Clazz.declarePackage("JS");
Clazz.load(["JU.Edge"], "JS.SmilesBond", ["JS.InvalidSmilesException"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.atom1 = null;
this.atom2 = null;
this.isNot = false;
this.matchingBond = null;
this.primitives = null;
this.nPrimitives = 0;
this.bondsOr = null;
this.nBondsOr = 0;
this.isConnection = false;
this.atropType = null;
this.isChain = false;
Clazz.instantialize(this, arguments);}, JS, "SmilesBond", JU.Edge);
Clazz.makeConstructor(c$, 
function(atom1, atom2, bondType, isNot){
Clazz.superConstructor (this, JS.SmilesBond, []);
this.set2(bondType, isNot);
this.set2a(atom1, atom2);
}, "JS.SmilesAtom,JS.SmilesAtom,~N,~B");
c$.getBondOrderString = Clazz.defineMethod(c$, "getBondOrderString", 
function(order){
switch (order) {
case 2:
return "=";
case 3:
return "#";
case 4:
return "$";
default:
return "";
}
}, "~N");
c$.getBondTypeFromCode = Clazz.defineMethod(c$, "getBondTypeFromCode", 
function(code){
switch ((code).charCodeAt(0)) {
case 46:
return 0;
case 45:
return 1;
case 61:
return 2;
case 35:
return 3;
case 36:
return 4;
case 58:
return 17;
case 47:
return 1025;
case 92:
return 1041;
case 94:
return 65537;
case 96:
return 65538;
case 64:
return 65;
case 126:
return 81;
case 43:
return 96;
}
return -1;
}, "~S");
Clazz.defineMethod(c$, "getAtom1", 
function(){
return this.atom1;
});
Clazz.defineMethod(c$, "set", 
function(bond){
this.order = bond.order;
this.isNot = bond.isNot;
this.primitives = bond.primitives;
this.nPrimitives = bond.nPrimitives;
this.bondsOr = bond.bondsOr;
this.nBondsOr = bond.nBondsOr;
this.atropType = bond.atropType;
}, "JS.SmilesBond");
Clazz.defineMethod(c$, "setAtropType", 
function(nn){
this.atropType =  Clazz.newIntArray(-1, [Clazz.doubleToInt(nn / 10) - 1, nn % 10 - 1]);
}, "~N");
Clazz.defineMethod(c$, "setPrimitive", 
function(i){
var p = this.primitives[i];
this.order = p.order;
this.isNot = p.isNot;
this.atropType = p.atropType;
return p;
}, "~N");
Clazz.defineMethod(c$, "addBondOr", 
function(){
if (this.bondsOr == null) this.bondsOr =  new Array(2);
if (this.nBondsOr >= this.bondsOr.length) {
var tmp =  new Array(this.bondsOr.length * 2);
System.arraycopy(this.bondsOr, 0, tmp, 0, this.bondsOr.length);
this.bondsOr = tmp;
}var sBond =  new JS.SmilesBond(null, null, -1, false);
this.bondsOr[this.nBondsOr] = sBond;
this.nBondsOr++;
return sBond;
});
Clazz.defineMethod(c$, "addPrimitive", 
function(){
if (this.primitives == null) this.primitives =  new Array(2);
if (this.nPrimitives >= this.primitives.length) {
var tmp =  new Array(this.primitives.length * 2);
System.arraycopy(this.primitives, 0, tmp, 0, this.primitives.length);
this.primitives = tmp;
}var sBond =  new JS.SmilesBond(null, null, -1, false);
this.primitives[this.nPrimitives] = sBond;
this.nPrimitives++;
return sBond;
});
Clazz.overrideMethod(c$, "toString", 
function(){
return this.atom1 + " -" + (this.isNot ? "!" : "") + this.order + "- " + this.atom2;
});
Clazz.defineMethod(c$, "set2", 
function(bondType, isNot){
this.order = bondType;
this.isNot = isNot;
}, "~N,~B");
Clazz.defineMethod(c$, "set2a", 
function(a1, a2){
if (a1 != null) {
this.atom1 = a1;
a1.addBond(this);
}if (a2 != null) {
this.atom2 = a2;
if (a2.isBioAtomWild && this.atom1.isBioAtomWild) this.order = 96;
a2.isFirst = false;
a2.addBond(this);
}}, "JS.SmilesAtom,JS.SmilesAtom");
Clazz.defineMethod(c$, "setAtom2", 
function(atom, molecule){
this.atom2 = atom;
if (this.atom2 != null) {
atom.addBond(this);
this.isConnection = true;
}}, "JS.SmilesAtom,JS.SmilesSearch");
Clazz.defineMethod(c$, "isFromPreviousTo", 
function(atom){
return (!this.isConnection && this.atom2 === atom);
}, "JS.SmilesAtom");
c$.isBondType = Clazz.defineMethod(c$, "isBondType", 
function(ch, isSearch, isBioSequence){
if (ch == '>') return 1;
if ("-=#$:/\\.~^`+!,&;@".indexOf(ch) < 0) return 0;
if (!isSearch && "-=#$:/\\.~^`".indexOf(ch) < 0) throw  new JS.InvalidSmilesException("SMARTS bond type " + ch + " not allowed in SMILES");
switch ((ch).charCodeAt(0)) {
case 126:
return (isBioSequence ? 0 : 1);
case 94:
case 96:
return -1;
default:
return 1;
}
}, "~S,~B,~B");
Clazz.defineMethod(c$, "getValence", 
function(){
return (this.order & 7);
});
Clazz.defineMethod(c$, "getOtherAtom", 
function(a){
return (this.atom1 === a ? this.atom2 : this.atom1);
}, "JS.SmilesAtom");
Clazz.overrideMethod(c$, "getAtomIndex1", 
function(){
return this.atom1.index;
});
Clazz.overrideMethod(c$, "getAtomIndex2", 
function(){
return this.atom2.index;
});
Clazz.overrideMethod(c$, "getCovalentOrder", 
function(){
return this.order & 131071;
});
Clazz.overrideMethod(c$, "getOtherNode", 
function(atom){
return (atom === this.atom1 ? this.atom2 : atom === this.atom2 || atom == null ? this.atom1 : null);
}, "JU.SimpleNode");
Clazz.overrideMethod(c$, "isCovalent", 
function(){
return this.order != 112;
});
Clazz.overrideMethod(c$, "isPartial", 
function(){
return false;
});
Clazz.overrideMethod(c$, "isHydrogen", 
function(){
return this.order == 112;
});
Clazz.defineMethod(c$, "switchAtoms", 
function(){
var a = this.atom1;
this.atom1 = this.atom2;
this.atom2 = a;
switch (this.order & 131071) {
case 65537:
this.order = 65538;
break;
case 65538:
this.order = 65537;
break;
case 1025:
this.order = 1041;
break;
case 1041:
this.order = 1025;
break;
}
});
Clazz.defineMethod(c$, "getRealCovalentOrder", 
function(){
switch (this.order & 131071) {
case 65537:
case 65538:
case 1025:
case 1041:
return 1;
}
return this.order & 131071;
});
Clazz.defineMethod(c$, "getMatchingBond", 
function(){
return this.matchingBond == null ? this : this.matchingBond;
});
Clazz.overrideMethod(c$, "getAtom", 
function(i){
return (i == 1 ? this.atom2 : this.atom1);
}, "~N");
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
