Clazz.declarePackage("JS");
Clazz.load(["JS.CIPData"], "JS.CIPDataSmiles", ["JU.Lst", "$.Measure", "JU.BSUtil"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.smiles = null;
this.nodes = null;
Clazz.instantialize(this, arguments);}, JS, "CIPDataSmiles", JS.CIPData);
Clazz.prepareFields (c$, function(){
this.nodes =  new Array(6);
});
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, JS.CIPDataSmiles, []);
});
Clazz.overrideMethod(c$, "isSmiles", 
function(){
return true;
});
Clazz.defineMethod(c$, "setAtomsForSmiles", 
function(vwr, smiles){
this.vwr = vwr;
this.smiles = smiles;
this.atoms = vwr.getSmilesAtoms(smiles);
this.bsAtoms = JU.BSUtil.newBitSet2(0, this.atoms.length);
this.bsMolecule = this.bsAtoms.clone();
this.init();
return this;
}, "JV.Viewer,~S");
Clazz.overrideMethod(c$, "getList", 
function(smarts){
return this.vwr.getSubstructureSetArrayForNodes(smarts, this.atoms, 2);
}, "~S");
Clazz.overrideMethod(c$, "match", 
function(smarts){
return this.vwr.getSmartsMatchForNodes(smarts, this.atoms);
}, "~S");
Clazz.overrideMethod(c$, "getBondOrder", 
function(bond){
return (bond).getRealCovalentOrder();
}, "JU.SimpleEdge");
Clazz.overrideMethod(c$, "isCis", 
function(a, b, c, d){
var stereo1 = this.getStereoEdge(b.atom, a.atom);
var stereo2 = this.getStereoEdge(c.atom, d.atom);
return (stereo1 == 0 || stereo2 == 0 ? 0 : stereo1 != stereo2 ? 14 : 13);
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom");
Clazz.defineMethod(c$, "getStereoEdge", 
function(atom, winner){
var edges = atom.getEdges();
var order = 0;
for (var i = edges.length; --i >= 0; ) {
var edge = edges[i];
switch (order = edge.getCovalentOrder()) {
case 1025:
return (edge.getOtherNode(atom) === winner) == (edge.getAtom1() === atom) ? 1041 : order;
case 1041:
return (edges[i].getOtherNode(atom) === winner) == (edge.getAtom1() === atom) ? 1025 : order;
}
}
return 0;
}, "JU.SimpleNode,JU.SimpleNode");
Clazz.overrideMethod(c$, "isPositiveTorsion", 
function(a, b, c, d){
var center = this.findCumulativeCenter(b, c);
if (center == null) return 0;
var jn = center.stereo.getAlleneAtoms(false, null, center, b.atom);
if (jn == null) return 0;
center.stereo.setTopoCoordinates(center, null, null, jn, false);
var angle = JU.Measure.computeTorsion(jn[0].getXYZ(), jn[1].getXYZ(), jn[2].getXYZ(), jn[3].getXYZ(), true);
return ((angle > 0) == ((a.atom.getIndex() == jn[0].getIndex()) && (d.atom.getIndex() == jn[3].getIndex()) || (a.atom.getIndex() == jn[1].getIndex()) && (d.atom.getIndex() == jn[2].getIndex())) ? 18 : 17);
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom");
Clazz.defineMethod(c$, "findCumulativeCenter", 
function(a, a2){
var center = a.atom;
var c = null;
var b = null;
while (center != null && center !== a2.atom) {
var edges = center.getEdges();
for (var i = edges.length; --i >= 0; ) {
if (edges[i].getCovalentOrder() == 2 && (c = edges[i].getOtherNode(center)) !== b) {
var sa = c;
if (sa.stereo != null) {
return sa;
}}}
b = center;
center = c;
}
return null;
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom");
Clazz.overrideMethod(c$, "setCoord", 
function(atom, atoms){
var a = atom;
if (a.stereo == null) return false;
var edges = a.getEdges();
for (var i = edges.length; --i >= 0; ) this.nodes[i] = edges[i].getOtherNode(a);

a.stereo.setTopoCoordinates(a, null, null, this.nodes, false);
return true;
}, "JU.SimpleNode,~A");
Clazz.defineMethod(c$, "getSmilesChiralityArray", 
function(){
var chirality =  new JU.Lst();
for (var i = 0; i < this.atoms.length; i++) {
var a = this.atoms[i];
var pt = a.getPatternIndex();
if (pt >= 0) {
var c = a.getCIPChirality(false);
chirality.addLast(c);
}}
return chirality.toArray( new Array(chirality.size()));
});
});
;//5.0.1-v7 Tue Jul 22 18:14:29 CDT 2025
