Clazz.declarePackage("J.adapter.readers.quantum");
Clazz.load(["J.adapter.readers.quantum.MopacSlaterReader"], "J.adapter.readers.quantum.MopacGraphfReader", ["java.util.Hashtable", "JU.AU", "$.Lst"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.ac = 0;
this.nCoefficients = 0;
this.invMatrix = null;
this.isNewFormat = false;
this.orbitalData = null;
this.orbitalInfo = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum, "MopacGraphfReader", J.adapter.readers.quantum.MopacSlaterReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.alphaBeta = "alpha";
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
this.readAtoms();
if (this.doReadMolecularOrbitals) {
this.readSlaterBasis();
this.readMolecularOrbitals(false);
if (this.readKeywords()) this.readMolecularOrbitals(true);
}this.continuing = false;
return false;
});
Clazz.defineMethod(c$, "readAtoms", 
function(){
this.asc.newAtomSet();
this.ac = this.parseIntStr(this.line);
this.atomicNumbers =  Clazz.newIntArray (this.ac, 0);
for (var i = 0; i < this.ac; i++) {
this.rd();
this.atomicNumbers[i] = this.parseIntRange(this.line, 0, 4);
var atom = this.asc.addNewAtom();
this.setAtomCoordXYZ(atom, this.parseFloatRange(this.line, 4, 17), this.parseFloatRange(this.line, 17, 29), this.parseFloatRange(this.line, 29, 41));
if (this.line.length > 41) atom.partialCharge = this.parseFloatStr(this.line.substring(41));
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(this.atomicNumbers[i]);
}
});
Clazz.defineMethod(c$, "readSlaterBasis", 
function(){
this.nCoefficients = 0;
this.getSlaters();
var values =  Clazz.newFloatArray (3, 0);
for (var iAtom = 0; iAtom < this.ac; iAtom++) {
J.adapter.smarter.AtomSetCollectionReader.getTokensFloat(this.rd(), values, 3);
var atomicNumber = this.atomicNumbers[iAtom];
this.createMopacSlaters(iAtom, atomicNumber, values, true);
}
this.nCoefficients = this.slaters.size();
this.setSlaters(false);
});
Clazz.defineMethod(c$, "readMolecularOrbitals", 
function(isBeta){
if (isBeta) this.alphaBeta = "beta";
var list = null;
if (this.rd() == null) return;
this.isNewFormat = (this.line.indexOf("ORBITAL") >= 0);
if (this.isNewFormat) {
this.orbitalData =  new JU.Lst();
if (this.line.length > 10) this.orbitalInfo =  new JU.Lst();
} else {
list =  Clazz.newFloatArray (this.nCoefficients, this.nCoefficients, 0);
}for (var iMo = 0; iMo < this.nCoefficients; iMo++) {
if (iMo != 0) this.rd();
var data;
if (this.isNewFormat) {
if (this.line == null || this.line.indexOf("ORBITAL") < 0 || this.line.indexOf("ORBITAL_LIST") >= 0) break;
this.orbitalData.addLast(data =  Clazz.newFloatArray (this.nCoefficients, 0));
if (this.orbitalInfo != null) this.orbitalInfo.addLast(this.line);
this.rd();
} else {
data = list[iMo];
}this.fillFloatArray(this.line, 15, data);
}
if (this.invMatrix == null) {
if (this.isNewFormat && this.line.indexOf("MATRIX") < 0) this.rd();
this.invMatrix = JU.AU.newFloat2(this.nCoefficients);
for (var iMo = 0; iMo < this.nCoefficients; iMo++) this.fillFloatArray(null, 15, this.invMatrix[iMo] =  Clazz.newFloatArray (iMo + 1, 0));

}this.nOrbitals = (this.orbitalData == null ? this.nCoefficients : this.orbitalData.size());
if (this.orbitalData != null) {
list = JU.AU.newFloat2(this.nOrbitals);
for (var i = this.nOrbitals; --i >= 0; ) list[i] = this.orbitalData.get(i);

}var list2 =  Clazz.newFloatArray (this.nOrbitals, this.nCoefficients, 0);
for (var i = 0; i < this.nOrbitals; i++) for (var j = 0; j < this.nCoefficients; j++) {
for (var k = 0; k < this.nCoefficients; k++) list2[i][j] += (list[i][k] * (k >= j ? this.invMatrix[k][j] : this.invMatrix[j][k]));

if (Math.abs(list2[i][j]) < 1.0E-4) list2[i][j] = 0;
}

if (this.isNewFormat && this.orbitalInfo == null && this.line != null && this.line.indexOf("ORBITAL_LIST") < 0) this.rd();
var values =  Clazz.newFloatArray (2, 0);
for (var iMo = 0; iMo < this.nOrbitals; iMo++) {
var mo =  new java.util.Hashtable();
if (this.orbitalInfo != null) {
this.line = this.orbitalInfo.get(iMo);
var tokens = this.getTokens();
mo.put("energy", Float.$valueOf(this.parseFloatStr(tokens[3])));
mo.put("occupancy", Float.$valueOf(this.parseFloatStr(tokens[1])));
} else if (this.rd() != null) {
J.adapter.smarter.AtomSetCollectionReader.getTokensFloat(this.line, values, 2);
mo.put("energy", Float.$valueOf(values[0]));
mo.put("occupancy", Float.$valueOf(values[1]));
}mo.put("coefficients", list2[iMo]);
if (isBeta) mo.put("type", "beta");
this.line = "\n";
if (this.filterMO()) this.setMO(mo);
}
this.setMOs("eV");
}, "~B");
Clazz.defineMethod(c$, "readKeywords", 
function(){
if (this.rd() == null || this.line.indexOf(" Keywords:") < 0) return false;
this.moData.put("calculationType", this.calculationType = this.line.substring(11).trim());
var isUHF = (this.line.indexOf("UHF") >= 0);
if (isUHF) {
for (var i = this.orbitals.size(); --i >= 0; ) {
this.orbitals.get(i).put("type", "alpha");
}
}return isUHF;
});
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
