Clazz.declarePackage("J.shapesurface");
Clazz.load(["J.shapesurface.Isosurface"], "J.shapesurface.MolecularOrbital", ["java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "$.SB", "J.jvxl.data.JvxlCoder", "J.quantum.QS", "JU.Escape"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.moTranslucency = null;
this.moTranslucentLevel = null;
this.moPlane = null;
this.moCutoff = null;
this.moResolution = null;
this.moScale = null;
this.moSelection = null;
this.moColorPos = null;
this.moColorNeg = null;
this.moMonteCarloCount = null;
this.moIsPositiveOnly = false;
this.moSquareData = null;
this.moSquareLinear = null;
this.moRandomSeed = null;
this.moFill = 1073742046;
this.moMesh = 1073742018;
this.moDots = 1073742042;
this.moFrontOnly = 1073741960;
this.moShell = 1073742057;
this.moTitleFormat = null;
this.moDebug = false;
this.myColorPt = 0;
this.strID = null;
this.$moNumber = 0;
this.$moLinearCombination = null;
this.htModels = null;
this.thisModel = null;
this.moSlab = null;
this.moSlabValue = null;
this.nboType = null;
Clazz.instantialize(this, arguments);}, J.shapesurface, "MolecularOrbital", J.shapesurface.Isosurface);
Clazz.defineMethod(c$, "initShape", 
function(){
Clazz.superCall(this, J.shapesurface.MolecularOrbital, "initShape", []);
this.myType = "mo";
this.setPropI("thisID", this.myType, null);
});
Clazz.overrideMethod(c$, "setProperty", 
function(propertyName, value, bs){
if ("init" === propertyName) {
this.myColorPt = 0;
this.moDebug = false;
var modelIndex = (value).intValue();
this.strID = this.getId(modelIndex);
this.setPropI("init", null, null);
this.setPropI("modelIndex", Integer.$valueOf(modelIndex), null);
if (this.htModels == null) this.htModels =  new java.util.Hashtable();
if (!this.htModels.containsKey(this.strID)) this.htModels.put(this.strID,  new java.util.Hashtable());
this.thisModel = this.htModels.get(this.strID);
this.$moNumber = (!this.thisModel.containsKey("moNumber") ? 0 : (this.thisModel.get("moNumber")).intValue());
this.$moLinearCombination = this.thisModel.get("moLinearCombination");
this.moSquareData = (this.$moLinearCombination != null ? null : this.thisModel.get("moSquareData"));
this.moSquareLinear = (this.$moLinearCombination == null ? null : this.thisModel.get("moSquareLinear"));
return;
}if (this.htModels != null && this.strID != null) this.thisModel = this.htModels.get(this.strID);
if ("slab" === propertyName) {
if (Clazz.instanceOf(value, Integer)) {
this.thisModel.put("slabValue", value);
} else {
var slabInfo = value;
var tok = (slabInfo[0]).intValue();
this.moSlab = this.thisModel.get("slab");
if (this.moSlab == null) this.thisModel.put("slab", this.moSlab =  new JU.Lst());
if (tok == 1073742333) {
this.moSlab = null;
this.thisModel.remove("slab");
return;
}this.moSlab.addLast(value);
}return;
}if ("cutoff" === propertyName) {
this.thisModel.put("moCutoff", value);
this.thisModel.put("moIsPositiveOnly", Boolean.FALSE);
return;
}if ("scale" === propertyName) {
this.thisModel.put("moScale", value);
return;
}if ("select" === propertyName) {
this.thisModel.put("moSelection", value);
return;
}if ("squareData" === propertyName) {
if (value === Boolean.TRUE) this.thisModel.put("moSquareData", Boolean.TRUE);
 else this.thisModel.remove("moSquareData");
this.moSquareData = value;
return;
}if ("squareLinear" === propertyName) {
if (value === Boolean.TRUE) this.thisModel.put("moSquareLinear", Boolean.TRUE);
 else this.thisModel.remove("moSquareLinear");
this.moSquareLinear = value;
return;
}if ("cutoffPositive" === propertyName) {
this.thisModel.put("moCutoff", value);
this.thisModel.put("moIsPositiveOnly", Boolean.TRUE);
return;
}if ("resolution" === propertyName) {
this.thisModel.put("moResolution", value);
return;
}if ("titleFormat" === propertyName) {
this.moTitleFormat = value;
return;
}if ("color" === propertyName) {
if (!(Clazz.instanceOf(value, Integer))) return;
this.thisModel.remove("moTranslucency");
this.setPropI("color", value, bs);
propertyName = "colorRGB";
this.myColorPt = 0;
}if ("colorRGB" === propertyName) {
this.moColorPos = value;
if (this.myColorPt++ == 0) this.moColorNeg = this.moColorPos;
this.thisModel.put("moColorNeg", this.moColorNeg);
this.thisModel.put("moColorPos", this.moColorPos);
return;
}if ("plane" === propertyName) {
if (value == null) this.thisModel.remove("moPlane");
 else this.thisModel.put("moPlane", value);
return;
}if ("monteCarloCount" === propertyName) {
this.thisModel.put("monteCarloCount", value);
return;
}if ("randomSeed" === propertyName) {
if (value == null) this.thisModel.remove("randomSeed");
 else this.thisModel.put("randomSeed", value);
return;
}if ("molecularOrbital" === propertyName) {
if (Clazz.instanceOf(value, Integer)) {
this.$moNumber = (value).intValue();
this.thisModel.put("moNumber", value);
this.thisModel.remove("moLinearCombination");
this.$moLinearCombination = null;
} else {
this.$moNumber = 0;
this.$moLinearCombination = value;
this.thisModel.put("moNumber", Integer.$valueOf(0));
this.thisModel.put("moLinearCombination", this.$moLinearCombination);
}if (this.moSquareData === Boolean.TRUE) this.thisModel.put("moSquareData", Boolean.TRUE);
 else this.thisModel.remove("moSquareData");
if (this.moSquareLinear === Boolean.TRUE) this.thisModel.put("moSquareLinear", Boolean.TRUE);
 else this.thisModel.remove("moSquareLinear");
this.setOrbital(this.$moNumber, this.$moLinearCombination);
return;
}if (propertyName === "deleteModelAtoms") {
var modelIndex = ((value)[2])[0];
var htModelsNew =  new java.util.Hashtable();
for (var i = this.meshCount; --i >= 0; ) {
if (this.meshes[i] == null) continue;
if (this.meshes[i].modelIndex == modelIndex) {
this.meshCount--;
if (this.meshes[i] === this.currentMesh) {
this.currentMesh = null;
this.thisModel = null;
}this.meshes = JU.AU.deleteElements(this.meshes, i, 1);
continue;
}var htModel = this.htModels.get(this.meshes[i].thisID);
if (this.meshes[i].modelIndex > modelIndex) {
this.meshes[i].modelIndex--;
this.meshes[i].thisID = this.getId(this.meshes[i].modelIndex);
}htModelsNew.put(this.meshes[i].thisID, htModel);
}
this.htModels = htModelsNew;
return;
}if ("moData" === propertyName) {
var moData = value;
this.nboType = moData.get("nboType");
this.thisModel = this.htModels.get(this.strID);
if (this.nboType == null) this.thisModel.remove("nboType");
 else this.thisModel.put("nboType", this.nboType);
} else if ("translucentLevel" === propertyName) {
if (this.thisModel == null) {
if (this.currentMesh == null) return;
this.thisModel = this.htModels.get(this.currentMesh.thisID);
}this.thisModel.put("moTranslucentLevel", value);
} else if ("delete" === propertyName) {
this.htModels.remove(this.strID);
this.$moNumber = 0;
this.$moLinearCombination = null;
} else if ("token" === propertyName) {
var tok = (value).intValue();
switch (tok) {
case 1112150019:
case 1073742042:
this.moDots = tok;
break;
case 1073741938:
case 1073742046:
this.moFill = tok;
break;
case 1073742018:
case 1073742052:
this.moMesh = tok;
break;
case 1073741862:
case 1073742057:
this.moShell = tok;
break;
case 1073741960:
case 1073742058:
this.moFrontOnly = tok;
break;
}
} else if ("translucency" === propertyName) {
if (this.thisModel == null) {
if (this.currentMesh == null) return;
this.thisModel = this.htModels.get(this.currentMesh.thisID);
}this.thisModel.put("moTranslucency", value);
}this.setPropI(propertyName, value, bs);
}, "~S,~O,JU.BS");
Clazz.defineMethod(c$, "getId", 
function(modelIndex){
return "mo_model" + this.vwr.getModelNumberDotted(modelIndex);
}, "~N");
Clazz.overrideMethod(c$, "getProperty", 
function(propertyName, index){
if (propertyName.startsWith("list")) {
var s = "";
if (propertyName.equals("list")) {
s = this.getPropI("list", index);
if (s.length > 1) s += "cutoff = " + this.jvxlData.cutoff + "\n";
s = "\n" + s;
}return this.getMoInfo(-1) + s;
}if (propertyName === "moLabel") {
var labels = this.sg.params.moData.get("nboLabels");
if (this.$moNumber > 0 && labels != null && labels.length != 0) return labels[(this.$moNumber - 1) % labels.length];
return "";
}if (propertyName === "moNumber") return Integer.$valueOf(this.$moNumber);
if (propertyName === "moLinearCombination") return this.$moLinearCombination;
if (propertyName === "moSquareData") return this.moSquareData;
if (propertyName === "moSquareLinear") return this.moSquareLinear;
if (propertyName === "showMO") {
var str =  new JU.SB();
var mos = (this.sg.params.moData.get("mos"));
var nOrb = (mos == null ? 0 : mos.size());
var thisMO = index;
var currentMO = this.$moNumber;
var isShowCurrent = (thisMO == -2147483648 || thisMO == 2147483647);
if (isShowCurrent) thisMO = currentMO;
if (nOrb == 0 || isShowCurrent && currentMO == 0) return "";
var doOneMo = (thisMO != 0);
if (currentMO == 0) thisMO = 0;
var haveHeader = false;
var nTotal = (thisMO > 0 ? 1 : nOrb);
var i0 = (nTotal == 1 && currentMO > 0 ? currentMO : 1);
for (var i = i0; i <= nOrb; i++) if (thisMO == 0 || thisMO == i || !doOneMo && i == currentMO) {
if (!doOneMo) {
this.setPropI("init", this.sg.params, null);
this.setOrbital(i, null);
}this.jvxlData.moleculeXml = this.vwr.getModelCml(this.vwr.getModelUndeletedAtomsBitSet(this.thisMesh.modelIndex), 100, true, false);
if (!haveHeader) {
str.append(J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData, null, null, "HEADERONLY", true, nTotal, null, null));
haveHeader = true;
}str.append(J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData, null, this.jvxlData.title, null, false, 1, this.thisMesh.getState(this.myType), (this.thisMesh.scriptCommand == null ? "" : this.thisMesh.scriptCommand)));
if (!doOneMo) this.setPropI("delete", "mo_show", null);
if (nTotal == 1) break;
}
str.append(J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData, null, null, "TRAILERONLY", true, 0, null, null));
return str.toString();
}return this.getPropI(propertyName, index);
}, "~S,~N");
Clazz.defineMethod(c$, "getMoInfo", 
function(modelIndex){
var sb =  new JU.SB();
for (var m = 0, mc = this.ms.mc; m < mc; m++) {
if (modelIndex >= 0 && m != modelIndex) continue;
var moData = this.ms.getInfo(m, "moData");
if (moData == null) continue;
var mos = (moData.get("mos"));
var nOrb = (mos == null ? 0 : mos.size());
if (nOrb == 0) continue;
var moType = moData.get("nboType");
if (moType == null) moType = "mo";
for (var i = nOrb; --i >= 0; ) {
var mo = mos.get(i);
var type = mo.get("type");
if (type == null) type = "";
var units = mo.get("energyUnits");
if (units == null) units = "";
var occ = mo.get("occupancy");
if (occ != null) type = "occupancy " + occ.floatValue() + " " + type;
var sym = mo.get("symmetry");
if (sym != null) type += sym;
var energy = "" + mo.get("energy");
if (Float.isNaN(JU.PT.parseFloat(energy))) sb.append(JU.PT.sprintf("model %-2s; %s %-2i # %s\n", "ssis",  Clazz.newArray(-1, [this.ms.getModelNumberDotted(m), moType, Integer.$valueOf(i + 1), type])));
 else sb.append(JU.PT.sprintf("model %-2s;  %s %-2i # energy %-8.3f %s %s\n", "ssifss",  Clazz.newArray(-1, [this.ms.getModelNumberDotted(m), moType, Integer.$valueOf(i + 1), mo.get("energy"), units, type])));
}
}
return sb.toString();
}, "~N");
Clazz.overrideMethod(c$, "clearSg", 
function(){
});
Clazz.defineMethod(c$, "getSettings", 
function(strID){
this.thisModel = this.htModels.get(strID);
if (this.thisModel == null || this.thisModel.get("moNumber") == null) return false;
this.nboType = this.thisModel.get("nboType");
this.moTranslucency = this.thisModel.get("moTranslucency");
this.moTranslucentLevel = this.thisModel.get("moTranslucentLevel");
this.moPlane = this.thisModel.get("moPlane");
this.moCutoff = this.thisModel.get("moCutoff");
if (this.moCutoff == null) this.moCutoff = this.sg.params.moData.get("defaultCutoff");
if (this.moCutoff == null) {
this.moCutoff = Float.$valueOf(0.05);
}this.thisModel.put("moCutoff", Float.$valueOf(this.moCutoff.floatValue()));
this.moResolution = this.thisModel.get("moResolution");
this.moScale = this.thisModel.get("moScale");
this.moSelection = this.thisModel.get("moSelection");
this.moColorPos = this.thisModel.get("moColorPos");
this.moColorNeg = this.thisModel.get("moColorNeg");
this.moSquareData = this.thisModel.get("moSquareData");
this.moSquareLinear = this.thisModel.get("moSquareLinear");
this.moMonteCarloCount = this.thisModel.get("monteCarloCount");
this.moRandomSeed = this.thisModel.get("randomSeed");
this.moSlabValue = this.thisModel.get("slabValue");
this.moSlab = this.thisModel.get("slab");
if (this.moRandomSeed == null) this.thisModel.put("randomSeed", this.moRandomSeed = Integer.$valueOf((-System.currentTimeMillis()) % 10000));
this.$moNumber = (this.thisModel.get("moNumber")).intValue();
this.$moLinearCombination = this.thisModel.get("moLinearCombination");
var b = this.thisModel.get("moIsPositiveOnly");
this.moIsPositiveOnly = (b != null && ((b)).booleanValue());
return true;
}, "~S");
Clazz.defineMethod(c$, "setOrbital", 
function(moNumber, linearCombination){
this.setPropI("reset", this.strID, null);
if (this.moDebug) this.setPropI("debug", Boolean.TRUE, null);
this.getSettings(this.strID);
if (this.moScale != null) this.setPropI("scale", this.moScale, null);
if (this.moSelection != null) this.setPropI("select", this.moSelection, null);
if (this.moResolution != null) this.setPropI("resolution", this.moResolution, null);
if (this.moPlane != null) {
this.setPropI("plane", this.moPlane, null);
if (this.moCutoff != null) {
var max = this.moCutoff.floatValue();
if (this.moSquareData === Boolean.TRUE || this.moSquareLinear === Boolean.TRUE) max = max * max;
this.setPropI("red", Float.$valueOf(-max), null);
this.setPropI("blue", Float.$valueOf(max), null);
}} else {
if (this.moCutoff != null) this.setPropI((this.moIsPositiveOnly ? "cutoffPositive" : "cutoff"), this.moCutoff, null);
if (this.moColorNeg != null) this.setPropI("colorRGB", this.moColorNeg, null);
if (this.moColorPos != null) this.setPropI("colorRGB", this.moColorPos, null);
if (this.moMonteCarloCount != null) {
this.setPropI("randomSeed", this.moRandomSeed, null);
this.setPropI("monteCarloCount", this.moMonteCarloCount, null);
}}this.setPropI("squareData", this.moSquareData, null);
this.setPropI("squareLinear", this.moSquareLinear, null);
this.setPropI("title", this.moTitleFormat, null);
this.setPropI("fileName", this.vwr.fm.getFileName(), null);
this.currentMesh.modelIndex = this.modelIndex;
this.setPropI("molecularOrbital", linearCombination == null ? Integer.$valueOf(moNumber) : linearCombination, null);
if (this.moPlane != null && this.moColorNeg != null) this.setPropI("colorRGB", this.moColorNeg, null);
if (this.moPlane != null && this.moColorPos != null) this.setPropI("colorRGB", this.moColorPos, null);
this.currentMesh.isColorSolid = false;
if (this.moSlabValue != null) this.setPropI("slab", this.moSlabValue, null);
if (this.moSlab != null) for (var i = 0; i < this.moSlab.size(); i++) this.setPropI("slab", this.moSlab.get(i), null);

if (this.moTranslucentLevel != null) this.setPropI("translucentLevel", this.moTranslucentLevel, null);
if (this.moTranslucency != null) this.setPropI("translucency", this.moTranslucency, null);
this.setPropI("token", Integer.$valueOf(this.moFill), null);
this.setPropI("token", Integer.$valueOf(this.moMesh), null);
this.setPropI("token", Integer.$valueOf(this.moShell), null);
this.setPropI("token", Integer.$valueOf(this.moDots), null);
this.setPropI("token", Integer.$valueOf(this.moFrontOnly), null);
this.thisModel.put("mesh", this.currentMesh);
return;
}, "~N,~A");
Clazz.overrideMethod(c$, "getShapeState", 
function(){
if (this.htModels == null) return "";
var s =  new JU.SB();
var modelCount = this.ms.mc;
for (var iModel = 0; iModel < modelCount; iModel++) {
if (!this.getSettings(this.getId(iModel))) continue;
if (modelCount > 1) J.shape.Shape.appendCmd(s, "frame " + this.vwr.getModelNumberDotted(iModel));
if (this.nboType != null) J.shape.Shape.appendCmd(s, "nbo type " + this.nboType);
if (this.moCutoff != null) J.shape.Shape.appendCmd(s, this.myType + " cutoff " + (this.sg.params.isPositiveOnly ? "+" : "") + this.moCutoff);
if (this.moScale != null) J.shape.Shape.appendCmd(s, this.myType + " scale " + this.moScale);
if (this.moSelection != null) {
s.append("try{/*16.2*/\n");
J.shape.Shape.appendCmd(s, this.myType + " select " + this.moSelection);
s.append("}catch{};\n");
}if (this.moMonteCarloCount != null) J.shape.Shape.appendCmd(s, this.myType + " points " + this.moMonteCarloCount + " " + this.moRandomSeed);
if (this.moResolution != null) J.shape.Shape.appendCmd(s, this.myType + " resolution " + this.moResolution);
if (this.moPlane != null) J.shape.Shape.appendCmd(s, this.myType + " plane {" + this.moPlane.x + " " + this.moPlane.y + " " + this.moPlane.z + " " + this.moPlane.w + "}");
if (this.moTitleFormat != null) J.shape.Shape.appendCmd(s, this.myType + " titleFormat " + JU.PT.esc(this.moTitleFormat));
if (this.moColorNeg != null) J.shape.Shape.appendCmd(s, this.myType + " color " + JU.Escape.escapeColor(this.moColorNeg.intValue()) + (this.moColorNeg.equals(this.moColorPos) ? "" : " " + JU.Escape.escapeColor(this.moColorPos.intValue())));
if (this.moSlab != null) {
if (this.thisMesh.slabOptions != null) J.shape.Shape.appendCmd(s, this.thisMesh.slabOptions.toString());
if (this.thisMesh.jvxlData.slabValue != -2147483648) J.shape.Shape.appendCmd(s, this.myType + " slab " + this.thisMesh.jvxlData.slabValue);
}if (this.$moLinearCombination == null) {
J.shape.Shape.appendCmd(s, this.myType + " " + (this.moSquareData === Boolean.TRUE ? "squared " : "") + this.$moNumber);
} else {
J.shape.Shape.appendCmd(s, this.myType + " " + J.quantum.QS.getMOString(this.$moLinearCombination) + (this.moSquareLinear === Boolean.TRUE ? " squared" : ""));
}if (this.moTranslucency != null) J.shape.Shape.appendCmd(s, this.myType + " translucent " + this.moTranslucentLevel);
if (this.thisModel == null) {
System.out.println("MolecularOrbital ???");
}J.shape.Shape.appendCmd(s, (this.thisModel.get("mesh")).getState(this.myType));
}
return s.toString();
});
Clazz.defineMethod(c$, "merge", 
function(shape){
var mo = shape;
this.moColorNeg = mo.moColorNeg;
this.moColorPos = mo.moColorPos;
this.moCutoff = mo.moCutoff;
this.moPlane = mo.moPlane;
this.moResolution = mo.moResolution;
this.moScale = mo.moScale;
this.moSlab = mo.moSlab;
this.moSlabValue = mo.moSlabValue;
this.moTitleFormat = mo.moTitleFormat;
this.moTranslucency = mo.moTranslucency;
if (this.htModels == null) this.htModels =  new java.util.Hashtable();
var ht = mo.htModels;
if (ht != null) {
for (var entry, $entry = ht.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
var key = entry.getKey();
this.htModels.put(key, entry.getValue());
}
}Clazz.superCall(this, J.shapesurface.MolecularOrbital, "merge", [shape]);
}, "J.shape.MeshCollection");
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
