Clazz.declarePackage("J.shapespecial");
Clazz.load(null, "J.shapespecial.Polyhedron", ["java.util.Hashtable", "JU.AU", "$.BS", "$.Lst", "$.Measure", "$.P3", "$.PT", "$.V3", "J.api.Interface", "JS.SV", "JU.C", "$.Elements", "$.Escape", "$.Logger", "$.Normix", "$.Point3fi"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.info = null;
this.id = null;
this.center = null;
this.centralAtom = null;
this.vertices = null;
this.triangles = null;
this.faces = null;
this.nVertices = 0;
this.collapsed = false;
this.bsFlat = null;
this.distanceRef = 0;
this.normals = null;
this.normixes = null;
this.planes = null;
this.smiles = null;
this.smarts = null;
this.polySmiles = null;
this.pointGroup = null;
this.pointGroupFamily = null;
this.volume = null;
this.visible = true;
this.isFullyLit = false;
this.isValid = true;
this.colixEdge = 0;
this.visibilityFlags = 0;
this.colix = 23;
this.modelIndex = -2147483648;
this.offset = null;
this.scale = 1;
this.pointScale = 0;
this.faceTriangles = null;
this.elemNos = null;
this.v0 = null;
Clazz.instantialize(this, arguments);}, J.shapespecial, "Polyhedron", null);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "set", 
function(id, modelIndex, atomOrPt, points, nPoints, vertexCount, triangles, triangleCount, faces, faceTriangles, normals, bsFlat, collapsed, distanceRef, pointScale){
this.pointScale = pointScale;
this.distanceRef = distanceRef;
if (id == null) {
this.centralAtom = atomOrPt;
this.modelIndex = this.centralAtom.mi;
} else {
this.id = id;
this.center = atomOrPt;
this.modelIndex = modelIndex;
}this.nVertices = vertexCount;
this.vertices =  new Array(nPoints + 1);
this.normals =  new Array(triangleCount);
this.faces = faces;
this.faceTriangles = faceTriangles;
this.bsFlat = bsFlat;
this.triangles = JU.AU.newInt2(triangleCount);
for (var i = nPoints + 1; --i >= 0; ) this.vertices[i] = points[i];

for (var i = triangleCount; --i >= 0; ) this.normals[i] = JU.V3.newV(normals[i]);

for (var i = triangleCount; --i >= 0; ) this.triangles[i] = triangles[i];

this.collapsed = collapsed;
return this;
}, "~S,~N,JU.P3,~A,~N,~N,~A,~N,~A,~A,~A,JU.BS,~B,~N,~N");
Clazz.defineMethod(c$, "setInfo", 
function(vwr, info, at){
try {
var o = info.get("id");
this.collapsed = info.containsKey("collapsed");
var isSV = (!((typeof(o)=='string')));
if (o != null) this.id = (isSV ? (info.get("id")).asString() : o.toString());
if (this.id == null) {
this.centralAtom = at[(info.get("atomIndex")).intValue];
this.modelIndex = this.centralAtom.mi;
} else {
o = info.get("center");
this.center = JU.P3.newP(isSV ? JS.SV.ptValue(o) : o);
o = info.get("modelIndex");
this.modelIndex = (o == null ? vwr.am.cmi : isSV ? (o).intValue : (o).intValue());
o = info.get("color");
this.colix = JU.C.getColixS(o == null ? "gold" : isSV ? (o).asString() : o);
o = info.get("colorEdge");
if (o != null) this.colixEdge = JU.C.getColixS(isSV ? (o).asString() : o.toString());
o = info.get("offset");
if (o != null) this.offset = JU.P3.newP(isSV ? JS.SV.ptValue(o) : o);
o = info.get("scale");
if (o != null) this.scale = (isSV ? JS.SV.fValue(o) : (o).floatValue());
}o = info.get("vertices");
var lst = (isSV ? (o).getList() : o);
o = info.get("vertexCount");
var needTriangles = false;
if (o != null) {
this.nVertices = (isSV ? (o).intValue : (o).intValue());
this.vertices =  new Array(lst.size());
o = info.get("r");
if (o != null) this.distanceRef = (isSV ? (o).asFloat() : (o).floatValue());
} else {
this.nVertices = lst.size();
this.vertices =  new Array(this.nVertices + 1);
if (this.center == null) {
this.vertices[this.nVertices] = JS.SV.ptValue(info.get("ptRef"));
} else {
this.vertices[this.nVertices] = this.center;
needTriangles = true;
}}for (var i = lst.size(); --i >= 0; ) {
o = lst.get(i);
this.vertices[i] = (isSV ? JS.SV.ptValue(o) : o);
}
o = info.get("explodeOffset");
if (o != null) this.setZeroOffset((o).floatValue());
o = info.get("elemNos");
if (o != null) {
lst = (isSV ? (o).getList() : o);
for (var i = this.nVertices; --i >= 0; ) {
o = lst.get(i);
var n = (isSV ? (o).intValue : (o).intValue());
if (n > 0) {
var p = JU.Point3fi.newPF(this.vertices[i], 0);
p.sD = n;
this.vertices[i] = p;
}}
}o = info.get("pointScale");
if (o != null) this.pointScale = Math.max(0, (isSV ? JS.SV.fValue(o) : (o).floatValue()));
this.faces = this.toInt2(isSV, info.get("faces"));
o = info.get("triangles");
if (o == null) {
if (needTriangles) {
this.faceTriangles = JU.AU.newInt2(this.faces.length);
this.triangles = (J.api.Interface.getInterface("JU.MeshCapper", vwr, "script")).set(null).triangulateFaces(this.faces, this.vertices, this.faceTriangles);
} else {
this.triangles = this.faces;
this.faces = null;
}} else {
this.triangles = this.toInt2(isSV, o);
}this.normals =  new Array(this.triangles.length);
var vAB =  new JU.V3();
for (var i = this.triangles.length; --i >= 0; ) {
this.normals[i] =  new JU.V3();
var a = this.triangles[i];
JU.Measure.getNormalThroughPoints(this.vertices[a[0]], this.vertices[a[1]], this.vertices[a[2]], this.normals[i], vAB);
}
o = info.get("bsFlat");
this.bsFlat = (o == null ?  new JU.BS() : isSV ? JS.SV.getBitSet(o, false) : o);
if (info.containsKey("volume")) info.put("volume", this.getVolume());
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
return null;
} else {
throw e;
}
}
return this;
}, "JV.Viewer,java.util.Map,~A");
Clazz.defineMethod(c$, "toInt2", 
function(isSV, o){
var lst = (isSV ? (o).getList() : o);
var ai = JU.AU.newInt2(lst.size());
for (var i = ai.length; --i >= 0; ) {
o = lst.get(i);
if (isSV) {
var lst2 = (o).getList();
var a = ai[i] =  Clazz.newIntArray (lst2.size(), 0);
for (var j = a.length; --j >= 0; ) a[j] = lst2.get(j).intValue;

} else {
ai[i] = o;
}}
return ai;
}, "~B,~O");
Clazz.defineMethod(c$, "getInfo", 
function(vwr, property){
var isState = (property == null);
var isFaceCalc = (!isState);
var info = this.info;
if (!isState && info != null && (!isFaceCalc || info.containsKey("face_types")) && !JU.Logger.debugging) return info;
info =  new java.util.Hashtable();
info.put("vertexCount", Integer.$valueOf(this.nVertices));
var nv = (isState ? this.vertices.length : this.nVertices);
var pts =  new Array(nv);
for (var i = 0; i < nv; i++) pts[i] = JU.P3.newP(this.vertices[i]);

info.put("vertices", pts);
info.put("elemNos", this.getElemNos(true));
if (this.id == null) {
info.put("atomIndex", Integer.$valueOf(this.centralAtom.i));
} else {
info.put("id", this.id);
info.put("center", JU.P3.newP(this.center));
info.put("color", JU.C.getHexCode(this.colix));
info.put("colorEdge", JU.C.getHexCode(this.colixEdge == 0 ? this.colix : this.colixEdge));
if (this.offset != null) info.put("offset", this.offset);
if (this.scale != 1) info.put("scale", Float.$valueOf(this.scale));
}if (this.id != null || !isState) info.put("modelIndex", Integer.$valueOf(this.modelIndex));
if (!isState) {
this.info = info;
if (this.id == null) {
info.put("center", JU.P3.newP(this.centralAtom));
info.put("modelNumber", Integer.$valueOf(this.centralAtom.getModelNumber()));
info.put("atomNumber", Integer.$valueOf(this.centralAtom.getAtomNumber()));
info.put("atomName", this.centralAtom.getInfo());
info.put("element", this.centralAtom.getElementSymbol());
var energy = vwr.ms.getInfo(this.centralAtom.mi, "Energy");
if (energy != null) info.put("energy", energy);
}info.put("triangleCount", Integer.$valueOf(this.triangles.length));
info.put("volume", this.getVolume());
var names =  new Array(this.nVertices);
var indices =  Clazz.newIntArray (this.nVertices, 0);
for (var i = this.nVertices; --i >= 0; ) {
var pt = this.vertices[i];
var isNode = Clazz.instanceOf(pt,"JM.Atom");
names[i] = (isNode ? (pt).getAtomName() : Clazz.instanceOf(pt,"JU.Point3fi") ? JU.Elements.elementSymbolFromNumber((pt).sD) : "");
indices[i] = (isNode ? (pt).getIndex() : -1);
}
info.put("atomNames", names);
info.put("vertexIndices", indices);
if (this.faces != null && !this.collapsed && this.faceTriangles != null) {
info.put("faceCount", Integer.$valueOf(this.faces.length));
info.put("faceTriangles", this.faceTriangles);
if (isFaceCalc) {
var faceTypes =  Clazz.newIntArray (this.faces.length, 0);
var faceAreas =  Clazz.newFloatArray (this.faces.length, 0);
var facePoints =  new JU.Lst();
var vAB =  new JU.V3();
var vAC =  new JU.V3();
var vTemp =  new JU.V3();
for (var i = this.faces.length; --i >= 0; ) {
var face = this.faces[i];
faceTypes[i] = face.length;
var f = 0;
var ft = this.faceTriangles[i];
for (var j = ft.length; --j >= 0; ) {
var t = this.triangles[ft[j]];
f += this.triangleArea(t[0], t[1], t[2], vAB, vAC, vTemp);
}
faceAreas[i] = f;
var fpts =  new Array(face.length);
for (var j = face.length; --j >= 0; ) fpts[j] = this.vertices[face[j]];

facePoints.addLast(fpts);
}
info.put("face_types", faceTypes);
info.put("face_areas", faceAreas);
info.put("face_points", facePoints);
}}if (this.smarts != null) info.put("smarts", this.smarts);
if (this.smiles != null) info.put("smiles", this.smiles);
if (this.polySmiles != null) info.put("polySmiles", this.polySmiles);
if (this.pointGroup != null) info.put("pointGroup", this.pointGroup.getPointGroupName());
if (this.pointGroupFamily != null) info.put("pointGroupFamily", this.pointGroupFamily.getPointGroupName());
}if (this.pointScale > 0) info.put("pointScale", Float.$valueOf(this.pointScale));
if (this.faces != null) info.put("faces", this.faces);
if (isState || JU.Logger.debugging) {
info.put("bsFlat", this.bsFlat);
if (this.collapsed) info.put("collapsed", Boolean.$valueOf(this.collapsed));
if (this.distanceRef != 0) info.put("r", Float.$valueOf(this.distanceRef));
var n =  new Array(this.normals.length);
for (var i = n.length; --i >= 0; ) n[i] = JU.P3.newP(this.normals[i]);

if (!isState) info.put("normals", n);
info.put("triangles", JU.AU.arrayCopyII(this.triangles, this.triangles.length));
}return info;
}, "JV.Viewer,~S");
Clazz.defineMethod(c$, "setPointScale", 
function(scale){
this.pointScale = scale;
this.elemNos = null;
}, "~N");
Clazz.defineMethod(c$, "getElemNos", 
function(forInfo){
if (forInfo) {
var a =  Clazz.newIntArray (this.nVertices, 0);
for (var i = 0; i < this.nVertices; i++) {
var pt = this.vertices[i];
a[i] = (Clazz.instanceOf(pt,"JM.Atom") ? (pt).getElementNumber() : Clazz.instanceOf(pt,"JU.Point3fi") ? (pt).sD : -2);
}
return a;
}if (this.elemNos == null) this.elemNos =  Clazz.newIntArray (this.nVertices, 0);
for (var i = 0; i < this.nVertices; i++) {
var pt = this.vertices[i];
this.elemNos[i] = (Clazz.instanceOf(pt,"JM.Atom") ? (pt).getAtomicAndIsotopeNumber() : Clazz.instanceOf(pt,"JU.Point3fi") ? (pt).sD : -2);
}
return this.elemNos;
}, "~B");
Clazz.defineMethod(c$, "getSymmetry", 
function(vwr, withPointGroup){
if (this.id == null) {
if (this.smarts == null) {
this.info = null;
var sm = vwr.getSmilesMatcher();
try {
var details = (this.distanceRef <= 0 ? null : "r=" + this.distanceRef);
this.polySmiles = sm.polyhedronToSmiles(this.centralAtom, this.faces, this.nVertices, this.vertices, 1 | 65536 | (JU.Logger.debugging ? 131072 : 0), details);
this.smarts = sm.polyhedronToSmiles(this.centralAtom, this.faces, this.nVertices, null, 16384, null);
this.smiles = sm.polyhedronToSmiles(this.centralAtom, this.faces, this.nVertices, this.vertices, 1, null);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
}}if (!withPointGroup) return null;
if (this.pointGroup == null) {
var pts =  new Array(this.nVertices);
for (var i = pts.length; --i >= 0; ) pts[i] = this.vertices[i];

this.pointGroup = vwr.getSymTemp().setPointGroup(vwr, null, null, pts, null, false, vwr.getFloat(570425382), vwr.getFloat(570425384), pts.length, true);
for (var i = pts.length; --i >= 0; ) pts[i] = JU.P3.newP(this.vertices[i]);

this.pointGroupFamily = vwr.getSymTemp().setPointGroup(vwr, null, null, pts, null, false, vwr.getFloat(570425382), vwr.getFloat(570425384), pts.length, true);
}return (this.center == null ? this.centralAtom : this.center) + "    \t" + this.pointGroup.getPointGroupName() + "\t" + this.pointGroupFamily.getPointGroupName();
}, "JV.Viewer,~B");
Clazz.defineMethod(c$, "getVolume", 
function(){
if (this.volume != null) return this.volume;
var vAB =  new JU.V3();
var vAC =  new JU.V3();
var vTemp =  new JU.V3();
var v = 0;
if (this.bsFlat.cardinality() < this.triangles.length) for (var i = this.triangles.length; --i >= 0; ) {
var t = this.triangles[i];
v += this.triangleVolume(t[0], t[1], t[2], vAB, vAC, vTemp);
}
return Float.$valueOf(v / 6);
});
Clazz.defineMethod(c$, "triangleArea", 
function(i, j, k, vAB, vAC, vTemp){
vAB.sub2(this.vertices[j], this.vertices[i]);
vAC.sub2(this.vertices[k], this.vertices[i]);
vTemp.cross(vAB, vAC);
return vTemp.length();
}, "~N,~N,~N,JU.V3,JU.V3,JU.V3");
Clazz.defineMethod(c$, "triangleVolume", 
function(i, j, k, vAB, vAC, vTemp){
vAB.setT(this.vertices[i]);
vAC.setT(this.vertices[j]);
vTemp.cross(vAB, vAC);
vAC.setT(this.vertices[k]);
return vAC.dot(vTemp);
}, "~N,~N,~N,JU.V3,JU.V3,JU.V3");
Clazz.defineMethod(c$, "getState", 
function(vwr){
var ident = (this.id == null ? "({" + this.centralAtom.i + "})" : "ID " + JU.Escape.e(this.id));
return "  polyhedron @{" + JU.Escape.e(this.getInfo(vwr, null)) + "} " + (this.isFullyLit ? " fullyLit" : "") + ";" + (this.visible ? "" : "polyhedra " + ident + " off;") + "\n";
}, "JV.Viewer");
Clazz.defineMethod(c$, "move", 
function(mat, bsMoved){
this.info = null;
for (var i = 0; i < this.nVertices; i++) {
var p = this.vertices[i];
if (Clazz.instanceOf(p,"JM.Atom")) {
if (bsMoved.get((p).i)) continue;
p = this.vertices[i] = JU.P3.newP(p);
}mat.rotTrans(p);
}
for (var i = this.normals.length; --i >= 0; ) mat.rotate(this.normals[i]);

this.normixes = null;
}, "JU.M4,JU.BS");
Clazz.defineMethod(c$, "getNormixes", 
function(){
if (this.normixes == null) {
this.normixes =  Clazz.newShortArray (this.normals.length, 0);
var bsTemp =  new JU.BS();
for (var i = this.normals.length; --i >= 0; ) this.normixes[i] = (this.bsFlat.get(i) ? JU.Normix.get2SidedNormix(this.normals[i], bsTemp) : JU.Normix.getNormixV(this.normals[i], bsTemp));

}return this.normixes;
});
Clazz.defineMethod(c$, "setOffset", 
function(value){
this.planes = null;
if (this.center == null) return;
var v = JU.P3.newP(value);
if (this.offset != null) value.sub(this.offset);
this.offset = v;
for (var i = this.vertices.length; --i >= 0; ) this.vertices[i].add(value);

}, "JU.P3");
Clazz.defineMethod(c$, "setZeroOffset", 
function(value){
if (this.id == null || this.center == null || value == 0) return;
var d = this.center.length();
if (d < 0.0001) return;
var v = JU.P3.newP(this.center);
v.scale(value / d);
this.setOffset(v);
}, "~N");
Clazz.defineMethod(c$, "list", 
function(sb){
if (this.id == null) {
sb.append(" atomIndex:" + this.centralAtom.i);
sb.append(" atomName:" + this.centralAtom.getAtomName());
sb.append(" element:" + this.centralAtom.getElementSymbol());
} else {
sb.append(" id:" + this.id);
sb.append("; center:" + JU.PT.sprintf("{%6.3p %6.3p %6.3p}", "p",  Clazz.newArray(-1, [this.center]))).append("; visible:" + this.visible);
}sb.append("; model:" + this.modelIndex).append("; vertices:" + this.nVertices).append("; faces:" + this.faces.length).append("; volume:" + JU.PT.formatD(this.getVolume().doubleValue(), 1, 3, false, false));
if (this.scale != 1) sb.append("; scale:" + this.scale);
sb.append("\n");
}, "JU.SB");
});
;//5.0.1-v7 Mon Mar 16 22:19:28 CDT 2026
