Clazz.declarePackage("J.adapter.readers.cif");
Clazz.load(["J.adapter.readers.cif.MMCifReader"], "J.adapter.readers.cif.MMTFReader", ["java.util.Hashtable", "JU.BS", "$.Lst", "$.M4", "$.MessagePackReader", "$.PT", "$.SB", "J.adapter.smarter.Atom", "$.Bond", "$.Structure", "JS.SV", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.haveStructure = false;
this.map = null;
this.fileAtomCount = 0;
this.opCount = 0;
this.groupModels = null;
this.groupMap = null;
this.groupDSSP = null;
this.atomGroup = null;
this.labelAsymList = null;
this.atomMap = null;
this.entities = null;
this.groupCount = 0;
this.ac0 = 0;
this.bsStructures = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.cif, "MMTFReader", J.adapter.readers.cif.MMCifReader);
Clazz.overrideMethod(c$, "addHeader", 
function(){
});
Clazz.overrideMethod(c$, "setup", 
function(fullPath, htParams, reader){
this.isBinary = true;
this.isMMCIF = true;
this.iHaveFractionalCoordinates = false;
this.setupASCR(fullPath, htParams, reader);
}, "~S,java.util.Map,~O");
Clazz.overrideMethod(c$, "processBinaryDocument", 
function(){
var t = System.currentTimeMillis();
var doDoubleBonds = (!this.isCourseGrained && !this.checkFilterKey("NODOUBLE"));
this.isDSSP1 = !this.checkFilterKey("DSSP2");
var mmtfImplementsDSSP2 = false;
this.applySymmetryToBonds = true;
this.map = ( new JU.MessagePackReader(this.binaryDoc, true)).readMap();
this.entities = this.map.get("entityList");
if (JU.Logger.debugging) {
for (var s, $s = this.map.keySet().iterator (); $s.hasNext()&& ((s = $s.next ()) || true);) JU.Logger.info(s);

}this.asc.setInfo("noAutoBond", Boolean.TRUE);
JU.Logger.info("MMTF version " + this.map.get("mmtfVersion"));
JU.Logger.info("MMTF Producer " + this.map.get("mmtfProducer"));
var title = this.map.get("title");
if (title != null) this.appendLoadNote(title);
this.pdbID = this.map.get("structureId");
if (this.pdbID == null) this.pdbID = this.map.get("pdbId");
this.fileAtomCount = (this.map.get("numAtoms")).intValue();
var nBonds = (this.map.get("numBonds")).intValue();
this.groupCount = (this.map.get("numGroups")).intValue();
this.groupModels =  Clazz.newIntArray (this.groupCount, 0);
this.groupDSSP =  Clazz.newIntArray (this.groupCount, 0);
this.groupMap =  Clazz.newIntArray (this.groupCount, 0);
var modelCount = (this.map.get("numModels")).intValue();
this.appendLoadNote("id=" + this.pdbID + " numAtoms=" + this.fileAtomCount + " numBonds=" + nBonds + " numGroups=" + this.groupCount + " numModels=" + modelCount);
this.getMMTFAtoms(doDoubleBonds);
System.out.println("MMTF read and parsed in " + (System.currentTimeMillis() - t) + " ms");
if (!this.isCourseGrained) {
var bo = this.decode("bondOrderList");
var bi = this.decode("bondAtomList");
this.addMMTFBonds(bo, bi, 0, doDoubleBonds, true);
if (this.isDSSP1 || mmtfImplementsDSSP2) this.getStructure();
}this.setMMTFSymmetry();
this.getMMTFBioAssembly();
this.setModelPDB(true);
if (JU.Logger.debuggingHigh) JU.Logger.info(JS.SV.getVariable(this.map).asString());
});
Clazz.defineMethod(c$, "applySymmetryAndSetTrajectory", 
function(){
this.ac0 = this.ac;
Clazz.superCall(this, J.adapter.readers.cif.MMTFReader, "applySymmetryAndSetTrajectory", []);
this.addStructureSymmetry();
});
Clazz.defineMethod(c$, "getMMTFAtoms", 
function(doMulti){
var chainsPerModel = this.map.get("chainsPerModel");
var groupsPerChain = this.map.get("groupsPerChain");
this.labelAsymList = this.decode("chainIdList");
var authAsymList = this.decode("chainNameList");
var groupTypeList = this.decode("groupTypeList");
var groupIdList = this.decode("groupIdList");
var groupList = this.map.get("groupList");
var insCodes = this.decode("insCodeList");
var atomId = this.decode("atomIdList");
var haveSerial = (atomId != null);
var altloc = this.decode("altLocList");
var occ = this.decode("occupancyList");
var x = this.decode("xCoordList");
var y = this.decode("yCoordList");
var z = this.decode("zCoordList");
var bf = this.decode("bFactorList");
var nameList = (this.useAuthorChainID ? authAsymList : this.labelAsymList);
var iModel = -1;
var iChain = 0;
var nChain = 0;
var iGroup = 0;
var nGroup = 0;
var chainpt = 0;
var seqNo = 0;
var iatom = 0;
var chainID = "";
var authAsym = "";
var labelAsym = "";
var insCode = '\u0000';
this.atomMap =  new Array(this.fileAtomCount);
this.atomGroup =  Clazz.newIntArray (this.fileAtomCount, 0);
for (var j = 0, thisGroup = -1; j < this.groupCount; j++) {
if (++iGroup >= nGroup) {
chainID = nameList[chainpt];
authAsym = authAsymList[chainpt];
labelAsym = this.labelAsymList[chainpt];
nGroup = groupsPerChain[chainpt++];
iGroup = 0;
if (++iChain >= nChain) {
this.groupModels[j] = ++iModel;
nChain = chainsPerModel[iModel];
iChain = 0;
this.setModelPDB(true);
this.incrementModel(iModel + 1);
this.asc.setCurrentModelInfo("pdbID", this.pdbID);
this.nAtoms0 = this.asc.ac;
if (this.done) return;
}}var g = groupList[groupTypeList[j]];
var atomNameList = g.get("atomNameList");
var len = atomNameList.length;
if (this.skipping) {
iatom += len;
continue;
}var a0 = iatom;
if (insCodes != null) insCode = insCodes[j];
seqNo = groupIdList[j];
var group3 = g.get("groupName");
var isHetero = this.vwr.getJBR().isHetero(group3);
if (isHetero) {
var groupType = "" + g.get("chemCompType");
if (this.htHetero == null || !this.htHetero.containsKey(group3)) {
var hetName = groupType;
if (this.entities != null && hetName.equals("NON-POLYMER")) {
out : for (var i = this.entities.length; --i >= 0; ) {
var entity = this.entities[i];
var chainList = entity.get("chainIndexList");
for (var k = chainList.length; --k >= 0; ) {
if (chainList[k] == iChain) {
hetName = "a component of the entity \"" + entity.get("description") + "\"";
break out;
}}
}
}this.addHetero(group3, hetName, groupType.toLowerCase(), false, true);
}}var elementList = g.get("elementList");
var haveAtom = false;
for (var ia = 0, pt = 0; ia < len; ia++, iatom++) {
var a =  new J.adapter.smarter.Atom();
a.isHetero = isHetero;
if (insCode.charCodeAt(0) != 0) a.insertionCode = insCode;
this.setAtomCoordXYZ(a, x[iatom], y[iatom], z[iatom]);
a.elementSymbol = elementList[pt];
a.atomName = atomNameList[pt++];
if (seqNo >= 0) this.maxSerial = Math.max(this.maxSerial, a.sequenceNumber = seqNo);
a.group3 = group3;
this.setChainID(a, chainID);
if (bf != null) a.bfactor = bf[iatom];
if (altloc != null) a.altLoc = altloc[iatom];
if (occ != null) a.foccupancy = occ[iatom];
if (haveSerial) a.atomSerial = atomId[iatom];
if (!this.filterAtom(a, -1) || !this.processSubclassAtom(a, labelAsym, authAsym)) continue;
if (!haveAtom) {
thisGroup++;
haveAtom = true;
}if (haveSerial) {
this.asc.addAtomWithMappedSerialNumber(a);
} else {
this.asc.addAtom(a);
}this.atomMap[iatom] = a;
this.atomGroup[this.ac] = j;
this.groupMap[j] = thisGroup;
this.ac++;
}
if (!this.isCourseGrained) {
var bo = g.get("bondOrderList");
var bi = g.get("bondAtomList");
this.addMMTFBonds(bo, bi, a0, doMulti, false);
}}
this.asc.setCurrentModelInfo("pdbID", this.pdbID);
}, "~B");
Clazz.defineMethod(c$, "addMMTFBonds", 
function(bo, bi, a0, doMulti, isInter){
if (bi == null) return;
doMulti = new Boolean (doMulti & (bo != null)).valueOf();
for (var bj = 0, pt = 0, nj = Clazz.doubleToInt(bi.length / 2); bj < nj; bj++) {
var a1 = this.atomMap[bi[pt++] + a0];
var a2 = this.atomMap[bi[pt++] + a0];
if (a1 != null && a2 != null) {
var bond =  new J.adapter.smarter.Bond(a1.index, a2.index, doMulti ? bo[bj] : 1);
this.asc.addBond(bond);
if (JU.Logger.debugging && isInter) {
JU.Logger.info("inter-group (" + (a1.atomSetIndex + 1) + "." + a1.index + "/" + (a2.atomSetIndex + 1) + "." + a2.index + ") bond " + a1.group3 + a1.sequenceNumber + "." + a1.atomName + " - " + a2.group3 + a2.sequenceNumber + "." + a2.atomName + " " + bond.order);
}}}
}, "~A,~A,~N,~B,~B");
Clazz.defineMethod(c$, "setMMTFSymmetry", 
function(){
this.setSpaceGroupName(this.map.get("spaceGroup"));
var o = this.map.get("unitCell");
if (o != null) for (var i = 0; i < 6; i++) this.setUnitCellItem(i, o[i]);

});
Clazz.defineMethod(c$, "getMMTFBioAssembly", 
function(){
var o = this.map.get("bioAssemblyList");
if (o == null) return;
if (this.vBiomolecules == null) this.vBiomolecules =  new JU.Lst();
for (var i = o.length; --i >= 0; ) {
var info =  new java.util.Hashtable();
this.vBiomolecules.addLast(info);
var iMolecule = i + 1;
info.put("id", "" + iMolecule);
this.checkFilterAssembly(info);
info.put("name", "biomolecule " + iMolecule);
info.put("molecule", Integer.$valueOf(iMolecule));
var assemb =  new JU.Lst();
var ops =  new JU.Lst();
info.put("biomts",  new JU.Lst());
info.put("chains",  new JU.Lst());
info.put("assemblies", assemb);
info.put("operators", ops);
var m = o[i];
var tlist = m.get("transformList");
var chlist =  new JU.SB();
for (var j = 0, n = tlist.length; j < n; j++) {
var t = tlist[j];
chlist.setLength(0);
var chainList = t.get("chainIndexList");
for (var k = 0, kn = chainList.length; k < kn; k++) chlist.append("$").append(this.labelAsymList[chainList[k]]);

assemb.addLast(chlist.append("$").toString());
var id = "" + (++this.opCount);
this.addMatrix(id, JU.M4.newA16(t.get("matrix")), false);
ops.addLast(id);
}
}
});
Clazz.defineMethod(c$, "getStructure", 
function(){
var a = this.decode("secStructList");
if (JU.Logger.debugging) JU.Logger.info(JU.PT.toJSON("secStructList", a));
this.bsStructures =  Clazz.newArray(-1, [ new JU.BS(), null,  new JU.BS(),  new JU.BS(),  new JU.BS(), null,  new JU.BS()]);
var lastGroup = -1;
for (var j = 0; j < a.length; j++) {
var type = a[j];
switch (type) {
case 0:
case 2:
case 3:
case 4:
case 6:
var igroup = this.groupMap[j];
this.bsStructures[type].set(igroup);
this.groupDSSP[igroup] = type + 1;
lastGroup = j;
}
}
var n = (this.isDSSP1 ? this.asc.iSet : this.groupModels[lastGroup]);
if (lastGroup >= 0) {
this.haveStructure = true;
this.asc.addStructure( new J.adapter.smarter.Structure(n, null, null, null, null, 0, this.bsStructures));
}});
Clazz.defineMethod(c$, "addStructureSymmetry", 
function(){
if (this.asc.ac == 0 || !this.haveStructure || this.thisBiomolecule == null || this.ac0 == this.asc.ac) return;
var atoms = this.asc.atoms;
var bsAtoms = this.asc.bsAtoms;
var ptGroup = -1;
var mygroup = -1;
for (var i = this.bsStructures.length; --i >= 0; ) if (this.bsStructures[i] != null) this.bsStructures[i].clearAll();

for (var i = this.ac0, n = this.asc.ac; i < n; i++) {
if (bsAtoms == null || bsAtoms.get(i)) {
var a = atoms[i];
var igroup = this.atomGroup[a.atomSite];
if (igroup != mygroup) {
mygroup = igroup;
ptGroup++;
var dssp = this.groupDSSP[igroup];
if (dssp > 0) {
this.bsStructures[dssp - 1].set(ptGroup);
}}}}
});
Clazz.defineMethod(c$, "decode", 
function(key){
return JU.MessagePackReader.decode(this.map.get(key));
}, "~S");
});
;//5.0.1-v7 Mon Aug 24 10:01:38 CDT 2026
