(function(Clazz
,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_defineStatics
,Clazz_newFloatArray
,Clazz_declareType
,Clazz_prepareFields
,Clazz_superConstructor
,Clazz_newByteArray
,Clazz_declareInterface
,Clazz_p0p
,Clazz_pu$h
,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_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$;
Clazz_declarePackage ("J.api");
Clazz_declareInterface (J.api, "JmolSceneGenerator");
Clazz_declarePackage ("J.adapter.readers.pymol");
Clazz_load (["java.util.Hashtable", "JU.Lst"], "J.adapter.readers.pymol.PickleReader", ["java.lang.Double", "$.Long", "JU.SB", "JU.Logger"], function () {
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.lastMark = 0;
this.retrieveCount = 0;
Clazz_instantialize (this, arguments);
}, J.adapter.readers.pymol, "PickleReader");
Clazz_prepareFields (c$, function () {
this.stack =  new JU.Lst ();
this.marks =  new JU.Lst ();
this.build =  new JU.Lst ();
this.memo =  new java.util.Hashtable ();
});
Clazz_makeConstructor (c$, 
function (doc, vwr) {
this.binaryDoc = doc;
this.vwr = vwr;
}, "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 s;
var b;
var i;
var mark;
var d;
var o;
var a;
var map;
var l;
var going = true;
while (going) {
b = this.binaryDoc.readByte ();
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);
if (o == null) {
JU.Logger.error ("did not find memo item for " + i);
this.push ("LONG_BINGET" + (++this.id));
} else {
this.push (o);
}break;
case 85:
i = this.binaryDoc.readByte () & 0xff;
a =  Clazz_newByteArray (i, 0);
this.binaryDoc.readByteArray (a, 0, i);
s =  String.instantialize (a, "UTF-8");
if (this.inNames && this.markCount == 3 && this.lastMark == this.stack.size ()) {
this.filePt = this.emptyListPt;
}this.push (s);
break;
case 84:
i = this.binaryDoc.readIntLE ();
a =  Clazz_newByteArray (i, 0);
this.binaryDoc.readByteArray (a, 0, i);
s =  String.instantialize (a, "UTF-8");
this.push (s);
break;
case 87:
i = this.binaryDoc.readIntLE ();
a =  Clazz_newByteArray (i, 0);
this.binaryDoc.readByteArray (a, 0, i);
s =  String.instantialize (a, "UTF-8");
this.push (s);
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.readString ());
l.addLast (this.readString ());
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 ();
if (!(Clazz_instanceOf (this.peek (), String))) JU.Logger.error (this.peek () + " is not a string");
s = 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++) (o).addLast (l.get (i));

} else {
map = o;
for (i = l.size (); --i >= 0; ) {
o = l.get (i);
s = l.get (--i);
map.put (s, o);
}
}break;
case 46:
going = false;
break;
case 116:
this.push (this.getObjects (this.getMark ()));
break;
case 73:
s = this.readString ();
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;
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);
this.memo = null;
map = this.stack.remove (0);
if (map.size () == 0) for (i = this.stack.size (); --i >= 0; ) {
o = this.stack.get (i--);
s = this.stack.get (i);
map.put (s, o);
}
return map;
}, "~B");
Clazz_defineMethod (c$, "putMemo", 
 function (i, doCheck) {
var o = this.peek ();
if (Clazz_instanceOf (o, String)) {
if (doCheck && this.markCount >= 6 || this.markCount == 3 && this.inMovie) return;
this.memo.put (Integer.$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 ();
for (var j = 0; j < n; j++) args.addLast (null);

for (var j = n, i = this.stack.size (); --i >= mark; ) args.set (--j, this.stack.remove (i));

return args;
}, "~N");
Clazz_defineMethod (c$, "readString", 
 function () {
var sb =  new JU.SB ();
while (true) {
var b = this.binaryDoc.readByte ();
if (b == 0xA) break;
sb.appendC (String.fromCharCode (b));
}
return sb.toString ();
});
Clazz_defineMethod (c$, "putMark", 
 function (i) {
if (this.logging) this.log ("\n " + Integer.toHexString (this.binaryDoc.getPosition ()) + " [");
this.marks.addLast (Integer.$valueOf (this.lastMark = i));
this.markCount++;
switch (this.markCount) {
case 2:
this.thisSection = this.stack.get (i - 2);
this.inMovie = "movie".equals (this.thisSection);
this.inNames = "names".equals (this.thisSection);
break;
default:
break;
}
}, "~N");
Clazz_defineMethod (c$, "getMark", 
 function () {
return this.marks.remove (--this.markCount).intValue ();
});
Clazz_defineMethod (c$, "push", 
 function (o) {
if (this.logging && (Clazz_instanceOf (o, String) || Clazz_instanceOf (o, Double) || Clazz_instanceOf (o, Integer))) this.log ((Clazz_instanceOf (o, String) ? "'" + o + "'" : o) + ", ");
this.stack.addLast (o);
}, "~O");
Clazz_defineMethod (c$, "peek", 
 function () {
return this.stack.get (this.stack.size () - 1);
});
Clazz_defineMethod (c$, "pop", 
 function () {
return this.stack.remove (this.stack.size () - 1);
});
Clazz_defineStatics (c$,
"APPEND", 97,
"APPENDS", 101,
"BINFLOAT", 71,
"BININT", 74,
"BININT1", 75,
"BININT2", 77,
"BINPUT", 113,
"BINSTRING", 84,
"BINUNICODE", 87,
"BUILD", 98,
"EMPTY_DICT", 125,
"EMPTY_LIST", 93,
"GLOBAL", 99,
"LONG_BINPUT", 114,
"MARK", 40,
"NONE", 78,
"OBJ", 111,
"SETITEM", 115,
"SETITEMS", 117,
"SHORT_BINSTRING", 85,
"STOP", 46,
"BINGET", 104,
"LONG_BINGET", 106,
"TUPLE", 116,
"INT", 73);
});
Clazz_declarePackage ("J.api");
Clazz_declareInterface (J.api, "PymolAtomReader");
Clazz_declarePackage ("J.adapter.readers.pymol");
Clazz_load (["java.util.Hashtable"], "J.adapter.readers.pymol.PyMOL", ["JU.Logger"], function () {
c$ = Clazz_declareType (J.adapter.readers.pymol, "PyMOL");
c$.getRGB = Clazz_defineMethod (c$, "getRGB", 
function (color) {
if (J.adapter.readers.pymol.PyMOL.moreColors != null) {
var key = Integer.$valueOf (color);
var c = J.adapter.readers.pymol.PyMOL.moreColors.get (key);
if (c != null) return c.intValue ();
}if (color < J.adapter.readers.pymol.PyMOL.colors.length) return (J.adapter.readers.pymol.PyMOL.colors[color]);
return 0;
}, "~N");
c$.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 453:
return 14;
case 236:
case 570:
case 235:
case 526:
case 376:
case 530:
case 531:
case 532:
return -1;
case 327:
case 569:
return 1;
default:
JU.Logger.info ("PyMOL " + pymolVersion + " does not have setting " + i);
case 571:
case 666:
case 524:
return 0;
}
}, "~N,~N");
Clazz_defineStatics (c$,
"OBJECT_SELECTION", -1,
"OBJECT_MOLECULE", 1,
"OBJECT_MAPDATA", 2,
"OBJECT_MAPMESH", 3,
"OBJECT_MEASURE", 4,
"OBJECT_CALLBACK", 5,
"OBJECT_CGO", 6,
"OBJECT_SURFACE", 7,
"OBJECT_GADGET", 8,
"OBJECT_CALCULATOR", 9,
"OBJECT_SLICE", 10,
"OBJECT_ALIGNMENT", 11,
"OBJECT_GROUP", 12);
c$.REP_LIST = c$.prototype.REP_LIST = ["sticks", "spheres", "surface", "labels", "nb_spheres", "cartoon", "ribbon", "lines", "mesh", "dots", "dashes", "nonbonded", "cell", "cgo", "callback", "extent", "slice", "angles", "dihedrals", "ellipsoid", "volume"];
Clazz_defineStatics (c$,
"REP_STICKS", 0,
"REP_SPHERES", 1,
"REP_SURFACE", 2,
"REP_LABELS", 3,
"REP_NBSPHERES", 4,
"REP_CARTOON", 5,
"REP_RIBBON", 6,
"REP_LINES", 7,
"REP_MESH", 8,
"REP_DOTS", 9,
"REP_DASHES", 10,
"REP_NONBONDED", 11,
"REP_CELL", 12,
"REP_CGO", 13,
"REP_CALLBACK", 14,
"REP_EXTENT", 15,
"REP_SLICE", 16,
"REP_ANGLES", 17,
"REP_DIHEDRALS", 18,
"REP_ELLIPSOID", 19,
"REP_VOLUME", 20,
"REP_MAX", 21,
"REP_JMOL_TRACE", 21,
"REP_JMOL_PUTTY", 22,
"REP_JMOL_MAX", 23,
"FLAG_exfoliate", 0x01000000,
"FLAG_ignore", 0x02000000,
"FLAG_no_smooth", 0x04000000,
"FLAG_polymer", 0x08000000,
"FLAG_solvent", 0x10000000,
"FLAG_organic", 0x20000000,
"FLAG_inorganic", 0x40000000);
c$.FLAG_NOSURFACE = c$.prototype.FLAG_NOSURFACE = J.adapter.readers.pymol.PyMOL.FLAG_ignore | J.adapter.readers.pymol.PyMOL.FLAG_exfoliate;
Clazz_defineStatics (c$,
"active_selections", 351,
"alignment_as_cylinders", 692,
"all_states", 49,
"ambient", 7,
"ambient_occlusion_mode", 702,
"ambient_occlusion_scale", 703,
"ambient_occlusion_smooth", 704,
"anaglyph_mode", 706,
"angle_color", 575,
"angle_label_position", 406,
"angle_size", 405,
"animation", 388,
"animation_duration", 389,
"antialias", 12,
"async_builds", 506,
"ati_bugs", 585,
"atom_name_wildcard", 413,
"atom_type_format", 660,
"auto_classify_atoms", 360,
"auto_color", 238,
"auto_color_next", 239,
"auto_copy_images", 557,
"auto_defer_atom_count", 653,
"auto_defer_builds", 567,
"auto_dss", 323,
"auto_hide_selections", 79,
"auto_indicate_flags", 147,
"auto_number_selections", 443,
"auto_overlay", 603,
"auto_remove_hydrogens", 158,
"auto_rename_duplicate_objects", 561,
"auto_sculpt", 162,
"auto_show_lines", 51,
"auto_show_nonbonded", 72,
"auto_show_selections", 78,
"auto_show_spheres", 420,
"auto_zoom", 60,
"autoclose_dialogs", 661,
"backface_cull", 75,
"batch_prefix", 187,
"bg_gradient", 662,
"bg_image_filename", 712,
"bg_image_mode", 713,
"bg_image_tilesize", 714,
"bg_image_linear", 715,
"bg_rgb", 6,
"bg_rgb_bottom", 664,
"bg_rgb_top", 663,
"bonding_vdw_cutoff", 0,
"button_mode", 63,
"button_mode_name", 330,
"cache_display", 73,
"cache_frames", 31,
"cache_max", 578,
"cache_memory", 264,
"cache_mode", 573,
"cartoon_color", 236,
"cartoon_cylindrical_helices", 180,
"cartoon_debug", 105,
"cartoon_discrete_colors", 125,
"cartoon_dumbbell_length", 115,
"cartoon_dumbbell_radius", 117,
"cartoon_dumbbell_width", 116,
"cartoon_fancy_helices", 118,
"cartoon_fancy_sheets", 119,
"cartoon_flat_cycles", 260,
"cartoon_flat_sheets", 113,
"cartoon_helix_radius", 181,
"cartoon_highlight_color", 241,
"cartoon_ladder_color", 450,
"cartoon_ladder_mode", 448,
"cartoon_ladder_radius", 449,
"cartoon_loop_cap", 432,
"cartoon_loop_quality", 93,
"cartoon_loop_radius", 92,
"cartoon_nucleic_acid_as_cylinders", 693,
"cartoon_nucleic_acid_color", 451,
"cartoon_nucleic_acid_mode", 361,
"cartoon_oval_length", 100,
"cartoon_oval_quality", 102,
"cartoon_oval_width", 101,
"cartoon_power", 94,
"cartoon_power_b", 95,
"cartoon_putty_quality", 378,
"cartoon_putty_radius", 377,
"cartoon_putty_range", 382,
"cartoon_putty_scale_max", 380,
"cartoon_putty_scale_min", 379,
"cartoon_putty_scale_power", 381,
"cartoon_putty_transform", 581,
"cartoon_rect_length", 96,
"cartoon_rect_width", 97,
"cartoon_refine", 123,
"cartoon_refine_normals", 112,
"cartoon_refine_tips", 124,
"cartoon_ring_color", 429,
"cartoon_ring_finder", 430,
"cartoon_ring_mode", 427,
"cartoon_ring_radius", 508,
"cartoon_ring_transparency", 452,
"cartoon_ring_width", 428,
"cartoon_round_helices", 111,
"cartoon_sampling", 91,
"cartoon_side_chain_helper", 383,
"cartoon_smooth_cycles", 259,
"cartoon_smooth_first", 257,
"cartoon_smooth_last", 258,
"cartoon_smooth_loops", 114,
"cartoon_throw", 122,
"cartoon_trace_atoms", 269,
"cartoon_transparency", 279,
"cartoon_tube_cap", 431,
"cartoon_tube_quality", 104,
"cartoon_tube_radius", 103,
"cartoon_use_shader", 643,
"cavity_cull", 13,
"cgo_debug", 674,
"cgo_dot_radius", 303,
"cgo_dot_width", 302,
"cgo_ellipsoid_quality", 564,
"cgo_lighting", 671,
"cgo_line_radius", 130,
"cgo_line_width", 129,
"cgo_ray_width_scale", 109,
"cgo_shader_ub_color", 669,
"cgo_shader_ub_flags", 694,
"cgo_shader_ub_normal", 670,
"cgo_sphere_quality", 189,
"cgo_transparency", 441,
"cgo_use_shader", 668,
"clamp_colors", 214,
"clean_electro_mode", 615,
"cone_quality", 583,
"connect_bonded", 487,
"connect_cutoff", 182,
"connect_mode", 179,
"coulomb_cutoff", 367,
"coulomb_dielectric", 243,
"coulomb_units_factor", 242,
"cull_spheres", 33,
"cylinder_shader_ff_workaround", 697,
"cylinders_shader_filter_faces", 687,
"dash_as_cylinders", 684,
"dash_color", 574,
"dash_gap", 59,
"dash_length", 58,
"dash_radius", 108,
"dash_round_ends", 280,
"dash_use_shader", 683,
"dash_width", 107,
"debug_pick", 209,
"default_2fofc_map_rep", 659,
"default_buster_names", 657,
"default_fofc_map_rep", 658,
"default_phenix_names", 655,
"default_phenix_no_fill_names", 656,
"default_refmac_names", 654,
"defer_builds_mode", 409,
"defer_updates", 304,
"depth_cue", 84,
"dihedral_color", 576,
"dihedral_label_position", 408,
"dihedral_size", 407,
"direct", 8,
"dist_counter", 57,
"distance_exclusion", 460,
"dot_as_spheres", 701,
"dot_color", 210,
"dot_density", 2,
"dot_hydrogens", 28,
"dot_lighting", 336,
"dot_mode", 3,
"dot_normals", 332,
"dot_radius", 29,
"dot_solvent", 206,
"dot_use_shader", 700,
"dot_width", 77,
"draw_frames", 436,
"draw_mode", 614,
"dynamic_measures", 637,
"dynamic_width", 610,
"dynamic_width_factor", 611,
"dynamic_width_max", 613,
"dynamic_width_min", 612,
"edit_light", 707,
"editor_auto_dihedral", 416,
"editor_auto_origin", 439,
"editor_bond_cycle_mode", 633,
"editor_label_fragments", 321,
"ellipsoid_color", 570,
"ellipsoid_probability", 568,
"ellipsoid_quality", 563,
"ellipsoid_scale", 569,
"ellipsoid_transparency", 571,
"excl_display_lists_shaders", 682,
"fast_idle", 54,
"fetch_host", 636,
"fetch_path", 507,
"field_of_view", 152,
"fit_iterations", 185,
"fit_kabsch", 608,
"fit_tolerance", 186,
"float_labels", 232,
"fog", 88,
"fog_start", 192,
"frame", 194,
"full_screen", 142,
"gamma", 76,
"gaussian_b_adjust", 255,
"gaussian_b_floor", 272,
"gaussian_resolution", 271,
"geometry_export_mode", 586,
"gl_ambient", 14,
"gradient_max_length", 539,
"gradient_min_length", 540,
"gradient_min_slope", 541,
"gradient_normal_min_dot", 542,
"gradient_spacing", 544,
"gradient_step_size", 543,
"gradient_symmetry", 545,
"grid_max", 580,
"grid_mode", 577,
"grid_slot", 579,
"group_arrow_prefix", 547,
"group_auto_mode", 537,
"group_full_member_names", 538,
"h_bond_cone", 286,
"h_bond_cutoff_center", 282,
"h_bond_cutoff_edge", 283,
"h_bond_exclusion", 461,
"h_bond_from_proton", 556,
"h_bond_max_angle", 281,
"h_bond_power_a", 284,
"h_bond_power_b", 285,
"half_bonds", 45,
"hash_max", 22,
"heavy_neighbor_cutoff", 639,
"hide_long_bonds", 560,
"hide_underscore_names", 458,
"idle_delay", 52,
"ignore_case", 414,
"ignore_pdb_segi", 120,
"image_copy_always", 601,
"image_dots_per_inch", 434,
"INIT", 710,
"internal_feedback", 128,
"internal_gui", 99,
"internal_gui_control_size", 322,
"internal_gui_mode", 341,
"internal_gui_width", 98,
"internal_prompt", 313,
"isomesh_auto_state", 89,
"keep_alive", 607,
"label_anchor", 635,
"label_angle_digits", 531,
"label_color", 66,
"label_digits", 529,
"label_dihedral_digits", 532,
"label_distance_digits", 530,
"label_font_id", 328,
"label_outline_color", 467,
"label_position", 471,
"label_shadow_mode", 462,
"label_size", 453,
"legacy_mouse_zoom", 442,
"legacy_vdw_radii", 177,
"light", 10,
"light_count", 455,
"light2", 456,
"light3", 457,
"light4", 463,
"light5", 464,
"light6", 465,
"light7", 466,
"light8", 489,
"light9", 490,
"line_as_cylinders", 679,
"line_color", 526,
"line_radius", 110,
"line_smooth", 43,
"line_stick_helper", 391,
"line_use_shader", 645,
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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 = c$.prototype.moreColors =  new java.util.Hashtable ();
});
Clazz_declarePackage ("J.adapter.readers.pymol");
Clazz_load (null, "J.adapter.readers.pymol.JmolObject", ["java.lang.Float", "JU.P3", "$.PT", "$.SB", "J.adapter.readers.pymol.PyMOLScene", "JU.BSUtil", "$.Escape"], function () {
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");
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 1073742032:
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 == 1060866) {
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 3145770:
sm.vwr.displayAtoms (this.bsAtoms, false, false, 1276118017, 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, 1276118017, true);
}return;
case 1060866:
sm.vwr.defineAtomSets (this.info);
return;
case 1073742032:
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, "textLabels", this.info, this.bsAtoms);
return;
case 1678770178:
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 1141899265:
this.id = 0;
break;
case 0:
break;
case 10:
case 9:
sm.loadShape (this.id);
var bsCarb = m.getAtoms (3145764, 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.PyMOLScene.floatAt (J.adapter.readers.pymol.PyMOLScene.listAt (mep, 3), 0);
var max = J.adapter.readers.pymol.PyMOLScene.floatAt (J.adapter.readers.pymol.PyMOLScene.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 within = J.adapter.readers.pymol.PyMOLScene.floatAt (J.adapter.readers.pymol.PyMOLScene.listAt (J.adapter.readers.pymol.PyMOLScene.listAt (mesh, 2), 0), 11);
var list = J.adapter.readers.pymol.PyMOLScene.listAt (J.adapter.readers.pymol.PyMOLScene.listAt (J.adapter.readers.pymol.PyMOLScene.listAt (mesh, 2), 0), 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.PyMOLScene.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 135271429:
sb = this.info;
break;
case 1113200654:
sm.loadShape (this.id = 10);
sm.setShapePropertyBs (this.id, "putty", this.info, this.bsAtoms);
break;
}
if (sb != null) {
sm.vwr.runScript (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 = [colixes, Float.$valueOf (translucency)];
}, "~A,~N");
Clazz_defineMethod (c$, "setSize", 
function (size) {
this.size = Clazz_floatToInt (size * 1000);
}, "~N");
});
Clazz_declarePackage ("J.adapter.readers.pymol");
Clazz_load (["java.util.Hashtable", "JU.BS"], "J.adapter.readers.pymol.PyMOLGroup", null, function () {
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.type = 0;
this.parent = null;
Clazz_instantialize (this, arguments);
}, J.adapter.readers.pymol, "PyMOLGroup");
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$, "addGroupAtoms", 
function (bs) {
this.bsAtoms.or (bs);
if (this.parent != null) this.parent.addGroupAtoms (this.bsAtoms);
return this.bsAtoms;
}, "JU.BS");
Clazz_overrideMethod (c$, "toString", 
function () {
return this.name;
});
});
Clazz_declarePackage ("J.adapter.readers.pymol");
Clazz_load (["J.api.JmolSceneGenerator", "java.util.Hashtable", "JU.BS", "$.Lst", "$.P3"], "J.adapter.readers.pymol.PyMOLScene", ["java.lang.Boolean", "$.Double", "$.Float", "JU.AU", "$.CU", "$.PT", "$.SB", "J.adapter.readers.pymol.JmolObject", "$.PyMOL", "$.PyMOLGroup", "J.atomdata.RadiusData", "J.c.VDW", "JM.Text", "JU.BSUtil", "$.C", "$.Escape", "$.Logger", "$.Point3fi"], function () {
c$ = 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.ssMapAtom = null;
this.atomColorList = null;
this.occludedObjects = null;
this.labels = null;
this.colixes = null;
this.frameObj = null;
this.groups = null;
this.objectSettings = 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.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;
Clazz_instantialize (this, arguments);
}, J.adapter.readers.pymol, "PyMOLScene", null, J.api.JmolSceneGenerator);
Clazz_prepareFields (c$, function () {
this.bsHidden =  new JU.BS ();
this.bsNucleic =  new JU.BS ();
this.bsNonbonded =  new JU.BS ();
this.bsLabeled =  new JU.BS ();
this.bsHydrogen =  new JU.BS ();
this.bsNoSurface =  new JU.BS ();
this.htSpacefill =  new java.util.Hashtable ();
this.ssMapAtom =  new java.util.Hashtable ();
this.atomColorList =  new JU.Lst ();
this.occludedObjects =  new java.util.Hashtable ();
this.labels =  new java.util.Hashtable ();
this.bsCartoon =  new JU.BS ();
this.htCarveSets =  new java.util.Hashtable ();
this.htDefinedAtoms =  new java.util.Hashtable ();
this.htHiddenObjects =  new java.util.Hashtable ();
this.moleculeNames =  new JU.Lst ();
this.jmolObjects =  new JU.Lst ();
this.htAtomMap =  new java.util.Hashtable ();
this.htObjectAtoms =  new java.util.Hashtable ();
this.htObjectGroups =  new java.util.Hashtable ();
this.htMeasures =  new java.util.Hashtable ();
this.htObjectSettings =  new java.util.Hashtable ();
this.objectInfo =  new java.util.Hashtable ();
this.htStateSettings =  new java.util.Hashtable ();
this.labelPosition0 =  new JU.P3 ();
this.bsLineBonds =  new JU.BS ();
this.bsStickBonds =  new JU.BS ();
});
Clazz_defineMethod (c$, "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_makeConstructor (c$, 
function (reader, vwr, settings, uniqueSettings, pymolVersion, haveScenes, baseAtomIndex, baseModelIndex, doCache, filePath) {
this.reader = reader;
this.vwr = vwr;
this.settings = settings;
this.uniqueSettings = uniqueSettings;
this.pymolVersion = pymolVersion;
this.haveScenes = haveScenes;
this.baseAtomIndex = baseAtomIndex;
this.baseModelIndex = baseModelIndex;
this.doCache = doCache;
this.surfaceInfoName = filePath + "##JmolSurfaceInfo##";
this.setVersionSettings ();
settings.trimToSize ();
this.bgRgb = J.adapter.readers.pymol.PyMOLScene.colorSetting (J.adapter.readers.pymol.PyMOLScene.listAt (settings, 6));
J.adapter.readers.pymol.PyMOLScene.pointAt (J.adapter.readers.pymol.PyMOLScene.listAt (settings, 471).get (2), 0, this.labelPosition0);
}, "J.api.PymolAtomReader,JV.Viewer,JU.Lst,java.util.Map,~N,~B,~N,~N,~B,~S");
Clazz_defineMethod (c$, "setReaderObjectInfo", 
function (name, type, groupName, isHidden, listObjSettings, listStateSettings, ext) {
this.objectName = name;
this.objectHidden = isHidden;
this.objectNameID = (this.objectName == null ? null : J.adapter.readers.pymol.PyMOLScene.fixName (this.objectName + ext));
this.objectSettings =  new java.util.Hashtable ();
this.stateSettings =  new java.util.Hashtable ();
if (this.objectName != null) {
this.objectJmolName = J.adapter.readers.pymol.PyMOLScene.getJmolName (name);
if (groupName != null) {
this.htObjectGroups.put (this.objectName, groupName);
this.htObjectGroups.put (this.objectNameID, groupName);
}this.objectInfo.put (this.objectName, [this.objectNameID, Integer.$valueOf (type)]);
if (this.htObjectSettings.get (this.objectName) == null) {
J.adapter.readers.pymol.PyMOLScene.listToSettings (listObjSettings, this.objectSettings);
this.htObjectSettings.put (this.objectName, this.objectSettings);
}if (this.htStateSettings.get (this.objectNameID) == null) {
J.adapter.readers.pymol.PyMOLScene.listToSettings (listStateSettings, this.stateSettings);
this.htStateSettings.put (this.objectNameID, this.stateSettings);
}}this.getObjectSettings ();
}, "~S,~N,~S,~B,JU.Lst,JU.Lst,~S");
c$.listToSettings = 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.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.PyMOLScene.pointAt (J.adapter.readers.pymol.PyMOLScene.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 = J.adapter.readers.pymol.PyMOLScene.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$, "buildScene", 
function (name, thisScene, htObjNames, htSecrets) {
var frame = thisScene.get (2);
var smap =  new java.util.Hashtable ();
smap.put ("pymolFrame", frame);
smap.put ("generator", this);
smap.put ("name", name);
var view = J.adapter.readers.pymol.PyMOLScene.listAt (thisScene, 0);
if (view != null) smap.put ("pymolView", this.getPymolView (view, false));
var visibilities = thisScene.get (1);
smap.put ("visibilities", visibilities);
var sname = "_scene_" + name + "_";
var reps =  new Array (J.adapter.readers.pymol.PyMOL.REP_LIST.length);
for (var j = J.adapter.readers.pymol.PyMOL.REP_LIST.length; --j >= 0; ) {
var list = htObjNames.get (sname + J.adapter.readers.pymol.PyMOL.REP_LIST[j]);
var data = J.adapter.readers.pymol.PyMOLScene.listAt (list, 5);
if (data != null && data.size () > 0) reps[j] = J.adapter.readers.pymol.PyMOLScene.listToMap (data);
}
smap.put ("moleculeReps", reps);
sname = "_!c_" + name + "_";
var colorection = J.adapter.readers.pymol.PyMOLScene.listAt (thisScene, 3);
var n = colorection.size ();
var colors =  new Array (Clazz_doubleToInt (n / 2));
for (var j = 0, i = 0; j < n; j += 2) {
var color = J.adapter.readers.pymol.PyMOLScene.intAt (colorection, j);
var c = htSecrets.get (sname + color);
if (c != null && c.size () > 1) colors[i++] = [Integer.$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);
if (!this.vwr.isJS) e.printStackTrace ();
} else {
throw e;
}
}
}, "java.util.Map");
Clazz_defineMethod (c$, "generateColors", 
 function (colors) {
if (colors == null) return;
for (var i = colors.length; --i >= 0; ) {
var item = colors[i];
var color = (item[0]).intValue ();
var icolor = J.adapter.readers.pymol.PyMOL.getRGB (color);
var molecules = item[1];
var bs = this.getSelectionAtoms (molecules, this.thisState,  new JU.BS ());
this.addJmolObject (1141899265, bs, null).argb = icolor;
}
}, "~A");
Clazz_defineMethod (c$, "getSelectionAtoms", 
 function (molecules, istate, bs) {
if (molecules != null) for (var j = molecules.size (); --j >= 0; ) this.selectAllAtoms (J.adapter.readers.pymol.PyMOLScene.listAt (molecules, j), istate, bs);

return bs;
}, "JU.Lst,~N,JU.BS");
Clazz_defineMethod (c$, "selectAllAtoms", 
 function (obj, istate, bs) {
var name = obj.get (0);
this.setSceneObject (name, istate);
var atomList = J.adapter.readers.pymol.PyMOLScene.listAt (obj, 1);
var k0 = (istate == 0 ? 1 : istate);
var k1 = (istate == 0 ? this.stateCount : istate);
for (var k = k0; k <= k1; k++) {
var atomMap = this.htAtomMap.get (J.adapter.readers.pymol.PyMOLScene.fixName (name + "_" + k));
if (atomMap == null) continue;
this.getBsAtoms (atomList, atomMap, bs);
}
}, "JU.Lst,~N,JU.BS");
Clazz_defineMethod (c$, "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.PyMOLScene.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 = $e.next ()) || true);) {
var name = e.getKey ();
if (name.equals ("all")) continue;
this.setSceneObject (name, this.thisState);
if (this.objectHidden) continue;
var list = e.getValue ();
var tok = (this.objectHidden ? 12294 : 1610625028);
bs = null;
var info = this.objectJmolName;
switch (this.objectType) {
case 0:
case 12:
continue;
case 1:
bs = this.vwr.getDefinedAtomSet (info);
if (bs.nextSetBit (0) < 0) continue;
break;
case 4:
if (tok == 1610625028) {
var mdList = this.htMeasures.get (name);
if (mdList != null) this.addMeasurements (mdList, mdList[0].points.size (), null, this.getBS (J.adapter.readers.pymol.PyMOLScene.listAt (list, 2)), J.adapter.readers.pymol.PyMOLScene.intAt (list, 3), null, true);
}info += "_*";
break;
case 6:
case 3:
case 2:
break;
}
this.addJmolObject (tok, bs, info);
}
}, "java.util.Map");
Clazz_defineMethod (c$, "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++) {
this.setSceneObject (this.moleculeNames.get (m), 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.PyMOLScene.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.PyMOLScene.intAt (list, i)]);

}, "JU.Lst,~A,JU.BS");
c$.getColorPt = Clazz_defineMethod (c$, "getColorPt", 
function (o) {
return (Clazz_instanceOf (o, Integer) ? (o).intValue () : JU.CU.colorPtToFFRGB (J.adapter.readers.pymol.PyMOLScene.pointAt (o, 0, J.adapter.readers.pymol.PyMOLScene.ptTemp)));
}, "~O");
c$.intAt = Clazz_defineMethod (c$, "intAt", 
function (list, i) {
return (list.get (i)).intValue ();
}, "JU.Lst,~N");
c$.colorSetting = Clazz_defineMethod (c$, "colorSetting", 
function (c) {
return J.adapter.readers.pymol.PyMOLScene.getColorPt (c.get (2));
}, "JU.Lst");
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);
if (!this.vwr.isJS) e.printStackTrace ();
} else {
throw e;
}
}
}
this.finalizeUniqueBonds ();
this.jmolObjects.clear ();
});
Clazz_defineMethod (c$, "offsetObjects", 
function () {
for (var i = 0; i < this.jmolObjects.size (); 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.PyMOLScene.floatAt (view, i++);

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

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

if (isViewObj) i += 5;
for (var j = 0; j < 8; j++) pymolView[pt++] = J.adapter.readers.pymol.PyMOLScene.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$, "globalSetting", 
function (i) {
try {
var setting = this.settings.get (i);
return (setting.get (2)).floatValue ();
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return J.adapter.readers.pymol.PyMOL.getDefaultSetting (i, this.pymolVersion);
} else {
throw e;
}
}
}, "~N");
Clazz_defineMethod (c$, "addGroup", 
function (object, parent, type) {
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);
return myGroup;
}, "JU.Lst,~S,~N");
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 (3145770, 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.PyMOLScene.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 (J.adapter.readers.pymol.PyMOLScene.getJmolName (name), bs);
}, "~S,JU.BS");
c$.getJmolName = Clazz_defineMethod (c$, "getJmolName", 
 function (name) {
return "__" + J.adapter.readers.pymol.PyMOLScene.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 (1141899265, 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, labelOffset, label) {
var icolor = Clazz_floatToInt (this.getUniqueFloatDef (uniqueID, 66, this.labelColor));
if (icolor == -7 || icolor == -6) {
} else if (icolor < 0) {
icolor = atomColor;
}var labelPos =  Clazz_newFloatArray (7, 0);
if (labelOffset == null) {
var offset = this.getUniquePoint (uniqueID, 471, null);
if (offset == null) offset = this.labelPosition;
 else offset.add (this.labelPosition);
J.adapter.readers.pymol.PyMOLScene.setLabelPosition (offset, labelPos);
} else {
for (var i = 0; i < 7; i++) labelPos[i] = J.adapter.readers.pymol.PyMOLScene.floatAt (labelOffset, i);

}this.labels.put (Integer.$valueOf (atomIndex), this.newTextLabel (label, labelPos, icolor, this.labelFontId, this.labelSize));
}, "~N,~N,~N,JU.Lst,~S");
Clazz_defineMethod (c$, "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.$valueOf ((id << 10) + key))) == null) return pt;
pt =  new JU.P3 ();
J.adapter.readers.pymol.PyMOLScene.pointAt (setting.get (2), 0, pt);
JU.Logger.info ("Pymol unique setting for " + id + ": " + key + " = " + pt);
return pt;
}, "~N,~N,JU.P3");
Clazz_defineMethod (c$, "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$, "floatSetting", 
function (i) {
try {
var setting = this.getSetting (i);
return (setting.get (2)).floatValue ();
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return J.adapter.readers.pymol.PyMOL.getDefaultSetting (i, this.pymolVersion);
} else {
throw e;
}
}
}, "~N");
Clazz_defineMethod (c$, "stringSetting", 
function (i) {
try {
var setting = this.getSetting (i);
return setting.get (2).toString ();
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
return null;
} else {
throw e;
}
}
}, "~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.$valueOf (i));
if (setting == null) setting = this.settings.get (i);
return setting;
}, "~N");
c$.pointAt = Clazz_defineMethod (c$, "pointAt", 
function (list, i, pt) {
pt.set (J.adapter.readers.pymol.PyMOLScene.floatAt (list, i++), J.adapter.readers.pymol.PyMOLScene.floatAt (list, i++), J.adapter.readers.pymol.PyMOLScene.floatAt (list, i));
return pt;
}, "JU.Lst,~N,JU.P3");
c$.floatAt = Clazz_defineMethod (c$, "floatAt", 
function (list, i) {
return (list == null ? 0 : (list.get (i)).floatValue ());
}, "JU.Lst,~N");
c$.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.PyMOLScene.floatAt (a, pt++);

return data;
}, "JU.Lst,~N,~A,~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$.setLabelPosition = Clazz_defineMethod (c$, "setLabelPosition", 
function (offset, labelPos) {
labelPos[0] = 1;
labelPos[1] = offset.x;
labelPos[2] = offset.y;
labelPos[3] = offset.z;
return labelPos;
}, "JU.P3,~A");
Clazz_defineMethod (c$, "addCGO", 
function (data, color) {
data.addLast (this.objectName);
var jo = this.addJmolObject (23, null, data);
jo.argb = color;
jo.translucency = this.floatSetting (441);
return J.adapter.readers.pymol.PyMOLScene.fixName (this.objectName);
}, "JU.Lst,~N");
Clazz_defineMethod (c$, "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.get (3);
var drawDashes = bsReps.get (10);
var rad = this.floatSetting (107) / 20;
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.pointAt (list, p,  new JU.Point3fi ()));

offset = J.adapter.readers.pymol.PyMOLScene.floatsAt (J.adapter.readers.pymol.PyMOLScene.listAt (offsets, index), 0,  Clazz_newFloatArray (7, 0), 7);
if (offset == null) offset = J.adapter.readers.pymol.PyMOLScene.setLabelPosition (this.labelPosition,  Clazz_newFloatArray (7, 0));
md = mdList[index] = this.vwr.newMeasurementData (this.objectNameID + "_" + (index + 1), points);
md.note = this.objectName;
} else {
md = mdList[index];
offset = md.text.pymolOffset;
}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 text = this.newTextLabel (strFormat, offset, clabel, Clazz_floatToInt (this.floatSetting (328)), this.floatSetting (453));
md.set (1060866, null, null, strFormat, "angstroms", null, false, false, null, false, Clazz_floatToInt (rad * 2000), colix, text);
this.addJmolObject (6, bs, md);
}
return true;
}, "~A,~N,JU.Lst,JU.BS,~N,JU.Lst,~B");
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.$valueOf (J.adapter.readers.pymol.PyMOL.getRGB (colorIndex))));
return JU.C.getColixTranslucent3 (colix, translucency > 0, translucency);
}, "~N,~N");
c$.colorSettingClamped = Clazz_defineMethod (c$, "colorSettingClamped", 
function (c) {
return (c.size () < 6 || J.adapter.readers.pymol.PyMOLScene.intAt (c, 4) == 0 ? J.adapter.readers.pymol.PyMOLScene.colorSetting (c) : J.adapter.readers.pymol.PyMOLScene.getColorPt (c.get (5)));
}, "JU.Lst");
Clazz_defineMethod (c$, "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");
c$.fixName = Clazz_defineMethod (c$, "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$, "setAtomMap", 
function (atomMap, ac0) {
this.htAtomMap.put (this.objectNameID, atomMap);
var bsAtoms = this.htDefinedAtoms.get (this.objectJmolName);
if (bsAtoms == null) {
bsAtoms = JU.BS.newN (ac0 + atomMap.length);
JU.Logger.info ("PyMOL molecule " + this.objectName);
this.htDefinedAtoms.put (this.objectJmolName, bsAtoms);
this.htObjectAtoms.put (this.objectName, bsAtoms);
this.moleculeNames.addLast (this.objectName);
}return bsAtoms;
}, "~A,~N");
Clazz_defineMethod (c$, "newTextLabel", 
 function (label, labelOffset, colorIndex, fontID, fontSize) {
var face;
var factor = 1;
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;
}
var font = this.vwr.getFont3D (face, style, fontSize == 0 ? 12 : fontSize * factor);
var t = JM.Text.newLabel (this.vwr, font, label, this.getColix (colorIndex, 0), 0, 0, 0, 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.$valueOf (2));
this.addSetting (471, 4, [1, 1, 0]);
if (this.pymolVersion < 99) {
this.addSetting (448, 2, Integer.$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$, "fixReps", 
 function (reps) {
this.htSpacefill.clear ();
this.bsCartoon.clearAll ();
for (var iAtom = this.bsAtoms.nextSetBit (0); iAtom >= 0; iAtom = this.bsAtoms.nextSetBit (iAtom + 1)) {
var rad = 0;
var uniqueID = (this.reader == null ? this.uniqueIDs[iAtom] : this.reader.getUniqueID (iAtom));
if (reps[1].get (iAtom)) {
rad = (this.reader == null ? this.radii[iAtom] : this.reader.getVDW (iAtom)) * this.getUniqueFloatDef (uniqueID, 155, this.sphereScale);
} else if (reps[4].get (iAtom)) {
rad = this.nonbondedSize;
}if (rad != 0) {
var r = Float.$valueOf (rad);
var bsr = this.htSpacefill.get (r);
if (bsr == null) this.htSpacefill.put (r, bsr =  new JU.BS ());
bsr.set (iAtom);
}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$, "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$, "createShapeObject", 
 function (shapeID, bs) {
if (bs.isEmpty ()) return;
var jo = null;
switch (shapeID) {
case 11:
bs.and (this.bsNonbonded);
if (bs.isEmpty ()) return;
this.setUniqueObjects (7, bs, 0, 0, 524, this.nonbondedTranslucency, 0, this.nonbondedSize, 0.5);
break;
case 4:
case 1:
this.setUniqueObjects (0, bs, 173, this.sphereColor, 172, this.sphereTranslucency, 155, this.sphereScale, 1);
break;
case 19:
var ellipsoidTranslucency = this.floatSetting (571);
var ellipsoidColor = Clazz_floatToInt (this.floatSetting (570));
var ellipsoidScale = this.floatSetting (569);
this.setUniqueObjects (20, bs, 570, ellipsoidColor, 571, ellipsoidTranslucency, 569, ellipsoidScale, 50);
break;
case 9:
this.setUniqueObjects (16, bs, 210, this.dotColor, 0, 0, 155, this.sphereScale, 1);
break;
case 2:
var withinDistance = this.floatSetting (344);
jo = this.addJmolObject (135180, bs, [this.booleanSetting (156) ? "FULLYLIT" : "FRONTLIT", (this.surfaceMode == 3 || this.surfaceMode == 4) ? " only" : "", this.bsCarve, Float.$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 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$, "setUniqueObjects", 
 function (shape, bs, setColor, color, setTrans, trans, setSize, size, f) {
var n = bs.cardinality ();
var colixes = (setColor == 0 ? null :  Clazz_newShortArray (n, 0));
var atrans = (setTrans == 0 ? null :  Clazz_newFloatArray (n, 0));
var sizes =  Clazz_newFloatArray (n, 0);
for (var pt = 0, i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1), pt++) {
var id = (this.reader == null ? this.uniqueIDs[i] : this.reader.getUniqueID (i));
if (colixes != null) {
var c = Clazz_floatToInt (this.getUniqueFloatDef (id, setColor, color));
if (c > 0) colixes[pt] = this.getColix (c, 0);
}if (atrans != null) {
atrans[pt] = this.getUniqueFloatDef (id, setTrans, trans);
}sizes[pt] = this.getUniqueFloatDef (id, setSize, size) * f;
}
return this.addJmolObject (shape, bs, [colixes, atrans, sizes]);
}, "~N,JU.BS,~N,~N,~N,~N,~N,~N,~N");
Clazz_defineMethod (c$, "createSpacefillObjects", 
 function () {
for (var e, $e = this.htSpacefill.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var r = e.getKey ().floatValue ();
var bs = e.getValue ();
this.addJmolObject (1141899265, bs, null).rd =  new J.atomdata.RadiusData (null, r, J.atomdata.RadiusData.EnumType.ABSOLUTE, J.c.VDW.AUTO);
}
this.htSpacefill.clear ();
});
Clazz_defineMethod (c$, "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 = [this.floatSetting (378), this.floatSetting (377), this.floatSetting (382), this.floatSetting (379), this.floatSetting (380), this.floatSetting (381), this.floatSetting (581)];
this.addJmolObject (1113200654, 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");
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.PyMOLScene.listAt (list, i);
if (item != null && item.size () > 0) map.put (item.get (0), item);
}
return map;
}, "JU.Lst");
Clazz_defineMethod (c$, "setAtomDefs", 
function () {
this.setGroupVisibilities ();
var defs =  new java.util.Hashtable ();
for (var e, $e = this.htDefinedAtoms.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var bs = e.getValue ();
if (!bs.isEmpty ()) defs.put (e.getKey (), bs);
}
this.addJmolObject (1060866, null, defs);
return defs;
});
Clazz_defineMethod (c$, "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$, "addMesh", 
function (tok, obj, objName, isMep) {
var jo = this.addJmolObject (tok, null, obj);
this.setSceneObject (objName, -1);
var meshColor = Clazz_floatToInt (this.floatSetting (146));
if (meshColor < 0) meshColor = J.adapter.readers.pymol.PyMOLScene.intAt (J.adapter.readers.pymol.PyMOLScene.listAt (obj, 0), 2);
if (!isMep) {
jo.setSize (this.meshWidth);
jo.argb = J.adapter.readers.pymol.PyMOL.getRGB (meshColor);
}jo.translucency = this.transparency;
jo.cacheID = this.surfaceInfoName;
}, "~N,JU.Lst,~S,~B");
Clazz_defineMethod (c$, "addIsosurface", 
function (objectName) {
var jo = this.addJmolObject (135180, null, objectName);
jo.cacheID = this.surfaceInfoName;
return jo;
}, "~S");
c$.ptTemp = c$.prototype.ptTemp =  new JU.P3 ();
Clazz_defineStatics (c$,
"MEAS_DIGITS", [530, 531, 532]);
});
Clazz_declarePackage ("J.adapter.readers.pymol");
Clazz_load (["J.adapter.readers.pdb.PdbReader", "J.api.PymolAtomReader", "JU.BS", "$.P3"], "J.adapter.readers.pymol.PyMOLReader", ["java.lang.Boolean", "java.util.Hashtable", "JU.Lst", "$.PT", "$.V3", "J.adapter.readers.pymol.PickleReader", "$.PyMOL", "$.PyMOLScene", "J.adapter.smarter.Atom", "$.Bond", "$.Structure", "J.c.STR", "JU.BSUtil", "$.BoxInfo", "$.Logger"], function () {
c$ = Clazz_decorateAsClass (function () {
this.allowSurface = true;
this.doResize = false;
this.doCache = false;
this.isStateScript = false;
this.sourcePNGJ = false;
this.ac0 = 0;
this.$ac = 0;
this.stateCount = 0;
this.structureCount = 0;
this.isHidden = false;
this.bsStructureDefined = null;
this.bsBytesExcluded = null;
this.atomMap = null;
this.ssMapSeq = null;
this.pymolScene = null;
this.xyzMin = null;
this.xyzMax = null;
this.nModels = 0;
this.logging = false;
this.reps = null;
this.isMovie = false;
this.pymolFrame = 0;
this.allStates = false;
this.totalAtomCount = 0;
this.pymolVersion = 0;
this.trajectoryStep = null;
this.trajectoryPtr = 0;
this.objectName = null;
this.volumeData = null;
this.mapObjects = null;
this.haveMeasurements = false;
this.frames = null;
this.uniqueSettings = null;
this.atoms = null;
this.haveScenes = false;
this.baseModelIndex = 0;
this.sceneOrder = null;
this.bondCount = 0;
Clazz_instantialize (this, arguments);
}, J.adapter.readers.pymol, "PyMOLReader", J.adapter.readers.pdb.PdbReader, J.api.PymolAtomReader);
Clazz_prepareFields (c$, function () {
this.bsStructureDefined =  new JU.BS ();
this.xyzMin = JU.P3.new3 (1e6, 1e6, 1e6);
this.xyzMax = JU.P3.new3 (-1000000.0, -1000000.0, -1000000.0);
this.reps =  new Array (23);
});
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.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 ();
this.logging = false;
Clazz_superCall (this, J.adapter.readers.pymol.PyMOLReader, "initializeReader", []);
});
Clazz_overrideMethod (c$, "processBinaryDocument", 
function () {
var reader =  new J.adapter.readers.pymol.PickleReader (this.binaryDoc, this.vwr);
var map = reader.getMap (this.logging);
reader = null;
this.process (map);
});
Clazz_overrideMethod (c$, "setAdditionalAtomParameters", 
function (atom) {
}, "J.adapter.smarter.Atom");
Clazz_overrideMethod (c$, "finalizeSubclassReader", 
function () {
this.finalizeReaderPDB ();
this.asc.setTensors ();
});
Clazz_overrideMethod (c$, "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] = this.sceneOrder.get (i);

this.vwr.getModelSetAuxiliaryInfo ().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"));
this.sceneOrder = J.adapter.readers.pymol.PyMOLReader.getMapList (map, "scene_order");
this.haveScenes = this.getFrameScenes (map);
var file = this.listAt (settings, 440);
if (file != null) 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);
this.logging = (this.vwr.getLogFileName ().length > 0);
var names = J.adapter.readers.pymol.PyMOLReader.getMapList (map, "names");
for (var e, $e = map.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var name = e.getKey ();
JU.Logger.info (name);
if (name.equals ("names")) {
for (var i = 1; i < names.size (); i++) {
var obj = this.listAt (names, i);
JU.Logger.info ("  " + J.adapter.readers.pymol.PyMOLReader.stringAt (obj, 0));
}
}}
if (this.logging) {
if (this.logging) this.vwr.log ("$CLEAR$");
for (var e, $e = map.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var name = e.getKey ();
if (!"names".equals (name)) {
this.vwr.log ("\n===" + name + "===");
this.vwr.log (JU.PT.rep (e.getValue ().toString (), "[", "\n["));
}}
this.vwr.log ("\n===names===");
for (var i = 1; i < names.size (); i++) {
this.vwr.log ("");
var list = names.get (i);
this.vwr.log (" =" + list.get (0).toString () + "=");
try {
this.vwr.log (JU.PT.rep (list.toString (), "[", "\n["));
} catch (e) {
}
}
}this.addColors (J.adapter.readers.pymol.PyMOLReader.getMapList (map, "colors"), this.pymolScene.globalSetting (214) != 0);
this.allStates = (this.pymolScene.globalSetting (49) != 0);
this.pymolFrame = Clazz_floatToInt (this.pymolScene.globalSetting (194));
this.getAtomAndStateCount (names);
this.pymolScene.setStateCount (this.stateCount);
var pymolState = Clazz_floatToInt (this.pymolScene.globalSetting (193));
if (!this.isMovie) this.pymolScene.setFrameObject (4115, (this.allStates ? Integer.$valueOf (-1) : Integer.$valueOf (pymolState - 1)));
this.appendLoadNote ("frame=" + this.pymolFrame + " state=" + pymolState + " all_states=" + this.allStates);
if (!this.isStateScript && this.doResize) {
var width = 0;
var height = 0;
try {
width = J.adapter.readers.pymol.PyMOLReader.intAt (J.adapter.readers.pymol.PyMOLReader.getMapList (map, "main"), 0);
height = J.adapter.readers.pymol.PyMOLReader.intAt (J.adapter.readers.pymol.PyMOLReader.getMapList (map, "main"), 1);
} catch (e) {
if (Clazz_exceptionOf (e, Exception)) {
} else {
throw e;
}
}
var note;
if (width > 0 && height > 0) {
note = "PyMOL dimensions width=" + width + " height=" + height;
this.asc.setInfo ("perferredWidthHeight", [width, height]);
this.vwr.resizeInnerPanel (width, height);
} else {
note = "PyMOL dimensions?";
}this.appendLoadNote (note);
}var mov;
if (!this.isStateScript && !this.allStates && (mov = J.adapter.readers.pymol.PyMOLReader.getMapList (map, "movie")) != null) {
var frameCount = J.adapter.readers.pymol.PyMOLReader.intAt (mov, 0);
if (frameCount > 0) this.processMovie (mov, frameCount);
}if (this.totalAtomCount == 0) this.asc.newAtomSet ();
if (this.allStates && this.desiredModelNumber == -2147483648) {
} else if (this.isMovie) {
switch (this.desiredModelNumber) {
case -2147483648:
break;
default:
this.desiredModelNumber = this.frames[(this.desiredModelNumber > 0 && this.desiredModelNumber <= this.frames.length ? this.desiredModelNumber : this.pymolFrame) - 1];
this.pymolScene.setFrameObject (4115, Integer.$valueOf (this.desiredModelNumber - 1));
break;
}
} else if (this.desiredModelNumber == 0) {
this.desiredModelNumber = pymolState;
} else {
}var n = names.size ();
for (var j = 0; j < this.stateCount; j++) {
if (!this.doGetModel (++this.nModels, null)) continue;
this.model (this.nModels);
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 (this.listAt (names, i), true, j);

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

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);
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 i2 = J.adapter.readers.pymol.PyMOLReader.intAt (settings.get (i), 0);
while (i < i2) {
JU.Logger.info ("PyMOL reader adding null settings #" + i);
settings.add (i++,  new JU.Lst ());
n++;
}
}
return settings;
}, "JU.Lst");
Clazz_defineMethod (c$, "getFrameScenes", 
 function (map) {
if (this.sceneOrder == null) return false;
var scenes = map.get ("scene_dict");
for (var i = 0; i < this.sceneOrder.size (); i++) {
var name = J.adapter.readers.pymol.PyMOLReader.stringAt (this.sceneOrder, i);
var thisScene = J.adapter.readers.pymol.PyMOLReader.getMapList (scenes, name);
if (thisScene == null || thisScene.get (2) == null) this.sceneOrder.remove (i--);
}
return (this.sceneOrder != null && this.sceneOrder.size () != 0);
}, "java.util.Map");
Clazz_defineMethod (c$, "setUniqueSettings", 
 function (list) {
this.uniqueSettings =  new java.util.Hashtable ();
var max = 0;
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 uid = (id << 10) + J.adapter.readers.pymol.PyMOLReader.intAt (setting, 0);
this.uniqueSettings.put (Integer.$valueOf (uid), setting);
JU.Logger.info ("PyMOL unique setting " + id + " " + setting);
}
}
}return max;
}, "JU.Lst");
Clazz_defineMethod (c$, "addColors", 
 function (colors, isClamped) {
if (colors == null || colors.size () == 0) return;
for (var i = colors.size (); --i >= 0; ) {
var c = this.listAt (colors, i);
J.adapter.readers.pymol.PyMOL.addColor (c.get (1), isClamped ? J.adapter.readers.pymol.PyMOLScene.colorSettingClamped (c) : J.adapter.readers.pymol.PyMOLScene.colorSetting (c));
}
}, "JU.Lst,~B");
Clazz_defineMethod (c$, "getAtomAndStateCount", 
 function (names) {
var n = 0;
for (var i = 1; i < names.size (); i++) {
var execObject = this.listAt (names, i);
var type = J.adapter.readers.pymol.PyMOLReader.intAt (execObject, 4);
if (!this.checkObject (execObject)) continue;
if (type == 1) {
var pymolObject = this.listAt (execObject, 5);
var states = this.listAt (pymolObject, 4);
var ns = states.size ();
if (ns > this.stateCount) this.stateCount = ns;
var nAtoms = this.listAt (pymolObject, 7).size ();
for (var j = 0; j < ns; j++) {
var state = this.listAt (states, j);
var idxToAtm = this.listAt (state, 3);
if (idxToAtm == null) {
this.isTrajectory = false;
} else {
var m = idxToAtm.size ();
n += m;
if (this.isTrajectory && m != nAtoms) this.isTrajectory = false;
}}
}}
this.totalAtomCount = n;
JU.Logger.info ("PyMOL total atom count = " + this.totalAtomCount);
JU.Logger.info ("PyMOL state count = " + this.stateCount);
}, "JU.Lst");
Clazz_defineMethod (c$, "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 = this.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 = this.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 = this.listAt (mov, 6);
var view;
for (var i = views.size (); --i >= 0; ) if ((view = this.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 (1073742032, 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) {
if (execObject == null) return;
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;
var pymolObject = this.listAt (execObject, 5);
var stateSettings = null;
if (type == 1) {
var states = this.listAt (pymolObject, 4);
var state = this.listAt (states, iState);
var idxToAtm = this.listAt (state, 3);
if (iState > 0 && (idxToAtm == null || idxToAtm.size () == 0)) return;
stateSettings = this.listAt (state, 7);
} else if (iState > 0) {
return;
}JU.Logger.info ("PyMOL model " + (this.nModels) + " Object " + this.objectName + (this.isHidden ? " (hidden)" : " (visible)"));
var objectHeader = this.listAt (pymolObject, 0);
var parentGroupName = (execObject.size () < 8 ? null : J.adapter.readers.pymol.PyMOLReader.stringAt (execObject, 6));
if (" ".equals (parentGroupName)) parentGroupName = null;
this.pymolScene.setReaderObjectInfo (this.objectName, type, parentGroupName, this.isHidden, this.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:
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) {
var group = this.pymolScene.addGroup (execObject, parentGroupName, type);
if (bsAtoms != null) bsAtoms = group.addGroupAtoms (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);
}, "JU.Lst,~B,~N");
Clazz_defineMethod (c$, "processCGO", 
 function (pymolObject) {
if (this.isStateScript) return;
if (this.isHidden) return;
var data = this.listAt (this.listAt (pymolObject, 2), 0);
var color = J.adapter.readers.pymol.PyMOL.getRGB (J.adapter.readers.pymol.PyMOLReader.intAt (this.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$, "processMeasure", 
 function (pymolObject) {
if (this.isStateScript) return;
if (this.isHidden) return;
JU.Logger.info ("PyMOL measure " + this.objectName);
var measure = this.listAt (this.listAt (pymolObject, 2), 0);
var pt;
var nCoord = (Clazz_instanceOf (measure.get (pt = 1), JU.Lst) ? 2 : Clazz_instanceOf (measure.get (pt = 4), JU.Lst) ? 3 : Clazz_instanceOf (measure.get (pt = 6), JU.Lst) ? 4 : 0);
if (nCoord == 0) return;
var setting = this.listAt (pymolObject, 0);
var bsReps = J.adapter.readers.pymol.PyMOLReader.getBsReps (this.listAt (setting, 3));
var list = this.listAt (measure, pt);
var offsets = this.listAt (measure, 8);
var haveLabels = (measure.size () > 8);
var color = J.adapter.readers.pymol.PyMOLReader.intAt (setting, 2);
if (this.pymolScene.addMeasurements (null, nCoord, list, bsReps, color, offsets, haveLabels)) this.haveMeasurements = true;
}, "JU.Lst");
Clazz_defineMethod (c$, "processMolecule", 
 function (pymolObject, iState) {
var states = this.listAt (pymolObject, 4);
var state = this.listAt (states, iState);
var idxToAtm = this.listAt (state, 3);
var n = (idxToAtm == null ? 0 : idxToAtm.size ());
if (n == 0) return null;
this.$ac = this.ac0 = this.asc.ac;
var nAtoms = J.adapter.readers.pymol.PyMOLReader.intAt (pymolObject, 3);
if (nAtoms == 0) return null;
this.ssMapSeq =  new java.util.Hashtable ();
if (iState == 0) this.processMolCryst (this.listAt (pymolObject, 10));
var bonds = this.getBondList (this.listAt (pymolObject, 6));
var pymolAtoms = this.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);

var coords = this.listAt (state, 2);
var labelPositions = this.listAt (state, 8);
if (iState == 0 || !this.isTrajectory) for (var idx = 0; idx < n; idx++) {
var a = this.addAtom (pymolAtoms, J.adapter.readers.pymol.PyMOLReader.intAt (idxToAtm, idx), idx, coords, labelPositions, bsAtoms, iState);
if (a != null) this.trajectoryStep[this.trajectoryPtr++] = a;
}
this.addBonds (bonds);
this.addMolStructures ();
this.atoms = this.asc.atoms;
if (!this.isStateScript) this.createShapeObjects ();
this.ssMapSeq = null;
JU.Logger.info ("reading " + (this.$ac - this.ac0) + " atoms");
JU.Logger.info ("----------");
return bsAtoms;
}, "JU.Lst,~N");
Clazz_defineMethod (c$, "processMolCryst", 
 function (cryst) {
if (cryst == null || cryst.size () == 0) return;
var l = this.listAt (this.listAt (cryst, 0), 0);
var a = this.listAt (this.listAt (cryst, 0), 1);
this.setUnitCell (this.floatAt (l, 0), this.floatAt (l, 1), this.floatAt (l, 2), this.floatAt (a, 0), this.floatAt (a, 1), this.floatAt (a, 2));
this.setSpaceGroupName (J.adapter.readers.pymol.PyMOLReader.stringAt (cryst, 1));
}, "JU.Lst");
Clazz_defineMethod (c$, "getBondList", 
 function (bonds) {
var bondList =  new JU.Lst ();
var asSingle = (this.pymolScene.booleanSetting (64) ? 0 : 65536);
var n = bonds.size ();
for (var i = 0; i < n; i++) {
var b = this.listAt (bonds, i);
var order = J.adapter.readers.pymol.PyMOLReader.intAt (b, 2);
if (order < 1 || order > 3) order = 1;
var ia = J.adapter.readers.pymol.PyMOLReader.intAt (b, 0);
var ib = J.adapter.readers.pymol.PyMOLReader.intAt (b, 1);
if (order > 1 && asSingle == 0) order |= 98304;
 else order |= asSingle;
var bond =  new J.adapter.smarter.Bond (ia, ib, order);
bond.uniqueID = (b.size () > 6 && J.adapter.readers.pymol.PyMOLReader.intAt (b, 6) != 0 ? J.adapter.readers.pymol.PyMOLReader.intAt (b, 5) : -1);
bondList.addLast (bond);
}
return bondList;
}, "JU.Lst");
Clazz_defineMethod (c$, "addAtom", 
 function (pymolAtoms, apt, icoord, coords, labelPositions, bsState, iState) {
this.atomMap[apt] = -1;
var a = this.listAt (pymolAtoms, apt);
var seqNo = J.adapter.readers.pymol.PyMOLReader.intAt (a, 0);
var chainID = J.adapter.readers.pymol.PyMOLReader.stringAt (a, 1);
var altLoc = J.adapter.readers.pymol.PyMOLReader.stringAt (a, 2);
var insCode = " ";
var name = J.adapter.readers.pymol.PyMOLReader.stringAt (a, 6);
var group3 = J.adapter.readers.pymol.PyMOLReader.stringAt (a, 5);
if (group3.length > 3) group3 = group3.substring (0, 3);
if (group3.equals (" ")) group3 = "UNK";
var sym = J.adapter.readers.pymol.PyMOLReader.stringAt (a, 7);
if (sym.equals ("A")) sym = "C";
var isHetero = (J.adapter.readers.pymol.PyMOLReader.intAt (a, 19) != 0);
var ichain = this.vwr.getChainID (chainID, true);
var atom = this.processAtom ( new J.adapter.smarter.Atom (), name, altLoc.charAt (0), group3, ichain, seqNo, insCode.charAt (0), isHetero, sym);
if (!this.filterPDBAtom (atom, this.fileAtomIndex++)) return null;
icoord *= 3;
var x = this.floatAt (coords, icoord);
var y = this.floatAt (coords, ++icoord);
var z = this.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.$ac);
var label = J.adapter.readers.pymol.PyMOLReader.stringAt (a, 9);
var ssType = J.adapter.readers.pymol.PyMOLReader.stringAt (a, 10);
if (seqNo >= -1000 && (!ssType.equals (" ") || name.equals ("CA") || isNucleic)) {
var bs = this.ssMapSeq.get (ssType);
if (bs == null) this.ssMapSeq.put (ssType, bs =  new JU.BS ());
bs.set (seqNo - -1000);
ssType += ichain;
bs = this.ssMapSeq.get (ssType);
if (bs == null) this.ssMapSeq.put (ssType, bs =  new JU.BS ());
bs.set (seqNo - -1000);
}atom.bfactor = this.floatAt (a, 14);
atom.foccupancy = this.floatAt (a, 15);
atom.radius = this.floatAt (a, 16);
if (atom.radius == 0) atom.radius = 1;
atom.partialCharge = this.floatAt (a, 17);
var formalCharge = J.adapter.readers.pymol.PyMOLReader.intAt (a, 18);
var bsReps = J.adapter.readers.pymol.PyMOLReader.getBsReps (this.listAt (a, 20));
var atomColor = J.adapter.readers.pymol.PyMOLReader.intAt (a, 21);
var serNo = J.adapter.readers.pymol.PyMOLReader.intAt (a, 22);
var cartoonType = J.adapter.readers.pymol.PyMOLReader.intAt (a, 23);
var flags = J.adapter.readers.pymol.PyMOLReader.intAt (a, 24);
var bonded = (J.adapter.readers.pymol.PyMOLReader.intAt (a, 25) != 0);
var uniqueID = (a.size () > 40 && J.adapter.readers.pymol.PyMOLReader.intAt (a, 40) == 1 ? J.adapter.readers.pymol.PyMOLReader.intAt (a, 32) : -1);
atom.vib = JU.V3.new3 (uniqueID, cartoonType, NaN);
if (a.size () > 46) {
var data = J.adapter.readers.pymol.PyMOLScene.floatsAt (a, 41,  Clazz_newFloatArray (8, 0), 6);
this.asc.setAnisoBorU (atom, data, 12);
}this.pymolScene.setAtomColor (atomColor);
this.processAtom2 (atom, serNo, x, y, z, formalCharge);
if (!bonded) this.pymolScene.bsNonbonded.set (this.$ac);
if (!label.equals (" ")) {
this.pymolScene.bsLabeled.set (this.$ac);
var labelOffset = this.listAt (labelPositions, apt);
this.pymolScene.addLabel (this.$ac, uniqueID, atomColor, labelOffset, 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.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.atomMap[apt] = this.$ac++;
return null;
}, "JU.Lst,~N,~N,JU.Lst,JU.Lst,JU.BS,~N");
Clazz_defineMethod (c$, "addBonds", 
 function (bonds) {
var n = bonds.size ();
for (var i = 0; i < n; i++) {
var bond = bonds.get (i);
bond.atomIndex1 = this.atomMap[bond.atomIndex1];
bond.atomIndex2 = this.atomMap[bond.atomIndex2];
if (bond.atomIndex1 < 0 || bond.atomIndex2 < 0) continue;
this.pymolScene.setUniqueBond (this.bondCount++, bond.uniqueID);
this.asc.addBond (bond);
}
}, "JU.Lst");
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);
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$, "processMeshes", 
 function () {
this.vwr.cachePut (this.pymolScene.surfaceInfoName, this.volumeData);
for (var i = this.mapObjects.size (); --i >= 0; ) {
var obj = this.mapObjects.get (i);
var objName = obj.get (obj.size () - 1).toString ();
var isMep = objName.endsWith ("_e_pot");
var mapName;
var tok;
if (isMep) {
tok = 1073742016;
var root = objName.substring (0, objName.length - 3);
mapName = root + "map";
var isosurfaceName = this.pymolScene.getObjectID (root + "chg");
if (isosurfaceName == null) continue;
obj.addLast (isosurfaceName);
this.pymolScene.mepList += ";" + isosurfaceName + ";";
} else {
tok = 1073742018;
mapName = J.adapter.readers.pymol.PyMOLReader.stringAt (this.listAt (this.listAt (obj, 2), 0), 1);
}var surface = this.volumeData.get (mapName);
if (surface == null) continue;
obj.addLast (mapName);
this.volumeData.put (objName, obj);
this.volumeData.put ("__pymolSurfaceData__", obj);
if (!this.isStateScript) this.pymolScene.addMesh (tok, obj, objName, isMep);
this.appendLoadNote ("PyMOL object " + objName + " references map " + mapName);
}
});
Clazz_defineMethod (c$, "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$, "processSelectionsAndScenes", 
 function (map) {
if (!this.pymolScene.needSelections ()) return;
var htObjNames = J.adapter.readers.pymol.PyMOLScene.listToMap (J.adapter.readers.pymol.PyMOLReader.getMapList (map, "names"));
if (this.haveScenes) {
var scenes = map.get ("scene_dict");
this.finalizeSceneData ();
var htSecrets = J.adapter.readers.pymol.PyMOLScene.listToMap (J.adapter.readers.pymol.PyMOLReader.getMapList (map, "selector_secrets"));
for (var i = 0; i < this.sceneOrder.size (); i++) {
var name = J.adapter.readers.pymol.PyMOLReader.stringAt (this.sceneOrder, i);
var thisScene = J.adapter.readers.pymol.PyMOLReader.getMapList (scenes, name);
if (thisScene == null) continue;
this.pymolScene.buildScene (name, thisScene, htObjNames, htSecrets);
this.appendLoadNote ("scene: " + name);
}
}this.pymolScene.setCarveSets (htObjNames);
}, "java.util.Map");
Clazz_defineMethod (c$, "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.get (i)).intValue ();
}, "JU.Lst,~N");
c$.stringAt = Clazz_defineMethod (c$, "stringAt", 
 function (list, i) {
var s = list.get (i).toString ();
return (s.length == 0 ? " " : s);
}, "JU.Lst,~N");
c$.getMapList = Clazz_defineMethod (c$, "getMapList", 
 function (map, key) {
return map.get (key);
}, "java.util.Map,~S");
c$.getBsReps = Clazz_defineMethod (c$, "getBsReps", 
 function (list) {
var bsReps =  new JU.BS ();
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");
Clazz_defineMethod (c$, "floatAt", 
 function (a, i) {
return J.adapter.readers.pymol.PyMOLScene.floatAt (a, i);
}, "JU.Lst,~N");
Clazz_defineMethod (c$, "listAt", 
 function (list, i) {
return J.adapter.readers.pymol.PyMOLScene.listAt (list, i);
}, "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$, "compareAtoms", 
function (iPrev, i) {
return this.atoms[iPrev].chainID != this.atoms[i].chainID;
}, "~N,~N");
Clazz_defineStatics (c$,
"MIN_RESNO", -1000,
"nucleic", " A C G T U ADE THY CYT GUA URI DA DC DG DT DU ");
});
})(Clazz
,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.defineStatics
,Clazz.newFloatArray
,Clazz.declareType
,Clazz.prepareFields
,Clazz.superConstructor
,Clazz.newByteArray
,Clazz.declareInterface
,Clazz.p0p
,Clazz.pu$h
,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.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
);
