Clazz.declarePackage("JS");
Clazz.load(null, "JS.MathExt", ["java.util.Date", "$.Hashtable", "$.Random", "JU.A4", "$.AU", "$.BArray", "$.BS", "$.CU", "$.Lst", "$.M3", "$.M4", "$.Measure", "$.OC", "$.P3", "$.P4", "$.PT", "$.Quat", "$.Rdr", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.bspt.PointIterator", "J.c.VDW", "J.i18n.GT", "JM.BondSet", "$.Measurement", "JS.SV", "$.T", "JU.BSUtil", "$.BoxInfo", "$.Edge", "$.Escape", "$.JmolMolecule", "$.Logger", "$.Parser", "$.Point3fi", "$.SimpleUnitCell", "JV.FileManager", "$.JC", "$.Viewer"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.e = null;
this.rand = null;
this.pm = null;
Clazz.instantialize(this, arguments);}, JS, "MathExt", null);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "init", 
function(se){
this.e = se;
this.vwr = this.e.vwr;
return this;
}, "~O");
Clazz.defineMethod(c$, "evaluate", 
function(mp, op, args, tok){
switch (tok) {
case 134218760:
return (args.length >= 1 && args[0].tok == 4 ? mp.addXStr((args.length == 1 ?  new java.util.Date().toString() : this.vwr.apiPlatform.getDateFormat(JS.SV.sValue(args[1]))) + "\t" + JS.SV.sValue(args[0]).trim()) : mp.addXInt(((System.currentTimeMillis() - JS.MathExt.t0)) - (args.length == 0 ? 0 : args[0].asInt())));
case 134218250:
return (args.length == 1 && args[0].tok == 2 ? mp.addXInt(Math.abs(args[0].intValue)) : mp.addXFloat(Math.abs(args[0].asFloat())));
case 134218241:
case 134218245:
case 134218244:
case 134218246:
case 134218255:
return (args.length == 1 && this.evaluateMath(mp, args, tok));
case 1275069441:
case 1275068435:
case 1275068928:
case 1275068929:
case 1275068930:
case 1275068931:
case 1275335685:
case 1275334681:
return this.evaluateList(mp, op.intValue, args);
case 268437504:
if (args.length == 0) mp.wasX = false;
case 1275068418:
return this.evaluateArray(mp, args, tok == 1275068418 && op.tok == 268442113);
case 134217766:
return this.evaluateMatrix(mp, args);
case 134217765:
return this.evaluateCallbackParam(mp, args);
case 134217731:
case 134221850:
return this.evaluateQuaternion(mp, args, tok);
case 1275068420:
return this.evaluateBin(mp, args);
case 134221829:
return this.evaluateCache(mp, args);
case 1275068934:
case 1275068935:
return this.evaluateRowCol(mp, args, tok);
case 1765808134:
return this.evaluateColor(mp, args);
case 134221831:
return this.evaluateCompare(mp, args);
case 1228931586:
case 134217736:
case 1275203608:
return this.evaluateConnected(mp, args, tok, op.intValue);
case 1812599299:
case 1814695966:
return this.evaluateUnitCell(mp, args, op.tok == 268442113, op.tok == 268442113 ? op.intValue : op.tok);
case 134353926:
return this.evaluateContact(mp, args);
case 134221834:
return this.evaluateData(mp, args);
case 1275069444:
case 1275069442:
return this.evaluateDotDist(mp, args, tok, op.intValue);
case 1275069443:
if (op.tok == 268442113) return this.evaluateDotDist(mp, args, tok, op.intValue);
case 134217729:
case 1745489939:
return this.evaluateMeasure(mp, args, op.tok);
case 1228935687:
case 134223363:
return this.evaluateLoad(mp, args, tok == 1228935687);
case 1275068427:
return this.evaluateFind(mp, args);
case 1275068433:
return this.evaluateInChI(mp, args);
case 1287653388:
case 1825200146:
return this.evaluateFormat(mp, op.intValue, args, tok == 1825200146);
case 134320141:
return this.evaluateUserFunction(mp, op.value, args, op.intValue, op.tok == 268442113);
case 1275068437:
tok = 1275068725;
case 1275068446:
case 1275068725:
case 1275082241:
case 1275072526:
return this.evaluateGetProperty(mp, args, tok, op.tok == 268442113);
case 136314895:
return this.evaluateHelix(mp, args);
case 134219777:
case 134217750:
case 134217763:
return this.evaluatePlane(mp, args, tok, op.tok == 268442113);
case 134218759:
case 134238732:
case 134222850:
case 134222350:
return this.evaluateScript(mp, args, tok);
case 1275069446:
case 1275069447:
case 1275068932:
return this.evaluateString(mp, op.intValue, args);
case 134217751:
return this.evaluatePoint(mp, args);
case 1275068447:
return this.evaluatePointGroup(mp, args, op.tok == 268442113);
case 134256129:
return this.evaluatePrompt(mp, args);
case 134219266:
return this.evaluateRandom(mp, args);
case 1275068432:
return this.evaluateIn(mp, args);
case 1275072532:
return this.evaluateModulation(mp, args);
case 1275068443:
return this.evaluateReplace(mp, args);
case 134218753:
case 134218756:
case 134218757:
case 1237320707:
return this.evaluateSubstructure(mp, args, tok, op.tok == 268442113);
case 1275068444:
case 1275068425:
return this.evaluateSort(mp, args, tok);
case 134217764:
return this.evaluateSpacegroup(mp, args);
case 1296041986:
return this.evaluateSymop(mp, args, op.tok == 268442113);
case 1275068445:
return this.evaluateTensor(mp, args);
case 134217759:
return this.evaluateWithin(mp, args, op.tok == 268442113);
case 134221856:
return this.evaluateWrite(mp, args);
}
return false;
}, "JS.ScriptMathProcessor,JS.T,~A,~N");
Clazz.defineMethod(c$, "evaluateMatrix", 
function(mp, args){
var n = args.length;
var m4 = null;
var m3 = null;
var sarg0 = (n > 0 && args[0].tok == 4 ? args[0].value : null);
var map = (n < 2 || sarg0 == null ? null : args[1].getMap());
var lst = (n < 2 || sarg0 == null ? null : args[1].getList());
var normalize = (n > 1 && args[n - 1].tok == 1073742335);
if (normalize) n--;
var retType = (n > 1 && args[n - 1].tok == 4 ? args[n - 1].value : null);
var asUVW = "uvw".equalsIgnoreCase(retType);
var asABC = "abc".equalsIgnoreCase(retType);
var asXYZ = asUVW || !asABC && "xyz".equalsIgnoreCase(retType);
var asRXYZ = !asUVW && !asABC && !asXYZ && "rxyz".equalsIgnoreCase(retType);
var a = null;
if (retType != null || lst != null || map != null) n--;
switch (n) {
case 0:
m4 =  new JU.M4();
m4.setIdentity();
break;
case 1:
switch (args[0].tok) {
case 9:
var q = JU.Quat.newP4(args[0].value);
m3 = q.getMatrix();
break;
case 11:
m3 = args[0].value;
break;
case 12:
m4 = args[0].value;
break;
case 4:
var s = args[0].value;
if (s.equals("h") || s.equals("r") || s.indexOf(",") >= 0 && s.indexOf(":") < 0) {
var sym;
if (s.indexOf('*') >= 0) {
sym = this.vwr.getCurrentUnitCell();
if (sym == null) return false;
} else {
sym = this.vwr.getSymTemp();
}m4 = sym.convertTransform(s, null);
if (s.indexOf("u") >= 0) {
m3 =  new JU.M3();
m4.getRotationScale(m3);
}}if (m4 != null) break;
var select = null;
if (retType != null && !asABC && !asXYZ && !asUVW) {
if ("map".equals(retType)) {
map =  new java.util.Hashtable();
retType = null;
} else if ("list".equals(retType)) {
lst =  new JU.Lst();
retType = null;
} else {
select = "[SELECT (" + retType + ")]";
lst =  new JU.Lst();
retType = null;
}}var returnM4 = (lst == null && map == null);
var retMap = (map == null ? null :  new java.util.Hashtable());
var retLst = (lst == null ? null :  new JU.Lst());
if (returnM4) {
retMap =  new java.util.Hashtable();
retMap.put("ASM4", Boolean.TRUE);
}m4 = this.vwr.getSymStatic().staticGetMatrixTransform(s, retMap == null ? retLst : retMap);
if (returnM4) break;
if (map != null) {
map.clear();
for (var e, $e = retMap.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
map.put(e.getKey(), JS.SV.getVariable(e.getValue()));
}
return mp.addXMap(map);
}if (lst != null) {
if (select != null) return mp.addXObj(this.vwr.extractProperty(retLst, select, -1));
lst.clear();
for (var i = 0, nl = retLst.size(); i < nl; i++) {
lst.addLast(JS.SV.getVariable(retLst.get(i)));
}
return mp.addXList(lst);
}break;
case 7:
lst = args[0].getList();
var len = lst.size();
switch (len) {
case 3:
case 4:
a =  Clazz.newFloatArray (len * len, 0);
for (var i = 0, pt = 0; i < len; i++) {
var row = lst.get(i);
switch (row.tok) {
case 8:
var p = row.value;
a[pt++] = p.x;
a[pt++] = p.y;
a[pt++] = p.z;
break;
case 9:
var p4 = row.value;
a[pt++] = p4.x;
a[pt++] = p4.y;
a[pt++] = p4.z;
a[pt++] = p4.w;
break;
case 7:
var a2 = lst.get(i).getList();
if (a2 == null || a2.size() != len) return false;
for (var j = 0; j < len; j++) {
a[pt++] = JS.SV.fValue(a2.get(j));
}
break;
}
}
break;
case 9:
case 16:
a = JS.SV.flistValue(args[0], 0);
break;
default:
return false;
}
break;
}
break;
case 2:
m3 =  new JU.M3();
if (args[0].tok != 8) return false;
var v = JU.V3.newV(JS.SV.ptValue(args[0]));
var angle = JS.SV.fValue(args[1]);
m3.setAA(JU.A4.newVA(v, (angle / 180 * 3.141592653589793)));
return mp.addXM3(m3);
case 3:
case 4:
if (args[0].tok == 7) {
a =  Clazz.newFloatArray (n == 3 ? 9 : 16, 0);
for (var p = 0, i = 0; i < n; i++) {
var row = JS.SV.flistValue(args[i], 0);
for (var j = 0; j < n; j++) a[p++] = row[j];

}
break;
}}
if (a != null) {
switch (a.length) {
case 9:
m3 = JU.M3.newA9(a);
break;
case 16:
m4 = JU.M4.newA16(a);
break;
default:
return false;
}
}if (asRXYZ || asABC || asUVW || asXYZ) {
if (m3 != null) {
m4 = JU.M4.newMV(m3,  new JU.P3());
}if (normalize) this.doNormalize(m4);
return mp.addXStr(this.matToString((asRXYZ && m3 != null ? m3 : m4), asRXYZ ? 0x1 : asABC ? 0xABC : asUVW ? 0xDEF : 0));
}if (normalize) this.doNormalize(m4);
return (m3 != null ? mp.addXM3(m3) : m4 != null ? mp.addXM4(m4) : false);
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "doNormalize", 
function(m4){
if (m4 == null) return;
var a = m4.m03 + (m4.m00 + m4.m01 + m4.m02) / 2;
var b = m4.m13 + (m4.m10 + m4.m11 + m4.m12) / 2;
var c = m4.m23 + (m4.m20 + m4.m21 + m4.m22) / 2;
m4.m03 -= Math.floor(a);
m4.m13 -= Math.floor(b);
m4.m23 -= Math.floor(c);
}, "JU.M4");
Clazz.defineMethod(c$, "matToString", 
function(m4, mode){
var sym = this.vwr.getSymStatic();
var smode;
switch (mode) {
case 47:
case 0x1:
smode = "rxyz";
break;
case 39:
case 0xABC:
if (Clazz.instanceOf(m4,"JU.M3")) {
var m = JU.M4.newM4(null);
m.setRotationScale(m4);
return sym.staticGetTransformABC(m, false);
}smode = "abc";
break;
case 43:
case 0xDEF:
smode = "uvw";
break;
default:
case 35:
smode = "xyz";
}
return this.vwr.getSymStatic().staticConvertOperation("", m4, smode);
}, "JU.M34,~N");
Clazz.defineMethod(c$, "evaluateCallbackParam", 
function(mp, args){
return mp.addX(this.e.getCallbackParameter(args.length == 0 ? -2147483648 : args[0].asInt()));
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateSpacegroup", 
function(mp, args){
var ucParams = null;
var nargs = args.length;
if (nargs == 0) return mp.addXObj(this.vwr.getSymTemp().getSpaceGroupInfo(this.vwr.ms, null, this.vwr.am.cmi, true, null));
var mode = (args[args.length - 1].tok == 4 ? args[args.length - 1].value : null);
var isSettings = "settings".equalsIgnoreCase(mode);
var isSetting = "setting".equalsIgnoreCase(mode);
var isSubgroups = (nargs > 1 && (nargs != 2 || !isSettings && !isSetting && !"list".equalsIgnoreCase(mode) && !"jmol".equalsIgnoreCase(mode)));
var xyzList = args[0].asString();
if (isSubgroups || "subgroups".equals(mode)) {
var ret = this.getSubgroupInfo(args, "subgroups".equals(mode) ? nargs : nargs + 1);
return (ret == null ? false : mp.addXObj(ret));
}var params = null;
var ret = null;
switch (nargs) {
default:
return false;
case 2:
if ("list".equals(mode)) {
params = Integer.$valueOf(this.vwr.getSymTemp().getSpaceGroupInfoObj("itaNumber", xyzList, false, false));
xyzList = "list";
break;
}if (args[1].tok != 4) {
ucParams = JS.SV.flistValue(args[1], 0);
if (ucParams == null || ucParams.length != 6) return false;
params = ucParams = JU.SimpleUnitCell.newParams(ucParams, NaN);
}case 1:
if (args[0].tok == 10) {
var atoms = JS.SV.getBitSet(args[0], true);
return mp.addXObj(this.vwr.findSpaceGroup(null, atoms, null, ucParams, null, null, 1));
}var itaNo = (args[0].tok == 2 ? args[0].intValue : nargs == 1 ? -2147483648 : 0);
if (isSettings || isSetting) {
if (isSettings && itaNo == 0) return false;
var data = (isSetting && nargs > 1 ? xyzList : null);
return mp.addXObj((itaNo == -2147483648 ? this.vwr.getCurrentUnitCell() : this.vwr.getSymTemp()).getSpaceGroupJSON(mode.toLowerCase(), data, itaNo));
}if ("setting".equalsIgnoreCase(xyzList) || "settings".equalsIgnoreCase(xyzList)) {
var sym = this.vwr.getOperativeSymmetry();
return mp.addXObj(sym == null ? null : sym.getSpaceGroupJSON(xyzList.toLowerCase(), null, -2147483648));
}if (xyzList.toUpperCase().startsWith("AFLOWLIB/")) {
return mp.addXObj(this.vwr.getSymTemp().getSpaceGroupJSON("AFLOWLIB", xyzList.substring(9), 0));
}if (xyzList.startsWith("Hall:") || xyzList.indexOf("x") >= 0 || ucParams != null) {
ret = this.vwr.findSpaceGroup(null, null, xyzList, ucParams, null, null, 1);
break;
}if (itaNo > 0 || args[0].tok == 3 || args[0].tok == 4) {
if (itaNo > 0 || xyzList.length > 1 && xyzList.charAt(1) == '/' || !xyzList.endsWith(":") && !Float.isNaN(JU.PT.parseFloat(xyzList))) xyzList = "ITA/" + xyzList;
if (xyzList.toUpperCase().startsWith("ITA/")) {
return mp.addXObj(this.vwr.getSymTemp().getSpaceGroupJSON("ITA", xyzList.substring(4), 0));
}}break;
}
if (ret == null) ret = this.vwr.getSymStatic().getSpaceGroupInfoObj(xyzList, params, true, false);
if (ret != null && !"jmol".equals(mode) && !"list".equals(mode)) {
var o = (ret).get("itaIndex");
if (o != null) {
ret = this.vwr.getSymTemp().getSpaceGroupJSON("ITA", o.toString(), 0);
}}return mp.addXObj(ret);
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "getSubgroupInfo", 
function(args, nargs){
var sym;
var index1 = -2147483648;
var index2 = -2147483648;
var nameFrom = null;
var nameTo = null;
switch (nargs) {
case 5:
index2 = args[3].intValue;
if (index2 < 0) return null;
case 4:
index1 = args[2].intValue;
if (index1 < 0 || index1 == 2147483647) return null;
case 3:
nameTo = (args[1].intValue == 0 ? "" : args[1].asString());
case 2:
nameFrom = args[0].asString();
case 1:
default:
if (nameFrom == null) {
sym = this.vwr.getOperativeSymmetry();
if (sym == null) return null;
nameFrom = sym.getSpaceGroupClegId();
} else {
sym = this.vwr.getSymStatic();
}break;
}
return sym.getSubgroupJSON(nameFrom, nameTo, index1, index2, 0, null, null);
}, "~A,~N");
Clazz.defineMethod(c$, "evaluatePointGroup", 
function(mp, args, isAtomProperty){
var pts = null;
var center = null;
var distanceTolerance = -1;
var linearTolerance = -1;
var bsAtoms = null;
var type = null;
var isSpaceGroup = false;
switch (args.length) {
case 4:
linearTolerance = args[3].asFloat();
case 3:
distanceTolerance = args[2].asFloat();
case 2:
switch (args[1].tok) {
case 8:
center = JS.SV.ptValue(args[1]);
break;
case 10:
bsAtoms = JS.SV.getBitSet(args[1], false);
if (args[0].asString().equalsIgnoreCase("spaceGroup")) {
isSpaceGroup = true;
if (args.length == 2) distanceTolerance = 0;
}break;
}
if (isSpaceGroup) break;
case 1:
switch (args[0].tok) {
case 7:
var points = args[0].getList();
pts =  new Array(points.size());
for (var i = pts.length; --i >= 0; ) pts[i] = JS.SV.ptValue(points.get(i));

break;
case 10:
bsAtoms = JS.SV.getBitSet(args[0], false);
pts = this.vwr.ms.at;
break;
case 4:
if (isAtomProperty) {
bsAtoms = JS.SV.getBitSet(mp.getX(), true);
if (bsAtoms == null || bsAtoms.isEmpty()) return false;
var s = args[0].asString();
if ("spacegroup".equals(s)) {
isSpaceGroup = true;
break;
}}default:
return false;
}
break;
case 0:
if (!isAtomProperty) {
return mp.addXObj(this.vwr.ms.getPointGroupInfo(null, type));
}bsAtoms = JS.SV.getBitSet(mp.getX(), false);
break;
default:
return false;
}
if (bsAtoms != null) {
var iatom = bsAtoms.nextSetBit(0);
if (iatom < 0 || iatom >= this.vwr.ms.ac || isSpaceGroup && bsAtoms.cardinality() != 1) return false;
if (isSpaceGroup) {
var lst = this.vwr.ms.generateCrystalClass(iatom, JU.P3.new3(NaN, NaN, NaN));
pts =  new Array(lst.size());
for (var i = pts.length; --i >= 0; ) pts[i] = lst.get(i);

center =  new JU.P3();
}}var pointGroup = this.vwr.getSymTemp().setPointGroup(this.vwr, null, center, (pts == null ? this.vwr.ms.at : pts), bsAtoms, false, distanceTolerance < 0 ? this.vwr.getFloat(570425382) : distanceTolerance, linearTolerance < 0 ? this.vwr.getFloat(570425384) : linearTolerance, (bsAtoms == null ? pts.length : bsAtoms.cardinality()), true);
return mp.addXMap(pointGroup.getPointGroupInfo(-1, null, true, type, 0, 1));
}, "JS.ScriptMathProcessor,~A,~B");
Clazz.defineMethod(c$, "evaluateUnitCell", 
function(mp, args, isSelector, tok){
var x1 = (isSelector ? JS.SV.getBitSet(mp.getX(), true) : tok == 1812599299 ? this.vwr.getAllAtoms() : null);
var iatom = ((x1 == null ? this.vwr.getAllAtoms() : x1).nextSetBit(0));
var lastParam = args.length - 1;
if (tok == 1812599299) {
if (lastParam > 1 || lastParam == 0 && args[0].tok != 4) return false;
var b = this.vwr.ms.getBoxInfo(x1, 1);
return mp.addXObj(b.getInfo(lastParam == 0 ? null : args[0].asString()));
}var isInfo = false;
var asMatrix = (lastParam >= 0 && args[lastParam].tok == 1073742335);
if (lastParam >= 0 && args[lastParam].tok == 4) {
var infoType = args[lastParam].value;
isInfo = "info".equals(infoType);
if (isInfo) {
if (isInfo && lastParam == 0) {
var sym = this.vwr.getCurrentUnitCell();
return mp.addXMap(sym.getUnitCellInfoMap());
}lastParam--;
} else {
var infoValue = this.vwr.getUnitCellInfoStr(infoType);
if (!Float.isNaN(infoValue)) {
return mp.addXFloat(infoValue);
}}}var o = this.getUnitCell(args, iatom, 0, lastParam);
if (JU.AU.isAP(o)) {
var oabc = o;
if (isInfo) {
var uc = this.vwr.getSymTemp().getUnitCell(oabc, false, null);
return mp.addXMap(uc.getUnitCellInfoMap());
}if (asMatrix) {
var sym = this.vwr.getCurrentUnitCell();
var m4 =  new JU.M4();
for (var i = 0; i < 4; i++) {
var p = oabc[i];
sym.toFractional(oabc[i], true);
if (i == 0) {
m4.m00 = p.x;
m4.m01 = p.y;
m4.m02 = p.z;
m4.m03 = 1;
} else {
m4.setColumn4(i - 1, p.x, p.y, p.z, 0);
}}
return mp.addXM4(m4);
}}return (o != null && mp.addXObj(o));
}, "JS.ScriptMathProcessor,~A,~B,~N");
Clazz.defineMethod(c$, "getUnitCell", 
function(args, iatom, ipt, lastParam){
var isWithin = (ipt > 0);
var scale = 1;
switch (lastParam < ipt ? 0 : args[lastParam].tok) {
case 2:
case 3:
scale = args[lastParam].asFloat();
lastParam--;
break;
}
var normalize = false;
var tok0 = (ipt >= args.length || lastParam < ipt ? 0 : args[ipt].tok);
var ucnew = null;
var uc = null;
var arg0 = null;
switch (tok0) {
case 7:
uc = args[ipt].getList();
break;
case 12:
if (isWithin) return null;
switch (lastParam > 1 ? 1073741936 : lastParam < ipt + 1 ? 0 : args[ipt + 1].tok) {
default:
case 1073741936:
return null;
case 0:
case 1073742334:
break;
case 1073742335:
normalize = true;
break;
}
return this.vwr.getSymStatic().staticGetTransformABC(args[ipt].value, normalize);
case 4:
arg0 = args[ipt].asString().toLowerCase();
if (arg0.indexOf("a=") == 0) {
ucnew =  new Array(4);
for (var i = 0; i < 4; i++) ucnew[i] =  new JU.P3();

JU.SimpleUnitCell.setAbc(arg0, null, ucnew);
arg0 = null;
} else if (arg0.indexOf(",") >= 0 || arg0.equals("r")) {
} else {
var isNot = arg0.startsWith("!");
if (isNot) {
arg0 = arg0.substring(1);
}if (arg0.startsWith("unitcell_")) {
arg0 = this.vwr.getCurrentModelAuxInfo().get(arg0);
if (arg0 == null) return null;
if (isNot) arg0 = "!" + arg0;
} else {
arg0 = null;
}}break;
}
if (arg0 != null) {
var asMatrix = (lastParam > ipt && JS.SV.bValue(args[ipt + 1]));
if (asMatrix) return (isWithin ? null : this.vwr.getSymTemp().convertTransform(arg0, null));
ucnew = this.vwr.getV0abc(-1, arg0);
if (ucnew == null) return null;
}if (ucnew == null) {
var u = null;
var haveUC = (uc != null);
if (haveUC && uc.size() < 4) return null;
var ptParam = ipt + (haveUC ? 1 : 0);
if (!haveUC && tok0 != 8) {
u = (iatom < 0 ? this.vwr.getCurrentUnitCell() : this.vwr.ms.getUnitCell(this.vwr.ms.at[iatom].mi));
ucnew = (u == null ?  Clazz.newArray(-1, [JU.P3.new3(0, 0, 0), JU.P3.new3(1, 0, 0), JU.P3.new3(0, 1, 0), JU.P3.new3(0, 0, 1)]) : u.getUnitCellVectors());
}if (ucnew == null) {
ucnew =  new Array(4);
if (haveUC) {
switch (uc.size()) {
case 3:
ucnew[0] =  new JU.P3();
for (var i = 0; i < 3; i++) ucnew[i + 1] = JU.P3.newP(JS.SV.ptValue(uc.get(i)));

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

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

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

break;
case 1:
var l = args[1].getList();
if (l != null && l.size() == 3) {
for (var i = 0; i < 3; i++) ucnew[i + 1] = JU.P3.newP(JS.SV.ptValue(l.get(i)));

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

return ucnew;
}, "~A,~N,~N,~N");
Clazz.defineMethod(c$, "evaluateArray", 
function(mp, args, isSelector){
if (isSelector) {
var x1 = mp.getX();
switch (x1.tok) {
case 11:
case 12:
return mp.addX(x1.toArray());
}
if (args.length == 0 || args.length > 2) return false;
var doCopy = (args.length == 1 || args[1].tok == 1073742334);
var id;
var m1;
switch (x1.tok) {
case 11:
case 12:
return mp.addX(x1.toArray());
case 6:
if (args.length != 1) return false;
var lst =  new JU.Lst();
var map = x1.getMap();
var keys = x1.getKeys(false);
for (var i = 0, n = keys.length; i < n; i++) if (map.get(keys[i]).getMap() == null) return false;

id = args[0].asString();
for (var i = 0, n = keys.length; i < n; i++) {
m1 = map.get(keys[i]).getMap();
if (doCopy) m1 = JS.SV.deepCopy(m1, true, false);
m1.put(id, JS.SV.newS(keys[i]));
lst.addLast(JS.SV.newV(6, m1));
}
return mp.addXList(lst);
case 7:
var toArray = true;
var bsIndex =  new JU.BS();
var map1 =  new java.util.Hashtable();
var lst1 = x1.getList();
id = args[0].asString();
for (var i = lst1.size(); --i > 0; ) {
m1 = lst1.get(i).getMap();
if (m1 == null || m1.get(id) == null) return false;
}
for (var i = 0, n = lst1.size(); i < n; i++) {
m1 = lst1.get(i).getMap();
if (m1 == null) return false;
if (doCopy) m1 = JS.SV.deepCopy(m1, true, false);
var mid = m1.remove(id);
if (toArray) {
if (mid.tok == 2 && mid.intValue >= 0 && mid.intValue <= 10000) {
bsIndex.set(mid.intValue);
} else {
toArray = false;
}}var key = mid.asString();
if (map1.containsKey(key)) return false;
map1.put(key, JS.SV.newV(6, m1));
}
if (toArray) {
var pt = bsIndex.nextSetBit(0);
if ( new Boolean (pt == 0 | pt == 1).valueOf()) {
var len = bsIndex.cardinality();
if (bsIndex.nextClearBit(pt) == len + pt) {
var a =  new Array(len);
for (var e, $e = map1.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
a[Integer.parseInt(e.getKey()) - pt] = e.getValue();
}
var list =  new JU.Lst();
for (var i = 0; i < len; i++) list.addLast(a[i]);

return mp.addXList(list);
}}}return mp.addXObj(map1);
}
return false;
}var a =  new Array(args.length);
for (var i = a.length; --i >= 0; ) a[i] = JS.SV.newT(args[i]);

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

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

return mp.addXList(lst);
}return mp.addXAI(array);
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateCache", 
function(mp, args){
if (args.length > 0) return false;
return mp.addXMap(this.vwr.fm.cacheList());
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateColor", 
function(mp, args){
var colorScheme = (args.length > 0 ? JS.SV.sValue(args[0]) : "");
var isIsosurface = colorScheme.startsWith("$");
if (args.length == 2 && colorScheme.equalsIgnoreCase("TOHSL")) return mp.addXPt(JU.CU.rgbToHSL(JU.P3.newP(args[1].tok == 8 ? JS.SV.ptValue(args[1]) : JU.CU.colorPtFromString(args[1].asString())), true));
if (args.length == 2 && colorScheme.equalsIgnoreCase("TORGB")) {
var pt = JU.P3.newP(args[1].tok == 8 ? JS.SV.ptValue(args[1]) : JU.CU.colorPtFromString(args[1].asString()));
return mp.addXPt(args[1].tok == 8 ? JU.CU.hslToRGB(pt) : pt);
}if (args.length == 4 && (args[3].tok == 1073742335 || args[3].tok == 1073742334)) {
var pt1 = JU.P3.newP(args[0].tok == 8 ? JS.SV.ptValue(args[0]) : JU.CU.colorPtFromString(args[0].asString()));
var pt2 = JU.P3.newP(args[1].tok == 8 ? JS.SV.ptValue(args[1]) : JU.CU.colorPtFromString(args[1].asString()));
var usingHSL = (args[3].tok == 1073742335);
if (usingHSL) {
pt1 = JU.CU.rgbToHSL(pt1, false);
pt2 = JU.CU.rgbToHSL(pt2, false);
}var sb =  new JU.SB();
var vd = JU.V3.newVsub(pt2, pt1);
var n = args[2].asInt();
if (n < 2) n = 20;
vd.scale(1 / (n - 1));
for (var i = 0; i < n; i++) {
sb.append(JU.Escape.escapeColor(JU.CU.colorPtToFFRGB(usingHSL ? JU.CU.hslToRGB(pt1) : pt1)));
pt1.add(vd);
}
return mp.addXStr(sb.toString());
}var ce = (isIsosurface ? null : this.vwr.cm.getColorEncoder(colorScheme));
if (!isIsosurface && ce == null) return mp.addXStr("");
var lo = (args.length > 1 ? JS.SV.fValue(args[1]) : 3.4028235E38);
var hi = (args.length > 2 ? JS.SV.fValue(args[2]) : 3.4028235E38);
var value = (args.length > 3 ? JS.SV.fValue(args[3]) : 3.4028235E38);
var getValue = (value != 3.4028235E38 || lo != 3.4028235E38 && hi == 3.4028235E38);
var haveRange = (hi != 3.4028235E38);
if (!haveRange && colorScheme.length == 0) {
value = lo;
var range = this.vwr.getCurrentColorRange();
lo = range[0];
hi = range[1];
}if (isIsosurface) {
var id = colorScheme.substring(1);
var data =  Clazz.newArray(-1, [id, null]);
if (!this.vwr.shm.getShapePropertyData(24, "colorEncoder", data)) return mp.addXStr("");
ce = data[1];
} else {
ce.setRange(lo, hi, lo > hi);
}var key = ce.getColorKey();
if (getValue) return mp.addXPt(JU.CU.colorPtFromInt(ce.getArgb(hi == 3.4028235E38 ? lo : value), null));
return mp.addX(JS.SV.getVariableMap(key));
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateCompare", 
function(mp, args){
var narg = args.length;
if (narg < 2 || narg > 5) return false;
var stddev;
var isTrue = (args[narg - 1].tok == 1073742335);
if (isTrue || args[narg - 1].tok == 1073742334) narg--;
var sOpt = JS.SV.sValue(args[narg - 1]);
var isStdDev = sOpt.equalsIgnoreCase("stddev");
var isIsomer = sOpt.equalsIgnoreCase("ISOMER");
var isTautomer = isIsomer && isTrue;
var isBonds = sOpt.equalsIgnoreCase("BONDS");
var isPoints = (args[0].tok == 7 && args[1].tok == 7);
var abmap = (narg >= 3 ? args[2].getList() : null);
var isSmiles = (abmap == null && !isPoints && !isIsomer && narg > (isStdDev ? 3 : 2));
var bs1 = (args[0].tok == 10 ? args[0].value : null);
var bs2 = (args[1].tok == 10 ? args[1].value : null);
var smiles1 = (bs1 == null ? JS.SV.sValue(args[0]) : "");
var smiles2 = (bs2 == null ? JS.SV.sValue(args[1]) : "");
stddev = NaN;
try {
if (isBonds) {
if (narg != 4) return false;
smiles1 = JS.SV.sValue(args[2]);
isSmiles = smiles1.equalsIgnoreCase("SMILES");
try {
if (isSmiles) smiles1 = this.vwr.getSmiles(bs1);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
this.e.evalError(ex.getMessage(), null);
} else {
throw ex;
}
}
var data = this.e.getSmilesExt().getFlexFitList(bs1, bs2, smiles1, !isSmiles);
return (data == null ? mp.addXStr("") : mp.addXAF(data));
}if (isIsomer) {
if (narg != 3) return false;
if (bs1 == null && bs2 == null) {
var ret = this.vwr.getSmilesMatcher().getRelationship(smiles1, smiles2).toUpperCase();
return mp.addXStr(ret);
}var mf1 = (bs1 == null ? this.vwr.getSmilesMatcher().getMolecularFormula(smiles1, false, false) : JU.JmolMolecule.getMolecularFormulaAtoms(this.vwr.ms.at, bs1, null, false));
var mf2 = (bs2 == null ? this.vwr.getSmilesMatcher().getMolecularFormula(smiles2, false, false) : JU.JmolMolecule.getMolecularFormulaAtoms(this.vwr.ms.at, bs2, null, false));
if (!mf1.equals(mf2)) return mp.addXStr("NONE");
if (bs1 != null) smiles1 = this.e.getSmilesExt().getSmilesMatches("/strict///", null, bs1, null, 1, true, false);
var check;
if (bs2 == null) {
check = (this.vwr.getSmilesMatcher().areEqual(smiles2, smiles1) > 0);
} else {
smiles2 = this.e.getSmilesExt().getSmilesMatches("/strict///", null, bs2, null, 1, true, false);
check = ((this.e.getSmilesExt().getSmilesMatches("/strict///" + smiles1, null, bs2, null, 1, true, false)).nextSetBit(0) >= 0);
}if (!check) {
var s = smiles1 + smiles2;
if (s.indexOf("/") >= 0 || s.indexOf("\\") >= 0 || s.indexOf("@") >= 0) {
if (smiles1.indexOf("@") >= 0 && (bs2 != null || smiles2.indexOf("@") >= 0) && smiles1.indexOf("@SP") < 0) {
var pt = smiles1.toLowerCase().indexOf("invertstereo");
smiles1 = (pt >= 0 ? "/strict/" + smiles1.substring(0, pt) + smiles1.substring(pt + 12) : "/invertstereo strict/" + smiles1);
if (bs2 == null) {
check = (this.vwr.getSmilesMatcher().areEqual(smiles1, smiles2) > 0);
} else {
check = ((this.e.getSmilesExt().getSmilesMatches(smiles1, null, bs2, null, 1, true, false)).nextSetBit(0) >= 0);
}if (check) return mp.addXStr("ENANTIOMERS");
}if (bs2 == null) {
check = (this.vwr.getSmilesMatcher().areEqual("/nostereo/" + smiles2, smiles1) > 0);
} else {
var ret = this.e.getSmilesExt().getSmilesMatches("/nostereo/" + smiles1, null, bs2, null, 1, true, false);
check = ((ret).nextSetBit(0) >= 0);
}if (check) return mp.addXStr("DIASTEREOMERS");
}var ret = "CONSTITUTIONAL ISOMERS";
if (isTautomer) {
var inchi = this.vwr.getInchi(bs1, null, null);
if (inchi != null && inchi.equals(this.vwr.getInchi(bs2, null, null))) ret = "TAUTOMERS";
}return mp.addXStr(ret);
}if (bs1 == null || bs2 == null) return mp.addXStr("IDENTICAL");
stddev = this.e.getSmilesExt().getSmilesCorrelation(bs1, bs2, smiles1, null, null, null, null, false, null, null, false, 1);
return mp.addXStr(stddev < 0.2 ? "IDENTICAL" : "IDENTICAL or CONFORMATIONAL ISOMERS (RMSD=" + stddev + ")");
}var m =  new JU.M4();
var ptsA = null;
var ptsB = null;
if (isSmiles) {
if (bs1 == null || bs2 == null) return false;
sOpt = JS.SV.sValue(args[2]);
var isMap = sOpt.equalsIgnoreCase("MAP");
isSmiles = sOpt.equalsIgnoreCase("SMILES");
var isSearch = (isMap || sOpt.equalsIgnoreCase("SMARTS"));
if (isSmiles || isSearch) sOpt = (narg > (isStdDev ? 4 : 3) ? JS.SV.sValue(args[3]) : null);
var hMaps = (("H".equalsIgnoreCase(sOpt) || "allH".equalsIgnoreCase(sOpt) || "bestH".equalsIgnoreCase(sOpt)));
var isPolyhedron = !hMaps && ("polyhedra".equalsIgnoreCase(sOpt) || "polyhedron".equalsIgnoreCase(sOpt));
if (isPolyhedron) {
stddev = this.e.getSmilesExt().mapPolyhedra(bs1.nextSetBit(0), bs2.nextSetBit(0), isSmiles, m);
} else {
ptsA =  new JU.Lst();
ptsB =  new JU.Lst();
var allMaps = (("all".equalsIgnoreCase(sOpt) || "allH".equalsIgnoreCase(sOpt)));
var bestMap = (("best".equalsIgnoreCase(sOpt) || "bestH".equalsIgnoreCase(sOpt)));
if ("stddev".equals(sOpt)) sOpt = null;
var pattern = sOpt;
if (sOpt == null || hMaps || allMaps || bestMap) {
if (!isMap && !isSmiles || hMaps && isPolyhedron) return false;
pattern = "/noaromatic" + (allMaps || bestMap ? "/" : " nostereo/") + this.e.getSmilesExt().getSmilesMatches((hMaps ? "H" : ""), null, bs1, null, 32769, true, false);
} else {
allMaps = true;
}stddev = this.e.getSmilesExt().getSmilesCorrelation(bs1, bs2, pattern, ptsA, ptsB, m, null, isMap, null, null, bestMap, (isSmiles ? 1 : 2) | (!allMaps && !bestMap ? 8 : 0));
if (isMap) {
var nAtoms = ptsA.size();
if (nAtoms == 0) return mp.addXStr("");
var nMatch = Clazz.doubleToInt(ptsB.size() / nAtoms);
var ret =  new JU.Lst();
for (var i = 0, pt = 0; i < nMatch; i++) {
var a = JU.AU.newInt2(nAtoms);
ret.addLast(a);
for (var j = 0; j < nAtoms; j++, pt++) a[j] =  Clazz.newIntArray(-1, [(ptsA.get(j)).i, (ptsB.get(pt)).i]);

}
return (allMaps ? mp.addXList(ret) : ret.size() > 0 ? mp.addXAII(ret.get(0)) : mp.addXStr(""));
}}} else {
ptsA = this.e.getPointVector(args[0], 0);
ptsB = this.e.getPointVector(args[1], 0);
if (ptsA == null || ptsB == null) return false;
if (abmap != null) {
narg--;
var n = abmap.size();
if (n > ptsA.size() || n != ptsB.size()) return false;
var list =  new JU.Lst();
for (var i = 0; i < n; i++) list.addLast(ptsA.get(abmap.get(i).intValue - 1));

ptsA = list;
}switch (narg) {
case 2:
break;
case 3:
if (isStdDev) break;
default:
return false;
}
if (ptsA.size() == ptsB.size()) {
J.api.Interface.getInterface("JU.Eigen", this.vwr, "script");
stddev = JU.Measure.getTransformMatrix4(ptsA, ptsB, m, null);
}}return (isStdDev || Float.isNaN(stddev) ? mp.addXFloat(stddev) : mp.addXM4(m.round(1e-7)));
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
this.e.evalError(ex.getMessage() == null ? ex.toString() : ex.getMessage(), null);
return false;
} else {
throw ex;
}
}
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateConnected", 
function(mp, args, tok, intValue){
if (args.length > 5) return false;
var min = -2147483648;
var max = 2147483647;
var fmin = 0;
var fmax = 3.4028235E38;
var order = 65535;
var atoms1 = null;
var atoms2 = null;
var haveDecimal = false;
var isBonds = false;
switch (tok) {
case 1275203608:
var nv = -2147483648;
var smiles = null;
if (args.length > 0) {
switch (args[0].tok) {
case 2:
nv = args[0].intValue;
break;
case 4:
smiles = JS.SV.sValue(args[0]);
break;
}
}if (intValue == 1275203608) atoms1 = JS.SV.getBitSet(mp.getX(), true);
var data =  Clazz.newArray(-1, [Integer.$valueOf(nv), smiles, atoms1]);
if (!this.vwr.shm.getShapePropertyData(21, "getCenters", data)) data[1] = null;
return mp.addXBs(data[1] == null ?  new JU.BS() : data[1]);
case 1228931586:
var x1 = mp.getX();
if (x1.tok != 10 || args.length != 1 || args[0].tok != 10) return false;
atoms1 = x1.value;
atoms2 = args[0].value;
var list =  new JU.Lst();
var atoms = this.vwr.ms.at;
for (var i = atoms1.nextSetBit(0); i >= 0; i = atoms1.nextSetBit(i + 1)) {
var n = 0;
var b = atoms[i].bonds;
for (var j = b.length; --j >= 0; ) if (atoms2.get(b[j].getOtherAtom(atoms[i]).i)) n++;

list.addLast(Integer.$valueOf(n));
}
return mp.addXList(list);
}
for (var i = 0; i < args.length; i++) {
var $var = args[i];
switch ($var.tok) {
case 10:
isBonds = (Clazz.instanceOf($var.value,"JM.BondSet"));
if (isBonds && atoms1 != null) return false;
if (atoms1 == null) atoms1 = $var.value;
 else if (atoms2 == null) atoms2 = $var.value;
 else return false;
break;
case 4:
var type = JS.SV.sValue($var);
if (type.equalsIgnoreCase("hbond")) order = 30720;
 else order = JU.Edge.getBondOrderFromString(type);
if (order == 131071) return false;
break;
case 3:
haveDecimal = true;
default:
var n = $var.asInt();
var f = $var.asFloat();
if (max != 2147483647) return false;
if (min == -2147483648) {
min = Math.max(n, 0);
fmin = f;
} else {
max = n;
fmax = f;
}}
}
if (min == -2147483648) {
min = 1;
max = 100;
fmin = 0.1;
fmax = 1.0E8;
} else if (max == 2147483647) {
max = min;
fmax = fmin;
fmin = 0.1;
}if (atoms1 == null) atoms1 = this.vwr.getAllAtoms();
if (haveDecimal && atoms2 == null) atoms2 = atoms1;
if (atoms2 != null) {
var bsBonds =  new JU.BS();
this.vwr.makeConnections(fmin, fmax, order, 1086324745, atoms1, atoms2, bsBonds, isBonds, false, 0);
return mp.addX(JS.SV.newV(10, JM.BondSet.newBS(bsBonds)));
}return mp.addXBs(this.vwr.ms.getAtomsConnected(min, max, order, atoms1));
}, "JS.ScriptMathProcessor,~A,~N,~N");
Clazz.defineMethod(c$, "evaluateContact", 
function(mp, args){
if (args.length < 1 || args.length > 3) return false;
var i = 0;
var distance = 100;
var tok = args[0].tok;
switch (tok) {
case 3:
case 2:
distance = JS.SV.fValue(args[i++]);
break;
case 10:
break;
default:
return false;
}
if (i == args.length || !(Clazz.instanceOf(args[i].value,"JU.BS"))) return false;
var bsA = JU.BSUtil.copy(args[i++].value);
var bsB = (i < args.length ? JU.BSUtil.copy(args[i].value) : null);
var rd =  new J.atomdata.RadiusData(null, (distance > 10 ? distance / 100 : distance), (distance > 10 ? J.atomdata.RadiusData.EnumType.FACTOR : J.atomdata.RadiusData.EnumType.OFFSET), J.c.VDW.AUTO);
bsB = this.setContactBitSets(bsA, bsB, true, NaN, rd, false);
bsB.or(bsA);
return mp.addXBs(bsB);
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateData", 
function(mp, args){
var selected = (args.length == 0 ? "" : JS.SV.sValue(args[0]));
switch (args.length) {
case 0:
case 1:
break;
case 2:
case 3:
if (args[0].tok == 10) return mp.addXStr(this.vwr.getModelFileData(selected, JS.SV.sValue(args[1]), args.length == 3 && JS.SV.bValue(args[2])));
break;
case 4:
var iField = args[1].asInt();
var nBytes = args[2].asInt();
var firstLine = args[3].asInt();
var f = JU.Parser.parseFloatArrayFromMatchAndField(JS.SV.sValue(args[0]), null, 0, 0, null, iField, nBytes, null, firstLine);
return mp.addXStr(JU.Escape.escapeFloatA(f, false));
default:
return false;
}
if (selected.indexOf("data2d_") == 0) {
var f1 = this.vwr.getDataObj(selected, null, 2);
if (f1 == null) return mp.addXStr("");
if (args.length == 2 && args[1].tok == 2) {
var pt = args[1].intValue;
if (pt < 0) pt += f1.length;
if (pt >= 0 && pt < f1.length) return mp.addXStr(JU.Escape.escapeFloatA(f1[pt], false));
return mp.addXStr("");
}return mp.addXStr(JU.Escape.escapeFloatAA(f1, false));
}if (selected.endsWith("*")) return mp.addXList(this.vwr.getDataObj(selected, null, 0));
if (selected.indexOf("property_") == 0) {
var f1 = this.vwr.getDataObj(selected, null, 1);
return (f1 == null ? mp.addXStr("") : mp.addXStr(JU.Escape.escapeFloatA(f1, false)));
}var data = this.vwr.getDataObj(selected, null, -1);
return mp.addXStr(data == null || data.length < 2 ? "" : "" + data[1]);
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateDotDist", 
function(mp, args, tok, op){
var isDist = (tok == 1275069443);
var x1;
var x2;
var x3 = null;
switch (args.length) {
case 2:
if (op == 2147483647) {
x1 = args[0];
x2 = args[1];
break;
}x3 = args[1];
case 1:
x1 = mp.getX();
x2 = args[0];
break;
case 0:
if (isDist) {
x1 = mp.getX();
x2 = JS.SV.getVariable( new JU.P3());
break;
}default:
return false;
}
var f = NaN;
try {
if (tok == 1275069442) {
var a = JU.P3.newP(mp.ptValue(x1, null));
a.cross(a, mp.ptValue(x2, null));
return mp.addXPt(a);
}var pt2 = (x2.tok == 7 ? null : mp.ptValue(x2, null));
var plane2 = this.e.planeValue(x2);
if (isDist) {
var minMax = (op == -2147483648 ? 0 : op & 480);
var isMinMax = (minMax == 32 || minMax == 64);
var isAll = minMax == 480;
switch (x1.tok) {
case 7:
case 10:
var isAtomSet1 = (x1.tok == 10);
var isAtomSet2 = (x2.tok == 10);
var isPoint2 = (x2.tok == 8);
var bs1 = (isAtomSet1 ? x1.value : null);
var bs2 = (isAtomSet2 ? x2.value : null);
var list1 = (isAtomSet1 ? null : x1.getList());
var list2 = (isAtomSet2 ? null : x2.getList());
var returnAtom = (isMinMax && x3 != null && x3.asBoolean());
switch (x2.tok) {
case 10:
case 7:
case 8:
var atoms = this.vwr.ms.at;
if (returnAtom) {
var dMinMax = NaN;
var iMinMax = 2147483647;
if (isAtomSet1) {
for (var i = bs1.nextSetBit(0); i >= 0; i = bs1.nextSetBit(i + 1)) {
var d = (isPoint2 ? atoms[i].distanceSquared(pt2) : (this.e.getBitsetProperty(bs2, list2, op, atoms[i], plane2, x1.value, null, false, x1.index, false)).floatValue());
if (minMax == 32 ? d >= dMinMax : d <= dMinMax) continue;
dMinMax = d;
iMinMax = i;
}
return mp.addXBs(iMinMax == 2147483647 ?  new JU.BS() : JU.BSUtil.newAndSetBit(iMinMax));
}for (var i = list1.size(); --i >= 0; ) {
var pt = JS.SV.ptValue(list1.get(i));
var d = (isPoint2 ? pt.distanceSquared(pt2) : (this.e.getBitsetProperty(bs2, list2, op, pt, plane2, x1.value, null, false, 2147483647, false)).floatValue());
if (minMax == 32 ? d >= dMinMax : d <= dMinMax) continue;
dMinMax = d;
iMinMax = i;
}
return mp.addXInt(iMinMax);
}if (isAll) {
if (bs2 == null) {
var data =  Clazz.newFloatArray (bs1.cardinality(), 0);
for (var p = 0, i = bs1.nextSetBit(0); i >= 0; i = bs1.nextSetBit(i + 1), p++) data[p] = atoms[i].distance(pt2);

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


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

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

return mp.addXAF(data);
}return mp.addXObj(this.e.getBitsetProperty(bs1, list1, op, pt2, plane2, x1.value, null, false, x1.index, false));
}
}
}var pt1 = mp.ptValue(x1, null);
var plane1 = this.e.planeValue(x1);
if (isDist) {
if (plane2 != null && x3 != null) f = JU.Measure.directedDistanceToPlane(pt1, plane2, JS.SV.ptValue(x3));
 else f = (plane1 == null ? (plane2 == null ? pt2.distance(pt1) : JU.Measure.distanceToPlane(plane2, pt1)) : JU.Measure.distanceToPlane(plane1, pt2));
} else {
if (plane1 != null && plane2 != null) {
f = plane1.x * plane2.x + plane1.y * plane2.y + plane1.z * plane2.z + plane1.w * plane2.w;
} else {
if (plane1 != null) pt1 = JU.P3.new3(plane1.x, plane1.y, plane1.z);
 else if (plane2 != null) pt2 = JU.P3.new3(plane2.x, plane2.y, plane2.z);
f = pt1.dot(pt2);
}}} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return mp.addXFloat(f);
}, "JS.ScriptMathProcessor,~A,~N,~N");
Clazz.defineMethod(c$, "evaluateHelix", 
function(mp, args){
if (args.length < 1 || args.length > 5) return false;
var pt = (args.length > 2 ? 3 : 1);
var type = (pt >= args.length ? "array" : JS.SV.sValue(args[pt]));
var tok = JS.T.getTokFromName(type);
if (args.length > 2) {
var pta = mp.ptValue(args[0], null);
var ptb = mp.ptValue(args[1], null);
if (tok == 0 || args[2].tok != 9 || pta == null || ptb == null) return false;
var dq = JU.Quat.newP4(args[2].value);
var data = JU.Measure.computeHelicalAxis(pta, ptb, dq);
return (data == null ? false : mp.addXObj(JU.Escape.escapeHelical(type, tok, pta, ptb, data)));
}var bs = (Clazz.instanceOf(args[0].value,"JU.BS") ? args[0].value : this.vwr.ms.getAtoms(1094715412, Integer.$valueOf(args[0].asInt())));
switch (tok) {
case 134217751:
case 1073741854:
case 1665140738:
return mp.addXObj(this.getHelixData(bs, tok));
case 134217729:
return mp.addXFloat((this.getHelixData(bs, 134217729)).floatValue());
case 135176:
case 1745489939:
return mp.addXObj(this.getHelixData(bs, tok));
case 1275068418:
var data = this.getHelixData(bs, 1073742001);
if (data == null) return false;
return mp.addXAS(data);
}
return false;
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "getHelixData", 
function(bs, tokType){
var iAtom = bs.nextSetBit(0);
return (iAtom < 0 ? "null" : this.vwr.ms.at[iAtom].group.getHelixData(tokType, this.vwr.getQuaternionFrame(), this.vwr.getInt(553648142)));
}, "JU.BS,~N");
Clazz.defineMethod(c$, "evaluateInChI", 
function(mp, args){
var x1 = mp.getX();
var flags = (args.length > 0 ? JS.SV.sValue(args[0]) : "fixedh?");
if (flags.toLowerCase().equals("standard")) flags = "";
var atoms = JS.SV.getBitSet(x1, true);
var molData = (atoms == null ? JS.SV.sValue(x1) : null);
var ret = this.vwr.getInchi(atoms, molData, flags);
return (flags.indexOf("model") >= 0 ? mp.addXMap(this.vwr.parseJSONMap(ret)) : mp.addXStr(ret));
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateFind", 
function(mp, args){
var x1 = mp.getX();
var isList = (x1.tok == 7);
var isAtoms = (x1.tok == 10);
var isEmpty = (args.length == 0);
var tok0 = (args.length == 0 ? 0 : args[0].tok);
var sFind = (isEmpty || tok0 != 4 ? "" : JS.SV.sValue(args[0]));
var isOff = (args.length > 1 && args[1].tok == 1073742334);
var tokLast = (tok0 == 0 ? 0 : args[args.length - 1].tok);
var argLast = (tokLast == 0 ? JS.SV.vF : args[args.length - 1]);
var isON = !isList && (tokLast == 1073742335);
var asIndex = (isList && argLast.tok == 4 && "index".equalsIgnoreCase(JS.SV.sValue(argLast)));
var flags = (args.length > 1 && args[1].tok != 1073742335 && args[1].tok != 1073742334 && args[1].tok != 10 ? JS.SV.sValue(args[1]) : "");
var isSequence = !isList && !isOff && sFind.equalsIgnoreCase("SEQUENCE");
var isSeq = !isList && !isOff && sFind.equalsIgnoreCase("SEQ");
if (sFind.toUpperCase().startsWith("SMILES/")) {
if (!sFind.endsWith("/")) sFind += "/";
var s = sFind.substring(6) + "//";
if (JV.JC.isSmilesCanonical(s)) {
flags = "SMILES";
sFind = "CHEMICAL";
} else {
sFind = "SMILES";
flags = s + flags;
}} else if (sFind.toUpperCase().startsWith("SMARTS/")) {
if (!sFind.endsWith("/")) sFind += "/";
flags = sFind.substring(6) + (flags.length == 0 ? "//" : flags);
sFind = "SMARTS";
}var smiles = null;
var isStr = false;
var isPatternObj = (args.length > 0 && args[0].tok == 134218753);
if (!isPatternObj && x1.tok == 4) {
switch (args.length) {
case 1:
if ((x1.value).startsWith("InChI=")) {
if (sFind.equalsIgnoreCase("SMILES")) {
return mp.addXStr(this.vwr.getInchi(null, x1.value, "SMILES" + flags));
}}isStr = !sFind.equalsIgnoreCase("SMILES");
break;
case 2:
case 3:
if (isOff || isON) {
isStr = true;
} else if ((x1.value).startsWith("InChI=")) {
if (sFind.equalsIgnoreCase("SMARTS")) {
smiles = this.vwr.getInchi(null, x1.value, "SMILES");
} else {
isStr = true;
}} else if (flags.length <= 3) {
if (flags.$replace('m', ' ').$replace('i', ' ').$replace('v', ' ').trim().length == 0) isStr = true;
}break;
}
}var isSmiles = !isStr && sFind.equalsIgnoreCase("SMILES");
var isSMARTS = isPatternObj || !isStr && sFind.equalsIgnoreCase("SMARTS");
var isChemical = !isList && !isStr && sFind.equalsIgnoreCase("CHEMICAL");
var isMF = !isList && !isStr && sFind.equalsIgnoreCase("MF");
var isCF = !isList && !isStr && sFind.equalsIgnoreCase("CELLFORMULA");
var isInchi = isAtoms && !isList && sFind.equalsIgnoreCase("INCHI");
var isInchiKey = isAtoms && !isList && sFind.equalsIgnoreCase("INCHIKEY");
var isStructureMap = (!isSmiles && !isSMARTS && tok0 == 10 && flags.toLowerCase().indexOf("map") >= 0);
var isEquivalent = !isSmiles && !isSMARTS && ((x1.tok == 10 || x1.tok == 8 || x1.tok == 7) && sFind.toLowerCase().startsWith("equivalent"));
try {
if (isEquivalent) {
switch (x1.tok) {
case 10:
return mp.addXBs(this.vwr.ms.getSymmetryEquivAtoms(x1.value, null, null));
case 8:
return mp.addXList(this.vwr.getSymmetryEquivPoints(JU.Point3fi.newPF(x1.value, 0), sFind + flags));
case 7:
var lst =  new JU.Lst();
var l0 = x1.getList();
for (var i = 0, n = l0.size(); i < n; i++) {
var p = JS.SV.ptValue(l0.get(i));
if (p == null) return false;
lst.addLast(JU.Point3fi.newPF(p, 0));
}
return mp.addXList(this.vwr.getSymmetryEquivPointList(lst, sFind + flags));
}
} else if (isInchi || isInchiKey) {
if (isInchiKey) flags += " key";
return mp.addXStr(this.vwr.getInchi(JS.SV.getBitSet(x1, true), null, flags));
}if (isChemical) {
var bsAtoms = (isAtoms ? x1.value : null);
var data = (bsAtoms == null ? JS.SV.sValue(x1) : this.vwr.getOpenSmiles(bsAtoms));
data = (data.length == 0 ? "" : this.vwr.getChemicalInfo(data, flags.toLowerCase(), bsAtoms)).trim();
if (data.startsWith("InChI")) data = JU.PT.rep(JU.PT.rep(data, "InChI=", ""), "InChIKey=", "");
return mp.addXStr(data);
}if (isSmiles || isSMARTS || isAtoms) {
var iPt = (isStructureMap ? 0 : isSmiles || isSMARTS ? 2 : 1);
var bs2 = (iPt < args.length && args[iPt].tok == 10 ? args[iPt++].value : null);
var asBonds = (argLast.tok == 4 && "bonds".equalsIgnoreCase(JS.SV.sValue(argLast)));
var isAll = (asBonds || isON);
var isSmilesObj = false;
var ret = null;
switch (x1.tok) {
case 134218753:
isSmilesObj = true;
case 7:
case 4:
if (smiles == null && !isList) {
smiles = x1.value;
}if ((isSmiles || isSMARTS) && args.length == 1 && flags == null) {
return false;
}if (bs2 != null) return false;
if (flags.equalsIgnoreCase("mf")) {
ret = this.vwr.getSmilesMatcher().getMolecularFormula(smiles.toString(), isSMARTS, isON);
} else {
var pattern = (isPatternObj ? args[0].value : flags);
var allMappings = true;
var asMap = false;
if (isPatternObj) {
switch (args.length) {
case 3:
allMappings = JS.SV.bValue(args[2]);
case 2:
asMap = JS.SV.bValue(args[1]);
break;
}
} else {
switch (args.length) {
case 4:
allMappings = JS.SV.bValue(args[3]);
case 3:
asMap = JS.SV.bValue(args[2]);
break;
}
}var isChirality = (!isPatternObj && pattern.equals("chirality"));
var justOne = (!asMap && (!allMappings || !isSMARTS && !isChirality));
try {
if (isList) {
var list = x1.getList();
var o =  new Array(list.size());
for (var i = o.length; --i >= 0; ) {
o[i] = list.get(i).value;
}
smiles = o;
}ret = this.e.getSmilesExt().getSmilesMatches(pattern, smiles, null, null, isSMARTS ? 2 : 1, !asMap, !allMappings);
if (isList) return mp.addXObj(ret);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
System.out.println(ex.getMessage());
return mp.addXInt(-1);
} else {
throw ex;
}
}
var len = (isChirality ? 1 : JU.AU.isAI(ret) ? (ret).length : (ret).length);
if (len == 0 && this.vwr.getSmilesMatcher().getLastException() !== "MF_FAILED" && (isSmilesObj || (smiles).toLowerCase().indexOf("noaromatic") < 0 && (smiles).toLowerCase().indexOf("strict") < 0)) {
ret = this.e.getSmilesExt().getSmilesMatches(pattern, smiles, null, null, 16 | (isSMARTS ? 2 : 1), !asMap, !allMappings);
}if (justOne) {
return mp.addXInt(!allMappings && len > 0 ? 1 : len);
}}break;
case 10:
var bs = x1.value;
if (sFind.equalsIgnoreCase("spacegroup")) {
var o = this.vwr.findSpaceGroup(null, bs, null, null, null, null, ("parent".equals(flags.toLowerCase()) ? 8 : 0));
if (o != null) {
var s = o.toString();
o = JU.PT.rep(s.substring(s.indexOf(" ") + 1), " #", "\t");
}return mp.addXStr(o.toString());
}if (sFind.equalsIgnoreCase("crystalClass")) {
var n = bs.nextSetBit(0);
var bsNew = null;
if (args.length != 2) {
bsNew =  new JU.BS();
bsNew.set(n);
}return mp.addXList(this.vwr.ms.generateCrystalClass(n, (bsNew != null ? this.vwr.ms.getAtomSetCenter(bsNew) : argLast.tok == 10 ? this.vwr.ms.getAtomSetCenter(argLast.value) : JS.SV.ptValue(argLast))));
}if (isMF && flags.length != 0) {
return mp.addXBs(JU.JmolMolecule.getBitSetForMF(this.vwr.ms.at, bs, flags));
}if (isMF || isCF) {
var isEmpirical = isON;
return mp.addXStr(this.vwr.getFormulaForAtoms(bs, (isMF ? "MF" : "CELLFORMULA"), isEmpirical));
}if (isSequence || isSeq) {
var isHH = (argLast.asString().equalsIgnoreCase("H"));
isAll = new Boolean (isAll | isHH).valueOf();
return mp.addXStr(this.vwr.getSmilesOpt(bs, -1, -1, (isAll ? 3145728 | 5242880 | (isHH ? 9437184 : 0) : 0) | (isSeq ? 34603008 : 1048576), null));
}if (isStructureMap) {
var map = null;
var map1 = null;
var map2 = null;
var mapNames = null;
var key = (args.length == 3 ? JS.SV.sValue(argLast) : null);
var itype = (key == null || key.equals("%i") || key.equals("number") ? 'i' : key.equals("%a") || key.equals("name") ? 'a' : key.equals("%D") || key.equals("index") ? 'D' : '?');
if (key == null) key = "number";
var err = null;
flags = flags.$replace("map", "").trim();
sFind = this.vwr.getSmilesOpt(bs, 0, 0, 0, flags);
if (bs.cardinality() != bs2.cardinality()) {
err = "atom sets are not the same size";
} else {
try {
var iflags = (137);
if (flags.length > 0) sFind = "/" + flags + "/" + sFind;
map1 = this.vwr.getSmilesMatcher().getCorrelationMaps(sFind, this.vwr.ms.at, this.vwr.ms.ac, bs, iflags)[0];
var m2 = this.vwr.getSmilesMatcher().getCorrelationMaps(sFind, this.vwr.ms.at, this.vwr.ms.ac, bs2, iflags);
if (m2.length > 0) {
map =  Clazz.newIntArray (bs.length(), 0);
for (var i = map.length; --i >= 0; ) map[i] = -1;

map2 = m2[0];
for (var i = map1.length; --i >= 0; ) map[map1[i]] = map2[i];

mapNames =  Clazz.newArray(map1.length, 2, null);
var bsAll = JU.BS.copy(bs);
bsAll.or(bs2);
var names = (itype == '?' ?  new Array(bsAll.length()) : null);
if (names != null) names = this.e.getCmdExt().getBitsetIdentFull(bsAll, key, false, 2147483647, false, names);
var at = this.vwr.ms.at;
for (var pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
var j = map[i];
if (j == -1) continue;
var a;
switch ((itype).charCodeAt(0)) {
case 97:
a =  Clazz.newArray(-1, [at[i].getAtomName(), at[j].getAtomName()]);
break;
case 105:
a =  Clazz.newArray(-1, [Integer.$valueOf(at[i].getAtomNumber()), Integer.$valueOf(at[j].getAtomNumber())]);
break;
case 68:
a =  Clazz.newArray(-1, [Integer.$valueOf(i), Integer.$valueOf(j)]);
break;
default:
a =  Clazz.newArray(-1, [names[i], names[j]]);
break;
}
mapNames[pt++] = a;
}
}} catch (ee) {
if (Clazz.exceptionOf(ee, Exception)){
err = ee.getMessage();
} else {
throw ee;
}
}
}var m =  new java.util.Hashtable();
m.put("BS1", bs);
m.put("BS2", bs2);
m.put("SMILES", sFind);
if (err == null) {
m.put("SMILEStoBS1", map1);
m.put("SMILEStoBS2", map2);
m.put("BS1toBS2", map);
m.put("MAP1to2", mapNames);
m.put("key", key);
} else {
m.put("error", err);
}return mp.addXMap(m);
}if (isSmiles || isSMARTS) {
sFind = (args.length > 1 && args[1].tok == 10 ? this.vwr.getSmilesOpt(args[1].value, 0, 0, 0, flags) : flags);
}flags = flags.toUpperCase();
var bsMatch3D = bs2;
if (flags.indexOf("INCHI") >= 0) {
return mp.addXStr(this.vwr.getInchi(bs, null, "SMILES/" + flags));
}if (flags.equals("MF")) {
smiles = this.e.getSmilesExt().getSmilesMatches("", null, bs, bsMatch3D, 1, true, false);
ret = this.vwr.getSmilesMatcher().getMolecularFormula(smiles.toString(), false, isON);
} else if (asBonds) {
var map = this.vwr.getSmilesMatcher().getCorrelationMaps(sFind, this.vwr.ms.at, this.vwr.ms.ac, bs, (isSmiles ? 1 : 2) | 8);
ret = (map.length > 0 ? this.vwr.ms.getDihedralMap(map[0]) :  Clazz.newIntArray (0, 0));
} else if (flags.equals("MAP")) {
var map = this.vwr.getSmilesMatcher().getCorrelationMaps(sFind, this.vwr.ms.at, this.vwr.ms.ac, bs, (isSmiles ? 1 : 2) | 128 | 16);
ret = map;
} else {
var smilesFlags = (isSmiles ? (flags.indexOf("OPEN") >= 0 ? 5 : 1) : 2) | (isON && sFind.length == 0 ? 22020096 : 0);
if (isSmiles && flags.indexOf("/ALL/") >= 0) {
smilesFlags |= 32768;
}if (flags.indexOf("/MOLECULE/") >= 0) {
var mols = this.vwr.ms.getMolecules();
var molList =  new JU.Lst();
for (var i = 0; i < mols.length; i++) {
if (mols[i].atomList.intersects(bs)) {
var bsRet = this.e.getSmilesExt().getSmilesMatches(sFind, null, mols[i].atomList, bsMatch3D, smilesFlags, !isON, false);
if (!bsRet.isEmpty()) molList.addLast(bsRet);
}}
ret = molList;
} else {
ret = this.e.getSmilesExt().getSmilesMatches(sFind, null, bs, bsMatch3D, smilesFlags, !isON, false);
}}break;
}
if (ret == null) this.e.invArg();
return mp.addXObj(ret);
}} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
this.e.evalError(ex.getMessage(), null);
} else {
throw ex;
}
}
var bs =  new JU.BS();
var svlist = (isList ? x1.getList() : null);
if (isList && tok0 != 4 && tok0 != 0) {
var v = args[0];
for (var i = 0, n = svlist.size(); i < n; i++) {
if (JS.SV.areEqual(svlist.get(i), v)) bs.set(i);
}
var ret =  Clazz.newIntArray (bs.cardinality(), 0);
for (var pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) ret[pt++] = i + 1;

return mp.addXAI(ret);
}var isReverse = (flags.indexOf("v") >= 0);
var isCaseInsensitive = (flags.indexOf("i") >= 0) || isOff;
var asMatch = (flags.indexOf("m") >= 0);
var checkEmpty = (sFind.length == 0);
var isPattern = (!checkEmpty && !isEquivalent && args.length == (asIndex ? 3 : 2));
if (isList || isPattern) {
var pm = (isPattern ? this.getPatternMatcher() : null);
var pattern = null;
if (isPattern) {
try {
pattern = pm.compile(sFind, isCaseInsensitive);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
this.e.evalError(ex.toString(), null);
} else {
throw ex;
}
}
}var list = (checkEmpty ? null : JS.SV.strListValue(x1));
var nlist = (checkEmpty ? svlist.size() : list.length);
if (JU.Logger.debugging) JU.Logger.debug("finding " + sFind);
var n = 0;
var matcher = null;
var v = (asMatch ?  new JU.Lst() : null);
var what = "";
for (var i = 0; i < nlist; i++) {
var isMatch;
if (checkEmpty) {
var o = svlist.get(i);
switch (o.tok) {
case 6:
isMatch = (o.getMap().isEmpty() != isEmpty);
break;
case 7:
isMatch = ((o.getList().size() == 0) != isEmpty);
break;
case 4:
isMatch = ((o.asString().length == 0) != isEmpty);
break;
default:
isMatch = true;
}
} else if (isPattern) {
what = list[i];
matcher = pattern.matcher(what);
isMatch = matcher.find();
} else {
isMatch = (JS.SV.sValue(svlist.get(i)).indexOf(sFind) >= 0);
}if (asMatch && isMatch || !asMatch && isMatch == !isReverse) {
n++;
bs.set(i);
if (asMatch) v.addLast(isReverse ? what.substring(0, matcher.start()) + what.substring(matcher.end()) : matcher.group());
}}
if (!isList) {
return (asMatch ? mp.addXStr(v.size() == 1 ? v.get(0) : "") : isReverse ? mp.addXBool(n == 1) : asMatch ? mp.addXStr(n == 0 ? "" : matcher.group()) : mp.addXInt(n == 0 ? 0 : matcher.start() + 1));
}if (asIndex) {
var lst =  new JU.Lst();
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
lst.addLast(JS.SV.newI(i + 1));
}
return mp.addXList(lst);
}if (asMatch) {
var listNew =  new Array(n);
if (n > 0) for (var i = list.length; --i >= 0; ) if (bs.get(i)) {
--n;
listNew[n] = (asMatch ? v.get(n) : list[i]);
}
return mp.addXAS(listNew);
}var l =  new JU.Lst();
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) l.addLast(svlist.get(i));

return mp.addXList(l);
}if (isSequence) {
return mp.addXStr(this.vwr.getJBR().toStdAmino3(JS.SV.sValue(x1)));
}return mp.addXInt(JS.SV.sValue(x1).indexOf(sFind) + 1);
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateGetProperty", 
function(mp, args, tok0, isAtomProperty){
var nargs = args.length;
var isSelect = (isAtomProperty && tok0 == 1275082241);
var isPivot = (isAtomProperty && tok0 == 1275068725);
var isAuxiliary = (tok0 == 1275068446);
var pt = 0;
var tok = (nargs == 0 ? 0 : args[0].tok);
if (nargs == 2 && (tok == 7 || tok == 6 || tok == 14)) {
return mp.addXObj(this.vwr.extractProperty(args[0].value, args[1].value.toString(), -1));
}var bsSelect = (isAtomProperty && nargs == 1 && args[0].tok == 10 ? args[0].value : null);
var pname = (bsSelect == null && nargs > 0 ? JS.SV.sValue(args[pt++]) : "");
var propertyName = pname;
var lc = propertyName.toLowerCase();
if (!isSelect && lc.indexOf("[select ") < 0) propertyName = lc;
var isJSON = false;
if (propertyName.equals("json") && nargs > pt) {
isJSON = true;
propertyName = JS.SV.sValue(args[pt++]);
}var x = null;
if (isAtomProperty) {
x = mp.getX();
switch (x.tok) {
case 10:
break;
case 4:
var name = x.value;
var data =  new Array(3);
var shapeID;
if (name.startsWith("$")) {
name = name.substring(1);
shapeID = this.vwr.shm.getShapeIdFromObjectName(name);
if (shapeID >= 0) {
data[0] = name;
this.vwr.shm.getShapePropertyData(shapeID, "index", data);
if (data[1] != null && !pname.equals("index")) {
var index = (data[1]).intValue();
data[1] = this.vwr.shm.getShapePropertyIndex(shapeID, pname.intern(), index);
}}} else {
shapeID = JV.JC.shapeTokenIndex(JS.T.getTokFromName(name));
if (shapeID >= 0) {
data[0] = pname;
data[1] = Integer.$valueOf(-1);
this.vwr.shm.getShapePropertyData(shapeID, pname.intern(), data);
}}return (data[1] == null ? mp.addXStr("") : mp.addXObj(data[1]));
case 7:
if (isPivot) {
var lstx = x.getList();
if (nargs == 0) return mp.addXObj(this.getMinMax(lstx, 1275068725, true));
var map =  new java.util.Hashtable();
var sep = (nargs > 1 ? JS.SV.sValue(args[nargs - 1]) : null);
if (sep != null) nargs--;
var keys =  new Array(nargs);
for (var i = 0; i < nargs; i++) keys[i] = JS.SV.sValue(args[i]);

for (var i = 0, n = lstx.size(); i < n; i++) {
var sv = lstx.get(i);
if (sv.tok != 6) continue;
var mapi = sv.getMap();
var key = "";
for (var j = 0; j < nargs; j++) {
var obj = mapi.get(keys[j]);
key += (j == 0 ? "" : sep) + JS.SV.sValue(obj);
}
var vlist = map.get(key);
if (vlist == null) map.put(key, vlist = JS.SV.newV(7,  new JU.Lst()));
vlist.getList().addLast(sv);
}
return mp.addXMap(map);
}if (bsSelect != null) {
var l0 = x.getList();
var lst =  new JU.Lst();
for (var i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect.nextSetBit(i + 1)) lst.addLast(l0.get(i));

return mp.addXList(lst);
}default:
if (tok0 == 1275068725 && x.tok == 6) {
var map =  new java.util.Hashtable();
var map0 = x.getMap();
for (var e, $e = map0.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var key = e.getKey();
var s = e.getValue().asString();
var l = map.get(s);
if (l == null) map.put(s, l =  new JU.Lst());
l.addLast(key);
}
if ("count".equals(lc)) {
for (var e, $e = map.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
e.setValue(Integer.$valueOf((e.getValue()).size()));
}
}return mp.addXMap(map);
}if (isSelect) propertyName = "[SELECT " + propertyName + "]";
return mp.addXObj(this.vwr.extractProperty(x, propertyName, -1));
}
if (!lc.startsWith("bondinfo") && !lc.startsWith("atominfo") && !lc.startsWith("modelkitinfo")) propertyName = "atomInfo." + propertyName;
}var propertyValue = "";
if (propertyName.equalsIgnoreCase("fileContents") && nargs >= 2) {
var s = JS.SV.sValue(args[1]);
for (var i = 2; i < nargs; i++) s += "|" + JS.SV.sValue(args[i]);

propertyValue = s;
pt = nargs;
} else if (nargs > pt) {
switch (args[pt].tok) {
case 10:
propertyValue = args[pt++].value;
if (propertyName.equalsIgnoreCase("bondInfo") && nargs > pt && args[pt].tok == 10) propertyValue =  Clazz.newArray(-1, [propertyValue, args[pt].value]);
break;
case 6:
case 4:
if (this.vwr.checkPropertyParameter(propertyName)) propertyValue = args[pt++].value;
break;
}
}if (isAtomProperty) {
var bs = x.value;
var iAtom = bs.nextSetBit(0);
if (iAtom < 0) return mp.addXStr("");
propertyValue = bs;
}if (isAuxiliary && !isAtomProperty) propertyName = "auxiliaryInfo.models." + propertyName;
propertyName = JU.PT.rep(propertyName, ".[", "[");
var property = this.vwr.getProperty(null, propertyName, propertyValue);
if (pt < nargs) property = this.vwr.extractProperty(property, args, pt);
return mp.addXObj(isJSON ? JS.SV.safeJSON("value", property) : JS.SV.isVariableType(property) ? property : JU.Escape.toReadable(propertyName, property));
}, "JS.ScriptMathProcessor,~A,~N,~B");
Clazz.defineMethod(c$, "evaluateFormat", 
function(mp, intValue, args, isLabel){
if (isLabel && args.length > 1) return false;
var x1 = (args.length < 2 || intValue == 1287653388 ? mp.getX() : null);
var format;
var pt = -1;
var x = null;
switch (args.length) {
case 0:
format = "%U";
break;
case 1:
if (x1 == null) return false;
switch (args[0].tok) {
case 7:
format = null;
break;
case 4:
format = args[0].value;
pt = JS.SV.getFormatType(format);
if (pt >= 0) x = x1;
break;
default:
return false;
}
break;
case 2:
if (args[0].tok != 4 || args[1].tok == 4 && JS.SV.getFormatType(args[1].value) >= 0) {
x = args[0];
format = JS.SV.sValue(args[1]);
} else {
format = args[0].value;
x = args[1];
}pt = JS.SV.getFormatType(format);
break;
default:
format = args[0].value;
pt = JS.SV.getFormatType(format);
if (pt >= 0) return false;
break;
}
switch (pt) {
case -1:
break;
case 35:
case 39:
case 43:
case 47:
return ((x.tok == 12 || x.tok == 11) && mp.addXStr(this.matToString(x.value, pt)));
case 28:
case 0:
return mp.addXStr(JS.SV.getFormat(x, pt));
default:
return mp.addXObj(JS.SV.getFormat(x, pt));
}
var bs = (x1 != null && x1.tok == 10 ? x1.value : null);
if (!isLabel && x1 != null && bs == null && args.length > 0 && format != null) {
if (args.length == 2) {
var listIn = x1.getList();
var formatList = x.getList();
if (listIn == null || formatList == null) return false;
x1 = JS.SV.getVariableList(this.getSublist(listIn, formatList));
}args =  Clazz.newArray(-1, [args[0], x1]);
x1 = null;
}if (x1 == null) {
if (format == null || pt >= 0 && pt != 28 && args.length != 2) return false;
if (pt >= 0 || args.length < 2 || args[1].tok != 7) {
var o = JS.SV.format(args, pt);
return ((typeof(o)=='string') ? mp.addXStr(o) : mp.addXObj(o));
}var a = args[1].getList();
var args2 =  Clazz.newArray(-1, [args[0], null]);
var sa =  new Array(a.size());
for (var i = sa.length; --i >= 0; ) {
args2[1] = a.get(i);
sa[i] = JS.SV.format(args2, pt).toString();
}
return mp.addXAS(sa);
}if (x1.tok == 7 && format == null) {
var listIn = x1.getList();
var formatList = args[0].getList();
var listOut = this.getSublist(listIn, formatList);
return mp.addXList(listOut);
}var ret = null;
if (format == null) {
ret = "";
} else if (bs == null) {
ret = JS.SV.sprintf(JU.PT.formatCheck(format), x1);
} else {
ret = this.e.getCmdExt().getBitsetIdent(bs, format, x1.value, true, x1.index, false);
}return mp.addXObj(ret);
}, "JS.ScriptMathProcessor,~N,~A,~B");
Clazz.defineMethod(c$, "getSublist", 
function(listIn, formatList){
var listOut =  new JU.Lst();
var map;
var v;
var list;
for (var i = 0, n = listIn.size(); i < n; i++) {
var element = listIn.get(i);
switch (element.tok) {
case 6:
map = element.getMap();
list =  new JU.Lst();
for (var j = 0, n1 = formatList.size(); j < n1; j++) {
v = map.get(JS.SV.sValue(formatList.get(j)));
list.addLast(v == null ? JS.SV.newS("") : v);
}
listOut.addLast(JS.SV.getVariableList(list));
break;
case 7:
map =  new java.util.Hashtable();
list = element.getList();
for (var j = 0, n1 = Math.min(list.size(), formatList.size()); j < n1; j++) {
map.put(JS.SV.sValue(formatList.get(j)), list.get(j));
}
listOut.addLast(JS.SV.getVariable(map));
}
}
return listOut;
}, "JU.Lst,JU.Lst");
Clazz.defineMethod(c$, "evaluateList", 
function(mp, tok, args){
var len = args.length;
var x1 = mp.getX();
var isArray1 = (x1.tok == 7);
var x2;
switch (tok) {
case 1275335685:
return (len == 2 && mp.addX(x1.pushPop(args[0], args[1])) || len == 1 && mp.addX(x1.pushPop(null, args[0])));
case 1275334681:
return (len == 1 && mp.addX(x1.pushPop(args[0], null)) || len == 0 && mp.addX(x1.pushPop(null, null)));
case 1275069441:
if (len != 1 && len != 2) return false;
break;
case 1275068435:
if (len != 0 || !isArray1) return false;
break;
case 1275069447:
case 1275069446:
break;
default:
if (len != 1) return false;
}
if (len == 2) {
var ret = this.listSpecial(tok, x1, JS.SV.sValue(args[0]), args[1], isArray1);
return (ret != null && mp.addXObj(ret));
}x2 = (tok == 1275068435 ? null : len == 0 ? JS.SV.newV(1073742327, "all") : args[0]);
var isAll = (x2 != null && x2.tok == 1073742327);
if (!isArray1 && x1.tok != 4) return mp.binaryOp(JS.MathExt.opTokenFor(tok), x1, x2);
var isScalar1 = JS.SV.isScalar(x1);
var isScalar2 = (x2 == null || JS.SV.isScalar(x2));
var list1 = null;
var list2 = null;
var alist1 = x1.getList();
var alist2 = (x2 == null ? null : x2.getList());
var sList1 = null;
var sList2 = null;
if (isArray1) {
len = alist1.size();
} else if (isScalar1) {
len = 2147483647;
} else {
sList1 = (JU.PT.split(JS.SV.sValue(x1), "\n"));
list1 =  Clazz.newFloatArray (len = sList1.length, 0);
JU.PT.parseFloatArrayData(sList1, list1);
}if (isAll && tok != 1275069446) {
var sum = 0;
if (isArray1) {
for (var i = len; --i >= 0; ) sum += JS.SV.fValue(alist1.get(i));

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

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

}return mp.addXStr(sb.toString());
}var scalar = null;
if (isScalar2) {
scalar = x2;
} else if (x2.tok == 7) {
len = Math.min(len, alist2.size());
} else {
sList2 = JU.PT.split(JS.SV.sValue(x2), "\n");
list2 =  Clazz.newFloatArray (sList2.length, 0);
JU.PT.parseFloatArrayData(sList2, list2);
len = Math.min(len, list2.length);
}var token = JS.MathExt.opTokenFor(tok);
if (isArray1 && isAll) {
var llist =  new JU.Lst();
return mp.addXList(this.addAllLists(x1.getList(), llist));
}var a = (isScalar1 ? x1 : null);
var b;
var justVal = (len == 2147483647);
if (justVal) len = 1;
var olist =  new Array(len);
for (var i = 0; i < len; i++) {
if (isScalar2) b = scalar;
 else if (x2.tok == 7) b = alist2.get(i);
 else if (Float.isNaN(list2[i])) b = JS.SV.getVariable(JS.SV.unescapePointOrBitsetAsVariable(sList2[i]));
 else b = JS.SV.newF(list2[i]);
if (!isScalar1) {
if (isArray1) a = alist1.get(i);
 else if (Float.isNaN(list1[i])) a = JS.SV.getVariable(JS.SV.unescapePointOrBitsetAsVariable(sList1[i]));
 else a = JS.SV.newF(list1[i]);
}if (tok == 1275069446) {
if (a.tok != 7) {
var l =  new JU.Lst();
l.addLast(a);
a = JS.SV.getVariableList(l);
}}if (b == null ? !mp.propOp(token, a) : !mp.binaryOp(token, a, b)) return false;
olist[i] = mp.getX();
}
return (justVal ? mp.addXObj(olist[0]) : mp.addXAV(olist));
}, "JS.ScriptMathProcessor,~N,~A");
c$.opTokenFor = Clazz.defineMethod(c$, "opTokenFor", 
function(tok){
switch (tok) {
case 1275069441:
case 1275069446:
return JS.T.tokenPlus;
case 1275068931:
return JS.T.tokenMinus;
case 1275068929:
return JS.T.tokenTimes;
case 1275068930:
return JS.T.tokenMul3;
case 1275068928:
return JS.T.tokenDivide;
case 1275068435:
return JS.T.tokenLength;
}
return null;
}, "~N");
Clazz.defineMethod(c$, "listSpecial", 
function(tok, x1, tab, x2, isArray1){
var sList1 = null;
var sList2 = null;
var sList3 = null;
if (tok == 1275069441) {
sList1 = (isArray1 ? JS.SV.strListValue(x1) : JU.PT.split(JS.SV.sValue(x1), "\n"));
sList2 = (x2.tok == 7 ? JS.SV.strListValue(x2) : JU.PT.split(JS.SV.sValue(x2), "\n"));
var len = Math.max(sList1.length, sList2.length);
sList3 =  new Array(len);
for (var i = 0; i < len; i++) sList3[i] = (i >= sList1.length ? "" : sList1[i]) + tab + (i >= sList2.length ? "" : sList2[i]);

return sList3;
}if (x2.tok != 1073742335) return null;
var l = x1.getList();
var isCSV = (tab.length == 0);
if (isCSV) tab = ",";
if (tok == 1275069446) {
var s2 =  new Array(l.size());
for (var i = l.size(); --i >= 0; ) {
var a = l.get(i).getList();
if (a == null) s2[i] = l.get(i);
 else {
var sb =  new JU.SB();
for (var j = 0, n = a.size(); j < n; j++) {
if (j > 0) sb.append(tab);
var sv = a.get(j);
var s = null;
if (sv.tok == 4) {
var st = sv.value;
if (isCSV) {
s = "\"" + JU.PT.rep(st, "\"", "\"\"") + "\"";
}}sb.append(s == null ? "" + sv.asString() : s);
}
s2[i] = JS.SV.newS(sb.toString());
}}
return s2;
}var sa =  new JU.Lst();
if (isCSV) tab = "\0";
var next =  Clazz.newIntArray (2, 0);
for (var i = 0, nl = l.size(); i < nl; i++) {
var line = l.get(i).asString();
if (isCSV) {
next[1] = 0;
next[0] = 0;
var last = 0;
while (true) {
var s = JU.PT.getCSVString(line, next);
if (s == null) {
if (next[1] == -1) {
line += (++i < nl ? "\n" + l.get(i).asString() : "\"");
next[1] = last;
continue;
}line = line.substring(0, last) + line.substring(last).$replace(',', '\0');
break;
}line = line.substring(0, last) + line.substring(last, next[0]).$replace(',', '\0') + s + line.substring(next[1]);
next[1] = last = next[0] + s.length;
}
}var linaa = line.$plit(tab);
var la =  new JU.Lst();
for (var j = 0, n = linaa.length; j < n; j++) {
var s = linaa[j];
if (s.indexOf(".") < 0) try {
la.addLast(JS.SV.newI(Integer.parseInt(s)));
continue;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
 else try {
la.addLast(JS.SV.getVariable(Float.$valueOf(Float.parseFloat(s))));
continue;
} catch (ee) {
if (Clazz.exceptionOf(ee, Exception)){
} else {
throw ee;
}
}
la.addLast(JS.SV.newS(s));
}
sa.addLast(JS.SV.getVariableList(la));
}
return JS.SV.getVariableList(sa);
}, "~N,JS.SV,~S,JS.SV,~B");
Clazz.defineMethod(c$, "addAllLists", 
function(list, l){
var n = list.size();
for (var i = 0; i < n; i++) {
var v = list.get(i);
if (v.tok == 7) this.addAllLists(v.getList(), l);
 else l.addLast(v);
}
return l;
}, "JU.Lst,JU.Lst");
Clazz.defineMethod(c$, "evaluateLoad", 
function(mp, args, isFile){
if (!this.checkAccess()) return false;
if (args.length < 1 || args.length > 3) return false;
var file = JV.FileManager.fixDOSName(JS.SV.sValue(args[0]));
var asMap = (args.length > 1 && args[1].tok == 1073742335);
var async = (this.vwr.async || args.length > 2 && args[args.length - 1].tok == 1073742335);
var nBytesMax = (args.length > 1 && args[1].tok == 2 ? args[1].asInt() : -1);
var asJSON = (args.length > 1 && args[1].asString().equalsIgnoreCase("JSON"));
if (asMap) return mp.addXMap(this.vwr.fm.getFileAsMap(file, null, false));
var isQues = file.startsWith("?");
if (JV.Viewer.isJS && (isQues || async)) {
if (isFile && isQues) return mp.addXStr("");
file = this.e.loadFileAsync("load()_", file, mp.oPt, true);
}var str = isFile ? this.vwr.fm.getFilePath(file, false, false) : this.vwr.getFileAsString4(file, nBytesMax, false, false, true, "script");
try {
return (asJSON ? mp.addXObj(this.vwr.parseJSON(str)) : mp.addXStr(str));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return false;
} else {
throw e;
}
}
}, "JS.ScriptMathProcessor,~A,~B");
Clazz.defineMethod(c$, "evaluateMath", 
function(mp, args, tok){
var x = JS.SV.fValue(args[0]);
switch (tok) {
case 134218246:
x = Math.sqrt(x);
break;
case 134218244:
x = Math.sin(x * 3.141592653589793 / 180);
break;
case 134218245:
x = Math.cos(x * 3.141592653589793 / 180);
break;
case 134218255:
x = Math.tan(x * 3.141592653589793 / 180);
break;
case 134218241:
x = Math.acos(x) * 180 / 3.141592653589793;
break;
}
return mp.addXFloat(x);
}, "JS.ScriptMathProcessor,~A,~N");
Clazz.defineMethod(c$, "evaluateMeasure", 
function(mp, args, tok){
var nPoints = 0;
switch (tok) {
case 1745489939:
var property = null;
var points =  new JU.Lst();
var rangeMinMax =  Clazz.newFloatArray(-1, [3.4028235E38, 3.4028235E38]);
var strFormat = null;
var units = null;
var isAllConnected = false;
var isNotConnected = false;
var rPt = 0;
var isNull = false;
var rd = null;
var nBitSets = 0;
var vdw = 3.4028235E38;
var asMinArray = false;
var asFloatArray = false;
for (var i = 0; i < args.length; i++) {
switch (args[i].tok) {
case 10:
var bs = args[i].value;
if (bs.length() == 0) isNull = true;
points.addLast(bs);
nPoints++;
nBitSets++;
break;
case 8:
points.addLast(JU.Point3fi.newPF(args[i].value, 0));
nPoints++;
break;
case 2:
case 3:
rangeMinMax[rPt++ % 2] = JS.SV.fValue(args[i]);
break;
case 4:
var s = JS.SV.sValue(args[i]);
if (s.startsWith("property_")) {
property = s;
break;
}if (s.equalsIgnoreCase("vdw") || s.equalsIgnoreCase("vanderwaals")) vdw = (i + 1 < args.length && args[i + 1].tok == 2 ? args[++i].asInt() : 100) / 100;
 else if (s.equalsIgnoreCase("notConnected")) isNotConnected = true;
 else if (s.equalsIgnoreCase("connected")) isAllConnected = true;
 else if (s.equalsIgnoreCase("minArray")) asMinArray = (nBitSets >= 1);
 else if (s.equalsIgnoreCase("asArray") || s.length == 0) asFloatArray = (nBitSets >= 1);
 else if (JM.Measurement.isUnits(s)) units = s.toLowerCase();
 else strFormat = nPoints + ":" + s;
break;
default:
return false;
}
}
if (nPoints < 2 || nPoints > 4 || rPt > 2 || isNotConnected && isAllConnected) return false;
if (isNull) return mp.addXStr("");
if (vdw != 3.4028235E38 && (nBitSets != 2 || nPoints != 2)) return mp.addXStr("");
rd = (vdw == 3.4028235E38 ?  new J.atomdata.RadiusData(rangeMinMax, 0, null, null) :  new J.atomdata.RadiusData(null, vdw, J.atomdata.RadiusData.EnumType.FACTOR, J.c.VDW.AUTO));
var obj = (this.vwr.newMeasurementData(null, points)).set(0, null, rd, property, strFormat, units, null, isAllConnected, isNotConnected, null, true, 0, 0, null, NaN, null).getMeasurements(asFloatArray, asMinArray);
return mp.addXObj(obj);
case 134217729:
if ((nPoints = args.length) != 3 && nPoints != 4) return false;
break;
default:
if ((nPoints = args.length) != 2) return false;
}
var pts =  new Array(nPoints);
for (var i = 0; i < nPoints; i++) {
if ((pts[i] = mp.ptValue(args[i], null)) == null) return false;
}
switch (nPoints) {
case 2:
return mp.addXFloat(pts[0].distance(pts[1]));
case 3:
return mp.addXFloat(JU.Measure.computeAngleABC(pts[0], pts[1], pts[2], true));
case 4:
return mp.addXFloat(JU.Measure.computeTorsion(pts[0], pts[1], pts[2], pts[3], true));
}
return false;
}, "JS.ScriptMathProcessor,~A,~N");
Clazz.defineMethod(c$, "evaluateModulation", 
function(mp, args){
var type = "";
var t = NaN;
var t456 = null;
switch (args.length) {
case 0:
break;
case 1:
switch (args[0].tok) {
case 8:
t456 = args[0].value;
break;
case 4:
type = args[0].asString();
break;
default:
t = JS.SV.fValue(args[0]);
}
break;
case 2:
type = JS.SV.sValue(args[0]);
t = JS.SV.fValue(args[1]);
break;
default:
return false;
}
if (t456 == null && t < 1e6) t456 = JU.P3.new3(t, t, t);
var x = mp.getX();
var bs = (x.tok == 10 ? x.value :  new JU.BS());
return mp.addXList(this.vwr.ms.getModulationList(bs, (type + "D").toUpperCase().charAt(0), t456));
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluatePlane", 
function(mp, args, tok, isSelector){
if (tok == 134219777 && args.length != 3 && args.length != 4 || tok == 134217763 && args.length != 2 && args.length != 3 && args.length != 4 || args.length == 0 || args.length > 4) return false;
var pt1;
var pt2;
var pt3;
var plane = this.e.planeValue(args[0]);
var norm;
var vTemp;
switch (args.length) {
case 1:
if (tok == 134217750) {
if (args[0].tok != 7) return false;
var uvw = JS.SV.flistValue(args[0], 3);
if (uvw.length != 3) return false;
var sym = this.vwr.getOperativeSymmetry();
if (sym == null) return false;
var ptuvw = JU.P3.new3(uvw[0], uvw[1], uvw[2]);
sym.toCartesian(ptuvw, false);
plane = JU.P4.new4(ptuvw.x, ptuvw.y, ptuvw.z, 0);
if (isSelector) {
break;
}}return (plane != null && mp.addXPt4(plane));
case 2:
if (tok == 134217763) {
var plane1 = this.e.planeValue(args[1]);
if (plane1 == null) return false;
pt3 =  new JU.P3();
norm =  new JU.V3();
vTemp =  new JU.V3();
if (plane != null) {
var list = JU.Measure.getIntersectionPP(plane, plane1);
if (list == null) return mp.addXStr("");
return mp.addXList(list);
}pt2 = mp.ptValue(args[0], null);
if (pt2 == null) return mp.addXStr("");
return mp.addXPt(JU.Measure.getIntersection(pt2, null, plane1, pt3, norm, vTemp));
}case 3:
case 4:
switch (tok) {
case 134219777:
var offset = (args.length == 4 ? JS.SV.fValue(args[3]) : NaN);
plane = this.e.getHklPlane(JU.P3.new3(JS.SV.fValue(args[0]), JS.SV.fValue(args[1]), JS.SV.fValue(args[2])), offset, null);
if (isSelector) {
break;
}return plane != null && mp.addXPt4(plane);
case 134217763:
pt1 = mp.ptValue(args[0], null);
pt2 = mp.ptValue(args[1], null);
if (pt1 == null || pt2 == null) return mp.addXStr("");
var vLine = JU.V3.newV(pt2);
vLine.normalize();
var plane2 = this.e.planeValue(args[2]);
if (plane2 != null) {
pt3 =  new JU.P3();
norm =  new JU.V3();
vTemp =  new JU.V3();
pt1 = JU.Measure.getIntersection(pt1, vLine, plane2, pt3, norm, vTemp);
if (pt1 == null) return mp.addXStr("");
return mp.addXPt(pt1);
}pt3 = mp.ptValue(args[2], null);
if (pt3 == null) return mp.addXStr("");
var v =  new JU.V3();
pt3 = JU.P3.newP(pt3);
if (args.length == 3) {
JU.Measure.projectOntoAxis(pt3, pt1, vLine, v);
return mp.addXPt(pt3);
}var r = JS.SV.fValue(args[3]);
var ptCenter = JU.P3.newP(pt3);
JU.Measure.projectOntoAxis(pt3, pt1, vLine, v);
var d = ptCenter.distance(pt3);
var l =  new JU.Lst();
if (d == r) {
l.addLast(pt3);
} else if (d < r) {
d = Math.sqrt(r * r - d * d);
v.scaleAdd2(d, vLine, pt3);
l.addLast(JU.P3.newP(v));
v.scaleAdd2(-d, vLine, pt3);
l.addLast(JU.P3.newP(v));
}return mp.addXList(l);
}
switch (args[0].tok) {
case 2:
case 3:
if (args.length == 3) {
var r = JS.SV.fValue(args[0]);
var theta = JS.SV.fValue(args[1]);
var phi = JS.SV.fValue(args[2]);
norm = JU.V3.new3(0, 0, 1);
pt2 = JU.P3.new3(0, 1, 0);
var q = JU.Quat.newVA(pt2, phi);
q.getMatrix().rotate(norm);
pt2.set(0, 0, 1);
q = JU.Quat.newVA(pt2, theta);
q.getMatrix().rotate(norm);
pt2.setT(norm);
pt2.scale(r);
plane =  new JU.P4();
JU.Measure.getPlaneThroughPoint(pt2, norm, plane);
return mp.addXPt4(plane);
}break;
case 10:
case 8:
pt1 = mp.ptValue(args[0], null);
pt2 = mp.ptValue(args[1], null);
if (pt2 == null) return false;
pt3 = (args.length > 2 && (args[2].tok == 10 || args[2].tok == 8) ? mp.ptValue(args[2], null) : null);
norm = JU.V3.newV(pt2);
if (pt3 == null) {
plane =  new JU.P4();
if (args.length == 2 || args[2].tok != 2 && args[2].tok != 3 && !args[2].asBoolean()) {
pt3 = JU.P3.newP(pt1);
pt3.add(pt2);
pt3.scale(0.5);
norm.sub(pt1);
norm.normalize();
} else if (args[2].tok == 1073742335) {
pt3 = pt1;
} else {
norm.sub(pt1);
pt3 =  new JU.P3();
pt3.scaleAdd2(args[2].asFloat(), norm, pt1);
}JU.Measure.getPlaneThroughPoint(pt3, norm, plane);
return mp.addXPt4(plane);
}var vAB =  new JU.V3();
var ptref = (args.length == 4 ? mp.ptValue(args[3], null) : null);
var nd = JU.Measure.getDirectedNormalThroughPoints(pt1, pt2, pt3, ptref, norm, vAB);
return mp.addXPt4(JU.P4.new4(norm.x, norm.y, norm.z, nd));
}
}
if (isSelector) {
var x1 = mp.getX();
switch (x1.tok) {
case 10:
var list =  new JU.Lst();
var bsAtoms = JS.SV.getBitSet(x1, false);
for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
var p =  new JU.P3();
JU.Measure.getPlaneProjection(this.vwr.ms.at[i], plane, p,  new JU.V3());
list.addLast(JS.SV.getVariable(p));
}
return mp.addXList(list);
case 8:
var pt = JS.SV.ptValue(x1);
var p =  new JU.P3();
JU.Measure.getPlaneProjection(pt, plane, p,  new JU.V3());
return mp.addXPt(p);
}
}if (args.length != 4) return false;
var x = JS.SV.fValue(args[0]);
var y = JS.SV.fValue(args[1]);
var z = JS.SV.fValue(args[2]);
var w = JS.SV.fValue(args[3]);
return mp.addXPt4(JU.P4.new4(x, y, z, w));
}, "JS.ScriptMathProcessor,~A,~N,~B");
Clazz.defineMethod(c$, "evaluatePoint", 
function(mp, args){
var s = null;
switch (args.length) {
default:
return false;
case 1:
switch (args[0].tok) {
case 3:
case 2:
return mp.addXInt(args[0].asInt());
case 4:
s = args[0].value;
if (s.startsWith("(") && s.charAt(s.length - 1) == ')') {
return mp.addXPt(this.getRealPointFromFraction(s));
}break;
case 7:
var list = args[0].getList();
var len = list.size();
if (len == 0) {
return false;
}switch (list.get(0).tok) {
case 2:
case 3:
switch (len) {
case 3:
return mp.addXPt(JU.P3.new3(list.get(0).asFloat(), list.get(1).asFloat(), list.get(2).asFloat()));
case 4:
return mp.addXPt4(JU.P4.new4(list.get(0).asFloat(), list.get(1).asFloat(), list.get(2).asFloat(), list.get(3).asFloat()));
}
return false;
case 7:
var ar =  new JU.Lst();
for (var i = 0; i < len; i++) {
ar.addLast(JS.SV.getVariable(JU.Escape.uP("{" + list.get(i).asString() + "}")));
}
return mp.addXList(ar);
case 4:
s = list.get(0).value;
if (!s.startsWith("{") || (typeof(JU.Escape.uP(s))=='string')) {
s = null;
break;
}var a =  new JU.Lst();
for (var i = 0; i < len; i++) {
a.addLast(JS.SV.getVariable(JU.Escape.uP(JS.SV.sValue(list.get(i)))));
}
return mp.addXList(a);
default:
return false;
}
s = "{" + s + "}";
}
if (s == null) s = JS.SV.sValue(args[0]);
var pt = JU.Escape.uP(s);
return (Clazz.instanceOf(pt,"JU.P3") ? mp.addXPt(pt) : mp.addXStr("" + pt));
case 2:
var pt3;
switch (args[1].tok) {
case 1073742334:
case 1073742335:
switch (args[0].tok) {
case 8:
pt3 = JU.P3.newP(args[0].value);
break;
case 10:
pt3 = this.vwr.ms.getAtomSetCenter(args[0].value);
break;
default:
return false;
}
if (args[1].tok == 1073742335) {
this.vwr.tm.transformPt3fSafe(pt3, pt3);
pt3.y = this.vwr.tm.height - pt3.y;
if (this.vwr.antialiased) pt3.scale(0.5);
} else {
if (this.vwr.antialiased) pt3.scale(2);
pt3.y = this.vwr.tm.height - pt3.y;
this.vwr.tm.unTransformPoint(pt3, pt3);
}break;
case 8:
var sv = args[0].getList();
if (sv == null || sv.size() != 4) return false;
var pt1 = JS.SV.ptValue(args[1]);
pt3 = JU.P3.newP(JS.SV.ptValue(sv.get(0)));
pt3.scaleAdd2(pt1.x, JS.SV.ptValue(sv.get(1)), pt3);
pt3.scaleAdd2(pt1.y, JS.SV.ptValue(sv.get(2)), pt3);
pt3.scaleAdd2(pt1.z, JS.SV.ptValue(sv.get(3)), pt3);
break;
default:
return false;
}
return mp.addXPt(pt3);
case 3:
return mp.addXPt(JU.P3.new3(args[0].asFloat(), args[1].asFloat(), args[2].asFloat()));
case 4:
return mp.addXPt4(JU.P4.new4(args[0].asFloat(), args[1].asFloat(), args[2].asFloat(), args[3].asFloat()));
}
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "getRealPointFromFraction", 
function(s){
s = JU.PT.rep(s.substring(1, s.length - 1).$replace(',', ' '), "  ", " ");
var xyz = JU.PT.split(s.trim(), " ");
if (xyz.length != 3) return null;
var pt = JU.P3.new3(JU.SimpleUnitCell.parseCalcFunctions(this.vwr, null, xyz[0]), JU.SimpleUnitCell.parseCalcFunctions(this.vwr, null, xyz[1]), JU.SimpleUnitCell.parseCalcFunctions(this.vwr, null, xyz[2]));
return pt;
}, "~S");
Clazz.defineMethod(c$, "evaluatePrompt", 
function(mp, args){
if (args.length != 1 && args.length != 2 && args.length != 3) return false;
var label = JS.SV.sValue(args[0]);
var buttonArray = (args.length > 1 && args[1].tok == 7 ? JS.SV.strListValue(args[1]) : null);
var asButtons = (buttonArray != null || args.length == 1 || args.length == 3 && args[2].asBoolean());
var input = (buttonArray != null ? null : args.length >= 2 ? JS.SV.sValue(args[1]) : "OK");
var s = "" + this.vwr.prompt(label, input, buttonArray, asButtons);
return (asButtons && buttonArray != null ? mp.addXInt(Integer.parseInt(s) + 1) : mp.addXStr(s));
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateQuaternion", 
function(mp, args, tok){
var pt0 = null;
var nArgs = args.length;
var nMax = 2147483647;
var isRelative = false;
if (tok == 134221850) {
if (nArgs > 1 && args[nArgs - 1].tok == 4 && (args[nArgs - 1].value).equalsIgnoreCase("relative")) {
nArgs--;
isRelative = true;
}if (nArgs > 1 && args[nArgs - 1].tok == 2 && args[0].tok == 10) {
nMax = args[nArgs - 1].asInt();
if (nMax <= 0) nMax = 2147483646;
nArgs--;
}}switch (nArgs) {
case 0:
case 1:
case 4:
break;
case 2:
if (tok == 134221850) {
if (args[0].tok == 7 && (args[1].tok == 7 || args[1].tok == 1073742335)) break;
if (args[0].tok == 10 && (args[1].tok == 2 || args[1].tok == 10)) break;
}if ((pt0 = mp.ptValue(args[0], null)) == null || tok != 134221850 && args[1].tok == 8) return false;
break;
case 3:
if (tok != 134221850) return false;
if (args[0].tok == 9) {
if (args[2].tok != 8 && args[2].tok != 10) return false;
break;
}for (var i = 0; i < 3; i++) if (args[i].tok != 8 && args[i].tok != 10) return false;

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

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

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

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

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

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

return mp.addXAS(list);
}
return mp.addXStr("");
}, "JS.ScriptMathProcessor,~N,~A");
Clazz.defineMethod(c$, "evaluateSubstructure", 
function(mp, args, tok, isSelector){
var x = (isSelector ? mp.getX() : null);
var sx = null;
var bsSelected = null;
if (x != null) {
switch (x.tok) {
case 10:
bsSelected = x.value;
break;
case 4:
sx = x.value;
if (sx.startsWith("InChI")) {
mp.addX(x);
return this.evaluateInChI(mp,  Clazz.newArray(-1, [JS.SV.newS("SMILES " + (args.length > 0 ? args[0].asString() : sx.indexOf("/f") >= 0 ? "fixedh" : "amide"))]));
}}
}var isSelectedSmiles = isSelector && tok == 134218757;
if (isSelectedSmiles) {
return mp.addXObj(this.e.getSmilesExt().getSmilesMatches("", null, bsSelected, null, 1, true, false));
}if (args.length == 0 || isSelector && (tok == 134218753 || args.length > 1)) return false;
var objTarget = (tok == 134218756 && !isSelector && args[0].tok == 134218756 ? args[0].value : null);
if (objTarget != null && args.length < 2) return false;
var compileSearch = (tok == 134218756 && !isSelector && args[0].tok == 10);
var objPattern = (args[0].tok == 134218753 ? args[0].value : objTarget != null && args[1].tok == 134218753 ? args[1].value : null);
if (objTarget != null && objPattern == null) return false;
var pattern = (compileSearch ? null : objPattern == null ? JS.SV.sValue(args[0]) : null);
var bs =  new JU.BS();
if (pattern == null || pattern.length > 0) try {
if (compileSearch) {
return mp.addX(JS.SV.newV(134218756, this.vwr.getSmilesMatcher().compileSearchTarget(this.vwr.ms.at, this.vwr.ms.ac, JS.SV.getBitSet(args[0], false))));
}if (objTarget != null) return mp.addXBs(this.vwr.getSmilesMatcher().getSubstructureSet(objPattern, objTarget, 0, null, 2));
if (tok == 134218753) {
return mp.addX(JS.SV.newV(134218753, this.vwr.getSmilesMatcher().compileSmartsPattern(pattern)));
}if (bsSelected == null) bsSelected = (args.length == 2 && args[1].tok == 10 ? args[1].value : this.vwr.getModelUndeletedAtomsBitSet(-1));
bs = this.vwr.getSmilesMatcher().getSubstructureSet((objPattern == null ? pattern : objPattern), this.vwr.ms.at, this.vwr.ms.ac, bsSelected, (tok == 134218757 ? 1 : 2));
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
this.e.evalError(ex.getMessage(), null);
} else {
throw ex;
}
}
return (tok != 134218753 && mp.addXBs(bs));
}, "JS.ScriptMathProcessor,~A,~N,~B");
Clazz.defineMethod(c$, "evaluateSymop", 
function(mp, args, isProperty){
var o;
if (!isProperty && args.length == 2 && args[0].tok == 7 && args[1].tok == 4) {
var ret =  new JU.Lst();
var list = args[0].value;
for (var i = 0, n = list.size(); i < n; i++) {
o = this.getSymopInfo(mp, null,  Clazz.newArray(-1, [list.get(i), args[1]]), i + 1, false);
if (o == null) return false;
ret.addLast(o);
}
return mp.addXList(ret);
}var x1 = (isProperty ? mp.getX() : null);
o = this.getSymopInfo(mp, x1, args, 0, isProperty);
return mp.addXObj(o);
}, "JS.ScriptMathProcessor,~A,~B");
Clazz.defineMethod(c$, "getSymopInfo", 
function(mp, x1, args, index, isProperty){
var o = null;
var narg = args.length;
var str1 = (narg == 2 && args[1].tok == 4 ? (args[1].value).toLowerCase() : null);
if (str1 != null) {
var m = null;
var xyz = null;
switch (args[0].tok) {
case 4:
switch (str1) {
case "rxyz":
case "matrix":
xyz = args[0].value;
}
break;
case 11:
switch (str1) {
case "rxyz":
case "xyz":
case "uvw":
m = args[0].value;
break;
}
break;
case 12:
switch (str1) {
case "rxyz":
case "xyz":
m = args[0].value;
break;
}
break;
}
if (m != null || xyz != null) return this.vwr.getSymStatic().staticConvertOperation(xyz, m, str1);
}var isPoint = false;
if (x1 != null && x1.tok != 10 && !(isPoint = (x1.tok == 8))) return null;
var bsAtoms = (x1 == null || isPoint ? null : x1.value);
var pt1 = (isPoint ? JS.SV.ptValue(x1) : null);
if (!isPoint && bsAtoms == null) bsAtoms = this.vwr.getThisModelAtoms();
if (narg == 0) {
var ops = JU.PT.split(JU.PT.trim(this.vwr.getSymTemp().getSpaceGroupInfo(this.vwr.ms, null, (bsAtoms == null || bsAtoms.isEmpty() ? Math.max(0, this.vwr.am.cmi) : this.vwr.ms.at[bsAtoms.nextSetBit(0)].mi), false, null).get("symmetryInfo"), "\n"), "\n");
var lst =  new JU.Lst();
for (var i = 0, n = ops.length; i < n; i++) lst.addLast(JU.PT.split(ops[i], "\t"));

return lst;
}var xyz = null;
var tok = 0;
var iOp = -2147483648;
var apt = 0;
var pt2 = null;
var bs1 = null;
var isWyckoff = false;
switch (args[0].tok) {
case 4:
xyz = JS.SV.sValue(args[0]);
switch (xyz == null ? "" : xyz.toLowerCase()) {
case "count":
var sym = this.vwr.getOperativeSymmetry();
return (narg != 1 ? null : Integer.$valueOf(sym == null ? 0 : sym.getSpaceGroupOperationCount()));
case "":
tok = 0;
break;
case "invariant":
tok = 36868;
break;
case "wyckoff":
tok = 1086324754;
isWyckoff = true;
break;
case "wyckoffm":
tok = 1086324755;
isWyckoff = true;
break;
}
apt++;
break;
case 11:
case 12:
xyz = args[0].escape();
apt++;
break;
case 2:
iOp = args[0].asInt();
apt++;
break;
case 10:
if (!isPoint) {
bs1 = args[0].value;
}break;
}
if (bsAtoms == null) {
if (apt < narg && args[apt].tok == 10) (bsAtoms =  new JU.BS()).or(args[apt].value);
if (apt + 1 < narg && args[apt + 1].tok == 10) (bsAtoms == null ? (bsAtoms =  new JU.BS()) : bsAtoms).or(args[apt + 1].value);
} else if (!bsAtoms.isEmpty()) {
bsAtoms = this.vwr.getModelUndeletedAtomsBitSet(this.vwr.getModelIndexForAtom(bsAtoms.nextSetBit(0)));
}var trans = null;
if (narg > apt && args[apt].tok == 7) {
var a = args[apt++].getList();
if (a.size() != 3) return null;
trans = JU.P3.new3(JS.SV.fValue(a.get(0)), JS.SV.fValue(a.get(1)), JS.SV.fValue(a.get(2)));
} else if (narg > apt && args[apt].tok == 2) {
JU.SimpleUnitCell.ijkToPoint3f(JS.SV.iValue(args[apt++]), trans =  new JU.P3(), 0, 0);
}if (pt1 == null && (pt1 = (narg > apt ? mp.ptValue(args[apt], bsAtoms) : null)) != null) apt++;
if ((pt2 = (narg > apt ? mp.ptValue(args[apt], bsAtoms) : null)) != null) apt++;
if (pt1 != null && pt2 == null && bs1 != null && !bs1.isEmpty()) {
pt2 = pt1;
bs1 = JU.BSUtil.copy(bs1);
bs1.and(bsAtoms);
var a0 = this.vwr.ms.getSymmetryEquivAtoms(bs1, null, null).nextSetBit(0);
if ("basis".equals(str1)) {
return JU.BSUtil.newAndSetBit(a0);
}pt1 = JU.P3.newP(this.vwr.ms.at[a0]);
}var nth = (pt2 != null && args.length > apt && iOp == -2147483648 && args[apt].tok == 2 ? args[apt].intValue : -1);
if (nth >= 0) apt++;
if (iOp == -2147483648 && tok != 36868) iOp = 0;
var map = null;
if (tok == 0 && xyz != null && xyz.indexOf(",") < 0) {
if (apt == narg) {
map = this.vwr.ms.getPointGroupInfo(null, null);
} else if (args[apt].tok == 6) {
map = args[apt].getMap();
}}if (map != null) {
var m;
var pt = xyz.indexOf('.');
var p1 = xyz.indexOf('^');
if (p1 > 0) {
nth = JU.PT.parseInt(xyz.substring(p1 + 1));
} else {
p1 = xyz.length;
nth = 1;
}if (pt > 0 && p1 > pt + 1) {
iOp = JU.PT.parseInt(xyz.substring(pt + 1, p1));
if (iOp < 1) iOp = 1;
p1 = pt;
} else {
iOp = 1;
}xyz = xyz.substring(0, p1);
o = map.get(xyz + "_m");
if (o == null) {
o = map.get(xyz);
return (o == null ? "" : o);
}var centerPt;
try {
if (Clazz.instanceOf(o,"JS.SV")) {
centerPt = (map.get("center")).value;
var obj = o;
if (obj.tok == 11) {
m = obj.value;
} else if (obj.tok == 7) {
m = obj.getList().get(iOp - 1).value;
} else {
return null;
}} else {
centerPt = map.get("center");
if (Clazz.instanceOf(o,"JU.M3")) {
m = o;
} else {
m = (o).get(iOp - 1);
}}var m0 = m;
m = JU.M3.newM3(m);
if (nth > 1) {
for (var i = 1; i < nth; i++) {
m.mul(m0);
}
}if (pt1 == null) return m;
pt1 = JU.P3.newP(pt1);
pt1.sub(centerPt);
m.rotate(pt1);
pt1.add(centerPt);
return pt1;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return null;
}var desc = (narg == apt ? (isWyckoff ? "" : tok == 36868 ? "id" : pt2 != null || pt1 == null ? "matrix" : "point") : JS.SV.sValue(args[apt++]));
var haveAtom = ((!isWyckoff || isProperty) && bsAtoms != null && !bsAtoms.isEmpty());
var iatom = (haveAtom ? bsAtoms.nextSetBit(0) : -1);
if (isWyckoff) {
var pt = (haveAtom ? this.vwr.ms.getAtom(iatom) : pt1);
while (desc.length > 0 && JU.PT.isDigit(desc.charAt(0))) desc = desc.substring(1);

if (pt == null) {
switch (desc) {
case "":
case "*":
desc = "*";
break;
default:
if (desc.length == 1) desc += "*";
 else return null;
}
}if (desc.length == 0 || desc.equalsIgnoreCase("label")) desc = null;
var letter = (desc == null ? (tok == 1086324755 ? "" : null) : desc.endsWith("*") || desc.equalsIgnoreCase("coord") || desc.equalsIgnoreCase("coords") ? desc : desc.substring(0, 1));
var sym = this.vwr.getOperativeSymmetry();
return (sym == null ? null : sym.getWyckoffPosition(pt, (letter == null ? (tok == 1086324755 ? "M" : null) : (tok == 1086324755 ? "M" : "") + letter)));
}desc = desc.toLowerCase();
if (tok == 36868 || desc.equals("invariant") && isProperty) {
if (haveAtom && pt1 == null) pt1 = this.vwr.ms.at[iatom];
haveAtom = (pt1 != null);
if (iatom < 0) iatom = this.vwr.getThisModelAtoms().nextSetBit(0);
}if (tok == 36868 && iOp == -2147483648) {
var ret = null;
var sym = this.vwr.getCurrentUnitCell();
if (pt1 != null) {
ret = (sym == null ?  Clazz.newIntArray (0, 0) : sym.getInvariantSymops(pt1, null));
} else if (bsAtoms != null && !bsAtoms.isEmpty()) {
var ia = bsAtoms.nextSetBit(0);
pt1 = this.vwr.ms.at[ia];
ret = this.vwr.ms.getSymmetryInvariant(ia);
}if (ret != null && ret.length > 0) {
var m =  new Array(ret.length);
for (var i = 0; i < m.length; i++) {
iOp = ret[i];
m[i] = this.vwr.getSymmetryInfo(iatom, null, iOp, null, pt1, pt1, 1275068418, desc, 0, -1, 0, null);
}
return m;
}return ret;
}var isUVW = (xyz != null && xyz.indexOf("u") >= 0);
o = (apt == args.length ? this.vwr.getSymmetryInfo(iatom, xyz, index > 0 ? index : iOp, trans, pt1, pt2, 1275068418, desc, 0, nth, 0, null) : null);
if (isUVW && Clazz.instanceOf(o,"JU.M4")) {
var m3 =  new JU.M3();
(o).getRotationScale(m3);
o = m3;
}return o;
}, "JS.ScriptMathProcessor,JS.SV,~A,~N,~B");
Clazz.defineMethod(c$, "evaluateTensor", 
function(mp, args){
var isTensor = (args.length == 2 && args[1].tok == 1275068445);
var x = (isTensor ? null : mp.getX());
if (args.length > 2 || !isTensor && x.tok != 10) return false;
var bs = x.value;
var tensorType = (isTensor || args.length == 0 ? null : JS.SV.sValue(args[0]).toLowerCase());
var calc = this.vwr.getNMRCalculation();
if ("unique".equals(tensorType)) return mp.addXBs(calc.getUniqueTensorSet(bs));
var infoType = (args.length < 2 ? null : JS.SV.sValue(args[1]).toLowerCase());
if (isTensor) {
return mp.addXObj((args[0].value).getInfo(infoType));
}return mp.addXList(calc.getTensorInfo(tensorType, infoType, bs));
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "evaluateUserFunction", 
function(mp, name, args, tok, isSelector){
var x1 = null;
if (isSelector) {
x1 = mp.getX();
switch (x1.tok) {
case 10:
break;
case 6:
if (args.length > 0) return false;
x1 = x1.getMap().get(name);
return (x1 == null ? mp.addXStr("") : mp.addX(x1));
default:
return false;
}
}name = name.toLowerCase();
mp.wasX = false;
var params =  new JU.Lst();
for (var i = 0; i < args.length; i++) {
params.addLast(args[i]);
}
if (isSelector) {
return mp.addXObj(this.e.getBitsetProperty(x1.value, null, tok, null, null, x1.value,  Clazz.newArray(-1, [name, params]), false, x1.index, false));
}var $var = this.e.getUserFunctionResult(name, params, null);
return ($var == null ? false : mp.addX($var));
}, "JS.ScriptMathProcessor,~S,~A,~N,~B");
Clazz.defineMethod(c$, "evaluateWithin", 
function(mp, args, isAtomProperty){
var len = args.length;
if (len < 1 || len > 5) return false;
if (len == 1 && args[0].tok == 10) return mp.addX(args[0]);
var bs = (isAtomProperty ? JS.SV.getBitSet(mp.getX(), false) : null);
var distance = 0;
var withinSpec = args[0].value;
var withinStr = "" + withinSpec;
var ms = this.vwr.ms;
var isVdw = false;
var isBooleanFlag = false;
var isWithinGroup = false;
var isDistance = false;
var bsSelected = null;
var rd = null;
var tok = args[0].tok;
var isUnitCell = false;
out : while (true) {
switch (tok == 4 ? tok = JS.T.getTokFromName(withinStr) : tok) {
case 1648363544:
isVdw = true;
withinSpec = null;
case 3:
case 2:
isDistance = true;
if (len < 2 || len == 3 && args[1].tok == 7 && args[2].tok != 7) return false;
distance = (isVdw ? 100 : JS.SV.fValue(args[0]));
switch (tok = args[1].tok) {
case 1073742335:
case 1073742334:
isBooleanFlag = args[1].asBoolean();
if (len > 2 && JS.SV.sValue(args[2]).equalsIgnoreCase("unitcell")) {
tok = 1814695966;
isUnitCell = (len == 3);
} else if (len > 2 && args[2].tok != 10) {
return false;
}if (!isUnitCell) len = 0;
break;
case 4:
var s = JS.SV.sValue(args[1]);
if (s.startsWith("$")) {
bsSelected = this.getAtomsNearSurface(distance, s.substring(1));
break out;
}if (s.equalsIgnoreCase("group")) {
isWithinGroup = true;
tok = 1086324742;
} else if (s.equalsIgnoreCase("vanderwaals") || s.equalsIgnoreCase("vdw")) {
withinSpec = null;
isVdw = true;
tok = 1648363544;
} else {
tok = JS.T.getTokFromName(s);
if (tok == 0) return false;
}break;
}
break;
case 7:
if (len == 1) {
withinSpec = args[0].asString();
tok = 0;
}break;
case 1073742328:
bsSelected = (len == 3 && Clazz.instanceOf(args[1].value,"JU.BS") && Clazz.instanceOf(args[2].value,"JU.BS") ? this.vwr.getBranchBitSet((args[2].value).nextSetBit(0), (args[1].value).nextSetBit(0), true) : null);
break out;
case 134218757:
case 1237320707:
case 134218756:
var isOK = true;
switch (len) {
case 2:
bsSelected = bs;
break;
case 3:
isOK = (args[2].tok == 10);
if (isOK) bsSelected = args[2].value;
break;
default:
isOK = false;
}
return isOK && mp.addXObj(this.e.getSmilesExt().getSmilesMatches(JS.SV.sValue(args[1]), null, bsSelected, null, tok == 134218756 ? 2 : 1, mp.asBitSet, false));
}
if ((typeof(withinSpec)=='string')) {
if (tok == 0) {
tok = 1073742362;
if (len > 2) return false;
len = 2;
}} else if (!isDistance) {
return false;
}switch (len) {
case 1:
switch (tok) {
case 2097184:
case 136314895:
case 1812599299:
case 1814695966:
bsSelected = ms.getAtoms(tok, null);
break out;
case 1073741863:
bsSelected = ms.getAtoms(tok, "");
break out;
case 1073742362:
bsSelected = ms.getAtoms(1086324744, withinStr);
break out;
}
return false;
case 2:
switch (tok) {
case 7:
break;
case 1073742362:
tok = 1086324744;
break;
case 1073741824:
case 1086326786:
case 1086326785:
case 1073741863:
case 1086324744:
case 1111490587:
case 1073742128:
case 1073741925:
case 1073742189:
bsSelected = this.vwr.ms.getAtoms(tok, JS.SV.sValue(args[1]));
break out;
case 1094713349:
case 1094713350:
bsSelected = this.vwr.ms.getAtoms(tok, JS.SV.ptValue(args[1]));
break out;
case 1814695966:
if (isDistance) {
bsSelected = this.vwr.ms.getAtoms(tok,  Clazz.newArray(-1, [null, Double.$valueOf(distance)]));
break out;
}isUnitCell = true;
break;
}
break;
case 3:
switch (tok) {
case 1073742335:
case 1073742334:
case 1086324742:
case 1648363544:
case 134217750:
case 134219777:
case 1073742329:
case 8:
case 7:
break;
case 1086324744:
withinStr = JS.SV.sValue(args[1]);
break;
case 2:
case 3:
if (!isDistance || !"unitcell".equals(args[2].value)) {
return false;
}isUnitCell = true;
case 1814695966:
if (isUnitCell) {
if (isDistance) {
isUnitCell = false;
bsSelected = this.vwr.ms.getAtoms(1814695966,  Clazz.newArray(-1, [null, Double.$valueOf(distance), Double.$valueOf(isBooleanFlag ? distance : -distance)]));
break out;
}} else {
isUnitCell = true;
}break;
default:
return false;
}
break;
case 4:
switch (tok) {
case 1814695966:
if (!isDistance) return false;
isUnitCell = true;
break;
default:
return false;
}
break;
}
if (isUnitCell) {
var o = this.getUnitCell(args, -1, (isDistance ? 2 : 1), args.length - 1);
if (o == null) return false;
var oabc = o;
var uc = this.vwr.getSymTemp().getUnitCell(oabc, false, null);
bsSelected = this.vwr.ms.getAtoms(tok,  Clazz.newArray(-1, [uc, isDistance ? Float.$valueOf(distance) : null]));
break;
}var plane = null;
var pt = null;
var pts1 = null;
var last = args.length - 1;
switch (args[last].tok) {
case 9:
plane = args[last].value;
break;
case 8:
pt = args[last].value;
if (JS.SV.sValue(args[1]).equalsIgnoreCase("hkl")) plane = this.e.getHklPlane(pt, NaN, null);
break;
case 7:
pts1 = (last == 2 && args[1].tok == 7 ? args[1].getList() : null);
pt = (last == 2 ? JS.SV.ptValue(args[1]) : last == 1 ? JU.P3.new3(NaN, 0, 0) : null);
break;
}
if (plane != null) {
bsSelected = ms.getAtomsNearPlane(distance, plane);
break out;
}var bsLast = (args[last].tok == 10 ? args[last].value : null);
if (bs == null) bs = bsLast;
if (last > 0 && pt == null && pts1 == null && bs == null) return false;
if (tok == 1814695966) {
var asMap = isBooleanFlag;
return ((bs != null || pt != null) && mp.addXObj(this.vwr.ms.getUnitCellPointsWithin(distance, bs, pt, asMap)));
}if (pt != null || pts1 != null) {
if (args[last].tok == 7) {
var sv = args[last].getList();
var ap3 =  new Array(sv.size());
for (var i = ap3.length; --i >= 0; ) ap3[i] = JS.SV.ptValue(sv.get(i));

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

}var ret =  new Array(1);
if (bs != null) {
bs.and(this.vwr.getAllAtoms());
ap31 = this.vwr.ms.at;
}switch (J.bspt.PointIterator.withinDistPoints(distance, pt, ap3, ap31, bs, ret)) {
case 10:
return mp.addXBs(ret[0]);
case 134217751:
return mp.addXPt(ret[0]);
case 1073742001:
return mp.addXList(ret[0]);
case 1275068418:
return mp.addXAI(ret[0]);
case 4:
return mp.addXStr(ret[0]);
default:
return false;
}
}return mp.addXBs(this.vwr.getAtomsNearPt(distance, pt, null));
}if (tok == 1086324744) {
return mp.addXBs(this.vwr.ms.getSequenceBits(withinStr, bs,  new JU.BS()));
}if (bs == null) bs =  new JU.BS();
if (!isDistance) {
try {
return mp.addXBs(this.vwr.ms.getAtoms(tok, bs));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return false;
} else {
throw e;
}
}
}if (isWithinGroup) return mp.addXBs(this.vwr.getGroupsWithin(Clazz.floatToInt(distance), bs));
if (isVdw) {
rd =  new J.atomdata.RadiusData(null, (distance > 10 ? distance / 100 : distance), (distance > 10 ? J.atomdata.RadiusData.EnumType.FACTOR : J.atomdata.RadiusData.EnumType.OFFSET), J.c.VDW.AUTO);
if (distance < 0) distance = 0;
}var bsret = this.vwr.ms.getAtomsWithinRadius(distance, (isAtomProperty ? bsLast : bs), isBooleanFlag, rd, isAtomProperty ? bs : null);
if (isAtomProperty) {
bsret.andNot(bsLast);
}return mp.addXBs(bsret);
}
if (bsSelected != null) {
if (bs != null) bsSelected.and(bs);
return mp.addXBs(bsSelected);
}return false;
}, "JS.ScriptMathProcessor,~A,~B");
Clazz.defineMethod(c$, "evaluateWrite", 
function(mp, args){
if (!this.checkAccess()) return false;
var n = args.length;
var asBytes = false;
if (n == 2 && args[1].tok == 1073742335) {
n = 1;
asBytes = true;
}switch (n) {
case 0:
return false;
case 1:
var type = args[0].asString().toUpperCase();
if (type.equals("PNGJ")) {
var o = this.vwr.fm.getFileAsMap(null, "PNGJ", asBytes);
return (asBytes ? mp.addX(JS.SV.newV(15,  new JU.BArray(o))) : mp.addXMap(o));
}if (JU.PT.isOneOf(type, ";ZIP;ZIPALL;JMOL;")) {
var params =  new java.util.Hashtable();
var oc =  new JU.OC();
params.put("outputChannel", oc);
this.vwr.createZip(null, type, params);
var bytes = oc.toByteArray();
if (asBytes) return mp.addX(JS.SV.newV(15,  new JU.BArray(bytes)));
params =  new java.util.Hashtable();
this.vwr.readFileAsMap(JU.Rdr.getBIS(bytes), params, null);
return mp.addXMap(params);
}break;
}
return mp.addXStr(this.e.getCmdExt().dispatch(134221856, true, args));
}, "JS.ScriptMathProcessor,~A");
Clazz.defineMethod(c$, "getAtomsNearSurface", 
function(distance, surfaceId){
var data =  Clazz.newArray(-1, [surfaceId, null, null]);
if (this.e.getShapePropertyData(24, "getVertices", data)) return this.getAtomsNearPts(distance, data[1], data[2]);
data[1] = Integer.$valueOf(0);
data[2] = Integer.$valueOf(-1);
if (this.e.getShapePropertyData(22, "getCenter", data)) {
return this.vwr.getAtomsNearPt(distance, data[2], null);
}data[1] = Float.$valueOf(distance);
if (this.e.getShapePropertyData(21, "getAtomsWithin", data)) return data[2];
return  new JU.BS();
}, "~N,~S");
Clazz.defineMethod(c$, "getAtomsNearPts", 
function(distance, points, bsInclude){
var bsResult =  new JU.BS();
if (points.length == 0 || bsInclude != null && bsInclude.isEmpty()) return bsResult;
if (bsInclude == null) bsInclude = JU.BSUtil.setAll(points.length);
var at = this.vwr.ms.at;
for (var i = this.vwr.ms.ac; --i >= 0; ) {
var atom = at[i];
if (atom == null) continue;
for (var j = bsInclude.nextSetBit(0); j >= 0; j = bsInclude.nextSetBit(j + 1)) if (atom.distance(points[j]) < distance) {
bsResult.set(i);
break;
}
}
return bsResult;
}, "~N,~A,JU.BS");
Clazz.defineMethod(c$, "getMinMax", 
function(floatOrSVArray, tok, isSV){
var data = null;
var sv = null;
var ndata = 0;
var htPivot = null;
while (true) {
if (JU.AU.isAF(floatOrSVArray)) {
if (tok == 1275068725) return Float.$valueOf(NaN);
data = floatOrSVArray;
ndata = data.length;
if (ndata == 0) break;
} else if (Clazz.instanceOf(floatOrSVArray,"JU.Lst")) {
sv = floatOrSVArray;
ndata = sv.size();
if (ndata == 0) {
if (tok != 1275068725) break;
} else {
if (tok != 1275068725) {
var sv0 = sv.get(0);
if (sv0.tok == 8) return this.getMinMaxPoint(sv, tok);
if (sv0.tok == 4 && (sv0.value).startsWith("{")) {
var pt = JS.SV.ptValue(sv0);
if (Clazz.instanceOf(pt,"JU.P3")) return this.getMinMaxPoint(sv, tok);
if (Clazz.instanceOf(pt,"JU.P4")) return this.getMinMaxQuaternion(sv, tok);
break;
}}}} else {
break;
}var sum;
var minMax;
var isMin = false;
switch (tok) {
case 1275068725:
htPivot =  new java.util.Hashtable();
sum = minMax = 0;
break;
case 32:
isMin = true;
sum = 3.4028235E38;
minMax = 2147483647;
break;
case 64:
sum = -3.4028235E38;
minMax = -2147483647;
break;
default:
sum = minMax = 0;
}
var sum2 = 0;
var n = 0;
var isInt = true;
var isPivot = (tok == 1275068725);
for (var i = ndata; --i >= 0; ) {
var o = (sv == null ? null : sv.get(i));
var svi = (!isSV ? null : o == null ? JS.SV.vF : o);
var v = (isPivot ? 1 : data == null ? JS.SV.fValue(svi) : data[i]);
if (Float.isNaN(v)) continue;
n++;
switch (tok) {
case 160:
case 192:
sum2 += (v) * v;
case 128:
case 96:
sum += v;
break;
case 1275068725:
var key = (svi == null ? o.toString() : svi.asString());
var ii = htPivot.get(key);
htPivot.put(key, (ii == null ? Integer.$valueOf(1) : Integer.$valueOf(ii.intValue() + 1)));
break;
case 32:
case 64:
isInt = new Boolean (isInt & (svi.tok == 2)).valueOf();
if (isMin == (v < sum)) {
sum = v;
if (isInt) minMax = svi.intValue;
}break;
}
}
if (tok == 1275068725) {
return htPivot;
}if (n == 0) break;
switch (tok) {
case 96:
sum /= n;
break;
case 192:
if (n == 1) break;
sum = Math.sqrt((sum2 - sum * sum / n) / (n - 1));
break;
case 32:
case 64:
if (isInt) return Integer.$valueOf(minMax);
break;
case 128:
break;
case 160:
sum = sum2;
break;
}
return Float.$valueOf(sum);
}
return JS.MathExt.nan;
}, "~O,~N,~B");
Clazz.defineMethod(c$, "getMinMaxPoint", 
function(pointOrSVArray, tok){
var data = null;
var sv = null;
var ndata = 0;
if (Clazz.instanceOf(pointOrSVArray,Array)) {
data = pointOrSVArray;
ndata = data.length;
} else if (Clazz.instanceOf(pointOrSVArray,"JU.Lst")) {
sv = pointOrSVArray;
ndata = sv.size();
}if (sv == null && data == null) return JS.MathExt.nan;
var result =  new JU.P3();
var fdata =  Clazz.newFloatArray (ndata, 0);
for (var xyz = 0; xyz < 3; xyz++) {
for (var i = 0; i < ndata; i++) {
var pt = (data == null ? JS.SV.ptValue(sv.get(i)) : data[i]);
if (pt == null) return JS.MathExt.nan;
switch (xyz) {
case 0:
fdata[i] = pt.x;
break;
case 1:
fdata[i] = pt.y;
break;
case 2:
fdata[i] = pt.z;
break;
}
}
var f = this.getMinMax(fdata, tok, true);
if (!(Clazz.instanceOf(f, Number))) return JS.MathExt.nan;
var value = (f).floatValue();
switch (xyz) {
case 0:
result.x = value;
break;
case 1:
result.y = value;
break;
case 2:
result.z = value;
break;
}
}
return result;
}, "~O,~N");
Clazz.defineMethod(c$, "getMinMaxQuaternion", 
function(svData, tok){
var data;
switch (tok) {
case 32:
case 64:
case 128:
case 160:
return JS.MathExt.nan;
}
while (true) {
data = this.e.getQuaternionArray(svData, 1073742001);
if (data == null) break;
var retStddev =  Clazz.newFloatArray (1, 0);
var result = JU.Quat.sphereMean(data, retStddev, 0.0001);
switch (tok) {
case 96:
return result;
case 192:
return Float.$valueOf(retStddev[0]);
}
break;
}
return JS.MathExt.nan;
}, "JU.Lst,~N");
Clazz.defineMethod(c$, "getPatternMatcher", 
function(){
return (this.pm == null ? this.pm = J.api.Interface.getUtil("PatternMatcher", this.e.vwr, "script") : this.pm);
});
Clazz.defineMethod(c$, "setContactBitSets", 
function(bsA, bsB, localOnly, distance, rd, warnMultiModel){
var withinAllModels;
var bs;
if (bsB == null) {
bsB = JU.BSUtil.setAll(this.vwr.ms.ac);
JU.BSUtil.andNot(bsB, this.vwr.slm.bsDeleted);
bsB.andNot(bsA);
withinAllModels = false;
} else {
bs = JU.BSUtil.copy(bsA);
bs.or(bsB);
var nModels = this.vwr.ms.getModelBS(bs, false).cardinality();
withinAllModels = (nModels > 1);
if (warnMultiModel && nModels > 1 && !this.e.tQuiet) this.e.showString(J.i18n.GT.$("Note: More than one model is involved in this contact!"));
}if (!bsA.equals(bsB)) {
var setBfirst = (!localOnly || bsA.cardinality() < bsB.cardinality());
if (setBfirst) {
bs = this.vwr.ms.getAtomsWithinRadius(distance, bsA, withinAllModels, (Float.isNaN(distance) ? rd : null), null);
bsB.and(bs);
}if (localOnly) {
bs = this.vwr.ms.getAtomsWithinRadius(distance, bsB, withinAllModels, (Float.isNaN(distance) ? rd : null), null);
bsA.and(bs);
if (!setBfirst) {
bs = this.vwr.ms.getAtomsWithinRadius(distance, bsA, withinAllModels, (Float.isNaN(distance) ? rd : null), null);
bsB.and(bs);
}bs = JU.BSUtil.copy(bsB);
bs.and(bsA);
if (bs.equals(bsA)) bsB.andNot(bsA);
 else if (bs.equals(bsB)) bsA.andNot(bsB);
}}return bsB;
}, "JU.BS,JU.BS,~B,~N,J.atomdata.RadiusData,~B");
c$.nan = Float.$valueOf(NaN);
c$.t0 = System.currentTimeMillis();
});
;//5.0.1-v7 Tue Feb 10 12:29:49 CST 2026
