Clazz.declarePackage("JS");
Clazz.load(["JS.ScriptExt"], "JS.CmdExt", ["java.util.Hashtable", "JU.AU", "$.BS", "$.Base64", "$.Lst", "$.M3", "$.M4", "$.Measure", "$.P3", "$.P4", "$.PT", "$.Quat", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.c.STER", "$.VDW", "J.i18n.GT", "JM.AtomCollection", "$.LabelToken", "$.Measurement", "$.Text", "JS.SV", "$.ScriptCompiler", "$.ScriptError", "$.ScriptEval", "$.ScriptInterruption", "$.ScriptMathProcessor", "$.ScriptParam", "$.T", "JU.BSUtil", "$.BoxInfo", "$.C", "$.Edge", "$.Elements", "$.Escape", "$.Logger", "$.Parser", "$.Point3fi", "$.SimpleUnitCell", "JV.FileManager", "$.JC", "$.StateManager", "$.Viewer"], function(){
var c$ = Clazz.declareType(JS, "CmdExt", JS.ScriptExt);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JS.CmdExt, []);
});
Clazz.overrideMethod(c$, "dispatch", 
function(iTok, flag, st){
this.chk = this.e.chk;
this.slen = this.e.slen;
this.st = st;
switch (iTok) {
case 4108:
this.audio();
break;
case 1073741866:
st[0].value = this.prepareBinaryOutput(st[0]);
return null;
case 4098:
this.assign(false);
break;
case 134221829:
this.cache();
break;
case 4102:
this.calculate();
break;
case 4103:
this.capture();
break;
case 4105:
this.centerAt();
break;
case 134221831:
this.compare();
break;
case 528395:
this.console();
break;
case 4106:
this.connect(1);
break;
case 1094717448:
this.configuration();
break;
case 134221834:
this.data();
break;
case 1613238294:
this.connect(0);
break;
case 4120:
this.image();
break;
case 4122:
this.invertSelected();
break;
case 4124:
this.macro();
break;
case 4125:
this.mapProperty();
break;
case 4126:
this.minimize(false);
break;
case 603983903:
this.modelkit();
break;
case 1275072532:
this.modulation();
break;
case 4130:
this.mutate();
break;
case 4131:
this.navigate();
break;
case 4133:
case 134221850:
case 4138:
this.plot(st);
break;
case 134222350:
this.show();
break;
case 528443:
this.stereo();
break;
case 4156:
this.sync();
break;
case 1814695966:
this.unitcell(flag ? 2 : 1, 0);
break;
case 20489:
this.varna();
break;
case 134221856:
return this.write(flag ? st : null);
case 6:
this.measure();
break;
case 21:
this.polyhedra();
break;
case 20:
this.ellipsoid();
break;
case 4:
this.struts();
break;
}
return null;
}, "~N,~B,~A");
Clazz.defineMethod(c$, "audio", 
function(){
var htParams =  new java.util.Hashtable();
var id = null;
var filter = null;
var filename = null;
var i = this.e.iToken + 1;
if (this.tokAt(i) == 1073742334) {
this.checkLength(i + 1);
if (!this.chk) this.vwr.sm.stopAudio(null);
return;
}for (; i < this.slen; i++) {
switch (this.tokAt(i)) {
case 1073741974:
if (id != null) this.invArg();
id = this.paramAsStr(++i);
break;
case 4:
filename = this.stringParameter(i);
htParams.put("audioFile", filename);
break;
case 1073741940:
filter = this.stringParameter(++i);
id = this.addFilterAttribute(htParams, filter, "id");
this.addFilterAttribute(htParams, filter, "loop");
this.addFilterAttribute(htParams, filter, "start");
this.addFilterAttribute(htParams, filter, "pause");
this.addFilterAttribute(htParams, filter, "play");
this.addFilterAttribute(htParams, filter, "ended");
this.addFilterAttribute(htParams, filter, "action");
break;
default:
this.checkLength(i + 1);
if (htParams.containsKey("action")) this.invArg();
var action = this.paramAsStr(i);
htParams.put("autoclose", Boolean.FALSE);
htParams.put("action", action);
break;
}
}
if (!this.chk && !htParams.isEmpty()) {
if (id == null) id = "audio1";
htParams.put("id", id);
this.vwr.sm.playAudio(htParams);
}});
Clazz.defineMethod(c$, "addFilterAttribute", 
function(htParams, filter, key){
var val = JU.PT.getQuotedOrUnquotedAttribute(filter, key);
if (val != null && val.length > 0) htParams.put(key, val);
return val;
}, "java.util.Map,~S,~S");
Clazz.defineMethod(c$, "macro", 
function(){
if (this.chk) return;
var key = this.e.optParameterAsString(1);
if (key.length == 0) {
this.showString(this.vwr.getMacro(null));
return;
}var macro = this.vwr.getMacro(key);
if (macro == null) {
this.showString("macro " + key + " could not be found. Current macros include:\n" + this.vwr.getMacro(null));
return;
}this.showString("running " + macro);
this.e.cmdScript(4124, macro, null, null);
});
Clazz.defineMethod(c$, "evalParallel", 
function(context, shapeManager){
this.chk = this.e.chk;
this.slen = this.e.slen;
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.setAllowJSThreads(false);
se.dispatchCommands(false, 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);
ex.printStackTrace();
}return false;
} else {
throw ex;
}
}
return true;
}, "JS.ScriptContext,JV.ShapeManager");
Clazz.defineMethod(c$, "getBitsetIdent", 
function(bs, label, tokenValue, useAtomMap, index, isExplicitlyAll){
return this.getBitsetIdentFull(bs, label, useAtomMap, index, isExplicitlyAll, null);
}, "JU.BS,~S,~O,~B,~N,~B");
Clazz.defineMethod(c$, "getBitsetIdentFull", 
function(bs, label, useAtomMap, index, isExplicitlyAll, sout){
var isAtoms = !(Clazz.instanceOf(bs,"JM.BondSet"));
if (isAtoms) {
if (label == null) {
label = this.vwr.getStandardLabelFormat(0);
} else if (label.length == 0) {
label = "%[label]";
}} else {
if (label != null && label.length == 0) {
label = "[%a1 #%i1] %4.3LENGTH [%a2 #%i2] #%#";
} else if ("%U".equals(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 ?  Clazz.newArray(-1, [label]) : label;
}var modelSet = this.vwr.ms;
var n = 0;
if (JS.CmdExt.labeler == null) JS.CmdExt.labeler = modelSet.getLabeler();
var indices = (isAtoms || !useAtomMap ? null : (bs).getAssociatedAtoms(modelSet));
var asIdentity = (label == null || label.length == 0);
var htValues = (isAtoms || asIdentity ? null : JS.CmdExt.labeler.getBondLabelValues());
var tokens = (asIdentity ? null : isAtoms ? JS.CmdExt.labeler.compile(this.vwr, label, '\0', null) : JS.CmdExt.labeler.compile(this.vwr, label, '\1', htValues));
var nmax = (haveIndex ? 1 : bs.cardinality());
var haveSout = (sout != null);
if (!haveSout) 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) {
str = (asIdentity ? modelSet.at[j].getInfo() : JS.CmdExt.labeler.formatLabelAtomArray(this.vwr, modelSet.at[j], tokens, '\0', indices, ptTemp));
} else {
var bond = modelSet.bo[j];
if (bond == null) continue;
str = (asIdentity ? bond.getIdentity() : JS.CmdExt.labeler.formatLabelBond(this.vwr, bond, tokens, htValues, indices, ptTemp));
}str = JU.PT.formatStringI(str, "#", (n + 1));
sout[haveSout ? j : n] = str;
n++;
if (haveIndex) break;
}
return nmax == 1 && !isExplicitlyAll ? sout[0] : sout;
}, "JU.BS,~S,~B,~N,~B,~A");
Clazz.defineMethod(c$, "getLoadSymmetryParams", 
function(i, sOptions, htParams){
var eval = this.e;
this.chk = eval.chk;
this.slen = eval.slen;
var isEmptyLoad = false;
var lattice = null;
var tok = this.tokAt(i);
if (tok == 1073742332 || tok == 8) {
lattice = eval.getFractionalPoint(i);
tok = this.tokAt(i = eval.iToken + 1);
}switch (tok) {
case 134217764:
isEmptyLoad = (htParams.get("isEmptyLoad") === Boolean.TRUE);
case 1073741938:
case 1073742080:
case 1094713350:
case 1073742163:
case 1073742114:
case 1814695966:
if (lattice == null) lattice = JU.P3.new3(555, 555, -1);
eval.iToken = i - 1;
break;
}
var offset = null;
if (lattice != null) {
htParams.put("lattice", lattice);
i = eval.iToken + 1;
sOptions.append(" " + JU.SimpleUnitCell.escapeMultiplier(lattice));
i = this.checkPacked(i, 0, htParams, sOptions);
if (this.tokAt(i) == 1094713350) {
htParams.put("centroid", Boolean.TRUE);
sOptions.append(" CENTROID");
var ptok = 0;
if (this.isFloatParameter(i + 1)) {
--i;
ptok = 1073742080;
}i = this.checkPacked(++i, ptok, htParams, sOptions);
}if (this.tokAt(i) == 1073742163) {
var supercell;
sOptions.append(" SUPERCELL ");
if (eval.isPoint3f(++i)) {
var pt = this.getPoint3f(i, false);
if (pt.x != Clazz.floatToInt(pt.x) || pt.y != Clazz.floatToInt(pt.y) || pt.z != Clazz.floatToInt(pt.z) || pt.x < 1 || pt.y < 1 || pt.z < 1) {
eval.iToken = i;
this.invArg();
}supercell = pt;
i = eval.iToken;
} else {
supercell = this.stringParameter(i);
}sOptions.append(JU.Escape.e(supercell));
htParams.put("supercell", supercell);
i = this.checkPacked(++i, 0, htParams, sOptions);
}var distance = 0;
if (this.tokAt(i) == 1073742114) {
i++;
distance = this.floatParameter(i++);
sOptions.append(" range " + distance);
}htParams.put("symmetryRange", Float.$valueOf(distance));
var spacegroup = null;
var sg;
var iGroup = -2147483648;
if (this.tokAt(i) == 134217764) {
++i;
spacegroup = JU.PT.rep(this.paramAsStr(i++), "''", "\"");
sOptions.append(" spacegroup " + JU.PT.esc(spacegroup));
if (spacegroup.equalsIgnoreCase("ignoreOperators")) {
iGroup = -999;
} else {
if (spacegroup.length == 0) {
sg = this.vwr.getCurrentUnitCell();
if (sg != null) spacegroup = sg.getSpaceGroupName();
} else {
if (spacegroup.indexOf(",") >= 0) if ((lattice.x < 9 && lattice.y < 9 && lattice.z == 0)) spacegroup += "#doNormalize=0";
}htParams.put("spaceGroupName", spacegroup);
iGroup = -2;
}}var fparams = null;
if (this.tokAt(i) == 1814695966) {
++i;
var s = eval.optParameterAsString(i);
if (s.length == 0) {
sg = this.vwr.getCurrentUnitCell();
if (sg != null) {
fparams = sg.getUnitCellAsArray(true);
offset = sg.getCartesianOffset();
}} else {
if (this.tokAt(i) == 4) {
fparams =  Clazz.newFloatArray (6, 0);
JU.SimpleUnitCell.setAbc(s, fparams, null);
} else {
fparams = eval.floatParameterSet(i, 6, 9);
}}if (fparams == null || fparams.length != 6 && fparams.length != 9) this.invArg();
sOptions.append(" unitcell [");
for (var j = 0; j < fparams.length; j++) sOptions.append((j == 0 ? "" : " ") + fparams[j]);

sOptions.append("]");
htParams.put("unitcell", fparams);
if (iGroup == -2147483648) iGroup = -1;
i = eval.iToken + 1;
}if (iGroup != -2147483648) htParams.put("spaceGroupIndex", Integer.$valueOf(iGroup));
if (isEmptyLoad && fparams == null && spacegroup != null && (iGroup = JU.PT.parseInt(spacegroup)) != -2147483648) {
}}var areFractional = false;
if (offset == null && this.tokAt(i) == 1073742066) {
offset = this.getPoint3f(++i, true);
areFractional = eval.coordinatesAreFractional;
}if (offset != null) {
if (areFractional) {
offset.setT(eval.fractionalPoint);
htParams.put("unitCellOffsetFractional", (areFractional ? Boolean.TRUE : Boolean.FALSE));
sOptions.append(" offset {" + offset.x + " " + offset.y + " " + offset.z + "/1}");
} else {
sOptions.append(" offset " + JU.Escape.eP(offset));
}htParams.put("unitCellOffset", offset);
i = eval.iToken + 1;
}return i;
}, "~N,JU.SB,java.util.Map");
Clazz.defineMethod(c$, "checkPacked", 
function(i, tok, htParams, sOptions){
if (tok == 0) tok = this.tokAt(i);
switch (tok) {
case 1073741938:
htParams.put("packed", Boolean.TRUE);
var oabc = null;
tok = this.tokAt(++i);
switch (tok) {
case 1812599299:
case 1814695966:
case 4:
break;
default:
if (this.e.isArrayParameter(i)) {
oabc = this.e.getPointArray(i, -1, false, true);
i = this.e.iToken;
} else if (this.isFloatParameter(i)) {
var d = this.floatParameter(i);
oabc =  Clazz.newArray(-1, [ new JU.P3(), JU.P3.new3(d, d, d)]);
} else {
oabc =  new Array(0);
--i;
}}
i++;
if (this.e.chk) return i;
var isRaw = false;
switch (tok) {
case 4:
case 1095241729:
isRaw = true;
i--;
case 1814695966:
var type = this.e.optParameterAsString(i++).toLowerCase();
if (isRaw || JU.PT.isOneOf(type, ";spin;conventional;primitive;rhombohedral;trigonal;") || type.indexOf(",") >= 0 && (type.indexOf("a") >= 0 && type.indexOf("b") >= 0 && type.indexOf("c") >= 0)) {
htParams.put("fillRange", type);
sOptions.append(" FILL " + (isRaw ? "" : "UNITCELL ") + "\"" + type + "\"");
return i;
}var unitCell = this.vwr.getCurrentUnitCell();
if (unitCell != null) {
oabc = JU.BoxInfo.toOABC(unitCell.getUnitCellVerticesNoOffset(), unitCell.getCartesianOffset());
break;
}case 1812599299:
oabc = JU.BoxInfo.toOABC(this.vwr.ms.getBBoxVertices(), null);
break;
}
switch (oabc.length) {
case 2:
var a = oabc[1];
oabc =  Clazz.newArray(-1, [oabc[0], JU.P3.newP(oabc[0]),  new JU.P3(),  new JU.P3()]);
oabc[1].x = a.x;
oabc[2].y = a.y;
oabc[3].z = a.z;
break;
case 3:
oabc =  Clazz.newArray(-1, [ new JU.P3(), oabc[0], oabc[1], oabc[2]]);
break;
case 4:
break;
default:
if (tok != 0) this.invArg();
oabc =  Clazz.newArray(-1, [ new JU.P3(), JU.P3.new3(10, 0, 0), JU.P3.new3(0, 10, 0), JU.P3.new3(0, 0, 10)]);
}
htParams.put("fillRange", oabc);
sOptions.append(" FILL [" + oabc[0] + oabc[1] + oabc[2] + oabc[3] + "]");
break;
case 1073742080:
var f = NaN;
if (this.isFloatParameter(++i)) f = this.floatParameter(i++);
if (!this.e.chk) {
htParams.put("packed", Boolean.TRUE);
sOptions.append(" PACKED");
if (!Float.isNaN(f)) {
htParams.put("packingRange", Float.$valueOf(f));
sOptions.append(" " + f);
}}break;
}
return i;
}, "~N,~N,java.util.Map,JU.SB");
Clazz.defineMethod(c$, "cache", 
function(){
var tok = this.tokAt(1);
var fileName = null;
var n = 2;
switch (tok) {
case 1275069441:
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 == 1275069441);
this.showString(nBytes < 0 ? "cache cleared" : nBytes + " bytes " + (tok == 1275069441 ? " cached" : " removed"));
}break;
default:
this.invArg();
}
});
Clazz.defineMethod(c$, "calculate", 
function(){
var isSurface = false;
var asDSSP = false;
var bs1 = null;
var bs2 = null;
var e = this.e;
var n = -2147483648;
var version = -1;
if ((e.iToken = e.slen) >= 2) {
e.clearDefinedVariableAtomSets();
switch (this.getToken(1).tok) {
case 2:
if (this.intParameter(1) != 3 || !this.paramAsStr(2).equalsIgnoreCase("D")) {
break;
}if (this.vwr.am.cmi < 0) e.errorStr(30, "calculate 3D");
var cmd = "load append $ filter '2D';select visible;center selected";
if (e.optParameterAsString(3).equalsIgnoreCase("ZAP")) {
cmd += ";zap modelIndex=" + Math.max(this.vwr.am.cmi, 0);
}if (!this.chk) e.runScript(cmd);
return;
case 1073741824:
this.checkLength(2);
break;
case 134217764:
e.iToken = 1;
bs1 = (this.slen == 2 ? null : this.atomExpressionAt(2));
e.checkLast(e.iToken);
if (!this.chk) e.showString("" + this.vwr.findSpaceGroup(null, bs1, null, null, null, null, 1));
return;
case 1086324752:
e.iToken = 1;
bs1 = (this.slen == 2 ? null : this.atomExpressionAt(2));
e.checkLast(e.iToken);
if (!this.chk) e.showString(this.vwr.calculateChirality(bs1));
return;
case 1631586315:
this.checkLength(2);
if (this.chk) return;
n = this.vwr.calculateFormalCharges(null);
this.showString(J.i18n.GT.i(J.i18n.GT.$("{0} charges modified"), n));
return;
case 1075838996:
this.checkLength(2);
if (!this.chk) this.vwr.ms.assignAromaticBondsBs(true, null);
return;
case 1613238294:
if (e.slen != 2) {
asDSSP = (this.tokAt(++e.iToken) == 1639976963);
if (asDSSP) bs1 = this.vwr.bsA();
 else bs1 = this.atomExpressionAt(e.iToken);
if (!asDSSP && !(asDSSP = (this.tokAt(++e.iToken) == 1639976963))) bs2 = this.atomExpressionAt(e.iToken);
}if (this.chk) return;
n = this.vwr.autoHbond(bs1, bs2, false);
if (n != -2147483648) e.report(J.i18n.GT.i(J.i18n.GT.$("{0} hydrogen bonds"), Math.abs(n)), false);
return;
case 1612709900:
var itok = this.tokAt(2);
var andBond = (itok == 1073742335);
if (andBond) {
e.iToken++;
} else if (itok == 528443) {
e.iToken++;
}bs1 = (this.slen == e.iToken + 1 ? null : this.atomExpressionAt(e.iToken + 1));
if (bs1 == null && itok == 528443) {
bs1 = this.vwr.getAtomBitSet("_C & connected(3) & !connected(double)");
}e.checkLast(e.iToken);
if (!this.chk) {
this.vwr.addHydrogens(bs1, 0);
if (andBond) {
if (bs1 == null) bs1 = this.vwr.bsA();
this.vwr.makeConnections(0.1, 1e8, 515, 1073742025, bs1, bs1, null, false, false, 0);
this.vwr.ms.assignAromaticBondsBs(true, null);
}}return;
case 1111492619:
e.iToken = 1;
bs1 = (this.slen == 2 ? null : this.atomExpressionAt(2));
e.checkLast(e.iToken);
if (!this.chk) e.getPartialCharges(bs1);
return;
case 1088421903:
case 1275068447:
if (!this.chk) {
if (this.tokAt(2) == 1275203608) {
var id = (this.tokAt(3) == 4 ? this.stringParameter(3) : null);
bs1 = (id != null || this.slen == 3 ? null : this.atomExpressionAt(3));
var data =  Clazz.newArray(-1, [id, null, bs1]);
this.showString(e.getShapePropertyData(21, "symmetry", data) ? data[1] : "");
} else {
bs1 = (this.slen == 2 ? this.vwr.bsA() : this.atomExpressionAt(2));
var center = null;
if (this.tokAt(e.iToken) == 12289) {
center = e.centerParameter(e.iToken + 1, null);
}this.showString(this.vwr.ms.calculatePointGroup(bs1, center));
}}return;
case 1111490574:
this.checkLength(2);
if (!this.chk) {
this.vwr.calculateStraightness();
this.vwr.addStateScript("set quaternionFrame '" + this.vwr.getQuaternionFrame() + "'; calculate straightness", false, true);
}return;
case 1639976963:
bs1 = (this.slen < 4 || this.isFloatParameter(3) ? null : this.atomExpressionAt(2));
switch (this.tokAt(++e.iToken)) {
case 4138:
break;
case 1111490587:
if (this.chk) return;
var s = this.vwr.getAnnotationParser(1111490587).calculateDSSRStructure(this.vwr, bs1);
e.showString(s);
this.vwr.notifyCalculation("dssr", bs1, s);
return;
case 1073741915:
asDSSP = true;
version = (this.slen == e.iToken + 1 ? -1 : Clazz.floatToInt(this.floatParameter(++e.iToken)));
break;
case 0:
asDSSP = this.vwr.getBoolean(603979826);
break;
default:
this.invArg();
}
if (!this.chk) this.showString(this.vwr.calculateStructures(bs1, asDSSP, true, version));
return;
case 659482:
bs1 = (e.iToken + 1 < this.slen ? this.atomExpressionAt(++e.iToken) : null);
bs2 = (e.iToken + 1 < this.slen ? this.atomExpressionAt(++e.iToken) : null);
this.checkLength(++e.iToken);
if (!this.chk) {
n = this.vwr.calculateStruts(bs1, bs2);
if (n > 0) {
this.setShapeProperty(1, "type", Integer.$valueOf(32768));
e.setShapePropertyBs(1, "color", Integer.$valueOf(0x0FFFFFF), null);
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 2097180:
isSurface = true;
case 1111490575:
var isFrom = false;
switch (this.tokAt(2)) {
case 134217759:
e.iToken++;
break;
case 0:
isFrom = !isSurface;
break;
case 1073741952:
isFrom = true;
e.iToken++;
break;
default:
isFrom = true;
}
bs1 = (e.iToken + 1 < this.slen ? this.atomExpressionAt(++e.iToken) : this.vwr.bsA());
this.checkLength(++e.iToken);
if (!this.chk) this.vwr.calculateSurface(bs1, (isFrom ? 3.4028235E38 : -1));
return;
}
}e.errorStr2(53, "CALCULATE", "3D? 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 params = this.vwr.captureParams;
var type = (params == null ? "GIF" : params.get("type"));
var endTime = 0;
var mode = 0;
var slen = this.e.slen;
var fileName = "";
var looping = (this.vwr.am.animationReplayMode != 1073742070);
var i = 1;
var tok = this.tokAt(i);
var isTransparent = (tok == 1111490588);
if (isTransparent) tok = this.tokAt(++i);
var s = null;
switch (tok == 0 ? (tok = 102409) : tok) {
case 4:
fileName = this.e.optParameterAsString(i++);
if (fileName.length == 0) {
mode = 102409;
break;
}var lc = fileName.toLowerCase();
if (lc.endsWith(".gift") || lc.endsWith(".pngt")) {
isTransparent = true;
fileName = fileName.substring(0, fileName.length - 1);
lc = fileName.toLowerCase();
} else if (!lc.endsWith(".gif") && !lc.contains(".png")) {
fileName += ".gif";
}if (lc.endsWith(".png")) {
if (!lc.endsWith("0.png")) fileName = fileName.substring(0, fileName.length - 4) + "0000.png";
type = "PNG";
} else {
type = "GIF";
}if (isTransparent) type += "T";
var pt = fileName.indexOf("0000.");
var streaming = (pt < 0 || pt != fileName.lastIndexOf(".") - 4);
var isRock = false;
if (this.tokAt(i) == 528411) {
looping = true;
tok = this.tokAt(++i);
}switch (this.tokAt(i)) {
case 134222850:
s = this.stringParameter(++i);
break;
case 1073742129:
isRock = true;
case 1095241729:
var axis = "y";
looping = true;
i++;
if (isRock) {
if (i < slen && this.tokAt(i) != 2) axis = this.e.optParameterAsString(i++).toLowerCase();
s = "rotate Y 10 10;rotate Y -10 -10;rotate Y -10 -10;rotate Y 10 10";
var n = (i < slen ? this.intParameter(i++) : 5);
if (n < 0) {
s = JU.PT.rep(s, "10;", "" + (-n) + ";");
} else {
s = JU.PT.rep(s, "10", "" + n);
}} else {
if (i < slen) axis = this.e.optParameterAsString(i++).toLowerCase();
s = "rotate Y 360 30;";
}if (this.chk) return;
this.vwr.setNavigationMode(false);
if (axis === "" || "xyz".indexOf(axis) < 0) axis = "y";
s = JU.PT.rep(s, "Y", axis);
break;
case 3:
case 2:
endTime = this.floatParameter(i++);
break;
}
if (this.chk) return;
if (s != null) {
var wf = this.vwr.g.waitForMoveTo;
s = "set waitformoveto true;" + s + ";set waitformoveto " + wf;
s = "capture " + (isTransparent ? "transparent " : "") + JU.PT.esc(fileName) + (looping ? " LOOP;" : ";") + s + ";capture end;";
this.e.cmdScript(0, null, s, null);
return;
}mode = 1073742031;
params =  new java.util.Hashtable();
var fps = this.vwr.getInt(553648132);
if (streaming) {
params.put("streaming", Boolean.TRUE);
if (!looping) this.showString(J.i18n.GT.o(J.i18n.GT.$("Note: Enable looping using the LOOP keyword just after the file name or {0}"),  Clazz.newArray(-1, ["ANIMATION MODE LOOP"])));
this.showString(J.i18n.GT.o(J.i18n.GT.$("Animation delay based on: {0}"),  Clazz.newArray(-1, ["ANIMATION FPS " + fps])));
}params.put("captureFps", Integer.$valueOf(fps));
break;
case 102409:
case 1073741874:
if (params != null) params.put("captureSilent", Boolean.TRUE);
case 1073742335:
case 1073742334:
this.checkLength(-2);
mode = tok;
break;
default:
this.invArg();
}
if (this.chk || params == null) return;
params.put("type", type);
var c = Integer.$valueOf(this.vwr.getBackgroundArgb());
params.put("backgroundColor", c);
params.put("fileName", fileName);
params.put("quality", Integer.$valueOf(-1));
params.put("endTime", Long.$valueOf(endTime <= 0 ? -1 : System.currentTimeMillis() + Clazz.floatToLong(endTime * 1000)));
params.put("captureMode", JS.T.nameOf(mode).toLowerCase());
params.put("captureLooping", looping ? Boolean.TRUE : Boolean.FALSE);
var msg = this.vwr.processWriteOrCapture(params);
if (msg == null) msg = "canceled";
JU.Logger.info(msg);
});
Clazz.defineMethod(c$, "centerAt", 
function(){
var tok = this.getToken(1).tok;
switch (tok) {
case 1073741826:
case 96:
case 1812599299:
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$, "compare", 
function(){
var eval = this.e;
var isQuaternion = false;
var doRotate = false;
var doTranslate = false;
var doAnimate = false;
var isFlexFit = false;
var doMorph = false;
var data1 = null;
var data2 = null;
var bsAtoms1 = null;
var bsAtoms2 = null;
var vAtomSets = null;
var vQuatSets = null;
eval.iToken = 0;
var nSeconds = (this.isFloatParameter(1) ? this.floatParameter(++eval.iToken) : NaN);
var coordTo = null;
var bsFrom = null;
var bsTo = null;
var tok = 0;
if (this.tokAt(1) == 4115) {
bsFrom = this.vwr.bsA();
} else {
bsFrom = this.atomExpressionAt(1);
if (eval.isArrayParameter(++eval.iToken)) {
coordTo = eval.getPointArray(eval.iToken, -1, false, true);
} else if ((tok = this.tokAt(eval.iToken)) != 1153433601 && tok != 4115) {
bsTo = this.atomExpressionAt(eval.iToken);
}}var bsSubset = null;
var isSmiles = false;
var isPolyhedral = 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;
var isAtoms = (tok == 1153433601);
var isCoords = false;
for (var i = eval.iToken + 1; i < this.slen; ++i) {
switch (this.getToken(i).tok) {
case 4115:
isFrames = true;
if (bsTo == null) bsTo = JU.BSUtil.copy(bsFrom);
break;
case 134218757:
isSmiles = true;
tok = this.tokAt(i + 1);
if (tok != 4 && tok != 1275203608) {
strSmiles = "*";
break;
}case 134218756:
isPolyhedral = (this.tokAt(++i) == 1275203608);
strSmiles = (isPolyhedral ? "polyhedra" : this.stringParameter(i));
if (strSmiles.equalsIgnoreCase("polyhedra") || strSmiles.equalsIgnoreCase("polyhedron")) isPolyhedral = true;
break;
case 1677721602:
isFlexFit = true;
doRotate = true;
strSmiles = this.paramAsStr(++i);
if (strSmiles.equalsIgnoreCase("SMILES")) {
isSmiles = true;
if (this.e.tokAt(i + 1) == 1612709900) {
strSmiles = "H";
i++;
} else {
strSmiles = "*";
}}break;
case 3:
case 2:
nSeconds = Math.abs(this.floatParameter(i));
if (nSeconds > 0) doAnimate = true;
break;
case 268436992:
break;
case 2109448:
bsSubset = this.atomExpressionAt(++i);
i = eval.iToken;
break;
case 10:
case 1073742325:
if (vQuatSets != null) this.invArg();
bsAtoms1 = this.atomExpressionAt(eval.iToken);
tok = (isToSubsetOfFrom ? 0 : this.tokAt(eval.iToken + 1));
bsAtoms2 = (coordTo == null && eval.isArrayParameter(eval.iToken + 1) ? null : (tok == 10 || tok == 1073742325 ? this.atomExpressionAt(++eval.iToken) : JU.BSUtil.copy(bsAtoms1)));
if (bsSubset != null) {
bsAtoms1.and(bsSubset);
if (bsAtoms2 != null) bsAtoms2.and(bsSubset);
}if (bsAtoms2 == null) {
var ipt = eval.iToken;
coordTo = eval.getPointArray(eval.iToken + 1, -1, false, true);
if (coordTo == null) eval.iToken = ipt;
 else isCoords = true;
} else if (bsTo != null) {
bsAtoms2.and(bsTo);
}if (vAtomSets == null) vAtomSets =  new JU.Lst();
vAtomSets.addLast( Clazz.newArray(-1, [bsAtoms1, (bsAtoms2 == null ? coordTo : bsAtoms2)]));
if (isAtoms) coordTo = null;
i = eval.iToken;
break;
case 1275203608:
isSmiles = isPolyhedral = true;
break;
case 4125:
break;
case 7:
if (vAtomSets != null) this.invArg();
isQuaternion = true;
data1 = eval.getQuaternionArray((eval.theToken).getList(), 1073742001);
this.getToken(++i);
data2 = eval.getQuaternionArray((eval.theToken).getList(), 1073742001);
if (vQuatSets == null) vQuatSets =  new JU.Lst();
vQuatSets.addLast( Clazz.newArray(-1, [data1, data2]));
break;
case 1073742077:
isQuaternion = true;
break;
case 1153433601:
isAtoms = true;
isQuaternion = false;
break;
case 134217751:
isQuaternion = false;
break;
case 1073742029:
doMorph = true;
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 (!doMorph && !doRotate && !doTranslate) doRotate = doTranslate = true;
doAnimate = (nSeconds != 0);
isAtoms = (!isQuaternion && strSmiles == null && !isPolyhedral || coordTo != null);
if (isAtoms) J.api.Interface.getInterface("JU.Eigen", this.vwr, "script");
if (vAtomSets == null && vQuatSets == null) {
if (isPolyhedral && bsSubset == null) {
bsSubset = this.vwr.getAtomBitSet("polyhedra");
}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);
bsAtoms1.and(bsFrom);
if (bsAtoms2 != null) {
bsAtoms2.and(bsSubset);
bsAtoms2.and(bsTo);
}}vAtomSets =  new JU.Lst();
vAtomSets.addLast( Clazz.newArray(-1, [bsAtoms1, bsAtoms2]));
}var bsFrames;
var bsModels = null;
if (isFrames) {
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 {
bsModels = JU.BSUtil.newAndSetBit(0);
bsFrames =  Clazz.newArray(-1, [bsFrom]);
}for (var iFrame = 0, iModel = bsModels.nextSetBit(0); iFrame < bsFrames.length; iFrame++, iModel = bsModels.nextSetBit(iModel + 1)) {
bsFrom = bsFrames[iFrame];
var retStddev =  Clazz.newFloatArray (2, 0);
if (isFrames && isPolyhedral && iFrame == 0) {
bsTo = bsFrom;
continue;
}var q = null;
var vQ =  new JU.Lst();
var centerAndPoints = null;
var vAtomSets2 = (isFrames ?  new JU.Lst() : vAtomSets);
if (!isCoords) {
for (var i = 0; i < vAtomSets.size(); ++i) {
var bss = vAtomSets.get(i);
if (isFrames) vAtomSets2.addLast(bss =  Clazz.newArray(-1, [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( Clazz.newArray(-1, [bsAtoms1, coordTo]));
}try {
centerAndPoints = this.vwr.getCenterAndPoints(vAtomSets2, !doMorph);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
this.invArg();
} else {
throw ex;
}
}
if (doMorph) {
} else {
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;
if (!isFrames) 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 (bsFrom != null && strSmiles != null && ("H".equals(strSmiles) || "*".equals(strSmiles) || "".equals(strSmiles))) try {
strSmiles = this.vwr.getSmilesOpt(bsAtoms1 == null ? bsFrom : bsAtoms1, -1, -1, 32768 | ("H".equals(strSmiles) ? 4096 : 0), null);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
eval.evalError(ex.getMessage(), null);
} else {
throw ex;
}
}
if (isFlexFit) {
var list;
if (bsFrom == null || bsTo == null || (list = eval.getSmilesExt().getFlexFitList(bsFrom, bsTo, strSmiles, !isSmiles)) == null) return;
this.vwr.setDihedrals(list, null, 1);
}var stddev;
if (isPolyhedral) {
var bs1 = JU.BS.copy(bsAtoms1);
bs1.and(bsFrom);
var bs2 = JU.BS.copy(bsAtoms2);
bs2.and(bsTo);
stddev = eval.getSmilesExt().mapPolyhedra(bs1.nextSetBit(0), bs2.nextSetBit(0), isSmiles, m4);
} else {
this.showString("COMPARE using " + (isSmiles ? "SMILES " : "SMARTS ") + strSmiles);
var ptsA =  new JU.Lst();
var ptsB =  new JU.Lst();
stddev = eval.getSmilesExt().getSmilesCorrelation(bsAtoms1 == null ? bsFrom : bsAtoms1, bsAtoms2 == null ? bsTo : bsAtoms2, strSmiles, ptsA, ptsB, m4, null, false, null, center, false, 32 | (isSmiles ? 1 : 2));
}if (Float.isNaN(stddev)) {
this.showString("structures do not match from " + bsFrom + " to " + bsTo);
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 (isFrames) {
var oabc = this.vwr.getV0abc(iModel,  Clazz.newArray(-1, [m4]));
if (oabc != null) this.vwr.ms.setModelCagePts(iModel, oabc, null);
}}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 (doMorph) {
endDegrees = 1e10;
} else {
if (doTranslate) {
if (translation == null) translation = JU.V3.newVsub(centerAndPoints[1][0], center);
endDegrees = 1e10;
}if (doRotate) {
if (q == null) eval.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 if (isFrames) continue;
 else doRotate = doTranslate = doAnimate = false;
}}}if (Float.isNaN(endDegrees) || Float.isNaN(pt1.x)) continue;
var ptsB = null;
if (doMorph) {
ptsB =  new JU.Lst();
for (var n = centerAndPoints[0].length, i = 0; i < n; i++) {
ptsB.addLast(centerAndPoints[1][i]);
}
} else if (doRotate && doTranslate && nSeconds != 0) {
var ptsA = this.vwr.ms.getAtomPointVector(bsFrom);
var m4 = JS.ScriptMathProcessor.getMatrix4f(q.getMatrix(), translation);
ptsB = JS.ScriptParam.transformPoints(ptsA, m4, center);
}if (!eval.useThreads(true)) doAnimate = false;
if (this.vwr.rotateAboutPointsInternal(eval, center, pt1, endDegrees / nSeconds, endDegrees, doAnimate, bsFrom, translation, ptsB, null, null, null, false, doMorph ? centerAndPoints : null) && doAnimate && eval.isJS) throw  new JS.ScriptInterruption(eval, "compare", 1);
}
});
Clazz.defineMethod(c$, "configuration", 
function(){
var bsAtoms = null;
var bsSelected = (this.chk ? null : this.vwr.bsA());
if (this.slen == 1) {
if (this.chk) return;
bsAtoms = this.vwr.ms.setConformation(bsSelected);
this.vwr.ms.addStateScript("select", null, bsSelected, null, ";configuration", true, false);
} else {
var n = -2147483648;
var bs = null;
if (this.tokAt(1) == 4) {
n = -1000 - (this.stringParameter(this.e.checkLast(1)) + " ").codePointAt(0);
} else if (this.tokAt(1) == 2) {
n = this.intParameter(this.e.checkLast(1));
} else {
bs = bsAtoms = this.atomExpressionAt(1);
if (this.tokAt(this.e.iToken) == 4) {
n = -1000 - (this.stringParameter(this.e.checkLast(this.e.iToken + 1)) + " ").codePointAt(0);
} else {
n = this.intParameter(this.e.checkLast(this.e.iToken + 1));
}}if (this.chk) return;
this.vwr.addStateScript("configuration " + (bs == null ? "" : JU.Escape.eBS(bsAtoms) + " ") + n + ";", true, false);
bsAtoms = this.vwr.ms.getConformation(this.vwr.am.cmi, n, true, bs);
}this.setShapeProperty(1, "type", Integer.$valueOf(30720));
this.e.setShapeSizeBs(1, 0, bsAtoms);
this.vwr.autoHbond(bsAtoms, bsAtoms, true);
this.vwr.selectStatus(bsAtoms, false, 0, !this.e.doReport(), false);
});
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 1073742334:
this.setShapeProperty(6, "hideAll", Boolean.TRUE);
return;
case 12291:
if (!this.chk) this.vwr.clearAllMeasurements();
return;
case 1113589787:
if (!this.chk) this.showMeasureCount(true);
return;
}
this.vwr.shm.loadShape(6);
switch (this.tokAt(1)) {
case 134218756:
var smarts = this.stringParameter(this.slen == 3 ? 2 : 4);
if (this.chk) return;
var atoms = this.vwr.ms.at;
var ac = this.vwr.ms.ac;
var maps = null;
try {
maps = this.vwr.getSmilesMatcher().getCorrelationMaps(smarts, atoms, ac, this.vwr.bsA(), 2);
} 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 1073742335:
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 == 1073742327) {
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 =  Clazz.newFloatArray(-1, [3.4028235E38, 3.4028235E38]);
var isAll = false;
var isAllConnected = false;
var isNotConnected = false;
var isRange = true;
var isRefreshID = false;
var rd = null;
var intramolecular = null;
var tokAction = 268438018;
var strFormat = null;
var property = null;
var units = null;
var font = null;
var points =  new JU.Lst();
var bs =  new JU.BS();
var bsSelected = null;
var target = null;
var tickInfo = null;
var nBitSets = 0;
var mad = 0;
var value = NaN;
var alignment = null;
for (var i = 1; i < this.slen; ++i) {
switch (this.getToken(i).tok) {
default:
this.error(15);
break;
case 1073741974:
if (i != 1) this.invArg();
id = eval.optParameterAsString(++i);
continue;
case 1073741824:
eval.errorStr(24, "ALL, ALLCONNECTED, DELETE");
break;
case 1275082241:
tokAction = 1275082241;
if (this.tokAt(i + 1) == 1073742327 && this.slen == i + 2) {
if (!this.chk) {
this.vwr.setShapeProperty(6, "selectall", null);
this.showMeasureCount(true);
}return;
}break;
case 1113589787:
if (points.size() > 0 || nBitSets > 0 || id != null) this.invArg();
tokAction = 1275082241;
if (this.chk) {
bsSelected =  new JU.BS();
} else {
bsSelected = this.vwr.getShapeProperty(6, "selected");
if (bsSelected.cardinality() == 0) return;
}isAll = true;
break;
case 268439040:
if (this.tokAt(i + 1) != 134217736) this.invArg();
i++;
isNotConnected = true;
break;
case 1073741832:
alignment = this.paramAsStr(++i).toLowerCase();
break;
case 134217736:
case 1073741834:
case 1073742327:
isAllConnected = (eval.theTok == 1073741834);
atomIndex = -1;
isAll = true;
if (isAllConnected && isNotConnected) this.invArg();
break;
case 1765808134:
colix = JU.C.getColix(eval.getArgbParam(++i));
i = eval.iToken;
break;
case 1073742066:
if (eval.isPoint3f(++i)) {
var p = this.getPoint3f(i, false);
offset =  Clazz.newFloatArray(-1, [1, p.x, p.y, p.z, 0, 0, 0]);
} else {
offset = eval.floatParameterSet(i, 7, 7);
}i = eval.iToken;
break;
case 1665140738:
case 1073741917:
mad = Clazz.floatToInt((eval.theTok == 1665140738 ? 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 != 268438018 && tokAction != 1275082241) 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.ms.getFirstAtomIndexFromAtomNumber(iParam, this.vwr.getVisibleFramesBitSet());
if (!this.chk && atomIndex < 0) return;
if (target != null) this.invArg();
if ((countPlusIndexes[0] = ++nAtoms) > 4) eval.bad();
countPlusIndexes[nAtoms] = atomIndex;
}break;
case 1094713359:
modelIndex = this.intParameter(++i);
break;
case 1073742334:
if (tokAction != 268438018) this.invArg();
tokAction = 1073742334;
break;
case 1073742335:
if (tokAction != 268438018) this.invArg();
tokAction = 1073742335;
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 1648363544:
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.ms.ac);
bs2.and(this.vwr.ms.getAtomsWithinRadius(5, bs, false, null, null));
points.addLast(bs2);
}break;
case 12290:
case 10:
case 1073742325:
nBitSets++;
case 1073742332:
case 8:
case 1073742330:
if (atomIndex >= 0 || bsSelected != null) this.invArg();
var ret =  new Array(1);
target = eval.centerParameter(i, ret);
if (Clazz.instanceOf(ret[0],"JU.BS")) {
target = bs = ret[0];
if (!this.chk && bs.length() == 0) return;
}if (Clazz.instanceOf(target,"JU.P3")) target = JU.Point3fi.newPF(target, modelIndex);
if ((nAtoms = ++expressionCount) > 4) eval.bad();
i = eval.iToken;
points.addLast(target);
break;
case 1715472409:
property = this.paramAsStr(i);
break;
case 1073742188:
value = this.floatParameter(++i);
break;
case 4:
var s = this.stringParameter(i);
if (JM.Measurement.isUnits(s) || s.equals("default")) {
units = s;
} else {
strFormat = s;
}break;
case 1073742164:
tickInfo = eval.tickParamAsStr(i, false, true, true);
i = eval.iToken;
tokAction = 12290;
break;
}
}
if (rd != null && (ptFloat >= 0 || nAtoms != 2) || tokAction != 1275082241 && bsSelected == null && 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;
isRefreshID = (id != null && target == null && tokAction == 268438018);
if (target != null || bsSelected != null || tickInfo != null || isRefreshID) {
if (rd == null) rd =  new J.atomdata.RadiusData(rangeMinMax, 0, null, null);
if (tickInfo != null) tickInfo.id = "default";
if (isRefreshID) {
tokAction = 266284;
} else if (target != null && (property != null || strFormat != null) && tokAction == 268438018) {
tokAction = 12290;
}var text = null;
if (font != null || alignment != null || colix != 0 || strFormat != null && (isRefreshID || strFormat.indexOf('\n') >= 0)) text = JM.Text.newMeasure(this.vwr, font, colix);
if (text != null) {
text.setPymolOffset(offset);
text.setAlignmentLCR(alignment);
}this.setShapeProperty(6, "measure", this.vwr.newMeasurementData(id, points).set(tokAction, null, rd, property, strFormat, units, tickInfo, isAllConnected, isNotConnected, intramolecular, isAll, mad, colix, text, value, bsSelected));
if (tokAction == 1275082241) {
this.showMeasureCount(false);
}return;
}var propertyValue = (id == null ? countPlusIndexes : id);
switch (tokAction) {
case 12291:
this.setShapeProperty(6, "delete", propertyValue);
break;
case 1073742335:
this.setShapeProperty(6, "show", propertyValue);
break;
case 1073742334:
this.setShapeProperty(6, "hide", propertyValue);
break;
default:
this.setShapeProperty(6, (strFormat == null && units == null ? "toggle" : "toggleOn"), propertyValue);
if (strFormat != null) this.setShapeProperty(6, "setFormats", strFormat);
}
});
Clazz.defineMethod(c$, "showMeasureCount", 
function(isFull){
var bs = this.vwr.getShapeProperty(6, "selected");
var n = bs.cardinality();
if (isFull) {
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
this.showString((this.vwr.shm.getShape(6)).getInfoAsString(i));
}
}this.showString(n + (n == 1 ? " measure" : " measures") + " selected");
}, "~B");
Clazz.defineMethod(c$, "connect", 
function(index){
var eval = this.e;
var distances =  Clazz.newFloatArray (2, 0);
var atomSets =  new Array(2);
atomSets[0] = atomSets[1] = this.vwr.bsA();
var radius = NaN;
var colorArgb =  Clazz.newIntArray(-1, [-2147483648]);
var distanceCount = 0;
var bondOrder = 131071;
var bo;
var operation = 1073742026;
var isDelete = false;
var haveType = false;
var haveOperation = false;
var translucentLevel = 3.4028235E38;
var isColorOrRadius = false;
var nAtomSets = 0;
var nDistances = 0;
var bsBonds =  new JU.BS();
var isBonds = false;
var expression2 = 0;
var ptColor = 0;
var energy = 0;
var addGroup = false;
if (this.slen == 1) {
if (!this.chk) this.vwr.rebondState(eval.$isStateScript);
return;
}if (this.tokAt(1) == 1073877011) {
if (!this.chk) this.vwr.connectNBO(this.e.optParameterAsString(2));
return;
}for (var i = index; i < this.slen; ++i) {
switch (this.getToken(i).tok) {
case 1073742335:
case 1073742334:
this.checkLength(2);
if (!this.chk) this.vwr.rebondState(eval.$isStateScript);
return;
case 2:
case 3:
if (nAtomSets > 0) {
if (haveType || isColorOrRadius) eval.error(23);
bo = JU.Edge.getBondOrderFromFloat(this.floatParameter(i));
if (bo == 131071) this.invArg();
bondOrder = bo;
haveType = true;
break;
}if (++nDistances > 2) eval.bad();
var dist = this.floatParameter(i);
if (this.tokAt(i + 1) == 268441090) {
dist = -dist / 100;
i++;
}distances[distanceCount++] = dist;
break;
case 12290:
case 10:
case 1073742325:
if (nAtomSets > 2 || isBonds && nAtomSets > 0) eval.bad();
if (haveType || isColorOrRadius) this.invArg();
atomSets[nAtomSets++] = this.atomExpressionAt(i);
isBonds = eval.isBondSet;
if (nAtomSets == 2) {
var pt = eval.iToken;
for (var j = i; j < pt; j++) if (this.tokAt(j) == 1073741824 && this.paramAsStr(j).equals("_1")) {
expression2 = i;
break;
}
eval.iToken = pt;
}i = eval.iToken;
break;
case 1086324742:
addGroup = true;
break;
case 1765808134:
case 1111490588:
case 1073742074:
isColorOrRadius = true;
translucentLevel = this.getColorTrans(eval, i, false, colorArgb);
i = eval.iToken;
break;
case 1073742086:
var isAuto = (this.tokAt(2) == 1073741852);
this.checkLength(isAuto ? 3 : 2);
if (this.chk) return;
this.vwr.clearModelDependentObjects();
this.vwr.ms.deleteAllBonds();
var bsExclude =  new JU.BS();
this.vwr.ms.setPdbConectBonding(0, 0, bsExclude);
if (isAuto) {
var isLegacy = eval.$isStateScript && this.vwr.getBoolean(603979872);
this.vwr.ms.autoBondBs4(null, null, bsExclude, null, this.vwr.getMadBond(), isLegacy, null);
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 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 659482:
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 1075838996:
case 1613238294:
var cmd = this.paramAsStr(i);
if ((bo = JU.Edge.getBondOrderFromString(cmd)) == 131071) this.invArg();
if (haveType) eval.error(18);
haveType = true;
switch (bo) {
case 33:
switch (this.tokAt(i + 1)) {
case 3:
bo = JU.Edge.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;
case 65537:
if (!haveOperation) {
operation = 1073742025;
haveOperation = true;
}break;
}
bondOrder = bo;
break;
case 1665140738:
radius = this.floatParameter(++i);
isColorOrRadius = true;
break;
case 1073742333:
if (++i != this.slen) this.invArg();
case 12291:
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();
this.vwr.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.$("{0} connections deleted"), nModified), false);
return;
}if (isColorOrRadius) {
this.vwr.selectBonds(bsBonds);
if (!Float.isNaN(radius)) eval.setShapeSizeBs(1, Math.round(radius * 2000), null);
this.finalizeObject(1, colorArgb[0], translucentLevel, 0, false, null, 0, bsBonds);
this.vwr.selectBonds(null);
}if (report) eval.report(J.i18n.GT.o(J.i18n.GT.$("{0} new bonds; {1} modified"),  Clazz.newArray(-1, [Integer.$valueOf(nNew), Integer.$valueOf(nModified)])), false);
}, "~N");
Clazz.defineMethod(c$, "console", 
function(){
switch (this.getToken(1).tok) {
case 1073742334:
if (!this.chk) this.vwr.showConsole(false);
break;
case 1073742335:
if (!this.chk) this.vwr.showConsole(true);
break;
case 1073741882:
if (!this.chk) this.vwr.sm.clearConsole();
break;
case 134221856:
this.showString(this.stringParameter(2));
break;
default:
this.invArg();
}
});
Clazz.defineMethod(c$, "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.substring(0, (dataLabel + " ").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.ms.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 =  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.ms.ac;
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.ms.at[j].getAtomNumber();
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.$valueOf(0);
this.vwr.setData(dataType, d, ac, atomNumberField, atomNumberFieldColumnCount, propertyField, propertyFieldColumnCount);
return;
}if ("occupany".equals(dataType)) dataType = "occupancy";
var userType = JM.AtomCollection.getUserSettableType(dataType);
if (userType > -1) {
this.vwr.setAtomData(userType, dataType, dataString, isDefault);
return;
}d[0] = dataLabel;
d[1] = dataString;
d[3] = Integer.$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 1073742335:
mad = 2147483647;
break;
case 1073742334:
break;
case 2:
mad = this.intParameter(1);
break;
case 36867:
this.e.sm.loadShape(20);
this.setShapeProperty(20, "select", this.paramAsStr(2));
i = eval.iToken;
checkMore = true;
isSet = true;
break;
case 1073741974:
case 268441089:
case 1073741824:
this.e.sm.loadShape(20);
if (eval.theTok == 1073741974) 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 =  Clazz.newIntArray(-1, [-2147483648]);
while (++i < this.slen) {
var key = this.paramAsStr(i);
var value = null;
this.getToken(i);
if (!isSet) switch (eval.theTok) {
case 1073742330:
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 1825200146:
value = this.e.optParameterAsString(++i);
if ((value).length == 0) continue;
break;
case 1611272194:
var axes =  new Array(3);
var l = null;
switch (this.getToken(i + 1).tok) {
case 11:
i++;
var m = eval.theToken.value;
for (var im = 3; --im >= 0; ) m.getColumnV(im, axes[im] =  new JU.V3());

break;
case 1073742195:
i += 2;
case 268437504:
l =  new JU.Lst();
for (var i1 = 3; --i1 >= 0; ) {
switch (this.tokAt(++i)) {
case 268437504:
break;
default:
if (eval.isCenterParameter(i)) {
l.addLast(JS.SV.newV(8, this.centerParameter(i)));
} else if (this.tokAt(i) == 268437504) {
} else {
l.addLast(this.getToken(i));
}}
i = eval.iToken;
}
if (this.getToken(++i).tok != 268437505) this.invArg();
break;
case 7:
l = (eval.theToken).getList();
switch (l.size()) {
case 1:
var l1 =  new JU.Lst();
for (var il = 3; --il >= 0; ) l1.addLast(this.getToken(++i));

l = l1;
break;
case 3:
break;
default:
this.invArg();
break;
}
break;
default:
for (var j = 0; j < 3; j++) {
axes[j] =  new JU.V3();
axes[j].setT(this.centerParameter(++i));
i = eval.iToken;
}
break;
}
if (l != null) {
for (var k = 3; --k >= 0; ) {
var v = l.get(k);
switch (v.tok) {
case 7:
axes[k] = JU.V3.new3(JS.SV.fValue(v.getList().get(0)), JS.SV.fValue(v.getList().get(1)), JS.SV.fValue(v.getList().get(2)));
break;
case 8:
axes[k] = JU.V3.newV(v.value);
break;
}
}
}i = eval.iToken;
value = axes;
break;
case 12289:
value = this.centerParameter(++i);
i = eval.iToken;
break;
case 1094713359:
value = Integer.$valueOf(this.intParameter(++i));
break;
case 12291:
value = Boolean.TRUE;
this.checkLength(i + 1);
break;
}
if (value == null) switch (eval.theTok) {
case 1073742335:
key = "on";
value = Boolean.TRUE;
break;
case 1073742334:
key = "on";
value = Boolean.FALSE;
break;
case 536875059:
if (this.isFloatParameter(i + 1)) {
value = Float.$valueOf(this.floatParameter(++i));
} else if (eval.isCenterParameter(i)) {
var p = this.centerParameter(i);
value =  Clazz.newFloatArray(-1, [p.x, p.y, p.z]);
} else {
value = eval.floatParameterSet(++i, 3, 3);
}i = eval.iToken;
break;
case 12290:
case 10:
case 1073742325:
key = "atoms";
value = this.atomExpressionAt(i);
i = eval.iToken;
break;
case 1765808134:
case 1111490588:
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$, "image", 
function(){
if (!this.chk) this.vwr.getConsole();
var pt = 1;
var id = null;
if (this.tokAt(1) == 1073741974) {
id = this.e.optParameterAsString(++pt);
pt++;
}var fileName = null;
var isClose = this.e.optParameterAsString(this.slen - 1).equalsIgnoreCase("close");
switch (this.tokAt(pt)) {
case 15:
if (isClose) this.invArg();
fileName = (this.getToken(pt).value).data;
break;
case 6:
if (isClose) this.invArg();
fileName = (this.getToken(pt)).getMap();
break;
case 4:
case 0:
fileName = this.e.optParameterAsString(pt);
if (!isClose && (this.slen == pt || this.slen == pt + 2)) {
var width = (this.slen == pt + 2 ? this.intParameter(pt++) : -1);
var height = (width < 0 ? -1 : this.intParameter(pt));
var params =  new java.util.Hashtable();
params.put("fileName", "\1\1" + id);
params.put("backgroundColor", Integer.$valueOf(this.vwr.getBackgroundArgb()));
params.put("type", "png");
params.put("quality", Integer.$valueOf(-1));
params.put("width", Integer.$valueOf(width));
params.put("height", Integer.$valueOf(height));
if (!this.chk) this.vwr.processWriteOrCapture(params);
return;
}break;
}
if (isClose) {
switch (this.slen) {
case 2:
fileName = "closeall";
break;
case 3:
case 4:
break;
default:
this.checkLength(0);
}
}if (!this.chk) {
var echoName = ((typeof(fileName)=='string') ? fileName : "");
this.vwr.fm.loadImage(isClose ? "\1close" : fileName, "\1" + echoName + "\1" + ("".equals(id) || id == null ? null : id), false);
}});
Clazz.defineMethod(c$, "invertSelected", 
function(){
var e = this.e;
var pt = null;
var plane = null;
var bs = null;
var iAtom = -2147483648;
var ipt = 1;
switch (this.tokAt(1)) {
case 0:
if (this.chk) return;
bs = this.vwr.bsA();
pt = this.vwr.ms.getAtomSetCenter(bs);
this.vwr.invertAtomCoord(pt, null, bs, -1, false);
return;
case 528443:
case 1153433601:
ipt++;
case 10:
case 1073742325:
case 12290:
bs = this.atomExpressionAt(ipt);
if (!e.isAtomExpression(e.iToken + 1)) {
e.checkLengthErrorPt(e.iToken + 1, e.iToken + 1);
if (!this.chk) {
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
this.vwr.invertAtomCoord(null, null, bs, i, false);
}
}return;
}iAtom = bs.nextSetBit(0);
bs = this.atomExpressionAt(e.iToken + 1);
break;
case 134217751:
pt = e.centerParameter(2, null);
break;
case 134217750:
plane = e.planeParameter(1, false);
break;
case 134219777:
plane = e.hklParameter(2, null, true, null);
break;
}
e.checkLengthErrorPt(e.iToken + 1, 1);
if (plane == null && pt == null && iAtom == -2147483648) this.invArg();
if (this.chk) return;
if (iAtom == -1) return;
this.vwr.invertSelected(pt, plane, iAtom, bs);
});
Clazz.defineMethod(c$, "mapProperty", 
function(){
var bsFrom;
var bsTo;
var property1;
var property2;
var mapKey;
var tokProp1 = 0;
var tokProp2 = 0;
var tokKey = 0;
var e = this.e;
while (true) {
if (this.tokAt(1) == 1113589787) {
bsFrom = this.vwr.bsA();
bsTo = this.atomExpressionAt(2);
property1 = property2 = "selected";
} else {
bsFrom = this.atomExpressionAt(1);
if (this.tokAt(++e.iToken) != 1073742336 || !JS.T.tokAttr(tokProp1 = this.tokAt(++e.iToken), 1077936128)) break;
property1 = this.paramAsStr(e.iToken);
bsTo = this.atomExpressionAt(++e.iToken);
if (this.tokAt(++e.iToken) != 1073742336 || !JS.T.tokAttr(tokProp2 = this.tokAt(++e.iToken), 2048)) break;
property2 = this.paramAsStr(e.iToken);
}if (JS.T.tokAttr(tokKey = this.tokAt(e.iToken + 1), 1077936128)) mapKey = this.paramAsStr(++e.iToken);
 else mapKey = JS.T.nameOf(tokKey = 1094715393);
e.checkLast(e.iToken);
if (this.chk) return;
var bsOut = null;
this.showString("mapping " + property1.toUpperCase() + " for " + bsFrom.cardinality() + " atoms to " + property2.toUpperCase() + " for " + bsTo.cardinality() + " atoms using " + mapKey.toUpperCase());
if (JS.T.tokAttrOr(tokProp1, 1094713344, 1111490560) && JS.T.tokAttrOr(tokProp2, 1094713344, 1111490560) && JS.T.tokAttrOr(tokKey, 1094713344, 1111490560)) {
var data1 = e.getBitsetPropertyFloat(bsFrom, tokProp1 | 224, null, NaN, NaN);
var data2 = e.getBitsetPropertyFloat(bsFrom, tokKey | 224, null, NaN, NaN);
var data3 = e.getBitsetPropertyFloat(bsTo, tokKey | 224, null, NaN, NaN);
var isProperty = (tokProp2 == 1715472409);
var dataOut =  Clazz.newFloatArray (isProperty ? this.vwr.ms.ac : data3.length, 0);
bsOut =  new JU.BS();
if (data1.length == data2.length) {
var ht =  new java.util.Hashtable();
for (var i = 0; i < data1.length; i++) {
ht.put(Float.$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,  Clazz.newArray(-1, [property2, dataOut, bsOut, Integer.$valueOf(1), Boolean.TRUE]), this.vwr.ms.ac, 0, 0, 2147483647, 0);
 else if (!JS.T.tokAttr(tokProp2, 2048)) this.error(56);
 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.slm.bsSubset);
this.vwr.slm.setSelectionSubset(bsTo);
try {
e.runScript(sb.toString());
} catch (e$$) {
if (Clazz.exceptionOf(e$$, Exception)){
var ex = e$$;
{
this.vwr.slm.setSelectionSubset(bsSubset);
e.errorStr(-1, "Error: " + ex.getMessage());
}
} else if (Clazz.exceptionOf(e$$, Error)){
var er = e$$;
{
this.vwr.slm.setSelectionSubset(bsSubset);
e.errorStr(-1, "Error: " + er.toString());
}
} else {
throw e$$;
}
}
this.vwr.slm.setSelectionSubset(bsSubset);
}this.showString("DONE");
return;
}
this.invArg();
});
Clazz.defineMethod(c$, "minimize", 
function(isModelkit){
var bsSelected = null;
var steps = 2147483647;
var crit = 0;
var addHydrogen = false;
var isSilent = false;
var bsFixed = null;
var selectedOnly = false;
var groupOnly = false;
var minimizer = this.vwr.getMinimizer(false);
var range = 0;
for (var i = (isModelkit ? 2 : 1); i < this.slen; i++) {
switch (this.getToken(i).tok) {
case 1073741905:
crit = this.floatParameter(++i);
continue;
case 1073742114:
range = this.floatParameter(++i);
continue;
case 1073741935:
steps = 0;
continue;
case 1073741874:
case 1073742162:
this.checkLength(2);
if (this.chk || minimizer == null) return;
minimizer.setProperty(this.paramAsStr(i), null);
return;
case 1073741882:
this.checkLength(2);
if (this.chk || minimizer == null) return;
minimizer.setProperty("clear", null);
return;
case 1073741894:
if (i != 1) this.invArg();
var n = 0;
var targetValue = 0;
var aList =  Clazz.newIntArray (5, 0);
if (this.tokAt(++i) == 1073741882) {
this.checkLength(3);
} else {
while (n < 4 && !this.isFloatParameter(i)) {
aList[++n] = this.atomExpressionAt(i).nextSetBit(0);
i = this.e.iToken + 1;
}
aList[0] = n;
if (n == 1) this.invArg();
targetValue = this.floatParameter(this.e.checkLast(i));
}if (!this.chk) this.vwr.getMinimizer(true).setProperty("constraint",  Clazz.newArray(-1, [aList, Float.$valueOf(targetValue)]));
return;
case 12293:
if (i != 1) this.invArg();
if (this.slen == ++i) {
if (!this.chk) {
var bs = this.vwr.getMinimizer(true).getProperty("fixed", 0);
if (bs == null) {
this.e.showString("no atoms are fixed for minimization");
} else {
n = bs.cardinality();
this.e.showString(n + (n == 1 ? " atom is" : " atoms are") + " fixed for minimization: " + bs + "\nunfix them with MINIMIZE FIX NONE");
}}return;
}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 1073741828:
addHydrogen = true;
continue;
case 1073742072:
case 1113589787:
selectedOnly = true;
break;
case 1086324742:
groupOnly = true;
break;
case 1073742148:
isSilent = true;
break;
case 266298:
steps = this.intParameter(++i);
continue;
case 10:
case 1073742325:
selectedOnly = true;
case 1275082241:
if (this.e.theTok == 1275082241) i++;
bsSelected = this.atomExpressionAt(i);
i = this.e.iToken;
if (this.tokAt(i + 1) == 1073742072) {
i++;
selectedOnly = true;
}continue;
default:
this.invArg();
break;
}
}
if (isModelkit && (addHydrogen || selectedOnly || groupOnly)) this.invArg();
if (!this.chk) try {
this.vwr.minimize(this.e, steps, crit, bsSelected, bsFixed, null, range, (addHydrogen ? 16 : 0) | (isModelkit ? 256 : 0) | (selectedOnly ? 32 : 0) | (groupOnly ? 64 : 0) | (isSilent ? 1 : 0));
} catch (e1) {
if (Clazz.exceptionOf(e1, Exception)){
throw  new JS.ScriptInterruption(this.e, "minimize", 1);
} else {
throw e1;
}
}
}, "~B");
Clazz.defineMethod(c$, "modulation", 
function(){
var qtOffset = null;
var eval = this.e;
var mod = true;
var isQ = false;
var bs = null;
var i = 1;
switch (this.getToken(i).tok) {
case 1073742334:
mod = false;
case 0:
case 1073742335:
break;
case 12290:
case 10:
case 1073742325:
bs = this.atomExpressionAt(1);
switch (this.tokAt(eval.iToken + 1)) {
case 0:
break;
case 1073742334:
mod = false;
case 1073742335:
eval.iToken++;
break;
}
eval.checkLast(eval.iToken);
break;
case 1073742332:
case 8:
qtOffset = eval.getPoint3f(1, false, true);
isQ = (this.tokAt(eval.iToken + 1) == 1073742335);
break;
default:
var s = eval.theToken.value.toString();
i++;
if (s.equalsIgnoreCase("t")) {
eval.theTok = 3;
} else if (s.equalsIgnoreCase("m") || s.equalsIgnoreCase("q")) {
eval.theTok = 2;
} else {
this.invArg();
}case 3:
case 2:
switch (eval.theTok) {
case 3:
if (this.isFloatParameter(i)) {
var t1 = this.floatParameter(i);
qtOffset = JU.P3.new3(t1, t1, t1);
} else {
qtOffset = eval.getPoint3f(i, false, true);
}break;
case 2:
if (this.tokAt(i) == 2) {
var t = this.intParameter(i);
qtOffset = JU.P3.new3(t, t, t);
} else {
qtOffset = eval.getPoint3f(i, false, true);
}isQ = true;
break;
}
break;
case 536875059:
var scale = this.floatParameter(2);
if (!this.chk) this.vwr.setFloatProperty("modulationScale", scale);
return;
}
if (!this.chk) {
this.vwr.tm.setVibrationPeriod(0);
this.vwr.setModulation(bs, mod, qtOffset, isQ);
}});
Clazz.defineMethod(c$, "mutate", 
function(){
var i = this.e.iToken;
var bs;
var alphaType = null;
var sequence = null;
var phipsi = null;
var isCreate = false;
switch (this.tokAt(++i)) {
case 1073741904:
alphaType = "alpha";
isCreate = true;
bs = null;
switch (this.tokAt(++i)) {
case 0:
this.invArg();
break;
default:
sequence = this.e.paramAsStr(i);
i = this.e.iToken;
switch (this.tokAt(i + 1)) {
case 0:
break;
case 268437504:
case 1073742195:
case 7:
alphaType = null;
phipsi = this.e.floatParameterSet(++i, 2, 2147483647);
if (phipsi.length % 2 == 1) this.invArg();
i = this.e.iToken;
break;
default:
alphaType = this.e.paramAsStr(++i);
i = this.e.iToken;
break;
}
break;
}
break;
case 2:
this.st[1] = JS.T.o(4, "" + this.st[1].value);
default:
bs = this.atomExpressionAt(i);
i = ++this.e.iToken;
break;
case 268441089:
bs = this.vwr.getFrameAtoms();
i = ++this.e.iToken;
break;
}
if (!this.chk && bs != null) {
bs.and(this.vwr.getFrameAtoms());
var iatom = bs.nextSetBit(0);
if (iatom < 0) this.invArg();
var imodel = this.vwr.ms.at[iatom].mi;
if (this.vwr.ms.isTrajectory(imodel) || !this.vwr.ms.am[imodel].isBioModel) return;
}if (sequence == null) sequence = this.e.optParameterAsString(i);
this.e.checkLast(i);
if (!isCreate && !this.vwr.ms.haveBioModels) this.invArg();
if (this.chk) return;
var isOneLetter = sequence.startsWith("~");
var isFile = (!isOneLetter && !isCreate && (sequence.indexOf(".") >= 0 || sequence.indexOf("-") < 0 && sequence.length > 3 && sequence.startsWith("==")));
var list;
if (isFile) {
list =  Clazz.newArray(-1, [sequence]);
sequence = null;
} else {
sequence = JU.PT.replaceAllCharacters(sequence, ",; \t\n", " ").trim().toUpperCase();
if (!isOneLetter && sequence.indexOf("-") >= 0) {
list = JU.PT.split(sequence, "-");
} else {
if (isOneLetter || sequence.length != 3 || !this.vwr.getJBR().isKnownPDBGroup(sequence, 20)) sequence = this.vwr.getJBR().toStdAmino3(isOneLetter ? sequence.substring(1) : sequence);
list = JU.PT.getTokens(sequence);
}}this.e.iToken = this.e.slen;
if (list.length > 0) {
var err = this.vwr.getJBR().getBioModelSet(this.vwr.ms).mutate(bs, sequence, list, alphaType, phipsi);
if (err != null) this.e.showString(err);
}});
Clazz.defineMethod(c$, "navigate", 
function(){
var eval = this.e;
if (this.slen == 1) {
eval.setBooleanProperty("navigationMode", true);
return;
}var rotAxis = JU.V3.new3(0, 1, 0);
var list =  new JU.Lst();
var pt;
if (this.slen == 2) {
switch (this.getToken(1).tok) {
case 1073742335:
case 1073742334:
if (this.chk) return;
eval.setObjectMad10(34, "axes", 10);
this.setShapeProperty(34, "position", JU.P3.new3(50, 50, 3.4028235E38));
eval.setBooleanProperty("navigationMode", true);
this.vwr.tm.setNavOn(eval.theTok == 1073742335);
return;
case 1073742162:
if (!this.chk) this.vwr.tm.setNavXYZ(0, 0, 0);
return;
case 8:
case 1112152078:
break;
default:
this.invArg();
}
}if (!this.chk && !this.vwr.getBoolean(603979889)) eval.setBooleanProperty("navigationMode", true);
for (var i = 1; i < this.slen; i++) {
var timeSec = (this.isFloatParameter(i) ? this.floatParameter(i++) : 2);
if (timeSec < 0) this.invArg();
if (!this.chk && timeSec > 0) eval.refresh(false);
switch (this.getToken(i).tok) {
case 8:
case 1073742332:
pt = this.getPoint3f(i, true);
eval.iToken++;
if (eval.iToken != this.slen) this.invArg();
if (!this.chk) this.vwr.tm.setNavXYZ(pt.x, pt.y, pt.z);
return;
case 554176526:
var depth = this.floatParameter(++i);
if (!this.chk) list.addLast( Clazz.newArray(-1, [Integer.$valueOf(554176526), Float.$valueOf(timeSec), Float.$valueOf(depth)]));
continue;
case 12289:
pt = this.centerParameter(++i);
i = eval.iToken;
if (!this.chk) list.addLast( Clazz.newArray(-1, [Integer.$valueOf(134217751), Float.$valueOf(timeSec), pt]));
continue;
case 528432:
switch (this.getToken(++i).tok) {
case 1111492629:
rotAxis.set(1, 0, 0);
i++;
break;
case 1111492630:
rotAxis.set(0, 1, 0);
i++;
break;
case 1111492631:
rotAxis.set(0, 0, 1);
i++;
break;
case 8:
case 1073742332:
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( Clazz.newArray(-1, [Integer.$valueOf(528432), Float.$valueOf(timeSec), rotAxis, Float.$valueOf(degrees)]));
continue;
case 4160:
var x = NaN;
var y = NaN;
if (this.isFloatParameter(++i)) {
x = this.floatParameter(i);
y = this.floatParameter(++i);
} else {
switch (this.tokAt(i)) {
case 1111492629:
x = this.floatParameter(++i);
break;
case 1111492630:
y = this.floatParameter(++i);
break;
default:
pt = this.centerParameter(i);
i = eval.iToken;
if (!this.chk) list.addLast( Clazz.newArray(-1, [Integer.$valueOf(4160), Float.$valueOf(timeSec), pt]));
continue;
}
}if (!this.chk) list.addLast( Clazz.newArray(-1, [Integer.$valueOf(268441090), Float.$valueOf(timeSec), Float.$valueOf(x), Float.$valueOf(y)]));
continue;
case 268441088:
continue;
case 1112152078:
var pathGuide;
var vp =  new JU.Lst();
var bs;
if (eval.isAtomExpression(i + 1)) {
bs = this.atomExpressionAt(++i);
i = eval.iToken;
} else {
bs = this.vwr.bsA();
}if (this.chk) return;
this.vwr.getPolymerPointsAndVectors(bs, vp);
var n;
if ((n = vp.size()) > 0) {
pathGuide =  new Array(n);
for (var j = 0; j < n; j++) {
pathGuide[j] = vp.get(j);
}
list.addLast( Clazz.newArray(-1, [Integer.$valueOf(1112152078), Float.$valueOf(timeSec), pathGuide]));
continue;
}break;
case 1073742084:
var path;
var theta = null;
if (this.getToken(i + 1).tok == 1073742330) {
i++;
var pathID = eval.objectNameParameter(++i);
if (this.chk) return;
this.setShapeProperty(22, "thisID", pathID);
path = this.getShapeProperty(22, "vertices");
eval.refresh(false);
if (path == null) this.invArg();
var indexStart = Clazz.floatToInt(this.isFloatParameter(i + 1) ? this.floatParameter(++i) : 0);
var indexEnd = Clazz.floatToInt(this.isFloatParameter(i + 1) ? this.floatParameter(++i) : 2147483647);
list.addLast( Clazz.newArray(-1, [Integer.$valueOf(1073742084), Float.$valueOf(timeSec), path, theta,  Clazz.newIntArray(-1, [indexStart, indexEnd])]));
continue;
}var v =  new JU.Lst();
while (eval.isCenterParameter(i + 1)) {
v.addLast(this.centerParameter(++i));
i = eval.iToken;
}
if (v.size() > 0) {
path = v.toArray( new Array(v.size()));
if (!this.chk) list.addLast( Clazz.newArray(-1, [Integer.$valueOf(1073742084), Float.$valueOf(timeSec), path, theta,  Clazz.newIntArray(-1, [0, 2147483647])]));
continue;
}default:
this.invArg();
}
}
if (!this.chk && !this.vwr.isJmolDataFrame() && !this.vwr.is2D()) this.vwr.tm.navigateList(eval, list);
});
Clazz.defineMethod(c$, "plot", 
function(args){
var e = this.e;
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) e.errorStr(30, "plot");
modelIndex = this.vwr.ms.getJmolDataSourceFrame(modelIndex);
var pt = args.length - 1;
var isReturnOnly = (args !== this.st);
var isQuaternion = false;
var isPdbFormat = true;
var isSplit = false;
var statementSave = this.st;
if (isReturnOnly) e.st = this.st = args;
var tokCmd = (isReturnOnly ? 134222350 : args[0].tok);
var pt0 = (isReturnOnly || tokCmd == 134221850 || tokCmd == 4138 ? 0 : 1);
var filename = null;
var makeNewFrame = true;
var isDraw = false;
var isSpinPointGroup = false;
switch (tokCmd) {
case 4133:
case 134221850:
case 4138:
isSplit = (this.tokAt(pt) == 1275069447);
if (isSplit) e.slen = this.slen = pt--;
break;
case 135176:
makeNewFrame = false;
isDraw = true;
break;
case 134222350:
makeNewFrame = false;
isPdbFormat = false;
break;
case 134221856:
makeNewFrame = false;
if (JS.CmdExt.tokAtArray(pt, args) == 4) {
filename = this.stringParameter(pt--);
} else if (JS.CmdExt.tokAtArray(pt - 1, args) == 1073742336) {
filename = this.paramAsStr(pt - 2) + "." + this.paramAsStr(pt);
pt -= 3;
} else {
e.st = this.st = statementSave;
e.iToken = this.st.length;
this.error(13);
}e.slen = this.slen = pt + 1;
break;
}
var qFrame = "";
var startScript = "";
var endScript = "";
var isDerivative = false;
var isSecondDerivative = false;
var isRamachandranRelative = false;
var props =  new Array(4);
var propToks =  Clazz.newIntArray (4, 0);
var bs = JU.BSUtil.copy(this.vwr.bsA());
var preselected = "; select " + JU.Escape.eBS(bs) + ";\n ";
var type = e.optParameterAsString(pt).toLowerCase();
var minXYZ = null;
var maxXYZ = null;
var format = null;
var tok = JS.CmdExt.tokAtArray(pt0, args);
if (tok == 4) tok = JS.T.getTokFromName(args[pt0].value);
switch (tok) {
default:
e.iToken = 1;
this.invArg();
break;
case 134221834:
e.iToken = 1;
type = "data";
preselected = "";
break;
case 1073741872:
type = "brillouin";
if (bs.nextSetBit(0) < 0) {
bs = this.vwr.getModelUndeletedAtomsBitSet(modelIndex);
}break;
case 1095241729:
if (!this.chk) {
type = "spin";
isSpinPointGroup = (this.tokAt(pt0 + 1) == 1275068447);
propToks[0] = 1111492626;
propToks[1] = 1111492627;
propToks[2] = 1111492628;
propToks[3] = 1095241729;
props[0] = "spinX";
props[1] = "spinY";
props[2] = "spinZ";
props[3] = "spin";
bs = this.vwr.fm.getJmolDataReader().getPlotSpinSet(this.vwr, bs, modelIndex, minXYZ =  new JU.P3(), maxXYZ =  new JU.P3());
if (bs == null || bs.cardinality() == 0) return null;
var spinModel = this.vwr.ms.getJmolDataFrameInt(modelIndex, 1095241729);
if (spinModel >= 0) this.vwr.deleteModels(spinModel, null);
this.vwr.setSelectionSet(bs);
}break;
case 1715472409:
e.iToken = pt0 + 1;
for (var i = 0; i < 3; i++) {
switch (this.tokAt(e.iToken)) {
case 4:
propToks[i] = JS.T.getTokFromName(e.getToken(e.iToken).value);
break;
default:
propToks[i] = this.tokAt(e.iToken);
break;
case 0:
if (i == 0) this.invArg();
case 1287653388:
case 32:
case 64:
i = 2;
continue;
}
if (propToks[i] != 1715472409 && !JS.T.tokAttr(propToks[i], 1077936128)) this.invArg();
props[i] = this.getToken(e.iToken).value.toString();
e.iToken++;
}
if (this.tokAt(e.iToken) == 1287653388) {
format = this.stringParameter(++e.iToken);
isPdbFormat = false;
e.iToken++;
}if (this.tokAt(e.iToken) == 32) {
minXYZ = this.getPoint3f(++e.iToken, false);
e.iToken++;
}if (this.tokAt(e.iToken) == 64) {
maxXYZ = this.getPoint3f(++e.iToken, false);
e.iToken++;
}type = "property " + props[0] + (props[1] == null ? "" : " " + props[1]) + (props[2] == null ? "" : " " + props[2]);
if (bs.nextSetBit(0) < 0) bs = this.vwr.getModelUndeletedAtomsBitSet(modelIndex);
startScript = "select " + JU.Escape.eBS(bs) + ";\n ";
break;
case 4138:
if (type.equalsIgnoreCase("draw")) {
isDraw = true;
type = e.optParameterAsString(--pt).toLowerCase();
}isRamachandranRelative = (pt > pt0 && type.startsWith("r"));
type = "ramachandran" + (isRamachandranRelative ? " r" : "") + (tokCmd == 135176 ? " draw" : "");
break;
case 134221850:
case 136314895:
qFrame = " \"" + this.vwr.getQuaternionFrame() + "\"";
startScript = "set quaternionFrame" + qFrame + ";\n  ";
isQuaternion = true;
if (type.equalsIgnoreCase("draw")) {
isDraw = true;
type = 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 ? "" : 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;")) 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) {
if (isSplit) endScript += " split";
startScript += "plot " + type + endScript;
var ptDataFrame = this.vwr.ms.getJmolDataFrameIndex(modelIndex, startScript);
if (ptDataFrame > 0 && tokCmd != 134221856 && tokCmd != 134222350) {
this.vwr.setCurrentModelIndexClear(ptDataFrame, true);
return "";
}}var reader = this.vwr.fm.getJmolDataReader();
var parameters = (tok == 1715472409 || tok == 1095241729 ? reader.getJmolDataFrameProperties(e, tok, propToks, props, bs, minXYZ, maxXYZ, format, isPdbFormat) : null);
if (tokCmd == 134221856) return this.vwr.writeFileData(filename, "PLOT_" + type, modelIndex, parameters);
var data;
switch (type.substring(0, 4)) {
case "data":
data = "1 0 H 0 0 0 # Jmol PDB-encoded data";
break;
case "spin":
case "bril":
default:
data = this.vwr.getPdbData(modelIndex, type, null, parameters, null, true);
break;
}
if (tokCmd == 134222350) return data;
if (JU.Logger.debugging) JU.Logger.debug(data);
if (tokCmd == 135176) {
e.runScript(data);
return "";
}var savedFileInfo = this.vwr.fm.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.fm.setFileInfo(savedFileInfo);
if (!isOK) return "";
var modelCount = this.vwr.ms.mc;
reader.setJmolDataFrame(this.vwr.ms, startScript, modelIndex, modelCount - 1);
if (tok != 1715472409) startScript += ";\n" + preselected;
var ss = this.vwr.addStateScript(startScript, true, false);
var scripts = reader.getJmolDataFrameScripts(this.vwr, tok, modelIndex, modelCount, type, qFrame, props, isSpinPointGroup);
e.runScript(scripts[0] + preselected);
ss.setModelIndex(this.vwr.am.cmi);
var radius;
switch (tok) {
case 1715472409:
case 4138:
case 134221850:
case 136314895:
case 1095241729:
radius = 180;
break;
default:
radius = 10;
break;
}
this.vwr.setRotationRadius(radius, true);
e.sm.loadShape(31);
if (scripts[1] != null) {
e.runScript(scripts[1]);
}if (isSplit) {
var m = this.vwr.getP("_modelNumber");
e.runScript("frame 1.1 " + m + " split;");
}this.showString("frame " + this.vwr.getModelNumberDotted(this.vwr.ms.mc - 1) + (type.length > 0 ? " created: " + type + (isQuaternion ? qFrame : "") : ""));
return "";
}, "~A");
Clazz.defineMethod(c$, "polyhedra", 
function(){
var eval = this.e;
var haveBonds = (this.slen == 1);
var haveCenter = false;
var needsGenerating = haveBonds;
var onOffDelete = false;
var typeSeen = false;
var edgeParameterSeen = false;
var scale = NaN;
var nAtomSets = 0;
eval.sm.loadShape(21);
this.setShapeProperty(21, "init", Boolean.TRUE);
var translucentLevel = 3.4028235E38;
var radius = -1;
var colorArgb =  Clazz.newIntArray(-1, [-2147483648]);
var noToParam = -1;
var atomPt = -1;
var offset = null;
var foffset = 0;
var id = null;
var ok = false;
var modifyOnly = false;
var faces = null;
var points = null;
if (this.slen == 2 && this.tokAt(1) == 1073742001) {
if (!this.chk) eval.showStringPrint(this.getShapeProperty(21, "list"), false);
return;
}for (var i = 1; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
switch (this.getToken(i).tok) {
case 1073742197:
scale = NaN;
case 1073741872:
var index = (this.e.theTok == 1073742197 ? -1 : (this.tokAt(i + 1) == 2 ? this.intParameter(++i) : 1));
if (index > 8) this.invArg();
if (!this.chk) (J.api.Interface.getInterface("JU.BZone", this.vwr, "script")).createBZ(this.vwr, index, null, false, id, scale, foffset, offset);
return;
case 6:
propertyName = "info";
propertyValue = this.e.theToken.value;
needsGenerating = true;
break;
case 134217751:
propertyName = "points";
propertyValue = Float.$valueOf(this.tokAt(++i) == 1073742334 ? 0 : this.e.floatParameter(i));
ok = true;
break;
case 536875059:
scale = this.floatParameter(++i);
ok = true;
continue;
case 1814695966:
if (id != null) this.invArg();
propertyName = "unitCell";
propertyValue = Boolean.TRUE;
needsGenerating = true;
break;
case 1073742072:
this.e.restrictSelected(false, false);
eval.theTok = 1073742335;
case 1073742335:
case 12291:
case 1073742334:
if (i + 1 != this.slen || needsGenerating || nAtomSets > 1) this.error(18);
propertyName = (eval.theTok == 1073742334 ? "off" : eval.theTok == 1073742335 ? "on" : "delete");
onOffDelete = true;
break;
case 7:
if (id == null || needsGenerating) this.invArg();
needsGenerating = true;
faces = this.getIntArray2(i);
points = this.getAllPoints(eval.iToken + 1, 3);
i = eval.iToken;
if (Clazz.instanceOf(points[0],"JM.Atom")) this.setShapeProperty(21, "model", Integer.$valueOf((points[0]).getModelIndex()));
propertyName = "definedFaces";
propertyValue =  Clazz.newArray(-1, [faces, points]);
break;
case 1073741961:
propertyName = "full";
break;
case 2:
if (id != null) this.invArg();
propertyName = "nVertices";
propertyValue = Integer.$valueOf(this.intParameter(i));
needsGenerating = true;
if (this.tokAt(i + 1) == 268436992) i++;
break;
case 1677721602:
if (id != null) this.invArg();
if (nAtomSets > 0) this.invPO();
needsGenerating = true;
propertyName = "bonds";
haveBonds = true;
break;
case 1073741852:
if (radius != -1) this.invArg();
radius = 0;
i--;
case 1665140738:
i++;
case 3:
if (id != null) this.invArg();
if (nAtomSets > 0) this.invPO();
propertyName = (radius <= 0 ? "radius" : "radius1");
propertyValue = Float.$valueOf(radius = (radius == 0 ? 0 : this.floatParameter(i)));
needsGenerating = true;
break;
case 1073742066:
if (this.isFloatParameter(i + 1)) {
foffset = this.floatParameter(++i);
} else {
offset = this.e.centerParameter(++i, null);
i = eval.iToken;
}ok = true;
continue;
case 1073741937:
this.setShapeProperty(21, "collapsed", null);
case 1073742099:
case 1073741924:
propertyName = JS.T.nameOf(eval.theTok);
switch (this.tokAt(i + 1)) {
case 268440324:
case 268436992:
i++;
break;
}
propertyValue = Float.$valueOf(this.floatParameter(++i));
break;
case 1094717454:
if (id == null) this.invArg();
propertyName = "model";
propertyValue = Integer.$valueOf(this.intParameter(++i));
break;
case 1073742170:
if (nAtomSets > 1 || id != null && !haveCenter || noToParam == i) this.invPO();
nAtomSets = 3;
if (eval.isAtomExpression(++i)) {
propertyName = (needsGenerating || haveCenter ? "to" : "toBitSet");
propertyValue = this.atomExpressionAt(i);
} else if (eval.isArrayParameter(i)) {
propertyName = "toVertices";
propertyValue = eval.getPointArray(i, -1, false, true);
} else {
this.error(19);
}i = eval.iToken;
needsGenerating = true;
break;
case 12290:
case 10:
case 1073742325:
if (typeSeen) this.invPO();
switch (++nAtomSets) {
case 1:
if (id != null) this.invArg();
propertyName = "centers";
break;
case 2:
propertyName = "to";
needsGenerating = true;
break;
default:
eval.bad();
}
propertyValue = this.atomExpressionAt(i);
atomPt = i = eval.iToken;
needsGenerating = new Boolean (needsGenerating | (i + 1 == this.slen)).valueOf();
break;
case 1073741948:
case 1073741886:
needsGenerating = true;
modifyOnly = (i == 1);
if (typeSeen) this.error(18);
typeSeen = true;
propertyName = (this.e.theTok == 1073741886 ? "collapsed" : null);
if (this.isFloatParameter(i + 1)) this.setShapeProperty(21, "faceCenterOffset", Float.$valueOf(this.floatParameter(++i)));
break;
case 1765808134:
case 1111490588:
case 1073742074:
if (atomPt == i - 1) needsGenerating = true;
translucentLevel = this.getColorTrans(eval, i, true, colorArgb);
ok = true;
i = eval.iToken;
continue;
case 1073742044:
case 1073741933:
case 1073741956:
case 1073741934:
if (atomPt == i - 1) needsGenerating = true;
if (edgeParameterSeen) this.error(18);
edgeParameterSeen = true;
ok = true;
propertyName = JS.T.nameOf(eval.theTok);
break;
case 1073742182:
case 1073742060:
case 1073741861:
case 1073741958:
case 1073741964:
continue;
case 1073741974:
case 268441089:
case 1073741824:
case 4:
if (!eval.isColorParam(i)) {
if (i != 1) this.invPO();
id = (eval.theTok == 1073741974 ? this.stringParameter(++i) : eval.optParameterAsString(i));
if (this.tokAt(i + 1) == 268441089) id += this.paramAsStr(++i);
this.setShapeProperty(21, "thisID", id);
this.setShapeProperty(21, "model", Integer.$valueOf(this.vwr.am.cmi));
if (!eval.isCenterParameter(i + 1)) continue;
propertyName = "center";
propertyValue = this.centerParameter(++i);
i = eval.iToken;
haveCenter = true;
break;
}default:
if (eval.isColorParam(i)) {
if (atomPt == i - 1) needsGenerating = true;
colorArgb[0] = eval.getArgbParam(i);
if (eval.isCenterParameter(i)) noToParam = eval.iToken + 1;
i = eval.iToken;
continue;
}this.invArg();
}
if (propertyName != null) this.setShapeProperty(21, propertyName, propertyValue);
if (onOffDelete) return;
}
if (needsGenerating) {
if (!typeSeen && haveBonds) this.setShapeProperty(21, "bonds", null);
this.setShapeProperty(21, "generate", Boolean.$valueOf(modifyOnly));
} else if (!ok) {
this.error(19);
}if (offset != null) this.setShapeProperty(21, "offset", offset);
if (!Float.isNaN(scale)) this.setShapeProperty(21, "scale", Float.$valueOf(scale));
if (colorArgb[0] != -2147483648) this.setShapeProperty(21, "colorThis", Integer.$valueOf(colorArgb[0]));
if (translucentLevel != 3.4028235E38) eval.setShapeTranslucency(21, "", "translucentThis", translucentLevel, null);
this.setShapeProperty(21, "init", Boolean.FALSE);
});
Clazz.defineMethod(c$, "write", 
function(args){
if (args == null && this.vwr.haveAccessInternal(null)) this.invArg();
var eval = this.e;
var pt = 1;
var pt0 = 1;
var scripts = null;
var msg = null;
var localPath = null;
var remotePath = null;
var type = "SPT";
var isCommand = true;
var showOnly = false;
var isContact = false;
if (args == null) {
args = this.st;
showOnly = (this.vwr.isApplet && !this.vwr.isSignedApplet || !this.vwr.haveAccess(JV.Viewer.ACCESS.ALL) || this.vwr.fm.getPathForAllFiles().length > 0);
} else {
pt = pt0 = 0;
isCommand = false;
showOnly = !isCommand;
}var tok = JS.CmdExt.tokAtArray(pt, args);
if (tok == 4 && !isCommand) {
var t0 = JS.T.getTokenFromName(JS.SV.sValue(args[0]).toLowerCase());
if (t0 != null) tok = t0.tok;
}switch (tok) {
case 0:
break;
case 15:
case 7:
case 6:
type = "VAR";
break;
case 1095241729:
case 1073741872:
this.invArg();
break;
case 134221850:
case 4138:
case 1715472409:
msg = this.plot(args);
return (showOnly ? msg : this.writeMsg(msg));
case 134222850:
if (eval.isArrayParameter(pt + 1)) {
scripts = eval.stringParameterSet(++pt);
localPath = ".";
remotePath = ".";
pt0 = pt = eval.iToken + 1;
tok = this.tokAt(pt);
}break;
default:
type = JS.SV.sValue(this.tokenAt(pt, args)).toUpperCase();
}
var driverList = this.vwr.getExportDriverList();
var data = null;
var argCount = (isCommand ? this.slen : args.length);
var type2 = "";
var val = null;
var is2D = false;
var tVar = null;
var nVibes = 0;
var sceneType = null;
var isCoord = false;
var bsFrames = null;
var width = -1;
var height = -1;
var isExport = false;
var asJSON = false;
var fileName = null;
var quality = -2147483648;
if (tok != 0 && isCommand && this.slen > 1 && this.tokAt(this.slen - 2) == 1073741848) {
var p = this.paramAsStr(this.slen - 1).toUpperCase();
if (p.equals("JSON")) {
asJSON = true;
argCount -= 2;
}if (asJSON && type.equals("VAR")) {
} else {
type = p;
pt0 = argCount;
tok = 0;
}argCount -= 2;
}switch (tok) {
case 0:
break;
case 15:
case 7:
case 6:
type = "VAR";
tVar = this.tokenAt(pt++, args);
break;
case 1073741984:
type = "INLINE";
data = JS.SV.sValue(this.tokenAt(++pt, args));
pt++;
break;
case 1275068447:
type = "PGRP";
pt++;
type2 = JS.SV.sValue(this.tokenAt(pt, args)).toLowerCase();
if (type2.equals("draw")) pt++;
break;
case 1073742329:
pt++;
isCoord = true;
break;
case 1073742158:
case 134222850:
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 1228935687:
case 134320141:
case 1610616855:
case 135180:
case 1073742015:
case 1073742018:
case 1073877011:
case 1073877010:
case 135188:
pt++;
break;
case 1073741991:
type = "ZIPALL";
pt++;
break;
case 36868:
type = "VAR";
pt += 2;
break;
case 1073741929:
case 4115:
case 4120:
case 1073742062:
case 1073742139:
case 4166:
case 1073741824:
case 4:
switch (tok) {
case 4115:
var bsAtoms;
if (pt + 1 < argCount && args[++pt].tok == 1073742325 || args[pt].tok == 10) {
bsAtoms = eval.atomExpression(args, pt, 0, true, false, null, true);
pt = eval.iToken + 1;
} else {
bsAtoms = this.vwr.getAllAtoms();
}if (!this.chk) bsFrames = this.vwr.ms.getModelBS(bsAtoms, true);
break;
case 1073741929:
tok = 4120;
is2D = true;
case 4120:
type = "IMAGE";
pt++;
break;
case 1073742139:
val = JS.SV.sValue(this.tokenAt(++pt, args)).toUpperCase();
if (JU.PT.isOneOf(val, ";PNG;PNGJ;")) {
sceneType = val;
pt++;
} else {
sceneType = "PNG";
}break;
case 4166:
nVibes = eval.intParameterRange(++pt, 1, 10);
if (nVibes == 2147483647) return "";
if (!this.chk) {
this.vwr.tm.setVibrationPeriod(0);
if (!eval.isJS) eval.delayScript(100);
}pt++;
break;
default:
tok = 4120;
break;
}
if (tok == 4120 && pt < args.length) {
var t = JS.T.getTokenFromName(JS.SV.sValue(args[pt]).toLowerCase());
if (t != null) type = JS.SV.sValue(t).toUpperCase();
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 {
type = "IMAGE";
}}if (JS.CmdExt.tokAtArray(pt, args) == 2) {
width = JS.SV.iValue(this.tokenAt(pt++, args));
if (width <= 0) this.invArg();
height = JS.SV.iValue(this.tokenAt(pt++, args));
if (height <= 0) this.invArg();
if (JS.CmdExt.tokAtArray(pt, args) == 2) {
quality = JS.SV.iValue(this.tokenAt(pt++, args));
}}break;
}
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;gift;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));
if (width <= 0) this.invArg();
height = JS.SV.iValue(this.tokenAt(++pt, args));
if (height <= 0) this.invArg();
}if (JS.CmdExt.tokAtArray(pt + 1, args) == 2) quality = JS.SV.iValue(this.tokenAt(++pt, args));
} else if (!"VAR".equals(type) && JU.PT.isOneOf(val.toLowerCase(), ";xyz;xyzrn;xyzvib;mol;mol67;sdf;v2000;v3000;json;pdb;pqr;cml;cif;scif;cifp1;pwmat;pwslab;qcjson;xsf;")) {
type = val.toUpperCase();
if (pt + 1 == argCount) pt++;
}if (type.equals("IMAGE") && JU.PT.isOneOf(val.toLowerCase(), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;")) {
type = val.toUpperCase();
pt++;
}}if (pt + 2 == argCount) {
++pt;
}switch (JS.CmdExt.tokAtArray(pt, args)) {
case 0:
showOnly = true;
break;
case 1073741884:
break;
case 805307393:
fileName = (type.equals("IMAGE") ? "?jmol.png" : "?jmol." + type.toLowerCase());
break;
case 15:
case 7:
case 6:
break;
case 1073741824:
case 4:
fileName = JS.SV.sValue(this.tokenAt(pt, args));
if (fileName.equalsIgnoreCase("clipboard") || !this.vwr.haveAccess(JV.Viewer.ACCESS.ALL)) fileName = null;
break;
default:
this.invArg();
}
switch (type) {
case "IMAGE":
case "FRAME":
case "VIBRATION":
type = this.getWriteType(fileName, "JPG");
break;
case "CONTACT":
isContact = true;
case "ISOSURFACE":
type = this.getWriteType(fileName, "JVXL");
case "PLB":
switch (type) {
case "PMESH":
type = "ISOMESH";
break;
case "PMB":
type = "ISOMESHBIN";
break;
case "PLY":
type = "ISOPLY";
break;
case "PLB":
type = "ISOPLYBIN";
break;
}
break;
}
var isImage = JU.PT.isOneOf(type.toLowerCase(), ";jpg;jpeg;jpg64;jpeg64;gif;gift;pdf;ppm;png;pngj;pngt;scene;");
if (!isImage) {
switch (type) {
case "MNU":
type = "MENU";
break;
case "WRL":
case "VRML":
type = "Vrml";
isExport = true;
break;
case "X3D":
type = "X3d";
isExport = true;
break;
case "STL":
type = "Stl";
isExport = true;
break;
case "IDTF":
type = "Idtf";
isExport = true;
break;
case "MA":
type = "Maya";
isExport = true;
break;
case "JS":
type = "Js";
isExport = true;
break;
case "OBJ":
type = "Obj";
isExport = true;
break;
case "JVXL":
case "XJVXL":
type = "ISOSURFACE";
break;
case "JMOL":
type = "ZIPALL";
break;
case "HIS":
type = "HISTORY";
break;
case "COORD":
case "COORDS":
type = this.getWriteType(fileName, "XYZ");
break;
}
}if (scripts != null) {
if (!JV.FileManager.isJmolType(type)) this.invArg();
if (type.equals("PNG")) type = "PNGJ";
}if (!isImage && !isExport && !JU.PT.isOneOf(type, ";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;PMB;PLY;PLB;ISOMESHBIN;ISOMESH;ISOPLY;ISOPLYBIN;VAR;FILE;FUNCTION;CFI;CIF;SCIF;CIFP1;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL67;PDB;PGRP;PQR;PWMAT;PWSLAB;QUAT;RAMA;SDF;V2000;V3000;QCJSON;XSF;INLINE;")) eval.errorStr2(54, "COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION [w,x,y,z] [derivative]|RAMACHANDRAN|SPT|STATE|VAR x|ZIP|ZIPALL|CLIPBOARD", "CIF|SCIF|CIFP1|CML|CFI|GIF|GIFT|JPG|JPG64|JMOL|JVXL|MESH|MOL|PDB|PMESH|PNG|PNGJ|PNGT|PPM|PQR|PWMAT|PWSLAB|SDF|CD|JSON|QCJSON|V2000|V3000|SPT|XJVXL|XSF|XYZ|XYZRN|XYZVIB|ZIP" + driverList.toUpperCase().$replace(';', '|'));
if (this.chk) return "";
var fullPath =  new Array(1);
var params;
var timeMsg = this.vwr.getBoolean(603979934);
if (isExport) {
if (timeMsg) JU.Logger.startTimer("export");
var eparams =  new java.util.Hashtable();
eparams.put("type", type);
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));
try {
data = this.vwr.generateOutputForExport(eparams);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
data = e.toString();
return data;
} else {
throw e;
}
}
if (data == null || data.length == 0) return "";
if (showOnly) return data;
if (!type.equals("Povray") && !type.equals("Idtf") || fullPath[0] == null) return this.writeMsg(data);
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));
if (msg != null) {
var isError = !msg.startsWith("OK");
if (isError) eval.evalError(msg, null);
eval.report(data, isError);
}return "";
}var bytes = null;
var writeFileData = false;
if (data == null) {
data = type.intern();
switch (data) {
case "MENU":
data = this.vwr.getMenu("");
break;
case "PGRP":
data = this.vwr.ms.getPointGroupAsString(this.vwr.bsA(), null, 0, 1, null, null, type2.equals("draw") ? "" : null);
break;
case "PDB":
case "PQR":
if (showOnly) {
data = this.vwr.getPdbAtomData(null, null, (data === "PQR"), isCoord);
} else {
writeFileData = true;
type = "PDB_" + data + "-coord " + isCoord;
}break;
case "FILE":
if ("?".equals(fileName)) fileName = "?Jmol." + this.vwr.getP("_fileType");
if (showOnly) data = this.vwr.getCurrentModelFile(null, false);
 else writeFileData = true;
break;
case "CFI":
data = this.vwr.getModelFileData("selected", "cfi", false);
break;
case "FUNCTION":
data = this.vwr.getFunctionCalls(null);
type = "TXT";
break;
case "VAR":
if (tVar == null) {
var vtoken = this.tokenAt(isCommand ? 2 : 1, args);
switch (vtoken.tok) {
case 15:
case 7:
case 6:
break;
default:
tVar = eval.getParameter(JS.SV.sValue(vtoken), 1073742190, true);
break;
}
}if (fileName != null && fileName.endsWith(".json")) asJSON = true;
var v = null;
switch (tVar.tok) {
case 7:
break;
case 15:
v =  new JU.Lst();
v.addLast((tVar.value).data);
break;
case 6:
v = (fileName == null ? null : this.prepareBinaryOutput(tVar));
break;
}
if (v == null) {
data = (asJSON ? tVar.toJSON() : tVar.asString());
type = "TXT";
} else if (fileName != null) {
params =  new java.util.Hashtable();
params.put("data", v);
if ((bytes = data = this.vwr.createZip(fileName, v.size() == 1 || fileName.endsWith(".png") || fileName.endsWith(".pngj") ? "BINARY" : "ZIPDATA", params)) == null) eval.evalError("#CANCELED#", null);
}break;
case "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);
}break;
case "ZIP":
case "ZIPALL":
if (fileName != null) {
params =  new java.util.Hashtable();
if (scripts != null) params.put("data", scripts);
if ((bytes = data = this.vwr.createZip(fileName, type, params)) == null) eval.evalError("#CANCELED#", null);
}break;
case "HISTORY":
data = this.vwr.getSetHistory(2147483647);
type = "SPT";
break;
case "MO":
case "NBO":
data = this.getMoJvxl(2147483647, data === "NBO");
type = "XJVXL";
break;
case "PMESH":
case "PMB":
if ((data = this.getIsosurfaceJvxl(29, data)) == null) this.error(31);
type = "XJVXL";
break;
case "ISOMESH":
if ((data = this.getIsosurfaceJvxl(24, data)) == null) this.error(31);
type = "PMESH";
break;
case "ISOMESHBIN":
if ((bytes = this.getIsosurfaceJvxl(24, "ISOMESHBIN")) == null) this.error(31);
type = "PMB";
break;
case "ISOPLY":
if ((data = this.getIsosurfaceJvxl(24, data)) == null) this.error(31);
type = "PLY";
break;
case "ISOPLYBIN":
if ((bytes = this.getIsosurfaceJvxl(24, "ISOPLYBIN")) == null) this.error(31);
type = "PLB";
break;
case "ISOSURFACE":
case "MESH":
if ((data = this.getIsosurfaceJvxl(isContact ? 25 : 24, data)) == null) this.error(31);
type = (data.indexOf("<?xml") >= 0 ? "XJVXL" : "JVXL");
if (!showOnly) this.showString(this.getShapeProperty(isContact ? 25 : 24, "jvxlFileInfo"));
break;
default:
if (JU.PT.isOneOf(data, ";CIF;SCIF;CIFP1;SDF;MOL;MOL67;V2000;V3000;CD;JSON;XYZ;XYZRN;XYZVIB;CML;QCJSON;PWMAT;PWSLAB;XSF;")) {
var selected = this.vwr.bsA();
var bsModel;
this.vwr.setErrorMessage(null, " (" + selected.cardinality() + " atoms)");
data = this.vwr.getModelExtract(selected, isCoord, false, data);
msg = this.vwr.getErrorMessageUn();
this.vwr.setErrorMessage(null, null);
if (this.vwr.am.cmi >= 0 && !selected.equals(bsModel = this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi))) msg += "\nNote! Selected atom set " + selected + " is not the same as the current model " + bsModel;
if (data.startsWith("ERROR:")) bytes = data;
} else {
if (isCommand && showOnly && fileName == null) {
showOnly = false;
fileName = "\1";
}if (sceneType == null && quality < 0) quality = -1;
}break;
}
if (data == null) data = "";
}if (!isCommand) return data;
if (showOnly) {
eval.showStringPrint(data, true);
return "";
}if (bytes != null && (typeof(bytes)=='string')) return this.writeMsg(bytes);
if (writeFileData) {
return this.writeMsg(this.vwr.writeFileData(fileName, type, 0, null));
}if (type.equals("SCENE")) bytes = sceneType;
 else if (bytes == null && (!isImage || fileName != null)) bytes = data;
if (timeMsg) JU.Logger.startTimer("write");
if (isImage) {
eval.refresh(false);
if (width < 0) width = (is2D ? 250 : this.vwr.getScreenWidth());
if (height < 0) height = (is2D ? 250 : this.vwr.getScreenHeight());
}params =  new java.util.Hashtable();
var isCache = false;
if (fileName != null) {
params.put("fileName", fileName);
isCache = fileName.startsWith("cache://");
}params.put("backgroundColor", Integer.$valueOf(this.vwr.getBackgroundArgb()));
params.put("type", type);
if (is2D) {
params.put("is2D", Boolean.TRUE);
var smiles;
var ret = "smiles could not be generated";
try {
smiles = this.vwr.getOpenSmiles(null);
if (smiles.length > 0) {
var fname = this.vwr.setLoadFormat(true, "_" + smiles, '2', false);
fname += "?width=" + width + "&height=" + height + "&format=" + type.toLowerCase();
this.showString(fname);
ret = this.vwr.fm.getFileAsBytes(fname, null);
}} catch (e1) {
if (Clazz.exceptionOf(e1, Exception)){
} else {
throw e1;
}
}
if ((typeof(ret)=='string')) {
this.showString(ret);
return null;
}bytes = ret;
}var btype = null;
if ((typeof(bytes)=='string') && quality == -2147483648) params.put(btype = "text", bytes);
 else if (Clazz.instanceOf(bytes,Array)) params.put(btype = "bytes", bytes);
if (isCache) {
if (btype == null) return null;
this.vwr.cachePut(fileName, bytes);
return this.writeMsg("OK " + (btype === "text" ? (bytes).length : (bytes).length));
}if (scripts != null) params.put("scripts", scripts);
if (bsFrames != null) params.put("bsFrames", bsFrames);
params.put("fullPath", fullPath);
params.put("quality", Integer.$valueOf(quality));
params.put("width", Integer.$valueOf(width));
params.put("height", Integer.$valueOf(height));
params.put("nVibes", Integer.$valueOf(nVibes));
var ret = this.vwr.processWriteOrCapture(params);
if (ret == null) ret = "canceled";
if (isImage && ret.startsWith("OK")) ret += "; width=" + width + "; height=" + height;
if (timeMsg) this.showString(JU.Logger.getTimerMsg("write", 0));
return this.writeMsg(ret + (msg == null ? "" : msg));
}, "~A");
Clazz.defineMethod(c$, "getWriteType", 
function(fileName, def){
if (fileName != null) {
var pt = fileName.indexOf('.');
if (pt >= 0) return fileName.substring(pt + 1).toUpperCase();
}return def;
}, "~S,~S");
Clazz.defineMethod(c$, "prepareBinaryOutput", 
function(tvar){
var m = tvar.getMap();
if (m == null || !m.containsKey("$_BINARY_$")) return null;
var v =  new JU.Lst();
for (var e, $e = m.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var key = e.getKey();
if (key.equals("$_BINARY_$")) continue;
var o = e.getValue();
var bytes = (o.tok == 15 ? (o.value).data : null);
if (bytes == null) {
var s = o.asString();
bytes = (s.startsWith(";base64,") ? JU.Base64.decodeBase64(s) : s.getBytes());
}if (key.equals("_DATA_")) {
v =  new JU.Lst();
v.addLast(bytes);
return v;
} else if (key.equals("_IMAGE_")) {
v.add(0, key);
v.add(1, null);
v.add(2, bytes);
} else {
v.addLast(key);
v.addLast(null);
v.addLast(bytes);
}}
return v;
}, "JS.SV");
Clazz.defineMethod(c$, "writeMsg", 
function(msg){
if (this.chk || msg == null) return "";
var isError = !msg.startsWith("OK");
if (isError) {
this.e.evalError(msg, null);
{
alert(msg);
}}this.e.report(msg, isError);
return msg;
}, "~S");
Clazz.defineMethod(c$, "show", 
function(){
var eval = this.e;
var value = null;
var str = this.paramAsStr(1);
var filter = null;
var filterLen = 0;
if (this.slen > 3 && this.tokAt(this.slen - 3) == 268441088 && this.tokAt(this.slen - 2) == 268439040) {
filter = "!/" + this.paramAsStr(this.slen - 1);
this.slen -= 3;
filterLen = 3;
} else if (this.slen > 2 && this.tokAt(this.slen - 2) == 268441088) {
filter = "/" + this.paramAsStr(this.slen - 1);
this.slen -= 2;
filterLen = 2;
} else if ((filter = this.paramAsStr(this.slen - 1)).lastIndexOf("/") == 0) {
this.slen--;
filterLen = 1;
} else {
filter = null;
}var msg = null;
var name = null;
var len = 2;
var token = this.getToken(1);
var tok = (Clazz.instanceOf(token,"JS.SV") && token.tok != 1073741824 ? 0 : token.tok);
if (tok == 4) {
token = JS.T.getTokenFromName(str.toLowerCase());
if (token != null) tok = token.tok;
}if (tok != 1296041986 && tok != 1073742158 && tok != 1715472409 && tok != 1228935687) this.checkLength(-3);
if (this.slen == 2 && str.indexOf("?") >= 0) {
msg = this.vwr.getAllSettings(str.substring(0, str.indexOf("?")));
tok = -1;
}switch (tok) {
case -1:
break;
case 0:
if (!this.chk) msg = (eval.theToken).escape();
break;
case 603984065:
if (!this.chk) msg = this.vwr.stm.getUndoInfo();
break;
case 1073741925:
eval.checkLength23();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.getModelInfo("domains");
if (Clazz.instanceOf(d,"JS.SV")) msg = this.vwr.getAnnotationInfo(d, eval.optParameterAsString(2), 1073741925);
 else msg = "domain information has not been loaded";
}break;
case 1715472409:
msg = this.plot(this.st);
len = this.st.length;
break;
case 1073742189:
eval.checkLength23();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.getModelInfo("validation");
if (Clazz.instanceOf(d,"JS.SV")) msg = this.vwr.getAnnotationInfo(d, eval.optParameterAsString(2), 1073742189);
 else msg = "validation information has not been loaded";
}break;
case 134221829:
if (!this.chk) msg = JU.Escape.e(this.vwr.fm.cacheList());
break;
case 1111490587:
eval.checkLength23();
len = this.st.length;
if (!this.chk) {
var d = this.vwr.getModelInfo("dssr");
msg = (d == null ? "no DSSR information has been read" : len > 2 ? JS.SV.getVariable(this.vwr.extractProperty(d, this.stringParameter(2), -1)).asString() : "" + JS.SV.getVariable(d).asString());
}break;
case 1073741915:
var version = 2;
if (this.slen == 3) version = (Clazz.floatToInt(this.floatParameter((len = 3) - 1)));
 else this.checkLength(2 + filterLen);
if (!this.chk) msg = this.vwr.calculateStructures(null, true, false, version);
break;
case 545259572:
this.checkLength(2 + filterLen);
if (!this.chk) msg = this.vwr.fm.getPathForAllFiles();
break;
case 1275203608:
if (!this.chk) {
var info =  new Array(2);
this.vwr.shm.getShapePropertyData(21, "allInfo", info);
msg = JS.SV.getVariable(info[1]).asString();
}break;
case 1073742038:
if (!this.chk) this.vwr.getNMRPredict(eval.optParameterAsString(2));
return;
case 603983903:
if (!this.chk && this.slen == 3) {
msg = "" + this.vwr.getModelkitPropertySafely(eval.stringParameter(2));
len = 3;
}break;
case 1275068433:
case 1073741978:
case 1073741929:
case 1073741879:
case 134218757:
this.checkLength((tok == 1073741879 || tok == 134218757 && this.tokAt(2) == 1073742335 ? len = 3 : 2) + filterLen);
if (this.chk) return;
var param2 = eval.optParameterAsString(2);
if (tok == 1073741879) {
if ("mf".equals(param2)) param2 = "formula";
if ("formula".equals(param2)) {
msg = this.vwr.getModelInfo("formula");
if (msg != null) msg = JU.PT.rep(msg, " ", "");
}}if (msg == null) {
try {
switch (tok) {
case 1275068433:
msg = this.vwr.getInchi(this.vwr.bsA(), null, null);
if (msg == null) msg = "?";
break;
case 1073741978:
msg = this.vwr.getInchi(this.vwr.bsA(), null, "key");
break;
case 134218757:
if (param2.equalsIgnoreCase("true")) {
msg = this.vwr.getBioSmiles(null);
filter = null;
} else if (filter != null) {
msg = this.vwr.getSmilesOpt(null, -1, -1, 1, filter + "///");
filter = null;
}break;
default:
msg = this.vwr.ms.getModelDataBaseName(this.vwr.bsA());
if (msg != null && (msg.startsWith("$") || msg.startsWith(":"))) {
msg = msg.substring(1);
} else {
msg = null;
}break;
}
if (msg == null) {
var level = JU.Logger.getLogLevel();
JU.Logger.setLogLevel(4);
msg = (tok == 134218757 ? this.vwr.getSmiles(null) : this.vwr.getOpenSmiles(null));
JU.Logger.setLogLevel(level);
}} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
msg = ex.getMessage();
if (msg == null) {
msg = "";
}ex.printStackTrace();
} else {
throw ex;
}
}
switch (tok) {
case 134218757:
break;
case 1073741929:
if (msg.length > 0) {
this.vwr.fm.loadImage(this.vwr.setLoadFormat(false, "_" + msg, '2', false), "\1" + msg, false);
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, param2, this.vwr.bsA());
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 1086324755:
case 1086324754:
if (this.chk) break;
msg = ("" + this.vwr.evaluateExpression("symop('wyckoff" + (tok == 1086324755 ? "m" : "") + "')")).trim();
break;
case 134217764:
case 1296041986:
var sym = this.vwr.getOperativeSymmetry();
switch (tok) {
case 134217764:
var sdiag = eval.optParameterAsString(2);
var isNames = sdiag.toLowerCase().equals("names");
var isSubgroup = sdiag.toLowerCase().startsWith("subgroups");
var isDiagram = sdiag.toLowerCase().startsWith("diagram");
var isDiagramITA = sdiag.startsWith("diagramITA");
var isTable = sdiag.toLowerCase().startsWith("table");
len = this.slen;
var ita = -1;
if (isNames) {
if (this.chk) break;
} else if (isSubgroup || isDiagram || isTable || isDiagramITA) {
if (this.chk) break;
sdiag = JU.PT.trim(sdiag.substring(isDiagramITA ? 10 : isSubgroup ? 9 : isDiagram ? 7 : 5).trim(), "\"");
if (sdiag.length == 0) {
if (sym == null) {
msg = "Include a space group name or number to view its diagram, table, or subgroups";
break;
}if (sym.getSpaceGroupClegId().charAt(1) == '/') {
msg = "special group information is not implemented yet";
break;
}sdiag = sym.getIntTableNumber();
if (sdiag == null || sdiag.equals("0")) {
msg = "Can't display a table; don't have an ITA number.";
break;
}}if (msg != null) break;
ita = JU.PT.parseInt(sdiag);
if (ita == -2147483648) {
if (sym == null) {
sym = this.vwr.getSymStatic();
}var info = sym.getSpaceGroupInfo(this.vwr.ms, JU.PT.rep(sdiag, "''", "\""), -1, true, null);
if (info == null) {
msg = "Could not find space group " + sdiag;
break;
}ita = ((info.get("spaceGroupInfo")).get("ita")).intValue();
}}if (isNames || ita > 0) {
var href = (isNames ? "https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-getgen" : JV.JC.resolveDataBase(isDiagramITA ? "itadiagramita" : isDiagram ? "itadiagram" : "itatable", JU.PT.formatS("" + ita, 3, 0, false, true), null));
msg = href;
this.vwr.showUrl(href);
break;
}case 1296041986:
msg = "";
var info = null;
if ((len = this.slen) == 2) {
if (this.chk) break;
if (sym == null) sym = this.vwr.getSymTemp();
info = sym.getSpaceGroupInfo(this.vwr.ms, null, -1, false, null);
} else if (tok == 134217764) {
var sg = this.paramAsStr(2);
len = 3;
if (this.chk) break;
if (sg.startsWith("list/")) {
filter = sg.substring(4);
sg = "list";
}info = this.vwr.getSymTemp().getSpaceGroupInfo(this.vwr.ms, JU.PT.rep(sg, "''", "\""), -1, false, null);
}if (info != null) {
msg = (tok == 134217764 ? "" + info.get("spaceGroupInfo") + info.get("spaceGroupNote") : "") + (info.containsKey("symmetryInfo") ? info.get("symmetryInfo") : "");
break;
}var iop = (this.tokAt(2) == 2 ? this.intParameter(2) : 0);
var xyz = (this.tokAt(2) == 4 || this.tokAt(2) == 12 ? this.paramAsStr(2) : null);
var pt1 = null;
var pt2 = null;
var nth = -1;
if (this.slen > 3 && this.tokAt(3) != 4) {
var ret =  Clazz.newArray(-1, [null, this.vwr.getFrameAtoms()]);
pt1 = eval.centerParameter(2 + (iop == 0 ? 0 : 1), ret);
if (ret[0] != null && (ret[0]).isEmpty()) {
len = this.slen;
break;
}ret[0] = null;
if (this.tokAt(eval.iToken + 1) != 0 && this.tokAt(eval.iToken + 1) != 4) {
pt2 = eval.centerParameter(++eval.iToken, ret);
if (ret[0] != null && (ret[0]).isEmpty()) {
len = this.slen;
break;
}}if (iop == 0 && this.tokAt(eval.iToken + 1) == 2) nth = eval.getToken(++eval.iToken).intValue;
}var type = (eval.iToken > 1 && this.tokAt(eval.iToken + 1) == 4 ? this.stringParameter(++eval.iToken) : pt1 == null && pt2 == null ? "label" : null);
this.checkLength((len = ++eval.iToken) + filterLen);
if (!this.chk) {
var o = this.vwr.getSymmetryInfo(this.vwr.getAllAtoms().nextSetBit(0), xyz, iop, null, pt1, pt2, 0, type, 0, nth, 0, null);
msg = (o == null ? "" : Clazz.instanceOf(o,"java.util.Map") ? JS.SV.getVariable(o).asString() : o.toString());
}break;
}
break;
case 1648363544:
var vdwType = null;
if (this.slen > 2) {
len = this.slen;
vdwType = J.c.VDW.getVdwType(this.paramAsStr(2));
if (vdwType == null) this.invArg();
}if (!this.chk) msg = this.vwr.getDefaultVdwNameOrData(0, vdwType, null);
break;
case 134320141:
eval.checkLength23();
len = this.slen;
var s = eval.optParameterAsString(2);
var pt;
if (filter == null && (pt = s.indexOf('/')) >= 0) {
filter = s.substring(pt + 1);
s = s.substring(0, pt);
}if (!this.chk) msg = this.vwr.getFunctionCalls(s);
break;
case 36867:
this.checkLength(2 + filterLen);
if (!this.chk) msg = this.vwr.getAllSettings(null);
break;
case 1073742166:
msg = this.vwr.getFrameTitle();
break;
case 1073742184:
if ((len = this.slen) == 2) {
if (!this.chk) this.vwr.showUrl(eval.getFullPathName(false));
} else {
name = this.paramAsStr(2);
if (!this.chk) this.vwr.showUrl(name);
}return;
case 1765808134:
str = "defaultColorScheme";
break;
case 1610612740:
str = "scaleAngstromsPerInch";
break;
case 134221850:
case 4138:
if (this.chk) return;
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) eval.errorStr(30, "show " + eval.theToken.value);
msg = this.plot(this.st);
len = this.slen;
break;
case 14:
case 1112152078:
if (!this.chk) msg = this.getContext(false);
break;
case 1073741888:
name = eval.optParameterAsString(2);
if (name.length > 0) len = 3;
if (!this.chk) value = this.vwr.cm.getColorSchemeList(name);
break;
case 1073742192:
if (!this.chk) msg = this.vwr.getAtomDefs(this.vwr.definedAtomSets) + this.vwr.g.getVariableList() + this.getContext(true);
break;
case 536870926:
if (!this.chk) msg = this.vwr.getTrajectoryState();
break;
case 553648144:
value = "" + JS.ScriptEval.commandHistoryLevelMax;
break;
case 553648148:
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 603979808:
msg = "set axesUnitcell";
break;
case 603979804:
msg = "set axesMolecular";
break;
default:
msg = "set axesWindow";
}
break;
case 1610612737:
msg = "set bondMode " + (this.vwr.getBoolean(603979812) ? "OR" : "AND");
break;
case 1649022989:
if (!this.chk) msg = "set strandCountForStrands " + this.vwr.getStrandCount(12) + "; set strandCountForMeshRibbon " + this.vwr.getStrandCount(13);
break;
case 1613238294:
msg = "set hbondsBackbone " + this.vwr.getBoolean(603979852) + ";set hbondsSolid " + this.vwr.getBoolean(603979854);
break;
case 1095241729:
if (!this.chk) msg = this.vwr.getSpinState();
break;
case 1611141176:
msg = "set ssbondsBackbone " + this.vwr.getBoolean(603979952);
break;
case 1610625028:
case 1611141172:
msg = "selectionHalos " + (this.vwr.getSelectionHalosEnabled() ? "ON" : "OFF");
break;
case 1612709894:
msg = "set selectHetero " + this.vwr.getBoolean(1612709894);
break;
case 1073741828:
msg = JU.Escape.eAP(this.vwr.getAdditionalHydrogens(null, null, 768));
break;
case 1612709900:
msg = "set selectHydrogens " + this.vwr.getBoolean(1612709900);
break;
case 553648130:
case 553648138:
case 536870924:
case 553648176:
case 553648172:
case 1073741995:
if (!this.chk) msg = this.vwr.getLightingState();
break;
case 1073742136:
case 4146:
if (!this.chk) msg = this.vwr.stm.listSavedStates();
break;
case 1814695966:
if (!this.chk) {
if ((len = this.slen) == 3) {
msg = this.vwr.stm.getSavedUnitCell(this.paramAsStr(2));
} else {
msg = this.vwr.getUnitCellInfoText();
}}break;
case 1073742329:
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 && eval.outputBuffer == null && filter == null) this.vwr.sm.clearConsole();
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.getStateInfo();
break;
}if (filter != null && this.slen == 3) {
if (!this.chk) msg = this.vwr.getStateInfo();
break;
} else if (this.tokAt(2) == 1228935687 && (len = this.slen) == 4) {
if (!this.chk) msg = this.vwr.fm.getEmbeddedFileState(this.paramAsStr(3), true, "state.spt");
break;
}len = 3;
name = this.paramAsStr(2);
if (!this.chk) msg = this.vwr.stm.getSavedState(name);
break;
case 1639976963:
if ((len = this.slen) == 2) {
if (!this.chk) msg = this.vwr.ms.getProteinStructureState(this.vwr.bsA(), 134222350);
break;
}var shape = this.paramAsStr(2);
if (!this.chk) msg = this.vwr.stm.getSavedStructure(shape);
break;
case 134221834:
var dtype = ((len = this.slen) == 3 ? this.paramAsStr(2) : null);
if (!this.chk) {
var data = this.vwr.getDataObj(dtype, null, -2);
var isType = (dtype != null && "types".equals(dtype.toLowerCase()));
var isAll = (isType || "*".equals(dtype));
if (data == null) {
msg = "no data";
} else if (Clazz.instanceOf(data,"JU.Lst")) {
var list = data;
data = list.toArray( new Array(list.size()));
} else if (!isAll) {
var odata = data;
msg = JU.Escape.encapsulateData(odata[0], odata[1], (odata[3]).intValue());
}if (msg == null) {
var sdata = data;
if (isType) {
sdata[1] = sdata[1].$replace('\n', ',');
}msg = JU.Escape.e(sdata);
}}break;
case 1073742330:
len = 3;
msg = eval.setObjectProperty();
break;
case 1812599299:
if (!this.chk) {
msg = this.vwr.ms.getBoundBoxCommand(true);
}break;
case 12289:
if (!this.chk) msg = "center " + JU.Escape.eP(this.vwr.tm.fixedRotationCenter);
break;
case 135176:
if (!this.chk) msg = this.getShapeProperty(22, "command");
break;
case 1228935687:
if (this.slen == 2) {
if (!this.chk) {
if (filter == null && !eval.isFuncReturn) this.vwr.sm.clearConsole();
msg = this.vwr.getCurrentModelFile(null, false);
}if (msg == null) msg = "<unavailable>";
break;
}len = 3;
value = this.paramAsStr(2);
if (!this.chk) {
if (filter == null) this.vwr.sm.clearConsole();
msg = this.vwr.getFileAsString3(value, true, null);
}break;
case 4115:
if (this.tokAt(2) == 1073742327 && (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 (eval.scriptLevel == 0) this.vwr.removeCommand();
msg = this.vwr.getSetHistory(n);
}break;
case 135180:
if (!this.chk) msg = this.getShapeProperty(24, "jvxlDataXml");
break;
case 1073877011:
case 1073877010:
if (eval.optParameterAsString(2).equalsIgnoreCase("list")) {
this.e.sm.loadShape(27);
msg = (this.chk ? "" : this.getShapeProperty(27, "list -1"));
len = 3;
} else {
var ptMO = ((len = this.slen) == 2 ? -2147483648 : this.intParameter(2));
if (!this.chk) msg = this.getMoJvxl(ptMO, tok == 1073877011);
}break;
case 1094717454:
if (!this.chk) msg = this.vwr.ms.getModelInfoAsString();
break;
case 537006096:
if (!this.chk) msg = this.vwr.getMeasurementInfoAsString();
break;
case 1073741864:
len = 3;
if (!this.chk && this.slen == len) {
msg = this.paramAsStr(2);
msg = this.vwr.getOrientation(JS.T.getTokFromName(msg.equals("box") ? "volume" : msg.equals("rotation") ? "best" : msg), "best", null, null).toString();
}break;
case 1073742132:
tok = this.tokAt(2);
if (tok == 0) tok = 1073742132;
 else len = 3;
case 1073742178:
case 4129:
if (!this.chk) msg = this.vwr.getOrientation(tok, null, null, null).toString();
break;
case 1073742077:
len = 2;
if (this.slen > 3) break;
switch (tok = this.tokAt(2)) {
case 1073742178:
case 1073742132:
case 4129:
case 0:
if (!this.chk) msg = this.vwr.getOrientation(tok, null, null, null).toString();
break;
default:
name = eval.optParameterAsString(2);
msg = this.vwr.getOrientation(1073742034, name, null, null).toString();
}
len = this.slen;
break;
case 1073742088:
if (!this.chk) msg = this.vwr.ms.getPDBHeader(this.vwr.am.cmi);
break;
case 1275068447:
var typ = eval.optParameterAsString(2);
if (typ.length == 0) typ = null;
len = this.slen;
if (!this.chk) msg = this.vwr.ms.getPointGroupAsString(this.vwr.bsA(), "show:" + typ, 0, 0, null, null, null);
break;
case 1088421903:
if (!this.chk) msg = this.vwr.ms.getSymmetryInfoAsString();
break;
case 1073742176:
if (!this.chk) msg = "transform:\n" + this.vwr.tm.matrixRotate.toString();
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 1665140738:
str = "solventProbeRadius";
break;
case 1086324744:
if ((len = this.slen) == 3 && this.tokAt(2) == 1073742334) tok = 1086324743;
case 1073741863:
case 1086326788:
case 1073742120:
case 1113589787:
case 1086324742:
case 1153433601:
case 1073741982:
if (!this.chk) msg = this.vwr.getChimeInfo(tok);
break;
case 537022465:
case 1610612738:
case 20482:
case 1612709912:
value = "?";
break;
case 1073742030:
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.ms.getPDBHeader(this.vwr.am.cmi);
}break;
case 1073741992:
case 36868:
str = this.paramAsStr(len++);
var v = eval.getParameter(str, 1073742190, true);
if (!this.chk) if (tok == 1073741992) {
msg = v.toJSON();
} else {
msg = v.escape();
}break;
}
this.checkLength(len + filterLen);
if (this.chk) return;
if (msg != null) this.showString(this.filterShow(msg, filter));
 else if (value != null) this.showString(str + " = " + value);
 else if (str != null) {
if (str.indexOf(" ") >= 0) this.showString(str);
 else this.showString(str + " = " + (eval.getParameter(str, 1073742190, true)).escape());
}});
Clazz.defineMethod(c$, "filterShow", 
function(msg, name){
if (name == null) return msg;
var isNot = name.startsWith("!/");
name = name.substring(isNot ? 2 : 1).toLowerCase();
var info = JU.PT.split(msg, "\n");
var sb =  new JU.SB();
for (var i = 0; i < info.length; i++) if ((info[i].toLowerCase().indexOf(name) < 0) == isNot) sb.append(info[i]).appendC('\n');

return sb.toString();
}, "~S,~S");
Clazz.defineMethod(c$, "stereo", 
function(){
var stereoMode = J.c.STER.DOUBLE;
var degrees = -5;
var degreesSeen = false;
var colors = null;
var colorpt = 0;
for (var i = 1; i < this.slen; ++i) {
if (this.e.isColorParam(i)) {
if (colorpt > 1) this.e.bad();
if (colorpt == 0) colors =  Clazz.newIntArray (2, 0);
if (!degreesSeen) degrees = 3;
colors[colorpt] = this.e.getArgbParam(i);
if (colorpt++ == 0) colors[1] = ~colors[0];
i = this.e.iToken;
continue;
}switch (this.getToken(i).tok) {
case 1073742335:
this.e.checkLast(this.e.iToken = 1);
this.e.iToken = 1;
break;
case 1073742334:
this.e.checkLast(this.e.iToken = 1);
stereoMode = J.c.STER.NONE;
break;
case 2:
case 3:
degrees = this.floatParameter(i);
degreesSeen = true;
break;
case 1073741824:
if (!degreesSeen) degrees = 3;
stereoMode = J.c.STER.getStereoMode(this.paramAsStr(i));
if (stereoMode != null) break;
default:
this.invArg();
}
}
if (this.chk) return;
this.vwr.setStereoMode(colors, stereoMode, degrees);
});
Clazz.defineMethod(c$, "struts", 
function(){
var eval = this.e;
var defOn = (this.tokAt(1) == 1073742072 || this.tokAt(1) == 1073742335 || 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$, "unitcell", 
function(i, tok2){
var justReset = (tok2 == 4141);
var eval = this.e;
var icell = 2147483647;
var mad10 = 2147483647;
var pt = null;
var tickInfo = (tok2 == 0 ? eval.tickParamAsStr(i, true, false, false) : null);
i = eval.iToken;
var id = null;
var oabc = null;
var newUC = null;
var ucname = null;
var isOffset = false;
var isReset = false;
var packing = -1;
var sym = (this.chk ? null : this.vwr.getCurrentUnitCell());
var tok = (justReset ? 4141 : this.tokAt(++i));
switch (tok) {
case 1073742333:
if (!this.chk) this.vwr.ms.clearUnitCell(this.vwr.am.cmi);
return;
case 4142:
case 4141:
isReset = true;
pt = JU.P4.new4(0, 0, 0, -1);
if (!justReset) {
eval.iToken++;
}break;
case 2097180:
var plane = eval.hklParameter(i + 1, null, false, null);
var hkl = eval.getPointOrPlane(i + 1, 7);
i = eval.iToken;
var zscale = NaN;
if (this.isFloatParameter(i + 1)) {
zscale = this.floatParameter(++i);
if (this.tokAt(i + 1) == 268441090) {
zscale = -zscale / 100;
i++;
}}var zoffset = NaN;
var zoffPercent = false;
if (this.isFloatParameter(i + 1)) {
zoffset = this.floatParameter(++i);
if (this.tokAt(i + 1) == 268441090) {
zoffPercent = true;
i++;
}}var refTop = (this.tokAt(i + 1) == 1073742172);
if (refTop) i++;
eval.iToken = i;
if (this.chk) break;
if (Clazz.instanceOf(hkl,"JU.P3")) {
hkl = JU.P4.new4(hkl.x, hkl.y, hkl.z, 0);
} else if (Float.isNaN(zoffset)) {
zoffset = (hkl).w;
}oabc = this.getUVBoxFromHKL(sym, hkl, plane);
var p =  new JU.P3();
var vt =  new JU.V3();
JU.Measure.getPlaneProjection( new JU.P3(), plane, p, vt);
if (zscale > 0) {
oabc[3].normalize();
oabc[3].scale(zscale);
} else if (zscale < 0) {
oabc[3].scale(-zscale);
}if (!Float.isNaN(zoffset) && zoffset != 0) {
if (zoffPercent) {
zoffset = zoffset / 100 * oabc[3].length();
}oabc[0].scaleAdd2(zoffset, vt, oabc[0]);
}if (refTop) oabc[0].scaleAdd2(-oabc[3].length(), vt, oabc[0]);
ucname = "surface" + (Clazz.floatToInt(hkl.x)) + (Clazz.floatToInt(hkl.y)) + (Clazz.floatToInt(hkl.z));
break;
case 536875059:
case 1073742163:
pt = (tok == 536875059 ? eval.getPointOrPlane(++i, 19) : eval.checkHKL(eval.getFractionalPoint(++i)));
i = eval.iToken;
if (this.chk) break;
oabc = sym.getUnitCellVectors();
oabc[1].scale(Math.abs(pt.x));
oabc[2].scale(Math.abs(pt.y));
oabc[3].scale(Math.abs(pt.z));
pt = null;
ucname = "supercell";
break;
case 1073741938:
pt = eval.getFractionalPoint(++i);
i = eval.iToken;
if (this.chk) break;
pt = JU.SimpleUnitCell.ptToIJK(eval.checkHKL(pt), 1);
break;
case 135180:
case 1073742330:
id = eval.objectNameParameter(++i);
break;
case 1812599299:
eval.iToken = i;
if (this.chk) break;
var o = JU.P3.newP(this.vwr.getBoundBoxCenter());
pt = this.vwr.getBoundBoxCornerVector();
o.sub(pt);
oabc =  Clazz.newArray(-1, [o, JU.P3.new3(pt.x * 2, 0, 0), JU.P3.new3(0, pt.y * 2, 0), JU.P3.new3(0, 0, pt.z * 2)]);
pt = null;
break;
case 1073742176:
if (this.tokAt(++i) != 12) this.invArg();
if (this.chk) break;
newUC =  Clazz.newArray(-1, [this.getToken(i).value]);
break;
case 11:
case 12:
newUC = this.getToken(i).value;
break;
case 12289:
switch (this.tokAt(++i)) {
case 12290:
case 10:
case 1073742325:
pt = this.vwr.ms.getAtomSetCenter(this.atomExpressionAt(i));
i = eval.iToken;
if (this.chk) break;
this.vwr.toFractional(pt, true);
break;
default:
if (eval.isCenterParameter(i)) {
pt = this.centerParameter(i);
i = eval.iToken;
break;
}this.invArg();
}
pt.x -= 0.5;
pt.y -= 0.5;
pt.z -= 0.5;
break;
case 12290:
case 10:
case 1073742325:
var iAtom = this.atomExpressionAt(i).nextSetBit(0);
i = eval.iToken;
if (!this.chk) this.vwr.setUnitCellAtomIndex(iAtom);
if (iAtom < 0) return;
break;
case 1073742066:
isOffset = true;
if (eval.isAtomExpression(i + 1)) {
pt = eval.centerParameter(++i, null);
i = eval.iToken;
if (this.chk) break;
this.vwr.toFractional(pt, false);
break;
}case 1073742114:
pt = eval.getFractionalPoint(++i);
if (Clazz.instanceOf(pt,"JU.P4")) {
if (isOffset) this.invArg();
} else {
i = eval.iToken;
if (this.chk) break;
if (!isOffset && pt.x < 555) {
pt = JU.SimpleUnitCell.ptToIJK(eval.checkHKL(pt), 1);
} else {
pt = JU.P4.new4(pt.x, pt.y, pt.z, (isOffset ? 1 : 0));
}}break;
case 3:
case 2:
var f = this.floatParameter(i);
if (f < 111) {
i--;
break;
}icell = this.intParameter(i);
break;
case 1095241729:
case 4:
case 1073741824:
var s = this.paramAsStr(i).toLowerCase();
if (s.equals("rhombohedral") || s.equals("r")) {
if (sym != null && sym.getUnitCellInfoType(8) == 0) return;
s = "2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3c";
} else if (s.equals("trigonal") || s.equals("hexagonal")) {
if (sym != null && sym.getUnitCellInfoType(9) == 0) return;
s = "a-b,b-c,a+b+c";
}ucname = s;
if (s.indexOf(",") >= 0 || this.chk) {
newUC = s;
break;
}if (s.startsWith("unitcell_")) {
this.unitcell(0, 4141);
} else {
var stype = null;
this.vwr.ms.setModelCagePts(-1, null, null);
newUC = this.vwr.getModelInfo("unitcell_conventional");
var modelIsPrimitive = this.vwr.getModelInfo("isprimitive") != null;
if (JU.PT.isOneOf(ucname, ";parent;standard;primitive;")) {
if (newUC == null && modelIsPrimitive) {
this.showString("Cannot convert unit cell when file data is primitive and have no lattice information");
return;
}if (ucname.equals("primitive") && this.tokAt(i + 1) == 4) stype = this.paramAsStr(++i).toUpperCase();
}if (Clazz.instanceOf(newUC,Array)) {
oabc = newUC;
}if (stype == null) stype = this.vwr.getModelInfo("latticeType");
if (newUC != null) {
this.vwr.ms.setModelCagePts(-1, this.vwr.getV0abc(-1, newUC), "" + newUC);
newUC = null;
}if (!ucname.equals("conventional")) {
this.setShapeProperty(34, "labels", null);
s = this.vwr.getModelInfo("unitcell_" + ucname);
if (s == null) {
var isPrimitive = ucname.equals("primitive");
if (isPrimitive || ucname.equals("reciprocal")) {
var scale = (this.slen == i + 1 ? 1 : this.tokAt(i + 1) == 2 ? this.intParameter(++i) * 3.141592653589793 : this.floatParameter(++i));
ucname = (sym == null ? "" : sym.getSpaceGroupName() + " ") + ucname;
oabc = (sym == 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)]) : sym.getUnitCellVectors());
if (stype == null) stype = this.vwr.getSymmetryInfo(this.vwr.getFrameAtoms().nextSetBit(0), null, 0, null, null, null, 1073741994, null, 0, -1, 0, null);
if (sym == null) sym = this.vwr.getSymTemp();
if (!modelIsPrimitive) sym.toFromPrimitive(true, stype.length == 0 ? 'P' : stype.charAt(0), oabc, this.vwr.getCurrentModelAuxInfo().get("primitiveToCrystal"));
if (!isPrimitive) {
JU.SimpleUnitCell.getReciprocal(oabc, oabc, scale);
}break;
}} else {
ucname = s;
if (s.indexOf(",") >= 0) newUC = s;
}}break;
}default:
var ret =  new Array(1);
if ( new Boolean (!justReset & this.getUnitCellParameter(i, ret)).valueOf()) {
oabc = ret[0];
} else {
newUC = ret[0];
}if (newUC == null && oabc == null) {
if (this.slen > i + 1) {
pt = eval.getFractionalPoint(i);
i = eval.iToken;
} else {
i--;
}} else if (newUC != null) {
if (!this.chk && tok2 != 0) {
if (sym == null) {
if (tok2 == 1073741938) return;
this.assignSpaceGroup(null, "P1", newUC, packing, false, "unitcell");
} else if (tok2 != 1073741938 && sym.fixUnitCell(newUC)) {
eval.invArgStr("Unit cell is incompatible with current space group");
}}i = eval.iToken;
} else if (oabc != null) {
i = eval.iToken;
}break;
}
switch (tok2) {
case 1073741938:
if (eval.isFloatParameter(i + 1)) {
packing = this.floatParameter(++i);
eval.iToken = i;
} else {
packing = 0;
}mad10 = 0;
break;
case 1814695966:
if (this.tokAt(i + 1) == 1073742080) {
packing = (eval.isFloatParameter(++i + 1) ? this.floatParameter(++i) : 0);
eval.iToken = i;
}default:
mad10 = (justReset ? 1 : eval.getSetAxesTypeMad10(++i));
break;
}
if (!justReset) eval.checkLast(eval.iToken);
if (this.chk || mad10 == 2147483647) return;
if (oabc == null && newUC != null) oabc = this.vwr.getV0abc(-1, newUC);
if (tok2 == 1073741938) {
if (sym == null || icell != 2147483647 || id != null || isReset) this.invArg();
if (oabc == null) {
oabc = sym.getUnitCellVectors();
if (pt == null) pt =  new JU.P3();
sym.toCartesian(pt, true);
oabc[0] = pt;
}this.vwr.getModelkit(false).cmdFillOABC(oabc, packing, this.e.fullCommand);
return;
}if (icell != 2147483647) {
if (sym != null) sym.setOffset(icell);
} else if (id != null) {
this.vwr.setCurrentCage(id);
} else if (isReset || oabc != null) {
isReset = (tok2 == 1814695966 || sym == null ? this.vwr.getModelkit(false).transformAtomsToUnitCell(sym, oabc, ucname) : true);
if (isReset) {
if (tok2 == 1814695966 && sym != null) {
this.vwr.ms.setSpaceGroup(this.vwr.am.cmi, sym.getUnitCell(oabc, false, null), null);
return;
}this.vwr.ms.setModelCagePts(-1, oabc, ucname);
if (sym == null) {
this.vwr.setNewRotationCenter(this.vwr.getUnitCellCenter());
}}}var sym0 = (tok2 == 1814695966 ? this.vwr.ms.getUnitCell(-1 - this.vwr.am.cmi) : null);
eval.setObjectMad10(33, "unitCell", mad10);
if (pt != null) {
sym = this.vwr.ms.getUnitCell(-2147483648);
if (sym != null) sym.setOffsetPt(pt);
}if (tok2 == 1814695966 && sym.getFractionalOffset(true) == null) {
sym.setSpaceGroupTo(sym0);
if (packing >= 0) this.vwr.getModelkit(false).cmdPackUnitCell(sym, this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi), packing);
}if (tickInfo != null) this.setShapeProperty(33, "tickInfo", tickInfo);
if (ucname != null) this.showString(ucname + (oabc == null ? "" : " " + JU.Escape.e(oabc)));
}, "~N,~N");
Clazz.defineMethod(c$, "getUVBoxFromHKL", 
function(uc, hkl, plane){
var h = Clazz.floatToInt(hkl.x);
var k = Clazz.floatToInt(hkl.y);
var l = Clazz.floatToInt(hkl.z);
if (h == 0 && k == 0 && l == 0 || h != hkl.x || k != hkl.y || l != hkl.z) this.invArg();
while ((h % 2) == 0 && (k % 2) == 0 && (l % 2) == 0) {
h /= 2;
k /= 2;
l /= 2;
}
var oabc = uc.getUnitCellVectors();
var dist0 = plane.w;
var p0 = JU.P4.new4(plane.x, plane.y, plane.z, 0);
var max = Math.max(Math.max(h, k), l);
var cpts = JU.Measure.getLatticePoints(uc.getLatticeCentering(), max, max, max);
for (var j = cpts.size(); --j >= 0; ) {
uc.toCartesian(cpts.get(j), true);
}
cpts = JU.Measure.getPointsOnPlane(cpts.toArray( new Array(cpts.size())), p0);
var zero =  new JU.P3();
var amin = -179;
var dmin = 3.4028235E38;
var dmin2 = 3.4028235E38;
var v = null;
var v1 = null;
var da = amin;
var damin = 3.4028235E38;
var d;
var okAng;
var isNew;
var isLinear;
for (var i = cpts.size(); --i >= 0; ) {
var pt = cpts.get(i);
d = pt.length();
isNew = isLinear = false;
if (d < 0.01 || v != null && ((da = Math.abs(JU.Measure.computeTorsion(v, zero, plane, pt, true))) > -amin)) continue;
isLinear = (da < 1);
if (v == null) {
v = pt;
dmin = d;
continue;
}if (d < dmin - 0.01) {
isNew = true;
damin = 3.4028235E38;
da = 3.4028235E38;
} else if (d < dmin2 - 0.01) {
damin = 3.4028235E38;
} else if (d >= dmin2 + 0.01) {
} else {
continue;
}if (isNew || (okAng = (da > 89)) && d < dmin + 0.1 && (pt.x >= -0.01 && pt.y <= 0.01) && (damin == 3.4028235E38 || damin < 89)) {
if (isLinear) {
v1 = null;
dmin2 = 3.4028235E38;
} else {
v1 = v;
dmin2 = dmin;
}v = pt;
dmin = d;
if (!isNew && da < damin) damin = da;
} else if (okAng && d < dmin2 + 0.1) {
v1 = pt;
dmin2 = d;
if (da < damin) damin = da;
}}
if (v == null) this.invArg();
var u = null;
if (v1 == null) {
for (var i = cpts.size(); --i >= 0; ) {
var pt = cpts.get(i);
da = JU.Measure.computeTorsion(v, zero, plane, pt, true);
if (da < -89.9 && da > amin + 0.01) {
amin = da;
u = pt;
}}
} else {
da = JU.Measure.computeTorsion(v, zero, plane, v1, true);
if (da > 1) {
u = v;
v = v1;
} else {
u = v1;
}}if (u == null) this.invArg();
oabc[1] = u;
oabc[2] = v;
var doReverse = ((((h < 0 ? 1 : 0) + (k < 0 ? 1 : 0) + (l < 0 ? 1 : 0)) % 2) == 1);
var w = oabc[3];
var a = JU.P3.newP(u);
var b = JU.P3.newP(v);
if (h == 0 && k == 0) {
b.scale(-1);
a.scale(-1);
oabc[1] = a;
oabc[2] = b;
} else if (h == 0 && l == 0) {
} else if (k == 0 && l == 0) {
a.scale(-1);
b.scale(-1);
oabc[1] = b;
oabc[2] = a;
}if (doReverse) {
a = oabc[1];
oabc[1] = oabc[2];
oabc[2] = a;
}w.cross(v, u);
w.normalize();
w.scale(dist0);
return oabc;
}, "J.api.SymmetryInterface,JU.P4,JU.P4");
Clazz.defineMethod(c$, "modelkit", 
function(){
var i = 0;
var tok = this.tokAt(1);
switch (tok) {
case 603984065:
case 4139:
if (this.chk) this.e.cmdUndoRedo(tok == 603984065 ? 4165 : 4140);
return;
case 1073742334:
if (this.e.$isStateScript) this.vwr.getModelkit(false).setProperty("updatekeysfromstate", null);
if (this.slen == 2 && this.vwr.getModelkitPropertySafely("exists") == null) return;
case 0:
case 1073742335:
if (!this.chk) this.vwr.setBooleanProperty("modelkitmode", tok != 1073742334);
if (this.tokAt(i + 1) == 0) return;
i = ++this.e.iToken;
break;
case 4126:
if (this.vwr.am.cmi < 0) this.e.errorStr(30, "MODELKIT MINIMIZE");
this.minimize(true);
return;
case 528432:
case 4145:
this.e.cmdRotate(false, true);
return;
case 4098:
++this.e.iToken;
case 134217764:
case 4106:
case 12291:
case 1275069441:
case 4129:
case 1073742080:
case 12297:
case 135176:
this.assign(true);
return;
case 4130:
++this.e.iToken;
this.mutate();
return;
}
var kit = this.vwr.getModelkit(false);
while ((tok = this.tokAt(++i)) != 0) {
var key = this.paramAsStr(i).toLowerCase();
var value = null;
switch (tok) {
case 1073742335:
case 1073742334:
if (!this.chk) {
this.vwr.setBooleanProperty("modelkitmode", tok == 1073742335);
if (tok == 1073742334) this.vwr.setStringProperty("picking", "identify");
}continue;
case 1610625028:
case 12294:
key = "hidden";
value = Boolean.$valueOf(tok != 1610625028);
break;
case 12293:
key = "constraint";
value = "";
var type = this.tokAt(++i);
var v1 = null;
var v2 = null;
var plane = null;
switch (type) {
case 1073742334:
case 1073742333:
if (!this.chk) this.vwr.setBooleanProperty("dragPicking", false);
break;
case 135198:
v1 = this.e.getPoint3f(++i, true, true);
i = this.e.iToken;
v2 = this.e.getPoint3f(++i, true, true);
value = null;
break;
case 134219777:
plane = this.e.hklParameter(++i, null, true, null);
value = null;
break;
case 134217750:
plane = this.e.planeParameter(++i, false);
value = null;
break;
default:
this.invArg();
}
if (value == null) {
if ((v1 == null || v2 == null) == (plane == null)) this.invArg();
value =  Clazz.newArray(-1, [v1, v2, plane]);
} else {
value = null;
}i = this.e.iToken;
break;
case 36867:
key = this.paramAsStr(++i);
value = (this.tokAt(++i) == 0 ? "true" : this.paramAsStr(i));
break;
case 4166:
key = "vibration";
switch (this.tokAt(++i)) {
case 1073742334:
value = "off";
break;
case 1086324754:
value = "wyckoff";
break;
default:
this.invArg();
break;
}
break;
case 1296041986:
switch (this.tokAt(++i)) {
case 4:
case 1073742333:
value = this.paramAsStr(i);
break;
case 12:
value = this.getToken(i).value;
break;
case 2:
value = Integer.$valueOf(this.getToken(i).intValue);
break;
default:
if (this.e.isCenterParameter(i)) {
key = "center";
value = this.e.centerParameter(i, null);
i = this.e.iToken;
} else {
this.invArg();
}break;
}
break;
case 1073742066:
value = this.paramAsStr(i + 1);
if (value.equals("none")) {
++i;
break;
}case 134217751:
case 12289:
value = this.e.atomCenterOrCoordinateParameter(++i, null);
i = this.e.iToken;
break;
case 1073742024:
value = this.paramAsStr(++i).toLowerCase();
if (!this.vwr.isModelKitOption('M', value)) this.invArg();
break;
case 1073741938:
case 1814695966:
if (this.e.isArrayParameter(i + 1)) {
this.unitcell(2, tok);
return;
}value = (this.tokAt(i + 1) == 4 || this.tokAt(i + 1) == 1814695966 ? this.paramAsStr(++i).toLowerCase() : null);
if (value == null || !this.vwr.isModelKitOption('U', value)) {
this.unitcell(2, tok);
return;
}break;
case 1088421903:
value = this.paramAsStr(++i).toLowerCase();
if (!this.vwr.isModelKitOption('S', value)) this.invArg();
break;
default:
if (this.vwr.isModelKitOption('B', key)) {
value = Boolean.$valueOf((tok = this.tokAt(++i)) == 0 || tok == 1073742335);
break;
}if (this.vwr.isModelKitOption('M', key)) {
value = key;
key = "mode";
break;
}if (this.vwr.isModelKitOption('U', key)) {
value = key;
key = "unitcell";
break;
}this.invArg();
}
if (!this.chk && value != null && (value = kit.setProperty(key, value)) != null && key !== "hidden" && !kit.isHidden()) this.vwr.showString("modelkit SET " + key + " " + value.toString(), false);
}
});
Clazz.defineMethod(c$, "assign", 
function(isModelkit){
if (this.vwr.am.cmi < 0) this.invArg();
var bsModelAtoms = this.vwr.getThisModelAtoms();
var i = ++this.e.iToken;
var doDraw = false;
var isZap = false;
var mode = this.tokAt(i);
if (mode == 135176) {
if (this.tokAt(2) != 134217764) this.invArg();
doDraw = true;
mode = 12297;
}if (mode == 12297) {
if (!isModelkit) this.invArg();
isZap = true;
mode = this.tokAt(++i);
if (mode == 0) return;
}var isAtom = (mode == 1153433601);
var isBond = (mode == 1677721602);
var isAdd = (mode == 1275069441);
var isConnect = (mode == 4106);
var isDelete = (mode == 12291);
var isMove = (mode == 4129);
var isSpacegroup = (mode == 134217764);
var packing = -1;
if (mode == 1073742080) {
packing = (this.e.isFloatParameter(i + 1) ? this.floatParameter(++i) : 0);
}if ((packing >= 0 || isSpacegroup) && !isModelkit) {
this.invArg();
}if (isAtom || isBond || isConnect || isSpacegroup || isDelete || isMove || isAdd || packing >= 0) {
i++;
} else {
isAtom = true;
mode = 1153433601;
}var index = -1;
var index2 = -1;
var bs = null;
if (isBond) {
if (this.tokAt(i) == 2) {
index = this.e.intParameter(i);
} else if (Clazz.instanceOf(this.getToken(i).value,"JM.BondSet")) {
index = (this.getToken(i).value).nextSetBit(0);
} else {
bs = this.expFor(i, bsModelAtoms);
index = bs.nextSetBit(0);
switch (bs.cardinality()) {
case 1:
bs = this.expFor(i = ++this.e.iToken, bsModelAtoms);
index2 = bs.nextSetBit(0);
if (index2 < 0) this.invArg();
bs.set(index);
case 2:
bs = this.vwr.ms.getBondsForSelectedAtoms(bs, false);
if (!bs.isEmpty()) {
index = bs.nextSetBit(0);
} else {
isConnect = true;
mode = 4106;
}break;
case 0:
default:
this.invArg();
}
}i = ++this.e.iToken;
} else if (packing >= 0) {
bs = bsModelAtoms;
} else if (isAtom && this.tokAt(i) == 4 || mode == 1275069441) {
} else if (!isSpacegroup || this.e.isAtomExpression(i)) {
bs = this.expFor(i, bsModelAtoms);
index = bs.nextSetBit(0);
if (index < 0) {
return;
}i = ++this.e.iToken;
}var sym = this.vwr.getOperativeSymmetry();
var type = null;
var pt = null;
var wyckoff = null;
var paramsOrUC = null;
var pts = null;
if (isAdd) {
if (this.e.isAtomExpression(i)) {
bs = this.expFor(++this.e.iToken, bsModelAtoms);
i = this.e.iToken;
type = this.e.optParameterAsString(i + 1);
i = this.e.iToken;
if (type.toLowerCase().equals("packed")) {
packing = (this.e.isFloatParameter(i + 1) ? this.floatParameter(++i) : 0);
this.e.iToken = i;
type = "";
}} else if (this.e.tokAt(i) == 1086324754) {
this.e.iToken = i - 1;
type = "O";
} else {
type = this.e.optParameterAsString(i);
}if (this.e.isPoint3f(this.e.iToken + 1)) {
pt = this.getPoint3f(++this.e.iToken, true);
} else if (this.e.isArrayParameter(this.e.iToken + 1)) {
pts = this.e.getPointArray(this.e.iToken + 1, -1, false, true);
}if (type.length == 0) type = null;
switch (this.tokAt(this.e.iToken + 1)) {
case 1073742080:
this.e.iToken++;
packing = (this.e.isFloatParameter(this.e.iToken + 1) ? this.floatParameter(++this.e.iToken) : 0);
break;
case 1086324754:
++this.e.iToken;
wyckoff = this.paramAsStr(++this.e.iToken);
var w = (wyckoff.equalsIgnoreCase("all") ? 'L' : wyckoff.equalsIgnoreCase("general") ? 'G' : (wyckoff.length > 1 || wyckoff.length == 0 ? '\0' : wyckoff.charAt(0)));
if (w < 'a' && w != 'A' && w != 'G' && w != 'L' || w > 'z') this.invArg();
wyckoff = "" + w;
if ("packed".equals(this.e.optParameterAsString(this.e.iToken + 1))) {
packing = (this.e.isFloatParameter(++this.e.iToken + 1) ? this.floatParameter(++this.e.iToken) : 0);
}break;
}
} else if (isMove) {
if (this.e.isArrayParameter(i)) {
pts = this.e.getPointArray(i, -1, false, true);
} else {
pt = this.getPoint3f(i, true);
}i = this.e.iToken;
} else if (isSpacegroup) {
type = this.e.optParameterAsString(i);
if (type.length == 0) type = ".";
sym = this.vwr.getOperativeSymmetry();
if (type.equals(".")) {
if (sym == null) type = "P1";
 else type = (i == this.slen ? null : sym.getSpaceGroupClegId());
}if ("packed".equalsIgnoreCase(type)) {
packing = (this.e.isFloatParameter(this.e.iToken + 1) ? this.floatParameter(++this.e.iToken) : 0);
type = sym.getSpaceGroupClegId();
}if (this.tokAt(this.e.iToken + 1) == 1814695966) {
var ret =  new Array(1);
this.getUnitCellParameter(this.e.iToken + 2, ret);
paramsOrUC = ret[0];
if (paramsOrUC == null) this.invArg();
}if (packing < 0 && this.tokAt(this.e.iToken + 1) == 1073742080) {
packing = (this.e.isFloatParameter(this.e.iToken + 1) ? this.floatParameter(++this.e.iToken) : 0);
}} else if (isConnect) {
if (index2 < 0) {
bs = this.expFor(i, bsModelAtoms);
index2 = bs.nextSetBit(0);
type = this.e.optParameterAsString(++this.e.iToken);
}} else {
type = this.e.optParameterAsString(i);
if (isAtom) pt = (++this.e.iToken < this.slen ? this.centerParameter(this.e.iToken) : null);
}if (this.chk) return;
this.vwr.pushState();
switch (mode) {
case 1153433601:
this.e.clearDefinedVariableAtomSets();
this.vwr.getModelkit(false).cmdAssignAtom(bs, pt, type, this.e.fullCommand);
break;
case 1677721602:
this.vwr.getModelkit(false).cmdAssignBond(index, (type + "-").charAt(0), this.e.fullCommand);
break;
case 4106:
this.vwr.getModelkit(false).cmdAssignConnect(index, index2, (type + "1").charAt(0), this.e.fullCommand);
break;
case 1073742080:
type = null;
case 1275069441:
case 1086324754:
if (pts == null) {
if (pt != null) {
pts =  Clazz.newArray(-1, [pt]);
} else if (bs == null && wyckoff == null) {
if (type == null) this.invArg();
 else wyckoff = "G";
}}var na = this.vwr.getModelkit(false).cmdAssignAddAtoms(type == null ? null : type + (wyckoff != null ? ":" + wyckoff : ""), pts, bs, packing, this.e.fullCommand);
if (this.e.doReport()) this.e.report(J.i18n.GT.i(J.i18n.GT.$("{0} atoms added"), na), false);
break;
case 12291:
var nd = this.vwr.getModelkit(false).cmdAssignDeleteAtoms(bs);
if (this.e.doReport()) this.e.report(J.i18n.GT.i(J.i18n.GT.$("{0} atoms deleted"), nd), false);
break;
case 4129:
var nm = this.vwr.getModelkit(false).cmdAssignMoveAtoms(bs, index, JU.P3.newP(pt), pts, true, false, true);
if (nm > 0) this.vwr.checkCoordinatesChanged(bs);
if (this.e.doReport()) this.e.report(J.i18n.GT.i(J.i18n.GT.$("{0} atoms moved"), nm), false);
break;
case 134217764:
if (isZap) {
this.vwr.zap(false, false, false);
sym = null;
}if (packing >= 0 && type.equalsIgnoreCase("packed")) {
type = null;
if (sym == null) this.invArg();
} else {
if (packing < 0) {
var ptend = i + 1;
for (var j = ptend; j < this.slen; j++) {
if (this.tokAt(j) == 1073742080) {
packing = (this.e.isFloatParameter(j + 1) ? this.floatParameter(++j) : 0);
ptend = j;
break;
}}
if (ptend < this.slen) type = null;
}if (type == null) type = this.concatString(i, (packing >= 0 ? "packed" : "unitcell"));
if (type.length > 0 && type.indexOf(":") < 0 && type.indexOf(">") < 0 && (type.indexOf(",") > 0 || "rh".indexOf(type) >= 0)) {
if (sym == null) this.invArg();
var cleg = sym.getSpaceGroupClegId();
type = (cleg == null ? "[" + sym.getSpaceGroupName() + "]:" : cleg.substring(0, cleg.indexOf(":") + 1)) + type;
}}var s = this.assignSpaceGroup(bs, type, paramsOrUC, packing, doDraw, this.e.fullCommand);
var isError = s.endsWith("!");
if (isError) this.e.invArgStr(s);
if (this.e.doReport()) this.e.showString(s);
break;
}
}, "~B");
Clazz.defineMethod(c$, "assignSpaceGroup", 
function(bs, cleg, paramsOrUC, packing, doDraw, cmd){
var sb =  new JU.SB();
var ret = this.vwr.getSymStatic().staticTransformSpaceGroup(bs, cleg, paramsOrUC, sb);
var isError = ret.endsWith("!");
if (isError) return ret;
if (packing >= 0 || doDraw) this.vwr.getModelkit(false).cmdAssignSpaceGroup(ret, sb, cmd, packing, doDraw);
return sb.toString();
}, "JU.BS,~S,~O,~N,~B,~S");
Clazz.defineMethod(c$, "concatString", 
function(i, butNot){
var s = "";
for (; i < this.slen; i++) {
var t = JS.SV.sValue(this.e.getToken(i));
if (t.equals(butNot)) {
this.e.iToken--;
break;
}s += t;
}
return s;
}, "~N,~S");
Clazz.defineMethod(c$, "getUnitCellParameter", 
function(i, ret){
ret[0] = null;
var tok = this.tokAt(i);
var ei = this.e.iToken;
var isNot = false;
if (tok == 268439040) {
isNot = true;
tok = this.tokAt(++i);
}switch (tok) {
case 8:
return false;
case 1073741824:
case 4:
case 1814695966:
var tr = this.paramAsStr(i).toLowerCase();
var uc = this.vwr.getCurrentUnitCell();
if (uc == null) this.invArg();
if (!this.chk) {
if (tr.equalsIgnoreCase("unitcell")) {
tr = "a,b,c";
} else if (tr.startsWith("unitcell_")) {
tr = this.vwr.getCurrentModelAuxInfo().get(tr);
} else {
tr = JU.SimpleUnitCell.parseSimpleMath(this.vwr, tr);
}if (isNot) tr = "!" + tr;
ret[0] = uc.getV0abc(tr, null);
}return true;
}
if (this.e.isArrayParameter(i)) {
this.e.ignoreError = true;
if (this.tokAt(i + 2) != 1073742332) {
try {
ret[0] = this.e.floatParameterSet(i, 6, 6);
this.e.ignoreError = false;
return false;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}try {
ret[0] = this.e.getPointArray(i, 4, false, true);
return true;
} catch (ee) {
if (Clazz.exceptionOf(ee, Exception)){
this.e.iToken = ei;
} else {
throw ee;
}
}
try {
if (this.tokAt(i) == 1073742195) {
i += 2;
var pts =  new Array(4);
for (var p = 0; p < 4; p++) {
if (this.e.isArrayParameter(i)) {
var a = this.e.floatParameterSet(i, 3, 3);
pts[p] = JU.P3.newA(a);
i = this.e.iToken + 1;
if (this.tokAt(i) == 268436992) i++;
this.e.iToken = i;
} else if (p == 3) {
for (i = p; i > 0; --i) {
pts[i] = pts[i - 1];
}
pts[0] =  new JU.P3();
} else {
break;
}if (p == 3) {
ret[0] = pts;
return true;
}}
}} catch (ee) {
if (Clazz.exceptionOf(ee, Exception)){
this.e.iToken = ei;
} else {
throw ee;
}
}
this.e.ignoreError = false;
}return true;
}, "~N,~A");
Clazz.defineMethod(c$, "expFor", 
function(i, bsAtoms){
var bs = JU.BS.copy(this.atomExpressionAt(i));
bs.and(bsAtoms);
return bs;
}, "~N,JU.BS");
Clazz.defineMethod(c$, "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$, "getIsosurfaceJvxl", 
function(iShape, type){
switch (type) {
case "PMESH":
case "MESH":
type = "jvxlMeshXml";
break;
case "ISOMESH":
type = "pmesh";
break;
case "ISOMESHBIN":
case "PMB":
type = "pmeshbin";
break;
case "ISOPLY":
type = "ply";
break;
case "ISOPLYBIN":
case "PLB":
type = "plybin";
break;
default:
type = "jvxlDataXml";
break;
}
return (this.chk ? "" : this.getShapeProperty(iShape, type));
}, "~N,~S");
Clazz.defineMethod(c$, "getMoJvxl", 
function(ptMO, isNBO){
var iShape = (isNBO ? 28 : 27);
this.e.sm.loadShape(iShape);
var modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) this.e.errorStr(30, "show/write MO/NBO");
var moData = this.vwr.ms.getInfo(modelIndex, "moData");
if (moData == null) this.error(27);
var n = this.getShapeProperty(iShape, "moNumber");
if (n == null || n.intValue() == 0) this.setShapeProperty(iShape, "init", Integer.$valueOf(modelIndex));
this.setShapeProperty(iShape, "moData", moData);
return this.e.sm.getShapePropertyIndex(iShape, "showMO", ptMO);
}, "~N,~B");
Clazz.defineMethod(c$, "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$, "tokenAt", 
function(i, args){
return (i < args.length ? args[i] : null);
}, "~N,~A");
c$.tokAtArray = Clazz.defineMethod(c$, "tokAtArray", 
function(i, args){
return (i < args.length && args[i] != null ? args[i].tok : 0);
}, "~N,~A");
Clazz.defineMethod(c$, "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.defineMethod(c$, "sync", 
function(){
var text = "";
var applet = "";
var port = JU.PT.parseInt(this.e.optParameterAsString(1));
if (port == -2147483648) {
this.checkLength(-3);
port = 0;
switch (this.slen) {
case 1:
applet = "*";
text = "ON";
break;
case 2:
applet = this.paramAsStr(1);
if (applet.indexOf("jmolApplet") == 0 || JU.PT.isOneOf(applet, ";*;.;^;")) {
text = "ON";
if (!this.chk) this.vwr.syncScript(text, applet, 0);
applet = ".";
break;
}text = applet;
applet = "*";
break;
case 3:
applet = this.paramAsStr(1);
text = (this.tokAt(2) == 528443 ? "GET_GRAPHICS" : this.paramAsStr(2));
break;
}
} else {
var v = null;
if (this.slen > 2 && (v = this.e.setVariable(2, -1, "", false)) == null) return;
text = (this.slen == 2 ? null : v.tok == 6 ? v.toJSON() : v.asString());
applet = null;
}if (this.chk) return;
this.vwr.syncScript(text, applet, port);
});
Clazz.defineMethod(c$, "varna", 
function(){
var message = this.e.paramAsStr(1);
if (this.chk) return;
var err = this.vwr.syncScriptErr("varna:" + message);
if (err != null) this.e.showString(err);
});
c$.labeler = null;
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
