Clazz.declarePackage("JM");
Clazz.load(["JU.Node", "$.Point3fi", "J.c.PAL"], "JM.Atom", ["JU.BS", "$.CU", "$.P3", "$.PT", "$.SB", "J.atomdata.RadiusData", "J.c.VDW", "JM.Group", "JU.C", "$.Elements", "JV.JC"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.altloc = '\0';
this.atomID = 0;
this.atomSite = 0;
this.group = null;
this.userDefinedVanDerWaalRadius = 0;
this.valence = 0;
this.atomNumberFlags = 0;
this.atomSymmetry = null;
this.formalChargeAndFlags = 0;
this.madAtom = 0;
this.colixAtom = 0;
this.paletteID = 0;
this.bonds = null;
this.nBondsDisplayed = 0;
this.nBackbonesDisplayed = 0;
this.clickabilityFlags = 0;
this.shapeVisibilityFlags = 0;
Clazz.instantialize(this, arguments);}, JM, "Atom", JU.Point3fi, JU.Node);
Clazz.prepareFields (c$, function(){
this.paletteID = J.c.PAL.CPK.id;
});
Clazz.overrideMethod(c$, "setAtom", 
function(modelIndex, atomIndex, xyz, radius, atomSymmetry, atomSite, atomicAndIsotopeNumber, formalCharge, isHetero, isNegDisorder){
this.mi = modelIndex;
this.atomSymmetry = atomSymmetry;
this.atomSite = atomSite;
this.i = atomIndex;
this.atomNumberFlags = atomicAndIsotopeNumber;
if (isHetero) this.formalChargeAndFlags = 2;
if (formalCharge != 0 && formalCharge != -2147483648) this.setFormalCharge(formalCharge);
this.userDefinedVanDerWaalRadius = radius;
if (xyz != null) this.setT(xyz);
return this;
}, "~N,~N,JU.P3,~N,JU.BS,~N,~N,~N,~B,~B");
Clazz.defineMethod(c$, "setShapeVisibility", 
function(flag, isVisible){
if (isVisible) this.shapeVisibilityFlags |= flag;
 else this.shapeVisibilityFlags &= ~flag;
}, "~N,~B");
Clazz.defineMethod(c$, "isCovalentlyBonded", 
function(atomOther){
if (this.bonds != null) for (var i = this.bonds.length; --i >= 0; ) if (this.bonds[i].isCovalent() && this.bonds[i].getOtherAtom(this) === atomOther) return true;

return false;
}, "JM.Atom");
Clazz.defineMethod(c$, "isBonded", 
function(atomOther){
if (this.bonds != null) for (var i = this.bonds.length; --i >= 0; ) if (this.bonds[i].getOtherAtom(this) === atomOther) return true;

return false;
}, "JM.Atom");
Clazz.defineMethod(c$, "getBond", 
function(atomOther){
if (this.bonds != null) for (var i = this.bonds.length; --i >= 0; ) if (this.bonds[i].getOtherAtom(atomOther) != null) return this.bonds[i];

return null;
}, "JM.Atom");
Clazz.defineMethod(c$, "addDisplayedBond", 
function(stickVisibilityFlag, isVisible){
this.nBondsDisplayed += (isVisible ? 1 : -1);
this.setShapeVisibility(stickVisibilityFlag, (this.nBondsDisplayed > 0));
}, "~N,~B");
Clazz.defineMethod(c$, "deleteBond", 
function(bond){
if (this.bonds != null) for (var i = this.bonds.length; --i >= 0; ) if (this.bonds[i] === bond) {
this.deleteBondAt(i);
return;
}
}, "JM.Bond");
Clazz.defineMethod(c$, "deleteBondAt", 
function(i){
this.setCIPChirality(0);
var newLength = this.bonds.length - 1;
if (newLength == 0) {
this.bonds = null;
return;
}var bondsNew =  new Array(newLength);
var j = 0;
for (; j < i; ++j) bondsNew[j] = this.bonds[j];

for (; j < newLength; ++j) bondsNew[j] = this.bonds[j + 1];

this.bonds = bondsNew;
}, "~N");
Clazz.overrideMethod(c$, "getBondedAtomIndex", 
function(bondIndex){
return this.bonds[bondIndex].getOtherAtom(this).i;
}, "~N");
Clazz.defineMethod(c$, "setMadAtom", 
function(vwr, rd){
this.madAtom = this.calculateMad(vwr, rd);
}, "JV.Viewer,J.atomdata.RadiusData");
Clazz.defineMethod(c$, "calculateMad", 
function(vwr, rd){
if (rd == null) return 0;
var f = rd.value;
if (f == 0) return 0;
switch (rd.factorType) {
case J.atomdata.RadiusData.EnumType.SCREEN:
return Clazz.floatToShort(f);
case J.atomdata.RadiusData.EnumType.FACTOR:
case J.atomdata.RadiusData.EnumType.OFFSET:
var r = 0;
switch (rd.vdwType) {
case J.c.VDW.TEMP:
var tmax = vwr.ms.getBfactor100Hi();
r = (tmax > 0 ? this.getBfactor100() / tmax : 0);
break;
case J.c.VDW.HYDRO:
r = Math.abs(this.getHydrophobicity());
break;
case J.c.VDW.BONDING:
r = this.getBondingRadius();
break;
case J.c.VDW.ADPMIN:
case J.c.VDW.ADPMAX:
r = this.getADPMinMax(rd.vdwType === J.c.VDW.ADPMAX);
break;
default:
r = this.getVanderwaalsRadiusFloat(vwr, rd.vdwType);
}
if (rd.factorType === J.atomdata.RadiusData.EnumType.FACTOR) f *= r;
 else f += r;
break;
case J.atomdata.RadiusData.EnumType.ABSOLUTE:
if (f == 16.1) return JM.Atom.MAD_GLOBAL;
break;
}
var mad = Clazz.floatToShort(f < 0 ? f : f * 2000);
if (mad < 0 && f > 0) mad = 0;
return mad;
}, "JV.Viewer,J.atomdata.RadiusData");
Clazz.defineMethod(c$, "getADPMinMax", 
function(isMax){
var tensors = this.getTensors();
if (tensors == null) return 0;
var t = tensors[0];
if (t == null || t.iType != 1) return 0;
if (this.group.chain.model.ms.isModulated(this.i) && t.isUnmodulated) t = tensors[1];
return t.getFactoredValue(isMax ? 2 : 1);
}, "~B");
Clazz.defineMethod(c$, "getTensors", 
function(){
return this.group.chain.model.ms.getAtomTensorList(this.i);
});
Clazz.defineMethod(c$, "getRasMolRadius", 
function(){
return Math.abs(Clazz.doubleToInt(this.madAtom / 8));
});
Clazz.overrideMethod(c$, "getEdges", 
function(){
return (this.bonds == null ?  new Array(0) : this.bonds);
});
Clazz.overrideMethod(c$, "getBondCount", 
function(){
return (this.bonds == null ? 0 : this.bonds.length);
});
Clazz.defineMethod(c$, "setTranslucent", 
function(isTranslucent, translucentLevel){
this.colixAtom = JU.C.getColixTranslucent3(this.colixAtom, isTranslucent, translucentLevel);
}, "~B,~N");
Clazz.overrideMethod(c$, "getElementNumber", 
function(){
return JU.Elements.getElementNumber(this.atomNumberFlags);
});
Clazz.overrideMethod(c$, "getIsotopeNumber", 
function(){
return JU.Elements.getIsotopeNumber(this.atomNumberFlags);
});
Clazz.overrideMethod(c$, "getAtomicAndIsotopeNumber", 
function(){
return this.atomNumberFlags;
});
Clazz.defineMethod(c$, "setAtomicAndIsotopeNumber", 
function(n){
if (n < 0 || (n & 127) >= JU.Elements.elementNumberMax || n > 32767) n = 0;
this.atomNumberFlags = n;
}, "~N");
Clazz.defineMethod(c$, "getElementSymbolIso", 
function(withIsotope){
return JU.Elements.elementSymbolFromNumber(withIsotope ? this.atomNumberFlags : this.atomNumberFlags & 127);
}, "~B");
Clazz.defineMethod(c$, "getElementSymbol", 
function(){
return this.getElementSymbolIso(true);
});
Clazz.defineMethod(c$, "isHetero", 
function(){
return (this.formalChargeAndFlags & 2) != 0;
});
Clazz.defineMethod(c$, "hasVibration", 
function(){
return (this.formalChargeAndFlags & 1) != 0;
});
Clazz.defineMethod(c$, "setFormalCharge", 
function(charge){
this.formalChargeAndFlags = (this.formalChargeAndFlags & 15) | ((charge == -2147483648 ? 0 : charge > 7 ? 7 : charge < -3 ? -3 : charge) << 24);
}, "~N");
Clazz.defineMethod(c$, "setVibrationVector", 
function(){
this.formalChargeAndFlags |= 1;
});
Clazz.defineMethod(c$, "setNegativeDisorder", 
function(){
this.formalChargeAndFlags |= 4;
});
Clazz.defineMethod(c$, "isNegativeDisorder", 
function(){
return ((this.formalChargeAndFlags & 4) != 0);
});
Clazz.overrideMethod(c$, "getFormalCharge", 
function(){
return this.formalChargeAndFlags >> 24;
});
Clazz.defineMethod(c$, "getOccupancy100", 
function(){
var occupancies = this.group.chain.model.ms.occupancies;
return (occupancies == null ? 100 : Math.round(occupancies[this.i]));
});
Clazz.defineMethod(c$, "isOccupied", 
function(){
var occupancies = this.group.chain.model.ms.occupancies;
return (occupancies == null || occupancies[this.i] >= 50);
});
Clazz.defineMethod(c$, "getBfactor100", 
function(){
var bfactor100s = this.group.chain.model.ms.bfactor100s;
return (bfactor100s == null ? 0 : bfactor100s[this.i]);
});
Clazz.defineMethod(c$, "getHydrophobicity", 
function(){
var values = this.group.chain.model.ms.hydrophobicities;
return (values == null ? JU.Elements.getHydrophobicity(this.group.groupID) : values[this.i]);
});
Clazz.defineMethod(c$, "setRadius", 
function(radius){
return !Float.isNaN(this.userDefinedVanDerWaalRadius = (radius > 0 ? radius : NaN));
}, "~N");
Clazz.defineMethod(c$, "$delete", 
function(bsBonds){
this.valence = -1;
if (this.bonds != null) for (var i = this.bonds.length; --i >= 0; ) {
var bond = this.bonds[i];
bond.getOtherAtom(this).deleteBond(bond);
bsBonds.set(bond.index);
}
this.bonds = null;
}, "JU.BS");
Clazz.overrideMethod(c$, "isDeleted", 
function(){
return (this.valence < 0);
});
Clazz.defineMethod(c$, "setValence", 
function(nBonds){
if (!this.isDeleted()) this.valence = (nBonds < 0 ? 0 : nBonds <= 0x7F ? nBonds : 0x7F);
}, "~N");
Clazz.overrideMethod(c$, "getValence", 
function(){
return (this.isDeleted() ? -1 : this.valence > 0 ? this.valence : this.getValenceAromatic(true));
});
Clazz.defineMethod(c$, "getValenceAromatic", 
function(checkAromatic){
if (this.isDeleted()) return -1;
var n = this.valence;
if (n == 0 && this.bonds != null) {
var npartial = 0;
for (var i = this.bonds.length; --i >= 0; ) {
n += this.bonds[i].getValence();
if (checkAromatic && this.bonds[i].is(515)) npartial++;
}
if (n > 0 && n < 3 && npartial != 0) n++;
}return n;
}, "~B");
Clazz.overrideMethod(c$, "getCovalentBondCount", 
function(){
if (this.bonds == null) return 0;
var n = 0;
for (var i = this.bonds.length; --i >= 0; ) {
var b = this.bonds[i];
if (b.isCovalentNotPartial0() && !b.getOtherAtom(this).isDeleted()) ++n;
}
return n;
});
Clazz.defineMethod(c$, "getCovalentOrPartialBondCount", 
function(){
if (this.bonds == null) return 0;
var n = 0;
for (var i = this.bonds.length; --i >= 0; ) {
var b = this.bonds[i];
if (b.isCovalent() && !b.getOtherAtom(this).isDeleted()) ++n;
}
return n;
});
Clazz.overrideMethod(c$, "getCovalentHydrogenCount", 
function(){
if (this.bonds == null) return 0;
var n = 0;
for (var i = this.bonds.length; --i >= 0; ) {
var b = this.bonds[i];
if (b.isCovalentNotPartial0()) {
var a = this.bonds[i].getOtherAtom(this);
if (a.valence >= 0 && a.getElementNumber() == 1) ++n;
}}
return n;
});
Clazz.overrideMethod(c$, "getImplicitHydrogenCount", 
function(){
return this.group.chain.model.ms.getMissingHydrogenCount(this, false);
});
Clazz.overrideMethod(c$, "getTotalHydrogenCount", 
function(){
return this.getCovalentHydrogenCount() + this.getImplicitHydrogenCount();
});
Clazz.overrideMethod(c$, "getTotalValence", 
function(){
var v = this.getValence();
if (v < 0) return v;
var h = this.getImplicitHydrogenCount();
var sp2 = this.group.chain.model.ms.aaRet[4];
return v + h + sp2;
});
Clazz.overrideMethod(c$, "getCovalentBondCountPlusMissingH", 
function(){
return this.getCovalentBondCount() + this.getImplicitHydrogenCount();
});
Clazz.defineMethod(c$, "getTargetValence", 
function(){
switch (this.getElementNumber()) {
case 6:
case 14:
case 32:
return 4;
case 5:
case 7:
case 15:
return 3;
case 8:
case 16:
return 2;
case 1:
case 9:
case 17:
case 35:
case 53:
return 1;
}
return -1;
});
Clazz.defineMethod(c$, "getDimensionValue", 
function(dimension){
return (dimension == 0 ? this.x : (dimension == 1 ? this.y : this.z));
}, "~N");
Clazz.defineMethod(c$, "getVanderwaalsRadiusFloat", 
function(vwr, type){
return (Float.isNaN(this.userDefinedVanDerWaalRadius) ? vwr.getVanderwaalsMarType(this.atomNumberFlags, this.getVdwType(type)) / 1000 : this.userDefinedVanDerWaalRadius);
}, "JV.Viewer,J.c.VDW");
Clazz.defineMethod(c$, "getVdwType", 
function(type){
switch (type) {
case J.c.VDW.AUTO:
type = this.group.chain.model.ms.getDefaultVdwType(this.mi);
break;
case J.c.VDW.NOJMOL:
type = this.group.chain.model.ms.getDefaultVdwType(this.mi);
if (type === J.c.VDW.AUTO_JMOL) type = J.c.VDW.AUTO_BABEL;
break;
}
return type;
}, "J.c.VDW");
Clazz.defineMethod(c$, "getBondingRadius", 
function(){
var rr = this.group.chain.model.ms.bondingRadii;
var r = (rr == null || this.i >= rr.length ? 0 : rr[this.i]);
return (r == 0 ? JU.Elements.getBondingRadius(this.atomNumberFlags, this.getFormalCharge()) : r);
});
Clazz.defineMethod(c$, "getVolume", 
function(vwr, vType){
var r1 = (vType == null ? this.userDefinedVanDerWaalRadius : NaN);
if (Float.isNaN(r1)) r1 = vwr.getVanderwaalsMarType(this.getElementNumber(), this.getVdwType(vType)) / 1000;
var volume = 0;
if (this.bonds != null) for (var j = 0; j < this.bonds.length; j++) {
if (!this.bonds[j].isCovalent()) continue;
var atom2 = this.bonds[j].getOtherAtom(this);
var r2 = (vType == null ? atom2.userDefinedVanDerWaalRadius : NaN);
if (Float.isNaN(r2)) r2 = vwr.getVanderwaalsMarType(atom2.getElementNumber(), atom2.getVdwType(vType)) / 1000;
var d = this.distance(atom2);
if (d > r1 + r2) continue;
if (d + r1 <= r2) return 0;
var h = r1 - (r1 * r1 + d * d - r2 * r2) / (2.0 * d);
volume -= 1.0471975511965976 * h * h * (3 * r1 - h);
}
return (volume + 4.1887902047863905 * r1 * r1 * r1);
}, "JV.Viewer,J.c.VDW");
Clazz.defineMethod(c$, "getCurrentBondCount", 
function(){
return this.bonds == null ? 0 : this.bonds.length;
});
Clazz.defineMethod(c$, "getRadius", 
function(){
return Math.abs(this.madAtom / 2000);
});
Clazz.overrideMethod(c$, "getIndex", 
function(){
return this.i;
});
Clazz.overrideMethod(c$, "getAtomSite", 
function(){
return this.atomSite;
});
Clazz.overrideMethod(c$, "getGroupBits", 
function(bs){
this.group.setAtomBits(bs);
}, "JU.BS");
Clazz.overrideMethod(c$, "getAtomName", 
function(){
return (this.atomID > 0 ? JM.Group.specialAtomNames[this.atomID] : this.group.chain.model.ms.atomNames == null ? "" : this.group.chain.model.ms.atomNames[this.i]);
});
Clazz.overrideMethod(c$, "getAtomType", 
function(){
var atomTypes = this.group.chain.model.ms.atomTypes;
var type = (atomTypes == null ? null : atomTypes[this.i]);
return (type == null ? this.getAtomName() : type);
});
Clazz.overrideMethod(c$, "getAtomNumber", 
function(){
var atomSerials = this.group.chain.model.ms.atomSerials;
return (atomSerials == null ? this.i : atomSerials[this.i]);
});
Clazz.defineMethod(c$, "getSeqID", 
function(){
var ids = this.group.chain.model.ms.atomSeqIDs;
return (ids == null ? 0 : ids[this.i]);
});
Clazz.defineMethod(c$, "isVisible", 
function(flags){
return ((this.shapeVisibilityFlags & flags) == flags);
}, "~N");
Clazz.defineMethod(c$, "getPartialCharge", 
function(){
var partialCharges = this.group.chain.model.ms.partialCharges;
return partialCharges == null ? 0 : partialCharges[this.i];
});
Clazz.defineMethod(c$, "getSymmetryTranslation", 
function(symop, cellRange, nOps){
var pt = symop;
for (var i = 0; i < cellRange.length; i++) if (this.atomSymmetry.get(pt += nOps)) return cellRange[i];

return 0;
}, "~N,~A,~N");
Clazz.defineMethod(c$, "getCellTranslation", 
function(cellNNN, cellRange, nOps){
var pt = nOps;
for (var i = 0; i < cellRange.length; i++) for (var j = 0; j < nOps; j++, pt++) if (this.atomSymmetry.get(pt) && cellRange[i] == cellNNN) return cellRange[i];


return 0;
}, "~N,~A,~N");
Clazz.defineMethod(c$, "getSymmetryOperatorList", 
function(isAll){
var str = "";
var f = this.group.chain.model.ms;
var nOps = f.getModelSymmetryCount(this.mi);
if (nOps == 0 || this.atomSymmetry == null) return "";
var cellRange = f.getModelCellRange(this.mi);
var pt = nOps;
var n = (cellRange == null ? 1 : cellRange.length);
var bs = (isAll ? null :  new JU.BS());
for (var i = 0; i < n; i++) for (var j = 0; j < nOps; j++) if (this.atomSymmetry.get(pt++)) if (isAll) {
str += "," + (j + 1) + (cellRange == null ? 555 : cellRange[i]);
} else {
bs.set(j + 1);
}

if (!isAll) for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) str += "," + i;

return (str.length == 0 ? "" : str.substring(1));
}, "~B");
Clazz.overrideMethod(c$, "getModelIndex", 
function(){
return this.mi;
});
Clazz.overrideMethod(c$, "getMoleculeNumber", 
function(inModel){
return (this.group.chain.model.ms.getMoleculeIndex(this.i, inModel) + 1);
}, "~B");
Clazz.defineMethod(c$, "getFractionalCoord", 
function(fixJavaFloat, ch, ignoreOffset, pt){
pt = this.getFractionalCoordPt(fixJavaFloat, ignoreOffset, pt);
return (ch == 'X' ? pt.x : ch == 'Y' ? pt.y : pt.z);
}, "~B,~S,~B,JU.P3");
Clazz.overrideMethod(c$, "getXYZ", 
function(){
return this;
});
Clazz.defineMethod(c$, "getFractionalCoordPt", 
function(fixJavaFloat, ignoreOffset, pt){
var c = this.getUnitCell();
if (pt == null) pt = JU.P3.newP(this);
 else pt.setT(this);
if (c != null) {
c = c.getUnitCellMultiplied();
c.toFractional(pt, ignoreOffset);
if (fixJavaFloat) JU.PT.fixPtFloats(pt, 100000.0);
}return pt;
}, "~B,~B,JU.P3");
Clazz.defineMethod(c$, "getUnitCell", 
function(){
return this.group.chain.model.ms.getUnitCellForAtom(this.i);
});
Clazz.defineMethod(c$, "getFractionalUnitCoord", 
function(fixJavaFloat, ch, pt){
pt = this.getFractionalUnitCoordPt(fixJavaFloat, false, pt);
return (ch == 'X' ? pt.x : ch == 'Y' ? pt.y : pt.z);
}, "~B,~S,JU.P3");
Clazz.defineMethod(c$, "getFractionalUnitCoordPt", 
function(fixJavaFloat, asCartesian, pt){
var c = this.getUnitCell();
if (pt == null) pt = JU.P3.newP(this);
 else pt.setT(this);
if (c == null) return pt;
c = c.getUnitCellMultiplied();
if (this.group.chain.model.isJmolDataFrame) {
c.toFractional(pt, false);
if (asCartesian) c.toCartesian(pt, false);
} else {
c.toUnitCell(pt, null);
if (!asCartesian) c.toFractional(pt, false);
}if (fixJavaFloat) JU.PT.fixPtFloats(pt, asCartesian ? 10000.0 : 100000.0);
return pt;
}, "~B,~B,JU.P3");
Clazz.defineMethod(c$, "getFractionalUnitDistance", 
function(pt, ptTemp1, ptTemp2){
var c = this.getUnitCell();
if (c == null) return this.distance(pt);
ptTemp1.setT(this);
ptTemp2.setT(pt);
if (this.group.chain.model.isJmolDataFrame) {
c.toFractional(ptTemp1, true);
c.toFractional(ptTemp2, true);
} else {
c.toUnitCell(ptTemp1, null);
c.toUnitCell(ptTemp2, null);
}return ptTemp1.distance(ptTemp2);
}, "JU.T3,JU.T3,JU.T3");
Clazz.defineMethod(c$, "setFractionalCoord", 
function(tok, fValue, asAbsolute){
var c = this.getUnitCell();
if (c != null) c.toFractional(this, asAbsolute);
switch (tok) {
case 1111492615:
case 1111492612:
this.x = fValue;
break;
case 1111492616:
case 1111492613:
this.y = fValue;
break;
case 1111492617:
case 1111492614:
this.z = fValue;
break;
}
if (c != null) c.toCartesian(this, asAbsolute);
}, "~N,~N,~B");
Clazz.defineMethod(c$, "setFractionalCoordTo", 
function(ptNew, asAbsolute){
this.setFractionalCoordPt(this, ptNew, asAbsolute);
}, "JU.P3,~B");
Clazz.defineMethod(c$, "setFractionalCoordPt", 
function(pt, ptNew, asAbsolute){
pt.setT(ptNew);
var c = this.getUnitCell();
if (c != null) c.toCartesian(pt, asAbsolute && !this.group.chain.model.isJmolDataFrame);
}, "JU.P3,JU.P3,~B");
Clazz.defineMethod(c$, "isCursorOnTopOf", 
function(xCursor, yCursor, minRadius, competitor){
var r = Clazz.doubleToInt(this.sD / 2);
if (r < minRadius) r = minRadius;
var r2 = r * r;
var dx = this.sX - xCursor;
var dx2 = dx * dx;
if (dx2 > r2) return false;
var dy = this.sY - yCursor;
var dy2 = dy * dy;
var dz2 = r2 - (dx2 + dy2);
if (dz2 < 0) return false;
if (competitor == null) return true;
var z = this.sZ;
var zCompetitor = competitor.sZ;
var rCompetitor = Clazz.doubleToInt(competitor.sD / 2);
if (z < zCompetitor - rCompetitor) return true;
var dxCompetitor = competitor.sX - xCursor;
var dx2Competitor = dxCompetitor * dxCompetitor;
var dyCompetitor = competitor.sY - yCursor;
var dy2Competitor = dyCompetitor * dyCompetitor;
var r2Competitor = rCompetitor * rCompetitor;
var dz2Competitor = r2Competitor - (dx2Competitor + dy2Competitor);
return (z - Math.sqrt(dz2) < zCompetitor - Math.sqrt(dz2Competitor));
}, "~N,~N,~N,JM.Atom");
Clazz.defineMethod(c$, "getInfo", 
function(){
return this.getIdentity(2);
});
Clazz.defineMethod(c$, "getIdentityXYZ", 
function(pt, mode){
pt = (mode == 3 || this.group.chain.model.isJmolDataFrame ? this.getFractionalCoordPt(!this.group.chain.model.ms.vwr.g.legacyJavaFloat, false, pt) : this);
var s = (mode == 3 ? "" : this.getIdentity(mode) + " ") + JU.PT.formatF(pt.x, 0, 3, true, true) + " " + JU.PT.formatF(pt.y, 0, 3, true, true) + " " + JU.PT.formatF(pt.z, 0, 3, true, true);
return s;
}, "JU.P3,~N");
Clazz.defineMethod(c$, "getIdentity", 
function(mode){
var info =  new JU.SB();
var group3 = this.getGroup3(true);
if (group3 != null && group3.length > 0 && (!group3.equals("UNK") || this.group.chain.model.isBioModel)) {
info.append("[");
info.append(group3);
info.append("]");
var seqcodeString = this.group.getSeqcodeString();
if (seqcodeString != null) info.append(seqcodeString);
var chainID = this.group.chain.chainID;
if (chainID != 0 && chainID != 32) {
info.append(":");
var s = this.getChainIDStr();
if (chainID >= 256) s = JU.PT.esc(s);
info.append(s);
}if (mode != 2 && mode != 5) return info.toString();
info.append(".");
}info.append(this.getAtomName());
if (info.length() == 0) {
info.append(this.getElementSymbolIso(false));
info.append(" ");
info.appendI(this.getAtomNumber());
}if (mode == 2) {
if (this.altloc != '\0') {
info.append("%");
info.appendC(this.altloc);
}if (this.group.chain.model.ms.mc > 1 && !this.group.chain.model.isJmolDataFrame) {
info.append("/");
info.append(this.getModelNumberForLabel());
}info.append(" #");
info.appendI(this.getAtomNumber());
}return info.toString();
}, "~N");
Clazz.overrideMethod(c$, "getGroup3", 
function(allowNull){
var group3 = this.group.getGroup3();
return (allowNull || group3 != null && group3.length > 0 ? group3 : "UNK");
}, "~B");
Clazz.overrideMethod(c$, "getGroup1", 
function(c0){
var c = this.group.getGroup1();
return (c != '\0' ? "" + c : c0 != '\0' ? "" + c0 : "");
}, "~S");
Clazz.overrideMethod(c$, "getBioSmilesType", 
function(){
return (this.group.isProtein() ? 'p' : this.group.isDna() ? 'd' : this.group.isRna() ? 'r' : this.group.isCarbohydrate() ? 'c' : ' ');
});
Clazz.overrideMethod(c$, "isPurine", 
function(){
return this.group.isPurine();
});
Clazz.overrideMethod(c$, "isPyrimidine", 
function(){
return this.group.isPyrimidine();
});
Clazz.overrideMethod(c$, "getResno", 
function(){
return this.group.getResno();
});
Clazz.defineMethod(c$, "isClickable", 
function(){
return (this.checkVisible() && this.clickabilityFlags != 0 && ((this.shapeVisibilityFlags | this.group.shapeVisibilityFlags) & this.clickabilityFlags) != 0);
});
Clazz.defineMethod(c$, "setClickable", 
function(flag){
if (flag == 0) {
this.clickabilityFlags = 0;
} else {
this.clickabilityFlags |= flag;
if (flag != 1040384) this.shapeVisibilityFlags |= flag;
}}, "~N");
Clazz.defineMethod(c$, "checkVisible", 
function(){
if (this.isVisible(2)) return this.isVisible(4);
var isVis = this.isVisible(9);
if (isVis) {
var flags = this.shapeVisibilityFlags;
if (this.group.shapeVisibilityFlags != 0 && (this.group.shapeVisibilityFlags != 8192 || this.isLeadAtom())) flags |= this.group.shapeVisibilityFlags;
flags &= -10;
if (flags == 32 && this.clickabilityFlags == 0) flags = 0;
isVis = (flags != 0);
if (isVis) this.shapeVisibilityFlags |= 4;
}this.shapeVisibilityFlags |= 2;
return isVis;
});
Clazz.overrideMethod(c$, "isLeadAtom", 
function(){
return this.group.isLeadAtom(this.i);
});
Clazz.overrideMethod(c$, "getChainID", 
function(){
return this.group.chain.chainID;
});
Clazz.overrideMethod(c$, "getChainIDStr", 
function(){
return this.group.chain.getIDStr();
});
Clazz.defineMethod(c$, "getSurfaceDistance100", 
function(){
return this.group.chain.model.ms.getSurfaceDistance100(this.i);
});
Clazz.defineMethod(c$, "getVibrationVector", 
function(){
return this.group.chain.model.ms.getVibration(this.i, false);
});
Clazz.defineMethod(c$, "getModulation", 
function(){
return this.group.chain.model.ms.getModulation(this.i);
});
Clazz.defineMethod(c$, "getModelNumberForLabel", 
function(){
return this.group.chain.model.ms.getModelNumberForAtomLabel(this.mi);
});
Clazz.defineMethod(c$, "getModelNumber", 
function(){
return this.group.chain.model.ms.getModelNumber(this.mi) % 1000000;
});
Clazz.overrideMethod(c$, "getBioStructureTypeName", 
function(){
return this.group.getProteinStructureType().getBioStructureTypeName(true);
});
Clazz.overrideMethod(c$, "equals", 
function(obj){
return (this === obj);
}, "~O");
Clazz.overrideMethod(c$, "hashCode", 
function(){
return this.i;
});
Clazz.defineMethod(c$, "findAromaticNeighbor", 
function(notAtomIndex){
if (this.bonds == null) return null;
for (var i = this.bonds.length; --i >= 0; ) {
var bondT = this.bonds[i];
var a = bondT.getOtherAtom(this);
if (bondT.isAromatic() && a.i != notAtomIndex) return a;
}
return null;
}, "~N");
Clazz.defineMethod(c$, "atomPropertyInt", 
function(tokWhat){
switch (tokWhat) {
case 1094715393:
return this.getAtomNumber();
case 1094713365:
return this.getSeqID();
case 1094713346:
return this.atomID;
case 1094713368:
return Math.max(0, this.altloc.charCodeAt(0) - 32);
case 1094713347:
return this.i;
case 1228931586:
return this.getCovalentBondCount();
case 1094713351:
return this.group.chain.chainNo;
case 1765808134:
return this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom);
case 1086326789:
case 1094715402:
return this.getElementNumber();
case 1094713353:
return this.atomNumberFlags;
case 1228935687:
return this.group.chain.model.fileIndex + 1;
case 1631586315:
return this.getFormalCharge();
case 1094713356:
return this.group.groupID;
case 1094713357:
return this.group.groupIndex;
case 1094717454:
return this.getModelNumber();
case -1094717454:
return this.group.chain.model.ms.modelFileNumbers[this.mi];
case 1094713359:
return this.mi;
case 1094713360:
return this.getMoleculeNumber(true);
case 1094713361:
return this.group.getMonomerIndex() + 1;
case 1128269825:
return this.getOccupancy100();
case 1094713362:
return this.group.getBioPolymerIndexInModel() + 1;
case 1094713363:
return this.group.getBioPolymerLength();
case 1665140738:
return this.getRasMolRadius();
case 1094715412:
return this.getResno();
case 1094713366:
return this.getAtomSite();
case 1639976963:
return this.group.getProteinStructureType().getId();
case 1237320707:
return this.group.getProteinStructureSubType().getId();
case 1094713367:
return this.group.getStrucNo();
case 1296041985:
return this.getSymOp();
case 1094715418:
return this.getValence();
}
return 0;
}, "~N");
Clazz.defineMethod(c$, "getSymOp", 
function(){
return (this.atomSymmetry == null ? 0 : this.atomSymmetry.nextSetBit(0) + 1);
});
Clazz.defineMethod(c$, "atomPropertyFloat", 
function(vwr, tokWhat, ptTemp){
switch (tokWhat) {
case 1111490561:
return this.getADPMinMax(true);
case 1111490562:
return this.getADPMinMax(false);
case 1111492609:
case 1111492629:
return this.x;
case 1111492610:
case 1111492630:
return this.y;
case 1111492611:
case 1111492631:
return this.z;
case 1111490587:
return this.group.chain.model.ms.getAtomicDSSRData(this.i);
case 1114249217:
case 1112152066:
case 1112150019:
case 1112150020:
case 1112150021:
case 1112152070:
case 1112152071:
case 1112152073:
case 1112152074:
case 1112152076:
case 1649022989:
case 1112152078:
return vwr.shm.getAtomShapeValue(tokWhat, this.group, this.i);
case 1111492618:
return this.getBondingRadius();
case 1111490563:
return vwr.getNMRCalculation().getChemicalShift(this);
case 1111490564:
return JU.Elements.getCovalentRadius(this.atomNumberFlags);
case 1111490565:
case 1111490576:
case 1111490574:
return this.group.getGroupParameter(tokWhat);
case 1111492615:
case 1111492612:
return this.getFractionalCoord(!vwr.g.legacyJavaFloat, 'X', false, ptTemp);
case 1111492616:
case 1111492613:
return this.getFractionalCoord(!vwr.g.legacyJavaFloat, 'Y', false, ptTemp);
case 1111492617:
case 1111492614:
return this.getFractionalCoord(!vwr.g.legacyJavaFloat, 'Z', false, ptTemp);
case 1113589786:
return this.getHydrophobicity();
case 1111490566:
return vwr.getNMRCalculation().getMagneticShielding(this);
case 1111490567:
return this.getMass();
case 1128269825:
return this.getOccupancy100() / 100;
case 1111492619:
return this.getPartialCharge();
case 1111490569:
case 1111490570:
case 1111490568:
if (this.group.chain.model.isJmolDataFrame && this.group.chain.model.jmolFrameType.startsWith("plot ramachandran")) {
switch (tokWhat) {
case 1111490569:
return this.getFractionalCoord(!vwr.g.legacyJavaFloat, 'X', false, ptTemp);
case 1111490570:
return this.getFractionalCoord(!vwr.g.legacyJavaFloat, 'Y', false, ptTemp);
case 1111490568:
var omega = this.getFractionalCoord(!vwr.g.legacyJavaFloat, 'Z', false, ptTemp) - 180;
return (omega < -180 ? 360 + omega : omega);
}
}return this.group.getGroupParameter(tokWhat);
case 1665140738:
case 1112152075:
return this.getRadius();
case 1111490571:
return (vwr.antialiased ? Clazz.doubleToInt(this.sX / 2) : this.sX);
case 1111490572:
return vwr.getScreenHeight() - (vwr.antialiased ? Clazz.doubleToInt(this.sY / 2) : this.sY);
case 1111490573:
return (vwr.antialiased ? Clazz.doubleToInt(this.sZ / 2) : this.sZ);
case 1113589787:
return (vwr.slm.isAtomSelected(this.i) ? 1 : 0);
case 1111490575:
vwr.ms.getSurfaceDistanceMax();
return this.getSurfaceDistance100() / 100;
case 1111492620:
return this.getBfactor100() / 100;
case 1111490577:
return this.getFractionalUnitCoord(!vwr.g.legacyJavaFloat, 'X', ptTemp);
case 1111490578:
return this.getFractionalUnitCoord(!vwr.g.legacyJavaFloat, 'Y', ptTemp);
case 1111490579:
return this.getFractionalUnitCoord(!vwr.g.legacyJavaFloat, 'Z', ptTemp);
case 1648363544:
return this.getVanderwaalsRadiusFloat(vwr, J.c.VDW.AUTO);
case 1648361473:
var v = this.getVibrationVector();
return (v == null ? 0 : v.length() * vwr.getFloat(1648361473));
case 1111492626:
return this.getVib('x');
case 1111492627:
return this.getVib('y');
case 1111492628:
return this.getVib('z');
case 1111490583:
return this.getVib('X');
case 1111490584:
return this.getVib('Y');
case 1111490585:
return this.getVib('Z');
case 1111490586:
return this.getVib('O');
case 1111490580:
return this.getVib('1');
case 1111490581:
return this.getVib('2');
case 1111490582:
return this.getVib('3');
case 1312817669:
return this.getVolume(vwr, J.c.VDW.AUTO);
case 1145047050:
case 1145047053:
case 1145045006:
case 1145047052:
case 1145047055:
case 1145045008:
case 1145047049:
var v3 = this.atomPropertyTuple(vwr, tokWhat, ptTemp);
return (v3 == null ? -1 : v3.length());
}
return this.atomPropertyInt(tokWhat);
}, "JV.Viewer,~N,JU.P3");
Clazz.defineMethod(c$, "getVib", 
function(ch){
return this.group.chain.model.ms.getVibCoord(this.i, ch);
}, "~S");
Clazz.defineMethod(c$, "getNominalMass", 
function(){
var mass = this.getIsotopeNumber();
return (mass > 0 ? mass : JU.Elements.getNaturalIsotope(this.getElementNumber()));
});
Clazz.overrideMethod(c$, "getMass", 
function(){
var mass = this.getIsotopeNumber();
return (mass > 0 ? mass : JU.Elements.getAtomicMass(this.getElementNumber()));
});
Clazz.defineMethod(c$, "atomPropertyString", 
function(vwr, tokWhat){
var ch;
var s;
switch (tokWhat) {
case 1153433601:
return this.getIdentity(5);
case 1086324739:
ch = this.altloc;
return (ch == '\0' ? "" : "" + ch);
case 1086326786:
return this.getAtomName();
case 1086326785:
return this.getAtomType();
case 1086326788:
return this.getChainIDStr();
case 1086324752:
return this.getCIPChirality(true);
case 1086324753:
return this.getCIPChiralityRule();
case 1140850705:
case 1086324754:
return this.getWyckoffPosition(false);
case 1086324755:
return this.getWyckoffPosition(true);
case 1086324744:
return this.getGroup1('?');
case 1086324747:
s = this.group.getSeqcodeString();
return (s == null ? "" : s);
case 1086324743:
return this.getGroup1('\0');
case 1086324742:
return this.getGroup3(false);
case 1086326789:
return this.getElementSymbolIso(true);
case 1086324745:
return this.getIdentity(2);
case 1086324746:
ch = this.group.getInsertionCode();
return (ch == '\0' ? "" : "" + ch);
case 1825200146:
case 1287653388:
s = vwr.shm.getShapePropertyIndex(5, "label", this.i);
if (s == null) s = "";
return s;
case 1145045003:
return vwr.getSymStatic().staticToRationalXYZ(this.getFractionalCoordPt(!vwr.g.legacyJavaFloat, false, null), " ");
case 1639976963:
return this.group.getProteinStructureType().getBioStructureTypeName(false);
case 1237320707:
return this.group.getProteinStructureSubType().getBioStructureTypeName(false);
case 1086324749:
return this.group.getStructureId();
case 1086324748:
return vwr.getHybridizationAndAxes(this.i, null, null, "d");
case 1086326798:
return this.getElementSymbolIso(false);
case 1088421903:
return this.getSymmetryOperatorList(true);
}
return "";
}, "JV.Viewer,~N");
Clazz.defineMethod(c$, "getWyckoffPosition", 
function(withMultiplicity){
var ms = this.group.chain.model.ms;
var a = ms.getBasisAtom(this.i, true);
var id = a.getSeqID();
if (id != 0) {
var m = id >> 16;
var c = String.fromCharCode(id & 0xFF);
return (withMultiplicity ? "" + m : "") + c;
}var sym = this.getUnitCell();
var s;
if (sym == null || (s = sym.getWyckoffPosition(ms.vwr, this, "M")) == null) {
s = "0?";
}ms.setAtomSeqID(this.i, (JU.PT.parseInt(s) << 16) + (s.charAt(s.length - 1)).charCodeAt(0));
return (withMultiplicity ? s : s.substring(s.length - 1));
}, "~B");
Clazz.overrideMethod(c$, "getCIPChirality", 
function(doCalculate){
var flags = (this.formalChargeAndFlags & 496) >> 4;
if (flags == 0 && this.atomNumberFlags > 1 && doCalculate) {
flags = this.group.chain.model.ms.getAtomCIPChiralityCode(this);
this.formalChargeAndFlags |= ((flags == 0 ? 3 : flags) << 4);
}return JV.JC.getCIPChiralityName(flags);
}, "~B");
Clazz.defineMethod(c$, "getCIPChiralityRule", 
function(){
var rs = this.getCIPChirality(true);
var flags = (rs.length == 0 ? -1 : (this.formalChargeAndFlags & 3584) >> 9);
return JV.JC.getCIPRuleName(flags + 1);
});
Clazz.overrideMethod(c$, "setCIPChirality", 
function(c){
this.formalChargeAndFlags = (this.formalChargeAndFlags & -4081) | (c << 4);
}, "~N");
Clazz.overrideMethod(c$, "getCIPChiralityCode", 
function(){
return (this.formalChargeAndFlags & 496) >> 4;
});
Clazz.overrideMethod(c$, "getInsertionCode", 
function(){
return this.group.getInsertionCode();
});
Clazz.defineMethod(c$, "atomPropertyTuple", 
function(vwr, tok, ptTemp){
switch (tok) {
case 1073742329:
return JU.P3.newP(this);
case 1145047050:
return this.getFractionalCoordPt(!vwr.g.legacyJavaFloat, false, ptTemp);
case 1145047053:
return this.getFractionalCoordPt(!vwr.g.legacyJavaFloat, false, ptTemp);
case 1145045006:
return (this.group.chain.model.isJmolDataFrame ? this.getFractionalCoordPt(!vwr.g.legacyJavaFloat, false, ptTemp) : this.getFractionalUnitCoordPt(!vwr.g.legacyJavaFloat, false, ptTemp));
case 1145047052:
return JU.P3.new3(vwr.antialiased ? Clazz.doubleToInt(this.sX / 2) : this.sX, vwr.getScreenHeight() - (vwr.antialiased ? Clazz.doubleToInt(this.sY / 2) : this.sY), vwr.antialiased ? Clazz.doubleToInt(this.sZ / 2) : this.sZ);
case 1145047055:
return this.getVibrationVector();
case 1145045008:
var ms = this.getModulation();
return (ms == null ? null : ms.getV3());
case 1145047049:
return this;
case 1765808134:
return JU.CU.colorPtFromInt(this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom), ptTemp);
}
return null;
}, "JV.Viewer,~N,JU.P3");
Clazz.overrideMethod(c$, "getOffsetResidueAtom", 
function(name, offset){
return this.group.getAtomIndex(name, offset);
}, "~S,~N");
Clazz.overrideMethod(c$, "isCrossLinked", 
function(node){
return this.group.isCrossLinked((node).group);
}, "JU.Node");
Clazz.overrideMethod(c$, "getCrossLinkVector", 
function(vReturn, crosslinkCovalent, crosslinkHBond){
return this.group.getCrossLinkVector(vReturn, crosslinkCovalent, crosslinkHBond);
}, "JU.Lst,~B,~B");
Clazz.overrideMethod(c$, "toString", 
function(){
return this.getInfo();
});
Clazz.overrideMethod(c$, "findAtomsLike", 
function(atomExpression){
return this.group.chain.model.ms.vwr.getAtomBitSet(atomExpression);
}, "~S");
Clazz.defineMethod(c$, "getUnitID", 
function(flags){
var m = this.group.chain.model;
return (m.isBioModel ? (m).getUnitID(this, flags) : "");
}, "~N");
Clazz.overrideMethod(c$, "getFloatProperty", 
function(property){
var data = this.group.chain.model.ms.vwr.getDataObj(property, null, 1);
var f = NaN;
if (data != null) {
try {
f = (data)[this.i];
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}return f;
}, "~S");
Clazz.overrideMethod(c$, "modelIsRawPDB", 
function(){
var m = this.group.chain.model;
return (m.isBioModel && !m.isPdbWithMultipleBonds && m.hydrogenCount == 0);
});
Clazz.defineMethod(c$, "setSymop", 
function(isym, andClear){
if (this.atomSymmetry == null) this.atomSymmetry =  new JU.BS();
if (andClear) this.atomSymmetry.clearAll();
if (isym > 0) this.atomSymmetry.set(isym - 1);
}, "~N,~B");
Clazz.overrideMethod(c$, "getExplicitHydrogenCount", 
function(){
return 0;
});
c$.MAD_GLOBAL = 32200;
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
