Clazz.declarePackage("J.adapter.readers.more");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.more.GromacsReader", ["JU.P3", "J.adapter.smarter.Atom", "JU.Logger"], function(){
var c$ = Clazz.declareType(J.adapter.readers.more, "GromacsReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.setIsPDB();
this.asc.newAtomSet();
this.setModelPDB(true);
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
this.checkCurrentLineForScript();
this.asc.setAtomSetName(this.line.trim());
this.readAtoms();
this.readUnitCell();
this.continuing = false;
return false;
});
Clazz.defineMethod(c$, "readAtoms", 
function(){
var modelAtomCount = this.parseIntStr(this.rd());
for (var i = 0; i < modelAtomCount; ++i) {
this.rd();
var len = this.line.length;
if (len != 44 && len != 68) {
JU.Logger.warn("line cannot be read for GROMACS atom data: " + this.line);
continue;
}var atom =  new J.adapter.smarter.Atom();
atom.sequenceNumber = this.parseIntRange(this.line, 0, 5);
this.setAtomName(atom, this.parseTokenRange(this.line, 5, 9).trim(), this.line.substring(11, 15).trim());
atom.atomSerial = this.parseIntRange(this.line, 15, 20);
atom.x = this.parseFloatRange(this.line, 20, 28) * 10;
atom.y = this.parseFloatRange(this.line, 28, 36) * 10;
atom.z = this.parseFloatRange(this.line, 36, 44) * 10;
if (Float.isNaN(atom.x) || Float.isNaN(atom.y) || Float.isNaN(atom.z)) {
JU.Logger.warn("line cannot be read for GROMACS atom data: " + this.line);
atom.set(0, 0, 0);
}this.setAtomCoord(atom);
atom.elementSymbol = this.deduceElementSymbol(atom.group3, atom.atomName);
if (!this.filterAtom(atom, i)) continue;
atom.isHetero = false;
this.asc.addAtom(atom);
if (len < 69) continue;
var vx = this.parseFloatRange(this.line, 44, 52) * 10;
var vy = this.parseFloatRange(this.line, 52, 60) * 10;
var vz = this.parseFloatRange(this.line, 60, 68) * 10;
if (Float.isNaN(vx) || Float.isNaN(vy) || Float.isNaN(vz)) continue;
this.asc.addVibrationVector(atom.index, vx, vy, vz);
}
});
Clazz.defineMethod(c$, "setAtomName", 
function(atom, gname, aname){
atom.atomName = aname;
if (gname.equals("SOL") && aname.length == 3 && "OW1;HW2;HW3".indexOf(aname) >= 0) gname = "WAT";
atom.group3 = gname;
}, "J.adapter.smarter.Atom,~S,~S");
Clazz.defineMethod(c$, "deduceElementSymbol", 
function(group3, atomName){
if (atomName.length <= 2 && group3.equals(atomName)) return atomName;
var ch1 = (atomName.length == 4 ? atomName.charAt(0) : '\0');
var ch2 = atomName.charAt(atomName.length == 4 ? 1 : 0);
var isHetero = this.vwr.getJBR().isHetero(group3);
if (J.adapter.smarter.Atom.isValidSymNoCase(ch1, ch2)) return (isHetero || ch1 != 'H' ? "" + ch1 + ch2 : "H");
if (J.adapter.smarter.Atom.isValidSym1(ch2)) return "" + ch2;
if (J.adapter.smarter.Atom.isValidSym1(ch1)) return "" + ch1;
return "Xx";
}, "~S,~S");
Clazz.defineMethod(c$, "readUnitCell", 
function(){
if (this.rd() == null) return;
var tokens = this.getTokens();
if (tokens.length < 3 || !this.doApplySymmetry) return;
var a = 10 * this.parseFloatStr(tokens[0]);
var b = 10 * this.parseFloatStr(tokens[1]);
var c = 10 * this.parseFloatStr(tokens[2]);
this.setUnitCell(a, b, c, 90, 90, 90);
this.setSpaceGroupName("P1");
var atoms = this.asc.atoms;
var pt = JU.P3.new3(0.5, 0.5, 0.5);
for (var i = this.asc.ac; --i >= 0; ) {
this.setAtomCoord(atoms[i]);
atoms[i].add(pt);
}
});
});
;//5.0.1-v7 Mon Aug 24 10:01:38 CDT 2026
