diff options
| author | Campbell Barton <ideasman42@gmail.com> | 2011-12-02 02:34:41 +0400 |
|---|---|---|
| committer | Campbell Barton <ideasman42@gmail.com> | 2011-12-02 02:34:41 +0400 |
| commit | 09a798bb6b371bc3f7fb3228b285bfbb8a867dda (patch) | |
| tree | c13d0e9977370a9faaa5c594204b967c1ad835b3 /io_mesh_pdb/import_pdb.py | |
| parent | dd829de739390b6d21910941d5ed9670fa112c37 (diff) | |
Moving PDB importer into trunk,
thanks to Clemens Barth for making all edits requested to have this in an acceptable quality level.
There are a few todo's still but at this point the script is better then the previous PDB importer in trink, so better to include this in the 2.61 release.
[[Split portion of a mixed commit.]]
Diffstat (limited to 'io_mesh_pdb/import_pdb.py')
| -rw-r--r-- | io_mesh_pdb/import_pdb.py | 1146 |
1 files changed, 1146 insertions, 0 deletions
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py new file mode 100644 index 00000000..eff89985 --- /dev/null +++ b/io_mesh_pdb/import_pdb.py @@ -0,0 +1,1146 @@ +# ##### 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 ##### + +# +# +# Authors : Clemens Barth (Blendphys@root-1.de), ... +# +# Homepage(Wiki) : http://development.root-1.de/Atomic_Blender.php +# Tracker : http://projects.blender.org/tracker/index.php?func=detail&aid=29226&group_id=153&atid=467 +# +# Start of project : 2011-08-31 by Clemens Barth +# First publication in Blender : 2011-11-11 +# Last modified : 2011-12-01 +# +# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon, +# dairin0d, PKHG, Valter, etc +# + +import bpy +import io +import sys +import math +import os +from math import pi, cos, sin +from mathutils import Vector, Matrix + +# These are variables, which contain the name of the PDB file and +# the path of the PDB file. +# They are used almost everywhere, which is the reason why they +# should stay global. First, they are empty and get 'filled' directly +# after having chosen the PDB file (see 'class LoadPDB' further below). + +ATOM_PDB_FILEPATH = "" + +# Some string stuff for the console. +ATOM_PDB_STRING = "Atomic Blender\n===================" + + +# ----------------------------------------------------------------------------- +# 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) + +ATOM_PDB_ELEMENTS_DEFAULT = ( +( 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 (CLASS_atom_pdb_Elements). 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. +ATOM_PDB_ELEMENTS = [] + +# This is the class, which stores the properties for one element. +class CLASS_atom_pdb_Elements: + 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 CLASS_atom_pdb_atom: + 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 CLASS_atom_pdb_stick: + def __init__(self, atom1, atom2): + self.atom1 = atom1 + self.atom2 = atom2 + + +# ----------------------------------------------------------------------------- +# Some small routines + + +# Routine which produces a cylinder. All is somewhat easy to undertsand. +def DEF_atom_pdb_build_stick(radius, length, sectors): + + vertices = [] + faces = [] + + dphi = 2.0 * pi/(float(sectors)-1) + + # Vertices + vertices_top = [Vector((0,0,length / 2.0))] + vertices_bottom = [Vector((0,0,-length / 2.0))] + 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 + + # Top facets + 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) + faces.append(face_top) + faces.append(face_bottom) + + # Side facets + for i in range(sectors-1): + if i == sectors-2: + faces.append( [i+1, 1, 1+sectors, i+1+sectors] ) + else: + faces.append( [i+1, i+2, i+2+sectors, i+1+sectors] ) + + # Build the mesh + cylinder = bpy.data.meshes.new("Sticks_Cylinder") + cylinder.from_pydata(vertices, [], faces) + cylinder.update() + new_cylinder = bpy.data.objects.new("Sticks_Cylinder", cylinder) + bpy.context.scene.objects.link(new_cylinder) + + return new_cylinder + + +# This function measures the distance between two objects (atoms), +# which are active. +def DEF_atom_pdb_distance(): + + if len(bpy.context.selected_bases) > 1: + object_1 = bpy.context.selected_objects[0] + object_2 = bpy.context.selected_objects[1] + else: + return "N.A." + + dv = object_2.location - object_1.location + return str(dv.length) + + +# Routine to modify the radii via the type: +# pre-defined, atomic or van der Waals +# Explanations here are also valid for the next 3 DEFs. +def DEF_atom_pdb_radius_type(rtype,how): + + if how == "ALL_IN_LAYER": + + # Note all layers that are active. + layers = [] + for i in range(20): + if bpy.context.scene.layers[i] == True: + layers.append(i) + + # Put all objects, which are in the layers, into a list. + change_objects = [] + for obj in bpy.context.scene.objects: + for layer in layers: + if obj.layers[layer] == True: + change_objects.append(obj) + + # Consider all objects, which are in the list 'change_objects'. + for obj in change_objects: + if len(obj.children) != 0: + if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH": + for element in ATOM_PDB_ELEMENTS: + if element.name in obj.name: + obj.children[0].scale = (element.radii[int(rtype)], + element.radii[int(rtype)], + element.radii[int(rtype)]) + else: + if obj.type == "SURFACE" or obj.type == "MESH": + for element in ATOM_PDB_ELEMENTS: + if element.name in obj.name: + obj.scale = (element.radii[int(rtype)], + element.radii[int(rtype)], + element.radii[int(rtype)]) + + if how == "ALL_ACTIVE": + for obj in bpy.context.selected_objects: + if len(obj.children) != 0: + if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH": + for element in ATOM_PDB_ELEMENTS: + if element.name in obj.name: + obj.children[0].scale = (element.radii[int(rtype)], + element.radii[int(rtype)], + element.radii[int(rtype)]) + else: + if obj.type == "SURFACE" or obj.type == "MESH": + for element in ATOM_PDB_ELEMENTS: + if element.name in obj.name: + obj.scale = (element.radii[int(rtype)], + element.radii[int(rtype)], + element.radii[int(rtype)]) + + +# Routine to modify the radii in picometer of a specific type of atom +def DEF_atom_pdb_radius_pm(atomname, radius_pm, how): + + if how == "ALL_IN_LAYER": + + layers = [] + for i in range(20): + if bpy.context.scene.layers[i] == True: + layers.append(i) + + change_objects = [] + for obj in bpy.context.scene.objects: + for layer in layers: + if obj.layers[layer] == True: + change_objects.append(obj) + + for obj in change_objects: + if len(obj.children) != 0: + if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH": + if atomname in obj.name: + obj.children[0].scale = (radius_pm/100, + radius_pm/100, + radius_pm/100) + else: + if obj.type == "SURFACE" or obj.type == "MESH": + if atomname in obj.name: + obj.scale = (radius_pm/100, + radius_pm/100, + radius_pm/100) + + if how == "ALL_ACTIVE": + for obj in bpy.context.selected_objects: + if len(obj.children) != 0: + if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH": + if atomname in obj.name: + obj.children[0].scale = (radius_pm/100, + radius_pm/100, + radius_pm/100) + else: + if obj.type == "SURFACE" or obj.type == "MESH": + if atomname in obj.name: + obj.scale = (radius_pm/100, + radius_pm/100, + radius_pm/100) + + +# Routine to scale the radii of all atoms +def DEF_atom_pdb_radius_all(scale, how): + + if how == "ALL_IN_LAYER": + + layers = [] + for i in range(20): + if bpy.context.scene.layers[i] == True: + layers.append(i) + + change_objects = [] + for obj in bpy.context.scene.objects: + for layer in layers: + if obj.layers[layer] == True: + change_objects.append(obj) + + + for obj in change_objects: + if len(obj.children) != 0: + if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH": + if "Stick" not in obj.name: + obj.children[0].scale *= scale + else: + if obj.type == "SURFACE" or obj.type == "MESH": + if "Stick" not in obj.name: + obj.scale *= scale + + if how == "ALL_ACTIVE": + for obj in bpy.context.selected_objects: + if len(obj.children) != 0: + if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH": + if "Stick" not in obj.name: + obj.children[0].scale *= scale + else: + if obj.type == "SURFACE" or obj.type == "MESH": + if "Stick" not in obj.name: + obj.scale *= scale + + +# This reads a custom data file. +def DEF_atom_pdb_custom_datafile(path_datafile): + + if path_datafile == "": + return False + + path_datafile = bpy.path.abspath(path_datafile) + + if os.path.isfile(path_datafile) == False: + return False + + # The whole list gets deleted! We build it new. + ATOM_PDB_ELEMENTS[:] = [] + + # Read the data file, which contains all data + # (atom name, radii, colors, etc.) + data_file_p = io.open(path_datafile, "r") + + for line in data_file_p: + + if "Atom" in line: + + line = data_file_p.readline() + + # Number + line = data_file_p.readline() + number = line[19:-1] + # Name + line = data_file_p.readline() + name = line[19:-1] + # Short name + line = data_file_p.readline() + short_name = line[19:-1] + # Color + line = data_file_p.readline() + color_value = line[19:-1].split(',') + color = [float(color_value[0]), + float(color_value[1]), + float(color_value[2])] + # Used radius + line = data_file_p.readline() + radius_used = float(line[19:-1]) + # Atomic radius + line = data_file_p.readline() + radius_atomic = float(line[19:-1]) + # Van der Waals radius + line = data_file_p.readline() + radius_vdW = float(line[19:-1]) + + radii = [radius_used,radius_atomic,radius_vdW] + radii_ionic = [] + + element = CLASS_atom_pdb_Elements(number,name,short_name,color, + radii, radii_ionic) + + ATOM_PDB_ELEMENTS.append(element) + + data_file_p.close() + + return True + + +# ----------------------------------------------------------------------------- +# The main routine + + +def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith, + Ball_radius_factor,radiustype,Ball_distance_factor, + use_stick,Stick_sectors,Stick_diameter,put_to_center, + use_camera,use_lamp,path_datafile): + + # The list of all atoms as read from the PDB file. + all_atoms = [] + + # The list of all sticks. + all_sticks = [] + + # 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 + + ATOM_PDB_ELEMENTS[:] = [] + + for item in ATOM_PDB_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 = CLASS_atom_pdb_Elements(item[0],item[1],item[2],item[3], + radii,radii_ionic) + ATOM_PDB_ELEMENTS.append(li) + + + # ------------------------------------------------------------------------ + # READING DATA OF ATOMS + + + if DEF_atom_pdb_custom_datafile(path_datafile): + print("Custom data file is loaded.") + + # Open the file ... + ATOM_PDB_FILEPATH_p = io.open(ATOM_PDB_FILEPATH, "r") + + #Go to the line, in which "ATOM" or "HETATM" appears. + for line in ATOM_PDB_FILEPATH_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 + color = [0,0,0] + location = Vector((0,0,0)) + # Append the TER into the list. Material remains empty so far. + all_atoms.append(CLASS_atom_pdb_atom(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 ... + short_name = line[13:14] + if short_name.isupper() == True: + if line[14:15].islower() == True: + short_name = short_name + line[14:15] + else: + short_name = line[12:13] + if short_name.isupper() == True: + if line[13:14].islower() == True: + short_name = short_name + line[13:14] + # ... to here. + + # Go through all elements and find the element of the current atom. + FLAG_FOUND = False + for element in ATOM_PDB_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(ATOM_PDB_ELEMENTS[-3].radii[int(radiustype)]) + color = ATOM_PDB_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(ATOM_PDB_ELEMENTS[-2].radii[int(radiustype)]) + color = ATOM_PDB_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(CLASS_atom_pdb_atom(short_name, + name, + location, + radius, + color,[])) + + line = ATOM_PDB_FILEPATH_p.readline() + line = line[:-1] + + ATOM_PDB_FILEPATH_p.close() + # From above it can be clearly seen that j is now the number of all atoms. + Number_of_total_atoms = j + + + # ------------------------------------------------------------------------ + # 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 + + + # Open the PDB file again such that the file pointer is in the first + # line ... . Stupid, I know ... ;-) + ATOM_PDB_FILEPATH_p = io.open(ATOM_PDB_FILEPATH, "r") + + split_list = line.split(' ') + + # Go to the first entry + if "CONECT" not in split_list[0]: + for line in ATOM_PDB_FILEPATH_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 + + # 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 many 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 each_atom in atom_list[1:]: + + # The second, third, ... partner atom + atom2 = each_atom + + # 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(CLASS_atom_pdb_stick(atom1,atom2)) + Number_of_sticks += 1 + j += 1 + + line = ATOM_PDB_FILEPATH_p.readline() + line = line.rstrip() + + ATOM_PDB_FILEPATH_p.close() + # So far, all atoms and sticks 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). + + 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 substracted + 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 farest 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 math.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((math.sqrt(object_size) * camera_factor, + 0.0, + math.sqrt(object_size) * camera_factor)) + camera_xyz_vec = object_center_vec + object_camera_vec + + # Create the camera + current_layers=bpy.context.scene.layers + bpy.ops.object.camera_add(view_align=False, enter_editmode=False, + location=camera_xyz_vec, + rotation=(0.0, 0.0, 0.0), layers=current_layers) + # Some properties of the camera are changed. + camera = bpy.context.scene.objects.active + camera.name = "A_camera" + camera.data.name = "A_camera" + camera.data.lens = 45 + camera.data.clip_end = 500.0 + + # 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. + euler = Matrix.Rotation(angle, 4, axis_vec).to_euler() + camera.rotation_euler = euler + + # Rotate the camera around its axis by 90° such that we have a nice + # camera position and view onto the object. + bpy.ops.transform.rotate(value=(90.0*2*math.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) + + + # This does not work, I don't know why. + # + #for area in bpy.context.screen.areas: + # if area.type == 'VIEW_3D': + # area.spaces[0].region_3d.view_perspective = 'CAMERA' + + + # 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 % + # of the camera distance. It is set onto 50% (1/2) distance. + lamp_dl = math.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 + + # Create the lamp + current_layers=bpy.context.scene.layers + bpy.ops.object.lamp_add (type = 'POINT', view_align=False, + location=lamp_xyz_vec, + rotation=(0.0, 0.0, 0.0), + layers=current_layers) + # Some properties of the lamp are changed. + lamp = bpy.context.scene.objects.active + lamp.data.name = "A_lamp" + lamp.name = "A_lamp" + lamp.data.distance = 500.0 + lamp.data.energy = 3.0 + lamp.data.shadow_method = 'RAY_SHADOW' + + bpy.context.scene.world.light_settings.use_ambient_occlusion = True + bpy.context.scene.world.light_settings.ao_factor = 0.2 + + + # ------------------------------------------------------------------------ + # SOME OUTPUT ON THE CONSOLE + + + print() + print() + print() + print(ATOM_PDB_STRING) + print() + print("Total number of atoms : " + str(Number_of_total_atoms)) + print("Total number of sticks : " + str(Number_of_sticks)) + print("Center of object : ", object_center_vec) + print("Size of object : ", object_size) + print() + + + # ------------------------------------------------------------------------ + # 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: + + # 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) + + + # ------------------------------------------------------------------------ + # DRAWING THE ATOMS + + + # This is the number of all atoms which are put into the scene. + number_loaded_atoms = 0 + 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 + + if atom[0] == "Vacancy": + bpy.ops.mesh.primitive_cube_add( + view_align=False, enter_editmode=False, + location=(0.0, 0.0, 0.0), + rotation=(0.0, 0.0, 0.0), + layers=current_layers) + else: + # NURBS balls + if use_mesh == False: + bpy.ops.surface.primitive_nurbs_surface_sphere_add( + 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), + layers=current_layers) + + ball = bpy.context.scene.objects.active + ball.scale = (atom[3]*Ball_radius_factor, + atom[3]*Ball_radius_factor, + atom[3]*Ball_radius_factor) + + if atom[0] == "Vacancy": + ball.name = "Cube_"+atom[0] + else: + ball.name = "Ball (NURBS)_"+atom[0] + 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) + + print() + + + # ------------------------------------------------------------------------ + # DRAWING THE STICKS + + + if use_stick == True and all_sticks != []: + + # Create a new material with the corresponding color. The + # color is taken from the all_atom list, it is the last entry + # in the data file (index -1). + bpy.ops.object.material_slot_add() + stick_material = bpy.data.materials.new(ATOM_PDB_ELEMENTS[-1].name) + stick_material.diffuse_color = ATOM_PDB_ELEMENTS[-1].color + + vertices = [] + faces = [] + dl = 0.2 + + i = 0 + # For all sticks, do ... + for stick in all_sticks: + + # What follows is school mathematics! :-) + v1 = all_atoms[stick.atom2-1].location + v2 = all_atoms[stick.atom1-1].location + + dv = (v1 - v2) + + n = dv / dv.length + m = v1 - dv / 2.0 + + gamma = -n * v1 + b = v1 + gamma * n + n_b = b / b.length + + loops = int(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") + mesh.from_pydata(vertices, [], faces) + mesh.update() + new_mesh = bpy.data.objects.new("Sticks", mesh) + bpy.context.scene.objects.link(new_mesh) + + current_layers = bpy.context.scene.layers + stick_cylinder = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors) + + + stick_cylinder.active_material = stick_material + stick_cylinder.parent = new_mesh + new_mesh.dupli_type = 'FACES' + atom_object_list.append(new_mesh) + + + # ------------------------------------------------------------------------ + # SELECT ALL LOADED OBJECTS + bpy.ops.object.select_all(action='DESELECT') + obj = None + for obj in atom_object_list: + obj.select = True + + # activate the last selected object (perhaps another should be active?) + if obj: + bpy.context.scene.objects.active = obj + + print("\n\nAll atoms (%d) and sticks (%d) have been drawn - finished.\n\n" + % (Number_of_total_atoms,Number_of_sticks)) + + + return Number_of_total_atoms |