io_mesh_atomic/pdb_import.py

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  17 # ##### END GPL LICENSE BLOCK #####
  18
  19 import os
  20 import bpy
  21 import bmesh
  22 from math import pi, cos, sin, sqrt, ceil
  23 from mathutils import Vector, Matrix
  24 from copy import copy
  25
  26 # -----------------------------------------------------------------------------
  27 #                                                  Atom, stick and element data
  28
  29
  30 # This is a list that contains some data of all possible elements. The structure
  31 # is as follows:
  32 #
  33 # 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54   means
  34 #
  35 # No., name, short name, color, radius (used), radius (covalent), radius (atomic),
  36 #
  37 # charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
  38 # charge states for any atom are listed, if existing.
  39 # The list is fixed and cannot be changed ... (see below)
  40
  41 ELEMENTS_DEFAULT = (
  42 ( 1,      "Hydrogen",        "H",  (  1.0,   1.0,   1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
  43 ( 2,        "Helium",       "He",  ( 0.85,   1.0,   1.0, 1.0), 0.93, 0.93, 0.49 ),
  44 ( 3,       "Lithium",       "Li",  (  0.8,  0.50,   1.0, 1.0), 1.23, 1.23, 2.05 ,  1 , 0.68 ),
  45 ( 4,     "Beryllium",       "Be",  ( 0.76,   1.0,   0.0, 1.0), 0.90, 0.90, 1.40 ,  1 , 0.44 ,  2 , 0.35 ),
  46 ( 5,         "Boron",        "B",  (  1.0,  0.70,  0.70, 1.0), 0.82, 0.82, 1.17 ,  1 , 0.35 ,  3 , 0.23 ),
  47 ( 6,        "Carbon",        "C",  ( 0.56,  0.56,  0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 ,  4 , 0.16 ),
  48 ( 7,      "Nitrogen",        "N",  ( 0.18,  0.31,  0.97, 1.0), 0.75, 0.75, 0.75 , -3 , 1.71 ,  1 , 0.25 ,  3 , 0.16 ,  5 , 0.13 ),
  49 ( 8,        "Oxygen",        "O",  (  1.0,  0.05,  0.05, 1.0), 0.73, 0.73, 0.65 , -2 , 1.32 , -1 , 1.76 ,  1 , 0.22 ,  6 , 0.09 ),
  50 ( 9,      "Fluorine",        "F",  ( 0.56,  0.87,  0.31, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 ,  7 , 0.08 ),
  51 (10,          "Neon",       "Ne",  ( 0.70,  0.89,  0.96, 1.0), 0.71, 0.71, 0.51 ,  1 , 1.12 ),
  52 (11,        "Sodium",       "Na",  ( 0.67,  0.36,  0.94, 1.0), 1.54, 1.54, 2.23 ,  1 , 0.97 ),
  53 (12,     "Magnesium",       "Mg",  ( 0.54,   1.0,   0.0, 1.0), 1.36, 1.36, 1.72 ,  1 , 0.82 ,  2 , 0.66 ),
  54 (13,     "Aluminium",       "Al",  ( 0.74,  0.65,  0.65, 1.0), 1.18, 1.18, 1.82 ,  3 , 0.51 ),
  55 (14,       "Silicon",       "Si",  ( 0.94,  0.78,  0.62, 1.0), 1.11, 1.11, 1.46 , -4 , 2.71 , -1 , 3.84 ,  1 , 0.65 ,  4 , 0.42 ),
  56 (15,    "Phosphorus",        "P",  (  1.0,  0.50,   0.0, 1.0), 1.06, 1.06, 1.23 , -3 , 2.12 ,  3 , 0.44 ,  5 , 0.35 ),
  57 (16,        "Sulfur",        "S",  (  1.0,   1.0,  0.18, 1.0), 1.02, 1.02, 1.09 , -2 , 1.84 ,  2 , 2.19 ,  4 , 0.37 ,  6 , 0.30 ),
  58 (17,      "Chlorine",       "Cl",  ( 0.12,  0.94,  0.12, 1.0), 0.99, 0.99, 0.97 , -1 , 1.81 ,  5 , 0.34 ,  7 , 0.27 ),
  59 (18,         "Argon",       "Ar",  ( 0.50,  0.81,  0.89, 1.0), 0.98, 0.98, 0.88 ,  1 , 1.54 ),
  60 (19,     "Potassium",        "K",  ( 0.56,  0.25,  0.83, 1.0), 2.03, 2.03, 2.77 ,  1 , 0.81 ),
  61 (20,       "Calcium",       "Ca",  ( 0.23,   1.0,   0.0, 1.0), 1.74, 1.74, 2.23 ,  1 , 1.18 ,  2 , 0.99 ),
  62 (21,      "Scandium",       "Sc",  ( 0.90,  0.90,  0.90, 1.0), 1.44, 1.44, 2.09 ,  3 , 0.73 ),
  63 (22,      "Titanium",       "Ti",  ( 0.74,  0.76,  0.78, 1.0), 1.32, 1.32, 2.00 ,  1 , 0.96 ,  2 , 0.94 ,  3 , 0.76 ,  4 , 0.68 ),
  64 (23,      "Vanadium",        "V",  ( 0.65,  0.65,  0.67, 1.0), 1.22, 1.22, 1.92 ,  2 , 0.88 ,  3 , 0.74 ,  4 , 0.63 ,  5 , 0.59 ),
  65 (24,      "Chromium",       "Cr",  ( 0.54,   0.6,  0.78, 1.0), 1.18, 1.18, 1.85 ,  1 , 0.81 ,  2 , 0.89 ,  3 , 0.63 ,  6 , 0.52 ),
  66 (25,     "Manganese",       "Mn",  ( 0.61,  0.47,  0.78, 1.0), 1.17, 1.17, 1.79 ,  2 , 0.80 ,  3 , 0.66 ,  4 , 0.60 ,  7 , 0.46 ),
  67 (26,          "Iron",       "Fe",  ( 0.87,   0.4,   0.2, 1.0), 1.17, 1.17, 1.72 ,  2 , 0.74 ,  3 , 0.64 ),
  68 (27,        "Cobalt",       "Co",  ( 0.94,  0.56,  0.62, 1.0), 1.16, 1.16, 1.67 ,  2 , 0.72 ,  3 , 0.63 ),
  69 (28,        "Nickel",       "Ni",  ( 0.31,  0.81,  0.31, 1.0), 1.15, 1.15, 1.62 ,  2 , 0.69 ),
  70 (29,        "Copper",       "Cu",  ( 0.78,  0.50,   0.2, 1.0), 1.17, 1.17, 1.57 ,  1 , 0.96 ,  2 , 0.72 ),
  71 (30,          "Zinc",       "Zn",  ( 0.49,  0.50,  0.69, 1.0), 1.25, 1.25, 1.53 ,  1 , 0.88 ,  2 , 0.74 ),
  72 (31,       "Gallium",       "Ga",  ( 0.76,  0.56,  0.56, 1.0), 1.26, 1.26, 1.81 ,  1 , 0.81 ,  3 , 0.62 ),
  73 (32,     "Germanium",       "Ge",  (  0.4,  0.56,  0.56, 1.0), 1.22, 1.22, 1.52 , -4 , 2.72 ,  2 , 0.73 ,  4 , 0.53 ),
  74 (33,       "Arsenic",       "As",  ( 0.74,  0.50,  0.89, 1.0), 1.20, 1.20, 1.33 , -3 , 2.22 ,  3 , 0.58 ,  5 , 0.46 ),
  75 (34,      "Selenium",       "Se",  (  1.0,  0.63,   0.0, 1.0), 1.16, 1.16, 1.22 , -2 , 1.91 , -1 , 2.32 ,  1 , 0.66 ,  4 , 0.50 ,  6 , 0.42 ),
  76 (35,       "Bromine",       "Br",  ( 0.65,  0.16,  0.16, 1.0), 1.14, 1.14, 1.12 , -1 , 1.96 ,  5 , 0.47 ,  7 , 0.39 ),
  77 (36,       "Krypton",       "Kr",  ( 0.36,  0.72,  0.81, 1.0), 1.31, 1.31, 1.24 ),
  78 (37,      "Rubidium",       "Rb",  ( 0.43,  0.18,  0.69, 1.0), 2.16, 2.16, 2.98 ,  1 , 1.47 ),
  79 (38,     "Strontium",       "Sr",  (  0.0,   1.0,   0.0, 1.0), 1.91, 1.91, 2.45 ,  2 , 1.12 ),
  80 (39,       "Yttrium",        "Y",  ( 0.58,   1.0,   1.0, 1.0), 1.62, 1.62, 2.27 ,  3 , 0.89 ),
  81 (40,     "Zirconium",       "Zr",  ( 0.58,  0.87,  0.87, 1.0), 1.45, 1.45, 2.16 ,  1 , 1.09 ,  4 , 0.79 ),
  82 (41,       "Niobium",       "Nb",  ( 0.45,  0.76,  0.78, 1.0), 1.34, 1.34, 2.08 ,  1 , 1.00 ,  4 , 0.74 ,  5 , 0.69 ),
  83 (42,    "Molybdenum",       "Mo",  ( 0.32,  0.70,  0.70, 1.0), 1.30, 1.30, 2.01 ,  1 , 0.93 ,  4 , 0.70 ,  6 , 0.62 ),
  84 (43,    "Technetium",       "Tc",  ( 0.23,  0.61,  0.61, 1.0), 1.27, 1.27, 1.95 ,  7 , 0.97 ),
  85 (44,     "Ruthenium",       "Ru",  ( 0.14,  0.56,  0.56, 1.0), 1.25, 1.25, 1.89 ,  4 , 0.67 ),
  86 (45,       "Rhodium",       "Rh",  ( 0.03,  0.49,  0.54, 1.0), 1.25, 1.25, 1.83 ,  3 , 0.68 ),
  87 (46,     "Palladium",       "Pd",  (  0.0,  0.41,  0.52, 1.0), 1.28, 1.28, 1.79 ,  2 , 0.80 ,  4 , 0.65 ),
  88 (47,        "Silver",       "Ag",  ( 0.75,  0.75,  0.75, 1.0), 1.34, 1.34, 1.75 ,  1 , 1.26 ,  2 , 0.89 ),
  89 (48,       "Cadmium",       "Cd",  (  1.0,  0.85,  0.56, 1.0), 1.48, 1.48, 1.71 ,  1 , 1.14 ,  2 , 0.97 ),
  90 (49,        "Indium",       "In",  ( 0.65,  0.45,  0.45, 1.0), 1.44, 1.44, 2.00 ,  3 , 0.81 ),
  91 (50,           "Tin",       "Sn",  (  0.4,  0.50,  0.50, 1.0), 1.41, 1.41, 1.72 , -4 , 2.94 , -1 , 3.70 ,  2 , 0.93 ,  4 , 0.71 ),
  92 (51,      "Antimony",       "Sb",  ( 0.61,  0.38,  0.70, 1.0), 1.40, 1.40, 1.53 , -3 , 2.45 ,  3 , 0.76 ,  5 , 0.62 ),
  93 (52,     "Tellurium",       "Te",  ( 0.83,  0.47,   0.0, 1.0), 1.36, 1.36, 1.42 , -2 , 2.11 , -1 , 2.50 ,  1 , 0.82 ,  4 , 0.70 ,  6 , 0.56 ),
  94 (53,        "Iodine",        "I",  ( 0.58,   0.0,  0.58, 1.0), 1.33, 1.33, 1.32 , -1 , 2.20 ,  5 , 0.62 ,  7 , 0.50 ),
  95 (54,         "Xenon",       "Xe",  ( 0.25,  0.61,  0.69, 1.0), 1.31, 1.31, 1.24 ),
  96 (55,       "Caesium",       "Cs",  ( 0.34,  0.09,  0.56, 1.0), 2.35, 2.35, 3.35 ,  1 , 1.67 ),
  97 (56,        "Barium",       "Ba",  (  0.0,  0.78,   0.0, 1.0), 1.98, 1.98, 2.78 ,  1 , 1.53 ,  2 , 1.34 ),
  98 (57,     "Lanthanum",       "La",  ( 0.43,  0.83,   1.0, 1.0), 1.69, 1.69, 2.74 ,  1 , 1.39 ,  3 , 1.06 ),
  99 (58,        "Cerium",       "Ce",  (  1.0,   1.0,  0.78, 1.0), 1.65, 1.65, 2.70 ,  1 , 1.27 ,  3 , 1.03 ,  4 , 0.92 ),
 100 (59,  "Praseodymium",       "Pr",  ( 0.85,   1.0,  0.78, 1.0), 1.65, 1.65, 2.67 ,  3 , 1.01 ,  4 , 0.90 ),
 101 (60,     "Neodymium",       "Nd",  ( 0.78,   1.0,  0.78, 1.0), 1.64, 1.64, 2.64 ,  3 , 0.99 ),
 102 (61,    "Promethium",       "Pm",  ( 0.63,   1.0,  0.78, 1.0), 1.63, 1.63, 2.62 ,  3 , 0.97 ),
 103 (62,      "Samarium",       "Sm",  ( 0.56,   1.0,  0.78, 1.0), 1.62, 1.62, 2.59 ,  3 , 0.96 ),
 104 (63,      "Europium",       "Eu",  ( 0.38,   1.0,  0.78, 1.0), 1.85, 1.85, 2.56 ,  2 , 1.09 ,  3 , 0.95 ),
 105 (64,    "Gadolinium",       "Gd",  ( 0.27,   1.0,  0.78, 1.0), 1.61, 1.61, 2.54 ,  3 , 0.93 ),
 106 (65,       "Terbium",       "Tb",  ( 0.18,   1.0,  0.78, 1.0), 1.59, 1.59, 2.51 ,  3 , 0.92 ,  4 , 0.84 ),
 107 (66,    "Dysprosium",       "Dy",  ( 0.12,   1.0,  0.78, 1.0), 1.59, 1.59, 2.49 ,  3 , 0.90 ),
 108 (67,       "Holmium",       "Ho",  (  0.0,   1.0,  0.61, 1.0), 1.58, 1.58, 2.47 ,  3 , 0.89 ),
 109 (68,        "Erbium",       "Er",  (  0.0,  0.90,  0.45, 1.0), 1.57, 1.57, 2.45 ,  3 , 0.88 ),
 110 (69,       "Thulium",       "Tm",  (  0.0,  0.83,  0.32, 1.0), 1.56, 1.56, 2.42 ,  3 , 0.87 ),
 111 (70,     "Ytterbium",       "Yb",  (  0.0,  0.74,  0.21, 1.0), 1.74, 1.74, 2.40 ,  2 , 0.93 ,  3 , 0.85 ),
 112 (71,      "Lutetium",       "Lu",  (  0.0,  0.67,  0.14, 1.0), 1.56, 1.56, 2.25 ,  3 , 0.85 ),
 113 (72,       "Hafnium",       "Hf",  ( 0.30,  0.76,   1.0, 1.0), 1.44, 1.44, 2.16 ,  4 , 0.78 ),
 114 (73,      "Tantalum",       "Ta",  ( 0.30,  0.65,   1.0, 1.0), 1.34, 1.34, 2.09 ,  5 , 0.68 ),
 115 (74,      "Tungsten",        "W",  ( 0.12,  0.58,  0.83, 1.0), 1.30, 1.30, 2.02 ,  4 , 0.70 ,  6 , 0.62 ),
 116 (75,       "Rhenium",       "Re",  ( 0.14,  0.49,  0.67, 1.0), 1.28, 1.28, 1.97 ,  4 , 0.72 ,  7 , 0.56 ),
 117 (76,        "Osmium",       "Os",  ( 0.14,   0.4,  0.58, 1.0), 1.26, 1.26, 1.92 ,  4 , 0.88 ,  6 , 0.69 ),
 118 (77,       "Iridium",       "Ir",  ( 0.09,  0.32,  0.52, 1.0), 1.27, 1.27, 1.87 ,  4 , 0.68 ),
 119 (78,      "Platinum",       "Pt",  ( 0.81,  0.81,  0.87, 1.0), 1.30, 1.30, 1.83 ,  2 , 0.80 ,  4 , 0.65 ),
 120 (79,          "Gold",       "Au",  (  1.0,  0.81,  0.13, 1.0), 1.34, 1.34, 1.79 ,  1 , 1.37 ,  3 , 0.85 ),
 121 (80,       "Mercury",       "Hg",  ( 0.72,  0.72,  0.81, 1.0), 1.49, 1.49, 1.76 ,  1 , 1.27 ,  2 , 1.10 ),
 122 (81,      "Thallium",       "Tl",  ( 0.65,  0.32,  0.30, 1.0), 1.48, 1.48, 2.08 ,  1 , 1.47 ,  3 , 0.95 ),
 123 (82,          "Lead",       "Pb",  ( 0.34,  0.34,  0.38, 1.0), 1.47, 1.47, 1.81 ,  2 , 1.20 ,  4 , 0.84 ),
 124 (83,       "Bismuth",       "Bi",  ( 0.61,  0.30,  0.70, 1.0), 1.46, 1.46, 1.63 ,  1 , 0.98 ,  3 , 0.96 ,  5 , 0.74 ),
 125 (84,      "Polonium",       "Po",  ( 0.67,  0.36,   0.0, 1.0), 1.46, 1.46, 1.53 ,  6 , 0.67 ),
 126 (85,      "Astatine",       "At",  ( 0.45,  0.30,  0.27, 1.0), 1.45, 1.45, 1.43 , -3 , 2.22 ,  3 , 0.85 ,  5 , 0.46 ),
 127 (86,         "Radon",       "Rn",  ( 0.25,  0.50,  0.58, 1.0), 1.00, 1.00, 1.34 ),
 128 (87,      "Francium",       "Fr",  ( 0.25,   0.0,   0.4, 1.0), 1.00, 1.00, 1.00 ,  1 , 1.80 ),
 129 (88,        "Radium",       "Ra",  (  0.0,  0.49,   0.0, 1.0), 1.00, 1.00, 1.00 ,  2 , 1.43 ),
 130 (89,      "Actinium",       "Ac",  ( 0.43,  0.67,  0.98, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.18 ),
 131 (90,       "Thorium",       "Th",  (  0.0,  0.72,   1.0, 1.0), 1.65, 1.65, 1.00 ,  4 , 1.02 ),
 132 (91,  "Protactinium",       "Pa",  (  0.0,  0.63,   1.0, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.13 ,  4 , 0.98 ,  5 , 0.89 ),
 133 (92,       "Uranium",        "U",  (  0.0,  0.56,   1.0, 1.0), 1.42, 1.42, 1.00 ,  4 , 0.97 ,  6 , 0.80 ),
 134 (93,     "Neptunium",       "Np",  (  0.0,  0.50,   1.0, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.10 ,  4 , 0.95 ,  7 , 0.71 ),
 135 (94,     "Plutonium",       "Pu",  (  0.0,  0.41,   1.0, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.08 ,  4 , 0.93 ),
 136 (95,     "Americium",       "Am",  ( 0.32,  0.36,  0.94, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.07 ,  4 , 0.92 ),
 137 (96,        "Curium",       "Cm",  ( 0.47,  0.36,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 138 (97,     "Berkelium",       "Bk",  ( 0.54,  0.30,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 139 (98,   "Californium",       "Cf",  ( 0.63,  0.21,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 140 (99,   "Einsteinium",       "Es",  ( 0.70,  0.12,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 141 (100,       "Fermium",       "Fm", ( 0.70,  0.12,  0.72, 1.0), 1.00, 1.00, 1.00 ),
 142 (101,   "Mendelevium",       "Md", ( 0.70,  0.05,  0.65, 1.0), 1.00, 1.00, 1.00 ),
 143 (102,      "Nobelium",       "No", ( 0.74,  0.05,  0.52, 1.0), 1.00, 1.00, 1.00 ),
 144 (103,    "Lawrencium",       "Lr", ( 0.78,   0.0,   0.4, 1.0), 1.00, 1.00, 1.00 ),
 145 (104,       "Vacancy",      "Vac", (  0.5,   0.5,   0.5, 1.0), 1.00, 1.00, 1.00),
 146 (105,       "Default",  "Default", (  1.0,   1.0,   1.0, 1.0), 1.00, 1.00, 1.00),
 147 (106,         "Stick",    "Stick", (  0.5,   0.5,   0.5, 1.0), 1.00, 1.00, 1.00),
 148 )
 149
 150 # This list here contains all data of the elements and will be used during
 151 # runtime. It is a list of classes.
 152 # During executing Atomic Blender, the list will be initialized with the fixed
 153 # data from above via the class structure below (ElementProp). We
 154 # have then one fixed list (above), which will never be changed, and a list of
 155 # classes with same data. The latter can be modified via loading a separate
 156 # custom data file.
 157 ELEMENTS = []
 158
 159 # This is the class, which stores the properties for one element.
 160 class ElementProp(object):
 161     __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
 162     def __init__(self, number, name, short_name, color, radii, radii_ionic):
 163         self.number = number
 164         self.name = name
 165         self.short_name = short_name
 166         self.color = color
 167         self.radii = radii
 168         self.radii_ionic = radii_ionic
 169
 170 # This is the class, which stores the properties of one atom.
 171 class AtomProp(object):
 172     __slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
 173     def __init__(self, element, name, location, radius, color, material):
 174         self.element = element
 175         self.name = name
 176         self.location = location
 177         self.radius = radius
 178         self.color = color
 179         self.material = material
 180
 181 # This is the class, which stores the two atoms of one stick.
 182 class StickProp(object):
 183     __slots__ = ('atom1', 'atom2', 'number', 'dist')
 184     def __init__(self, atom1, atom2, number, dist):
 185         self.atom1 = atom1
 186         self.atom2 = atom2
 187         self.number = number
 188         self.dist = dist
 189
 190 # -----------------------------------------------------------------------------
 191 #                                                           Some basic routines
 192
 193
 194 # The function, which reads all necessary properties of the elements.
 195 def read_elements():
 196
 197     del ELEMENTS[:]
 198
 199     for item in ELEMENTS_DEFAULT:
 200
 201         # All three radii into a list
 202         radii = [item[4],item[5],item[6]]
 203         # The handling of the ionic radii will be done later. So far, it is an
 204         # empty list.
 205         radii_ionic = []
 206
 207         li = ElementProp(item[0],item[1],item[2],item[3],
 208                                      radii,radii_ionic)
 209         ELEMENTS.append(li)
 210
 211
 212 # The function, which reads the x,y,z positions of all atoms in a PDB
 213 # file.
 214 #
 215 # filepath_pdb: path to pdb file
 216 # radiustype  : '0' default
 217 #               '1' atomic radii
 218 #               '2' van der Waals
 219 def read_pdb_file(filepath_pdb, radiustype):
 220
 221     # The list of all atoms as read from the PDB file.
 222     all_atoms  = []
 223
 224     # Open the pdb file ...
 225     filepath_pdb_p = open(filepath_pdb, "r")
 226
 227     #Go to the line, in which "ATOM" or "HETATM" appears.
 228     for line in filepath_pdb_p:
 229         split_list = line.split(' ')
 230         if "ATOM" in split_list[0]:
 231             break
 232         if "HETATM" in split_list[0]:
 233             break
 234
 235     j = 0
 236     # This is in fact an endless 'while loop', ...
 237     while j > -1:
 238
 239         # ... the loop is broken here (EOF) ...
 240         if line == "":
 241             break
 242
 243         # If there is a "TER" we need to put empty entries into the lists
 244         # in order to not destroy the order of atom numbers and same numbers
 245         # used for sticks. "TER? What is that?" TER indicates the end of a
 246         # list of ATOM/HETATM records for a chain.
 247         if "TER" in line:
 248             short_name = "TER"
 249             name = "TER"
 250             radius = 0.0
 251             # 2019-03-14, New
 252             color = [0,0,0, 0]
 253             location = Vector((0,0,0))
 254             # Append the TER into the list. Material remains empty so far.
 255             all_atoms.append(AtomProp(short_name,
 256                                       name,
 257                                       location,
 258                                       radius,
 259                                       color,[]))
 260
 261         # If 'ATOM or 'HETATM' appears in the line then do ...
 262         elif "ATOM" in line or "HETATM" in line:
 263
 264             # What follows is due to deviations which appear from PDB to
 265             # PDB file. It is very special!
 266             #
 267             # PLEASE, DO NOT CHANGE! ............................... from here
 268             if line[12:13] == " " or line[12:13].isdigit() == True:
 269                 short_name = line[13:14]
 270                 if line[14:15].islower() == True:
 271                     short_name = short_name + line[14:15]
 272             elif line[12:13].isupper() == True:
 273                 short_name = line[12:13]
 274                 if line[13:14].isalpha() == True:
 275                     short_name = short_name + line[13:14]
 276             else:
 277                 print("Atomic Blender: Strange error in PDB file.\n"
 278                       "Look for element names at positions 13-16 and 78-79.\n")
 279                 return -1
 280
 281             if len(line) >= 78:
 282
 283                 if line[76:77] == " ":
 284                     short_name2 = line[76:77]
 285                 else:
 286                     short_name2 = line[76:78]
 287
 288                 if short_name2.isalpha() == True:
 289                     FOUND = False
 290                     for element in ELEMENTS:
 291                         if str.upper(short_name2) == str.upper(element.short_name):
 292                             FOUND = True
 293                             break
 294                     if FOUND == False:
 295                         short_name = short_name2
 296
 297             # ....................................................... to here.
 298
 299             # Go through all elements and find the element of the current atom.
 300             FLAG_FOUND = False
 301             for element in ELEMENTS:
 302                 if str.upper(short_name) == str.upper(element.short_name):
 303                     # Give the atom its proper names, color and radius:
 304                     short_name = str.upper(element.short_name)
 305                     name = element.name
 306                     # int(radiustype) => type of radius:
 307                     # pre-defined (0), atomic (1) or van der Waals (2)
 308                     radius = float(element.radii[int(radiustype)])
 309                     color = element.color
 310                     FLAG_FOUND = True
 311                     break
 312
 313             # Is it a vacancy or an 'unknown atom' ?
 314             if FLAG_FOUND == False:
 315                 # Give this atom also a name. If it is an 'X' then it is a
 316                 # vacancy. Otherwise ...
 317                 if "X" in short_name:
 318                     short_name = "VAC"
 319                     name = "Vacancy"
 320                     radius = float(ELEMENTS[-3].radii[int(radiustype)])
 321                     color = ELEMENTS[-3].color
 322                 # ... take what is written in the PDB file. These are somewhat
 323                 # unknown atoms. This should never happen, the element list is
 324                 # almost complete. However, we do this due to security reasons.
 325                 else:
 326                     short_name = str.upper(short_name)
 327                     name = str.upper(short_name)
 328                     radius = float(ELEMENTS[-2].radii[int(radiustype)])
 329                     color = ELEMENTS[-2].color
 330
 331             # x,y and z are at fixed positions in the PDB file.
 332             x = float(line[30:38].rsplit()[0])
 333             y = float(line[38:46].rsplit()[0])
 334             z = float(line[46:55].rsplit()[0])
 335
 336             location = Vector((x,y,z))
 337
 338             j += 1
 339
 340             # Append the atom to the list. Material remains empty so far.
 341             all_atoms.append(AtomProp(short_name,
 342                                       name,
 343                                       location,
 344                                       radius,
 345                                       color,[]))
 346
 347         line = filepath_pdb_p.readline()
 348         line = line[:-1]
 349
 350     filepath_pdb_p.close()
 351     # From above it can be clearly seen that j is now the number of all atoms.
 352     Number_of_total_atoms = j
 353
 354     return (Number_of_total_atoms, all_atoms)
 355
 356
 357 # The function, which reads the sticks in a PDB file.
 358 def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms):
 359
 360     # The list of all sticks.
 361     all_sticks = []
 362
 363     # Open the PDB file.
 364     filepath_pdb_p = open(filepath_pdb, "r")
 365
 366     line = filepath_pdb_p.readline()
 367     split_list = line.split(' ')
 368
 369     # Go to the first entry
 370     if "CONECT" not in split_list[0]:
 371         for line in filepath_pdb_p:
 372             split_list = line.split(' ')
 373             if "CONECT" in split_list[0]:
 374                 break
 375
 376     Number_of_sticks = 0
 377     sticks_double = 0
 378     j = 0
 379     # This is in fact an endless while loop, ...
 380     while j > -1:
 381
 382         # ... which is broken here (EOF) ...
 383         if line == "":
 384             break
 385         # ... or here, when no 'CONECT' appears anymore.
 386         if "CONECT" not in line:
 387             break
 388
 389         # Note 2019-03-16: in a PDB file the identifier for sticks is called
 390         # 'CONECT' and NOT 'CONNECT'! Please leave this as is, otherwise the
 391         # sticks are NOT correctly loaded.
 392
 393         # The strings of the atom numbers do have a clear position in the file
 394         # (From 7 to 12, from 13 to 18 and so on.) and one needs to consider
 395         # this. One could also use the split function but then one gets into
 396         # trouble if there are lots of atoms: For instance, it may happen that
 397         # one has
 398         #                   CONECT 11111  22244444
 399         #
 400         # In Fact it means that atom No. 11111 has a connection with atom
 401         # No. 222 but also with atom No. 44444. The split function would give
 402         # me only two numbers (11111 and 22244444), which is wrong.
 403
 404         # Cut spaces from the right and 'CONECT' at the beginning
 405         line = line.rstrip()
 406         line = line[6:]
 407         # Amount of loops
 408         length = len(line)
 409         loops  = int(length/5)
 410
 411         # List of atoms
 412         atom_list = []
 413         for i in range(loops):
 414             number = line[5*i:5*(i+1)].rsplit()
 415             if number != []:
 416                 if number[0].isdigit() == True:
 417                     atom_number = int(number[0])
 418                     atom_list.append(atom_number)
 419
 420         # The first atom is connected with all the others in the list.
 421         atom1 = atom_list[0]
 422
 423         # For all the other atoms in the list do:
 424         for atom2 in atom_list[1:]:
 425
 426             if use_sticks_bonds == True:
 427                 number = atom_list[1:].count(atom2)
 428
 429                 if number == 2 or number == 3:
 430                     basis_list = list(set(atom_list[1:]))
 431
 432                     if len(basis_list) > 1:
 433                         basis1 = (all_atoms[atom1-1].location
 434                                 - all_atoms[basis_list[0]-1].location)
 435                         basis2 = (all_atoms[atom1-1].location
 436                                 - all_atoms[basis_list[1]-1].location)
 437                         plane_n = basis1.cross(basis2)
 438
 439                         dist_n = (all_atoms[atom1-1].location
 440                                 - all_atoms[atom2-1].location)
 441                         dist_n = dist_n.cross(plane_n)
 442                         dist_n = dist_n / dist_n.length
 443                     else:
 444                         dist_n = (all_atoms[atom1-1].location
 445                                 - all_atoms[atom2-1].location)
 446                         dist_n = Vector((dist_n[1],-dist_n[0],0))
 447                         dist_n = dist_n / dist_n.length
 448
 449                 elif number > 3:
 450                     number = 1
 451                     dist_n = None
 452                 else:
 453                     dist_n = None
 454             else:
 455                 number = 1
 456                 dist_n = None
 457
 458             # Note that in a PDB file, sticks of one atom pair can appear a
 459             # couple of times. (Only god knows why ...)
 460             # So, does a stick between the considered atoms already exist?
 461             FLAG_BAR = False
 462             for k in range(Number_of_sticks):
 463                 if ((all_sticks[k].atom1 == atom1 and all_sticks[k].atom2 == atom2) or
 464                     (all_sticks[k].atom2 == atom1 and all_sticks[k].atom1 == atom2)):
 465                     sticks_double += 1
 466                     # If yes, then FLAG on 'True'.
 467                     FLAG_BAR       = True
 468                     break
 469
 470             # If the stick is not yet registered (FLAG_BAR == False), then
 471             # register it!
 472             if FLAG_BAR == False:
 473                 all_sticks.append(StickProp(atom1,atom2,number,dist_n))
 474                 Number_of_sticks += 1
 475                 j += 1
 476
 477         line = filepath_pdb_p.readline()
 478         line = line.rstrip()
 479
 480     filepath_pdb_p.close()
 481
 482     return all_sticks
 483
 484
 485 # Function, which produces a cylinder. All is somewhat easy to understand.
 486 def build_stick(radius, length, sectors, element_name):
 487
 488     dphi = 2.0 * pi/(float(sectors)-1)
 489
 490     # Vertices
 491     vertices_top    = [Vector((0,0,length / 2.0))]
 492     vertices_bottom = [Vector((0,0,-length / 2.0))]
 493     vertices = []
 494     for i in range(sectors-1):
 495         x = radius * cos( dphi * i )
 496         y = radius * sin( dphi * i )
 497         z =  length / 2.0
 498         vertex = Vector((x,y,z))
 499         vertices_top.append(vertex)
 500         z = -length / 2.0
 501         vertex = Vector((x,y,z))
 502         vertices_bottom.append(vertex)
 503     vertices = vertices_top + vertices_bottom
 504
 505     # Side facets (Cylinder)
 506     faces1 = []
 507     for i in range(sectors-1):
 508         if i == sectors-2:
 509             faces1.append(  [i+1, 1, 1+sectors, i+1+sectors] )
 510         else:
 511             faces1.append(  [i+1, i+2, i+2+sectors, i+1+sectors] )
 512
 513     # Top facets
 514     faces2 = []
 515     for i in range(sectors-1):
 516         if i == sectors-2:
 517             face_top = [0,sectors-1,1]
 518             face_bottom = [sectors,2*sectors-1,sectors+1]
 519         else:
 520             face_top    = [0]
 521             face_bottom = [sectors]
 522             for j in range(2):
 523                 face_top.append(i+j+1)
 524                 face_bottom.append(i+j+1+sectors)
 525         faces2.append(face_top)
 526         faces2.append(face_bottom)
 527
 528     # Build the mesh, Cylinder
 529     cylinder = bpy.data.meshes.new(element_name+"_sticks_cylinder")
 530     cylinder.from_pydata(vertices, [], faces1)
 531     cylinder.update()
 532     new_cylinder = bpy.data.objects.new(element_name+"_sticks_cylinder", cylinder)
 533     # Attention: the linking will be done a few moments later, after this
 534     # is done definition.
 535
 536     # Build the mesh, Cups
 537     cups = bpy.data.meshes.new(element_name+"_sticks_cup")
 538     cups.from_pydata(vertices, [], faces2)
 539     cups.update()
 540     new_cups = bpy.data.objects.new(element_name+"_sticks_cup", cups)
 541     # Attention: the linking will be done a few moments later, after this
 542     # is done definition.
 543
 544     return (new_cylinder, new_cups)
 545
 546
 547 # Rotate an object.
 548 def rotate_object(rot_mat, obj):
 549
 550     bpy.ops.object.select_all(action='DESELECT')
 551     obj.select_set(True)
 552
 553     # Decompose world_matrix's components, and from them assemble 4x4 matrices.
 554     orig_loc, orig_rot, orig_scale = obj.matrix_world.decompose()
 555
 556     orig_loc_mat   = Matrix.Translation(orig_loc)
 557     orig_rot_mat   = orig_rot.to_matrix().to_4x4()
 558     orig_scale_mat = (Matrix.Scale(orig_scale[0],4,(1,0,0)) @
 559                       Matrix.Scale(orig_scale[1],4,(0,1,0)) @
 560                       Matrix.Scale(orig_scale[2],4,(0,0,1)))
 561
 562     # Assemble the new matrix.
 563     obj.matrix_world = orig_loc_mat @ rot_mat @ orig_rot_mat @ orig_scale_mat
 564
 565
 566 # Function, which puts a camera and light source into the 3D scene
 567 def camera_light_source(use_camera,
 568                         use_light,
 569                         object_center_vec,
 570                         object_size):
 571
 572     camera_factor = 15.0
 573
 574     # If chosen a camera is put into the scene.
 575     if use_camera == True:
 576
 577         # Assume that the object is put into the global origin. Then, the
 578         # camera is moved in x and z direction, not in y. The object has its
 579         # size at distance sqrt(object_size) from the origin. So, move the
 580         # camera by this distance times a factor of camera_factor in x and z.
 581         # Then add x, y and z of the origin of the object.
 582         object_camera_vec = Vector((sqrt(object_size) * camera_factor,
 583                                     0.0,
 584                                     sqrt(object_size) * camera_factor))
 585         camera_xyz_vec = object_center_vec + object_camera_vec
 586
 587         # Create the camera
 588         camera_data = bpy.data.cameras.new("A_camera")
 589         camera_data.lens = 45
 590         camera_data.clip_end = 500.0
 591         camera = bpy.data.objects.new("A_camera", camera_data)
 592         camera.location = camera_xyz_vec
 593         bpy.context.collection.objects.link(camera)
 594
 595         # Here the camera is rotated such it looks towards the center of
 596         # the object. The [0.0, 0.0, 1.0] vector along the z axis
 597         z_axis_vec             = Vector((0.0, 0.0, 1.0))
 598         # The angle between the last two vectors
 599         angle                  = object_camera_vec.angle(z_axis_vec, 0)
 600         # The cross-product of z_axis_vec and object_camera_vec
 601         axis_vec               = z_axis_vec.cross(object_camera_vec)
 602         # Rotate 'axis_vec' by 'angle' and convert this to euler parameters.
 603         # 4 is the size of the matrix.
 604         camera.rotation_euler  = Matrix.Rotation(angle, 4, axis_vec).to_euler()
 605
 606         # Rotate the camera around its axis by 90° such that we have a nice
 607         # camera position and view onto the object.
 608         bpy.ops.object.select_all(action='DESELECT')
 609         camera.select_set(True)
 610
 611         # Rotate the camera around its axis 'object_camera_vec' by 90° such
 612         # that we have a nice camera view onto the object.
 613         matrix_rotation = Matrix.Rotation(90/360*2*pi, 4, object_camera_vec)
 614         rotate_object(matrix_rotation, camera)
 615
 616     # Here a lamp is put into the scene, if chosen.
 617     if use_light == True:
 618
 619         # This is the distance from the object measured in terms of %
 620         # of the camera distance. It is set onto 50% (1/2) distance.
 621         light_dl = sqrt(object_size) * 15 * 0.5
 622         # This is a factor to which extend the lamp shall go to the right
 623         # (from the camera  point of view).
 624         light_dy_right = light_dl * (3.0/4.0)
 625
 626         # Create x, y and z for the lamp.
 627         object_light_vec = Vector((light_dl,light_dy_right,light_dl))
 628         light_xyz_vec = object_center_vec + object_light_vec
 629
 630         # Create the lamp
 631         light_data = bpy.data.lights.new(name="A_light", type="SUN")
 632         light_data.distance = 500.0
 633         light_data.energy = 3.0
 634         lamp = bpy.data.objects.new("A_light", light_data)
 635         lamp.location = light_xyz_vec
 636         bpy.context.collection.objects.link(lamp)
 637
 638         # Some settings for the World: a bit ambient occlusion
 639         bpy.context.scene.world.light_settings.use_ambient_occlusion = True
 640         bpy.context.scene.world.light_settings.ao_factor = 0.1
 641         # Some properties for cycles
 642         lamp.data.use_nodes = True
 643         lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
 644         lmp_P_BSDF.inputs['Strength'].default_value = 5
 645
 646
 647 # Function, which draws the atoms of one type (balls). This is one
 648 # dupliverts structure then.
 649 # Return: the dupliverts structure
 650 def draw_atoms_one_type(draw_all_atoms_type,
 651                         Ball_type,
 652                         Ball_azimuth,
 653                         Ball_zenith,
 654                         Ball_radius_factor,
 655                         object_center_vec,
 656                         collection_molecule):
 657
 658     # Create the vertices composed of the coordinates of all atoms of one type
 659     atom_vertices = []
 660     for atom in draw_all_atoms_type:
 661         # In fact, the object is created in the World's origin.
 662         # This is why 'object_center_vec' is subtracted. At the end
 663         # the whole object is translated back to 'object_center_vec'.
 664         atom_vertices.append(atom[2] - object_center_vec)
 665
 666     # IMPORTANT: First, we create a collection of the element, which contains
 667     # the atoms (balls + mesh) AND the sticks! The definition dealing with the
 668     # sticks will put the sticks inside this collection later on.
 669     coll_element_name = atom[0] # the element name
 670     # Create the new collection and ...
 671     coll_element = bpy.data.collections.new(coll_element_name)
 672     # ... link it to the collection, which contains all parts of the
 673     # molecule.
 674     collection_molecule.children.link(coll_element)
 675
 676     # Now, create a collection for the atoms, which includes the representative
 677     # ball and the mesh.
 678     coll_atom_name = atom[0] + "_atom"
 679     # Create the new collection and ...
 680     coll_atom = bpy.data.collections.new(coll_atom_name)
 681     # ... link it to the collection, which contains all parts of the
 682     # element (ball and mesh).
 683     coll_element.children.link(coll_atom)
 684
 685     # Build the mesh
 686     atom_mesh = bpy.data.meshes.new("Mesh_"+atom[0])
 687     atom_mesh.from_pydata(atom_vertices, [], [])
 688     atom_mesh.update()
 689     new_atom_mesh = bpy.data.objects.new(atom[0] + "_mesh", atom_mesh)
 690
 691     # Link active object to the new collection
 692     coll_atom.objects.link(new_atom_mesh)
 693
 694     # Now, build a representative sphere (atom).
 695     if atom[0] == "Vacancy":
 696         bpy.ops.mesh.primitive_cube_add(
 697                         view_align=False, enter_editmode=False,
 698                         location=(0.0, 0.0, 0.0),
 699                         rotation=(0.0, 0.0, 0.0))
 700     else:
 701         # NURBS balls
 702         if Ball_type == "0":
 703             bpy.ops.surface.primitive_nurbs_surface_sphere_add(
 704                         view_align=False, enter_editmode=False,
 705                         location=(0,0,0), rotation=(0.0, 0.0, 0.0))
 706         # UV balls
 707         elif Ball_type == "1":
 708             bpy.ops.mesh.primitive_uv_sphere_add(
 709                         segments=Ball_azimuth, ring_count=Ball_zenith,
 710                         view_align=False, enter_editmode=False,
 711                         location=(0,0,0), rotation=(0, 0, 0))
 712         # Meta balls
 713         elif Ball_type == "2":
 714             bpy.ops.object.metaball_add(type='BALL', view_align=False,
 715                         enter_editmode=False, location=(0, 0, 0),
 716                         rotation=(0, 0, 0))
 717
 718     ball = bpy.context.view_layer.objects.active
 719     # Hide this ball because its appearance has no meaning. It is just the
 720     # representative ball. The ball is visible at the vertices of the mesh.
 721     # Rememmber, this is a dupliverts construct!
 722     # However, hiding does not work with meta balls!
 723     if Ball_type == "0" or Ball_type == "1":
 724         ball.hide_set(True)
 725     # Scale up/down the ball radius.
 726     ball.scale  = (atom[3]*Ball_radius_factor,) * 3
 727
 728     if atom[0] == "Vacancy":
 729         ball.name = atom[0] + "_cube"
 730     else:
 731         ball.name = atom[0] + "_ball"
 732
 733     ball.active_material = atom[1]
 734     ball.parent = new_atom_mesh
 735     new_atom_mesh.instance_type = 'VERTS'
 736     # The object is back translated to 'object_center_vec'.
 737     new_atom_mesh.location = object_center_vec
 738
 739     # Note the collection where the ball was placed into.
 740     coll_all = ball.users_collection
 741     if len(coll_all) > 0:
 742         coll_past = coll_all[0]
 743     else:
 744         coll_past = bpy.context.scene.collection
 745
 746     # Put the atom into the new collection 'atom' and ...
 747     coll_atom.objects.link(ball)
 748     # ... unlink the atom from the other collection.
 749     coll_past.objects.unlink(ball)
 750
 751     return new_atom_mesh, coll_element
 752
 753
 754 # Function, which draws the sticks with help of the dupliverts technique.
 755 # Return: list of dupliverts structures.
 756 def draw_sticks_dupliverts(all_atoms,
 757                            atom_all_types_list,
 758                            center,
 759                            all_sticks,
 760                            Stick_diameter,
 761                            Stick_sectors,
 762                            Stick_unit,
 763                            Stick_dist,
 764                            use_sticks_smooth,
 765                            use_sticks_color,
 766                            list_coll_elements):
 767
 768     dl = Stick_unit
 769
 770     if use_sticks_color == False:
 771         stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
 772         stick_material.diffuse_color = ELEMENTS[-1].color
 773
 774     # Sort the sticks and put them into a new list such that ...
 775     sticks_all_lists = []
 776     if use_sticks_color == True:
 777         for atom_type in atom_all_types_list:
 778             if atom_type[0] == "TER":
 779                 continue
 780             sticks_list = []
 781             for stick in all_sticks:
 782                 for repeat in range(stick.number):
 783
 784                     atom1 = copy(all_atoms[stick.atom1-1].location)-center
 785                     atom2 = copy(all_atoms[stick.atom2-1].location)-center
 786
 787                     dist =  Stick_diameter * Stick_dist
 788
 789                     if stick.number == 2:
 790                         if repeat == 0:
 791                             atom1 += (stick.dist * dist)
 792                             atom2 += (stick.dist * dist)
 793                         if repeat == 1:
 794                             atom1 -= (stick.dist * dist)
 795                             atom2 -= (stick.dist * dist)
 796
 797                     if stick.number == 3:
 798                         if repeat == 0:
 799                             atom1 += (stick.dist * dist)
 800                             atom2 += (stick.dist * dist)
 801                         if repeat == 2:
 802                             atom1 -= (stick.dist * dist)
 803                             atom2 -= (stick.dist * dist)
 804
 805                     dv = atom1 - atom2
 806                     n  = dv / dv.length
 807                     if atom_type[0] == all_atoms[stick.atom1-1].name:
 808                         location = atom1
 809                         name     = "_" + all_atoms[stick.atom1-1].name
 810                         material = all_atoms[stick.atom1-1].material
 811                         sticks_list.append([name, location, dv, material])
 812                     if atom_type[0] == all_atoms[stick.atom2-1].name:
 813                         location = atom1 - n * dl * int(ceil(dv.length / (2.0 * dl)))
 814                         name     = "_" + all_atoms[stick.atom2-1].name
 815                         material = all_atoms[stick.atom2-1].material
 816                         sticks_list.append([name, location, dv, material])
 817
 818             if sticks_list != []:
 819                 sticks_all_lists.append(sticks_list)
 820     else:
 821         sticks_list = []
 822         for stick in all_sticks:
 823
 824             if stick.number > 3:
 825                 stick.number = 1
 826
 827             for repeat in range(stick.number):
 828
 829                 atom1 = copy(all_atoms[stick.atom1-1].location)-center
 830                 atom2 = copy(all_atoms[stick.atom2-1].location)-center
 831
 832                 dist =  Stick_diameter * Stick_dist
 833
 834                 if stick.number == 2:
 835                     if repeat == 0:
 836                         atom1 += (stick.dist * dist)
 837                         atom2 += (stick.dist * dist)
 838                     if repeat == 1:
 839                         atom1 -= (stick.dist * dist)
 840                         atom2 -= (stick.dist * dist)
 841                 if stick.number == 3:
 842                     if repeat == 0:
 843                         atom1 += (stick.dist * dist)
 844                         atom2 += (stick.dist * dist)
 845                     if repeat == 2:
 846                         atom1 -= (stick.dist * dist)
 847                         atom2 -= (stick.dist * dist)
 848
 849                 dv = atom1 - atom2
 850                 n  = dv / dv.length
 851                 location = atom1
 852                 material = stick_material
 853                 sticks_list.append(["", location, dv, material])
 854
 855         sticks_all_lists.append(sticks_list)
 856
 857     atom_object_list = []
 858     # ... the sticks in the list can be drawn:
 859     for stick_list in sticks_all_lists:
 860         vertices = []
 861         faces    = []
 862         i = 0
 863
 864         # What follows is school mathematics! :-)
 865         for stick in stick_list:
 866
 867             dv = stick[2]
 868             v1 = stick[1]
 869             n  = dv / dv.length
 870             gamma = -n.dot(v1)
 871             b     = v1 + gamma * n
 872             n_b   = b / b.length
 873
 874             if use_sticks_color == True:
 875                 loops = int(ceil(dv.length / (2.0 * dl)))
 876             else:
 877                 loops = int(ceil(dv.length / dl))
 878
 879             for j in range(loops):
 880
 881                 g  = v1 - n * dl / 2.0 - n * dl * j
 882                 p1 = g + n_b * Stick_diameter
 883                 p2 = g - n_b * Stick_diameter
 884                 p3 = g - n_b.cross(n) * Stick_diameter
 885                 p4 = g + n_b.cross(n) * Stick_diameter
 886
 887                 vertices.append(p1)
 888                 vertices.append(p2)
 889                 vertices.append(p3)
 890                 vertices.append(p4)
 891                 faces.append((i*4+0,i*4+2,i*4+1,i*4+3))
 892                 i += 1
 893
 894         # Create a collection for the sticks, which includes the representative
 895         # cylinders, cups and the mesh.
 896         coll_name = stick[0][1:] + "_sticks"
 897         # Create the collection and ...
 898         coll = bpy.data.collections.new(coll_name)
 899         # ... link it to the collection, which contains all parts of the
 900         # element. 'stick[0][1:]' contains the name of the element!
 901         for coll_element_from_list in list_coll_elements:
 902             if stick[0][1:] in coll_element_from_list.name:
 903                 break
 904         coll_element_from_list.children.link(coll)
 905
 906         # Build the mesh.
 907         mesh = bpy.data.meshes.new("Sticks_"+stick[0][1:])
 908         mesh.from_pydata(vertices, [], faces)
 909         mesh.update()
 910         new_mesh = bpy.data.objects.new(stick[0][1:]+"_sticks_mesh", mesh)
 911         # Link active object to the new collection
 912         coll.objects.link(new_mesh)
 913
 914         # Build the object.
 915         # Get the cylinder from the 'build_stick' function.
 916         object_stick = build_stick(Stick_diameter,
 917                                    dl,
 918                                    Stick_sectors,
 919                                    stick[0][1:])
 920         # Link active object to the new collection
 921         coll.objects.link(object_stick[0])
 922         coll.objects.link(object_stick[1])
 923
 924         # Hide these objects because their appearance has no meaning. They are
 925         # just the representative objects. The cylinder and cups are visible at
 926         # the vertices of the mesh. Rememmber, this is a dupliverts construct!
 927         object_stick[0].hide_set(True)
 928         object_stick[1].hide_set(True)
 929
 930         stick_cylinder = object_stick[0]
 931         stick_cylinder.active_material = stick[3]
 932         stick_cups = object_stick[1]
 933         stick_cups.active_material = stick[3]
 934
 935         # Smooth the cylinders.
 936         if use_sticks_smooth == True:
 937             bpy.ops.object.select_all(action='DESELECT')
 938             stick_cylinder.select_set(True)
 939             stick_cups.select_set(True)
 940             bpy.ops.object.shade_smooth()
 941
 942         # Parenting the mesh to the cylinder.
 943         stick_cylinder.parent = new_mesh
 944         stick_cups.parent = new_mesh
 945         new_mesh.instance_type = 'FACES'
 946         new_mesh.location = center
 947         atom_object_list.append(new_mesh)
 948
 949     # Return the list of dupliverts structures.
 950     return atom_object_list
 951
 952
 953 # Function, which draws the sticks with help of the skin and subdivision
 954 # modifiers.
 955 def draw_sticks_skin(all_atoms,
 956                      all_sticks,
 957                      Stick_diameter,
 958                      use_sticks_smooth,
 959                      sticks_subdiv_view,
 960                      sticks_subdiv_render,
 961                      coll_molecule):
 962
 963     # These counters are for the edges, in the shape [i,i+1].
 964     i = 0
 965
 966     # This is the list of vertices, containing the atom position
 967     # (vectors)).
 968     stick_vertices = []
 969     # This is the 'same' list, which contains not vector position of
 970     # the atoms but their numbers. It is used to handle the edges.
 971     stick_vertices_nr = []
 972     # This is the list of edges.
 973     stick_edges = []
 974
 975     # Go through the list of all sticks. For each stick do:
 976     for stick in all_sticks:
 977
 978         # Each stick has two atoms = two vertices.
 979
 980         """
 981         [ 0,1 ,  3,4 ,  0,8 ,  7,3]
 982         [[0,1], [2,3], [4,5], [6,7]]
 983
 984         [ 0,1 ,  3,4 ,  x,8 ,   7,x]    x:deleted
 985         [[0,1], [2,3], [0,5], [6,2]]
 986         """
 987
 988         # Check, if the vertex (atom) is already in the vertex list.
 989         # edge: [s1,s2]
 990         FLAG_s1 = False
 991         s1 = 0
 992         for stick2 in stick_vertices_nr:
 993             if stick2 == stick.atom1-1:
 994                 FLAG_s1 = True
 995                 break
 996             s1 += 1
 997         FLAG_s2 = False
 998         s2 = 0
 999         for stick2 in stick_vertices_nr:
1000             if stick2 == stick.atom2-1:
1001                 FLAG_s2 = True
1002                 break
1003             s2 += 1
1004
1005         # If the vertex (atom) is not yet in the vertex list:
1006         # append the number of atom and the vertex to the two lists.
1007         # For the first atom:
1008         if FLAG_s1 == False:
1009             atom1 = copy(all_atoms[stick.atom1-1].location)
1010             stick_vertices.append(atom1)
1011             stick_vertices_nr.append(stick.atom1-1)
1012         # For the second atom:
1013         if FLAG_s2 == False:
1014             atom2 = copy(all_atoms[stick.atom2-1].location)
1015             stick_vertices.append(atom2)
1016             stick_vertices_nr.append(stick.atom2-1)
1017
1018         # Build the edges:
1019
1020         # If both vertices (atoms) were not in the lists, then
1021         # the edge is simply [i,i+1]. These are two new vertices
1022         # (atoms), so increase i by 2.
1023         if FLAG_s1 == False and FLAG_s2 == False:
1024             stick_edges.append([i,i+1])
1025             i += 2
1026         # Both vertices (atoms) were already in the list, so then
1027         # use the vertices (atoms), which already exist. They are
1028         # at positions s1 and s2.
1029         if FLAG_s1 == True and FLAG_s2 == True:
1030             stick_edges.append([s1,s2])
1031         # The following two if cases describe the situation that
1032         # only one vertex (atom) was in the list. Since only ONE
1033         # new vertex was added, increase i by one.
1034         if FLAG_s1 == True and FLAG_s2 == False:
1035             stick_edges.append([s1,i])
1036             i += 1
1037         if FLAG_s1 == False and FLAG_s2 == True:
1038             stick_edges.append([i,s2])
1039             i += 1
1040
1041     # Build the mesh of the sticks
1042     stick_mesh = bpy.data.meshes.new("Mesh_sticks")
1043     stick_mesh.from_pydata(stick_vertices, stick_edges, [])
1044     stick_mesh.update()
1045     new_stick_mesh = bpy.data.objects.new("Sticks", stick_mesh)
1046     # Link the active mesh to the molecule collection
1047     coll_molecule.objects.link(new_stick_mesh)
1048
1049     # Apply the skin modifier.
1050     new_stick_mesh.modifiers.new(name="Sticks_skin", type='SKIN')
1051     # Smooth the skin surface if this option has been chosen.
1052     new_stick_mesh.modifiers[0].use_smooth_shade = use_sticks_smooth
1053     # Apply the Subdivision modifier.
1054     new_stick_mesh.modifiers.new(name="Sticks_subsurf", type='SUBSURF')
1055     # Options: choose the levels
1056     new_stick_mesh.modifiers[1].levels = sticks_subdiv_view
1057     new_stick_mesh.modifiers[1].render_levels = sticks_subdiv_render
1058
1059     stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
1060     stick_material.diffuse_color = ELEMENTS[-1].color
1061     new_stick_mesh.active_material = stick_material
1062
1063     # This is for putting the radius of the sticks onto
1064     # the desired value 'Stick_diameter'
1065     bpy.context.view_layer.objects.active = new_stick_mesh
1066     # EDIT mode
1067     bpy.ops.object.mode_set(mode='EDIT', toggle=False)
1068     bm = bmesh.from_edit_mesh(new_stick_mesh.data)
1069     bpy.ops.mesh.select_all(action='DESELECT')
1070
1071     # Select all vertices
1072     for v in bm.verts:
1073         v.select = True
1074
1075     # This is somewhat a factor for the radius.
1076     r_f = 4.0
1077     # Apply operator 'skin_resize'.
1078     bpy.ops.transform.skin_resize(
1079         value=(
1080             Stick_diameter * r_f,
1081             Stick_diameter * r_f,
1082             Stick_diameter * r_f,
1083         ),
1084         constraint_axis=(False, False, False),
1085         orient_type='GLOBAL',
1086         mirror=False,
1087         use_proportional_edit=False,
1088         snap=False,
1089         snap_target='CLOSEST',
1090         snap_point=(0, 0, 0),
1091         snap_align=False,
1092         snap_normal=(0, 0, 0),
1093         release_confirm=False,
1094     )
1095     # Back to the OBJECT mode.
1096     bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
1097
1098     return new_stick_mesh
1099
1100
1101 # Draw the sticks the normal way: connect the atoms by simple cylinders.
1102 # Two options: 1. single cylinders parented to an empty
1103 #              2. one single mesh object
1104 def draw_sticks_normal(all_atoms,
1105                        all_sticks,
1106                        center,
1107                        Stick_diameter,
1108                        Stick_sectors,
1109                        use_sticks_smooth,
1110                        use_sticks_one_object,
1111                        use_sticks_one_object_nr,
1112                        coll_molecule):
1113
1114     stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
1115     stick_material.diffuse_color = ELEMENTS[-1].color
1116
1117     up_axis = Vector([0.0, 0.0, 1.0])
1118
1119     # For all sticks, do ...
1120     list_group = []
1121     list_group_sub = []
1122     counter = 0
1123     for stick in all_sticks:
1124
1125         # The vectors of the two atoms
1126         atom1 = all_atoms[stick.atom1-1].location-center
1127         atom2 = all_atoms[stick.atom2-1].location-center
1128         # Location
1129         location = (atom1 + atom2) * 0.5
1130         # The difference of both vectors
1131         v = (atom2 - atom1)
1132         # Angle with respect to the z-axis
1133         angle = v.angle(up_axis, 0)
1134         # Cross-product between v and the z-axis vector. It is the
1135         # vector of rotation.
1136         axis = up_axis.cross(v)
1137         # Calculate Euler angles
1138         euler = Matrix.Rotation(angle, 4, axis).to_euler()
1139         # Create stick
1140         stick = bpy.ops.mesh.primitive_cylinder_add(vertices=Stick_sectors,
1141                                                     radius=Stick_diameter,
1142                                                     depth=v.length,
1143                                                     end_fill_type='NGON',
1144                                                     view_align=False,
1145                                                     enter_editmode=False,
1146                                                     location=location,
1147                                                     rotation=(0, 0, 0))
1148         # Put the stick into the scene ...
1149         stick = bpy.context.view_layer.objects.active
1150         # ... and rotate the stick.
1151         stick.rotation_euler = euler
1152         # ... and name
1153         stick.name = "Stick_Cylinder"
1154         counter += 1
1155
1156         # Smooth the cylinder.
1157         if use_sticks_smooth == True:
1158             bpy.ops.object.select_all(action='DESELECT')
1159             stick.select_set(True)
1160             bpy.ops.object.shade_smooth()
1161
1162         list_group_sub.append(stick)
1163
1164         if use_sticks_one_object == True:
1165             if counter == use_sticks_one_object_nr:
1166                 bpy.ops.object.select_all(action='DESELECT')
1167                 for stick in list_group_sub:
1168                     stick.select_set(True)
1169                 bpy.ops.object.join()
1170                 list_group.append(bpy.context.view_layer.objects.active)
1171                 bpy.ops.object.select_all(action='DESELECT')
1172                 list_group_sub = []
1173                 counter = 0
1174         else:
1175             # Material ...
1176             stick.active_material = stick_material
1177
1178     if use_sticks_one_object == True:
1179         bpy.ops.object.select_all(action='DESELECT')
1180         for stick in list_group_sub:
1181             stick.select_set(True)
1182         bpy.ops.object.join()
1183         list_group.append(bpy.context.view_layer.objects.active)
1184         bpy.ops.object.select_all(action='DESELECT')
1185
1186         for group in list_group:
1187             group.select_set(True)
1188         bpy.ops.object.join()
1189         bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY',
1190                                    center='MEDIAN')
1191         sticks = bpy.context.view_layer.objects.active
1192         sticks.active_material = stick_material
1193
1194         sticks.location += center
1195
1196         # Collections
1197         # ===========
1198         # Note the collection where the sticks were placed into.
1199         coll_all = sticks.users_collection
1200         if len(coll_all) > 0:
1201             coll_past = coll_all[0]
1202         else:
1203             coll_past = bpy.context.scene.collection
1204
1205         # Link the sticks with the collection of the molecule ...
1206         coll_molecule.objects.link(sticks)
1207         # ... and unlink them from the collection it has been before.
1208         coll_past.objects.unlink(sticks)
1209
1210         return sticks
1211     else:
1212         # Here we use an empty ...
1213         bpy.ops.object.empty_add(type='ARROWS',
1214                                   view_align=False,
1215                                   location=(0, 0, 0),
1216                                   rotation=(0, 0, 0))
1217         sticks_empty = bpy.context.view_layer.objects.active
1218         sticks_empty.name = "A_sticks_empty"
1219         # ... that is parent to all sticks. With this, we can better move
1220         # all sticks if necessary.
1221         for stick in list_group_sub:
1222             stick.parent = sticks_empty
1223
1224         sticks_empty.location += center
1225
1226         # Collections
1227         # ===========
1228         # Create a collection that will contain all sticks + the empty and ...
1229         coll = bpy.data.collections.new("Sticks")
1230         # ... link it to the collection, which contains all parts of the
1231         # molecule.
1232         coll_molecule.children.link(coll)
1233         # Now, create a collection that only contains the sticks and ...
1234         coll_cylinder = bpy.data.collections.new("Sticks_cylinders")
1235         # ... link it to the collection, which contains the sticks and empty.
1236         coll.children.link(coll_cylinder)
1237
1238         # Note the collection where the empty was placed into, ...
1239         coll_all = sticks_empty.users_collection
1240         if len(coll_all) > 0:
1241             coll_past = coll_all[0]
1242         else:
1243             coll_past = bpy.context.scene.collection
1244         # ... link the empty with the new collection  ...
1245         coll.objects.link(sticks_empty)
1246         # ... and unlink it from the old collection where it has been before.
1247         coll_past.objects.unlink(sticks_empty)
1248
1249         # Note the collection where the cylinders were placed into, ...
1250         coll_all = list_group_sub[0].users_collection
1251         if len(coll_all) > 0:
1252             coll_past = coll_all[0]
1253         else:
1254             coll_past = bpy.context.scene.collection
1255
1256         for stick in list_group_sub:
1257             # ... link each stick with the new collection  ...
1258             coll_cylinder.objects.link(stick)
1259             # ... and unlink it from the old collection.
1260             coll_past.objects.unlink(stick)
1261
1262         return sticks_empty
1263
1264
1265 # -----------------------------------------------------------------------------
1266 #                                                            The main routine
1267
1268 def import_pdb(Ball_type,
1269                Ball_azimuth,
1270                Ball_zenith,
1271                Ball_radius_factor,
1272                radiustype,
1273                Ball_distance_factor,
1274                use_sticks,
1275                use_sticks_type,
1276                sticks_subdiv_view,
1277                sticks_subdiv_render,
1278                use_sticks_color,
1279                use_sticks_smooth,
1280                use_sticks_bonds,
1281                use_sticks_one_object,
1282                use_sticks_one_object_nr,
1283                Stick_unit, Stick_dist,
1284                Stick_sectors,
1285                Stick_diameter,
1286                put_to_center,
1287                use_camera,
1288                use_light,
1289                filepath_pdb):
1290
1291     # List of materials
1292     atom_material_list = []
1293
1294     # A list of ALL objects which are loaded (needed for selecting the loaded
1295     # structure.
1296     atom_object_list = []
1297
1298     # ------------------------------------------------------------------------
1299     # INITIALIZE THE ELEMENT LIST
1300
1301     read_elements()
1302
1303     # ------------------------------------------------------------------------
1304     # READING DATA OF ATOMS
1305
1306     (Number_of_total_atoms, all_atoms) = read_pdb_file(filepath_pdb, radiustype)
1307
1308     # ------------------------------------------------------------------------
1309     # MATERIAL PROPERTIES FOR ATOMS
1310
1311     # The list that contains info about all types of atoms is created
1312     # here. It is used for building the material properties for
1313     # instance (see below).
1314     atom_all_types_list = []
1315
1316     for atom in all_atoms:
1317         FLAG_FOUND = False
1318         for atom_type in atom_all_types_list:
1319             # If the atom name is already in the list, FLAG on 'True'.
1320             if atom_type[0] == atom.name:
1321                 FLAG_FOUND = True
1322                 break
1323         # No name in the current list has been found? => New entry.
1324         if FLAG_FOUND == False:
1325             # Stored are: Atom label (e.g. 'Na'), the corresponding atom
1326             # name (e.g. 'Sodium') and its color.
1327             atom_all_types_list.append([atom.name, atom.element, atom.color])
1328
1329     # The list of materials is built.
1330     # Note that all atoms of one type (e.g. all hydrogens) get only ONE
1331     # material! This is good because then, by activating one atom in the
1332     # Blender scene and changing the color of this atom, one changes the color
1333     # of ALL atoms of the same type at the same time.
1334
1335     # Create first a new list of materials for each type of atom
1336     # (e.g. hydrogen)
1337     for atom_type in atom_all_types_list:
1338         material = bpy.data.materials.new(atom_type[1])
1339         material.name = atom_type[0]
1340         material.diffuse_color = atom_type[2]
1341         atom_material_list.append(material)
1342
1343     # Now, we go through all atoms and give them a material. For all atoms ...
1344     for atom in all_atoms:
1345         # ... and all materials ...
1346         for material in atom_material_list:
1347             # ... select the correct material for the current atom via
1348             # comparison of names ...
1349             if atom.name in material.name:
1350                 # ... and give the atom its material properties.
1351                 # However, before we check, if it is a vacancy, because then it
1352                 # gets some additional preparation. The vacancy is represented
1353                 # by a transparent cube.
1354                 if atom.name == "Vacancy":
1355                     material.metallic = 0.8
1356                     material.specular_intensity = 0.5
1357                     material.roughness = 0.3
1358                     material.blend_method = 'ADD'
1359                     material.show_transparent_back = False
1360                     # Some properties for cycles
1361                     material.use_nodes = True
1362                     mat_P_BSDF = material.node_tree.nodes['Principled BSDF']
1363                     mat_P_BSDF.inputs['Metallic'].default_value = 0.1
1364                     mat_P_BSDF.inputs['Roughness'].default_value = 0.2
1365                     mat_P_BSDF.inputs['Transmission'].default_value = 0.97
1366                     mat_P_BSDF.inputs['IOR'].default_value = 0.8
1367                 # The atom gets its properties.
1368                 atom.material = material
1369
1370     # ------------------------------------------------------------------------
1371     # READING DATA OF STICKS
1372
1373     all_sticks = read_pdb_file_sticks(filepath_pdb,
1374                                       use_sticks_bonds,
1375                                       all_atoms)
1376     #
1377     # So far, all atoms, sticks and materials have been registered.
1378     #
1379
1380     # ------------------------------------------------------------------------
1381     # TRANSLATION OF THE STRUCTURE TO THE ORIGIN
1382
1383     # It may happen that the structure in a PDB file already has an offset
1384     # If chosen, the structure is first put into the center of the scene
1385     # (the offset is subtracted).
1386
1387     if put_to_center == True:
1388         sum_vec = Vector((0.0,0.0,0.0))
1389         # Sum of all atom coordinates
1390         sum_vec = sum([atom.location for atom in all_atoms], sum_vec)
1391         # Then the average is taken
1392         sum_vec = sum_vec / Number_of_total_atoms
1393         # After, for each atom the center of gravity is subtracted
1394         for atom in all_atoms:
1395             atom.location -= sum_vec
1396
1397     # ------------------------------------------------------------------------
1398     # SCALING
1399
1400     # Take all atoms and adjust their radii and scale the distances.
1401     for atom in all_atoms:
1402         atom.location *= Ball_distance_factor
1403
1404     # ------------------------------------------------------------------------
1405     # DETERMINATION OF SOME GEOMETRIC PROPERTIES
1406
1407     # In the following, some geometric properties of the whole object are
1408     # determined: center, size, etc.
1409     sum_vec = Vector((0.0,0.0,0.0))
1410
1411     # First the center is determined. All coordinates are summed up ...
1412     sum_vec = sum([atom.location for atom in all_atoms], sum_vec)
1413
1414     # ... and the average is taken. This gives the center of the object.
1415     object_center_vec = sum_vec / Number_of_total_atoms
1416
1417     # Now, we determine the size.The farthest atom from the object center is
1418     # taken as a measure. The size is used to place well the camera and light
1419     # into the scene.
1420     object_size_vec = [atom.location - object_center_vec for atom in all_atoms]
1421     object_size = max(object_size_vec).length
1422
1423     # ------------------------------------------------------------------------
1424     # SORTING THE ATOMS
1425
1426     # Lists of atoms of one type are created. Example:
1427     # draw_all_atoms = [ data_hydrogen,data_carbon,data_nitrogen ]
1428     # data_hydrogen = [["Hydrogen", Material_Hydrogen, Vector((x,y,z)), 109], ...]
1429
1430     # Go through the list which contains all types of atoms. It is the list,
1431     # which has been created on the top during reading the PDB file.
1432     # Example: atom_all_types_list = ["hydrogen", "carbon", ...]
1433     draw_all_atoms = []
1434     for atom_type in atom_all_types_list:
1435
1436         # Don't draw 'TER atoms'.
1437         if atom_type[0] == "TER":
1438             continue
1439
1440         # This is the draw list, which contains all atoms of one type (e.g.
1441         # all hydrogens) ...
1442         draw_all_atoms_type = []
1443
1444         # Go through all atoms ...
1445         for atom in all_atoms:
1446             # ... select the atoms of the considered type via comparison ...
1447             if atom.name == atom_type[0]:
1448                 # ... and append them to the list 'draw_all_atoms_type'.
1449                 draw_all_atoms_type.append([atom.name,
1450                                             atom.material,
1451                                             atom.location,
1452                                             atom.radius])
1453
1454         # Now append the atom list to the list of all types of atoms
1455         draw_all_atoms.append(draw_all_atoms_type)
1456
1457     # ------------------------------------------------------------------------
1458     # COLLECTION
1459
1460     # Before we start to draw the atoms and sticks, we first create a
1461     # collection for the molecule. All atoms (balls) and sticks (cylinders)
1462     # are put into this collection.
1463     coll_molecule_name = os.path.basename(filepath_pdb)
1464     scene = bpy.context.scene
1465     coll_molecule = bpy.data.collections.new(coll_molecule_name)
1466     scene.collection.children.link(coll_molecule)
1467
1468     # ------------------------------------------------------------------------
1469     # DRAWING THE ATOMS
1470
1471     bpy.ops.object.select_all(action='DESELECT')
1472
1473     list_coll_elements = []
1474     # For each list of atoms of ONE type (e.g. Hydrogen)
1475     for draw_all_atoms_type in draw_all_atoms:
1476
1477         atom_mesh, coll_element = draw_atoms_one_type(draw_all_atoms_type,
1478                                                       Ball_type,
1479                                                       Ball_azimuth,
1480                                                       Ball_zenith,
1481                                                       Ball_radius_factor,
1482                                                       object_center_vec,
1483                                                       coll_molecule)
1484         atom_object_list.append(atom_mesh)
1485         list_coll_elements.append(coll_element)
1486
1487     # ------------------------------------------------------------------------
1488     # DRAWING THE STICKS: cylinders in a dupliverts structure
1489
1490     if use_sticks == True and use_sticks_type == '0' and all_sticks != []:
1491
1492         sticks = draw_sticks_dupliverts(all_atoms,
1493                                         atom_all_types_list,
1494                                         object_center_vec,
1495                                         all_sticks,
1496                                         Stick_diameter,
1497                                         Stick_sectors,
1498                                         Stick_unit,
1499                                         Stick_dist,
1500                                         use_sticks_smooth,
1501                                         use_sticks_color,
1502                                         list_coll_elements)
1503         for stick in sticks:
1504             atom_object_list.append(stick)
1505
1506     # ------------------------------------------------------------------------
1507     # DRAWING THE STICKS: skin and subdivision modifier
1508
1509     if use_sticks == True and use_sticks_type == '1' and all_sticks != []:
1510
1511         sticks = draw_sticks_skin(all_atoms,
1512                                   all_sticks,
1513                                   Stick_diameter,
1514                                   use_sticks_smooth,
1515                                   sticks_subdiv_view,
1516                                   sticks_subdiv_render,
1517                                   coll_molecule)
1518         atom_object_list.append(sticks)
1519
1520     # ------------------------------------------------------------------------
1521     # DRAWING THE STICKS: normal cylinders
1522
1523     if use_sticks == True and use_sticks_type == '2' and all_sticks != []:
1524
1525         sticks = draw_sticks_normal(all_atoms,
1526                                     all_sticks,
1527                                     object_center_vec,
1528                                     Stick_diameter,
1529                                     Stick_sectors,
1530                                     use_sticks_smooth,
1531                                     use_sticks_one_object,
1532                                     use_sticks_one_object_nr,
1533                                     coll_molecule)
1534         atom_object_list.append(sticks)
1535
1536     # ------------------------------------------------------------------------
1537     # CAMERA and LIGHT SOURCES
1538
1539     camera_light_source(use_camera,
1540                         use_light,
1541                         object_center_vec,
1542                         object_size)
1543
1544     # ------------------------------------------------------------------------
1545     # SELECT ALL LOADED OBJECTS
1546     bpy.ops.object.select_all(action='DESELECT')
1547     obj = None
1548     for obj in atom_object_list:
1549         obj.select_set(True)
1550
1551     # activate the last selected object
1552     if obj:
1553         bpy.context.view_layer.objects.active = obj