File pymol.changes of Package pymol
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Wed Jul 17 17:21:56 UTC 2013 - dhall@wustl.edu
- update to svn rev 4035
* fixed load_traj with stop/max arguments. Thanks to David Osguthorpe for the patch.
* fix pymol.importing.read_mmodstr
* proper numpy support (ObjectMap.c)
* take out broken experimenting.expfit
* fetch_path: graceful error handling when writing file fails
* fixed flickering ortho problems on some machines
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Thu Jun 27 12:49:30 UTC 2013 - dhall@wustl.edu
- update to svn rev 4033
* fixed selection indicators
* invalidation of selection indicators when selections change
* wrong sized selection indicators are shown after zoom
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Tue Jun 18 12:32:11 UTC 2013 - dhall@wustl.edu
- update to svn rev 4032
* fixed loading in bg_rgb settings from old project pse files
* add URL support for run command
* some setup.py adjustments
* fixed labels when use_shaders is 0 and show_frame_rate is on
* update APBS Tools plugin
* fix spectrumany when minimum/maximum are provided
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Wed Jun 12 13:01:11 UTC 2013 - dhall@wustl.edu
- PyMOL v1.6.0.0 Release
* freeing VBOs properly when deleting volumes
* added quiet flag for SettingGenerateSideEffects() and SettingCheckUseShaders()
* fix 15bit color picking
* fix surface memory leak
* fix CGO demo
* internal.file_read: use urllib2 instead of urllib
* fix ellipsoid transparency OpenGL rendering
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Tue Jun 4 10:32:00 UTC 2013 - dhall@wustl.edu
- update to sven rev 4029
* fix Scripts ending with ...pymol.py do not execute
https://sourceforge.net/p/pymol/bugs/46/
* several CGO fixes
* several python fixes
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Fri Apr 26 22:45:26 UTC 2013 - dhall@wustl.edu
- update to svn rev 4028, pymol 1.6beta1
* refactored importing.fetch
* spectrum enhancements (arbitrary expressions and colors)
* pymol2.cmd2: implement proxy pattern
* chempy model improvements
* fix bg_color, which sometimes did not apply instantly
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Mon Apr 22 22:25:07 UTC 2013 - dhall@wustl.edu
- update to svn rev 4027
* support full path for "matrix" argument
https://sourceforge.net/p/pymol/patches/4/
* use PyMOL API in pymol.rpc module
https://sourceforge.net/p/pymol/patches/3/
* doc string for cmd.find_pairs
https://sourceforge.net/p/pymol/patches/2/
* rotate ANISOU vector when transforming objects
* new command: split_chains
* fix create/extract bug with movie
* fixed cartoon VBO memory leak
* always draw rounded caps with sticks shaders
* several shader fixes and performance improvements
* fixed screen z-offset for labels
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Mon Apr 22 20:02:56 UTC 2013 - dimstar@opensuse.org
- Add freetype2-devel: the source #includes ft2build.h, so it's
only correct to build require it.
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Sun Mar 24 13:18:19 UTC 2013 - dhall@wustl.edu
- version bump: pymol 1.6
* improved rendering performance using shaders, including
dynamically updated shaders based on settings
(see data/shaders directory)
* implemented shaders for menus, labels, selection indicators,
background, and other graphics that were not using shaders.
* consolidated textures used for labels and selection indicators
to one texture, which helps performance
* added memory checking to help avoid crashing when memory is
low or not available
* cleaned up code base, took out extraneous preprocessor code and
code that was not used.
* refactor pmg_tk.Settings
* Do not clear atom names with chempy.champ.assign.amber99
* fix some plugin manager exception handling
* fix create with name=None
* Plugin override search path: Always include "startup"
from installation directory in plugin search path
* Movie > Program > Scene Loop > Nutate > by degrees
* ObjectMeshRenderImpl refactoring: color isomesh and isodot with
mesh_color and dot_color settings
* merging alignment objects: eliminate orphaned atoms
* fix cealign alignment object creation: rms_cur arguments swapped
* improved the alignto command to take additional keyword arguments
which get passed to the used method -> object=aln supported now
* remove _PYMOL_MODULE constant
* fix LITERAL mode command parsing: ignore leading whitespace
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Wed Mar 20 16:24:45 UTC 2013 - dhall@wustl.edu
- update to svn rev 4023
* setup.py: unify Linux and Mac platform-specific stuff
* disable shaders for nouveau driver
* setup.py: add support for incremental build
* add missing file "qmplugin.h"
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Sat Feb 16 02:46:15 UTC 2013 - dhall@wustl.edu
- update to svn rev 4020
* enable VMD plugins by default
* apply patch #120 "pymol" import in launcher ambiguous
http://sourceforge.net/p/pymol/bugs/120/
* always import _cmd from pymol or pymol.cmd instead of relative
* add bz2 support for reading PDB and some other file formats
* support width/height units with the png command
* support decorator syntax for cmd.extend
* setup.py refactoring, setup2.py no longer needed
* Exit on error with "-y" flag
* shortcut and auto-completion refactoring
* fix setting angle_color or dihedral_color
* ramp_new: exception handling on argument parsing
* feedback fixes
* speed up iterate and alter - https://sourceforge.net/p/pymol/patches/5/
* command line (Tk GUI) history improvements
* add angles to the Movie-Program-SceneLoop menu
* Fixed fab hydro argument
* Fixed #3539436: right justified resn in PDB
* Fixed #3506103: alignment objects from "super" do not contain N atoms
* Fixed #3496006: END before ENDMDL bug reintroduced
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Thu Aug 16 15:33:22 UTC 2012 - dhall@wustl.edu
- update to svn rev 4005
* Fixed longstanding annoyance: 'as rep, vis' now works
* Added autocomplete for 'group' command.
* Adding autocomplete for 'dss'.
* Fixed bug where FASTA strings aren't returned for multiple objects.
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Sun Jun 10 14:56:06 UTC 2012 - dhall@wustl.edu
- update to svn rev 4001
* FIXED: fails to align chains of length < 2*window+1
* FIXED: if chain length is a multiple of window, only (length-window) residues get aligned
* FIXED: only evaluates every 2nd path of the best 20 (increments k twice in the loop)
* FIXED: if no alignment is found, the return value is NULL which raises a SystemError instead of a graceful error message.
* FIXED: finally, it's not possible to obtain the alignment as an object (like with align ..., object=aln)
* FIXED: fixed auto complete names on for cealign
* Fixing the exception handling of get_names_of_type
* Fixing get_unused_names
* Fixing locking on get_names_of_type
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Sat May 5 17:30:03 UTC 2012 - dhall@wustl.edu
- Adding checks for Quadro cards
- Improved Plugin Manager; Thomas Holder's PyMOL OSFP project
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Fri Apr 13 03:52:00 UTC 2012 - dhall@wustl.edu
- update to svn rev 3996
* Fixed ID: 3512313 TER records before residues like MSE, patch submitted by Thomas Holder
* Fixed ID:3513708, cmd.get_unused_name fix; thanks to Thomas Holder
* Default all Intel cards to not use shaders
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Tue Mar 6 02:21:51 UTC 2012 - dhall@wustl.edu
- update to svn rev 3993
* fixed crash when reading in long lines from stdin
- update to 1.5.0.3
* fixed error showing Cell on map with attached file
* fixed reading in symmetry
* fixed problem with symmetry copying/setting where map doesn't get updated
* get_symmetry should return None if argument is not an ObjectMolecule or ObjectMap
* fixed Volume extents only get shown when volume is rendered
* fixed reading in legacy sessions with version # less than 1
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Sat Feb 18 23:44:14 UTC 2012 - dhall@wustl.edu
- update to 1.5.0.2
* stack trace when saving movie as MPEG (ID: 3488608)
* error loading from pse that don't have Crystal/Symmetry info (ID: 3488609)
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Mon Feb 13 22:41:59 UTC 2012 - dhall@wustl.edu
- update to 1.5.0.1 release
* improved rendering Performance
* improved rendering Quality
* bg_gradient now ray traces
* improved cartoon support for non-standard nucleotides
* surface color smoothing
* surface-based picking
* frame buffer-based antialiasing for real-time rendering
* optimized anaglyph colors and intensities for an improved 3D
viewing experience
* real-time and ray-traceable ambient occlusion
* molecular weight calculuations; A > Compute > Molceular Weight
* selection generation A > Generate > Selection
* new mouse mode for repositioning lights
* many bug fixes
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Fri Feb 10 08:54:07 UTC 2012 - cfarrell@suse.com
- license update: Python-2.0
Use the SPDX identifier (http://www.spdx.org/licenses)
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Wed Jan 4 20:21:01 UTC 2012 - dhall@wustl.edu
- update to svn rev 3975
* improved callback rendering
* fixed object creation when merging two objects
* fixed get_mass
* fixed create to reorder IDs when combining objects
* Cleaned up 'fitting.py'
* alignto updated; can now take a method for alignment
* cealign updated; made faster and cleaner
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Fri Oct 14 21:22:58 UTC 2011 - dhall@wustl.edu
- update to svn rev 3971
* Added the get_viewport function and updated the viewport function
* Added support for some non-standard nucleic acids (PSU)
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Mon Oct 3 15:28:14 UTC 2011 - dhall@wustl.edu
- update to svn rev 3969
* PyMOL now respects the h_bond_from_proton setting
* Doc fixes
* Added Display > Roving Detail
* Removed AttributeError on coloring volumes
* Added polar contacts/hydrogen bonds to the measurement wizard
* Fixed distance invalidation problem
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Fri Sep 16 01:54:16 UTC 2011 - dhall@wustl.edu
- update to svn rev 3965
* Fixed a conversion bug in util.cbc; thanks Hongbo.
* Added A > Compute > Molecular Weight and cleaned up the compute menu in general
* Fixed click-flash that happens when middle-clicking when showing the background
gradient (thanks, Blaine)
* Added A > Generate > Selection > polar, non_polar, acceptor/donator options
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Fri Aug 5 22:22:56 UTC 2011 - dhall@wustl.edu
- update to svn rev 3962:
* code cleanup
* fix opengl from python
* read and importing fixes
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Thu Jul 7 19:32:39 UTC 2011 - dhall@wustl.edu
- Small state bugfix
- Feedback bugfix
- Updated TNT to 3.0b
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Sun Jul 3 13:44:10 UTC 2011 - saschpe@gmx.de
- Spec file cleanup:
* Added proper license header
* Removed authors from description
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Fri Jun 17 13:51:09 UTC 2011 - dhall@wustl.edu
- have just one package rather than pymol+python-pymol, maybe chempy
will split out later
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Thu Jun 16 21:56:32 UTC 2011 - dhall@wustl.edu
- update to svn version 3955
- fixed stick coloring
- fixed save mol file
- fixed shading/fog
- fixed volume shaders
- supress guess valences
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Thu Jun 2 19:02:45 UTC 2011 - dhall@wustl.edu
- update to svn version 3951
- fix clipped group names
- much faster ribbons
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Tue May 10 20:02:06 UTC 2011 - dhall@wustl.edu
- move pymol_path stuff into python module
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Tue May 10 19:42:45 UTC 2011 - dhall@wustl.edu
- fix dependencies
- mark file as executable
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Tue May 10 17:49:20 UTC 2011 - dhall@wustl.edu
correct separation between pymol and python-pymol-
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Tue May 10 16:25:06 UTC 2011 - dhall@wustl.edu
Initial checkin of pymol 1.4.1-
