[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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