Clazz.declarePackage("JM");
Clazz.load(["JU.V3"], "JM.AtomCollection", ["java.util.Arrays", "$.Hashtable", "JU.A4", "$.AU", "$.BS", "$.Lst", "$.M3", "$.Measure", "$.P3", "$.PT", "J.api.Interface", "J.atomdata.RadiusData", "J.c.PAL", "$.VDW", "JM.Group", "JS.T", "JU.BSUtil", "$.Elements", "$.Logger", "$.Parser", "$.Vibration"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.g3d = null;
this.bioModelset = null;
this.at = null;
this.ac = 0;
this.trajectory = null;
this.pointGroup = null;
this.labeler = null;
this.maxBondingRadius = 1.4E-45;
this.maxVanderwaalsRadius = 1.4E-45;
this.hasBfactorRange = false;
this.bfactor100Lo = 0;
this.bfactor100Hi = 0;
this.haveBSVisible = false;
this.haveBSClickable = false;
this.bsSurface = null;
this.nSurfaceAtoms = 0;
this.surfaceDistanceMax = 0;
this.haveChirality = false;
this.bspf = null;
this.preserveState = true;
this.canSkipLoad = true;
this.haveStraightness = false;
this.bsHidden = null;
this.bsVisible = null;
this.bsClickable = null;
this.bsModulated = null;
this.atomTensorList = null;
this.atomTensors = null;
this.surfaceDistance100s = null;
this.tainted = null;
this.atomNames = null;
this.atomTypes = null;
this.atomSerials = null;
this.atomResnos = null;
this.atomSeqIDs = null;
this.dssrData = null;
this.vibrations = null;
this.occupancies = null;
this.bfactor100s = null;
this.partialCharges = null;
this.bondingRadii = null;
this.hydrophobicities = null;
this.bsPartialCharges = null;
this.aaRet = null;
if (!Clazz.isClassDefined("JM.AtomCollection.AtomSorter")) {
JM.AtomCollection.$AtomCollection$AtomSorter$ ();
}
this.atomCapacity = 0;
Clazz.instantialize(this, arguments);}, JM, "AtomCollection", null);
Clazz.defineMethod(c$, "getAtom", 
function(iatom){
return (iatom >= 0 && iatom < this.at.length ? this.at[iatom] : null);
}, "~N");
Clazz.defineMethod(c$, "setupAC", 
function(){
this.bsHidden =  new JU.BS();
this.bsVisible =  new JU.BS();
this.bsClickable =  new JU.BS();
if (JM.AtomCollection.userSettableValues == null) JM.AtomCollection.userSettableValues = ("atomName atomType coord element formalCharge hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals vibrationVector atomNo seqID resNo chain site").$plit(" ");
});
Clazz.defineMethod(c$, "releaseModelSetAC", 
function(){
this.ac = 0;
this.at = null;
this.vwr = null;
this.g3d = null;
this.bspf = null;
this.surfaceDistance100s = null;
this.bsSurface = null;
this.tainted = null;
this.atomNames = null;
this.atomTypes = null;
this.atomResnos = null;
this.dssrData = null;
this.atomSerials = null;
this.atomSeqIDs = null;
this.vibrations = null;
this.occupancies = null;
this.bfactor100s = null;
this.resetPartialCharges();
this.bondingRadii = null;
this.atomTensors = null;
});
Clazz.defineMethod(c$, "mergeAtomArrays", 
function(mergeModelSet){
this.tainted = mergeModelSet.tainted;
this.atomNames = mergeModelSet.atomNames;
this.atomTypes = mergeModelSet.atomTypes;
this.atomResnos = mergeModelSet.atomResnos;
this.dssrData = mergeModelSet.dssrData;
this.atomSerials = mergeModelSet.atomSerials;
this.atomSeqIDs = mergeModelSet.atomSeqIDs;
this.vibrations = mergeModelSet.vibrations;
this.occupancies = mergeModelSet.occupancies;
this.bfactor100s = mergeModelSet.bfactor100s;
this.bondingRadii = mergeModelSet.bondingRadii;
this.partialCharges = mergeModelSet.partialCharges;
this.bsPartialCharges = mergeModelSet.bsPartialCharges;
this.atomTensors = mergeModelSet.atomTensors;
this.atomTensorList = mergeModelSet.atomTensorList;
this.bsModulated = mergeModelSet.bsModulated;
this.haveStraightness = false;
this.surfaceDistance100s = null;
}, "JM.AtomCollection");
Clazz.defineMethod(c$, "getAtomPointVector", 
function(bs){
var v =  new JU.Lst();
var n = this.ac;
if (bs != null) {
for (var i = bs.nextSetBit(0); i >= 0 && i < n; i = bs.nextSetBit(i + 1)) {
v.addLast(this.at[i]);
}
}return v;
}, "JU.BS");
Clazz.defineMethod(c$, "modelSetHasVibrationVectors", 
function(){
return (this.vibrations != null);
});
Clazz.defineMethod(c$, "getAtomTypes", 
function(){
return this.atomTypes;
});
Clazz.defineMethod(c$, "getPartialCharges", 
function(){
return this.partialCharges;
});
Clazz.defineMethod(c$, "getBondingRadii", 
function(){
return this.bondingRadii;
});
Clazz.defineMethod(c$, "getBFactors", 
function(){
return this.bfactor100s;
});
Clazz.defineMethod(c$, "getHydrophobicity", 
function(){
return this.hydrophobicities;
});
Clazz.defineMethod(c$, "setBsHidden", 
function(bs){
this.bsHidden = bs;
}, "JU.BS");
Clazz.defineMethod(c$, "isAtomHidden", 
function(iAtom){
return this.bsHidden.get(iAtom);
}, "~N");
Clazz.defineMethod(c$, "getLabeler", 
function(){
return (this.labeler == null ? this.labeler = J.api.Interface.getInterface("JM.LabelToken", this.vwr, "ms") : this.labeler);
});
Clazz.defineMethod(c$, "getAtomInfo", 
function(i, format, ptTemp){
return (format == null ? this.at[i].getInfo() : this.getLabeler().formatLabel(this.vwr, this.at[i], format, ptTemp));
}, "~N,~S,JU.P3");
Clazz.defineMethod(c$, "getElementName", 
function(i){
return JU.Elements.elementNameFromNumber(this.at[i].getAtomicAndIsotopeNumber());
}, "~N");
Clazz.defineMethod(c$, "getQuaternion", 
function(i, qtype){
return (i < 0 ? null : this.at[i].group.getQuaternion(qtype));
}, "~N,~S");
Clazz.defineMethod(c$, "getFirstAtomIndexFromAtomNumber", 
function(atomNumber, bsVisibleFrames){
for (var i = 0; i < this.ac; i++) {
var atom = this.at[i];
if (!JM.AtomCollection.isDeleted(atom) && atom.getAtomNumber() == atomNumber && bsVisibleFrames.get(atom.mi)) return i;
}
return -1;
}, "~N,JU.BS");
Clazz.defineMethod(c$, "setFormalCharges", 
function(bs, formalCharge){
if (bs != null) {
this.resetPartialCharges();
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
this.at[i].setFormalCharge(formalCharge);
this.taintAtom(i, 4);
}
}}, "JU.BS,~N");
Clazz.defineMethod(c$, "getAtomicCharges", 
function(){
var charges =  Clazz.newFloatArray (this.ac, 0);
for (var i = this.ac; --i >= 0; ) charges[i] = (JM.AtomCollection.isDeleted(this.at[i]) ? 0 : this.at[i].getElementNumber());

return charges;
});
Clazz.defineMethod(c$, "getRadiusVdwJmol", 
function(atom){
return JU.Elements.getVanderwaalsMar(atom.getElementNumber(), J.c.VDW.JMOL) / 1000;
}, "JM.Atom");
Clazz.defineMethod(c$, "getMaxVanderwaalsRadius", 
function(){
if (this.maxVanderwaalsRadius == 1.4E-45) this.findMaxRadii();
return this.maxVanderwaalsRadius;
});
Clazz.defineMethod(c$, "findMaxRadii", 
function(){
var r;
for (var i = this.ac; --i >= 0; ) {
var atom = this.at[i];
if (JM.AtomCollection.isDeleted(atom)) continue;
if ((r = atom.getBondingRadius()) > this.maxBondingRadius) this.maxBondingRadius = r;
if ((r = atom.getVanderwaalsRadiusFloat(this.vwr, J.c.VDW.AUTO)) > this.maxVanderwaalsRadius) this.maxVanderwaalsRadius = r;
}
});
Clazz.defineMethod(c$, "clearBfactorRange", 
function(){
this.hasBfactorRange = false;
});
Clazz.defineMethod(c$, "calcBfactorRange", 
function(bs){
if (this.hasBfactorRange) return;
this.bfactor100Lo = 2147483647;
this.bfactor100Hi = -2147483648;
if (bs == null) {
for (var i = 0; i < this.ac; i++) this.setBf(i);

} else {
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) this.setBf(i);

}this.hasBfactorRange = true;
}, "JU.BS");
Clazz.defineMethod(c$, "setBf", 
function(i){
if (JM.AtomCollection.isDeleted(this.at[i])) return;
var bf = this.at[i].getBfactor100();
if (bf < this.bfactor100Lo) this.bfactor100Lo = bf;
 else if (bf > this.bfactor100Hi) this.bfactor100Hi = bf;
}, "~N");
Clazz.defineMethod(c$, "getBfactor100Lo", 
function(){
if (!this.hasBfactorRange) {
if (this.vwr.g.rangeSelected) {
this.calcBfactorRange(this.vwr.bsA());
} else {
this.calcBfactorRange(null);
}}return this.bfactor100Lo;
});
Clazz.defineMethod(c$, "getBfactor100Hi", 
function(){
this.getBfactor100Lo();
return this.bfactor100Hi;
});
Clazz.defineMethod(c$, "getSurfaceDistanceMax", 
function(){
if (this.surfaceDistance100s == null) this.calcSurfaceDistances();
return this.surfaceDistanceMax;
});
Clazz.defineMethod(c$, "calculateVolume", 
function(bs, vType){
var volume = 0;
if (bs != null) for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) volume += this.at[i].getVolume(this.vwr, vType);

return volume;
}, "JU.BS,J.c.VDW");
Clazz.defineMethod(c$, "getSurfaceDistance100", 
function(atomIndex){
if (this.nSurfaceAtoms == 0) return -1;
if (this.surfaceDistance100s == null) this.calcSurfaceDistances();
return this.surfaceDistance100s[atomIndex];
}, "~N");
Clazz.defineMethod(c$, "calcSurfaceDistances", 
function(){
this.calculateSurface(null, -1);
});
Clazz.defineMethod(c$, "calculateSurface", 
function(bsSelected, envelopeRadius){
if (envelopeRadius < 0) envelopeRadius = 3.0;
var ec = (J.api.Interface.getOption("geodesic.EnvelopeCalculation", this.vwr, "ms")).set(this.vwr, this.ac, null);
ec.calculate( new J.atomdata.RadiusData(null, envelopeRadius, J.atomdata.RadiusData.EnumType.ABSOLUTE, null), 3.4028235E38, bsSelected, JU.BSUtil.copyInvert(bsSelected, this.ac), false, false, false, true);
var points = ec.getPoints();
this.surfaceDistanceMax = 0;
this.bsSurface = ec.getBsSurfaceClone();
this.surfaceDistance100s =  Clazz.newIntArray (this.ac, 0);
this.nSurfaceAtoms = JU.BSUtil.cardinalityOf(this.bsSurface);
if (this.nSurfaceAtoms == 0 || points == null || points.length == 0) return points;
var radiusAdjust = (envelopeRadius == 3.4028235E38 ? 0 : envelopeRadius);
for (var i = 0; i < this.ac; i++) {
if (this.bsSurface.get(i) || JM.AtomCollection.isDeleted(this.at[i])) {
this.surfaceDistance100s[i] = 0;
} else {
var dMin = 3.4028235E38;
var atom = this.at[i];
for (var j = points.length; --j >= 0; ) {
dMin = Math.min(Math.abs(points[j].distance(atom) - radiusAdjust), dMin);
}
var d = this.surfaceDistance100s[i] = Clazz.doubleToInt(Math.floor(dMin * 100));
this.surfaceDistanceMax = Math.max(this.surfaceDistanceMax, d);
}}
return points;
}, "JU.BS,~N");
Clazz.defineMethod(c$, "setAtomCoord2", 
function(bs, tokType, xyzValues){
var xyz = null;
var values = null;
var v = null;
var type = 0;
var nValues = 1;
if (Clazz.instanceOf(xyzValues,"JU.P3")) {
xyz = xyzValues;
} else if (Clazz.instanceOf(xyzValues,"JU.Lst")) {
v = xyzValues;
if ((nValues = v.size()) == 0) return;
type = 1;
} else if (JU.AU.isAP(xyzValues)) {
values = xyzValues;
if ((nValues = values.length) == 0) return;
type = 2;
} else {
return;
}var n = 0;
if (bs != null) for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
switch (type) {
case 1:
if (n >= nValues) return;
xyz = v.get(n++);
break;
case 2:
if (n >= nValues) return;
xyz = values[n++];
break;
}
if (xyz != null) switch (tokType) {
case 1145047049:
this.setAtomCoord(i, xyz.x, xyz.y, xyz.z);
break;
case 1145047050:
case 1145047053:
this.at[i].setFractionalCoordTo(xyz, false);
this.taintAtom(i, 2);
break;
case 1145047055:
this.setAtomVibrationVector(i, xyz);
break;
}
}
}, "JU.BS,~N,~O");
Clazz.defineMethod(c$, "setAtomVibrationVector", 
function(atomIndex, vib){
this.setVibrationVector(atomIndex, vib);
this.taintAtom(atomIndex, 12);
}, "~N,JU.T3");
Clazz.defineMethod(c$, "setAtomCoord", 
function(atomIndex, x, y, z){
if (atomIndex < 0 || atomIndex >= this.ac) return;
var a = this.at[atomIndex];
a.set(x, y, z);
this.fixTrajectory(a);
this.taintAtom(atomIndex, 2);
}, "~N,~N,~N,~N");
Clazz.defineMethod(c$, "fixTrajectory", 
function(a){
if ((this).isTrajectory(a.mi)) this.trajectory.fixAtom(a);
}, "JM.Atom");
Clazz.defineMethod(c$, "setAtomCoordRelative", 
function(atomIndex, x, y, z){
if (atomIndex < 0 || atomIndex >= this.ac) return;
var a = this.at[atomIndex];
a.add3(x, y, z);
this.fixTrajectory(a);
this.taintAtom(atomIndex, 2);
}, "~N,~N,~N,~N");
Clazz.defineMethod(c$, "setAtomsCoordRelative", 
function(bs, x, y, z){
if (bs != null) for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) this.setAtomCoordRelative(i, x, y, z);

}, "JU.BS,~N,~N,~N");
Clazz.defineMethod(c$, "setAPa", 
function(bs, tok, iValue, fValue, sValue, values, list){
var n = 0;
if (values != null && values.length == 0 || bs == null) return;
var isAll = (values != null && values.length == this.ac || list != null && list.length == this.ac);
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
if (isAll) n = i;
if (values != null) {
if (n >= values.length) return;
fValue = values[n++];
if (Float.isNaN(fValue)) continue;
iValue = Clazz.floatToInt(fValue);
} else if (list != null) {
if (n >= list.length) return;
sValue = list[n++];
}var atom = this.at[i];
var f;
switch (tok) {
case 1086326786:
this.setAtomName(i, sValue, true);
break;
case 1086326785:
this.setAtomType(i, sValue);
break;
case 1086326788:
this.setChainID(i, sValue);
break;
case 1094715393:
this.setAtomNumber(i, iValue, true);
break;
case 1094713365:
this.setAtomSeqID(i, iValue);
break;
case 1111492609:
case 1111492629:
this.setAtomCoord(i, fValue, atom.y, atom.z);
break;
case 1111492610:
case 1111492630:
this.setAtomCoord(i, atom.x, fValue, atom.z);
break;
case 1111492611:
case 1111492631:
this.setAtomCoord(i, atom.x, atom.y, fValue);
break;
case 1111492626:
case 1111492627:
case 1111492628:
this.setVibrationVector2(i, tok, fValue);
break;
case 1111492612:
case 1111492613:
case 1111492614:
case 1111492615:
case 1111492616:
case 1111492617:
atom.setFractionalCoord(tok, fValue, false);
this.taintAtom(i, 2);
break;
case 1094715402:
case 1086326789:
this.setElement(atom, iValue, true);
break;
case 1631586315:
this.resetPartialCharges();
atom.setFormalCharge(iValue);
this.taintAtom(i, 4);
break;
case 1113589786:
this.setHydrophobicity(i, fValue);
break;
case 1128269825:
f = (fValue < 2 && fValue >= 0.01 ? 100 * fValue : fValue);
this.setOccupancy(i, f, true);
break;
case 1111492619:
this.setPartialCharge(i, fValue, true);
break;
case 1111492618:
this.setBondingRadius(i, fValue);
break;
case 1111492620:
this.setBFactor(i, fValue, true);
break;
case 1094715412:
this.setAtomResno(i, iValue);
break;
case 1825200146:
case 1287653388:
this.vwr.shm.setAtomLabel(sValue, i);
break;
case 1665140738:
case 1112152075:
f = fValue;
if (f < 0) f = 0;
 else if (f > 16) f = 16.1;
atom.madAtom = (Clazz.floatToShort(f * 2000));
break;
case 1113589787:
this.vwr.slm.setSelectedAtom(atom.i, (fValue != 0));
break;
case 1094715418:
atom.setValence(iValue);
this.taintAtom(i, 10);
break;
case 1648363544:
if (atom.setRadius(fValue)) this.taintAtom(i, 11);
 else this.untaint(i, 11);
break;
default:
JU.Logger.error("unsettable atom property: " + JS.T.nameOf(tok));
return;
}
}
switch (tok) {
case 1113589787:
this.vwr.slm.setSelectedAtom(-1, false);
break;
case 1665140738:
case 1112152075:
this.vwr.setShapeSize(0, 2147483647, bs);
}
}, "JU.BS,~N,~N,~N,~S,~A,~A");
Clazz.defineMethod(c$, "getVibCoord", 
function(atomIndex, c){
var ms = null;
var v = null;
switch ((c).charCodeAt(0)) {
case 120:
case 121:
case 122:
v = this.getVibration(atomIndex, false);
break;
default:
ms = this.getModulation(atomIndex);
if (ms != null) {
v = ms.getVibration(false);
if (v == null) v = ms;
}}
if (v == null && ms == null) return NaN;
switch ((c).charCodeAt(0)) {
case 120:
case 88:
return v.x;
case 121:
case 89:
return v.y;
case 122:
case 90:
return v.z;
case 79:
return (ms.getModulation('O', null, true)).floatValue();
case 49:
case 50:
case 51:
var t = ms.getModulation('T', null, true);
var x = (c == '1' ? t.x : c == '2' ? t.y : t.z);
return (x - Math.floor(x));
default:
return NaN;
}
}, "~N,~S");
Clazz.defineMethod(c$, "getVibration", 
function(atomIndex, forceNew){
var v = (this.vibrations == null ? null : this.vibrations[atomIndex]);
return (Clazz.instanceOf(v,"J.api.JmolModulationSet") ? (v).getVibration(forceNew) : v == null && forceNew ?  new JU.Vibration() : v);
}, "~N,~B");
Clazz.defineMethod(c$, "getModulation", 
function(iAtom){
var v = (this.vibrations == null ? null : this.vibrations[iAtom]);
return (v != null && v.modDim > 0 ? v : null);
}, "~N");
Clazz.defineMethod(c$, "setVibrationVector", 
function(atomIndex, vib){
if (vib == null) {
if (this.vibrations != null && this.vibrations.length > atomIndex) this.vibrations[atomIndex] = null;
return;
}if (Double.isNaN(vib.x) || Double.isNaN(vib.y) || Double.isNaN(vib.z)) return;
if (this.vibrations == null || this.vibrations.length <= atomIndex) this.vibrations =  new Array(this.at.length);
if (Clazz.instanceOf(vib,"JU.Vibration")) {
this.vibrations[atomIndex] = vib;
} else {
if (this.vibrations[atomIndex] == null) this.vibrations[atomIndex] =  new JU.Vibration();
this.vibrations[atomIndex].setXYZ(vib);
}this.at[atomIndex].setVibrationVector();
}, "~N,JU.T3");
Clazz.defineMethod(c$, "setVibrationVector2", 
function(atomIndex, tok, fValue){
var v = this.getVibration(atomIndex, true);
if (v == null) return;
switch (tok) {
case 1111492626:
v.x = fValue;
break;
case 1111492627:
v.y = fValue;
break;
case 1111492628:
v.z = fValue;
break;
}
this.setAtomVibrationVector(atomIndex, v);
}, "~N,~N,~N");
Clazz.defineMethod(c$, "setAtomName", 
function(atomIndex, name, doTaint){
if (doTaint && name.equals(this.at[atomIndex].getAtomName())) return;
var id = ((this).am[this.at[atomIndex].mi].isBioModel ? this.vwr.getJBR().lookupSpecialAtomID(name) : 0);
this.at[atomIndex].atomID = id;
if (id <= 0) {
if (this.atomNames == null) this.atomNames =  new Array(this.at.length);
this.atomNames[atomIndex] = name;
}if (doTaint) this.taintAtom(atomIndex, 0);
}, "~N,~S,~B");
Clazz.defineMethod(c$, "setAtomType", 
function(atomIndex, type){
if (type.equals(this.at[atomIndex].getAtomType())) return;
if (this.atomTypes == null) this.atomTypes =  new Array(this.at.length);
this.atomTypes[atomIndex] = type;
return;
}, "~N,~S");
Clazz.defineMethod(c$, "setChainID", 
function(atomIndex, id){
if (id.equals(this.at[atomIndex].getChainIDStr())) return;
var intid = this.at[atomIndex].getChainID();
var bs = this.getChainBits(intid);
var c = this.at[atomIndex].group.chain;
c.chainID = this.vwr.getChainID(id, true);
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) this.taintAtom(i, 16);

}, "~N,~S");
Clazz.defineMethod(c$, "setAtomNumber", 
function(atomIndex, atomno, doTaint){
if (doTaint && atomno == this.at[atomIndex].getAtomNumber()) return;
if (this.atomSerials == null) this.atomSerials =  Clazz.newIntArray (this.at.length, 0);
this.atomSerials[atomIndex] = atomno;
if (doTaint) this.taintAtom(atomIndex, 13);
}, "~N,~N,~B");
Clazz.defineMethod(c$, "setElement", 
function(atom, atomicNumber, doTaint){
if (doTaint && atom.getElementNumber() == atomicNumber) return;
atom.setAtomicAndIsotopeNumber(atomicNumber);
atom.paletteID = J.c.PAL.CPK.id;
atom.colixAtom = this.vwr.cm.getColixAtomPalette(atom, J.c.PAL.CPK.id);
this.resetPartialCharges();
if (doTaint) this.taintAtom(atom.i, 3);
}, "JM.Atom,~N,~B");
Clazz.defineMethod(c$, "setSite", 
function(atom, site, doTaint){
if (atom.atomSite == site) return;
atom.atomSite = site;
if (doTaint) this.taintAtom(atom.i, 17);
}, "JM.Atom,~N,~B");
Clazz.defineMethod(c$, "resetPartialCharges", 
function(){
this.partialCharges = null;
this.bsPartialCharges = null;
});
Clazz.defineMethod(c$, "setAtomResno", 
function(atomIndex, resno){
if (resno == this.at[atomIndex].getResno()) return;
this.at[atomIndex].group.setResno(resno);
if (this.atomResnos == null) this.atomResnos =  Clazz.newIntArray (this.at.length, 0);
this.atomResnos[atomIndex] = resno;
this.taintAtom(atomIndex, 15);
}, "~N,~N");
Clazz.defineMethod(c$, "setAtomSeqID", 
function(atomIndex, seqID){
if (seqID == this.at[atomIndex].getSeqID()) return;
if (this.atomSeqIDs == null) this.atomSeqIDs =  Clazz.newIntArray (this.at.length, 0);
this.atomSeqIDs[atomIndex] = seqID;
this.taintAtom(atomIndex, 14);
}, "~N,~N");
Clazz.defineMethod(c$, "setOccupancy", 
function(atomIndex, occupancy, doTaint){
if (doTaint && occupancy == this.at[atomIndex].getOccupancy100()) return;
if (this.occupancies == null) {
if (occupancy == 100) return;
this.occupancies =  Clazz.newFloatArray (this.at.length, 0);
for (var i = this.at.length; --i >= 0; ) this.occupancies[i] = 100;

}this.occupancies[atomIndex] = occupancy;
if (doTaint) this.taintAtom(atomIndex, 7);
}, "~N,~N,~B");
Clazz.defineMethod(c$, "getOccupancyFloat", 
function(i){
return (this.occupancies == null || i >= this.occupancies.length ? 100 : this.occupancies[i]);
}, "~N");
Clazz.defineMethod(c$, "setPartialCharge", 
function(atomIndex, partialCharge, doTaint){
if (Float.isNaN(partialCharge)) return;
if (this.partialCharges == null) {
this.bsPartialCharges =  new JU.BS();
if (partialCharge == 0) return;
this.partialCharges =  Clazz.newFloatArray (this.at.length, 0);
}this.bsPartialCharges.set(atomIndex);
this.partialCharges[atomIndex] = partialCharge;
if (doTaint) this.taintAtom(atomIndex, 8);
}, "~N,~N,~B");
Clazz.defineMethod(c$, "setBondingRadius", 
function(atomIndex, radius){
if (Float.isNaN(radius) || radius == this.at[atomIndex].getBondingRadius()) return;
if (this.bondingRadii == null) {
this.bondingRadii =  Clazz.newFloatArray (this.at.length, 0);
} else if (this.bondingRadii.length < this.at.length) {
this.bondingRadii = JU.AU.ensureLengthA(this.bondingRadii, this.at.length);
}this.bondingRadii[atomIndex] = radius;
this.taintAtom(atomIndex, 6);
}, "~N,~N");
Clazz.defineMethod(c$, "setBFactor", 
function(atomIndex, bfactor, doTaint){
if (Float.isNaN(bfactor) || doTaint && bfactor == this.at[atomIndex].getBfactor100()) return;
if (this.bfactor100s == null) {
if (bfactor == 0) return;
this.bfactor100s =  Clazz.newShortArray (this.at.length, 0);
}this.bfactor100s[atomIndex] = Clazz.doubleToShort((bfactor < -327.68 ? -327.68 : bfactor > 327.67 ? 327.67 : bfactor) * 100 + (bfactor < 0 ? -0.5 : 0.5));
if (doTaint) this.taintAtom(atomIndex, 9);
}, "~N,~N,~B");
Clazz.defineMethod(c$, "setHydrophobicity", 
function(atomIndex, value){
if (Float.isNaN(value) || value == this.at[atomIndex].getHydrophobicity()) return;
if (this.hydrophobicities == null) {
this.hydrophobicities =  Clazz.newFloatArray (this.at.length, 0);
for (var i = 0; i < this.at.length; i++) this.hydrophobicities[i] = JU.Elements.getHydrophobicity(this.at[i].group.groupID);

}this.hydrophobicities[atomIndex] = value;
this.taintAtom(atomIndex, 5);
}, "~N,~N");
Clazz.defineMethod(c$, "setAtomData", 
function(type, name, dataString, isDefault){
var fData = null;
var bs = null;
switch (type) {
case 2:
this.loadCoordinates(dataString, false, !isDefault);
return;
case 12:
this.loadCoordinates(dataString, true, true);
return;
case 18:
fData =  Clazz.newFloatArray (this.ac, 0);
bs = JU.BS.newN(this.ac);
break;
}
var lines = JU.Parser.markLines(dataString, ';');
var n = 0;
try {
var nData = JU.PT.parseInt(dataString.substring(0, lines[0] - 1));
for (var i = 1; i <= nData; i++) {
var tokens = JU.PT.getTokens(JU.PT.parseTrimmed(dataString.substring(lines[i], lines[i + 1] - 1)));
var atomIndex = JU.PT.parseInt(tokens[0]) - 1;
if (atomIndex < 0 || atomIndex >= this.ac) continue;
var atom = this.at[atomIndex];
n++;
var pt = tokens.length - 1;
var x = JU.PT.parseFloat(tokens[pt]);
switch (type) {
case 18:
fData[atomIndex] = x;
bs.set(atomIndex);
continue;
case 0:
this.setAtomName(atomIndex, tokens[pt], true);
break;
case 13:
this.setAtomNumber(atomIndex, Clazz.floatToInt(x), true);
break;
case 15:
this.setAtomResno(atomIndex, Clazz.floatToInt(x));
break;
case 14:
this.setAtomSeqID(atomIndex, Clazz.floatToInt(x));
break;
case 1:
this.setAtomType(atomIndex, tokens[pt]);
break;
case 16:
this.setChainID(atomIndex, tokens[pt]);
break;
case 17:
atom.atomSite = Clazz.floatToInt(x);
break;
case 3:
atom.setAtomicAndIsotopeNumber(Clazz.floatToInt(x));
atom.paletteID = J.c.PAL.CPK.id;
atom.colixAtom = this.vwr.cm.getColixAtomPalette(atom, J.c.PAL.CPK.id);
break;
case 4:
atom.setFormalCharge(Clazz.floatToInt(x));
break;
case 5:
this.setHydrophobicity(atomIndex, x);
break;
case 6:
this.setBondingRadius(atomIndex, x);
break;
case 8:
this.setPartialCharge(atomIndex, x, true);
break;
case 9:
this.setBFactor(atomIndex, x, true);
break;
case 10:
atom.setValence(Clazz.floatToInt(x));
break;
case 11:
atom.setRadius(x);
break;
}
this.taintAtom(atomIndex, type);
}
if (type == 18 && n > 0) this.vwr.setData(name,  Clazz.newArray(-1, [name, fData, bs, Integer.$valueOf(1)]), 0, 0, 0, 0, 0);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error("loadData error: " + e);
} else {
throw e;
}
}
}, "~N,~S,~S,~B");
Clazz.defineMethod(c$, "loadCoordinates", 
function(data, isVibrationVectors, doTaint){
var lines = JU.Parser.markLines(data, ';');
var v = (isVibrationVectors ?  new JU.V3() : null);
try {
var nData = JU.PT.parseInt(data.substring(0, lines[0] - 1));
for (var i = 1; i <= nData; i++) {
var tokens = JU.PT.getTokens(JU.PT.parseTrimmed(data.substring(lines[i], lines[i + 1])));
var atomIndex = JU.PT.parseInt(tokens[0]) - 1;
var x = (tokens[3].equalsIgnoreCase("1.4E-45") ? 1.4e-45 : JU.PT.parseFloat(tokens[3]));
var y = (tokens[4].equalsIgnoreCase("1.4E-45") ? 1.4e-45 : JU.PT.parseFloat(tokens[4]));
var z = JU.PT.parseFloat(tokens[5]);
if (isVibrationVectors) {
v.set(x, y, z);
this.setAtomVibrationVector(atomIndex, v);
} else {
this.setAtomCoord(atomIndex, x, y, z);
if (!doTaint) this.untaint(atomIndex, 2);
}}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error("Frame.loadCoordinate error: " + e);
} else {
throw e;
}
}
}, "~S,~B,~B");
Clazz.defineMethod(c$, "validateBspf", 
function(isValid){
if (this.bspf != null) this.bspf.isValid = isValid;
}, "~B");
Clazz.defineMethod(c$, "validateBspfForModel", 
function(modelIndex, isValid){
if (this.bspf != null) this.bspf.validateModel(modelIndex, isValid);
}, "~N,~B");
Clazz.defineMethod(c$, "setPreserveState", 
function(TF){
this.preserveState = TF;
}, "~B");
c$.getUserSettableType = Clazz.defineMethod(c$, "getUserSettableType", 
function(dataType){
var isExplicit = (dataType.indexOf("property_") == 0);
var check = (isExplicit ? dataType.substring(9) : dataType);
for (var i = 0; i < 18; i++) if (JM.AtomCollection.userSettableValues[i].equalsIgnoreCase(check)) return i;

return (isExplicit ? 18 : -1);
}, "~S");
Clazz.defineMethod(c$, "getTaintedAtoms", 
function(type){
return this.tainted == null ? null : this.tainted[type];
}, "~N");
Clazz.defineMethod(c$, "taintAtoms", 
function(bsAtoms, type){
this.canSkipLoad = false;
if (!this.preserveState) return;
for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) this.taintAtom(i, type);

}, "JU.BS,~N");
Clazz.defineMethod(c$, "taintAtom", 
function(atomIndex, type){
if (this.preserveState) {
if (this.tainted == null) this.tainted =  new Array(18);
if (this.tainted[type] == null) this.tainted[type] = JU.BS.newN(this.ac);
this.tainted[type].set(atomIndex);
}if (type == 2) this.taintModelCoord(atomIndex);
}, "~N,~N");
Clazz.defineMethod(c$, "taintModelCoord", 
function(atomIndex){
var m = (this).am[this.at[atomIndex].mi];
this.validateBspfForModel(m.trajectoryBaseIndex, false);
if (m.isBioModel) m.resetDSSR(true);
this.pointGroup = null;
}, "~N");
Clazz.defineMethod(c$, "untaint", 
function(atomIndex, type){
if (!this.preserveState) return;
if (this.tainted == null || this.tainted[type] == null) return;
this.tainted[type].clear(atomIndex);
}, "~N,~N");
Clazz.defineMethod(c$, "setTaintedAtoms", 
function(bs, type){
if (this.preserveState) {
if (bs == null) {
if (this.tainted == null) return;
this.tainted[type] = null;
return;
}if (this.tainted == null) this.tainted =  new Array(18);
if (this.tainted[type] == null) this.tainted[type] = JU.BS.newN(this.ac);
JU.BSUtil.copy2(bs, this.tainted[type]);
}if (type == 2) {
var i = bs.nextSetBit(0);
if (i >= 0) this.taintModelCoord(i);
}}, "JU.BS,~N");
Clazz.defineMethod(c$, "unTaintAtoms", 
function(bs, type){
if (this.tainted == null || this.tainted[type] == null) return;
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) this.tainted[type].clear(i);

if (this.tainted[type].nextSetBit(0) < 0) this.tainted[type] = null;
}, "JU.BS,~N");
Clazz.defineMethod(c$, "findNearest2", 
function(x, y, closest, bsNot, min){
var champion = null;
var contender;
for (var i = this.ac; --i >= 0; ) {
if (bsNot != null && bsNot.get(i) || (contender = this.at[i]) == null) continue;
if (contender.isClickable() && this.isCursorOnTopOf(contender, x, y, min, champion)) champion = contender;
}
closest[0] = champion;
}, "~N,~N,~A,JU.BS,~N");
Clazz.defineMethod(c$, "isCursorOnTopOf", 
function(contender, x, y, radius, champion){
return contender.sZ > 1 && !this.g3d.isClippedZ(contender.sZ) && this.g3d.isInDisplayRange(contender.sX, contender.sY) && contender.isCursorOnTopOf(x, y, radius, champion);
}, "JM.Atom,~N,~N,~N,JM.Atom");
Clazz.defineMethod(c$, "fillADa", 
function(atomData, mode){
atomData.xyz = atomData.atoms = this.at;
atomData.ac = this.ac;
atomData.atomicNumber =  Clazz.newIntArray (this.ac, 0);
var includeRadii = ((mode & 2) != 0);
if (includeRadii) atomData.atomRadius =  Clazz.newFloatArray (this.ac, 0);
var isMultiModel = ((mode & 16) != 0);
for (var i = 0; i < this.ac; i++) {
var atom = this.at[i];
if (JM.AtomCollection.isDeleted(atom) || !isMultiModel && atomData.modelIndex >= 0 && atom.mi != atomData.firstModelIndex) {
if (atomData.bsIgnored == null) atomData.bsIgnored =  new JU.BS();
atomData.bsIgnored.set(i);
continue;
}atomData.atomicNumber[i] = atom.getElementNumber();
atomData.lastModelIndex = atom.mi;
if (includeRadii) atomData.atomRadius[i] = this.getWorkingRadius(atom, atomData);
}
}, "J.atomdata.AtomData,~N");
Clazz.defineMethod(c$, "getWorkingRadius", 
function(atom, atomData){
var r = 0;
var rd = atomData.radiusData;
switch (rd.factorType) {
case J.atomdata.RadiusData.EnumType.ABSOLUTE:
r = rd.value;
break;
case J.atomdata.RadiusData.EnumType.FACTOR:
case J.atomdata.RadiusData.EnumType.OFFSET:
switch (rd.vdwType) {
case J.c.VDW.BONDING:
r = atom.getBondingRadius();
break;
case J.c.VDW.ADPMAX:
r = atom.getADPMinMax(true);
break;
case J.c.VDW.ADPMIN:
r = atom.getADPMinMax(false);
break;
default:
r = atom.getVanderwaalsRadiusFloat(this.vwr, atomData.radiusData.vdwType);
}
if (rd.factorType === J.atomdata.RadiusData.EnumType.FACTOR) r *= rd.value;
 else r += rd.value;
}
return r + rd.valueExtended;
}, "JM.Atom,J.atomdata.AtomData");
Clazz.defineMethod(c$, "calculateHydrogens", 
function(bs, nTotal, vConnect, flags){
var doAll = ((flags & 256) == 256);
var justCarbon = ((flags & 512) == 512);
var isQuick = ((flags & 8) == 8);
var ignoreH = ((flags & 2048) == 2048);
var allowH = ((flags & 4096) == 4096);
var z =  new JU.V3();
var x =  new JU.V3();
var hAtoms =  new Array(this.ac);
var bsDeleted = this.vwr.slm.bsDeleted;
var pt;
var nH = nTotal[0] = 0;
if (bs == null) {
return hAtoms;
}var sym = this.vwr.getOperativeSymmetry();
if (sym != null && this.vwr.getObjectMad10(5) == 0) sym = null;
var ptTemp = (sym == null ? null :  new JU.P3());
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
if (bsDeleted != null && bsDeleted.get(i)) continue;
var atom = this.at[i];
var atomicNumber = atom.getElementNumber();
if (justCarbon && atomicNumber != 6) continue;
var dHX = (atomicNumber <= 6 ? 1.1 : atomicNumber <= 10 ? 1.0 : 1.3);
switch (atomicNumber) {
case 7:
case 8:
dHX = 1.0;
break;
case 6:
}
var n = (doAll || ignoreH || allowH ? atom.getCovalentHydrogenCount() : 0);
if (doAll && n > 0 || ignoreH && n == 0) continue;
var nMissing = this.getMissingHydrogenCount(atom, false);
if (doAll && nMissing == 0) continue;
if (!ignoreH) n = nMissing;
var targetValence = this.aaRet[0];
var hybridization = this.aaRet[2];
var nBonds = this.aaRet[3] - (ignoreH ? n : 0);
if (nBonds == 0 && atom.isHetero()) continue;
hAtoms[i] =  new Array(n);
var hPt = 0;
if (nBonds == 0) {
switch (n) {
case 4:
z.set(0.635, 0.635, 0.635);
pt = JU.P3.newP(z);
pt.add(atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
case 3:
z.set(-0.635, -0.635, 0.635);
pt = JU.P3.newP(z);
pt.add(atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
case 2:
z.set(-0.635, 0.635, -0.635);
pt = JU.P3.newP(z);
pt.add(atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
case 1:
z.set(0.635, -0.635, -0.635);
pt = JU.P3.newP(z);
pt.add(atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
}
} else {
switch (n) {
default:
break;
case 3:
this.getHybridizationAndAxes(i, atomicNumber, z, x, "sp3b", false, true, isQuick, null);
pt =  new JU.P3();
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
this.getHybridizationAndAxes(i, atomicNumber, z, x, "sp3c", false, true, isQuick, null);
pt =  new JU.P3();
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
this.getHybridizationAndAxes(i, atomicNumber, z, x, "sp3d", false, true, isQuick, null);
pt =  new JU.P3();
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
break;
case 2:
var isEne = (hybridization == 2 || atomicNumber == 5 || nBonds == 1 && targetValence == 4 || atomicNumber == 7 && this.isAdjacentSp2(atom));
this.getHybridizationAndAxes(i, atomicNumber, z, x, (isEne ? "sp2b" : targetValence == 3 ? "sp3c" : "lpa"), false, true, isQuick, null);
pt = JU.P3.newP(z);
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
this.getHybridizationAndAxes(i, atomicNumber, z, x, (isEne ? "sp2c" : targetValence == 3 ? "sp3d" : "lpb"), false, true, isQuick, null);
pt = JU.P3.newP(z);
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
break;
case 1:
switch (targetValence - nBonds) {
case 1:
if (atomicNumber == 8 && atom === atom.group.getCarbonylOxygenAtom()) {
hAtoms[i] = null;
continue;
}if (this.getHybridizationAndAxes(i, atomicNumber, z, x, (hybridization == 2 || atomicNumber == 5 || atomicNumber == 6 && this.aaRet[1] == 1 || atomicNumber == 7 && ( new Boolean ( new Boolean (atom.group.getNitrogenAtom() === atom & atom.getFormalCharge() == 0).valueOf() || this.isAdjacentSp2(atom)).valueOf()) ? "sp2c" : "sp3d"), true, false, isQuick, null) != null) {
pt = JU.P3.newP(z);
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
}break;
case 2:
this.getHybridizationAndAxes(i, atomicNumber, z, x, (targetValence == 4 ? "sp2c" : "sp2b"), false, false, isQuick, null);
pt = JU.P3.newP(z);
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
break;
case 3:
this.getHybridizationAndAxes(i, atomicNumber, z, x, "spb", false, true, isQuick, null);
pt = JU.P3.newP(z);
pt.scaleAdd2(dHX, z, atom);
hPt = JM.AtomCollection.addH(hAtoms[i], hPt, pt, atom, vConnect, sym, ptTemp);
break;
}
}
}if (hPt < n) {
var a =  new Array(hPt);
for (var j = 0; j < hPt; j++) a[j] = hAtoms[i][j];

hAtoms[i] = a;
}nH += hPt;
}
nTotal[0] = nH;
return hAtoms;
}, "JU.BS,~A,JU.Lst,~N");
c$.addH = Clazz.defineMethod(c$, "addH", 
function(hAtoms, hPt, pt, atom, vConnect, sym, ptTemp){
if (sym != null) {
ptTemp.setT(pt);
sym.toFractional(ptTemp, false);
if (!sym.isWithinUnitCell(ptTemp, 1, 1, 1)) {
return hPt;
}}hAtoms[hPt++] = pt;
if (vConnect != null) vConnect.addLast(atom);
return hPt;
}, "~A,~N,JU.P3,JM.Atom,JU.Lst,J.api.SymmetryInterface,JU.P3");
Clazz.defineMethod(c$, "isAdjacentSp2", 
function(atom){
var bonds = atom.bonds;
for (var i = 0; i < bonds.length; i++) {
var b2 = bonds[i].getOtherAtom(atom).bonds;
for (var j = 0; j < b2.length; j++) switch (b2[j].getCovalentOrder()) {
case 2:
case 3:
return true;
}

}
return false;
}, "JM.Atom");
Clazz.defineMethod(c$, "getMissingHydrogenCount", 
function(atom, allowNegative){
if (this.aaRet == null) this.aaRet =  Clazz.newIntArray (5, 0);
var targetCount = atom.getTargetValence();
if (targetCount < 0) return 0;
var charge = atom.getFormalCharge();
var valence = atom.getValence();
var model = (this).am[atom.mi];
var s = (model.isBioModel && !model.isPdbWithMultipleBonds ? atom.group.getGroup3() : null);
this.aaRet[0] = targetCount;
this.aaRet[1] = charge;
this.aaRet[2] = 0;
this.aaRet[3] = atom.getCovalentBondCount();
this.aaRet[4] = (s == null ? 0 : valence);
if (s != null && charge == 0) {
if (this.bioModelset.getAminoAcidValenceAndCharge(s, atom.getAtomName(), this.aaRet)) {
targetCount = this.aaRet[0];
charge = this.aaRet[1];
}}if (charge != 0) {
targetCount += (targetCount == 4 ? -Math.abs(charge) : charge);
this.aaRet[0] = targetCount;
}var n = targetCount - valence;
return (n < 0 && !allowNegative ? 0 : n);
}, "JM.Atom,~B");
Clazz.defineMethod(c$, "fixFormalCharges", 
function(bs){
var n = 0;
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
var a = this.at[i];
var nH = this.getMissingHydrogenCount(a, true);
if (nH != 0) {
var c0 = a.getFormalCharge();
var c = c0 - nH;
a.setFormalCharge(c);
this.taintAtom(i, 4);
if (JU.Logger.debugging) JU.Logger.debug("atom " + a + " formal charge " + c0 + " -> " + c);
n++;
}}
return n;
}, "JU.BS");
Clazz.defineMethod(c$, "getHybridizationAndAxes", 
function(atomIndex, atomicNumber, z, x, lcaoTypeRaw, hybridizationCompatible, doAlignZ, isQuick, ref){
var lcaoType = (lcaoTypeRaw.length > 0 && lcaoTypeRaw.charAt(0) == '-' ? lcaoTypeRaw.substring(1) : lcaoTypeRaw);
if (lcaoTypeRaw.indexOf("d") >= 0 && !lcaoTypeRaw.endsWith("sp3d")) return this.getHybridizationAndAxesD(atomIndex, z, x, lcaoType);
var atom = this.at[atomIndex];
if (atomicNumber == 0) atomicNumber = atom.getElementNumber();
var attached = this.getAttached(atom, 4, hybridizationCompatible, isQuick);
var nAttached = attached.length;
var pt = (lcaoType.charAt(lcaoType.length - 1)).charCodeAt(0) - 97;
if (pt < 0 || pt > 6) pt = 0;
z.set(0, 0, 0);
x.set(0, 0, 0);
var v =  new Array(4);
for (var i = 0; i < nAttached; i++) {
var a = attached[i];
if (a == null) {
nAttached = i;
break;
}v[i] = JU.V3.newVsub(atom, a);
v[i].normalize();
z.add(v[i]);
}
if (nAttached > 0) x.setT(v[0]);
var isPlanar = false;
var vTemp =  new JU.V3();
if (nAttached >= 3) {
if (x.angle(v[1]) < 2.9845130209103035) vTemp.cross(x, v[1]);
 else vTemp.cross(x, v[2]);
vTemp.normalize();
var vTemp2 =  new JU.V3();
if (v[1].angle(v[2]) < 2.9845130209103035) vTemp2.cross(v[1], v[2]);
 else vTemp2.cross(x, v[2]);
vTemp2.normalize();
isPlanar = (Math.abs(vTemp2.dot(vTemp)) >= 0.95);
}var isSp3 = (lcaoType.indexOf("sp3") == 0);
var isSp2 = (!isSp3 && lcaoType.indexOf("sp2") == 0);
var isSp = (!isSp3 && !isSp2 && lcaoType.indexOf("sp") == 0);
var isP = (lcaoType.indexOf("p") == 0);
var isLp = (lcaoType.indexOf("lp") == 0);
var hybridization = null;
if (hybridizationCompatible) {
if (nAttached == 0) return null;
if (isSp3) {
if (pt > 3 || nAttached > 4) return null;
} else if (isSp2) {
if (pt > 2 || nAttached > 3) return null;
} else if (isSp) {
if (pt > 1 || nAttached > 2) return null;
}switch (nAttached) {
case 1:
if (atomicNumber == 1 && !isSp3) return null;
if (isSp3) {
hybridization = "sp3";
break;
}switch (attached[0].getCovalentBondCount()) {
case 1:
if (attached[0].getValence() != 2) {
hybridization = "sp";
break;
}case 2:
hybridization = (isSp ? "sp" : "sp2");
break;
case 3:
if (!isSp2 && !isP) return null;
hybridization = "sp2";
break;
}
break;
case 2:
if (z.length() < 0.1) {
if (lcaoType.indexOf("2") >= 0 || lcaoType.indexOf("3") >= 0) return null;
hybridization = "sp";
break;
}hybridization = (isSp3 ? "sp3" : "sp2");
if (lcaoType.indexOf("sp") == 0) {
break;
}if (isLp) {
hybridization = "lp";
break;
}hybridization = lcaoType;
break;
default:
if (isPlanar && !isQuick) {
hybridization = "sp2";
} else {
if (isPlanar) z.setT(vTemp);
if (isLp && nAttached == 3) {
hybridization = "lp";
break;
}hybridization = "sp3";
}}
if (hybridization == null) return null;
if (lcaoType.indexOf("p") == 0) {
if (hybridization === "sp3") return null;
} else if (lcaoType.indexOf(hybridization) < 0) {
return null;
}}if (pt < nAttached && !lcaoType.startsWith("p") && !lcaoType.startsWith("l")) {
z.sub2(attached[pt], atom);
z.normalize();
return hybridization;
}switch (nAttached) {
case 0:
if (lcaoType.equals("sp3c") || lcaoType.equals("sp2d") || lcaoType.equals("lpa")) {
z.set(-0.5, -0.7, 1);
x.set(1, 0, 0);
} else if (lcaoType.equals("sp3b") || lcaoType.equals("lpb")) {
z.set(0.5, -0.7, -1.0);
x.set(1, 0, 0);
} else if (lcaoType.equals("sp3a")) {
z.set(0, 1, 0);
x.set(1, 0, 0);
} else {
z.set(0, 0, 1);
x.set(1, 0, 0);
}break;
case 1:
vTemp.setT(JM.AtomCollection.vRef);
x.cross(vTemp, z);
if (isSp3) {
for (var i = attached[0].getBondCount(); --i >= 0; ) {
if (attached[0].bonds[i].isCovalentNotPartial0() && attached[0].getBondedAtomIndex(i) != atom.i) {
x.sub2(attached[0], attached[0].bonds[i].getOtherAtom(attached[0]));
x.cross(z, x);
if (x.length() == 0) continue;
x.cross(x, z);
break;
}}
x.normalize();
if (Float.isNaN(x.x)) {
x.setT(JM.AtomCollection.vRef);
x.cross(x, z);
}vTemp.cross(z, x);
vTemp.normalize();
z.normalize();
x.scaleAdd2(2.828, x, z);
if (pt != 3) {
x.normalize();
 new JU.M3().setAA(JU.A4.new4(z.x, z.y, z.z, (pt == 2 ? 1 : -1) * 2.09439507)).rotate(x);
}z.setT(x);
x.cross(vTemp, z);
break;
}vTemp.cross(x, z);
var na = attached[0].getCovalentBondCount();
switch (na) {
case 3:
if (ref !== attached[0]) {
this.getHybridizationAndAxes(attached[0].i, 0, x, vTemp, "pz", false, doAlignZ, isQuick, atom);
vTemp.setT(x);
if (isSp2) {
x.cross(x, z);
if (pt == 1) x.scale(-1);
x.scale(JM.AtomCollection.sqrt3_2);
z.scaleAdd2(0.5, z, x);
} else if (isSp) {
} else {
vTemp.setT(z);
z.setT(x);
}x.cross(vTemp, z);
break;
}na = 2;
case 1:
if (na == 1 && attached[0].getValence() != 2) {
break;
}case 2:
var isCumulated = false;
var a0 = attached[0];
x.setT(z);
vTemp.setT(JM.AtomCollection.vRef);
while (a0 != null && a0.getCovalentBondCount() == 2) {
var bonds = a0.bonds;
var a = null;
isCumulated = !isCumulated;
for (var i = 0; i < bonds.length; i++) if (bonds[i].isCovalentNotPartial0()) {
a = bonds[i].getOtherAtom(a0);
if (a !== atom) {
vTemp.sub2(a, a0);
break;
}}
vTemp.cross(vTemp, x);
if (vTemp.length() > 0.1 || a.getCovalentBondCount() != 2) break;
atom = a0;
a0 = a;
}
if (isSp) {
} else if (vTemp.length() > 0.1) {
z.cross(vTemp, x);
z.normalize();
if (pt == 1) z.scale(-1);
z.scale(JM.AtomCollection.sqrt3_2);
z.scaleAdd2(0.5, x, z);
if (isP) {
vTemp.cross(z, x);
z.setT(vTemp);
vTemp.setT(x);
}x.cross(vTemp, z);
} else {
z.setT(x);
x.cross(JM.AtomCollection.vRef, x);
}break;
}
break;
case 2:
if (z.length() < 0.1) {
if (!lcaoType.equals("pz")) {
var a = attached[0];
var ok = (a.getCovalentBondCount() == 3);
if (!ok) ok = ((a = attached[1]).getCovalentBondCount() == 3);
if (ok) {
this.getHybridizationAndAxes(a.i, 0, x, z, "pz", false, doAlignZ, isQuick, null);
if (lcaoType.equals("px")) x.scale(-1);
z.setT(v[0]);
break;
}vTemp.setT(JM.AtomCollection.vRef);
z.cross(vTemp, x);
vTemp.cross(z, x);
}z.setT(x);
x.cross(vTemp, z);
break;
}vTemp.cross(z, x);
if (isSp2) {
x.cross(z, vTemp);
break;
}if (isSp3 || isLp) {
vTemp.normalize();
z.normalize();
if (!lcaoType.equals("lp")) {
if (pt == 0 || pt == 2) z.scaleAdd2(-1.2, vTemp, z);
 else z.scaleAdd2(1.2, vTemp, z);
}x.cross(z, vTemp);
break;
}x.cross(z, vTemp);
z.setT(vTemp);
if (z.z < 0) {
z.scale(-1);
x.scale(-1);
}break;
default:
if (isSp3) break;
if (!isPlanar) {
x.cross(z, x);
break;
}z.setT(vTemp);
if (z.z < 0 && doAlignZ) {
z.scale(-1);
x.scale(-1);
}}
x.normalize();
z.normalize();
return hybridization;
}, "~N,~N,JU.V3,JU.V3,~S,~B,~B,~B,JU.T3");
Clazz.defineMethod(c$, "getHybridizationAndAxesD", 
function(atomIndex, z, x, lcaoType){
if (lcaoType.startsWith("sp3d2")) lcaoType = "d2sp3" + (lcaoType.length == 5 ? "a" : lcaoType.substring(5));
if (lcaoType.startsWith("sp3d")) lcaoType = "dsp3" + (lcaoType.length == 4 ? "a" : lcaoType.substring(4));
if (lcaoType.equals("d2sp3") || lcaoType.equals("dsp3")) lcaoType += "a";
var isTrigonal = lcaoType.startsWith("dsp3");
var pt = (lcaoType.charAt(lcaoType.length - 1)).charCodeAt(0) - 97;
if (z != null && (!isTrigonal && (pt > 5 || !lcaoType.startsWith("d2sp3")) || isTrigonal && pt > 4)) return null;
var atom = this.at[atomIndex];
var attached = this.getAttached(atom, 6, true, false);
if (attached == null) return (z == null ? null : "?");
var nAttached = attached.length;
if (nAttached < 3 && z != null) return null;
var isLP = (pt >= nAttached);
var nAngles = Clazz.doubleToInt(nAttached * (nAttached - 1) / 2);
var angles = JU.AU.newInt2(nAngles);
var ntypes =  Clazz.newIntArray (3, 0);
var typePtrs =  Clazz.newIntArray (3, nAngles, 0);
var n = 0;
var _90 = 0;
var _120 = 1;
var _180 = 2;
var n120_atom0 = 0;
for (var i = 0; i < nAttached - 1; i++) for (var j = i + 1; j < nAttached; j++) {
var angle = JU.Measure.computeAngleABC(attached[i], atom, attached[j], true);
var itype = (angle < 105 ? _90 : angle >= 150 ? _180 : _120);
typePtrs[itype][ntypes[itype]] = n;
ntypes[itype]++;
angles[n++] =  Clazz.newIntArray(-1, [i, j]);
if (i == 0 && itype == _120) n120_atom0++;
}

n = ntypes[_90] * 100 + ntypes[_120] * 10 + ntypes[_180];
if (z == null) {
switch (n) {
default:
return "";
case 0:
return "";
case 1:
return "linear";
case 100:
case 10:
return "bent";
case 111:
case 201:
return "T-shaped";
case 30:
case 120:
case 210:
case 300:
if (Math.abs(JU.Measure.computeTorsion(attached[0], atom, attached[1], attached[2], true)) > 162) return "trigonal planar";
return "trigonal pyramidal";
case 330:
return (n120_atom0 % 2 == 1 ? "tetrahedral" : "uncapped trigonal pyramid");
case 60:
case 150:
case 240:
return "tetrahedral";
case 402:
return "square planar";
case 411:
case 501:
return "see-saw";
case 631:
return "trigonal bipyramidal";
case 802:
return "uncapped square pyramid";
case 1203:
return "octahedral";
}
}switch (n) {
default:
return null;
case 201:
break;
case 210:
case 330:
case 411:
case 631:
if (!isTrigonal) return null;
break;
case 300:
case 402:
case 501:
case 802:
case 1203:
if (isTrigonal) return null;
break;
}
if (isLP) {
var a;
var bs;
if (isTrigonal) {
switch (ntypes[_120]) {
case 0:
z.sub2(attached[angles[typePtrs[_90][0]][0]], atom);
x.sub2(attached[angles[typePtrs[_90][0]][1]], atom);
z.cross(z, x);
z.normalize();
if (pt == 4) z.scale(-1);
bs = this.findNotAttached(nAttached, angles, typePtrs[_180], ntypes[_180]);
var i = bs.nextSetBit(0);
x.sub2(attached[i], atom);
x.normalize();
x.scale(0.5);
z.scaleAdd2(JM.AtomCollection.sqrt3_2, z, x);
pt = -1;
break;
case 1:
if (pt == 4) {
a = angles[typePtrs[_120][0]];
z.add2(attached[a[0]], attached[a[1]]);
z.scaleAdd2(-2, atom, z);
pt = -1;
} else {
bs = this.findNotAttached(nAttached, angles, typePtrs[_120], ntypes[_120]);
pt = bs.nextSetBit(0);
}break;
default:
bs = this.findNotAttached(nAttached, angles, typePtrs[_120], ntypes[_120]);
pt = bs.nextSetBit(0);
}
} else {
var isPlanar = false;
if (nAttached == 4) {
switch (ntypes[_180]) {
case 1:
bs = this.findNotAttached(nAttached, angles, typePtrs[_180], ntypes[_180]);
var i = bs.nextSetBit(0);
if (pt == 4) pt = i;
 else pt = bs.nextSetBit(i + 1);
break;
default:
isPlanar = true;
}
} else {
bs = this.findNotAttached(nAttached, angles, typePtrs[_180], ntypes[_180]);
var i = bs.nextSetBit(0);
for (var j = nAttached; j < pt && i >= 0; j++) i = bs.nextSetBit(i + 1);

if (i == -1) isPlanar = true;
 else pt = i;
}if (isPlanar) {
z.sub2(attached[angles[typePtrs[_90][0]][0]], atom);
x.sub2(attached[angles[typePtrs[_90][0]][1]], atom);
z.cross(z, x);
if (pt == 4) z.scale(-1);
pt = -1;
}}}if (pt >= 0) z.sub2(attached[pt], atom);
if (isLP) z.scale(-1);
z.normalize();
return (isTrigonal ? "dsp3" : "d2sp3");
}, "~N,JU.V3,JU.V3,~S");
Clazz.defineMethod(c$, "getAttached", 
function(atom, nMax, doSort, isQuick){
var nAttached = atom.getCovalentBondCount();
if (nAttached > nMax) return null;
var attached =  new Array(nAttached);
if (nAttached > 0) {
var bonds = atom.bonds;
var n = 0;
for (var i = 0; i < bonds.length; i++) if (bonds[i].isCovalentNotPartial0()) {
var a = bonds[i].getOtherAtom(atom);
if (!isQuick || a.getAtomicAndIsotopeNumber() != 1) attached[n++] = a;
}
if (doSort && !isQuick) java.util.Arrays.sort(attached, Clazz.innerTypeInstance(JM.AtomCollection.AtomSorter, this, null));
}return attached;
}, "JM.Atom,~N,~B,~B");
Clazz.defineMethod(c$, "findNotAttached", 
function(nAttached, angles, ptrs, nPtrs){
var bs = JU.BS.newN(nAttached);
bs.setBits(0, nAttached);
for (var i = 0; i < nAttached; i++) for (var j = 0; j < nPtrs; j++) {
var a = angles[ptrs[j]];
if (a[0] == i || a[1] == i) bs.clear(i);
}

return bs;
}, "~N,~A,~A,~N");
Clazz.defineMethod(c$, "getAtomBitsMDa", 
function(tokType, specInfo, bs){
var iSpec = (Clazz.instanceOf(specInfo, Integer) ? (specInfo).intValue() : 0);
switch (tokType) {
case 1086326786:
case 1086326785:
var isType = (tokType == 1086326785);
var names = "," + specInfo + ",";
for (var i = this.ac; --i >= 0; ) {
if (JM.AtomCollection.isDeleted(this.at[i])) continue;
var s = (isType ? this.at[i].getAtomType() : this.at[i].getAtomName());
if (names.indexOf("," + s + ",") >= 0) bs.set(i);
}
return bs;
case 1094715393:
for (var i = this.ac; --i >= 0; ) {
if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].getAtomNumber() == iSpec) bs.set(i);
}
return bs;
case 2097155:
for (var i = this.ac; --i >= 0; ) {
if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].getCovalentBondCount() > 0) bs.set(i);
}
return bs;
case 2097188:
case 2097156:
case 136314895:
case 2097166:
case 2097168:
case 2097170:
case 2097172:
case 2097174:
case 2097184:
return ((this).haveBioModels ? (this).bioModelset.getAtomBitsBS(tokType, null, bs) : bs);
case 1612709900:
iSpec = 1;
case 1094715402:
for (var i = this.ac; --i >= 0; ) {
if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].getElementNumber() == iSpec) bs.set(i);
}
return bs;
case 1612709894:
for (var i = this.ac; --i >= 0; ) {
if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].isHetero()) bs.set(i);
}
return bs;
case 1073741824:
return this.getIdentifierOrNull(specInfo);
case 2097165:
for (var i = this.ac; --i >= 0; ) {
if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].isLeadAtom()) bs.set(i);
}
return bs;
case 1094713362:
case 1639976963:
return ((this).haveBioModels ? (this).bioModelset.getAtomBitsBS(tokType, specInfo, bs) : bs);
case 1094715412:
for (var i = this.ac; --i >= 0; ) {
if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].getResno() == iSpec) bs.set(i);
}
return bs;
case 1612709912:
var hs =  Clazz.newIntArray (2, 0);
var a;
for (var i = this.ac; --i >= 0; ) {
if (JM.AtomCollection.isDeleted(this.at[i])) continue;
var g = this.at[i].group.groupID;
if (g >= 42 && g < 45) {
bs.set(i);
} else if ((a = this.at[i]).getElementNumber() == 8 && a.getCovalentBondCount() == 2) {
var bonds = a.bonds;
var n = 0;
var b;
for (var j = bonds.length; --j >= 0 && n < 3; ) if (bonds[j].isCovalentNotPartial0() && (b = bonds[j].getOtherAtom(a)).getElementNumber() == 1) hs[n++ % 2] = b.i;

if (n == 2) {
bs.set(hs[1]);
bs.set(hs[0]);
bs.set(i);
}}}
return bs;
case 1073742355:
var spec = specInfo;
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.isAltLoc(this.at[i].altloc, spec)) bs.set(i);

return bs;
case 1073742356:
var atomSpec = (specInfo).toUpperCase();
if (atomSpec.indexOf("\\?") >= 0) atomSpec = JU.PT.rep(atomSpec, "\\?", "\1");
var allowStar = atomSpec.startsWith("?*");
if (allowStar) atomSpec = atomSpec.substring(1);
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.isAtomNameMatch(this.at[i], atomSpec, allowStar, allowStar)) bs.set(i);

return bs;
case 1073742357:
return JU.BSUtil.copy(this.getChainBits(iSpec));
case 1073742360:
return this.getSpecName(specInfo);
case 1073742361:
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].group.groupID == iSpec) bs.set(i);

return bs;
case 1073742362:
return JU.BSUtil.copy(this.getSeqcodeBits(iSpec, true));
case 5:
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].group.getInsCode() == iSpec) bs.set(i);

return bs;
case 1296041985:
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].getSymOp() == iSpec) bs.set(i);

return bs;
}
var bsTemp;
var bsInfo = specInfo;
var i0 = bsInfo.nextSetBit(0);
if (i0 < 0) return bs;
switch (tokType) {
case 1094717454:
bsTemp = JU.BSUtil.copy(bsInfo);
for (var i = i0; i >= 0; i = bsTemp.nextSetBit(i + 1)) {
bs.or((this).am[this.at[i].mi].bsAtoms);
bsTemp.andNot(bs);
}
return bs;
case 1086326788:
bsTemp = JU.BSUtil.copy(bsInfo);
for (var i = i0; i >= 0; i = bsTemp.nextSetBit(i + 1)) {
this.at[i].group.chain.setAtomBits(bs);
bsTemp.andNot(bs);
}
return bs;
case 1086326789:
bsTemp =  new JU.BS();
for (var i = i0; i >= 0; i = bsInfo.nextSetBit(i + 1)) bsTemp.set(this.at[i].getElementNumber());

for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && bsTemp.get(this.at[i].getElementNumber())) bs.set(i);

return bs;
case 1086324742:
bsTemp = JU.BSUtil.copy(bsInfo);
for (var i = i0; i >= 0; i = bsTemp.nextSetBit(i + 1)) {
this.at[i].group.setAtomBits(bs);
bsTemp.andNot(bs);
}
return bs;
case 1094713366:
bsTemp =  new JU.BS();
for (var i = i0; i >= 0; i = bsInfo.nextSetBit(i + 1)) bsTemp.set(this.at[i].atomSite);

for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && bsTemp.get(this.at[i].atomSite)) bs.set(i);

return bs;
}
JU.Logger.error("MISSING getAtomBits entry for " + JS.T.nameOf(tokType));
return bs;
}, "~N,~O,JU.BS");
Clazz.defineMethod(c$, "getChainBits", 
function(chainID){
var caseSensitive = this.vwr.getBoolean(603979822);
if (caseSensitive) {
if (chainID >= 97 && chainID <= 122) chainID += 159;
} else {
if (chainID >= 0 && chainID < 300) chainID = this.chainToUpper(chainID);
}var bs =  new JU.BS();
var bsDone = JU.BS.newN(this.ac);
var id;
for (var i = bsDone.nextClearBit(0); i < this.ac; i = bsDone.nextClearBit(i + 1)) {
if (JM.AtomCollection.isDeleted(this.at[i])) continue;
var chain = this.at[i].group.chain;
if (chainID == (id = chain.chainID) || !caseSensitive && id >= 0 && id < 300 && chainID == this.chainToUpper(id)) {
chain.setAtomBits(bs);
bsDone.or(bs);
} else {
chain.setAtomBits(bsDone);
}}
return bs;
}, "~N");
Clazz.defineMethod(c$, "chainToUpper", 
function(chainID){
return (chainID >= 97 && chainID <= 122 ? chainID - 32 : chainID >= 256 && chainID < 300 ? chainID - 191 : chainID);
}, "~N");
Clazz.defineMethod(c$, "isAltLoc", 
function(altloc, strPattern){
if (strPattern == null) return (altloc == '\0');
if (strPattern.length != 1) return false;
var ch = strPattern.charAt(0);
return (ch == '*' || ch == '?' && altloc != '\0' || altloc == ch);
}, "~S,~S");
Clazz.defineMethod(c$, "getSeqcodeBits", 
function(seqcode, returnEmpty){
var bs =  new JU.BS();
var seqNum = JM.Group.getSeqNumberFor(seqcode);
var haveSeqNumber = (seqNum != 2147483647);
var isEmpty = true;
var insCode = JM.Group.getInsertionCodeChar(seqcode);
switch ((insCode).charCodeAt(0)) {
case 63:
for (var i = this.ac; --i >= 0; ) {
if (JM.AtomCollection.isDeleted(this.at[i])) continue;
var atomSeqcode = this.at[i].group.seqcode;
if ((!haveSeqNumber || seqNum == JM.Group.getSeqNumberFor(atomSeqcode)) && JM.Group.getInsertionCodeFor(atomSeqcode) != 0) {
bs.set(i);
isEmpty = false;
}}
break;
default:
for (var i = this.ac; --i >= 0; ) {
if (JM.AtomCollection.isDeleted(this.at[i])) continue;
var atomSeqcode = this.at[i].group.seqcode;
if (seqcode == atomSeqcode || !haveSeqNumber && seqcode == JM.Group.getInsertionCodeFor(atomSeqcode) || insCode == '*' && seqNum == JM.Group.getSeqNumberFor(atomSeqcode)) {
bs.set(i);
isEmpty = false;
}}
}
return (!isEmpty || returnEmpty ? bs : null);
}, "~N,~B");
Clazz.defineMethod(c$, "getIdentifierOrNull", 
function(identifier){
var bs = this.getSpecNameOrNull(identifier, false);
if (identifier.indexOf("\\?") >= 0) identifier = JU.PT.rep(identifier, "\\?", "\1");
return (bs != null || identifier.indexOf("?") > 0 ? bs : identifier.indexOf("*") > 0 ? this.getSpecNameOrNull(identifier, true) : (this).haveBioModels ? (this).bioModelset.getIdentifierOrNull(identifier) : null);
}, "~S");
Clazz.defineMethod(c$, "getSpecName", 
function(name){
var bs = this.getSpecNameOrNull(name, false);
if (bs != null) return bs;
if (name.indexOf("*") > 0) bs = this.getSpecNameOrNull(name, true);
return (bs == null ?  new JU.BS() : bs);
}, "~S");
Clazz.defineMethod(c$, "getSpecNameOrNull", 
function(name, checkStar){
var bs = null;
name = name.toUpperCase();
if (name.indexOf("\\?") >= 0) name = JU.PT.rep(name, "\\?", "\1");
var allowInitialStar = name.startsWith("?*");
if (allowInitialStar) name = name.substring(1);
for (var i = this.ac; --i >= 0; ) {
if (JM.AtomCollection.isDeleted(this.at[i])) continue;
var g3 = this.at[i].getGroup3(true);
if (g3 != null && g3.length > 0) {
if (JU.PT.isMatch(g3, name, checkStar, true)) {
if (bs == null) bs = JU.BS.newN(i + 1);
bs.set(i);
while (--i >= 0) {
if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].getGroup3(true).equals(g3)) bs.set(i);
}
i++;
}} else if (this.isAtomNameMatch(this.at[i], name, checkStar, allowInitialStar)) {
if (bs == null) bs = JU.BS.newN(i + 1);
bs.set(i);
}}
return bs;
}, "~S,~B");
Clazz.defineMethod(c$, "isAtomNameMatch", 
function(atom, strPattern, checkStar, allowInitialStar){
return JU.PT.isMatch(atom.getAtomName().toUpperCase(), strPattern, checkStar, allowInitialStar);
}, "JM.Atom,~S,~B,~B");
Clazz.defineMethod(c$, "getAtomIndices", 
function(bs){
var n = 0;
var indices =  Clazz.newIntArray (this.ac, 0);
for (var j = bs.nextSetBit(0); j >= 0 && j < this.ac; j = bs.nextSetBit(j + 1)) indices[j] = ++n;

return indices;
}, "JU.BS");
Clazz.defineMethod(c$, "getAtomsNearPlane", 
function(distance, plane){
var bsResult =  new JU.BS();
for (var i = this.ac; --i >= 0; ) {
var atom = this.at[i];
if (JM.AtomCollection.isDeleted(atom)) continue;
var d = JU.Measure.distanceToPlane(plane, atom);
if (distance > 0 && d >= -0.1 && d <= distance || distance < 0 && d <= 0.1 && d >= distance || distance == 0 && Math.abs(d) < 0.01) bsResult.set(atom.i);
}
return bsResult;
}, "~N,JU.P4");
Clazz.defineMethod(c$, "clearVisibleSets", 
function(){
this.haveBSVisible = false;
this.haveBSClickable = false;
});
Clazz.defineMethod(c$, "getAtomsInFrame", 
function(bsAtoms){
this.clearVisibleSets();
bsAtoms.clearAll();
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].isVisible(1)) bsAtoms.set(i);

}, "JU.BS");
Clazz.defineMethod(c$, "getVisibleSet", 
function(forceNew){
if (forceNew) {
this.vwr.setModelVisibility();
this.vwr.shm.finalizeAtoms(null, true);
} else if (this.haveBSVisible) {
return this.bsVisible;
}this.bsVisible.clearAll();
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].checkVisible()) this.bsVisible.set(i);

if (this.vwr.shm.bsSlabbedInternal != null) this.bsVisible.andNot(this.vwr.shm.bsSlabbedInternal);
this.haveBSVisible = true;
return this.bsVisible;
}, "~B");
Clazz.defineMethod(c$, "getClickableSet", 
function(forceNew){
if (forceNew) this.vwr.setModelVisibility();
 else if (this.haveBSClickable) return this.bsClickable;
this.bsClickable.clearAll();
for (var i = this.ac; --i >= 0; ) if (!JM.AtomCollection.isDeleted(this.at[i]) && this.at[i].isClickable()) this.bsClickable.set(i);

this.haveBSClickable = true;
return this.bsClickable;
}, "~B");
Clazz.defineMethod(c$, "isModulated", 
function(i){
return this.bsModulated != null && this.bsModulated.get(i);
}, "~N");
Clazz.defineMethod(c$, "deleteModelAtoms", 
function(firstAtomIndex, nAtoms, bsAtoms){
this.at = JU.AU.deleteElements(this.at, firstAtomIndex, nAtoms);
this.ac = this.at.length;
for (var j = firstAtomIndex; j < this.ac; j++) {
this.at[j].i = j;
this.at[j].mi--;
}
if (this.bsModulated != null) JU.BSUtil.deleteBits(this.bsModulated, bsAtoms);
this.deleteAtomTensors(bsAtoms);
this.atomNames = JU.AU.deleteElements(this.atomNames, firstAtomIndex, nAtoms);
this.atomTypes = JU.AU.deleteElements(this.atomTypes, firstAtomIndex, nAtoms);
this.atomResnos = JU.AU.deleteElements(this.atomResnos, firstAtomIndex, nAtoms);
this.atomSerials = JU.AU.deleteElements(this.atomSerials, firstAtomIndex, nAtoms);
this.atomSeqIDs = JU.AU.deleteElements(this.atomSeqIDs, firstAtomIndex, nAtoms);
this.dssrData = JU.AU.deleteElements(this.dssrData, firstAtomIndex, nAtoms);
this.bfactor100s = JU.AU.deleteElements(this.bfactor100s, firstAtomIndex, nAtoms);
this.hasBfactorRange = false;
this.occupancies = JU.AU.deleteElements(this.occupancies, firstAtomIndex, nAtoms);
this.resetPartialCharges();
this.atomTensorList = JU.AU.deleteElements(this.atomTensorList, firstAtomIndex, nAtoms);
this.vibrations = JU.AU.deleteElements(this.vibrations, firstAtomIndex, nAtoms);
this.nSurfaceAtoms = 0;
this.bsSurface = null;
this.surfaceDistance100s = null;
if (this.tainted != null) for (var i = 0; i < 18; i++) JU.BSUtil.deleteBits(this.tainted[i], bsAtoms);

}, "~N,~N,JU.BS");
Clazz.defineMethod(c$, "getAtomIdentityInfo", 
function(i, info, ptTemp){
info.put("_ipt", Integer.$valueOf(i));
info.put("atomIndex", Integer.$valueOf(i));
info.put("atomno", Integer.$valueOf(this.at[i].getAtomNumber()));
info.put("info", this.getAtomInfo(i, null, ptTemp));
info.put("sym", this.at[i].getElementSymbol());
}, "~N,java.util.Map,JU.P3");
Clazz.defineMethod(c$, "getAtomTensorList", 
function(i){
return (i < 0 || this.atomTensorList == null || i >= this.atomTensorList.length ? null : this.atomTensorList[i]);
}, "~N");
Clazz.defineMethod(c$, "deleteAtomTensors", 
function(bsAtoms){
if (this.atomTensors == null) return;
var toDelete =  new JU.Lst();
for (var key, $key = this.atomTensors.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) {
var list = this.atomTensors.get(key);
for (var i = list.size(); --i >= 0; ) {
var t = list.get(i);
if (bsAtoms.get(t.atomIndex1) || t.atomIndex2 >= 0 && bsAtoms.get(t.atomIndex2)) list.removeItemAt(i);
}
if (list.size() == 0) toDelete.addLast(key);
}
for (var i = toDelete.size(); --i >= 0; ) this.atomTensors.remove(toDelete.get(i));

}, "JU.BS");
Clazz.defineMethod(c$, "setCapacity", 
function(nAtoms){
this.atomCapacity += nAtoms;
}, "~N");
Clazz.defineMethod(c$, "setAtomTensors", 
function(atomIndex, list){
if (list == null || list.size() == 0) return;
if (this.atomTensors == null) this.atomTensors =  new java.util.Hashtable();
if (this.atomTensorList == null) this.atomTensorList =  new Array(this.at.length);
this.atomTensorList = JU.AU.ensureLength(this.atomTensorList, this.at.length);
this.atomTensorList[atomIndex] = JM.AtomCollection.getTensorList(list);
for (var i = list.size(); --i >= 0; ) {
var t = list.get(i);
t.atomIndex1 = atomIndex;
t.atomIndex2 = -1;
t.modelIndex = this.at[atomIndex].mi;
this.addTensor(t, t.type);
if (t.altType != null) this.addTensor(t, t.altType);
}
}, "~N,JU.Lst");
Clazz.defineMethod(c$, "addTensor", 
function(t, type){
type = type.toLowerCase();
var tensors = this.atomTensors.get(type);
if (tensors == null) {
this.atomTensors.put(type, tensors =  new JU.Lst());
tensors.ensureCapacity(this.atomCapacity);
}tensors.addLast(t);
}, "JU.Tensor,~S");
c$.getTensorList = Clazz.defineMethod(c$, "getTensorList", 
function(list){
var pt = -1;
var haveTLS = false;
var n = list.size();
for (var i = n; --i >= 0; ) {
var t = list.get(i);
if (t.forThermalEllipsoid) pt = i;
 else if (t.iType == 2) haveTLS = true;
}
var a =  new Array((pt >= 0 || !haveTLS ? 0 : 1) + n);
if (pt >= 0) {
a[0] = list.get(pt);
if (list.size() == 1) return a;
}if (haveTLS) {
pt = 0;
for (var i = n; --i >= 0; ) {
var t = list.get(i);
if (t.forThermalEllipsoid) continue;
a[++pt] = t;
}
} else {
for (var i = 0; i < n; i++) a[i] = list.get(i);

}return a;
}, "JU.Lst");
Clazz.defineMethod(c$, "getAtomTensor", 
function(i, type){
var tensors = this.getAtomTensorList(i);
if (tensors != null && type != null) {
type = type.toLowerCase();
for (var j = 0; j < tensors.length; j++) {
var t = tensors[j];
if (t != null && (type.equals(t.type) || type.equals(t.altType))) return t;
}
}return null;
}, "~N,~S");
Clazz.defineMethod(c$, "getAllAtomTensors", 
function(type){
if (this.atomTensors == null) return null;
if (type != null) return this.atomTensors.get(type.toLowerCase());
var list =  new JU.Lst();
for (var e, $e = this.atomTensors.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) list.addAll(e.getValue());

return list;
}, "~S");
Clazz.defineMethod(c$, "scaleVectorsToMax", 
function(max){
if (this.vibrations == null) return;
var m = 0;
var bsVib = JU.BS.newN(this.ac);
for (var i = this.vibrations.length; --i >= 0; ) {
var v = this.getVibration(i, false);
if (v != null && (v.modDim == -1 || v.modDim == -2)) {
m = Math.max(m, v.length());
bsVib.set(i);
}}
if (m == max || m == 0) return;
m = max / m;
var ok = false;
for (var i = bsVib.nextSetBit(0); i >= 0; i = bsVib.nextSetBit(i + 1)) {
var v = this.getVibration(i, false);
var mod = this.getModulation(i);
if (mod == null) {
if (m == 0) return;
v.scale(m);
} else {
mod.scaleVibration(m);
}if (!ok) {
this.taintAtom(i, 12);
ok = true;
}}
this.tainted[12].or(bsVib);
}, "~N");
Clazz.defineMethod(c$, "getAtomsFromAtomNumberInFrame", 
function(atomNumber){
var bs = this.vwr.getFrameAtoms();
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) if (this.at[i].getAtomNumber() != atomNumber) bs.clear(i);

return bs;
}, "~N");
Clazz.defineMethod(c$, "generateCrystalClass", 
function(atomIndex, pt){
var sym = (atomIndex < 0 || atomIndex >= this.ac ? this.vwr.getOperativeSymmetry() : this.at[atomIndex].getUnitCell());
var isRandom = (pt != null && Float.isNaN(pt.x));
var ret = (sym == null ? null : sym.generateCrystalClass(isRandom ? null : pt != null ? pt : this.at[atomIndex]));
return (ret == null ?  new JU.Lst() : ret);
}, "~N,JU.P3");
c$.isDeleted = Clazz.defineMethod(c$, "isDeleted", 
function(atom){
return (atom == null || atom.isDeleted());
}, "JM.Atom");
c$.$AtomCollection$AtomSorter$ = function(){
/*if4*/;(function(){
var c$ = Clazz.decorateAsClass(function(){
Clazz.prepareCallback(this, arguments);
Clazz.instantialize(this, arguments);}, JM.AtomCollection, "AtomSorter", null, java.util.Comparator);
Clazz.overrideMethod(c$, "compare", 
function(a1, a2){
return (a1.i > a2.i ? 1 : a1.i < a2.i ? -1 : 0);
}, "JM.Atom,JM.Atom");
/*eoif4*/})();
};
c$.sqrt3_2 = Math.sqrt(3) / 2;
c$.vRef = JU.V3.new3(3.14159, 2.71828, 1.41421);
c$.userSettableValues = null;
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
