Clazz.declarePackage("J.quantum");
Clazz.load(["J.quantum.QuantumCalculation"], "J.quantum.MepCalculation", ["java.util.Hashtable", "JU.PT", "$.Rdr", "JU.Logger", "JV.FileManager"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.distanceMode = 0;
this.potentials = null;
this.atomCoordAngstroms = null;
this.bsSelected = null;
this.vwr = null;
this.htAtomicPotentials = null;
this.resourceName = null;
Clazz.instantialize(this, arguments);}, J.quantum, "MepCalculation", J.quantum.QuantumCalculation);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.quantum.MepCalculation, []);
this.rangeBohrOrAngstroms = 8;
this.distanceMode = 0;
this.unitFactor = 1;
});
Clazz.defineMethod(c$, "set", 
function(vwr){
this.vwr = vwr;
}, "JV.Viewer");
Clazz.defineMethod(c$, "assignPotentials", 
function(atoms, potentials, bsAromatic, bsCarbonyl, bsIgnore, data){
this.getAtomicPotentials(data, null);
for (var i = 0; i < atoms.length; i++) {
var f;
if (bsIgnore != null && bsIgnore.get(i)) {
f = NaN;
} else {
f = this.getTabulatedPotential(atoms[i]);
if (Float.isNaN(f)) f = 0;
}if (JU.Logger.debugging) JU.Logger.debug(atoms[i].getInfo() + " " + f);
potentials[i] = f;
}
}, "~A,~A,JU.BS,JU.BS,JU.BS,~S");
Clazz.defineMethod(c$, "setup", 
function(calcType, potentials, atomCoordAngstroms, bsSelected){
if (calcType >= 0) this.distanceMode = calcType;
this.potentials = potentials;
this.atomCoordAngstroms = atomCoordAngstroms;
this.bsSelected = bsSelected;
}, "~N,~A,~A,JU.BS");
Clazz.defineMethod(c$, "calculate", 
function(volumeData, bsSelected, xyz, atoms, potentials, calcType){
this.setup(calcType, potentials, atoms, bsSelected);
this.voxelData = volumeData.getVoxelData();
this.countsXYZ = volumeData.getVoxelCounts();
this.initialize(this.countsXYZ[0], this.countsXYZ[1], this.countsXYZ[2], null);
this.setupCoordinates(volumeData.getOriginFloat(), volumeData.getVolumetricVectorLengths(), bsSelected, xyz, atoms, null, false);
this.setXYZBohr(this.points);
this.process();
}, "J.jvxl.data.VolumeData,JU.BS,~A,~A,~A,~N");
Clazz.defineMethod(c$, "getValueAtPoint", 
function(pt){
var value = 0;
for (var i = this.bsSelected.nextSetBit(0); i >= 0; i = this.bsSelected.nextSetBit(i + 1)) {
var x = this.potentials[i];
var d2 = pt.distanceSquared(this.atomCoordAngstroms[i]);
value += this.valueFor(x, d2, this.distanceMode);
}
return value;
}, "JU.P3");
Clazz.overrideMethod(c$, "process", 
function(){
for (var atomIndex = this.qmAtoms.length; --atomIndex >= 0; ) {
if ((this.thisAtom = this.qmAtoms[atomIndex]) == null) continue;
var x0 = this.potentials[atomIndex];
if (JU.Logger.debugging) JU.Logger.debug("process map for atom " + atomIndex + this.thisAtom + "  charge=" + x0);
this.thisAtom.setXYZ(this, true);
for (var ix = this.xMax; --ix >= this.xMin; ) {
var dX = this.X2[ix];
for (var iy = this.yMax; --iy >= this.yMin; ) {
var dXY = dX + this.Y2[iy];
for (var iz = this.zMax; --iz >= this.zMin; ) {
this.voxelData[ix][iy][iz] += this.valueFor(x0, dXY + this.Z2[iz], this.distanceMode);
}
}
}
}
});
Clazz.defineMethod(c$, "valueFor", 
function(x0, d2, distanceMode){
switch (distanceMode) {
case 0:
return (d2 == 0 ? x0 * Infinity : x0 / Math.sqrt(d2));
case 2:
return x0 / (1 + Math.sqrt(d2));
case 1:
return x0 * Math.exp(-Math.sqrt(d2) / 2);
case 3:
return x0 * Math.exp(-Math.sqrt(d2));
}
return x0;
}, "~N,~N,~N");
Clazz.defineMethod(c$, "getTabulatedPotential", 
function(atom){
var name = atom.getAtomType();
var g1 = atom.getGroup1('\0');
var type = atom.getBioStructureTypeName();
if (g1.length == 0) {
g1 = atom.getGroup3(true);
if (g1 == null) g1 = "";
}var key = g1 + name;
var o = this.htAtomicPotentials.get(key);
if (o == null && type.length > 0) o = this.htAtomicPotentials.get("_" + type.charAt(0) + name);
return (Clazz.instanceOf(o, Float) ? (o).floatValue() : NaN);
}, "JM.Atom");
Clazz.defineMethod(c$, "getAtomicPotentials", 
function(data, resourceName){
var br = null;
this.htAtomicPotentials =  new java.util.Hashtable();
try {
br = (data == null ? JV.FileManager.getBufferedReaderForResource(this.vwr, J.quantum.MepCalculation, "J/quantum/", resourceName) : JU.Rdr.getBR(data));
var line;
while ((line = br.readLine()) != null) {
if (line.startsWith("#")) continue;
var vs = JU.PT.getTokens(line);
if (vs.length < 2) continue;
if (JU.Logger.debugging) JU.Logger.debug(line);
this.htAtomicPotentials.put(vs[0], Float.$valueOf(JU.PT.parseFloat(vs[1])));
}
br.close();
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error("Exception " + e.toString() + " in getResource " + resourceName);
try {
br.close();
} catch (ee) {
if (Clazz.exceptionOf(ee, Exception)){
} else {
throw ee;
}
}
} else {
throw e;
}
}
}, "~S,~S");
Clazz.overrideMethod(c$, "createCube", 
function(){
});
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
