Clazz.declarePackage("J.dssx");
Clazz.load(["J.dssx.AnnotationParser"], "J.dssx.DSSR1", ["JU.BS", "$.Lst", "$.P3", "$.PT", "JM.HBond", "JM.BasePair", "JU.Escape", "$.Logger"], function(){
var c$ = Clazz.declareType(J.dssx, "DSSR1", J.dssx.AnnotationParser);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.dssx.DSSR1, []);
});
Clazz.overrideMethod(c$, "calculateDSSRStructure", 
function(vwr, bsAtoms){
var bs = vwr.ms.getModelBS(bsAtoms == null ? vwr.bsA() : bsAtoms, true);
var s = "";
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) s += this.getDSSRForModel(vwr, i) + "\n";

return s;
}, "JV.Viewer,JU.BS");
Clazz.defineMethod(c$, "getDSSRForModel", 
function(vwr, modelIndex){
var info = null;
var out = null;
while (true) {
if (!vwr.ms.am[modelIndex].isBioModel) break;
info = vwr.ms.getModelAuxiliaryInfo(modelIndex);
if (info.containsKey("dssr")) break;
var bs = vwr.restrictToModel(vwr.ms.getAtoms(2097166, null), modelIndex);
if (bs.nextClearBit(0) < 0) {
info = null;
break;
}try {
var name = vwr.setLoadFormat(false, "=dssrModel/", '=', false);
name = JU.PT.rep(name, "%20", " ");
JU.Logger.info("fetching " + name + "[pdb data]");
var data = vwr.getPdbAtomData(bs, null, false, false);
var modelNumber = vwr.getModelNumber(vwr.ms.getModelBS(bs, false).nextSetBit(0));
var s = "          " + modelNumber;
data = "MODEL" + s.substring(s.length - 9) + "\n" + data + "ENDMDL\n";
data = vwr.getFileAsString3(name + data, false, null);
var x = vwr.parseJSONMap(data);
if (x != null) {
info.put("dssr", x);
this.setGroup1(vwr.ms, modelIndex);
this.fixDSSRJSONMap(x);
this.setBioPolymers(vwr.ms.am[modelIndex], false);
}} catch (e) {
info = null;
out = "" + e;
}
break;
}
return (info != null ? JU.PT.rep(JU.Escape.escapeMap((info.get("dssr")).get("counts")), ",", ",\n") : out == null ? "model has no nucleotides" : out);
}, "JV.Viewer,~N");
Clazz.overrideMethod(c$, "fixDSSRJSONMap", 
function(map){
var s = "";
try {
this.fixIndices(map, "kissingLoops", "hairpin");
this.fixIndices(map, "coaxStacks", "stem");
if (map.containsKey("counts")) s += "_M.dssr.counts = " + map.get("counts").toString() + "\n";
if (map.containsKey("dbn")) s += "_M.dssr.dbn = " + map.get("dbn").toString();
} catch (e) {
}
return s;
}, "java.util.Map");
Clazz.defineMethod(c$, "fixIndices", 
function(map, key, root){
var indices = root + "_indices";
var original = root + "s";
var lst = map.get(key);
if (lst != null) {
var hpins = map.get(original);
for (var i = lst.size(); --i >= 0; ) {
var kmap = lst.get(i);
var khlist = kmap.get(indices);
var n = khlist.size();
if (n > 0) {
var khpins =  new JU.Lst();
kmap.put(original, khpins);
for (var j = n; --j >= 0; ) khpins.addLast(hpins.get((khlist.get(j)).intValue() - 1));

}}
}}, "java.util.Map,~S,~S");
Clazz.overrideMethod(c$, "getBasePairs", 
function(vwr, modelIndex){
var ms = vwr.ms;
var info = ms.getInfo(modelIndex, "dssr");
var pairs = (info == null ? null : info.get("pairs"));
var singles = (info == null ? null : info.get("ssSegments"));
if (pairs == null && singles == null) {
this.setBioPolymers(vwr.ms.am[modelIndex], true);
return;
}var bsAtoms = ms.am[modelIndex].bsAtoms;
try {
var bs =  new JU.BS();
var atoms = ms.at;
if (pairs != null) for (var i = pairs.size(); --i >= 0; ) {
var map = pairs.get(i);
var unit1 = map.get("nt1");
var unit2 = map.get("nt2");
var a1 = ms.getSequenceBits(unit1, bsAtoms, bs).nextSetBit(0);
bs.clearAll();
var a2 = ms.getSequenceBits(unit2, bsAtoms, bs).nextSetBit(0);
bs.clearAll();
JM.BasePair.add(map, this.setRes(atoms[a1]), this.setRes(atoms[a2]));
}
if (singles != null) for (var i = singles.size(); --i >= 0; ) {
var map = singles.get(i);
var units = map.get("nts_long");
ms.getSequenceBits(units, bsAtoms, bs);
for (var j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1)) this.setRes(atoms[j]);

}
} catch (e) {
JU.Logger.error("Exception " + e + " in DSSRParser.getBasePairs");
}
}, "JV.Viewer,~N");
Clazz.defineMethod(c$, "setBioPolymers", 
function(m, b){
var n = m.getBioPolymerCount();
for (var i = n; --i >= 0; ) {
var bp = m.bioPolymers[i];
if (bp.isNucleic()) (bp).isDssrSet = b;
}
}, "JM.BioModel,~B");
Clazz.defineMethod(c$, "setRes", 
function(atom){
if (atom.group.getBioPolymerLength() == 0) return null;
var m = atom.group;
(m.bioPolymer).isDssrSet = true;
return m;
}, "JM.Atom");
Clazz.overrideMethod(c$, "getAtomBits", 
function(vwr, key, dbObj, annotationCache, type, modelIndex, bsModel){
if (dbObj == null) return  new JU.BS();
var doCache = !key.contains("NOCACHE");
if (!doCache) {
key = JU.PT.rep(key, "NOCACHE", "").trim();
}var bs = null;
bs =  new JU.BS();
if (doCache) annotationCache.put(key, bs);
try {
key = JU.PT.rep(key, "[where", "[select * where");
key = JU.PT.rep(key, "[WHERE", "[select * where");
var ext = "";
var n = -2147483648;
var pt = key.toLowerCase().indexOf("[select");
if (pt >= 0) {
ext = key.substring(pt);
key = key.substring(0, pt);
pt = ext.lastIndexOf("]..");
if (pt >= 0 && (n = JU.PT.parseInt(ext.substring(pt + 3))) != -2147483648) ext = ext.substring(0, pt + 1);
}pt = key.toLowerCase().indexOf(" where ");
if (pt < 0) {
key = key.toLowerCase();
pt = (n == -2147483648 ? key.lastIndexOf('.') : -1);
var haveIndex = false;
if (pt >= 0 && (haveIndex = (n = JU.PT.parseInt(key.substring(pt + 1))) != -2147483648)) key = key.substring(0, pt);
pt = "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".indexOf(".." + key) + 2;
var len = key.length;
if (pt < 2) return bs;
var ptLast = (haveIndex ? pt + len : 2147483647);
while (pt >= 2 && pt < ptLast && len > 0) {
if (key.indexOf(".") < 0 && "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".substring(pt + len, pt + len + 2).equals("..")) {
key = "[select (" + key + ")]";
}dbObj = vwr.extractProperty(dbObj, key, -1);
pt += len + 1;
if (ext.length > 0) {
dbObj = vwr.extractProperty(dbObj, ext, -1);
ext = "";
}var pt1 = "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".indexOf(".", pt);
key = "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".substring(pt, pt1);
len = key.length;
}
} else {
key = key.substring(0, pt).trim() + "[select * " + key.substring(pt + 1) + "]" + ext;
dbObj = vwr.extractProperty(dbObj, key, -1);
}if (n != -2147483648 && Clazz.instanceOf(dbObj,"JU.Lst")) {
if (n <= 0) n += (dbObj).size();
dbObj = (dbObj).get(n - 1);
}bs.or(vwr.ms.getAtoms(1086324744, dbObj.toString()));
bs.and(bsModel);
} catch (e) {
System.out.println(e.toString() + " in AnnotationParser");
bs.clearAll();
}
return bs;
}, "JV.Viewer,~S,~O,java.util.Map,~N,~N,JU.BS");
Clazz.overrideMethod(c$, "getHBonds", 
function(ms, modelIndex, vHBonds, doReport){
var info = ms.getInfo(modelIndex, "dssr");
var list;
if (info == null || (list = info.get("hbonds")) == null) return "no DSSR hydrogen-bond data";
var bsAtoms = ms.am[modelIndex].bsAtoms;
var unit1 = null;
var unit2 = null;
var a1 = 0;
var a2 = 0;
try {
var bs =  new JU.BS();
for (var i = list.size(); --i >= 0; ) {
var map = list.get(i);
unit1 = map.get("atom1_id");
a1 = ms.getSequenceBits(unit1, bsAtoms, bs).nextSetBit(0);
if (a1 < 0) {
JU.Logger.error("Atom " + unit1 + " was not found");
continue;
}unit2 = map.get("atom2_id");
bs.clearAll();
a2 = ms.getSequenceBits(unit2, bsAtoms, bs).nextSetBit(0);
if (a2 < 0) {
JU.Logger.error("Atom " + unit2 + " was not found");
continue;
}bs.clearAll();
var energy = 0;
vHBonds.addLast( new JM.HBond(ms.at[a1], ms.at[a2], 2048, 1, 0, energy));
}
} catch (e) {
}
return "DSSR reports " + list.size() + " hydrogen bonds";
}, "JM.ModelSet,~N,JU.Lst,~B");
Clazz.overrideMethod(c$, "setGroup1", 
function(ms, modelIndex){
var info = ms.getInfo(modelIndex, "dssr");
var list;
if (info == null || (list = info.get("nts")) == null) return;
var m = ms.am[modelIndex];
var bsAtoms = m.bsAtoms;
var atoms = ms.at;
var bs =  new JU.BS();
for (var i = list.size(); --i >= 0; ) {
var map = list.get(i);
var ch = (map.get("nt_code")).charAt(0);
var unit1 = map.get("nt_id");
ms.bioModelset.getAllSequenceBits(unit1, bsAtoms, bs);
var pt = bs.nextSetBit(0);
if (pt < 0) continue;
if ("ACGTU".indexOf(ch) < 0) atoms[pt].group.group1 = ch;
atoms[pt].group.dssrNT = map;
bs.clearAll();
}
}, "JM.ModelSet,~N");
Clazz.overrideMethod(c$, "getAtomicDSSRData", 
function(ms, modelIndex, dssrData, dataType){
var info = ms.getInfo(modelIndex, "dssr");
var list;
if (info == null || (list = info.get(dataType)) == null) return;
var bsAtoms = ms.am[modelIndex].bsAtoms;
try {
var bs =  new JU.BS();
for (var i = list.size(); --i >= 0; ) {
var map = list.get(i);
bs.clearAll();
ms.getSequenceBits(map.toString(), bsAtoms, bs);
for (var j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1)) dssrData[j] = i;

}
} catch (e) {
}
}, "JM.ModelSet,~N,~A,~S");
Clazz.overrideMethod(c$, "getDSSRFrame", 
function(nt){
var frame = nt.get("frame");
if (frame == null) return null;
var oxyz =  new Array(4);
for (var i = 4; --i >= 0; ) oxyz[i] =  new JU.P3();

this.getPoint(frame, "origin", oxyz[0]);
this.getPoint(frame, "x_axis", oxyz[1]);
this.getPoint(frame, "y_axis", oxyz[2]);
this.getPoint(frame, "z_axis", oxyz[3]);
return oxyz;
}, "java.util.Map");
Clazz.defineMethod(c$, "getPoint", 
function(frame, item, pt){
var xyz = frame.get(item);
pt.x = xyz.get(0).floatValue();
pt.y = xyz.get(1).floatValue();
pt.z = xyz.get(2).floatValue();
}, "java.util.Map,~S,JU.P3");
});
;//5.0.1-v7 Tue Jul 22 18:14:29 CDT 2025
