[Bf-extensions-cvs] SVN commit: /data/svn/bf-extensions [2644] contrib/py/scripts/addons/ io_import_pdb_atomic_blender.py:
Clemens Barth
barth at root-1.de
Tue Nov 22 19:20:22 CET 2011
Revision: 2644
http://projects.blender.org/scm/viewvc.php?view=rev&root=bf-extensions&revision=2644
Author: blendphys
Date: 2011-11-22 18:20:22 +0000 (Tue, 22 Nov 2011)
Log Message:
-----------
Changes have been done according to this
http://codereview.appspot.com/5433045/diff/1/io_import_pdb_atomic_blender.py
and the email with subject 'Anotations for atomic (issue 5433045)'
Cheers,
Blendphys.
Modified Paths:
--------------
contrib/py/scripts/addons/io_import_pdb_atomic_blender.py
Modified: contrib/py/scripts/addons/io_import_pdb_atomic_blender.py
===================================================================
--- contrib/py/scripts/addons/io_import_pdb_atomic_blender.py 2011-11-22 10:10:32 UTC (rev 2643)
+++ contrib/py/scripts/addons/io_import_pdb_atomic_blender.py 2011-11-22 18:20:22 UTC (rev 2644)
@@ -52,7 +52,10 @@
import io
import sys
import math
+import os
from mathutils import Vector, Matrix
+from bpy_extras.io_utils import ExportHelper
+from bpy.props import StringProperty, BoolProperty, EnumProperty
# These are variables, which contain the name of the PDB file and
@@ -77,102 +80,102 @@
# ... then the charge state: charge state, radius (ionic), charge state, radius (ionic), ... all charge states
# for any atom are listed, if existing.
-Data_all_atoms = [
-[ 1, "Hydrogen", "H", [ 0.0, 0.0, 1.0], 0.32, 0.32, 0.32 , -1 , 1.54 ],
-[ 2, "Helium", "He", [ 0.20, 0.56, 0.20], 0.93, 0.93, 0.93 , 1 , 0.68 ],
-[ 3, "Beryllium", "Be", [ 0.44, 0.72, 0.30], 0.90, 0.90, 0.90 , 1 , 0.44 , 2 , 0.35 ],
-[ 4, "Boron", "B", [ 1.0, 1.0, 1.0], 0.82, 0.82, 0.82 , 1 , 0.35 , 3 , 0.23 ],
-[ 5, "Carbon", "C", [ 0.0, 0.0, 0.0], 0.77, 0.77, 0.77 , -4 , 2.60 , 4 , 0.16 ],
-[ 6, "Nitrogen", "N", [ 0.0, 0.0, 1.0], 0.75, 0.75, 0.75 , -3 , 1.71 , 1 , 0.25 , 3 , 0.16 , 5 , 0.13 ],
-[ 7, "Oxygen", "O", [ 1.0, 0.0, 0.0], 0.73, 0.73, 0.73 , -2 , 1.32 , -1 , 1.76 , 1 , 0.22 , 6 , 0.09 ],
-[ 8, "Fluorine", "F", [ 0.0, 1.0, 0.0], 0.72, 0.72, 0.72 , -1 , 1.33 , 7 , 0.08 ],
-[ 9, "Neon", "Ne", [ 0.53, 0.60, 0.52], 0.71, 0.71, 0.71 , 1 , 1.12 ],
-[10, "Sodium", "Na", [ 0.0, 0.0, 1.0], 1.54, 1.54, 1.54 , 1 , 0.97 ],
-[11, "Magnesium", "Mg", [ 1.0, 1.0, 1.0], 1.36, 1.36, 1.36 , 1 , 0.82 , 2 , 0.66 ],
-[12, "Aluminium", "Al", [ 0.70, 0.2, 0.62], 1.18, 1.18, 1.18 , 3 , 0.51 ],
-[13, "Silicon", "Si", [ 0.65, 0.64, 0.27], 1.11, 1.11, 1.11 , -4 , 2.71 , -1 , 3.84 , 1 , 0.65 , 4 , 0.42 ],
-[14, "Phosphorus", "P", [ 1.0, 1.0, 0.0], 1.06, 1.06, 1.06 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ],
-[15, "Sulfur", "S", [ 1.0, 1.0, 0.50], 1.02, 1.02, 1.02 , -2 , 1.84 , 2 , 2.19 , 4 , 0.37 , 6 , 0.30 ],
-[16, "Chlorine", "Cl", [ 0.0, 1.0, 0.0], 0.99, 0.99, 0.99 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ],
-[17, "Argon", "Ar", [ 0.31, 0.32, 0.74], 0.98, 0.98, 0.98 , 1 , 1.54 ],
-[18, "Potassium", "K", [ 0.81, 0.23, 0.42], 2.03, 2.03, 2.03 , 1 , 0.81 ],
-[19, "Calcium", "Ca", [ 1.0, 1.0, 1.0], 1.74, 1.74, 1.74 , 1 , 1.18 , 2 , 0.99 ],
-[20, "Scandium", "Sc", [ 0.66, 0.44, 0.31], 1.44, 1.44, 1.44 , 3 , 0.73 ],
-[21, "Titanium", "Ti", [ 0.27, 0.53, 0.68], 1.32, 1.32, 1.32 , 1 , 0.96 , 2 , 0.94 , 3 , 0.76 , 4 , 0.68 ],
-[22, "Vanadium", "V", [ 0.27, 0.24, 0.63], 1.22, 1.22, 1.22 , 2 , 0.88 , 3 , 0.74 , 4 , 0.63 , 5 , 0.59 ],
-[23, "Chromium", "Cr", [ 0.80, 0.28, 0.81], 1.18, 1.18, 1.18 , 1 , 0.81 , 2 , 0.89 , 3 , 0.63 , 6 , 0.52 ],
-[24, "Manganese", "Mn", [ 0.75, 0.35, 0.55], 1.17, 1.17, 1.17 , 2 , 0.80 , 3 , 0.66 , 4 , 0.60 , 7 , 0.46 ],
-[25, "Iron", "Fe", [ 1.0, 0.0, 0.0], 1.17, 1.17, 1.17 , 2 , 0.74 , 3 , 0.64 ],
-[26, "Cobalt", "Co", [ 0.27, 0.21, 0.75], 1.16, 1.16, 1.16 , 2 , 0.72 , 3 , 0.63 ],
-[27, "Nickel", "Ni", [ 0.43, 0.36, 0.86], 1.15, 1.15, 1.15 , 2 , 0.69 ],
-[28, "Copper", "Cu", [ 0.60, 0.0, 0.0], 1.17, 1.17, 1.17 , 1 , 0.96 , 2 , 0.72 ],
-[29, "Zinc", "Zn", [ 0.42, 0.36, 0.45], 1.25, 1.25, 1.25 , 1 , 0.88 , 2 , 0.74 ],
-[30, "Gallium", "Ga", [ 0.63, 0.72, 0.33], 1.26, 1.26, 1.26 , 1 , 0.81 , 3 , 0.62 ],
-[31, "Germanium", "Ge", [ 0.42, 0.75, 0.30], 1.22, 1.22, 1.22 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ],
-[32, "Arsenic", "As", [ 0.39, 0.77, 0.25], 1.20, 1.20, 1.20 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ],
-[33, "Selenium", "Se", [ 0.95, 0.27, 0.90], 1.16, 1.16, 1.16 , -2 , 1.91 , -1 , 2.32 , 1 , 0.66 , 4 , 0.50 , 6 , 0.42 ],
-[34, "Bromine", "Br", [ 0.0, 0.49, 0.0], 1.14, 1.14, 1.14 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ],
-[35, "Krypton", "Kr", [ 0.22, 0.43, 0.19], 1.31, 1.31, 1.31 , 1 , 1.47 ],
-[36, "Strontium", "Sr", [ 1.0, 1.0, 1.0], 1.91, 1.91, 1.91 , 2 , 1.12 ],
-[37, "Yttrium", "Y", [ 1.0, 1.0, 1.0], 1.62, 1.62, 1.62 , 3 , 0.89 ],
-[38, "Zirconium", "Zr", [ 1.0, 1.0, 1.0], 1.45, 1.45, 1.45 , 1 , 1.09 , 4 , 0.79 ],
-[39, "Niobium", "Nb", [ 1.0, 1.0, 1.0], 1.34, 1.34, 1.34 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ],
-[40, "Molybdenum", "Mo", [ 1.0, 1.0, 1.0], 1.30, 1.30, 1.30 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ],
-[41, "Technetium", "Tc", [ 1.0, 1.0, 1.0], 1.27, 1.27, 1.27 , 7 , 0.97 ],
-[42, "Ruthenium", "Ru", [ 1.0, 1.0, 1.0], 1.25, 1.25, 1.25 , 4 , 0.67 ],
-[43, "Rhodium", "Rh", [ 1.0, 1.0, 1.0], 1.25, 1.25, 1.25 , 3 , 0.68 ],
-[44, "Palladium", "Pd", [ 1.0, 1.0, 1.0], 1.28, 1.28, 1.28 , 2 , 0.80 , 4 , 0.65 ],
-[45, "Silver", "Ag", [ 1.0, 1.0, 1.0], 1.34, 1.34, 1.34 , 1 , 1.26 , 2 , 0.89 ],
-[46, "Cadmium", "Cd", [ 1.0, 1.0, 1.0], 1.48, 1.48, 1.48 , 1 , 1.14 , 2 , 0.97 ],
-[47, "Indium", "In", [ 1.0, 1.0, 1.0], 1.44, 1.44, 1.44 , 3 , 0.81 ],
-[48, "Tin", "Sn", [ 1.0, 1.0, 1.0], 1.41, 1.41, 1.41 , -4 , 2.94 , -1 , 3.70 , 2 , 0.93 , 4 , 0.71 ],
-[49, "Antimony", "Sb", [ 1.0, 1.0, 1.0], 1.40, 1.40, 1.40 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ],
-[50, "Tellurium", "Te", [ 1.0, 1.0, 1.0], 1.36, 1.36, 1.36 , -2 , 2.11 , -1 , 2.50 , 1 , 0.82 , 4 , 0.70 , 6 , 0.56 ],
-[51, "Iodine", "I", [ 0.0, 0.49, 0.49], 1.33, 1.33, 1.33 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ],
-[52, "Xenon", "Xe", [ 1.0, 1.0, 1.0], 1.31, 1.31, 1.31 , 1 , 1.67 ],
-[53, "Barium", "Ba", [ 1.0, 1.0, 1.0], 1.98, 1.98, 1.98 , 1 , 1.53 , 2 , 1.34 ],
-[54, "Lanthanum", "La", [ 1.0, 1.0, 1.0], 1.69, 1.69, 1.69 , 1 , 1.39 , 3 , 1.06 ],
-[55, "Cerium", "Ce", [ 1.0, 1.0, 1.0], 1.65, 1.65, 1.65 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ],
-[56, "Praseodymium", "Pr", [ 1.0, 1.0, 1.0], 1.65, 1.65, 1.65 , 3 , 1.01 , 4 , 0.90 ],
-[57, "Neodymium", "Nd", [ 1.0, 1.0, 1.0], 1.64, 1.64, 1.64 , 3 , 0.99 ],
-[58, "Promethium", "Pm", [ 1.0, 1.0, 1.0], 1.63, 1.63, 1.63 , 3 , 0.97 ],
-[59, "Samarium", "Sm", [ 1.0, 1.0, 1.0], 1.62, 1.62, 1.62 , 3 , 0.96 ],
-[60, "Europium", "Eu", [ 1.0, 1.0, 1.0], 1.85, 1.85, 1.85 , 2 , 1.09 , 3 , 0.95 ],
-[61, "Gadolinium", "Gd", [ 1.0, 1.0, 1.0], 1.61, 1.61, 1.61 , 3 , 0.93 ],
-[62, "Terbium", "Tb", [ 1.0, 1.0, 1.0], 1.59, 1.59, 1.59 , 3 , 0.92 , 4 , 0.84 ],
-[63, "Dysprosium", "Dy", [ 1.0, 1.0, 1.0], 1.59, 1.59, 1.59 , 3 , 0.90 ],
-[64, "Holmium", "Ho", [ 1.0, 1.0, 1.0], 1.58, 1.58, 1.58 , 3 , 0.89 ],
-[65, "Erbium", "Er", [ 0.48, 0.48, 0.48], 1.57, 1.57, 1.57 , 3 , 0.88 ],
-[66, "Thulium", "Tm", [ 1.0, 1.0, 1.0], 1.56, 1.56, 1.56 , 3 , 0.87 ],
-[67, "Ytterbium", "Yb", [ 1.0, 1.0, 1.0], 1.74, 1.74, 1.74 , 2 , 0.93 , 3 , 0.85 ],
-[68, "Lutetium", "Lu", [ 1.0, 1.0, 1.0], 1.56, 1.56, 1.56 , 3 , 0.85 ],
-[69, "Hafnium", "Hf", [ 1.0, 1.0, 1.0], 1.44, 1.44, 1.44 , 4 , 0.78 ],
-[70, "Tantalum", "Ta", [ 1.0, 1.0, 1.0], 1.34, 1.34, 1.34 , 5 , 0.68 ],
-[71, "Tungsten", "W", [ 1.0, 1.0, 1.0], 1.30, 1.30, 1.30 , 4 , 0.70 , 6 , 0.62 ],
-[72, "Rhenium", "Re", [ 1.0, 1.0, 1.0], 1.28, 1.28, 1.28 , 4 , 0.72 , 7 , 0.56 ],
-[73, "Osmium", "Os", [ 1.0, 1.0, 1.0], 1.26, 1.26, 1.26 , 4 , 0.88 , 6 , 0.69 ],
-[74, "Iridium", "Ir", [ 1.0, 1.0, 1.0], 1.27, 1.27, 1.27 , 4 , 0.68 ],
-[75, "Platinium", "Pt", [ 1.0, 1.0, 1.0], 1.30, 1.30, 1.30 , 2 , 0.80 , 4 , 0.65 ],
-[76, "Gold", "Au", [ 1.0, 1.0, 1.0], 1.34, 1.34, 1.34 , 1 , 1.37 , 3 , 0.85 ],
-[77, "Mercury", "Hg", [ 1.0, 1.0, 1.0], 1.49, 1.49, 1.49 , 1 , 1.27 , 2 , 1.10 ],
-[78, "Thallium", "Tl", [ 1.0, 1.0, 1.0], 1.48, 1.48, 1.48 , 1 , 1.47 , 3 , 0.95 ],
-[79, "Lead", "Pb", [ 0.49, 0.49, 0.49], 1.47, 1.47, 1.47 , 2 , 1.20 , 4 , 0.84 ],
-[80, "Bismuth", "Bi", [ 1.0, 1.0, 1.0], 1.46, 1.46, 1.46 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ],
-[81, "Polonium", "Po", [ 1.0, 1.0, 1.0], 1.46, 1.46, 1.46 , 6 , 0.67 ],
-[82, "Astatine", "At", [ 1.0, 1.0, 1.0], 1.45, 1.45, 1.45 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ],
-[83, "Radon", "Rn", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 , 1 , 1.80 ],
-[84, "Radium", "Ra", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 , 2 , 1.43 ],
-[85, "Actinium", "Ac", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 , 3 , 1.18 ],
-[86, "Thorium", "Th", [ 1.0, 1.0, 1.0], 1.65, 1.65, 1.65 , 4 , 1.02 ],
-[87, "Protactinium", "Pa", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 , 3 , 1.13 , 4 , 0.98 , 5 , 0.89 ],
-[88, "Uranium", "U", [ 1.0, 1.0, 1.0], 1.42, 1.42, 1.42 , 4 , 0.97 , 6 , 0.80 ],
-[89, "Neptunium", "Np", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 , 3 , 1.10 , 4 , 0.95 , 7 , 0.71 ],
-[90, "Plutonium", "Pu", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ],
-[91, "Americium", "Am", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ],
-[92, "Curium", "Cm", [ 1.0, 1.0, 1.0], 1.00, 1.00, 1.00 ],
-[93, "Vacancy", "Vac", [ 0.5, 0.5, 0.5], 1.00, 0.00, 0.00],
@@ Diff output truncated at 10240 characters. @@
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