Importing a PDB structure where the atoms are shown as mesh balls created an
error. This bug was fixed. 
 
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2. Small cleanups of the code

3. New feature: The sticks can be represented as entire cylinders. One can 
choose either single cylinders, which are parented to an empty, or one single
mesh object including all sticks. 
This feature is quite suitable for structures, which count more than 1000 
sticks. When the sticks are represented by one single mesh object the
handling in the 3D scene is much faster.
Note that the layout of the preferences in the file dialog had to be also 
changed since there are more options for sticks now.
 
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The new feature: the sticks represented by a skin and subdivision modifier
do also have a material now. - I simply forgot that to include.
 
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been removed and put into a separate function.
 
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been removed and put into a separate function.
 
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source into the 3D scene has been removed and put into a separate function.
 
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in Blender, which both can be used to draw the sticks. This is what I have 
done and implemented.

The code has become a bit 'unreadable' there will be after some other commitments
including some code cleanups.
 
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Quite annoying: When importing an atomic structure with sticks, the sticks
were not automatically smoothened. I changed the default value from False to
True.

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make addons blender versions consistent

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

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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.

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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.

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

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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)

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Some cosmetics ...

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

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- 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 ...

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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

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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.

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* Remove api info, this is not used anymore. 

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


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Importer
========

+ normalization ...

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Importer
========

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

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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.

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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.

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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.


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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.

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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