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File pymol.changes of Package pymol
------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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" ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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) ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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 ------------------------------------------------------------------- Thu Jul 7 19:32:39 UTC 2011 - dhall@wustl.edu - Small state bugfix - Feedback bugfix - Updated TNT to 3.0b ------------------------------------------------------------------- Sun Jul 3 13:44:10 UTC 2011 - saschpe@gmx.de - Spec file cleanup: * Added proper license header * Removed authors from description ------------------------------------------------------------------- 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 ------------------------------------------------------------------- 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 ------------------------------------------------------------------- Thu Jun 2 19:02:45 UTC 2011 - dhall@wustl.edu - update to svn version 3951 - fix clipped group names - much faster ribbons ------------------------------------------------------------------- Tue May 10 20:02:06 UTC 2011 - dhall@wustl.edu - move pymol_path stuff into python module ------------------------------------------------------------------- Tue May 10 19:42:45 UTC 2011 - dhall@wustl.edu - fix dependencies - mark file as executable ------------------------------------------------------------------- Tue May 10 17:49:20 UTC 2011 - dhall@wustl.edu correct separation between pymol and python-pymol- ------------------------------------------------------------------- Tue May 10 16:25:06 UTC 2011 - dhall@wustl.edu Initial checkin of pymol 1.4.1-
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