(function(Clazz
,Clazz_getClassName
,Clazz_newLongArray
,Clazz_doubleToByte
,Clazz_doubleToInt
,Clazz_doubleToLong
,Clazz_declarePackage
,Clazz_instanceOf
,Clazz_load
,Clazz_instantialize
,Clazz_decorateAsClass
,Clazz_floatToInt
,Clazz_floatToLong
,Clazz_makeConstructor
,Clazz_defineEnumConstant
,Clazz_exceptionOf
,Clazz_newIntArray
,Clazz_newFloatArray
,Clazz_declareType
,Clazz_prepareFields
,Clazz_superConstructor
,Clazz_newByteArray
,Clazz_declareInterface
,Clazz_newShortArray
,Clazz_innerTypeInstance
,Clazz_isClassDefined
,Clazz_prepareCallback
,Clazz_newArray
,Clazz_castNullAs
,Clazz_floatToShort
,Clazz_superCall
,Clazz_decorateAsType
,Clazz_newBooleanArray
,Clazz_newCharArray
,Clazz_implementOf
,Clazz_newDoubleArray
,Clazz_overrideConstructor
,Clazz_clone
,Clazz_doubleToShort
,Clazz_getInheritedLevel
,Clazz_getParamsType
,Clazz_isAF
,Clazz_isAB
,Clazz_isAI
,Clazz_isAS
,Clazz_isASS
,Clazz_isAP
,Clazz_isAFloat
,Clazz_isAII
,Clazz_isAFF
,Clazz_isAFFF
,Clazz_tryToSearchAndExecute
,Clazz_getStackTrace
,Clazz_inheritArgs
,Clazz_alert
,Clazz_defineMethod
,Clazz_overrideMethod
,Clazz_declareAnonymous
//,Clazz_checkPrivateMethod
,Clazz_cloneFinals
){
var $t$;
//var c$;
Clazz_declarePackage("J.api");
Clazz_declareInterface(J.api, "JmolSceneGenerator");
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
Clazz_declarePackage("J.adapter.readers.pymol");
Clazz_load(["java.util.Hashtable", "JU.Lst"], "J.adapter.readers.pymol.PickleReader", ["JU.AU", "JU.Logger"], function(){
var c$ = Clazz_decorateAsClass(function(){
this.vwr = null;
this.binaryDoc = null;
this.stack = null;
this.marks = null;
this.build = null;
this.memo = null;
this.logging = false;
this.id = 0;
this.markCount = 0;
this.filePt = 0;
this.emptyListPt = 0;
this.thisSection = null;
this.inMovie = false;
this.inNames = false;
this.thisName = null;
this.lastMark = 0;
this.retrieveCount = 0;
this.ipt = 0;
this.aTemp = null;
Clazz_instantialize(this, arguments);}, J.adapter.readers.pymol, "PickleReader", null);
Clazz_prepareFields (c$, function(){
this.stack =  new JU.Lst();
this.marks =  new JU.Lst();
this.build =  new JU.Lst();
this.memo =  new java.util.Hashtable();
this.aTemp =  Clazz_newByteArray (16, 0);
});
Clazz_makeConstructor(c$, 
function(doc, vwr){
this.binaryDoc = doc;
this.vwr = vwr;
this.stack.ensureCapacity(1000);
}, "javajs.api.GenericBinaryDocument,JV.Viewer");
Clazz_defineMethod(c$, "log", 
function(s){
this.vwr.log(s + "\0");
}, "~S");
Clazz_defineMethod(c$, "getMap", 
function(logging){
this.logging = logging;
var b;
var i;
var mark;
var d;
var o;
var a;
var map;
var l;
this.ipt = 0;
var going = true;
while (going) {
b = this.binaryDoc.readByte();
this.ipt++;
switch (b) {
case 125:
this.push( new java.util.Hashtable());
break;
case 97:
o = this.pop();
(this.peek()).addLast(o);
break;
case 101:
l = this.getObjects(this.getMark());
if (this.inNames && this.markCount == 2) {
var pt = this.binaryDoc.getPosition();
var l2 =  new JU.Lst();
l2.addLast(Integer.$valueOf(this.filePt));
l2.addLast(Integer.$valueOf(pt - this.filePt));
l.addLast(l2);
}(this.peek()).addAll(l);
break;
case 71:
d = this.binaryDoc.readDouble();
this.push(Double.$valueOf(d));
break;
case 74:
i = this.binaryDoc.readIntLE();
this.push(Integer.$valueOf(i));
break;
case 75:
i = this.binaryDoc.readByte() & 0xff;
this.push(Integer.$valueOf(i));
break;
case 77:
i = (this.binaryDoc.readByte() & 0xff | ((this.binaryDoc.readByte() & 0xff) << 8)) & 0xffff;
this.push(Integer.$valueOf(i));
break;
case 113:
i = this.binaryDoc.readByte();
this.putMemo(i, false);
break;
case 114:
i = this.binaryDoc.readIntLE();
this.putMemo(i, true);
break;
case 104:
i = this.binaryDoc.readByte();
o = this.getMemo(i);
this.push(o == null ? "BINGET" + (++this.id) : o);
break;
case 106:
i = this.binaryDoc.readIntLE();
o = this.getMemo(i);
this.push(o == null ? "LONG_BINGET" + (++this.id) : o);
break;
case 85:
i = this.binaryDoc.readByte() & 0xff;
a =  Clazz_newByteArray (i, 0);
this.binaryDoc.readByteArray(a, 0, i);
if (this.inNames && this.markCount == 3 && this.lastMark == this.stack.size()) {
this.thisName = this.bytesToString(a);
this.filePt = this.emptyListPt;
}this.push(a);
break;
case 84:
i = this.binaryDoc.readIntLE();
a =  Clazz_newByteArray (i, 0);
this.binaryDoc.readByteArray(a, 0, i);
this.push(a);
break;
case 88:
i = this.binaryDoc.readIntLE();
a =  Clazz_newByteArray (i, 0);
this.binaryDoc.readByteArray(a, 0, i);
this.push(a);
break;
case 93:
this.emptyListPt = this.binaryDoc.getPosition() - 1;
this.push( new JU.Lst());
break;
case 99:
l =  new JU.Lst();
l.addLast("global");
l.addLast(this.readStringAsBytes());
l.addLast(this.readStringAsBytes());
this.push(l);
break;
case 98:
o = this.pop();
this.build.addLast(o);
break;
case 40:
this.putMark(this.stack.size());
break;
case 78:
this.push(null);
break;
case 111:
this.push(this.getObjects(this.getMark()));
break;
case 115:
o = this.pop();
var s = this.bytesToString(this.pop());
(this.peek()).put(s, o);
break;
case 117:
mark = this.getMark();
l = this.getObjects(mark);
o = this.peek();
if (Clazz_instanceOf(o,"JU.Lst")) {
for (i = 0; i < l.size(); i++) {
var oo = l.get(i);
(o).addLast(oo);
}
} else {
map = o;
for (i = l.size(); --i >= 0; ) {
o = l.get(i);
var key = this.bytesToString(l.get(--i));
map.put(key, o);
}
}break;
case 46:
going = false;
break;
case 116:
this.push(this.getObjects(this.getMark()));
break;
case 76:
var val =  String.instantialize(this.readStringAsBytes());
if (val.endsWith("L")) {
val = val.substring(0, val.length - 1);
}this.push(Long.$valueOf(val));
break;
case 82:
this.pop();
break;
case 73:
s = this.bytesToString(this.readStringAsBytes());
try {
this.push(Integer.$valueOf(Integer.parseInt(s)));
} catch (e) {
if (Clazz_exceptionOf(e, Exception)){
var ll = Long.parseLong(s);
this.push(Integer.$valueOf((ll & 0xFFFFFFFF)));
} else {
throw e;
}
}
break;
case 41:
this.push( new JU.Lst());
break;
default:
JU.Logger.error("Pickle reader error: " + b + " " + this.binaryDoc.getPosition());
}
}
if (logging) this.log("");
JU.Logger.info("PyMOL Pickle reader cached " + this.memo.size() + " tokens; retrieved " + this.retrieveCount);
map = this.stack.removeItemAt(0);
if (map.size() == 0) for (i = this.stack.size(); --i >= 0; ) {
o = this.stack.get(i--);
a = this.stack.get(i);
map.put(this.bytesToString(a), o);
}
this.memo = null;
return map;
}, "~B");
Clazz_defineMethod(c$, "bytesToString", 
function(o){
try {
return (JU.AU.isAB(o) ?  String.instantialize(o, "UTF-8") : o.toString());
} catch (e) {
if (Clazz_exceptionOf(e,"java.io.UnsupportedEncodingException")){
return "";
} else {
throw e;
}
}
}, "~O");
Clazz_defineMethod(c$, "putMemo", 
function(i, doCheck){
var o = this.peek();
if (JU.AU.isAB(o)) o = this.bytesToString(o);
if ((typeof(o)=='string')) {
this.memo.put(Integer.$valueOf(i), o);
}}, "~N,~B");
Clazz_defineMethod(c$, "getMemo", 
function(i){
var o = this.memo.get(Integer.$valueOf(i));
if (o == null) return o;
this.retrieveCount++;
return o;
}, "~N");
Clazz_defineMethod(c$, "getObjects", 
function(mark){
var n = this.stack.size() - mark;
var args =  new JU.Lst();
args.ensureCapacity(n);
for (var i = mark; i < this.stack.size(); ++i) {
var oo = this.stack.get(i);
args.addLast(oo);
}
for (var i = this.stack.size(); --i >= mark; ) this.stack.removeItemAt(i);

return args;
}, "~N");
Clazz_defineMethod(c$, "readStringAsBytes", 
function(){
var n = 0;
var a = this.aTemp;
while (true) {
var b = this.binaryDoc.readByte();
if (b == 0xA) break;
if (n >= a.length) a = this.aTemp = JU.AU.arrayCopyByte(a, a.length * 2);
a[n++] = b;
}
return JU.AU.arrayCopyByte(a, n);
});
Clazz_defineMethod(c$, "putMark", 
function(i){
if (this.logging) this.log("\n " + Integer.toHexString(this.binaryDoc.getPosition()) + " [");
this.marks.addLast(Integer.$valueOf(this.lastMark = i));
this.markCount++;
switch (this.markCount) {
case 2:
var o = this.stack.get(i - 2);
if (JU.AU.isAB(o)) {
this.thisSection = this.bytesToString(o);
this.inMovie = "movie".equals(this.thisSection);
this.inNames = "names".equals(this.thisSection);
}break;
default:
break;
}
}, "~N");
Clazz_defineMethod(c$, "getMark", 
function(){
return this.marks.removeItemAt(--this.markCount).intValue();
});
Clazz_defineMethod(c$, "push", 
function(o){
if (this.logging && ((typeof(o)=='string') || Clazz_instanceOf(o, Double) || Clazz_instanceOf(o, Integer))) this.log(((typeof(o)=='string') ? "'" + o + "'" : o) + ", ");
this.stack.addLast(o);
}, "~O");
Clazz_defineMethod(c$, "peek", 
function(){
return this.stack.get(this.stack.size() - 1);
});
Clazz_defineMethod(c$, "pop", 
function(){
return this.stack.removeItemAt(this.stack.size() - 1);
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
Clazz_declarePackage("J.api");
Clazz_declareInterface(J.api, "PymolAtomReader");
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
Clazz_declarePackage("J.adapter.readers.pymol");
Clazz_load(["java.util.Hashtable"], "J.adapter.readers.pymol.PyMOL", ["JU.Logger"], function(){
var c$ = Clazz_declareType(J.adapter.readers.pymol, "PyMOL", null);
c$.getRGB = Clazz_defineMethod(c$, "getRGB", 
function(color){
if ((color & 0xFF000000) != 0) return color;
if (J.adapter.readers.pymol.PyMOL.moreColors != null) {
var key = Integer.$valueOf(color);
var c = J.adapter.readers.pymol.PyMOL.moreColors.get(key);
if (c != null) return c.intValue();
}return (color < J.adapter.readers.pymol.PyMOL.colors.length ? J.adapter.readers.pymol.PyMOL.colors[color] : color);
}, "~N");
c$.addColor = Clazz_defineMethod(c$, "addColor", 
function(id, value){
J.adapter.readers.pymol.PyMOL.moreColors.put(id, Integer.$valueOf(value));
}, "Integer,~N");
c$.getDefaultSetting = Clazz_defineMethod(c$, "getDefaultSetting", 
function(i, pymolVersion){
switch (i) {
case 173:
case 236:
case 570:
case 235:
case 526:
case 210:
case 376:
case 144:
case 574:
case 146:
case 378:
case 530:
case 531:
case 532:
case 156:
return -1;
case 327:
case 569:
case 155:
case 90:
case 448:
case 214:
case 194:
case 193:
case 84:
case 88:
case 111:
case 529:
case 19:
return 1;
case 420:
case 172:
case 571:
case 666:
case 524:
case 279:
case 198:
case 138:
case 6:
case 180:
case 143:
case 338:
case 49:
case 441:
case 118:
case 581:
case 749:
case 23:
case 20:
case 237:
case 203:
case 276:
case 344:
case 64:
return 0;
case 92:
return 0.2;
case 96:
return 1.4;
case 277:
return 1.0;
case 65:
return 0.25;
case 192:
return 0.45;
case 453:
return 14;
case 66:
return -6;
case 328:
return 5;
case 213:
case 382:
case 431:
return 2;
case 361:
case 380:
return 4;
case 377:
return 0.4;
case 379:
return 0.6;
case 381:
return 1.5;
case 103:
return 0.5;
case 4:
return 1.4;
case 107:
return 2.5;
case 44:
return 1.49;
case 106:
return 3;
case 152:
return 20;
case 550:
return 30;
case 21:
return 0.25;
case 100:
return 1.2;
case 101:
return 0.25;
default:
JU.Logger.error("PyMOL " + pymolVersion + " default float setting not found: " + i);
return 0;
}
}, "~N,~N");
c$.getDefaultSettingPt = Clazz_defineMethod(c$, "getDefaultSettingPt", 
function(i, pymolVersion, pt){
switch (i) {
case 471:
pt.set(0, 0, 1.75);
break;
default:
JU.Logger.error("PyMOL " + pymolVersion + " default point setting not found: " + i);
break;
}
return pt;
}, "~N,~N,JU.P3");
c$.getDefaultSettingS = Clazz_defineMethod(c$, "getDefaultSettingS", 
function(i, pymolVersion){
switch (i) {
case 342:
break;
default:
JU.Logger.info("PyMOL " + pymolVersion + " does not have String setting " + i);
break;
}
return "";
}, "~N,~N");
c$.getVArray = Clazz_defineMethod(c$, "getVArray", 
function(version){
var va = null;
var varray = null;
switch (version) {
case 176:
va = J.adapter.readers.pymol.PyMOL.v176;
break;
case 177:
va = J.adapter.readers.pymol.PyMOL.v177;
break;
case 181:
va = J.adapter.readers.pymol.PyMOL.v181;
break;
}
if (va != null) {
varray =  Clazz_newIntArray (60, 0);
for (var i = 0; i < va.length; ) varray[va[i++]] = va[i++];

}return varray;
}, "~N");
c$.getVArrayB = Clazz_defineMethod(c$, "getVArrayB", 
function(version){
var va = null;
var varray = null;
switch (version) {
case 176:
va = J.adapter.readers.pymol.PyMOL.v176b;
break;
case 177:
va = J.adapter.readers.pymol.PyMOL.v177b;
break;
case 181:
va = J.adapter.readers.pymol.PyMOL.v181b;
break;
}
if (va != null) {
varray =  Clazz_newIntArray (10, 0);
for (var i = 0; i < va.length; ) varray[va[i++]] = va[i++];

}return varray;
}, "~N");
c$.fixAllZeroLabelPosition = Clazz_defineMethod(c$, "fixAllZeroLabelPosition", 
function(labelPos){
for (var i = 0; i < 7; i++) {
if (labelPos[i] != 0) return labelPos;
}
return null;
}, "~A");
c$.REP_LIST =  Clazz_newArray(-1, ["sticks", "spheres", "surface", "labels", "nb_spheres", "cartoon", "ribbon", "lines", "mesh", "dots", "dashes", "nonbonded", "cell", "cgo", "callback", "extent", "slice", "angles", "dihedrals", "ellipsoid", "volume"]);
c$.FLAG_exfoliate = 0x01000000;
c$.FLAG_ignore = 0x02000000;
c$.FLAG_no_smooth = 0x04000000;
c$.FLAG_polymer = 0x08000000;
c$.FLAG_solvent = 0x10000000;
c$.FLAG_organic = 0x20000000;
c$.FLAG_inorganic = 0x40000000;
c$.FLAG_NOSURFACE = J.adapter.readers.pymol.PyMOL.FLAG_ignore | J.adapter.readers.pymol.PyMOL.FLAG_exfoliate;
c$.colors =  Clazz_newIntArray(-1, [0xFFFFFFFF, 0xFF000000, 0xFF0000FF, 0xFF00FF00, 0xFFFF0000, 0xFF00FFFF, 0xFFFFFF00, 0xFFFFFF00, 0xFFFF00FF, 0xFFFF9999, 0xFF7FFF7F, 0xFF7F7FFF, 0xFFFF007F, 0xFFFF7F00, 0xFF7FFF00, 0xFF00FF7F, 0xFF7F00FF, 0xFF007FFF, 0xFFC4B200, 0xFFBF00BF, 0xFF00BFBF, 0xFF993333, 0xFF339933, 0xFF3F3FA5, 0xFF7F7F7F, 0xFF7F7F7F, 0xFF33FF33, 0xFF3333FF, 0xFFFF4C4C, 0xFFE5E5E5, 0xFFFFB233, 0xFFE5C53F, 0xFFFF3333, 0xFF33FF33, 0xFF4C4CFF, 0xFFFFFF33, 0xFFFFDD5E, 0xFFFF8C26, 0xFF1919FF, 0xFF3319E5, 0xFF4C19CC, 0xFF6619B2, 0xFF7F1999, 0xFF99197F, 0xFFB21966, 0xFFCC194C, 0xFFE51933, 0xFFFF1919, 0xFFFFA5D8, 0xFFB12121, 0xFF8D381C, 0xFFA5512B, 0xFFFCD1A5, 0xFFFF7FFF, 0xFF000000, 0xFF020202, 0xFF050505, 0xFF070707, 0xFF0A0A0A, 0xFF0C0C0C, 0xFF0F0F0F, 0xFF121212, 0xFF141414, 0xFF171717, 0xFF191919, 0xFF1C1C1C, 0xFF1E1E1E, 0xFF212121, 0xFF242424, 0xFF262626, 0xFF292929, 0xFF2B2B2B, 0xFF2E2E2E, 0xFF303030, 0xFF333333, 0xFF363636, 0xFF383838, 0xFF3B3B3B, 0xFF3D3D3D, 0xFF404040, 0xFF424242, 0xFF454545, 0xFF484848, 0xFF4A4A4A, 0xFF4D4D4D, 0xFF4F4F4F, 0xFF525252, 0xFF555555, 0xFF575757, 0xFF5A5A5A, 0xFF5C5C5C, 0xFF5F5F5F, 0xFF616161, 0xFF646464, 0xFF676767, 0xFF696969, 0xFF6C6C6C, 0xFF6E6E6E, 0xFF717171, 0xFF737373, 0xFF767676, 0xFF797979, 0xFF7B7B7B, 0xFF7E7E7E, 0xFF808080, 0xFF838383, 0xFF858585, 0xFF888888, 0xFF8B8B8B, 0xFF8D8D8D, 0xFF909090, 0xFF929292, 0xFF959595, 0xFF979797, 0xFF9A9A9A, 0xFF9D9D9D, 0xFF9F9F9F, 0xFFA2A2A2, 0xFFA4A4A4, 0xFFA7A7A7, 0xFFAAAAAA, 0xFFACACAC, 0xFFAFAFAF, 0xFFB1B1B1, 0xFFB4B4B4, 0xFFB6B6B6, 0xFFB9B9B9, 0xFFBCBCBC, 0xFFBEBEBE, 0xFFC1C1C1, 0xFFC3C3C3, 0xFFC6C6C6, 0xFFC8C8C8, 0xFFCBCBCB, 0xFFCECECE, 0xFFD0D0D0, 0xFFD3D3D3, 0xFFD5D5D5, 0xFFD8D8D8, 0xFFDADADA, 0xFFDDDDDD, 0xFFE0E0E0, 0xFFE2E2E2, 0xFFE5E5E5, 0xFFE7E7E7, 0xFFEAEAEA, 0xFFECECEC, 0xFFEFEFEF, 0xFFF2F2F2, 0xFFF4F4F4, 0xFFF7F7F7, 0xFFF9F9F9, 0xFFFCFCFC, 0xFFFFFFFF, 0xFFFF33CC, 0xFFFF00FF, 0xFFFD00FF, 0xFFFB00FF, 0xFFFA00FF, 0xFFF800FF, 0xFFF700FF, 0xFFF500FF, 0xFFF400FF, 0xFFF200FF, 0xFFF100FF, 0xFFEF00FF, 0xFFEE00FF, 0xFFEC00FF, 0xFFEB00FF, 0xFFE900FF, 0xFFE800FF, 0xFFE600FF, 0xFFE400FF, 0xFFE300FF, 0xFFE100FF, 0xFFE000FF, 0xFFDE00FF, 0xFFDD00FF, 0xFFDB00FF, 0xFFDA00FF, 0xFFD800FF, 0xFFD700FF, 0xFFD500FF, 0xFFD400FF, 0xFFD200FF, 0xFFD100FF, 0xFFCF00FF, 0xFFCE00FF, 0xFFCC00FF, 0xFFCA00FF, 0xFFC900FF, 0xFFC700FF, 0xFFC600FF, 0xFFC400FF, 0xFFC300FF, 0xFFC100FF, 0xFFC000FF, 0xFFBE00FF, 0xFFBD00FF, 0xFFBB00FF, 0xFFBA00FF, 0xFFB800FF, 0xFFB700FF, 0xFFB500FF, 0xFFB400FF, 0xFFB200FF, 0xFFB000FF, 0xFFAF00FF, 0xFFAD00FF, 0xFFAC00FF, 0xFFAA00FF, 0xFFA900FF, 0xFFA700FF, 0xFFA600FF, 0xFFA400FF, 0xFFA300FF, 0xFFA100FF, 0xFFA000FF, 0xFF9E00FF, 0xFF9D00FF, 0xFF9B00FF, 0xFF9A00FF, 0xFF9800FF, 0xFF9600FF, 0xFF9500FF, 0xFF9300FF, 0xFF9200FF, 0xFF9000FF, 0xFF8F00FF, 0xFF8D00FF, 0xFF8C00FF, 0xFF8A00FF, 0xFF8900FF, 0xFF8700FF, 0xFF8600FF, 0xFF8400FF, 0xFF8300FF, 0xFF8100FF, 0xFF8000FF, 0xFF7E00FF, 0xFF7C00FF, 0xFF7B00FF, 0xFF7900FF, 0xFF7800FF, 0xFF7600FF, 0xFF7500FF, 0xFF7300FF, 0xFF7200FF, 0xFF7000FF, 0xFF6F00FF, 0xFF6D00FF, 0xFF6C00FF, 0xFF6A00FF, 0xFF6900FF, 0xFF6700FF, 0xFF6600FF, 0xFF6400FF, 0xFF6200FF, 0xFF6100FF, 0xFF5F00FF, 0xFF5E00FF, 0xFF5C00FF, 0xFF5B00FF, 0xFF5900FF, 0xFF5800FF, 0xFF5600FF, 0xFF5500FF, 0xFF5300FF, 0xFF5200FF, 0xFF5000FF, 0xFF4F00FF, 0xFF4D00FF, 0xFF4B00FF, 0xFF4A00FF, 0xFF4800FF, 0xFF4700FF, 0xFF4500FF, 0xFF4400FF, 0xFF4200FF, 0xFF4100FF, 0xFF3F00FF, 0xFF3E00FF, 0xFF3C00FF, 0xFF3B00FF, 0xFF3900FF, 0xFF3800FF, 0xFF3600FF, 0xFF3500FF, 0xFF3300FF, 0xFF3100FF, 0xFF3000FF, 0xFF2E00FF, 0xFF2D00FF, 0xFF2B00FF, 0xFF2A00FF, 0xFF2800FF, 0xFF2700FF, 0xFF2500FF, 0xFF2400FF, 0xFF2200FF, 0xFF2100FF, 0xFF1F00FF, 0xFF1E00FF, 0xFF1C00FF, 0xFF1B00FF, 0xFF1900FF, 0xFF1700FF, 0xFF1600FF, 0xFF1400FF, 0xFF1300FF, 0xFF1100FF, 0xFF1000FF, 0xFF0E00FF, 0xFF0D00FF, 0xFF0B00FF, 0xFF0A00FF, 0xFF0800FF, 0xFF0700FF, 0xFF0500FF, 0xFF0400FF, 0xFF0200FF, 0xFF0100FF, 0xFF0000FF, 0xFF0002FF, 0xFF0003FF, 0xFF0005FF, 0xFF0006FF, 0xFF0008FF, 0xFF0009FF, 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0xFFFA04FA, 0xFFFD01FD, 0xFFFC02FF, 0xFFF905FF, 0xFFF608FF, 0xFFF30BFF, 0xFFF00EFF, 0xFFED11FF, 0xFFEA14FF, 0xFFE717FF, 0xFFE41AFF, 0xFFE11DFF, 0xFFDE20FF, 0xFFDB23FF, 0xFFD826FF, 0xFFD529FF, 0xFFD22CFF, 0xFFCF2FFF, 0xFFCC32FF, 0xFFC836FF, 0xFFC539FF, 0xFFC23CFF, 0xFFBF3FFF, 0xFFBC42FF, 0xFFB945FF, 0xFFB648FF, 0xFFB34BFF, 0xFFB04EFF, 0xFFAD51FF, 0xFFAA54FF, 0xFFA757FF, 0xFFA45AFF, 0xFFA15DFF, 0xFF9E60FF, 0xFF9B63FF, 0xFF9767FF, 0xFF946AFF, 0xFF916DFF, 0xFF8E70FF, 0xFF8B73FF, 0xFF8876FF, 0xFF8579FF, 0xFF827CFF, 0xFF7F7FFF, 0xFF7C82FF, 0xFF7985FF, 0xFF7688FF, 0xFF738BFF, 0xFF708EFF, 0xFF6D91FF, 0xFF6A94FF, 0xFF6797FF, 0xFF639BFF, 0xFF609EFF, 0xFF5DA1FF, 0xFF5AA4FF, 0xFF57A7FF, 0xFF54AAFF, 0xFF51ADFF, 0xFF4EB0FF, 0xFF4BB3FF, 0xFF48B6FF, 0xFF45B9FF, 0xFF42BCFF, 0xFF3FBFFF, 0xFF3CC2FF, 0xFF39C5FF, 0xFF36C8FF, 0xFF33CBFF, 0xFF2FCFFF, 0xFF2CD2FF, 0xFF29D5FF, 0xFF26D8FF, 0xFF23DBFF, 0xFF20DEFF, 0xFF1DE1FF, 0xFF1AE4FF, 0xFF17E7FF, 0xFF14EAFF, 0xFF11EDFF, 0xFF0EF0FF, 0xFF0BF3FF, 0xFF08F6FF, 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0xFFFF0B00, 0xFFFF0800, 0xFFFF0500, 0xFFFF0200, 0xFFFD0101, 0xFFFA0404, 0xFFF70707, 0xFFF40A0A, 0xFFF10D0D, 0xFFEE1010, 0xFFEB1313, 0xFFE81616, 0xFFE51919, 0xFFE21C1C, 0xFFDF1F1F, 0xFFDC2222, 0xFFD92525, 0xFFD62828, 0xFFD32B2B, 0xFFD02E2E, 0xFFCD3131, 0xFFC93535, 0xFFC63838, 0xFFC33B3B, 0xFFC03E3E, 0xFFBD4141, 0xFFBA4444, 0xFFB74747, 0xFFB44A4A, 0xFFB14D4D, 0xFFAE5050, 0xFFAB5353, 0xFFA85656, 0xFFA55959, 0xFFA25C5C, 0xFF9F5F5F, 0xFF9C6262, 0xFF996565, 0xFF956969, 0xFF926C6C, 0xFF8F6F6F, 0xFF8C7272, 0xFF897575, 0xFF867878, 0xFF837B7B, 0xFF807E7E, 0xFF7D8181, 0xFF7A8484, 0xFF778787, 0xFF748A8A, 0xFF718D8D, 0xFF6E9090, 0xFF6B9393, 0xFF689696, 0xFF649A9A, 0xFF619D9D, 0xFF5EA0A0, 0xFF5BA3A3, 0xFF58A6A6, 0xFF55A9A9, 0xFF52ACAC, 0xFF4FAFAF, 0xFF4CB2B2, 0xFF49B5B5, 0xFF46B8B8, 0xFF43BBBB, 0xFF40BEBE, 0xFF3DC1C1, 0xFF3AC4C4, 0xFF37C7C7, 0xFF34CACA, 0xFF30CECE, 0xFF2DD1D1, 0xFF2AD4D4, 0xFF27D7D7, 0xFF24DADA, 0xFF21DDDD, 0xFF1EE0E0, 0xFF1BE3E3, 0xFF18E6E6, 0xFF15E9E9, 0xFF12ECEC, 0xFF0FEFEF, 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0xFF1A1AFF, 0xFF1414FF, 0xFF0E0EFF, 0xFF0808FF, 0xFF0202FF, 0xFF0404FF, 0xFF0A0AFF, 0xFF1010FF, 0xFF1616FF, 0xFF1C1CFF, 0xFF2222FF, 0xFF2828FF, 0xFF2E2EFF, 0xFF3535FF, 0xFF3B3BFF, 0xFF4141FF, 0xFF4747FF, 0xFF4D4DFF, 0xFF5353FF, 0xFF5959FF, 0xFF5F5FFF, 0xFF6565FF, 0xFF6C6CFF, 0xFF7272FF, 0xFF7878FF, 0xFF7E7EFF, 0xFF8484FF, 0xFF8A8AFF, 0xFF9090FF, 0xFF9696FF, 0xFF9D9DFF, 0xFFA3A3FF, 0xFFA9A9FF, 0xFFAFAFFF, 0xFFB5B5FF, 0xFFBBBBFF, 0xFFC1C1FF, 0xFFC7C7FF, 0xFFCECEFF, 0xFFD4D4FF, 0xFFDADAFF, 0xFFE0E0FF, 0xFFE6E6FF, 0xFFECECFF, 0xFFF2F2FF, 0xFFF8F8FF, 0xFFFEFEFF, 0xFFFFF8F8, 0xFFFFF2F2, 0xFFFFECEC, 0xFFFFE6E6, 0xFFFFE0E0, 0xFFFFDADA, 0xFFFFD4D4, 0xFFFFCECE, 0xFFFFC7C7, 0xFFFFC1C1, 0xFFFFBBBB, 0xFFFFB5B5, 0xFFFFAFAF, 0xFFFFA9A9, 0xFFFFA3A3, 0xFFFF9D9D, 0xFFFF9696, 0xFFFF9090, 0xFFFF8A8A, 0xFFFF8484, 0xFFFF7E7E, 0xFFFF7878, 0xFFFF7272, 0xFFFF6C6C, 0xFFFF6666, 0xFFFF5F5F, 0xFFFF5959, 0xFFFF5353, 0xFFFF4D4D, 0xFFFF4747, 0xFFFF4141, 0xFFFF3B3B, 0xFFFF3535, 0xFFFF2E2E, 0xFFFF2828, 0xFFFF2222, 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0xFF00FF3B, 0xFF00FF39, 0xFF00FF36, 0xFF00FF34, 0xFF00FF32, 0xFF00FF31, 0xFF00FF2F, 0xFF00FF2E, 0xFF00FF2D, 0xFF00FF2B, 0xFF00FF2A, 0xFF00FF28, 0xFF00FF27, 0xFF00FF25, 0xFF00FF24, 0xFF00FF23, 0xFF00FF21, 0xFF00FF20, 0xFF00FF1E, 0xFF00FF1D, 0xFF00FF1B, 0xFF00FF1A, 0xFF00FF19, 0xFF00FF17, 0xFF00FF16, 0xFF00FF14, 0xFF00FF13, 0xFF00FF11, 0xFF00FF10, 0xFF00FF0F, 0xFF00FF0D, 0xFF00FF0C, 0xFF00FF0A, 0xFF00FF09, 0xFF00FF07, 0xFF00FF06, 0xFF00FF05, 0xFF00FF03, 0xFF00FF02, 0xFF00FF00, 0xFF00FF00, 0xFF02FF00, 0xFF03FF00, 0xFF04FF00, 0xFF06FF00, 0xFF07FF00, 0xFF09FF00, 0xFF0AFF00, 0xFF0CFF00, 0xFF0DFF00, 0xFF0EFF00, 0xFF10FF00, 0xFF11FF00, 0xFF13FF00, 0xFF14FF00, 0xFF16FF00, 0xFF17FF00, 0xFF18FF00, 0xFF1AFF00, 0xFF1BFF00, 0xFF1DFF00, 0xFF1EFF00, 0xFF20FF00, 0xFF21FF00, 0xFF22FF00, 0xFF24FF00, 0xFF25FF00, 0xFF27FF00, 0xFF28FF00, 0xFF2AFF00, 0xFF2BFF00, 0xFF2CFF00, 0xFF2EFF00, 0xFF2FFF00, 0xFF31FF00, 0xFF32FF00, 0xFF34FF00, 0xFF36FF00, 0xFF38FF00, 0xFF3AFF00, 0xFF3DFF00, 0xFF3FFF00, 0xFF41FF00, 0xFF43FF00, 0xFF45FF00, 0xFF47FF00, 0xFF49FF00, 0xFF4CFF00, 0xFF4EFF00, 0xFF50FF00, 0xFF52FF00, 0xFF54FF00, 0xFF56FF00, 0xFF58FF00, 0xFF5BFF00, 0xFF5DFF00, 0xFF5FFF00, 0xFF61FF00, 0xFF63FF00, 0xFF65FF00, 0xFF67FF00, 0xFF6AFF00, 0xFF6CFF00, 0xFF6EFF00, 0xFF70FF00, 0xFF72FF00, 0xFF74FF00, 0xFF76FF00, 0xFF79FF00, 0xFF7BFF00, 0xFF7DFF00, 0xFF7FFF00, 0xFF81FF00, 0xFF83FF00, 0xFF85FF00, 0xFF88FF00, 0xFF8AFF00, 0xFF8CFF00, 0xFF8EFF00, 0xFF90FF00, 0xFF92FF00, 0xFF94FF00, 0xFF97FF00, 0xFF99FF00, 0xFF9BFF00, 0xFF9DFF00, 0xFF9FFF00, 0xFFA1FF00, 0xFFA3FF00, 0xFFA6FF00, 0xFFA8FF00, 0xFFAAFF00, 0xFFACFF00, 0xFFAEFF00, 0xFFB0FF00, 0xFFB2FF00, 0xFFB5FF00, 0xFFB7FF00, 0xFFB9FF00, 0xFFBBFF00, 0xFFBDFF00, 0xFFBFFF00, 0xFFC1FF00, 0xFFC4FF00, 0xFFC6FF00, 0xFFC8FF00, 0xFFCAFF00, 0xFFCCFF00, 0xFFCDFF00, 0xFFCFFF00, 0xFFD0FF00, 0xFFD2FF00, 0xFFD3FF00, 0xFFD4FF00, 0xFFD6FF00, 0xFFD7FF00, 0xFFD9FF00, 0xFFDAFF00, 0xFFDCFF00, 0xFFDDFF00, 0xFFDEFF00, 0xFFE0FF00, 0xFFE1FF00, 0xFFE3FF00, 0xFFE4FF00, 0xFFE6FF00, 0xFFE7FF00, 0xFFE8FF00, 0xFFEAFF00, 0xFFEBFF00, 0xFFEDFF00, 0xFFEEFF00, 0xFFF0FF00, 0xFFF1FF00, 0xFFF2FF00, 0xFFF4FF00, 0xFFF5FF00, 0xFFF7FF00, 0xFFF8FF00, 0xFFFAFF00, 0xFFFBFF00, 0xFFFCFF00, 0xFFFEFF00, 0xFFFFFE00, 0xFFFFFD00, 0xFFFFFD00, 0xFFFFFC00, 0xFFFFFB00, 0xFFFFFB00, 0xFFFFFA00, 0xFFFFF900, 0xFFFFF800, 0xFFFFF800, 0xFFFFF700, 0xFFFFF600, 0xFFFFF600, 0xFFFFF500, 0xFFFFF400, 0xFFFFF300, 0xFFFFF300, 0xFFFFF200, 0xFFFFF100, 0xFFFFF100, 0xFFFFF000, 0xFFFFEF00, 0xFFFFEE00, 0xFFFFEE00, 0xFFFFED00, 0xFFFFEC00, 0xFFFFEC00, 0xFFFFEB00, 0xFFFFEA00, 0xFFFFE900, 0xFFFFE900, 0xFFFFE800, 0xFFFFE700, 0xFFFFE700, 0xFFFFE600, 0xFFFFE500, 0xFFFFE400, 0xFFFFE300, 0xFFFFE200, 0xFFFFE100, 0xFFFFE000, 0xFFFFDF00, 0xFFFFDE00, 0xFFFFDD00, 0xFFFFDC00, 0xFFFFDA00, 0xFFFFD900, 0xFFFFD800, 0xFFFFD700, 0xFFFFD600, 0xFFFFD500, 0xFFFFD400, 0xFFFFD300, 0xFFFFD200, 0xFFFFD100, 0xFFFFD000, 0xFFFFCF00, 0xFFFFCE00, 0xFFFFCD00, 0xFFFFCB00, 0xFFFFCA00, 0xFFFFC900, 0xFFFFC800, 0xFFFFC700, 0xFFFFC600, 0xFFFFC500, 0xFFFFC400, 0xFFFFC300, 0xFFFFC200, 0xFFFFC100, 0xFFFFC000, 0xFFFFBF00, 0xFFFFBE00, 0xFFFFBC00, 0xFFFFBB00, 0xFFFFBA00, 0xFFFFB900, 0xFFFFB800, 0xFFFFB700, 0xFFFFB600, 0xFFFFB500, 0xFFFFB400, 0xFFFFB300, 0xFFFFB200, 0xFFFFB100, 0xFFFFB000, 0xFFFFAF00, 0xFFFFAD00, 0xFFFFAC00, 0xFFFFAB00, 0xFFFFAA00, 0xFFFFA900, 0xFFFFA800, 0xFFFFA700, 0xFFFFA600, 0xFFFFA500, 0xFFFFA400, 0xFFFFA300, 0xFFFFA200, 0xFFFFA100, 0xFFFFA000, 0xFFFF9E00, 0xFFFF9D00, 0xFFFF9C00, 0xFFFF9B00, 0xFFFF9A00, 0xFFFF9900, 0xFFFF9800, 0xFFFF9700, 0xFFFF9700, 0xFFFF9600, 0xFFFF9500, 0xFFFF9500, 0xFFFF9400, 0xFFFF9300, 0xFFFF9200, 0xFFFF9200, 0xFFFF9100, 0xFFFF9000, 0xFFFF9000, 0xFFFF8F00, 0xFFFF8E00, 0xFFFF8D00, 0xFFFF8D00, 0xFFFF8C00, 0xFFFF8B00, 0xFFFF8B00, 0xFFFF8A00, 0xFFFF8900, 0xFFFF8800, 0xFFFF8800, 0xFFFF8700, 0xFFFF8600, 0xFFFF8600, 0xFFFF8500, 0xFFFF8400, 0xFFFF8300, 0xFFFF8300, 0xFFFF8200, 0xFFFF8100, 0xFFFF8100, 0xFFFF8000, 0xFFFF7F00, 0xFFFF7E00, 0xFFFF7E00, 0xFFFF7D00, 0xFFFF7C00, 0xFFFF7C00, 0xFFFF7B00, 0xFFFF7A00, 0xFFFF7900, 0xFFFF7900, 0xFFFF7800, 0xFFFF7700, 0xFFFF7700, 0xFFFF7600, 0xFFFF7500, 0xFFFF7400, 0xFFFF7400, 0xFFFF7300, 0xFFFF7200, 0xFFFF7200, 0xFFFF7100, 0xFFFF7000, 0xFFFF6F00, 0xFFFF6F00, 0xFFFF6E00, 0xFFFF6D00, 0xFFFF6D00, 0xFFFF6C00, 0xFFFF6B00, 0xFFFF6A00, 0xFFFF6A00, 0xFFFF6900, 0xFFFF6800, 0xFFFF6800, 0xFFFF6700, 0xFFFF6600, 0xFFFF6600, 0xFFFF6500, 0xFFFF6400, 0xFFFF6300, 0xFFFF6300, 0xFFFF6200, 0xFFFF6100, 0xFFFF6100, 0xFFFF6000, 0xFFFF5F00, 0xFFFF5E00, 0xFFFF5E00, 0xFFFF5D00, 0xFFFF5C00, 0xFFFF5C00, 0xFFFF5B00, 0xFFFF5A00, 0xFFFF5900, 0xFFFF5900, 0xFFFF5800, 0xFFFF5700, 0xFFFF5700, 0xFFFF5600, 0xFFFF5500, 0xFFFF5400, 0xFFFF5400, 0xFFFF5300, 0xFFFF5200, 0xFFFF5200, 0xFFFF5100, 0xFFFF5000, 0xFFFF4F00, 0xFFFF4F00, 0xFFFF4E00, 0xFFFF4D00, 0xFFFF4D00, 0xFFFF4C00, 0xFFFF4B00, 0xFFFF4A00, 0xFFFF4A00, 0xFFFF4900, 0xFFFF4800, 0xFFFF4800, 0xFFFF4700, 0xFFFF4600, 0xFFFF4500, 0xFFFF4500, 0xFFFF4400, 0xFFFF4300, 0xFFFF4300, 0xFFFF4200, 0xFFFF4100, 0xFFFF4000, 0xFFFF4000, 0xFFFF3F00, 0xFFFF3E00, 0xFFFF3E00, 0xFFFF3D00, 0xFFFF3C00, 0xFFFF3B00, 0xFFFF3B00, 0xFFFF3A00, 0xFFFF3900, 0xFFFF3900, 0xFFFF3800, 0xFFFF3700, 0xFFFF3600, 0xFFFF3600, 0xFFFF3500, 0xFFFF3400, 0xFFFF3400, 0xFFFF3300, 0xFFFF3200, 0xFFFF3000, 0xFFFF2F00, 0xFFFF2D00, 0xFFFF2C00, 0xFFFF2B00, 0xFFFF2900, 0xFFFF2800, 0xFFFF2600, 0xFFFF2500, 0xFFFF2300, 0xFFFF2200, 0xFFFF2100, 0xFFFF1F00, 0xFFFF1E00, 0xFFFF1C00, 0xFFFF1B00, 0xFFFF1900, 0xFFFF1800, 0xFFFF1700, 0xFFFF1500, 0xFFFF1400, 0xFFFF1200, 0xFFFF1100, 0xFFFF0F00, 0xFFFF0E00, 0xFFFF0D00, 0xFFFF0B00, 0xFFFF0A00, 0xFFFF0800, 0xFFFF0700, 0xFFFF0500, 0xFFFF0400, 0xFFFF0300, 0xFFFF0100, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0000, 0xFFFF0004, 0xFFFF0007, 0xFFFF000B, 0xFFFF000E, 0xFFFF0012, 0xFFFF0015, 0xFFFF0019, 0xFFFF001D, 0xFFFF0020, 0xFFFF0024, 0xFFFF0027, 0xFFFF002B, 0xFFFF002E, 0xFFFF0032, 0xFFFF0036, 0xFFFF0039, 0xFFFF003D, 0xFFFF0040, 0xFFFF0044, 0xFFFF0047, 0xFFFF004B, 0xFFFF004F, 0xFFFF0052, 0xFFFF0056, 0xFFFF0059, 0xFFFF005D, 0xFFFF0060, 0xFFFF0064, 0xFFFF0068, 0xFFFF006B, 0xFFFF006F, 0xFFFF0072, 0xFFFF0076, 0xFFFF0079, 0xFFFF007D, 0xFFFF0080, 0xFFFF0082, 0xFFFF0084, 0xFFFF0086, 0xFFFF0088, 0xFFFF008B, 0xFFFF008D, 0xFFFF008F, 0xFFFF0091, 0xFFFF0093, 0xFFFF0095, 0xFFFF0097, 0xFFFF009A, 0xFFFF009C, 0xFFFF009E, 0xFFFF00A0, 0xFFFF00A2, 0xFFFF00A4, 0xFFFF00A6, 0xFFFF00A9, 0xFFFF00AB, 0xFFFF00AD, 0xFFFF00AF, 0xFFFF00B1, 0xFFFF00B3, 0xFFFF00B5, 0xFFFF00B8, 0xFFFF00BA, 0xFFFF00BC, 0xFFFF00BE, 0xFFFF00C0, 0xFFFF00C2, 0xFFFF00C4, 0xFFFF00C7, 0xFFFF00C9, 0xFFFF00CB, 0xFFFF00CD, 0xFFFF00CE, 0xFFFF00CF, 0xFFFF00D1, 0xFFFF00D2, 0xFFFF00D4, 0xFFFF00D5, 0xFFFF00D7, 0xFFFF00D8, 0xFFFF00D9, 0xFFFF00DB, 0xFFFF00DC, 0xFFFF00DE, 0xFFFF00DF, 0xFFFF00E1, 0xFFFF00E2, 0xFFFF00E3, 0xFFFF00E5, 0xFFFF00E6, 0xFFFF00E8, 0xFFFF00E9, 0xFFFF00EB, 0xFFFF00EC, 0xFFFF00ED, 0xFFFF00EF, 0xFFFF00F0, 0xFFFF00F2, 0xFFFF00F3, 0xFFFF00F5, 0xFFFF00F6, 0xFFFF00F7, 0xFFFF00F9, 0xFFFF00FA, 0xFFFF00FC, 0xFFFF00FD, 0xFFFFFF7F, 0xFF7FFFFF, 0xFFFF7F7F, 0xFFA5E5A5, 0xFF999919, 0xFF991999, 0xFF199999, 0xFFBFBFFF, 0xFFFFCC7F, 0xFFCCFFFF, 0xFF66B2B2, 0xFF84BF00, 0xFFB24C66, 0xFFB78C4C, 0xFF8CB266, 0xFF8C3F99, 0xFFB27F7F, 0xFFFF7F7F, 0xFFFFBFDD, 0xFF3FFFBF, 0xFFBFFF3F, 0xFF337FCC, 0xFFD8D8FF, 0xFFD8337F, 0xFFBA8C84, 0xFFD9FFFF, 0xFFCC7FFF, 0xFFC2FF00, 0xFFFFB5B5, 0xFFB3FFFF, 0xFFB3E3F5, 0xFFAB5CF2, 0xFF8AFF00, 0xFFBFA6A6, 0xFFF0C8A0, 0xFFFF7F00, 0xFF1FF01F, 0xFF7FD1E3, 0xFF8F3FD4, 0xFF3DFF00, 0xFFE6E6E6, 0xFFBFC2C7, 0xFFA6A6AB, 0xFF8A99C7, 0xFF9C7AC7, 0xFFE06633, 0xFFF090A0, 0xFF50D050, 0xFFC87F33, 0xFF7D7FB0, 0xFFC28F8F, 0xFF668F8F, 0xFFBD7FE3, 0xFFFFA100, 0xFFA62929, 0xFF5CB8D1, 0xFF702EB0, 0xFF00FF00, 0xFF94FFFF, 0xFF94E0E0, 0xFF73C2C9, 0xFF54B5B5, 0xFF3B9E9E, 0xFF248F8F, 0xFF0A7D8C, 0xFF006985, 0xFFC0C0C0, 0xFFFFD98F, 0xFFA67573, 0xFF667F7F, 0xFF9E63B5, 0xFFD47A00, 0xFF940094, 0xFF429EB0, 0xFF57178F, 0xFF00C900, 0xFF70D4FF, 0xFFFFFFC7, 0xFFD9FFC7, 0xFFC7FFC7, 0xFFA3FFC7, 0xFF8FFFC7, 0xFF61FFC7, 0xFF45FFC7, 0xFF30FFC7, 0xFF1FFFC7, 0xFF00FF9C, 0xFF00E675, 0xFF00D452, 0xFF00BF38, 0xFF00AB24, 0xFF4DC2FF, 0xFF4DA6FF, 0xFF2194D6, 0xFF267DAB, 0xFF266696, 0xFF175487, 0xFFD0D0E0, 0xFFFFD123, 0xFFB8B8D0, 0xFFA6544D, 0xFF575961, 0xFF9E4FB5, 0xFFAB5C00, 0xFF754F45, 0xFF428296, 0xFF420066, 0xFF007D00, 0xFF70ABFA, 0xFF00BAFF, 0xFF00A1FF, 0xFF008FFF, 0xFF007FFF, 0xFF006BFF, 0xFF545CF2, 0xFF785CE3, 0xFF8A4FE3, 0xFFA136D4, 0xFFB31FD4, 0xFFB31FBA, 0xFFB30DA6, 0xFFBD0D87, 0xFFC70066, 0xFFCC0059, 0xFFD1004F, 0xFFD90045, 0xFFE00038, 0xFFE6002E, 0xFFEB0026, 0xFFE5E5E5]);
c$.moreColors =  new java.util.Hashtable();
c$.v176 =  Clazz_newIntArray(-1, [0, 164, 1, 0, 2, 4, 3, 8, 4, 12, 5, 16, 6, 20, 7, 24, 9, 32, 10, 36, 11, 40, 13, 48, 14, 52, 15, 56, 16, 60, 17, -64, 18, -68, 19, -72, 20, 76, 28, 80, 29, 82, 30, 83, 21, 84, 22, 85, 43, 86, 31, 87, 32, 88, 24, 90, 44, 91, 33, 92, 25, 93, 26, 94, 27, 95, 46, 0x01, 47, 0x01, 48, 0x01, 49, 0x01, 50, 0x01, 51, 0x01, 34, 96, 35, 100, 36, 105, 37, 110, 38, 115, 39, 122, 40, 124, 41, 126, 45, 132]);
c$.v177 =  Clazz_newIntArray(-1, [0, 144, 1, 8, 2, 12, 3, 16, 4, 20, 5, 24, 6, 28, 7, 32, 9, 40, 10, 44, 11, 48, 13, 56, 14, 60, 15, 64, 16, 68, 17, -72, 18, -76, 19, -80, 20, 84, 21, 96, 22, 96, 24, 96, 25, 97, 26, 97, 27, 97, 46, 0x01, 47, 0x02, 48, 0x08, 49, 0x01, 50, 0x02, 51, 0x04, 28, 98, 29, 99, 30, 100, 31, 101, 32, 102, 33, 103, 34, 104, 35, 108, 36, 113, 37, 118, 38, 123, 39, 129, 40, 131, 41, 133, 43, 140, 44, 141]);
c$.v181 =  Clazz_newIntArray(-1, [0, 120, 45, 0, 35, -12, 34, -16, 41, -20, 36, -24, 17, -28, 18, -32, 19, -36, 1, 40, 2, 44, 3, 48, 4, 52, 5, 56, 6, 60, 7, 64, 9, 68, 10, 72, 11, 76, 13, 80, 14, 84, 15, 88, 16, 92, 20, 96, 21, 100, 22, 100, 24, 100, 25, 100, 26, 100, 27, 100, 46, 0x01, 47, 0x02, 48, 0x04, 49, 0x08, 50, 0x10, 51, 0x20, 28, 101, 30, 102, 31, 103, 32, 104, 33, 105, 42, 106, 37, 107, 39, 112, 40, 114, 29, 116, 43, 117, 44, 118]);
c$.v176b =  Clazz_newIntArray(-1, [0, 32, 1, 0, 2, 4, 3, 8, 4, 12, 5, 16, 6, 26]);
c$.v177b =  Clazz_newIntArray(-1, [0, 24, 1, 0, 2, 4, 4, 8, 5, 12, 3, 20, 6, 23]);
c$.v181b =  Clazz_newIntArray(-1, [0, 20, 1, 0, 2, 4, 4, 8, 5, 12, 3, 16, 6, 18]);
});
;//5.0.1-v2 Fri Jul 26 07:31:06 CDT 2024
Clazz_declarePackage("J.adapter.readers.pymol");
Clazz_load(null, "J.adapter.readers.pymol.JmolObject", ["JU.P3", "$.PT", "$.SB", "J.adapter.readers.pymol.PyMOLReader", "JU.BSUtil", "$.Escape"], function(){
var c$ = Clazz_decorateAsClass(function(){
this.id = 0;
this.bsAtoms = null;
this.info = null;
this.size = -1;
this.colors = null;
this.modelIndex = -2147483648;
this.jmolName = null;
this.argb = 0;
this.translucency = 0;
this.visible = true;
this.rd = null;
this.cacheID = null;
Clazz_instantialize(this, arguments);}, J.adapter.readers.pymol, "JmolObject", null);
Clazz_makeConstructor(c$, 
function(id, branchNameID, bsAtoms, info){
this.id = id;
this.bsAtoms = bsAtoms;
this.info = info;
this.jmolName = branchNameID;
}, "~N,~S,JU.BS,~O");
Clazz_defineMethod(c$, "offset", 
function(modelOffset, atomOffset){
if (modelOffset > 0) {
if (this.modelIndex != -2147483648) this.modelIndex += modelOffset;
switch (this.id) {
case 1610625028:
case 12294:
return;
case 4115:
var i = (this.info).intValue();
if (i >= 0) this.info = Integer.$valueOf(modelOffset + i);
return;
case 1073742031:
var movie = this.info;
var frames = movie.get("frames");
for (var j = frames.length; --j >= 0; ) frames[j] += modelOffset;

return;
}
}if (atomOffset <= 0) return;
if (this.id == 12290) {
var map = (this.info).values();
for (var o, $o = map.iterator (); $o.hasNext()&& ((o = $o.next ()) || true);) JU.BSUtil.offset(o, 0, atomOffset);

return;
}if (this.bsAtoms != null) JU.BSUtil.offset(this.bsAtoms, 0, atomOffset);
if (this.colors != null) {
var colixes = this.colors[0];
var c =  Clazz_newShortArray (colixes.length + atomOffset, 0);
System.arraycopy(colixes, 0, c, atomOffset, colixes.length);
this.colors[0] = c;
}}, "~N,~N");
Clazz_defineMethod(c$, "finalizeObject", 
function(pymolScene, m, mepList, doCache){
var sm = m.sm;
var color = "color";
var sID;
var sb = null;
if (this.bsAtoms != null) this.modelIndex = this.getModelIndex(m);
switch (this.id) {
case 2097194:
sm.vwr.displayAtoms(this.bsAtoms, false, false, 1275069441, true);
return;
case 12295:
var bs = sm.vwr.getModelUndeletedAtomsBitSet(this.argb);
JU.BSUtil.invertInPlace(bs, sm.vwr.ms.ac);
sm.vwr.select(bs, false, 0, true);
sm.restrictSelected(false, true);
return;
case 1610625028:
case 12294:
if (this.bsAtoms == null) {
if (this.info == null) {
sm.vwr.displayAtoms(null, true, false, 0, true);
}sm.vwr.setObjectProp(this.info, this.id);
} else {
sm.vwr.displayAtoms(this.bsAtoms, this.id == 1610625028, false, 1275069441, true);
}return;
case 12290:
sm.vwr.defineAtomSets(this.info);
return;
case 1073742031:
sm.vwr.am.setMovie(this.info);
return;
case 4115:
var frame = (this.info).intValue();
if (frame >= 0) {
sm.vwr.setCurrentModelIndex(frame);
} else {
sm.vwr.setAnimationRange(-1, -1);
sm.vwr.setCurrentModelIndex(-1);
}return;
case 1073742139:
sm.vwr.stm.saveScene(this.jmolName, this.info);
sm.vwr.stm.saveOrientation(this.jmolName, (this.info).get("pymolView"));
return;
case 5:
sm.loadShape(this.id);
sm.setShapePropertyBs(this.id, "pymolLabels", this.info, this.bsAtoms);
return;
case 1677721602:
break;
case 659488:
case 1:
if (this.size != -1) {
sm.setShapeSizeBs(1, this.size, null, this.bsAtoms);
var bsBonds = (sm.getShapePropertyIndex(1, "sets", 0))[1];
pymolScene.setUniqueBonds(bsBonds, this.id == 1);
this.size = -1;
}this.id = 1;
break;
case 1153433601:
this.id = 0;
break;
case 0:
break;
case 10:
case 9:
sm.loadShape(this.id);
var bsCarb = m.getAtoms(2097188, null);
JU.BSUtil.andNot(this.bsAtoms, bsCarb);
break;
case 16:
sm.loadShape(this.id);
sm.setShapePropertyBs(this.id, "ignore", JU.BSUtil.copyInvert(this.bsAtoms, sm.vwr.ms.ac), null);
break;
default:
if (!this.visible) return;
break;
}
switch (this.id) {
case 23:
sm.vwr.setCGO(this.info);
break;
case 16:
case 0:
case 7:
case 20:
case 11:
case 9:
case 10:
case 24:
if (Clazz_instanceOf(this.info,Array)) {
sm.loadShape(this.id);
sm.setShapePropertyBs(this.id, "params", this.info, this.bsAtoms);
}break;
case 6:
if (this.modelIndex < 0) return;
sm.loadShape(this.id);
var md = this.info;
md.setModelSet(m);
var points = md.points;
for (var i = points.size(); --i >= 0; ) (points.get(i)).mi = this.modelIndex;

sm.setShapePropertyBs(this.id, "measure", md, this.bsAtoms);
return;
case 135180:
sID = (this.bsAtoms == null ? this.info : this.jmolName);
if (sm.getShapeIdFromObjectName(sID) >= 0) {
sm.vwr.setObjectProp(sID, 1610625028);
return;
}sb =  new JU.SB();
sb.append("isosurface ID ").append(JU.PT.esc(sID));
if (this.modelIndex < 0) this.modelIndex = sm.vwr.am.cmi;
if (this.bsAtoms == null) {
sb.append(" model ").append(m.getModelNumberDotted(this.modelIndex)).append(" color density sigma 1.0 ").append(JU.PT.esc(this.cacheID)).append(" ").append(JU.PT.esc(sID));
if (doCache) sb.append(";isosurface cache");
} else {
var lighting = (this.info)[0];
var only = (this.info)[1];
only = " only";
var bsCarve = (this.info)[2];
var carveDistance = ((this.info)[3]).floatValue();
var resolution = "";
if (lighting == null) {
lighting = "mesh nofill";
resolution = " resolution 1.5";
}var haveMep = JU.PT.isOneOf(sID, mepList);
var model = m.getModelNumberDotted(this.modelIndex);
var ignore = "";
var type = (this.size < 0 ? " sasurface " : " solvent ");
sb.append(" model ").append(model).append(resolution).append(" select ").append(JU.Escape.eBS(this.bsAtoms)).append(only).append(ignore).append(type).appendF(Math.abs(this.size / 1000));
if (!haveMep) {
if (this.argb == 0) sb.append(" map property color");
 else sb.append(";color isosurface ").append(JU.Escape.escapeColor(this.argb));
}sb.append(";isosurface frontOnly ").append(lighting);
if (this.translucency > 0) sb.append(";color isosurface translucent " + this.translucency);
if (bsCarve != null && !bsCarve.isEmpty()) sb.append(";isosurface slab within " + carveDistance + " {" + model + " and " + JU.Escape.eBS(bsCarve) + "}");
if (doCache && !haveMep) sb.append(";isosurface cache");
}break;
case 1073742016:
var mep = this.info;
sID = mep.get(mep.size() - 2).toString();
var mapID = mep.get(mep.size() - 1).toString();
var min = J.adapter.readers.pymol.PyMOLReader.floatAt(J.adapter.readers.pymol.PyMOLReader.listAt(mep, 3), 0);
var max = J.adapter.readers.pymol.PyMOLReader.floatAt(J.adapter.readers.pymol.PyMOLReader.listAt(mep, 3), 2);
sb =  new JU.SB();
sb.append(";isosurface ID ").append(JU.PT.esc(sID)).append(" map ").append(JU.PT.esc(this.cacheID)).append(" ").append(JU.PT.esc(mapID)).append(";color isosurface range " + min + " " + max + ";isosurface colorscheme rwb;set isosurfacekey true");
if (this.translucency > 0) sb.append(";color isosurface translucent " + this.translucency);
if (doCache) sb.append(";isosurface cache");
break;
case 1073742018:
this.modelIndex = sm.vwr.am.cmi;
var mesh = this.info;
sID = mesh.get(mesh.size() - 2).toString();
sb =  new JU.SB();
sb.append("isosurface ID ").append(JU.PT.esc(sID)).append(" model ").append(m.getModelNumberDotted(this.modelIndex)).append(" color ").append(JU.Escape.escapeColor(this.argb)).append("  ").append(JU.PT.esc(this.cacheID)).append(" ").append(JU.PT.esc(sID)).append(" mesh nofill frontonly");
var list = J.adapter.readers.pymol.PyMOLReader.sublistAt(mesh, [2, 0]);
var within = J.adapter.readers.pymol.PyMOLReader.floatAt(list, 11);
list = J.adapter.readers.pymol.PyMOLReader.listAt(list, 12);
if (within > 0) {
var pt =  new JU.P3();
sb.append(";isosurface slab within ").appendF(within).append(" [ ");
for (var j = list.size() - 3; j >= 0; j -= 3) {
J.adapter.readers.pymol.PyMOLReader.pointAt(list, j, pt);
sb.append(JU.Escape.eP(pt));
}
sb.append(" ]");
}if (doCache && !JU.PT.isOneOf(sID, mepList)) sb.append(";isosurface cache");
sb.append(";set meshScale ").appendI(Clazz_doubleToInt(this.size / 500));
break;
case 134222850:
sb = this.info;
break;
case 1112152078:
sm.loadShape(this.id = 10);
sm.setShapePropertyBs(this.id, "putty", this.info, this.bsAtoms);
break;
}
if (sb != null) {
sm.vwr.runScriptCautiously(sb.toString());
return;
}if (this.size != -1 || this.rd != null) sm.setShapeSizeBs(this.id, this.size, this.rd, this.bsAtoms);
if (this.argb != 0) sm.setShapePropertyBs(this.id, color, Integer.$valueOf(this.argb), this.bsAtoms);
if (this.translucency > 0) {
sm.setShapePropertyBs(this.id, "translucentLevel", Float.$valueOf(this.translucency), this.bsAtoms);
sm.setShapePropertyBs(this.id, "translucency", "translucent", this.bsAtoms);
} else if (this.colors != null) sm.setShapePropertyBs(this.id, "colors", this.colors, this.bsAtoms);
}, "J.adapter.readers.pymol.PyMOLScene,JM.ModelSet,~S,~B");
Clazz_defineMethod(c$, "getModelIndex", 
function(m){
if (this.bsAtoms == null) return -1;
var iAtom = this.bsAtoms.nextSetBit(0);
if (iAtom >= m.at.length) System.out.println("PyMOL LOADING ERROR IN MERGE");
return (iAtom < 0 ? -1 : m.at[iAtom].mi);
}, "JM.ModelSet");
Clazz_defineMethod(c$, "setColors", 
function(colixes, translucency){
this.colors =  Clazz_newArray(-1, [colixes, Float.$valueOf(translucency)]);
}, "~A,~N");
Clazz_defineMethod(c$, "setSize", 
function(size){
this.size = Clazz_floatToInt(size * 1000);
}, "~N");
Clazz_defineMethod(c$, "toString", 
function(){
return "[JmolObject " + this.id + " " + (this.bsAtoms == null ? "" : this.bsAtoms.cardinality() + " atoms") + "]";
});
});
;//5.0.1-v2 Fri Jul 26 07:56:23 CDT 2024
Clazz_declarePackage("J.adapter.readers.pymol");
Clazz_load(["java.util.Hashtable", "JU.BS"], "J.adapter.readers.pymol.PyMOLGroup", null, function(){
var c$ = Clazz_decorateAsClass(function(){
this.name = null;
this.objectNameID = null;
this.list = null;
this.object = null;
this.visible = true;
this.occluded = false;
this.bsAtoms = null;
this.firstAtom = 0;
this.type = 0;
this.parent = null;
Clazz_instantialize(this, arguments);}, J.adapter.readers.pymol, "PyMOLGroup", null);
Clazz_prepareFields (c$, function(){
this.list =  new java.util.Hashtable();
this.bsAtoms =  new JU.BS();
});
Clazz_makeConstructor(c$, 
function(name){
this.name = name;
}, "~S");
Clazz_defineMethod(c$, "addList", 
function(child){
var group = this.list.get(child.name);
if (group != null) return;
this.list.put(child.name, child);
child.parent = this;
}, "J.adapter.readers.pymol.PyMOLGroup");
Clazz_defineMethod(c$, "set", 
function(){
if (this.parent != null) return;
});
Clazz_defineMethod(c$, "addGroupAtoms", 
function(bs){
this.bsAtoms.or(bs);
if (this.parent != null) this.parent.addGroupAtoms(this.bsAtoms);
}, "JU.BS");
Clazz_overrideMethod(c$, "toString", 
function(){
return this.name;
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
Clazz_declarePackage("J.adapter.readers.pymol");
Clazz_load(["J.api.JmolSceneGenerator", "java.util.Hashtable", "JU.BS", "$.Lst", "$.P3"], "J.adapter.readers.pymol.PyMOLScene", ["JU.AU", "$.CU", "$.PT", "$.SB", "J.adapter.readers.pymol.JmolObject", "$.PyMOL", "$.PyMOLGroup", "$.PyMOLReader", "J.atomdata.RadiusData", "J.c.VDW", "JM.Text", "JU.BSUtil", "$.C", "$.Escape", "$.Logger", "$.Point3fi"], function(){
var c$ = Clazz_decorateAsClass(function(){
this.vwr = null;
this.pymolVersion = 0;
this.bsHidden = null;
this.bsNucleic = null;
this.bsNonbonded = null;
this.bsLabeled = null;
this.bsHydrogen = null;
this.bsNoSurface = null;
this.htSpacefill = null;
this.bsSpacefillSphere = null;
this.ssMapAtom = null;
this.atomColorList = null;
this.occludedObjects = null;
this.labels = null;
this.colixes = null;
this.frameObj = null;
this.groups = null;
this.objectSettings = null;
this.ptTemp = null;
this.bsCartoon = null;
this.htCarveSets = null;
this.htDefinedAtoms = null;
this.htHiddenObjects = null;
this.moleculeNames = null;
this.jmolObjects = null;
this.htAtomMap = null;
this.htObjectAtoms = null;
this.htObjectGroups = null;
this.htMeasures = null;
this.htObjectSettings = null;
this.objectInfo = null;
this.settings = null;
this.htStateSettings = null;
this.stateSettings = null;
this.uniqueSettings = null;
this.uniqueList = null;
this.bsUniqueBonds = null;
this.bgRgb = 0;
this.dotColor = 0;
this.surfaceMode = 0;
this.surfaceColor = 0;
this.cartoonColor = 0;
this.ribbonColor = 0;
this.sphereColor = 0;
this.labelFontId = 0;
this.labelColor = 0;
this.cartoonTranslucency = 0;
this.ribbonTranslucency = 0;
this.labelSize = 0;
this.meshWidth = 0;
this.nonbondedSize = 0;
this.nonbondedTranslucency = 0;
this.sphereScale = 0;
this.sphereTranslucency = 0;
this.stickTranslucency = 0;
this.transparency = 0;
this.stickBallRatio = 0;
this.stickBalls = 0;
this.stickRadius = 0;
this.valence = 0;
this.cartoonLadderMode = false;
this.cartoonRockets = false;
this.haveNucleicLadder = false;
this.labelPosition = null;
this.labelPosition0 = null;
this.objectName = null;
this.objectNameID = null;
this.objectJmolName = null;
this.objectType = 0;
this.bsAtoms = null;
this.objectHidden = false;
this.reader = null;
this.uniqueIDs = null;
this.cartoonTypes = null;
this.sequenceNumbers = null;
this.newChain = null;
this.radii = null;
this.baseModelIndex = 0;
this.baseAtomIndex = 0;
this.stateCount = 0;
this.mepList = "";
this.doCache = false;
this.haveScenes = false;
this.bsCarve = null;
this.solventAccessible = false;
this.bsLineBonds = null;
this.bsStickBonds = null;
this.thisState = 0;
this.currentAtomSetIndex = 0;
this.surfaceInfoName = null;
this.modelName = null;
Clazz_instantialize(this, arguments);}, J.adapter.readers.pymol, "PyMOLScene", null, J.api.JmolSceneGenerator);
Clazz_prepareFields (c$, function(){
this.bsHidden =  new JU.BS();
this.bsNucleic =  new JU.BS();
this.bsNonbonded =  new JU.BS();
this.bsLabeled =  new JU.BS();
this.bsHydrogen =  new JU.BS();
this.bsNoSurface =  new JU.BS();
this.htSpacefill =  new java.util.Hashtable();
this.bsSpacefillSphere =  new JU.BS();
this.ssMapAtom =  new java.util.Hashtable();
this.atomColorList =  new JU.Lst();
this.occludedObjects =  new java.util.Hashtable();
this.labels =  new java.util.Hashtable();
this.ptTemp =  new JU.P3();
this.bsCartoon =  new JU.BS();
this.htCarveSets =  new java.util.Hashtable();
this.htDefinedAtoms =  new java.util.Hashtable();
this.htHiddenObjects =  new java.util.Hashtable();
this.moleculeNames =  new JU.Lst();
this.jmolObjects =  new JU.Lst();
this.htAtomMap =  new java.util.Hashtable();
this.htObjectAtoms =  new java.util.Hashtable();
this.htObjectGroups =  new java.util.Hashtable();
this.htMeasures =  new java.util.Hashtable();
this.htObjectSettings =  new java.util.Hashtable();
this.objectInfo =  new java.util.Hashtable();
this.htStateSettings =  new java.util.Hashtable();
this.labelPosition0 =  new JU.P3();
this.bsLineBonds =  new JU.BS();
this.bsStickBonds =  new JU.BS();
});
Clazz_makeConstructor(c$, 
function(reader, vwr, settings, uniqueSettings, pymolVersion, haveScenes, baseAtomIndex, baseModelIndex, doCache, filePath){
this.reader = reader;
this.vwr = vwr;
this.settings = settings;
this.uniqueSettings = uniqueSettings;
this.pymolVersion = pymolVersion;
this.haveScenes = haveScenes;
this.baseAtomIndex = baseAtomIndex;
this.baseModelIndex = baseModelIndex;
this.doCache = doCache;
this.surfaceInfoName = filePath + "##JmolSurfaceInfo##";
this.setVersionSettings();
settings.trimToSize();
this.bgRgb = J.adapter.readers.pymol.PyMOL.getRGB(this.colorSetting(6));
this.labelPosition0 = this.pointSetting(471);
}, "J.api.PymolAtomReader,JV.Viewer,JU.Lst,java.util.Map,~N,~B,~N,~N,~B,~S");
Clazz_defineMethod(c$, "clearReaderData", 
function(){
this.reader = null;
this.colixes = null;
this.atomColorList = null;
this.objectSettings = null;
this.stateSettings = null;
if (this.haveScenes) return;
this.settings = null;
this.groups = null;
this.labels = null;
this.ssMapAtom = null;
this.htSpacefill = null;
this.htAtomMap = null;
this.htMeasures = null;
this.htObjectGroups = null;
this.htObjectAtoms = null;
this.htObjectSettings = null;
this.htStateSettings = null;
this.htHiddenObjects = null;
this.objectInfo = null;
this.occludedObjects = null;
this.bsHidden = this.bsNucleic = this.bsNonbonded = this.bsLabeled = this.bsHydrogen = this.bsNoSurface = this.bsCartoon = null;
});
Clazz_defineMethod(c$, "setUniqueBond", 
function(index, uniqueID){
if (uniqueID < 0) return;
if (this.uniqueList == null) {
this.uniqueList =  new java.util.Hashtable();
this.bsUniqueBonds =  new JU.BS();
}this.uniqueList.put(Integer.$valueOf(index), Integer.$valueOf(uniqueID));
this.bsUniqueBonds.set(index);
}, "~N,~N");
Clazz_defineMethod(c$, "setStateCount", 
function(stateCount){
this.stateCount = stateCount;
}, "~N");
Clazz_defineMethod(c$, "colorSetting", 
function(i){
var pos = J.adapter.readers.pymol.PyMOLReader.listAt(this.settings, i);
var o = (pos == null || pos.size() != 3 ? null : pos.get(2));
if (o == null) return Clazz_floatToInt(J.adapter.readers.pymol.PyMOL.getDefaultSetting(i, this.pymolVersion));
return (Clazz_instanceOf(o, Integer) ? (o).intValue() : JU.CU.colorPtToFFRGB(J.adapter.readers.pymol.PyMOLReader.pointAt(o, 0, this.ptTemp)));
}, "~N");
Clazz_defineMethod(c$, "pointSetting", 
function(i){
var pt =  new JU.P3();
var pos = J.adapter.readers.pymol.PyMOLReader.listAt(this.settings, i);
if (pos != null && pos.size() == 3) return J.adapter.readers.pymol.PyMOLReader.pointAt(pos.get(2), 0, pt);
return J.adapter.readers.pymol.PyMOL.getDefaultSettingPt(i, this.pymolVersion, pt);
}, "~N");
Clazz_defineMethod(c$, "ensureCapacity", 
function(n){
this.atomColorList.ensureCapacity(this.atomColorList.size() + n);
}, "~N");
Clazz_defineMethod(c$, "setReaderObjectInfo", 
function(name, type, groupName, isHidden, listObjSettings, listStateSettings, ext){
this.objectName = name;
this.objectHidden = isHidden;
this.objectNameID = (this.objectName == null ? null : this.fixName(this.objectName + ext));
this.objectSettings =  new java.util.Hashtable();
this.stateSettings =  new java.util.Hashtable();
if (this.objectName != null) {
this.objectJmolName = this.getJmolName(name);
if (groupName != null) {
this.htObjectGroups.put(this.objectName, groupName);
this.htObjectGroups.put(this.objectNameID, groupName);
}this.objectInfo.put(this.objectName,  Clazz_newArray(-1, [this.objectNameID, Integer.$valueOf(type)]));
if (this.htObjectSettings.get(this.objectName) == null) {
this.listToSettings(listObjSettings, this.objectSettings);
this.htObjectSettings.put(this.objectName, this.objectSettings);
}if (this.htStateSettings.get(this.objectNameID) == null) {
this.listToSettings(listStateSettings, this.stateSettings);
this.htStateSettings.put(this.objectNameID, this.stateSettings);
}}this.getObjectSettings();
}, "~S,~N,~S,~B,JU.Lst,JU.Lst,~S");
Clazz_defineMethod(c$, "listToSettings", 
function(list, objectSettings){
if (list != null && list.size() != 0) {
for (var i = list.size(); --i >= 0; ) {
var setting = list.get(i);
objectSettings.put(setting.get(0), setting);
}
}}, "JU.Lst,java.util.Map");
Clazz_defineMethod(c$, "getObjectSettings", 
function(){
this.stickBallRatio = this.floatSetting(277);
this.stickBalls = this.floatSetting(276);
this.stickRadius = this.floatSetting(21);
this.valence = this.floatSetting(64);
this.transparency = this.floatSetting(138);
this.dotColor = Clazz_floatToInt(this.floatSetting(210));
this.nonbondedSize = this.floatSetting(65);
this.nonbondedTranslucency = this.floatSetting(524);
this.sphereScale = this.floatSetting(155);
this.cartoonColor = Clazz_floatToInt(this.floatSetting(236));
this.ribbonColor = Clazz_floatToInt(this.floatSetting(235));
this.sphereColor = Clazz_floatToInt(this.floatSetting(173));
this.cartoonTranslucency = this.floatSetting(279);
this.ribbonTranslucency = this.floatSetting(666);
this.stickTranslucency = this.floatSetting(198);
this.sphereTranslucency = this.floatSetting(172);
this.cartoonLadderMode = this.booleanSetting(448);
this.cartoonRockets = this.booleanSetting(180);
this.surfaceMode = Clazz_floatToInt(this.floatSetting(143));
this.surfaceColor = Clazz_floatToInt(this.floatSetting(144));
this.solventAccessible = this.booleanSetting(338);
this.meshWidth = this.floatSetting(90);
var carveSet = this.stringSetting(342).trim();
if (carveSet.length == 0) {
this.bsCarve = null;
} else {
this.bsCarve = this.htCarveSets.get(carveSet);
if (this.bsCarve == null) this.htCarveSets.put(carveSet, this.bsCarve =  new JU.BS());
}this.labelPosition =  new JU.P3();
try {
var setting = this.getObjectSetting(471);
J.adapter.readers.pymol.PyMOLReader.pointAt(J.adapter.readers.pymol.PyMOLReader.listAt(setting, 2), 0, this.labelPosition);
} catch (e) {
if (Clazz_exceptionOf(e, Exception)){
} else {
throw e;
}
}
this.labelPosition.add(this.labelPosition0);
this.labelColor = Clazz_floatToInt(this.floatSetting(66));
this.labelSize = this.floatSetting(453);
this.labelFontId = Clazz_floatToInt(this.floatSetting(328));
});
Clazz_defineMethod(c$, "setAtomInfo", 
function(uniqueIDs, cartoonTypes, sequenceNumbers, newChain, radii){
this.uniqueIDs = uniqueIDs;
this.cartoonTypes = cartoonTypes;
this.sequenceNumbers = sequenceNumbers;
this.newChain = newChain;
this.radii = radii;
}, "~A,~A,~A,~A,~A");
Clazz_defineMethod(c$, "setSceneObject", 
function(name, istate){
this.objectName = name;
this.objectType = this.getObjectType(name);
this.objectJmolName = this.getJmolName(name);
this.objectNameID = (istate == 0 && this.objectType != 0 ? this.getObjectID(name) : this.objectJmolName + "_" + istate);
this.bsAtoms = this.htObjectAtoms.get(name);
this.objectSettings = this.htObjectSettings.get(name);
this.stateSettings = this.htStateSettings.get(name + "_" + istate);
var groupName = this.htObjectGroups.get(name);
this.objectHidden = (this.htHiddenObjects.containsKey(name) || groupName != null && !this.groups.get(groupName).visible);
this.getObjectSettings();
}, "~S,~N");
Clazz_defineMethod(c$, "buildScene", 
function(name, thisScene, htObjNames, htSecrets){
var frame = thisScene.get(2);
var smap =  new java.util.Hashtable();
smap.put("pymolFrame", frame);
smap.put("generator", this);
smap.put("name", name);
var view = J.adapter.readers.pymol.PyMOLReader.listAt(thisScene, 0);
if (view != null) smap.put("pymolView", this.getPymolView(view, false));
var visibilities = thisScene.get(1);
smap.put("visibilities", visibilities);
var sname = "_scene_" + name + "_";
var reps =  new Array(J.adapter.readers.pymol.PyMOL.REP_LIST.length);
for (var j = J.adapter.readers.pymol.PyMOL.REP_LIST.length; --j >= 0; ) {
var list = htObjNames.get(sname + J.adapter.readers.pymol.PyMOL.REP_LIST[j]);
var data = J.adapter.readers.pymol.PyMOLReader.listAt(list, 5);
if (data != null && data.size() > 0) reps[j] = J.adapter.readers.pymol.PyMOLReader.listToMap(data);
}
smap.put("moleculeReps", reps);
sname = "_!c_" + name + "_";
var colorection = J.adapter.readers.pymol.PyMOLReader.listAt(thisScene, 3);
var n = colorection.size();
n -= n % 2;
var colors =  new Array(Clazz_doubleToInt(n / 2));
for (var j = 0, i = 0; j < n; j += 2) {
var color = J.adapter.readers.pymol.PyMOLReader.intAt(colorection, j);
var c = htSecrets.get(sname + color);
if (c != null && c.size() > 1) colors[i++] =  Clazz_newArray(-1, [Integer.$valueOf(color), c.get(1)]);
}
smap.put("colors", colors);
this.addJmolObject(1073742139, null, smap).jmolName = name;
}, "~S,JU.Lst,java.util.Map,java.util.Map");
Clazz_overrideMethod(c$, "generateScene", 
function(scene){
JU.Logger.info("PyMOLScene - generateScene " + scene.get("name"));
this.jmolObjects.clear();
this.bsHidden.clearAll();
this.occludedObjects.clear();
this.htHiddenObjects.clear();
var frame = scene.get("pymolFrame");
this.thisState = frame.intValue();
this.addJmolObject(4115, null, Integer.$valueOf(this.thisState - 1));
try {
this.generateVisibilities(scene.get("visibilities"));
this.generateColors(scene.get("colors"));
this.generateShapes(scene.get("moleculeReps"));
this.finalizeVisibility();
this.offsetObjects();
this.finalizeObjects();
} catch (e) {
if (Clazz_exceptionOf(e, Exception)){
JU.Logger.info("PyMOLScene exception " + e);
e.printStackTrace();
} else {
throw e;
}
}
}, "java.util.Map");
Clazz_defineMethod(c$, "generateColors", 
function(colors){
if (colors == null) return;
for (var i = colors.length; --i >= 0; ) {
var item = colors[i];
var color = (item[0]).intValue();
var icolor = J.adapter.readers.pymol.PyMOL.getRGB(color);
var molecules = item[1];
var bs = this.getSelectionAtoms(molecules, this.thisState,  new JU.BS());
this.addJmolObject(1153433601, bs, null).argb = icolor;
}
}, "~A");
Clazz_defineMethod(c$, "processSelection", 
function(selection){
var id = J.adapter.readers.pymol.PyMOLReader.stringAt(selection, 0);
id = "_" + (id.equals("sele") ? id : "sele_" + id);
var g = this.getGroup(id);
this.getSelectionAtoms(J.adapter.readers.pymol.PyMOLReader.listAt(selection, 5), 0, g.bsAtoms);
}, "JU.Lst");
Clazz_defineMethod(c$, "getSelectionAtoms", 
function(molecules, istate, bs){
if (molecules != null) for (var j = molecules.size(); --j >= 0; ) this.selectAllAtoms(J.adapter.readers.pymol.PyMOLReader.listAt(molecules, j), istate, bs);

return bs;
}, "JU.Lst,~N,JU.BS");
Clazz_defineMethod(c$, "selectAllAtoms", 
function(obj, istate, bs){
var name = J.adapter.readers.pymol.PyMOLReader.stringAt(obj, 0);
this.setSceneObject(name, istate);
var atomList = J.adapter.readers.pymol.PyMOLReader.listAt(obj, 1);
var k0 = (istate == 0 ? 1 : istate);
var k1 = (istate == 0 ? this.stateCount : istate);
for (var k = k0; k <= k1; k++) {
var atomMap = this.htAtomMap.get(this.fixName(name + "_" + k));
if (atomMap == null) continue;
this.getBsAtoms(atomList, atomMap, bs);
}
}, "JU.Lst,~N,JU.BS");
Clazz_defineMethod(c$, "generateVisibilities", 
function(vis){
if (vis == null) return;
var bs =  new JU.BS();
this.addJmolObject(12294, null, null);
for (var e, $e = this.groups.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) e.getValue().visible = true;

for (var e, $e = vis.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var name = e.getKey();
if (name.equals("all")) continue;
var list = e.getValue();
var tok = (J.adapter.readers.pymol.PyMOLReader.intAt(list, 0) == 1 ? 1610625028 : 12294);
if (tok == 12294) this.htHiddenObjects.put(name, Boolean.TRUE);
switch (this.getObjectType(name)) {
case 12:
var g = this.groups.get(name);
if (g != null) g.visible = (tok == 1610625028);
break;
}
}
this.setGroupVisibilities();
for (var e, $e = vis.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var name = e.getKey();
if (name.equals("all")) continue;
this.setSceneObject(name, this.thisState);
if (this.objectHidden) continue;
var list = e.getValue();
var tok = (this.objectHidden ? 12294 : 1610625028);
bs = null;
var info = this.objectJmolName;
switch (this.objectType) {
case 0:
case 12:
continue;
case 1:
bs = this.vwr.getDefinedAtomSet(info);
if (bs.nextSetBit(0) < 0) continue;
break;
case 4:
if (tok == 1610625028) {
var mdList = this.htMeasures.get(name);
if (mdList != null) this.addMeasurements(mdList, mdList[0].points.size(), null, this.getBS(J.adapter.readers.pymol.PyMOLReader.listAt(list, 2)), J.adapter.readers.pymol.PyMOLReader.intAt(list, 3), null, true);
}info += "_*";
break;
case 6:
case 3:
case 2:
break;
}
this.addJmolObject(tok, bs, info);
}
}, "java.util.Map");
Clazz_defineMethod(c$, "generateShapes", 
function(reps){
if (reps == null) return;
this.addJmolObject(12295, null, null).argb = this.thisState - 1;
for (var m = 0; m < this.moleculeNames.size(); m++) {
var name = this.moleculeNames.get(m);
this.setSceneObject(name, this.thisState);
if (this.objectHidden) continue;
var molReps =  new Array(23);
for (var i = 0; i < 23; i++) molReps[i] =  new JU.BS();

for (var i = reps.length; --i >= 0; ) {
var repMap = reps[i];
var list = (repMap == null ? null : repMap.get(this.objectName));
if (list != null) this.selectAllAtoms(list, this.thisState, molReps[i]);
}
this.createShapeObjects(molReps, true, -1, -1);
}
}, "~A");
Clazz_defineMethod(c$, "getBS", 
function(list){
var bs =  new JU.BS();
for (var i = list.size(); --i >= 0; ) bs.set(J.adapter.readers.pymol.PyMOLReader.intAt(list, i));

return bs;
}, "JU.Lst");
Clazz_defineMethod(c$, "getBsAtoms", 
function(list, atomMap, bs){
for (var i = list.size(); --i >= 0; ) bs.set(atomMap[J.adapter.readers.pymol.PyMOLReader.intAt(list, i)]);

}, "JU.Lst,~A,JU.BS");
Clazz_defineMethod(c$, "setReaderObjects", 
function(){
this.clearReaderData();
this.finalizeObjects();
if (!this.haveScenes) {
this.uniqueSettings = null;
this.bsUniqueBonds = this.bsStickBonds = this.bsLineBonds = null;
}});
Clazz_defineMethod(c$, "finalizeObjects", 
function(){
this.vwr.setStringProperty("defaults", "PyMOL");
for (var i = 0; i < this.jmolObjects.size(); i++) {
try {
var obj = this.jmolObjects.get(i);
obj.finalizeObject(this, this.vwr.ms, this.mepList, this.doCache);
} catch (e) {
if (Clazz_exceptionOf(e, Exception)){
System.out.println(e);
e.printStackTrace();
} else {
throw e;
}
}
}
this.finalizeUniqueBonds();
this.jmolObjects.clear();
});
Clazz_defineMethod(c$, "offsetObjects", 
function(){
for (var i = 0, n = this.jmolObjects.size(); i < n; i++) this.jmolObjects.get(i).offset(this.baseModelIndex, this.baseAtomIndex);

});
Clazz_defineMethod(c$, "getJmolObject", 
function(id, bsAtoms, info){
if (this.baseAtomIndex > 0) bsAtoms = JU.BSUtil.copy(bsAtoms);
return  new J.adapter.readers.pymol.JmolObject(id, this.objectNameID, bsAtoms, info);
}, "~N,JU.BS,~O");
Clazz_defineMethod(c$, "addJmolObject", 
function(id, bsAtoms, info){
return this.addObject(this.getJmolObject(id, bsAtoms, info));
}, "~N,JU.BS,~O");
Clazz_defineMethod(c$, "getPymolView", 
function(view, isViewObj){
var pymolView =  Clazz_newFloatArray (21, 0);
var depthCue = this.booleanSetting(84);
var fog = this.booleanSetting(88);
var fog_start = this.floatSetting(192);
var pt = 0;
var i = 0;
for (var j = 0; j < 3; j++) pymolView[pt++] = J.adapter.readers.pymol.PyMOLReader.floatAt(view, i++);

if (isViewObj) i++;
for (var j = 0; j < 3; j++) pymolView[pt++] = J.adapter.readers.pymol.PyMOLReader.floatAt(view, i++);

if (isViewObj) i++;
for (var j = 0; j < 3; j++) pymolView[pt++] = J.adapter.readers.pymol.PyMOLReader.floatAt(view, i++);

if (isViewObj) i += 5;
for (var j = 0; j < 8; j++) pymolView[pt++] = J.adapter.readers.pymol.PyMOLReader.floatAt(view, i++);

var isOrtho = this.booleanSetting(23);
var fov = this.floatSetting(152);
pymolView[pt++] = (isOrtho ? fov : -fov);
pymolView[pt++] = (depthCue ? 1 : 0);
pymolView[pt++] = (fog ? 1 : 0);
pymolView[pt++] = fog_start;
return pymolView;
}, "JU.Lst,~B");
Clazz_defineMethod(c$, "globalSetting", 
function(i){
var setting = J.adapter.readers.pymol.PyMOLReader.listAt(this.settings, i);
if (setting != null && setting.size() == 3) return (setting.get(2)).floatValue();
return J.adapter.readers.pymol.PyMOL.getDefaultSetting(i, this.pymolVersion);
}, "~N");
Clazz_defineMethod(c$, "addGroup", 
function(object, parent, type, bsAtoms){
if (this.groups == null) this.groups =  new java.util.Hashtable();
var myGroup = this.getGroup(this.objectName);
myGroup.object = object;
myGroup.objectNameID = this.objectNameID;
myGroup.visible = !this.objectHidden;
myGroup.type = type;
if (!myGroup.visible) {
this.occludedObjects.put(this.objectNameID, Boolean.TRUE);
this.htHiddenObjects.put(this.objectName, Boolean.TRUE);
}if (parent != null && parent.length != 0) this.getGroup(parent).addList(myGroup);
if (bsAtoms != null) myGroup.addGroupAtoms(bsAtoms);
return myGroup;
}, "JU.Lst,~S,~N,JU.BS");
Clazz_defineMethod(c$, "getGroup", 
function(name){
var g = this.groups.get(name);
if (g == null) {
this.groups.put(name, (g =  new J.adapter.readers.pymol.PyMOLGroup(name)));
this.defineAtoms(name, g.bsAtoms);
}return g;
}, "~S");
Clazz_defineMethod(c$, "finalizeVisibility", 
function(){
this.setGroupVisibilities();
if (this.groups != null) for (var i = this.jmolObjects.size(); --i >= 0; ) {
var obj = this.jmolObjects.get(i);
if (obj.jmolName != null && this.occludedObjects.containsKey(obj.jmolName)) obj.visible = false;
}
if (!this.bsHidden.isEmpty()) this.addJmolObject(2097194, this.bsHidden, null);
});
Clazz_defineMethod(c$, "setCarveSets", 
function(htObjNames){
if (this.htCarveSets.isEmpty()) return;
for (var e, $e = this.htCarveSets.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) this.getSelectionAtoms(J.adapter.readers.pymol.PyMOLReader.listAt(htObjNames.get(e.getKey()), 5), 0, e.getValue());

}, "java.util.Map");
Clazz_defineMethod(c$, "setGroupVisibilities", 
function(){
if (this.groups == null) return;
var list = this.groups.values();
var bsAll =  new JU.BS();
for (var g, $g = list.iterator (); $g.hasNext()&& ((g = $g.next ()) || true);) {
bsAll.or(g.bsAtoms);
if (g.parent == null) this.setGroupVisible(g, true);
 else if (g.list.isEmpty()) g.addGroupAtoms( new JU.BS());
}
this.defineAtoms("all", bsAll);
});
Clazz_defineMethod(c$, "defineAtoms", 
function(name, bs){
this.htDefinedAtoms.put(this.getJmolName(name), bs);
}, "~S,JU.BS");
Clazz_defineMethod(c$, "getJmolName", 
function(name){
return "__" + this.fixName(name);
}, "~S");
Clazz_defineMethod(c$, "createShapeObjects", 
function(reps, allowSurface, ac0, ac){
if (ac >= 0) {
this.bsAtoms = JU.BSUtil.newBitSet2(ac0, ac);
var jo;
jo = this.addJmolObject(1153433601, this.bsAtoms, null);
this.colixes = JU.AU.ensureLengthShort(this.colixes, ac);
for (var i = ac; --i >= ac0; ) this.colixes[i] = this.atomColorList.get(i).intValue();

jo.setColors(this.colixes, 0);
jo.setSize(0);
jo = this.addJmolObject(1, this.bsAtoms, null);
jo.setSize(0);
}this.createShapeObject(7, reps[7]);
this.createShapeObject(0, reps[0]);
this.fixReps(reps);
this.createSpacefillObjects();
for (var i = 0; i < 23; i++) switch (i) {
case 7:
case 0:
continue;
case 8:
case 2:
if (!allowSurface) continue;
switch (this.surfaceMode) {
case 0:
reps[i].andNot(this.bsNoSurface);
break;
case 1:
case 3:
break;
case 2:
case 4:
reps[i].andNot(this.bsHydrogen);
break;
}
default:
this.createShapeObject(i, reps[i]);
continue;
}

this.bsAtoms = null;
}, "~A,~B,~N,~N");
Clazz_defineMethod(c$, "addLabel", 
function(atomIndex, uniqueID, atomColor, labelPos, label){
var icolor = Clazz_floatToInt(this.getUniqueFloatDef(uniqueID, 66, this.labelColor));
if (icolor == -7 || icolor == -6) {
} else if (icolor < 0) {
icolor = atomColor;
}if (labelPos == null) {
labelPos = this.setLabelPosition(this.getUniquePoint(uniqueID, 471, this.labelPosition), labelPos, false);
}var offset = this.getUniquePoint(uniqueID, 718, null);
if (offset != null) {
labelPos = this.setLabelPosition(offset, labelPos, true);
}this.labels.put(Integer.$valueOf(atomIndex), this.newTextLabel(label, labelPos, icolor, this.labelFontId, this.labelSize));
}, "~N,~N,~N,~A,~S");
Clazz_defineMethod(c$, "getUniqueFloatDef", 
function(id, key, defaultValue){
var setting;
if (id <= 0 || (setting = this.uniqueSettings.get(Integer.$valueOf((id << 10) + key))) == null) return defaultValue;
var v = (setting.get(2)).floatValue();
if (JU.Logger.debugging) JU.Logger.debug("Pymol unique setting for " + id + ": [" + key + "] = " + v);
return v;
}, "~N,~N,~N");
Clazz_defineMethod(c$, "getUniquePoint", 
function(id, key, pt){
var setting;
if (id <= 0 || (setting = this.uniqueSettings.get(Integer.$valueOf((id << 10) + key))) == null) return pt;
pt =  new JU.P3();
J.adapter.readers.pymol.PyMOLReader.pointAt(setting.get(2), 0, pt);
JU.Logger.info("Pymol unique setting for " + id + ": " + key + " = " + pt);
return pt;
}, "~N,~N,JU.P3");
Clazz_defineMethod(c$, "getObjectSetting", 
function(i){
return this.objectSettings.get(Integer.$valueOf(i));
}, "~N");
Clazz_defineMethod(c$, "booleanSetting", 
function(i){
return (this.floatSetting(i) != 0);
}, "~N");
Clazz_defineMethod(c$, "floatSetting", 
function(i){
var setting = this.getSetting(i);
if (setting != null && setting.size() == 3) return (setting.get(2)).floatValue();
return J.adapter.readers.pymol.PyMOL.getDefaultSetting(i, this.pymolVersion);
}, "~N");
Clazz_defineMethod(c$, "stringSetting", 
function(i){
var setting = this.getSetting(i);
if (setting != null && setting.size() == 3) return J.adapter.readers.pymol.PyMOLReader.stringAt(setting, 2);
return J.adapter.readers.pymol.PyMOL.getDefaultSettingS(i, this.pymolVersion);
}, "~N");
Clazz_defineMethod(c$, "getSetting", 
function(i){
var setting = null;
if (this.stateSettings != null) setting = this.stateSettings.get(Integer.$valueOf(i));
if (setting == null && this.objectSettings != null) setting = this.objectSettings.get(Integer.$valueOf(i));
if (setting == null && i < this.settings.size()) setting = this.settings.get(i);
return setting;
}, "~N");
Clazz_defineMethod(c$, "setLabelPosition", 
function(offset, labelPos, isPlacement){
if (labelPos == null) labelPos =  Clazz_newFloatArray (7, 0);
labelPos[0] = 1;
if (isPlacement) {
labelPos[4] = offset.x;
labelPos[5] = offset.y;
labelPos[6] = offset.z;
} else {
labelPos[1] = offset.x;
labelPos[2] = offset.y;
labelPos[3] = offset.z;
}return labelPos;
}, "JU.P3,~A,~B");
Clazz_defineMethod(c$, "addCGO", 
function(data, color){
data.addLast(this.objectName);
var jo = this.addJmolObject(23, null, data);
jo.argb = color;
jo.translucency = this.floatSetting(441);
return this.fixName(this.objectName);
}, "JU.Lst,~N");
Clazz_defineMethod(c$, "addMeasurements", 
function(mdList, nCoord, list, bsReps, color, offsets, haveLabels){
var isNew = (mdList == null);
var n = (isNew ? Clazz_doubleToInt(Clazz_doubleToInt(list.size() / 3) / nCoord) : mdList.length);
if (n == 0) return false;
var drawLabel = haveLabels && (bsReps == null || bsReps.get(3));
var drawDashes = (bsReps == null || bsReps.get(10));
var rad = this.floatSetting(107);
rad /= 400;
if (rad == 0) rad = 0.05;
if (!drawDashes) rad = -5.0E-4;
if (color < 0) color = Clazz_floatToInt(this.floatSetting(574));
var c = J.adapter.readers.pymol.PyMOL.getRGB(color);
var colix = JU.C.getColix(c);
var clabel = (this.labelColor < 0 ? color : this.labelColor);
if (isNew) {
mdList =  new Array(n);
this.htMeasures.put(this.objectName, mdList);
}var bs = JU.BSUtil.newAndSetBit(0);
for (var index = 0, p = 0; index < n; index++) {
var md;
var offset;
if (isNew) {
var points =  new JU.Lst();
for (var i = 0; i < nCoord; i++, p += 3) points.addLast(J.adapter.readers.pymol.PyMOLScene.newP3i(J.adapter.readers.pymol.PyMOLReader.pointAt(list, p,  new JU.P3())));

offset = (J.adapter.readers.pymol.PyMOLReader.floatsAt(J.adapter.readers.pymol.PyMOLReader.listAt(offsets, index), 0,  Clazz_newFloatArray (7, 0), 7));
if (offset == null) offset = this.setLabelPosition(this.labelPosition,  Clazz_newFloatArray (7, 0), false);
md = mdList[index] = this.vwr.newMeasurementData(this.objectNameID + "_" + (index + 1), points);
md.note = this.objectName;
} else {
md = mdList[index];
offset = md.text.pymolOffset;
}offset = J.adapter.readers.pymol.PyMOL.fixAllZeroLabelPosition(offset);
if (offset == null) offset =  Clazz_newFloatArray(-1, [1, 0, 0, 0, 0, 0, 0]);
var nDigits = Clazz_floatToInt(this.floatSetting(J.adapter.readers.pymol.PyMOLScene.MEAS_DIGITS[nCoord - 2]));
var strFormat = nCoord + ": " + (drawLabel ? "%0." + (nDigits < 0 ? 1 : nDigits) + "VALUE" : "");
var fontSize = this.floatSetting(453);
var text = this.newTextLabel(strFormat, offset, clabel, Clazz_floatToInt(this.floatSetting(328)), fontSize);
md.set(12290, null, null, null, strFormat, "angstroms", null, false, false, null, false, Clazz_floatToInt(rad * 2000), colix, text, NaN, null);
this.addJmolObject(6, bs, md);
}
return true;
}, "~A,~N,JU.Lst,JU.BS,~N,JU.Lst,~B");
c$.newP3i = Clazz_defineMethod(c$, "newP3i", 
function(p){
var pi =  new JU.Point3fi();
pi.set(p.x, p.y, p.z);
return pi;
}, "JU.P3");
Clazz_defineMethod(c$, "getViewScript", 
function(view){
var sb =  new JU.SB();
var pymolView = this.getPymolView(view, true);
sb.append(";set translucent " + (this.globalSetting(213) != 2) + ";set zshadePower 1;set traceAlpha " + (this.globalSetting(111) != 0));
var rockets = this.cartoonRockets;
sb.append(";set cartoonRockets " + rockets);
if (rockets) sb.append(";set rocketBarrels " + rockets);
sb.append(";set cartoonLadders " + this.haveNucleicLadder);
sb.append(";set ribbonBorder " + (this.globalSetting(118) != 0));
sb.append(";set cartoonFancy " + (this.globalSetting(118) == 0));
var s = "000000" + Integer.toHexString(this.bgRgb & 0xFFFFFF);
s = "[x" + s.substring(s.length - 6) + "]";
sb.append(";background " + s);
sb.append(";moveto 0 PyMOL " + JU.Escape.eAF(pymolView));
sb.append(";save orientation 'default';");
return sb;
}, "JU.Lst");
Clazz_defineMethod(c$, "getColix", 
function(colorIndex, translucency){
var colix = (colorIndex == -7 ? (JU.C.getBgContrast(this.bgRgb) == 8 ? 4 : 8) : colorIndex == -6 ? JU.C.getBgContrast(this.bgRgb) : JU.C.getColixO(Integer.$valueOf(J.adapter.readers.pymol.PyMOL.getRGB(colorIndex))));
return JU.C.getColixTranslucent3(colix, translucency > 0, translucency);
}, "~N,~N");
Clazz_defineMethod(c$, "setAtomColor", 
function(atomColor){
this.atomColorList.addLast(Integer.$valueOf(this.getColix(atomColor, 0)));
}, "~N");
Clazz_defineMethod(c$, "setFrameObject", 
function(type, info){
if (info != null) {
this.frameObj = this.getJmolObject(type, null, info);
return;
}if (this.frameObj == null) return;
this.frameObj.finalizeObject(this, this.vwr.ms, null, false);
this.frameObj = null;
}, "~N,~O");
Clazz_defineMethod(c$, "fixName", 
function(name){
var chars = name.toLowerCase().toCharArray();
for (var i = chars.length; --i >= 0; ) if (!JU.PT.isLetterOrDigit(chars[i])) chars[i] = '_';

return String.valueOf(chars);
}, "~S");
Clazz_defineMethod(c$, "getObjectID", 
function(name){
return this.objectInfo.get(name)[0];
}, "~S");
Clazz_defineMethod(c$, "getObjectType", 
function(name){
var o = this.objectInfo.get(name);
return (o == null ? 0 : (o[1]).intValue());
}, "~S");
Clazz_defineMethod(c$, "setAtomMap", 
function(atomMap, ac0){
this.htAtomMap.put(this.objectNameID, atomMap);
var bsAtoms = this.htDefinedAtoms.get(this.objectJmolName);
if (bsAtoms == null) {
bsAtoms = JU.BS.newN(ac0 + atomMap.length);
JU.Logger.info("PyMOL molecule " + this.objectName + " " + this.objectHidden);
this.htDefinedAtoms.put(this.objectJmolName, bsAtoms);
this.htObjectAtoms.put(this.objectName, bsAtoms);
this.moleculeNames.addLast(this.objectName);
this.modelName = this.objectName;
}return bsAtoms;
}, "~A,~N");
Clazz_defineMethod(c$, "newTextLabel", 
function(label, labelOffset, colorIndex, fontID, fontSize){
var face;
switch (fontID) {
default:
case 11:
case 12:
case 13:
case 14:
face = "SansSerif";
break;
case 0:
case 1:
face = "Monospaced";
break;
case 9:
case 10:
case 15:
case 16:
case 17:
case 18:
face = "Serif";
break;
}
var style;
switch (fontID) {
default:
style = "Plain";
break;
case 6:
case 12:
case 16:
case 17:
style = "Italic";
break;
case 7:
case 10:
case 13:
style = "Bold";
break;
case 8:
case 14:
case 18:
style = "BoldItalic";
break;
}
if (fontSize > 0) fontSize *= 1.25;
var font = this.vwr.getFont3D(face, style, fontSize == 0 ? 12 : fontSize);
var t = JM.Text.newLabel(this.vwr, font, label, this.getColix(colorIndex, 0), 0, 0, 0);
if (t != null) t.pymolOffset = labelOffset;
return t;
}, "~S,~A,~N,~N,~N");
Clazz_defineMethod(c$, "setVersionSettings", 
function(){
if (this.pymolVersion < 100) {
this.addSetting(550, 2, Integer.$valueOf(0));
this.addSetting(529, 2, Integer.$valueOf(2));
this.addSetting(471, 4,  Clazz_newDoubleArray(-1, [1, 1, 0]));
if (this.pymolVersion < 99) {
this.addSetting(448, 2, Integer.$valueOf(0));
this.addSetting(431, 2, Integer.$valueOf(0));
this.addSetting(361, 2, Integer.$valueOf(1));
}}});
Clazz_defineMethod(c$, "addSetting", 
function(key, type, val){
var settingCount = this.settings.size();
if (settingCount <= key) for (var i = key + 1; --i >= settingCount; ) this.settings.addLast(null);

if (type == 4) {
var d = val;
var list;
val = list =  new JU.Lst();
for (var i = 0; i < 3; i++) list.addLast(Double.$valueOf(d[i]));

}var setting =  new JU.Lst();
setting.addLast(Integer.$valueOf(key));
setting.addLast(Integer.$valueOf(type));
setting.addLast(val);
this.settings.set(key, setting);
}, "~N,~N,~O");
Clazz_defineMethod(c$, "fixReps", 
function(reps){
this.bsCartoon.clearAll();
for (var iAtom = this.bsAtoms.nextSetBit(0); iAtom >= 0; iAtom = this.bsAtoms.nextSetBit(iAtom + 1)) {
var rad = 0;
var uniqueID = (this.reader == null ? this.uniqueIDs[iAtom] : this.reader.getUniqueID(iAtom));
if (reps[1].get(iAtom)) {
rad = (this.reader == null ? this.radii[iAtom] : this.reader.getVDW(iAtom)) * this.getUniqueFloatDef(uniqueID, 155, this.sphereScale);
} else if (reps[4].get(iAtom)) {
rad = this.nonbondedSize;
}if (rad != 0) {
this.addSpacefill(iAtom, rad, true);
}var cartoonType = (this.reader == null ? this.cartoonTypes[iAtom] : this.reader.getCartoonType(iAtom));
if (reps[5].get(iAtom)) {
switch (cartoonType) {
case 1:
case 4:
reps[21].set(iAtom);
case -1:
reps[5].clear(iAtom);
this.bsCartoon.clear(iAtom);
break;
case 7:
reps[22].set(iAtom);
reps[5].clear(iAtom);
this.bsCartoon.clear(iAtom);
break;
default:
this.bsCartoon.set(iAtom);
}
}}
reps[5].and(this.bsCartoon);
this.cleanSingletons(reps[5]);
this.cleanSingletons(reps[6]);
this.cleanSingletons(reps[21]);
this.cleanSingletons(reps[22]);
this.bsCartoon.and(reps[5]);
}, "~A");
Clazz_defineMethod(c$, "addSpacefill", 
function(iAtom, rad, doCheck){
if (doCheck && this.bsSpacefillSphere.get(iAtom)) return;
this.bsSpacefillSphere.set(iAtom);
var r = Float.$valueOf(rad);
var bsr = this.htSpacefill.get(r);
if (bsr == null) this.htSpacefill.put(r, bsr =  new JU.BS());
bsr.set(iAtom);
}, "~N,~N,~B");
Clazz_defineMethod(c$, "cleanSingletons", 
function(bs){
if (bs.isEmpty()) return;
bs.and(this.bsAtoms);
var bsr =  new JU.BS();
var n = bs.length();
var pass = 0;
while (true) {
for (var i = 0, offset = 0, iPrev = -2147483648, iSeqLast = -2147483648, iSeq = -2147483648; i < n; i++) {
if (iPrev < 0 || (this.reader == null ? this.newChain[i] : this.reader.compareAtoms(iPrev, i))) offset++;
iSeq = (this.reader == null ? this.sequenceNumbers[i] : this.reader.getSequenceNumber(i));
if (iSeq != iSeqLast) {
iSeqLast = iSeq;
offset++;
}if (pass == 0) {
if (bs.get(i)) bsr.set(offset);
} else if (!bsr.get(offset)) bs.clear(i);
iPrev = i;
}
if (++pass == 2) break;
var bsnot =  new JU.BS();
for (var i = bsr.nextSetBit(0); i >= 0; i = bsr.nextSetBit(i + 1)) if (!bsr.get(i - 1) && !bsr.get(i + 1)) bsnot.set(i);

bsr.andNot(bsnot);
}
}, "JU.BS");
Clazz_defineMethod(c$, "createShapeObject", 
function(shapeID, bs){
if (bs.isEmpty()) return;
var jo = null;
switch (shapeID) {
case 11:
bs.and(this.bsNonbonded);
if (bs.isEmpty()) return;
this.setUniqueObjects(7, bs, 0, 0, 524, this.nonbondedTranslucency, 0, this.nonbondedSize, 0.5);
break;
case 4:
case 1:
this.setUniqueObjects(0, bs, 173, this.sphereColor, 172, this.sphereTranslucency, 155, this.sphereScale, 1);
break;
case 19:
var ellipsoidTranslucency = this.floatSetting(571);
var ellipsoidColor = Clazz_floatToInt(this.floatSetting(570));
var ellipsoidScale = this.floatSetting(569);
this.setUniqueObjects(20, bs, 570, ellipsoidColor, 571, ellipsoidTranslucency, 569, ellipsoidScale, 50);
break;
case 9:
this.setUniqueObjects(16, bs, 210, this.dotColor, 0, 0, 155, this.sphereScale, 1);
break;
case 2:
var withinDistance = this.floatSetting(344);
jo = this.addJmolObject(135180, bs,  Clazz_newArray(-1, [this.booleanSetting(156) ? "FULLYLIT" : "FRONTLIT", (this.surfaceMode == 3 || this.surfaceMode == 4) ? " only" : "", this.bsCarve, Float.$valueOf(withinDistance)]));
jo.setSize(this.floatSetting(4) * (this.solventAccessible ? -1 : 1));
jo.translucency = this.transparency;
if (this.surfaceColor >= 0) jo.argb = J.adapter.readers.pymol.PyMOL.getRGB(this.surfaceColor);
jo.modelIndex = this.currentAtomSetIndex;
jo.cacheID = this.surfaceInfoName;
this.setUniqueObjects(24, bs, 144, this.surfaceColor, 138, this.transparency, 0, 0, 0);
break;
case 8:
jo = this.addJmolObject(135180, bs, null);
jo.setSize(this.floatSetting(4));
jo.translucency = this.transparency;
this.setUniqueObjects(24, bs, 144, this.surfaceColor, 138, this.transparency, 0, 0, 0);
break;
case 3:
bs.and(this.bsLabeled);
if (bs.isEmpty()) return;
jo = this.addJmolObject(5, bs, this.labels);
break;
case 10:
case 7:
jo = this.addJmolObject(659488, bs, null);
jo.setSize(this.floatSetting(44) / 15);
var color = Clazz_floatToInt(this.floatSetting(526));
if (color >= 0) jo.argb = J.adapter.readers.pymol.PyMOL.getRGB(color);
break;
case 0:
jo = this.addJmolObject(1, bs, null);
jo.setSize(this.floatSetting(21) * 2);
jo.translucency = this.stickTranslucency;
var col = Clazz_floatToInt(this.floatSetting(376));
if (col >= 0) jo.argb = J.adapter.readers.pymol.PyMOL.getRGB(col);
break;
case 5:
this.createCartoonObject("H", (this.cartoonRockets ? 181 : 100));
this.createCartoonObject("S", 96);
this.createCartoonObject("L", 92);
this.createCartoonObject(" ", 92);
break;
case 22:
this.createPuttyObject(bs);
break;
case 21:
this.createTraceObject(bs);
break;
case 6:
this.createRibbonObject(bs);
break;
default:
JU.Logger.error("Unprocessed representation type " + shapeID);
}
}, "~N,JU.BS");
Clazz_defineMethod(c$, "setUniqueObjects", 
function(shape, bs, setColor, color, setTrans, trans, setSize, size, f){
var n = bs.cardinality();
var colixes = (setColor == 0 ? null :  Clazz_newShortArray (n, 0));
var atrans = (setTrans == 0 ? null :  Clazz_newFloatArray (n, 0));
var sizes =  Clazz_newFloatArray (n, 0);
for (var pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1), pt++) {
var id = (this.reader == null ? this.uniqueIDs[i] : this.reader.getUniqueID(i));
if (setColor == 0) {
} else {
var c = Clazz_floatToInt(this.getUniqueFloatDef(id, setColor, color));
if (c > 0) colixes[pt] = this.getColix(c, 0);
}if (atrans != null) {
atrans[pt] = this.getUniqueFloatDef(id, setTrans, trans);
}sizes[pt] = this.getUniqueFloatDef(id, setSize, size) * f;
}
return this.addJmolObject(shape, bs,  Clazz_newArray(-1, [colixes, atrans, sizes]));
}, "~N,JU.BS,~N,~N,~N,~N,~N,~N,~N");
Clazz_defineMethod(c$, "createSpacefillObjects", 
function(){
for (var e, $e = this.htSpacefill.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var r = e.getKey().floatValue();
var bs = e.getValue();
this.addJmolObject(1153433601, bs, null).rd =  new J.atomdata.RadiusData(null, r, J.atomdata.RadiusData.EnumType.ABSOLUTE, J.c.VDW.AUTO);
}
this.htSpacefill.clear();
});
Clazz_defineMethod(c$, "createTraceObject", 
function(bs){
this.checkNucleicObject(bs, true);
if (bs.isEmpty()) return;
var r = this.floatSetting(103);
var jo = this.setUniqueObjects(10, bs, 236, this.cartoonColor, 0, 0, 0, 0, 0);
jo.setSize(r * 2);
jo.translucency = this.cartoonTranslucency;
}, "JU.BS");
Clazz_defineMethod(c$, "checkNucleicObject", 
function(bs, isTrace){
var jo;
var bsNuc = JU.BSUtil.copy(this.bsNucleic);
bsNuc.and(bs);
if (!bsNuc.isEmpty()) {
if (isTrace && this.cartoonLadderMode) this.haveNucleicLadder = true;
jo = this.addJmolObject(11, bsNuc, null);
jo.translucency = this.cartoonTranslucency;
jo.setSize(this.floatSetting(103) * 2);
bs.andNot(bsNuc);
}}, "JU.BS,~B");
Clazz_defineMethod(c$, "createPuttyObject", 
function(bs){
var info =  Clazz_newFloatArray(-1, [this.floatSetting(378), this.floatSetting(377), this.floatSetting(382), this.floatSetting(379), this.floatSetting(380), this.floatSetting(381), this.floatSetting(581)]);
this.addJmolObject(1112152078, bs, info).translucency = this.cartoonTranslucency;
}, "JU.BS");
Clazz_defineMethod(c$, "createRibbonObject", 
function(bs){
var isTrace = (this.floatSetting(19) > 1);
var r = this.floatSetting(20) * 2;
var rayScale = this.floatSetting(327);
if (r == 0) r = this.floatSetting(106) * (isTrace ? 1 : (rayScale <= 1 ? 0.5 : rayScale)) * 0.1;
var jo = this.setUniqueObjects((isTrace ? 10 : 9), bs, 235, this.ribbonColor, 0, 0, 0, 0, 0);
jo.setSize(r);
jo.translucency = this.ribbonTranslucency;
}, "JU.BS");
Clazz_defineMethod(c$, "createCartoonObject", 
function(key, sizeID){
var bs = JU.BSUtil.copy(this.ssMapAtom.get(key));
if (bs == null) return;
bs.and(this.bsCartoon);
if (bs.isEmpty()) return;
if (key.equals(" ")) {
this.checkNucleicObject(bs, false);
if (bs.isEmpty()) return;
}var jo = this.setUniqueObjects(11, bs, 236, this.cartoonColor, 0, 0, 0, 0, 0);
jo.setSize(this.floatSetting(sizeID) * 2);
jo.translucency = this.cartoonTranslucency;
}, "~S,~N");
Clazz_defineMethod(c$, "addObject", 
function(obj){
this.jmolObjects.addLast(obj);
return obj;
}, "J.adapter.readers.pymol.JmolObject");
Clazz_defineMethod(c$, "setGroupVisible", 
function(g, parentVis){
var vis = parentVis && g.visible;
if (vis) return;
g.visible = false;
this.occludedObjects.put(g.objectNameID, Boolean.TRUE);
this.htHiddenObjects.put(g.name, Boolean.TRUE);
switch (g.type) {
case 1:
this.bsHidden.or(g.bsAtoms);
break;
default:
g.occluded = true;
break;
}
for (var gg, $gg = g.list.values().iterator (); $gg.hasNext()&& ((gg = $gg.next ()) || true);) {
this.setGroupVisible(gg, vis);
}
}, "J.adapter.readers.pymol.PyMOLGroup,~B");
Clazz_defineMethod(c$, "getSSMapAtom", 
function(ssType){
var bs = this.ssMapAtom.get(ssType);
if (bs == null) this.ssMapAtom.put(ssType, bs =  new JU.BS());
return bs;
}, "~S");
Clazz_defineMethod(c$, "setAtomDefs", 
function(){
this.setGroupVisibilities();
var defs =  new java.util.Hashtable();
for (var e, $e = this.htDefinedAtoms.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var bs = e.getValue();
if (!bs.isEmpty()) defs.put(e.getKey(), bs);
}
this.addJmolObject(12290, null, defs);
return defs;
});
Clazz_defineMethod(c$, "needSelections", 
function(){
return this.haveScenes || !this.htCarveSets.isEmpty();
});
Clazz_defineMethod(c$, "setUniqueBonds", 
function(bsBonds, isSticks){
if (isSticks) {
this.bsStickBonds.or(bsBonds);
this.bsStickBonds.andNot(this.bsLineBonds);
} else {
this.bsLineBonds.or(bsBonds);
this.bsLineBonds.andNot(this.bsStickBonds);
}}, "JU.BS,~B");
Clazz_defineMethod(c$, "finalizeUniqueBonds", 
function(){
if (this.uniqueList == null) return;
var bondCount = this.vwr.ms.bondCount;
var bonds = this.vwr.ms.bo;
for (var i = this.bsUniqueBonds.nextSetBit(0); i >= 0; i = this.bsUniqueBonds.nextSetBit(i + 1)) {
var rad = NaN;
var id = this.uniqueList.get(Integer.$valueOf(i)).intValue();
if (this.bsLineBonds.get(i)) {
rad = this.getUniqueFloatDef(id, 44, NaN) / 30;
} else if (this.bsStickBonds.get(i)) {
rad = this.getUniqueFloatDef(id, 21, NaN);
}var c = Clazz_floatToInt(this.getUniqueFloatDef(id, 376, 2147483647));
if (c != 2147483647) c = J.adapter.readers.pymol.PyMOL.getRGB(c);
var valence = this.getUniqueFloatDef(id, 64, NaN);
var t = this.getUniqueFloatDef(id, 198, NaN);
if (i < 0 || i >= bondCount) return;
var b = bonds[i];
this.setBondParameters(b, this.thisState - 1, rad, valence, c, t);
}
});
Clazz_defineMethod(c$, "setBondParameters", 
function(b, modelIndex, rad, pymolValence, argb, trans){
if (modelIndex >= 0 && b.atom1.mi != modelIndex) return;
if (!Float.isNaN(rad)) b.mad = Clazz_floatToShort(rad * 2000);
var colix = b.colix;
if (argb != 2147483647) colix = JU.C.getColix(argb);
if (!Float.isNaN(trans)) b.colix = JU.C.getColixTranslucent3(colix, trans != 0, trans);
 else if (b.colix != colix) b.colix = JU.C.copyColixTranslucency(b.colix, colix);
if (pymolValence == 1) b.order |= 98304;
 else if (pymolValence == 0) b.order |= 65536;
}, "JM.Bond,~N,~N,~N,~N,~N");
Clazz_defineMethod(c$, "addMesh", 
function(tok, obj, objName, isMep){
var jo = this.addJmolObject(tok, null, obj);
this.setSceneObject(objName, -1);
var meshColor = Clazz_floatToInt(this.floatSetting(146));
if (meshColor < 0) meshColor = J.adapter.readers.pymol.PyMOLReader.intAt(J.adapter.readers.pymol.PyMOLReader.listAt(obj, 0), 2);
if (!isMep) {
jo.setSize(this.meshWidth);
jo.argb = J.adapter.readers.pymol.PyMOL.getRGB(meshColor);
}jo.translucency = this.transparency;
jo.cacheID = this.surfaceInfoName;
}, "~N,JU.Lst,~S,~B");
Clazz_defineMethod(c$, "addIsosurface", 
function(objectName){
var jo = this.addJmolObject(135180, null, objectName);
jo.cacheID = this.surfaceInfoName;
return jo;
}, "~S");
c$.MEAS_DIGITS =  Clazz_newIntArray(-1, [530, 531, 532]);
});
;//5.0.1-v2 Fri Jul 26 07:56:23 CDT 2024
Clazz_declarePackage("J.adapter.readers.pymol");
Clazz_load(["J.adapter.readers.pdb.PdbReader", "J.api.PymolAtomReader", "JU.BS", "$.P3"], "J.adapter.readers.pymol.PyMOLReader", ["java.util.Hashtable", "JU.AU", "$.BC", "$.CU", "$.Lst", "$.PT", "$.V3", "J.adapter.readers.pymol.PickleReader", "$.PyMOL", "$.PyMOLScene", "J.adapter.smarter.Atom", "$.Bond", "$.Structure", "J.c.STR", "JU.BSUtil", "$.BoxInfo", "$.Logger"], function(){
var c$ = Clazz_decorateAsClass(function(){
this.allowSurface = true;
this.doResize = false;
this.doCache = false;
this.isStateScript = false;
this.sourcePNGJ = false;
this.ac0 = 0;
this.$ac = 0;
this.stateCount = 0;
this.structureCount = 0;
this.isHidden = false;
this.bsStructureDefined = null;
this.bsBytesExcluded = null;
this.bsValence = null;
this.atomMap = null;
this.jmolToUniqueID = null;
this.ssMapSeq = null;
this.pymolScene = null;
this.xyzMin = null;
this.xyzMax = null;
this.nModels = 0;
this.logging = false;
this.reps = null;
this.isMovie = false;
this.pymolFrame = 0;
this.allStates = false;
this.totalAtomCount = 0;
this.pymolVersion = 0;
this.trajectoryStep = null;
this.trajectoryPtr = 0;
this.objectName = null;
this.volumeData = null;
this.mapObjects = null;
this.haveMeasurements = false;
this.frames = null;
this.uniqueSettings = null;
this.atoms = null;
this.haveScenes = false;
this.baseModelIndex = 0;
this.sceneOrder = null;
this.bondCount = 0;
this.haveBinaryArrays = true;
this.aTemp = null;
this.ptTemp = null;
this.forceValence = false;
Clazz_instantialize(this, arguments);}, J.adapter.readers.pymol, "PyMOLReader", J.adapter.readers.pdb.PdbReader, J.api.PymolAtomReader);
Clazz_prepareFields (c$, function(){
this.bsStructureDefined =  new JU.BS();
this.bsValence =  new JU.BS();
this.xyzMin = JU.P3.new3(1e6, 1e6, 1e6);
this.xyzMax = JU.P3.new3(-1000000.0, -1000000.0, -1000000.0);
this.reps =  new Array(23);
this.aTemp =  Clazz_newByteArray (16, 0);
this.ptTemp =  new JU.P3();
});
Clazz_overrideMethod(c$, "setup", 
function(fullPath, htParams, reader){
this.isBinary = this.mustFinalizeModelSet = true;
this.setupASCR(fullPath, htParams, reader);
}, "~S,java.util.Map,~O");
Clazz_defineMethod(c$, "initializeReader", 
function(){
this.baseAtomIndex = (this.htParams.get("baseAtomIndex")).intValue();
this.baseModelIndex = (this.htParams.get("baseModelIndex")).intValue();
this.forceValence = this.checkFilterKey("SHOWVALENCE");
this.asc.setInfo("noAutoBond", Boolean.TRUE);
this.asc.setCurrentModelInfo("pdbNoHydrogens", Boolean.TRUE);
this.asc.setInfo("isPyMOL", Boolean.TRUE);
if (this.isTrajectory) this.trajectorySteps =  new JU.Lst();
this.isStateScript = this.htParams.containsKey("isStateScript");
this.sourcePNGJ = this.htParams.containsKey("sourcePNGJ");
this.doResize = this.checkFilterKey("DORESIZE");
this.allowSurface = !this.checkFilterKey("NOSURFACE");
this.doCache = this.checkFilterKey("DOCACHE");
if (this.doCache && this.sourcePNGJ) this.doCache = false;
 else if (this.sourcePNGJ && !this.doCache) this.sourcePNGJ = false;
if (this.doCache) this.bsBytesExcluded =  new JU.BS();
Clazz_superCall(this, J.adapter.readers.pymol.PyMOLReader, "initializeReader", []);
});
Clazz_overrideMethod(c$, "processBinaryDocument", 
function(){
var logFile = this.vwr.getLogFileName();
this.logging = (logFile.length > 0);
JU.Logger.info(this.logging ? "PyMOL (1) file data streaming to " + logFile : "To view raw PyMOL file data, use 'set logFile \"some_filename\" ");
var reader =  new J.adapter.readers.pymol.PickleReader(this.binaryDoc, this.vwr);
var map = reader.getMap(this.logging && JU.Logger.debuggingHigh);
reader = null;
this.process(map);
});
Clazz_overrideMethod(c$, "setAdditionalAtomParameters", 
function(atom){
}, "J.adapter.smarter.Atom");
Clazz_defineMethod(c$, "finalizeSubclassReader", 
function(){
if (this.asc.atomSetCount == 1 && this.pymolScene.modelName != null && this.pymolScene.modelName.length == 4) this.pdbID = this.pymolScene.modelName;
Clazz_superCall(this, J.adapter.readers.pymol.PyMOLReader, "finalizeSubclassReader", []);
this.asc.setTensors();
});
Clazz_overrideMethod(c$, "finalizeModelSet", 
function(){
this.pymolScene.setReaderObjects();
if (this.haveMeasurements) {
this.appendLoadNote(this.vwr.getMeasurementInfoAsString());
this.setLoadNote();
}if (this.haveScenes) {
var scenes =  new Array(this.sceneOrder.size());
for (var i = scenes.length; --i >= 0; ) scenes[i] = J.adapter.readers.pymol.PyMOLReader.stringAt(this.sceneOrder, i);

this.vwr.ms.msInfo.put("scenes", scenes);
}this.vwr.ms.setTrajectoryBs(JU.BSUtil.newBitSet2(this.baseModelIndex, this.vwr.ms.mc));
if (!this.isStateScript) this.pymolScene.setFrameObject(0, null);
if (this.bsBytesExcluded != null) {
var nExcluded = this.bsBytesExcluded.cardinality();
var bytes0 = this.vwr.fm.getFileAsBytes(this.filePath, null);
var bytes =  Clazz_newByteArray (bytes0.length - nExcluded, 0);
for (var i = this.bsBytesExcluded.nextClearBit(0), n = bytes0.length, pt = 0; i < n; i = this.bsBytesExcluded.nextClearBit(i + 1)) bytes[pt++] = bytes0[i];

bytes0 = null;
var fileName = this.filePath;
this.vwr.cachePut(fileName, bytes);
}});
Clazz_defineMethod(c$, "process", 
function(map){
this.pymolVersion = (map.get("version")).intValue();
this.appendLoadNote("PyMOL version: " + this.pymolVersion);
var settings = this.fixSettings(J.adapter.readers.pymol.PyMOLReader.getMapList(map, "settings"));
var lst = J.adapter.readers.pymol.PyMOLReader.listAt(settings, 749);
this.haveBinaryArrays = (lst != null && J.adapter.readers.pymol.PyMOLReader.floatAt(lst, 2) == 1);
this.sceneOrder = J.adapter.readers.pymol.PyMOLReader.getMapList(map, "scene_order");
this.haveScenes = this.getFrameScenes(map);
var file = J.adapter.readers.pymol.PyMOLReader.listAt(settings, 440);
if (file != null && file.size() > 2) JU.Logger.info("PyMOL session file: " + file.get(2));
this.setUniqueSettings(J.adapter.readers.pymol.PyMOLReader.getMapList(map, "unique_settings"));
this.pymolScene =  new J.adapter.readers.pymol.PyMOLScene(this, this.vwr, settings, this.uniqueSettings, this.pymolVersion, this.haveScenes, this.baseAtomIndex, this.baseModelIndex, this.doCache, this.filePath);
var logFile = this.vwr.getLogFileName();
this.logging = (logFile.length > 0);
JU.Logger.info(this.logging ? "PyMOL file data streaming to " + logFile : "To view raw PyMOL file data, use 'set logFile \"some_filename\" ");
var names = J.adapter.readers.pymol.PyMOLReader.getMapList(map, "names");
for (var e, $e = map.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var name = e.getKey();
JU.Logger.info(name);
if (name.equals("names")) {
for (var i = 1; i < names.size(); i++) {
var obj = J.adapter.readers.pymol.PyMOLReader.listAt(names, i);
JU.Logger.info("  " + J.adapter.readers.pymol.PyMOLReader.stringAt(obj, 0));
}
}}
if (this.logging) {
if (this.logging) this.vwr.log("$CLEAR$");
for (var e, $e = map.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var name = e.getKey();
if (!"names".equals(name)) {
this.vwr.log("\n===" + name + "===");
this.vwr.log(JU.PT.rep(e.getValue().toString(), "[", "\n["));
}}
this.vwr.log("\n===names===");
for (var i = 1; i < names.size(); i++) {
this.vwr.log("");
var list = names.get(i);
this.vwr.log(" =" + J.adapter.readers.pymol.PyMOLReader.bytesToString(list.get(0)) + "=");
try {
this.vwr.log(JU.PT.rep(list.toString(), "[", "\n["));
} catch (e) {
}
}
}this.addColors(J.adapter.readers.pymol.PyMOLReader.getMapList(map, "colors"), this.pymolScene.globalSetting(214) != 0);
this.allStates = (this.pymolScene.globalSetting(49) != 0);
this.pymolFrame = Clazz_floatToInt(this.pymolScene.globalSetting(194));
this.getAtomAndStateCount(names);
this.pymolScene.setStateCount(this.stateCount);
var pymolState = Clazz_floatToInt(this.pymolScene.globalSetting(193));
if (!this.isMovie) this.pymolScene.setFrameObject(4115, (this.allStates ? Integer.$valueOf(-1) : Integer.$valueOf(pymolState - 1)));
this.appendLoadNote("frame=" + this.pymolFrame + " state=" + pymolState + " all_states=" + this.allStates);
if (!this.isStateScript && this.doResize) {
var width = 0;
var height = 0;
var main = J.adapter.readers.pymol.PyMOLReader.getMapList(map, "main");
if (main != null) {
width = J.adapter.readers.pymol.PyMOLReader.intAt(main, 0);
height = J.adapter.readers.pymol.PyMOLReader.intAt(main, 1);
}var note;
if (width > 0 && height > 0) {
note = "PyMOL dimensions width=" + width + " height=" + height;
this.asc.setInfo("preferredWidthHeight",  Clazz_newIntArray(-1, [width, height]));
this.vwr.resizeInnerPanel(width, height);
} else {
note = "PyMOL dimensions?";
}this.appendLoadNote(note);
}var mov;
if (!this.isStateScript && !this.allStates && (mov = J.adapter.readers.pymol.PyMOLReader.getMapList(map, "movie")) != null) {
var frameCount = J.adapter.readers.pymol.PyMOLReader.intAt(mov, 0);
if (frameCount > 0) this.processMovie(mov, frameCount);
}if (this.totalAtomCount == 0) this.asc.newAtomSet();
if (this.allStates && this.desiredModelNumber == -2147483648) {
} else if (this.isMovie) {
switch (this.desiredModelNumber) {
case -2147483648:
break;
default:
this.desiredModelNumber = this.frames[(this.desiredModelNumber > 0 && this.desiredModelNumber <= this.frames.length ? this.desiredModelNumber : this.pymolFrame) - 1];
this.pymolScene.setFrameObject(4115, Integer.$valueOf(this.desiredModelNumber - 1));
break;
}
} else if (this.desiredModelNumber == 0) {
this.desiredModelNumber = pymolState;
} else {
}var n = names.size();
var nAtomsJmol = 0;
for (var j = 0; j < this.stateCount; j++) {
for (var i = 1; i < n; i++) nAtomsJmol += this.processObject(J.adapter.readers.pymol.PyMOLReader.listAt(names, i), true, j, true);

}
this.jmolToUniqueID =  Clazz_newIntArray (nAtomsJmol, 0);
for (var j = 0; j < this.stateCount; j++) {
if (!this.doGetModel(++this.nModels, null)) continue;
this.model(this.nModels, null);
this.pymolScene.currentAtomSetIndex = this.asc.iSet;
if (this.isTrajectory) {
this.trajectoryStep =  new Array(this.totalAtomCount);
this.trajectorySteps.addLast(this.trajectoryStep);
this.trajectoryPtr = 0;
}for (var i = 1; i < n; i++) this.processObject(J.adapter.readers.pymol.PyMOLReader.listAt(names, i), true, j, false);

}
for (var i = 1; i < n; i++) this.processObject(J.adapter.readers.pymol.PyMOLReader.listAt(names, i), false, 0, false);

this.pymolScene.setReaderObjectInfo(null, 0, null, false, null, null, null);
if (this.mapObjects != null && this.allowSurface) this.processMeshes();
if (this.isTrajectory) {
this.appendLoadNote("PyMOL trajectories read: " + this.trajectorySteps.size());
this.asc.finalizeTrajectoryAs(this.trajectorySteps, null);
}this.processDefinitions();
this.processSelectionsAndScenes(map);
this.pymolScene.finalizeVisibility();
if (!this.isStateScript) {
this.vwr.initialize(false, true);
this.addJmolScript(this.pymolScene.getViewScript(J.adapter.readers.pymol.PyMOLReader.getMapList(map, "view")).toString());
}if (this.$ac == 0) this.asc.setInfo("dataOnly", Boolean.TRUE);
this.pymolScene.offsetObjects();
}, "java.util.Map");
Clazz_defineMethod(c$, "fixSettings", 
function(settings){
var n = settings.size();
for (var i = 0; i < n; i++) {
var setting = settings.get(i);
var i2 = J.adapter.readers.pymol.PyMOLReader.intAt(setting, 0);
if (i2 == -1) {
settings.set(i,  new JU.Lst());
} else {
while (i < i2) {
settings.add(i++,  new JU.Lst());
n++;
}
System.out.println("PyMOL global setting " + setting);
}}
return settings;
}, "JU.Lst");
Clazz_defineMethod(c$, "getFrameScenes", 
function(map){
if (this.sceneOrder == null) return false;
var scenes = map.get("scene_dict");
for (var i = 0; i < this.sceneOrder.size(); i++) {
var name = J.adapter.readers.pymol.PyMOLReader.stringAt(this.sceneOrder, i);
var thisScene = J.adapter.readers.pymol.PyMOLReader.getMapList(scenes, name);
if (thisScene == null || thisScene.get(2) == null) this.sceneOrder.removeItemAt(i--);
}
return (this.sceneOrder != null && this.sceneOrder.size() != 0);
}, "java.util.Map");
Clazz_defineMethod(c$, "setUniqueSettings", 
function(list){
this.uniqueSettings =  new java.util.Hashtable();
var max = 0;
var n = 0;
if (list != null && list.size() != 0) {
for (var i = list.size(); --i >= 0; ) {
var atomSettings = list.get(i);
var id = J.adapter.readers.pymol.PyMOLReader.intAt(atomSettings, 0);
if (id > max) max = id;
var mySettings = atomSettings.get(1);
for (var j = mySettings.size(); --j >= 0; ) {
var setting = mySettings.get(j);
var type = J.adapter.readers.pymol.PyMOLReader.intAt(setting, 0);
var uid = (id << 10) + type;
this.uniqueSettings.put(Integer.$valueOf(uid), setting);
n++;
if (type != 64) System.out.println("UniqueSetting " + id + " " + setting);
if (JU.Logger.debugging) JU.Logger.info("PyMOL unique setting " + id + " " + setting);
}
}
}JU.Logger.info("PyMOL uniqueSettings: " + n);
return max;
}, "JU.Lst");
Clazz_defineMethod(c$, "addColors", 
function(colors, isClamped){
if (colors == null || colors.size() == 0) return;
for (var i = colors.size(); --i >= 0; ) {
var c = J.adapter.readers.pymol.PyMOLReader.listAt(colors, i);
J.adapter.readers.pymol.PyMOL.addColor(c.get(1), isClamped ? J.adapter.readers.pymol.PyMOLReader.colorSettingClamped(c, this.ptTemp) : J.adapter.readers.pymol.PyMOLReader.getColorPt(c.get(2), this.ptTemp));
}
}, "JU.Lst,~B");
Clazz_defineMethod(c$, "getAtomAndStateCount", 
function(names){
var n = 0;
for (var i = 1; i < names.size(); i++) {
var execObject = J.adapter.readers.pymol.PyMOLReader.listAt(names, i);
var type = J.adapter.readers.pymol.PyMOLReader.intAt(execObject, 4);
if (!this.checkObject(execObject)) continue;
if (type == 1) {
var pymolObject = J.adapter.readers.pymol.PyMOLReader.listAt(execObject, 5);
var states = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 4);
var ns = states.size();
if (ns > this.stateCount) this.stateCount = ns;
var nAtoms;
var nBonds;
if (this.haveBinaryArrays) {
nBonds = Clazz_doubleToInt((J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 6).get(1)).length / 20);
nAtoms = Clazz_doubleToInt((J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 7).get(1)).length / 120);
n += nAtoms;
} else {
nBonds = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 6).size();
nAtoms = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 7).size();
}System.out.println("Object " + this.objectName + " nBonds=" + nBonds + ", nAtoms = " + nAtoms);
for (var j = 0; j < ns; j++) {
var state = J.adapter.readers.pymol.PyMOLReader.listAt(states, j);
var idxToAtm = J.adapter.readers.pymol.PyMOLReader.listAt(state, 3);
if (idxToAtm == null) {
this.isTrajectory = false;
} else {
var m = idxToAtm.size();
n += m;
if (this.isTrajectory && m != nAtoms) this.isTrajectory = false;
}}
}}
this.totalAtomCount = n;
JU.Logger.info("PyMOL total atom count = " + this.totalAtomCount);
JU.Logger.info("PyMOL state count = " + this.stateCount);
}, "JU.Lst");
Clazz_defineMethod(c$, "checkObject", 
function(execObject){
this.objectName = J.adapter.readers.pymol.PyMOLReader.stringAt(execObject, 0);
this.isHidden = (J.adapter.readers.pymol.PyMOLReader.intAt(execObject, 2) != 1);
return (this.objectName.indexOf("_") != 0);
}, "JU.Lst");
Clazz_defineMethod(c$, "processMovie", 
function(mov, frameCount){
var movie =  new java.util.Hashtable();
movie.put("frameCount", Integer.$valueOf(frameCount));
movie.put("currentFrame", Integer.$valueOf(this.pymolFrame - 1));
var haveCommands = false;
var haveViews = false;
var haveFrames = false;
var list = J.adapter.readers.pymol.PyMOLReader.listAt(mov, 4);
for (var i = list.size(); --i >= 0; ) if (J.adapter.readers.pymol.PyMOLReader.intAt(list, i) != 0) {
this.frames =  Clazz_newIntArray (list.size(), 0);
for (var j = this.frames.length; --j >= 0; ) this.frames[j] = J.adapter.readers.pymol.PyMOLReader.intAt(list, j) + 1;

movie.put("frames", this.frames);
haveFrames = true;
break;
}
var cmds = J.adapter.readers.pymol.PyMOLReader.listAt(mov, 5);
var cmd;
for (var i = cmds.size(); --i >= 0; ) if ((cmd = J.adapter.readers.pymol.PyMOLReader.stringAt(cmds, i)) != null && cmd.length > 1) {
cmds = J.adapter.readers.pymol.PyMOLReader.fixMovieCommands(cmds);
if (cmds != null) {
movie.put("commands", cmds);
haveCommands = true;
break;
}}
var views = J.adapter.readers.pymol.PyMOLReader.listAt(mov, 6);
var view;
for (var i = views.size(); --i >= 0; ) if ((view = J.adapter.readers.pymol.PyMOLReader.listAt(views, i)) != null && view.size() >= 12 && view.get(1) != null) {
haveViews = true;
views = J.adapter.readers.pymol.PyMOLReader.fixMovieViews(views);
if (views != null) {
movie.put("views", views);
break;
}}
this.appendLoadNote("PyMOL movie frameCount = " + frameCount);
if (haveFrames && !haveCommands && !haveViews) {
this.isMovie = true;
this.pymolScene.setReaderObjectInfo(null, 0, null, false, null, null, null);
this.pymolScene.setFrameObject(1073742031, movie);
} else {
}}, "JU.Lst,~N");
c$.fixMovieViews = Clazz_defineMethod(c$, "fixMovieViews", 
function(views){
return views;
}, "JU.Lst");
c$.fixMovieCommands = Clazz_defineMethod(c$, "fixMovieCommands", 
function(cmds){
return cmds;
}, "JU.Lst");
Clazz_defineMethod(c$, "processObject", 
function(execObject, moleculeOnly, iState, justCountJmolAtoms){
if (execObject == null) return 0;
var type = J.adapter.readers.pymol.PyMOLReader.intAt(execObject, 4);
var startLen = execObject.get(execObject.size() - 1);
if ((type == 1) != moleculeOnly || !this.checkObject(execObject)) return 0;
var pymolObject = J.adapter.readers.pymol.PyMOLReader.listAt(execObject, 5);
var stateSettings = null;
if (type == 1) {
var states = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 4);
var state = J.adapter.readers.pymol.PyMOLReader.listAt(states, iState);
var idxToAtm = J.adapter.readers.pymol.PyMOLReader.listAt(state, 3);
if (iState > 0 && (idxToAtm == null || idxToAtm.size() == 0)) return 0;
stateSettings = J.adapter.readers.pymol.PyMOLReader.listAt(state, 7);
if (justCountJmolAtoms) {
return J.adapter.readers.pymol.PyMOLReader.intAt(pymolObject, 3);
}} else if (iState > 0) {
return 0;
}JU.Logger.info("PyMOL model " + (this.nModels) + " Object " + this.objectName + (this.isHidden ? " (hidden)" : " (visible)"));
if (!this.isHidden && !this.isMovie && !this.allStates) {
if (this.pymolFrame > 0 && this.pymolFrame != this.nModels) {
this.pymolFrame = this.nModels;
this.allStates = true;
this.pymolScene.setFrameObject(4115, Integer.$valueOf(-1));
}}var objectHeader = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 0);
var parentGroupName = (execObject.size() < 8 ? null : J.adapter.readers.pymol.PyMOLReader.stringAt(execObject, 6));
if (parentGroupName != null && "".equals(parentGroupName.trim())) parentGroupName = null;
this.pymolScene.setReaderObjectInfo(this.objectName, type, parentGroupName, this.isHidden, J.adapter.readers.pymol.PyMOLReader.listAt(objectHeader, 8), stateSettings, (moleculeOnly ? "_" + (iState + 1) : ""));
var bsAtoms = null;
var doExclude = (this.bsBytesExcluded != null);
var msg = null;
switch (type) {
default:
msg = "" + type;
break;
case -1:
this.pymolScene.processSelection(execObject);
break;
case 1:
doExclude = false;
bsAtoms = this.processMolecule(pymolObject, iState);
break;
case 4:
doExclude = false;
this.processMeasure(pymolObject);
break;
case 3:
case 2:
this.processMap(pymolObject, type == 3, false);
break;
case 8:
this.processGadget(pymolObject);
break;
case 12:
if (parentGroupName == null) parentGroupName = "";
break;
case 6:
msg = "CGO";
this.processCGO(pymolObject);
break;
case 11:
msg = "ALIGNEMENT";
break;
case 9:
msg = "CALCULATOR";
break;
case 5:
msg = "CALLBACK";
break;
case 10:
msg = "SLICE";
break;
case 7:
msg = "SURFACE";
break;
}
if (parentGroupName != null || bsAtoms != null) this.pymolScene.addGroup(execObject, parentGroupName, type, bsAtoms);
if (doExclude) {
var i0 = J.adapter.readers.pymol.PyMOLReader.intAt(startLen, 0);
var len = J.adapter.readers.pymol.PyMOLReader.intAt(startLen, 1);
this.bsBytesExcluded.setBits(i0, i0 + len);
JU.Logger.info("cached PSE file excludes PyMOL object type " + type + " name=" + this.objectName + " len=" + len);
}if (msg != null) JU.Logger.error("Unprocessed object type " + msg + " " + this.objectName);
return 0;
}, "JU.Lst,~B,~N,~B");
Clazz_defineMethod(c$, "processCGO", 
function(pymolObject){
if (this.isStateScript) return;
if (this.isHidden) return;
var data = J.adapter.readers.pymol.PyMOLReader.sublistAt(pymolObject, [2, 0]);
var color = J.adapter.readers.pymol.PyMOL.getRGB(J.adapter.readers.pymol.PyMOLReader.intAt(J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 0), 2));
var name = this.pymolScene.addCGO(data, color);
if (name != null) this.appendLoadNote("CGO " + name);
}, "JU.Lst");
Clazz_defineMethod(c$, "processGadget", 
function(pymolObject){
if (this.objectName.endsWith("_e_pot")) this.processMap(pymolObject, true, true);
}, "JU.Lst");
Clazz_defineMethod(c$, "processMap", 
function(pymolObject, isObject, isGadget){
if (isObject) {
if (this.sourcePNGJ) return;
if (this.isHidden && !isGadget) return;
if (this.mapObjects == null) this.mapObjects =  new JU.Lst();
this.mapObjects.addLast(pymolObject);
} else {
if (this.volumeData == null) this.volumeData =  new java.util.Hashtable();
this.volumeData.put(this.objectName, pymolObject);
if (!this.isHidden && !this.isStateScript) this.pymolScene.addIsosurface(this.objectName);
}pymolObject.addLast(this.objectName);
}, "JU.Lst,~B,~B");
Clazz_defineMethod(c$, "processMeasure", 
function(pymolObject){
if (this.isStateScript) return;
if (this.isHidden) return;
JU.Logger.info("PyMOL measure " + this.objectName);
var measure = J.adapter.readers.pymol.PyMOLReader.sublistAt(pymolObject, [2, 0]);
var pt;
var nCoord = (Clazz_instanceOf(measure.get(pt = 1),"JU.Lst") ? 2 : Clazz_instanceOf(measure.get(pt = 4),"JU.Lst") ? 3 : Clazz_instanceOf(measure.get(pt = 6),"JU.Lst") ? 4 : 0);
if (nCoord == 0) return;
var setting = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 0);
var bsReps = J.adapter.readers.pymol.PyMOLReader.getBsReps(setting, 3);
var list = J.adapter.readers.pymol.PyMOLReader.listAt(measure, pt);
var offsets = J.adapter.readers.pymol.PyMOLReader.listAt(measure, 8);
var haveLabels = (measure.size() > 8);
var color = J.adapter.readers.pymol.PyMOLReader.intAt(setting, 2);
if (this.pymolScene.addMeasurements(null, nCoord, list, bsReps, color, offsets, haveLabels)) this.haveMeasurements = true;
}, "JU.Lst");
Clazz_defineMethod(c$, "processMolecule", 
function(pymolObject, iState){
var states = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 4);
var state = J.adapter.readers.pymol.PyMOLReader.listAt(states, iState);
var idxToAtm;
var coords;
var labelPositions;
var uniqueIds = J.adapter.readers.pymol.PyMOLReader.listAt(state, 11);
var idxArray = null;
var coordsArray = null;
var labelArray = null;
var nBonds = J.adapter.readers.pymol.PyMOLReader.intAt(pymolObject, 2);
var nAtoms = J.adapter.readers.pymol.PyMOLReader.intAt(pymolObject, 3);
var n = nAtoms;
if (this.haveBinaryArrays && JU.AU.isAB(state.get(3))) {
idxToAtm = coords = labelPositions = null;
idxArray =  Clazz_newIntArray (nAtoms, 0);
coordsArray =  Clazz_newFloatArray (nAtoms * 3, 0);
this.fillFloatArrayFromBytes(state.get(2), coordsArray);
this.fillIntArrayFromBytes(state.get(3), idxArray);
var b = state.get(8);
if (b != null) {
labelArray =  Clazz_newFloatArray (nAtoms * 7, 0);
this.fillFloatArrayFromBytes(b, labelArray);
}} else {
coords = J.adapter.readers.pymol.PyMOLReader.listAt(state, 2);
idxToAtm = J.adapter.readers.pymol.PyMOLReader.listAt(state, 3);
labelPositions = J.adapter.readers.pymol.PyMOLReader.listAt(state, 8);
if (idxToAtm != null) n = idxToAtm.size();
}if (n == 0) return null;
this.$ac = this.ac0 = this.asc.ac;
if (nAtoms == 0) return null;
this.ssMapSeq =  new java.util.Hashtable();
if (iState == 0) this.processMolCryst(J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 10));
var pymolAtoms = J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 7);
this.atomMap =  Clazz_newIntArray (nAtoms, 0);
var bsAtoms = this.pymolScene.setAtomMap(this.atomMap, this.ac0);
for (var i = 0; i < 23; i++) this.reps[i] = JU.BS.newN(1000);

this.pymolScene.htSpacefill.clear();
if (iState == 0 || !this.isTrajectory) {
this.pymolScene.ensureCapacity(n);
var lexStr = null;
var atomArray = null;
var vArray = null;
if (this.haveBinaryArrays) {
var ver = J.adapter.readers.pymol.PyMOLReader.intAt(pymolAtoms, 0);
atomArray = pymolAtoms.get(1);
lexStr = this.getLexStr(pymolAtoms.get(2));
System.out.println("PyMOL atom dump version " + ver);
vArray = (this.haveBinaryArrays ? J.adapter.readers.pymol.PyMOL.getVArray(ver) : null);
}for (var idx = 0; idx < n; idx++) {
var index = (idxToAtm != null ? J.adapter.readers.pymol.PyMOLReader.intAt(idxToAtm, idx) : idxArray != null ? idxArray[idx] : idx);
var a = this.addAtom(pymolAtoms, index, atomArray, vArray, lexStr, idx, coords, coordsArray, labelPositions, uniqueIds, labelArray, bsAtoms, iState);
if (a != null) this.trajectoryStep[this.trajectoryPtr++] = a;
}
}this.addBonds(this.getBondList(J.adapter.readers.pymol.PyMOLReader.listAt(pymolObject, 6)));
this.addMolStructures();
this.atoms = this.asc.atoms;
if (!this.isStateScript) {
this.asc.setCurrentModelInfo("name", this.pymolScene.modelName);
this.createShapeObjects();
}this.ssMapSeq = null;
JU.Logger.info("reading " + (this.$ac - this.ac0) + " atoms and " + nBonds + " bonds");
JU.Logger.info("----------");
return bsAtoms;
}, "JU.Lst,~N");
Clazz_defineMethod(c$, "getLexStr", 
function(lex){
var pt = 0;
var n = JU.BC.bytesToInt(lex, pt, false);
var index =  Clazz_newIntArray (n, 0);
var imax = 0;
for (var i = 0; i < n; i++) {
pt += 4;
var ipt = index[i] = JU.BC.bytesToInt(lex, pt, false);
if (ipt > imax) imax = ipt;
}
var tokens =  new Array(imax + 1);
tokens[0] = " ";
pt += 4;
for (var i = 0; i < n; i++) {
var s = tokens[index[i]] = this.getCStr(lex, pt);
pt += s.length + 1;
}
return tokens;
}, "~A");
Clazz_defineMethod(c$, "getCStr", 
function(lex, pt){
try {
var a = this.aTemp;
var apt = 0;
var b = 0;
while ((b = lex[pt++]) != 0) {
if (apt >= a.length) a = this.aTemp = JU.AU.doubleLengthByte(a);
a[apt++] = b;
}
return  String.instantialize(JU.AU.arrayCopyByte(a, apt), "UTF-8");
} catch (e) {
if (Clazz_exceptionOf(e,"java.io.UnsupportedEncodingException")){
return null;
} else {
throw e;
}
}
}, "~A,~N");
Clazz_defineMethod(c$, "processMolCryst", 
function(cryst){
if (cryst == null || cryst.size() == 0) return;
var l = J.adapter.readers.pymol.PyMOLReader.sublistAt(cryst, [0, 0]);
var a = J.adapter.readers.pymol.PyMOLReader.sublistAt(cryst, [0, 1]);
this.setUnitCell(J.adapter.readers.pymol.PyMOLReader.floatAt(l, 0), J.adapter.readers.pymol.PyMOLReader.floatAt(l, 1), J.adapter.readers.pymol.PyMOLReader.floatAt(l, 2), J.adapter.readers.pymol.PyMOLReader.floatAt(a, 0), J.adapter.readers.pymol.PyMOLReader.floatAt(a, 1), J.adapter.readers.pymol.PyMOLReader.floatAt(a, 2));
this.setSpaceGroupName(J.adapter.readers.pymol.PyMOLReader.stringAt(cryst, 1));
}, "JU.Lst");
Clazz_defineMethod(c$, "getBondList", 
function(bonds){
var asSingle = !this.pymolScene.booleanSetting(64);
var b = null;
var vArray = null;
var n = bonds.size();
var len = 0;
if (this.haveBinaryArrays && n == 2) {
var ver = J.adapter.readers.pymol.PyMOLReader.intAt(bonds, 0);
System.out.println("PyMOL bond dump version " + ver);
vArray = J.adapter.readers.pymol.PyMOL.getVArrayB(ver);
b = bonds.get(1);
len = vArray[0];
n = Clazz_doubleToInt(b.length / len);
}var bondList =  new JU.Lst();
bondList.ensureCapacity(n);
var ia;
var ib;
var order;
var uid = -1;
for (var i = 0, apt = 0; i < n; i++) {
if (this.haveBinaryArrays) {
ia = JU.BC.bytesToInt(b, apt + vArray[1], false);
ib = JU.BC.bytesToInt(b, apt + vArray[2], false);
uid = (b[apt + vArray[6]] == 0 ? -1 : JU.BC.bytesToInt(b, apt + vArray[5], false));
order = b[apt + vArray[3]];
apt += len;
} else {
var lst = J.adapter.readers.pymol.PyMOLReader.listAt(bonds, i);
ia = J.adapter.readers.pymol.PyMOLReader.intAt(lst, 0);
ib = J.adapter.readers.pymol.PyMOLReader.intAt(lst, 1);
order = J.adapter.readers.pymol.PyMOLReader.intAt(lst, 2);
uid = (lst.size() > 6 && J.adapter.readers.pymol.PyMOLReader.intAt(lst, 6) != 0 ? J.adapter.readers.pymol.PyMOLReader.intAt(lst, 5) : -1);
}if (order < 1 || order > 3) order = 1;
var isSpecial = (order > 1 && this.bsValence.get(ia) && this.bsValence.get(ib));
order |= (order == 1 || asSingle && !isSpecial ? 65536 : 98304);
var bond =  new J.adapter.smarter.Bond(ia, ib, order);
bond.uniqueID = uid;
bondList.addLast(bond);
}
return bondList;
}, "JU.Lst");
Clazz_defineMethod(c$, "fillIntArrayFromBytes", 
function(b, array){
for (var i = 0, pt = 0; i < b.length; i += 4) array[pt++] = JU.BC.bytesToInt(b, i, false);

}, "~A,~A");
Clazz_defineMethod(c$, "fillFloatArrayFromBytes", 
function(b, array){
try {
for (var i = 0, pt = 0; i < b.length; i += 4) array[pt++] = JU.BC.bytesToFloat(b, i, false);

} catch (e) {
if (Clazz_exceptionOf(e, Exception)){
} else {
throw e;
}
}
}, "~A,~A");
Clazz_defineMethod(c$, "addAtom", 
function(pymolAtoms, apt, atomArray, vArray, lexStr, idx, coords, coordArray, labelPositions, uniqueIds, labelArray, bsState, iState){
this.atomMap[apt] = -1;
var chainID;
var altLoc;
var group3;
var name;
var sym;
var label;
var ssType;
var resi;
var insCode = null;
var bfactor;
var occupancy;
var radius;
var partialCharge;
var seqNo;
var intReps;
var formalCharge;
var atomColor;
var serNo;
var cartoonType;
var flags;
var uniqueID = -1;
var isHetero;
var bonded;
var anisou = null;
var bsReps = null;
if (this.haveBinaryArrays) {
var vpt;
var pt = apt * vArray[0];
seqNo = this.atomInt(atomArray, pt, vArray[1]);
chainID = this.atomStr(atomArray, pt, vArray[34], lexStr);
resi = this.atomStr(atomArray, pt, vArray[38], lexStr);
group3 = this.atomStr(atomArray, pt, vArray[41], lexStr);
if (group3.length > 3) group3 = group3.substring(0, 3);
name = this.atomStr(atomArray, pt, vArray[36], lexStr);
sym = this.atomStr(atomArray, pt, vArray[37], lexStr);
label = this.atomStr(atomArray, pt, vArray[19], lexStr);
ssType = this.atomStr(atomArray, pt, vArray[39], null);
altLoc = this.atomStr(atomArray, pt, vArray[40], null);
if ((vpt = vArray[42]) == 0) {
resi = this.atomStr(atomArray, pt, vArray[38], null);
} else {
var b = atomArray[pt + vpt];
insCode = (b == 0 ? " " : "" + String.fromCharCode(b));
}bfactor = this.atomFloat(atomArray, pt, vArray[4]);
occupancy = this.atomFloat(atomArray, pt, vArray[5]);
radius = this.atomFloat(atomArray, pt, vArray[6]);
partialCharge = this.atomFloat(atomArray, pt, vArray[7]);
formalCharge = atomArray[pt + vArray[28]];
if (formalCharge > 125) formalCharge -= 512;
intReps = this.atomInt(atomArray, pt, vArray[20]);
atomColor = this.atomInt(atomArray, pt, vArray[9]);
serNo = this.atomInt(atomArray, pt, vArray[10]);
cartoonType = this.atomInt(atomArray, pt, vArray[30]);
flags = this.atomInt(atomArray, pt, vArray[11]);
uniqueID = this.atomInt(atomArray, pt, vArray[13]);
anisou =  Clazz_newFloatArray (8, 0);
if ((vpt = vArray[45]) > 0) for (var i = 0; i < 6; i++) anisou[i] = JU.BC.bytesToShort(atomArray, pt + vpt + (i << 1), false);

bonded = this.atomBool(atomArray, pt, vArray[22], vArray[47]);
isHetero = this.atomBool(atomArray, pt, vArray[21], vArray[46]);
} else {
var a = J.adapter.readers.pymol.PyMOLReader.listAt(pymolAtoms, apt);
seqNo = J.adapter.readers.pymol.PyMOLReader.intAt(a, 0);
chainID = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 1);
if (chainID.length == 0) chainID = " ";
altLoc = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 2);
resi = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 3);
group3 = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 5);
name = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 6);
sym = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 7);
label = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 9);
ssType = J.adapter.readers.pymol.PyMOLReader.stringAt(a, 10);
if (ssType.length == 0) ssType = " ";
ssType = ssType.substring(0, 1);
bfactor = J.adapter.readers.pymol.PyMOLReader.floatAt(a, 14);
occupancy = J.adapter.readers.pymol.PyMOLReader.floatAt(a, 15);
radius = J.adapter.readers.pymol.PyMOLReader.floatAt(a, 16);
partialCharge = J.adapter.readers.pymol.PyMOLReader.floatAt(a, 17);
formalCharge = J.adapter.readers.pymol.PyMOLReader.intAt(a, 18);
isHetero = (J.adapter.readers.pymol.PyMOLReader.intAt(a, 19) != 0);
bsReps = J.adapter.readers.pymol.PyMOLReader.getBsReps(a, 20);
intReps = (bsReps == null ? J.adapter.readers.pymol.PyMOLReader.intAt(a, 20) : 0);
atomColor = J.adapter.readers.pymol.PyMOLReader.intAt(a, 21);
serNo = J.adapter.readers.pymol.PyMOLReader.intAt(a, 22);
cartoonType = J.adapter.readers.pymol.PyMOLReader.intAt(a, 23);
flags = J.adapter.readers.pymol.PyMOLReader.intAt(a, 24);
bonded = (J.adapter.readers.pymol.PyMOLReader.intAt(a, 25) != 0);
uniqueID = (a.size() > 40 && J.adapter.readers.pymol.PyMOLReader.intAt(a, 40) == 1 ? J.adapter.readers.pymol.PyMOLReader.intAt(a, 32) : 0);
if (a.size() > 46) anisou = J.adapter.readers.pymol.PyMOLReader.floatsAt(a, 41,  Clazz_newFloatArray (8, 0), 6);
}if (uniqueID == 0) {
uniqueID = -1;
if (uniqueIds != null) {
var id = uniqueIds.get(idx);
if (id != null) {
uniqueID = id.intValue();
}}}if (this.forceValence || this.pymolScene.getUniqueFloatDef(uniqueID, 64, this.pymolScene.valence) == 1) {
this.bsValence.set(apt);
}if (insCode == null) {
var len = resi.length;
var ch = (len > 0 ? resi.charAt(len - 1) : ' ');
insCode = (JU.PT.isDigit(ch) ? " " : "" + ch);
}if (group3.length > 3) group3 = group3.substring(0, 3);
if (group3.equals(" ")) group3 = "UNK";
if (sym.equals("A")) sym = "C";
var ichain = this.vwr.getChainID(chainID, true);
var atom = this.processAtom( new J.adapter.smarter.Atom(), name, (altLoc.length == 0 ? ' ' : altLoc.charAt(0)), group3, ichain, seqNo, insCode.charAt(0), isHetero, sym);
if (!this.filterPDBAtom(atom, this.fileAtomIndex++)) return null;
var x;
var y;
var z;
var icoord = idx * 3;
if (this.haveBinaryArrays) {
x = coordArray[icoord];
y = coordArray[++icoord];
z = coordArray[++icoord];
} else {
x = J.adapter.readers.pymol.PyMOLReader.floatAt(coords, icoord);
y = J.adapter.readers.pymol.PyMOLReader.floatAt(coords, ++icoord);
z = J.adapter.readers.pymol.PyMOLReader.floatAt(coords, ++icoord);
}JU.BoxInfo.addPointXYZ(x, y, z, this.xyzMin, this.xyzMax, 0);
if (this.isTrajectory && iState > 0) return null;
var isNucleic = (J.adapter.readers.pymol.PyMOLReader.nucleic.indexOf(group3) >= 0);
if (bsState != null) bsState.set(this.$ac);
if (seqNo >= -1000 && (!ssType.equals(" ") || name.equals("CA") || isNucleic)) {
var bs = this.ssMapSeq.get(ssType);
if (bs == null) this.ssMapSeq.put(ssType, bs =  new JU.BS());
bs.set(seqNo - -1000);
ssType += ichain;
bs = this.ssMapSeq.get(ssType);
if (bs == null) this.ssMapSeq.put(ssType, bs =  new JU.BS());
bs.set(seqNo - -1000);
}atom.bfactor = bfactor;
atom.foccupancy = occupancy;
atom.radius = radius;
if (atom.radius == 0) atom.radius = 1;
atom.partialCharge = partialCharge;
atom.vib = JU.V3.new3(uniqueID, cartoonType, NaN);
if (anisou != null && anisou[0] != 0) this.asc.setAnisoBorU(atom, anisou, 12);
this.pymolScene.setAtomColor(atomColor);
if (this.pymolScene.getUniqueFloatDef(uniqueID, 64, this.pymolScene.valence) == 1) {
this.bsValence.set(apt);
}this.processAtom2(atom, serNo, x, y, z, formalCharge);
if (!bonded) {
this.pymolScene.bsNonbonded.set(this.$ac);
}if (label.trim().length > 0) {
this.pymolScene.bsLabeled.set(this.$ac);
var labelPos =  Clazz_newFloatArray (7, 0);
if (labelArray != null) {
for (var i = 0; i < 7; i++) labelPos[i] = labelArray[apt * 7 + i];

} else {
var labelOffset = J.adapter.readers.pymol.PyMOLReader.listAt(labelPositions, apt);
if (labelOffset != null) {
for (var i = 0; i < 7; i++) labelPos[i] = J.adapter.readers.pymol.PyMOLReader.floatAt(labelOffset, i);

}}labelPos = J.adapter.readers.pymol.PyMOL.fixAllZeroLabelPosition(labelPos);
this.pymolScene.addLabel(this.$ac, uniqueID, atomColor, labelPos, label);
}if (this.isHidden) this.pymolScene.bsHidden.set(this.$ac);
if (isNucleic) this.pymolScene.bsNucleic.set(this.$ac);
for (var i = 0; i < 21; i++) if (bsReps == null ? ((intReps & (1 << i)) != 0) : bsReps.get(i)) this.reps[i].set(this.$ac);

if (atom.elementSymbol.equals("H")) this.pymolScene.bsHydrogen.set(this.$ac);
if ((flags & J.adapter.readers.pymol.PyMOL.FLAG_NOSURFACE) != 0) this.pymolScene.bsNoSurface.set(this.$ac);
this.jmolToUniqueID[this.$ac] = uniqueID;
this.atomMap[apt] = this.$ac++;
return null;
}, "JU.Lst,~N,~A,~A,~A,~N,JU.Lst,~A,JU.Lst,JU.Lst,~A,JU.BS,~N");
Clazz_defineMethod(c$, "atomBool", 
function(atomArray, pt, offset, mask){
return ((atomArray[pt + offset] & mask) != 0);
}, "~A,~N,~N,~N");
Clazz_defineMethod(c$, "atomFloat", 
function(atomArray, pt, offset){
try {
return JU.BC.bytesToFloat(atomArray, pt + offset, false);
} catch (e) {
if (Clazz_exceptionOf(e, Exception)){
return 0;
} else {
throw e;
}
}
}, "~A,~N,~N");
Clazz_defineMethod(c$, "atomStr", 
function(atomArray, pt, offset, lexStr){
if (offset < 0) return lexStr[JU.BC.bytesToInt(atomArray, pt - offset, false)];
var s = this.getCStr(atomArray, pt + offset);
return (s.length == 0 ? " " : s);
}, "~A,~N,~N,~A");
Clazz_defineMethod(c$, "atomInt", 
function(atomArray, pt, offset){
return JU.BC.bytesToInt(atomArray, pt + offset, false);
}, "~A,~N,~N");
Clazz_defineMethod(c$, "addBonds", 
function(bonds){
var n = bonds.size();
for (var i = 0; i < n; i++) {
var bond = bonds.get(i);
var a1 = this.atomMap[bond.atomIndex1];
var a2 = this.atomMap[bond.atomIndex2];
if (a1 < 0 || a2 < 0) continue;
bond.atomIndex1 = a1;
bond.atomIndex2 = a2;
this.checkStickBall(a1);
this.checkStickBall(a2);
this.pymolScene.setUniqueBond(this.bondCount++, bond.uniqueID);
this.asc.addBond(bond);
}
}, "JU.Lst");
Clazz_defineMethod(c$, "checkStickBall", 
function(iatom){
var id = this.jmolToUniqueID[iatom];
var radius = (this.pymolScene.getUniqueFloatDef(id, 276, this.pymolScene.stickBalls));
if (radius == 1) {
radius = this.pymolScene.getUniqueFloatDef(id, 21, this.pymolScene.stickRadius) * this.pymolScene.getUniqueFloatDef(id, 277, this.pymolScene.stickBallRatio);
} else {
radius = 0;
}this.pymolScene.addSpacefill(iatom, radius, false);
}, "~N");
Clazz_defineMethod(c$, "addMolStructures", 
function(){
this.addMolSS("H", J.c.STR.HELIX);
this.addMolSS("S", J.c.STR.SHEET);
this.addMolSS("L", J.c.STR.TURN);
this.addMolSS(" ", J.c.STR.NONE);
});
Clazz_defineMethod(c$, "addMolSS", 
function(ssType, type){
if (this.ssMapSeq.get(ssType) == null) return;
var istart = -1;
var iend = -1;
var ichain = 0;
var atoms = this.asc.atoms;
var bsSeq = null;
var bsAtom = this.pymolScene.getSSMapAtom(ssType);
var n = this.$ac + 1;
var seqNo = -1;
var thischain = 0;
var imodel = -1;
var thisModel = -1;
for (var i = this.ac0; i < n; i++) {
if (i == this.$ac) {
thischain = 0;
} else {
seqNo = atoms[i].sequenceNumber;
thischain = atoms[i].chainID;
thisModel = atoms[i].atomSetIndex;
}if (thischain != ichain || thisModel != imodel) {
ichain = thischain;
imodel = thisModel;
bsSeq = this.ssMapSeq.get(ssType + thischain);
--i;
if (istart < 0) continue;
} else if (bsSeq != null && seqNo >= -1000 && bsSeq.get(seqNo - -1000)) {
iend = i;
if (istart < 0) istart = i;
continue;
} else if (istart < 0) {
continue;
}if (type !== J.c.STR.NONE) {
var pt = this.bsStructureDefined.nextSetBit(istart);
if (pt >= 0 && pt <= iend) continue;
this.bsStructureDefined.setBits(istart, iend + 1);
var structure =  new J.adapter.smarter.Structure(imodel, type, type, type.toString(), "" + (++this.structureCount), type === J.c.STR.SHEET ? 1 : 0, null);
var a = atoms[istart];
var b = atoms[iend];
var i0 = this.asc.getAtomSetAtomIndex(thisModel);
structure.set(a.chainID, a.sequenceNumber, a.insertionCode, b.chainID, b.sequenceNumber, b.insertionCode, istart - i0, iend - i0);
this.asc.addStructure(structure);
}bsAtom.setBits(istart, iend + 1);
istart = -1;
}
}, "~S,J.c.STR");
Clazz_defineMethod(c$, "createShapeObjects", 
function(){
this.pymolScene.createShapeObjects(this.reps, this.allowSurface && !this.isHidden, this.ac0, this.$ac);
});
Clazz_defineMethod(c$, "processMeshes", 
function(){
var fileName = this.vwr.fm.getFilePath(this.pymolScene.surfaceInfoName, true, false);
this.vwr.cachePut(fileName, this.volumeData);
for (var i = this.mapObjects.size(); --i >= 0; ) {
var obj = this.mapObjects.get(i);
var objName = obj.get(obj.size() - 1).toString();
var isMep = objName.endsWith("_e_pot");
var mapName;
var tok;
if (isMep) {
tok = 1073742016;
var root = objName.substring(0, objName.length - 3);
mapName = root + "map";
var isosurfaceName = this.pymolScene.getObjectID(root + "chg");
if (isosurfaceName == null) continue;
obj.addLast(isosurfaceName);
this.pymolScene.mepList += ";" + isosurfaceName + ";";
} else {
tok = 1073742018;
mapName = J.adapter.readers.pymol.PyMOLReader.stringAt(J.adapter.readers.pymol.PyMOLReader.sublistAt(obj, [2, 0]), 1);
}var surface = this.volumeData.get(mapName);
if (surface == null) continue;
obj.addLast(mapName);
this.volumeData.put(objName, obj);
this.volumeData.put("__pymolSurfaceData__", obj);
if (!this.isStateScript) this.pymolScene.addMesh(tok, obj, objName, isMep);
this.appendLoadNote("PyMOL object " + objName + " references map " + mapName);
}
});
Clazz_defineMethod(c$, "processDefinitions", 
function(){
var s = this.vwr.getAtomDefs(this.pymolScene.setAtomDefs());
if (s.length > 2) s = s.substring(0, s.length - 2);
this.appendLoadNote(s);
});
Clazz_defineMethod(c$, "processSelectionsAndScenes", 
function(map){
if (!this.pymolScene.needSelections()) return;
var htObjNames = J.adapter.readers.pymol.PyMOLReader.listToMap(J.adapter.readers.pymol.PyMOLReader.getMapList(map, "names"));
if (this.haveScenes) {
var scenes = map.get("scene_dict");
this.finalizeSceneData();
var htSecrets = J.adapter.readers.pymol.PyMOLReader.listToMap(J.adapter.readers.pymol.PyMOLReader.getMapList(map, "selector_secrets"));
for (var i = 0; i < this.sceneOrder.size(); i++) {
var name = J.adapter.readers.pymol.PyMOLReader.stringAt(this.sceneOrder, i);
var thisScene = J.adapter.readers.pymol.PyMOLReader.getMapList(scenes, name);
if (thisScene == null) continue;
this.pymolScene.buildScene(name, thisScene, htObjNames, htSecrets);
this.appendLoadNote("scene: " + name);
}
}this.pymolScene.setCarveSets(htObjNames);
}, "java.util.Map");
Clazz_defineMethod(c$, "finalizeSceneData", 
function(){
var cartoonTypes =  Clazz_newIntArray (this.$ac, 0);
var uniqueIDs =  Clazz_newIntArray (this.$ac, 0);
var sequenceNumbers =  Clazz_newIntArray (this.$ac, 0);
var newChain =  Clazz_newBooleanArray(this.$ac, false);
var radii =  Clazz_newFloatArray (this.$ac, 0);
var lastAtomChain = -2147483648;
var lastAtomSet = -2147483648;
for (var i = 0; i < this.$ac; i++) {
cartoonTypes[i] = this.getCartoonType(i);
uniqueIDs[i] = this.getUniqueID(i);
sequenceNumbers[i] = this.getSequenceNumber(i);
radii[i] = this.getVDW(i);
if (lastAtomChain != this.atoms[i].chainID || lastAtomSet != this.atoms[i].atomSetIndex) {
newChain[i] = true;
lastAtomChain = this.atoms[i].chainID;
lastAtomSet = this.atoms[i].atomSetIndex;
}}
this.pymolScene.setAtomInfo(uniqueIDs, cartoonTypes, sequenceNumbers, newChain, radii);
});
c$.intAt = Clazz_defineMethod(c$, "intAt", 
function(list, i){
return (list == null ? -1 : (list.get(i)).intValue());
}, "JU.Lst,~N");
c$.pointAt = Clazz_defineMethod(c$, "pointAt", 
function(list, i, pt){
pt.set(J.adapter.readers.pymol.PyMOLReader.floatAt(list, i++), J.adapter.readers.pymol.PyMOLReader.floatAt(list, i++), J.adapter.readers.pymol.PyMOLReader.floatAt(list, i));
return pt;
}, "JU.Lst,~N,JU.P3");
c$.floatsAt = Clazz_defineMethod(c$, "floatsAt", 
function(a, pt, data, len){
if (a == null) return null;
for (var i = 0; i < len; i++) data[i] = J.adapter.readers.pymol.PyMOLReader.floatAt(a, pt++);

return data;
}, "JU.Lst,~N,~A,~N");
c$.floatAt = Clazz_defineMethod(c$, "floatAt", 
function(list, i){
return (list == null || i >= list.size() ? 0 : (list.get(i)).floatValue());
}, "JU.Lst,~N");
c$.listAt = Clazz_defineMethod(c$, "listAt", 
function(list, i){
if (list == null || i >= list.size()) return null;
var o = list.get(i);
return (Clazz_instanceOf(o,"JU.Lst") ? o : null);
}, "JU.Lst,~N");
c$.sublistAt = Clazz_defineMethod(c$, "sublistAt", 
function(mesh, pt){
for (var i = 0; i < pt.length; i++) mesh = mesh.get(pt[i]);

return mesh;
}, "JU.Lst,~A");
c$.listToMap = Clazz_defineMethod(c$, "listToMap", 
function(list){
var map =  new java.util.Hashtable();
for (var i = list.size(); --i >= 0; ) {
var item = J.adapter.readers.pymol.PyMOLReader.listAt(list, i);
if (item != null && item.size() > 0) map.put(J.adapter.readers.pymol.PyMOLReader.stringAt(item, 0), item);
}
return map;
}, "JU.Lst");
c$.stringAt = Clazz_defineMethod(c$, "stringAt", 
function(list, i){
var o = list.get(i);
if ((typeof(o)=='string')) return o;
var a = list.get(i);
return (a.length == 0 ? " " : J.adapter.readers.pymol.PyMOLReader.bytesToString(a));
}, "JU.Lst,~N");
c$.bytesToString = Clazz_defineMethod(c$, "bytesToString", 
function(object){
try {
return  String.instantialize(object, "UTF-8");
} catch (e) {
if (Clazz_exceptionOf(e, Exception)){
return object.toString();
} else {
throw e;
}
}
}, "~O");
c$.colorSettingClamped = Clazz_defineMethod(c$, "colorSettingClamped", 
function(c, ptTemp){
return J.adapter.readers.pymol.PyMOLReader.getColorPt(c.get(c.size() < 6 || J.adapter.readers.pymol.PyMOLReader.intAt(c, 4) == 0 ? 2 : 5), ptTemp);
}, "JU.Lst,JU.P3");
c$.getColorPt = Clazz_defineMethod(c$, "getColorPt", 
function(o, ptTemp){
return (o == null ? 0 : Clazz_instanceOf(o, Integer) ? (o).intValue() : JU.CU.colorPtToFFRGB(J.adapter.readers.pymol.PyMOLReader.pointAt(o, 0, ptTemp)));
}, "~O,JU.P3");
c$.getMapList = Clazz_defineMethod(c$, "getMapList", 
function(map, key){
return map.get(key);
}, "java.util.Map,~S");
c$.getBsReps = Clazz_defineMethod(c$, "getBsReps", 
function(setting, pt){
if (setting.size() <= pt) return null;
var bsReps =  new JU.BS();
var o = setting.get(pt);
if (Clazz_instanceOf(o, Integer)) {
var bits = (o).intValue();
for (var i = 0, b = 1; i < 32; i++) {
if ((bits & b) != 0) {
bsReps.set(i);
}b <<= 1;
}
} else {
var list = o;
var n = Math.min(list.size(), 21);
for (var i = 0; i < n; i++) {
if (J.adapter.readers.pymol.PyMOLReader.intAt(list, i) == 1) bsReps.set(i);
}
}return bsReps;
}, "JU.Lst,~N");
Clazz_overrideMethod(c$, "getUniqueID", 
function(iAtom){
return Clazz_floatToInt(this.atoms[iAtom].vib.x);
}, "~N");
Clazz_overrideMethod(c$, "getCartoonType", 
function(iAtom){
return Clazz_floatToInt(this.atoms[iAtom].vib.y);
}, "~N");
Clazz_overrideMethod(c$, "getVDW", 
function(iAtom){
return this.atoms[iAtom].radius;
}, "~N");
Clazz_overrideMethod(c$, "getSequenceNumber", 
function(iAtom){
return this.atoms[iAtom].sequenceNumber;
}, "~N");
Clazz_overrideMethod(c$, "compareAtoms", 
function(iPrev, i){
return this.atoms[iPrev].chainID != this.atoms[i].chainID;
}, "~N,~N");
c$.nucleic = " A C G T U ADE THY CYT GUA URI DA DC DG DT DU ";
});
;//5.0.1-v2 Fri Jul 26 07:57:22 CDT 2024
})(Clazz
,Clazz.getClassName
,Clazz.newLongArray
,Clazz.doubleToByte
,Clazz.doubleToInt
,Clazz.doubleToLong
,Clazz.declarePackage
,Clazz.instanceOf
,Clazz.load
,Clazz.instantialize
,Clazz.decorateAsClass
,Clazz.floatToInt
,Clazz.floatToLong
,Clazz.makeConstructor
,Clazz.defineEnumConstant
,Clazz.exceptionOf
,Clazz.newIntArray
,Clazz.newFloatArray
,Clazz.declareType
,Clazz.prepareFields
,Clazz.superConstructor
,Clazz.newByteArray
,Clazz.declareInterface
,Clazz.newShortArray
,Clazz.innerTypeInstance
,Clazz.isClassDefined
,Clazz.prepareCallback
,Clazz.newArray
,Clazz.castNullAs
,Clazz.floatToShort
,Clazz.superCall
,Clazz.decorateAsType
,Clazz.newBooleanArray
,Clazz.newCharArray
,Clazz.implementOf
,Clazz.newDoubleArray
,Clazz.overrideConstructor
,Clazz.clone
,Clazz.doubleToShort
,Clazz.getInheritedLevel
,Clazz.getParamsType
,Clazz.isAF
,Clazz.isAB
,Clazz.isAI
,Clazz.isAS
,Clazz.isASS
,Clazz.isAP
,Clazz.isAFloat
,Clazz.isAII
,Clazz.isAFF
,Clazz.isAFFF
,Clazz.tryToSearchAndExecute
,Clazz.getStackTrace
,Clazz.inheritArgs
,Clazz.alert
,Clazz.defineMethod
,Clazz.overrideMethod
,Clazz.declareAnonymous
//,Clazz.checkPrivateMethod
,Clazz.cloneFinals
);
