Clazz.declarePackage("J.adapter.readers.more");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.more.MdCrdReader", ["JU.P3", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.ptFloat = 0;
this.lenLine = 0;
Clazz.instantialize(this, arguments);}, J.adapter.readers.more, "MdCrdReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "setup", 
function(fullPath, htParams, readerOrDocument){
this.requiresBSFilter = true;
this.setupASCR(fullPath, htParams, readerOrDocument);
}, "~S,java.util.Map,~O");
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.initializeTrajectoryFile();
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
this.readCoordinates();
JU.Logger.info("Total number of trajectory steps=" + this.trajectorySteps.size());
this.continuing = false;
return false;
});
Clazz.defineMethod(c$, "readCoordinates", 
function(){
this.line = null;
var ac = (this.bsFilter == null ? this.templateAtomCount : (this.htParams.get("filteredAtomCount")).intValue());
var isPeriodic = this.htParams.containsKey("isPeriodic");
var floatCount = this.templateAtomCount * 3 + (isPeriodic ? 3 : 0);
while (true) if (this.doGetModel(++this.modelNumber, null)) {
var trajectoryStep =  new Array(ac);
if (!this.getTrajectoryStep(trajectoryStep, isPeriodic)) return;
this.trajectorySteps.addLast(trajectoryStep);
if (this.isLastModel(this.modelNumber)) return;
} else {
if (!this.skipFloats(floatCount)) return;
}
});
Clazz.defineMethod(c$, "getFloat", 
function(){
while (this.line == null || this.ptFloat >= this.lenLine) {
if (this.rd() == null) return NaN;
this.ptFloat = 0;
this.lenLine = this.line.length;
}
this.ptFloat += 8;
return this.parseFloatRange(this.line, this.ptFloat - 8, this.ptFloat);
});
Clazz.defineMethod(c$, "getPoint", 
function(){
var x = this.getFloat();
var y = this.getFloat();
var z = this.getFloat();
return (Float.isNaN(z) ? null : JU.P3.new3(x, y, z));
});
Clazz.defineMethod(c$, "getTrajectoryStep", 
function(trajectoryStep, isPeriodic){
var ac = trajectoryStep.length;
var n = -1;
for (var i = 0; i < this.templateAtomCount; i++) {
var pt = this.getPoint();
if (pt == null) return false;
if (this.bsFilter == null || this.bsFilter.get(i)) {
if (++n == ac) return false;
trajectoryStep[n] = pt;
}}
if (isPeriodic) this.getPoint();
return (this.line != null);
}, "~A,~B");
Clazz.defineMethod(c$, "skipFloats", 
function(n){
var i = 0;
while (i < n && this.rd() != null) i += this.getTokens().length;

return (this.line != null);
}, "~N");
});
;//5.0.1-v7 Thu May 08 14:17:10 CDT 2025
