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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 os
import bpy
import bmesh
from math import pi, cos, sin, sqrt, ceil
from mathutils import Vector, Matrix
from copy import copy
# -----------------------------------------------------------------------------
# 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 = (
( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
( 2, "Helium", "He", ( 0.85, 1.0, 1.0, 1.0), 0.93, 0.93, 0.49 ),
( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0, 1.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
( 5, "Boron", "B", ( 1.0, 0.70, 0.70, 1.0), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
( 6, "Carbon", "C", ( 0.56, 0.56, 0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
( 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 ),
( 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 ),
( 9, "Fluorine", "F", ( 0.56, 0.87, 0.31, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
(10, "Neon", "Ne", ( 0.70, 0.89, 0.96, 1.0), 0.71, 0.71, 0.51 , 1 , 1.12 ),
(11, "Sodium", "Na", ( 0.67, 0.36, 0.94, 1.0), 1.54, 1.54, 2.23 , 1 , 0.97 ),
(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0, 1.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65, 1.0), 1.18, 1.18, 1.82 , 3 , 0.51 ),
(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 ),
(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 ),
(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 ),
(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 ),
(18, "Argon", "Ar", ( 0.50, 0.81, 0.89, 1.0), 0.98, 0.98, 0.88 , 1 , 1.54 ),
(19, "Potassium", "K", ( 0.56, 0.25, 0.83, 1.0), 2.03, 2.03, 2.77 , 1 , 0.81 ),
(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0, 1.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90, 1.0), 1.44, 1.44, 2.09 , 3 , 0.73 ),
(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 ),
(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 ),
(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 ),
(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 ),
(26, "Iron", "Fe", ( 0.87, 0.4, 0.2, 1.0), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62, 1.0), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31, 1.0), 1.15, 1.15, 1.62 , 2 , 0.69 ),
(29, "Copper", "Cu", ( 0.78, 0.50, 0.2, 1.0), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69, 1.0), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56, 1.0), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
(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 ),
(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 ),
(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 ),
(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 ),
(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81, 1.0), 1.31, 1.31, 1.24 ),
(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69, 1.0), 2.16, 2.16, 2.98 , 1 , 1.47 ),
(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0, 1.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87, 1.0), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
(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 ),
(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 ),
(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61, 1.0), 1.27, 1.27, 1.95 , 7 , 0.97 ),
(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56, 1.0), 1.25, 1.25, 1.89 , 4 , 0.67 ),
(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54, 1.0), 1.25, 1.25, 1.83 , 3 , 0.68 ),
(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52, 1.0), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
(47, "Silver", "Ag", ( 0.75, 0.75, 0.75, 1.0), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56, 1.0), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
(49, "Indium", "In", ( 0.65, 0.45, 0.45, 1.0), 1.44, 1.44, 2.00 , 3 , 0.81 ),
(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 ),
(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 ),
(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 ),
(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 ),
(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69, 1.0), 1.31, 1.31, 1.24 ),
(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56, 1.0), 2.35, 2.35, 3.35 , 1 , 1.67 ),
(56, "Barium", "Ba", ( 0.0, 0.78, 0.0, 1.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
(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 ),
(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78, 1.0), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78, 1.0), 1.64, 1.64, 2.64 , 3 , 0.99 ),
(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78, 1.0), 1.63, 1.63, 2.62 , 3 , 0.97 ),
(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78, 1.0), 1.62, 1.62, 2.59 , 3 , 0.96 ),
(63, "Europium", "Eu", ( 0.38, 1.0, 0.78, 1.0), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78, 1.0), 1.61, 1.61, 2.54 , 3 , 0.93 ),
(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78, 1.0), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78, 1.0), 1.59, 1.59, 2.49 , 3 , 0.90 ),
(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61, 1.0), 1.58, 1.58, 2.47 , 3 , 0.89 ),
(68, "Erbium", "Er", ( 0.0, 0.90, 0.45, 1.0), 1.57, 1.57, 2.45 , 3 , 0.88 ),
(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32, 1.0), 1.56, 1.56, 2.42 , 3 , 0.87 ),
(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21, 1.0), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14, 1.0), 1.56, 1.56, 2.25 , 3 , 0.85 ),
(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
(74, "Tungsten", "W", ( 0.12, 0.58, 0.83, 1.0), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67, 1.0), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
(76, "Osmium", "Os", ( 0.14, 0.4, 0.58, 1.0), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52, 1.0), 1.27, 1.27, 1.87 , 4 , 0.68 ),
(78, "Platinum", "Pt", ( 0.81, 0.81, 0.87, 1.0), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
(79, "Gold", "Au", ( 1.0, 0.81, 0.13, 1.0), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81, 1.0), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30, 1.0), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
(82, "Lead", "Pb", ( 0.34, 0.34, 0.38, 1.0), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
(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 ),
(84, "Polonium", "Po", ( 0.67, 0.36, 0.0, 1.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
(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 ),
(86, "Radon", "Rn", ( 0.25, 0.50, 0.58, 1.0), 1.00, 1.00, 1.34 ),
(87, "Francium", "Fr", ( 0.25, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 , 1 , 1.80 ),
(88, "Radium", "Ra", ( 0.0, 0.49, 0.0, 1.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98, 1.0), 1.00, 1.00, 1.00 , 3 , 1.18 ),
(90, "Thorium", "Th", ( 0.0, 0.72, 1.0, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
(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 ),
(92, "Uranium", "U", ( 0.0, 0.56, 1.0, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
(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 ),
(94, "Plutonium", "Pu", ( 0.0, 0.41, 1.0, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
(95, "Americium", "Am", ( 0.32, 0.36, 0.94, 1.0), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
(96, "Curium", "Cm", ( 0.47, 0.36, 0.89, 1.0), 1.00, 1.00, 1.00 ),
(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89, 1.0), 1.00, 1.00, 1.00 ),
(98, "Californium", "Cf", ( 0.63, 0.21, 0.83, 1.0), 1.00, 1.00, 1.00 ),
(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83, 1.0), 1.00, 1.00, 1.00 ),
(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
(102, "Nobelium", "No", ( 0.74, 0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 ),
(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
(105, "Default", "Default", ( 1.0, 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
(106, "Stick", "Stick", ( 0.5, 0.5, 0.5, 1.0), 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 = []
# This is the class, which stores the properties for one element.
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):
self.atom1 = atom1
self.atom2 = atom2
self.number = number
self.dist = dist
# -----------------------------------------------------------------------------
# Some basic routines
# The function, which reads all necessary properties of the elements.
def read_elements():
del 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.
radii_ionic = []
li = ElementProp(item[0],item[1],item[2],item[3],
radii,radii_ionic)
ELEMENTS.append(li)
# The function, which reads the x,y,z positions of all atoms in a PDB
# file.
#
# 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")
#Go to the line, in which "ATOM" or "HETATM" appears.
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 == "":
break
# 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
# 2019-03-14, New
color = [0,0,0, 0]
location = Vector((0,0,0))
# Append the TER into the list. Material remains empty so far.
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]
if line[14:15].islower() == True:
short_name = short_name + line[14:15]
elif line[12:13].isupper() == True:
short_name = line[12:13]
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.
FLAG_FOUND = False
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' ?
if FLAG_FOUND == False:
# 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
# ... take what is written in the PDB file. These are somewhat
# 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
# Append the atom to the list. Material remains empty so far.
all_atoms.append(AtomProp(short_name,
name,
location,
radius,
color,[]))
line = filepath_pdb_p.readline()
line = line[:-1]
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)
# The function, which reads the sticks in a PDB file.
def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms):
# The list of all sticks.
all_sticks = []
# Open the PDB file.
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
Number_of_sticks = 0
sticks_double = 0
j = 0
# This is in fact an endless while loop, ...
while j > -1:
# ... which is broken here (EOF) ...
if line == "":
break
# ... or here, when no 'CONECT' appears anymore.
if "CONECT" not in line:
break
# Note 2019-03-16: in a PDB file the identifier for sticks is called
# 'CONECT' and NOT 'CONNECT'! Please leave this as is, otherwise the
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# sticks are NOT correctly loaded.
# 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
# CONECT 11111 22244444
#
# 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.
# Cut spaces from the right and 'CONECT' at the beginning
line = line.rstrip()
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 != []:
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 all the other atoms in the list do:
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:]))
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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
# Note that in a PDB file, sticks of one atom pair can appear a
# 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
# register it!
if FLAG_BAR == False:
all_sticks.append(StickProp(atom1,atom2,number,dist_n))
Number_of_sticks += 1
j += 1
line = filepath_pdb_p.readline()
line = line.rstrip()
filepath_pdb_p.close()
return all_sticks
# Function, which produces a cylinder. All is somewhat easy to understand.
def build_stick(radius, length, sectors, element_name):
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(element_name+"_sticks_cylinder")
cylinder.from_pydata(vertices, [], faces1)
cylinder.update()
new_cylinder = bpy.data.objects.new(element_name+"_sticks_cylinder", cylinder)
# Attention: the linking will be done a few moments later, after this
# is done definition.
# Build the mesh, Cups
cups = bpy.data.meshes.new(element_name+"_sticks_cup")
cups.from_pydata(vertices, [], faces2)
cups.update()
new_cups = bpy.data.objects.new(element_name+"_sticks_cup", cups)
# Attention: the linking will be done a few moments later, after this
return (new_cylinder, new_cups)
# Rotate an object.
def rotate_object(rot_mat, obj):
bpy.ops.object.select_all(action='DESELECT')
obj.select_set(True)
# Decompose world_matrix's components, and from them assemble 4x4 matrices.
orig_loc, orig_rot, orig_scale = obj.matrix_world.decompose()
orig_loc_mat = Matrix.Translation(orig_loc)
orig_rot_mat = orig_rot.to_matrix().to_4x4()
orig_scale_mat = (Matrix.Scale(orig_scale[0],4,(1,0,0)) @
Matrix.Scale(orig_scale[1],4,(0,1,0)) @
Matrix.Scale(orig_scale[2],4,(0,0,1)))
# Assemble the new matrix.
obj.matrix_world = orig_loc_mat @ rot_mat @ orig_rot_mat @ orig_scale_mat
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# Function, which puts a camera and light source into the 3D scene
def camera_light_source(use_camera,
use_light,
object_center_vec,
object_size):
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,
0.0,
sqrt(object_size) * camera_factor))
camera_xyz_vec = object_center_vec + object_camera_vec
# Create the camera
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
bpy.context.collection.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
# camera position and view onto the object.
bpy.ops.object.select_all(action='DESELECT')
camera.select_set(True)
# Rotate the camera around its axis 'object_camera_vec' by 90° such
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# that we have a nice camera view onto the object.
matrix_rotation = Matrix.Rotation(90/360*2*pi, 4, object_camera_vec)
rotate_object(matrix_rotation, camera)
# Here a lamp is put into the scene, if chosen.
if use_light == True:
# This is the distance from the object measured in terms of %
# of the camera distance. It is set onto 50% (1/2) distance.
light_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).
light_dy_right = light_dl * (3.0/4.0)
# Create x, y and z for the lamp.
object_light_vec = Vector((light_dl,light_dy_right,light_dl))
light_xyz_vec = object_center_vec + object_light_vec
# Create the lamp
light_data = bpy.data.lights.new(name="A_light", type="SUN")
light_data.distance = 500.0
light_data.energy = 3.0
lamp = bpy.data.objects.new("A_light", light_data)
lamp.location = light_xyz_vec
bpy.context.collection.objects.link(lamp)
# Some settings for the World: a bit ambient occlusion
bpy.context.scene.world.light_settings.use_ambient_occlusion = True
bpy.context.scene.world.light_settings.ao_factor = 0.1
# Some properties for cycles
lamp.data.use_nodes = True
lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
lmp_P_BSDF.inputs['Strength'].default_value = 5
# Function, which draws the atoms of one type (balls). This is one
# dupliverts structure then.
# Return: the dupliverts structure
def draw_atoms_one_type(draw_all_atoms_type,
Ball_type,
Ball_azimuth,
Ball_zenith,
Ball_radius_factor,
object_center_vec,
collection_molecule):
# Create 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 subtracted. At the end
# the whole object is translated back to 'object_center_vec'.
atom_vertices.append(atom[2] - object_center_vec)
# IMPORTANT: First, we create a collection of the element, which contains
# the atoms (balls + mesh) AND the sticks! The definition dealing with the
# sticks will put the sticks inside this collection later on.
coll_element_name = atom[0] # the element name
# Create the new collection and ...
coll_element = bpy.data.collections.new(coll_element_name)
# ... link it to the collection, which contains all parts of the
# molecule.
collection_molecule.children.link(coll_element)
# Now, create a collection for the atoms, which includes the representative
# ball and the mesh.
coll_atom_name = atom[0] + "_atom"
# Create the new collection and ...
coll_atom = bpy.data.collections.new(coll_atom_name)
# ... link it to the collection, which contains all parts of the
# element (ball and mesh).
coll_element.children.link(coll_atom)
# 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] + "_mesh", atom_mesh)
# Link active object to the new collection
coll_atom.objects.link(new_atom_mesh)
# Now, build a representative sphere (atom).
if atom[0] == "Vacancy":
bpy.ops.mesh.primitive_cube_add(
align='WORLD', enter_editmode=False,
location=(0.0, 0.0, 0.0),
rotation=(0.0, 0.0, 0.0))
else:
# NURBS balls
if Ball_type == "0":
bpy.ops.surface.primitive_nurbs_surface_sphere_add(
align='WORLD', enter_editmode=False,
location=(0,0,0), rotation=(0.0, 0.0, 0.0))
# UV balls
elif Ball_type == "1":
bpy.ops.mesh.primitive_uv_sphere_add(
segments=Ball_azimuth, ring_count=Ball_zenith,
align='WORLD', enter_editmode=False,
location=(0,0,0), rotation=(0, 0, 0))
# Meta balls
elif Ball_type == "2":
bpy.ops.object.metaball_add(type='BALL', align='WORLD',
enter_editmode=False, location=(0, 0, 0),
rotation=(0, 0, 0))
ball = bpy.context.view_layer.objects.active
# Hide this ball because its appearance has no meaning. It is just the
# representative ball. The ball is visible at the vertices of the mesh.
# Rememmber, this is a dupliverts construct!
Clemens Barth
committed
# However, hiding does not work with meta balls!
if Ball_type == "0" or Ball_type == "1":
ball.hide_set(True)
# Scale up/down the ball radius.
ball.scale = (atom[3]*Ball_radius_factor,) * 3
if atom[0] == "Vacancy":
ball.name = atom[0] + "_cube"
else:
ball.name = atom[0] + "_ball"
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ball.active_material = atom[1]
ball.parent = new_atom_mesh
new_atom_mesh.instance_type = 'VERTS'
# The object is back translated to 'object_center_vec'.
new_atom_mesh.location = object_center_vec
# Note the collection where the ball was placed into.
coll_all = ball.users_collection
if len(coll_all) > 0:
coll_past = coll_all[0]
else:
coll_past = bpy.context.scene.collection
# Put the atom into the new collection 'atom' and ...
coll_atom.objects.link(ball)
# ... unlink the atom from the other collection.
coll_past.objects.unlink(ball)
return new_atom_mesh, coll_element
# Function, which draws the sticks with help of the dupliverts technique.
# Return: list of dupliverts structures.
def draw_sticks_dupliverts(all_atoms,
atom_all_types_list,
center,
all_sticks,
Stick_diameter,
Stick_sectors,
Stick_unit,
Stick_dist,
use_sticks_smooth,
use_sticks_color,
list_coll_elements):
dl = Stick_unit
if use_sticks_color == False:
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:
for repeat in range(stick.number):
atom1 = copy(all_atoms[stick.atom1-1].location)-center
atom2 = copy(all_atoms[stick.atom2-1].location)-center
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])
if sticks_list != []:
sticks_all_lists.append(sticks_list)
else:
sticks_list = []
for stick in all_sticks:
if stick.number > 3:
stick.number = 1
for repeat in range(stick.number):
atom1 = copy(all_atoms[stick.atom1-1].location)-center
atom2 = copy(all_atoms[stick.atom2-1].location)-center
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)
atom_object_list = []
# ... the sticks in the list can be drawn:
for stick_list in sticks_all_lists:
vertices = []
faces = []
i = 0
# What follows is school mathematics! :-)
for stick in stick_list:
dv = stick[2]
v1 = stick[1]
n = dv / dv.length
gamma = -n.dot(v1)
b = v1 + gamma * n
n_b = b / b.length
if use_sticks_color == True:
loops = int(ceil(dv.length / (2.0 * dl)))
else:
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
# Create a collection for the sticks, which includes the representative
# cylinders, cups and the mesh.
coll_name = stick[0][1:] + "_sticks"
# Create the collection and ...
coll = bpy.data.collections.new(coll_name)
# ... link it to the collection, which contains all parts of the
# element. 'stick[0][1:]' contains the name of the element!
for coll_element_from_list in list_coll_elements:
if stick[0][1:] in coll_element_from_list.name:
break
coll_element_from_list.children.link(coll)
# Build the mesh.
mesh = bpy.data.meshes.new("Sticks_"+stick[0][1:])
mesh.from_pydata(vertices, [], faces)
mesh.update()
new_mesh = bpy.data.objects.new(stick[0][1:]+"_sticks_mesh", mesh)
# Link active object to the new collection
coll.objects.link(new_mesh)
# Build the object.
# Get the cylinder from the 'build_stick' function.
object_stick = build_stick(Stick_diameter,
dl,
Stick_sectors,
stick[0][1:])
# Link active object to the new collection
coll.objects.link(object_stick[0])
coll.objects.link(object_stick[1])
# Hide these objects because their appearance has no meaning. They are
# just the representative objects. The cylinder and cups are visible at
# the vertices of the mesh. Rememmber, this is a dupliverts construct!
object_stick[0].hide_set(True)
object_stick[1].hide_set(True)
stick_cylinder = object_stick[0]
stick_cylinder.active_material = stick[3]
stick_cups = object_stick[1]
stick_cups.active_material = stick[3]
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# Smooth the cylinders.
if use_sticks_smooth == True:
bpy.ops.object.select_all(action='DESELECT')
stick_cylinder.select_set(True)
stick_cups.select_set(True)
bpy.ops.object.shade_smooth()
# Parenting the mesh to the cylinder.
stick_cylinder.parent = new_mesh
stick_cups.parent = new_mesh
new_mesh.instance_type = 'FACES'
new_mesh.location = center
atom_object_list.append(new_mesh)
# Return the list of dupliverts structures.
return atom_object_list
# Function, which draws the sticks with help of the skin and subdivision
# modifiers.
def draw_sticks_skin(all_atoms,
all_sticks,
Stick_diameter,
use_sticks_smooth,
sticks_subdiv_view,
sticks_subdiv_render,
coll_molecule):
# These counters are for the edges, in the shape [i,i+1].
i = 0
# This is the list of vertices, containing the atom position
# (vectors)).
stick_vertices = []
# This is the 'same' list, which contains not vector position of
# the atoms but their numbers. It is used to handle the edges.
stick_vertices_nr = []
# This is the list of edges.
stick_edges = []
# Go through the list of all sticks. For each stick do:
for stick in all_sticks:
# Each stick has two atoms = two vertices.
"""
[ 0,1 , 3,4 , 0,8 , 7,3]
[[0,1], [2,3], [4,5], [6,7]]
[ 0,1 , 3,4 , x,8 , 7,x] x:deleted
[[0,1], [2,3], [0,5], [6,2]]
"""
# Check, if the vertex (atom) is already in the vertex list.
# edge: [s1,s2]
FLAG_s1 = False
s1 = 0
for stick2 in stick_vertices_nr:
if stick2 == stick.atom1-1:
FLAG_s1 = True
break
s1 += 1
FLAG_s2 = False
s2 = 0
for stick2 in stick_vertices_nr:
if stick2 == stick.atom2-1: