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error. This bug was fixed.
Blendphys.
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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.
Blendphys.
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do also have a material now. - I simply forgot that to include.
Blendphys.
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been removed and put into a separate function.
Blendphys.
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been removed and put into a separate function.
Blendphys.
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source into the 3D scene has been removed and put into a separate function.
Blendphys.
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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.
Blendphys.
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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
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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.
Blendphys
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Blendphys
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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.
Blendphys
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import. I have no idea why that happened out of a sudden. Anyway, I removed
this bug.
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Blendphys.
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Blendphys.
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- 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
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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
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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
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=======================
- Update of date
Blendphys
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========
+ normalization ...
Blendphys
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========
I forgot a '-' in the vector ...
Blendphys
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========
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
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========
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
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- 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
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least the script does not crash.
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I updated the date of change.
Blendphys
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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
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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
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Cheers,
Blendphys
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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
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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
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Some changes in the code, which reads PDB files, have
been done.
If you find bugs, please let me know. Thx.
Cheers,
Blendphys.
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Some large data classes (elements, atoms and sticks) use
__slots__
now.
Cheers,
Blendphys.
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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.]]
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which supports more file types
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by Mariusz Maximus & Jong89
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