static/j2s/core/corescriptmath.js

(function(Clazz
,Clazz_getClassName
,Clazz_newLongArray
,Clazz_doubleToByte
,Clazz_doubleToInt
,Clazz_doubleToLong
,Clazz_declarePackage
,Clazz_instanceOf
,Clazz_load
,Clazz_instantialize
,Clazz_decorateAsClass
,Clazz_floatToInt
,Clazz_floatToLong
,Clazz_makeConstructor
,Clazz_defineEnumConstant
,Clazz_exceptionOf
,Clazz_newIntArray
,Clazz_defineStatics
,Clazz_newFloatArray
,Clazz_declareType
,Clazz_prepareFields
,Clazz_superConstructor
,Clazz_newByteArray
,Clazz_declareInterface
,Clazz_p0p
,Clazz_pu$h
,Clazz_newShortArray
,Clazz_innerTypeInstance
,Clazz_isClassDefined
,Clazz_prepareCallback
,Clazz_newArray
,Clazz_castNullAs
,Clazz_floatToShort
,Clazz_superCall
,Clazz_decorateAsType
,Clazz_newBooleanArray
,Clazz_newCharArray
,Clazz_implementOf
,Clazz_newDoubleArray
,Clazz_overrideConstructor
,Clazz_clone
,Clazz_doubleToShort
,Clazz_getInheritedLevel
,Clazz_getParamsType
,Clazz_isAF
,Clazz_isAB
,Clazz_isAI
,Clazz_isAS
,Clazz_isASS
,Clazz_isAP
,Clazz_isAFloat
,Clazz_isAII
,Clazz_isAFF
,Clazz_isAFFF
,Clazz_tryToSearchAndExecute
,Clazz_getStackTrace
,Clazz_inheritArgs
,Clazz_alert
,Clazz_defineMethod
,Clazz_overrideMethod
,Clazz_declareAnonymous
//,Clazz_checkPrivateMethod
,Clazz_cloneFinals
){
var $t$;
//var c$;
Clazz_declarePackage ("JS");
Clazz_load (null, "JS.MathExt", ["java.lang.Float", "$.Number", "java.util.Date", "$.Hashtable", "$.Random", "JU.AU", "$.BS", "$.CU", "$.Lst", "$.M4", "$.Measure", "$.OC", "$.P3", "$.P4", "$.PT", "$.Quat", "$.Rdr", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.bspt.PointIterator", "J.c.VDW", "J.i18n.GT", "JM.BondSet", "JS.SV", "$.ScriptParam", "$.T", "JU.BSUtil", "$.Escape", "$.JmolMolecule", "$.Logger", "$.Parser", "$.Point3fi", "$.SimpleUnitCell", "JV.FileManager", "$.JC", "$.Viewer"], function () {
c$ = Clazz_decorateAsClass (function () {
this.vwr = null;
this.e = null;
this.rand = null;
this.pm = null;
Clazz_instantialize (this, arguments);
}, JS, "MathExt");
Clazz_makeConstructor (c$, 
function () {
});
Clazz_defineMethod (c$, "init", 
function (se) {
this.e = se;
this.vwr = this.e.vwr;
return this;
}, "~O");
Clazz_defineMethod (c$, "evaluate", 
function (mp, op, args, tok) {
switch (tok) {
case 134218250:
case 134218242:
case 134218245:
case 134217749:
case 134218244:
case 134218246:
return this.evaluateMath (mp, args, tok);
case 1275069441:
case 1275068928:
case 1275068929:
case 1275068930:
case 1275068931:
case 1275335685:
case 1275334681:
return this.evaluateList (mp, op.intValue, args);
case 268435520:
if (args.length == 0) mp.wasX = false;
case 1275068418:
return this.evaluateArray (mp, args, tok == 1275068418 && op.tok == 268435665);
case 134217731:
case 134221850:
return this.evaluateQuaternion (mp, args, tok);
case 1275068420:
return this.evaluateBin (mp, args);
case 134221829:
return this.evaluateCache (mp, args);
case 1275068934:
case 1275068935:
return this.evaluateRowCol (mp, args, tok);
case 1765808134:
return this.evaluateColor (mp, args);
case 134221831:
return this.evaluateCompare (mp, args);
case 1228931587:
case 134217736:
case 1275203608:
return this.evaluateConnected (mp, args, tok, op.intValue);
case 1814695966:
return this.evaluateUnitCell (mp, args, op.tok == 268435665);
case 134353926:
return this.evaluateContact (mp, args);
case 134221834:
return this.evaluateData (mp, args);
case 1275069444:
case 1275069442:
return this.evaluateDotDist (mp, args, tok, op.intValue);
case 1275069443:
if (op.tok == 268435665) return this.evaluateDotDist (mp, args, tok, op.intValue);
case 134217729:
case 1745489939:
return this.evaluateMeasure (mp, args, op.tok);
case 1228935687:
case 134222849:
return this.evaluateLoad (mp, args, tok == 1228935687);
case 1275068427:
return this.evaluateFind (mp, args);
case 1287653388:
case 1825200146:
return this.evaluateFormat (mp, op.intValue, args, tok == 1825200146);
case 134320141:
return this.evaluateUserFunction (mp, op.value, args, op.intValue, op.tok == 268435665);
case 1275068449:
case 1275082245:
case 1275072526:
return this.evaluateGetProperty (mp, args, tok, op.tok == 268435665);
case 136314895:
return this.evaluateHelix (mp, args);
case 134219265:
case 134217750:
case 134217763:
return this.evaluatePlane (mp, args, tok);
case 134218759:
case 134238732:
case 134222850:
case 134222350:
return this.evaluateScript (mp, args, tok);
case 1275069446:
case 1275069447:
case 1275068932:
return this.evaluateString (mp, op.intValue, args);
case 134217751:
return this.evaluatePoint (mp, args);
case 134217762:
return this.evaluatePointGroup (mp, args);
case 134256131:
return this.evaluatePrompt (mp, args);
case 134219268:
return this.evaluateRandom (mp, args);
case 1275068432:
return this.evaluateIn (mp, args);
case 1275072532:
return this.evaluateModulation (mp, args);
case 1275068443:
return this.evaluateReplace (mp, args);
case 134218756:
case 134218757:
case 1237320707:
return this.evaluateSubstructure (mp, args, tok, op.tok == 268435665);
case 1275068444:
case 1275068425:
return this.evaluateSort (mp, args, tok);
case 1296041986:
return this.evaluateSymop (mp, args, op.tok == 268435665);
case 1275068445:
return this.evaluateTensor (mp, args);
case 134217759:
return this.evaluateWithin (mp, args);
case 134221856:
return this.evaluateWrite (mp, args);
}
return false;
}, "JS.ScriptMathProcessor,JS.T,~A,~N");
Clazz_defineMethod (c$, "evaluatePointGroup", 
 function (mp, args) {
var pts = null;
var center = null;
var distanceTolerance = NaN;
var linearTolerance = NaN;
var bsAtoms;
switch (args.length) {
case 4:
linearTolerance = args[3].asFloat ();
case 3:
distanceTolerance = args[2].asFloat ();
case 2:
switch (args[1].tok) {
case 8:
center = JS.SV.ptValue (args[1]);
break;
case 10:
bsAtoms = JS.SV.getBitSet (args[1], false);
var iatom = bsAtoms.nextSetBit (0);
if (iatom < 0 || iatom >= this.vwr.ms.ac || bsAtoms.cardinality () != 1) return false;
if (JS.SV.sValue (args[0]).equalsIgnoreCase ("spaceGroup")) {
var lst = this.vwr.ms.generateCrystalClass (iatom, JU.P3.new3 (NaN, NaN, NaN));
pts =  new Array (lst.size ());
for (var i = pts.length; --i >= 0; ) pts[i] = lst.get (i);

center =  new JU.P3 ();
if (args.length == 2) distanceTolerance = 0;
} else {
center = this.vwr.ms.at[iatom];
}}
if (pts != null) break;
case 1:
switch (args[0].tok) {
case 7:
var points = args[0].getList ();
pts =  new Array (points.size ());
for (var i = pts.length; --i >= 0; ) pts[i] = JS.SV.ptValue (points.get (i));

break;
case 10:
bsAtoms = JS.SV.getBitSet (args[0], false);
var atoms = this.vwr.ms.getAtomPointVector (bsAtoms);
pts =  new Array (atoms.size ());
for (var i = pts.length; --i >= 0; ) pts[i] = atoms.get (i);

break;
default:
return false;
}
break;
default:
return false;
}
var pointGroup = this.vwr.getSymTemp ().setPointGroup (null, center, pts, null, false, Float.isNaN (distanceTolerance) ? this.vwr.getFloat (570425382) : distanceTolerance, Float.isNaN (linearTolerance) ? this.vwr.getFloat (570425384) : linearTolerance, true);
return mp.addXMap (pointGroup.getPointGroupInfo (-1, null, true, null, 0, 1));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateUnitCell", 
 function (mp, args, isSelector) {
var x1 = (isSelector ? JS.SV.getBitSet (mp.getX (), true) : null);
var iatom = ((x1 == null ? this.vwr.getAllAtoms () : x1).nextSetBit (0));
var lastParam = args.length - 1;
var scale = 1;
switch (lastParam < 0 ? 0 : args[lastParam].tok) {
case 2:
case 3:
scale = args[lastParam].asFloat ();
lastParam--;
break;
}
var tok0 = (lastParam < 0 ? 0 : args[0].tok);
var ucnew = null;
var uc = null;
switch (tok0) {
case 7:
uc = args[0].getList ();
break;
case 4:
var s = args[0].asString ();
if (s.indexOf ("a=") == 0) {
ucnew =  new Array (4);
for (var i = 0; i < 4; i++) ucnew[i] =  new JU.P3 ();

JU.SimpleUnitCell.setOabc (s, null, ucnew);
} else if (s.indexOf (",") >= 0) {
return mp.addXObj (this.vwr.getV0abc (s));
}break;
}
var u = null;
var haveUC = (uc != null);
if (ucnew == null && haveUC && uc.size () < 4) return false;
var ptParam = (haveUC ? 1 : 0);
if (ucnew == null && !haveUC && tok0 != 8) {
u = (iatom < 0 ? null : this.vwr.ms.getUnitCell (this.vwr.ms.at[iatom].mi));
ucnew = (u == null ?  Clazz_newArray (-1, [JU.P3.new3 (0, 0, 0), JU.P3.new3 (1, 0, 0), JU.P3.new3 (0, 1, 0), JU.P3.new3 (0, 0, 1)]) : u.getUnitCellVectors ());
}if (ucnew == null) {
ucnew =  new Array (4);
if (haveUC) {
switch (uc.size ()) {
case 3:
ucnew[0] =  new JU.P3 ();
for (var i = 0; i < 3; i++) ucnew[i + 1] = JU.P3.newP (JS.SV.ptValue (uc.get (i)));

break;
case 4:
for (var i = 0; i < 4; i++) ucnew[i] = JU.P3.newP (JS.SV.ptValue (uc.get (i)));

break;
case 6:
var params =  Clazz_newFloatArray (6, 0);
for (var i = 0; i < 6; i++) params[i] = uc.get (i).asFloat ();

JU.SimpleUnitCell.setOabc (null, params, ucnew);
break;
default:
return false;
}
} else {
ucnew[0] = JS.SV.ptValue (args[0]);
switch (lastParam) {
case 3:
for (var i = 1; i < 4; i++) (ucnew[i] = JU.P3.newP (JS.SV.ptValue (args[i]))).sub (ucnew[0]);

break;
case 1:
var l = args[1].getList ();
if (l != null && l.size () == 3) {
for (var i = 0; i < 3; i++) ucnew[i + 1] = JS.SV.ptValue (l.get (i));

break;
}default:
return false;
}
}}var op = (ptParam <= lastParam ? args[ptParam].asString () : null);
var toPrimitive = "primitive".equalsIgnoreCase (op);
if (toPrimitive || "conventional".equalsIgnoreCase (op)) {
var stype = (++ptParam > lastParam ? "" : args[ptParam].asString ().toUpperCase ());
if (stype.equals ("BCC")) stype = "I";
 else if (stype.length == 0) stype = this.vwr.getSymTemp ().getSymmetryInfoAtom (this.vwr.ms, iatom, null, 0, null, null, null, 1073741994, 0, -1);
if (stype == null || stype.length == 0) return false;
if (u == null) u = this.vwr.getSymTemp ();
var m3 = this.vwr.getModelForAtomIndex (iatom).auxiliaryInfo.get ("primitiveToCrystal");
if (!u.toFromPrimitive (toPrimitive, stype.charAt (0), ucnew, m3)) return false;
} else if ("reciprocal".equalsIgnoreCase (op)) {
ucnew = JU.SimpleUnitCell.getReciprocal (ucnew, null, scale);
scale = 1;
}if (scale != 1) for (var i = 1; i < 4; i++) ucnew[i].scale (scale);

return mp.addXObj (ucnew);
}, "JS.ScriptMathProcessor,~A,~B");
Clazz_defineMethod (c$, "evaluateArray", 
 function (mp, args, isSelector) {
if (isSelector) {
var x1 = mp.getX ();
switch (args.length == 1 ? x1.tok : 0) {
case 6:
var lst =  new JU.Lst ();
var id = args[0].asString ();
var map = x1.getMap ();
var keys = x1.getKeys (false);
for (var i = 0, n = keys.length; i < n; i++) if (map.get (keys[i]).getMap () == null) return false;

for (var i = 0, n = keys.length; i < n; i++) {
var m = map.get (keys[i]);
var m1 = m.getMap ();
var m2 = JS.SV.deepCopy (m1, true, false);
m2.put (id, JS.SV.newS (keys[i]));
lst.addLast (JS.SV.newV (6, m2));
}
return mp.addXList (lst);
case 7:
var map1 =  new java.util.Hashtable ();
var lst1 = x1.getList ();
var id1 = args[0].asString ();
for (var i = 0, n = lst1.size (); i < n; i++) {
var m0 = lst1.get (i).getMap ();
if (m0 == null || m0.get (id1) == null) return false;
}
for (var i = 0, n = lst1.size (); i < n; i++) {
var m = lst1.get (i);
var m1 = JS.SV.deepCopy (m.getMap (), true, false);
var mid = m1.remove (id1);
map1.put (mid.asString (), JS.SV.newV (6, m1));
}
return mp.addXObj (map1);
}
return false;
}var a =  new Array (args.length);
for (var i = a.length; --i >= 0; ) a[i] = JS.SV.newT (args[i]);

return mp.addXAV (a);
}, "JS.ScriptMathProcessor,~A,~B");
Clazz_defineMethod (c$, "evaluateBin", 
 function (mp, args) {
var n = args.length;
if (n < 3 || n > 5) return false;
var x1 = mp.getX ();
var isListf = (x1.tok == 13);
if (!isListf && x1.tok != 7) return mp.addX (x1);
var f0 = JS.SV.fValue (args[0]);
var f1 = JS.SV.fValue (args[1]);
var df = JS.SV.fValue (args[2]);
var addBins = (n >= 4 && args[n - 1].tok == 1073742335);
var key = ((n == 5 || n == 4 && !addBins) && args[3].tok != 1073742334 ? JS.SV.sValue (args[3]) : null);
var data;
var maps = null;
if (isListf) {
data = x1.value;
} else {
var list = x1.getList ();
data =  Clazz_newFloatArray (list.size (), 0);
if (key != null) maps = JU.AU.createArrayOfHashtable (list.size ());
try {
for (var i = list.size (); --i >= 0; ) data[i] = JS.SV.fValue (key == null ? list.get (i) : (maps[i] = list.get (i).getMap ()).get (key));

} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return false;
} else {
throw e;
}
}
}var nbins = Math.max (Clazz_doubleToInt (Math.floor ((f1 - f0) / df + 0.01)), 1);
var array =  Clazz_newIntArray (nbins, 0);
var nPoints = data.length;
for (var i = 0; i < nPoints; i++) {
var v = data[i];
var bin = Clazz_doubleToInt (Math.floor ((v - f0) / df));
if (bin < 0 || bin >= nbins) continue;
array[bin]++;
if (key != null) {
var map = maps[i];
if (map == null) continue;
map.put ("_bin", JS.SV.newI (bin));
var v1 = f0 + df * bin;
var v2 = v1 + df;
map.put ("_binMin", JS.SV.newF (bin == 0 ? -3.4028235E38 : v1));
map.put ("_binMax", JS.SV.newF (bin == nbins - 1 ? 3.4028235E38 : v2));
}}
if (addBins) {
var lst =  new JU.Lst ();
for (var i = 0; i < nbins; i++) lst.addLast ( Clazz_newFloatArray (-1, [f0 + df * i, array[i]]));

return mp.addXList (lst);
}return mp.addXAI (array);
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateCache", 
 function (mp, args) {
if (args.length > 0) return false;
return mp.addXMap (this.vwr.fm.cacheList ());
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateColor", 
 function (mp, args) {
var colorScheme = (args.length > 0 ? JS.SV.sValue (args[0]) : "");
var isIsosurface = colorScheme.startsWith ("$");
if (args.length == 2 && colorScheme.equalsIgnoreCase ("TOHSL")) return mp.addXPt (JU.CU.rgbToHSL (JU.P3.newP (args[1].tok == 8 ? JS.SV.ptValue (args[1]) : JU.CU.colorPtFromString (args[1].asString ())), true));
if (args.length == 2 && colorScheme.equalsIgnoreCase ("TORGB")) {
var pt = JU.P3.newP (args[1].tok == 8 ? JS.SV.ptValue (args[1]) : JU.CU.colorPtFromString (args[1].asString ()));
return mp.addXPt (args[1].tok == 8 ? JU.CU.hslToRGB (pt) : pt);
}if (args.length == 4 && (args[3].tok == 1073742335 || args[3].tok == 1073742334)) {
var pt1 = JU.P3.newP (args[0].tok == 8 ? JS.SV.ptValue (args[0]) : JU.CU.colorPtFromString (args[0].asString ()));
var pt2 = JU.P3.newP (args[1].tok == 8 ? JS.SV.ptValue (args[1]) : JU.CU.colorPtFromString (args[1].asString ()));
var usingHSL = (args[3].tok == 1073742335);
if (usingHSL) {
pt1 = JU.CU.rgbToHSL (pt1, false);
pt2 = JU.CU.rgbToHSL (pt2, false);
}var sb =  new JU.SB ();
var vd = JU.V3.newVsub (pt2, pt1);
var n = args[2].asInt ();
if (n < 2) n = 20;
vd.scale (1 / (n - 1));
for (var i = 0; i < n; i++) {
sb.append (JU.Escape.escapeColor (JU.CU.colorPtToFFRGB (usingHSL ? JU.CU.hslToRGB (pt1) : pt1)));
pt1.add (vd);
}
return mp.addXStr (sb.toString ());
}var ce = (isIsosurface ? null : this.vwr.cm.getColorEncoder (colorScheme));
if (!isIsosurface && ce == null) return mp.addXStr ("");
var lo = (args.length > 1 ? JS.SV.fValue (args[1]) : 3.4028235E38);
var hi = (args.length > 2 ? JS.SV.fValue (args[2]) : 3.4028235E38);
var value = (args.length > 3 ? JS.SV.fValue (args[3]) : 3.4028235E38);
var getValue = (value != 3.4028235E38 || lo != 3.4028235E38 && hi == 3.4028235E38);
var haveRange = (hi != 3.4028235E38);
if (!haveRange && colorScheme.length == 0) {
value = lo;
var range = this.vwr.getCurrentColorRange ();
lo = range[0];
hi = range[1];
}if (isIsosurface) {
var id = colorScheme.substring (1);
var data =  Clazz_newArray (-1, [id, null]);
if (!this.vwr.shm.getShapePropertyData (24, "colorEncoder", data)) return mp.addXStr ("");
ce = data[1];
} else {
ce.setRange (lo, hi, lo > hi);
}var key = ce.getColorKey ();
if (getValue) return mp.addXPt (JU.CU.colorPtFromInt (ce.getArgb (hi == 3.4028235E38 ? lo : value), null));
return mp.addX (JS.SV.getVariableMap (key));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateCompare", 
 function (mp, args) {
if (args.length < 2 || args.length > 5) return false;
var stddev;
var sOpt = JS.SV.sValue (args[args.length - 1]);
var isStdDev = sOpt.equalsIgnoreCase ("stddev");
var isIsomer = sOpt.equalsIgnoreCase ("ISOMER");
var isBonds = sOpt.equalsIgnoreCase ("BONDS");
var isSmiles = (!isIsomer && args.length > (isStdDev ? 3 : 2));
var bs1 = (args[0].tok == 10 ? args[0].value : null);
var bs2 = (args[1].tok == 10 ? args[1].value : null);
var smiles1 = (bs1 == null ? JS.SV.sValue (args[0]) : "");
var smiles2 = (bs2 == null ? JS.SV.sValue (args[1]) : "");
var m =  new JU.M4 ();
stddev = NaN;
var ptsA;
var ptsB;
try {
if (isSmiles) {
if (bs1 == null || bs2 == null) return false;
}if (isBonds) {
if (args.length != 4) return false;
smiles1 = JS.SV.sValue (args[2]);
isSmiles = smiles1.equalsIgnoreCase ("SMILES");
try {
if (isSmiles) smiles1 = this.vwr.getSmiles (bs1);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.e.evalError (ex.getMessage (), null);
} else {
throw ex;
}
}
var data = this.e.getSmilesExt ().getFlexFitList (bs1, bs2, smiles1, !isSmiles);
return (data == null ? mp.addXStr ("") : mp.addXAF (data));
}if (isIsomer) {
if (args.length != 3) return false;
if (bs1 == null && bs2 == null) return mp.addXStr (this.vwr.getSmilesMatcher ().getRelationship (smiles1, smiles2).toUpperCase ());
var mf1 = (bs1 == null ? this.vwr.getSmilesMatcher ().getMolecularFormula (smiles1, false) : JU.JmolMolecule.getMolecularFormulaAtoms (this.vwr.ms.at, bs1, null, false));
var mf2 = (bs2 == null ? this.vwr.getSmilesMatcher ().getMolecularFormula (smiles2, false) : JU.JmolMolecule.getMolecularFormulaAtoms (this.vwr.ms.at, bs2, null, false));
if (!mf1.equals (mf2)) return mp.addXStr ("NONE");
if (bs1 != null) smiles1 = this.e.getSmilesExt ().getSmilesMatches ("/strict///", null, bs1, null, 1, true, false);
var check;
if (bs2 == null) {
check = (this.vwr.getSmilesMatcher ().areEqual (smiles2, smiles1) > 0);
} else {
smiles2 = this.e.getSmilesExt ().getSmilesMatches ("/strict///", null, bs2, null, 1, true, false);
check = ((this.e.getSmilesExt ().getSmilesMatches ("/strict///" + smiles1, null, bs2, null, 1, true, false)).nextSetBit (0) >= 0);
}if (!check) {
var s = smiles1 + smiles2;
if (s.indexOf ("/") >= 0 || s.indexOf ("\\") >= 0 || s.indexOf ("@") >= 0) {
if (smiles1.indexOf ("@") >= 0 && (bs2 != null || smiles2.indexOf ("@") >= 0) && smiles1.indexOf ("@SP") < 0) {
var pt = smiles1.toLowerCase ().indexOf ("invertstereo");
smiles1 = (pt >= 0 ? "/strict/" + smiles1.substring (0, pt) + smiles1.substring (pt + 12) : "/invertstereo strict/" + smiles1);
if (bs2 == null) {
check = (this.vwr.getSmilesMatcher ().areEqual (smiles1, smiles2) > 0);
} else {
check = ((this.e.getSmilesExt ().getSmilesMatches (smiles1, null, bs2, null, 1, true, false)).nextSetBit (0) >= 0);
}if (check) return mp.addXStr ("ENANTIOMERS");
}if (bs2 == null) {
check = (this.vwr.getSmilesMatcher ().areEqual ("/nostereo/" + smiles2, smiles1) > 0);
} else {
var ret = this.e.getSmilesExt ().getSmilesMatches ("/nostereo/" + smiles1, null, bs2, null, 1, true, false);
check = ((ret).nextSetBit (0) >= 0);
}if (check) return mp.addXStr ("DIASTEREOMERS");
}return mp.addXStr ("CONSTITUTIONAL ISOMERS");
}if (bs1 == null || bs2 == null) return mp.addXStr ("IDENTICAL");
stddev = this.e.getSmilesExt ().getSmilesCorrelation (bs1, bs2, smiles1, null, null, null, null, false, null, null, false, 1);
return mp.addXStr (stddev < 0.2 ? "IDENTICAL" : "IDENTICAL or CONFORMATIONAL ISOMERS (RMSD=" + stddev + ")");
}if (isSmiles) {
ptsA =  new JU.Lst ();
ptsB =  new JU.Lst ();
sOpt = JS.SV.sValue (args[2]);
var isMap = sOpt.equalsIgnoreCase ("MAP");
isSmiles = sOpt.equalsIgnoreCase ("SMILES");
var isSearch = (isMap || sOpt.equalsIgnoreCase ("SMARTS"));
if (isSmiles || isSearch) sOpt = (args.length > (isStdDev ? 4 : 3) ? JS.SV.sValue (args[3]) : null);
var hMaps = (("H".equalsIgnoreCase (sOpt) || "allH".equalsIgnoreCase (sOpt) || "bestH".equalsIgnoreCase (sOpt)));
var isPolyhedron = ("polyhedra".equalsIgnoreCase (sOpt));
if (isPolyhedron) sOpt = (args.length > (isStdDev ? 5 : 4) ? JS.SV.sValue (args[4]) : null);
var allMaps = (("all".equalsIgnoreCase (sOpt) || "allH".equalsIgnoreCase (sOpt)));
var bestMap = (("best".equalsIgnoreCase (sOpt) || "bestH".equalsIgnoreCase (sOpt)));
if ("stddev".equals (sOpt)) sOpt = null;
var pattern = sOpt;
if (sOpt == null || hMaps || allMaps || bestMap) {
if (!isMap && !isSmiles || hMaps && isPolyhedron) return false;
pattern = "/noaromatic" + (allMaps || bestMap ? "/" : " nostereo/") + this.e.getSmilesExt ().getSmilesMatches ((hMaps ? "H" : ""), null, bs1, null, 1, true, false);
} else {
allMaps = true;
}stddev = this.e.getSmilesExt ().getSmilesCorrelation (bs1, bs2, pattern, ptsA, ptsB, m, null, isMap, null, null, bestMap, (isSmiles ? 1 : 2) | (!allMaps && !bestMap ? 8 : 0));
if (isMap) {
var nAtoms = ptsA.size ();
if (nAtoms == 0) return mp.addXStr ("");
var nMatch = Clazz_doubleToInt (ptsB.size () / nAtoms);
var ret =  new JU.Lst ();
for (var i = 0, pt = 0; i < nMatch; i++) {
var a = JU.AU.newInt2 (nAtoms);
ret.addLast (a);
for (var j = 0; j < nAtoms; j++, pt++) a[j] =  Clazz_newIntArray (-1, [(ptsA.get (j)).i, (ptsB.get (pt)).i]);

}
return (allMaps ? mp.addXList (ret) : ret.size () > 0 ? mp.addXAII (ret.get (0)) : mp.addXStr (""));
}} else {
switch (args.length) {
case 2:
break;
case 3:
if (isStdDev) break;
default:
return false;
}
ptsA = this.e.getPointVector (args[0], 0);
ptsB = this.e.getPointVector (args[1], 0);
if (ptsA != null && ptsB != null) {
J.api.Interface.getInterface ("JU.Eigen", this.vwr, "script");
stddev = JU.Measure.getTransformMatrix4 (ptsA, ptsB, m, null);
}}return (isStdDev || Float.isNaN (stddev) ? mp.addXFloat (stddev) : mp.addXM4 (m.round (1e-7)));
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.e.evalError (ex.getMessage () == null ? ex.toString () : ex.getMessage (), null);
return false;
} else {
throw ex;
}
}
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateConnected", 
 function (mp, args, tok, intValue) {
if (args.length > 5) return false;
var min = -2147483648;
var max = 2147483647;
var fmin = 0;
var fmax = 3.4028235E38;
var order = 65535;
var atoms1 = null;
var atoms2 = null;
var haveDecimal = false;
var isBonds = false;
switch (tok) {
case 1275203608:
var nv = -2147483648;
var smiles = null;
if (args.length > 0) {
switch (args[0].tok) {
case 2:
nv = args[0].intValue;
break;
case 4:
smiles = JS.SV.sValue (args[0]);
break;
}
}if (intValue == 1275203608) atoms1 = JS.SV.getBitSet (mp.getX (), true);
var data =  Clazz_newArray (-1, [Integer.$valueOf (nv), smiles, atoms1]);
if (!this.vwr.shm.getShapePropertyData (21, "getCenters", data)) data[1] = null;
return mp.addXBs (data[1] == null ?  new JU.BS () : data[1]);
case 1228931587:
var x1 = mp.getX ();
if (x1.tok != 10 || args.length != 1 || args[0].tok != 10) return false;
atoms1 = x1.value;
atoms2 = args[0].value;
var list =  new JU.Lst ();
var atoms = this.vwr.ms.at;
for (var i = atoms1.nextSetBit (0); i >= 0; i = atoms1.nextSetBit (i + 1)) {
var n = 0;
var b = atoms[i].bonds;
for (var j = b.length; --j >= 0; ) if (atoms2.get (b[j].getOtherAtom (atoms[i]).i)) n++;

list.addLast (Integer.$valueOf (n));
}
return mp.addXList (list);
}
for (var i = 0; i < args.length; i++) {
var $var = args[i];
switch ($var.tok) {
case 10:
isBonds = (Clazz_instanceOf ($var.value, JM.BondSet));
if (isBonds && atoms1 != null) return false;
if (atoms1 == null) atoms1 = $var.value;
 else if (atoms2 == null) atoms2 = $var.value;
 else return false;
break;
case 4:
var type = JS.SV.sValue ($var);
if (type.equalsIgnoreCase ("hbond")) order = 30720;
 else order = JS.ScriptParam.getBondOrderFromString (type);
if (order == 131071) return false;
break;
case 3:
haveDecimal = true;
default:
var n = $var.asInt ();
var f = $var.asFloat ();
if (max != 2147483647) return false;
if (min == -2147483648) {
min = Math.max (n, 0);
fmin = f;
} else {
max = n;
fmax = f;
}}
}
if (min == -2147483648) {
min = 1;
max = 100;
fmin = 0.1;
fmax = 1.0E8;
} else if (max == 2147483647) {
max = min;
fmax = fmin;
fmin = 0.1;
}if (atoms1 == null) atoms1 = this.vwr.getAllAtoms ();
if (haveDecimal && atoms2 == null) atoms2 = atoms1;
if (atoms2 != null) {
var bsBonds =  new JU.BS ();
this.vwr.makeConnections (fmin, fmax, order, 1086324745, atoms1, atoms2, bsBonds, isBonds, false, 0);
return mp.addX (JS.SV.newV (10, JM.BondSet.newBS (bsBonds, this.vwr.ms.getAtomIndices (this.vwr.ms.getAtoms (1677721602, bsBonds)))));
}return mp.addXBs (this.vwr.ms.getAtomsConnected (min, max, order, atoms1));
}, "JS.ScriptMathProcessor,~A,~N,~N");
Clazz_defineMethod (c$, "evaluateContact", 
 function (mp, args) {
if (args.length < 1 || args.length > 3) return false;
var i = 0;
var distance = 100;
var tok = args[0].tok;
switch (tok) {
case 3:
case 2:
distance = JS.SV.fValue (args[i++]);
break;
case 10:
break;
default:
return false;
}
if (i == args.length || !(Clazz_instanceOf (args[i].value, JU.BS))) return false;
var bsA = JU.BSUtil.copy (args[i++].value);
var bsB = (i < args.length ? JU.BSUtil.copy (args[i].value) : null);
var rd =  new J.atomdata.RadiusData (null, (distance > 10 ? distance / 100 : distance), (distance > 10 ? J.atomdata.RadiusData.EnumType.FACTOR : J.atomdata.RadiusData.EnumType.OFFSET), J.c.VDW.AUTO);
bsB = this.setContactBitSets (bsA, bsB, true, NaN, rd, false);
bsB.or (bsA);
return mp.addXBs (bsB);
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateData", 
 function (mp, args) {
var selected = (args.length == 0 ? "" : JS.SV.sValue (args[0]));
var type = "";
switch (args.length) {
case 0:
case 1:
break;
case 2:
case 3:
if (args[0].tok == 10) return mp.addXStr (this.vwr.getModelFileData (selected, JS.SV.sValue (args[1]), args.length == 3 && JS.SV.bValue (args[2])));
break;
case 4:
var iField = args[1].asInt ();
var nBytes = args[2].asInt ();
var firstLine = args[3].asInt ();
var f = JU.Parser.parseFloatArrayFromMatchAndField (JS.SV.sValue (args[0]), null, 0, 0, null, iField, nBytes, null, firstLine);
return mp.addXStr (JU.Escape.escapeFloatA (f, false));
default:
return false;
}
if (selected.indexOf ("data2d_") == 0) {
var f1 = this.vwr.getDataObj (selected, null, 2);
if (f1 == null) return mp.addXStr ("");
if (args.length == 2 && args[1].tok == 2) {
var pt = args[1].intValue;
if (pt < 0) pt += f1.length;
if (pt >= 0 && pt < f1.length) return mp.addXStr (JU.Escape.escapeFloatA (f1[pt], false));
return mp.addXStr ("");
}return mp.addXStr (JU.Escape.escapeFloatAA (f1, false));
}if (selected.indexOf ("property_") == 0) {
var f1 = this.vwr.getDataObj (selected, null, 1);
if (f1 == null) return mp.addXStr ("");
var f2 = (type.indexOf ("property_") == 0 ? this.vwr.getDataObj (selected, null, 1) : null);
if (f2 != null) {
f1 = JU.AU.arrayCopyF (f1, -1);
for (var i = Math.min (f1.length, f2.length); --i >= 0; ) f1[i] += f2[i];

}return mp.addXStr (JU.Escape.escapeFloatA (f1, false));
}var data = this.vwr.getDataObj (selected, null, -1);
return mp.addXStr (data == null ? "" : "" + data[1]);
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateDotDist", 
 function (mp, args, tok, op) {
var isDist = (tok == 1275069443);
var x1;
var x2;
var x3 = null;
switch (args.length) {
case 2:
if (op == 2147483647) {
x1 = args[0];
x2 = args[1];
break;
}x3 = args[1];
case 1:
x1 = mp.getX ();
x2 = args[0];
break;
default:
return false;
}
if (tok == 1275069442) {
var a = JU.P3.newP (mp.ptValue (x1, null));
a.cross (a, mp.ptValue (x2, null));
return mp.addXPt (a);
}var pt2 = (x2.tok == 7 ? null : mp.ptValue (x2, null));
var plane2 = mp.planeValue (x2);
var f = NaN;
try {
if (isDist) {
var minMax = (op == -2147483648 ? 0 : op & 480);
var isMinMax = (minMax == 32 || minMax == 64);
var isAll = minMax == 480;
switch (x1.tok) {
case 7:
case 10:
var isAtomSet1 = (x1.tok == 10);
var isAtomSet2 = (x2.tok == 10);
var isPoint2 = (x2.tok == 8);
var bs1 = (isAtomSet1 ? x1.value : null);
var bs2 = (isAtomSet2 ? x2.value : null);
var list1 = (isAtomSet1 ? null : x1.getList ());
var list2 = (isAtomSet2 ? null : x2.getList ());
var returnAtom = (isMinMax && x3 != null && x3.asBoolean ());
switch (x2.tok) {
case 10:
case 7:
case 8:
var atoms = this.vwr.ms.at;
if (returnAtom) {
var dMinMax = NaN;
var iMinMax = 2147483647;
if (isAtomSet1) {
for (var i = bs1.nextSetBit (0); i >= 0; i = bs1.nextSetBit (i + 1)) {
var d = (isPoint2 ? atoms[i].distanceSquared (pt2) : (this.e.getBitsetProperty (bs2, list2, op, atoms[i], plane2, x1.value, null, false, x1.index, false)).floatValue ());
if (minMax == 32 ? d >= dMinMax : d <= dMinMax) continue;
dMinMax = d;
iMinMax = i;
}
return mp.addXBs (iMinMax == 2147483647 ?  new JU.BS () : JU.BSUtil.newAndSetBit (iMinMax));
}for (var i = list1.size (); --i >= 0; ) {
var pt = JS.SV.ptValue (list1.get (i));
var d = (isPoint2 ? pt.distanceSquared (pt2) : (this.e.getBitsetProperty (bs2, list2, op, pt, plane2, x1.value, null, false, 2147483647, false)).floatValue ());
if (minMax == 32 ? d >= dMinMax : d <= dMinMax) continue;
dMinMax = d;
iMinMax = i;
}
return mp.addXInt (iMinMax);
}if (isAll) {
if (bs2 == null) {
var data =  Clazz_newFloatArray (bs1.cardinality (), 0);
for (var p = 0, i = bs1.nextSetBit (0); i >= 0; i = bs1.nextSetBit (i + 1), p++) data[p] = atoms[i].distance (pt2);

return mp.addXAF (data);
}var data2 =  Clazz_newFloatArray (bs1.cardinality (), bs2.cardinality (), 0);
for (var p = 0, i = bs1.nextSetBit (0); i >= 0; i = bs1.nextSetBit (i + 1), p++) for (var q = 0, j = bs2.nextSetBit (0); j >= 0; j = bs2.nextSetBit (j + 1), q++) data2[p][q] = atoms[i].distance (atoms[j]);


return mp.addXAFF (data2);
}if (isMinMax) {
var data =  Clazz_newFloatArray (isAtomSet1 ? bs1.cardinality () : list1.size (), 0);
if (isAtomSet1) {
for (var i = bs1.nextSetBit (0), p = 0; i >= 0; i = bs1.nextSetBit (i + 1)) data[p++] = (this.e.getBitsetProperty (bs2, list2, op, atoms[i], plane2, x1.value, null, false, x1.index, false)).floatValue ();

return mp.addXAF (data);
}for (var i = data.length; --i >= 0; ) data[i] = (this.e.getBitsetProperty (bs2, list2, op, JS.SV.ptValue (list1.get (i)), plane2, null, null, false, 2147483647, false)).floatValue ();

return mp.addXAF (data);
}return mp.addXObj (this.e.getBitsetProperty (bs1, list1, op, pt2, plane2, x1.value, null, false, x1.index, false));
}
}
}var pt1 = mp.ptValue (x1, null);
var plane1 = mp.planeValue (x1);
if (isDist) {
if (plane2 != null && x3 != null) f = JU.Measure.directedDistanceToPlane (pt1, plane2, JS.SV.ptValue (x3));
 else f = (plane1 == null ? (plane2 == null ? pt2.distance (pt1) : JU.Measure.distanceToPlane (plane2, pt1)) : JU.Measure.distanceToPlane (plane1, pt2));
} else {
if (plane1 != null && plane2 != null) {
f = plane1.x * plane2.x + plane1.y * plane2.y + plane1.z * plane2.z + plane1.w * plane2.w;
} else {
if (plane1 != null) pt1 = JU.P3.new3 (plane1.x, plane1.y, plane1.z);
 else if (plane2 != null) pt2 = JU.P3.new3 (plane2.x, plane2.y, plane2.z);
f = pt1.dot (pt2);
}}} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
return mp.addXFloat (f);
}, "JS.ScriptMathProcessor,~A,~N,~N");
Clazz_defineMethod (c$, "evaluateHelix", 
 function (mp, args) {
if (args.length < 1 || args.length > 5) return false;
var pt = (args.length > 2 ? 3 : 1);
var type = (pt >= args.length ? "array" : JS.SV.sValue (args[pt]));
var tok = JS.T.getTokFromName (type);
if (args.length > 2) {
var pta = mp.ptValue (args[0], null);
var ptb = mp.ptValue (args[1], null);
if (tok == 0 || args[2].tok != 9 || pta == null || ptb == null) return false;
var dq = JU.Quat.newP4 (args[2].value);
var data = JU.Measure.computeHelicalAxis (pta, ptb, dq);
return (data == null ? false : mp.addXObj (JU.Escape.escapeHelical (type, tok, pta, ptb, data)));
}var bs = (Clazz_instanceOf (args[0].value, JU.BS) ? args[0].value : this.vwr.ms.getAtoms (1094715412,  new Integer (args[0].asInt ())));
switch (tok) {
case 134217751:
case 1073741854:
case 1665140738:
return mp.addXObj (this.getHelixData (bs, tok));
case 134217729:
return mp.addXFloat ((this.getHelixData (bs, 134217729)).floatValue ());
case 135176:
case 1745489939:
return mp.addXObj (this.getHelixData (bs, tok));
case 1275068418:
var data = this.getHelixData (bs, 1073742001);
if (data == null) return false;
return mp.addXAS (data);
}
return false;
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "getHelixData", 
 function (bs, tokType) {
var iAtom = bs.nextSetBit (0);
return (iAtom < 0 ? "null" : this.vwr.ms.at[iAtom].group.getHelixData (tokType, this.vwr.getQuaternionFrame (), this.vwr.getInt (553648145)));
}, "JU.BS,~N");
Clazz_defineMethod (c$, "evaluateFind", 
 function (mp, args) {
var x1 = mp.getX ();
var isList = (x1.tok == 7);
var isEmpty = (args.length == 0);
var sFind = (isEmpty ? "" : JS.SV.sValue (args[0]));
var flags = (args.length > 1 && args[1].tok != 1073742335 && args[1].tok != 1073742334 && args[1].tok != 10 ? JS.SV.sValue (args[1]) : "");
var isSequence = !isList && sFind.equalsIgnoreCase ("SEQUENCE");
var isSeq = !isList && sFind.equalsIgnoreCase ("SEQ");
if (sFind.toUpperCase ().startsWith ("SMILES/")) {
if (!sFind.endsWith ("/")) sFind += "/";
var s = sFind.substring (6) + "//";
if (JV.JC.isSmilesCanonical (s)) {
flags = "SMILES";
sFind = "CHEMICAL";
} else {
sFind = "SMILES";
flags = s + flags;
}} else if (sFind.toUpperCase ().startsWith ("SMARTS/")) {
if (!sFind.endsWith ("/")) sFind += "/";
flags = sFind.substring (6) + (flags.length == 0 ? "//" : flags);
sFind = "SMARTS";
}var isSmiles = !isList && sFind.equalsIgnoreCase ("SMILES");
var isSMARTS = !isList && sFind.equalsIgnoreCase ("SMARTS");
var isChemical = !isList && sFind.equalsIgnoreCase ("CHEMICAL");
var isMF = !isList && sFind.equalsIgnoreCase ("MF");
var isCF = !isList && sFind.equalsIgnoreCase ("CELLFORMULA");
var argLast = (args.length > 0 ? args[args.length - 1] : JS.SV.vF);
var isON = !isList && (argLast.tok == 1073742335);
try {
if (isChemical) {
var bsAtoms = (x1.tok == 10 ? x1.value : null);
var data = (bsAtoms == null ? JS.SV.sValue (x1) : this.vwr.getOpenSmiles (bsAtoms));
data = (data.length == 0 ? "" : this.vwr.getChemicalInfo (data, flags.toLowerCase (), bsAtoms)).trim ();
if (data.startsWith ("InChI")) data = JU.PT.rep (JU.PT.rep (data, "InChI=", ""), "InChIKey=", "");
return mp.addXStr (data);
}if (isSmiles || isSMARTS || x1.tok == 10) {
var iPt = (isSmiles || isSMARTS ? 2 : 1);
var bs2 = (iPt < args.length && args[iPt].tok == 10 ? args[iPt++].value : null);
var asBonds = ("bonds".equalsIgnoreCase (JS.SV.sValue (args[args.length - 1])));
var isAll = (asBonds || isON);
var ret = null;
switch (x1.tok) {
case 4:
var smiles = JS.SV.sValue (x1);
if (bs2 != null || isSmiles && args.length == 1) return false;
if (flags.equalsIgnoreCase ("mf")) {
ret = this.vwr.getSmilesMatcher ().getMolecularFormula (smiles, isSMARTS);
} else {
var pattern = flags;
var allMappings = true;
var asMap = false;
switch (args.length) {
case 4:
allMappings = JS.SV.bValue (args[3]);
case 3:
asMap = JS.SV.bValue (args[2]);
break;
}
var justOne = (!asMap && (!allMappings || !isSMARTS && !pattern.equals ("chirality")));
try {
ret = this.e.getSmilesExt ().getSmilesMatches (pattern, smiles, null, null, isSMARTS ? 2 : 1, !asMap, !allMappings);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
System.out.println (ex.getMessage ());
return mp.addXInt (-1);
} else {
throw ex;
}
}
if (justOne) {
var len = (ret).length;
return mp.addXInt (!allMappings && len > 0 ? 1 : len);
}}break;
case 10:
var bs = x1.value;
if (isMF && flags.length != 0) return mp.addXBs (JU.JmolMolecule.getBitSetForMF (this.vwr.ms.at, bs, flags));
if (isMF || isCF) return mp.addXStr (JU.JmolMolecule.getMolecularFormulaAtoms (this.vwr.ms.at, bs, (isMF ? null : this.vwr.ms.getCellWeights (bs)), isON));
if (isSequence || isSeq) {
var isHH = (argLast.asString ().equalsIgnoreCase ("H"));
isAll = new Boolean (isAll | isHH).valueOf ();
return mp.addXStr (this.vwr.getSmilesOpt (bs, -1, -1, (isAll ? 3145728 | 5242880 | (isHH ? 9437184 : 0) : 0) | (isSeq ? 34603008 : 1048576), null));
}if (isSmiles || isSMARTS) sFind = (args.length > 1 && args[1].tok == 10 ? this.vwr.getSmilesOpt (args[1].value, 0, 0, 0, flags) : flags);
flags = flags.toUpperCase ();
var bsMatch3D = bs2;
if (asBonds) {
var map = this.vwr.getSmilesMatcher ().getCorrelationMaps (sFind, this.vwr.ms.at, this.vwr.ms.ac, bs, (isSmiles ? 1 : 2) | 8);
ret = (map.length > 0 ? this.vwr.ms.getDihedralMap (map[0]) :  Clazz_newIntArray (0, 0));
} else if (flags.equalsIgnoreCase ("map")) {
var map = this.vwr.getSmilesMatcher ().getCorrelationMaps (sFind, this.vwr.ms.at, this.vwr.ms.ac, bs, (isSmiles ? 1 : 2) | 128);
ret = map;
} else if (sFind.equalsIgnoreCase ("crystalClass")) {
ret = this.vwr.ms.generateCrystalClass (bs.nextSetBit (0), (args.length != 2 ? null : argLast.tok == 10 ? this.vwr.ms.getAtomSetCenter (argLast.value) : JS.SV.ptValue (argLast)));
} else {
var smilesFlags = (isSmiles ? (flags.indexOf ("OPEN") >= 0 ? 5 : 1) : 2) | (isON && sFind.length == 0 ? 22020096 : 0);
if (flags.indexOf ("/MOLECULE/") >= 0) {
var mols = this.vwr.ms.getMolecules ();
var molList =  new JU.Lst ();
for (var i = 0; i < mols.length; i++) {
if (mols[i].atomList.intersects (bs)) {
var bsRet = this.e.getSmilesExt ().getSmilesMatches (sFind, null, mols[i].atomList, bsMatch3D, smilesFlags, !isON, false);
if (!bsRet.isEmpty ()) molList.addLast (bsRet);
}}
ret = molList;
} else {
ret = this.e.getSmilesExt ().getSmilesMatches (sFind, null, bs, bsMatch3D, smilesFlags, !isON, false);
}}break;
}
if (ret == null) this.e.invArg ();
return mp.addXObj (ret);
}} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.e.evalError (ex.getMessage (), null);
} else {
throw ex;
}
}
var isReverse = (flags.indexOf ("v") >= 0);
var isCaseInsensitive = (flags.indexOf ("i") >= 0);
var asMatch = (flags.indexOf ("m") >= 0);
var checkEmpty = (sFind.length == 0);
var isPattern = (!checkEmpty && args.length == 2);
if (isList || isPattern) {
var pm = (isPattern ? this.getPatternMatcher () : null);
var pattern = null;
var svlist = (isList ? x1.getList () : null);
if (isPattern) {
try {
pattern = pm.compile (sFind, isCaseInsensitive);
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.e.evalError (ex.toString (), null);
} else {
throw ex;
}
}
}var list = (checkEmpty ? null : JS.SV.strListValue (x1));
var nlist = (checkEmpty ? svlist.size () : list.length);
if (JU.Logger.debugging) JU.Logger.debug ("finding " + sFind);
var bs =  new JU.BS ();
var n = 0;
var matcher = null;
var v = (asMatch ?  new JU.Lst () : null);
var what = "";
for (var i = 0; i < nlist; i++) {
var isMatch;
if (checkEmpty) {
var o = svlist.get (i);
switch (o.tok) {
case 6:
isMatch = (o.getMap ().isEmpty () != isEmpty);
break;
case 7:
isMatch = ((o.getList ().size () == 0) != isEmpty);
break;
case 4:
isMatch = ((o.asString ().length == 0) != isEmpty);
break;
default:
isMatch = true;
}
} else if (isPattern) {
what = list[i];
matcher = pattern.matcher (what);
isMatch = matcher.find ();
} else {
isMatch = (JS.SV.sValue (svlist.get (i)).indexOf (sFind) >= 0);
}if (asMatch && isMatch || !asMatch && isMatch == !isReverse) {
n++;
bs.set (i);
if (asMatch) v.addLast (isReverse ? what.substring (0, matcher.start ()) + what.substring (matcher.end ()) : matcher.group ());
}}
if (!isList) {
return (asMatch ? mp.addXStr (v.size () == 1 ? v.get (0) : "") : isReverse ? mp.addXBool (n == 1) : asMatch ? mp.addXStr (n == 0 ? "" : matcher.group ()) : mp.addXInt (n == 0 ? 0 : matcher.start () + 1));
}if (asMatch) {
var listNew =  new Array (n);
if (n > 0) for (var i = list.length; --i >= 0; ) if (bs.get (i)) {
--n;
listNew[n] = (asMatch ? v.get (n) : list[i]);
}
return mp.addXAS (listNew);
}var l =  new JU.Lst ();
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) l.addLast (svlist.get (i));

return mp.addXList (l);
}if (isSequence) {
return mp.addXStr (this.vwr.getJBR ().toStdAmino3 (JS.SV.sValue (x1)));
}return mp.addXInt (JS.SV.sValue (x1).indexOf (sFind) + 1);
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateGetProperty", 
 function (mp, args, tok0, isAtomProperty) {
var isSelect = (isAtomProperty && tok0 == 1275082245);
var isAuxiliary = (tok0 == 1275068449);
var pt = 0;
var tok = (args.length == 0 ? 0 : args[0].tok);
if (args.length == 2 && (tok == 7 || tok == 6 || tok == 14)) {
return mp.addXObj (this.vwr.extractProperty (args[0].value, args[1].value.toString (), -1));
}var bsSelect = (isAtomProperty && args.length == 1 && args[0].tok == 10 ? args[0].value : null);
var pname = (bsSelect == null && args.length > 0 ? JS.SV.sValue (args[pt++]) : "");
var propertyName = pname;
var lc = propertyName.toLowerCase ();
if (!isSelect && lc.indexOf ("[select ") < 0) propertyName = lc;
var isJSON = false;
if (propertyName.equals ("json") && args.length > pt) {
isJSON = true;
propertyName = JS.SV.sValue (args[pt++]);
}var x = null;
if (isAtomProperty) {
x = mp.getX ();
switch (x.tok) {
case 10:
break;
case 4:
var name = x.value;
var data =  new Array (3);
var shapeID;
if (name.startsWith ("$")) {
name = name.substring (1);
shapeID = this.vwr.shm.getShapeIdFromObjectName (name);
if (shapeID >= 0) {
data[0] = name;
this.vwr.shm.getShapePropertyData (shapeID, "index", data);
if (data[1] != null && !pname.equals ("index")) {
var index = (data[1]).intValue ();
data[1] = this.vwr.shm.getShapePropertyIndex (shapeID, pname.intern (), index);
}}} else {
shapeID = JV.JC.shapeTokenIndex (JS.T.getTokFromName (name));
if (shapeID >= 0) {
data[0] = pname;
data[1] = Integer.$valueOf (-1);
this.vwr.shm.getShapePropertyData (shapeID, pname.intern (), data);
}}return (data[1] == null ? mp.addXStr ("") : mp.addXObj (data[1]));
case 7:
if (bsSelect != null) {
var l0 = x.getList ();
var lst =  new JU.Lst ();
for (var i = bsSelect.nextSetBit (0); i >= 0; i = bsSelect.nextSetBit (i + 1)) lst.addLast (l0.get (i));

return mp.addXList (lst);
}default:
if (isSelect) propertyName = "[SELECT " + propertyName + "]";
return mp.addXObj (this.vwr.extractProperty (x, propertyName, -1));
}
if (!lc.startsWith ("bondinfo") && !lc.startsWith ("atominfo")) propertyName = "atomInfo." + propertyName;
}var propertyValue = "";
if (propertyName.equalsIgnoreCase ("fileContents") && args.length > 2) {
var s = JS.SV.sValue (args[1]);
for (var i = 2; i < args.length; i++) s += "|" + JS.SV.sValue (args[i]);

propertyValue = s;
pt = args.length;
} else if (args.length > pt) {
switch (args[pt].tok) {
case 10:
propertyValue = args[pt++].value;
if (propertyName.equalsIgnoreCase ("bondInfo") && args.length > pt && args[pt].tok == 10) propertyValue =  Clazz_newArray (-1, [propertyValue, args[pt].value]);
break;
case 6:
case 4:
if (this.vwr.checkPropertyParameter (propertyName)) propertyValue = args[pt++].value;
break;
}
}if (isAtomProperty) {
var bs = x.value;
var iAtom = bs.nextSetBit (0);
if (iAtom < 0) return mp.addXStr ("");
propertyValue = bs;
}if (isAuxiliary && !isAtomProperty) propertyName = "auxiliaryInfo.models." + propertyName;
propertyName = JU.PT.rep (propertyName, ".[", "[");
var property = this.vwr.getProperty (null, propertyName, propertyValue);
if (pt < args.length) property = this.vwr.extractProperty (property, args, pt);
return mp.addXObj (isJSON ? JS.SV.safeJSON ("value", property) : JS.SV.isVariableType (property) ? property : JU.Escape.toReadable (propertyName, property));
}, "JS.ScriptMathProcessor,~A,~N,~B");
Clazz_defineMethod (c$, "evaluateFormat", 
 function (mp, intValue, args, isLabel) {
var x1 = (args.length < 2 || intValue == 1287653388 ? mp.getX () : null);
var format = (args.length == 0 ? "%U" : args[0].tok == 7 ? null : JS.SV.sValue (args[0]));
if (!isLabel && args.length > 0 && x1 != null && x1.tok != 10 && format != null) {
if (args.length == 2) {
var listIn = x1.getList ();
var formatList = args[1].getList ();
if (listIn == null || formatList == null) return false;
x1 = JS.SV.getVariableList (this.getSublist (listIn, formatList));
}args =  Clazz_newArray (-1, [args[0], x1]);
x1 = null;
}if (x1 == null) {
var pt = (isLabel ? -1 : JS.SV.getFormatType (format));
if (pt >= 0 && args.length != 2) return false;
if (pt >= 0 || args.length < 2 || args[1].tok != 7) {
var o = JS.SV.format (args, pt);
return (format.equalsIgnoreCase ("json") ? mp.addXStr (o) : mp.addXObj (o));
}var a = args[1].getList ();
var args2 =  Clazz_newArray (-1, [args[0], null]);
var sa =  new Array (a.size ());
for (var i = sa.length; --i >= 0; ) {
args2[1] = a.get (i);
sa[i] = JS.SV.format (args2, pt).toString ();
}
return mp.addXAS (sa);
}if (x1.tok == 7 && format == null) {
var listIn = x1.getList ();
var formatList = args[0].getList ();
var listOut = this.getSublist (listIn, formatList);
return mp.addXList (listOut);
}var bs = (x1.tok == 10 ? x1.value : null);
var asArray = JS.T.tokAttr (intValue, 480);
return mp.addXObj (format == null ? "" : bs == null ? JS.SV.sprintf (JU.PT.formatCheck (format), x1) : this.e.getCmdExt ().getBitsetIdent (bs, format, x1.value, true, x1.index, asArray));
}, "JS.ScriptMathProcessor,~N,~A,~B");
Clazz_defineMethod (c$, "getSublist", 
 function (listIn, formatList) {
var listOut =  new JU.Lst ();
var map;
var v;
var list;
for (var i = 0, n = listIn.size (); i < n; i++) {
var element = listIn.get (i);
switch (element.tok) {
case 6:
map = element.getMap ();
list =  new JU.Lst ();
for (var j = 0, n1 = formatList.size (); j < n1; j++) {
v = map.get (JS.SV.sValue (formatList.get (j)));
list.addLast (v == null ? JS.SV.newS ("") : v);
}
listOut.addLast (JS.SV.getVariableList (list));
break;
case 7:
map =  new java.util.Hashtable ();
list = element.getList ();
for (var j = 0, n1 = Math.min (list.size (), formatList.size ()); j < n1; j++) {
map.put (JS.SV.sValue (formatList.get (j)), list.get (j));
}
listOut.addLast (JS.SV.getVariable (map));
}
}
return listOut;
}, "JU.Lst,JU.Lst");
Clazz_defineMethod (c$, "evaluateList", 
 function (mp, tok, args) {
var len = args.length;
var x1 = mp.getX ();
var isArray1 = (x1.tok == 7);
var x2;
switch (tok) {
case 1275335685:
return (len == 2 && mp.addX (x1.pushPop (args[0], args[1])) || len == 1 && mp.addX (x1.pushPop (null, args[0])));
case 1275334681:
return (len == 1 && mp.addX (x1.pushPop (args[0], null)) || len == 0 && mp.addX (x1.pushPop (null, null)));
case 1275069441:
if (len != 1 && len != 2) return false;
break;
case 1275069447:
case 1275069446:
break;
default:
if (len != 1) return false;
}
var sList1 = null;
var sList2 = null;
var sList3 = null;
if (len == 2) {
var tab = JS.SV.sValue (args[0]);
x2 = args[1];
if (tok == 1275069441) {
sList1 = (isArray1 ? JS.SV.strListValue (x1) : JU.PT.split (JS.SV.sValue (x1), "\n"));
sList2 = (x2.tok == 7 ? JS.SV.strListValue (x2) : JU.PT.split (JS.SV.sValue (x2), "\n"));
sList3 =  new Array (len = Math.max (sList1.length, sList2.length));
for (var i = 0; i < len; i++) sList3[i] = (i >= sList1.length ? "" : sList1[i]) + tab + (i >= sList2.length ? "" : sList2[i]);

return mp.addXAS (sList3);
}if (x2.tok != 1073742335) return false;
var l = x1.getList ();
var isCSV = (tab.length == 0);
if (isCSV) tab = ",";
if (tok == 1275069446) {
var s2 =  new Array (l.size ());
for (var i = l.size (); --i >= 0; ) {
var a = l.get (i).getList ();
if (a == null) s2[i] = l.get (i);
 else {
var sb =  new JU.SB ();
for (var j = 0, n = a.size (); j < n; j++) {
if (j > 0) sb.append (tab);
var sv = a.get (j);
sb.append (isCSV && sv.tok == 4 ? "\"" + JU.PT.rep (sv.value, "\"", "\"\"") + "\"" : "" + sv.asString ());
}
s2[i] = JS.SV.newS (sb.toString ());
}}
return mp.addXAV (s2);
}var sa =  new JU.Lst ();
if (isCSV) tab = "\0";
var next =  Clazz_newIntArray (2, 0);
for (var i = 0, nl = l.size (); i < nl; i++) {
var line = l.get (i).asString ();
if (isCSV) {
next[1] = 0;
next[0] = 0;
var last = 0;
while (true) {
var s = JU.PT.getCSVString (line, next);
if (s == null) {
if (next[1] == -1) {
line += (++i < nl ? "\n" + l.get (i).asString () : "\"");
next[1] = last;
continue;
}line = line.substring (0, last) + line.substring (last).$replace (',', '\0');
break;
}line = line.substring (0, last) + line.substring (last, next[0]).$replace (',', '\0') + s + line.substring (next[1]);
next[1] = last = next[0] + s.length;
}
}var linaa = line.$plit (tab);
var la =  new JU.Lst ();
for (var j = 0, n = linaa.length; j < n; j++) {
var s = linaa[j];
if (s.indexOf (".") < 0) try {
la.addLast (JS.SV.newI (Integer.parseInt (s)));
continue;
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
 else try {
la.addLast (JS.SV.getVariable (Float.$valueOf (Float.parseFloat (s))));
continue;
} catch (ee) {
if (Clazz_exceptionOf (ee, Exception)) {
} else {
throw ee;
}
}
la.addLast (JS.SV.newS (s));
}
sa.addLast (JS.SV.getVariableList (la));
}
return mp.addXObj (JS.SV.getVariableList (sa));
}x2 = (len == 0 ? JS.SV.newV (1073742327, "all") : args[0]);
var isAll = (x2.tok == 1073742327);
if (!isArray1 && x1.tok != 4) return mp.binaryOp (this.opTokenFor (tok), x1, x2);
var isScalar1 = JS.SV.isScalar (x1);
var isScalar2 = JS.SV.isScalar (x2);
var list1 = null;
var list2 = null;
var alist1 = x1.getList ();
var alist2 = x2.getList ();
if (isArray1) {
len = alist1.size ();
} else if (isScalar1) {
len = 2147483647;
} else {
sList1 = (JU.PT.split (JS.SV.sValue (x1), "\n"));
list1 =  Clazz_newFloatArray (len = sList1.length, 0);
JU.PT.parseFloatArrayData (sList1, list1);
}if (isAll && tok != 1275069446) {
var sum = 0;
if (isArray1) {
for (var i = len; --i >= 0; ) sum += JS.SV.fValue (alist1.get (i));

} else if (!isScalar1) {
for (var i = len; --i >= 0; ) sum += list1[i];

}return mp.addXFloat (sum);
}if (tok == 1275069446 && x2.tok == 4) {
var sb =  new JU.SB ();
if (isScalar1) {
sb.append (JS.SV.sValue (x1));
} else {
var s = (isAll ? "" : x2.value.toString ());
for (var i = 0; i < len; i++) sb.append (i > 0 ? s : "").append (JS.SV.sValue (alist1.get (i)));

}return mp.addXStr (sb.toString ());
}var scalar = null;
if (isScalar2) {
scalar = x2;
} else if (x2.tok == 7) {
len = Math.min (len, alist2.size ());
} else {
sList2 = JU.PT.split (JS.SV.sValue (x2), "\n");
list2 =  Clazz_newFloatArray (sList2.length, 0);
JU.PT.parseFloatArrayData (sList2, list2);
len = Math.min (len, list2.length);
}var token = this.opTokenFor (tok);
var olist =  new Array (len);
if (isArray1 && isAll) {
var llist =  new JU.Lst ();
return mp.addXList (this.addAllLists (x1.getList (), llist));
}var a = (isScalar1 ? x1 : null);
var b;
for (var i = 0; i < len; i++) {
if (isScalar2) b = scalar;
 else if (x2.tok == 7) b = alist2.get (i);
 else if (Float.isNaN (list2[i])) b = JS.SV.getVariable (JS.SV.unescapePointOrBitsetAsVariable (sList2[i]));
 else b = JS.SV.newF (list2[i]);
if (!isScalar1) {
if (isArray1) a = alist1.get (i);
 else if (Float.isNaN (list1[i])) a = JS.SV.getVariable (JS.SV.unescapePointOrBitsetAsVariable (sList1[i]));
 else a = JS.SV.newF (list1[i]);
}if (tok == 1275069446) {
if (a.tok != 7) {
var l =  new JU.Lst ();
l.addLast (a);
a = JS.SV.getVariableList (l);
}}if (!mp.binaryOp (token, a, b)) return false;
olist[i] = mp.getX ();
}
return mp.addXAV (olist);
}, "JS.ScriptMathProcessor,~N,~A");
Clazz_defineMethod (c$, "addAllLists", 
 function (list, l) {
var n = list.size ();
for (var i = 0; i < n; i++) {
var v = list.get (i);
if (v.tok == 7) this.addAllLists (v.getList (), l);
 else l.addLast (v);
}
return l;
}, "JU.Lst,JU.Lst");
Clazz_defineMethod (c$, "evaluateLoad", 
 function (mp, args, isFile) {
if (args.length < 1 || args.length > 3) return false;
var file = JV.FileManager.fixDOSName (JS.SV.sValue (args[0]));
var asBytes = (args.length > 1 && args[1].tok == 1073742335);
var async = (this.vwr.async || args.length > 2 && args[args.length - 1].tok == 1073742335);
var nBytesMax = (args.length > 1 && args[1].tok == 2 ? args[1].asInt () : -1);
var asJSON = (args.length > 1 && args[1].asString ().equalsIgnoreCase ("JSON"));
if (asBytes) return mp.addXMap (this.vwr.fm.getFileAsMap (file, null));
var isQues = file.startsWith ("?");
if (JV.Viewer.isJS && (isQues || async)) {
if (isFile && isQues) return mp.addXStr ("");
file = this.e.loadFileAsync ("load()_", file, mp.oPt, true);
}var str = isFile ? this.vwr.fm.getFilePath (file, false, false) : this.vwr.getFileAsString4 (file, nBytesMax, false, false, true, "script");
try {
return (asJSON ? mp.addXObj (this.vwr.parseJSON (str)) : mp.addXStr (str));
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return false;
} else {
throw e;
}
}
}, "JS.ScriptMathProcessor,~A,~B");
Clazz_defineMethod (c$, "evaluateMath", 
 function (mp, args, tok) {
if (tok == 134217749) {
if (args.length == 1 && args[0].tok == 4) return mp.addXStr (( new java.util.Date ()) + "\t" + JS.SV.sValue (args[0]));
return mp.addXInt ((System.currentTimeMillis () & 0x7FFFFFFF) - (args.length == 0 ? 0 : args[0].asInt ()));
}if (args.length != 1) return false;
if (tok == 134218250) {
if (args[0].tok == 2) return mp.addXInt (Math.abs (args[0].asInt ()));
return mp.addXFloat (Math.abs (args[0].asFloat ()));
}var x = JS.SV.fValue (args[0]);
switch (tok) {
case 134218242:
return mp.addXFloat ((Math.acos (x) * 180 / 3.141592653589793));
case 134218245:
return mp.addXFloat (Math.cos (x * 3.141592653589793 / 180));
case 134218244:
return mp.addXFloat (Math.sin (x * 3.141592653589793 / 180));
case 134218246:
return mp.addXFloat (Math.sqrt (x));
}
return false;
}, "JS.ScriptMathProcessor,~A,~N");
Clazz_defineMethod (c$, "evaluateMeasure", 
 function (mp, args, tok) {
var nPoints = 0;
switch (tok) {
case 1745489939:
var points =  new JU.Lst ();
var rangeMinMax =  Clazz_newFloatArray (-1, [3.4028235E38, 3.4028235E38]);
var strFormat = null;
var units = null;
var isAllConnected = false;
var isNotConnected = false;
var rPt = 0;
var isNull = false;
var rd = null;
var nBitSets = 0;
var vdw = 3.4028235E38;
var asMinArray = false;
var asArray = false;
for (var i = 0; i < args.length; i++) {
switch (args[i].tok) {
case 10:
var bs = args[i].value;
if (bs.length () == 0) isNull = true;
points.addLast (bs);
nPoints++;
nBitSets++;
break;
case 8:
var v =  new JU.Point3fi ();
v.setT (args[i].value);
points.addLast (v);
nPoints++;
break;
case 2:
case 3:
rangeMinMax[rPt++ % 2] = JS.SV.fValue (args[i]);
break;
case 4:
var s = JS.SV.sValue (args[i]);
if (s.equalsIgnoreCase ("vdw") || s.equalsIgnoreCase ("vanderwaals")) vdw = (i + 1 < args.length && args[i + 1].tok == 2 ? args[++i].asInt () : 100) / 100;
 else if (s.equalsIgnoreCase ("notConnected")) isNotConnected = true;
 else if (s.equalsIgnoreCase ("connected")) isAllConnected = true;
 else if (s.equalsIgnoreCase ("minArray")) asMinArray = (nBitSets >= 1);
 else if (s.equalsIgnoreCase ("asArray")) asArray = (nBitSets >= 1);
 else if (JU.PT.isOneOf (s.toLowerCase (), ";nm;nanometers;pm;picometers;angstroms;ang;au;") || s.endsWith ("hz")) units = s.toLowerCase ();
 else strFormat = nPoints + ":" + s;
break;
default:
return false;
}
}
if (nPoints < 2 || nPoints > 4 || rPt > 2 || isNotConnected && isAllConnected) return false;
if (isNull) return mp.addXStr ("");
if (vdw != 3.4028235E38 && (nBitSets != 2 || nPoints != 2)) return mp.addXStr ("");
rd = (vdw == 3.4028235E38 ?  new J.atomdata.RadiusData (rangeMinMax, 0, null, null) :  new J.atomdata.RadiusData (null, vdw, J.atomdata.RadiusData.EnumType.FACTOR, J.c.VDW.AUTO));
return mp.addXObj ((this.vwr.newMeasurementData (null, points)).set (0, null, rd, strFormat, units, null, isAllConnected, isNotConnected, null, true, 0, 0, null).getMeasurements (asArray, asMinArray));
case 134217729:
if ((nPoints = args.length) != 3 && nPoints != 4) return false;
break;
default:
if ((nPoints = args.length) != 2) return false;
}
var pts =  new Array (nPoints);
for (var i = 0; i < nPoints; i++) {
if ((pts[i] = mp.ptValue (args[i], null)) == null) return false;
}
switch (nPoints) {
case 2:
return mp.addXFloat (pts[0].distance (pts[1]));
case 3:
return mp.addXFloat (JU.Measure.computeAngleABC (pts[0], pts[1], pts[2], true));
case 4:
return mp.addXFloat (JU.Measure.computeTorsion (pts[0], pts[1], pts[2], pts[3], true));
}
return false;
}, "JS.ScriptMathProcessor,~A,~N");
Clazz_defineMethod (c$, "evaluateModulation", 
 function (mp, args) {
var type = "";
var t = NaN;
var t456 = null;
switch (args.length) {
case 0:
break;
case 1:
switch (args[0].tok) {
case 8:
t456 = args[0].value;
break;
case 4:
type = args[0].asString ();
break;
default:
t = JS.SV.fValue (args[0]);
}
break;
case 2:
type = JS.SV.sValue (args[0]);
t = JS.SV.fValue (args[1]);
break;
default:
return false;
}
if (t456 == null && t < 1e6) t456 = JU.P3.new3 (t, t, t);
var x = mp.getX ();
var bs = (x.tok == 10 ? x.value :  new JU.BS ());
return mp.addXList (this.vwr.ms.getModulationList (bs, (type + "D").toUpperCase ().charAt (0), t456));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluatePlane", 
 function (mp, args, tok) {
if (tok == 134219265 && args.length != 3 || tok == 134217763 && args.length != 2 && args.length != 3 && args.length != 4 || args.length == 0 || args.length > 4) return false;
var pt1;
var pt2;
var pt3;
var plane;
var norm;
var vTemp;
switch (args.length) {
case 1:
if (args[0].tok == 10) {
var bs = args[0].value;
if (bs.cardinality () == 3) {
var pts = this.vwr.ms.getAtomPointVector (bs);
return mp.addXPt4 (JU.Measure.getPlaneThroughPoints (pts.get (0), pts.get (1), pts.get (2),  new JU.V3 (),  new JU.V3 (),  new JU.P4 ()));
}}var pt = JU.Escape.uP (JS.SV.sValue (args[0]));
if (Clazz_instanceOf (pt, JU.P4)) return mp.addXPt4 (pt);
return mp.addXStr ("" + pt);
case 2:
if (tok == 134217763) {
if (args[1].tok != 9) return false;
pt3 =  new JU.P3 ();
norm =  new JU.V3 ();
vTemp =  new JU.V3 ();
plane = args[1].value;
if (args[0].tok == 9) {
var list = JU.Measure.getIntersectionPP (args[0].value, plane);
if (list == null) return mp.addXStr ("");
return mp.addXList (list);
}pt2 = mp.ptValue (args[0], null);
if (pt2 == null) return mp.addXStr ("");
return mp.addXPt (JU.Measure.getIntersection (pt2, null, plane, pt3, norm, vTemp));
}case 3:
case 4:
switch (tok) {
case 134219265:
return mp.addXPt4 (this.e.getHklPlane (JU.P3.new3 (JS.SV.fValue (args[0]), JS.SV.fValue (args[1]), JS.SV.fValue (args[2]))));
case 134217763:
pt1 = mp.ptValue (args[0], null);
pt2 = mp.ptValue (args[1], null);
if (pt1 == null || pt2 == null) return mp.addXStr ("");
var vLine = JU.V3.newV (pt2);
vLine.normalize ();
if (args[2].tok == 9) {
pt3 =  new JU.P3 ();
norm =  new JU.V3 ();
vTemp =  new JU.V3 ();
pt1 = JU.Measure.getIntersection (pt1, vLine, args[2].value, pt3, norm, vTemp);
if (pt1 == null) return mp.addXStr ("");
return mp.addXPt (pt1);
}pt3 = mp.ptValue (args[2], null);
if (pt3 == null) return mp.addXStr ("");
var v =  new JU.V3 ();
pt3 = JU.P3.newP (pt3);
if (args.length == 3) {
JU.Measure.projectOntoAxis (pt3, pt1, vLine, v);
return mp.addXPt (pt3);
}var r = JS.SV.fValue (args[3]);
var ptCenter = JU.P3.newP (pt3);
JU.Measure.projectOntoAxis (pt3, pt1, vLine, v);
var d = ptCenter.distance (pt3);
var l =  new JU.Lst ();
if (d == r) {
l.addLast (pt3);
} else if (d < r) {
d = Math.sqrt (r * r - d * d);
v.scaleAdd2 (d, vLine, pt3);
l.addLast (JU.P3.newP (v));
v.scaleAdd2 (-d, vLine, pt3);
l.addLast (JU.P3.newP (v));
}return mp.addXList (l);
}
switch (args[0].tok) {
case 2:
case 3:
if (args.length == 3) {
var r = JS.SV.fValue (args[0]);
var theta = JS.SV.fValue (args[1]);
var phi = JS.SV.fValue (args[2]);
norm = JU.V3.new3 (0, 0, 1);
pt2 = JU.P3.new3 (0, 1, 0);
var q = JU.Quat.newVA (pt2, phi);
q.getMatrix ().rotate (norm);
pt2.set (0, 0, 1);
q = JU.Quat.newVA (pt2, theta);
q.getMatrix ().rotate (norm);
pt2.setT (norm);
pt2.scale (r);
plane =  new JU.P4 ();
JU.Measure.getPlaneThroughPoint (pt2, norm, plane);
return mp.addXPt4 (plane);
}break;
case 10:
case 8:
pt1 = mp.ptValue (args[0], null);
pt2 = mp.ptValue (args[1], null);
if (pt2 == null) return false;
pt3 = (args.length > 2 && (args[2].tok == 10 || args[2].tok == 8) ? mp.ptValue (args[2], null) : null);
norm = JU.V3.newV (pt2);
if (pt3 == null) {
plane =  new JU.P4 ();
if (args.length == 2 || args[2].tok != 2 && args[2].tok != 3 && !args[2].asBoolean ()) {
pt3 = JU.P3.newP (pt1);
pt3.add (pt2);
pt3.scale (0.5);
norm.sub (pt1);
norm.normalize ();
} else if (args[2].tok == 1073742335) {
pt3 = pt1;
} else {
norm.sub (pt1);
pt3 =  new JU.P3 ();
pt3.scaleAdd2 (args[2].asFloat (), norm, pt1);
}JU.Measure.getPlaneThroughPoint (pt3, norm, plane);
return mp.addXPt4 (plane);
}var vAB =  new JU.V3 ();
var ptref = (args.length == 4 ? mp.ptValue (args[3], null) : null);
var nd = JU.Measure.getDirectedNormalThroughPoints (pt1, pt2, pt3, ptref, norm, vAB);
return mp.addXPt4 (JU.P4.new4 (norm.x, norm.y, norm.z, nd));
}
}
if (args.length != 4) return false;
var x = JS.SV.fValue (args[0]);
var y = JS.SV.fValue (args[1]);
var z = JS.SV.fValue (args[2]);
var w = JS.SV.fValue (args[3]);
return mp.addXPt4 (JU.P4.new4 (x, y, z, w));
}, "JS.ScriptMathProcessor,~A,~N");
Clazz_defineMethod (c$, "evaluatePoint", 
 function (mp, args) {
switch (args.length) {
default:
return false;
case 1:
if (args[0].tok == 3 || args[0].tok == 2) return mp.addXInt (args[0].asInt ());
var s = JS.SV.sValue (args[0]);
if (args[0].tok == 7) s = "{" + s + "}";
var pt = JU.Escape.uP (s);
return (Clazz_instanceOf (pt, JU.P3) ? mp.addXPt (pt) : mp.addXStr ("" + pt));
case 2:
var pt3;
switch (args[1].tok) {
case 1073742334:
case 1073742335:
switch (args[0].tok) {
case 8:
pt3 = JU.P3.newP (args[0].value);
break;
case 10:
pt3 = this.vwr.ms.getAtomSetCenter (args[0].value);
break;
default:
return false;
}
if (args[1].tok == 1073742335) {
this.vwr.tm.transformPt3f (pt3, pt3);
pt3.y = this.vwr.tm.height - pt3.y;
if (this.vwr.antialiased) pt3.scale (0.5);
} else {
if (this.vwr.antialiased) pt3.scale (2);
pt3.y = this.vwr.tm.height - pt3.y;
this.vwr.tm.unTransformPoint (pt3, pt3);
}break;
case 8:
var sv = args[0].getList ();
if (sv == null || sv.size () != 4) return false;
var pt1 = JS.SV.ptValue (args[1]);
pt3 = JU.P3.newP (JS.SV.ptValue (sv.get (0)));
pt3.scaleAdd2 (pt1.x, JS.SV.ptValue (sv.get (1)), pt3);
pt3.scaleAdd2 (pt1.y, JS.SV.ptValue (sv.get (2)), pt3);
pt3.scaleAdd2 (pt1.z, JS.SV.ptValue (sv.get (3)), pt3);
break;
default:
return false;
}
return mp.addXPt (pt3);
case 3:
return mp.addXPt (JU.P3.new3 (args[0].asFloat (), args[1].asFloat (), args[2].asFloat ()));
case 4:
return mp.addXPt4 (JU.P4.new4 (args[0].asFloat (), args[1].asFloat (), args[2].asFloat (), args[3].asFloat ()));
}
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluatePrompt", 
 function (mp, args) {
if (args.length != 1 && args.length != 2 && args.length != 3) return false;
var label = JS.SV.sValue (args[0]);
var buttonArray = (args.length > 1 && args[1].tok == 7 ? JS.SV.strListValue (args[1]) : null);
var asButtons = (buttonArray != null || args.length == 1 || args.length == 3 && args[2].asBoolean ());
var input = (buttonArray != null ? null : args.length >= 2 ? JS.SV.sValue (args[1]) : "OK");
var s = "" + this.vwr.prompt (label, input, buttonArray, asButtons);
return (asButtons && buttonArray != null ? mp.addXInt (Integer.parseInt (s) + 1) : mp.addXStr (s));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateQuaternion", 
 function (mp, args, tok) {
var pt0 = null;
var nArgs = args.length;
var nMax = 2147483647;
var isRelative = false;
if (tok == 134221850) {
if (nArgs > 1 && args[nArgs - 1].tok == 4 && (args[nArgs - 1].value).equalsIgnoreCase ("relative")) {
nArgs--;
isRelative = true;
}if (nArgs > 1 && args[nArgs - 1].tok == 2 && args[0].tok == 10) {
nMax = args[nArgs - 1].asInt ();
if (nMax <= 0) nMax = 2147483646;
nArgs--;
}}switch (nArgs) {
case 0:
case 1:
case 4:
break;
case 2:
if (tok == 134221850) {
if (args[0].tok == 7 && (args[1].tok == 7 || args[1].tok == 1073742335)) break;
if (args[0].tok == 10 && (args[1].tok == 2 || args[1].tok == 10)) break;
}if ((pt0 = mp.ptValue (args[0], null)) == null || tok != 134221850 && args[1].tok == 8) return false;
break;
case 3:
if (tok != 134221850) return false;
if (args[0].tok == 9) {
if (args[2].tok != 8 && args[2].tok != 10) return false;
break;
}for (var i = 0; i < 3; i++) if (args[i].tok != 8 && args[i].tok != 10) return false;

break;
default:
return false;
}
var q = null;
var qs = null;
var p4 = null;
switch (nArgs) {
case 0:
return mp.addXPt4 (this.vwr.tm.getRotationQ ().toPoint4f ());
case 1:
default:
if (tok == 134221850 && args[0].tok == 7) {
var data1 = this.e.getQuaternionArray (args[0].getList (), 1073742001);
var mean = JU.Quat.sphereMean (data1, null, 0.0001);
q = (Clazz_instanceOf (mean, JU.Quat) ? mean : null);
break;
} else if (tok == 134221850 && args[0].tok == 10) {
qs = this.vwr.getAtomGroupQuaternions (args[0].value, nMax);
} else if (args[0].tok == 11) {
q = JU.Quat.newM (args[0].value);
} else if (args[0].tok == 9) {
p4 = args[0].value;
} else {
var s = JS.SV.sValue (args[0]);
var v = JU.Escape.uP (s.equalsIgnoreCase ("best") ? this.vwr.getOrientationText (1073741864, "best", null).toString () : s);
if (!(Clazz_instanceOf (v, JU.P4))) return false;
p4 = v;
}if (tok == 134217731) q = JU.Quat.newVA (JU.P3.new3 (p4.x, p4.y, p4.z), p4.w);
break;
case 2:
if (tok == 134221850) {
if (args[0].tok == 7 && args[1].tok == 7) {
var data1 = this.e.getQuaternionArray (args[0].getList (), 1073742001);
var data2 = this.e.getQuaternionArray (args[1].getList (), 1073742001);
qs = JU.Quat.div (data2, data1, nMax, isRelative);
break;
}if (args[0].tok == 7 && args[1].tok == 1073742335) {
var data1 = this.e.getQuaternionArray (args[0].getList (), 1073742001);
var stddev =  Clazz_newFloatArray (1, 0);
JU.Quat.sphereMean (data1, stddev, 0.0001);
return mp.addXFloat (stddev[0]);
}if (args[0].tok == 10 && args[1].tok == 10) {
var data1 = this.vwr.getAtomGroupQuaternions (args[0].value, 2147483647);
var data2 = this.vwr.getAtomGroupQuaternions (args[1].value, 2147483647);
qs = JU.Quat.div (data2, data1, nMax, isRelative);
break;
}}var pt1 = mp.ptValue (args[1], null);
p4 = mp.planeValue (args[0]);
if (pt1 != null) q = JU.Quat.getQuaternionFrame (JU.P3.new3 (0, 0, 0), pt0, pt1);
 else q = JU.Quat.newVA (pt0, JS.SV.fValue (args[1]));
break;
case 3:
if (args[0].tok == 9) {
var pt = (args[2].tok == 8 ? args[2].value : this.vwr.ms.getAtomSetCenter (args[2].value));
return mp.addXStr (JU.Escape.drawQuat (JU.Quat.newP4 (args[0].value), "q", JS.SV.sValue (args[1]), pt, 1));
}var pts =  new Array (3);
for (var i = 0; i < 3; i++) pts[i] = (args[i].tok == 8 ? args[i].value : this.vwr.ms.getAtomSetCenter (args[i].value));

q = JU.Quat.getQuaternionFrame (pts[0], pts[1], pts[2]);
break;
case 4:
if (tok == 134221850) p4 = JU.P4.new4 (JS.SV.fValue (args[1]), JS.SV.fValue (args[2]), JS.SV.fValue (args[3]), JS.SV.fValue (args[0]));
 else q = JU.Quat.newVA (JU.P3.new3 (JS.SV.fValue (args[0]), JS.SV.fValue (args[1]), JS.SV.fValue (args[2])), JS.SV.fValue (args[3]));
break;
}
if (qs != null) {
if (nMax != 2147483647) {
var list =  new JU.Lst ();
for (var i = 0; i < qs.length; i++) list.addLast (qs[i].toPoint4f ());

return mp.addXList (list);
}q = (qs.length > 0 ? qs[0] : null);
}return mp.addXPt4 ((q == null ? JU.Quat.newP4 (p4) : q).toPoint4f ());
}, "JS.ScriptMathProcessor,~A,~N");
Clazz_defineMethod (c$, "evaluateRandom", 
 function (mp, args) {
if (args.length > 3) return false;
if (this.rand == null) this.rand =  new java.util.Random ();
var lower = 0;
var upper = 1;
switch (args.length) {
case 3:
this.rand.setSeed (Clazz_floatToInt (JS.SV.fValue (args[2])));
case 2:
upper = JS.SV.fValue (args[1]);
case 1:
lower = JS.SV.fValue (args[0]);
case 0:
break;
default:
return false;
}
return mp.addXFloat ((this.rand.nextFloat () * (upper - lower)) + lower);
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateRowCol", 
 function (mp, args, tok) {
if (args.length != 1) return false;
var n = args[0].asInt () - 1;
var x1 = mp.getX ();
var f;
switch (x1.tok) {
case 11:
if (n < 0 || n > 2) return false;
var m = x1.value;
switch (tok) {
case 1275068935:
f =  Clazz_newFloatArray (3, 0);
m.getRow (n, f);
return mp.addXAF (f);
case 1275068934:
default:
f =  Clazz_newFloatArray (3, 0);
m.getColumn (n, f);
return mp.addXAF (f);
}
case 12:
if (n < 0 || n > 2) return false;
var m4 = x1.value;
switch (tok) {
case 1275068935:
f =  Clazz_newFloatArray (4, 0);
m4.getRow (n, f);
return mp.addXAF (f);
case 1275068934:
default:
f =  Clazz_newFloatArray (4, 0);
m4.getColumn (n, f);
return mp.addXAF (f);
}
case 7:
var l1 = x1.getList ();
var l2 =  new JU.Lst ();
for (var i = 0, len = l1.size (); i < len; i++) {
var l3 = l1.get (i).getList ();
if (l3 == null) return mp.addXStr ("");
l2.addLast (n < l3.size () ? l3.get (n) : JS.SV.newS (""));
}
return mp.addXList (l2);
}
return false;
}, "JS.ScriptMathProcessor,~A,~N");
Clazz_defineMethod (c$, "evaluateIn", 
 function (mp, args) {
var x1 = mp.getX ();
switch (args.length) {
case 1:
var lst = args[0].getList ();
if (lst != null) for (var i = 0, n = lst.size (); i < n; i++) if (JS.SV.areEqual (x1, lst.get (i))) return mp.addXInt (i + 1);

break;
default:
for (var i = 0; i < args.length; i++) if (JS.SV.areEqual (x1, args[i])) return mp.addXInt (i + 1);

break;
}
return mp.addXInt (0);
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateReplace", 
 function (mp, args) {
var isAll = false;
var sFind;
var sReplace;
switch (args.length) {
case 0:
isAll = true;
sFind = sReplace = null;
break;
case 3:
isAll = JS.SV.bValue (args[2]);
case 2:
sFind = JS.SV.sValue (args[0]);
sReplace = JS.SV.sValue (args[1]);
break;
default:
return false;
}
var x = mp.getX ();
if (x.tok == 7) {
var list = JS.SV.strListValue (x);
var l =  new Array (list.length);
for (var i = list.length; --i >= 0; ) l[i] = (sFind == null ? JU.PT.clean (list[i]) : isAll ? JU.PT.replaceAllCharacters (list[i], sFind, sReplace) : JU.PT.rep (list[i], sFind, sReplace));

return mp.addXAS (l);
}var s = JS.SV.sValue (x);
return mp.addXStr (sFind == null ? JU.PT.clean (s) : isAll ? JU.PT.replaceAllCharacters (s, sFind, sReplace) : JU.PT.rep (s, sFind, sReplace));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateScript", 
 function (mp, args, tok) {
if ((tok == 134222350 || tok == 134238732) && args.length != 1 || args.length == 0) return false;
var s = JS.SV.sValue (args[0]);
var sb =  new JU.SB ();
switch (tok) {
case 134218759:
return (args.length == 2 ? s.equalsIgnoreCase ("JSON") && mp.addXObj (this.vwr.parseJSONMap (JS.SV.sValue (args[1]))) : mp.addXObj (this.vwr.evaluateExpressionAsVariable (s)));
case 134222850:
var appID = (args.length == 2 ? JS.SV.sValue (args[1]) : ".");
if (!appID.equals (".")) sb.append (this.vwr.jsEval (appID + "\1" + s));
if (appID.equals (".") || appID.equals ("*")) this.e.runScriptBuffer (s, sb, true);
break;
case 134222350:
this.e.runScriptBuffer ("show " + s, sb, true);
break;
case 134238732:
return mp.addX (this.vwr.jsEvalSV (s));
}
s = sb.toString ();
var f;
return (Float.isNaN (f = JU.PT.parseFloatStrict (s)) ? mp.addXStr (s) : s.indexOf (".") >= 0 ? mp.addXFloat (f) : mp.addXInt (JU.PT.parseInt (s)));
}, "JS.ScriptMathProcessor,~A,~N");
Clazz_defineMethod (c$, "evaluateSort", 
 function (mp, args, tok) {
if (args.length > 1) return false;
if (tok == 1275068444) {
if (args.length == 1 && args[0].tok == 4) {
return mp.addX (mp.getX ().sortMapArray (args[0].asString ()));
}var n = (args.length == 0 ? 0 : args[0].asInt ());
return mp.addX (mp.getX ().sortOrReverse (n));
}var x = mp.getX ();
var match = (args.length == 0 ? null : args[0]);
if (x.tok == 4) {
var n = 0;
var s = JS.SV.sValue (x);
if (match == null) return mp.addXInt (0);
var m = JS.SV.sValue (match);
for (var i = 0; i < s.length; i++) {
var pt = s.indexOf (m, i);
if (pt < 0) break;
n++;
i = pt;
}
return mp.addXInt (n);
}var counts =  new JU.Lst ();
var last = null;
var count = null;
var xList = JS.SV.getVariable (x.value).sortOrReverse (0).getList ();
if (xList == null) return (match == null ? mp.addXStr ("") : mp.addXInt (0));
for (var i = 0, nLast = xList.size (); i <= nLast; i++) {
var a = (i == nLast ? null : xList.get (i));
if (match != null && a != null && !JS.SV.areEqual (a, match)) continue;
if (JS.SV.areEqual (a, last)) {
count.intValue++;
continue;
} else if (last != null) {
var y =  new JU.Lst ();
y.addLast (last);
y.addLast (count);
counts.addLast (JS.SV.getVariableList (y));
}count = JS.SV.newI (1);
last = a;
}
if (match == null) return mp.addX (JS.SV.getVariableList (counts));
if (counts.isEmpty ()) return mp.addXInt (0);
return mp.addX (counts.get (0).getList ().get (1));
}, "JS.ScriptMathProcessor,~A,~N");
Clazz_defineMethod (c$, "evaluateString", 
 function (mp, tok, args) {
var x = mp.getX ();
var sArg = (args.length > 0 ? JS.SV.sValue (args[0]) : tok == 1275068932 ? "" : "\n");
switch (args.length) {
case 0:
break;
case 1:
if (args[0].tok == 1073742335) {
return mp.addX (JS.SV.getVariable (JU.PT.getTokens (x.asString ())));
}break;
case 2:
if (x.tok == 7) break;
if (tok == 1275069447) {
x = JS.SV.getVariable (JU.PT.split (JU.PT.rep (x.value, "\n\r", "\n").$replace ('\r', '\n'), "\n"));
break;
}default:
return false;
}
if (x.tok == 7 && tok != 1275068932 && (tok != 1275069447 || args.length == 2)) {
mp.addX (x);
return this.evaluateList (mp, tok, args);
}var s = (tok == 1275069447 && x.tok == 10 || tok == 1275068932 && x.tok == 7 ? null : JS.SV.sValue (x));
switch (tok) {
case 1275069447:
if (x.tok == 10) {
var bsSelected = x.value;
var modelCount = this.vwr.ms.mc;
var lst =  new JU.Lst ();
for (var i = 0; i < modelCount; i++) {
var bs = this.vwr.getModelUndeletedAtomsBitSet (i);
bs.and (bsSelected);
lst.addLast (JS.SV.getVariable (bs));
}
return mp.addXList (lst);
}return mp.addXAS (JU.PT.split (s, sArg));
case 1275069446:
if (s.length > 0 && s.charAt (s.length - 1) == '\n') s = s.substring (0, s.length - 1);
return mp.addXStr (JU.PT.rep (s, "\n", sArg));
case 1275068932:
if (s != null) return mp.addXStr (JU.PT.trim (s, sArg));
var list = JS.SV.strListValue (x);
for (var i = list.length; --i >= 0; ) list[i] = JU.PT.trim (list[i], sArg);

return mp.addXAS (list);
}
return mp.addXStr ("");
}, "JS.ScriptMathProcessor,~N,~A");
Clazz_defineMethod (c$, "evaluateSubstructure", 
 function (mp, args, tok, isSelector) {
if (args.length == 0 || isSelector && args.length > 1) return false;
var bs =  new JU.BS ();
var pattern = JS.SV.sValue (args[0]);
if (pattern.length > 0) try {
var bsSelected = (isSelector ? mp.getX ().value : args.length == 2 && args[1].tok == 10 ? args[1].value : null);
bs = this.vwr.getSmilesMatcher ().getSubstructureSet (pattern, this.vwr.ms.at, this.vwr.ms.ac, bsSelected, (tok == 134218757 ? 1 : 2));
} catch (ex) {
if (Clazz_exceptionOf (ex, Exception)) {
this.e.evalError (ex.getMessage (), null);
} else {
throw ex;
}
}
return mp.addXBs (bs);
}, "JS.ScriptMathProcessor,~A,~N,~B");
Clazz_defineMethod (c$, "evaluateSymop", 
 function (mp, args, haveBitSet) {
var x1 = (haveBitSet ? mp.getX () : null);
if (x1 != null && x1.tok != 10) return false;
var bsAtoms = (x1 == null ? null : x1.value);
if (bsAtoms == null && this.vwr.ms.mc == 1) bsAtoms = this.vwr.getModelUndeletedAtomsBitSet (0);
var narg = args.length;
if (narg == 0) {
if (bsAtoms.isEmpty ()) return false;
var ops = JU.PT.split (JU.PT.trim (this.vwr.getSymTemp ().getSpaceGroupInfo (this.vwr.ms, null, this.vwr.ms.at[bsAtoms.nextSetBit (0)].mi, false).get ("symmetryInfo"), "\n"), "\n");
var lst =  new JU.Lst ();
for (var i = 0, n = ops.length; i < n; i++) lst.addLast (JU.PT.split (ops[i], "\t"));

return mp.addXList (lst);
}var xyz = null;
var iOp = -2147483648;
var apt = 0;
switch (args[0].tok) {
case 4:
xyz = JS.SV.sValue (args[0]);
apt++;
break;
case 12:
xyz = args[0].escape ();
apt++;
break;
case 2:
iOp = args[0].asInt ();
apt++;
break;
}
if (bsAtoms == null) {
if (apt < narg && args[apt].tok == 10) (bsAtoms =  new JU.BS ()).or (args[apt].value);
if (apt + 1 < narg && args[apt + 1].tok == 10) (bsAtoms == null ? (bsAtoms =  new JU.BS ()) : bsAtoms).or (args[apt + 1].value);
}var pt1 = null;
var pt2 = null;
if ((pt1 = (narg > apt ? mp.ptValue (args[apt], bsAtoms) : null)) != null) apt++;
if ((pt2 = (narg > apt ? mp.ptValue (args[apt], bsAtoms) : null)) != null) apt++;
var nth = (pt2 != null && args.length > apt && iOp == -2147483648 && args[apt].tok == 2 ? args[apt].intValue : 0);
if (nth > 0) apt++;
if (iOp == -2147483648) iOp = 0;
var desc = (narg == apt ? (pt2 != null ? "all" : pt1 != null ? "point" : "matrix") : JS.SV.sValue (args[apt++]).toLowerCase ());
return (bsAtoms != null && !bsAtoms.isEmpty () && apt == args.length && mp.addXObj (this.vwr.getSymTemp ().getSymmetryInfoAtom (this.vwr.ms, bsAtoms.nextSetBit (0), xyz, iOp, pt1, pt2, desc, 0, 0, nth)));
}, "JS.ScriptMathProcessor,~A,~B");
Clazz_defineMethod (c$, "evaluateTensor", 
 function (mp, args) {
var x = mp.getX ();
if (args.length > 2 || x.tok != 10) return false;
var bs = x.value;
var tensorType = (args.length == 0 ? null : JS.SV.sValue (args[0]).toLowerCase ());
var calc = this.vwr.getNMRCalculation ();
if ("unique".equals (tensorType)) return mp.addXBs (calc.getUniqueTensorSet (bs));
var infoType = (args.length < 2 ? null : JS.SV.sValue (args[1]).toLowerCase ());
return mp.addXList (calc.getTensorInfo (tensorType, infoType, bs));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateUserFunction", 
 function (mp, name, args, tok, isSelector) {
var x1 = null;
if (isSelector) {
x1 = mp.getX ();
switch (x1.tok) {
case 10:
break;
case 6:
if (args.length > 0) return false;
x1 = x1.getMap ().get (name);
return (x1 == null ? mp.addXStr ("") : mp.addX (x1));
default:
return false;
}
}name = name.toLowerCase ();
mp.wasX = false;
var params =  new JU.Lst ();
for (var i = 0; i < args.length; i++) {
params.addLast (args[i]);
}
if (isSelector) {
return mp.addXObj (this.e.getBitsetProperty (x1.value, null, tok, null, null, x1.value,  Clazz_newArray (-1, [name, params]), false, x1.index, false));
}var $var = this.e.getUserFunctionResult (name, params, null);
return ($var == null ? false : mp.addX ($var));
}, "JS.ScriptMathProcessor,~S,~A,~N,~B");
Clazz_defineMethod (c$, "evaluateWithin", 
 function (mp, args) {
if (args.length < 1 || args.length > 5) return false;
var len = args.length;
if (len == 1 && args[0].tok == 10) return mp.addX (args[0]);
var distance = 0;
var withinSpec = args[0].value;
var withinStr = "" + withinSpec;
var tok = args[0].tok;
if (tok == 4) tok = JS.T.getTokFromName (withinStr);
var ms = this.vwr.ms;
var isVdw = false;
var isWithinModelSet = false;
var isWithinGroup = false;
var isDistance = false;
var rd = null;
switch (tok) {
case 1648363544:
isVdw = true;
withinSpec = null;
case 3:
case 2:
isDistance = true;
if (len < 2 || len == 3 && args[1].tok == 7 && args[2].tok != 7) return false;
distance = (isVdw ? 100 : JS.SV.fValue (args[0]));
switch (tok = args[1].tok) {
case 1073742335:
case 1073742334:
isWithinModelSet = args[1].asBoolean ();
if (len > 2 && JS.SV.sValue (args[2]).equalsIgnoreCase ("unitcell")) tok = 1814695966;
len = 0;
break;
case 4:
var s = JS.SV.sValue (args[1]);
if (s.startsWith ("$")) return mp.addXBs (this.getAtomsNearSurface (distance, s.substring (1)));
if (s.equalsIgnoreCase ("group")) {
isWithinGroup = true;
tok = 1086324742;
} else if (s.equalsIgnoreCase ("vanderwaals") || s.equalsIgnoreCase ("vdw")) {
withinSpec = null;
isVdw = true;
tok = 1648363544;
} else if (s.equalsIgnoreCase ("unitcell")) {
tok = 1814695966;
} else {
return false;
}break;
}
break;
case 7:
if (len == 1) {
withinSpec = args[0].asString ();
tok = 0;
}break;
case 1073742328:
return (len == 3 && Clazz_instanceOf (args[1].value, JU.BS) && Clazz_instanceOf (args[2].value, JU.BS) && mp.addXBs (this.vwr.getBranchBitSet ((args[2].value).nextSetBit (0), (args[1].value).nextSetBit (0), true)));
case 134218757:
case 1237320707:
case 134218756:
var bsSelected = null;
var isOK = true;
switch (len) {
case 2:
break;
case 3:
isOK = (args[2].tok == 10);
if (isOK) bsSelected = args[2].value;
break;
default:
isOK = false;
}
if (!isOK) this.e.invArg ();
return mp.addXObj (this.e.getSmilesExt ().getSmilesMatches (JS.SV.sValue (args[1]), null, bsSelected, null, tok == 134218756 ? 2 : 1, mp.asBitSet, false));
}
if (Clazz_instanceOf (withinSpec, String)) {
if (tok == 0) {
tok = 1073742362;
if (len > 2) return false;
len = 2;
}} else if (!isDistance) {
return false;
}switch (len) {
case 1:
switch (tok) {
case 136314895:
case 2097184:
case 1678381065:
return mp.addXBs (ms.getAtoms (tok, null));
case 1073741863:
return mp.addXBs (ms.getAtoms (tok, ""));
case 1073742362:
return mp.addXBs (ms.getAtoms (1086324744, withinStr));
}
return false;
case 2:
switch (tok) {
case 1073742362:
tok = 1086324744;
break;
case 1073741824:
case 1086326786:
case 1086326785:
case 1073741863:
case 1086324744:
case 1111490587:
case 1073742128:
case 1073741925:
case 1073742189:
return mp.addXBs (this.vwr.ms.getAtoms (tok, JS.SV.sValue (args[args.length - 1])));
}
break;
case 3:
switch (tok) {
case 1073742335:
case 1073742334:
case 1086324742:
case 1648363544:
case 1814695966:
case 134217750:
case 134219265:
case 1073742329:
case 8:
case 7:
break;
case 1086324744:
withinStr = JS.SV.sValue (args[2]);
break;
default:
return false;
}
break;
}
var plane = null;
var pt = null;
var pts1 = null;
var last = args.length - 1;
switch (args[last].tok) {
case 9:
plane = args[last].value;
break;
case 8:
pt = args[last].value;
if (JS.SV.sValue (args[1]).equalsIgnoreCase ("hkl")) plane = this.e.getHklPlane (pt);
break;
case 7:
pts1 = (last == 2 && args[1].tok == 7 ? args[1].getList () : null);
pt = (last == 2 ? JS.SV.ptValue (args[1]) : last == 1 ? JU.P3.new3 (NaN, 0, 0) : null);
break;
}
if (plane != null) return mp.addXBs (ms.getAtomsNearPlane (distance, plane));
var bs = (args[last].tok == 10 ? args[last].value : null);
if (last > 0 && pt == null && pts1 == null && bs == null) return false;
if (tok == 1814695966) {
var asMap = isWithinModelSet;
return ((bs != null || pt != null) && mp.addXObj (this.vwr.ms.getUnitCellPointsWithin (distance, bs, pt, asMap)));
}if (pt != null || pts1 != null) {
if (args[last].tok == 7) {
var sv = args[last].getList ();
var ap3 =  new Array (sv.size ());
for (var i = ap3.length; --i >= 0; ) ap3[i] = JS.SV.ptValue (sv.get (i));

var ap31 = null;
if (pts1 != null) {
ap31 =  new Array (pts1.size ());
for (var i = ap31.length; --i >= 0; ) ap31[i] = JS.SV.ptValue (pts1.get (i));

}var ret =  new Array (1);
switch (J.bspt.PointIterator.withinDistPoints (distance, pt, ap3, ap31, ret)) {
case 134217751:
return mp.addXPt (ret[0]);
case 1073742001:
return mp.addXList (ret[0]);
case 1275068418:
return mp.addXAI (ret[0]);
case 4:
return mp.addXStr (ret[0]);
default:
return false;
}
}return mp.addXBs (this.vwr.getAtomsNearPt (distance, pt));
}if (tok == 1086324744) return mp.addXBs (this.vwr.ms.getSequenceBits (withinStr, bs,  new JU.BS ()));
if (bs == null) bs =  new JU.BS ();
if (!isDistance) return mp.addXBs (this.vwr.ms.getAtoms (tok, bs));
if (isWithinGroup) return mp.addXBs (this.vwr.getGroupsWithin (Clazz_floatToInt (distance), bs));
if (isVdw) {
rd =  new J.atomdata.RadiusData (null, (distance > 10 ? distance / 100 : distance), (distance > 10 ? J.atomdata.RadiusData.EnumType.FACTOR : J.atomdata.RadiusData.EnumType.OFFSET), J.c.VDW.AUTO);
if (distance < 0) distance = 0;
}return mp.addXBs (this.vwr.ms.getAtomsWithinRadius (distance, bs, isWithinModelSet, rd));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "evaluateWrite", 
 function (mp, args) {
switch (args.length) {
case 0:
return false;
case 1:
var type = args[0].asString ().toUpperCase ();
if (type.equals ("PNGJ")) {
return mp.addXMap (this.vwr.fm.getFileAsMap (null, "PNGJ"));
}if (JU.PT.isOneOf (type, ";ZIP;ZIPALL;JMOL;")) {
var params =  new java.util.Hashtable ();
var oc =  new JU.OC ();
params.put ("outputChannel", oc);
this.vwr.createZip (null, type, params);
var bis = JU.Rdr.getBIS (oc.toByteArray ());
params =  new java.util.Hashtable ();
this.vwr.getJzt ().readFileAsMap (bis, params, null);
return mp.addXMap (params);
}break;
}
return mp.addXStr (this.e.getCmdExt ().dispatch (134221856, true, args));
}, "JS.ScriptMathProcessor,~A");
Clazz_defineMethod (c$, "getAtomsNearSurface", 
 function (distance, surfaceId) {
var data =  Clazz_newArray (-1, [surfaceId, null, null]);
if (this.e.getShapePropertyData (24, "getVertices", data)) return this.getAtomsNearPts (distance, data[1], data[2]);
data[1] = Integer.$valueOf (0);
data[2] = Integer.$valueOf (-1);
if (this.e.getShapePropertyData (22, "getCenter", data)) return this.vwr.getAtomsNearPt (distance, data[2]);
data[1] = Float.$valueOf (distance);
if (this.e.getShapePropertyData (21, "getAtomsWithin", data)) return data[2];
return  new JU.BS ();
}, "~N,~S");
Clazz_defineMethod (c$, "getAtomsNearPts", 
 function (distance, points, bsInclude) {
var bsResult =  new JU.BS ();
if (points.length == 0 || bsInclude != null && bsInclude.isEmpty ()) return bsResult;
if (bsInclude == null) bsInclude = JU.BSUtil.setAll (points.length);
var at = this.vwr.ms.at;
for (var i = this.vwr.ms.ac; --i >= 0; ) {
var atom = at[i];
for (var j = bsInclude.nextSetBit (0); j >= 0; j = bsInclude.nextSetBit (j + 1)) if (atom.distance (points[j]) < distance) {
bsResult.set (i);
break;
}
}
return bsResult;
}, "~N,~A,JU.BS");
Clazz_defineMethod (c$, "getMinMax", 
function (floatOrSVArray, tok) {
var data = null;
var sv = null;
var ndata = 0;
var htPivot = null;
while (true) {
if (JU.AU.isAF (floatOrSVArray)) {
if (tok == 1140850707) return "NaN";
data = floatOrSVArray;
ndata = data.length;
if (ndata == 0) break;
} else if (Clazz_instanceOf (floatOrSVArray, JU.Lst)) {
sv = floatOrSVArray;
ndata = sv.size ();
if (ndata == 0) {
if (tok != 1140850707) break;
} else {
var sv0 = sv.get (0);
if (sv0.tok == 8) return this.getMinMaxPoint (sv, tok);
if (sv0.tok == 4 && (sv0.value).startsWith ("{")) {
var pt = JS.SV.ptValue (sv0);
if (Clazz_instanceOf (pt, JU.P3)) return this.getMinMaxPoint (sv, tok);
if (Clazz_instanceOf (pt, JU.P4)) return this.getMinMaxQuaternion (sv, tok);
break;
}}} else {
break;
}var sum;
var minMax;
var isMin = false;
switch (tok) {
case 1140850707:
htPivot =  new java.util.Hashtable ();
sum = minMax = 0;
break;
case 32:
isMin = true;
sum = 3.4028235E38;
minMax = 2147483647;
break;
case 64:
sum = -3.4028235E38;
minMax = -2147483647;
break;
default:
sum = minMax = 0;
}
var sum2 = 0;
var n = 0;
var isInt = true;
var isPivot = (tok == 1140850707);
for (var i = ndata; --i >= 0; ) {
var svi = (sv == null ? JS.SV.vF : sv.get (i));
var v = (isPivot ? 1 : data == null ? JS.SV.fValue (svi) : data[i]);
if (Float.isNaN (v)) continue;
n++;
switch (tok) {
case 160:
case 192:
sum2 += (v) * v;
case 128:
case 96:
sum += v;
break;
case 1140850707:
isInt = new Boolean (isInt & (svi.tok == 2)).valueOf ();
var key = svi.asString ();
var ii = htPivot.get (key);
htPivot.put (key, (ii == null ?  new Integer (1) :  new Integer (ii.intValue () + 1)));
break;
case 32:
case 64:
isInt = new Boolean (isInt & (svi.tok == 2)).valueOf ();
if (isMin == (v < sum)) {
sum = v;
if (isInt) minMax = svi.intValue;
}break;
}
}
if (tok == 1140850707) {
return htPivot;
}if (n == 0) break;
switch (tok) {
case 96:
sum /= n;
break;
case 192:
if (n == 1) break;
sum = Math.sqrt ((sum2 - sum * sum / n) / (n - 1));
break;
case 32:
case 64:
if (isInt) return Integer.$valueOf (minMax);
break;
case 128:
break;
case 160:
sum = sum2;
break;
}
return Float.$valueOf (sum);
}
return "NaN";
}, "~O,~N");
Clazz_defineMethod (c$, "getMinMaxPoint", 
 function (pointOrSVArray, tok) {
var data = null;
var sv = null;
var ndata = 0;
if (Clazz_instanceOf (pointOrSVArray, Array)) {
data = pointOrSVArray;
ndata = data.length;
} else if (Clazz_instanceOf (pointOrSVArray, JU.Lst)) {
sv = pointOrSVArray;
ndata = sv.size ();
}if (sv == null && data == null) return "NaN";
var result =  new JU.P3 ();
var fdata =  Clazz_newFloatArray (ndata, 0);
for (var xyz = 0; xyz < 3; xyz++) {
for (var i = 0; i < ndata; i++) {
var pt = (data == null ? JS.SV.ptValue (sv.get (i)) : data[i]);
if (pt == null) return "NaN";
switch (xyz) {
case 0:
fdata[i] = pt.x;
break;
case 1:
fdata[i] = pt.y;
break;
case 2:
fdata[i] = pt.z;
break;
}
}
var f = this.getMinMax (fdata, tok);
if (!(Clazz_instanceOf (f, Number))) return "NaN";
var value = (f).floatValue ();
switch (xyz) {
case 0:
result.x = value;
break;
case 1:
result.y = value;
break;
case 2:
result.z = value;
break;
}
}
return result;
}, "~O,~N");
Clazz_defineMethod (c$, "getMinMaxQuaternion", 
 function (svData, tok) {
var data;
switch (tok) {
case 32:
case 64:
case 128:
case 160:
return "NaN";
}
while (true) {
data = this.e.getQuaternionArray (svData, 1073742001);
if (data == null) break;
var retStddev =  Clazz_newFloatArray (1, 0);
var result = JU.Quat.sphereMean (data, retStddev, 0.0001);
switch (tok) {
case 96:
return result;
case 192:
return Float.$valueOf (retStddev[0]);
}
break;
}
return "NaN";
}, "JU.Lst,~N");
Clazz_defineMethod (c$, "getPatternMatcher", 
 function () {
return (this.pm == null ? this.pm = J.api.Interface.getUtil ("PatternMatcher", this.e.vwr, "script") : this.pm);
});
Clazz_defineMethod (c$, "opTokenFor", 
 function (tok) {
switch (tok) {
case 1275069441:
case 1275069446:
return JS.T.tokenPlus;
case 1275068931:
return JS.T.tokenMinus;
case 1275068929:
return JS.T.tokenTimes;
case 1275068930:
return JS.T.tokenMul3;
case 1275068928:
return JS.T.tokenDivide;
}
return null;
}, "~N");
Clazz_defineMethod (c$, "setContactBitSets", 
function (bsA, bsB, localOnly, distance, rd, warnMultiModel) {
var withinAllModels;
var bs;
if (bsB == null) {
bsB = JU.BSUtil.setAll (this.vwr.ms.ac);
JU.BSUtil.andNot (bsB, this.vwr.slm.bsDeleted);
bsB.andNot (bsA);
withinAllModels = false;
} else {
bs = JU.BSUtil.copy (bsA);
bs.or (bsB);
var nModels = this.vwr.ms.getModelBS (bs, false).cardinality ();
withinAllModels = (nModels > 1);
if (warnMultiModel && nModels > 1 && !this.e.tQuiet) this.e.showString (J.i18n.GT.$ ("Note: More than one model is involved in this contact!"));
}if (!bsA.equals (bsB)) {
var setBfirst = (!localOnly || bsA.cardinality () < bsB.cardinality ());
if (setBfirst) {
bs = this.vwr.ms.getAtomsWithinRadius (distance, bsA, withinAllModels, (Float.isNaN (distance) ? rd : null));
bsB.and (bs);
}if (localOnly) {
bs = this.vwr.ms.getAtomsWithinRadius (distance, bsB, withinAllModels, (Float.isNaN (distance) ? rd : null));
bsA.and (bs);
if (!setBfirst) {
bs = this.vwr.ms.getAtomsWithinRadius (distance, bsA, withinAllModels, (Float.isNaN (distance) ? rd : null));
bsB.and (bs);
}bs = JU.BSUtil.copy (bsB);
bs.and (bsA);
if (bs.equals (bsA)) bsB.andNot (bsA);
 else if (bs.equals (bsB)) bsA.andNot (bsB);
}}return bsB;
}, "JU.BS,JU.BS,~B,~N,J.atomdata.RadiusData,~B");
});
})(Clazz
,Clazz.getClassName
,Clazz.newLongArray
,Clazz.doubleToByte
,Clazz.doubleToInt
,Clazz.doubleToLong
,Clazz.declarePackage
,Clazz.instanceOf
,Clazz.load
,Clazz.instantialize
,Clazz.decorateAsClass
,Clazz.floatToInt
,Clazz.floatToLong
,Clazz.makeConstructor
,Clazz.defineEnumConstant
,Clazz.exceptionOf
,Clazz.newIntArray
,Clazz.defineStatics
,Clazz.newFloatArray
,Clazz.declareType
,Clazz.prepareFields
,Clazz.superConstructor
,Clazz.newByteArray
,Clazz.declareInterface
,Clazz.p0p
,Clazz.pu$h
,Clazz.newShortArray
,Clazz.innerTypeInstance
,Clazz.isClassDefined
,Clazz.prepareCallback
,Clazz.newArray
,Clazz.castNullAs
,Clazz.floatToShort
,Clazz.superCall
,Clazz.decorateAsType
,Clazz.newBooleanArray
,Clazz.newCharArray
,Clazz.implementOf
,Clazz.newDoubleArray
,Clazz.overrideConstructor
,Clazz.clone
,Clazz.doubleToShort
,Clazz.getInheritedLevel
,Clazz.getParamsType
,Clazz.isAF
,Clazz.isAB
,Clazz.isAI
,Clazz.isAS
,Clazz.isASS
,Clazz.isAP
,Clazz.isAFloat
,Clazz.isAII
,Clazz.isAFF
,Clazz.isAFFF
,Clazz.tryToSearchAndExecute
,Clazz.getStackTrace
,Clazz.inheritArgs
,Clazz.alert
,Clazz.defineMethod
,Clazz.overrideMethod
,Clazz.declareAnonymous
//,Clazz.checkPrivateMethod
,Clazz.cloneFinals
);