I also updated the Wiki page.
2. There was a small mistake introduced by the last commits. This has been 
   fixed.
3. Code cleaning

Blendphys

according to the "Style Guide for Python Code" 
(http://www.python.org/dev/peps/pep-0008/) and the recent review
(http://codereview.appspot.com/6815052). Some slight changes were done, too. 
Extensive tests have shown that the code is still well working.

Blendphys

Blendphys

panel from the import/export addons. This means that the panel has had to be 
removed also from the PDB importer/exporter. This is what I have done.

Attention, this is a major change of the Atomic Blender PDB importer/exporter!

A lot of test today have shown, that the new version of the PDB 
importer/exporter has not lost its stability. In the next days, I will perform 
other stability tests.

Blendphys

Also in the PDB IO: relict from old times, which has been removed

Blendphys.

Some cosmetics ... .

When exporting structures from Blender into a PDB file it happened 
sometimes that the xyz positions of the atoms weren't correctly 
stored. Bug fixed.

import. I have no idea why that happened out of a sudden. Anyway, I removed
this bug.

1. There was a bug when separating a single ball from a dupliverts
structure upon pushing the button "Separate atom" in the Atomic Blender
panel. 

2. Thanks to an inspirations from <CoDEmanX> I changed the code such that 
all selected atoms (vertices) in the "Edit Mode" are seperated at once.
(new feature)

Blendphys.

Some cosmetics ...

Blendphys.

The Atomic Blender panel is loaded correctly when a blend file is loaded.

Blendphys.

- Option 'smooth' permits now a better 'polishing' of the sticks.

- The default value for the precision of the sticks (unit length)
  has been put from 0.2 onto 0.05. If the sticks are shown, they do not 
  overlapp anymore.

- Code cleaning

- Due to the recent large changes of the code the addon has been tested 
  with even more PDB files.
  
  
Blendphys 

PS: see recent comment here: http://blenderartists.org/forum/showthread.php?235003-Atomic-Blender-for-loading-PDB-files-into-Blender-2.5&p=2079416&viewfull=1#post2079416

Some code cleaning ...

Blendphys 

1. New: The user can now decide whether the panel is always, once or never shown 
after a PDB file is loaded. Note that the panel is quite essential since it 
helps quickly modifying PDB structures.
2. Some code cleaning
3. Wiki has been updated

Blendphys 

Attention: big changes in __init__.py, almost no changes in import_pdb.py
and export_pdb.py

1. With respect to the propositions made by Campbell and Sebastian
(see http://projects.blender.org/tracker/?func=detail&group_id=153&aid=29226&atid=469)
I changed the code. The PDB IO has now the preset option in the file dialog
of the importer and exporter.

2. Furthermore, I have put all properties into one group, which is located
in bpy.contect.scene. 

3. Some code cleaning

Soon, I will put in a new option (next days): the user can decide whether the 
panel is always, once or never shown after a PDB file is loaded. Note that
the panel is essential for me and also my students. It helps quickly modifying
PDB structures.

Blendphys 

* Remove api info, this is not used anymore. 

PDB - Importer/Exporter
=======================
- Update of date


Blendphys 

Importer
========

+ normalization ...

Blendphys 

Importer
========

I forgot a '-' in the vector ...

Blendphys 

Importer
========

I removed a small bug: Double or triple bonds were not shown for atoms, which
have only one neighbour.

BTW: I updated the wiki.

Blendphys 

Importer
========
The length of the 'unit stick' of the dupliface structure that is used for 
representing the sticks can now be explicitly chosen before loading a PDB 
structure.
 
It was always on 0.05 Angstrom, which is a quite small value. Loading 
structures with lots of sticks was therefore very slow. The value can now be 
changed [from 0 to infinity]. I have set the default value onto 0.2 Angstrom,
which should be sufficient.

Note: The smaller the value, the better is the length precision. However, the 
more single units need to be drawn (more vertices).

By time, I will change the wiki ... in some days.

Blendphys 

Exporter
- Either active objects with a proper element name or all active objects are
  exported depending on EnumProperty in File dialog: all <-> element 
- Removed a bug in the exporter: 'import_pdb.ATOM_PDB_ELEMENTS_DEFAULT' is
  used instead of 'import_pdb.ATOM_PDB_ELEMENTS' <= is sometimes empty list

Importer
- The name of the representive ball of a dupliverts technique is now shorter:
  from 'Ball (NURBS)_<element>' to  'Ball_<element>'; The name of the element 
  is not cut in the outliner.


Blendphys 

MHX importer: temporary commit for Bmesh. UV coordinates are ignored, but at least the script does not crash.

Dear all.

I updated the date of change.

Blendphys 

Dear all.

Bug: The script crashed when sticks with the colors of atoms
were drawn in the presence of TER lines in the PDB file. 
This bug has been removed.

Blendphys 

- Check for keymap availability to suppress warning messages when running
  blender in background mode

Dear all.

Here comes version 1.2 !

New 
===
1. Double and tripple bonds can now be displayed. The option 'bonds' needs to be
checked. One can also choose the distance between the sticks.

2. If the bool 'smooth' is checked the shape of the sticks is more round.  

Changes
=======
- Buttons, which depend on other buttons, are grayed out as soon as the
'master button' is deactivated.
- Other small bug fixes


With this version 1.2 I consider the PDB project as 'accomplished' so far. 
Of course, I will keep an eye on any critics, changes, bug fixes and so on. 
Please, let me know if you find any bugs. Thanks.



Happy New Year!




Blendphys 

... only small changes, that's it ...

Cheers,

Blendphys 

Dear all.

1. New option: sticks connecting atoms can have now the color of the atoms.
2. New button in the panel: 'Show sticks' scales the atom radii such that only
   the sticks are visible.  
3. A bug was removed: Scaling atoms with a specific name scaled also the sticks.
   This does not happen anymore.  

- Due to the changes, the script has version 1.1
- To be done: Update of both Wiki pages (next days)
- Probably, I commit a 2nd time today.

Merry Christams,

Blendphys 

Dear all.

1. Changes of the 'Atomic Blender - PDB importer' panel. I've 
grouped specific in/outputs and buttons by using boxes. Now,
there is some order in the panel.
2. Better precision for sticks
3. No other changes otherwise ...

Merry Christams,

Blendphys 

Dear all.

Some changes in the code, which reads PDB files, have
been done.

If you find bugs, please let me know. Thx. 

Cheers,

Blendphys.

Dear all.

Some large data classes (elements, atoms and sticks) use 

           __slots__

now.


Cheers,

Blendphys.

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.]]

removing this PDB importer in preparation to replace with a re-written one which supports more file types