# SPDX-License-Identifier: GPL-2.0-or-later 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 # DO NOT CHANGE 'CONECT', read below. 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 # sticks are NOT correctly imported. # 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:])) 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 # is done definition. 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 # 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 # 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. 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 length = lamp_xyz_vec.length # As a lamp we use a point source. lamp_data = bpy.data.lights.new(name="A_lamp", type="POINT") # We now determine the emission strength of the lamp. Note that the # intensity depends on 1/r^2. For this we use a value of 100000.0 at a # distance of 58. This value was determined manually inside Blender. lamp_data.energy = 500000.0 * ( (length * length) / (58.0 * 58.0) ) lamp = bpy.data.objects.new("A_lamp", lamp_data) lamp.location = lamp_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 # 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! # 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" 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.use_nodes = True mat_P_BSDF = stick_material.node_tree.nodes['Principled BSDF'] mat_P_BSDF.inputs['Base Color'].default_value = 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! :-) We construct equidistant # planes, on which the stcik sections (cylinders) are perpendicular on. 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): # The plane, which is normal to the length of the cylinder, # will have a 1/100 of the stick diameter. => When decreasing # the size of the stick diameter, the plane will not be visible. f = 0.01 g = v1 - n * dl / 2.0 - n * dl * j p1 = g + n_b * Stick_diameter * f p2 = g - n_b * Stick_diameter * f p3 = g - n_b.cross(n) * Stick_diameter * f p4 = g + n_b.cross(n) * Stick_diameter * f 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. stick_cylinder, stick_cups = build_stick(Stick_diameter, dl, Stick_sectors, stick[0][1:]) # Link active object to the new collection. coll.objects.link(stick_cylinder) coll.objects.link(stick_cups) # Assign the material. stick_cylinder.active_material = stick[3] stick_cups.active_material = stick[3] # 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() # 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! stick_cylinder.hide_set(True) stick_cups.hide_set(True) # 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: FLAG_s2 = True break s2 += 1 # If the vertex (atom) is not yet in the vertex list: # append the number of atom and the vertex to the two lists. # For the first atom: if FLAG_s1 == False: atom1 = copy(all_atoms[stick.atom1-1].location) stick_vertices.append(atom1) stick_vertices_nr.append(stick.atom1-1) # For the second atom: if FLAG_s2 == False: atom2 = copy(all_atoms[stick.atom2-1].location) stick_vertices.append(atom2) stick_vertices_nr.append(stick.atom2-1) # Build the edges: # If both vertices (atoms) were not in the lists, then # the edge is simply [i,i+1]. These are two new vertices # (atoms), so increase i by 2. if FLAG_s1 == False and FLAG_s2 == False: stick_edges.append([i,i+1]) i += 2 # Both vertices (atoms) were already in the list, so then # use the vertices (atoms), which already exist. They are # at positions s1 and s2. if FLAG_s1 == True and FLAG_s2 == True: stick_edges.append([s1,s2]) # The following two if cases describe the situation that # only one vertex (atom) was in the list. Since only ONE # new vertex was added, increase i by one. if FLAG_s1 == True and FLAG_s2 == False: stick_edges.append([s1,i]) i += 1 if FLAG_s1 == False and FLAG_s2 == True: stick_edges.append([i,s2]) i += 1 # Build the mesh of the sticks stick_mesh = bpy.data.meshes.new("Mesh_sticks") stick_mesh.from_pydata(stick_vertices, stick_edges, []) stick_mesh.update() new_stick_mesh = bpy.data.objects.new("Sticks", stick_mesh) # Link the active mesh to the molecule collection coll_molecule.objects.link(new_stick_mesh) # Apply the skin modifier. new_stick_mesh.modifiers.new(name="Sticks_skin", type='SKIN') # Smooth the skin surface if this option has been chosen. new_stick_mesh.modifiers[0].use_smooth_shade = use_sticks_smooth # Apply the Subdivision modifier. new_stick_mesh.modifiers.new(name="Sticks_subsurf", type='SUBSURF') # Options: choose the levels new_stick_mesh.modifiers[1].levels = sticks_subdiv_view new_stick_mesh.modifiers[1].render_levels = sticks_subdiv_render stick_material = bpy.data.materials.new(ELEMENTS[-1].name) stick_material.use_nodes = True mat_P_BSDF = stick_material.node_tree.nodes['Principled BSDF'] mat_P_BSDF.inputs['Base Color'].default_value = ELEMENTS[-1].color new_stick_mesh.active_material = stick_material # This is for putting the radius of the sticks onto # the desired value 'Stick_diameter' bpy.context.view_layer.objects.active = new_stick_mesh # EDIT mode bpy.ops.object.mode_set(mode='EDIT', toggle=False) bm = bmesh.from_edit_mesh(new_stick_mesh.data) bpy.ops.mesh.select_all(action='DESELECT') # Select all vertices for v in bm.verts: v.select = True # This is somewhat a factor for the radius. r_f = 4.0 # Apply operator 'skin_resize'. bpy.ops.transform.skin_resize( value=( Stick_diameter * r_f, Stick_diameter * r_f, Stick_diameter * r_f, ), constraint_axis=(False, False, False), orient_type='GLOBAL', mirror=False, use_proportional_edit=False, snap=False, snap_target='CLOSEST', snap_point=(0, 0, 0), snap_align=False, snap_normal=(0, 0, 0), release_confirm=False, ) # Back to the OBJECT mode. bpy.ops.object.mode_set(mode='OBJECT', toggle=False) return new_stick_mesh # Draw the sticks the normal way: connect the atoms by simple cylinders. # Two options: 1. single cylinders parented to an empty # 2. one single mesh object def draw_sticks_normal(all_atoms, all_sticks, center, Stick_diameter, Stick_sectors, use_sticks_smooth, use_sticks_one_object, use_sticks_one_object_nr, coll_molecule): stick_material = bpy.data.materials.new(ELEMENTS[-1].name) stick_material.use_nodes = True mat_P_BSDF = stick_material.node_tree.nodes['Principled BSDF'] mat_P_BSDF.inputs['Base Color'].default_value = ELEMENTS[-1].color up_axis = Vector([0.0, 0.0, 1.0]) # For all sticks, do ... list_group = [] list_group_sub = [] counter = 0 for stick in all_sticks: # The vectors of the two atoms atom1 = all_atoms[stick.atom1-1].location-center atom2 = all_atoms[stick.atom2-1].location-center # Location location = (atom1 + atom2) * 0.5 # The difference of both vectors v = (atom2 - atom1) # Angle with respect to the z-axis angle = v.angle(up_axis, 0) # Cross-product between v and the z-axis vector. It is the # vector of rotation. axis = up_axis.cross(v) # Calculate Euler angles euler = Matrix.Rotation(angle, 4, axis).to_euler() # Create stick stick = bpy.ops.mesh.primitive_cylinder_add(vertices=Stick_sectors, radius=Stick_diameter, depth=v.length, end_fill_type='NGON', align='WORLD', enter_editmode=False, location=location, rotation=(0, 0, 0)) # Put the stick into the scene ... stick = bpy.context.view_layer.objects.active # ... and rotate the stick. stick.rotation_euler = euler # ... and name stick.name = "Stick_Cylinder" counter += 1 # Smooth the cylinder. if use_sticks_smooth == True: bpy.ops.object.select_all(action='DESELECT') stick.select_set(True) bpy.ops.object.shade_smooth() list_group_sub.append(stick) if use_sticks_one_object == True: if counter == use_sticks_one_object_nr: bpy.ops.object.select_all(action='DESELECT') for stick in list_group_sub: stick.select_set(True) bpy.ops.object.join() list_group.append(bpy.context.view_layer.objects.active) bpy.ops.object.select_all(action='DESELECT') list_group_sub = [] counter = 0 else: # Material ... stick.active_material = stick_material if use_sticks_one_object == True: bpy.ops.object.select_all(action='DESELECT') for stick in list_group_sub: stick.select_set(True) bpy.ops.object.join() list_group.append(bpy.context.view_layer.objects.active) bpy.ops.object.select_all(action='DESELECT') for group in list_group: group.select_set(True) bpy.ops.object.join() bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY', center='MEDIAN') sticks = bpy.context.view_layer.objects.active sticks.active_material = stick_material sticks.location += center # Collections # =========== # Note the collection where the sticks were placed into. coll_all = sticks.users_collection if len(coll_all) > 0: coll_past = coll_all[0] else: coll_past = bpy.context.scene.collection # Link the sticks with the collection of the molecule ... coll_molecule.objects.link(sticks) # ... and unlink them from the collection it has been before. coll_past.objects.unlink(sticks) return sticks else: # Here we use an empty ... bpy.ops.object.empty_add(type='ARROWS', align='WORLD', location=(0, 0, 0), rotation=(0, 0, 0)) sticks_empty = bpy.context.view_layer.objects.active sticks_empty.name = "A_sticks_empty" # ... that is parent to all sticks. With this, we can better move # all sticks if necessary. for stick in list_group_sub: stick.parent = sticks_empty sticks_empty.location += center # Collections # =========== # Create a collection that will contain all sticks + the empty and ... coll = bpy.data.collections.new("Sticks") # ... link it to the collection, which contains all parts of the # molecule. coll_molecule.children.link(coll) # Now, create a collection that only contains the sticks and ... coll_cylinder = bpy.data.collections.new("Sticks_cylinders") # ... link it to the collection, which contains the sticks and empty. coll.children.link(coll_cylinder) # Note the collection where the empty was placed into, ... coll_all = sticks_empty.users_collection if len(coll_all) > 0: coll_past = coll_all[0] else: coll_past = bpy.context.scene.collection # ... link the empty with the new collection ... coll.objects.link(sticks_empty) # ... and unlink it from the old collection where it has been before. coll_past.objects.unlink(sticks_empty) # Note the collection where the cylinders were placed into, ... coll_all = list_group_sub[0].users_collection if len(coll_all) > 0: coll_past = coll_all[0] else: coll_past = bpy.context.scene.collection for stick in list_group_sub: # ... link each stick with the new collection ... coll_cylinder.objects.link(stick) # ... and unlink it from the old collection. coll_past.objects.unlink(stick) return sticks_empty # ----------------------------------------------------------------------------- # The main routine def import_pdb(Ball_type, Ball_azimuth, Ball_zenith, Ball_radius_factor, radiustype, Ball_distance_factor, use_sticks, use_sticks_type, sticks_subdiv_view, sticks_subdiv_render, use_sticks_color, use_sticks_smooth, use_sticks_bonds, use_sticks_one_object, use_sticks_one_object_nr, Stick_unit, Stick_dist, Stick_sectors, Stick_diameter, put_to_center, use_camera, use_light, 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) # ------------------------------------------------------------------------ # 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.diffuse_color = atom_type[2] material.use_nodes = True mat_P_BSDF = material.node_tree.nodes['Principled BSDF'] mat_P_BSDF.inputs['Base Color'].default_value = atom_type[2] material.name = atom_type[0] 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. # The vacancy is represented by a transparent cube. if atom.name == "Vacancy": # For cycles and eevee. material.use_nodes = True mat_P_BSDF = material.node_tree.nodes['Principled BSDF'] mat_P_BSDF.inputs['Metallic'].default_value = 0.1 mat_P_BSDF.inputs['Specular'].default_value = 0.15 mat_P_BSDF.inputs['Roughness'].default_value = 0.05 mat_P_BSDF.inputs['Clearcoat Roughness'].default_value = 0.37 mat_P_BSDF.inputs['IOR'].default_value = 0.8 mat_P_BSDF.inputs['Transmission'].default_value = 0.6 mat_P_BSDF.inputs['Transmission Roughness'].default_value = 0.0 mat_P_BSDF.inputs['Alpha'].default_value = 0.5 # Some additional stuff for eevee. material.blend_method = 'HASHED' material.shadow_method = 'HASHED' material.use_backface_culling = False # The atom gets its properties. atom.material = material # ------------------------------------------------------------------------ # READING DATA OF STICKS all_sticks = read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms) # # 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 subtracted). if put_to_center == True: 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 subtracted for atom in all_atoms: atom.location -= sum_vec # ------------------------------------------------------------------------ # SCALING # 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 = max(object_size_vec).length # ------------------------------------------------------------------------ # 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], ...] # 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", ...] draw_all_atoms = [] for atom_type in atom_all_types_list: # Don't draw 'TER atoms'. if atom_type[0] == "TER": continue # This is the draw list, which contains all atoms of one type (e.g. # all hydrogens) ... 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, atom.location, atom.radius]) # Now append the atom list to the list of all types of atoms draw_all_atoms.append(draw_all_atoms_type) # ------------------------------------------------------------------------ # COLLECTION # Before we start to draw the atoms and sticks, we first create a # collection for the molecule. All atoms (balls) and sticks (cylinders) # are put into this collection. coll_molecule_name = os.path.basename(filepath_pdb) scene = bpy.context.scene coll_molecule = bpy.data.collections.new(coll_molecule_name) scene.collection.children.link(coll_molecule) # ------------------------------------------------------------------------ # DRAWING THE ATOMS bpy.ops.object.select_all(action='DESELECT') list_coll_elements = [] # For each list of atoms of ONE type (e.g. Hydrogen) for draw_all_atoms_type in draw_all_atoms: atom_mesh, coll_element = draw_atoms_one_type(draw_all_atoms_type, Ball_type, Ball_azimuth, Ball_zenith, Ball_radius_factor, object_center_vec, coll_molecule) atom_object_list.append(atom_mesh) list_coll_elements.append(coll_element) # ------------------------------------------------------------------------ # DRAWING THE STICKS: cylinders in a dupliverts structure if use_sticks == True and use_sticks_type == '0' and all_sticks != []: sticks = draw_sticks_dupliverts(all_atoms, atom_all_types_list, object_center_vec, all_sticks, Stick_diameter, Stick_sectors, Stick_unit, Stick_dist, use_sticks_smooth, use_sticks_color, list_coll_elements) for stick in sticks: atom_object_list.append(stick) # ------------------------------------------------------------------------ # DRAWING THE STICKS: skin and subdivision modifier if use_sticks == True and use_sticks_type == '1' and all_sticks != []: sticks = draw_sticks_skin(all_atoms, all_sticks, Stick_diameter, use_sticks_smooth, sticks_subdiv_view, sticks_subdiv_render, coll_molecule) atom_object_list.append(sticks) # ------------------------------------------------------------------------ # DRAWING THE STICKS: normal cylinders if use_sticks == True and use_sticks_type == '2' and all_sticks != []: sticks = draw_sticks_normal(all_atoms, all_sticks, object_center_vec, Stick_diameter, Stick_sectors, use_sticks_smooth, use_sticks_one_object, use_sticks_one_object_nr, coll_molecule) atom_object_list.append(sticks) # ------------------------------------------------------------------------ # CAMERA and LIGHT SOURCES camera_light_source(use_camera, use_light, object_center_vec, object_size) # ------------------------------------------------------------------------ # SELECT ALL LOADED OBJECTS bpy.ops.object.select_all(action='DESELECT') obj = None for obj in atom_object_list: obj.select_set(True) # activate the last selected object if obj: bpy.context.view_layer.objects.active = obj