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# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# ##### END GPL LICENSE BLOCK #####
import bpy
import os
from math import pi, cos, sin, sqrt, ceil
# -----------------------------------------------------------------------------
# Atom, stick and element data
# This is a list that contains some data of all possible elements. The structure
# is as follows:
#
# 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54 means
#
# No., name, short name, color, radius (used), radius (covalent), radius (atomic),
#
# charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
# charge states for any atom are listed, if existing.
# The list is fixed and cannot be changed ... (see below)
ELEMENTS_DEFAULT = (
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
( 2, "Helium", "He", ( 0.85, 1.0, 1.0), 0.93, 0.93, 0.49 ),
( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
( 5, "Boron", "B", ( 1.0, 0.70, 0.70), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
( 6, "Carbon", "C", ( 0.56, 0.56, 0.56), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97), 0.75, 0.75, 0.75 , -3 , 1.71 , 1 , 0.25 , 3 , 0.16 , 5 , 0.13 ),
( 8, "Oxygen", "O", ( 1.0, 0.05, 0.05), 0.73, 0.73, 0.65 , -2 , 1.32 , -1 , 1.76 , 1 , 0.22 , 6 , 0.09 ),
( 9, "Fluorine", "F", ( 0.56, 0.87, 0.31), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
(10, "Neon", "Ne", ( 0.70, 0.89, 0.96), 0.71, 0.71, 0.51 , 1 , 1.12 ),
(11, "Sodium", "Na", ( 0.67, 0.36, 0.94), 1.54, 1.54, 2.23 , 1 , 0.97 ),
(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65), 1.18, 1.18, 1.82 , 3 , 0.51 ),
(14, "Silicon", "Si", ( 0.94, 0.78, 0.62), 1.11, 1.11, 1.46 , -4 , 2.71 , -1 , 3.84 , 1 , 0.65 , 4 , 0.42 ),
(15, "Phosphorus", "P", ( 1.0, 0.50, 0.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
(16, "Sulfur", "S", ( 1.0, 1.0, 0.18), 1.02, 1.02, 1.09 , -2 , 1.84 , 2 , 2.19 , 4 , 0.37 , 6 , 0.30 ),
(17, "Chlorine", "Cl", ( 0.12, 0.94, 0.12), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
(18, "Argon", "Ar", ( 0.50, 0.81, 0.89), 0.98, 0.98, 0.88 , 1 , 1.54 ),
(19, "Potassium", "K", ( 0.56, 0.25, 0.83), 2.03, 2.03, 2.77 , 1 , 0.81 ),
(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90), 1.44, 1.44, 2.09 , 3 , 0.73 ),
(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78), 1.32, 1.32, 2.00 , 1 , 0.96 , 2 , 0.94 , 3 , 0.76 , 4 , 0.68 ),
(23, "Vanadium", "V", ( 0.65, 0.65, 0.67), 1.22, 1.22, 1.92 , 2 , 0.88 , 3 , 0.74 , 4 , 0.63 , 5 , 0.59 ),
(24, "Chromium", "Cr", ( 0.54, 0.6, 0.78), 1.18, 1.18, 1.85 , 1 , 0.81 , 2 , 0.89 , 3 , 0.63 , 6 , 0.52 ),
(25, "Manganese", "Mn", ( 0.61, 0.47, 0.78), 1.17, 1.17, 1.79 , 2 , 0.80 , 3 , 0.66 , 4 , 0.60 , 7 , 0.46 ),
(26, "Iron", "Fe", ( 0.87, 0.4, 0.2), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31), 1.15, 1.15, 1.62 , 2 , 0.69 ),
(29, "Copper", "Cu", ( 0.78, 0.50, 0.2), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
(33, "Arsenic", "As", ( 0.74, 0.50, 0.89), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
(34, "Selenium", "Se", ( 1.0, 0.63, 0.0), 1.16, 1.16, 1.22 , -2 , 1.91 , -1 , 2.32 , 1 , 0.66 , 4 , 0.50 , 6 , 0.42 ),
(35, "Bromine", "Br", ( 0.65, 0.16, 0.16), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81), 1.31, 1.31, 1.24 ),
(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69), 2.16, 2.16, 2.98 , 1 , 1.47 ),
(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61), 1.27, 1.27, 1.95 , 7 , 0.97 ),
(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56), 1.25, 1.25, 1.89 , 4 , 0.67 ),
(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54), 1.25, 1.25, 1.83 , 3 , 0.68 ),
(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
(47, "Silver", "Ag", ( 0.75, 0.75, 0.75), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
(49, "Indium", "In", ( 0.65, 0.45, 0.45), 1.44, 1.44, 2.00 , 3 , 0.81 ),
(50, "Tin", "Sn", ( 0.4, 0.50, 0.50), 1.41, 1.41, 1.72 , -4 , 2.94 , -1 , 3.70 , 2 , 0.93 , 4 , 0.71 ),
(51, "Antimony", "Sb", ( 0.61, 0.38, 0.70), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0), 1.36, 1.36, 1.42 , -2 , 2.11 , -1 , 2.50 , 1 , 0.82 , 4 , 0.70 , 6 , 0.56 ),
(53, "Iodine", "I", ( 0.58, 0.0, 0.58), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69), 1.31, 1.31, 1.24 ),
(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56), 2.35, 2.35, 3.35 , 1 , 1.67 ),
(56, "Barium", "Ba", ( 0.0, 0.78, 0.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78), 1.64, 1.64, 2.64 , 3 , 0.99 ),
(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78), 1.63, 1.63, 2.62 , 3 , 0.97 ),
(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78), 1.62, 1.62, 2.59 , 3 , 0.96 ),
(63, "Europium", "Eu", ( 0.38, 1.0, 0.78), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78), 1.61, 1.61, 2.54 , 3 , 0.93 ),
(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78), 1.59, 1.59, 2.49 , 3 , 0.90 ),
(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61), 1.58, 1.58, 2.47 , 3 , 0.89 ),
(68, "Erbium", "Er", ( 0.0, 0.90, 0.45), 1.57, 1.57, 2.45 , 3 , 0.88 ),
(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32), 1.56, 1.56, 2.42 , 3 , 0.87 ),
(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14), 1.56, 1.56, 2.25 , 3 , 0.85 ),
(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
(74, "Tungsten", "W", ( 0.12, 0.58, 0.83), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
(76, "Osmium", "Os", ( 0.14, 0.4, 0.58), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52), 1.27, 1.27, 1.87 , 4 , 0.68 ),
(78, "Platinium", "Pt", ( 0.81, 0.81, 0.87), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
(79, "Gold", "Au", ( 1.0, 0.81, 0.13), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
(82, "Lead", "Pb", ( 0.34, 0.34, 0.38), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
(84, "Polonium", "Po", ( 0.67, 0.36, 0.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
(85, "Astatine", "At", ( 0.45, 0.30, 0.27), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
(86, "Radon", "Rn", ( 0.25, 0.50, 0.58), 1.00, 1.00, 1.34 ),
(87, "Francium", "Fr", ( 0.25, 0.0, 0.4), 1.00, 1.00, 1.00 , 1 , 1.80 ),
(88, "Radium", "Ra", ( 0.0, 0.49, 0.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98), 1.00, 1.00, 1.00 , 3 , 1.18 ),
(90, "Thorium", "Th", ( 0.0, 0.72, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0), 1.00, 1.00, 1.00 , 3 , 1.13 , 4 , 0.98 , 5 , 0.89 ),
(92, "Uranium", "U", ( 0.0, 0.56, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0), 1.00, 1.00, 1.00 , 3 , 1.10 , 4 , 0.95 , 7 , 0.71 ),
(94, "Plutonium", "Pu", ( 0.0, 0.41, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
(95, "Americium", "Am", ( 0.32, 0.36, 0.94), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
(96, "Curium", "Cm", ( 0.47, 0.36, 0.89), 1.00, 1.00, 1.00 ),
(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89), 1.00, 1.00, 1.00 ),
(98, "Californium", "Cf", ( 0.63, 0.21, 0.83), 1.00, 1.00, 1.00 ),
(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83), 1.00, 1.00, 1.00 ),
(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72), 1.00, 1.00, 1.00 ),
(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65), 1.00, 1.00, 1.00 ),
(102, "Nobelium", "No", ( 0.74, 0.05, 0.52), 1.00, 1.00, 1.00 ),
(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4), 1.00, 1.00, 1.00 ),
(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
(105, "Default", "Default", ( 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
(106, "Stick", "Stick", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
)
# This list here contains all data of the elements and will be used during
# runtime. It is a list of classes.
# During executing Atomic Blender, the list will be initialized with the fixed
# data from above via the class structure below (ElementProp). We
# have then one fixed list (above), which will never be changed, and a list of
# classes with same data. The latter can be modified via loading a separate
# custom data file.
ELEMENTS = []
class ElementProp(object):
__slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
def __init__(self, number, name, short_name, color, radii, radii_ionic):
self.number = number
self.name = name
self.short_name = short_name
self.color = color
self.radii = radii
self.radii_ionic = radii_ionic
# This is the class, which stores the properties of one atom.
class AtomProp(object):
__slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
def __init__(self, element, name, location, radius, color, material):
self.element = element
self.name = name
self.location = location
self.radius = radius
self.color = color
self.material = material
# This is the class, which stores the two atoms of one stick.
class StickProp(object):
__slots__ = ('atom1', 'atom2', 'number', 'dist')
def __init__(self, atom1, atom2, number, dist):
# -----------------------------------------------------------------------------
# Some basic routines
def read_elements():
ELEMENTS[:] = []
for item in ELEMENTS_DEFAULT:
# All three radii into a list
radii = [item[4],item[5],item[6]]
# The handling of the ionic radii will be done later. So far, it is an
# empty list.
li = ElementProp(item[0],item[1],item[2],item[3],
ELEMENTS.append(li)
# filepath_pdb: path to pdb file
# radiustype : '0' default
# '1' atomic radii
# '2' van der Waals
def read_pdb_file(filepath_pdb, radiustype):
# The list of all atoms as read from the PDB file.
all_atoms = []
# Open the pdb file ...
filepath_pdb_p = open(filepath_pdb, "r")
for line in filepath_pdb_p:
split_list = line.split(' ')
if "ATOM" in split_list[0]:
break
if "HETATM" in split_list[0]:
break
j = 0
# This is in fact an endless 'while loop', ...
while j > -1:
# ... the loop is broken here (EOF) ...
if line == "":
# If there is a "TER" we need to put empty entries into the lists
# in order to not destroy the order of atom numbers and same numbers
# used for sticks. "TER? What is that?" TER indicates the end of a
# list of ATOM/HETATM records for a chain.
if "TER" in line:
short_name = "TER"
name = "TER"
radius = 0.0
color = [0,0,0]
location = Vector((0,0,0))
all_atoms.append(AtomProp(short_name,
name,
location,
radius,
color,[]))
# If 'ATOM or 'HETATM' appears in the line then do ...
elif "ATOM" in line or "HETATM" in line:
# What follows is due to deviations which appear from PDB to
# PDB file. It is very special!
#
# PLEASE, DO NOT CHANGE! ............................... from here
if line[12:13] == " " or line[12:13].isdigit() == True:
short_name = line[13:14]
short_name = short_name + line[14:15]
elif line[12:13].isupper() == True:
if line[13:14].isalpha() == True:
short_name = short_name + line[13:14]
else:
print("Atomic Blender: Strange error in PDB file.\n"
"Look for element names at positions 13-16 and 78-79.\n")
return -1
if len(line) >= 78:
if line[76:77] == " ":
short_name2 = line[76:77]
else:
short_name2 = line[76:78]
if short_name2.isalpha() == True:
FOUND = False
for element in ELEMENTS:
if str.upper(short_name2) == str.upper(element.short_name):
FOUND = True
break
if FOUND == False:
short_name = short_name2
# ....................................................... to here.
# Go through all elements and find the element of the current atom.
for element in ELEMENTS:
if str.upper(short_name) == str.upper(element.short_name):
# Give the atom its proper names, color and radius:
short_name = str.upper(element.short_name)
name = element.name
# int(radiustype) => type of radius:
# pre-defined (0), atomic (1) or van der Waals (2)
radius = float(element.radii[int(radiustype)])
color = element.color
FLAG_FOUND = True
break
# Is it a vacancy or an 'unknown atom' ?
# Give this atom also a name. If it is an 'X' then it is a
# vacancy. Otherwise ...
if "X" in short_name:
short_name = "VAC"
name = "Vacancy"
radius = float(ELEMENTS[-3].radii[int(radiustype)])
color = ELEMENTS[-3].color
# unknown atoms. This should never happen, the element list is
# almost complete. However, we do this due to security reasons.
else:
short_name = str.upper(short_name)
name = str.upper(short_name)
radius = float(ELEMENTS[-2].radii[int(radiustype)])
color = ELEMENTS[-2].color
# x,y and z are at fixed positions in the PDB file.
x = float(line[30:38].rsplit()[0])
y = float(line[38:46].rsplit()[0])
z = float(line[46:55].rsplit()[0])
location = Vector((x,y,z))
j += 1
all_atoms.append(AtomProp(short_name,
name,
location,
radius,
color,[]))
line = filepath_pdb_p.readline()
filepath_pdb_p.close()
# From above it can be clearly seen that j is now the number of all atoms.
Number_of_total_atoms = j
return (Number_of_total_atoms, all_atoms)
def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds):
# The list of all sticks.
all_sticks = []
# Open the PDB file again.
filepath_pdb_p = open(filepath_pdb, "r")
line = filepath_pdb_p.readline()
split_list = line.split(' ')
# Go to the first entry
if "CONECT" not in split_list[0]:
for line in filepath_pdb_p:
split_list = line.split(' ')
if "CONECT" in split_list[0]:
break
# This is in fact an endless while loop, ...
# ... or here, when no 'CONECT' appears anymore.
if "CONECT" not in line:
break
# The strings of the atom numbers do have a clear position in the file
# (From 7 to 12, from 13 to 18 and so on.) and one needs to consider
# this. One could also use the split function but then one gets into
# trouble if there are lots of atoms: For instance, it may happen that
# one has
# In Fact it means that atom No. 11111 has a connection with atom
# No. 222 but also with atom No. 44444. The split function would give
# me only two numbers (11111 and 22244444), which is wrong.
line = line[6:]
# Amount of loops
length = len(line)
loops = int(length/5)
# List of atoms
atom_list = []
for i in range(loops):
number = line[5*i:5*(i+1)].rsplit()
if number[0].isdigit() == True:
atom_number = int(number[0])
atom_list.append(atom_number)
# The first atom is connected with all the others in the list.
atom1 = atom_list[0]
for atom2 in atom_list[1:]:
if use_sticks_bonds == True:
number = atom_list[1:].count(atom2)
if number == 2 or number == 3:
basis_list = list(set(atom_list[1:]))
if len(basis_list) > 1:
basis1 = (all_atoms[atom1-1].location
- all_atoms[basis_list[0]-1].location)
basis2 = (all_atoms[atom1-1].location
- all_atoms[basis_list[1]-1].location)
plane_n = basis1.cross(basis2)
dist_n = (all_atoms[atom1-1].location
- all_atoms[atom2-1].location)
dist_n = dist_n.cross(plane_n)
dist_n = dist_n / dist_n.length
else:
dist_n = (all_atoms[atom1-1].location
- all_atoms[atom2-1].location)
dist_n = Vector((dist_n[1],-dist_n[0],0))
dist_n = dist_n / dist_n.length
elif number > 3:
number = 1
dist_n = None
else:
dist_n = None
else:
number = 1
dist_n = None
# couple of times. (Only god knows why ...)
# So, does a stick between the considered atoms already exist?
FLAG_BAR = False
for k in range(Number_of_sticks):
if ((all_sticks[k].atom1 == atom1 and all_sticks[k].atom2 == atom2) or
(all_sticks[k].atom2 == atom1 and all_sticks[k].atom1 == atom2)):
sticks_double += 1
# If yes, then FLAG on 'True'.
FLAG_BAR = True
break
# If the stick is not yet registered (FLAG_BAR == False), then
all_sticks.append(StickProp(atom1,atom2,number,dist_n))
line = filepath_pdb_p.readline()
filepath_pdb_p.close()
return all_sticks
# Routine which produces a cylinder. All is somewhat easy to undertsand.
def build_stick(radius, length, sectors):
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dphi = 2.0 * pi/(float(sectors)-1)
# Vertices
vertices_top = [Vector((0,0,length / 2.0))]
vertices_bottom = [Vector((0,0,-length / 2.0))]
vertices = []
for i in range(sectors-1):
x = radius * cos( dphi * i )
y = radius * sin( dphi * i )
z = length / 2.0
vertex = Vector((x,y,z))
vertices_top.append(vertex)
z = -length / 2.0
vertex = Vector((x,y,z))
vertices_bottom.append(vertex)
vertices = vertices_top + vertices_bottom
# Side facets (Cylinder)
faces1 = []
for i in range(sectors-1):
if i == sectors-2:
faces1.append( [i+1, 1, 1+sectors, i+1+sectors] )
else:
faces1.append( [i+1, i+2, i+2+sectors, i+1+sectors] )
# Top facets
faces2 = []
for i in range(sectors-1):
if i == sectors-2:
face_top = [0,sectors-1,1]
face_bottom = [sectors,2*sectors-1,sectors+1]
else:
face_top = [0]
face_bottom = [sectors]
for j in range(2):
face_top.append(i+j+1)
face_bottom.append(i+j+1+sectors)
faces2.append(face_top)
faces2.append(face_bottom)
# Build the mesh, Cylinder
cylinder = bpy.data.meshes.new("Sticks_Cylinder")
cylinder.from_pydata(vertices, [], faces1)
cylinder.update()
new_cylinder = bpy.data.objects.new("Sticks_Cylinder", cylinder)
bpy.context.scene.objects.link(new_cylinder)
# Build the mesh, Cups
cups = bpy.data.meshes.new("Sticks_Cups")
cups.from_pydata(vertices, [], faces2)
cups.update()
new_cups = bpy.data.objects.new("Sticks_Cups", cups)
bpy.context.scene.objects.link(new_cups)
return (new_cylinder, new_cups)
# -----------------------------------------------------------------------------
# The main routine
def import_pdb(use_mesh,
Ball_azimuth,
Ball_zenith,
Ball_radius_factor,
radiustype,
Ball_distance_factor,
use_sticks,
use_sticks_color,
use_sticks_smooth,
use_sticks_bonds,
Stick_unit, Stick_dist,
Stick_sectors,
Stick_diameter,
put_to_center,
use_camera,
use_lamp,
filepath_pdb):
# List of materials
atom_material_list = []
# A list of ALL objects which are loaded (needed for selecting the loaded
# structure.
atom_object_list = []
# ------------------------------------------------------------------------
# INITIALIZE THE ELEMENT LIST
read_elements()
# ------------------------------------------------------------------------
# READING DATA OF ATOMS
(Number_of_total_atoms, all_atoms) = read_pdb_file(filepath_pdb, radiustype)
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# ------------------------------------------------------------------------
# MATERIAL PROPERTIES FOR ATOMS
# The list that contains info about all types of atoms is created
# here. It is used for building the material properties for
# instance (see below).
atom_all_types_list = []
for atom in all_atoms:
FLAG_FOUND = False
for atom_type in atom_all_types_list:
# If the atom name is already in the list, FLAG on 'True'.
if atom_type[0] == atom.name:
FLAG_FOUND = True
break
# No name in the current list has been found? => New entry.
if FLAG_FOUND == False:
# Stored are: Atom label (e.g. 'Na'), the corresponding atom
# name (e.g. 'Sodium') and its color.
atom_all_types_list.append([atom.name, atom.element, atom.color])
# The list of materials is built.
# Note that all atoms of one type (e.g. all hydrogens) get only ONE
# material! This is good because then, by activating one atom in the
# Blender scene and changing the color of this atom, one changes the color
# of ALL atoms of the same type at the same time.
# Create first a new list of materials for each type of atom
# (e.g. hydrogen)
for atom_type in atom_all_types_list:
material = bpy.data.materials.new(atom_type[1])
material.name = atom_type[0]
material.diffuse_color = atom_type[2]
atom_material_list.append(material)
# Now, we go through all atoms and give them a material. For all atoms ...
for atom in all_atoms:
# ... and all materials ...
for material in atom_material_list:
# ... select the correct material for the current atom via
# comparison of names ...
if atom.name in material.name:
# ... and give the atom its material properties.
# However, before we check, if it is a vacancy, because then it
# gets some additional preparation. The vacancy is represented
# by a transparent cube.
if atom.name == "Vacancy":
material.transparency_method = 'Z_TRANSPARENCY'
material.alpha = 1.3
material.raytrace_transparency.fresnel = 1.6
material.raytrace_transparency.fresnel_factor = 1.6
material.use_transparency = True
# The atom gets its properties.
atom.material = material
# ------------------------------------------------------------------------
# READING DATA OF STICKS
all_sticks = read_pdb_file_sticks(filepath_pdb, use_sticks_bonds)
# So far, all atoms, sticks and materials have been registered.
# ------------------------------------------------------------------------
# TRANSLATION OF THE STRUCTURE TO THE ORIGIN
# It may happen that the structure in a PDB file already has an offset
# If chosen, the structure is first put into the center of the scene
# (the offset is substracted).
sum_vec = Vector((0.0,0.0,0.0))
# Sum of all atom coordinates
sum_vec = sum([atom.location for atom in all_atoms], sum_vec)
# Then the average is taken
sum_vec = sum_vec / Number_of_total_atoms
# After, for each atom the center of gravity is substracted
for atom in all_atoms:
atom.location -= sum_vec
# ------------------------------------------------------------------------
# Take all atoms and adjust their radii and scale the distances.
for atom in all_atoms:
atom.location *= Ball_distance_factor
# ------------------------------------------------------------------------
# DETERMINATION OF SOME GEOMETRIC PROPERTIES
# In the following, some geometric properties of the whole object are
# determined: center, size, etc.
sum_vec = Vector((0.0,0.0,0.0))
# First the center is determined. All coordinates are summed up ...
sum_vec = sum([atom.location for atom in all_atoms], sum_vec)
# ... and the average is taken. This gives the center of the object.
object_center_vec = sum_vec / Number_of_total_atoms
# Now, we determine the size.The farthest atom from the object center is
# taken as a measure. The size is used to place well the camera and light
# into the scene.
object_size_vec = [atom.location - object_center_vec for atom in all_atoms]
object_size = 0.0
object_size = max(object_size_vec).length
# ------------------------------------------------------------------------
# CAMERA AND LAMP
camera_factor = 15.0
# If chosen a camera is put into the scene.
if use_camera == True:
# Assume that the object is put into the global origin. Then, the
# camera is moved in x and z direction, not in y. The object has its
# size at distance sqrt(object_size) from the origin. So, move the
# camera by this distance times a factor of camera_factor in x and z.
# Then add x, y and z of the origin of the object.
object_camera_vec = Vector((sqrt(object_size) * camera_factor,
sqrt(object_size) * camera_factor))
camera_xyz_vec = object_center_vec + object_camera_vec
# Create the camera
current_layers=bpy.context.scene.layers
camera_data = bpy.data.cameras.new("A_camera")
camera_data.lens = 45
camera_data.clip_end = 500.0
camera = bpy.data.objects.new("A_camera", camera_data)
camera.location = camera_xyz_vec
camera.layers = current_layers
bpy.context.scene.objects.link(camera)
# Here the camera is rotated such it looks towards the center of
# the object. The [0.0, 0.0, 1.0] vector along the z axis
z_axis_vec = Vector((0.0, 0.0, 1.0))
# The angle between the last two vectors
angle = object_camera_vec.angle(z_axis_vec, 0)
# The cross-product of z_axis_vec and object_camera_vec
axis_vec = z_axis_vec.cross(object_camera_vec)
# Rotate 'axis_vec' by 'angle' and convert this to euler parameters.
# 4 is the size of the matrix.
camera.rotation_euler = Matrix.Rotation(angle, 4, axis_vec).to_euler()
# Rotate the camera around its axis by 90° such that we have a nice
bpy.ops.object.select_all(action='DESELECT')
camera.select = True
bpy.ops.transform.rotate(value=(90.0*2*pi/360.0),
axis=object_camera_vec,
constraint_axis=(False, False, False),
constraint_orientation='GLOBAL',
mirror=False, proportional='DISABLED',
proportional_edit_falloff='SMOOTH',
proportional_size=1, snap=False,
snap_target='CLOSEST', snap_point=(0, 0, 0),
snap_align=False, snap_normal=(0, 0, 0),
release_confirm=False)
# Here a lamp is put into the scene, if chosen.
if use_lamp == True:
# This is the distance from the object measured in terms of %
lamp_dl = sqrt(object_size) * 15 * 0.5
# This is a factor to which extend the lamp shall go to the right
# (from the camera point of view).
lamp_dy_right = lamp_dl * (3.0/4.0)
# Create x, y and z for the lamp.
object_lamp_vec = Vector((lamp_dl,lamp_dy_right,lamp_dl))
lamp_xyz_vec = object_center_vec + object_lamp_vec
lamp_data = bpy.data.lamps.new(name="A_lamp", type="POINT")
lamp_data.distance = 500.0
lamp_data.energy = 3.0
lamp_data.shadow_method = 'RAY_SHADOW'
lamp = bpy.data.objects.new("A_lamp", lamp_data)
lamp.location = lamp_xyz_vec
lamp.layers = current_layers
bpy.context.scene.objects.link(lamp)
bpy.context.scene.world.light_settings.use_ambient_occlusion = True
bpy.context.scene.world.light_settings.ao_factor = 0.2
# ------------------------------------------------------------------------
# SORTING THE ATOMS
# Lists of atoms of one type are created. Example:
# draw_all_atoms = [ data_hydrogen,data_carbon,data_nitrogen ]
# data_hydrogen = [["Hydrogen", Material_Hydrogen, Vector((x,y,z)), 109], ...]
draw_all_atoms = []
# Go through the list which contains all types of atoms. It is the list,
# which has been created on the top during reading the PDB file.
# Example: atom_all_types_list = ["hydrogen", "carbon", ...]
for atom_type in atom_all_types_list:
# This is the draw list, which contains all atoms of one type (e.g.
draw_all_atoms_type = []
# Go through all atoms ...
for atom in all_atoms:
# ... select the atoms of the considered type via comparison ...
if atom.name == atom_type[0]:
# ... and append them to the list 'draw_all_atoms_type'.
draw_all_atoms_type.append([atom.name,
atom.material,
# Now append the atom list to the list of all types of atoms
draw_all_atoms.append(draw_all_atoms_type)
# ------------------------------------------------------------------------
# DRAWING THE ATOMS
# This is the number of all atoms which are put into the scene.
bpy.ops.object.select_all(action='DESELECT')
# For each list of atoms of ONE type (e.g. Hydrogen)
for draw_all_atoms_type in draw_all_atoms:
# Create first the vertices composed of the coordinates of all
# atoms of one type
atom_vertices = []
for atom in draw_all_atoms_type:
# In fact, the object is created in the World's origin.
# This is why 'object_center_vec' is substracted. At the end
# the whole object is translated back to 'object_center_vec'.
atom_vertices.append( atom[2] - object_center_vec )
# Build the mesh
atom_mesh = bpy.data.meshes.new("Mesh_"+atom[0])
atom_mesh.from_pydata(atom_vertices, [], [])
atom_mesh.update()
new_atom_mesh = bpy.data.objects.new(atom[0], atom_mesh)
bpy.context.scene.objects.link(new_atom_mesh)
# Now, build a representative sphere (atom)
current_layers=bpy.context.scene.layers
view_align=False, enter_editmode=False,
location=(0.0, 0.0, 0.0),
rotation=(0.0, 0.0, 0.0),
view_align=False, enter_editmode=False,
location=(0,0,0), rotation=(0.0, 0.0, 0.0),
layers=current_layers)
# UV balls
else:
bpy.ops.mesh.primitive_uv_sphere_add(
segments=Ball_azimuth, ring_count=Ball_zenith,
size=1, view_align=False, enter_editmode=False,
location=(0,0,0), rotation=(0, 0, 0),
ball.scale = (atom[3]*Ball_radius_factor,) * 3
ball.active_material = atom[1]
ball.parent = new_atom_mesh
new_atom_mesh.dupli_type = 'VERTS'
# The object is back translated to 'object_center_vec'.
new_atom_mesh.location = object_center_vec
atom_object_list.append(new_atom_mesh)
# ------------------------------------------------------------------------
# DRAWING THE STICKS
if use_sticks_color == False:
bpy.ops.object.material_slot_add()
stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
stick_material.diffuse_color = ELEMENTS[-1].color
# Sort the sticks and put them into a new list such that ...
sticks_all_lists = []
if use_sticks_color == True:
for atom_type in atom_all_types_list:
if atom_type[0] == "TER":
continue
sticks_list = []
for stick in all_sticks:
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for repeat in range(stick.number):
atom1 = copy(all_atoms[stick.atom1-1].location)
atom2 = copy(all_atoms[stick.atom2-1].location)
dist = Stick_diameter * Stick_dist
if stick.number == 2:
if repeat == 0:
atom1 += (stick.dist * dist)
atom2 += (stick.dist * dist)
if repeat == 1:
atom1 -= (stick.dist * dist)
atom2 -= (stick.dist * dist)
if stick.number == 3:
if repeat == 0:
atom1 += (stick.dist * dist)
atom2 += (stick.dist * dist)
if repeat == 2:
atom1 -= (stick.dist * dist)
atom2 -= (stick.dist * dist)
dv = atom1 - atom2
n = dv / dv.length
if atom_type[0] == all_atoms[stick.atom1-1].name:
location = atom1
name = "_" + all_atoms[stick.atom1-1].name
material = all_atoms[stick.atom1-1].material
sticks_list.append([name, location, dv, material])
if atom_type[0] == all_atoms[stick.atom2-1].name:
location = atom1 - n * dl * int(ceil(dv.length / (2.0 * dl)))
name = "_" + all_atoms[stick.atom2-1].name
material = all_atoms[stick.atom2-1].material
sticks_list.append([name, location, dv, material])
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if stick.number > 3:
stick.number = 1
for repeat in range(stick.number):
atom1 = copy(all_atoms[stick.atom1-1].location)
atom2 = copy(all_atoms[stick.atom2-1].location)
dist = Stick_diameter * Stick_dist
if stick.number == 2:
if repeat == 0:
atom1 += (stick.dist * dist)
atom2 += (stick.dist * dist)
if repeat == 1:
atom1 -= (stick.dist * dist)
atom2 -= (stick.dist * dist)
if stick.number == 3:
if repeat == 0:
atom1 += (stick.dist * dist)
atom2 += (stick.dist * dist)
if repeat == 2:
atom1 -= (stick.dist * dist)
atom2 -= (stick.dist * dist)
dv = atom1 - atom2
n = dv / dv.length
location = atom1
material = stick_material
sticks_list.append(["", location, dv, material])
sticks_all_lists.append(sticks_list)
# ... the sticks in the list can be drawn:
for stick_list in sticks_all_lists:
vertices = []
faces = []
i = 0
for stick in stick_list:
dv = stick[2]
v1 = stick[1]
n = dv / dv.length
gamma = -n * v1
b = v1 + gamma * n
n_b = b / b.length
if use_sticks_color == True:
loops = int(ceil(dv.length / (2.0 * dl)))
loops = int(ceil(dv.length / dl))
for j in range(loops):
g = v1 - n * dl / 2.0 - n * dl * j
p1 = g + n_b * Stick_diameter
p2 = g - n_b * Stick_diameter
p3 = g - n_b.cross(n) * Stick_diameter
p4 = g + n_b.cross(n) * Stick_diameter
vertices.append(p1)
vertices.append(p2)
vertices.append(p3)
vertices.append(p4)
faces.append((i*4+0,i*4+2,i*4+1,i*4+3))
i += 1
mesh = bpy.data.meshes.new("Sticks"+stick[0])
mesh.from_pydata(vertices, [], faces)
mesh.update()
new_mesh = bpy.data.objects.new("Sticks"+stick[0], mesh)
bpy.context.scene.objects.link(new_mesh)
object_stick = build_stick(Stick_diameter, dl, Stick_sectors)