File pymol.changes of Package pymol
-------------------------------------------------------------------
Mon Sep 15 19:20:49 UTC 2014 - dhall@wustl.edu
- update to svnrev 4093
* fix ObjectMoleculeCopy lex ref counting
* added missing function pymol.menu.measurement_color
* multi-letter chain support
* c++ for all PyMOL c files
- renaming files c -> cpp
- c++ specific syntax (::)
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Mon Aug 25 22:52:17 UTC 2014 - dhall@wustl.edu
- update to svnrev 4088
* port pdb_conect_nodup to open-source PyMOL
* reimplement volume carving
- use a carve mask texture
* fix boxed volume around selection (with or without carving)
- this only worked for symmetry expanded volumes
- still limited to maps with symmetry information (TODO)
* removed ObjectVolumeGetIsUpdated, deprecate get_volume_is_updated
* refactored ObjectVolumeStateGetField, ObjectVolumeGetField
- don't keep a redundant vs->volume copy in memory
* revert a 1.7.2 opaque_background change
- real-time rendering background was always black with
opaque_background=0
- removes opaque_background support for "draw"
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Fri Aug 8 01:28:03 UTC 2014 - dhall@wustl.edu
- update to svnrev 4086
* chempy.cif: fix symmetry loading
* Improve ObjectVolume rendering latency
* Improve label edge pixel rounding
* alter_state auto completion
* improve "Label" wizard
* re-implemented ObjectMoleculeSetDiscrete
* fix ObjectMoleculeSetDiscrete for empty molecules (crashed PyMOL)
regression by rev 4083
* fix mutagenesis bump_scores error: after apply or clear, bump_scores must be cleared
regression by rev 4081
* improve "Label" wizard
* re-implemented ObjectMoleculeSetDiscrete
* fix label_digits crash
* fixed get_angle3f to use doubles internally
* avoid ZeroDivisionError in Volume Panel
* support opaque_background with "draw"
* fix spheroid command for use_shaders=0
* report clash score in mutagenesis wizard
* change defaults for settings "ribbon_as_cylinders" and
"nonbonded_as_cylinders" to 0
* new commands (ported from PSICO): join_states, alphatoall, loadall,
centerofmass, extra_fit, api
* pubchem and emd fetch support
* support to run pml and py script with the "load" command
* Fix text mode (text=1) with white background color
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Fri Jun 27 16:35:20 UTC 2014 - dhall@wustl.edu
- update to svnrev 4080
* chempy.cif: don't bond metalc and hydrog
* chempy.cif: fix copy/paste typo in read_struct_conn_
* better CIF support, etc.
* refactor chempy.cif
- support for multi-model
- read secondary structure
- rewritten tokenizer
* atom sorting: make segi match case sensitive
* fix/improve:
A > compute > surface area > ...
A > generate > selection > surface atoms
* PDB parser: factor out SS handling for readability
* open file dialog in CWD until the first file was selected, then
remember that directory
* with -J immediatly cd to $HOME (or $HOME/Documents on Windows).
This allowes to put a "cd ..." in pymolrc
* fix stereo shader invalidation
* add missing header
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Wed May 14 20:19:36 UTC 2014 - dhall@wustl.edu
- update to svn rev 4076
* fix label depth issues with label_position
* fix label reappeared when zoomed in too far
* fix "scene auto, update" with wizard message
* fix setting surface_circumscribe
* volume improvments:
- grid_mode support
- adjust volume ramp alphas by number of layers
- support TTT matrix
- bind mouse wheel to volume panel to adjust all alphas at once
* CCP4 map type 0 support
* fixed polymer detection for intra-residue N->C and O3'->P bonds
* raise exception when assigning arbitrary string to int setting
* fix group visibility issue in movie making
-------------------------------------------------------------------
Thu Apr 24 17:25:55 UTC 2014 - drhall@bu.edu
- update to svn rev 4074
* never assign atom_type (noInvalidateMMStereoAndTextType)
* fix ExecutivePurgeSpec memory leak
* fix cartoon memory leak
* fixed small solvent_radius crashes surface generation
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Thu Mar 13 14:30:29 UTC 2014 - dhall@wustl.edu
- update to svn rev 4073
* fix CGO ALPHA should not make colors get ignored
* volume API and panel improvements
* volume presets
* new commands: volume_color, volume_ramp_new
* improved volume panel/UI
* custom volume ramps/presets
* support for volumes from maps with transformation matrix (matrix_copy on map)
* fix distorted labels with stereo walleye/crosseye
* fix broken label scaling on Linux
* update splash
* bugfix: labels missing on some ATI cards
* th_assert -> ok_assert
* fix typo in menu: isolevel -1.5
* set PYMOL_PATH=. if unknown and cannot be guessed
* use PYMOL_DATA in ShaderMgr
* remove some old code in pymol/__init__.py
* http://sourceforge.net/p/pymol/bugs/147/
* add method chempy.brick.Brick.from_numpy
* mutagenesis wizard: use PYMOL_DATA
* fix pymolrc lookup on Windows from users home directory broken
* read space group from CCP4 maps
* handle empty space group like P1 (for best support of map formats
which do not have a space group)
* map_auto_expand_sym: take symmetry from map if molecular object
doesn't have symmetry information
* gracefully reject writing MOL format with >999 atoms
* fix: saving MOL2 format with empty atom name
* fix: ray+png in batch mode ray traces twice
* disable seq_view in mpng
* change movie_quality default to 90 (was 60)
* fix needs_alpha_reset
* apbs_tools PDB writing: disable putting spaces before dashes
-------------------------------------------------------------------
Sat Jan 4 13:17:00 UTC 2014 - dhall@wustl.edu
- update to svn rev 4058
* fix ramp coloring when loaded from PSE
* don't set use_shaders with PSE or reinitialize
* delete duplicates when loading PSE w/ partial=1
* fix incomplete CGO loading from session file
* fix viewport logging syntax error
* fixed typo in RepDihehral "ok &+" -> "ok &="
http://sourceforge.net/p/pymol/bugs/146/
* fix warnings about unused data argument
* submenus can be callables which return a list
* fix antialiasing internal edges, ray tracing
* fix clicking volume panel dots at zero alpha
* fix molecular weight w/ aromatic bonds & missing hydrogens
* fixed sequence text/background when scrollbar isn't shown
* remove deprecated mray command
-------------------------------------------------------------------
Fri Dec 6 20:00:16 UTC 2013 - dhall@wustl.edu
- update to svn rev 4053
* remove self assignments
http://sourceforge.net/p/pymol/bugs/143/
* cmd.load_callback: import fixed version to api
* don't sort atoms in discrete objects
* fix resizing issue for lines on ATI cards
* fix reset stereo with reinitialize
* fix draw stereo
* fix label shader fog blending
-------------------------------------------------------------------
Mon Nov 11 21:31:02 UTC 2013 - dhall@wustl.edu
- update to svn rev 4051
* fix segfault in SceneImagePrepareImpl
* fix dihedral rep for objects with >20 states
* cmd.png: consider image_dots_per_inch with _unit2px
* preset.py: delete temporary selections
* fixed CGO demo crash in CGOSimplify
* print OpenGL info not only to STDOUT, but to PyMOL text output
* fix tcl/tk window placement on OS X 10.9
* get_viewport: do not print int as float
* fix: do not set wiz.cmd to None when saving PSE
* fix cartoon picking bug
* fix crash during selection
* fix two_sided_lighting cartoon shader bug
* fix isolevel command for isosurface with shaders
* mol2 writing with multiple objects
* fix removing non-polar hydrogens
* fix crash during select bychain
* fixed line_as_cylinder bug
* fixed smooth half bonds with line as cylinders
* get_bond command
-------------------------------------------------------------------
Mon Nov 11 21:22:50 UTC 2013 - dhall@wustl.edu
- Add no-build-date.patch : eliminates build date in executable
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Mon Nov 11 17:18:28 UTC 2013 - dhall@wustl.edu
- update to svn rev 4050
* fix splash.png sRGB profile, https://sourceforge.net/p/pymol/bugs/136/
* fix get_setting_updates
* improve Filter Wizard, "Create Filtered Object"
* consider "ignore_pdb_segi" setting when saving to PDB
* delete obsolete files (sglite, ExtensionClass)
* some C code refactoring
* remove out-dated pymol.opengl module
* enhance get_version command, quiet=-1 gives build information
* remove max_triangles setting (was unused)
* fcmp equals operator approximate match
* fix Tcl/Tk save multiple to one file
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Mon Oct 7 01:56:36 UTC 2013 - dhall@wustl.edu
- Drop setup.patch: upstream fixed bug
- update to svn rev 4045
* fix setup.py sys.argv
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Sat Oct 5 01:56:22 UTC 2013 - dhall@wustl.edu
- update to svn rev 4044
* fix segfault in OrthoRenderCGO https://sourceforge.net/p/pymol/bugs/137/
* importing.load_coords
* improve util.chainbow
* fix plugin manager PyMOLWiki URL install: strip whitespace
* major re-work/organization of RepSphere.c and fixed sphere picking
* fix color type settings return format for hex colors (0x prefix)
* fix special keys in wizard input prompt
-------------------------------------------------------------------
Mon Sep 9 15:56:23 UTC 2013 - dhall@wustl.edu
- update to svn rev 4042
* add "x" "y" "z" selection operators
* fix seq viewer background color
* add "backbone" and "sidechain" selection keywords
* fix: cealign inverts target structure
* fix [bugs:#135] array overrun
* apply one part of [patches:#6]
* preserve "use_shaders" setting when loading session files
* simplify pymolrc search routine
* fix CtSh-M click on group members in object menu panel
* set_key string support
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Fri Aug 23 21:27:13 UTC 2013 - dhall@wustl.edu
- Add setup.patch: Makes pymol build using standard distutils commands
- update to svn rev 4039
* fix h_add atom sorting
* add "metals" keyword to selection language
* improve amber rst/crd support
* fix pair_fitting with one atom pair
* setup.py: add --osx-frameworks agument
* rpc server: use register_instance
* fix numpy/ndarrayobject.h import
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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.
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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.
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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)
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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)
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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-
