Clazz.declarePackage("J.adapter.readers.quantum");
Clazz.load(["J.adapter.readers.quantum.GamessReader"], "J.adapter.readers.quantum.GamessUKReader", ["JU.Lst", "$.PT"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.symmetries = null;
this.occupancies = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum, "GamessUKReader", J.adapter.readers.quantum.GamessReader);
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.indexOf("BASIS OPTIONS") >= 0) {
this.readBasisInfo();
return true;
}if (this.line.indexOf("$CONTRL OPTIONS") >= 0) {
this.readControlInfo();
return true;
}if (this.line.indexOf("contracted primitive functions") >= 0) {
this.readGaussianBasis("======================================================", "======");
return false;
}if (this.line.indexOf("molecular geometry") >= 0) {
if (!this.doGetModel(++this.modelNumber, null)) return this.checkLastModel();
this.atomNames =  new JU.Lst();
this.readAtomsInBohrCoordinates();
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf("FREQUENCY_INFO_WOULD_BE_HERE") >= 0) {
return true;
}if (this.line.indexOf("SYMMETRY ASSIGNMENT") >= 0) {
this.readOrbitalSymmetryAndOccupancy();
return false;
}if (this.line.indexOf("- ALPHA SET -") >= 0) this.alphaBeta = "alpha";
 else if (this.line.indexOf("- BETA SET -") >= 0) this.alphaBeta = "beta";
 else if (this.line.indexOf("eigenvectors") >= 0) {
this.readMolecularOrbitals(3);
this.setOrbitalSymmetryAndOccupancy();
return false;
}return this.checkNboLine();
});
Clazz.overrideMethod(c$, "readAtomsInBohrCoordinates", 
function(){
this.discardLinesUntilContains("*****");
this.discardLinesUntilContains("atom");
this.discardLinesUntilContains("*****");
this.asc.newAtomSet();
while (this.rd() != null && this.line.indexOf("*****") < 0) {
if (this.line.charAt(14) == ' ') continue;
var tokens = this.getTokens();
var atomicNumber = Clazz.floatToInt(this.parseFloatStr(tokens[2]));
var atom = this.setAtomCoordScaled(null, tokens, 3, 0.5291772);
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(atomicNumber);
this.setAtom(atom, atomicNumber, tokens[1], null);
}
});
Clazz.overrideMethod(c$, "fixShellTag", 
function(tag){
return tag.substring(1).toUpperCase();
}, "~S");
Clazz.defineMethod(c$, "readOrbitalSymmetryAndOccupancy", 
function(){
this.readLines(4);
this.symmetries =  new JU.Lst();
this.occupancies =  new JU.Lst();
while (this.rd() != null && this.line.indexOf("====") < 0) {
var tokens = JU.PT.getTokens(this.line.substring(20));
this.symmetries.addLast(tokens[0] + " " + tokens[1]);
this.occupancies.addLast(Float.$valueOf(this.parseFloatStr(tokens[5])));
}
});
Clazz.defineMethod(c$, "setOrbitalSymmetryAndOccupancy", 
function(){
if (this.symmetries.size() < this.orbitals.size()) return;
for (var i = this.orbitals.size(); --i >= 0; ) {
var mo = this.orbitals.get(i);
mo.put("symmetry", this.symmetries.get(i));
mo.put("occupancy", this.occupancies.get(i));
}
});
});
;//5.0.1-v7 Thu Feb 05 13:38:23 CST 2026
