Clazz.declarePackage("JM");
Clazz.load(["JU.Edge", "JV.JC"], "JM.Bond", ["JU.C"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.atom1 = null;
this.atom2 = null;
this.mad = 0;
this.colix = 0;
this.shapeVisibilityFlags = 0;
Clazz.instantialize(this, arguments);}, JM, "Bond", JU.Edge);
Clazz.makeConstructor(c$, 
function(atom1, atom2, order, mad, colix){
Clazz.superConstructor (this, JM.Bond, []);
this.atom1 = atom1;
this.atom2 = atom2;
this.colix = colix;
this.setOrder(order);
this.setMad(mad);
}, "JM.Atom,JM.Atom,~N,~N,~N");
Clazz.defineMethod(c$, "setMad", 
function(mad){
this.mad = mad;
this.setShapeVisibility(mad != 0);
}, "~N");
Clazz.defineMethod(c$, "setShapeVisibility", 
function(isVisible){
var wasVisible = ((this.shapeVisibilityFlags & JM.Bond.myVisibilityFlag) != 0);
if (wasVisible == isVisible) return;
this.atom1.addDisplayedBond(JM.Bond.myVisibilityFlag, isVisible);
this.atom2.addDisplayedBond(JM.Bond.myVisibilityFlag, isVisible);
if (isVisible) this.shapeVisibilityFlags |= JM.Bond.myVisibilityFlag;
 else this.shapeVisibilityFlags &= ~JM.Bond.myVisibilityFlag;
}, "~B");
Clazz.defineMethod(c$, "getIdentity", 
function(){
return (this.index + 1) + " " + JU.Edge.getBondOrderNumberFromOrder(this.order) + " " + this.atom1.getInfo() + " -- " + this.atom2.getInfo() + " " + this.atom1.distance(this.atom2);
});
Clazz.overrideMethod(c$, "isCovalent", 
function(){
return (this.order & 1023) != 0;
});
Clazz.overrideMethod(c$, "isHydrogen", 
function(){
return JU.Edge.isOrderH(this.order);
});
Clazz.defineMethod(c$, "isStereo", 
function(){
return (this.order & 1024) != 0;
});
Clazz.overrideMethod(c$, "isPartial", 
function(){
return (this.order & 224) != 0;
});
Clazz.defineMethod(c$, "isAromatic", 
function(){
return (this.order & 512) != 0;
});
Clazz.defineMethod(c$, "getEnergy", 
function(){
return 0;
});
Clazz.defineMethod(c$, "getValence", 
function(){
return (!this.isCovalent() || this.order == 33 ? 0 : this.is(515) ? 1 : this.order & 7);
});
Clazz.defineMethod(c$, "deleteAtomReferences", 
function(){
if (this.atom1 != null) this.atom1.deleteBond(this);
if (this.atom2 != null) this.atom2.deleteBond(this);
this.atom1 = this.atom2 = null;
});
Clazz.defineMethod(c$, "setTranslucent", 
function(isTranslucent, translucentLevel){
this.colix = JU.C.getColixTranslucent3(this.colix, isTranslucent, translucentLevel);
}, "~B,~N");
Clazz.defineMethod(c$, "setOrder", 
function(order){
if (this.atom1.getElementNumber() == 16 && this.atom2.getElementNumber() == 16) order |= 256;
if (order == 512) order = 515;
this.order = order | (this.order & 131072);
}, "~N");
Clazz.overrideMethod(c$, "getAtomIndex1", 
function(){
return this.atom1.i;
});
Clazz.overrideMethod(c$, "getAtomIndex2", 
function(){
return this.atom2.i;
});
Clazz.overrideMethod(c$, "getCovalentOrder", 
function(){
return JU.Edge.getCovalentBondOrder(this.order);
});
Clazz.defineMethod(c$, "getOtherAtom", 
function(thisAtom){
return (this.atom1 === thisAtom ? this.atom2 : this.atom2 === thisAtom ? this.atom1 : null);
}, "JM.Atom");
Clazz.defineMethod(c$, "is", 
function(bondType){
return (this.order & 131071) == bondType;
}, "~N");
Clazz.overrideMethod(c$, "getOtherNode", 
function(thisAtom){
return (this.atom1 === thisAtom ? this.atom2 : this.atom2 === thisAtom || thisAtom == null ? this.atom1 : null);
}, "JU.SimpleNode");
Clazz.defineMethod(c$, "setAtropisomerOptions", 
function(){
var i1;
var i2 = 2147483647;
var bonds = this.atom1.bonds;
for (i1 = 0; i1 < bonds.length; i1++) {
var a = bonds[i1].getOtherAtom(this.atom1);
if (a !== this.atom2) break;
}
if (i1 < bonds.length) {
bonds = this.atom2.bonds;
for (i2 = 0; i2 < bonds.length; i2++) {
var a = bonds[i2].getOtherAtom(this.atom2);
if (a !== this.atom1) break;
}
}this.order = (i1 > 2 || i2 >= bonds.length || i2 > 2 ? 1 : JU.Edge.getAtropismOrder(i1 + 1, i2 + 1));
});
Clazz.overrideMethod(c$, "getCIPChirality", 
function(doCalculate){
return "";
}, "~B");
Clazz.overrideMethod(c$, "setCIPChirality", 
function(c){
}, "~N");
Clazz.overrideMethod(c$, "toString", 
function(){
return this.atom1 + " - " + this.atom2;
});
Clazz.overrideMethod(c$, "getAtom", 
function(i){
return (i == 1 ? this.atom2 : this.atom1);
}, "~N");
Clazz.defineMethod(c$, "isCovalentNotPartial0", 
function(){
return ((this.order & 1023) != 0 && this.order != 33);
});
c$.myVisibilityFlag = JV.JC.getShapeVisibilityFlag(1);
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
