Clazz.declarePackage("J.jvxl.readers");
Clazz.load(["J.jvxl.readers.AtomDataReader"], "J.jvxl.readers.IsoMOReader", ["java.util.Random", "JU.AU", "$.Measure", "$.P3", "$.PT", "$.V3", "J.api.Interface", "J.quantum.QS", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.random = null;
this.points = null;
this.vTemp = null;
this.q = null;
this.mos = null;
this.isNci = false;
this.coef = null;
this.dfCoefMaps = null;
this.linearCombination = null;
this.coefs = null;
this.isElectronDensityCalc = false;
this.mo = null;
this.vDist = null;
this.qSetupDone = false;
Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoMOReader", J.jvxl.readers.AtomDataReader);
Clazz.prepareFields (c$, function(){
this.vDist =  Clazz.newFloatArray (3, 0);
});
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.jvxl.readers.IsoMOReader, []);
});
Clazz.overrideMethod(c$, "init", 
function(sg){
this.initADR(sg);
this.isNci = (this.params.qmOrbitalType == 3);
if (this.isNci) {
this.isXLowToHigh = this.hasColorData = true;
this.precalculateVoxelData = false;
this.params.insideOut = !this.params.insideOut;
}}, "J.jvxl.readers.SurfaceGenerator");
Clazz.overrideMethod(c$, "setup", 
function(isMapData){
this.mos = this.params.moData.get("mos");
this.linearCombination = this.params.qm_moLinearCombination;
this.mo = (this.mos != null && this.linearCombination == null ? this.mos.get(this.params.qm_moNumber - 1) : null);
var haveVolumeData = this.params.moData.containsKey("haveVolumeData");
if (haveVolumeData && this.mo != null) this.params.volumeData = this.mo.get("volumeData");
this.setup2();
this.doAddHydrogens = false;
this.getAtoms(this.params.bsSelected, this.doAddHydrogens, !this.isNci, this.isNci, this.isNci, false, false, this.params.qm_marginAngstroms, (this.isNci ? null : this.params.modelInvRotation));
var className;
if (this.isNci) {
className = "quantum.NciCalculation";
this.setHeader("NCI (promolecular)", "see NCIPLOT: A Program for Plotting Noncovalent Interaction Regions, Julia Contreras-Garcia, et al., J. of Chemical Theory and Computation, 2011, 7, 625-632");
} else {
className = "quantum.MOCalculation";
this.setHeader("MO", "calculation type: " + this.params.moData.get("calculationType"));
}this.setRanges(this.params.qm_ptsPerAngstrom, this.params.qm_gridMax, 0);
if (haveVolumeData) {
for (var i = this.params.title.length; --i >= 0; ) this.fixTitleLine(i, this.mo);

} else {
this.q = J.api.Interface.getOption(className, this.sg.atomDataServer, "file");
if (this.isNci) {
this.qpc = this.q;
} else {
if (this.linearCombination == null) {
for (var i = this.params.title.length; --i >= 0; ) this.fixTitleLine(i, this.mo);

this.coef = this.mo.get("coefficients");
this.dfCoefMaps = this.mo.get("dfCoefMaps");
} else {
this.coefs = JU.AU.newFloat2(this.mos.size());
for (var i = 1; i < this.linearCombination.length; i += 2) {
var j = Clazz.floatToInt(this.linearCombination[i]);
if (j > this.mos.size() || j < 1) return;
this.coefs[j - 1] = this.mos.get(j - 1).get("coefficients");
}
for (var i = this.params.title.length; --i >= 0; ) this.fixTitleLine(i, null);

}}this.isElectronDensityCalc = (this.coef == null && this.linearCombination == null && !this.isNci);
}this.volumeData.sr = null;
if (isMapData && !this.isElectronDensityCalc && !haveVolumeData) {
this.volumeData.doIterate = false;
this.volumeData.setVoxelDataAsArray(this.voxelData =  Clazz.newFloatArray (1, 1, 1, 0));
this.volumeData.sr = this;
this.points =  new Array(1);
this.points[0] =  new JU.P3();
if (!this.setupCalculation()) this.q = null;
} else if (this.params.psi_monteCarloCount > 0) {
this.vertexDataOnly = true;
this.random =  new java.util.Random(this.params.randomSeed);
}}, "~B");
Clazz.overrideMethod(c$, "readVolumeParameters", 
function(isMapData){
this.setup(isMapData);
if (this.volumeData.sr == null) this.initializeVolumetricData();
return true;
}, "~B");
Clazz.defineMethod(c$, "fixTitleLine", 
function(iLine, mo){
if (this.params.title == null) return;
var line = this.params.title[iLine];
if (line.indexOf(" MO ") >= 0) {
var nboType = this.params.moData.get("nboType");
if (nboType != null) line = JU.PT.rep(line, " MO ", " " + nboType + " ");
}if (line.indexOf("%M") >= 0) line = this.params.title[iLine] = JU.PT.formatStringS(line, "M", this.atomData.modelName);
if (line.indexOf("%F") >= 0) line = this.params.title[iLine] = JU.PT.formatStringS(line, "F", JU.PT.rep(this.params.fileName, "DROP_", ""));
var pt = line.indexOf("%");
if (line.length == 0 || pt < 0) return;
var rep = 0;
if (line.indexOf("%I") >= 0) line = JU.PT.formatStringS(line, "I", this.params.qm_moLinearCombination == null ? "" + this.params.qm_moNumber : J.quantum.QS.getMOString(this.params.qm_moLinearCombination));
if (line.indexOf("%N") >= 0) line = JU.PT.formatStringS(line, "N", "" + this.params.qmOrbitalCount);
var energy = null;
if (mo == null) {
for (var i = 0; i < this.linearCombination.length; i += 2) if (this.linearCombination[i] != 0) {
mo = this.mos.get(Clazz.floatToInt(this.linearCombination[i + 1]) - 1);
var e = mo.get("energy");
if (energy == null) {
if (e == null) break;
energy = e;
} else if (!energy.equals(e)) {
energy = null;
break;
}}
} else {
if (mo.containsKey("energy")) energy = mo.get("energy");
}if (line.indexOf("%E") >= 0) {
line = JU.PT.formatStringS(line, "E", energy != null && ++rep != 0 ? "" + energy : "");
} else if (energy != null) {
var s = JU.PT.formatStringF(line, "E", energy.floatValue());
if (s !== line) {
line = s;
rep++;
}}if (line.indexOf("%U") >= 0) line = JU.PT.formatStringS(line, "U", energy != null && this.params.moData.containsKey("energyUnits") && ++rep != 0 ? this.params.moData.get("energyUnits") : "");
if (line.indexOf("%S") >= 0) line = JU.PT.formatStringS(line, "S", mo != null && mo.containsKey("symmetry") && ++rep != 0 ? "" + mo.get("symmetry") : "");
if (line.indexOf("%O") >= 0) {
var obj = (mo == null ? null : mo.get("occupancy"));
var o = (obj == null ? 0 : obj.floatValue());
line = JU.PT.formatStringS(line, "O", obj != null && this.params.qm_moLinearCombination == null && ++rep != 0 ? (o == Clazz.floatToInt(o) ? "" + Clazz.floatToInt(o) : JU.PT.formatF(o, 0, 4, false, false)) : "");
}if (line.indexOf("%T") >= 0) line = JU.PT.formatStringS(line, "T", mo != null && mo.containsKey("type") ? (this.params.qm_moLinearCombination == null && ++rep != 0 ? "" + mo.get("type") : "") + ((this.params.isSquared || this.params.isSquaredLinear) && ++rep != 0 ? " ^2" : "") : "");
if (line.equals("string")) {
this.params.title[iLine] = "";
return;
}var isOptional = (line.indexOf("?") == 0);
this.params.title[iLine] = (!isOptional ? line : rep > 0 && !line.trim().endsWith("=") ? line.substring(1) : "");
}, "~N,java.util.Map");
Clazz.overrideMethod(c$, "readSurfaceData", 
function(isMapData){
if (this.volumeData.sr != null) return;
if (this.params.psi_monteCarloCount <= 0) {
this.readSurfaceDataVDR(isMapData);
return;
}if (this.points != null) return;
this.points =  new Array(1000);
for (var j = 0; j < 1000; j++) this.points[j] =  new JU.P3();

if (this.params.thePlane != null) this.vTemp =  new JU.V3();
for (var i = 0; i < 3; i++) this.vDist[i] = this.volumeData.volumetricVectorLengths[i] * this.volumeData.voxelCounts[i];

this.volumeData.setVoxelDataAsArray(this.voxelData =  Clazz.newFloatArray (1000, 1, 1, 0));
this.getValues();
var value;
var f = 0;
for (var j = 0; j < 1000; j++) if ((value = Math.abs(this.voxelData[j][0][0])) > f) f = value;

if (f < 0.0001) return;
for (var i = 0; i < this.params.psi_monteCarloCount; ) {
this.getValues();
for (var j = 0; j < 1000; j++) {
value = this.voxelData[j][0][0];
var absValue = Math.abs(value);
if (absValue <= this.getRnd(f)) continue;
this.addVC(this.points[j], value, 0, false);
if (++i == this.params.psi_monteCarloCount) break;
}
}
}, "~B");
Clazz.overrideMethod(c$, "postProcessVertices", 
function(){
});
Clazz.defineMethod(c$, "getValues", 
function(){
for (var j = 0; j < 1000; j++) {
this.voxelData[j][0][0] = 0;
this.points[j].set(this.volumeData.volumetricOrigin.x + this.getRnd(this.vDist[0]), this.volumeData.volumetricOrigin.y + this.getRnd(this.vDist[1]), this.volumeData.volumetricOrigin.z + this.getRnd(this.vDist[2]));
if (this.params.thePlane != null) JU.Measure.getPlaneProjection(this.points[j], this.params.thePlane, this.points[j], this.vTemp);
}
this.createOrbital();
});
Clazz.overrideMethod(c$, "getValueAtPoint", 
function(pt, getSource){
return (this.q == null ? 0 : this.q.processPt(pt));
}, "JU.T3,~B");
Clazz.defineMethod(c$, "getRnd", 
function(f){
return this.random.nextFloat() * f;
}, "~N");
Clazz.overrideMethod(c$, "generateCube", 
function(){
if (this.params.volumeData != null) return;
this.newVoxelDataCube();
this.createOrbital();
});
Clazz.defineMethod(c$, "createOrbital", 
function(){
var isMonteCarlo = (this.params.psi_monteCarloCount > 0);
if (this.isElectronDensityCalc) {
if (this.mos == null || isMonteCarlo) return;
System.out.println("createOrbital " + this.params.qm_moNumber);
for (var i = this.params.qm_moNumber; --i >= 0; ) {
JU.Logger.info(" generating isosurface data for MO " + (i + 1));
var mo = this.mos.get(i);
this.coef = mo.get("coefficients");
this.dfCoefMaps = mo.get("dfCoefMaps");
if (!this.setupCalculation()) return;
this.q.createCube();
}
} else {
if (!isMonteCarlo) JU.Logger.info("generating isosurface data for MO using cutoff " + this.params.cutoff);
if (!this.setupCalculation()) return;
this.q.createCube();
this.jvxlData.integration = this.q.getIntegration();
if (this.mo != null) this.mo.put("integration", Float.$valueOf(this.jvxlData.integration));
}});
Clazz.overrideMethod(c$, "getPlane", 
function(x){
if (!this.qSetupDone) this.setupCalculation();
return this.getPlaneSR(x);
}, "~N");
Clazz.defineMethod(c$, "setupCalculation", 
function(){
this.qSetupDone = true;
switch (this.params.qmOrbitalType) {
case 5:
break;
case 2:
case 1:
return (this.q).setupCalculation(this.params.moData, this.params.qmOrbitalType == 2, this.volumeData, this.bsMySelected, this.atomData.xyz, this.atomData.atoms, this.atomData.firstAtomIndex, this.dfCoefMaps, this.coef, this.linearCombination, this.params.isSquaredLinear, this.coefs, this.points);
case 3:
return (this.q).setupCalculation(this.volumeData, this.bsMySelected, this.params.bsSolvent, this.atomData.bsMolecules, this.atomData.atoms, this.atomData.firstAtomIndex, true, this.points, this.params.parameters, this.params.testFlags);
}
return false;
});
Clazz.overrideMethod(c$, "getSurfacePointAndFraction", 
function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn){
var zero = this.getSPF(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
if (this.q != null && !Float.isNaN(zero)) {
zero = this.q.processPt(ptReturn);
if (this.params.isSquared) zero *= zero;
}return zero;
}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
});
;//5.0.1-v7 Sat Feb 21 18:17:38 CST 2026
