[Bf-extensions-cvs] SVN commit: /data/svn/bf-extensions [2670] contrib/py/scripts/addons:
Clemens Barth
barth at root-1.de
Sun Nov 27 16:28:16 CET 2011
Revision: 2670
http://projects.blender.org/scm/viewvc.php?view=rev&root=bf-extensions&revision=2670
Author: blendphys
Date: 2011-11-27 15:28:11 +0000 (Sun, 27 Nov 2011)
Log Message:
-----------
Dear all.
Yet again an overall polishing of my script. I'm sorry but there are lots
of changes in the code and treatment of the structures. However, the script is
much more convenient now.
Basic changes
=============
1. I removed my first loading procedure, which has taken simply too much time
for loading a many-atom scenario. Only the dupliverts technique is used now.
2. Ideasman told me that care must be taken when changing the properties of
objects. For instance, the objects in other layers or scenes should not be
modified. Following the advices, I was dealing with this issue.
1. One can now change the radii either of all objects, which are activated
(marked) in the current scene and layer.
2. Or one can change the radii of all atoms in one scene and in all layers
which are active. This is useful since one wishes to do that from time
to time.
3. The type of radii can be changed: pre-defined radii (pre-defined in a custom
data file), atomic radii and van der Waals radii. The pre-defined radii in the
script are in fact atomic radii.
4. An issue with this dupliverts technique is that a single representative ball is
reproduced on a mesh, which reflects the structure of one type of atom (sub
atomic structure) - a single atom cannot be really independently treated. To
extract an atom that has been chosen via the vertex in the 'edit mode' by the
user, a button has been introduced into the panel. The button appears as soon
as one is in the 'edit mode'. Pushing the button executes code, which separates
the marked atom from the mesh or dupliverts structure such that the atom is a
separate ball. This ball is completely independent, and its properties can be
changed accordingly independently (shape, color, etc.).
5. There were some bugs in the code which reads PDB files. Also, the element
list was 'strange' at some places (some elements were missing and all types of
radii had the values of the atomic radii). All bugs could be removed.
6. I forgot to mention that a part of the buttons are now in the file dialog
window. This is more convenient.
I consider the script as finished. I give it the version 0.9 since some changes
will be done in future during refereeing the manuscript. Here are some PDB
files which you can try out. Have fun to try out all the stuff:
http://qsad.bu.edu/data/pdbfiles/
http://www.pdb.org/pdb/home/home.do
http://development.root-1.de/Atomic_Blender/
At the end I recognize that it is not much. I have spent most of the time with
the Blender specific Python code - it is not easy and not at all fast to get
what one wishes! So far, I somewhat familiar with Blender python and changes
with respect to PDB etc. are easy.
Isssues
=======
- Measuring distance between two active objects in the object mode works.
However, the same doesn't work with two vertices marked in the edit mode
so far. The latter is due to the fact that I cannot determine the active
vertices. ... otherwise you tell me how ...
- Separating an atom from a dupliverts structure works. However, it does not
work if one wants to do the same with more than 1 activated atom. It is again
due to the issue of active vertices, which cannot be determined.
- I don't really like the place where the panel appears (VIEW_3D, TOOL_PROPS).
I want to have my own tab! :-)
Why? Right now, there are many other panels above my on always pushing my nice
'Atomic Blender' panel to the bottom. Hmmm ... but I have no idea where to put
it elsewhere.
To be done in future
====================
- I would like to make more order in the structures, which appear in the
outliner. For instance, sub-atomic structures (hydrogens, carbons, etc) should
be put into a single structure called 'molecule' or 'crystal' or 'structure'.
This can obviously be done via parenting.
- Double or triple bonds are not represented by sticks so far. However, this is
needed. <= Very easy to do and is next to get included
- I would like to choose also the ionic radii. But this is not easy to integrate
into the script: Note that not all atoms have same charge states and that a
single atom can have several charge states.
- Theorists use a file type which is called .xyz. This file can include many
configurations of a molecule, surface or complex atomic structure. For instance,
such files are used to represent structures composed by atoms which move in
time. <= My next project.
Integrating this should be easy since I have learned a lot about Blender's
python interface. <= Is next to be done.
Ackknowledgements:
==================
Thanks to ideasman, meta_androcto, truman, kilon, dairin0d, PKHG, Valte, etc.
for helping me with the code. I feel sorry for the many 'stupid' questions I
have been posing. (and don't fell on the save side now since I stop working on
the script: I'm going to annoy you also in the next future. ;-))
So, I wait now for feedback. What do you all think about the manuscript?
Cheers all,
Blendphys.
Modified Paths:
--------------
contrib/py/scripts/addons/io_import_pdb_atomic_blender.dat
contrib/py/scripts/addons/io_import_pdb_atomic_blender.py
Modified: contrib/py/scripts/addons/io_import_pdb_atomic_blender.dat
===================================================================
--- contrib/py/scripts/addons/io_import_pdb_atomic_blender.dat 2011-11-27 15:07:23 UTC (rev 2669)
+++ contrib/py/scripts/addons/io_import_pdb_atomic_blender.dat 2011-11-27 15:28:11 UTC (rev 2670)
@@ -20,13 +20,24 @@
Radius used : 0.930000
Radius, covalent : 0.930000
Radius, atomic : 0.490000
+
+
+Atom
+====
+Number : 3
+Name : Lithium
+Short name : Li
+Color : 0.729411764706,0.278431372549,0.254901960784
+Radius used : 1.230000
+Radius, covalent : 1.230000
+Radius, atomic : 2.050000
Charge state : 1
Radius, ionic : 0.680000
Atom
====
-Number : 3
+Number : 4
Name : Beryllium
Short name : Be
Color : 0.447058823529,0.725490196078,0.309803921569
@@ -41,7 +52,7 @@
Atom
====
-Number : 4
+Number : 5
Name : Boron
Short name : B
Color : 1.0,1.0,1.0
@@ -56,7 +67,7 @@
Atom
====
-Number : 5
+Number : 6
Name : Carbon
Short name : C
Color : 0.0,0.0,0.0
@@ -71,7 +82,7 @@
Atom
====
-Number : 6
+Number : 7
Name : Nitrogen
Short name : N
Color : 0.0,0.0,1.0
@@ -90,7 +101,7 @@
Atom
====
-Number : 7
+Number : 8
Name : Oxygen
Short name : O
Color : 1.0,0.0,0.0
@@ -109,7 +120,7 @@
Atom
====
-Number : 8
+Number : 9
Name : Fluorine
Short name : F
Color : 0.0,1.0,0.0
@@ -124,7 +135,7 @@
Atom
====
-Number : 9
+Number : 10
Name : Neon
Short name : Ne
Color : 0.537254901961,0.607843137255,0.525490196078
@@ -137,7 +148,7 @@
Atom
====
-Number : 10
+Number : 11
Name : Sodium
Short name : Na
Color : 0.0,0.0,1.0
@@ -150,7 +161,7 @@
Atom
====
-Number : 11
+Number : 12
Name : Magnesium
Short name : Mg
Color : 1.0,1.0,1.0
@@ -165,7 +176,7 @@
Atom
====
-Number : 12
+Number : 13
Name : Aluminium
Short name : Al
Color : 0.701960784314,0.2,0.623529411765
@@ -178,7 +189,7 @@
Atom
====
-Number : 13
+Number : 14
Name : Silicon
Short name : Si
Color : 0.654901960784,0.647058823529,0.278431372549
@@ -197,7 +208,7 @@
Atom
====
-Number : 14
+Number : 15
Name : Phosphorus
Short name : P
Color : 1.0,1.0,0.0
@@ -214,7 +225,7 @@
Atom
====
-Number : 15
+Number : 16
Name : Sulfur
Short name : S
Color : 1.0,1.0,0.501960784314
@@ -233,7 +244,7 @@
Atom
====
-Number : 16
+Number : 17
Name : Chlorine
Short name : Cl
Color : 0.0,1.0,0.0
@@ -250,7 +261,7 @@
Atom
====
-Number : 17
+Number : 18
Name : Argon
Short name : Ar
Color : 0.317647058824,0.329411764706,0.749019607843
@@ -263,7 +274,7 @@
Atom
====
-Number : 18
+Number : 19
Name : Potassium
Short name : K
Color : 0.811764705882,0.239215686275,0.423529411765
@@ -276,7 +287,7 @@
Atom
====
-Number : 19
+Number : 20
Name : Calcium
Short name : Ca
Color : 1.0,1.0,1.0
@@ -291,7 +302,7 @@
Atom
====
-Number : 20
+Number : 21
Name : Scandium
Short name : Sc
Color : 0.662745098039,0.447058823529,0.313725490196
@@ -304,7 +315,7 @@
Atom
====
-Number : 21
+Number : 22
Name : Titanium
Short name : Ti
Color : 0.270588235294,0.533333333333,0.686274509804
@@ -323,7 +334,7 @@
Atom
====
-Number : 22
+Number : 23
Name : Vanadium
Short name : V
Color : 0.270588235294,0.243137254902,0.635294117647
@@ -342,7 +353,7 @@
Atom
====
-Number : 23
+Number : 24
Name : Chromium
Short name : Cr
Color : 0.807843137255,0.286274509804,0.819607843137
@@ -361,7 +372,7 @@
Atom
====
-Number : 24
+Number : 25
Name : Manganese
Short name : Mn
Color : 0.752941176471,0.352941176471,0.552941176471
@@ -380,7 +391,7 @@
Atom
====
-Number : 25
+Number : 26
Name : Iron
Short name : Fe
Color : 1.0,0.0,0.0
@@ -395,7 +406,7 @@
Atom
====
-Number : 26
+Number : 27
Name : Cobalt
Short name : Co
Color : 0.274509803922,0.219607843137,0.752941176471
@@ -410,7 +421,7 @@
Atom
====
-Number : 27
+Number : 28
Name : Nickel
Short name : Ni
Color : 0.439215686275,0.360784313725,0.862745098039
@@ -423,7 +434,7 @@
Atom
====
-Number : 28
+Number : 29
Name : Copper
Short name : Cu
Color : 0.607843137255,0.0,0.0
@@ -438,7 +449,7 @@
Atom
====
-Number : 29
+Number : 30
Name : Zinc
Short name : Zn
Color : 0.423529411765,0.36862745098,0.450980392157
@@ -453,7 +464,7 @@
Atom
====
-Number : 30
+Number : 31
Name : Gallium
Short name : Ga
Color : 0.635294117647,0.729411764706,0.337254901961
@@ -468,7 +479,7 @@
Atom
====
-Number : 31
+Number : 32
Name : Germanium
Short name : Ge
Color : 0.423529411765,0.756862745098,0.301960784314
@@ -485,7 +496,7 @@
Atom
====
-Number : 32
+Number : 33
Name : Arsenic
Short name : As
Color : 0.396078431373,0.776470588235,0.250980392157
@@ -502,7 +513,7 @@
Atom
====
-Number : 33
+Number : 34
Name : Selenium
Short name : Se
Color : 0.952941176471,0.270588235294,0.905882352941
@@ -523,7 +534,7 @@
Atom
====
-Number : 34
+Number : 35
Name : Bromine
Short name : Br
Color : 0.0,0.498039215686,0.0
@@ -540,20 +551,31 @@
Atom
====
-Number : 35
+Number : 36
Name : Krypton
Short name : Kr
Color : 0.227450980392,0.435294117647,0.192156862745
Radius used : 1.310000
Radius, covalent : 1.310000
Radius, atomic : 1.240000
+
+
+Atom
+====
+Number : 37
+Name : Rubidium
+Short name : Rb
+Color : 1.0,1.0,1.0
+Radius used : 2.160000
+Radius, covalent : 2.160000
+Radius, atomic : 2.980000
Charge state : 1
Radius, ionic : 1.470000
Atom
====
-Number : 36
+Number : 38
Name : Strontium
Short name : Sr
Color : 1.0,1.0,1.0
@@ -566,7 +588,7 @@
Atom
====
-Number : 37
+Number : 39
Name : Yttrium
Short name : Y
Color : 1.0,1.0,1.0
@@ -579,7 +601,7 @@
Atom
====
-Number : 38
+Number : 40
Name : Zirconium
Short name : Zr
Color : 1.0,1.0,1.0
@@ -594,7 +616,7 @@
Atom
====
-Number : 39
+Number : 41
Name : Niobium
Short name : Nb
Color : 1.0,1.0,1.0
@@ -611,7 +633,7 @@
Atom
====
-Number : 40
+Number : 42
Name : Molybdenum
Short name : Mo
Color : 1.0,1.0,1.0
@@ -628,7 +650,7 @@
Atom
====
-Number : 41
+Number : 43
Name : Technetium
Short name : Tc
Color : 1.0,1.0,1.0
@@ -641,7 +663,7 @@
Atom
====
-Number : 42
+Number : 44
Name : Ruthenium
Short name : Ru
Color : 1.0,1.0,1.0
@@ -654,7 +676,7 @@
Atom
====
-Number : 43
+Number : 45
Name : Rhodium
Short name : Rh
Color : 1.0,1.0,1.0
@@ -667,7 +689,7 @@
Atom
====
-Number : 44
+Number : 46
Name : Palladium
Short name : Pd
Color : 1.0,1.0,1.0
@@ -682,7 +704,7 @@
Atom
====
-Number : 45
+Number : 47
Name : Silver
Short name : Ag
Color : 1.0,1.0,1.0
@@ -697,7 +719,7 @@
Atom
====
-Number : 46
+Number : 48
Name : Cadmium
Short name : Cd
Color : 1.0,1.0,1.0
@@ -712,7 +734,7 @@
Atom
====
-Number : 47
+Number : 49
Name : Indium
Short name : In
Color : 1.0,1.0,1.0
@@ -725,7 +747,7 @@
Atom
====
-Number : 48
+Number : 50
Name : Tin
Short name : Sn
Color : 1.0,1.0,1.0
@@ -744,7 +766,7 @@
Atom
====
-Number : 49
+Number : 51
Name : Antimony
Short name : Sb
Color : 1.0,1.0,1.0
@@ -761,7 +783,7 @@
Atom
====
-Number : 50
+Number : 52
Name : Tellurium
Short name : Te
Color : 1.0,1.0,1.0
@@ -782,7 +804,7 @@
Atom
====
-Number : 51
+Number : 53
Name : Iodine
Short name : I
Color : 0.0,0.498039215686,0.498039215686
@@ -799,20 +821,31 @@
Atom
====
-Number : 52
+Number : 54
Name : Xenon
Short name : Xe
Color : 1.0,1.0,1.0
Radius used : 1.310000
Radius, covalent : 1.310000
Radius, atomic : 1.240000
+
+
+Atom
+====
+Number : 55
+Name : Caesium
+Short name : Cs
+Color : 1.0,1.0,1.0
+Radius used : 2.350000
+Radius, covalent : 2.350000
+Radius, atomic : 3.350000
Charge state : 1
Radius, ionic : 1.670000
Atom
====
-Number : 53
+Number : 56
Name : Barium
Short name : Ba
Color : 1.0,1.0,1.0
@@ -827,7 +860,7 @@
Atom
====
-Number : 54
+Number : 57
Name : Lanthanum
Short name : La
Color : 1.0,1.0,1.0
@@ -842,7 +875,7 @@
Atom
====
-Number : 55
+Number : 58
Name : Cerium
Short name : Ce
Color : 1.0,1.0,1.0
@@ -859,7 +892,7 @@
Atom
====
-Number : 56
+Number : 59
@@ Diff output truncated at 10240 characters. @@
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