Clazz.declarePackage("JM");
Clazz.load(null, "JM.BioModelSet", ["java.util.Hashtable", "JU.AU", "$.BS", "$.Lst", "$.PT", "$.SB", "J.api.Interface", "J.c.STR", "JM.Group", "$.ModelSet", "JM.BioResolver", "JS.T", "JU.BSUtil", "$.Escape", "$.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.haveDSSR = false;
this.vwr = null;
this.ms = null;
this.ext = null;
this.unitIdSets = null;
this.dssrDataMap = null;
Clazz.instantialize(this, arguments);}, JM, "BioModelSet", null);
Clazz.defineMethod(c$, "getBioExt", 
function(){
return (this.ext == null ? (this.ext = (J.api.Interface.getInterface("JM.BioExt", this.vwr, "script"))).set(this.vwr, this.vwr.ms) : this.ext);
});
Clazz.defineMethod(c$, "set", 
function(vwr, ms){
this.vwr = vwr;
this.ms = ms;
System.err.println("BioModelset need to delete the DataList map");
this.unitIdSets = null;
if (this.ext != null) this.ext.set(vwr, ms);
return this;
}, "JV.Viewer,JM.ModelSet");
Clazz.defineMethod(c$, "calcAllRasmolHydrogenBonds", 
function(bsA, bsB, vHBonds, nucleicOnly, nMax, dsspIgnoreHydrogens, bsHBonds, dsspVersion){
var am = this.ms.am;
if (vHBonds == null) {
var bsAtoms = bsA;
if (bsB != null && !bsA.equals(bsB)) (bsAtoms = JU.BSUtil.copy(bsA)).or(bsB);
var bsDelete =  new JU.BS();
var bsOK =  new JU.BS();
var models = this.ms.am;
var bonds = this.ms.bo;
for (var i = this.ms.bondCount; --i >= 0; ) {
var bond = bonds[i];
if (bond == null || (bond.order & 28672) == 0) continue;
if (bsAtoms.get(bond.atom1.i)) bsDelete.set(i);
 else bsOK.set(models[bond.atom1.mi].trajectoryBaseIndex);
}
for (var i = this.ms.mc; --i >= 0; ) if (models[i].isBioModel) models[i].hasRasmolHBonds = bsOK.get(i);

if (bsDelete.nextSetBit(0) >= 0) this.ms.deleteBonds(bsDelete, false);
}for (var i = this.ms.mc; --i >= 0; ) if (am[i].isBioModel && !this.ms.isTrajectorySubFrame(i)) (am[i]).getRasmolHydrogenBonds(bsA, bsB, vHBonds, nucleicOnly, nMax, dsspIgnoreHydrogens, bsHBonds, dsspVersion);

}, "JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS,~N");
Clazz.defineMethod(c$, "calcSelectedMonomersCount", 
function(){
var bsSelected = this.vwr.bsA();
for (var i = this.ms.mc; --i >= 0; ) if (this.ms.am[i].isBioModel) {
var m = this.ms.am[i];
for (var j = m.bioPolymerCount; --j >= 0; ) m.bioPolymers[j].calcSelectedMonomersCount(bsSelected);

}
});
Clazz.defineMethod(c$, "calculateAllPolymers", 
function(groups, groupCount, baseGroupIndex, modelsExcluded){
var checkConnections = !this.vwr.getBoolean(603979896);
if (groupCount < 0) groupCount = groups.length;
if (modelsExcluded != null) for (var j = 0; j < groupCount; ++j) {
var group = groups[j];
if (Clazz.instanceOf(group,"JM.Monomer")) {
if ((group).bioPolymer != null && (!modelsExcluded.get(group.chain.model.modelIndex))) (group).setBioPolymer(null, -1);
}}
for (var i = 0, mc = this.ms.mc; i < mc; i++) if ((modelsExcluded == null || !modelsExcluded.get(i)) && this.ms.am[i].isBioModel) {
for (var pt = 0, j = baseGroupIndex; j < groupCount; ++j, pt++) {
var g = groups[j];
var model = g.getModel();
if (!model.isBioModel || !(Clazz.instanceOf(g,"JM.Monomer")) || g.getLeadAtom() == null) continue;
var doCheck = checkConnections && !this.ms.isJmolDataFrame(this.ms.at[g.getLeadAtom().i].mi);
var bp = ((g).bioPolymer == null ? JM.BioResolver.allocateBioPolymer(groups, j, doCheck, pt) : null);
if (bp == null || bp.monomerCount == 0) continue;
var n = (model).addBioPolymer(bp);
j += n - 1;
pt += n - 1;
}
}
}, "~A,~N,~N,JU.BS");
Clazz.defineMethod(c$, "calculateAllStructuresExcept", 
function(alreadyDefined, asDSSP, doReport, dsspIgnoreHydrogen, setStructure, includeAlpha, version){
var ret = "";
var bsModels = JU.BSUtil.copyInvert(alreadyDefined, this.ms.mc);
if (setStructure) this.setAllDefaultStructure(bsModels);
for (var i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) if (this.ms.am[i].isBioModel) ret += (this.ms.am[i]).calculateStructures(asDSSP, doReport, dsspIgnoreHydrogen, setStructure, includeAlpha, version);

if (setStructure) this.ms.setStructureIndexes();
return ret;
}, "JU.BS,~B,~B,~B,~B,~B,~N");
Clazz.defineMethod(c$, "calculateAllStuctures", 
function(bsAtoms, asDSSP, doReport, dsspIgnoreHydrogen, setStructure, version){
if (version <= 0) version = 2;
var bsAllAtoms =  new JU.BS();
var bsModelsExcluded = JU.BSUtil.copyInvert(this.modelsOf(bsAtoms, bsAllAtoms), this.ms.mc);
if (!setStructure) return this.ms.calculateStructuresAllExcept(bsModelsExcluded, asDSSP, doReport, dsspIgnoreHydrogen, false, false, version);
this.ms.recalculatePolymers(bsModelsExcluded);
var ret = this.ms.calculateStructuresAllExcept(bsModelsExcluded, asDSSP, doReport, dsspIgnoreHydrogen, true, false, version);
this.vwr.shm.resetBioshapes(bsAllAtoms);
this.ms.setStructureIndexes();
return ret;
}, "JU.BS,~B,~B,~B,~B,~N");
Clazz.defineMethod(c$, "calculateStraightnessAll", 
function(){
this.getBioExt().calculateStraightnessAll();
});
Clazz.defineMethod(c$, "calculateStruts", 
function(bs1, bs2){
return this.getBioExt().calculateAllstruts(this.vwr, this.ms, bs1, bs2);
}, "JU.BS,JU.BS");
Clazz.defineMethod(c$, "getAllDefaultStructures", 
function(bsAtoms, bsModified){
var bsModels = this.modelsOf(bsAtoms, bsModified);
var ret =  new JU.SB();
for (var i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) if (this.ms.am[i].isBioModel && (this.ms.am[i]).defaultStructure != null) ret.append((this.ms.am[i]).defaultStructure);

return ret.toString();
}, "JU.BS,JU.BS");
Clazz.defineMethod(c$, "getAllHeteroList", 
function(modelIndex){
var htFull =  new java.util.Hashtable();
var ok = false;
for (var i = this.ms.mc; --i >= 0; ) if (modelIndex < 0 || i == modelIndex) {
var ht = this.ms.getInfo(i, "hetNames");
if (ht == null) continue;
ok = true;
for (var entry, $entry = ht.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
var key = entry.getKey();
htFull.put(key, entry.getValue());
}
}
return (ok ? htFull : null);
}, "~N");
Clazz.defineMethod(c$, "getAllPolymerInfo", 
function(bs, info){
this.getBioExt().getAllPolymerInfo(bs, info);
}, "JU.BS,java.util.Map");
Clazz.defineMethod(c$, "getAllPolymerPointsAndVectors", 
function(bs, vList, isTraceAlpha, sheetSmoothing){
for (var i = 0; i < this.ms.mc; ++i) if (this.ms.am[i].isBioModel) {
var m = this.ms.am[i];
var last = 2147483646;
for (var ip = 0; ip < m.bioPolymerCount; ip++) last = m.bioPolymers[ip].getPolymerPointsAndVectors(last, bs, vList, isTraceAlpha, sheetSmoothing);

}
}, "JU.BS,JU.Lst,~B,~N");
Clazz.defineMethod(c$, "getAllSequenceBits", 
function(specInfo, bsAtoms, bsResult){
if (specInfo.length > 0) {
if (bsAtoms == null) bsAtoms = this.vwr.getAllAtoms();
if (specInfo.indexOf('|') < specInfo.lastIndexOf('|')) return this.getAllUnitIds(specInfo, bsAtoms, bsResult);
var am = this.ms.am;
for (var i = this.ms.mc; --i >= 0; ) if (am[i].isBioModel) {
var m = am[i];
var lenInfo = specInfo.length;
for (var ip = 0; ip < m.bioPolymerCount; ip++) {
var sequence = m.bioPolymers[ip].getSequence();
var j = -1;
while ((j = sequence.indexOf(specInfo, ++j)) >= 0) m.bioPolymers[ip].getPolymerSequenceAtoms(j, lenInfo, bsAtoms, bsResult);

}
}
}return bsResult;
}, "~S,JU.BS,JU.BS");
Clazz.defineMethod(c$, "getAtomBitsBS", 
function(tokType, bsInfo, bs){
var at = this.ms.at;
var ac = this.ms.ac;
var i = 0;
var g;
switch (tokType) {
case 136314895:
case 2097184:
var type = (tokType == 136314895 ? J.c.STR.HELIX : J.c.STR.SHEET);
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isWithinStructure(type)) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
case 2097188:
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isCarbohydrate()) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
case 2097156:
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isDna()) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
case 2097166:
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isNucleic()) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
case 2097168:
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isProtein()) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
case 2097170:
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isPurine()) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
case 2097172:
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isPyrimidine()) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
case 2097174:
for (i = ac; --i >= 0; ) {
if (at[i] == null) continue;
if ((g = at[i].group).isRna()) g.setAtomBits(bs);
i = g.firstAtomIndex;
}
break;
}
if (i < 0) return bs;
var i0 = bsInfo.nextSetBit(0);
if (i0 < 0) return bs;
i = 0;
switch (tokType) {
case 1094713362:
for (i = i0; i >= 0; i = bsInfo.nextSetBit(i + 1)) {
var iPolymer = at[i].group.getBioPolymerIndexInModel();
if (iPolymer >= 0) (at[i].group).bioPolymer.setAtomBitsAndClear(bs, bsInfo);
}
break;
case 1639976963:
for (i = i0; i >= 0; i = bsInfo.nextSetBit(i + 1)) {
var structure = at[i].group.getStructure();
if (structure != null) structure.setAtomBitsAndClear(bs, bsInfo);
}
break;
}
if (i == 0) JU.Logger.error("MISSING getAtomBits entry for " + JS.T.nameOf(tokType));
return bs;
}, "~N,JU.BS,JU.BS");
Clazz.defineMethod(c$, "getAtomBitsStr", 
function(tokType, specInfo, bs){
switch (tokType) {
default:
return  new JU.BS();
case 1073741925:
return this.getAnnotationBits("domains", 1073741925, specInfo, null);
case 1073742189:
return this.getAnnotationBits("validation", 1073742189, specInfo, null);
case 1073742128:
return this.getAnnotationBits("rna3d", 1073742128, specInfo, null);
case 1073741863:
var s = specInfo;
bs =  new JU.BS();
return (s.length % 2 != 0 ? bs : this.ms.getAtomBitsMDa(1086324742, this.getAllBasePairBits(s), bs));
case 1111490587:
return this.getAnnotationBits("dssr", 1111490587, specInfo, null);
case 1086324744:
return this.getAllSequenceBits(specInfo, null, bs);
}
}, "~N,~S,JU.BS");
Clazz.defineMethod(c$, "getBioPolymerCountInModel", 
function(modelIndex){
if (modelIndex < 0) {
var polymerCount = 0;
for (var i = this.ms.mc; --i >= 0; ) if (!this.ms.isTrajectorySubFrame(i) && this.ms.am[i].isBioModel) polymerCount += (this.ms.am[i]).getBioPolymerCount();

return polymerCount;
}return (this.ms.isTrajectorySubFrame(modelIndex) || !this.ms.am[modelIndex].isBioModel ? 0 : (this.ms.am[modelIndex]).getBioPolymerCount());
}, "~N");
Clazz.defineMethod(c$, "getFullProteinStructureState", 
function(bsAtoms, mode){
var taintedOnly = (mode == 1073742327);
if (taintedOnly && !this.ms.proteinStructureTainted) return "";
var scriptMode = (mode == 1073742158 || mode == 1073742327);
var atoms = this.ms.at;
var at0 = (bsAtoms == null ? this.vwr.getAllAtoms() : bsAtoms).nextSetBit(0);
if (at0 < 0) return "";
if (bsAtoms != null && mode == 4138) {
bsAtoms = JU.BSUtil.copy(bsAtoms);
for (var i = this.ms.ac; --i >= 0; ) if (atoms[i] == null || Float.isNaN(atoms[i].group.getGroupParameter(1111490569)) || Float.isNaN(atoms[i].group.getGroupParameter(1111490570))) bsAtoms.clear(i);

}var at1 = (bsAtoms == null ? this.vwr.getAllAtoms() : bsAtoms).length() - 1;
var im0 = atoms[at0].mi;
var im1 = atoms[at1].mi;
var lstStr =  new JU.Lst();
var map =  new java.util.Hashtable();
var cmd =  new JU.SB();
for (var im = im0; im <= im1; im++) {
if (!this.ms.am[im].isBioModel) continue;
var m = this.ms.am[im];
if (taintedOnly && !m.structureTainted) continue;
var bsA =  new JU.BS();
bsA.or(m.bsAtoms);
bsA.andNot(m.bsAtomsDeleted);
var i0 = bsA.nextSetBit(0);
if (i0 < 0) continue;
if (scriptMode) {
cmd.append("  structure none ").append(JU.Escape.eBS(this.ms.getModelAtomBitSetIncludingDeleted(im, false))).append("    \t# model=" + this.ms.getModelNumberDotted(im)).append(";\n");
}var ps;
for (var i = i0; i >= 0; i = bsA.nextSetBit(i + 1)) {
var a = atoms[i];
if (a == null || !(Clazz.instanceOf(a.group,"JM.AlphaMonomer")) || (ps = (a.group).proteinStructure) == null || map.containsKey(ps)) continue;
lstStr.addLast(ps);
map.put(ps, Boolean.TRUE);
}
}
this.getStructureLines(bsAtoms, cmd, lstStr, J.c.STR.HELIX, scriptMode, mode);
this.getStructureLines(bsAtoms, cmd, lstStr, J.c.STR.SHEET, scriptMode, mode);
this.getStructureLines(bsAtoms, cmd, lstStr, J.c.STR.TURN, scriptMode, mode);
return cmd.toString();
}, "JU.BS,~N");
Clazz.defineMethod(c$, "getGroupsWithinAll", 
function(nResidues, bs){
var bsResult =  new JU.BS();
var bsCheck = this.ms.getIterativeModels(false);
for (var iModel = this.ms.mc; --iModel >= 0; ) if (bsCheck.get(iModel) && this.ms.am[iModel].isBioModel) {
var m = this.ms.am[iModel];
for (var i = m.bioPolymerCount; --i >= 0; ) m.bioPolymers[i].getRangeGroups(nResidues, bs, bsResult);

}
return bsResult;
}, "~N,JU.BS");
Clazz.defineMethod(c$, "getIdentifierOrNull", 
function(identifier){
var len = identifier.length;
var pt = 0;
while (pt < len && JU.PT.isLetter(identifier.charAt(pt))) ++pt;

var bs = this.ms.getSpecNameOrNull(identifier.substring(0, pt), false);
if (pt == len) return bs;
if (bs == null) bs =  new JU.BS();
var pt0 = pt;
while (pt < len && JU.PT.isDigit(identifier.charAt(pt))) ++pt;

if (pt == pt0) return null;
var seqNumber = 0;
try {
seqNumber = Integer.parseInt(identifier.substring(pt0, pt));
} catch (nfe) {
if (Clazz.exceptionOf(nfe,"NumberFormatException")){
return null;
} else {
throw nfe;
}
}
var insertionCode = ' ';
if (pt < len && identifier.charAt(pt) == '^') if (++pt < len) insertionCode = identifier.charAt(pt);
var seqcode = JM.Group.getSeqcodeFor(seqNumber, insertionCode);
var bsInsert = this.ms.getSeqcodeBits(seqcode, false);
if (bsInsert == null) {
if (insertionCode != ' ') bsInsert = this.ms.getSeqcodeBits(Character.toUpperCase(identifier.charAt(pt)).charCodeAt(0), false);
if (bsInsert == null) return null;
pt++;
}bs.and(bsInsert);
if (pt >= len) return bs;
if (pt != len - 1) return null;
bs.and(this.ms.getChainBits(identifier.charAt(pt).charCodeAt(0)));
return bs;
}, "~S");
Clazz.defineMethod(c$, "mutate", 
function(bs, group, sequence, alphaType, phipsi){
return this.getBioExt().mutate(this.vwr, bs, group, sequence, alphaType, phipsi);
}, "JU.BS,~S,~A,~S,~A");
Clazz.defineMethod(c$, "recalculateAllPolymers", 
function(bsModelsExcluded, groups){
for (var i = 0; i < this.ms.mc; i++) if (this.ms.am[i].isBioModel && !bsModelsExcluded.get(i)) (this.ms.am[i]).clearBioPolymers();

this.calculateAllPolymers(groups, -1, 0, bsModelsExcluded);
}, "JU.BS,~A");
Clazz.defineMethod(c$, "recalculatePoints", 
function(modelIndex){
if (modelIndex < 0) {
for (var i = this.ms.mc; --i >= 0; ) if (!this.ms.isTrajectorySubFrame(i) && this.ms.am[i].isBioModel) (this.ms.am[i]).recalculateLeadMidpointsAndWingVectors();

return;
}if (!this.ms.isTrajectorySubFrame(modelIndex) && this.ms.am[modelIndex].isBioModel) (this.ms.am[modelIndex]).recalculateLeadMidpointsAndWingVectors();
}, "~N");
Clazz.defineMethod(c$, "setAllConformation", 
function(bsAtoms){
this.vwr.ms.recalculatePositionDependentQuantities(bsAtoms, null);
var bsModels = this.ms.getModelBS(bsAtoms, false);
for (var i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) if (this.ms.am[i].isBioModel) {
var m = this.ms.am[i];
if (m.altLocCount > 0) for (var j = m.bioPolymerCount; --j >= 0; ) m.bioPolymers[j].setConformation(bsAtoms);

}
}, "JU.BS");
Clazz.defineMethod(c$, "setAllProteinType", 
function(bs, type){
var monomerIndexCurrent = -1;
var bsModels = this.ms.getModelBS(bs, false);
this.setAllDefaultStructure(bsModels);
var groups = this.ms.getGroups();
var lastStrucNo = 0;
var lastResNo = -2147483648;
var lastPolymer = null;
var lastModel = null;
var isNone = (type === J.c.STR.NONE);
for (var i = 0; i < groups.length; i++) {
var g = groups[i];
if (g.getBioPolymerLength() == 0 || !bs.get(g.firstAtomIndex)) continue;
var m = g.getModel();
if (!isNone) {
if (m !== lastModel) {
lastModel = m;
lastStrucNo = 0;
lastPolymer = null;
}if (lastPolymer !== (g).bioPolymer) {
lastResNo = -2147483648;
lastPolymer = (g).bioPolymer;
}var resno = g.getResno();
if (resno != lastResNo + 1) {
monomerIndexCurrent = -1;
}lastResNo = resno;
}monomerIndexCurrent = g.setProteinStructureType(type, monomerIndexCurrent);
if (g.getStrucNo() > 1000) g.setStrucNo(++lastStrucNo);
this.ms.proteinStructureTainted = m.structureTainted = true;
}
}, "JU.BS,J.c.STR");
Clazz.defineMethod(c$, "setAllStructureList", 
function(structureList){
for (var iModel = this.ms.mc; --iModel >= 0; ) if (this.ms.am[iModel].isBioModel) {
var m = this.ms.am[iModel];
m.bioPolymers = JU.AU.arrayCopyObject(m.bioPolymers, m.bioPolymerCount);
for (var i = m.bioPolymerCount; --i >= 0; ) {
var bp = m.bioPolymers[i];
if (Clazz.instanceOf(bp,"JM.AminoPolymer")) (bp).setStructureList(structureList);
}
}
}, "java.util.Map");
Clazz.defineMethod(c$, "getAllBasePairBits", 
function(specInfo){
var bsA = null;
var bsB = null;
var vHBonds =  new JU.Lst();
if (specInfo.length == 0) {
bsA = bsB = this.vwr.getAllAtoms();
this.calcAllRasmolHydrogenBonds(bsA, bsB, vHBonds, true, 1, false, null, 0);
} else {
for (var i = 0; i < specInfo.length; ) {
bsA = this.ms.getSequenceBits(specInfo.substring(i, ++i), null,  new JU.BS());
if (bsA.nextSetBit(0) < 0) continue;
bsB = this.ms.getSequenceBits(specInfo.substring(i, ++i), null,  new JU.BS());
if (bsB.nextSetBit(0) < 0) continue;
this.calcAllRasmolHydrogenBonds(bsA, bsB, vHBonds, true, 1, false, null, 0);
}
}var bsAtoms =  new JU.BS();
for (var i = vHBonds.size(); --i >= 0; ) {
var b = vHBonds.get(i);
bsAtoms.set(b.atom1.i);
bsAtoms.set(b.atom2.i);
}
return bsAtoms;
}, "~S");
Clazz.defineMethod(c$, "getAllUnitIds", 
function(specInfo, bsSelected, bsResult){
var maps = this.unitIdSets;
if (maps == null) {
maps = this.unitIdSets =  new Array(7);
for (var i = 0; i < 7; i++) maps[i] =  new java.util.Hashtable();

for (var i = this.ms.mc; --i >= 0; ) {
var m = this.ms.am[i];
if (!m.isBioModel) continue;
if (this.ms.isTrajectory(i)) m = this.ms.am[i = m.trajectoryBaseIndex];
var num = "|" + this.ms.getInfo(i, "modelNumber");
this.checkMap(maps[0], this.ms.getInfo(i, "modelName") + num, m.bsAtoms);
this.checkMap(maps[0], num, m.bsAtoms);
}
}var bsModelChain = null;
var lastModelChain = null;
var bsTemp =  new JU.BS();
var units = JU.PT.getTokens(JU.PT.replaceAllCharacters(specInfo, ", \t\n[]\"=", " "));
var ptrs =  Clazz.newIntArray (8, 0);
for (var i = units.length; --i >= 0; ) {
var unit = units[i] + "|";
if (unit.length < 5) continue;
var bsPtr = 0;
for (var j = 0, n = 0, pt = unit.lastIndexOf('|') + 1; j < pt && n < 8; j++) {
if (unit.charAt(j) == '|') ptrs[n++] = j;
 else bsPtr |= 1 << n;
}
if ((bsPtr & 0x16) != 0x16) continue;
bsTemp.clearAll();
bsTemp.or(bsSelected);
var mchain = unit.substring(0, ptrs[2]);
if (lastModelChain != null && lastModelChain.equals(mchain)) {
bsTemp.and(bsModelChain);
} else {
if (!this.addUnit(1094717454, unit.substring(0, ptrs[1]).toUpperCase(), bsTemp, maps[0]) || !this.addUnit(1073742357, unit.substring(ptrs[1] + 1, ptrs[2]), bsTemp, maps[1])) continue;
bsModelChain = JU.BSUtil.copy(bsTemp);
lastModelChain = mchain;
}var haveAtom = ((bsPtr & (32)) != 0);
var haveAlt = ((bsPtr & (64)) != 0);
if (!this.addUnit(1094715412, unit.substring(ptrs[3] + 1, ptrs[4]), bsTemp, maps[2]) || !this.addUnit(5, ((bsPtr & (128)) == 0 ? "\0" : unit.substring(ptrs[6] + 1, ptrs[7])), bsTemp, maps[3]) || (haveAtom ? !this.addUnit(1086326786, unit.substring(ptrs[4] + 1, ptrs[5]).toUpperCase(), bsTemp, maps[4]) || !this.addUnit(1073742355, unit.substring(ptrs[5] + 1, ptrs[6]), bsTemp, maps[5]) : haveAlt && !this.addUnit(1094717448, unit.substring(ptrs[5] + 1, ptrs[6]), bsTemp, maps[6]))) continue;
bsResult.or(bsTemp);
}
return bsResult;
}, "~S,JU.BS,JU.BS");
Clazz.defineMethod(c$, "checkMap", 
function(map, key, bsAtoms){
var bs = JU.BSUtil.copy(bsAtoms);
var bs0 = map.get(key);
if (bs0 == null) map.put(key, bs0 = bs);
 else bs0.or(bs);
return bs0;
}, "java.util.Map,~S,JU.BS");
Clazz.defineMethod(c$, "addUnit", 
function(tok, key, bsTemp, map){
var bs = map.get(key);
if (bs == null) {
var o;
switch (tok) {
default:
return false;
case 1073742357:
o = Integer.$valueOf(this.vwr.getChainID(key, false));
break;
case 1094715412:
o = Integer.$valueOf(JU.PT.parseInt(key));
break;
case 5:
o = Integer.$valueOf(key.charAt(0).charCodeAt(0));
break;
case 1094717448:
bs = this.ms.getAtomBitsMDa(tok = 1073742355, null,  new JU.BS());
case 1086326786:
o = key;
break;
case 1073742355:
o = (key.length == 0 ? null : key);
break;
}
map.put(key, bs = this.ms.getAtomBitsMDa(tok, o, (bs == null ?  new JU.BS() : bs)));
}bsTemp.and(bs);
return (bsTemp.nextSetBit(0) >= 0);
}, "~N,~S,JU.BS,java.util.Map");
Clazz.defineMethod(c$, "getAnnotationBits", 
function(key, tok, specInfo, type){
var bs =  new JU.BS();
if (tok == 1111490587 && !this.haveDSSR) return bs;
var pa = this.vwr.getAnnotationParser(tok);
var ann;
var keyV = key + " V ";
for (var i = this.ms.mc; --i >= 0; ) {
if ((ann = this.ms.getInfo(i, key)) != null) {
var b = pa.getAtomBits(this.vwr, specInfo, (this.ms.am[i]).getCachedAnnotationMap(keyV, ann), this.ms.am[i].annotationCache, tok, i, this.ms.am[i].bsAtoms);
bs.or(b);
}}
if (tok == 1111490587 && type != null) {
var groups = this.ms.getGroupsForAtoms(bs);
for (var i = groups.size(); --i >= 0; ) {
groups.get(i).setDSSRStructureSubType(type);
}
}return bs;
}, "~S,~N,~S,J.c.STR");
Clazz.defineMethod(c$, "getStructureLines", 
function(bsAtoms, cmd, lstStr, type, scriptMode, mode){
var showMode = (mode == 134222350);
var nHelix = 0;
var nSheet = 0;
var nTurn = 0;
var sid = null;
var bs =  new JU.BS();
var n = 0;
for (var i = 0, ns = lstStr.size(); i < ns; i++) {
var ps = lstStr.get(i);
if (ps.type !== type) continue;
var m1 = ps.findMonomer(bsAtoms, true);
var m2 = ps.findMonomer(bsAtoms, false);
if (m1 == null || m2 == null) continue;
var iModel = ps.apolymer.model.modelIndex;
var comment = (scriptMode ? "    \t# model=" + this.ms.getModelNumberDotted(iModel) : null);
var res1 = m1.getResno();
var res2 = m2.getResno();
var subtype = ps.subtype;
switch (type) {
case J.c.STR.HELIX:
case J.c.STR.TURN:
case J.c.STR.SHEET:
n++;
if (scriptMode) {
bs.clearAll();
ps.setAtomBits(bs);
var stype = subtype.getBioStructureTypeName(false);
cmd.append("  structure ").append(stype).append(" ").append(JU.Escape.eBS(bs)).append(comment).append(" & (" + res1 + " - " + res2 + ")").append(";\n");
} else {
var str;
var nx;
switch (type) {
case J.c.STR.HELIX:
nx = ++nHelix;
sid = JU.PT.formatStringI("%3N %3N", "N", nx);
str = "HELIX  %ID %3GROUPA %1CA %4RESA  %3GROUPB %1CB %4RESB";
var stype = null;
switch (subtype) {
case J.c.STR.HELIX:
case J.c.STR.HELIXALPHA:
stype = "  1";
break;
case J.c.STR.HELIX310:
stype = "  5";
break;
case J.c.STR.HELIXPI:
stype = "  3";
break;
}
if (stype != null) str += stype;
break;
case J.c.STR.SHEET:
nx = ++nSheet;
sid = JU.PT.formatStringI("%3N %3A 0", "N", nx);
sid = JU.PT.formatStringS(sid, "A", "S" + nx);
str = "SHEET  %ID %3GROUPA %1CA%4RESA  %3GROUPB %1CB%4RESB";
break;
case J.c.STR.TURN:
default:
nx = ++nTurn;
sid = JU.PT.formatStringI("%3N %3N", "N", nx);
str = "TURN   %ID %3GROUPA %1CA%4RESA  %3GROUPB %1CB%4RESB";
break;
}
str = JU.PT.formatStringS(str, "ID", sid);
str = JU.PT.formatStringS(str, "GROUPA", m1.getGroup3());
str = JU.PT.formatStringS(str, "CA", m1.getLeadAtom().getChainIDStr());
str = JU.PT.formatStringI(str, "RESA", res1);
str = JU.PT.formatStringS(str, "GROUPB", m2.getGroup3());
str = JU.PT.formatStringS(str, "CB", m2.getLeadAtom().getChainIDStr());
str = JU.PT.formatStringI(str, "RESB", res2);
cmd.append(str);
if (showMode) cmd.append(" strucno= ").appendI(ps.strucNo);
cmd.append("\n");
}}
}
if (n > 0) cmd.append("\n");
return n;
}, "JU.BS,JU.SB,JU.Lst,J.c.STR,~B,~N");
Clazz.defineMethod(c$, "modelsOf", 
function(bsAtoms, bsAtomsRet){
var bsModels = JU.BS.newN(this.ms.mc);
var isAll = (bsAtoms == null);
var i0 = (isAll ? this.ms.ac - 1 : bsAtoms.nextSetBit(0));
for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsAtoms.nextSetBit(i + 1))) {
if (this.ms.at[i] == null) continue;
var modelIndex = this.ms.am[this.ms.at[i].mi].trajectoryBaseIndex;
if (this.ms.isJmolDataFrame(modelIndex)) continue;
bsModels.set(modelIndex);
bsAtomsRet.set(i);
}
return bsModels;
}, "JU.BS,JU.BS");
Clazz.defineMethod(c$, "setAllDefaultStructure", 
function(bsModels){
for (var i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) if (this.ms.am[i].isBioModel) {
var m = this.ms.am[i];
if (m.defaultStructure == null) m.defaultStructure = this.getFullProteinStructureState(m.bsAtoms, 1073742158);
}
}, "JU.BS");
Clazz.defineMethod(c$, "getAminoAcidValenceAndCharge", 
function(s, atomName, aaRet){
return this.getBioExt().getAminoAcidValenceAndCharge(s, atomName, aaRet);
}, "~S,~S,~A");
Clazz.defineMethod(c$, "getStructureDSSRAssignments", 
function(){
if (!this.haveDSSR) return;
this.getAnnotationBits("dssr", 1111490587, "iloops", J.c.STR.DSSRINTERNALLOOP);
this.getAnnotationBits("dssr", 1111490587, "hairpins", J.c.STR.DSSRHAIRPINLOOP);
this.getAnnotationBits("dssr", 1111490587, "bulges", J.c.STR.DSSRBULGELOOP);
this.getAnnotationBits("dssr", 1111490587, "junctions", J.c.STR.DSSRJUNCTIONLOOP);
this.getAnnotationBits("dssr", 1111490587, "stems", J.c.STR.DSSRSTEM);
});
Clazz.defineMethod(c$, "setHaveDSSR", 
function(b){
this.haveDSSR = b;
}, "~B");
Clazz.defineMethod(c$, "getDSSRProperties", 
function(dataType){
if (!this.haveDSSR || dataType == null) return null;
var dataPath = (dataType.indexOf('.') < 0 ? "dssr" + "." + dataType : dataType);
if (this.dssrDataMap == null) {
this.dssrDataMap =  new java.util.Hashtable();
}var dataList = this.dssrDataMap.get(dataType);
if (dataList == null) {
this.dssrDataMap.put(dataType, dataList =  new JM.ModelSet.DataList(dataPath));
}for (var i = this.ms.mc; --i >= 0; ) if (this.ms.am[i].isBioModel && (this.ms.am[i]).haveDSSR) this.vwr.getAnnotationParser(1111490587).getAtomicDSSRData(this.ms, i, dataList);

return dataList;
}, "~S");
Clazz.defineMethod(c$, "getAtomicDSSRDataFloat", 
function(dataType, atomIndex){
var dl = (this.dssrDataMap == null ? null : this.dssrDataMap.get(dataType));
return (dl != null && dl.floatData != null && dl.floatData.length > atomIndex ? dl.floatData[atomIndex] : NaN);
}, "~S,~N");
Clazz.defineMethod(c$, "getAtomicDSSRDataString", 
function(dataType, atomIndex){
var dl = (this.dssrDataMap == null ? null : this.dssrDataMap.get(dataType));
return (dl != null && dl.stringData != null && dl.stringData.length > atomIndex ? dl.stringData[atomIndex] : null);
}, "~S,~N");
Clazz.defineMethod(c$, "releaseModelSet", 
function(){
System.err.println("can't remove ms here??");
});
Clazz.defineMethod(c$, "clearDSSR", 
function(){
this.dssrDataMap = null;
});
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
