Clazz.declarePackage("J.shape");
Clazz.load(["J.shape.Shape", "JU.P3i"], "J.shape.Sticks", ["java.util.Hashtable", "JU.BS", "$.P3", "J.c.PAL", "JU.BSUtil", "$.C", "$.Edge", "$.Escape"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.myMask = 0;
this.reportAll = false;
this.haveStrutPoints = false;
this.bsOrderSet = null;
this.selectedBonds = null;
this.closestAtom = null;
this.ptXY = null;
Clazz.instantialize(this, arguments);}, J.shape, "Sticks", J.shape.Shape);
Clazz.prepareFields (c$, function(){
this.closestAtom =  Clazz.newIntArray (1, 0);
this.ptXY =  new JU.P3i();
});
Clazz.overrideMethod(c$, "initShape", 
function(){
this.myMask = 1023;
this.reportAll = false;
});
Clazz.overrideMethod(c$, "setSize", 
function(size, bsSelected){
if (size == 2147483647) {
this.selectedBonds = JU.BSUtil.copy(bsSelected);
return;
}if (size == -2147483648) {
if (this.bsOrderSet == null) this.bsOrderSet =  new JU.BS();
this.bsOrderSet.or(bsSelected);
return;
}if (this.bsSizeSet == null) this.bsSizeSet =  new JU.BS();
var iter = (this.selectedBonds != null ? this.ms.getBondIterator(this.selectedBonds) : this.ms.getBondIteratorForType(this.myMask, bsSelected));
var mad = size;
while (iter.hasNext()) {
this.bsSizeSet.set(iter.nextIndex());
var b = iter.next();
if (b != null) b.setMad(mad);
}
}, "~N,JU.BS");
Clazz.overrideMethod(c$, "setProperty", 
function(propertyName, value, bs){
if ("type" === propertyName) {
this.myMask = (value).intValue();
return;
}if ("reportAll" === propertyName) {
this.reportAll = true;
return;
}if ("reset" === propertyName) {
this.bsOrderSet = null;
this.bsSizeSet = null;
this.bsColixSet = null;
this.selectedBonds = null;
return;
}if ("bondOrder" === propertyName) {
if (this.bsOrderSet == null) this.bsOrderSet =  new JU.BS();
var order = (value).intValue();
var iter = (this.selectedBonds != null ? this.ms.getBondIterator(this.selectedBonds) : this.ms.getBondIteratorForType(65535, bs));
while (iter.hasNext()) {
this.bsOrderSet.set(iter.nextIndex());
iter.next().setOrder(order);
}
return;
}if ("color" === propertyName) {
if (this.bsColixSet == null) this.bsColixSet =  new JU.BS();
var colix = JU.C.getColixO(value);
var pal = (Clazz.instanceOf(value,"J.c.PAL") ? value : null);
if (pal === J.c.PAL.TYPE || pal === J.c.PAL.ENERGY) {
var isEnergy = (pal === J.c.PAL.ENERGY);
var iter = (this.selectedBonds != null ? this.ms.getBondIterator(this.selectedBonds) : this.ms.getBondIteratorForType(this.myMask, bs));
while (iter.hasNext()) {
this.bsColixSet.set(iter.nextIndex());
var bond = iter.next();
bond.colix = (isEnergy ? this.getColixB(colix, pal.id, bond) : JU.C.getColix(JU.Edge.getArgbHbondType(bond.order)));
}
return;
}if (colix == 2 && pal !== J.c.PAL.CPK) return;
var iter = (this.selectedBonds != null ? this.ms.getBondIterator(this.selectedBonds) : this.ms.getBondIteratorForType(this.myMask, bs));
while (iter.hasNext()) {
var iBond = iter.nextIndex();
iter.next().colix = colix;
this.bsColixSet.setBitTo(iBond, (colix != 0 && colix != 2));
}
return;
}if ("translucency" === propertyName) {
if (this.bsColixSet == null) this.bsColixSet =  new JU.BS();
var isTranslucent = ((value).equals("translucent"));
var iter = (this.selectedBonds != null ? this.ms.getBondIterator(this.selectedBonds) : this.ms.getBondIteratorForType(this.myMask, bs));
while (iter.hasNext()) {
this.bsColixSet.set(iter.nextIndex());
iter.next().setTranslucent(isTranslucent, this.translucentLevel);
}
return;
}if ("deleteModelAtoms" === propertyName) {
return;
}this.setPropS(propertyName, value, bs);
}, "~S,~O,JU.BS");
Clazz.overrideMethod(c$, "getProperty", 
function(property, index){
if (property.equals("selectionState")) return (this.selectedBonds != null ? "select BONDS " + JU.Escape.eBS(this.selectedBonds) + "\n" : "");
if (property.equals("sets")) return  Clazz.newArray(-1, [this.bsOrderSet, this.bsSizeSet, this.bsColixSet]);
return null;
}, "~S,~N");
Clazz.overrideMethod(c$, "setAtomClickability", 
function(){
var bonds = this.ms.bo;
for (var i = this.ms.bondCount; --i >= 0; ) {
var bond = bonds[i];
if (bond == null || (bond.shapeVisibilityFlags & this.vf) == 0 || this.ms.isAtomHidden(bond.atom1.i) || this.ms.isAtomHidden(bond.atom2.i)) continue;
bond.atom1.setClickable(this.vf);
bond.atom2.setClickable(this.vf);
}
});
Clazz.overrideMethod(c$, "getShapeState", 
function(){
return null;
});
Clazz.overrideMethod(c$, "checkObjectHovered", 
function(x, y, bsVisible){
var pt =  new JU.P3();
var bond = this.findPickedBond(x, y, bsVisible, pt, this.closestAtom);
if (bond == null) return false;
this.vwr.highlightBond(bond.index, this.closestAtom[0], x, y);
return true;
}, "~N,~N,JU.BS");
Clazz.overrideMethod(c$, "checkObjectClicked", 
function(x, y, modifiers, bsVisible, drawPicking){
var pt =  new JU.P3();
var bond = this.findPickedBond(x, y, bsVisible, pt, this.closestAtom);
if (bond == null) return null;
var modelIndex = bond.atom1.mi;
var info = bond.getIdentity();
var map =  new java.util.Hashtable();
map.put("pt", pt);
map.put("index", Integer.$valueOf(bond.index));
map.put("modelIndex", Integer.$valueOf(modelIndex));
map.put("model", this.vwr.getModelNumberDotted(modelIndex));
map.put("type", "bond");
map.put("info", info);
this.vwr.setStatusAtomPicked(-3, "[\"bond\",\"" + bond.getIdentity() + "\"," + pt.x + "," + pt.y + "," + pt.z + "]", map, false);
return map;
}, "~N,~N,~N,JU.BS,~B");
Clazz.defineMethod(c$, "findPickedBond", 
function(x, y, bsVisible, pt, closestAtom){
var dmin2 = 100;
if (this.vwr.gdata.isAntialiased()) {
x <<= 1;
y <<= 1;
dmin2 <<= 1;
}var pickedBond = null;
var v =  new JU.P3();
var bonds = this.ms.bo;
for (var i = this.ms.bondCount; --i >= 0; ) {
var bond = bonds[i];
if (bond == null || bond.shapeVisibilityFlags == 0) continue;
var atom1 = bond.atom1;
var atom2 = bond.atom2;
if (!atom1.checkVisible() || !atom2.checkVisible()) continue;
v.ave(atom1, atom2);
var d2 = this.coordinateInRange(x, y, v, dmin2, this.ptXY);
if (d2 >= 0 && Math.abs(atom1.sY - atom2.sY) + Math.abs(atom1.sX - atom2.sX) > 40) {
var f = 1 * (this.ptXY.x - atom1.sX) / (atom2.sX - atom1.sX);
if (f < 0.4 || f > 0.6) continue;
dmin2 = d2;
pickedBond = bond;
if (closestAtom != null) closestAtom[0] = (f < 0.5 ? atom1.i : atom2.i);
pt.setT(v);
}}
return pickedBond;
}, "~N,~N,JU.BS,JU.P3,~A");
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
