Clazz.declarePackage("JS");
Clazz.load(["JS.ScriptExt"], "JS.IsoExt", ["JU.AU", "$.BS", "$.Lst", "$.M4", "$.Measure", "$.P3", "$.PT", "$.Quat", "$.SB", "$.V3", "J.api.Interface", "J.atomdata.RadiusData", "J.c.VDW", "JS.SV", "$.ScriptEval", "$.ScriptInterruption", "$.T", "JU.BSUtil", "$.BoxInfo", "$.C", "$.Escape", "$.Logger", "$.Parser", "$.TempArray", "$.Triangulator", "JV.JC"], function(){
var c$ = Clazz.declareType(JS, "IsoExt", JS.ScriptExt);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JS.IsoExt, []);
});
Clazz.overrideMethod(c$, "dispatch", 
function(iTok, b, st){
this.chk = this.e.chk;
this.slen = this.e.slen;
this.st = st;
switch (iTok) {
case 23:
this.cgo();
break;
case 25:
this.contact();
break;
case 17:
this.dipole();
break;
case 22:
this.draw();
break;
case 24:
case 30:
case 29:
this.isosurface(iTok);
break;
case 26:
this.lcaoCartoon();
break;
case 27:
case 28:
this.mo(b, iTok);
break;
}
return null;
}, "~N,~B,~A");
Clazz.defineMethod(c$, "dipole", 
function(){
var eval = this.e;
var propertyName = null;
var propertyValue = null;
var iHaveAtoms = false;
var iHaveCoord = false;
var idSeen = false;
var getCharges = false;
var bsSelected = null;
eval.sm.loadShape(17);
if (this.tokAt(1) == 1073742001 && this.listIsosurface(17)) return;
this.setShapeProperty(17, "init", null);
if (this.slen == 1) {
this.setShapeProperty(17, "thisID", null);
return;
}for (var i = 1; i < this.slen; ++i) {
propertyName = null;
propertyValue = null;
switch (this.getToken(i).tok) {
case 1073742327:
propertyName = "all";
getCharges = true;
break;
case 1073742335:
propertyName = "on";
break;
case 1073742334:
propertyName = "off";
break;
case 12291:
propertyName = "delete";
break;
case 2:
case 3:
propertyName = "value";
propertyValue = Float.$valueOf(this.floatParameter(i));
break;
case 10:
if (this.tokAt(i + 1) == 10) {
this.setShapeProperty(17, "startSet", this.atomExpressionAt(i++));
} else {
propertyName = "atomBitset";
}case 1073742325:
if (propertyName == null) propertyName = (iHaveAtoms || iHaveCoord ? "endSet" : "startSet");
propertyValue = bsSelected = this.atomExpressionAt(i);
i = eval.iToken;
if (this.tokAt(i + 1) == 0 && propertyName === "startSet") propertyName = "atomBitset";
iHaveAtoms = true;
getCharges = true;
break;
case 1073742332:
case 8:
var pt = this.getPoint3f(i, true);
i = eval.iToken;
propertyName = (iHaveAtoms || iHaveCoord ? "endCoord" : "startCoord");
propertyValue = pt;
iHaveCoord = true;
break;
case 1677721602:
propertyName = "bonds";
getCharges = true;
break;
case 4102:
getCharges = true;
propertyName = "calculate";
if (eval.isAtomExpression(i + 1)) {
propertyValue = bsSelected = this.atomExpressionAt(++i);
i = eval.iToken;
}break;
case 1073741974:
this.setShapeId(17, ++i, idSeen);
i = eval.iToken;
break;
case 1275069442:
propertyName = "cross";
propertyValue = Boolean.TRUE;
break;
case 1073742040:
propertyName = "cross";
propertyValue = Boolean.FALSE;
break;
case 1073742066:
if (this.isFloatParameter(i + 1)) {
var v = this.floatParameter(++i);
if (eval.theTok == 2) {
propertyName = "offsetPercent";
propertyValue = Integer.$valueOf(Clazz.floatToInt(v));
} else {
propertyName = "offset";
propertyValue = Float.$valueOf(v);
}} else {
propertyName = "offsetPt";
propertyValue = this.centerParameter(++i);
i = eval.iToken;
}break;
case 1073742068:
propertyName = "offsetSide";
propertyValue = Float.$valueOf(this.floatParameter(++i));
break;
case 1073742188:
propertyName = "value";
propertyValue = Float.$valueOf(this.floatParameter(++i));
break;
case 1073742196:
propertyName = "width";
propertyValue = Float.$valueOf(this.floatParameter(++i));
break;
default:
if (eval.theTok == 268441089 || JS.T.tokAttr(eval.theTok, 1073741824)) {
this.setShapeId(17, i, idSeen);
i = eval.iToken;
break;
}this.invArg();
}
idSeen = (eval.theTok != 12291 && eval.theTok != 4102);
if (getCharges) {
if (!this.chk) eval.getPartialCharges(bsSelected);
getCharges = false;
}if (propertyName != null) this.setShapeProperty(17, propertyName, propertyValue);
}
if (iHaveCoord || iHaveAtoms) this.setShapeProperty(17, "set", null);
});
Clazz.defineMethod(c$, "draw", 
function(){
var eval = this.e;
eval.sm.loadShape(22);
switch (this.tokAt(1)) {
case 1073742001:
if (this.listIsosurface(22)) return;
break;
case 136314895:
case 134221850:
case 4138:
this.e.getCmdExt().dispatch(4133, false, this.st);
return;
}
var havePoints = false;
var isInitialized = false;
var isSavedState = false;
var isIntersect = false;
var isFrame = false;
var plane;
var pts = null;
var tokIntersectBox = 0;
var translucentLevel = 3.4028235E38;
var colorArgb =  Clazz.newIntArray(-1, [-2147483648]);
var intScale = 0;
var swidth = "";
var iptDisplayProperty = 0;
var center = null;
var thisId = this.initIsosurface(22);
var idSeen = (thisId != null);
var isWild = (idSeen && this.getShapeProperty(22, "ID") == null);
var connections = null;
var iConnect = 0;
var iArray = -1;
var iOn = -1;
var isBest = false;
var meshNoFill = false;
var tok = 0;
var lattice = null;
for (var i = eval.iToken; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
tok = this.getToken(i).tok;
switch (tok) {
case 134217763:
switch (tok = this.getToken(i + (this.tokAt(i + 1) == 1073741864 ? 2 : 1)).tok) {
case 1814695966:
case 1812599299:
tokIntersectBox = tok;
isIntersect = true;
continue;
case 1073742330:
++i;
propertyName = "intersect";
propertyValue = eval.objectNameParameter(++i);
isIntersect = true;
havePoints = true;
break;
default:
this.invArg();
}
break;
case 1073741864:
isBest = true;
if (iOn == i - 1) iOn++;
switch (this.tokAt(i + 1)) {
case 134217750:
case 1073741998:
case 1812599299:
continue;
default:
this.invArg();
}
break;
case 1611272194:
if (!this.chk) this.vwr.getModelkit(false).drawAxes(thisId, swidth);
return;
case 1073741994:
case 1814695966:
case 1812599299:
lattice = null;
var uc = null;
var ucLattice = null;
var bs = null;
switch (tok) {
case 1812599299:
switch (this.tokAt(i + 1)) {
case 1073741864:
switch (this.tokAt(i + 2)) {
case 134217750:
case 1073741998:
break;
case 1073742330:
var data =  Clazz.newArray(-1, [eval.objectNameParameter(i + 3), null]);
if (this.chk) return;
this.vwr.shm.getShapePropertyData(24, "points", data);
pts = data[1];
if (pts == null) this.invArg();
i += 2;
default:
isBest = true;
i++;
}
break;
case 10:
case 1073742325:
bs = eval.getAtomsStartingAt(i + 1);
i = eval.iToken;
}
break;
case 1814695966:
if (isBest) this.invArg();
if (eval.isArrayParameter(i + 1)) {
uc = this.vwr.getSymTemp().getUnitCell(eval.getPointArray(i + 1, -1, false), false, null);
i = eval.iToken;
} else {
switch (this.tokAt(i + 1)) {
case 4:
var tr = this.stringParameter(i + 1);
if (tr.length > 0 && (uc = this.vwr.getCurrentUnitCell()) != null) {
uc = this.vwr.getSymTemp().getUnitCell(uc.getV0abc(tr, null), false, "draw");
}i = eval.iToken;
break;
case 8:
case 1073742332:
ucLattice = eval.getFractionalPoint(i + 1);
i = eval.iToken;
break;
}
}if (this.tokAt(i + 1) == 1073741994) {
if (tokIntersectBox == 1814695966) tokIntersectBox = 1073741994;
++i;
lattice = eval.checkHKL(eval.getPointOrPlane(++i, 3));
i = eval.iToken;
}if (this.tokAt(i + 1) == 1611272194) {
if (ucLattice == null) ucLattice = JU.P3.new3(555, 555, 1);
i++;
}break;
}
if (this.chk) break;
if (bs != null) {
if (isBest) {
uc = this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966, "array", bs, null), false, null);
}} else if (isBest) {
uc = this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966, "array", null, pts), false, null);
} else if (tok == 1814695966 && uc == null) {
if (ucLattice != null) {
this.vwr.getModelkit(false).drawUnitCell(thisId, ucLattice, swidth);
return;
}uc = this.vwr.getCurrentUnitCell();
}if (lattice == null) {
pts = this.getBoxPoints(uc != null ? 1814695966 : tok, uc, bs, intScale / 100);
} else {
var cpts = JU.Measure.getLatticePoints(uc.getLatticeCentering(), Clazz.floatToInt(lattice.x), Clazz.floatToInt(lattice.y), Clazz.floatToInt(lattice.z));
pts =  new Array(cpts.size());
for (var j = 0; j < cpts.size(); j++) {
pts[j] = cpts.get(j);
uc.toCartesian(pts[j], true);
}
}isBest = false;
if (!isIntersect) {
if (pts == null) this.invArg();
propertyName = "polygon";
var v =  new JU.Lst();
v.addLast(pts);
if (lattice == null) {
this.vwr.getTriangulator();
v.addLast(JU.Triangulator.fullCubePolygon);
} else {
v.addLast(null);
}propertyValue = v;
havePoints = true;
intScale = 0;
meshNoFill = true;
break;
}if (this.tokAt(i + 1) == 1073742335) {
iOn = ++i;
}break;
case 1073741998:
case 134219777:
case 134217750:
var isProjection = (iOn == i - 1);
if (!havePoints && !isIntersect && tokIntersectBox == 0) {
if (eval.theTok == 134219777) {
havePoints = true;
this.setShapeProperty(22, "plane", null);
var list =  new JU.Lst();
plane = eval.hklParameter(++i, list, true);
i = eval.iToken;
propertyName = "coords";
propertyValue = list;
break;
}if (!isBest) {
propertyName = (tok == 134217750 ? "plane" : "line");
iArray = i + 1;
break;
}if (!this.chk && tok != 1073741998 && pts == null) {
uc = this.vwr.getCurrentUnitCell();
tokIntersectBox = (uc == null ? 1812599299 : 1814695966);
pts = this.getBoxPoints(tokIntersectBox, uc, null, intScale / 100);
isIntersect = true;
}}plane = null;
var linePts = null;
var isAll = false;
switch (tok) {
case 134217750:
plane = eval.planeParameter(i, isBest);
break;
case 134219777:
plane = eval.hklParameter(++i, null, true);
if (this.tokAt(eval.iToken + 1) == 1073742327) {
isAll = true;
eval.iToken++;
}break;
case 1073741998:
if (tokIntersectBox == 1073741994) this.invArg();
if (isBest) {
linePts = this.bsToArray(eval.getAtomsStartingAt(++i));
} else if (eval.isCenterParameter(i + 1)) {
linePts =  Clazz.newArray(-1, [this.centerParameter(++i), this.centerParameter(eval.iToken + 1)]);
} else {
linePts = eval.getPointArray(++i, 2, false);
}if (linePts.length < 2) this.invArg();
break;
}
i = eval.iToken;
havePoints = true;
if (this.chk) break;
if (tok == 1073741998) {
linePts = JU.Measure.getBestLineThroughPoints(linePts, -1);
if (tokIntersectBox != 0) {
var v = JU.V3.newVsub(linePts[1], linePts[0]);
v.scale(1 / v.length());
linePts = (isProjection ? JU.Measure.getProjectedLineSegment(pts, -1, linePts[0], v, null) : this.vwr.getTriangulator().intersectLine(pts, -1, linePts[0], v));
if (linePts == null || linePts[1] == null) return;
}if (!isInitialized) {
this.setShapeProperty(22, "points", Integer.$valueOf(intScale));
isInitialized = true;
}var l =  new JU.Lst();
l.addLast(linePts[0]);
l.addLast(linePts[1]);
this.setShapeProperty(22, "coords", l);
break;
}if (tokIntersectBox == 0) {
propertyValue = plane;
propertyName = "planedef";
} else if (tokIntersectBox == 1073741994) {
propertyName = "polygon";
var cpts = JU.Measure.getPointsOnPlane(pts, plane);
pts = cpts.toArray( new Array(cpts.size()));
var v =  new JU.Lst();
v.addLast(pts);
v.addLast(null);
propertyValue = v;
intScale = 0;
} else {
if (isAll && tokIntersectBox == 1814695966) {
(J.api.Interface.getInterface("JU.BZone", this.vwr, "script")).drawHKL(this.vwr, thisId, plane, pts);
}propertyName = "polygon";
propertyValue = this.vwr.getTriangulator().intersectPlane(plane, pts, isProjection ? -1 : 0);
intScale = 0;
}break;
case 1275068447:
pts = (eval.isArrayParameter(++i) ? eval.getPointArray(i, -1, false) : null);
if (pts == null && eval.isAtomExpression(i)) {
bs = eval.atomExpressionAt(i);
pts = this.vwr.ms.getAtomPointVector(bs).toArray( new Array(bs.cardinality()));
}if (pts != null) {
i = eval.iToken + 1;
if (this.tokAt(i) == 12289) {
center = eval.centerParameter(++i, null);
i = eval.iToken + 1;
}}var type;
switch (this.tokAt(i)) {
case 536875059:
type = "";
break;
case 1111490563:
type = "Cs";
break;
case 1073742330:
var data =  Clazz.newArray(-1, [eval.objectNameParameter(++i), null]);
if (this.chk) return;
this.vwr.shm.getShapePropertyData(21, "points", data);
pts = data[1];
if (pts == null) this.invArg();
type = "";
break;
case 1275203608:
type = ":poly";
break;
case 134217764:
if (center == null) center =  new JU.P3();
var crpts = this.vwr.ms.generateCrystalClass(this.vwr.bsA().nextSetBit(0), JU.P3.new3(NaN, NaN, NaN));
if (pts != null) this.invArg();
pts =  new Array(crpts.size());
for (var j = crpts.size(); --j >= 0; ) pts[j] = crpts.get(j);

i++;
type = "";
break;
default:
type = eval.optParameterAsString(i);
break;
}
var scale = (intScale == 0 ? 1 : intScale / 100);
var index = 0;
if (type.length > 0) {
if (this.isFloatParameter(++i)) index = this.intParameter(i++);
}if (this.tokAt(i) == 536875059) scale = this.floatParameter(++i);
if (!this.chk) eval.runScript(this.vwr.ms.getPointGroupAsString(this.vwr.bsA(), type, index, scale, pts, center, thisId == null ? "" : thisId));
return;
case 4106:
connections =  Clazz.newIntArray (4, 0);
iConnect = 4;
var farray = eval.floatParameterSet(++i, 4, 4);
i = eval.iToken;
for (var j = 0; j < 4; j++) connections[j] = Clazz.floatToInt(farray[j]);

havePoints = true;
break;
case 1677721602:
case 1153433601:
if (connections == null || iConnect > (eval.theTok == 1228931586 ? 2 : 3)) {
iConnect = 0;
connections =  Clazz.newIntArray(-1, [-1, -1, -1, -1]);
}connections[iConnect++] = this.atomExpressionAt(++i).nextSetBit(0);
i = eval.iToken;
connections[iConnect++] = (eval.theTok == 1677721602 ? this.atomExpressionAt(++i).nextSetBit(0) : -1);
i = eval.iToken;
havePoints = true;
break;
case 554176565:
switch (this.getToken(++i).tok) {
case 1073742330:
propertyName = "slab";
propertyValue = eval.objectNameParameter(++i);
i = eval.iToken;
havePoints = true;
break;
default:
this.invArg();
}
break;
case 1275203608:
case 134217751:
case 1073742106:
var isPoints = (tok == 134217751);
propertyName = "polygon";
havePoints = true;
var v =  new JU.Lst();
var nVertices = 0;
var nTriangles = 0;
var points = null;
var vpolygons = null;
var polygons = null;
if (eval.isArrayParameter(++i)) {
points = eval.getPointArray(i, -1, true);
if (points.length > 0 && points[0] == null) {
var faces;
if (tok == 1275203608) {
faces = this.getIntArray2(i);
} else {
faces = JU.AU.newInt2(1);
faces[0] = eval.expandFloatArray(eval.floatParameterSet(i, -1, 2147483647), -1, false);
}points = this.getAllPoints(this.e.iToken + 1, 3);
try {
polygons = (J.api.Interface.getInterface("JU.MeshCapper", this.vwr, "script")).set(null).triangulateFaces(faces, points, null);
} catch (e) {
this.invArg();
}
}nVertices = points.length;
}if (tok == 1275203608) {
nVertices = points.length;
}if (points == null) {
nVertices = Math.max(0, this.intParameter(i));
points =  new Array(nVertices);
for (var j = 0; j < nVertices; j++) points[j] = this.centerParameter(++eval.iToken);

}i = eval.iToken;
switch (this.tokAt(i + 1)) {
case 11:
case 12:
vpolygons = JS.SV.newT(this.getToken(++i)).toArray().getList();
nTriangles = vpolygons.size();
break;
case 7:
vpolygons = (this.getToken(++i)).getList();
nTriangles = vpolygons.size();
break;
case 2:
nTriangles = this.intParameter(++i);
if (nTriangles < 0) isPoints = true;
break;
default:
if (polygons == null && !isPoints && !this.chk) polygons = (J.api.Interface.getInterface("JU.MeshCapper", this.vwr, "script")).set(null).triangulatePolygon(points, -1);
break;
}
if (polygons == null && !isPoints) {
polygons = JU.AU.newInt2(nTriangles);
for (var j = 0; j < nTriangles; j++) {
var f = (vpolygons == null ? eval.floatParameterSet(++eval.iToken, 3, 4) : JS.SV.flistValue(vpolygons.get(j), 0));
if (f.length < 3 || f.length > 4) this.invArg();
polygons[j] =  Clazz.newIntArray(-1, [Clazz.floatToInt(f[0]), Clazz.floatToInt(f[1]), Clazz.floatToInt(f[2]), (f.length == 3 ? 7 : Clazz.floatToInt(f[3]))]);
}
}if (nVertices > 0) {
v.addLast(points);
v.addLast(polygons);
} else {
v = null;
}propertyValue = v;
i = eval.iToken;
break;
case 134217764:
case 1296041985:
var xyz = null;
var iSym = 2147483647;
plane = null;
var target = null;
var bsAtoms = null;
var options = 0;
var trans = null;
var opList = null;
var isSymop = (tok == 1296041985);
var nth = -1;
var ret =  Clazz.newArray(-1, [null, this.vwr.getFrameAtoms()]);
if (isSymop) {
iSym = 0;
switch (this.tokAt(++i)) {
case 4:
xyz = this.stringParameter(i);
break;
case 12:
xyz = this.vwr.getSymStatic().convertTransform("xyz", this.getToken(i).value);
break;
case 2:
default:
if (!eval.isCenterParameter(i)) {
if (eval.isArrayParameter(i)) {
var params = eval.floatParameterSet(i, 1, 2147483647);
opList =  Clazz.newIntArray (params.length, 0);
for (var j = opList.length; --j >= 0; ) opList[j] = Clazz.floatToInt(params[j]);

i = eval.iToken + 1;
} else {
iSym = this.intParameter(i++);
if (eval.isArrayParameter(i)) {
trans = JU.P3.newA(eval.floatParameterSet(i, 3, 3));
i = eval.iToken + 1;
}}}if (eval.isCenterParameter(i)) center = eval.centerParameter(i, ret);
if (opList == null && eval.isCenterParameter(eval.iToken + 1)) target = eval.centerParameter(++eval.iToken, ret);
if (this.chk) return;
i = eval.iToken;
if (center == null && i + 1 < this.slen) {
center = this.centerParameter(++i);
bsAtoms = (eval.isAtomExpression(i) ? this.atomExpressionAt(i) : null);
i = eval.iToken;
}nth = ((!isSymop || target != null) && this.tokAt(i + 1) == 2 ? eval.getToken(++i).intValue : -1);
if (nth < -1) this.invArg();
if (this.tokAt(i + 1) == 1814695966) {
target =  new JU.P3();
options = 1073742066;
eval.iToken = ++i;
} else if (this.tokAt(i + 1) == 1073742066) {
i++;
target = this.getPoint3f(i + 1, false);
options = 1073742066;
i = eval.iToken;
}break;
}
} else if (this.tokAt(i + 1) == 1073742327) {
nth = -2;
eval.iToken = ++i;
}if (xyz != null) {
i++;
if (eval.isCenterParameter(i)) {
center = eval.centerParameter(i, ret);
i = eval.iToken;
}}eval.checkLast(eval.iToken);
if (this.chk) return;
var s = "";
var iatom = (bsAtoms != null ? bsAtoms.nextSetBit(0) : -1);
if (bsAtoms == null && this.vwr.am.cmi >= 0) bsAtoms = this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi);
if (bsAtoms != null) {
s = this.vwr.getModelkit(false).drawSymmetry(thisId, isSymop, iatom, xyz, iSym, trans, center, target, intScale, nth, options, opList, false);
if (s == null) return;
if (isSymop && Clazz.instanceOf(target,"JM.Atom") && Clazz.instanceOf(center,"JM.Atom")) {
if (eval.fullCommand.indexOf("#quiet") >= 0) s = JU.PT.rep(s, "print", "#print");
s += "\nmodelkit set atomset " + JU.PT.esc(thisId + "|" + (center).i + "|" + (target).i + "|" + eval.fullCommand) + ";";
}}eval.runBufferedSafely(s.length > 0 ? s : "draw ID \"" + thisId + "*\" delete", eval.outputBuffer);
return;
case 4115:
isFrame = true;
continue;
case 1073742332:
case 9:
case 8:
if (eval.theTok == 9 || !eval.isPoint3f(i)) {
propertyValue = eval.getPoint4f(i);
if (isFrame) {
eval.checkLast(eval.iToken);
if (!this.chk) eval.runScript(JU.Escape.drawQuat(JU.Quat.newP4(propertyValue), (thisId == null ? "frame" : thisId), " " + swidth, (center == null ?  new JU.P3() : center), intScale / 100));
return;
}propertyName = "planedef";
} else {
propertyValue = center = this.getPoint3f(i, true);
propertyName = "coord";
}i = eval.iToken;
havePoints = true;
break;
case 1073742000:
propertyName = "lineData";
propertyValue = eval.floatParameterSet(++i, 0, 2147483647);
i = eval.iToken;
havePoints = true;
break;
case 12290:
case 10:
case 1073742325:
propertyName = "atomSet";
propertyValue = this.atomExpressionAt(i);
if (isFrame) center = this.centerParameter(i);
i = eval.iToken;
havePoints = true;
break;
case 7:
havePoints = true;
propertyName = (iArray == i ? "coords" : "modelBasedPoints");
propertyValue = eval.theToken.value;
break;
case 1073742195:
case 268436992:
break;
case 268437504:
propertyValue = eval.xypParameter(i);
if (propertyValue != null) {
i = eval.iToken;
propertyName = "coord";
havePoints = true;
break;
}if (isSavedState) this.invArg();
isSavedState = true;
break;
case 268437505:
if (!isSavedState) this.invArg();
isSavedState = false;
break;
case 1140850693:
propertyName = "reverse";
break;
case 1073742166:
if (this.tokAt(++i) == 1765808134) {
propertyValue = Integer.$valueOf(this.e.getArgbParamOrNone(++i, false));
propertyName = "titlecolor";
i = this.e.iToken;
break;
}if (this.tokAt(i) == 4114) {
--i;
continue;
}case 4:
propertyValue = this.stringParameter(i);
propertyName = "title";
break;
case 545259562:
propertyValue = this.stringParameter(++i);
propertyName = "hoverlabel";
break;
case 4114:
var fontSize = this.floatParameter(++i);
var fontFace = (this.tokAt(i + 1) == 1073741824 ? this.paramAsStr(++i) : null);
var fontStyle = (this.tokAt(i + 1) == 1073741824 ? this.paramAsStr(++i) : null);
if (this.tokAt(i + 1) != 4 && ++i != this.slen || fontSize <= 0 || fontSize > 0xFF) this.invArg();
propertyName = "myfont";
if (fontFace == null || fontStyle == null) {
var f = this.vwr.shm.getShapePropertyIndex(22, "font", -1);
if (fontFace == null) fontFace = f.fontFace;
if (fontStyle == null) fontStyle = f.fontStyle;
}propertyValue = this.vwr.getFont3D(fontFace, fontStyle, fontSize);
break;
case 135198:
propertyName = "vector";
break;
case 1140850691:
propertyValue = Float.$valueOf(this.floatParameter(++i));
propertyName = "length";
break;
case 3:
propertyValue = Float.$valueOf(this.floatParameter(i));
propertyName = "length";
break;
case 1094713359:
propertyName = "modelIndex";
propertyValue = Integer.$valueOf(this.intParameter(++i));
break;
case 2:
if (isSavedState) {
propertyName = "modelIndex";
propertyValue = Integer.$valueOf(this.intParameter(i));
} else {
intScale = this.intParameter(i);
}break;
case 536875059:
intScale = Math.round(this.floatParameter(++i) * (this.getToken(i).tok == 2 ? 1 : 100));
continue;
case 1073741974:
thisId = this.setShapeId(22, ++i, idSeen);
isWild = (this.getShapeProperty(22, "ID") == null);
i = eval.iToken;
break;
case 1073742027:
propertyName = "fixed";
propertyValue = Boolean.FALSE;
break;
case 12293:
propertyName = "fixed";
propertyValue = Boolean.TRUE;
break;
case 1073742066:
var pt = this.getPoint3f(++i, true);
i = eval.iToken;
propertyName = "offset";
propertyValue = pt;
break;
case 1073741906:
propertyName = "crossed";
break;
case 1073742196:
propertyValue = Float.$valueOf(this.floatParameter(++i));
propertyName = "width";
swidth = propertyName + " " + propertyValue;
break;
case 1073741908:
propertyName = "curve";
iArray = i + 1;
break;
case 1073741840:
propertyName = "arc";
iArray = i + 1;
break;
case 1073741846:
propertyName = "arrow";
iArray = i + 1;
break;
case 1073742194:
propertyName = "vertices";
iArray = i + 1;
break;
case 1073741880:
propertyName = "circle";
break;
case 1073741912:
propertyName = "cylinder";
break;
case 1073742048:
propertyName = "nohead";
break;
case 1073741860:
propertyName = "isbarb";
break;
case 1073742130:
propertyName = "rotate45";
break;
case 1073742092:
propertyName = "perp";
break;
case 1665140738:
case 1073741917:
var isRadius = (eval.theTok == 1665140738);
var f = this.floatParameter(++i);
if (isRadius) f *= 2;
propertyValue = Float.$valueOf(f);
propertyName = (isRadius || this.tokAt(i) == 3 ? "width" : "diameter");
swidth = propertyName + (this.tokAt(i) == 3 ? " " + f : " " + (Clazz.floatToInt(f)));
break;
case 1073742330:
if ((this.tokAt(i + 2) == 268437504 || isFrame)) {
var pto = center = this.centerParameter(i);
i = eval.iToken;
propertyName = "coord";
propertyValue = pto;
havePoints = true;
break;
}propertyValue = eval.objectNameParameter(++i);
propertyName = "identifier";
havePoints = true;
break;
case 1765808134:
case 603979967:
case 1073742074:
idSeen = true;
translucentLevel = this.getColorTrans(eval, i, false, colorArgb);
i = eval.iToken;
continue;
default:
if (!eval.setMeshDisplayProperty(22, 0, eval.theTok)) {
if (eval.theTok == 268441089 || JS.T.tokAttr(eval.theTok, 1073741824)) {
thisId = this.setShapeId(22, i, idSeen);
i = eval.iToken;
break;
}this.invArg();
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = eval.iToken;
continue;
}
idSeen = (eval.theTok != 12291);
if (havePoints && !isInitialized && !isFrame) {
this.setShapeProperty(22, "points", Integer.$valueOf(intScale));
isInitialized = true;
intScale = 0;
}if (havePoints && isWild) this.invArg();
if (propertyName != null) {
this.setShapeProperty(22, propertyName, propertyValue);
}}
if (meshNoFill) {
iptDisplayProperty = -1 - iptDisplayProperty;
}this.finalizeObject(22, colorArgb[0], translucentLevel, intScale, havePoints, connections, iptDisplayProperty, null);
});
Clazz.defineMethod(c$, "mo", 
function(isInitOnly, iShape){
var eval = this.e;
var offset = 2147483647;
var isNegOffset = false;
var nboType = null;
var bsModels = this.vwr.getVisibleFramesBitSet();
var propertyList =  new JU.Lst();
var isBeta = false;
var isNBO = (this.tokAt(0) == 1073877011);
var i0 = 1;
if (isNBO) {
var isViewOnly = this.e.optParameterAsString(1).equals("view");
if (this.e.slen == 1 || isViewOnly || this.e.optParameterAsString(1).equals("options")) {
if (!this.chk) {
var options = (isViewOnly ? "VIEW" : this.e.optParameterAsString(2));
this.vwr.startNBO(options);
}return;
}}if (this.tokAt(1) == 1094717454 || this.tokAt(1) == 4115) {
i0 = eval.modelNumberParameter(2);
if (i0 < 0) this.invArg();
bsModels.clearAll();
bsModels.set(i0);
i0 = 3;
}eval.sm.loadShape(iShape);
for (var iModel = bsModels.nextSetBit(0); iModel >= 0; iModel = bsModels.nextSetBit(iModel + 1)) {
var i = i0;
if (this.tokAt(i) == 1073742001 && this.listIsosurface(iShape)) return;
this.setShapeProperty(iShape, "init", Integer.$valueOf(iModel));
if (isInitOnly) return;
var title = null;
var moNumber = (this.getShapeProperty(iShape, "moNumber")).intValue();
var linearCombination = this.getShapeProperty(iShape, "moLinearCombination");
var squared = this.getShapeProperty(iShape, "moSquareData");
var linearSquared = (linearCombination == null ? null : this.getShapeProperty(iShape, "moSquareLinear"));
if (moNumber == 0) moNumber = 2147483647;
var propertyName = null;
var propertyValue = null;
var ignoreSquared = false;
var nboName = null;
switch (this.getToken(i).tok) {
case 1140850696:
if (iShape == 1073877010) {
this.mo(isInitOnly, 28);
return;
}nboType = this.paramAsStr(++i).toUpperCase();
if (eval.tokAt(i + 1) == 4) {
nboName = this.paramAsStr(++eval.iToken);
}break;
case 1073741875:
case 554176565:
propertyName = eval.theToken.value;
propertyValue = this.getCapSlabObject(i, false);
i = eval.iToken;
break;
case 1073741914:
linearSquared = Boolean.TRUE;
linearCombination =  Clazz.newFloatArray(-1, [1]);
offset = moNumber = 0;
break;
case 2:
moNumber = this.intParameter(i);
if (this.tokAt(i + 1) == 1073741865) {
isBeta = true;
i++;
}linearCombination = this.moCombo(propertyList);
if (linearCombination == null && moNumber < 0) linearCombination =  Clazz.newFloatArray(-1, [-100, -moNumber]);
ignoreSquared = true;
break;
case 268440576:
switch (this.tokAt(++i)) {
case 1073741973:
case 1073742008:
break;
default:
this.invArg();
}
isNegOffset = true;
case 1073741973:
case 1073742008:
if ((offset = this.moOffset(i)) == 2147483647) this.invArg();
moNumber = 0;
linearCombination = this.moCombo(propertyList);
ignoreSquared = true;
break;
case 1073742037:
moNumber = 1073742037;
isBeta = false;
linearCombination = this.moCombo(propertyList);
ignoreSquared = true;
break;
case 1073742108:
moNumber = 1073742108;
isBeta = false;
linearCombination = this.moCombo(propertyList);
ignoreSquared = true;
break;
case 1765808134:
this.setColorOptions(null, i + 1, iShape, 2);
break;
case 134217750:
propertyName = "plane";
propertyValue = (this.tokAt(this.e.iToken = ++i) == 1073742333 ? null : eval.planeParameter(i, false));
break;
case 134217751:
this.addShapeProperty(propertyList, "randomSeed", this.tokAt(i + 2) == 2 ? Integer.$valueOf(this.intParameter(i + 2)) : null);
propertyName = "monteCarloCount";
propertyValue = Integer.$valueOf(this.intParameter(i + 1));
break;
case 536875059:
propertyName = "scale";
propertyValue = Float.$valueOf(this.floatParameter(i + 1));
break;
case 1073741910:
if (this.tokAt(i + 1) == 268440577) {
propertyName = "cutoffPositive";
propertyValue = Float.$valueOf(this.floatParameter(i + 2));
} else {
propertyName = "cutoff";
propertyValue = Float.$valueOf(this.floatParameter(i + 1));
}break;
case 536870916:
propertyName = "debug";
break;
case 1073742054:
propertyName = "plane";
break;
case 1073742104:
case 1073742122:
propertyName = "resolution";
propertyValue = Float.$valueOf(this.floatParameter(i + 1));
break;
case 1073742156:
if (linearCombination == null) squared = Boolean.TRUE;
 else linearSquared = Boolean.TRUE;
ignoreSquared = false;
break;
case 1073742168:
if (i + 1 < this.slen && this.tokAt(i + 1) == 4) {
propertyName = "titleFormat";
propertyValue = this.paramAsStr(i + 1);
}break;
case 1073741824:
this.invArg();
break;
case 4:
if (isNBO && i == 1) {
nboName = eval.stringParameter(i);
break;
}default:
if (isNBO && eval.tokAt(i) == 4) {
nboName = this.paramAsStr(i++);
}if (eval.isArrayParameter(i)) {
linearCombination = eval.floatParameterSet(i, 1, 2147483647);
if (this.tokAt(eval.iToken + 1) == 1073742156) {
ignoreSquared = false;
linearSquared = Boolean.TRUE;
eval.iToken++;
}break;
}var ipt = eval.iToken;
if (!eval.setMeshDisplayProperty(iShape, 0, eval.theTok)) this.invArg();
this.setShapeProperty(iShape, "setProperties", propertyList);
eval.setMeshDisplayProperty(iShape, ipt, this.tokAt(ipt));
return;
}
if (propertyName != null) this.addShapeProperty(propertyList, propertyName, propertyValue);
var haveMO = (moNumber != 2147483647 || linearCombination != null);
if (this.chk) return;
if (nboType != null || nboName != null || haveMO) {
if (haveMO && this.tokAt(eval.iToken + 1) == 4) {
title = this.paramAsStr(++eval.iToken);
}eval.setCursorWait(true);
if (nboType != null || nboName != null) nboType = nboType + ":" + nboName;
this.setMoData(propertyList, moNumber, linearCombination, offset, isNegOffset, iModel, title, nboType, isBeta);
if (haveMO) {
this.addShapeProperty(propertyList, "finalize", null);
}}if (!ignoreSquared) {
this.setShapeProperty(iShape, "squareLinear", linearSquared);
this.setShapeProperty(iShape, "squareData", squared);
}if (propertyList.size() > 0) this.setShapeProperty(iShape, "setProperties", propertyList);
if (haveMO && !eval.tQuiet) {
var moLabel = "";
if (isNBO) {
moLabel = this.getShapeProperty(iShape, "moLabel");
} else {
moNumber = (this.getShapeProperty(iShape, "moNumber")).intValue();
moLabel = "" + moNumber;
}this.showString(JS.T.nameOf(this.tokAt(0)) + " " + moLabel + " " + (isBeta ? "beta " : "") + this.getShapeProperty(iShape, "message"));
}propertyList.clear();
}
}, "~B,~N");
Clazz.defineMethod(c$, "setNBOType", 
function(moData, type){
var nboNumber = -1;
var name = null;
var pt = type.indexOf(":");
if (pt > 0) {
name = type.substring(pt + 1);
type = type.substring(0, pt);
if (type.equals("null")) type = null;
if (name.equals("null")) name = null;
}if ((type == null ? 0 : JV.JC.getNBOTypeFromName(type)) < 0) this.invArg();
if (!moData.containsKey("nboLabels")) this.error(27);
if (this.chk) return -1;
if (type != null && !(J.api.Interface.getInterface("J.adapter.readers.quantum.GenNBOReader", this.vwr, "script")).readNBOCoefficients(moData, type, this.vwr)) this.error(27);
var auxFiles = moData.get("auxFiles");
var auxFiles0 = this.vwr.getCurrentModelAuxInfo().get("auxFiles");
if (auxFiles0 == null) {
this.vwr.getCurrentModelAuxInfo().put("auxFiles", auxFiles);
} else {
auxFiles0.addAll(auxFiles);
}if (name != null) {
pt = name.indexOf(".");
if (pt > 0) {
var ipt = JU.PT.parseInt(name.substring(pt + 1));
name = name.substring(0, pt);
pt = ipt;
}var labels = moData.get("nboLabels");
for (var i = 0, n = labels.length; i < n; i++) {
if (name.equals(labels[i])) {
if (pt < 0 || --pt == 0) {
nboNumber = i + 1;
break;
}}}
if (nboNumber < 0) this.error(27);
}return nboNumber;
}, "java.util.Map,~S");
Clazz.defineMethod(c$, "moCombo", 
function(propertyList){
if (this.tokAt(this.e.iToken + 1) != 1073742156) return null;
this.addShapeProperty(propertyList, "squareLinear", Boolean.TRUE);
this.e.iToken++;
return  Clazz.newFloatArray (0, 0);
}, "JU.Lst");
Clazz.defineMethod(c$, "moOffset", 
function(index){
var isHomo = (this.getToken(index).tok == 1073741973);
var offset = (isHomo ? 0 : 1);
var tok = this.tokAt(++index);
if (tok == 2 && (this.e.st[index].value).charAt(0) == '-') offset += this.intParameter(index);
 else if (tok == 268440577) offset += this.intParameter(++index);
 else if (tok == 268440576) offset -= this.intParameter(++index);
return offset;
}, "~N");
Clazz.defineMethod(c$, "setMoData", 
function(propertyList, moNumber, lc, offset, isNegOffset, modelIndex, title, nboType, isBeta){
var eval = this.e;
if (modelIndex < 0) {
modelIndex = this.vwr.am.cmi;
if (modelIndex < 0) eval.errorStr(30, "MO isosurfaces");
}var moData = this.vwr.ms.getInfo(modelIndex, "moData");
if (moData == null) this.error(27);
this.vwr.checkMenuUpdate();
if (nboType != null) {
var nboNumber = this.setNBOType(moData, nboType);
var nOrbitals = (moData.get("nboLabels")).length;
eval.showString(nOrbitals + " orbitals of type " + nboType.substring(0, nboType.indexOf(":") + 1) + " modelIndex=" + this.vwr.getModelNumberDotted(modelIndex));
if (nboNumber > 0) moNumber = nboNumber;
if (lc == null && moNumber == 2147483647) return;
}var mos = null;
var mo;
var nOrb = 0;
var f = null;
if (lc == null || lc.length < 2) {
if (lc != null && lc.length == 1) offset = 0;
 else if (isBeta && moData.containsKey("firstBeta")) offset = (moData.get("firstBeta")).intValue();
var lastMoNumber = (moData.containsKey("lastMoNumber") ? (moData.get("lastMoNumber")).intValue() : 0);
var lastMoCount = (moData.containsKey("lastMoCount") ? (moData.get("lastMoCount")).intValue() : 1);
if (moNumber == 1073742108) moNumber = lastMoNumber - 1;
 else if (moNumber == 1073742037) moNumber = lastMoNumber + lastMoCount;
mos = (moData.get("mos"));
nOrb = (mos == null ? 0 : mos.size());
if (nOrb == 0) this.error(25);
if (nOrb == 1 && moNumber > 1) this.error(29);
if (offset != 2147483647) {
if (isBeta) {
} else if (moData.containsKey("HOMO")) {
moNumber = (moData.get("HOMO")).intValue() + offset;
offset = 0;
} else {
moNumber = nOrb;
for (var i = 0; i < nOrb; i++) {
mo = mos.get(i);
if ((f = mo.get("occupancy")) != null) {
if (f.floatValue() < 0.5) {
moNumber = i;
break;
}continue;
} else if ((f = mo.get("energy")) != null) {
if (f.floatValue() > 0) {
moNumber = i;
break;
}continue;
}break;
}
if (f == null) this.error(28);
}moNumber += offset;
if (!this.chk) JU.Logger.info("MO " + moNumber);
}if (moNumber < 1 || moNumber > nOrb) eval.errorStr(26, "" + nOrb);
}moNumber = Math.abs(moNumber);
moData.put("lastMoNumber", Integer.$valueOf(moNumber));
moData.put("lastMoCount", Integer.$valueOf(1));
if (isNegOffset && lc == null) lc =  Clazz.newFloatArray(-1, [-100, moNumber]);
if (lc != null && lc.length < 2) {
mo = mos.get(moNumber - 1);
if ((f = mo.get("energy")) == null) {
lc =  Clazz.newFloatArray(-1, [100, moNumber]);
} else {
var energy = f.floatValue();
var bs = JU.BS.newN(nOrb);
var n = 0;
var isAllElectrons = (lc.length == 1 && lc[0] == 1);
for (var i = 0; i < nOrb; i++) {
if ((f = mos.get(i).get("energy")) == null) continue;
var e = f.floatValue();
if (isAllElectrons ? e <= energy : e == energy) {
bs.set(i + 1);
n += 2;
}}
lc =  Clazz.newFloatArray (n, 0);
for (var i = 0, pt = 0; i < n; i += 2) {
lc[i] = 1;
lc[i + 1] = (pt = bs.nextSetBit(pt + 1));
}
moData.put("lastMoNumber", Integer.$valueOf(bs.nextSetBit(0)));
moData.put("lastMoCount", Integer.$valueOf(Clazz.doubleToInt(n / 2)));
}this.addShapeProperty(propertyList, "squareLinear", Boolean.TRUE);
}this.addShapeProperty(propertyList, "moData", moData);
if (title != null) this.addShapeProperty(propertyList, "title", title);
this.addShapeProperty(propertyList, "molecularOrbital", lc != null ? lc : Integer.$valueOf(Math.abs(moNumber)));
this.addShapeProperty(propertyList, "clear", null);
}, "JU.Lst,~N,~A,~N,~B,~N,~S,~S,~B");
Clazz.defineMethod(c$, "isosurface", 
function(iShape){
var eval = this.e;
eval.sm.loadShape(iShape);
if (this.tokAt(1) == 1073742001 && this.listIsosurface(iShape)) return;
var iptDisplayProperty = 0;
var isDisplay = false;
var isBest = false;
var isIsosurface = (iShape == 24);
var isPmesh = (iShape == 29);
var isPlot3d = (iShape == 30);
var isLcaoCartoon = (iShape == 26);
var isSilent = (isLcaoCartoon || this.tokAt(1) == 12291 || eval.$isStateScript);
var surfaceObjectSeen = false;
var planeSeen = false;
var isMapped = false;
var isBicolor = false;
var isPhased = false;
var doCalcArea = false;
var doCalcVolume = false;
var isBeta = false;
var isCavity = false;
var haveRadius = false;
var toCache = false;
var isFxy = false;
var haveSlab = false;
var haveIntersection = false;
var isFrontOnly = false;
var nbotype = null;
var data = null;
var cmd = null;
var thisSet = null;
var nFiles = 0;
var nX;
var nY;
var nZ;
var ptX;
var ptY;
var sigma = NaN;
var cutoff = NaN;
var ptWithin = 0;
var smoothing = null;
var smoothingPower = 2147483647;
var bs = null;
var bsSelect = null;
var bsIgnore = null;
var sbCommand =  new JU.SB();
var pt;
var plane = null;
var lattice = null;
var fixLattice = false;
var pts = null;
var color = 0;
var str = null;
var modelIndex = (this.chk ? 0 : -2147483648);
eval.setCursorWait(true);
var idSeen = (this.initIsosurface(iShape) != null);
var isWild = (idSeen && this.getShapeProperty(iShape, "ID") == null);
var isColorSchemeTranslucent = false;
var isInline = false;
var isSign = false;
var colorDensity = false;
var onlyOneModel = null;
var filesData = null;
var translucency = null;
var colorScheme = null;
var mepOrMlp = null;
var symops = null;
var discreteColixes = null;
var propertyList =  new JU.Lst();
var defaultMesh = false;
if (isPmesh || isPlot3d) this.addShapeProperty(propertyList, "fileType", "Pmesh");
for (var i = eval.iToken; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
var tok = this.getToken(i).tok;
if (tok == 1073741824) {
str = this.paramAsStr(i);
if (str.equalsIgnoreCase("map")) tok = 4125;
}switch (tok) {
case 1073742148:
isSilent = true;
sbCommand.append(" silent");
propertyName = "silent";
break;
case 603979868:
smoothing = (this.getToken(++i).tok == 1073742335 ? Boolean.TRUE : eval.theTok == 1073742334 ? Boolean.FALSE : null);
if (smoothing == null) this.invArg();
continue;
case 553648146:
smoothingPower = this.intParameter(++i);
continue;
case 4128:
propertyName = "moveIsosurface";
if (this.tokAt(++i) != 12) this.invArg();
propertyValue = this.getToken(i++).value;
break;
case 1296041985:
var ff = this.floatArraySet(i + 2, this.intParameter(i + 1), 16);
symops =  new Array(ff.length);
for (var j = symops.length; --j >= 0; ) symops[j] = JU.M4.newA16(ff[j]);

i = eval.iToken;
break;
case 1088421903:
if (modelIndex < 0) modelIndex = Math.min(this.vwr.am.cmi, 0);
var needIgnore = (bsIgnore == null);
if (bsSelect == null) bsSelect = JU.BSUtil.copy(this.vwr.bsA());
bsSelect.and(this.vwr.ms.getAtoms(1296041985, Integer.$valueOf(1)));
if (!needIgnore) bsSelect.andNot(bsIgnore);
this.addShapeProperty(propertyList, "select", bsSelect);
if (needIgnore) {
bsIgnore = JU.BSUtil.copy(bsSelect);
JU.BSUtil.invertInPlace(bsIgnore, this.vwr.ms.ac);
isFrontOnly = true;
this.addShapeProperty(propertyList, "ignore", bsIgnore);
sbCommand.append(" ignore ").append(JU.Escape.eBS(bsIgnore));
}sbCommand.append(" symmetry");
if (color == 0) this.addShapeProperty(propertyList, "colorRGB", Integer.$valueOf(1296041985));
symops = this.vwr.ms.getSymMatrices(modelIndex);
break;
case 1073742066:
propertyName = "offset";
propertyValue = this.centerParameter(++i);
i = eval.iToken;
break;
case 528432:
propertyName = "rotate";
propertyValue = (this.tokAt(eval.iToken = ++i) == 1073742333 ? null : eval.getPoint4f(i));
i = eval.iToken;
break;
case 1610612740:
propertyName = "scale3d";
propertyValue = Float.$valueOf(this.floatParameter(++i));
break;
case 1073742090:
sbCommand.append(" periodic");
propertyName = "periodic";
break;
case 1073742078:
case 266298:
case 134217751:
propertyName = eval.theToken.value.toString();
sbCommand.append(" ").appendO(eval.theToken.value);
propertyValue = this.centerParameter(++i);
sbCommand.append(" ").append(JU.Escape.eP(propertyValue));
i = eval.iToken;
break;
case 1812599299:
if (eval.fullCommand.indexOf("# BBOX=") >= 0) {
var bbox = JU.PT.split(JU.PT.getQuotedAttribute(eval.fullCommand, "# BBOX"), ",");
pts =  Clazz.newArray(-1, [JU.Escape.uP(bbox[0]), JU.Escape.uP(bbox[1])]);
} else if (eval.isCenterParameter(i + 1)) {
pts =  Clazz.newArray(-1, [this.getPoint3f(i + 1, true), this.getPoint3f(eval.iToken + 1, true)]);
i = eval.iToken;
} else {
pts = this.vwr.ms.getBBoxVertices();
}sbCommand.append(" boundBox " + JU.Escape.eP(pts[0]) + " " + JU.Escape.eP(pts[pts.length - 1]));
propertyName = "boundingBox";
propertyValue = pts;
break;
case 135188:
isPmesh = true;
sbCommand.append(" pmesh");
propertyName = "fileType";
propertyValue = "Pmesh";
break;
case 134217763:
bsSelect = this.atomExpressionAt(++i);
if (this.chk) {
bs =  new JU.BS();
} else if (this.tokAt(eval.iToken + 1) == 1073742325 || this.tokAt(eval.iToken + 1) == 10) {
bs = this.atomExpressionAt(++eval.iToken);
bs.and(this.vwr.ms.getAtomsWithinRadius(5.0, bsSelect, false, null, null));
} else {
bs = this.vwr.ms.getAtomsWithinRadius(5.0, bsSelect, true, null, null);
bs.andNot(this.vwr.ms.getAtoms(1094713360, bsSelect));
}bs.andNot(bsSelect);
sbCommand.append(" intersection ").append(JU.Escape.eBS(bsSelect)).append(" ").append(JU.Escape.eBS(bs));
i = eval.iToken;
if (this.tokAt(i + 1) == 134320141) {
i++;
var f = this.getToken(++i).value;
sbCommand.append(" function ").append(JU.PT.esc(f));
if (!this.chk) this.addShapeProperty(propertyList, "func", (f.equals("a+b") || f.equals("a-b") ? f : this.createFunction("__iso__", "a,b", f)));
} else {
haveIntersection = true;
}propertyName = "intersection";
propertyValue =  Clazz.newArray(-1, [bsSelect, bs]);
break;
case 1610625028:
case 134217759:
isDisplay = (tok == 1610625028);
if (isDisplay) {
sbCommand.append(" display");
iptDisplayProperty = i;
tok = this.tokAt(i + 1);
if (tok == 0) continue;
i++;
this.addShapeProperty(propertyList, "token", Integer.$valueOf(1073742335));
if (tok == 10 || tok == 1073742327) {
propertyName = "bsDisplay";
if (tok == 1073742327) {
sbCommand.append(" all");
} else {
propertyValue = this.st[i].value;
sbCommand.append(" ").append(JU.Escape.eBS(propertyValue));
}eval.checkLast(i);
break;
} else if (tok != 134217759) {
eval.iToken = i;
this.invArg();
}} else {
ptWithin = i;
}var distance;
var ptc = null;
bs = null;
var ret =  new Array(1);
if (this.tokAt(i + 1) == 1073742325) {
distance = this.floatParameter(i + 3);
if (eval.isPoint3f(i + 4)) {
ptc = eval.centerParameter(i + 4, null);
eval.iToken += 2;
} else if (eval.isPoint3f(i + 5)) {
ptc = eval.centerParameter(i + 5, null);
eval.iToken += 2;
} else {
bs = eval.atomExpression(this.st, i + 5, this.slen, true, false, ret, true);
if (bs == null) this.invArg();
}} else {
distance = this.floatParameter(++i);
ptc = eval.centerParameter(++i, ret);
bs = (Clazz.instanceOf(ret[0],"JU.BS") ? ret[0] : null);
}if (isDisplay) eval.checkLast(eval.iToken);
i = eval.iToken;
if (eval.fullCommand.indexOf("# WITHIN=") >= 0) bs = JU.BS.unescape(JU.PT.getQuotedAttribute(eval.fullCommand, "# WITHIN"));
if (!this.chk) {
if (bs != null && modelIndex >= 0) bs = this.vwr.restrictToModel(bs, modelIndex);
if (ptc == null) ptc = (bs == null ?  new JU.P3() : this.vwr.ms.getAtomSetCenter(bs));
pts = this.getWithinDistanceVector(propertyList, distance, ptc, bs, isDisplay);
sbCommand.append(" within ").appendF(distance).append(" ").append(bs == null ? JU.Escape.eP(ptc) : JU.Escape.eBS(bs));
}continue;
case 1073742083:
propertyName = "parameters";
var fparams = eval.floatParameterSet(++i, 1, 10);
i = eval.iToken;
propertyValue = fparams;
sbCommand.append(" parameters ").append(JU.Escape.eAF(fparams));
break;
case 1715472409:
case 1073742190:
onlyOneModel = eval.theToken.value;
var isVariable = (tok == 1073742190);
var tokProperty = this.tokAt(i + 1);
if (mepOrMlp == null) {
if (!surfaceObjectSeen && !isMapped && !planeSeen) {
this.addShapeProperty(propertyList, "sasurface", Float.$valueOf(0));
sbCommand.append(" vdw");
surfaceObjectSeen = true;
}propertyName = "property";
if (smoothing == null) {
var allowSmoothing = JS.T.tokAttr(tokProperty, 1111490560);
smoothing = (allowSmoothing && this.vwr.getIsosurfacePropertySmoothing(false) == 1 ? Boolean.TRUE : Boolean.FALSE);
}this.addShapeProperty(propertyList, "propertySmoothing", smoothing);
sbCommand.append(" isosurfacePropertySmoothing " + smoothing);
if (smoothing === Boolean.TRUE) {
if (smoothingPower == 2147483647) smoothingPower = this.vwr.getIsosurfacePropertySmoothing(true);
this.addShapeProperty(propertyList, "propertySmoothingPower", Integer.$valueOf(smoothingPower));
sbCommand.append(" isosurfacePropertySmoothingPower " + smoothingPower);
}if (this.vwr.g.rangeSelected) this.addShapeProperty(propertyList, "rangeSelected", Boolean.TRUE);
} else {
propertyName = mepOrMlp;
}str = this.paramAsStr(i);
sbCommand.append(" ").append(str);
if (str.toLowerCase().indexOf("property_") == 0) {
data =  Clazz.newFloatArray (this.vwr.ms.ac, 0);
if (this.chk) continue;
data = this.vwr.getDataObj(str, null, 1);
if (data == null) this.invArg();
this.addShapeProperty(propertyList, propertyName, data);
continue;
}var ac = this.vwr.ms.ac;
data =  Clazz.newFloatArray (ac, 0);
if (isVariable) {
var vname = this.paramAsStr(++i);
if (vname.length == 0) {
data = eval.floatParameterSet(i, ac, ac);
} else {
data =  Clazz.newFloatArray (ac, 0);
if (!this.chk) JU.Parser.parseStringInfestedFloatArray("" + eval.getParameter(vname, 4, true), null, data);
}if (!this.chk) sbCommand.append(" \"\" ").append(JU.Escape.eAF(data));
} else {
this.getToken(++i);
if (!this.chk) {
sbCommand.append(" " + eval.theToken.value);
var atoms = this.vwr.ms.at;
this.vwr.autoCalculate(tokProperty, null);
if (tokProperty != 1765808134) {
pt =  new JU.P3();
for (var iAtom = ac; --iAtom >= 0; ) data[iAtom] = atoms[iAtom].atomPropertyFloat(this.vwr, tokProperty, pt);

}}if (tokProperty == 1765808134) colorScheme = "inherit";
if (this.tokAt(i + 1) == 134217759) {
var d = this.floatParameter(i = i + 2);
sbCommand.append(" within " + d);
this.addShapeProperty(propertyList, "propertyDistanceMax", Float.$valueOf(d));
}}propertyValue = data;
break;
case 1094713359:
case 1094717454:
if (surfaceObjectSeen) this.invArg();
modelIndex = (tok == 1094713359 ? this.intParameter(++i) : eval.modelNumberParameter(++i));
sbCommand.append(" modelIndex " + modelIndex);
if (modelIndex < 0) {
propertyName = "fixed";
propertyValue = Boolean.TRUE;
break;
}propertyName = "modelIndex";
propertyValue = Integer.$valueOf(modelIndex);
break;
case 1275082241:
propertyName = "select";
var bs1 = this.atomExpressionAt(++i);
propertyValue = bs1;
i = eval.iToken;
var isOnly = (this.tokAt(i + 1) == 1073742072);
if (isOnly) {
i++;
bsIgnore = JU.BSUtil.copy(bs1);
JU.BSUtil.invertInPlace(bsIgnore, this.vwr.ms.ac);
this.addShapeProperty(propertyList, "ignore", bsIgnore);
sbCommand.append(" ignore ").append(JU.Escape.eBS(bsIgnore));
isFrontOnly = true;
}if (surfaceObjectSeen || isMapped) {
sbCommand.append(" select " + JU.Escape.eBS(bs1));
} else {
bsSelect = propertyValue;
if (modelIndex < 0 && bsSelect.nextSetBit(0) >= 0) modelIndex = this.vwr.ms.at[bsSelect.nextSetBit(0)].mi;
}break;
case 2109448:
if (eval.getToken(++i).tok == 10) {
thisSet = eval.theToken.value;
} else {
thisSet = eval.expandFloatArray(eval.floatParameterSet(i, 1, 2147483647), 1, true);
}i = eval.iToken;
break;
case 36867:
var ns = this.intParameter(++i);
if (ns > 0) thisSet = JU.BSUtil.newAndSetBit(ns - 1);
 else thisSet =  new JU.BS();
break;
case 12289:
propertyName = "center";
propertyValue = this.centerParameter(++i);
sbCommand.append(" center " + JU.Escape.eP(propertyValue));
i = eval.iToken;
break;
case 1073742147:
case 1765808134:
idSeen = true;
if (tok == 1073742147) {
isSign = true;
sbCommand.append(" sign");
this.addShapeProperty(propertyList, "sign", Boolean.TRUE);
} else {
if (this.tokAt(i + 1) == 1073741914) {
i++;
propertyName = "colorDensity";
sbCommand.append(" color density");
colorDensity = true;
if (this.isFloatParameter(i + 1)) {
var ptSize = this.floatParameter(++i);
sbCommand.append(" " + ptSize);
propertyValue = Float.$valueOf(ptSize);
}break;
}if (this.getToken(i + 1).tok == 4) {
colorScheme = this.paramAsStr(++i);
if (colorScheme.indexOf(" ") > 0) {
discreteColixes = JU.C.getColixArray(colorScheme);
if (discreteColixes == null) this.error(4);
}} else if (eval.theTok == 1073742018) {
i++;
sbCommand.append(" color mesh");
color = eval.getArgbParam(++i);
this.addShapeProperty(propertyList, "meshcolor", Integer.$valueOf(color));
sbCommand.append(" ").append(JU.Escape.escapeColor(color));
i = eval.iToken;
continue;
}if ((eval.theTok = this.tokAt(i + 1)) == 603979967 || eval.theTok == 1073742074) {
sbCommand.append(" color");
translucency = this.setColorOptions(sbCommand, i + 1, 24, -2);
i = eval.iToken;
continue;
}switch (this.tokAt(i + 1)) {
case 1073741826:
case 1073742114:
this.getToken(++i);
sbCommand.append(" color range");
this.addShapeProperty(propertyList, "rangeAll", null);
if (this.tokAt(i + 1) == 1073742327) {
i++;
sbCommand.append(" all");
continue;
}var min = this.floatParameter(++i);
var max = this.floatParameter(++i);
this.addShapeProperty(propertyList, "red", Float.$valueOf(min));
this.addShapeProperty(propertyList, "blue", Float.$valueOf(max));
sbCommand.append(" ").appendF(min).append(" ").appendF(max);
continue;
}
if (eval.isColorParam(i + 1)) {
color = eval.getArgbParam(i + 1);
if (this.tokAt(i + 2) == 1073742170) {
colorScheme = eval.getColorRange(i + 1);
i = eval.iToken;
break;
}}sbCommand.append(" color");
}if (eval.isColorParam(i + 1)) {
color = eval.getArgbParam(++i);
sbCommand.append(" ").append(JU.Escape.escapeColor(color));
i = eval.iToken;
this.addShapeProperty(propertyList, "colorRGB", Integer.$valueOf(color));
idSeen = true;
if (eval.isColorParam(i + 1)) {
color = eval.getArgbParam(++i);
i = eval.iToken;
this.addShapeProperty(propertyList, "colorRGB", Integer.$valueOf(color));
sbCommand.append(" ").append(JU.Escape.escapeColor(color));
isBicolor = true;
} else if (isSign) {
this.invPO();
}} else if (!isSign && discreteColixes == null && colorScheme == null) {
this.invPO();
}continue;
case 134221829:
if (!isIsosurface) this.invArg();
toCache = !this.chk;
continue;
case 1228935687:
if (this.tokAt(i + 1) != 4) this.invPO();
continue;
case 1111492618:
case 1648363544:
sbCommand.append(" ").appendO(eval.theToken.value);
var rd = eval.encodeRadiusParameter(i, false, true);
if (rd == null) return;
sbCommand.append(" ").appendO(rd);
if (Float.isNaN(rd.value)) rd.value = 100;
propertyValue = rd;
propertyName = "radius";
haveRadius = true;
if (isMapped) surfaceObjectSeen = false;
i = eval.iToken;
break;
case 1073741864:
isBest = true;
continue;
case 134217750:
planeSeen = true;
propertyName = "plane";
propertyValue = eval.planeParameter(i, isBest);
i = eval.iToken;
sbCommand.append(" plane ").append(JU.Escape.eP4(propertyValue));
break;
case 536875059:
propertyName = "scale";
propertyValue = Float.$valueOf(this.floatParameter(++i));
sbCommand.append(" scale ").appendO(propertyValue);
break;
case 1073742327:
if (idSeen) this.invArg();
propertyName = "thisID";
break;
case 1112150020:
surfaceObjectSeen = true;
++i;
propertyValue = eval.getPoint4f(i);
propertyName = "ellipsoid";
i = eval.iToken;
sbCommand.append(" ellipsoid ").append(JU.Escape.eP4(propertyValue));
break;
case 134219777:
planeSeen = true;
propertyName = "plane";
propertyValue = eval.hklParameter(++i, null, true);
i = eval.iToken;
sbCommand.append(" plane ").append(JU.Escape.eP4(propertyValue));
break;
case 135182:
surfaceObjectSeen = true;
var lcaoType = this.paramAsStr(++i);
this.addShapeProperty(propertyList, "lcaoType", lcaoType);
sbCommand.append(" lcaocartoon ").append(JU.PT.esc(lcaoType));
switch (this.getToken(++i).tok) {
case 12290:
case 10:
case 1073742325:
propertyName = "lcaoCartoon";
bs = this.atomExpressionAt(i);
i = eval.iToken;
if (this.chk) continue;
var atomIndex = bs.nextSetBit(0);
if (atomIndex < 0) this.error(14);
sbCommand.append(" ({").appendI(atomIndex).append("})");
modelIndex = this.vwr.ms.at[atomIndex].mi;
this.addShapeProperty(propertyList, "modelIndex", Integer.$valueOf(modelIndex));
var axes =  Clazz.newArray(-1, [ new JU.V3(),  new JU.V3(), JU.V3.newV(this.vwr.ms.at[atomIndex]),  new JU.V3()]);
if (!lcaoType.equalsIgnoreCase("s") && this.vwr.getHybridizationAndAxes(atomIndex, axes[0], axes[1], lcaoType) == null) return;
propertyValue = axes;
break;
default:
this.error(14);
}
break;
case 1073877011:
nbotype = this.paramAsStr(++i).toUpperCase();
sbCommand.append(" nbo ").append(nbotype).append(" ");
case 1073877010:
if (nbotype == null) sbCommand.append(" mo ");
var moNumber = 2147483647;
var offset = 2147483647;
var isNegOffset = (this.tokAt(i + 1) == 268440576);
if (isNegOffset) i++;
var linearCombination = null;
switch (this.tokAt(++i)) {
case 0:
eval.bad();
break;
case 1073741914:
sbCommand.append("[1] squared ");
this.addShapeProperty(propertyList, "squareLinear", Boolean.TRUE);
linearCombination =  Clazz.newFloatArray(-1, [1]);
offset = moNumber = 0;
i++;
break;
case 1073741973:
case 1073742008:
offset = this.moOffset(i);
moNumber = 0;
i = eval.iToken;
sbCommand.append((isNegOffset ? "-" : "") + "HOMO ");
if (offset > 0) sbCommand.append("+");
if (offset != 0) sbCommand.appendI(offset);
break;
case 2:
moNumber = this.intParameter(i);
sbCommand.appendI(moNumber);
if (this.tokAt(i + 1) == 1073741865) {
isBeta = true;
i++;
}break;
default:
if (eval.isArrayParameter(i)) {
linearCombination = eval.floatParameterSet(i, 1, 2147483647);
i = eval.iToken;
}}
var squared = (this.tokAt(i + 1) == 1073742156);
if (squared) {
this.addShapeProperty(propertyList, "squareLinear", Boolean.TRUE);
sbCommand.append(" squared");
if (linearCombination == null) linearCombination =  Clazz.newFloatArray (0, 0);
} else if (this.tokAt(i + 1) == 134217751) {
++i;
var monteCarloCount = this.intParameter(++i);
var seed = (this.tokAt(i + 1) == 2 ? this.intParameter(++i) : (-System.currentTimeMillis()) % 10000);
this.addShapeProperty(propertyList, "monteCarloCount", Integer.$valueOf(monteCarloCount));
this.addShapeProperty(propertyList, "randomSeed", Integer.$valueOf(seed));
sbCommand.append(" points ").appendI(monteCarloCount).appendC(' ').appendI(seed);
}this.setMoData(propertyList, moNumber, linearCombination, offset, isNegOffset, modelIndex, null, nbotype, isBeta);
surfaceObjectSeen = true;
continue;
case 1073742036:
propertyName = "nci";
sbCommand.append(" " + propertyName);
tok = this.tokAt(i + 1);
var isPromolecular = (tok != 1228935687 && tok != 4 && tok != 1073742032);
propertyValue = Boolean.$valueOf(isPromolecular);
if (isPromolecular) surfaceObjectSeen = true;
break;
case 1073742016:
case 1073742022:
var isMep = (tok == 1073742016);
propertyName = (isMep ? "mep" : "mlp");
sbCommand.append(" " + propertyName);
var fname = null;
var calcType = -1;
surfaceObjectSeen = true;
if (this.tokAt(i + 1) == 2) {
calcType = this.intParameter(++i);
sbCommand.append(" " + calcType);
this.addShapeProperty(propertyList, "mepCalcType", Integer.$valueOf(calcType));
}if (this.tokAt(i + 1) == 4) {
fname = this.stringParameter(++i);
sbCommand.append(" /*file*/" + JU.PT.esc(fname));
} else if (this.tokAt(i + 1) == 1715472409) {
mepOrMlp = propertyName;
continue;
}if (!this.chk) try {
data = (fname == null && isMep ? this.vwr.getOrCalcPartialCharges(bsSelect, bsIgnore) : this.getAtomicPotentials(bsSelect, bsIgnore, fname));
} catch (e1) {
if (Clazz.exceptionOf(e1,"JV.JmolAsyncException")){
throw  new JS.ScriptInterruption(this.e, "partialcharge", 1);
} else {
throw e1;
}
}
if (!this.chk && data == null) this.error(32);
propertyValue = data;
break;
case 1312817669:
doCalcVolume = !this.chk;
sbCommand.append(" volume");
break;
case 1073741974:
this.setShapeId(iShape, ++i, idSeen);
isWild = (this.getShapeProperty(iShape, "ID") == null);
i = eval.iToken;
break;
case 1073741888:
if (this.tokAt(i + 1) == 603979967) {
isColorSchemeTranslucent = true;
i++;
}colorScheme = this.paramAsStr(++i).toLowerCase();
if (colorScheme.equals("sets")) {
sbCommand.append(" colorScheme \"sets\"");
} else if (eval.isColorParam(i)) {
colorScheme = eval.getColorRange(i);
i = eval.iToken;
}break;
case 1073741828:
propertyName = "addHydrogens";
propertyValue = Boolean.TRUE;
sbCommand.append(" addHydrogens");
break;
case 1073741836:
propertyName = "angstroms";
sbCommand.append(" angstroms");
break;
case 1073741837:
propertyName = "anisotropy";
propertyValue = this.getPoint3f(++i, false);
sbCommand.append(" anisotropy").append(JU.Escape.eP(propertyValue));
i = eval.iToken;
break;
case 1073741842:
doCalcArea = !this.chk;
sbCommand.append(" area");
break;
case 1073741850:
case 1073742076:
surfaceObjectSeen = true;
if (isBicolor && !isPhased) {
sbCommand.append(" phase \"_orb\"");
this.addShapeProperty(propertyList, "phase", "_orb");
}var nlmZprs =  Clazz.newFloatArray (7, 0);
nlmZprs[0] = this.intParameter(++i);
nlmZprs[1] = this.intParameter(++i);
nlmZprs[2] = this.intParameter(++i);
nlmZprs[3] = (this.isFloatParameter(i + 1) ? this.floatParameter(++i) : 6);
sbCommand.append(" atomicOrbital ").appendI(Clazz.floatToInt(nlmZprs[0])).append(" ").appendI(Clazz.floatToInt(nlmZprs[1])).append(" ").appendI(Clazz.floatToInt(nlmZprs[2])).append(" ").appendF(nlmZprs[3]);
if (this.tokAt(i + 1) == 134217751) {
i += 2;
nlmZprs[4] = this.intParameter(i);
nlmZprs[5] = (this.tokAt(i + 1) == 3 ? this.floatParameter(++i) : 0);
nlmZprs[6] = (this.tokAt(i + 1) == 2 ? this.intParameter(++i) : (-System.currentTimeMillis()) % 10000);
sbCommand.append(" points ").appendI(Clazz.floatToInt(nlmZprs[4])).appendC(' ').appendF(nlmZprs[5]).appendC(' ').appendI(Clazz.floatToInt(nlmZprs[6]));
}propertyName = "hydrogenOrbital";
propertyValue = nlmZprs;
break;
case 1073741866:
sbCommand.append(" binary");
continue;
case 1073741868:
sbCommand.append(" blockData");
propertyName = "blockData";
propertyValue = Boolean.TRUE;
break;
case 1073741875:
case 554176565:
haveSlab = true;
propertyName = eval.theToken.value;
propertyValue = this.getCapSlabObject(i, false);
i = eval.iToken;
break;
case 1073741876:
if (!isIsosurface) this.invArg();
isCavity = true;
var cavityRadius = (this.isFloatParameter(i + 1) ? this.floatParameter(++i) : 1.2);
var envelopeRadius = (this.isFloatParameter(i + 1) ? this.floatParameter(++i) : 10);
if (this.chk) continue;
if (envelopeRadius > 50) {
eval.integerOutOfRange(0, 50);
return;
}sbCommand.append(" cavity ").appendF(cavityRadius).append(" ").appendF(envelopeRadius);
this.addShapeProperty(propertyList, "envelopeRadius", Float.$valueOf(envelopeRadius));
this.addShapeProperty(propertyList, "cavityRadius", Float.$valueOf(cavityRadius));
propertyName = "cavity";
break;
case 1073741896:
case 1073741900:
propertyName = "contour";
sbCommand.append(" contour");
switch (this.tokAt(i + 1)) {
case 1073741920:
propertyValue = eval.floatParameterSet(i + 2, 1, 2147483647);
sbCommand.append(" discrete ").append(JU.Escape.eAF(propertyValue));
i = eval.iToken;
break;
case 1073741981:
pt = this.getPoint3f(i + 2, false);
if (pt.z <= 0 || pt.y < pt.x) this.invArg();
if (pt.z == Clazz.floatToInt(pt.z) && pt.z > (pt.y - pt.x)) pt.z = (pt.y - pt.x) / pt.z;
propertyValue = pt;
i = eval.iToken;
sbCommand.append(" increment ").append(JU.Escape.eP(pt));
break;
default:
propertyValue = Integer.$valueOf(this.tokAt(i + 1) == 2 ? this.intParameter(++i) : 0);
sbCommand.append(" ").appendO(propertyValue);
if (this.tokAt(i + 1) == 2) {
this.addShapeProperty(propertyList, propertyName, propertyValue);
propertyValue = Integer.$valueOf(-Math.abs(this.intParameter(++i)));
sbCommand.append(" ").appendO(propertyValue);
}}
break;
case 1073741910:
sbCommand.append(" cutoff ");
if (this.tokAt(++i) == 268440577) {
propertyName = "cutoffPositive";
propertyValue = Float.$valueOf(cutoff = this.floatParameter(++i));
sbCommand.append("+").appendO(propertyValue);
} else if (this.isFloatParameter(i)) {
propertyName = "cutoff";
propertyValue = Float.$valueOf(cutoff = this.floatParameter(i));
sbCommand.appendO(propertyValue);
} else if (colorDensity) {
propertyName = "cutoffRange";
propertyValue = eval.floatParameterSet(i, 2, 2);
this.addShapeProperty(propertyList, "cutoff", Float.$valueOf(0));
sbCommand.append(JU.Escape.eAF(propertyValue));
i = eval.iToken;
} else {
this.invArg();
}break;
case 1073741928:
propertyName = "downsample";
propertyValue = Integer.$valueOf(this.intParameter(++i));
sbCommand.append(" downsample ").appendO(propertyValue);
break;
case 1073741931:
propertyName = "eccentricity";
propertyValue = eval.getPoint4f(++i);
sbCommand.append(" eccentricity ").append(JU.Escape.eP4(propertyValue));
i = eval.iToken;
break;
case 1073741932:
sbCommand.append(" ed");
this.setMoData(propertyList, -1, null, 0, false, modelIndex, null, null, false);
surfaceObjectSeen = true;
continue;
case 536870916:
case 1073742041:
sbCommand.append(" ").appendO(eval.theToken.value);
propertyName = "debug";
propertyValue = (tok == 536870916 ? Boolean.TRUE : Boolean.FALSE);
break;
case 12293:
sbCommand.append(" fixed");
propertyName = "fixed";
propertyValue = Boolean.TRUE;
break;
case 1073741962:
sbCommand.append(" fullPlane");
propertyName = "fullPlane";
propertyValue = Boolean.TRUE;
break;
case 1073741966:
case 1073741968:
var isFxyz = (tok == 1073741968);
propertyName = "" + eval.theToken.value;
var vxy =  new JU.Lst();
propertyValue = vxy;
isFxy = surfaceObjectSeen = true;
sbCommand.append(" ").append(propertyName);
var name = this.paramAsStr(++i);
if (name.equals("=")) {
sbCommand.append(" =");
name = this.paramAsStr(++i);
sbCommand.append(" ").append(JU.PT.esc(name));
vxy.addLast(name);
if (!this.chk) this.addShapeProperty(propertyList, "func", this.createFunction("__iso__", "x,y,z", name));
break;
}var dName = JU.PT.getQuotedAttribute(eval.fullCommand, "# DATA" + (isFxy ? "2" : ""));
if (dName == null) dName = "inline";
 else name = dName;
var isXYZ = (name.indexOf("data2d_") == 0);
var isXYZV = (name.indexOf("data3d_") == 0);
isInline = name.equals("inline");
sbCommand.append(" inline");
vxy.addLast(name);
var pt3 = this.getPoint3f(++i, false);
sbCommand.append(" ").append(JU.Escape.eP(pt3));
vxy.addLast(pt3);
var pt4;
ptX = ++eval.iToken;
vxy.addLast(pt4 = eval.getPoint4f(ptX));
sbCommand.append(" ").append(JU.Escape.eP4(pt4));
nX = Clazz.floatToInt(pt4.x);
ptY = ++eval.iToken;
vxy.addLast(pt4 = eval.getPoint4f(ptY));
sbCommand.append(" ").append(JU.Escape.eP4(pt4));
nY = Clazz.floatToInt(pt4.x);
vxy.addLast(pt4 = eval.getPoint4f(++eval.iToken));
sbCommand.append(" ").append(JU.Escape.eP4(pt4));
nZ = Clazz.floatToInt(pt4.x);
if (nX == 0 || nY == 0 || nZ == 0) this.invArg();
if (!this.chk) {
var fdata = null;
var xyzdata = null;
if (isFxyz) {
if (isInline) {
nX = Math.abs(nX);
nY = Math.abs(nY);
nZ = Math.abs(nZ);
xyzdata = this.floatArraySetXYZ(++eval.iToken, nX, nY, nZ);
} else if (isXYZV) {
xyzdata = this.vwr.getDataObj(name, null, 3);
} else {
xyzdata = this.vwr.functionXYZ(name, nX, nY, nZ);
}nX = Math.abs(nX);
nY = Math.abs(nY);
nZ = Math.abs(nZ);
if (xyzdata == null) {
eval.iToken = ptX;
eval.errorStr(53, "xyzdata is null.");
}if (xyzdata.length != nX || xyzdata[0].length != nY || xyzdata[0][0].length != nZ) {
eval.iToken = ptX;
eval.errorStr(53, "xyzdata[" + xyzdata.length + "][" + xyzdata[0].length + "][" + xyzdata[0][0].length + "] is not of size [" + nX + "][" + nY + "][" + nZ + "]");
}vxy.addLast(xyzdata);
sbCommand.append(" ").append(JU.Escape.e(xyzdata));
} else {
if (isInline) {
nX = Math.abs(nX);
nY = Math.abs(nY);
fdata = this.floatArraySet(++eval.iToken, nX, nY);
} else if (isXYZ) {
fdata = this.vwr.getDataObj(name, null, 2);
nX = (fdata == null ? 0 : fdata.length);
nY = 3;
} else {
fdata = this.vwr.functionXY(name, nX, nY);
nX = Math.abs(nX);
nY = Math.abs(nY);
}if (fdata == null) {
eval.iToken = ptX;
eval.errorStr(53, "fdata is null.");
}if (fdata.length != nX && !isXYZ) {
eval.iToken = ptX;
eval.errorStr(53, "fdata length is not correct: " + fdata.length + " " + nX + ".");
}for (var j = 0; j < nX; j++) {
if (fdata[j] == null) {
eval.iToken = ptY;
eval.errorStr(53, "fdata[" + j + "] is null.");
}if (fdata[j].length != nY) {
eval.iToken = ptY;
eval.errorStr(53, "fdata[" + j + "] is not the right length: " + fdata[j].length + " " + nY + ".");
}}
vxy.addLast(fdata);
sbCommand.append(" ").append(JU.Escape.e(fdata));
}}i = eval.iToken;
break;
case 1073742188:
var isBS = this.e.isAtomExpression(++i);
var probes = this.getAllPoints(i, 1);
sbCommand.append(" value " + (isBS ? this.e.atomExpressionAt(i).toString() : JU.Escape.eAP(probes)));
propertyName = "probes";
propertyValue = probes;
i = this.e.iToken;
break;
case 1073741970:
propertyName = "gridPoints";
sbCommand.append(" gridPoints");
break;
case 1073741976:
propertyName = "ignore";
propertyValue = bsIgnore = this.atomExpressionAt(++i);
sbCommand.append(" ignore ").append(JU.Escape.eBS(bsIgnore));
i = eval.iToken;
break;
case 1073741985:
propertyName = "insideOut";
sbCommand.append(" insideout");
break;
case 1073741988:
case 1073741986:
case 1073742100:
sbCommand.append(" ").appendO(eval.theToken.value);
propertyName = "pocket";
propertyValue = (tok == 1073742100 ? Boolean.TRUE : Boolean.FALSE);
break;
case 1073742002:
propertyName = "lobe";
propertyValue = eval.getPoint4f(++i);
i = eval.iToken;
sbCommand.append(" lobe ").append(JU.Escape.eP4(propertyValue));
surfaceObjectSeen = true;
break;
case 1073742004:
case 1073742006:
propertyName = "lp";
propertyValue = eval.getPoint4f(++i);
i = eval.iToken;
sbCommand.append(" lp ").append(JU.Escape.eP4(propertyValue));
surfaceObjectSeen = true;
break;
case 4125:
if (isMapped || this.slen == i + 1) this.invArg();
isMapped = true;
if ((isCavity || haveRadius || haveIntersection) && !surfaceObjectSeen) {
surfaceObjectSeen = true;
this.addShapeProperty(propertyList, "bsSolvent", (haveRadius || haveIntersection ?  new JU.BS() : eval.lookupIdentifierValue("solvent")));
this.addShapeProperty(propertyList, "sasurface", Float.$valueOf(0));
}if (sbCommand.length() == 0) {
plane = this.getShapeProperty(24, "plane");
if (plane == null) {
if (this.getShapeProperty(24, "contours") != null) {
this.addShapeProperty(propertyList, "nocontour", null);
}} else {
this.addShapeProperty(propertyList, "plane", plane);
sbCommand.append("plane ").append(JU.Escape.eP4(plane));
planeSeen = true;
plane = null;
}} else if (!surfaceObjectSeen && !planeSeen) {
this.invArg();
}sbCommand.append("; isosurface map");
this.addShapeProperty(propertyList, "map", (surfaceObjectSeen ? Boolean.TRUE : Boolean.FALSE));
break;
case 1073742014:
propertyName = "maxset";
propertyValue = Integer.$valueOf(this.intParameter(++i));
sbCommand.append(" maxSet ").appendO(propertyValue);
break;
case 1073742020:
propertyName = "minset";
propertyValue = Integer.$valueOf(this.intParameter(++i));
sbCommand.append(" minSet ").appendO(propertyValue);
break;
case 1073742112:
surfaceObjectSeen = true;
propertyName = "rad";
propertyValue = eval.getPoint4f(++i);
i = eval.iToken;
sbCommand.append(" radical ").append(JU.Escape.eP4(propertyValue));
break;
case 1073742027:
propertyName = "fixed";
propertyValue = Boolean.FALSE;
sbCommand.append(" modelBased");
break;
case 1073742028:
case 1073742135:
case 1612709912:
onlyOneModel = eval.theToken.value;
var radius;
if (tok == 1073742028) {
propertyName = "molecular";
sbCommand.append(" molecular");
radius = (this.isFloatParameter(i + 1) ? this.floatParameter(++i) : 1.4);
} else {
this.addShapeProperty(propertyList, "bsSolvent", eval.lookupIdentifierValue("solvent"));
propertyName = (tok == 1073742135 ? "sasurface" : "solvent");
sbCommand.append(" ").appendO(eval.theToken.value);
radius = (this.isFloatParameter(i + 1) ? this.floatParameter(++i) : this.vwr.getFloat(570425394));
}sbCommand.append(" ").appendF(radius);
propertyValue = Float.$valueOf(radius);
if (this.tokAt(i + 1) == 1073741961) {
this.addShapeProperty(propertyList, "doFullMolecular", null);
sbCommand.append(" full");
i++;
}surfaceObjectSeen = true;
break;
case 1073742032:
this.addShapeProperty(propertyList, "fileType", "Mrc");
sbCommand.append(" mrc");
continue;
case 1140850696:
var s = eval.stringParameter(++i);
this.addShapeProperty(propertyList, "fileType", s);
sbCommand.append(" type \"" + s + "\"");
continue;
case 1073742064:
case 1073742062:
this.addShapeProperty(propertyList, "fileType", "Obj");
sbCommand.append(" obj");
continue;
case 1073742033:
this.addShapeProperty(propertyList, "fileType", "Msms");
sbCommand.append(" msms");
continue;
case 1073742094:
if (surfaceObjectSeen) this.invArg();
propertyName = "phase";
isPhased = true;
propertyValue = (this.tokAt(i + 1) == 4 ? this.stringParameter(++i) : "_orb");
sbCommand.append(" phase ").append(JU.PT.esc(propertyValue));
break;
case 1073742104:
case 1073742122:
propertyName = "resolution";
propertyValue = Float.$valueOf(this.floatParameter(++i));
sbCommand.append(" resolution ").appendO(propertyValue);
break;
case 1073742124:
propertyName = "reverseColor";
propertyValue = Boolean.TRUE;
sbCommand.append(" reversecolor");
break;
case 1073742127:
case 1073742146:
propertyName = "sigma";
propertyValue = Float.$valueOf(sigma = this.floatParameter(++i));
sbCommand.append(" sigma ").appendO(propertyValue);
break;
case 1112150021:
propertyName = "geodesic";
propertyValue = Float.$valueOf(this.floatParameter(++i));
sbCommand.append(" geosurface ").appendO(propertyValue);
surfaceObjectSeen = true;
break;
case 1073742154:
propertyName = "sphere";
propertyValue = Float.$valueOf(this.floatParameter(++i));
sbCommand.append(" sphere ").appendO(propertyValue);
surfaceObjectSeen = true;
break;
case 1073742156:
propertyName = "squareData";
propertyValue = Boolean.TRUE;
sbCommand.append(" squared");
break;
case 1073741984:
propertyName = (!surfaceObjectSeen && !planeSeen && !isMapped ? "readFile" : "mapColor");
str = this.stringParameter(++i);
if (str == null) this.invArg();
if (isPmesh) str = JU.PT.replaceWithCharacter(str, "{,}|", ' ');
if (eval.debugHigh) JU.Logger.debug("pmesh inline data:\n" + str);
propertyValue = (this.chk ? null : str);
this.addShapeProperty(propertyList, "fileName", "");
sbCommand.append(" INLINE ").append(JU.PT.esc(str));
surfaceObjectSeen = true;
break;
case 268437504:
case 1073742195:
case 7:
if (filesData != null || isWild) this.invArg();
var list = eval.listParameter4(i, 2, 2147483647, true);
i = eval.iToken;
var n = Clazz.doubleToInt(list.size() / 2);
if (n == 0 || n * 2 != list.size()) this.invArg();
var files =  new Array(n);
var factors =  Clazz.newFloatArray (n, 0);
sbCommand.append("[");
try {
for (var j = 0, ptf = 0; j < n; j++) {
factors[j] = (list.get(ptf++)).floatValue();
files[j] = this.e.checkFileExists("ISOSURFACE_" + j + "_", false, list.get(ptf++), i, false);
sbCommand.appendF(factors[j]);
sbCommand.append(" /*file*/").append(JU.PT.esc(files[j]));
}
sbCommand.append("]");
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
this.invArg();
} else {
throw e;
}
}
filesData =  Clazz.newArray(-1, [files, factors]);
propertyName = (!surfaceObjectSeen && !planeSeen && !isMapped ? "readFile" : "mapColor");
surfaceObjectSeen = true;
if (this.chk) break;
this.addShapeProperty(propertyList, "filesData", filesData);
break;
case 545259556:
case 545259557:
case 1073741914:
case 4:
var firstPass = (!surfaceObjectSeen && !planeSeen);
var filename = null;
propertyName = (firstPass && !isMapped ? "readFile" : "mapColor");
if (tok == 4) {
filename = this.paramAsStr(i);
var ipt = filename.indexOf("::");
if (ipt > 0) {
var ftype = filename.substring(0, ipt);
ftype = ftype.substring(0, 1).toUpperCase() + ftype.substring(1).toLowerCase();
this.addShapeProperty(propertyList, "fileType", ftype);
filename = filename.substring(ipt + 2);
}} else if (tok == 1073741914) {
filename = "=density/";
}if (filename == null || filename.length == 0 || filename.equals("*") || filename.equals("=")) {
var pdbID = this.vwr.getPdbID();
if (pdbID == null) eval.errorStr(22, "no PDBID available");
filename = "*" + (tok == 545259557 ? "*" : "") + pdbID;
}var checkWithin = false;
if (filename.startsWith("http://eds.bmc.uu.se/eds/dfs/cb/") && filename.endsWith(".omap")) {
filename = (filename.indexOf("_diff") >= 0 ? "*" : "") + "*" + filename.substring(32, 36);
}if (filename.startsWith("*") || filename.startsWith("=")) {
var haveCutoff = (!Float.isNaN(cutoff) || !Float.isNaN(sigma));
var isFull = (filename.indexOf("/full") >= 0);
if (isFull) filename = JU.PT.rep(filename, "/full", "");
if (filename.indexOf("/diff") >= 0) filename = "*" + filename.substring(0, filename.indexOf("/diff"));
if (filename.startsWith("**")) {
if (!haveCutoff) this.addShapeProperty(propertyList, "sigma", Float.$valueOf(sigma = 3));
if (!isSign) {
isSign = true;
sbCommand.append(" sign");
this.addShapeProperty(propertyList, "sign", Boolean.TRUE);
}}var fn = filename;
filename = this.vwr.setLoadFormat(false, filename, (this.chk ? '?' : isFull ? '_' : '-'), false);
if (filename == null) eval.errorStr(22, "error parsing filename: " + fn);
checkWithin = !isFull;
}if (checkWithin) {
if (pts == null && ptWithin == 0) {
onlyOneModel = filename;
if (modelIndex < 0) modelIndex = this.vwr.am.cmi;
bs = this.vwr.getModelUndeletedAtomsBitSet(modelIndex);
if (bs.nextSetBit(0) >= 0) {
pts = this.getWithinDistanceVector(propertyList, 2.0, null, bs, false);
sbCommand.append(" within 2.0 ").append(JU.Escape.eBS(bs));
}}if (pts != null && filename.indexOf("/0,0,0/0,0,0?") >= 0) {
filename = filename.$replace("0,0,0/0,0,0", pts[0].x + "," + pts[0].y + "," + pts[0].z + "/" + pts[pts.length - 1].x + "," + pts[pts.length - 1].y + "," + pts[pts.length - 1].z);
}if (firstPass) defaultMesh = true;
}var p = (filename == null ? -1 : filename.indexOf("#-"));
if (Float.isNaN(sigma) && Float.isNaN(cutoff)) {
if ((p = filename.indexOf("#-cutoff=")) >= 0) {
this.addShapeProperty(propertyList, "cutoff", Float.$valueOf(cutoff = Float.parseFloat(filename.substring(p + 9))));
sbCommand.append(" cutoff " + cutoff);
} else if ((p = filename.indexOf("#-sigma=")) >= 0) {
this.addShapeProperty(propertyList, "sigma", Float.$valueOf(sigma = Float.parseFloat(filename.substring(p + 8))));
sbCommand.append(" sigma " + sigma);
}}if (!Float.isNaN(sigma)) this.showString("using sigma = " + sigma);
 else if (!Float.isNaN(cutoff)) this.showString("using cutoff = " + cutoff);
if (firstPass && this.vwr.getP("_fileType").equals("Pdb") && Float.isNaN(sigma) && Float.isNaN(cutoff)) {
this.addShapeProperty(propertyList, "sigma", Float.$valueOf(-1));
sbCommand.append(" sigma -1.0");
}if (filename.length == 0) {
if (modelIndex < 0) modelIndex = this.vwr.am.cmi;
filename = eval.getFullPathName(false);
propertyValue = this.vwr.ms.getInfo(modelIndex, "jmolSurfaceInfo");
}var fileIndex = -1;
if (propertyValue == null && this.tokAt(i + 1) == 2) this.addShapeProperty(propertyList, "fileIndex", Integer.$valueOf(fileIndex = this.intParameter(++i)));
var stype = (this.tokAt(i + 1) == 4 ? this.stringParameter(++i) : null);
surfaceObjectSeen = true;
if (this.chk) {
break;
}var fullPathNameOrError;
var localName = null;
if (propertyValue == null) {
if (eval.fullCommand.indexOf("# FILE" + nFiles + "=") >= 0) {
filename = JU.PT.getQuotedAttribute(eval.fullCommand, "# FILE" + nFiles);
if (this.tokAt(i + 1) == 1073741848) i += 2;
} else if (this.tokAt(i + 1) == 1073741848) {
localName = this.vwr.fm.getFilePath(this.stringParameter(eval.iToken = (i = i + 2)), false, false);
fullPathNameOrError = this.vwr.getFullPathNameOrError(localName);
localName = fullPathNameOrError[0];
if (this.vwr.fm.getPathForAllFiles() !== "") {
filename = localName;
localName = null;
} else {
this.addShapeProperty(propertyList, "localName", localName);
}}}if (stype == null) {
filename = this.e.checkFileExists("ISOSURFACE_" + (isMapped ? "MAP_" : ""), false, filename, i, false);
}this.showString("reading isosurface data from " + filename);
if (stype != null) {
propertyValue = this.vwr.fm.cacheGet(filename, false);
this.addShapeProperty(propertyList, "calculationType", stype);
}if (propertyValue == null) {
this.addShapeProperty(propertyList, "fileName", filename);
if (localName != null) filename = localName;
if (fileIndex >= 0) sbCommand.append(" ").appendI(fileIndex);
}sbCommand.append(" /*file*/").append(JU.PT.esc(filename));
if (stype != null) sbCommand.append(" ").append(JU.PT.esc(stype));
break;
case 4106:
propertyName = "connections";
switch (this.tokAt(++i)) {
case 12290:
case 10:
case 1073742325:
propertyValue =  Clazz.newIntArray(-1, [this.atomExpressionAt(i).nextSetBit(0)]);
break;
default:
propertyValue =  Clazz.newIntArray(-1, [Clazz.floatToInt(eval.floatParameterSet(i, 1, 1)[0])]);
break;
}
i = eval.iToken;
break;
case 1094713347:
propertyName = "atomIndex";
propertyValue = Integer.$valueOf(this.intParameter(++i));
break;
case 1073741999:
propertyName = "link";
sbCommand.append(" link");
break;
case 1814695966:
if (iShape != 24) this.invArg();
if (this.tokAt(i + 1) == 268440577) i++;
propertyName = "extendGrid";
propertyValue = Float.$valueOf(this.floatParameter(++i));
sbCommand.append(" unitcell " + propertyValue);
break;
case 1073741994:
if (iShape != 24) this.invArg();
pt = this.getPoint3f(++i, false);
i = eval.iToken;
if (pt.x <= 0 || pt.y <= 0 || pt.z <= 0) break;
pt.x = Clazz.floatToInt(pt.x);
pt.y = Clazz.floatToInt(pt.y);
pt.z = Clazz.floatToInt(pt.z);
sbCommand.append(" lattice ").append(JU.Escape.eP(pt));
if (isMapped) {
propertyName = "mapLattice";
propertyValue = pt;
} else {
lattice = pt;
if (this.tokAt(i + 1) == 12293) {
sbCommand.append(" fixed");
fixLattice = true;
i++;
}}break;
default:
if (tok == 1073741824) {
propertyName = "thisID";
propertyValue = str;
}if (!eval.setMeshDisplayProperty(iShape, 0, tok)) {
if (JS.T.tokAttr(tok, 1073741824) && !idSeen) {
this.setShapeId(iShape, i, idSeen);
i = eval.iToken;
break;
}this.invArg();
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = this.slen - 1;
break;
}
idSeen = (tok != 12291);
if (isWild && surfaceObjectSeen) this.invArg();
if (propertyName != null) this.addShapeProperty(propertyList, propertyName, propertyValue);
}
if (!this.chk) {
if ((isCavity || haveRadius) && !surfaceObjectSeen) {
surfaceObjectSeen = true;
this.addShapeProperty(propertyList, "bsSolvent", (haveRadius ?  new JU.BS() : eval.lookupIdentifierValue("solvent")));
this.addShapeProperty(propertyList, "sasurface", Float.$valueOf(0));
}if (planeSeen && !surfaceObjectSeen && !isMapped) {
this.addShapeProperty(propertyList, "nomap", Float.$valueOf(0));
surfaceObjectSeen = true;
}if (thisSet != null) this.addShapeProperty(propertyList, "getSurfaceSets", thisSet);
if (discreteColixes != null) {
this.addShapeProperty(propertyList, "colorDiscrete", discreteColixes);
} else if ("sets".equals(colorScheme)) {
this.addShapeProperty(propertyList, "setColorScheme", null);
} else if (colorScheme != null) {
var ce = this.vwr.cm.getColorEncoder(colorScheme);
if (ce != null) {
ce.isTranslucent = isColorSchemeTranslucent;
ce.hi = 3.4028235E38;
this.addShapeProperty(propertyList, "remapColor", ce);
}}if (surfaceObjectSeen && !isLcaoCartoon && sbCommand.indexOf(";") != 0) {
propertyList.add(0,  Clazz.newArray(-1, ["newObject", null]));
var needSelect = (bsSelect == null);
if (needSelect) bsSelect = JU.BSUtil.copy(this.vwr.bsA());
if (modelIndex < 0) modelIndex = this.vwr.am.cmi;
bsSelect.and(this.vwr.getModelUndeletedAtomsBitSet(modelIndex));
if (onlyOneModel != null) {
var bsModels = this.vwr.ms.getModelBS(bsSelect, false);
if (bsModels.cardinality() > 1) eval.errorStr(30, "ISOSURFACE " + onlyOneModel);
if (needSelect) {
propertyList.add(0,  Clazz.newArray(-1, ["select", bsSelect]));
if (sbCommand.indexOf("; isosurface map") == 0) {
sbCommand =  new JU.SB().append("; isosurface map select ").append(JU.Escape.eBS(bsSelect)).append(sbCommand.substring(16));
}}}}if (haveIntersection && !haveSlab) {
if (!surfaceObjectSeen) this.addShapeProperty(propertyList, "sasurface", Float.$valueOf(0));
if (!isMapped) {
this.addShapeProperty(propertyList, "map", Boolean.TRUE);
this.addShapeProperty(propertyList, "select", bs);
this.addShapeProperty(propertyList, "sasurface", Float.$valueOf(0));
}this.addShapeProperty(propertyList, "slab", this.getCapSlabObject(-100, false));
}var timeMsg = (surfaceObjectSeen && this.vwr.getBoolean(603979934));
if (timeMsg) JU.Logger.startTimer("isosurface");
this.setShapeProperty(iShape, "setProperties", propertyList);
if (timeMsg) this.showString(JU.Logger.getTimerMsg("isosurface", 0));
if (defaultMesh) {
this.setShapeProperty(iShape, "token", Integer.$valueOf(1073742018));
this.setShapeProperty(iShape, "token", Integer.$valueOf(1073742046));
isFrontOnly = true;
sbCommand.append(" mesh nofill frontOnly");
}}if (lattice != null) {
this.setShapeProperty(iShape, "lattice", lattice);
if (fixLattice) this.setShapeProperty(iShape, "fixLattice", Boolean.TRUE);
}if (symops != null) this.setShapeProperty(iShape, "symops", symops);
if (isFrontOnly) this.setShapeProperty(iShape, "token", Integer.$valueOf(1073741960));
if (iptDisplayProperty > 0) {
if (!eval.setMeshDisplayProperty(iShape, iptDisplayProperty, 0)) this.invArg();
}if (this.chk) return;
var area = null;
var volume = null;
if (doCalcArea) {
area = this.getShapeProperty(iShape, "area");
if (Clazz.instanceOf(area, Float)) this.vwr.setFloatProperty("isosurfaceArea", (area).floatValue());
 else this.vwr.g.setUserVariable("isosurfaceArea", JS.SV.getVariableAD(area));
}if (doCalcVolume) {
volume = (doCalcVolume ? this.getShapeProperty(iShape, "volume") : null);
if (Clazz.instanceOf(volume, Float)) this.vwr.setFloatProperty("isosurfaceVolume", (volume).floatValue());
 else this.vwr.g.setUserVariable("isosurfaceVolume", JS.SV.getVariableAD(volume));
}if (!isLcaoCartoon) {
var s = null;
if (isMapped && !surfaceObjectSeen) {
this.setShapeProperty(iShape, "finalize", sbCommand.toString());
} else if (surfaceObjectSeen) {
cmd = sbCommand.toString();
this.setShapeProperty(iShape, "finalize", (cmd.indexOf("; isosurface map") == 0 ? "" : " select " + JU.Escape.eBS(bsSelect) + " ") + cmd);
s = this.getShapeProperty(iShape, "ID");
if (s != null && !eval.tQuiet && !isSilent) {
cutoff = (this.getShapeProperty(iShape, "cutoff")).floatValue();
if (Float.isNaN(cutoff) && !Float.isNaN(sigma)) JU.Logger.error("sigma not supported");
s += " created " + this.getShapeProperty(iShape, "message");
}}var sarea;
var svol;
if (doCalcArea || doCalcVolume) {
sarea = (doCalcArea ? "isosurfaceArea = " + (Clazz.instanceOf(area, Float) ? "" + area : JU.Escape.eAD(area)) : null);
svol = (doCalcVolume ? "isosurfaceVolume = " + (Clazz.instanceOf(volume, Float) ? "" + volume : JU.Escape.eAD(volume)) : null);
if (s == null) {
if (doCalcArea) this.showString(sarea);
if (doCalcVolume) this.showString(svol);
} else {
if (doCalcArea) s += "\n" + sarea;
if (doCalcVolume) s += "\n" + svol;
}}if (s != null && !isSilent) this.showString(s);
if (surfaceObjectSeen) {
s = this.getShapeProperty(iShape, "output");
if (s != null && !isSilent) this.showString(s);
}}if (translucency != null) this.setShapeProperty(iShape, "translucency", translucency);
this.setShapeProperty(iShape, "clear", null);
if (toCache) this.setShapeProperty(iShape, "cache", null);
if (!isSilent && !isDisplay && !haveSlab && eval.theTok != 12291) this.listIsosurface(iShape);
}, "~N");
Clazz.defineMethod(c$, "lcaoCartoon", 
function(){
var eval = this.e;
eval.sm.loadShape(26);
if (eval.tokAt(1) == 1073742001 && this.listIsosurface(26)) return;
this.setShapeProperty(26, "init", eval.fullCommand);
if (this.slen == 1) {
this.setShapeProperty(26, "lcaoID", null);
return;
}var idSeen = false;
var translucency = null;
for (var i = 1; i < this.slen; i++) {
var propertyName = null;
var propertyValue = null;
switch (this.getToken(i).tok) {
case 1073741875:
case 554176565:
propertyName = eval.theToken.value;
if (this.tokAt(i + 1) == 1073742334) eval.iToken = i + 1;
propertyValue = this.getCapSlabObject(i, true);
i = eval.iToken;
break;
case 12289:
this.isosurface(26);
return;
case 528432:
var degx = 0;
var degy = 0;
var degz = 0;
switch (this.getToken(++i).tok) {
case 1111492629:
degx = (this.floatParameter(++i) * 0.017453292519943295);
break;
case 1111492630:
degy = (this.floatParameter(++i) * 0.017453292519943295);
break;
case 1111492631:
degz = (this.floatParameter(++i) * 0.017453292519943295);
break;
default:
this.invArg();
}
propertyName = "rotationAxis";
propertyValue = JU.V3.new3(degx, degy, degz);
break;
case 1073742335:
case 1610625028:
case 2097192:
propertyName = "on";
break;
case 1073742334:
case 12294:
case 2097194:
propertyName = "off";
break;
case 12291:
propertyName = "delete";
break;
case 12290:
case 10:
case 1073742325:
propertyName = "select";
propertyValue = this.atomExpressionAt(i);
i = eval.iToken;
break;
case 1140850693:
propertyName = "reversecolor";
propertyValue = Boolean.TRUE;
if (this.tokAt(i + 1) == 1073742335) {
++i;
} else if (this.tokAt(i + 1) == 1073742334) {
propertyValue = Boolean.FALSE;
++i;
}break;
case 1765808134:
translucency = this.setColorOptions(null, i + 1, 26, -2);
if (translucency != null) this.setShapeProperty(26, "settranslucency", translucency);
i = eval.iToken;
idSeen = true;
continue;
case 603979967:
case 1073742074:
eval.setMeshDisplayProperty(26, i, eval.theTok);
i = eval.iToken;
idSeen = true;
continue;
case 1112152075:
case 4:
propertyValue = this.paramAsStr(i).toLowerCase();
if (propertyValue.equals("spacefill")) propertyValue = "cpk";
propertyName = "create";
if (eval.optParameterAsString(i + 1).equalsIgnoreCase("molecular")) {
i++;
propertyName = "molecular";
}break;
case 1275082241:
if (eval.isAtomExpression(i + 1)) {
propertyName = "select";
propertyValue = this.atomExpressionAt(i + 1);
i = eval.iToken;
} else {
propertyName = "selectType";
propertyValue = this.paramAsStr(++i);
if (propertyValue.equals("spacefill")) propertyValue = "cpk";
}break;
case 536875059:
propertyName = "scale";
propertyValue = Float.$valueOf(this.floatParameter(++i));
break;
case 1073742004:
case 1073742006:
propertyName = "lonePair";
break;
case 1073742112:
case 1073742111:
propertyName = "radical";
break;
case 1073742028:
propertyName = "molecular";
break;
case 1073741904:
propertyValue = this.paramAsStr(++i);
propertyName = "create";
if (eval.optParameterAsString(i + 1).equalsIgnoreCase("molecular")) {
i++;
propertyName = "molecular";
}break;
case 1073741974:
propertyValue = eval.setShapeNameParameter(++i);
i = eval.iToken;
if (idSeen) this.invArg();
propertyName = "lcaoID";
break;
default:
if (eval.theTok == 268441089 || JS.T.tokAttr(eval.theTok, 1073741824)) {
if (eval.theTok != 268441089) propertyValue = this.paramAsStr(i);
if (idSeen) this.invArg();
propertyName = "lcaoID";
break;
}break;
}
if (eval.theTok != 12291) idSeen = true;
if (propertyName == null) this.invArg();
this.setShapeProperty(26, propertyName, propertyValue);
}
this.setShapeProperty(26, "clear", null);
});
Clazz.defineMethod(c$, "contact", 
function(){
var eval = this.e;
eval.sm.loadShape(25);
if (this.tokAt(1) == 1073742001 && this.listIsosurface(25)) return false;
var iptDisplayProperty = 0;
eval.iToken = 1;
var thisId = this.initIsosurface(25);
var idSeen = (thisId != null);
var isWild = (idSeen && this.getShapeProperty(25, "ID") == null);
var bsA = null;
var bsB = null;
var bs = null;
var rd = null;
var params = null;
var colorDensity = false;
var sbCommand =  new JU.SB();
var minSet = 2147483647;
var displayType = 134217750;
var contactType = 0;
var distance = NaN;
var saProbeRadius = NaN;
var localOnly = true;
var intramolecular = null;
var userSlabObject = null;
var colorpt = 0;
var colorByType = false;
var tok;
var modelIndex = -2147483648;
var okNoAtoms = (eval.iToken > 1);
for (var i = eval.iToken; i < this.slen; ++i) {
switch (tok = this.getToken(i).tok) {
default:
okNoAtoms = true;
if (!eval.setMeshDisplayProperty(25, 0, eval.theTok)) {
if (eval.theTok != 268441089 && !JS.T.tokAttr(eval.theTok, 1073741824)) this.invArg();
thisId = this.setShapeId(25, i, idSeen);
i = eval.iToken;
break;
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = eval.iToken;
continue;
case 1073741974:
okNoAtoms = true;
this.setShapeId(25, ++i, idSeen);
isWild = (this.getShapeProperty(25, "ID") == null);
i = eval.iToken;
break;
case 1765808134:
switch (this.tokAt(i + 1)) {
case 1073741914:
tok = 0;
colorDensity = true;
sbCommand.append(" color density");
i++;
break;
case 1140850696:
tok = 0;
colorByType = true;
sbCommand.append(" color type");
i++;
break;
}
if (tok == 0) break;
case 603979967:
case 1073742074:
okNoAtoms = true;
if (colorpt == 0) colorpt = i;
eval.setMeshDisplayProperty(25, i, eval.theTok);
i = eval.iToken;
break;
case 554176565:
okNoAtoms = true;
userSlabObject = this.getCapSlabObject(i, false);
this.setShapeProperty(25, "slab", userSlabObject);
i = eval.iToken;
break;
case 1073741914:
colorDensity = true;
sbCommand.append(" density");
if (this.isFloatParameter(i + 1)) {
if (params == null) params =  Clazz.newFloatArray (1, 0);
params[0] = -Math.abs(this.floatParameter(++i));
sbCommand.append(" " + -params[0]);
}break;
case 1073742122:
var resolution = this.floatParameter(++i);
if (resolution > 0) {
sbCommand.append(" resolution ").appendF(resolution);
this.setShapeProperty(25, "resolution", Float.$valueOf(resolution));
}break;
case 1094717454:
case 1094713359:
modelIndex = (eval.theTok == 1094713359 ? this.intParameter(++i) : eval.modelNumberParameter(++i));
sbCommand.append(" modelIndex " + modelIndex);
break;
case 134217759:
case 1275069443:
distance = this.floatParameter(++i);
sbCommand.append(" within ").appendF(distance);
break;
case 268440577:
case 2:
case 3:
rd = eval.encodeRadiusParameter(i, false, false);
if (rd == null) return false;
sbCommand.append(" ").appendO(rd);
i = eval.iToken;
break;
case 1073741990:
case 1073741989:
intramolecular = (tok == 1073741989 ? Boolean.TRUE : Boolean.FALSE);
sbCommand.append(" ").appendO(eval.theToken.value);
break;
case 1073742020:
minSet = this.intParameter(++i);
break;
case 1613238294:
case 1073741881:
case 1648363544:
contactType = tok;
sbCommand.append(" ").appendO(eval.theToken.value);
break;
case 1073742135:
if (this.isFloatParameter(i + 1)) saProbeRadius = this.floatParameter(++i);
case 1073741875:
case 1073742036:
case 2097180:
localOnly = false;
case 1275068932:
case 1073741961:
case 134217750:
case 4106:
displayType = tok;
sbCommand.append(" ").appendO(eval.theToken.value);
if (tok == 1073742135) sbCommand.append(" ").appendF(saProbeRadius);
break;
case 1073742083:
params = eval.floatParameterSet(++i, 1, 10);
i = eval.iToken;
break;
case 12290:
case 10:
case 1073742325:
if (isWild || bsB != null) this.invArg();
bs = JU.BSUtil.copy(this.atomExpressionAt(i));
i = eval.iToken;
if (bsA == null) bsA = bs;
 else bsB = bs;
sbCommand.append(" ").append(JU.Escape.eBS(bs));
break;
}
idSeen = (eval.theTok != 12291);
}
if (!okNoAtoms && bsA == null) this.error(13);
if (this.chk) return false;
if (bsA != null) {
if (contactType == 1648363544 && rd == null) rd =  new J.atomdata.RadiusData(null, 0, J.atomdata.RadiusData.EnumType.OFFSET, J.c.VDW.AUTO);
var rd1 = (rd == null ?  new J.atomdata.RadiusData(null, 0.26, J.atomdata.RadiusData.EnumType.OFFSET, J.c.VDW.AUTO) : rd);
if (displayType == 1073742036 && bsB == null && intramolecular != null && intramolecular.booleanValue()) bsB = bsA;
 else bsB = eval.getMathExt().setContactBitSets(bsA, bsB, localOnly, distance, rd1, true);
switch (displayType) {
case 1073741875:
case 1073742135:
var bsSolvent = eval.lookupIdentifierValue("solvent");
bsA.andNot(bsSolvent);
bsB.andNot(bsSolvent);
bsB.andNot(bsA);
break;
case 2097180:
bsB.andNot(bsA);
break;
case 1073742036:
if (minSet == 2147483647) minSet = 100;
this.setShapeProperty(25, "minset", Integer.$valueOf(minSet));
sbCommand.append(" minSet ").appendI(minSet);
if (params == null) params =  Clazz.newFloatArray(-1, [0.5, 2]);
}
if (intramolecular != null) {
params = (params == null ?  Clazz.newFloatArray (2, 0) : JU.AU.ensureLengthA(params, 2));
params[1] = (intramolecular.booleanValue() ? 1 : 2);
}if (params != null) sbCommand.append(" parameters ").append(JU.Escape.eAF(params));
this.setShapeProperty(25, "set",  Clazz.newArray(-1, [Integer.$valueOf(contactType), Integer.$valueOf(displayType), Boolean.$valueOf(colorDensity), Boolean.$valueOf(colorByType), bsA, bsB, rd, Float.$valueOf(saProbeRadius), params, Integer.$valueOf(modelIndex), sbCommand.toString()]));
if (colorpt > 0) eval.setMeshDisplayProperty(25, colorpt, 0);
}if (iptDisplayProperty > 0) {
if (!eval.setMeshDisplayProperty(25, iptDisplayProperty, 0)) this.invArg();
}if (userSlabObject != null && bsA != null) this.setShapeProperty(25, "slab", userSlabObject);
if (bsA != null && (displayType == 1073742036 || localOnly)) {
var volume = this.getShapeProperty(25, "volume");
var v;
var isFull = (displayType == 1073741961);
if (JU.AU.isAD(volume)) {
var vs = volume;
v = 0;
for (var i = 0; i < vs.length; i++) v += (isFull ? vs[i] : Math.abs(vs[i]));

} else {
v = (volume).floatValue();
}v = (Math.round(v * 1000) / 1000.);
if (colorDensity || displayType != 1275068932) {
var nsets = (this.getShapeProperty(25, "nSets")).intValue();
var s = "Contacts: " + (nsets < 0 ? Clazz.doubleToInt(-nsets / 2) : nsets);
if (v != 0) s += ", with " + (isFull ? "approx " : "net ") + "volume " + v + " A^3";
this.showString(s);
}}return true;
});
Clazz.defineMethod(c$, "cgo", 
function(){
var eval = this.e;
eval.sm.loadShape(23);
if (this.tokAt(1) == 1073742001 && this.listIsosurface(23)) return false;
var iptDisplayProperty = 0;
var thisId = this.initIsosurface(23);
var idSeen = (thisId != null);
var isWild = (idSeen && this.getShapeProperty(23, "ID") == null);
var isInitialized = false;
var modelIndex = -1;
var data = null;
var translucentLevel = 3.4028235E38;
var colorArgb =  Clazz.newIntArray(-1, [-2147483648]);
var intScale = 0;
for (var i = eval.iToken; i < this.slen; ++i) {
var propertyName = null;
var propertyValue = null;
var tok = this.getToken(i).tok;
switch (tok) {
case 268437504:
case 1073742195:
case 7:
if (data != null || isWild) this.invArg();
data =  new JU.Lst();
var ai =  Clazz.newIntArray(-1, [i, this.slen]);
if (!eval.getShapePropertyData(23, "data",  Clazz.newArray(-1, [this.st, ai, data, this.vwr]))) this.invArg();
i = ai[0];
continue;
case 536875059:
if (++i >= this.slen) this.error(34);
switch (this.getToken(i).tok) {
case 2:
intScale = this.intParameter(i);
continue;
case 3:
intScale = Math.round(this.floatParameter(i) * 100);
continue;
}
this.error(34);
break;
case 12293:
propertyName = "modelIndex";
propertyValue = Integer.$valueOf(-1);
break;
case 1094713359:
case 1094717454:
modelIndex = (eval.theTok == 1094713359 ? this.intParameter(++i) : eval.modelNumberParameter(++i));
propertyName = "modelIndex";
propertyValue = Integer.$valueOf(modelIndex);
break;
case 1765808134:
case 603979967:
case 1073742074:
translucentLevel = this.getColorTrans(eval, i, false, colorArgb);
i = eval.iToken;
idSeen = true;
continue;
case 1073741974:
thisId = this.setShapeId(23, ++i, idSeen);
isWild = (this.getShapeProperty(23, "ID") == null);
i = eval.iToken;
break;
default:
if (!eval.setMeshDisplayProperty(23, 0, eval.theTok)) {
if (eval.theTok == 268441089 || JS.T.tokAttr(eval.theTok, 1073741824)) {
thisId = this.setShapeId(23, i, idSeen);
i = eval.iToken;
break;
}this.invArg();
}if (iptDisplayProperty == 0) iptDisplayProperty = i;
i = eval.iToken;
continue;
}
idSeen = (eval.theTok != 12291);
if (data != null && !isInitialized) {
propertyName = "points";
propertyValue = Integer.$valueOf(intScale);
isInitialized = true;
intScale = 0;
}if (propertyName != null) this.setShapeProperty(23, propertyName, propertyValue);
}
this.finalizeObject(23, colorArgb[0], translucentLevel, intScale, data != null, data, iptDisplayProperty, null);
return true;
});
Clazz.defineMethod(c$, "getAtomicPotentials", 
function(bsSelected, bsIgnore, fileName){
var potentials =  Clazz.newFloatArray (this.vwr.ms.ac, 0);
var m = J.api.Interface.getOption("quantum.MlpCalculation", this.vwr, "script");
m.set(this.vwr);
var data = (fileName == null ? null : this.vwr.getFileAsString3(fileName, false, null));
try {
m.assignPotentials(this.vwr.ms.at, potentials, this.vwr.getSmartsMatch("a", bsSelected), this.vwr.getSmartsMatch("/noAromatic/[$(C=O),$(O=C),$(NC=O)]", bsSelected), bsIgnore, data);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
return potentials;
}, "JU.BS,JU.BS,~S");
Clazz.defineMethod(c$, "getCapSlabObject", 
function(i, isLcaoCartoon){
if (i < 0) {
return JU.TempArray.getSlabWithinRange(i, 0);
}var eval = this.e;
var data = null;
var tok0 = this.tokAt(i);
var isSlab = (tok0 == 554176565);
var tok = this.tokAt(i + 1);
var plane = null;
var pts = null;
var d;
var d2;
var bs = null;
var slabColix = null;
var slabMeshType = null;
if (tok == 603979967) {
var slabTranslucency = (this.isFloatParameter(++i + 1) ? this.floatParameter(++i) : 0.5);
if (eval.isColorParam(i + 1)) {
slabColix = Short.$valueOf(JU.C.getColixTranslucent3(JU.C.getColix(eval.getArgbParam(i + 1)), slabTranslucency != 0, slabTranslucency));
i = eval.iToken;
} else {
slabColix = Short.$valueOf(JU.C.getColixTranslucent3(1, slabTranslucency != 0, slabTranslucency));
}switch (tok = this.tokAt(i + 1)) {
case 1073742018:
case 1073741938:
slabMeshType = Integer.$valueOf(tok);
tok = this.tokAt(++i + 1);
break;
default:
slabMeshType = Integer.$valueOf(1073741938);
break;
}
}switch (tok) {
case 1073742334:
eval.iToken = i + 1;
return Integer.$valueOf(-2147483648);
case 1073742333:
eval.iToken = i + 1;
break;
case 1073742330:
i++;
data =  Clazz.newArray(-1, [Float.$valueOf(1), this.paramAsStr(++i)]);
tok = 1073742018;
break;
case 134217759:
i++;
if (this.tokAt(++i) == 1073742114) {
d = this.floatParameter(++i);
d2 = this.floatParameter(++i);
data =  Clazz.newArray(-1, [Float.$valueOf(d), Float.$valueOf(d2)]);
tok = 1073742114;
} else if (this.isFloatParameter(i)) {
d = this.floatParameter(i);
if (eval.isCenterParameter(++i)) {
var ret =  new Array(1);
var pt = eval.centerParameter(i, ret);
if (this.chk || !(Clazz.instanceOf(ret[0],"JU.BS"))) {
pts =  Clazz.newArray(-1, [pt]);
} else {
var atoms = this.vwr.ms.at;
bs = ret[0];
pts =  new Array(bs.cardinality());
for (var k = 0, j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1), k++) pts[k] = atoms[j];

}} else {
pts = eval.getPointArray(i, -1, false);
}if (pts.length == 0) {
eval.iToken = i;
this.invArg();
}data =  Clazz.newArray(-1, [Float.$valueOf(d), pts, bs]);
} else {
data = eval.getPointArray(i, 4, false);
tok = 1812599299;
}break;
case 1812599299:
eval.iToken = i + 1;
data = JU.BoxInfo.toOABC(this.vwr.ms.getBBoxVertices(), null);
break;
case 1073741872:
case 1814695966:
eval.iToken = i + 1;
var unitCell = this.vwr.getCurrentUnitCell();
if (unitCell == null) {
if (tok == 1814695966) this.invArg();
} else {
pts = JU.BoxInfo.toOABC(unitCell.getUnitCellVerticesNoOffset(), unitCell.getCartesianOffset());
var iType = Clazz.floatToInt(unitCell.getUnitCellInfoType(6));
var v1 = null;
var v2 = null;
switch (iType) {
case 3:
break;
case 1:
v2 = JU.V3.newVsub(pts[2], pts[0]);
v2.scale(1000);
case 2:
v1 = JU.V3.newVsub(pts[1], pts[0]);
v1.scale(1000);
pts[0].sub(v1);
pts[1].scale(2000);
if (iType == 1) {
pts[0].sub(v2);
pts[2].scale(2000);
}break;
}
data = pts;
}break;
case 12290:
case 10:
case 1073742325:
data = this.atomExpressionAt(i + 1);
tok = 3;
if (!eval.isCenterParameter(++eval.iToken)) {
isSlab = true;
break;
}data = null;
default:
if (!isLcaoCartoon && isSlab && this.isFloatParameter(i + 1)) {
d = this.floatParameter(++i);
if (!this.isFloatParameter(i + 1)) return Integer.$valueOf(Clazz.floatToInt(d));
d2 = this.floatParameter(++i);
data =  Clazz.newArray(-1, [Float.$valueOf(d), Float.$valueOf(d2)]);
tok = 1073742114;
break;
}plane = eval.planeParameter(++i, false);
var off = (this.isFloatParameter(eval.iToken + 1) ? this.floatParameter(++eval.iToken) : NaN);
if (!Float.isNaN(off)) plane.w -= off;
data = plane;
tok = 134217750;
}
var colorData = (slabMeshType == null ? null :  Clazz.newArray(-1, [slabMeshType, slabColix]));
return JU.TempArray.getSlabObjectType(tok, data, !isSlab, colorData);
}, "~N,~B");
Clazz.defineMethod(c$, "setColorOptions", 
function(sb, index, iShape, nAllowed){
var eval = this.e;
this.getToken(index);
var translucency = "opaque";
if (eval.theTok == 603979967) {
translucency = "translucent";
if (nAllowed < 0) {
var value = (this.isFloatParameter(index + 1) ? this.floatParameter(++index) : 3.4028235E38);
eval.setShapeTranslucency(iShape, null, "translucent", value, null);
if (sb != null) {
sb.append(" translucent");
if (value != 3.4028235E38) sb.append(" ").appendF(value);
}} else {
eval.setMeshDisplayProperty(iShape, index, eval.theTok);
}} else if (eval.theTok == 1073742074) {
if (nAllowed >= 0) eval.setMeshDisplayProperty(iShape, index, eval.theTok);
} else {
eval.iToken--;
}nAllowed = Math.abs(nAllowed);
for (var i = 0; i < nAllowed; i++) {
if (eval.isColorParam(eval.iToken + 1)) {
var color = eval.getArgbParam(++eval.iToken);
this.setShapeProperty(iShape, "colorRGB", Integer.$valueOf(color));
if (sb != null) sb.append(" ").append(JU.Escape.escapeColor(color));
} else if (eval.iToken < index) {
this.invArg();
} else {
break;
}}
return translucency;
}, "JU.SB,~N,~N,~N");
Clazz.defineMethod(c$, "createFunction", 
function(fname, xyz, ret){
var e = ( new JS.ScriptEval()).setViewer(this.vwr);
try {
e.compileScript(null, "function " + fname + "(" + xyz + ") { return " + ret + "}", false);
var params =  new JU.Lst();
for (var i = 0; i < xyz.length; i += 2) params.addLast(JS.SV.newF(0).setName(xyz.substring(i, i + 1)));

return  Clazz.newArray(-1, [e.aatoken[0][1].value, params]);
} catch (ex) {
if (Clazz.exceptionOf(ex, Exception)){
return null;
} else {
throw ex;
}
}
}, "~S,~S,~S");
Clazz.defineMethod(c$, "getWithinDistanceVector", 
function(propertyList, distance, ptc, bs, isShow){
var v =  new JU.Lst();
var pts =  new Array(2);
if (bs == null) {
var pt1 = JU.P3.new3(distance, distance, distance);
var pt0 = JU.P3.newP(ptc);
pt0.sub(pt1);
pt1.add(ptc);
pts[0] = pt0;
pts[1] = pt1;
v.addLast(ptc);
} else {
var bbox = this.vwr.ms.getBoxInfo(bs, -Math.abs(distance * 2));
pts[0] = bbox.getBoundBoxVertices()[0];
pts[1] = bbox.getBoundBoxVertices()[7];
if (bs.cardinality() == 1) v.addLast(this.vwr.ms.at[bs.nextSetBit(0)]);
}if (v.size() == 1 && !isShow) {
this.addShapeProperty(propertyList, "withinDistance", Float.$valueOf(distance));
this.addShapeProperty(propertyList, "withinPoint", v.get(0));
}this.addShapeProperty(propertyList, (isShow ? "displayWithin" : "withinPoints"),  Clazz.newArray(-1, [Float.$valueOf(distance), pts, bs, v]));
return pts;
}, "JU.Lst,~N,JU.P3,JU.BS,~B");
Clazz.defineMethod(c$, "addShapeProperty", 
function(propertyList, key, value){
if (this.chk) return;
propertyList.addLast( Clazz.newArray(-1, [key, value]));
}, "JU.Lst,~S,~O");
Clazz.defineMethod(c$, "floatArraySetXYZ", 
function(i, nX, nY, nZ){
var eval = this.e;
var tok = this.tokAt(i++);
if (tok == 1073742195) tok = this.tokAt(i++);
if (tok != 268437504 || nX <= 0) this.invArg();
var fparams = JU.AU.newFloat3(nX, -1);
var n = 0;
while (tok != 268437505) {
tok = this.getToken(i).tok;
switch (tok) {
case 1073742195:
case 268437505:
continue;
case 268436992:
i++;
break;
case 268437504:
fparams[n++] = this.floatArraySet(i, nY, nZ);
i = ++eval.iToken;
tok = 0;
if (n == nX && this.tokAt(i) != 268437505) this.invArg();
break;
default:
this.invArg();
}
}
return fparams;
}, "~N,~N,~N,~N");
Clazz.defineMethod(c$, "floatArraySet", 
function(i, nX, nY){
var tok = this.tokAt(i++);
if (tok == 1073742195) tok = this.tokAt(i++);
if (tok != 268437504) this.invArg();
var fparams = JU.AU.newFloat2(nX);
var n = 0;
while (tok != 268437505) {
tok = this.getToken(i).tok;
switch (tok) {
case 1073742195:
case 268437505:
continue;
case 268436992:
i++;
break;
case 268437504:
i++;
var f =  Clazz.newFloatArray (nY, 0);
fparams[n++] = f;
for (var j = 0; j < nY; j++) {
f[j] = this.floatParameter(i++);
if (this.tokAt(i) == 268436992) i++;
}
if (this.tokAt(i++) != 268437505) this.invArg();
tok = 0;
if (n == nX && this.tokAt(i) != 268437505) this.invArg();
break;
default:
this.invArg();
}
}
return fparams;
}, "~N,~N,~N");
Clazz.defineMethod(c$, "initIsosurface", 
function(iShape){
var eval = this.e;
this.setShapeProperty(iShape, "init", eval.fullCommand);
eval.iToken = 0;
var tok1 = this.tokAt(1);
var tok2 = this.tokAt(2);
if (tok1 == 12291 || tok2 == 12291 && this.tokAt(++eval.iToken) == 1073742327) {
this.setShapeProperty(iShape, "delete", null);
eval.iToken += 2;
if (this.slen > eval.iToken) {
this.setShapeProperty(iShape, "init", eval.fullCommand);
this.setShapeProperty(iShape, "thisID", "+PREVIOUS_MESH+");
}return null;
}eval.iToken = 1;
if (!eval.setMeshDisplayProperty(iShape, 0, tok1)) {
this.setShapeProperty(iShape, "thisID", "+PREVIOUS_MESH+");
if (iShape != 22) this.setShapeProperty(iShape, "title",  Clazz.newArray(-1, [eval.thisCommand]));
if (tok1 != 1073741974 && (tok2 == 268441089 || tok1 == 268441089 && eval.setMeshDisplayProperty(iShape, 0, tok2))) {
var id = this.setShapeId(iShape, 1, false);
eval.iToken++;
return id;
}}return null;
}, "~N");
Clazz.defineMethod(c$, "listIsosurface", 
function(iShape){
var s = (this.slen > 3 ? "0" : this.tokAt(2) == 0 ? "" : " " + this.getToken(2).value);
if (!this.chk) this.showString(this.getShapeProperty(iShape, "list" + s));
return true;
}, "~N");
Clazz.defineMethod(c$, "getBoxPoints", 
function(type, uc, bsAtoms, scale){
switch (type) {
case 1814695966:
return (uc == null ? null : uc.getCanonicalCopy(scale, true));
case 1812599299:
var box;
if (bsAtoms == null) {
box = this.vwr.ms.getBoxInfo();
} else {
box =  new JU.BoxInfo();
this.vwr.calcAtomsMinMax(bsAtoms, box);
}return JU.BoxInfo.getCanonicalCopy(box.getBoundBoxVertices(), scale);
default:
return null;
}
}, "~N,J.api.SymmetryInterface,JU.BS,~N");
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
