCount = JU.PT.parseInt (tokens[2]);
propertyField = JU.PT.parseInt (tokens[3]);
propertyFieldColumnCount = JU.PT.parseInt (tokens[4]);
}}if (atomNumberField < 0) atomNumberField = 0;
if (propertyField < 0) propertyField = 0;
var ac = this.vwr.getAtomCount ();
var atomMap = null;
var bsTemp = JU.BS.newN (ac);
if (atomNumberField > 0) {
atomMap =  Clazz_newIntArray (ac + 2, 0);
for (var j = 0; j <= ac; j++) atomMap[j] = -1;

for (var j = bs.nextSetBit (0); j >= 0; j = bs.nextSetBit (j + 1)) {
var atomNo = this.vwr.getAtomNumber (j);
if (atomNo > ac + 1 || atomNo < 0 || bsTemp.get (atomNo)) continue;
bsTemp.set (atomNo);
atomMap[atomNo] = j;
}
d[2] = atomMap;
} else {
d[2] = JU.BSUtil.copy (bs);
}d[1] = dataString;
d[3] = Integer.$valueOf (0);
this.vwr.setData (dataType, d, ac, atomNumberField, atomNumberFieldColumnCount, propertyField, propertyFieldColumnCount);
return;
}var userType = JM.AtomCollection.getUserSettableType (dataType);
if (userType >= 0) {
this.vwr.setAtomData (userType, dataType, dataString, isDefault);
return;
}d[0] = dataLabel;
d[1] = dataString;
d[3] = Integer.$valueOf (0);
this.vwr.setData (dataType, d, 0, 0, 0, 0, 0);
});
Clazz_defineMethod (c$, "ellipsoid", 
 function () {
var eval = this.e;
var mad = 0;
var i = 1;
var translucentLevel = 3.4028235E38;
var checkMore = false;
var isSet = false;
this.setShapeProperty (20, "thisID", null);
switch (this.getToken (1).tok) {
case 1048589:
mad = 2147483647;
break;
case 1048588:
break;
case 2:
mad = this.intParameter (1);
break;
case 1085443:
this.sm.loadShape (20);
this.setShapeProperty (20, "select", this.paramAsStr (2));
i = eval.iToken;
checkMore = true;
isSet = true;
break;
case 1074790550:
case 269484209:
case 1073741824:
this.sm.loadShape (20);
if (eval.theTok == 1074790550) i++;
this.setShapeId (20, i, false);
i = eval.iToken;
checkMore = true;
break;
default:
this.invArg ();
}
if (!checkMore) {
eval.setShapeSizeBs (20, mad, null);
return;
}var colorArgb = [-2147483648];
while (++i < this.slen) {
var key = this.paramAsStr (i);
var value = null;
this.getToken (i);
if (!isSet) switch (eval.theTok) {
case 1048582:
key = "points";
var data =  new Array (3);
data[0] = eval.objectNameParameter (++i);
if (this.chk) continue;
eval.getShapePropertyData (24, "getVertices", data);
value = data;
break;
case 1611272194:
var axes =  new Array (3);
for (var j = 0; j < 3; j++) {
axes[j] =  new JU.V3 ();
axes[j].setT (this.centerParameter (++i));
i = eval.iToken;
}
value = axes;
break;
case 12289:
value = this.centerParameter (++i);
i = eval.iToken;
break;
case 1095761935:
value = Integer.$valueOf (this.intParameter (++i));
break;
case 12291:
value = Boolean.TRUE;
this.checkLength (i + 1);
break;
}
if (value == null) switch (eval.theTok) {
case 1048589:
key = "on";
value = Boolean.TRUE;
break;
case 1048588:
key = "on";
value = Boolean.FALSE;
break;
case 1073742138:
value = Float.$valueOf (this.floatParameter (++i));
break;
case 10:
case 1048577:
key = "atoms";
value = this.atomExpressionAt (i);
i = eval.iToken;
break;
case 1766856708:
case 603979967:
case 1073742074:
translucentLevel = this.getColorTrans (eval, i, true, colorArgb);
i = eval.iToken;
continue;
case 1073742075:
value = this.paramAsStr (++i);
break;
}
if (value == null) this.invArg ();
this.setShapeProperty (20, key.toLowerCase (), value);
}
this.finalizeObject (20, colorArgb[0], translucentLevel, 0, false, null, 0, null);
this.setShapeProperty (20, "thisID", null);
});
Clazz_defineMethod (c$, "isosurface", 
 function (iShape) {
var eval = this.e;
this.sm.loadShape (iShape);
if (this.tokAt (1) == 1073742001 && this.listIsosurface (iShape)) return false;
var iptDisplayProperty = 0;
var isIsosurface = (iShape == 24);
var isPmesh = (iShape == 28);
var isPlot3d = (iShape == 29);
var isLcaoCartoon = (iShape == 26);
var surfaceObjectSeen = false;
var planeSeen = false;
var isMapped = false;
var isBicolor = false;
var isPhased = false;
var doCalcArea = false;
var doCalcVolume = false;
var isCavity = false;
var haveRadius = false;
var toCache = false;
var isFxy = false;
var haveSlab = false;
var haveIntersection = false;
var isFrontOnly = false;
var data = null;
var cmd = null;
var thisSetNumber = -2147483648;
var nFiles = 0;
var nX;
var nY;
var nZ;
var ptX;
var ptY;
var sigma = NaN;
var cutoff = NaN;
var ptWithin = 0;
var smoothing = null;
var smoothingPower = 2147483647;
var bs = null;
var bsSelect = null;
var bsIgnore = null;
var sbCommand =  new JU.SB ();
var pt;
var plane = null;
var lattice = null;
var pts;
var color = 0;
var str = null;
var modelIndex = (this.chk ? 0 : -2147483648);
eval.setCursorWait (true);
var idSeen = (this.initIsosurface (iShape) != null);
var isWild = (idSeen && this.getShapeProperty (iShape, "ID") == null);
var isColorSchemeTranslucent = false;
var isInline = false;
var onlyOneModel = null;
var translucency = null;
var colorScheme = null;
var mepOrMlp = null;
var symops = null;
var discreteColixes = null;
var propertyList =  new JU.Lst ();
var defaultMesh = false;
if (isPmesh || isPlot3d) this.addShapeProperty (propertyList, "fileType", "Pmesh");
for (var i = eval.iToken; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
this.getToken (i);
if (eval.theTok == 1073741824) str = this.paramAsStr (i);
switch (eval.theTok) {
case 603979871:
smoothing = (this.getToken (++i).tok == 1048589 ? Boolean.TRUE : eval.theTok == 1048588 ? Boolean.FALSE : null);
if (smoothing == null) this.invArg ();
continue;
case 553648149:
smoothingPower = this.intParameter (++i);
continue;
case 4128:
propertyName = "moveIsosurface";
if (this.tokAt (++i) != 12) this.invArg ();
propertyValue = this.getToken (i++).value;
break;
case 1297090050:
var ff = this.floatArraySet (i + 2, this.intParameter (i + 1), 16);
symops =  new Array (ff.length);
for (var j = symops.length; --j >= 0; ) symops[j] = JU.M4.newA16 (ff[j]);

i = eval.iToken;
break;
case 1089470478:
if (modelIndex < 0) modelIndex = Math.min (this.vwr.am.cmi, 0);
var needIgnore = (bsIgnore == null);
if (bsSelect == null) bsSelect = JU.BSUtil.copy (this.vwr.bsA ());
bsSelect.and (this.vwr.ms.getAtoms (1297090050, Integer.$valueOf (1)));
if (!needIgnore) bsSelect.andNot (bsIgnore);
this.addShapeProperty (propertyList, "select", bsSelect);
if (needIgnore) {
bsIgnore = JU.BSUtil.copy (bsSelect);
JU.BSUtil.invertInPlace (bsIgnore, this.vwr.getAtomCount ());
isFrontOnly = true;
this.addShapeProperty (propertyList, "ignore", bsIgnore);
sbCommand.append (" ignore ").append (JU.Escape.eBS (bsIgnore));
}sbCommand.append (" symmetry");
if (color == 0) this.addShapeProperty (propertyList, "colorRGB", Integer.$valueOf (1297090050));
symops = this.vwr.ms.getSymMatrices (modelIndex);
break;
case 1073742066:
propertyName = "offset";
propertyValue = this.centerParameter (++i);
i = eval.iToken;
break;
case 528432:
propertyName = "rotate";
propertyValue = (this.tokAt (eval.iToken = ++i) == 1048587 ? null : this.getPoint4f (i));
i = eval.iToken;
break;
case 1610612740:
propertyName = "scale3d";
propertyValue = Float.$valueOf (this.floatParameter (++i));
break;
case 1073742090:
sbCommand.append (" periodic");
propertyName = "periodic";
break;
case 1073742078:
case 266298:
case 135266320:
propertyName = eval.theToken.value.toString ();
sbCommand.append (" ").appendO (eval.theToken.value);
propertyValue = this.centerParameter (++i);
sbCommand.append (" ").append (JU.Escape.eP (propertyValue));
i = eval.iToken;
break;
case 1679429641:
if (this.fullCommand.indexOf ("# BBOX=") >= 0) {
var bbox = JU.PT.split (JU.PT.getQuotedAttribute (this.fullCommand, "# BBOX"), ",");
pts = [JU.Escape.uP (bbox[0]), JU.Escape.uP (bbox[1])];
} else if (eval.isCenterParameter (i + 1)) {
pts = [this.getPoint3f (i + 1, true), this.getPoint3f (eval.iToken + 1, true)];
i = eval.iToken;
} else {
pts = this.vwr.ms.getBBoxVertices ();
}sbCommand.append (" boundBox " + JU.Escape.eP (pts[0]) + " " + JU.Escape.eP (pts[pts.length - 1]));
propertyName = "boundingBox";
propertyValue = pts;
break;
case 135188:
isPmesh = true;
sbCommand.append (" pmesh");
propertyName = "fileType";
propertyValue = "Pmesh";
break;
case 135267842:
bsSelect = this.atomExpressionAt (++i);
if (this.chk) {
bs =  new JU.BS ();
} else if (this.tokAt (eval.iToken + 1) == 1048577 || this.tokAt (eval.iToken + 1) == 10) {
bs = this.atomExpressionAt (++eval.iToken);
bs.and (this.vwr.ms.getAtomsWithinRadius (5.0, bsSelect, false, null));
} else {
bs = this.vwr.ms.getAtomsWithinRadius (5.0, bsSelect, true, null);
bs.andNot (this.vwr.ms.getAtoms (1095761936, bsSelect));
}bs.andNot (bsSelect);
sbCommand.append (" intersection ").append (JU.Escape.eBS (bsSelect)).append (" ").append (JU.Escape.eBS (bs));
i = eval.iToken;
if (this.tokAt (i + 1) == 135368713) {
i++;
var f = this.getToken (++i).value;
sbCommand.append (" function ").append (JU.PT.esc (f));
if (!this.chk) this.addShapeProperty (propertyList, "func", (f.equals ("a+b") || f.equals ("a-b") ? f : this.createFunction ("__iso__", "a,b", f)));
} else {
haveIntersection = true;
}propertyName = "intersection";
propertyValue = [bsSelect, bs];
break;
case 1610625028:
case 135266325:
var isDisplay = (eval.theTok == 1610625028);
if (isDisplay) {
sbCommand.append (" display");
iptDisplayProperty = i;
var tok = this.tokAt (i + 1);
if (tok == 0) continue;
i++;
this.addShapeProperty (propertyList, "token", Integer.$valueOf (1048589));
if (tok == 10 || tok == 1048579) {
propertyName = "bsDisplay";
if (tok == 1048579) {
sbCommand.append (" all");
} else {
propertyValue = this.st[i].value;
sbCommand.append (" ").append (JU.Escape.eBS (propertyValue));
}eval.checkLast (i);
break;
} else if (tok != 135266325) {
eval.iToken = i;
this.invArg ();
}} else {
ptWithin = i;
}var distance;
var ptc = null;
bs = null;
var havePt = false;
if (this.tokAt (i + 1) == 1048577) {
distance = this.floatParameter (i + 3);
if (eval.isPoint3f (i + 4)) {
ptc = this.centerParameter (i + 4);
havePt = true;
eval.iToken = eval.iToken + 2;
} else if (eval.isPoint3f (i + 5)) {
ptc = this.centerParameter (i + 5);
havePt = true;
eval.iToken = eval.iToken + 2;
} else {
bs = eval.atomExpression (this.st, i + 5, this.slen, true, false, false, true);
if (bs == null) this.invArg ();
}} else {
distance = this.floatParameter (++i);
ptc = this.centerParameter (++i);
}if (isDisplay) eval.checkLast (eval.iToken);
i = eval.iToken;
if (this.fullCommand.indexOf ("# WITHIN=") >= 0) bs = JU.BS.unescape (JU.PT.getQuotedAttribute (this.fullCommand, "# WITHIN"));
 else if (!havePt) bs = (Clazz_instanceOf (eval.expressionResult, JU.BS) ? eval.expressionResult : null);
if (!this.chk) {
if (bs != null && modelIndex >= 0) {
bs.and (this.vwr.getModelUndeletedAtomsBitSet (modelIndex));
}if (ptc == null) ptc = (bs == null ?  new JU.P3 () : this.vwr.ms.getAtomSetCenter (bs));
this.getWithinDistanceVector (propertyList, distance, ptc, bs, isDisplay);
sbCommand.append (" within ").appendF (distance).append (" ").append (bs == null ? JU.Escape.eP (ptc) : JU.Escape.eBS (bs));
}continue;
case 1073742083:
propertyName = "parameters";
var fparams = eval.floatParameterSet (++i, 1, 10);
i = eval.iToken;
propertyValue = fparams;
sbCommand.append (" parameters ").append (JU.Escape.eAF (fparams));
break;
case 1716520985:
case 1073742190:
onlyOneModel = eval.theToken.value;
var isVariable = (eval.theTok == 1073742190);
var tokProperty = this.tokAt (i + 1);
if (mepOrMlp == null) {
if (!surfaceObjectSeen && !isMapped && !planeSeen) {
this.addShapeProperty (propertyList, "sasurface", Float.$valueOf (0));
sbCommand.append (" vdw");
surfaceObjectSeen = true;
}propertyName = "property";
if (smoothing == null) {
var allowSmoothing = JS.T.tokAttr (tokProperty, 1112539136);
smoothing = (allowSmoothing && this.vwr.getIsosurfacePropertySmoothing (false) == 1 ? Boolean.TRUE : Boolean.FALSE);
}this.addShapeProperty (propertyList, "propertySmoothing", smoothing);
sbCommand.append (" isosurfacePropertySmoothing " + smoothing);
if (smoothing === Boolean.TRUE) {
if (smoothingPower == 2147483647) smoothingPower = this.vwr.getIsosurfacePropertySmoothing (true);
this.addShapeProperty (propertyList, "propertySmoothingPower", Integer.$valueOf (smoothingPower));
sbCommand.append (" isosurfacePropertySmoothingPower " + smoothingPower);
}if (this.vwr.g.rangeSelected) this.addShapeProperty (propertyList, "rangeSelected", Boolean.TRUE);
} else {
propertyName = mepOrMlp;
}str = this.paramAsStr (i);
sbCommand.append (" ").append (str);
if (str.toLowerCase ().indexOf ("property_") == 0) {
data =  Clazz_newFloatArray (this.vwr.getAtomCount (), 0);
if (this.chk) continue;
data = this.vwr.getDataFloat (str);
if (data == null) this.invArg ();
this.addShapeProperty (propertyList, propertyName, data);
continue;
}var ac = this.vwr.getAtomCount ();
data =  Clazz_newFloatArray (ac, 0);
if (isVariable) {
var vname = this.paramAsStr (++i);
if (vname.length == 0) {
data = eval.floatParameterSet (i, ac, ac);
} else {
data =  Clazz_newFloatArray (ac, 0);
if (!this.chk) JU.Parser.parseStringInfestedFloatArray ("" + eval.getParameter (vname, 4, true), null, data);
}if (!this.chk) sbCommand.append (" \"\" ").append (JU.Escape.eAF (data));
} else {
this.getToken (++i);
if (!this.chk) {
sbCommand.append (" " + eval.theToken.value);
var atoms = this.vwr.ms.at;
this.vwr.autoCalculate (tokProperty);
if (tokProperty != 1766856708) {
pt =  new JU.P3 ();
for (var iAtom = ac; --iAtom >= 0; ) data[iAtom] = JM.Atom.atomPropertyFloat (this.vwr, atoms[iAtom], tokProperty, pt);

}}if (tokProperty == 1766856708) colorScheme = "inherit";
if (this.tokAt (i + 1) == 135266325) {
var d = this.floatParameter (i = i + 2);
sbCommand.append (" within " + d);
this.addShapeProperty (propertyList, "propertyDistanceMax", Float.$valueOf (d));
}}propertyValue = data;
break;
case 1095761935:
case 1095766030:
if (surfaceObjectSeen) this.invArg ();
modelIndex = (eval.theTok == 1095761935 ? this.intParameter (++i) : eval.modelNumberParameter (++i));
sbCommand.append (" modelIndex " + modelIndex);
if (modelIndex < 0) {
propertyName = "fixed";
propertyValue = Boolean.TRUE;
break;
}propertyName = "modelIndex";
propertyValue = Integer.$valueOf (modelIndex);
break;
case 135280132:
propertyName = "select";
var bs1 = this.atomExpressionAt (++i);
propertyValue = bs1;
i = eval.iToken;
var isOnly = (this.tokAt (i + 1) == 1073742072);
if (isOnly) {
i++;
bsIgnore = JU.BSUtil.copy (bs1);
JU.BSUtil.invertInPlace (bsIgnore, this.vwr.getAtomCount ());
this.addShapeProperty (propertyList, "ignore", bsIgnore);
sbCommand.append (" ignore ").append (JU.Escape.eBS (bsIgnore));
isFrontOnly = true;
}if (surfaceObjectSeen || isMapped) {
sbCommand.append (" select " + JU.Escape.eBS (bs1));
} else {
bsSelect = propertyValue;
if (modelIndex < 0 && bsSelect.nextSetBit (0) >= 0) modelIndex = this.vwr.getAtomModelIndex (bsSelect.nextSetBit (0));
}break;
case 1085443:
thisSetNumber = this.intParameter (++i);
break;
case 12289:
propertyName = "center";
propertyValue = this.centerParameter (++i);
sbCommand.append (" center " + JU.Escape.eP (propertyValue));
i = eval.iToken;
break;
case 1073742147:
case 1766856708:
idSeen = true;
var isSign = (eval.theTok == 1073742147);
if (isSign) {
sbCommand.append (" sign");
this.addShapeProperty (propertyList, "sign", Boolean.TRUE);
} else {
if (this.tokAt (i + 1) == 1073741914) {
i++;
propertyName = "colorDensity";
sbCommand.append (" color density");
if (this.isFloatParameter (i + 1)) {
var ptSize = this.floatParameter (++i);
sbCommand.append (" " + ptSize);
propertyValue = Float.$valueOf (ptSize);
}break;
}if (this.getToken (i + 1).tok == 4) {
colorScheme = this.paramAsStr (++i);
if (colorScheme.indexOf (" ") > 0) {
discreteColixes = JU.C.getColixArray (colorScheme);
if (discreteColixes == null) this.error (4);
}} else if (eval.theTok == 1073742018) {
i++;
sbCommand.append (" color mesh");
color = eval.getArgbParam (++i);
this.addShapeProperty (propertyList, "meshcolor", Integer.$valueOf (color));
sbCommand.append (" ").append (JU.Escape.escapeColor (color));
i = eval.iToken;
continue;
}if ((eval.theTok = this.tokAt (i + 1)) == 603979967 || eval.theTok == 1073742074) {
sbCommand.append (" color");
translucency = this.setColorOptions (sbCommand, i + 1, 24, -2);
i = eval.iToken;
continue;
}switch (this.tokAt (i + 1)) {
case 1073741826:
case 1073742114:
this.getToken (++i);
sbCommand.append (" color range");
this.addShapeProperty (propertyList, "rangeAll", null);
if (this.tokAt (i + 1) == 1048579) {
i++;
sbCommand.append (" all");
continue;
}var min = this.floatParameter (++i);
var max = this.floatParameter (++i);
this.addShapeProperty (propertyList, "red", Float.$valueOf (min));
this.addShapeProperty (propertyList, "blue", Float.$valueOf (max));
sbCommand.append (" ").appendF (min).append (" ").appendF (max);
continue;
}
if (eval.isColorParam (i + 1)) {
color = eval.getArgbParam (i + 1);
if (this.tokAt (i + 2) == 1074790746) {
colorScheme = eval.getColorRange (i + 1);
i = eval.iToken;
break;
}}sbCommand.append (" color");
}if (eval.isColorParam (i + 1)) {
color = eval.getArgbParam (++i);
sbCommand.append (" ").append (JU.Escape.escapeColor (color));
i = eval.iToken;
this.addShapeProperty (propertyList, "colorRGB", Integer.$valueOf (color));
idSeen = true;
if (eval.isColorParam (i + 1)) {
color = eval.getArgbParam (++i);
i = eval.iToken;
this.addShapeProperty (propertyList, "colorRGB", Integer.$valueOf (color));
sbCommand.append (" ").append (JU.Escape.escapeColor (color));
isBicolor = true;
} else if (isSign) {
this.invPO ();
}} else if (!isSign && discreteColixes == null) {
this.invPO ();
}continue;
case 135270423:
if (!isIsosurface) this.invArg ();
toCache = !this.chk;
continue;
case 1229984263:
if (this.tokAt (i + 1) != 4) this.invPO ();
continue;
case 1112541195:
case 1649412120:
sbCommand.append (" ").appendO (eval.theToken.value);
var rd = eval.encodeRadiusParameter (i, false, true);
if (rd == null) return false;
sbCommand.append (" ").appendO (rd);
if (Float.isNaN (rd.value)) rd.value = 100;
propertyValue = rd;
propertyName = "radius";
haveRadius = true;
if (isMapped) surfaceObjectSeen = false;
i = eval.iToken;
break;
case 135266319:
planeSeen = true;
propertyName = "plane";
propertyValue = eval.planeParameter (i);
i = eval.iToken;
sbCommand.append (" plane ").append (JU.Escape.eP4 (propertyValue));
break;
case 1073742138:
propertyName = "scale";
propertyValue = Float.$valueOf (this.floatParameter (++i));
sbCommand.append (" scale ").appendO (propertyValue);
break;
case 1048579:
if (idSeen) this.invArg ();
propertyName = "thisID";
break;
case 1113198596:
surfaceObjectSeen = true;
++i;
propertyValue = this.getPoint4f (i);
propertyName = "ellipsoid";
i = eval.iToken;
sbCommand.append (" ellipsoid ").append (JU.Escape.eP4 (propertyValue));
break;
case 135267841:
planeSeen = true;
propertyName = "plane";
propertyValue = eval.hklParameter (++i);
i = eval.iToken;
sbCommand.append (" plane ").append (JU.Escape.eP4 (propertyValue));
break;
case 135182:
surfaceObjectSeen = true;
var lcaoType = this.paramAsStr (++i);
this.addShapeProperty (propertyList, "lcaoType", lcaoType);
sbCommand.append (" lcaocartoon ").append (JU.PT.esc (lcaoType));
switch (this.getToken (++i).tok) {
case 10:
case 1048577:
propertyName = "lcaoCartoon";
bs = this.atomExpressionAt (i);
i = eval.iToken;
if (this.chk) continue;
var atomIndex = bs.nextSetBit (0);
if (atomIndex < 0) this.error (14);
sbCommand.append (" ({").appendI (atomIndex).append ("})");
modelIndex = this.vwr.getAtomModelIndex (atomIndex);
this.addShapeProperty (propertyList, "modelIndex", Integer.$valueOf (modelIndex));
var axes = [ new JU.V3 (),  new JU.V3 (), JU.V3.newV (this.vwr.getAtomPoint3f (atomIndex)),  new JU.V3 ()];
if (!lcaoType.equalsIgnoreCase ("s") && this.vwr.getHybridizationAndAxes (atomIndex, axes[0], axes[1], lcaoType) == null) return false;
propertyValue = axes;
break;
default:
this.error (14);
}
break;
case 1183762:
var moNumber = 2147483647;
var offset = 2147483647;
var isNegOffset = (this.tokAt (i + 1) == 269484192);
if (isNegOffset) i++;
var linearCombination = null;
switch (this.tokAt (++i)) {
case 0:
eval.bad ();
break;
case 1073741914:
sbCommand.append ("mo [1] squared ");
this.addShapeProperty (propertyList, "squareLinear", Boolean.TRUE);
linearCombination = [1];
offset = moNumber = 0;
i++;
break;
case 1073741973:
case 1073742008:
offset = this.moOffset (i);
moNumber = 0;
i = eval.iToken;
sbCommand.append (" mo " + (isNegOffset ? "-" : "") + "HOMO ");
if (offset > 0) sbCommand.append ("+");
if (offset != 0) sbCommand.appendI (offset);
break;
case 2:
moNumber = this.intParameter (i);
sbCommand.append (" mo ").appendI (moNumber);
break;
default:
if (eval.isArrayParameter (i)) {
linearCombination = eval.floatParameterSet (i, 1, 2147483647);
i = eval.iToken;
}}
var squared = (this.tokAt (i + 1) == 1073742156);
if (squared) {
this.addShapeProperty (propertyList, "squareLinear", Boolean.TRUE);
sbCommand.append (" squared");
if (linearCombination == null) linearCombination =  Clazz_newFloatArray (0, 0);
} else if (this.tokAt (i + 1) == 135266320) {
++i;
var monteCarloCount = this.intParameter (++i);
var seed = (this.tokAt (i + 1) == 2 ? this.intParameter (++i) : (-System.currentTimeMillis ()) % 10000);
this.addShapeProperty (propertyList, "monteCarloCount", Integer.$valueOf (monteCarloCount));
this.addShapeProperty (propertyList, "randomSeed", Integer.$valueOf (seed));
sbCommand.append (" points ").appendI (monteCarloCount).appendC (' ').appendI (seed);
}this.setMoData (propertyList, moNumber, linearCombination, offset, isNegOffset, modelIndex, null);
surfaceObjectSeen = true;
continue;
case 1073742036:
propertyName = "nci";
sbCommand.append (" " + propertyName);
var tok = this.tokAt (i + 1);
var isPromolecular = (tok != 1229984263 && tok != 4 && tok != 1073742033);
propertyValue = Boolean.$valueOf (isPromolecular);
if (isPromolecular) surfaceObjectSeen = true;
break;
case 1073742016:
case 1073742022:
var isMep = (eval.theTok == 1073742016);
propertyName = (isMep ? "mep" : "mlp");
sbCommand.append (" " + propertyName);
var fname = null;
var calcType = -1;
surfaceObjectSeen = true;
if (this.tokAt (i + 1) == 2) {
calcType = this.intParameter (++i);
sbCommand.append (" " + calcType);
this.addShapeProperty (propertyList, "mepCalcType", Integer.$valueOf (calcType));
}if (this.tokAt (i + 1) == 4) {
fname = this.stringParameter (++i);
sbCommand.append (" /*file*/" + JU.PT.esc (fname));
} else if (this.tokAt (i + 1) == 1716520985) {
mepOrMlp = propertyName;
continue;
}if (!this.chk) try {
data = (fname == null && isMep ? this.vwr.getPartialCharges () : this.getAtomicPotentials (bsSelect, bsIgnore, fname));
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
} else {
throw ex;
}
}
if (!this.chk && data == null) this.error (32);
propertyValue = data;
break;
case 1313866249:
doCalcVolume = !this.chk;
sbCommand.append (" volume");
break;
case 1074790550:
this.setShapeId (iShape, ++i, idSeen);
isWild = (this.getShapeProperty (iShape, "ID") == null);
i = eval.iToken;
break;
case 1073741888:
if (this.tokAt (i + 1) == 603979967) {
isColorSchemeTranslucent = true;
i++;
}colorScheme = this.paramAsStr (++i).toLowerCase ();
if (colorScheme.equals ("sets")) {
sbCommand.append (" colorScheme \"sets\"");
} else if (eval.isColorParam (i)) {
colorScheme = eval.getColorRange (i);
i = eval.iToken;
}break;
case 1073741828:
propertyName = "addHydrogens";
propertyValue = Boolean.TRUE;
sbCommand.append (" mp.addHydrogens");
break;
case 1073741836:
propertyName = "angstroms";
sbCommand.append (" angstroms");
break;
case 1073741837:
propertyName = "anisotropy";
propertyValue = this.getPoint3f (++i, false);
sbCommand.append (" anisotropy").append (JU.Escape.eP (propertyValue));
i = eval.iToken;
break;
case 1073741842:
doCalcArea = !this.chk;
sbCommand.append (" area");
break;
case 1073741850:
case 1073742076:
surfaceObjectSeen = true;
if (isBicolor && !isPhased) {
sbCommand.append (" phase \"_orb\"");
this.addShapeProperty (propertyList, "phase", "_orb");
}var nlmZprs =  Clazz_newFloatArray (7, 0);
nlmZprs[0] = this.intParameter (++i);
nlmZprs[1] = this.intParameter (++i);
nlmZprs[2] = this.intParameter (++i);
nlmZprs[3] = (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 6);
sbCommand.append (" atomicOrbital ").appendI (Clazz_floatToInt (nlmZprs[0])).append (" ").appendI (Clazz_floatToInt (nlmZprs[1])).append (" ").appendI (Clazz_floatToInt (nlmZprs[2])).append (" ").appendF (nlmZprs[3]);
if (this.tokAt (i + 1) == 135266320) {
i += 2;
nlmZprs[4] = this.intParameter (i);
nlmZprs[5] = (this.tokAt (i + 1) == 3 ? this.floatParameter (++i) : 0);
nlmZprs[6] = (this.tokAt (i + 1) == 2 ? this.intParameter (++i) : (-System.currentTimeMillis ()) % 10000);
sbCommand.append (" points ").appendI (Clazz_floatToInt (nlmZprs[4])).appendC (' ').appendF (nlmZprs[5]).appendC (' ').appendI (Clazz_floatToInt (nlmZprs[6]));
}propertyName = "hydrogenOrbital";
propertyValue = nlmZprs;
break;
case 1073741866:
sbCommand.append (" binary");
continue;
case 1073741868:
sbCommand.append (" blockData");
propertyName = "blockData";
propertyValue = Boolean.TRUE;
break;
case 1074790451:
case 554176565:
haveSlab = true;
propertyName = eval.theToken.value;
propertyValue = this.getCapSlabObject (i, false);
i = eval.iToken;
break;
case 1073741876:
if (!isIsosurface) this.invArg ();
isCavity = true;
if (this.chk) continue;
var cavityRadius = (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 1.2);
var envelopeRadius = (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 10);
if (envelopeRadius > 10) {
eval.integerOutOfRange (0, 10);
return false;
}sbCommand.append (" cavity ").appendF (cavityRadius).append (" ").appendF (envelopeRadius);
this.addShapeProperty (propertyList, "envelopeRadius", Float.$valueOf (envelopeRadius));
this.addShapeProperty (propertyList, "cavityRadius", Float.$valueOf (cavityRadius));
propertyName = "cavity";
break;
case 1073741896:
case 1073741900:
propertyName = "contour";
sbCommand.append (" contour");
switch (this.tokAt (i + 1)) {
case 1073741920:
propertyValue = eval.floatParameterSet (i + 2, 1, 2147483647);
sbCommand.append (" discrete ").append (JU.Escape.eAF (propertyValue));
i = eval.iToken;
break;
case 1073741981:
pt = this.getPoint3f (i + 2, false);
if (pt.z <= 0 || pt.y < pt.x) this.invArg ();
if (pt.z == Clazz_floatToInt (pt.z) && pt.z > (pt.y - pt.x)) pt.z = (pt.y - pt.x) / pt.z;
propertyValue = pt;
i = eval.iToken;
sbCommand.append (" increment ").append (JU.Escape.eP (pt));
break;
default:
propertyValue = Integer.$valueOf (this.tokAt (i + 1) == 2 ? this.intParameter (++i) : 0);
sbCommand.append (" ").appendO (propertyValue);
}
break;
case 3:
case 2:
case 269484193:
case 1073741910:
sbCommand.append (" cutoff ");
if (eval.theTok == 1073741910) i++;
if (this.tokAt (i) == 269484193) {
propertyName = "cutoffPositive";
propertyValue = Float.$valueOf (cutoff = this.floatParameter (++i));
sbCommand.append ("+").appendO (propertyValue);
} else if (this.isFloatParameter (i)) {
propertyName = "cutoff";
propertyValue = Float.$valueOf (cutoff = this.floatParameter (i));
sbCommand.appendO (propertyValue);
} else {
propertyName = "cutoffRange";
propertyValue = eval.floatParameterSet (i, 2, 2);
this.addShapeProperty (propertyList, "cutoff", Float.$valueOf (0));
sbCommand.append (JU.Escape.eAF (propertyValue));
i = eval.iToken;
}break;
case 1073741928:
propertyName = "downsample";
propertyValue = Integer.$valueOf (this.intParameter (++i));
sbCommand.append (" downsample ").appendO (propertyValue);
break;
case 1073741930:
propertyName = "eccentricity";
propertyValue = this.getPoint4f (++i);
sbCommand.append (" eccentricity ").append (JU.Escape.eP4 (propertyValue));
i = eval.iToken;
break;
case 1074790508:
sbCommand.append (" ed");
this.setMoData (propertyList, -1, null, 0, false, modelIndex, null);
surfaceObjectSeen = true;
continue;
case 536870916:
case 1073742041:
sbCommand.append (" ").appendO (eval.theToken.value);
propertyName = "debug";
propertyValue = (eval.theTok == 536870916 ? Boolean.TRUE : Boolean.FALSE);
break;
case 1060869:
sbCommand.append (" fixed");
propertyName = "fixed";
propertyValue = Boolean.TRUE;
break;
case 1073741962:
sbCommand.append (" fullPlane");
propertyName = "fullPlane";
propertyValue = Boolean.TRUE;
break;
case 1073741966:
case 1073741968:
var isFxyz = (eval.theTok == 1073741968);
propertyName = "" + eval.theToken.value;
var vxy =  new JU.Lst ();
propertyValue = vxy;
isFxy = surfaceObjectSeen = true;
sbCommand.append (" ").append (propertyName);
var name = this.paramAsStr (++i);
if (name.equals ("=")) {
sbCommand.append (" =");
name = this.paramAsStr (++i);
sbCommand.append (" ").append (JU.PT.esc (name));
vxy.addLast (name);
if (!this.chk) this.addShapeProperty (propertyList, "func", this.createFunction ("__iso__", "x,y,z", name));
break;
}var dName = JU.PT.getQuotedAttribute (this.fullCommand, "# DATA" + (isFxy ? "2" : ""));
if (dName == null) dName = "inline";
 else name = dName;
var isXYZ = (name.indexOf ("data2d_") == 0);
var isXYZV = (name.indexOf ("data3d_") == 0);
isInline = name.equals ("inline");
sbCommand.append (" inline");
vxy.addLast (name);
var pt3 = this.getPoint3f (++i, false);
sbCommand.append (" ").append (JU.Escape.eP (pt3));
vxy.addLast (pt3);
var pt4;
ptX = ++eval.iToken;
vxy.addLast (pt4 = this.getPoint4f (ptX));
sbCommand.append (" ").append (JU.Escape.eP4 (pt4));
nX = Clazz_floatToInt (pt4.x);
ptY = ++eval.iToken;
vxy.addLast (pt4 = this.getPoint4f (ptY));
sbCommand.append (" ").append (JU.Escape.eP4 (pt4));
nY = Clazz_floatToInt (pt4.x);
vxy.addLast (pt4 = this.getPoint4f (++eval.iToken));
sbCommand.append (" ").append (JU.Escape.eP4 (pt4));
nZ = Clazz_floatToInt (pt4.x);
if (nX == 0 || nY == 0 || nZ == 0) this.invArg ();
if (!this.chk) {
var fdata = null;
var xyzdata = null;
if (isFxyz) {
if (isInline) {
nX = Math.abs (nX);
nY = Math.abs (nY);
nZ = Math.abs (nZ);
xyzdata = this.floatArraySetXYZ (++eval.iToken, nX, nY, nZ);
} else if (isXYZV) {
xyzdata = this.vwr.getDataFloat3D (name);
} else {
xyzdata = this.vwr.functionXYZ (name, nX, nY, nZ);
}nX = Math.abs (nX);
nY = Math.abs (nY);
nZ = Math.abs (nZ);
if (xyzdata == null) {
eval.iToken = ptX;
eval.errorStr (53, "xyzdata is null.");
}if (xyzdata.length != nX || xyzdata[0].length != nY || xyzdata[0][0].length != nZ) {
eval.iToken = ptX;
eval.errorStr (53, "xyzdata[" + xyzdata.length + "][" + xyzdata[0].length + "][" + xyzdata[0][0].length + "] is not of size [" + nX + "][" + nY + "][" + nZ + "]");
}vxy.addLast (xyzdata);
sbCommand.append (" ").append (JU.Escape.e (xyzdata));
} else {
if (isInline) {
nX = Math.abs (nX);
nY = Math.abs (nY);
fdata = this.floatArraySet (++eval.iToken, nX, nY);
} else if (isXYZ) {
fdata = this.vwr.getDataFloat2D (name);
nX = (fdata == null ? 0 : fdata.length);
nY = 3;
} else {
fdata = this.vwr.functionXY (name, nX, nY);
nX = Math.abs (nX);
nY = Math.abs (nY);
}if (fdata == null) {
eval.iToken = ptX;
eval.errorStr (53, "fdata is null.");
}if (fdata.length != nX && !isXYZ) {
eval.iToken = ptX;
eval.errorStr (53, "fdata length is not correct: " + fdata.length + " " + nX + ".");
}for (var j = 0; j < nX; j++) {
if (fdata[j] == null) {
eval.iToken = ptY;
eval.errorStr (53, "fdata[" + j + "] is null.");
}if (fdata[j].length != nY) {
eval.iToken = ptY;
eval.errorStr (53, "fdata[" + j + "] is not the right length: " + fdata[j].length + " " + nY + ".");
}}
vxy.addLast (fdata);
sbCommand.append (" ").append (JU.Escape.e (fdata));
}}i = eval.iToken;
break;
case 1073741970:
propertyName = "gridPoints";
sbCommand.append (" gridPoints");
break;
case 1073741976:
propertyName = "ignore";
propertyValue = bsIgnore = this.atomExpressionAt (++i);
sbCommand.append (" ignore ").append (JU.Escape.eBS (bsIgnore));
i = eval.iToken;
break;
case 1073741984:
propertyName = "insideOut";
sbCommand.append (" insideout");
break;
case 1073741988:
case 1073741986:
case 1073742100:
sbCommand.append (" ").appendO (eval.theToken.value);
propertyName = "pocket";
propertyValue = (eval.theTok == 1073742100 ? Boolean.TRUE : Boolean.FALSE);
break;
case 1073742002:
propertyName = "lobe";
propertyValue = this.getPoint4f (++i);
i = eval.iToken;
sbCommand.append (" lobe ").append (JU.Escape.eP4 (propertyValue));
surfaceObjectSeen = true;
break;
case 1073742004:
case 1073742006:
propertyName = "lp";
propertyValue = this.getPoint4f (++i);
i = eval.iToken;
sbCommand.append (" lp ").append (JU.Escape.eP4 (propertyValue));
surfaceObjectSeen = true;
break;
case 1052700:
if (isMapped || this.slen == i + 1) this.invArg ();
isMapped = true;
if ((isCavity || haveRadius || haveIntersection) && !surfaceObjectSeen) {
surfaceObjectSeen = true;
this.addShapeProperty (propertyList, "bsSolvent", (haveRadius || haveIntersection ?  new JU.BS () : eval.lookupIdentifierValue ("solvent")));
this.addShapeProperty (propertyList, "sasurface", Float.$valueOf (0));
}if (sbCommand.length () == 0) {
plane = this.getShapeProperty (24, "plane");
if (plane == null) {
if (this.getShapeProperty (24, "contours") != null) {
this.addShapeProperty (propertyList, "nocontour", null);
}} else {
this.addShapeProperty (propertyList, "plane", plane);
sbCommand.append ("plane ").append (JU.Escape.eP4 (plane));
planeSeen = true;
plane = null;
}} else if (!surfaceObjectSeen && !planeSeen) {
this.invArg ();
}sbCommand.append ("; isosurface map");
this.addShapeProperty (propertyList, "map", (surfaceObjectSeen ? Boolean.TRUE : Boolean.FALSE));
break;
case 1073742014:
propertyName = "maxset";
propertyValue = Integer.$valueOf (this.intParameter (++i));
sbCommand.append (" maxSet ").appendO (propertyValue);
break;
case 1073742020:
propertyName = "minset";
propertyValue = Integer.$valueOf (this.intParameter (++i));
sbCommand.append (" minSet ").appendO (propertyValue);
break;
case 1073742112:
surfaceObjectSeen = true;
propertyName = "rad";
propertyValue = this.getPoint4f (++i);
i = eval.iToken;
sbCommand.append (" radical ").append (JU.Escape.eP4 (propertyValue));
break;
case 1073742027:
propertyName = "fixed";
propertyValue = Boolean.FALSE;
sbCommand.append (" modelBased");
break;
case 1073742028:
case 1073742135:
case 1613758488:
onlyOneModel = eval.theToken.value;
var radius;
if (eval.theTok == 1073742028) {
propertyName = "molecular";
sbCommand.append (" molecular");
radius = (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 1.4);
} else {
this.addShapeProperty (propertyList, "bsSolvent", eval.lookupIdentifierValue ("solvent"));
propertyName = (eval.theTok == 1073742135 ? "sasurface" : "solvent");
sbCommand.append (" ").appendO (eval.theToken.value);
radius = (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : this.vwr.getFloat (570425394));
}sbCommand.append (" ").appendF (radius);
propertyValue = Float.$valueOf (radius);
if (this.tokAt (i + 1) == 1073741961) {
this.addShapeProperty (propertyList, "doFullMolecular", null);
sbCommand.append (" full");
i++;
}surfaceObjectSeen = true;
break;
case 1073742033:
this.addShapeProperty (propertyList, "fileType", "Mrc");
sbCommand.append (" mrc");
continue;
case 1073742064:
case 1073742062:
this.addShapeProperty (propertyList, "fileType", "Obj");
sbCommand.append (" obj");
continue;
case 1073742034:
this.addShapeProperty (propertyList, "fileType", "Msms");
sbCommand.append (" msms");
continue;
case 1073742094:
if (surfaceObjectSeen) this.invArg ();
propertyName = "phase";
isPhased = true;
propertyValue = (this.tokAt (i + 1) == 4 ? this.stringParameter (++i) : "_orb");
sbCommand.append (" phase ").append (JU.PT.esc (propertyValue));
break;
case 1073742104:
case 1073742122:
propertyName = "resolution";
propertyValue = Float.$valueOf (this.floatParameter (++i));
sbCommand.append (" resolution ").appendO (propertyValue);
break;
case 1073742124:
propertyName = "reverseColor";
propertyValue = Boolean.TRUE;
sbCommand.append (" reversecolor");
break;
case 1073742146:
propertyName = "sigma";
propertyValue = Float.$valueOf (sigma = this.floatParameter (++i));
sbCommand.append (" sigma ").appendO (propertyValue);
break;
case 1113198597:
propertyName = "geodesic";
propertyValue = Float.$valueOf (this.floatParameter (++i));
sbCommand.append (" geosurface ").appendO (propertyValue);
surfaceObjectSeen = true;
break;
case 1073742154:
propertyName = "sphere";
propertyValue = Float.$valueOf (this.floatParameter (++i));
sbCommand.append (" sphere ").appendO (propertyValue);
surfaceObjectSeen = true;
break;
case 1073742156:
propertyName = "squareData";
propertyValue = Boolean.TRUE;
sbCommand.append (" squared");
break;
case 1073741983:
propertyName = (!surfaceObjectSeen && !planeSeen && !isMapped ? "readFile" : "mapColor");
str = this.stringParameter (++i);
if (str == null) this.invArg ();
if (isPmesh) str = JU.PT.replaceWithCharacter (str, "{,}|", ' ');
if (eval.debugHigh) JU.Logger.debug ("pmesh inline data:\n" + str);
propertyValue = (this.chk ? null : str);
this.addShapeProperty (propertyList, "fileName", "");
sbCommand.append (" INLINE ").append (JU.PT.esc (str));
surfaceObjectSeen = true;
break;
case 4:
var firstPass = (!surfaceObjectSeen && !planeSeen);
propertyName = (firstPass && !isMapped ? "readFile" : "mapColor");
var filename = this.paramAsStr (i);
if (filename.startsWith ("=") && filename.length > 1) {
var info = this.vwr.setLoadFormat (filename, '_', false);
filename = info[0];
var strCutoff = (!firstPass || !Float.isNaN (cutoff) ? null : info[1]);
if (strCutoff != null && !this.chk) {
cutoff = NaN;
try {
var sfdat = this.vwr.getFileAsString (strCutoff, false);
JU.Logger.info (sfdat);
sfdat = JU.PT.split (sfdat, "MAP_SIGMA_DENS")[1];
cutoff = JU.PT.parseFloat (sfdat);
this.showString ("using cutoff = " + cutoff);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
JU.Logger.error ("MAP_SIGMA_DENS -- could  not read " + info[1]);
} else {
throw e;
}
}
if (cutoff > 0) {
if (!Float.isNaN (sigma)) {
cutoff *= sigma;
sigma = NaN;
this.addShapeProperty (propertyList, "sigma", Float.$valueOf (sigma));
}this.addShapeProperty (propertyList, "cutoff", Float.$valueOf (cutoff));
sbCommand.append (" cutoff ").appendF (cutoff);
}}if (ptWithin == 0) {
onlyOneModel = "=xxxx";
if (modelIndex < 0) modelIndex = this.vwr.am.cmi;
bs = this.vwr.getModelUndeletedAtomsBitSet (modelIndex);
if (bs.nextSetBit (0) >= 0) {
this.getWithinDistanceVector (propertyList, 2.0, null, bs, false);
sbCommand.append (" within 2.0 ").append (JU.Escape.eBS (bs));
}}if (firstPass) defaultMesh = true;
}if (firstPass && this.vwr.getP ("_fileType").equals ("Pdb") && Float.isNaN (sigma) && Float.isNaN (cutoff)) {
this.addShapeProperty (propertyList, "sigma", Float.$valueOf (-1));
sbCommand.append (" sigma -1.0");
}if (filename.length == 0) {
if (modelIndex < 0) modelIndex = this.vwr.am.cmi;
filename = eval.getFullPathName ();
propertyValue = this.vwr.getModelAuxiliaryInfoValue (modelIndex, "jmolSurfaceInfo");
}var fileIndex = -1;
if (propertyValue == null && this.tokAt (i + 1) == 2) this.addShapeProperty (propertyList, "fileIndex", Integer.$valueOf (fileIndex = this.intParameter (++i)));
var stype = (this.tokAt (i + 1) == 4 ? this.stringParameter (++i) : null);
surfaceObjectSeen = true;
if (this.chk) {
break;
}var fullPathNameOrError;
var localName = null;
if (propertyValue == null) {
if (this.fullCommand.indexOf ("# FILE" + nFiles + "=") >= 0) {
filename = JU.PT.getQuotedAttribute (this.fullCommand, "# FILE" + nFiles);
if (this.tokAt (i + 1) == 1073741848) i += 2;
} else if (this.tokAt (i + 1) == 1073741848) {
localName = this.vwr.getFilePath (this.stringParameter (eval.iToken = (i = i + 2)), false);
fullPathNameOrError = this.vwr.getFullPathNameOrError (localName);
localName = fullPathNameOrError[0];
if (this.vwr.getPathForAllFiles () !== "") {
filename = localName;
localName = null;
} else {
this.addShapeProperty (propertyList, "localName", localName);
}}}if (!filename.startsWith ("cache://") && stype == null) {
fullPathNameOrError = this.vwr.getFullPathNameOrError (filename);
filename = fullPathNameOrError[0];
if (fullPathNameOrError[1] != null) eval.errorStr (17, filename + ":" + fullPathNameOrError[1]);
}this.showString ("reading isosurface data from " + filename);
if (stype != null) {
propertyValue = this.vwr.cacheGet (filename);
this.addShapeProperty (propertyList, "calculationType", stype);
}if (propertyValue == null) {
this.addShapeProperty (propertyList, "fileName", filename);
if (localName != null) filename = localName;
if (fileIndex >= 0) sbCommand.append (" ").appendI (fileIndex);
}sbCommand.append (" /*file*/").append (JU.PT.esc (filename));
if (stype != null) sbCommand.append (" ").append (JU.PT.esc (stype));
break;
case 4106:
propertyName = "connections";
switch (this.tokAt (++i)) {
case 10:
case 1048577:
propertyValue = [this.atomExpressionAt (i).nextSetBit (0)];
break;
default:
propertyValue = [Clazz_floatToInt (eval.floatParameterSet (i, 1, 1)[0])];
break;
}
i = eval.iToken;
break;
case 1095761923:
propertyName = "atomIndex";
propertyValue = Integer.$valueOf (this.intParameter (++i));
break;
case 1073741999:
propertyName = "link";
sbCommand.append (" link");
break;
case 1073741994:
if (iShape != 24) this.invArg ();
pt = this.getPoint3f (eval.iToken + 1, false);
i = eval.iToken;
if (pt.x <= 0 || pt.y <= 0 || pt.z <= 0) break;
pt.x = Clazz_floatToInt (pt.x);
pt.y = Clazz_floatToInt (pt.y);
pt.z = Clazz_floatToInt (pt.z);
sbCommand.append (" lattice ").append (JU.Escape.eP (pt));
if (isMapped) {
propertyName = "mapLattice";
propertyValue = pt;
} else {
lattice = pt;
}break;
default:
if (eval.theTok == 1073741824) {
propertyName = "thisID";
propertyValue = str;
}if (!eval.setMeshDisplayProperty (iShape, 0, eval.theTok)) {
if (JS.T.tokAttr (eval.theTok, 1073741824) && !idSeen) {
this.setShapeId (iShape, i, idSeen);
i = eval.iToken;
break;
}this.invArg ();
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = this.slen - 1;
break;
}
idSeen = (eval.theTok != 12291);
if (isWild && surfaceObjectSeen) this.invArg ();
if (propertyName != null) this.addShapeProperty (propertyList, propertyName, propertyValue);
}
if (!this.chk) {
if ((isCavity || haveRadius) && !surfaceObjectSeen) {
surfaceObjectSeen = true;
this.addShapeProperty (propertyList, "bsSolvent", (haveRadius ?  new JU.BS () : eval.lookupIdentifierValue ("solvent")));
this.addShapeProperty (propertyList, "sasurface", Float.$valueOf (0));
}if (planeSeen && !surfaceObjectSeen && !isMapped) {
this.addShapeProperty (propertyList, "nomap", Float.$valueOf (0));
surfaceObjectSeen = true;
}if (thisSetNumber >= -1) this.addShapeProperty (propertyList, "getSurfaceSets", Integer.$valueOf (thisSetNumber - 1));
if (discreteColixes != null) {
this.addShapeProperty (propertyList, "colorDiscrete", discreteColixes);
} else if ("sets".equals (colorScheme)) {
this.addShapeProperty (propertyList, "setColorScheme", null);
} else if (colorScheme != null) {
var ce = this.vwr.cm.getColorEncoder (colorScheme);
if (ce != null) {
ce.isTranslucent = isColorSchemeTranslucent;
ce.hi = 3.4028235E38;
this.addShapeProperty (propertyList, "remapColor", ce);
}}if (surfaceObjectSeen && !isLcaoCartoon && sbCommand.indexOf (";") != 0) {
propertyList.add (0, ["newObject", null]);
var needSelect = (bsSelect == null);
if (needSelect) bsSelect = JU.BSUtil.copy (this.vwr.bsA ());
if (modelIndex < 0) modelIndex = this.vwr.am.cmi;
bsSelect.and (this.vwr.getModelUndeletedAtomsBitSet (modelIndex));
if (onlyOneModel != null) {
var bsModels = this.vwr.ms.getModelBS (bsSelect, false);
if (bsModels.cardinality () > 1) eval.errorStr (30, "ISOSURFACE " + onlyOneModel);
if (needSelect) {
propertyList.add (0, ["select", bsSelect]);
if (sbCommand.indexOf ("; isosurface map") == 0) {
sbCommand =  new JU.SB ().append ("; isosurface map select ").append (JU.Escape.eBS (bsSelect)).append (sbCommand.substring (16));
}}}}if (haveIntersection && !haveSlab) {
if (!surfaceObjectSeen) this.addShapeProperty (propertyList, "sasurface", Float.$valueOf (0));
if (!isMapped) {
this.addShapeProperty (propertyList, "map", Boolean.TRUE);
this.addShapeProperty (propertyList, "select", bs);
this.addShapeProperty (propertyList, "sasurface", Float.$valueOf (0));
}this.addShapeProperty (propertyList, "slab", this.getCapSlabObject (-100, false));
}var timeMsg = (surfaceObjectSeen && this.vwr.getBoolean (603979934));
if (timeMsg) JU.Logger.startTimer ("isosurface");
this.setShapeProperty (iShape, "setProperties", propertyList);
if (timeMsg) this.showString (JU.Logger.getTimerMsg ("isosurface", 0));
if (defaultMesh) {
this.setShapeProperty (iShape, "token", Integer.$valueOf (1073742018));
this.setShapeProperty (iShape, "token", Integer.$valueOf (1073742046));
isFrontOnly = true;
sbCommand.append (" mesh nofill frontOnly");
}}if (lattice != null) this.setShapeProperty (iShape, "lattice", lattice);
if (symops != null) this.setShapeProperty (iShape, "symops", symops);
if (isFrontOnly) this.setShapeProperty (iShape, "token", Integer.$valueOf (1073741960));
if (iptDisplayProperty > 0) {
if (!eval.setMeshDisplayProperty (iShape, iptDisplayProperty, 0)) this.invArg ();
}if (this.chk) return false;
var area = null;
var volume = null;
if (doCalcArea) {
area = this.getShapeProperty (iShape, "area");
if (Clazz_instanceOf (area, Float)) this.vwr.setFloatProperty ("isosurfaceArea", (area).floatValue ());
 else this.vwr.g.setUserVariable ("isosurfaceArea", JS.SV.getVariableAD (area));
}if (doCalcVolume) {
volume = (doCalcVolume ? this.getShapeProperty (iShape, "volume") : null);
if (Clazz_instanceOf (volume, Float)) this.vwr.setFloatProperty ("isosurfaceVolume", (volume).floatValue ());
 else this.vwr.g.setUserVariable ("isosurfaceVolume", JS.SV.getVariableAD (volume));
}if (!isLcaoCartoon) {
var s = null;
if (isMapped && !surfaceObjectSeen) {
this.setShapeProperty (iShape, "finalize", sbCommand.toString ());
} else if (surfaceObjectSeen) {
cmd = sbCommand.toString ();
this.setShapeProperty (iShape, "finalize", (cmd.indexOf ("; isosurface map") == 0 ? "" : " select " + JU.Escape.eBS (bsSelect) + " ") + cmd);
s = this.getShapeProperty (iShape, "ID");
if (s != null && !eval.tQuiet) {
cutoff = (this.getShapeProperty (iShape, "cutoff")).floatValue ();
if (Float.isNaN (cutoff) && !Float.isNaN (sigma)) {
JU.Logger.error ("sigma not supported");
}s += " created";
if (isIsosurface) s += " with cutoff=" + cutoff;
var minMax = this.getShapeProperty (iShape, "minMaxInfo");
if (minMax[0] != 3.4028235E38) s += " min=" + minMax[0] + " max=" + minMax[1];
s += "; " + JV.JC.shapeClassBases[iShape].toLowerCase () + " count: " + this.getShapeProperty (iShape, "count");
s += eval.getIsosurfaceDataRange (iShape, "\n");
}}var sarea;
var svol;
if (doCalcArea || doCalcVolume) {
sarea = (doCalcArea ? "isosurfaceArea = " + (Clazz_instanceOf (area, Float) ? "" + area : JU.Escape.eAD (area)) : null);
svol = (doCalcVolume ? "isosurfaceVolume = " + (Clazz_instanceOf (volume, Float) ? "" + volume : JU.Escape.eAD (volume)) : null);
if (s == null) {
if (doCalcArea) this.showString (sarea);
if (doCalcVolume) this.showString (svol);
} else {
if (doCalcArea) s += "\n" + sarea;
if (doCalcVolume) s += "\n" + svol;
}}if (s != null) this.showString (s);
}if (translucency != null) this.setShapeProperty (iShape, "translucency", translucency);
this.setShapeProperty (iShape, "clear", null);
if (toCache) this.setShapeProperty (iShape, "cache", null);
if (iShape != 26) this.listIsosurface (iShape);
return true;
}, "~N");
Clazz_defineMethod (c$, "lcaoCartoon", 
 function () {
var eval = this.e;
this.sm.loadShape (26);
if (this.tokAt (1) == 1073742001 && this.listIsosurface (26)) return false;
this.setShapeProperty (26, "init", this.fullCommand);
if (this.slen == 1) {
this.setShapeProperty (26, "lcaoID", null);
return false;
}var idSeen = false;
var translucency = null;
for (var i = 1; i < this.slen; i++) {
var propertyName = null;
var propertyValue = null;
switch (this.getToken (i).tok) {
case 1074790451:
case 554176565:
propertyName = eval.theToken.value;
if (this.tokAt (i + 1) == 1048588) eval.iToken = i + 1;
propertyValue = this.getCapSlabObject (i, true);
i = eval.iToken;
break;
case 12289:
this.isosurface (26);
return false;
case 528432:
var degx = 0;
var degy = 0;
var degz = 0;
switch (this.getToken (++i).tok) {
case 1112541205:
degx = this.floatParameter (++i) * 0.017453292;
break;
case 1112541206:
degy = this.floatParameter (++i) * 0.017453292;
break;
case 1112541207:
degz = this.floatParameter (++i) * 0.017453292;
break;
default:
this.invArg ();
}
propertyName = "rotationAxis";
propertyValue = JU.V3.new3 (degx, degy, degz);
break;
case 1048589:
case 1610625028:
case 3145768:
propertyName = "on";
break;
case 1048588:
case 12294:
case 3145770:
propertyName = "off";
break;
case 12291:
propertyName = "delete";
break;
case 10:
case 1048577:
propertyName = "select";
propertyValue = this.atomExpressionAt (i);
i = eval.iToken;
break;
case 1766856708:
translucency = this.setColorOptions (null, i + 1, 26, -2);
if (translucency != null) this.setShapeProperty (26, "settranslucency", translucency);
i = eval.iToken;
idSeen = true;
continue;
case 603979967:
case 1073742074:
eval.setMeshDisplayProperty (26, i, eval.theTok);
i = eval.iToken;
idSeen = true;
continue;
case 1113200651:
case 4:
propertyValue = this.paramAsStr (i).toLowerCase ();
if (propertyValue.equals ("spacefill")) propertyValue = "cpk";
propertyName = "create";
if (eval.optParameterAsString (i + 1).equalsIgnoreCase ("molecular")) {
i++;
propertyName = "molecular";
}break;
case 135280132:
if (this.tokAt (i + 1) == 10 || this.tokAt (i + 1) == 1048577) {
propertyName = "select";
propertyValue = this.atomExpressionAt (i + 1);
i = eval.iToken;
} else {
propertyName = "selectType";
propertyValue = this.paramAsStr (++i);
if (propertyValue.equals ("spacefill")) propertyValue = "cpk";
}break;
case 1073742138:
propertyName = "scale";
propertyValue = Float.$valueOf (this.floatParameter (++i));
break;
case 1073742004:
case 1073742006:
propertyName = "lonePair";
break;
case 1073742112:
case 1073742111:
propertyName = "radical";
break;
case 1073742028:
propertyName = "molecular";
break;
case 1073741904:
propertyValue = this.paramAsStr (++i);
propertyName = "create";
if (eval.optParameterAsString (i + 1).equalsIgnoreCase ("molecular")) {
i++;
propertyName = "molecular";
}break;
case 1074790550:
propertyValue = eval.setShapeNameParameter (++i);
i = eval.iToken;
if (idSeen) this.invArg ();
propertyName = "lcaoID";
break;
default:
if (eval.theTok == 269484209 || JS.T.tokAttr (eval.theTok, 1073741824)) {
if (eval.theTok != 269484209) propertyValue = this.paramAsStr (i);
if (idSeen) this.invArg ();
propertyName = "lcaoID";
break;
}break;
}
if (eval.theTok != 12291) idSeen = true;
if (propertyName == null) this.invArg ();
this.setShapeProperty (26, propertyName, propertyValue);
}
this.setShapeProperty (26, "clear", null);
return true;
});
Clazz_defineMethod (c$, "mapProperty", 
 function () {
var bsFrom;
var bsTo;
var property1;
var property2;
var mapKey;
var tokProp1 = 0;
var tokProp2 = 0;
var tokKey = 0;
while (true) {
if (this.tokAt (1) == 1114638363) {
bsFrom = this.vwr.bsA ();
bsTo = this.atomExpressionAt (2);
property1 = property2 = "selected";
} else {
bsFrom = this.atomExpressionAt (1);
if (this.tokAt (++this.e.iToken) != 1048583 || !JS.T.tokAttr (tokProp1 = this.tokAt (++this.e.iToken), 1078984704)) break;
property1 = this.paramAsStr (this.e.iToken);
bsTo = this.atomExpressionAt (++this.e.iToken);
if (this.tokAt (++this.e.iToken) != 1048583 || !JS.T.tokAttr (tokProp2 = this.tokAt (++this.e.iToken), 2048)) break;
property2 = this.paramAsStr (this.e.iToken);
}if (JS.T.tokAttr (tokKey = this.tokAt (this.e.iToken + 1), 1078984704)) mapKey = this.paramAsStr (++this.e.iToken);
 else mapKey = JS.T.nameOf (tokKey = 1095763969);
this.e.checkLast (this.e.iToken);
if (this.chk) return;
var bsOut = null;
this.showString ("mapping " + property1.toUpperCase () + " for " + bsFrom.cardinality () + " atoms to " + property2.toUpperCase () + " for " + bsTo.cardinality () + " atoms using " + mapKey.toUpperCase ());
if (JS.T.tokAttrOr (tokProp1, 1095761920, 1112539136) && JS.T.tokAttrOr (tokProp2, 1095761920, 1112539136) && JS.T.tokAttrOr (tokKey, 1095761920, 1112539136)) {
var data1 = this.e.getBitsetPropertyFloat (bsFrom, tokProp1 | 224, NaN, NaN);
var data2 = this.e.getBitsetPropertyFloat (bsFrom, tokKey | 224, NaN, NaN);
var data3 = this.e.getBitsetPropertyFloat (bsTo, tokKey | 224, NaN, NaN);
var isProperty = (tokProp2 == 1716520985);
var dataOut =  Clazz_newFloatArray (isProperty ? this.vwr.getAtomCount () : data3.length, 0);
bsOut =  new JU.BS ();
if (data1.length == data2.length) {
var ht =  new java.util.Hashtable ();
for (var i = 0; i < data1.length; i++) {
ht.put (Float.$valueOf (data2[i]), Float.$valueOf (data1[i]));
}
var pt = -1;
var nOut = 0;
for (var i = 0; i < data3.length; i++) {
pt = bsTo.nextSetBit (pt + 1);
var F = ht.get (Float.$valueOf (data3[i]));
if (F == null) continue;
bsOut.set (pt);
dataOut[(isProperty ? pt : nOut)] = F.floatValue ();
nOut++;
}
if (isProperty) this.vwr.setData (property2, [property2, dataOut, bsOut, Integer.$valueOf (1), Boolean.TRUE], this.vwr.getAtomCount (), 0, 0, 2147483647, 0);
 else this.vwr.setAtomProperty (bsOut, tokProp2, 0, 0, null, dataOut, null);
}}if (bsOut == null) {
var format = "{" + mapKey + "=%[" + mapKey + "]}." + property2 + " = %[" + property1 + "]";
var data = this.getBitsetIdent (bsFrom, format, null, false, 2147483647, false);
var sb =  new JU.SB ();
for (var i = 0; i < data.length; i++) if (data[i].indexOf ("null") < 0) sb.append (data[i]).appendC ('\n');

if (JU.Logger.debugging) JU.Logger.debug (sb.toString ());
var bsSubset = JU.BSUtil.copy (this.vwr.getSelectionSubset ());
this.vwr.setSelectionSubset (bsTo);
try {
this.e.runScript (sb.toString ());
} catch (e$$) {
if (Clazz_exceptionOf (e$$, Exception)) {
var ex = e$$;
{
this.vwr.setSelectionSubset (bsSubset);
this.e.errorStr (-1, "Error: " + ex.getMessage ());
}
} else if (Clazz_exceptionOf (e$$, Error)) {
var er = e$$;
{
this.vwr.setSelectionSubset (bsSubset);
this.e.errorStr (-1, "Error: " + er.toString ());
}
} else {
throw e$$;
}
}
this.vwr.setSelectionSubset (bsSubset);
}this.showString ("DONE");
return;
}
this.invArg ();
});
Clazz_defineMethod (c$, "minimize", 
 function () {
var bsSelected = null;
var steps = 2147483647;
var crit = 0;
var addHydrogen = false;
var isSilent = false;
var bsFixed = null;
var isOnly = false;
var minimizer = this.vwr.getMinimizer (false);
for (var i = 1; i < this.slen; i++) switch (this.getToken (i).tok) {
case 1073741828:
addHydrogen = true;
continue;
case 1073741874:
case 1073742162:
this.checkLength (2);
if (this.chk || minimizer == null) return;
minimizer.setProperty (this.paramAsStr (i), null);
return;
case 1073741882:
this.checkLength (2);
if (this.chk || minimizer == null) return;
minimizer.setProperty ("clear", null);
return;
case 1073741894:
if (i != 1) this.invArg ();
var n = 0;
var targetValue = 0;
var aList =  Clazz_newIntArray (5, 0);
if (this.tokAt (++i) == 1073741882) {
this.checkLength (3);
} else {
while (n < 4 && !this.isFloatParameter (i)) {
aList[++n] = this.atomExpressionAt (i).nextSetBit (0);
i = this.e.iToken + 1;
}
aList[0] = n;
if (n == 1) this.invArg ();
targetValue = this.floatParameter (this.e.checkLast (i));
}if (!this.chk) this.vwr.getMinimizer (true).setProperty ("constraint", [aList,  Clazz_newIntArray (n, 0), Float.$valueOf (targetValue)]);
return;
case 1073741905:
crit = this.floatParameter (++i);
continue;
case 1073741934:
steps = 0;
continue;
case 1060869:
if (i != 1) this.invArg ();
bsFixed = this.atomExpressionAt (++i);
if (bsFixed.nextSetBit (0) < 0) bsFixed = null;
i = this.e.iToken;
if (!this.chk) this.vwr.getMinimizer (true).setProperty ("fixed", bsFixed);
if (i + 1 == this.slen) return;
continue;
case 10:
case 1048577:
isOnly = true;
case 135280132:
if (this.e.theTok == 135280132) i++;
bsSelected = this.atomExpressionAt (i);
i = this.e.iToken;
if (this.tokAt (i + 1) == 1073742072) {
i++;
isOnly = true;
}continue;
case 1073742148:
isSilent = true;
break;
case 266298:
steps = this.intParameter (++i);
continue;
default:
this.invArg ();
break;
}

if (!this.chk) this.vwr.minimize (steps, crit, bsSelected, bsFixed, 0, addHydrogen, isOnly, isSilent, false);
});
Clazz_defineMethod (c$, "mo", 
 function (isInitOnly) {
var eval = this.e;
var offset = 2147483647;
var isNegOffset = false;
var bsModels = this.vwr.getVisibleFramesBitSet ();
var propertyList =  new JU.Lst ();
var i0 = 1;
if (this.tokAt (1) == 1095766030 || this.tokAt (1) == 4115) {
i0 = eval.modelNumberParameter (2);
if (i0 < 0) this.invArg ();
bsModels.clearAll ();
bsModels.set (i0);
i0 = 3;
}for (var iModel = bsModels.nextSetBit (0); iModel >= 0; iModel = bsModels.nextSetBit (iModel + 1)) {
this.sm.loadShape (27);
var i = i0;
if (this.tokAt (i) == 1073742001 && this.listIsosurface (27)) return true;
this.setShapeProperty (27, "init", Integer.$valueOf (iModel));
var title = null;
var moNumber = (this.getShapeProperty (27, "moNumber")).intValue ();
var linearCombination = this.getShapeProperty (27, "moLinearCombination");
if (isInitOnly) return true;
if (moNumber == 0) moNumber = 2147483647;
var propertyName = null;
var propertyValue = null;
switch (this.getToken (i).tok) {
case 1074790451:
case 554176565:
propertyName = eval.theToken.value;
propertyValue = this.getCapSlabObject (i, false);
i = eval.iToken;
break;
case 1073741914:
propertyName = "squareLinear";
propertyValue = Boolean.TRUE;
linearCombination = [1];
offset = moNumber = 0;
break;
case 2:
moNumber = this.intParameter (i);
linearCombination = this.moCombo (propertyList);
if (linearCombination == null && moNumber < 0) linearCombination = [-100, -moNumber];
break;
case 269484192:
switch (this.tokAt (++i)) {
case 1073741973:
case 1073742008:
break;
default:
this.invArg ();
}
isNegOffset = true;
case 1073741973:
case 1073742008:
if ((offset = this.moOffset (i)) == 2147483647) this.invArg ();
moNumber = 0;
linearCombination = this.moCombo (propertyList);
break;
case 1073742037:
moNumber = 1073742037;
linearCombination = this.moCombo (propertyList);
break;
case 1073742108:
moNumber = 1073742108;
linearCombination = this.moCombo (propertyList);
break;
case 1766856708:
this.setColorOptions (null, i + 1, 27, 2);
break;
case 135266319:
propertyName = "plane";
propertyValue = eval.planeParameter (i);
break;
case 135266320:
this.addShapeProperty (propertyList, "randomSeed", this.tokAt (i + 2) == 2 ? Integer.$valueOf (this.intParameter (i + 2)) : null);
propertyName = "monteCarloCount";
propertyValue = Integer.$valueOf (this.intParameter (i + 1));
break;
case 1073742138:
propertyName = "scale";
propertyValue = Float.$valueOf (this.floatParameter (i + 1));
break;
case 1073741910:
if (this.tokAt (i + 1) == 269484193) {
propertyName = "cutoffPositive";
propertyValue = Float.$valueOf (this.floatParameter (i + 2));
} else {
propertyName = "cutoff";
propertyValue = Float.$valueOf (this.floatParameter (i + 1));
}break;
case 536870916:
propertyName = "debug";
break;
case 1073742054:
propertyName = "plane";
break;
case 1073742104:
case 1073742122:
propertyName = "resolution";
propertyValue = Float.$valueOf (this.floatParameter (i + 1));
break;
case 1073742156:
propertyName = "squareData";
propertyValue = Boolean.TRUE;
break;
case 1073742168:
if (i + 1 < this.slen && this.tokAt (i + 1) == 4) {
propertyName = "titleFormat";
propertyValue = this.paramAsStr (i + 1);
}break;
case 1073741824:
this.invArg ();
break;
default:
if (eval.isArrayParameter (i)) {
linearCombination = eval.floatParameterSet (i, 1, 2147483647);
if (this.tokAt (eval.iToken + 1) == 1073742156) {
this.addShapeProperty (propertyList, "squareLinear", Boolean.TRUE);
eval.iToken++;
}break;
}var ipt = eval.iToken;
if (!eval.setMeshDisplayProperty (27, 0, eval.theTok)) this.invArg ();
this.setShapeProperty (27, "setProperties", propertyList);
eval.setMeshDisplayProperty (27, ipt, this.tokAt (ipt));
return true;
}
if (propertyName != null) this.addShapeProperty (propertyList, propertyName, propertyValue);
if (moNumber != 2147483647 || linearCombination != null) {
if (this.tokAt (eval.iToken + 1) == 4) title = this.paramAsStr (++eval.iToken);
eval.setCursorWait (true);
this.setMoData (propertyList, moNumber, linearCombination, offset, isNegOffset, iModel, title);
this.addShapeProperty (propertyList, "finalize", null);
}if (propertyList.size () > 0) this.setShapeProperty (27, "setProperties", propertyList);
propertyList.clear ();
}
return true;
}, "~B");
Clazz_defineMethod (c$, "modulation", 
 function () {
var qtOffset = null;
var mod = true;
var isQ = false;
var bs = null;
switch (this.getToken (1).tok) {
case 1048588:
mod = false;
case 0:
case 1048589:
break;
case 10:
case 1048577:
bs = this.atomExpressionAt (1);
switch (this.tokAt (this.e.iToken + 1)) {
case 0:
break;
case 1048588:
mod = false;
case 1048589:
this.e.iToken++;
break;
}
this.e.checkLast (this.e.iToken);
break;
case 1048586:
case 8:
qtOffset = this.e.getPoint3f (1, false);
isQ = (this.tokAt (this.e.iToken + 1) == 1048589);
break;
case 3:
var t1 = this.floatParameter (1);
qtOffset = JU.P3.new3 (t1, t1, t1);
break;
case 2:
var t = this.intParameter (1);
qtOffset = JU.P3.new3 (t, t, t);
isQ = true;
break;
case 1073742138:
var scale = this.floatParameter (2);
if (!this.chk) this.vwr.setFloatProperty ("modulationScale", scale);
return;
default:
this.invArg ();
}
if (!this.chk) {
this.vwr.setVibrationOff ();
this.vwr.setModulation (bs, mod, qtOffset, isQ);
}});
Clazz_defineMethod (c$, "navigate", 
function () {
var eval = this.e;
if (this.slen == 1) {
eval.setBooleanProperty ("navigationMode", true);
return;
}var rotAxis = JU.V3.new3 (0, 1, 0);
var list =  new JU.Lst ();
var pt;
if (this.slen == 2) {
switch (this.getToken (1).tok) {
case 1048589:
case 1048588:
if (this.chk) return;
eval.setObjectMad (33, "axes", 1);
this.setShapeProperty (33, "position", JU.P3.new3 (50, 50, 3.4028235E38));
eval.setBooleanProperty ("navigationMode", true);
this.vwr.tm.setNavOn (eval.theTok == 1048589);
return;
case 1073742162:
if (!this.chk) this.vwr.tm.setNavXYZ (0, 0, 0);
return;
case 8:
case 1113200654:
break;
default:
this.invArg ();
}
}if (!this.chk && !this.vwr.getBoolean (603979887)) eval.setBooleanProperty ("navigationMode", true);
for (var i = 1; i < this.slen; i++) {
var timeSec = (this.isFloatParameter (i) ? this.floatParameter (i++) : 2);
if (timeSec < 0) this.invArg ();
if (!this.chk && timeSec > 0) eval.refresh (false);
switch (this.getToken (i).tok) {
case 8:
case 1048586:
pt = this.getPoint3f (i, true);
eval.iToken++;
if (eval.iToken != this.slen) this.invArg ();
if (!this.chk) this.vwr.tm.setNavXYZ (pt.x, pt.y, pt.z);
return;
case 554176526:
var depth = this.floatParameter (++i);
if (!this.chk) list.addLast ([Integer.$valueOf (554176526), Float.$valueOf (timeSec), Float.$valueOf (depth)]);
continue;
case 12289:
pt = this.centerParameter (++i);
i = eval.iToken;
if (!this.chk) list.addLast ([Integer.$valueOf (135266320), Float.$valueOf (timeSec), pt]);
continue;
case 528432:
switch (this.getToken (++i).tok) {
case 1112541205:
rotAxis.set (1, 0, 0);
i++;
break;
case 1112541206:
rotAxis.set (0, 1, 0);
i++;
break;
case 1112541207:
rotAxis.set (0, 0, 1);
i++;
break;
case 8:
case 1048586:
rotAxis.setT (this.getPoint3f (i, true));
i = eval.iToken + 1;
break;
case 1073741824:
this.invArg ();
break;
}
var degrees = this.floatParameter (i);
if (!this.chk) list.addLast ([Integer.$valueOf (528432), Float.$valueOf (timeSec), rotAxis, Float.$valueOf (degrees)]);
continue;
case 4160:
var x = NaN;
var y = NaN;
if (this.isFloatParameter (++i)) {
x = this.floatParameter (i);
y = this.floatParameter (++i);
} else {
switch (this.tokAt (i)) {
case 1112541205:
x = this.floatParameter (++i);
break;
case 1112541206:
y = this.floatParameter (++i);
break;
default:
pt = this.centerParameter (i);
i = eval.iToken;
if (!this.chk) list.addLast ([Integer.$valueOf (4160), Float.$valueOf (timeSec), pt]);
continue;
}
}if (!this.chk) list.addLast ([Integer.$valueOf (269484210), Float.$valueOf (timeSec), Float.$valueOf (x), Float.$valueOf (y)]);
continue;
case 269484208:
continue;
case 1113200654:
var pathGuide;
var vp =  new JU.Lst ();
var bs;
if (this.tokAt (i + 1) == 10 || this.tokAt (i + 1) == 1048577) {
bs = this.atomExpressionAt (++i);
i = eval.iToken;
} else {
bs = this.vwr.bsA ();
}if (this.chk) return;
this.vwr.getPolymerPointsAndVectors (bs, vp);
var n;
if ((n = vp.size ()) > 0) {
pathGuide =  new Array (n);
for (var j = 0; j < n; j++) {
pathGuide[j] = vp.get (j);
}
list.addLast ([Integer.$valueOf (1113200654), Float.$valueOf (timeSec), pathGuide]);
continue;
}break;
case 1073742084:
var path;
var theta = null;
if (this.getToken (i + 1).tok == 1048582) {
i++;
var pathID = eval.objectNameParameter (++i);
if (this.chk) return;
this.setShapeProperty (22, "thisID", pathID);
path = this.getShapeProperty (22, "vertices");
eval.refresh (false);
if (path == null) this.invArg ();
var indexStart = Clazz_floatToInt (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 0);
var indexEnd = Clazz_floatToInt (this.isFloatParameter (i + 1) ? this.floatParameter (++i) : 2147483647);
list.addLast ([Integer.$valueOf (1073742084), Float.$valueOf (timeSec), path, theta, [indexStart, indexEnd]]);
continue;
}var v =  new JU.Lst ();
while (eval.isCenterParameter (i + 1)) {
v.addLast (this.centerParameter (++i));
i = eval.iToken;
}
if (v.size () > 0) {
path = v.toArray ( new Array (v.size ()));
if (!this.chk) list.addLast ([Integer.$valueOf (1073742084), Float.$valueOf (timeSec), path, theta, [0, 2147483647]]);
continue;
}default:
this.invArg ();
}
}
if (!this.chk && !this.vwr.isJmolDataFrame ()) this.vwr.tm.navigateList (eval, list);
});
Clazz_overrideMethod (c$, "plot", 
function (args) {
this.st = this.e.st;
this.chk = this.e.chk;
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) this.e.errorStr (30, "plot");
modelIndex = this.vwr.ms.getJmolDataSourceFrame (modelIndex);
var pt = args.length - 1;
var isReturnOnly = (args !== this.st);
var statementSave = this.st;
if (isReturnOnly) this.e.st = this.st = args;
var tokCmd = (isReturnOnly ? 135270926 : args[0].tok);
var pt0 = (isReturnOnly || tokCmd == 135270418 || tokCmd == 1052714 ? 0 : 1);
var filename = null;
var makeNewFrame = true;
var isDraw = false;
switch (tokCmd) {
case 4133:
case 135270418:
case 1052714:
break;
case 135176:
makeNewFrame = false;
isDraw = true;
break;
case 135270926:
makeNewFrame = false;
break;
case 135270422:
makeNewFrame = false;
if (JS.CmdExt.tokAtArray (pt, args) == 4) {
filename = this.stringParameter (pt--);
} else if (JS.CmdExt.tokAtArray (pt - 1, args) == 1048583) {
filename = this.paramAsStr (pt - 2) + "." + this.paramAsStr (pt);
pt -= 3;
} else {
this.e.st = this.st = statementSave;
this.e.iToken = this.st.length;
this.error (13);
}break;
}
var qFrame = "";
var parameters = null;
var stateScript = "";
var isQuaternion = false;
var isDerivative = false;
var isSecondDerivative = false;
var isRamachandranRelative = false;
var propertyX = 0;
var propertyY = 0;
var propertyZ = 0;
var bs = JU.BSUtil.copy (this.vwr.bsA ());
var preSelected = "; select " + JU.Escape.eBS (bs) + ";\n ";
var type = this.e.optParameterAsString (pt).toLowerCase ();
var minXYZ = null;
var maxXYZ = null;
var tok = JS.CmdExt.tokAtArray (pt0, args);
if (tok == 4) tok = JS.T.getTokFromName (args[pt0].value);
switch (tok) {
default:
this.e.iToken = 1;
this.invArg ();
break;
case 135270408:
this.e.iToken = 1;
type = "data";
preSelected = "";
break;
case 1716520985:
this.e.iToken = pt0 + 1;
if (!JS.T.tokAttr (propertyX = this.tokAt (this.e.iToken++), 1078984704) || !JS.T.tokAttr (propertyY = this.tokAt (this.e.iToken++), 1078984704)) this.invArg ();
if (JS.T.tokAttr (propertyZ = this.tokAt (this.e.iToken), 1078984704)) this.e.iToken++;
 else propertyZ = 0;
if (this.tokAt (this.e.iToken) == 32) {
minXYZ = this.getPoint3f (++this.e.iToken, false);
this.e.iToken++;
}if (this.tokAt (this.e.iToken) == 64) {
maxXYZ = this.getPoint3f (++this.e.iToken, false);
this.e.iToken++;
}type = "property " + JS.T.nameOf (propertyX) + " " + JS.T.nameOf (propertyY) + (propertyZ == 0 ? "" : " " + JS.T.nameOf (propertyZ));
if (bs.nextSetBit (0) < 0) bs = this.vwr.getModelUndeletedAtomsBitSet (modelIndex);
stateScript = "select " + JU.Escape.eBS (bs) + ";\n ";
break;
case 1052714:
if (type.equalsIgnoreCase ("draw")) {
isDraw = true;
type = this.e.optParameterAsString (--pt).toLowerCase ();
}isRamachandranRelative = (pt > pt0 && type.startsWith ("r"));
type = "ramachandran" + (isRamachandranRelative ? " r" : "") + (tokCmd == 135176 ? " draw" : "");
break;
case 135270418:
case 137363467:
qFrame = " \"" + this.vwr.getQuaternionFrame () + "\"";
stateScript = "set quaternionFrame" + qFrame + ";\n  ";
isQuaternion = true;
if (type.equalsIgnoreCase ("draw")) {
isDraw = true;
type = this.e.optParameterAsString (--pt).toLowerCase ();
}isDerivative = (type.startsWith ("deriv") || type.startsWith ("diff"));
isSecondDerivative = (isDerivative && type.indexOf ("2") > 0);
if (isDerivative) pt--;
if (type.equalsIgnoreCase ("helix") || type.equalsIgnoreCase ("axis")) {
isDraw = true;
isDerivative = true;
pt = -1;
}type = ((pt <= pt0 ? "" : this.e.optParameterAsString (pt)) + "w").substring (0, 1);
if (type.equals ("a") || type.equals ("r")) isDerivative = true;
if (!JU.PT.isOneOf (type, ";w;x;y;z;r;a;")) this.e.evalError ("QUATERNION [w,x,y,z,a,r] [difference][2]", null);
type = "quaternion " + type + (isDerivative ? " difference" : "") + (isSecondDerivative ? "2" : "") + (isDraw ? " draw" : "");
break;
}
this.st = statementSave;
if (this.chk) return "";
if (makeNewFrame) {
stateScript += "plot " + type;
var ptDataFrame = this.vwr.ms.getJmolDataFrameIndex (modelIndex, stateScript);
if (ptDataFrame > 0 && tokCmd != 135270422 && tokCmd != 135270926) {
this.vwr.setCurrentModelIndexClear (ptDataFrame, true);
return "";
}}var dataX = null;
var dataY = null;
var dataZ = null;
var factors = JU.P3.new3 (1, 1, 1);
if (tok == 1716520985) {
dataX = this.e.getBitsetPropertyFloat (bs, propertyX | 224, (minXYZ == null ? NaN : minXYZ.x), (maxXYZ == null ? NaN : maxXYZ.x));
dataY = this.e.getBitsetPropertyFloat (bs, propertyY | 224, (minXYZ == null ? NaN : minXYZ.y), (maxXYZ == null ? NaN : maxXYZ.y));
if (propertyZ != 0) dataZ = this.e.getBitsetPropertyFloat (bs, propertyZ | 224, (minXYZ == null ? NaN : minXYZ.z), (maxXYZ == null ? NaN : maxXYZ.z));
if (minXYZ == null) minXYZ = JU.P3.new3 (this.getPlotMinMax (dataX, false, propertyX), this.getPlotMinMax (dataY, false, propertyY), this.getPlotMinMax (dataZ, false, propertyZ));
if (maxXYZ == null) maxXYZ = JU.P3.new3 (this.getPlotMinMax (dataX, true, propertyX), this.getPlotMinMax (dataY, true, propertyY), this.getPlotMinMax (dataZ, true, propertyZ));
JU.Logger.info ("plot min/max: " + minXYZ + " " + maxXYZ);
var center =  new JU.P3 ();
center.ave (maxXYZ, minXYZ);
factors.sub2 (maxXYZ, minXYZ);
factors.set (factors.x / 200, factors.y / 200, factors.z / 200);
if (JS.T.tokAttr (propertyX, 1095761920)) {
factors.x = 1;
center.x = 0;
} else if (factors.x > 0.1 && factors.x <= 10) {
factors.x = 1;
}if (JS.T.tokAttr (propertyY, 1095761920)) {
factors.y = 1;
center.y = 0;
} else if (factors.y > 0.1 && factors.y <= 10) {
factors.y = 1;
}if (JS.T.tokAttr (propertyZ, 1095761920)) {
factors.z = 1;
center.z = 0;
} else if (factors.z > 0.1 && factors.z <= 10) {
factors.z = 1;
}if (propertyZ == 0) center.z = minXYZ.z = maxXYZ.z = factors.z = 0;
for (var i = 0; i < dataX.length; i++) dataX[i] = (dataX[i] - center.x) / factors.x;

for (var i = 0; i < dataY.length; i++) dataY[i] = (dataY[i] - center.y) / factors.y;

if (propertyZ != 0) for (var i = 0; i < dataZ.length; i++) dataZ[i] = (dataZ[i] - center.z) / factors.z;

parameters = [bs, dataX, dataY, dataZ, minXYZ, maxXYZ, factors, center];
}if (tokCmd == 135270422) return this.vwr.writeFileData (filename, "PLOT_" + type, modelIndex, parameters);
var data = (type.equals ("data") ? "1 0 H 0 0 0 # Jmol PDB-encoded data" : this.vwr.getPdbData (modelIndex, type, null, parameters, null, true));
if (tokCmd == 135270926) return data;
if (JU.Logger.debugging) JU.Logger.debug (data);
if (tokCmd == 135176) {
this.e.runScript (data);
return "";
}var savedFileInfo = this.vwr.getFileInfo ();
var oldAppendNew = this.vwr.getBoolean (603979792);
this.vwr.g.appendNew = true;
var isOK = (data != null && this.vwr.openStringInlineParamsAppend (data, null, true) == null);
this.vwr.g.appendNew = oldAppendNew;
this.vwr.setFileInfo (savedFileInfo);
if (!isOK) return "";
var modelCount = this.vwr.getModelCount ();
this.vwr.ms.setJmolDataFrame (stateScript, modelIndex, modelCount - 1);
if (tok != 1716520985) stateScript += ";\n" + preSelected;
var ss = this.vwr.addStateScript (stateScript, true, false);
var radius = 150;
var script;
switch (tok) {
default:
script = "frame 0.0; frame last; reset;select visible;wireframe only;";
radius = 10;
break;
case 1716520985:
this.vwr.setFrameTitle (modelCount - 1, type + " plot for model " + this.vwr.getModelNumberDotted (modelIndex));
var f = 3;
script = "frame 0.0; frame last; reset;select visible; spacefill " + f + "; wireframe 0;" + "draw plotAxisX" + modelCount + " {100 -100 -100} {-100 -100 -100} \"" + JS.T.nameOf (propertyX) + "\";" + "draw plotAxisY" + modelCount + " {-100 100 -100} {-100 -100 -100} \"" + JS.T.nameOf (propertyY) + "\";";
if (propertyZ != 0) script += "draw plotAxisZ" + modelCount + " {-100 -100 100} {-100 -100 -100} \"" + JS.T.nameOf (propertyZ) + "\";";
break;
case 1052714:
this.vwr.setFrameTitle (modelCount - 1, "ramachandran plot for model " + this.vwr.getModelNumberDotted (modelIndex));
script = "frame 0.0; frame last; reset;select visible; color structure; spacefill 3.0; wireframe 0;draw ramaAxisX" + modelCount + " {100 0 0} {-100 0 0} \"phi\";" + "draw ramaAxisY" + modelCount + " {0 100 0} {0 -100 0} \"psi\";";
break;
case 135270418:
case 137363467:
this.vwr.setFrameTitle (modelCount - 1, type.$replace ('w', ' ') + qFrame + " for model " + this.vwr.getModelNumberDotted (modelIndex));
var color = (JU.C.getHexCode (this.vwr.getColixBackgroundContrast ()));
script = "frame 0.0; frame last; reset;select visible; wireframe 0; spacefill 3.0; isosurface quatSphere" + modelCount + " color " + color + " sphere 100.0 mesh nofill frontonly translucent 0.8;" + "draw quatAxis" + modelCount + "X {100 0 0} {-100 0 0} color red \"x\";" + "draw quatAxis" + modelCount + "Y {0 100 0} {0 -100 0} color green \"y\";" + "draw quatAxis" + modelCount + "Z {0 0 100} {0 0 -100} color blue \"z\";" + "color structure;" + "draw quatCenter" + modelCount + "{0 0 0} scale 0.02;";
break;
}
this.e.runScript (script + preSelected);
ss.setModelIndex (this.vwr.am.cmi);
this.vwr.setRotationRadius (radius, true);
this.sm.loadShape (30);
this.showString ("frame " + this.vwr.getModelNumberDotted (modelCount - 1) + (type.length > 0 ? " created: " + type + (isQuaternion ? qFrame : "") : ""));
return "";
}, "~A");
Clazz_defineMethod (c$, "polyhedra", 
 function () {
var eval = this.e;
var needsGenerating = false;
var onOffDelete = false;
var typeSeen = false;
var edgeParameterSeen = false;
var isDesignParameter = false;
var lighting = 0;
var nAtomSets = 0;
this.sm.loadShape (21);
this.setShapeProperty (21, "init", Boolean.TRUE);
var setPropertyName = "centers";
var decimalPropertyName = "radius_";
var translucentLevel = 3.4028235E38;
var colorArgb = [-2147483648];
for (var i = 1; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
switch (this.getToken (i).tok) {
case 12291:
case 1048589:
case 1048588:
if (i + 1 != this.slen || needsGenerating || nAtomSets > 1 || nAtomSets == 0 && "to".equals (setPropertyName)) this.error (18);
propertyName = (eval.theTok == 1048588 ? "off" : eval.theTok == 1048589 ? "on" : "delete");
onOffDelete = true;
break;
case 269484436:
case 269484080:
continue;
case 1678770178:
if (nAtomSets > 0) this.invPO ();
needsGenerating = true;
propertyName = "bonds";
break;
case 1666189314:
decimalPropertyName = "radius";
continue;
case 2:
case 3:
if (nAtomSets > 0 && !isDesignParameter) this.invPO ();
if (eval.theTok == 2) {
if (decimalPropertyName === "radius_") {
propertyName = "nVertices";
propertyValue = Integer.$valueOf (this.intParameter (i));
needsGenerating = true;
break;
}}propertyName = (decimalPropertyName === "radius_" ? "radius" : decimalPropertyName);
propertyValue = Float.$valueOf (this.floatParameter (i));
decimalPropertyName = "radius_";
isDesignParameter = false;
needsGenerating = true;
break;
case 10:
case 1048577:
if (typeSeen) this.invPO ();
if (++nAtomSets > 2) eval.bad ();
if ("to".equals (setPropertyName)) needsGenerating = true;
propertyName = setPropertyName;
setPropertyName = "to";
propertyValue = this.atomExpressionAt (i);
i = eval.iToken;
break;
case 1074790746:
if (nAtomSets > 1) this.invPO ();
if (this.tokAt (i + 1) == 10 || this.tokAt (i + 1) == 1048577 && !needsGenerating) {
propertyName = "toBitSet";
propertyValue = this.atomExpressionAt (++i);
i = eval.iToken;
needsGenerating = true;
break;
} else if (!needsGenerating) {
this.error (19);
}setPropertyName = "to";
continue;
case 1073741937:
if (!needsGenerating) this.error (19);
decimalPropertyName = "faceCenterOffset";
isDesignParameter = true;
continue;
case 1073741924:
if (nAtomSets == 0) this.error (19);
decimalPropertyName = "distanceFactor";
isDesignParameter = true;
continue;
case 1766856708:
case 603979967:
case 1073742074:
translucentLevel = this.getColorTrans (eval, i, true, colorArgb);
i = eval.iToken;
continue;
case 1073741886:
case 1073741948:
propertyName = "collapsed";
propertyValue = (eval.theTok == 1073741886 ? Boolean.TRUE : Boolean.FALSE);
if (typeSeen) this.error (18);
typeSeen = true;
break;
case 1073742044:
case 1073741933:
case 1073741956:
if (edgeParameterSeen) this.error (18);
propertyName = this.paramAsStr (i);
edgeParameterSeen = true;
break;
case 1073741964:
lighting = eval.theTok;
continue;
default:
if (eval.isColorParam (i)) {
colorArgb[0] = eval.getArgbParam (i);
i = eval.iToken;
continue;
}this.invArg ();
}
this.setShapeProperty (21, propertyName, propertyValue);
if (onOffDelete) return false;
}
if (!needsGenerating && !typeSeen && !edgeParameterSeen && lighting == 0) this.error (19);
if (needsGenerating) this.setShapeProperty (21, "generate", null);
if (colorArgb[0] != -2147483648) this.setShapeProperty (21, "colorThis", Integer.$valueOf (colorArgb[0]));
if (translucentLevel != 3.4028235E38) eval.setShapeTranslucency (21, "", "translucentThis", translucentLevel, null);
if (lighting != 0) this.setShapeProperty (21, "token", Integer.$valueOf (lighting));
this.setShapeProperty (21, "init", Boolean.FALSE);
return true;
});
Clazz_overrideMethod (c$, "evalParallel", 
function (context, shapeManager) {
var se =  new JS.ScriptEval ().setViewer (this.vwr);
se.historyDisabled = true;
se.compiler =  new JS.ScriptCompiler (this.vwr);
se.sm = shapeManager;
try {
se.restoreScriptContext (context, true, false, false);
se.allowJSThreads = false;
se.dispatchCommands (false, false);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.e.vwr.setStringProperty ("_errormessage", "" + ex);
if (se.thisContext == null) {
JU.Logger.error ("Error evaluating context " + ex);
if (!this.vwr.isJS) ex.printStackTrace ();
}return false;
} else {
throw ex;
}
}
return true;
}, "JS.ScriptContext,JV.ShapeManager");
Clazz_overrideMethod (c$, "write", 
function (args) {
var pt = 0;
var pt0 = 0;
var isCommand;
var isShow;
if (args == null) {
args = this.st;
pt = pt0 = 1;
isCommand = true;
isShow = (this.vwr.isApplet () && !this.vwr.isSignedApplet () || !this.vwr.haveAccess (JV.Viewer.ACCESS.ALL) || this.vwr.getPathForAllFiles ().length > 0);
} else {
isCommand = false;
isShow = true;
}var argCount = (isCommand ? this.slen : args.length);
var len = 0;
var nVibes = 0;
var width = -1;
var height = -1;
var quality = -2147483648;
var timeMsg = this.vwr.getBoolean (603979934);
var driverList = this.vwr.getExportDriverList ();
var sceneType = "PNGJ";
var data = null;
var type2 = "";
var fileName = null;
var localPath = null;
var remotePath = null;
var val = null;
var msg = null;
var tVar = null;
var fullPath =  new Array (1);
var isCoord = false;
var isExport = false;
var isImage = false;
var bsFrames = null;
var scripts = null;
var params;
var type = "SPT";
var tok = (isCommand && args.length == 1 ? 1073741884 : JS.CmdExt.tokAtArray (pt, args));
switch (tok) {
case 0:
break;
case 135271429:
if (this.e.isArrayParameter (pt + 1)) {
scripts = this.e.stringParameterSet (++pt);
localPath = ".";
remotePath = ".";
pt0 = pt = this.e.iToken + 1;
tok = this.tokAt (pt);
}break;
default:
type = JS.SV.sValue (this.tokenAt (pt, args)).toUpperCase ();
}
if (isCommand && this.tokAt (this.slen - 2) == 1073741848) {
type = this.paramAsStr (this.slen - 1).toUpperCase ();
pt0 = argCount;
argCount -= 2;
tok = 0;
}switch (tok) {
case 0:
break;
case 15:
case 6:
type = "VAR";
tVar = this.tokenAt (pt++, args);
break;
case 135270418:
case 1052714:
case 1716520985:
msg = this.plot (args);
if (!isCommand) return msg;
break;
case 1073741983:
type = "INLINE";
data = JS.SV.sValue (this.tokenAt (++pt, args));
pt++;
break;
case 1073742102:
type = "PGRP";
pt++;
type2 = JS.SV.sValue (this.tokenAt (pt, args)).toLowerCase ();
if (type2.equals ("draw")) pt++;
break;
case 1048581:
pt++;
isCoord = true;
break;
case 1073742158:
case 135271429:
val = JS.SV.sValue (this.tokenAt (++pt, args)).toLowerCase ();
while (val.equals ("localpath") || val.equals ("remotepath")) {
if (val.equals ("localpath")) localPath = JS.SV.sValue (this.tokenAt (++pt, args));
 else remotePath = JS.SV.sValue (this.tokenAt (++pt, args));
val = JS.SV.sValue (this.tokenAt (++pt, args)).toLowerCase ();
}
type = "SPT";
break;
case 1229984263:
case 135368713:
case 1610616855:
case 135180:
case 1073742015:
case 1073742018:
case 1183762:
case 135188:
pt++;
break;
case 1073741991:
type = "ZIPALL";
pt++;
break;
case 36868:
type = "VAR";
pt += 2;
break;
case 4115:
case 1073741824:
case 1073741979:
case 1073742139:
case 4:
case 4166:
switch (tok) {
case 1073741979:
pt++;
break;
case 4166:
nVibes = this.e.intParameterRange (++pt, 1, 10);
if (nVibes == 2147483647) return "";
if (!this.chk) {
this.vwr.setVibrationOff ();
if (!this.e.isJS) this.e.delayScript (100);
}pt++;
break;
case 4115:
var bsAtoms;
if (pt + 1 < argCount && args[++pt].tok == 1048577 || args[pt].tok == 10) {
bsAtoms = this.e.atomExpression (args, pt, 0, true, false, true, true);
pt = this.e.iToken + 1;
} else {
bsAtoms = this.vwr.getAllAtoms ();
}if (!this.chk) bsFrames = this.vwr.ms.getModelBS (bsAtoms, true);
break;
case 1073742139:
val = JS.SV.sValue (this.tokenAt (++pt, args)).toUpperCase ();
if (JU.PT.isOneOf (val, ";PNG;PNGJ;")) {
sceneType = val;
pt++;
}break;
default:
tok = 1073741979;
break;
}
if (tok == 1073741979) {
var t = JS.T.getTokenFromName (JS.SV.sValue (args[pt]).toLowerCase ());
if (t != null) {
type = JS.SV.sValue (t).toUpperCase ();
isCoord = (t.tok == 1048581);
if (isCoord) pt++;
}if (JU.PT.isOneOf (type, driverList.toUpperCase ())) {
pt++;
type = type.substring (0, 1).toUpperCase () + type.substring (1).toLowerCase ();
isExport = true;
if (isCommand) fileName = "Jmol." + type.toLowerCase ();
break;
} else if (JU.PT.isOneOf (type, ";ZIP;ZIPALL;SPT;STATE;")) {
pt++;
break;
} else if (!isCoord) {
type = "(image)";
}}if (JS.CmdExt.tokAtArray (pt, args) == 2) {
width = JS.SV.iValue (this.tokenAt (pt++, args));
height = JS.SV.iValue (this.tokenAt (pt++, args));
}break;
}
if (msg == null) {
if (pt0 < argCount) {
val = JS.SV.sValue (this.tokenAt (pt, args));
if (val.equalsIgnoreCase ("clipboard")) {
if (this.chk) return "";
} else if (JU.PT.isOneOf (val.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;pdf;ppm;png;pngj;pngt;")) {
if (JS.CmdExt.tokAtArray (pt + 1, args) == 2 && JS.CmdExt.tokAtArray (pt + 2, args) == 2) {
width = JS.SV.iValue (this.tokenAt (++pt, args));
height = JS.SV.iValue (this.tokenAt (++pt, args));
}if (JS.CmdExt.tokAtArray (pt + 1, args) == 2) quality = JS.SV.iValue (this.tokenAt (++pt, args));
} else if (JU.PT.isOneOf (val.toLowerCase (), ";xyz;xyzrn;xyzvib;mol;sdf;v2000;v3000;json;pdb;pqr;cml;")) {
type = val.toUpperCase ();
if (pt + 1 == argCount) pt++;
}if (type.equals ("(image)") && JU.PT.isOneOf (val.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;pdf;ppm;png;pngj;pngt;scene;")) {
type = val.toUpperCase ();
pt++;
}}if (pt + 2 == argCount) {
var s = JS.SV.sValue (this.tokenAt (++pt, args));
if (s.length > 0 && s.charAt (0) != '.') type = val.toUpperCase ();
}switch (JS.CmdExt.tokAtArray (pt, args)) {
case 0:
isShow = true;
break;
case 1073741884:
break;
case 1073741824:
case 4:
fileName = JS.SV.sValue (this.tokenAt (pt, args));
if (pt == argCount - 3 && JS.CmdExt.tokAtArray (pt + 1, args) == 1048583) {
fileName += "." + JS.SV.sValue (this.tokenAt (pt + 2, args));
}if (type !== "VAR" && pt == pt0 && !isCoord) type = "IMAGE";
 else if (fileName.length > 0 && fileName.charAt (0) == '.' && (pt == pt0 + 1 || pt == pt0 + 2)) {
fileName = JS.SV.sValue (this.tokenAt (pt - 1, args)) + fileName;
if (type !== "VAR" && pt == pt0 + 1) type = "IMAGE";
}if (fileName.equalsIgnoreCase ("clipboard") || !this.vwr.haveAccess (JV.Viewer.ACCESS.ALL)) fileName = null;
break;
default:
this.invArg ();
}
if (type.equals ("IMAGE") || type.equals ("(image)") || type.equals ("FRAME") || type.equals ("VIBRATION")) {
type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "JPG");
}if (type.equals ("MNU")) {
type = "MENU";
} else if (type.equals ("WRL") || type.equals ("VRML")) {
type = "Vrml";
isExport = true;
} else if (type.equals ("X3D")) {
type = "X3d";
isExport = true;
} else if (type.equals ("IDTF")) {
type = "Idtf";
isExport = true;
} else if (type.equals ("MA")) {
type = "Maya";
isExport = true;
} else if (type.equals ("JS")) {
type = "Js";
isExport = true;
} else if (type.equals ("OBJ")) {
type = "Obj";
isExport = true;
} else if (type.equals ("JVXL")) {
type = "ISOSURFACE";
} else if (type.equals ("XJVXL")) {
type = "ISOSURFACE";
} else if (type.equals ("JMOL")) {
type = "ZIPALL";
} else if (type.equals ("HIS")) {
type = "HISTORY";
}if (type.equals ("COORD") || type.equals ("COORDS")) type = (fileName != null && fileName.indexOf (".") >= 0 ? fileName.substring (fileName.lastIndexOf (".") + 1).toUpperCase () : "XYZ");
isImage = JU.PT.isOneOf (type.toLowerCase (), ";jpg;jpeg;jpg64;jpeg64;gif;pdf;ppm;png;pngj;pngt;scene;");
if (scripts != null) {
if (type.equals ("PNG")) type = "PNGJ";
if (!type.equals ("PNGJ") && !type.equals ("ZIPALL")) this.invArg ();
}if (!isImage && !isExport && !JU.PT.isOneOf (type, ";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;")) this.e.errorStr2 (54, "COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|POINTGROUP|QUATERNION [w,x,y,z] [derivative]|RAMACHANDRAN|SPT|STATE|VAR x|ZIP|ZIPALL  CLIPBOARD", "CML|GIF|JPG|JPG64|JMOL|JVXL|MESH|MOL|PDB|PMESH|PNG|PNGJ|PNGT|PPM|PQR|SDF|CD|JSON|V2000|V3000|SPT|XJVXL|XYZ|XYZRN|XYZVIB|ZIP" + driverList.toUpperCase ().$replace (';', '|'));
if (this.chk) return "";
var bytes = null;
var doDefer = false;
if (data == null || isExport) {
data = type.intern ();
if (isExport) {
if (timeMsg) JU.Logger.startTimer ("export");
var eparams =  new java.util.Hashtable ();
eparams.put ("type", data);
if (fileName != null) eparams.put ("fileName", fileName);
if (isCommand || fileName != null) eparams.put ("fullPath", fullPath);
eparams.put ("width", Integer.$valueOf (width));
eparams.put ("height", Integer.$valueOf (height));
data = this.vwr.generateOutputForExport (eparams);
if (data == null || data.length == 0) return "";
if (!isCommand) return data;
if ((type.equals ("Povray") || type.equals ("Idtf")) && fullPath[0] != null) {
var ext = (type.equals ("Idtf") ? ".tex" : ".ini");
fileName = fullPath[0] + ext;
params =  new java.util.Hashtable ();
params.put ("fileName", fileName);
params.put ("type", ext);
params.put ("text", data);
params.put ("fullPath", fullPath);
msg = this.vwr.processWriteOrCapture (params);
if (type.equals ("Idtf")) data = data.substring (0, data.indexOf ("\\begin{comment}"));
data = "Created " + fullPath[0] + ":\n\n" + data;
if (timeMsg) this.showString (JU.Logger.getTimerMsg ("export", 0));
} else {
msg = data;
}if (msg != null) {
if (!msg.startsWith ("OK")) this.e.evalError (msg, null);
this.e.report (data);
}return "";
} else if (data === "MENU") {
data = this.vwr.getMenu ("");
} else if (data === "PGRP") {
data = this.vwr.getPointGroupAsString (type2.equals ("draw"), null, 0, 1.0);
} else if (data === "PDB" || data === "PQR") {
if (isShow) {
data = this.vwr.getPdbAtomData (null, null);
} else {
doDefer = true;
}} else if (data === "FILE") {
if (isShow) data = this.vwr.getCurrentFileAsString ();
 else doDefer = true;
if ("?".equals (fileName)) fileName = "?Jmol." + this.vwr.getP ("_fileType");
} else if ((data === "SDF" || data === "MOL" || data === "V2000" || data === "V3000" || data === "CD" || data === "JSON") && isCoord) {
data = this.vwr.getModelExtract ("selected", true, false, data);
if (data.startsWith ("ERROR:")) bytes = data;
} else if (data === "XYZ" || data === "XYZRN" || data === "XYZVIB" || data === "MOL" || data === "SDF" || data === "V2000" || data === "V3000" || data === "CML" || data === "CD" || data === "JSON") {
data = this.vwr.getData ("selected", data);
if (data.startsWith ("ERROR:")) bytes = data;
} else if (data === "FUNCTION") {
data = this.vwr.getFunctionCalls (null);
type = "TXT";
} else if (data === "VAR") {
if (tVar == null) {
tVar = this.e.getParameter (JS.SV.sValue (this.tokenAt (isCommand ? 2 : 1, args)), 1073742190, true);
}var v = null;
if (tVar.tok == 15) {
v =  new JU.Lst ();
v.addLast ((tVar.value).data);
} else if (tVar.tok == 6) {
var m = tVar.value;
if (m.containsKey ("$_BINARY_$")) {
v =  new JU.Lst ();
if (fileName != null) for (var e, $e = m.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var key = e.getKey ();
if (key.equals ("$_BINARY_$")) continue;
var o = e.getValue ();
bytes = (o.tok == 15 ? (o.value).data : null);
if (bytes == null) {
var s = o.asString ();
bytes = (s.startsWith (";base64,") ? JU.Base64.decodeBase64 (s) : s.getBytes ());
}if (key.equals ("_DATA_")) {
v = null;
if (bytes == null) bytes = (o.value).data;
break;
} else if (key.equals ("_IMAGE_")) {
v.add (0, key);
v.add (1, bytes);
} else {
v.addLast (key);
v.addLast (null);
v.addLast (bytes);
}}
}}if (v == null) {
if (bytes == null) {
data = tVar.asString ();
type = "TXT";
}} else {
if (fileName != null && (bytes = data = this.vwr.createZip (fileName, v.size () == 1 ? "BINARY" : "ZIPDATA", v)) == null) this.e.evalError ("#CANCELED#", null);
}} else if (data === "SPT") {
if (isCoord) {
var tainted = this.vwr.ms.getTaintedAtoms (2);
this.vwr.setAtomCoordsRelative (JU.P3.new3 (0, 0, 0), null);
data = this.vwr.getStateInfo ();
this.vwr.ms.setTaintedAtoms (tainted, 2);
} else {
data = this.vwr.getStateInfo ();
if (localPath != null || remotePath != null) data = JV.FileManager.setScriptFileReferences (data, localPath, remotePath, null);
}} else if (data === "ZIP" || data === "ZIPALL") {
if (fileName != null && (bytes = data = this.vwr.createZip (fileName, type, scripts)) == null) this.e.evalError ("#CANCELED#", null);
} else if (data === "HISTORY") {
data = this.vwr.getSetHistory (2147483647);
type = "SPT";
} else if (data === "MO") {
data = this.getMoJvxl (2147483647);
type = "XJVXL";
} else if (data === "PMESH") {
if ((data = this.getIsosurfaceJvxl (true, 28)) == null) this.error (31);
type = "XJVXL";
} else if (data === "ISOSURFACE" || data === "MESH") {
if ((data = this.getIsosurfaceJvxl (data === "MESH", 24)) == null) this.error (31);
type = (data.indexOf ("<?xml") >= 0 ? "XJVXL" : "JVXL");
if (!isShow) this.showString (this.getShapeProperty (24, "jvxlFileInfo"));
} else {
len = -1;
if (quality < 0) quality = -1;
}if (data == null && !doDefer) data = "";
if (len == 0 && !doDefer) len = (bytes == null ? data.length : Clazz_instanceOf (bytes, String) ? (bytes).length : (bytes).length);
if (isImage) {
this.e.refresh (false);
if (width < 0) width = this.vwr.getScreenWidth ();
if (height < 0) height = this.vwr.getScreenHeight ();
}}if (!isCommand) return data;
if (isShow) {
this.e.showStringPrint (data, true);
return "";
}if (bytes != null && Clazz_instanceOf (bytes, String)) {
{
if (bytes.indexOf("OK") != 0)alert(bytes);
}this.e.report (bytes);
return bytes;
}if (type.equals ("SCENE")) bytes = sceneType;
 else if (bytes == null && (!isImage || fileName != null)) bytes = data;
if (timeMsg) JU.Logger.startTimer ("write");
if (doDefer) {
msg = this.vwr.writeFileData (fileName, type, 0, null);
} else {
params =  new java.util.Hashtable ();
if (fileName != null) params.put ("fileName", fileName);
params.put ("type", type);
if (Clazz_instanceOf (bytes, String) && quality == -2147483648) params.put ("text", bytes);
 else if (Clazz_instanceOf (bytes, Array)) params.put ("bytes", bytes);
if (scripts != null) params.put ("scripts", scripts);
if (bsFrames != null) params.put ("bsFrames", bsFrames);
params.put ("fullPath", fullPath);
params.put ("quality", Integer.$valueOf (quality));
params.put ("width", Integer.$valueOf (width));
params.put ("height", Integer.$valueOf (height));
params.put ("nVibes", Integer.$valueOf (nVibes));
msg = this.vwr.processWriteOrCapture (params);
}if (timeMsg) this.showString (JU.Logger.getTimerMsg ("write", 0));
}if (!this.chk && msg != null) {
if (!msg.startsWith ("OK")) {
this.e.evalError (msg, null);
{
alert(msg);
}}this.e.report (msg + (isImage ? "; width=" + width + "; height=" + height : ""));
return msg;
}return "";
}, "~A");
Clazz_defineMethod (c$, "show", 
 function () {
var value = null;
var str = this.paramAsStr (1);
var msg = null;
var name = null;
var len = 2;
var token = this.getToken (1);
var tok = (Clazz_instanceOf (token, JS.SV) ? 0 : token.tok);
if (tok == 4) {
token = JS.T.getTokenFromName (str.toLowerCase ());
if (token != null) tok = token.tok;
}if (tok != 1297090050 && tok != 1073742158) this.checkLength (-3);
if (this.slen == 2 && str.indexOf ("?") >= 0) {
this.showString (this.vwr.getAllSettings (str.substring (0, str.indexOf ("?"))));
return;
}switch (tok) {
case 0:
if (!this.chk) msg = (this.e.theToken).escape ();
break;
case 1073741925:
this.e.checkLength23 ();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.ms.getInfo (this.vwr.am.cmi, "domains");
if (Clazz_instanceOf (d, JS.SV)) msg = this.vwr.getAnnotationInfo (d, this.e.optParameterAsString (2), 1073741925);
 else msg = "domain information has not been loaded";
}break;
case 1073742189:
this.e.checkLength23 ();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.ms.getInfo (this.vwr.am.cmi, "validation");
if (Clazz_instanceOf (d, JS.SV)) msg = this.vwr.getAnnotationInfo (d, this.e.optParameterAsString (2), 1073742189);
 else msg = "validation information has not been loaded";
}break;
case 135270423:
if (!this.chk) msg = JU.Escape.e (this.vwr.cacheList ());
break;
case 1073741916:
this.e.checkLength23 ();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.ms.getInfo (this.vwr.am.cmi, "dssr");
if (d == null) msg = "no DSSR information has been read";
 else if (len > 2) msg = JS.SV.getVariable (this.vwr.extractProperty (d, this.stringParameter (2), -1)).asString ();
 else msg = "" + JS.SV.getVariable (d).asString ();
}break;
case 1073741915:
this.checkLength (2);
if (!this.chk) msg = this.vwr.calculateStructures (null, true, false);
break;
case 545259571:
this.checkLength (2);
if (!this.chk) msg = this.vwr.getPathForAllFiles ();
break;
case 1073742038:
if (this.e.optParameterAsString (2).equalsIgnoreCase ("1H")) {
len = 3;
if (!this.chk) msg = this.vwr.getNMRPredict (false);
break;
}if (!this.chk) this.vwr.getNMRPredict (true);
return;
case 135267336:
case 1073741929:
case 1073741879:
this.checkLength (tok == 1073741879 ? 3 : 2);
if (this.chk) return;
try {
msg = this.vwr.getSmiles (null);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
msg = ex.getMessage ();
} else {
throw ex;
}
}
switch (tok) {
case 1073741929:
if (msg.length > 0) {
this.vwr.show2D (msg);
return;
}msg = "Could not show drawing -- Either insufficient atoms are selected or the model is a PDB file.";
break;
case 1073741879:
len = 3;
if (msg.length > 0) {
msg = this.vwr.getChemicalInfo (msg, this.getToken (2));
if (msg.indexOf ("FileNotFound") >= 0) msg = "?";
} else {
msg = "Could not show name -- Either insufficient atoms are selected or the model is a PDB file.";
}}
break;
case 1297090050:
var type;
var iop = 0;
var pt1 = null;
var pt2 = null;
if (this.slen > 3 && this.tokAt (3) != 4) {
pt1 = this.centerParameter (2);
pt2 = this.centerParameter (++this.e.iToken);
} else {
iop = (this.tokAt (2) == 2 ? this.intParameter (2) : 0);
}type = (this.tokAt (this.e.iToken + 1) == 4 ? this.stringParameter (++this.e.iToken) : null);
this.checkLength (len = ++this.e.iToken);
if (!this.chk) msg = this.vwr.getSymmetryOperation (iop, pt1, pt2, type);
break;
case 1649412120:
var vdwType = null;
if (this.slen > 2) {
vdwType = J.c.VDW.getVdwType (this.paramAsStr (2));
if (vdwType == null) this.invArg ();
}if (!this.chk) this.showString (this.vwr.getDefaultVdwNameOrData (0, vdwType, null));
return;
case 135368713:
this.e.checkLength23 ();
if (!this.chk) this.showString (this.vwr.getFunctionCalls (this.e.optParameterAsString (2)));
return;
case 1085443:
this.checkLength (2);
if (!this.chk) this.showString (this.vwr.getAllSettings (null));
return;
case 1074790760:
if ((len = this.slen) == 2) {
if (!this.chk) this.vwr.showUrl (this.e.getFullPathName ());
return;
}name = this.paramAsStr (2);
if (!this.chk) this.vwr.showUrl (name);
return;
case 1766856708:
str = "defaultColorScheme";
break;
case 1610612740:
str = "scaleAngstromsPerInch";
break;
case 135270418:
case 1052714:
if (this.chk) return;
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) this.e.errorStr (30, "show " + this.e.theToken.value);
msg = this.plot (this.st);
len = this.slen;
break;
case 14:
case 1113200654:
if (!this.chk) msg = this.getContext (false);
break;
case 1073741888:
name = this.e.optParameterAsString (2);
if (name.length > 0) len = 3;
if (!this.chk) value = this.vwr.getColorSchemeList (name);
break;
case 1073742192:
if (!this.chk) msg = this.vwr.getAtomDefs (this.e.definedAtomSets) + this.vwr.g.getVariableList () + this.getContext (true);
break;
case 536870926:
if (!this.chk) msg = this.vwr.getTrajectoryState ();
break;
case 553648148:
value = "" + this.e.commandHistoryLevelMax;
break;
case 553648150:
value = "" + JU.Logger.getLogLevel ();
break;
case 603979825:
value = "" + this.vwr.getBoolean (603979825);
break;
case 553648178:
msg = "set strandCountForStrands " + this.vwr.getStrandCount (12) + "; set strandCountForMeshRibbon " + this.vwr.getStrandCount (13);
break;
case 536875070:
msg = this.vwr.showTimeout ((len = this.slen) == 2 ? null : this.paramAsStr (2));
break;
case 536870918:
value = JU.Escape.eP (this.vwr.getDefaultLattice ());
break;
case 4126:
if (!this.chk) msg = this.vwr.getMinimizationInfo ();
break;
case 1611272194:
switch (this.vwr.g.axesMode) {
case J.c.AXES.UNITCELL:
msg = "set axesUnitcell";
break;
case J.c.AXES.BOUNDBOX:
msg = "set axesWindow";
break;
default:
msg = "set axesMolecular";
}
break;
case 1610612737:
msg = "set bondMode " + (this.vwr.getBoolean (603979812) ? "OR" : "AND");
break;
case 1650071565:
if (!this.chk) msg = "set strandCountForStrands " + this.vwr.getStrandCount (12) + "; set strandCountForMeshRibbon " + this.vwr.getStrandCount (13);
break;
case 1612189718:
msg = "set hbondsBackbone " + this.vwr.getBoolean (603979852) + ";set hbondsSolid " + this.vwr.getBoolean (603979854);
break;
case 1611141175:
if (!this.chk) msg = this.vwr.getSpinState ();
break;
case 1611141176:
msg = "set ssbondsBackbone " + this.vwr.getBoolean (603979952);
break;
case 1610625028:
case 1611141171:
msg = "selectionHalos " + (this.vwr.getSelectionHaloEnabled (false) ? "ON" : "OFF");
break;
case 1613758470:
msg = "set selectHetero " + this.vwr.getBoolean (1613758470);
break;
case 1073741828:
msg = JU.Escape.eAP (this.vwr.getAdditionalHydrogens (null, true, true, null));
break;
case 1613758476:
msg = "set selectHydrogens " + this.vwr.getBoolean (1613758476);
break;
case 553648130:
case 553648142:
case 536870924:
case 553648176:
case 553648172:
case 1073741995:
if (!this.chk) msg = this.vwr.getSpecularState ();
break;
case 1073742136:
case 4146:
if (!this.chk) msg = this.vwr.stm.listSavedStates ();
break;
case 1614417948:
if (!this.chk) msg = this.vwr.getUnitCellInfoText ();
break;
case 1048581:
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.getCoordinateState (this.vwr.bsA ());
break;
}var nameC = this.paramAsStr (2);
if (!this.chk) msg = this.vwr.stm.getSavedCoordinates (nameC);
break;
case 1073742158:
if (!this.chk && this.e.outputBuffer == null) this.vwr.sm.clearConsole ();
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.getStateInfo ();
break;
}name = this.paramAsStr (2);
if (name.equals ("/") && (len = this.slen) == 4) {
name = this.paramAsStr (3).toLowerCase ();
if (!this.chk) {
var info = JU.PT.split (this.vwr.getStateInfo (), "\n");
var sb =  new JU.SB ();
for (var i = 0; i < info.length; i++) if (info[i].toLowerCase ().indexOf (name) >= 0) sb.append (info[i]).appendC ('\n');

msg = sb.toString ();
}break;
} else if (this.tokAt (2) == 1229984263 && (len = this.slen) == 4) {
if (!this.chk) msg = this.vwr.getEmbeddedFileState (this.paramAsStr (3), true);
break;
}len = 3;
if (!this.chk) msg = this.vwr.stm.getSavedState (name);
break;
case 1641025539:
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.getProteinStructureState ();
break;
}var shape = this.paramAsStr (2);
if (!this.chk) msg = this.vwr.stm.getSavedStructure (shape);
break;
case 135270408:
type = ((len = this.slen) == 3 ? this.paramAsStr (2) : null);
if (!this.chk) {
var data = (type == null ? this.lastData : this.vwr.getData (type));
msg = (data == null ? "no data" : JU.Escape.encapsulateData (data[0], data[1], (data[3]).intValue ()));
}break;
case 1073742152:
var info = null;
if ((len = this.slen) == 2) {
if (!this.chk) {
info = this.vwr.getSpaceGroupInfo (null);
}} else {
var sg = this.paramAsStr (2);
if (!this.chk) info = this.vwr.getSpaceGroupInfo (JU.PT.rep (sg, "''", "\""));
}if (info != null) msg = "" + info.get ("spaceGroupInfo") + info.get ("symmetryInfo");
break;
case 1048582:
len = 3;
msg = this.e.setObjectProperty ();
break;
case 1679429641:
if (!this.chk) {
msg = this.vwr.ms.getBoundBoxCommand (true);
}break;
case 12289:
if (!this.chk) msg = "center " + JU.Escape.eP (this.vwr.tm.getRotationCenter ());
break;
case 135176:
if (!this.chk) msg = this.getShapeProperty (22, "command");
break;
case 1229984263:
if (!this.chk) this.vwr.sm.clearConsole ();
if (this.slen == 2) {
if (!this.chk) msg = this.vwr.getCurrentFileAsString ();
if (msg == null) msg = "<unavailable>";
break;
}len = 3;
value = this.paramAsStr (2);
if (!this.chk) msg = this.vwr.getFileAsString (value, true);
break;
case 4115:
if (this.tokAt (2) == 1048579 && (len = 3) > 0) msg = this.vwr.getModelFileInfoAll ();
 else msg = this.vwr.getModelFileInfo ();
break;
case 1610616855:
var n = ((len = this.slen) == 2 ? 2147483647 : this.intParameter (2));
if (n < 1) this.invArg ();
if (!this.chk) {
this.vwr.sm.clearConsole ();
if (this.e.scriptLevel == 0) this.vwr.removeCommand ();
msg = this.vwr.getSetHistory (n);
}break;
case 135180:
if (!this.chk) msg = this.getShapeProperty (24, "jvxlDataXml");
break;
case 1183762:
if (this.e.optParameterAsString (2).equalsIgnoreCase ("list")) {
msg = this.vwr.getMoInfo (-1);
len = 3;
} else {
var ptMO = ((len = this.slen) == 2 ? -2147483648 : this.intParameter (2));
if (!this.chk) msg = this.getMoJvxl (ptMO);
}break;
case 1095766030:
if (!this.chk) msg = this.vwr.ms.getModelInfoAsString ();
break;
case 537006096:
if (!this.chk) msg = this.vwr.getMeasurementInfoAsString ();
break;
case 1073741863:
len = 3;
if (!this.chk && this.slen == len) msg = this.vwr.getOrientationText (this.tokAt (2), null);
break;
case 1073742132:
tok = this.tokAt (2);
if (tok == 0) tok = 1073742132;
 else len = 3;
case 1073742178:
case 4130:
if (!this.chk) msg = this.vwr.getOrientationText (tok, null);
break;
case 1073742077:
len = 2;
if (this.slen > 3) break;
switch (tok = this.tokAt (2)) {
case 1073742178:
case 1073742132:
case 4130:
case 0:
if (!this.chk) msg = this.vwr.getOrientationText (tok, null);
break;
default:
name = this.e.optParameterAsString (2);
msg = this.vwr.getOrientationText (1073742035, name);
}
len = this.slen;
break;
case 1073742088:
if (!this.chk) msg = this.vwr.getPDBHeader ();
break;
case 1073742102:
if (!this.chk) this.showString (this.vwr.getPointGroupAsString (false, null, 0, 0));
return;
case 1089470478:
if (!this.chk) msg = this.vwr.ms.getSymmetryInfoAsString ();
break;
case 1073742176:
if (!this.chk) msg = "transform:\n" + this.vwr.tm.getTransformText ();
break;
case 4168:
msg = "zoom " + (this.vwr.tm.zoomEnabled ? ("" + this.vwr.tm.getZoomSetting ()) : "off");
break;
case 1611272202:
msg = (this.vwr.getShowFrank () ? "frank ON" : "frank OFF");
break;
case 1666189314:
str = "solventProbeRadius";
break;
case 1087373320:
if ((len = this.slen) == 3 && this.tokAt (2) == 1048588) tok = 1087373319;
case 1073741864:
case 1087373316:
case 1073742120:
case 1114638363:
case 1087373318:
case 1141899265:
case 1073741982:
if (!this.chk) msg = this.vwr.getChimeInfo (tok);
break;
case 537022465:
case 1610612738:
case 1716520985:
case 20482:
case 1613758488:
value = "?";
break;
case 1073742031:
var qualifiers = ((len = this.slen) == 2 ? null : this.paramAsStr (2));
if (!this.chk) msg = this.vwr.getBindingInfo (qualifiers);
break;
case 1073742015:
if (!this.chk) value = this.vwr.getMenu ("");
break;
case 1073741824:
if (str.equalsIgnoreCase ("fileHeader")) {
if (!this.chk) msg = this.vwr.getPDBHeader ();
}break;
case 1073741992:
case 36868:
str = this.paramAsStr (len++);
var v = this.e.getParameter (str, 1073742190, true);
if (!this.chk) if (tok == 1073741992) {
msg = v.toJSON ();
} else {
msg = v.escape ();
}break;
}
this.checkLength (len);
if (this.chk) return;
if (msg != null) this.showString (msg);
 else if (value != null) this.showString (str + " = " + value);
 else if (str != null) {
if (str.indexOf (" ") >= 0) this.showString (str);
 else this.showString (str + " = " + (this.e.getParameter (str, 1073742190, true)).escape ());
}});
Clazz_defineMethod (c$, "stereo", 
 function () {
var stereoMode = J.c.STER.DOUBLE;
var degrees = -5;
var degreesSeen = false;
var colors = null;
var colorpt = 0;
for (var i = 1; i < this.slen; ++i) {
if (this.e.isColorParam (i)) {
if (colorpt > 1) this.e.bad ();
if (colorpt == 0) colors =  Clazz_newIntArray (2, 0);
if (!degreesSeen) degrees = 3;
colors[colorpt] = this.e.getArgbParam (i);
if (colorpt++ == 0) colors[1] = ~colors[0];
i = this.e.iToken;
continue;
}switch (this.getToken (i).tok) {
case 1048589:
this.e.checkLast (this.e.iToken = 1);
this.e.iToken = 1;
break;
case 1048588:
this.e.checkLast (this.e.iToken = 1);
stereoMode = J.c.STER.NONE;
break;
case 2:
case 3:
degrees = this.floatParameter (i);
degreesSeen = true;
break;
case 1073741824:
if (!degreesSeen) degrees = 3;
stereoMode = J.c.STER.getStereoMode (this.paramAsStr (i));
if (stereoMode != null) break;
default:
this.invArg ();
}
}
if (this.chk) return;
this.vwr.setStereoMode (colors, stereoMode, degrees);
});
Clazz_defineMethod (c$, "struts", 
 function () {
var eval = this.e;
var defOn = (this.tokAt (1) == 1073742072 || this.tokAt (1) == 1048589 || this.slen == 1);
var mad = eval.getMadParameter ();
if (mad == 2147483647) return false;
if (defOn) mad = Math.round (this.vwr.getFloat (570425406) * 2000);
this.setShapeProperty (1, "type", Integer.$valueOf (32768));
eval.setShapeSizeBs (1, mad, null);
this.setShapeProperty (1, "type", Integer.$valueOf (1023));
return true;
});
Clazz_defineMethod (c$, "addShapeProperty", 
 function (propertyList, key, value) {
if (this.chk) return;
propertyList.addLast ([key, value]);
}, "JU.Lst,~S,~O");
Clazz_defineMethod (c$, "assign", 
 function () {
var atomsOrBonds = this.tokAt (1);
var index = this.atomExpressionAt (2).nextSetBit (0);
var index2 = -1;
var type = null;
if (index < 0) return;
if (atomsOrBonds == 4106) {
index2 = this.atomExpressionAt (++this.e.iToken).nextSetBit (0);
} else {
type = this.paramAsStr (++this.e.iToken);
}var pt = (++this.e.iToken < this.slen ? this.centerParameter (this.e.iToken) : null);
if (this.chk) return;
switch (atomsOrBonds) {
case 1141899265:
this.e.clearDefinedVariableAtomSets ();
this.assignAtom (index, pt, type);
break;
case 1678770178:
this.assignBond (index, (type + "p").charAt (0));
break;
case 4106:
this.assignConnect (index, index2);
}
});
Clazz_defineMethod (c$, "assignAtom", 
 function (atomIndex, pt, type) {
if (type.equals ("X")) this.vwr.setRotateBondIndex (-1);
if (this.vwr.ms.at[atomIndex].mi != this.vwr.ms.mc - 1) return;
this.vwr.clearModelDependentObjects ();
var ac = this.vwr.ms.getAtomCount ();
if (pt == null) {
this.vwr.sm.modifySend (atomIndex, this.vwr.ms.at[atomIndex].mi, 1, this.e.fullCommand);
this.vwr.ms.assignAtom (atomIndex, type, true);
if (!JU.PT.isOneOf (type, ";Mi;Pl;X;")) this.vwr.ms.setAtomNamesAndNumbers (atomIndex, -ac, null);
this.vwr.sm.modifySend (atomIndex, this.vwr.ms.at[atomIndex].mi, -1, "OK");
this.vwr.refresh (3, "assignAtom");
return;
}var atom = this.vwr.ms.at[atomIndex];
var bs = JU.BSUtil.newAndSetBit (atomIndex);
var pts = [pt];
var vConnections =  new JU.Lst ();
vConnections.addLast (atom);
var modelIndex = atom.mi;
this.vwr.sm.modifySend (atomIndex, modelIndex, 3, this.e.fullCommand);
try {
bs = this.vwr.addHydrogensInline (bs, vConnections, pts);
atomIndex = bs.nextSetBit (0);
this.vwr.ms.assignAtom (atomIndex, type, false);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
} else {
throw ex;
}
}
this.vwr.ms.setAtomNamesAndNumbers (atomIndex, -ac, null);
this.vwr.sm.modifySend (atomIndex, modelIndex, -3, "OK");
}, "~N,JU.P3,~S");
Clazz_defineMethod (c$, "assignBond", 
 function (bondIndex, type) {
var modelIndex = -1;
try {
modelIndex = this.vwr.getAtomModelIndex (this.vwr.ms.bo[bondIndex].getAtomIndex1 ());
this.vwr.sm.modifySend (bondIndex, modelIndex, 2, this.e.fullCommand);
var bsAtoms = this.vwr.ms.setBondOrder (bondIndex, type);
if (bsAtoms == null || type == '0') this.vwr.refresh (3, "setBondOrder");
 else this.vwr.addHydrogens (bsAtoms, false, true);
this.vwr.sm.modifySend (bondIndex, modelIndex, -2, "" + type);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
JU.Logger.error ("assignBond failed");
this.vwr.sm.modifySend (bondIndex, modelIndex, -2, "ERROR " + ex);
} else {
throw ex;
}
}
}, "~N,~S");
Clazz_defineMethod (c$, "assignConnect", 
 function (index, index2) {
this.vwr.clearModelDependentObjects ();
var connections = JU.AU.newFloat2 (1);
connections[0] = [index, index2];
var modelIndex = this.vwr.ms.at[index].mi;
this.vwr.sm.modifySend (index, modelIndex, 2, this.e.fullCommand);
this.vwr.ms.connect (connections);
this.vwr.ms.assignAtom (index, ".", true);
this.vwr.ms.assignAtom (index2, ".", true);
this.vwr.sm.modifySend (index, modelIndex, -2, "OK");
this.vwr.refresh (3, "assignConnect");
}, "~N,~N");
Clazz_defineMethod (c$, "getContext", 
 function (withVariables) {
var sb =  new JU.SB ();
var context = this.e.thisContext;
while (context != null) {
if (withVariables) {
if (context.vars != null) {
sb.append (this.getScriptID (context));
sb.append (JV.StateManager.getVariableList (context.vars, 80, true, false));
}} else {
sb.append (JS.ScriptError.getErrorLineMessage (context.functionName, context.scriptFileName, this.e.getLinenumber (context), context.pc, JS.ScriptEval.statementAsString (this.vwr, context.statement, -9999, this.e.debugHigh)));
}context = context.parentContext;
}
if (withVariables) {
if (this.e.contextVariables != null) {
sb.append (this.getScriptID (null));
sb.append (JV.StateManager.getVariableList (this.e.contextVariables, 80, true, false));
}} else {
sb.append (this.e.getErrorLineMessage2 ());
}return sb.toString ();
}, "~B");
Clazz_defineMethod (c$, "getAtomicPotentials", 
 function (bsSelected, bsIgnore, fileName) {
var potentials =  Clazz_newFloatArray (this.vwr.getAtomCount (), 0);
var m = J.api.Interface.getOption ("quantum.MlpCalculation");
m.set (this.vwr);
var data = (fileName == null ? null : this.vwr.getFileAsString (fileName, false));
m.assignPotentials (this.vwr.ms.at, potentials, this.vwr.getSmartsMatch ("a", bsSelected), this.vwr.getSmartsMatch ("/noAromatic/[$(C=O),$(O=C),$(NC=O)]", bsSelected), bsIgnore, data);
return potentials;
}, "JU.BS,JU.BS,~S");
Clazz_defineMethod (c$, "getColorTrans", 
 function (eval, i, allowNone, ret) {
var translucentLevel = 3.4028235E38;
if (eval.theTok != 1766856708) --i;
switch (this.tokAt (i + 1)) {
case 603979967:
i++;
translucentLevel = (this.isFloatParameter (i + 1) ? eval.getTranslucentLevel (++i) : this.vwr.getFloat (570425354));
break;
case 1073742074:
i++;
translucentLevel = 0;
break;
}
if (eval.isColorParam (i + 1)) {
ret[0] = eval.getArgbParam (++i);
} else if (this.tokAt (i + 1) == 1048587) {
ret[0] = 0;
eval.iToken = i + 1;
} else if (translucentLevel == 3.4028235E38) {
this.invArg ();
} else {
ret[0] = -2147483648;
}i = eval.iToken;
return translucentLevel;
}, "JS.ScriptEval,~N,~B,~A");
Clazz_defineMethod (c$, "getCapSlabObject", 
 function (i, isLcaoCartoon) {
if (i < 0) {
return JU.TempArray.getSlabWithinRange (i, 0);
}var eval = this.e;
var data = null;
var tok0 = this.tokAt (i);
var isSlab = (tok0 == 554176565);
var tok = this.tokAt (i + 1);
var plane = null;
var pts = null;
var d;
var d2;
var bs = null;
var slabColix = null;
var slabMeshType = null;
if (tok == 603979967) {
var slabTranslucency = (this.isFloatParameter (++i + 1) ? this.floatParameter (++i) : 0.5);
if (eval.isColorParam (i + 1)) {
slabColix = Short.$valueOf (JU.C.getColixTranslucent3 (JU.C.getColix (eval.getArgbParam (i + 1)), slabTranslucency != 0, slabTranslucency));
i = eval.iToken;
} else {
slabColix = Short.$valueOf (JU.C.getColixTranslucent3 (1, slabTranslucency != 0, slabTranslucency));
}switch (tok = this.tokAt (i + 1)) {
case 1073742018:
case 1073741938:
slabMeshType = Integer.$valueOf (tok);
tok = this.tokAt (++i + 1);
break;
default:
slabMeshType = Integer.$valueOf (1073741938);
break;
}
}switch (tok) {
case 1048588:
eval.iToken = i + 1;
return Integer.$valueOf (-2147483648);
case 1048587:
eval.iToken = i + 1;
break;
case 1048582:
i++;
data = [Float.$valueOf (1), this.paramAsStr (++i)];
tok = 1073742018;
break;
case 135266325:
i++;
if (this.tokAt (++i) == 1073742114) {
d = this.floatParameter (++i);
d2 = this.floatParameter (++i);
data = [Float.$valueOf (d), Float.$valueOf (d2)];
tok = 1073742114;
} else if (this.isFloatParameter (i)) {
d = this.floatParameter (i);
if (eval.isCenterParameter (++i)) {
var pt = this.centerParameter (i);
if (this.chk || !(Clazz_instanceOf (eval.expressionResult, JU.BS))) {
pts = [pt];
} else {
var atoms = this.vwr.ms.at;
bs = eval.expressionResult;
pts =  new Array (bs.cardinality ());
for (var k = 0, j = bs.nextSetBit (0); j >= 0; j = bs.nextSetBit (j + 1), k++) pts[k] = atoms[j];

}} else {
pts = eval.getPointArray (i, -1);
}if (pts.length == 0) {
eval.iToken = i;
this.invArg ();
}data = [Float.$valueOf (d), pts, bs];
} else {
data = eval.getPointArray (i, 4);
tok = 1679429641;
}break;
case 1679429641:
eval.iToken = i + 1;
data = JU.BoxInfo.getCriticalPoints (this.vwr.ms.getBBoxVertices (), null);
break;
case 1073741872:
case 1614417948:
eval.iToken = i + 1;
var unitCell = this.vwr.getCurrentUnitCell ();
if (unitCell == null) {
if (tok == 1614417948) this.invArg ();
} else {
pts = JU.BoxInfo.getCriticalPoints (unitCell.getUnitCellVertices (), unitCell.getCartesianOffset ());
var iType = Clazz_floatToInt (unitCell.getUnitCellInfoType (6));
var v1 = null;
var v2 = null;
switch (iType) {
case 3:
break;
case 1:
v2 = JU.V3.newVsub (pts[2], pts[0]);
v2.scale (1000);
case 2:
v1 = JU.V3.newVsub (pts[1], pts[0]);
v1.scale (1000);
pts[0].sub (v1);
pts[1].scale (2000);
if (iType == 1) {
pts[0].sub (v2);
pts[2].scale (2000);
}break;
}
data = pts;
}break;
case 10:
case 1048577:
data = this.atomExpressionAt (i + 1);
tok = 3;
if (!eval.isCenterParameter (++eval.iToken)) break;
data = null;
default:
if (!isLcaoCartoon && isSlab && this.isFloatParameter (i + 1)) {
d = this.floatParameter (++i);
if (!this.isFloatParameter (i + 1)) return Integer.$valueOf (Clazz_floatToInt (d));
d2 = this.floatParameter (++i);
data = [Float.$valueOf (d), Float.$valueOf (d2)];
tok = 1073742114;
break;
}plane = eval.planeParameter (++i);
var off = (this.isFloatParameter (eval.iToken + 1) ? this.floatParameter (++eval.iToken) : NaN);
if (!Float.isNaN (off)) plane.w -= off;
data = plane;
tok = 135266319;
}
var colorData = (slabMeshType == null ? null : [slabMeshType, slabColix]);
return JU.TempArray.getSlabObjectType (tok, data, !isSlab, colorData);
}, "~N,~B");
Clazz_defineMethod (c$, "getIsosurfaceJvxl", 
 function (asMesh, iShape) {
if (this.chk) return "";
return this.getShapeProperty (iShape, asMesh ? "jvxlMeshX" : "jvxlDataXml");
}, "~B,~N");
Clazz_defineMethod (c$, "getMoJvxl", 
 function (ptMO) {
this.sm.loadShape (27);
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) this.e.errorStr (30, "MO isosurfaces");
var moData = this.vwr.getModelAuxiliaryInfoValue (modelIndex, "moData");
if (moData == null) this.error (27);
var n = this.getShapeProperty (27, "moNumber");
if (n == null || n.intValue () == 0) {
this.setShapeProperty (27, "init", Integer.$valueOf (modelIndex));
}this.setShapeProperty (27, "moData", moData);
return this.getShapePropertyIndex (27, "showMO", ptMO);
}, "~N");
Clazz_defineMethod (c$, "getScriptID", 
 function (context) {
var fuName = (context == null ? this.e.functionName : "function " + context.functionName);
var fiName = (context == null ? this.e.scriptFileName : context.scriptFileName);
return "\n# " + fuName + " (file " + fiName + (context == null ? "" : " context " + context.id) + ")\n";
}, "JS.ScriptContext");
Clazz_defineMethod (c$, "getShapePropertyIndex", 
 function (shapeType, propertyName, index) {
return this.sm.getShapePropertyIndex (shapeType, propertyName, index);
}, "~N,~S,~N");
Clazz_defineMethod (c$, "tokenAt", 
 function (i, args) {
return (i < args.length ? args[i] : null);
}, "~N,~A");
c$.tokAtArray = Clazz_defineMethod (c$, "tokAtArray", 
 function (i, args) {
return (i < args.length && args[i] != null ? args[i].tok : 0);
}, "~N,~A");
Clazz_defineMethod (c$, "finalizeObject", 
 function (shapeID, colorArgb, translucentLevel, intScale, doSet, data, iptDisplayProperty, bs) {
if (doSet) {
this.setShapeProperty (shapeID, "set", data);
}if (colorArgb != -2147483648) this.e.setShapePropertyBs (shapeID, "color", Integer.$valueOf (colorArgb), bs);
if (translucentLevel != 3.4028235E38) this.e.setShapeTranslucency (shapeID, "", "translucent", translucentLevel, bs);
if (intScale != 0) {
this.setShapeProperty (shapeID, "scale", Integer.$valueOf (intScale));
}if (iptDisplayProperty > 0) {
if (!this.e.setMeshDisplayProperty (shapeID, iptDisplayProperty, 0)) this.invArg ();
}}, "~N,~N,~N,~N,~B,~O,~N,JU.BS");
Clazz_defineMethod (c$, "moCombo", 
 function (propertyList) {
if (this.tokAt (this.e.iToken + 1) != 1073742156) return null;
this.addShapeProperty (propertyList, "squareLinear", Boolean.TRUE);
this.e.iToken++;
return  Clazz_newFloatArray (0, 0);
}, "JU.Lst");
Clazz_defineMethod (c$, "moOffset", 
 function (index) {
var isHomo = (this.getToken (index).tok == 1073741973);
var offset = (isHomo ? 0 : 1);
var tok = this.tokAt (++index);
if (tok == 2 && this.intParameter (index) < 0) offset += this.intParameter (index);
 else if (tok == 269484193) offset += this.intParameter (++index);
 else if (tok == 269484192) offset -= this.intParameter (++index);
return offset;
}, "~N");
Clazz_defineMethod (c$, "setMoData", 
 function (propertyList, moNumber, lc, offset, isNegOffset, modelIndex, title) {
var eval = this.e;
if (this.chk) return;
if (modelIndex < 0) {
modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) eval.errorStr (30, "MO isosurfaces");
}var moData = this.vwr.getModelAuxiliaryInfoValue (modelIndex, "moData");
var mos = null;
var mo;
var f;
var nOrb = 0;
if (lc == null || lc.length < 2) {
if (lc != null && lc.length == 1) offset = 0;
if (moData == null) this.error (27);
var lastMoNumber = (moData.containsKey ("lastMoNumber") ? (moData.get ("lastMoNumber")).intValue () : 0);
var lastMoCount = (moData.containsKey ("lastMoCount") ? (moData.get ("lastMoCount")).intValue () : 1);
if (moNumber == 1073742108) moNumber = lastMoNumber - 1;
 else if (moNumber == 1073742037) moNumber = lastMoNumber + lastMoCount;
mos = (moData.get ("mos"));
nOrb = (mos == null ? 0 : mos.size ());
if (nOrb == 0) this.error (25);
if (nOrb == 1 && moNumber > 1) this.error (29);
if (offset != 2147483647) {
if (moData.containsKey ("HOMO")) {
moNumber = (moData.get ("HOMO")).intValue () + offset;
} else {
moNumber = -1;
for (var i = 0; i < nOrb; i++) {
mo = mos.get (i);
if ((f = mo.get ("occupancy")) != null) {
if (f.floatValue () < 0.5) {
moNumber = i;
break;
}continue;
} else if ((f = mo.get ("energy")) != null) {
if (f.floatValue () > 0) {
moNumber = i;
break;
}continue;
}break;
}
if (moNumber < 0) this.error (28);
moNumber += offset;
}JU.Logger.info ("MO " + moNumber);
}if (moNumber < 1 || moNumber > nOrb) eval.errorStr (26, "" + nOrb);
}moNumber = Math.abs (moNumber);
moData.put ("lastMoNumber", Integer.$valueOf (moNumber));
moData.put ("lastMoCount", Integer.$valueOf (1));
if (isNegOffset && lc == null) lc = [-100, moNumber];
if (lc != null && lc.length < 2) {
mo = mos.get (moNumber - 1);
if ((f = mo.get ("energy")) == null) {
lc = [100, moNumber];
} else {
var energy = f.floatValue ();
var bs = JU.BS.newN (nOrb);
var n = 0;
var isAllElectrons = (lc.length == 1 && lc[0] == 1);
for (var i = 0; i < nOrb; i++) {
if ((f = mos.get (i).get ("energy")) == null) continue;
var e = f.floatValue ();
if (isAllElectrons ? e <= energy : e == energy) {
bs.set (i + 1);
n += 2;
}}
lc =  Clazz_newFloatArray (n, 0);
for (var i = 0, pt = 0; i < n; i += 2) {
lc[i] = 1;
lc[i + 1] = (pt = bs.nextSetBit (pt + 1));
}
moData.put ("lastMoNumber", Integer.$valueOf (bs.nextSetBit (0)));
moData.put ("lastMoCount", Integer.$valueOf (Clazz_doubleToInt (n / 2)));
}this.addShapeProperty (propertyList, "squareLinear", Boolean.TRUE);
}this.addShapeProperty (propertyList, "moData", moData);
if (title != null) this.addShapeProperty (propertyList, "title", title);
this.addShapeProperty (propertyList, "molecularOrbital", lc != null ? lc : Integer.$valueOf (Math.abs (moNumber)));
this.addShapeProperty (propertyList, "clear", null);
}, "JU.Lst,~N,~A,~N,~B,~N,~S");
Clazz_defineMethod (c$, "getPlotMinMax", 
 function (data, isMax, tok) {
if (data == null) return 0;
switch (tok) {
case 1112539144:
case 1112539145:
case 1112539146:
return (isMax ? 180 : -180);
case 1112539141:
case 1112539152:
return (isMax ? 360 : 0);
case 1112539150:
return (isMax ? 1 : -1);
}
var fmax = (isMax ? -1.0E10 : 1E10);
for (var i = data.length; --i >= 0; ) {
var f = data[i];
if (Float.isNaN (f)) continue;
if (isMax == (f > fmax)) fmax = f;
}
return fmax;
}, "~A,~B,~N");
Clazz_defineMethod (c$, "initIsosurface", 
 function (iShape) {
var eval = this.e;
this.setShapeProperty (iShape, "init", this.fullCommand);
eval.iToken = 0;
var tok1 = this.tokAt (1);
var tok2 = this.tokAt (2);
if (tok1 == 12291 || tok2 == 12291 && this.tokAt (++eval.iToken) == 1048579) {
this.setShapeProperty (iShape, "delete", null);
eval.iToken += 2;
if (this.slen > eval.iToken) {
this.setShapeProperty (iShape, "init", this.fullCommand);
this.setShapeProperty (iShape, "thisID", "+PREVIOUS_MESH+");
}return null;
}eval.iToken = 1;
if (!eval.setMeshDisplayProperty (iShape, 0, tok1)) {
this.setShapeProperty (iShape, "thisID", "+PREVIOUS_MESH+");
if (iShape != 22) this.setShapeProperty (iShape, "title", [this.thisCommand]);
if (tok1 != 1074790550 && (tok2 == 269484209 || tok1 == 269484209 && eval.setMeshDisplayProperty (iShape, 0, tok2))) {
var id = this.setShapeId (iShape, 1, false);
eval.iToken++;
return id;
}}return null;
}, "~N");
Clazz_defineMethod (c$, "getWithinDistanceVector", 
 function (propertyList, distance, ptc, bs, isShow) {
var v =  new JU.Lst ();
var pts =  new Array (2);
if (bs == null) {
var pt1 = JU.P3.new3 (distance, distance, distance);
var pt0 = JU.P3.newP (ptc);
pt0.sub (pt1);
pt1.add (ptc);
pts[0] = pt0;
pts[1] = pt1;
v.addLast (ptc);
} else {
var bbox = this.vwr.ms.getBoxInfo (bs, -Math.abs (distance));
pts[0] = bbox.getBoundBoxVertices ()[0];
pts[1] = bbox.getBoundBoxVertices ()[7];
if (bs.cardinality () == 1) v.addLast (this.vwr.getAtomPoint3f (bs.nextSetBit (0)));
}if (v.size () == 1 && !isShow) {
this.addShapeProperty (propertyList, "withinDistance", Float.$valueOf (distance));
this.addShapeProperty (propertyList, "withinPoint", v.get (0));
}this.addShapeProperty (propertyList, (isShow ? "displayWithin" : "withinPoints"), [Float.$valueOf (distance), pts, bs, v]);
}, "JU.Lst,~N,JU.P3,JU.BS,~B");
Clazz_defineMethod (c$, "setColorOptions", 
 function (sb, index, iShape, nAllowed) {
var eval = this.e;
this.getToken (index);
var translucency = "opaque";
if (eval.theTok == 603979967) {
translucency = "translucent";
if (nAllowed < 0) {
var value = (this.isFloatParameter (index + 1) ? this.floatParameter (++index) : 3.4028235E38);
eval.setShapeTranslucency (iShape, null, "translucent", value, null);
if (sb != null) {
sb.append (" translucent");
if (value != 3.4028235E38) sb.append (" ").appendF (value);
}} else {
eval.setMeshDisplayProperty (iShape, index, eval.theTok);
}} else if (eval.theTok == 1073742074) {
if (nAllowed >= 0) eval.setMeshDisplayProperty (iShape, index, eval.theTok);
} else {
eval.iToken--;
}nAllowed = Math.abs (nAllowed);
for (var i = 0; i < nAllowed; i++) {
if (eval.isColorParam (eval.iToken + 1)) {
var color = eval.getArgbParam (++eval.iToken);
this.setShapeProperty (iShape, "colorRGB", Integer.$valueOf (color));
if (sb != null) sb.append (" ").append (JU.Escape.escapeColor (color));
} else if (eval.iToken < index) {
this.invArg ();
} else {
break;
}}
return translucency;
}, "JU.SB,~N,~N,~N");
Clazz_defineMethod (c$, "createFunction", 
 function (fname, xyz, ret) {
var e = ( new JS.ScriptEval ()).setViewer (this.vwr);
try {
e.compileScript (null, "function " + fname + "(" + xyz + ") { return " + ret + "}", false);
var params =  new JU.Lst ();
for (var i = 0; i < xyz.length; i += 2) params.addLast (JS.SV.newV (3, Float.$valueOf (0)).setName (xyz.substring (i, i + 1)));

return [e.aatoken[0][1].value, params];
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
return null;
} else {
throw ex;
}
}
}, "~S,~S,~S");
Clazz_defineMethod (c$, "floatArraySet", 
 function (i, nX, nY) {
var tok = this.tokAt (i++);
if (tok == 1073742195) tok = this.tokAt (i++);
if (tok != 269484096) this.invArg ();
var fparams = JU.AU.newFloat2 (nX);
var n = 0;
while (tok != 269484097) {
tok = this.getToken (i).tok;
switch (tok) {
case 1073742195:
case 269484097:
continue;
case 269484080:
i++;
break;
case 269484096:
i++;
var f =  Clazz_newFloatArray (nY, 0);
fparams[n++] = f;
for (var j = 0; j < nY; j++) {
f[j] = this.floatParameter (i++);
if (this.tokAt (i) == 269484080) i++;
}
if (this.tokAt (i++) != 269484097) this.invArg ();
tok = 0;
if (n == nX && this.tokAt (i) != 269484097) this.invArg ();
break;
default:
this.invArg ();
}
}
return fparams;
}, "~N,~N,~N");
Clazz_defineMethod (c$, "floatArraySetXYZ", 
 function (i, nX, nY, nZ) {
var eval = this.e;
var tok = this.tokAt (i++);
if (tok == 1073742195) tok = this.tokAt (i++);
if (tok != 269484096 || nX <= 0) this.invArg ();
var fparams = JU.AU.newFloat3 (nX, -1);
var n = 0;
while (tok != 269484097) {
tok = this.getToken (i).tok;
switch (tok) {
case 1073742195:
case 269484097:
continue;
case 269484080:
i++;
break;
case 269484096:
fparams[n++] = this.floatArraySet (i, nY, nZ);
i = ++eval.iToken;
tok = 0;
if (n == nX && this.tokAt (i) != 269484097) this.invArg ();
break;
default:
this.invArg ();
}
}
return fparams;
}, "~N,~N,~N,~N");
Clazz_overrideMethod (c$, "getBitsetIdent", 
function (bs, label, tokenValue, useAtomMap, index, isExplicitlyAll) {
var isAtoms = !(Clazz_instanceOf (tokenValue, JM.BondSet));
if (isAtoms) {
if (label == null) label = this.vwr.getStandardLabelFormat (0);
 else if (label.length == 0) label = "%[label]";
}var pt = (label == null ? -1 : label.indexOf ("%"));
var haveIndex = (index != 2147483647);
if (bs == null || this.chk || isAtoms && pt < 0) {
if (label == null) label = "";
return isExplicitlyAll ? [label] : label;
}var modelSet = this.vwr.ms;
var n = 0;
var labeler = modelSet.getLabeler ();
var indices = (isAtoms || !useAtomMap ? null : (tokenValue).getAssociatedAtoms ());
if (indices == null && label != null && label.indexOf ("%D") > 0) indices = this.vwr.ms.getAtomIndices (bs);
var asIdentity = (label == null || label.length == 0);
var htValues = (isAtoms || asIdentity ? null : JM.LabelToken.getBondLabelValues ());
var tokens = (asIdentity ? null : isAtoms ? labeler.compile (this.vwr, label, '\0', null) : labeler.compile (this.vwr, label, '\1', htValues));
var nmax = (haveIndex ? 1 : JU.BSUtil.cardinalityOf (bs));
var sout =  new Array (nmax);
var ptTemp =  new JU.P3 ();
for (var j = (haveIndex ? index : bs.nextSetBit (0)); j >= 0; j = bs.nextSetBit (j + 1)) {
var str;
if (isAtoms) {
if (asIdentity) str = modelSet.at[j].getInfo ();
 else str = labeler.formatLabelAtomArray (this.vwr, modelSet.at[j], tokens, '\0', indices, ptTemp);
} else {
var bond = modelSet.getBondAt (j);
if (asIdentity) str = bond.getIdentity ();
 else str = labeler.formatLabelBond (this.vwr, bond, tokens, htValues, indices, ptTemp);
}str = JU.Txt.formatStringI (str, "#", (n + 1));
sout[n++] = str;
if (haveIndex) break;
}
return nmax == 1 && !isExplicitlyAll ? sout[0] : sout;
}, "JU.BS,~S,~O,~B,~N,~B");
Clazz_defineMethod (c$, "listIsosurface", 
 function (iShape) {
var s = (this.slen > 3 ? "0" : this.tokAt (2) == 0 ? "" : " " + this.getToken (2).value);
if (!this.chk) this.showString (this.getShapeProperty (iShape, "list" + s));
return true;
}, "~N");
Clazz_defineMethod (c$, "setShapeId", 
 function (iShape, i, idSeen) {
if (idSeen) this.invArg ();
var name = this.e.setShapeNameParameter (i).toLowerCase ();
this.setShapeProperty (iShape, "thisID", name);
return name;
}, "~N,~N,~B");
Clazz_defineMethod (c$, "parseDataArray", 
 function (str, is3D) {
str = JU.Parser.fixDataString (str);
var lines = JU.Parser.markLines (str, '\n');
var nLines = lines.length;
if (!is3D) {
var data = JU.AU.newFloat2 (nLines);
for (var iLine = 0, pt = 0; iLine < nLines; pt = lines[iLine++]) {
var tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
JU.PT.parseFloatArrayData (tokens, data[iLine] =  Clazz_newFloatArray (tokens.length, 0));
}
return data;
}var tokens = JU.PT.getTokens (str.substring (0, lines[0]));
if (tokens.length != 3) return  Clazz_newFloatArray (0, 0, 0, 0);
var nX = JU.PT.parseInt (tokens[0]);
var nY = JU.PT.parseInt (tokens[1]);
var nZ = JU.PT.parseInt (tokens[2]);
if (nX < 1 || nY < 1 || nZ < 1) return  Clazz_newFloatArray (1, 1, 1, 0);
var data = JU.AU.newFloat3 (nX, nY);
var iX = 0;
var iY = 0;
for (var iLine = 1, pt = lines[0]; iLine < nLines && iX < nX; pt = lines[iLine++]) {
tokens = JU.PT.getTokens (str.substring (pt, lines[iLine]));
if (tokens.length < nZ) continue;
JU.PT.parseFloatArrayData (tokens, data[iX][iY] =  Clazz_newFloatArray (tokens.length, 0));
if (++iY == nY) {
iX++;
iY = 0;
}}
if (iX != nX) {
System.out.println ("Error reading 3D data -- nX = " + nX + ", but only " + iX + " blocks read");
return  Clazz_newFloatArray (1, 1, 1, 0);
}return data;
}, "~S,~B");
Clazz_defineStatics (c$,
"ERROR_invalidArgument", 22);
});
})(Clazz
,Clazz.newLongArray
,Clazz.doubleToByte
,Clazz.doubleToInt
,Clazz.doubleToLong
,Clazz.declarePackage
,Clazz.instanceOf
,Clazz.load
,Clazz.instantialize
,Clazz.decorateAsClass
,Clazz.floatToInt
,Clazz.makeConstructor
,Clazz.defineEnumConstant
,Clazz.exceptionOf
,Clazz.newIntArray
,Clazz.defineStatics
,Clazz.newFloatArray
,Clazz.declareType
,Clazz.prepareFields
,Clazz.superConstructor
,Clazz.newByteArray
,Clazz.declareInterface
,Clazz.p0p
,Clazz.pu$h
,Clazz.newShortArray
,Clazz.innerTypeInstance
,Clazz.isClassDefined
,Clazz.prepareCallback
,Clazz.newArray
,Clazz.castNullAs
,Clazz.floatToShort
,Clazz.superCall
,Clazz.decorateAsType
,Clazz.newBooleanArray
,Clazz.newCharArray
,Clazz.implementOf
,Clazz.newDoubleArray
,Clazz.overrideConstructor
,Clazz.clone
,Clazz.doubleToShort
,Clazz.getInheritedLevel
,Clazz.getParamsType
,Clazz.isAF
,Clazz.isAI
,Clazz.isAS
,Clazz.isASS
,Clazz.isAP
,Clazz.isAFloat
,Clazz.isAII
,Clazz.isAFF
,Clazz.isAFFF
,Clazz.tryToSearchAndExecute
,Clazz.getStackTrace
,Clazz.inheritArgs
,Clazz.alert
,Clazz.defineMethod
,Clazz.overrideMethod
,Clazz.declareAnonymous
//,Clazz.checkPrivateMethod
,Clazz.cloneFinals
);