Clazz.declarePackage("J.adapter.smarter");
Clazz.load(["J.api.JmolAdapterAtomIterator"], "J.adapter.smarter.AtomIterator", ["J.api.JmolAdapter"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.iatom = 0;
this.atom = null;
this.ac = 0;
this.atoms = null;
this.bsAtoms = null;
Clazz.instantialize(this, arguments);}, J.adapter.smarter, "AtomIterator", null, J.api.JmolAdapterAtomIterator);
Clazz.makeConstructor(c$, 
function(asc){
this.ac = asc.ac;
this.atoms = asc.atoms;
this.bsAtoms = asc.bsAtoms;
this.iatom = 0;
}, "J.adapter.smarter.AtomSetCollection");
Clazz.overrideMethod(c$, "hasNext", 
function(){
if (this.iatom == this.ac) return false;
while ((this.atom = this.atoms[this.iatom++]) == null || (this.bsAtoms != null && !this.bsAtoms.get(this.atom.index))) if (this.iatom == this.ac) return false;

this.atoms[this.iatom - 1] = null;
return true;
});
Clazz.overrideMethod(c$, "getAtomSetIndex", 
function(){
return this.atom.atomSetIndex;
});
Clazz.overrideMethod(c$, "getSymmetry", 
function(){
return this.atom.bsSymmetry;
});
Clazz.overrideMethod(c$, "getAtomSite", 
function(){
return this.atom.atomSite + 1;
});
Clazz.overrideMethod(c$, "getUniqueID", 
function(){
return Integer.$valueOf(this.atom.index);
});
Clazz.overrideMethod(c$, "getElementNumber", 
function(){
return (this.atom.elementNumber > 0 ? this.atom.elementNumber : J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol()));
});
Clazz.overrideMethod(c$, "getAtomName", 
function(){
return this.atom.atomName;
});
Clazz.overrideMethod(c$, "getFormalCharge", 
function(){
return (this.atom.formalCharge == -2147483648 ? 0 : this.atom.formalCharge);
});
Clazz.overrideMethod(c$, "getPartialCharge", 
function(){
return this.atom.partialCharge;
});
Clazz.overrideMethod(c$, "getTensors", 
function(){
return this.atom.tensors;
});
Clazz.overrideMethod(c$, "getRadius", 
function(){
return this.atom.radius;
});
Clazz.overrideMethod(c$, "getBondRadius", 
function(){
return this.atom.bondingRadius;
});
Clazz.overrideMethod(c$, "getVib", 
function(){
return (this.atom.vib == null || Float.isNaN(this.atom.vib.z) ? null : this.atom.vib);
});
Clazz.overrideMethod(c$, "getSeqID", 
function(){
return (this.atom.vib == null || !Float.isNaN(this.atom.vib.y) || this.atom.vib.z != 1094713365 ? 0 : Clazz.floatToInt(this.atom.vib.x));
});
Clazz.overrideMethod(c$, "getBfactor", 
function(){
return this.atom.bfactor;
});
Clazz.overrideMethod(c$, "getOccupancy", 
function(){
return this.atom.foccupancy * 100;
});
Clazz.overrideMethod(c$, "getIsHetero", 
function(){
return this.atom.isHetero;
});
Clazz.overrideMethod(c$, "getSerial", 
function(){
return this.atom.atomSerial;
});
Clazz.overrideMethod(c$, "getChainID", 
function(){
return this.atom.chainID;
});
Clazz.overrideMethod(c$, "getAltLoc", 
function(){
return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc);
});
Clazz.overrideMethod(c$, "getGroup3", 
function(){
return this.atom.group3;
});
Clazz.overrideMethod(c$, "getSequenceNumber", 
function(){
return this.atom.sequenceNumber;
});
Clazz.overrideMethod(c$, "getInsertionCode", 
function(){
return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode);
});
Clazz.overrideMethod(c$, "getXYZ", 
function(){
return this.atom;
});
Clazz.overrideMethod(c$, "getElement", 
function(){
return this.getElementNumber() & 0x7F;
});
Clazz.overrideMethod(c$, "getIsotope", 
function(){
return this.getElementNumber() >> 7;
});
Clazz.overrideMethod(c$, "getIsNegDisorder", 
function(){
return this.atom.isNegDisorder;
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
