Clazz.declarePackage("J.adapter.readers.spartan");
Clazz.load(["J.adapter.readers.quantum.BasisFunctionReader"], "J.adapter.readers.spartan.SpartanInputReader", ["JU.PT", "J.adapter.smarter.Bond", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.modelAtomCount = 0;
this.bondData = "";
this.constraints = "";
Clazz.instantialize(this, arguments);}, J.adapter.readers.spartan, "SpartanInputReader", J.adapter.readers.quantum.BasisFunctionReader);
Clazz.defineMethod(c$, "readInputRecords", 
function(){
var ac0 = this.asc.ac;
var modelName = this.readInputHeader();
while (this.rd() != null) {
var tokens = this.getTokens();
if (tokens.length == 2 && this.parseIntStr(tokens[0]) != -2147483648 && this.parseIntStr(tokens[1]) >= 0) break;
}
if (this.line == null) return null;
this.readInputAtoms();
this.discardLinesUntilContains("ATOMLABELS");
if (this.line != null) this.readAtomNames();
if (this.modelAtomCount > 1) {
this.discardLinesUntilContains("HESSIAN");
if (this.line != null) this.readBonds(ac0);
if (this.line != null && this.line.indexOf("BEGINCONSTRAINTS") >= 0) this.readConstraints();
}return modelName;
});
Clazz.defineMethod(c$, "readConstraints", 
function(){
this.constraints = "";
while (this.rd() != null && this.line.indexOf("END") < 0) this.constraints += (this.constraints === "" ? "" : "\n") + this.line;

this.rd();
if (this.constraints.length == 0) return;
this.asc.setCurrentModelInfo("constraints", this.constraints);
this.asc.setAtomSetModelProperty(".PATH", "EnergyProfile");
this.asc.setAtomSetModelProperty("Constraint", this.constraints);
});
Clazz.defineMethod(c$, "readTransform", 
function(){
this.rd();
var tokens = JU.PT.getTokens(this.rd() + " " + this.rd());
this.setTransform(this.parseFloatStr(tokens[0]), this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[4]), this.parseFloatStr(tokens[5]), this.parseFloatStr(tokens[6]), this.parseFloatStr(tokens[8]), this.parseFloatStr(tokens[9]), this.parseFloatStr(tokens[10]));
});
Clazz.defineMethod(c$, "readInputHeader", 
function(){
while (this.rd() != null && !this.line.startsWith(" ")) {
}
this.rd();
return this.line.substring(0, (this.line + ";").indexOf(";")).trim();
});
Clazz.defineMethod(c$, "readInputAtoms", 
function(){
this.modelAtomCount = 0;
while (this.rd() != null && !this.line.startsWith("ENDCART")) {
var tokens = this.getTokens();
this.addAtomXYZSymName(tokens, 1, J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(this.parseIntStr(tokens[0])), null);
this.modelAtomCount++;
}
if (this.debugging) JU.Logger.debug(this.asc.ac + " atoms read");
});
Clazz.defineMethod(c$, "readAtomNames", 
function(){
var atom0 = this.asc.ac - this.modelAtomCount;
for (var i = 0; i < this.modelAtomCount; i++) {
this.line = this.rd().trim();
var name = this.line.substring(1, this.line.length - 1);
this.asc.atoms[atom0 + i].atomName = name;
}
});
Clazz.defineMethod(c$, "readBonds", 
function(ac0){
var nAtoms = this.modelAtomCount;
this.bondData = "";
while (this.rd() != null && !this.line.startsWith("ENDHESS")) {
var tokens = this.getTokens();
this.bondData += this.line + " ";
if (nAtoms == 0) {
var sourceIndex = this.parseIntStr(tokens[0]) - 1 + ac0;
var targetIndex = this.parseIntStr(tokens[1]) - 1 + ac0;
var bondOrder = this.parseIntStr(tokens[2]);
if (bondOrder > 0) {
this.asc.addBond( new J.adapter.smarter.Bond(sourceIndex, targetIndex, bondOrder < 4 ? bondOrder : bondOrder == 5 ? 515 : 1));
}} else {
nAtoms -= tokens.length;
}}
this.rd();
if (this.debugging) JU.Logger.debug(this.asc.bondCount + " bonds read");
}, "~N");
});
;//5.0.1-v2 Mon Mar 04 12:59:58 CST 2024
