Clazz.declarePackage("J.adapter.readers.more");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.more.BinaryDcdReader", ["JU.BS", "$.P3", "$.SB", "JU.Escape", "$.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.nModels = 0;
this.nAtoms = 0;
this.nFree = 0;
this.bsFree = null;
this.xAll = null;
this.yAll = null;
this.zAll = null;
this.crystGroup = 0;
Clazz.instantialize(this, arguments);}, J.adapter.readers.more, "BinaryDcdReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "setup", 
function(fullPath, htParams, reader){
this.isBinary = true;
this.requiresBSFilter = true;
this.setupASCR(fullPath, htParams, reader);
}, "~S,java.util.Map,~O");
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.initializeTrajectoryFile();
this.asc.setInfo("ignoreUnitCell", Boolean.TRUE);
});
Clazz.overrideMethod(c$, "processBinaryDocument", 
function(){
var bytes =  Clazz.newByteArray (40, 0);
this.binaryDoc.setStream(null, this.binaryDoc.readInt() == 0x54);
this.binaryDoc.readInt();
this.nModels = this.binaryDoc.readInt();
var nPriv = this.binaryDoc.readInt();
var nSaveC = this.binaryDoc.readInt();
var nStep = this.binaryDoc.readInt();
this.binaryDoc.readInt();
this.binaryDoc.readInt();
this.binaryDoc.readInt();
var ndegf = this.binaryDoc.readInt();
this.nFree = Clazz.doubleToInt(ndegf / 3);
var nFixed = this.binaryDoc.readInt();
var delta4 = this.binaryDoc.readInt();
this.crystGroup = this.binaryDoc.readInt();
this.binaryDoc.readByteArray(bytes, 0, 32);
this.binaryDoc.readInt();
this.binaryDoc.readInt();
this.binaryDoc.readInt();
var sb =  new JU.SB();
for (var i = 0, n = this.binaryDoc.readInt(); i < n; i++) sb.append(this.trimString(this.binaryDoc.readString(80))).appendC('\n');

this.binaryDoc.readInt();
JU.Logger.info("BinaryDcdReadaer:\n" + sb);
this.binaryDoc.readInt();
this.nAtoms = this.binaryDoc.readInt();
this.binaryDoc.readInt();
this.nFree = this.nAtoms - nFixed;
if (nFixed != 0) {
this.binaryDoc.readInt();
this.bsFree = JU.BS.newN(this.nFree);
for (var i = 0; i < this.nFree; i++) this.bsFree.set(this.binaryDoc.readInt() - 1);

this.binaryDoc.readInt();
JU.Logger.info("free: " + this.bsFree.cardinality() + " " + JU.Escape.eBS(this.bsFree));
}this.readCoordinates();
JU.Logger.info("Total number of trajectory steps=" + this.trajectorySteps.size());
});
Clazz.defineMethod(c$, "trimString", 
function(s){
var pt = s.indexOf('\0');
if (pt >= 0) s = s.substring(0, pt);
return s.trim();
}, "~S");
Clazz.defineMethod(c$, "readFloatArray", 
function(){
var n = Clazz.doubleToInt(this.binaryDoc.readInt() / 4);
var data =  Clazz.newFloatArray (n, 0);
for (var i = 0; i < n; i++) data[i] = this.binaryDoc.readFloat();

this.binaryDoc.readInt();
return data;
});
Clazz.defineMethod(c$, "readDoubleArray", 
function(){
var n = Clazz.doubleToInt(this.binaryDoc.readInt() / 8);
var data =  Clazz.newDoubleArray (n, 0);
for (var i = 0; i < n; i++) data[i] = this.binaryDoc.readDouble();

this.binaryDoc.readInt();
return data;
});
Clazz.defineMethod(c$, "readCoordinates", 
function(){
var ac = (this.bsFilter == null ? this.templateAtomCount : (this.htParams.get("filteredAtomCount")).intValue());
for (var i = 0; i < this.nModels; i++) if (this.doGetModel(++this.modelNumber, null)) {
var trajectoryStep =  new Array(ac);
if (!this.getTrajectoryStep(trajectoryStep)) return;
this.trajectorySteps.addLast(trajectoryStep);
if (this.isLastModel(this.modelNumber)) return;
} else {
if (this.crystGroup > 0) this.readDoubleArray();
this.readFloatArray();
this.readFloatArray();
this.readFloatArray();
}
});
Clazz.defineMethod(c$, "getTrajectoryStep", 
function(trajectoryStep){
try {
var ac = trajectoryStep.length;
var n = -1;
if (this.crystGroup > 0) this.calcUnitCell(this.readDoubleArray());
var x = this.readFloatArray();
var y = this.readFloatArray();
var z = this.readFloatArray();
var bs = (this.xAll == null ? null : this.bsFree);
if (bs == null) {
this.xAll = x;
this.yAll = y;
this.zAll = z;
}for (var i = 0, vpt = 0; i < this.nAtoms; i++) {
var pt =  new JU.P3();
if (bs == null || bs.get(i)) {
pt.set(x[vpt], y[vpt], z[vpt]);
vpt++;
} else {
pt.set(this.xAll[i], this.yAll[i], this.zAll[i]);
}if (this.bsFilter == null || this.bsFilter.get(i)) {
if (++n == ac) return true;
trajectoryStep[n] = pt;
}}
return true;
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return false;
} else {
throw e;
}
}
}, "~A");
Clazz.defineMethod(c$, "calcUnitCell", 
function(abc){
var a = abc[0];
var angle1 = abc[1];
var b = abc[2];
var angle2 = abc[3];
var angle3 = abc[4];
var c = abc[5];
var alpha = (1.5707963267948966 - Math.asin(angle3)) * 180 / 3.141592653589793;
var beta = (1.5707963267948966 - Math.asin(angle2)) * 180 / 3.141592653589793;
var gamma = (1.5707963267948966 - Math.asin(angle1)) * 180 / 3.141592653589793;
System.out.println("unitcell:[" + a + " " + b + " " + c + " " + alpha + " " + beta + " " + gamma + "]");
return  Clazz.newFloatArray(-1, [a, b, c, alpha, beta, gamma]);
}, "~A");
});
;//5.0.1-v7 Sat Feb 21 18:17:38 CST 2026
