Clazz.declarePackage("J.adapter.readers.cif");
Clazz.load(["J.adapter.smarter.MSInterface"], "J.adapter.readers.cif.MSRdr", ["java.util.Hashtable", "JU.Lst", "$.M3", "$.Matrix", "$.P3", "$.PT", "J.adapter.readers.cif.Subsystem", "J.adapter.smarter.AtomSetCollectionReader", "JU.BoxInfo", "$.Escape", "$.Logger", "$.Modulation", "$.ModulationSet", "JV.JC"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.cr = null;
this.modDim = 0;
this.modAxes = null;
this.modAverage = false;
this.isCommensurate = false;
this.commensurateSection1 = 0;
this.modPack = false;
this.modVib = false;
this.modType = null;
this.modCell = null;
this.modDebug = false;
this.modSelected = -1;
this.modLast = false;
this.sigma = null;
this.htModulation = null;
this.htAtomMods = null;
this.iopLast = -1;
this.gammaE = null;
this.nOps = 0;
this.haveOccupancy = false;
this.atoms = null;
this.ac = 0;
this.haveAtomMods = false;
this.modCoord = false;
this.finalized = false;
this.symmetry = null;
this.supercellSymmetry = null;
this.legendres = null;
this.atModel = "@0";
this.modMatrices = null;
this.qlist100 = null;
this.qs = null;
this.modCount = 0;
this.modTUV = null;
this.htSubsystems = null;
this.minXYZ0 = null;
this.maxXYZ0 = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.cif, "MSRdr", null, J.adapter.smarter.MSInterface);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "getSigma", 
function(){
return this.sigma;
});
Clazz.overrideMethod(c$, "initialize", 
function(r, modDim){
this.cr = r;
this.modCoord = r.checkFilterKey("MODCOORD");
this.modDebug = r.checkFilterKey("MODDEBUG");
this.modPack = !r.checkFilterKey("MODNOPACK");
this.modLast = r.checkFilterKey("MODLAST");
this.modAxes = r.getFilter("MODAXES=");
this.modType = r.getFilter("MODTYPE=");
this.modCell = r.getFilter("MODCELL=");
this.modSelected = r.parseIntStr("" + r.getFilter("MOD="));
this.modVib = r.checkFilterKey("MODVIB");
this.modAverage = r.checkFilterKey("MODAVE");
var smodTUV = r.getFilter("MODT=");
if (smodTUV != null || (smodTUV = r.getFilter("MODTUV=")) != null) {
this.modTUV =  new JU.P3();
var tuv = (JU.PT.replaceAllCharacters(smodTUV, "{}()", "") + ",0,0,0").$plit(",");
this.modTUV.x = JU.PT.parseFloatFraction(tuv[0]);
this.modTUV.y = JU.PT.parseFloatFraction(tuv[1]);
this.modTUV.z = JU.PT.parseFloatFraction(tuv[2]);
if (Float.isNaN(this.modTUV.lengthSquared())) {
JU.Logger.error("MSRdr cannot read modTUV=" + smodTUV);
this.modTUV = null;
}}this.setModDim(modDim);
return modDim;
}, "J.adapter.smarter.AtomSetCollectionReader,~N");
Clazz.defineMethod(c$, "setSubsystemOptions", 
function(){
this.cr.forceSymmetry(this.modPack);
if (this.modCell != null) this.cr.addJmolScript("unitcell {%" + this.modCell + "}");
});
Clazz.defineMethod(c$, "setModDim", 
function(ndim){
this.htModulation =  new java.util.Hashtable();
this.modDim = ndim;
this.cr.appendLoadNote("Modulation dimension = " + this.modDim);
}, "~N");
Clazz.overrideMethod(c$, "addModulation", 
function(map, id, pt, iModel){
var ch = id.charAt(0);
switch ((ch).charCodeAt(0)) {
case 79:
case 68:
case 77:
case 85:
if (this.modType != null && this.modType.indexOf(ch) < 0 || this.modSelected > 0 && this.modSelected != 1) return;
break;
}
var isOK = false;
for (var i = pt.length; --i >= 0; ) {
if (this.modSelected > 0 && i + 1 != this.modSelected && id.contains("_coefs_")) {
pt[i] = 0;
} else if (pt[i] != 0) {
isOK = true;
break;
}}
if (!isOK) return;
if (map == null) map = this.htModulation;
if (id.indexOf("@") < 0) id += "@" + (iModel >= 0 ? iModel : this.cr.asc.iSet);
if (id.startsWith("D_L#") || id.startsWith("U_L")) {
if (this.legendres == null) this.legendres =  new JU.Lst();
this.legendres.addLast(id);
}JU.Logger.info("Adding " + id + " " + JU.Escape.e(pt));
map.put(id, pt);
}, "java.util.Map,~S,~A,~N");
Clazz.overrideMethod(c$, "setModulation", 
function(isPost, symmetry){
if (this.modDim == 0 || this.htModulation == null) return;
if (this.modDebug) JU.Logger.debugging = JU.Logger.debuggingHigh = true;
this.cr.asc.setInfo(JV.JC.getBoolName(9), Boolean.TRUE);
this.symmetry = symmetry;
this.setModulationForStructure(this.cr.asc.iSet, isPost);
if (this.modDebug) JU.Logger.debugging = JU.Logger.debuggingHigh = false;
}, "~B,J.adapter.smarter.XtalSymmetry.FileSymmetry");
Clazz.overrideMethod(c$, "finalizeModulation", 
function(){
if (!this.finalized && this.modDim > 0 && !this.modVib) {
if (this.modTUV != null) this.cr.appendLoadNote("modTUV=" + this.modTUV);
this.cr.asc.setInfo("modulationOn", this.modTUV == null ? Boolean.TRUE : this.modTUV);
this.cr.addJmolScript("set modulateOccupancy " + (this.haveOccupancy && !this.isCommensurate ? true : false));
}this.finalized = true;
});
Clazz.defineMethod(c$, "checkKey", 
function(key, checkQ){
var pt = key.indexOf(this.atModel);
return (pt < 0 || key.indexOf("_pos#") >= 0 || key.indexOf("*;*") >= 0 || checkQ && key.indexOf("?") >= 0 ? null : key.substring(0, pt));
}, "~S,~B");
Clazz.overrideMethod(c$, "getMod", 
function(key){
return this.htModulation.get(key + this.atModel);
}, "~S");
Clazz.overrideMethod(c$, "getModulationMap", 
function(){
return this.htModulation;
});
Clazz.defineMethod(c$, "setModulationForStructure", 
function(iModel, isPost){
this.atModel = "@" + iModel;
if (this.htModulation.containsKey("X_" + this.atModel)) return;
if (!isPost) {
this.initModForStructure(iModel);
return;
}this.htModulation.put("X_" + this.atModel,  Clazz.newDoubleArray (/*org.eclipse.jdt.core.dom.NumberLiteral*/0, 0));
this.cr.appendLoadNote(this.modCount + " modulations for " + this.ac + " modulated atoms");
if (!this.haveAtomMods) return;
var n = this.cr.asc.ac;
this.atoms = this.cr.asc.atoms;
if (this.symmetry != null) this.nOps = this.symmetry.getSpaceGroupOperationCount();
this.supercellSymmetry = this.cr.asc.getXSymmetry().getSymmetry();
if (this.supercellSymmetry === this.symmetry) this.supercellSymmetry = null;
this.iopLast = -1;
var i0 = this.cr.asc.getLastAtomSetAtomIndex();
for (var i = i0; i < n; i++) this.modulateAtom(this.atoms[i]);

this.htAtomMods = null;
if (this.minXYZ0 != null) this.trimAtomSet();
this.htSubsystems = null;
}, "~N,~B");
Clazz.defineMethod(c$, "initModForStructure", 
function(iModel){
var key;
if (this.legendres != null) this.fixLegendre();
this.sigma =  new JU.Matrix(null, this.modDim, 3);
this.qs = null;
this.qlist100 = null;
this.modMatrices =  Clazz.newArray(-1, [this.sigma, null]);
var pt;
for (var i = 0; i < this.modDim; i++) {
pt = this.getMod("W_" + (i + 1));
if (pt == null) {
this.cr.appendLoadNote("NOTE!: Not enough cell wave vectors for d=" + this.modDim);
return;
}this.cr.fixDoubleA(pt);
this.cr.appendLoadNote("W_" + (i + 1) + " = " + JU.Escape.e(pt));
this.cr.appendUnitCellInfo("q" + (i + 1) + "=" + pt[0] + " " + pt[1] + " " + pt[2]);
this.sigma.getArray()[i] =  Clazz.newDoubleArray(-1, [pt[0], pt[1], pt[2]]);
}
var map =  new java.util.Hashtable();
for (var e, $e = this.htModulation.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var k = e.getKey();
if ((key = this.checkKey(k, false)) == null) continue;
pt = e.getValue();
var ch = key.charAt(0);
switch ((ch).charCodeAt(0)) {
case 79:
this.haveOccupancy = true;
case 68:
case 77:
case 85:
if (pt[2] == 1 && key.charAt(2) != 'S' && key.charAt(2) != 'T' && key.charAt(2) != 'L') {
var ipt = key.indexOf("?");
if (ipt >= 0) {
k = key.substring(0, 2) + "_" + key.substring(ipt + 1) + "#*;*";
pt = this.getMod(k);
if (pt == null) {
k = key.substring(0, 1) + "_" + key.substring(ipt + 1) + "#*;*";
pt = this.getMod(k);
}if (pt != null) this.addModulation(map, key = key.substring(0, ipt), pt, iModel);
} else {
var a = pt[0];
var d = 2 * 3.141592653589793 * pt[1];
pt[0] = (a * Math.cos(d));
pt[1] = (a * Math.sin(-d));
pt[2] = 0;
JU.Logger.info("msCIF setting " + key + " " + JU.Escape.e(pt));
}}break;
case 87:
if (this.modDim > 1) {
continue;
}case 70:
if (key.indexOf("_coefs_") >= 0) {
this.cr.appendLoadNote("Wave vector " + key + "=" + JU.Escape.eAD(pt));
} else {
var ptHarmonic = this.calculateQCoefs(pt);
if (ptHarmonic == null) {
this.cr.appendLoadNote("Cannot match atom wave vector " + key + " " + JU.Escape.eAD(pt) + " to a cell wave vector or its harmonic");
} else {
var k2 = key + "_coefs_";
if (!this.htModulation.containsKey(k2 + this.atModel)) {
this.addModulation(map, k2, ptHarmonic, iModel);
if (key.startsWith("F_")) this.cr.appendLoadNote("atom wave vector " + key + " = " + JU.Escape.e(pt) + " fn = " + JU.Escape.e(ptHarmonic));
}}}break;
}
}
if (!map.isEmpty()) this.htModulation.putAll(map);
if (this.htSubsystems == null) {
this.haveAtomMods = false;
} else {
this.cr.strSupercell = null;
this.haveAtomMods = true;
this.htAtomMods =  new java.util.Hashtable();
}for (var e, $e = this.htModulation.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var k = e.getKey();
if ((key = this.checkKey(k, true)) == null) continue;
var params = e.getValue();
var atomName = key.substring(key.indexOf(";") + 1);
var pt_ = atomName.indexOf("#=");
if (pt_ >= 0) {
params = this.getMod(atomName.substring(pt_ + 2));
atomName = atomName.substring(0, pt_);
}if (JU.Logger.debuggingHigh) JU.Logger.debug("SetModulation: " + key + " " + JU.Escape.e(params));
var type = key.charAt(0);
pt_ = key.indexOf("#") + 1;
var utens = null;
switch ((type).charCodeAt(0)) {
case 85:
utens = key.substring(pt_, key.indexOf(";"));
case 79:
case 68:
case 77:
if (this.modAverage) break;
var axis = key.charAt(pt_);
type = this.getModType(key);
if (this.htAtomMods == null) this.htAtomMods =  new java.util.Hashtable();
var p =  Clazz.newDoubleArray (/*org.eclipse.jdt.core.dom.QualifiedName*/params.length, 0);
for (var i = p.length; --i >= 0; ) p[i] = params[i];

var qcoefs = this.getQCoefs(key);
if (qcoefs == null) {
System.err.println("MSRdr missing cell wave vector for atom wave vector for " + key + " " + JU.Escape.e(params));
break;
}this.addAtomModulation(atomName, axis, type, p, utens, qcoefs);
this.haveAtomMods = true;
break;
}
}
}, "~N");
Clazz.defineMethod(c$, "fixLegendre", 
function(){
for (var i = this.legendres.size(); --i >= 0; ) {
var key = this.legendres.get(i);
var pt = this.htModulation.get(key);
if (pt != null) {
var key1 = "O_0#0" + key.substring(key.indexOf(";"));
var pt1 = this.htModulation.get(key1);
if (pt1 == null) {
JU.Logger.error("Crenel " + key1 + " not found for legendre modulation " + key);
pt[2] = NaN;
} else {
this.htModulation.put(key,  Clazz.newDoubleArray(-1, [pt1[0], pt1[1], pt[0], pt[1]]));
}}}
});
Clazz.overrideMethod(c$, "getQCoefs", 
function(key){
var id = key.charAt(2);
var fn = ("STL0".indexOf(id) >= 0 ? 0 : this.cr.parseIntAt(key, 2));
if (fn < 0) System.err.println("warning only -- MSRdr missing cell wave vector for atom wave vector for " + key + " 1 assumed");
if (fn <= 0) {
if (this.qlist100 == null) {
this.qlist100 =  Clazz.newDoubleArray (/*org.eclipse.jdt.core.dom.SimpleName*/this.modDim, 0);
this.qlist100[0] = 1;
}return this.qlist100;
}var p = this.getMod("F_" + fn + "_coefs_");
if (p == null) {
p = this.getMod("F_coefs_" + fn);
}return p;
}, "~S");
Clazz.overrideMethod(c$, "getModType", 
function(key){
var type = key.charAt(0);
var id = key.charAt(2);
return (type == 'D' && id == 'S' ? 's' : type == 'D' && id == 'L' ? 'l' : type == 'O' && id == '0' ? 'c' : type == 'M' && id == 'T' ? 't' : type == 'U' && id == 'L' ? 'L' : type == 'D' ? 'f' : type == 'O' ? 'o' : type == 'M' ? 'm' : type == 'U' ? 'u' : '?');
}, "~S");
Clazz.defineMethod(c$, "calculateQCoefs", 
function(p){
if (this.qs == null) {
this.qs =  new Array(this.modDim);
for (var i = 0; i < this.modDim; i++) {
this.qs[i] = this.toP3(this.getMod("W_" + (i + 1)));
}
}var pt = this.toP3(p);
for (var i = 0; i < this.modDim; i++) if (this.qs[i] != null) {
var ifn = this.approxInt(pt.dot(this.qs[i]) / this.qs[i].dot(this.qs[i]));
if (ifn != 0) {
p =  Clazz.newDoubleArray (/*org.eclipse.jdt.core.dom.SimpleName*/this.modDim, 0);
p[i] = ifn;
return p;
}}
var p3 = this.toP3(p);
var jmin = (this.modDim < 2 ? 0 : -3);
var jmax = (this.modDim < 2 ? 0 : 3);
var kmin = (this.modDim < 3 ? 0 : -3);
var kmax = (this.modDim < 3 ? 0 : 3);
for (var i = -4; i <= 4; i++) for (var j = jmin; j <= jmax; j++) for (var k = kmin; k <= kmax; k++) {
pt.setT(this.qs[0]);
pt.scale(i);
if (this.modDim > 1 && this.qs[1] != null) pt.scaleAdd2(j, this.qs[1], pt);
if (this.modDim > 2 && this.qs[2] != null) pt.scaleAdd2(k, this.qs[2], pt);
if (pt.distanceSquared(p3) < 0.0001) {
p =  Clazz.newDoubleArray (/*org.eclipse.jdt.core.dom.SimpleName*/this.modDim, 0);
switch (this.modDim) {
default:
p[2] = k;
case 2:
p[1] = j;
case 1:
p[0] = i;
break;
}
return p;
}pt.setT(this.qs[0]);
pt.scale(1 / i);
if (this.modDim > 1 && this.qs[1] != null) pt.scaleAdd2(1 / j, this.qs[1], pt);
if (this.modDim > 2 && this.qs[2] != null) pt.scaleAdd2(1 / k, this.qs[2], pt);
if (pt.distanceSquared(p3) < 0.0001) {
p =  Clazz.newDoubleArray (/*org.eclipse.jdt.core.dom.SimpleName*/this.modDim, 0);
switch (this.modDim) {
default:
p[2] = 1 / k;
case 2:
p[1] = 1 / j;
case 1:
p[0] = 1 / i;
break;
}
return p;
}}


pt = this.toP3(p);
for (var i = 0; i < this.modDim; i++) if (this.qs[i] != null) {
p3 = this.qs[i];
var ifn = 0;
if (pt.x != 0) ifn = this.approxInt(pt.x / p3.x);
if (pt.y != 0) ifn = Math.max(this.approxInt(pt.y / p3.y), ifn);
if (ifn == 0 && pt.z != 0) ifn = Math.max(this.approxInt(pt.z / p3.z), ifn);
if (ifn == 0) continue;
if (p3.x != 0 && this.approxInt(10 + p3.x * ifn - pt.x) == 0 || p3.y != 0 && this.approxInt(10 + p3.y * ifn - pt.y) == 0 || p3.z != 0 && this.approxInt(10 + p3.z * ifn - pt.z) == 0) continue;
p =  Clazz.newDoubleArray (/*org.eclipse.jdt.core.dom.SimpleName*/this.modDim, 0);
p[i] = ifn;
return p;
}
return null;
}, "~A");
Clazz.defineMethod(c$, "approxInt", 
function(fn){
var ifn = Math.round(fn);
return (Math.abs(fn - ifn) < 0.001 ? ifn : 0);
}, "~N");
Clazz.defineMethod(c$, "toP3", 
function(x){
return JU.P3.new3(x[0], x[1], x[2]);
}, "~A");
Clazz.defineMethod(c$, "addAtomModulation", 
function(atomName, axis, type, params, utens, qcoefs){
var list = this.htAtomMods.get(atomName);
if (list == null) {
this.ac++;
this.htAtomMods.put(atomName, list =  new JU.Lst());
}list.addLast( new JU.Modulation(axis, type, params, utens, qcoefs));
this.modCount++;
}, "~S,~S,~S,~A,~S,~A");
Clazz.overrideMethod(c$, "addSubsystem", 
function(code, w){
if (code == null) return;
var ss =  new J.adapter.readers.cif.Subsystem(this, code, w);
this.cr.appendLoadNote("subsystem " + code + "\n" + w);
this.setSubsystem(code, ss);
}, "~S,JU.Matrix");
Clazz.defineMethod(c$, "addUStr", 
function(atom, id, val){
var i = Clazz.doubleToInt("U11U22U33U12U13U23UISO".indexOf(id) / 3);
if (JU.Logger.debuggingHigh) JU.Logger.debug("MOD RDR adding " + id + " " + i + " " + val + " to " + atom.anisoBorU[i]);
this.cr.asc.setU(atom, i, val + atom.anisoBorU[i]);
}, "J.adapter.smarter.Atom,~S,~N");
Clazz.defineMethod(c$, "modulateAtom", 
function(a){
var list = this.htAtomMods.get(a.atomName);
if (list == null && a.altLoc != '\0' && this.htSubsystems != null) {
list =  new JU.Lst();
}if (list == null || this.symmetry == null || a.bsSymmetry == null) return;
var iop = Math.max(a.bsSymmetry.nextSetBit(0), 0);
if (this.modLast) iop = Math.max((a.bsSymmetry.length() - 1) % this.nOps, iop);
if (JU.Logger.debuggingHigh) JU.Logger.info("\nsetModulation: i=" + a.index + " " + a.atomName + " xyz=" + a + " occ=" + a.foccupancy);
if (iop != this.iopLast) {
this.iopLast = iop;
this.gammaE =  new JU.M3();
this.getSymmetry(a).getSpaceGroupOperation(iop).getRotationScale(this.gammaE);
}if (JU.Logger.debugging) {
JU.Logger.debug("setModulation iop = " + iop + " " + this.symmetry.getSpaceGroupXyz(iop, false) + " " + a.bsSymmetry);
}var ms =  new JU.ModulationSet().setMod(a.index + " " + a.atomName, this.getAtomR0(this.cr.asc.atoms[a.atomSite]), this.getAtomR0(a), this.modDim, list, this.gammaE, this.getMatrices(a), this.getSymmetry(a), this.nOps, iop, Clazz.instanceOf(a.vib,"JU.Vibration") ? a.vib : null, this.isCommensurate);
ms.calculate(this.modTUV, false);
if (!Float.isNaN(ms.vOcc)) {
a.foccupancy = ms.setOccupancy(this.getMod("J_O#0;" + a.atomName), a.foccupancy, (a.vib == null ? 0 : a.vib.x));
}if (ms.htUij != null) {
var t = (a.tensors == null ? null : a.tensors.get(0));
if (t != null && t.parBorU != null) {
a.anisoBorU =  Clazz.newFloatArray (/*org.eclipse.jdt.core.dom.NumberLiteral*/8, 0);
for (var i = 0; i < 8; i++) a.anisoBorU[i] = t.parBorU[i];

t.isUnmodulated = true;
}if (a.anisoBorU == null) {
JU.Logger.error("MOD RDR cannot modulate nonexistent atom anisoBorU for atom " + a.atomName);
} else {
if (JU.Logger.debuggingHigh) {
JU.Logger.info("setModulation Uij(initial) " + a.atomName + " =" + JU.Escape.eAF(a.anisoBorU));
JU.Logger.info("setModulation tensor " + a.atomName + "=" + JU.Escape.e((a.tensors.get(0)).getInfo("all")));
}for (var e, $e = ms.htUij.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) this.addUStr(a, e.getKey(), e.getValue().floatValue());

var sym = this.getAtomSymmetry(a, this.symmetry);
t = this.cr.asc.getXSymmetry().addRotatedTensor(a, sym.getTensor(this.cr.vwr, a.anisoBorU), iop, false, sym);
t.isModulated = true;
t.id = JU.Escape.e(a.anisoBorU);
a.bfactor = a.anisoBorU[7] * 100;
a.anisoBorU = null;
if (JU.Logger.debuggingHigh) {
JU.Logger.debug("setModulation Uij(final)=" + JU.Escape.eAF(a.anisoBorU) + "\n");
JU.Logger.debug("setModulation tensor=" + JU.Escape.e((a.tensors.get(1)).getInfo("all")));
}}}if (Float.isNaN(ms.x)) ms.set(0, 0, 0);
a.vib = ms;
}, "J.adapter.smarter.Atom");
Clazz.defineMethod(c$, "getAtomR0", 
function(atom){
var r0 = JU.P3.newP(atom);
if (this.supercellSymmetry != null) {
this.supercellSymmetry.toCartesian(r0, true);
this.symmetry.toFractional(r0, true);
}return r0;
}, "J.adapter.smarter.Atom");
Clazz.overrideMethod(c$, "getAtomSymmetry", 
function(a, defaultSymmetry){
var ss;
return (this.htSubsystems == null || (ss = this.getSubsystem(a)) == null ? defaultSymmetry : ss.getSymmetry());
}, "J.adapter.smarter.Atom,J.adapter.smarter.XtalSymmetry.FileSymmetry");
Clazz.defineMethod(c$, "setSubsystem", 
function(code, system){
if (this.htSubsystems == null) this.htSubsystems =  new java.util.Hashtable();
this.htSubsystems.put(code, system);
this.setSubsystemOptions();
}, "~S,J.adapter.readers.cif.Subsystem");
Clazz.defineMethod(c$, "getMatrices", 
function(a){
var ss = this.getSubsystem(a);
return (ss == null ? this.modMatrices : ss.getModMatrices());
}, "J.adapter.smarter.Atom");
Clazz.defineMethod(c$, "getSymmetry", 
function(a){
var ss = this.getSubsystem(a);
return (ss == null ? this.symmetry : ss.getSymmetry());
}, "J.adapter.smarter.Atom");
Clazz.defineMethod(c$, "getSubsystem", 
function(a){
return (this.htSubsystems == null ? null : this.htSubsystems.get("" + a.altLoc));
}, "J.adapter.smarter.Atom");
Clazz.overrideMethod(c$, "setMinMax0", 
function(minXYZ, maxXYZ){
if (this.htSubsystems == null) {
this.minXYZ0 = this.maxXYZ0 = null;
return;
}var symmetry = this.getDefaultUnitCell();
this.minXYZ0 = JU.P3.newP(minXYZ);
this.maxXYZ0 = JU.P3.newP(maxXYZ);
var pt0 = JU.P3.newP(minXYZ);
var pt1 = JU.P3.newP(maxXYZ);
var pt =  new JU.P3();
symmetry.toCartesian(pt0, true);
symmetry.toCartesian(pt1, true);
var pts = JU.BoxInfo.unitCubePoints;
if (this.sigma == null) {
JU.Logger.error("Why are we in MSRdr.setMinMax0 without modulation init?");
return;
}for (var e, $e = this.htSubsystems.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var sym = e.getValue().getSymmetry();
for (var i = 8; --i >= 0; ) {
pt.x = (pts[i].x == 0 ? pt0.x : pt1.x);
pt.y = (pts[i].y == 0 ? pt0.y : pt1.y);
pt.z = (pts[i].z == 0 ? pt0.z : pt1.z);
this.expandMinMax(pt, sym, minXYZ, maxXYZ);
}
}
}, "JU.P3,JU.P3");
Clazz.defineMethod(c$, "expandMinMax", 
function(pt, sym, minXYZ, maxXYZ){
var pt2 = JU.P3.newP(pt);
var slop = 0.0001;
sym.toFractional(pt2, false);
if (minXYZ.x > pt2.x + slop) minXYZ.x = Clazz.doubleToInt(Math.floor(pt2.x + slop)) - 1;
if (minXYZ.y > pt2.y + slop) minXYZ.y = Clazz.doubleToInt(Math.floor(pt2.y + slop)) - 1;
if (minXYZ.z > pt2.z + slop) minXYZ.z = Clazz.doubleToInt(Math.floor(pt2.z + slop)) - 1;
if (maxXYZ.x < pt2.x - slop) maxXYZ.x = Clazz.doubleToInt(Math.ceil(pt2.x - slop)) + 1;
if (maxXYZ.y < pt2.y - slop) maxXYZ.y = Clazz.doubleToInt(Math.ceil(pt2.y - slop)) + 1;
if (maxXYZ.z < pt2.z - slop) maxXYZ.z = Clazz.doubleToInt(Math.ceil(pt2.z - slop)) + 1;
}, "JU.P3,J.adapter.smarter.XtalSymmetry.FileSymmetry,JU.P3,JU.P3");
Clazz.defineMethod(c$, "trimAtomSet", 
function(){
if (!this.cr.doApplySymmetry) return;
var asc = this.cr.asc;
var sym = this.getDefaultUnitCell();
var atoms = asc.atoms;
var pt =  new JU.P3();
var bs = asc.getBSAtoms(-1);
var i0 = this.cr.asc.getLastAtomSetAtomIndex();
var packing = this.cr.getPackingRangeValue(0.001);
for (var i = bs.nextSetBit(i0); i >= 0; i = bs.nextSetBit(i + 1)) {
var a = atoms[i];
var isOK = (!this.isCommensurate || this.modAverage || a.foccupancy >= 0.5);
if (isOK) {
pt.setT(a);
if (a.vib != null) pt.add(a.vib);
this.getSymmetry(a).toCartesian(pt, false);
sym.toFractional(pt, false);
this.cr.fixFloatPt(pt, 100000.0);
isOK = asc.xtalSymmetry.isWithinCell(3, pt, this.minXYZ0.x, this.maxXYZ0.x, this.minXYZ0.y, this.maxXYZ0.y, this.minXYZ0.z, this.maxXYZ0.z, packing);
}if (isOK) {
this.cr.fixFloatPt(a, 100000.0);
} else {
bs.clear(i);
}}
});
Clazz.defineMethod(c$, "getDefaultUnitCell", 
function(){
return (this.modCell != null && this.htSubsystems.containsKey(this.modCell) ? this.htSubsystems.get(this.modCell).getSymmetry() : this.cr.asc.getSymmetry());
});
Clazz.overrideMethod(c$, "getSymmetryFromCode", 
function(code){
return this.htSubsystems.get(code).getSymmetry();
}, "~S");
Clazz.overrideMethod(c$, "addLatticeVector", 
function(lattvecs, data){
var a = null;
var c = data.charAt(0);
var dim = this.modDim + 3;
switch ((c).charCodeAt(0)) {
case 80:
case 88:
break;
case 65:
case 66:
case 67:
case 73:
a =  Clazz.newFloatArray(-1, [0.5, 0.5, 0.5]);
if (c != 'I') a[c.charCodeAt(0) - 65] = 0;
break;
case 70:
this.addLatticeVector(lattvecs, "A");
this.addLatticeVector(lattvecs, "B");
this.addLatticeVector(lattvecs, "C");
break;
case 77:
dim++;
case 48:
if (data.indexOf(".") >= 0) a = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat(data, null, dim);
break;
default:
return false;
}
if (a != null) lattvecs.addLast(a);
return true;
}, "JU.Lst,~S");
});
;//5.0.1-v4 Thu Feb 20 12:29:54 CST 2025
