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-------------------------------------------------------------------
Sun Jun 8 15:58:57 UTC 2025 - Ben Greiner <code@bnavigator.de>
- Enable test suite for x86_64
-------------------------------------------------------------------
Fri Jun 6 08:29:17 UTC 2025 - Friedrich Haubensak <hsk17@mail.de>
- require Mesa-libGL-devel to build, require one of PyQt6 or
PySide6 to run, recommend Pmw (for legacy plugin manager)
-------------------------------------------------------------------
Fri Mar 14 17:31:28 UTC 2025 - Friedrich Haubensak <hsk17@mail.de>
- changes to .spec file:
* to make build work on leap 15.6, add sle15_python_module_pythons
and conditional BuildRequires: gcc12-c++
* drop skip_python2 and oldpython
-------------------------------------------------------------------
Wed Mar 12 22:14:37 UTC 2025 - Friedrich Haubensak <hsk17@mail.de>
- update to 3.1.0
* File Support
- BCIF import support
- gzipped-compressed SDF (SDFGZ) import support
* Python API
- "delete_states" command (removal of one or more states)
- "declare_command" extension for improved ergonomics of introducing
and customizing PyMOL functionality
- "cell_color" setting for altering unit cell colors
* Developer & Infrastructure
- Migration from distutils to setuptools
-------------------------------------------------------------------
Tue Nov 12 14:18:22 UTC 2024 - Bernhard Wiedemann <bwiedemann@suse.com>
- Add reproducible.patch to normalize build date (boo#1047218)
- Remove no-build-date.patch
-------------------------------------------------------------------
Thu Oct 10 23:20:52 UTC 2024 - mcepl@cepl.eu
- Update to version 3.0.0+git.1725549602.9d3061c:
* Symbol renaming in molfile_plugin and internal linkage
* New command: delete_states
* mark bind() calls with override where needed
* Separate CGO to VBO logic out into functions
* Remove unused returnData
* Use vector for memory alloc
* Use struct for total vert counts in CGO.cpp
* Remove _PYMOL_IOS (Discontinued; prep for MVK)
* Python 3.12 TypeError: convert progress to int for progress bar
* Fix ray/draw panel error when modifying units
- Remove upstream patches:
* pymol3-version-compare.patch
* no-o3.patch
* pymol3-numpy2.patch
-------------------------------------------------------------------
Tue Oct 1 19:23:57 UTC 2024 - <hsk17@mail.de>
- add patches:
* pymol3-numpy2.patch: add numpy-2 compatability
* pymol3-version-compare.patch: fix tests/helpers/test_utils.py
-------------------------------------------------------------------
Tue Jun 18 15:42:12 UTC 2024 - <hsk17@mail.de>
- update to 3.0.0
* Panels
- Nucleic Acid Builder supported
- Scenes Panel (Basic version)
- Improved APBS electrostatics plugin integrated
* Distance/Bonding detection
- Halogen-bond detection and display
* Python API
- "fnab" command (sequence to nucleic acid chain)
- Improved CGO builder API
- get_sasa_relative() "subsele" argument added
- new clip modes/API
- iterate() adds "explicit_valence" and "explicit_degree"
- "cell_centered" setting added
- by grid-cell background gradient "bg_gradient=2"
- look_at() added
- experimental "curve_new" / "move_on_curve"
* Developer
- C++17 required
- pymol-testing integrated
- pytest introduced
- Github Actions CI
* And many other fixes and small additions provided by
developers and the community...
- spec file:
* re-add test related stuff as upstream introduced a pytest
based testing
* drop TestExporting.testglTF - requires an executable from
Schrodinger
* on Leap, drop / tweak some tests to fit old package versions
-------------------------------------------------------------------
Wed Aug 11 12:23:17 UTC 2023 - <hsk17@mail.de>
- update to 2.5.0
* File Import/Export
- DX binary map import (*dxbin)
- PDB/MMTF export: symmetry information now added
- Improved FASTA import
- Support for map.gz and mrc.gz extensions
* Builder & Panels
- Improved Fuse command (disallows hypervalent bonds,
substitute monovalent atoms instead of attaching to them)
- Customizable keyboard shortcut menu
- Properties inspector now supports unsetting settings with
“Delete” key
* Graphics & Visualization
- Ray interior colors now match primitives with
`set ray_interior_color, atomic`
- Isomesh transparency support
- `sphere_mode` 5 removed (9 as replacement)
- Curved cartoon cylindrical helices
- Isosurface generation via marching cubes with setting
`isosurface_algorithm, (0, 1)` (0 requires VTKm)
* PBC Handling
- Periodic boundary conditions supported in rebond, smooth,
and intra_fit
* Python API
- Python 2 support removed
- pbc argument added to rebond, smooth, and intra_fit
- png(None) returns bytes
- scene_order() allows list for `names`
- pbc_wrap() and pbc_unwrap added
- matrix_reset() supports `state=0` for all states
- editing_ring() added
- unset now restores the default value for global settings
- load_traj now uses state=1 by default
- get_area command and dots representation: Exclude
“flag ignore” atoms
- no-o3.patch: adapt to 2.5.0
- spec file:
* some tweaks to adapt to 2.5.0
* remove test related stuff; test run commands are removed
from 2.5.0 as unmaintained and useless
-------------------------------------------------------------------
Wed May 19 04:27:29 UTC 2021 - Steve Kowalik <steven.kowalik@suse.com>
- Remove the execute bit from some test scripts to remove a spurious
requirement.
-------------------------------------------------------------------
Sun Feb 21 10:23:25 UTC 2021 - andy great <andythe_great@pm.me>
- Skip python3.6 because numpy no longer support it.
- Add mmtf-cpp-devel and use msgpackc.
- Attempt to get the test to run.
* Use _service to download pymol-testing for test data.
* Use bcond to enable/disable testing arguments.
* Pymol seems to need itself to test.
* Add %check section.
-------------------------------------------------------------------
Tue Sep 1 16:19:42 UTC 2020 - Matej Cepl <mcepl@suse.com>
- Update to 2.4.0:
* load_traj
- support netcdf format
- support `selection` argument with all file formats
* CCP4/MRC Map Support
- Distinguish .ccp4 and .mrc extensions (regarding origin)
- .map extension: auto-detect the format
* New distance mode 8
* MMTF export: Consider `pdb_retain_ids` setting
* GLTF export (based on collada2gltf)
* New `internal_gui_name_color_mode` setting
* MPEG4 Movie export: Apply `movie_fps` setting to exported
file
* Python API
- Improved error handling with exceptions
- New: cmd.rebond()
- New: cmd.get_capabilities()
- Fix: cmd.get_bonds() state off by one
- cmd.fit() et al.: raise on error
* Launch Options
- Restore `-V` launch argument for external GUI height
- macOS: `open` event opens new window
-------------------------------------------------------------------
Sat Feb 1 18:34:11 UTC 2020 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
- Remove glew runtime dependency (only contains debug tools and
documentation).
- Remove freeglut build dependency (unused unless enabled with
'--glut' setup.py option).
- Use https for URL.
-------------------------------------------------------------------
Mon Feb 11 15:49:44 CET 2019 - Matej Cepl <mcepl@suse.com>
- Upgrade to 2.3.0:
* atom-level cartoon_transparency
* aln export for Nucleic Acids
* new API function: cmd.set_raw_alignment()
* fetch async=0 by default
* fast MMTF export (requires mmtf-cpp)
* new setting: seq_view_gap_mode
-------------------------------------------------------------------
Thu Jan 03 22:17:20 UTC 2019 - opensuse-packaging@opensuse.org
- Update to version 2.2.0+git.1544795767.c481a7c1:
* fix SettingUniqueFromPyList w/ float3
* remove pymol::Image::Image(T&& vec, ...)
* refactor: pymol::Image tweaks
* rewrite "get_raw_alignment"
* refactor: pymol::vla::operator->() usage
* fix #16 pymol::vla::operator[] for VS2015 32bit
* fix pymol::vla::operator+ for VS2015
* pymol::Image::pixels()
* fix build
* fix macOS build
- Switch off msgpackc as we don't have mmtf-cpp packaged.
-------------------------------------------------------------------
Thu Aug 23 11:33:41 UTC 2018 - tchvatal@suse.com
- Version update to 2.2.0:
* Switch devel links to github
* No finegraned news file see ChangeLog for commit info
- Rebase patch no-o3.patch
-------------------------------------------------------------------
Thu Aug 23 11:30:41 UTC 2018 - tchvatal@suse.com
- Fix fdupes call
- Install license and docu files
-------------------------------------------------------------------
Wed Jun 6 11:46:38 UTC 2018 - jengelh@inai.de
- Trim marketing words from description.
-------------------------------------------------------------------
Wed May 2 11:38:24 UTC 2018 - tchvatal@suse.com
- Update to normal release that was released on 2018-03-19, 2 commits
changing tiny stuff compared to svn rev 4187
- Rename pymol to python-pymol to respect the packaging guidelines
- Fix qt5 devel python dependency to pull py3 and py2 both
- Obey system optflags instead of passing -O3
* no-o3.patch
-------------------------------------------------------------------
Tue Mar 13 22:33:00 UTC 2018 - dhall@wustl.edu
- update to svn rev 4187
* PyQt interface (2.1.0)
* stick_round_nub for COLLADA export
* UTF-8 in feedback
* display_scale_factor (ported from Incentive PyMOL)
* dx map import: support "type float" and skewed delta
* new selection keywords: polymer.protein polymer.nucleic
* new command: multifilesave
* MMTF export (requires simplemmtf python module)
* select: present, state -1 -> current object state
* create: source_state = -1 -> current
(was: source_state = -1/0 -> all)
* cif: support quoted '?' and '.' as values
cif_get_array -> None instead of empty string for ? and .
* fix copy discrete object w/o coords
* fix loading pdbqr AutoDock 4 atom types
* fix get_model('none') and get_str('mol', 'none')
* h_add refactored: 5x faster, support discrete objects-
-------------------------------------------------------------------
Tue Jan 16 16:35:27 UTC 2018 - dhall@wustl.edu
- update to svn rev 4184
* Python 3.7 support (https://sf.net/p/pymol/bugs/197/)
* enable align with alt-codes
- allow matching of non-alt-code to alt-code atoms in alignments
- swap sorting priority of 'name' and 'alt' identifiers
- sort empty 'alt' before non-empty 'alt'
* flags 6 and 7 for protein and nucleic acid
* mmCIF: read _atom_site.pdbx_formal_charge
* improve coordinate loading from mmcif chem_comp files
- ignore columns with all ? (missing) values
- select columns with "chem_comp_cartn_use" setting
* fix h_add: skip missing coordinates
* Python API: New "auto library mode". Automatically start a
non-GUI PyMOL instance if the pymol.cmd API is used without
running pymol.launch() first
* pdb_echo_tags for mmCIF and MMTF
* command parser: improve exception handling
* fix some PSE export memory leaks
* pymol2.cmd2: eliminate (non-weak) circular references
* movie making: reinterpolate after add_nutate/add_roll etc.
* support "module:callable" in loadfunctions/safefunctions
* yellow state indicator for discrete objects
* mpng modal draw improvements
* fix elements from .gro files (pymol/bugs/196, r4181 regression)
* save .mtl: raise exception
* Python 3:
- fix "GUI Font Size" dialog (pmw/bugs/47)
- fix COLLADA export
* some elements wrong from SDF and XYZ
* pse_export_version support with Python 3
-------------------------------------------------------------------
Fri Oct 20 22:03:33 UTC 2017 - dhall@wustl.edu
- 1.9.0.0
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session
-------------------------------------------------------------------
Wed Sep 20 18:39:35 UTC 2017 - dhall@wustl.edu
- update to svn rev 4177
* expose "oneletter" to label/iterate
* sequence viewer: MSE=M SEC=U
* wire/licorice rep aliases
* menu: A > copy to object
* new commands: copy_to, uniquify
* fix slow 'extract' performance
-------------------------------------------------------------------
Wed Aug 16 21:30:00 UTC 2017 - dhall@wustl.edu
- obsolete and provide pymol
-------------------------------------------------------------------
Fri Aug 4 16:49:23 UTC 2017 - dhall@wustl.edu
- move to python singlespec
-------------------------------------------------------------------
Fri Aug 4 15:47:20 UTC 2017 - dhall@wustl.edu
- 1.8.7.0
* support "not ..." and "enabled" in name patterns (e.g.: delete not enabled)
* improve/fix unicode+utf-8 handling for labels
* iterate color settings: type int (e.g.: iterate all, print(s.sphere_color))
* fix cmd.load with contents https://sf.net/p/pymol/mailman/message/35966326/
* fix ray tracing of stick_ball + valence https://sf.net/p/pymol/mailman/message/35928857/
* web.pymolhttpd -> pymol.pymolhttpd
Generic "web" name conflicts with webpy
https://sf.net/p/pymol/bugs/148/
* make build reproducible
https://sf.net/p/pymol/patches/12/
* delete obsolete packaging files
* internal command line: consistent behavior across platforms
* new "label" selection operator
* alter_state: remove restriction on x/y/z/flags
* iterate/label: expose "state" for discrete atoms
* CTRL+L drag/click -> move/center in 3-Button-Viewing mode
* auto-detect $PREFIX/share/pymol as $PYMOL_PATH
* locale LC_NUMERIC=C float parsing/formatting
* Python 3: fix wrong PyCapsule_New destructor
* PSE compatibility between Python 2 and 3
-------------------------------------------------------------------
Fri May 5 17:03:12 UTC 2017 - dhall@wustl.edu
- 1.8.6.1 fixes
* Python 3.6 fixes
* Python 3: fix builder bond order buttons (Red Hat Bug 1442127)
* fix MAE export PDB residue/atom names
* restored "scene_animation" setting (1.7.6 regression)
* restored "import cmd" prevention (1.8.6.0 regression)
-------------------------------------------------------------------
Mon Mar 13 18:02:44 UTC 2017 - dhall@wustl.edu
- remove explicity library dependency
-------------------------------------------------------------------
Mon Mar 13 17:51:51 UTC 2017 - dhall@wustl.edu
- require libmsgpack
-------------------------------------------------------------------
Mon Mar 13 17:25:19 UTC 2017 - dhall@wustl.edu
- 1.8.6.0 release
* mmtf: "ignore" flag for hetatm
* mmtf: msgpack version check
* INSTALL: env variables documentation
* Tcl/Tk menu updates
* fast MMTF load support in C++ (adds msgpack-c dependency)
* extra_fit: report RMS for method=cealign; Thanks to Hongbo Zhu
* CTRL-L ligand zoom
* preset > classified (auto_show_classified equivalent)
* preset > interface (ported from Incentive PyMOL 1.8.0)
* set_key auto-completion
* command completion for selection language
* fix connect_mode=4 for N-H1 and N-H3
* fix CGO ALPHA and dup COLOR issue
* width/height arguments for movie export (mpng, movie.produce)
* fetch: support "fetch EMD-3489"
* auto_show_classified -1 => 3 for 500k+ atoms
* pick_shading => surface_color_smoothing off
* cleanup: eliminate pymol.pymol_launch variable
* update molfile plugins to VMD version 1.9.3
* fetch 2fofc/fofc: update URLs, EDS will retire in 2017
* fix sf#102 pseudoatom multi-state problem
* editor.attach_amino_acid: fix PRO/N geometry
* avoid selection keyword name conflicts, append underscore
* load: allow format=plugin (by extension) and format=plugin:PLUGIN (with PLUGIN being a molfile plugin identifier)
* load format "vdb": VIPERdb PDB variant with retain_order=1
* load/load_traj: guess trajectory object
* fetch
* new setting "fetch_type_default"
* type=mmtf: fetch MMTF format
* type=2fofc/fofc: get spacegroup from PDBe API
* update download URLs
* new setting: editor_auto_measure
* new default: ray_transparency_oblique_power=4.0
* "update" command: support "current state" (-1)
* alter elem -> update protons and vdw
* don't allow "import cmd" (corrupts PyMOL namespace)
* support "python -m pymol" to launch PyMOL
-------------------------------------------------------------------
Thu Dec 1 14:43:24 UTC 2016 - dhall@wustl.edu
- 1.8.4.0 release
-------------------------------------------------------------------
Thu Sep 29 16:21:32 UTC 2016 - dhall@wustl.edu
- update to svn rev 4161
* pse_export_version: legacy scenes support
* use ignore_case setting with set_name command
* setup.py: detect anaconda prefix
-------------------------------------------------------------------
Thu Sep 22 16:10:17 UTC 2016 - dhall@wustl.edu
- update to svn rev 4160
* experimental MMTF load support
* map export in CCP4 format
* SDF V3000 import/export support
* refactor molecular file formats export: Unified handling of PDB, PQR, mmCIF, MOL2, SDF, XYZ, MAE
* PLY geometry import (as CGO)
* new command: unset_deep
* new setting: cartoon_all_alt: Create cartoon for every alt code
* stick_h_scale: default=1.0 (was: 0.4) but remove dependency on negative stick_radius
* auto_show_classified: Visualize small (< 50 atoms) polymer classified molecules like organic
* bymol selection operator: ignore zero-order bonds
* menu: isomesh/surface negative color
* improve alignment of residues with unknown resn (e.g. ligands):
give a match score of 5 to perfect matches of unknown residue codes.
Previously, those got match score -1.
* remove broken and obsolete "PMO" file support
* use "label_digits" setting with "label" command
* do not resize window when loading a session file
* fix ignored SCALE w/ identity rotation (e.g. 1WAP)
* fix "scene auto, clear" (Scene > Delete)
* new setting: pick_shading: do flat shading for programmable image color analysis
* experimental cmd.raw_image_callback: post cmd.draw() callback
-------------------------------------------------------------------
Mon Jun 20 15:54:38 UTC 2016 - dhall@wustl.edu
- update to svn rev 4159
* fix crash with ray tracing very large images
- use size_t instead of int for ray trace image buffer size
- correct image buffer size for antialias (was oversampled twice)
* fix crash with "align" and atoms without coordinates
* fix mutagenesis wizard "No Mutation" (update and rms commands)
* experimental FreeBSD support
* fix/silence various compiler warnings
* partly fixes sf#177, sf#178
* fix crash when loading PSE with bg_image_filenamefix ray trace memory limit; fix align crash
-------------------------------------------------------------------
Tue Apr 19 17:41:31 UTC 2016 - dhall@wustl.edu
- update to svnrev 4155
* experimental setting "pse_binary_dump"
* get_sasa_relative (command ported from Incentive PyMOL)
* Color menu uses util.color_deep (ported from Incentive PyMOL)
* C > by rep (ported from Incentive PyMOL)
* fix crash when saving mesh PSE without map
* fix isosurface invalidation when setting surface_negative_visible
* new setting: collada_background_box (by Jared Sampson)
* improve unicode filename loading
* fix "unset" of non-numeric settings
-------------------------------------------------------------------
Mon Mar 21 22:14:13 UTC 2016 - dhall@wustl.edu
- update to svnrev 4153/1.8.1.2
* new setting: auto_show_classified
* cartoon/ribbon: auto-detect CA-only models
* fix selection macros with wildcards and colon (:) residue ranges (1.8.0 regression)
* mmCIF: load missing residues independent of cif_use_auth setting
* fix pdb_insure_orthogonal for multi-model PDBs
-------------------------------------------------------------------
Mon Feb 8 20:00:49 UTC 2016 - dhall@wustl.edu
- update to svnrev 4149
* restore ignore_case=on default
* new setting: ignore_case_chain (default off)
* new setting: cartoon_gap_cutoff
* increase PYMOL_MAX_THREADS
* amber topology loading: bond order 1 for all bonds
* improve MOL2 file handling
* new grid_mode=3: grid per object-state
* distance mode=4: distance between centroids
* byring: new selection operator
* "Distances to Rings" mode in measurement wizard
* basic atom typing for MOL2 export
* cartoon dash: new dashed loop-like cartoon type
* object-level settings for measurements
* iterate: use Python exceptions
* iterate_state: ignore atomic=0 (fixes crash)
* format 'xyzstr': enable .gz and URL loading
* fix crash with object sele length >= 1024
* re-add -Wno-write-strings
* fix pmg_tk.skins.normal.encode()
* fix askopenfilename CANCEL case with multiple=0
* support segi, resn and name of arbitrary string length
* expose settings to iterate/alter via "s.<name>"
* Python 3 compatibility for champ module
* apbs_tools: apply fixes from Pymol-script-repo
* Tested with Python 2.6, 2.7, 3.4
* fix crash with empty alignment object from PSE
* fix cartoon ray tracing crash
* fix xyz export and emd fetch
* backport to pre-c++11 for OS X <= 10.8
* Tcl/Tk Settings GUI: feedback, radio buttons
* default alignment_as_cylinders changed to off
* fix restore legacy scenes with spaces
* fix invalid write in ObjectGadgetRampUpdate
-------------------------------------------------------------------
Thu Nov 5 20:59:23 UTC 2015 - dhall@wustl.edu
- update to svnrev 4139
* color autocomplete for ramps, improve volume blending
* new default: scene_buttons=on
* normalize_ccp4_maps=2 -> use mean and stdev from file header
* fix alignment with atoms w/o coords in a state
* new filetypes: pdbml, pdbqt, cml
* cell/symmetry: accept alpha=beta=gamma=0.0 as 90.0
* leave unknown protons as -1 instead of 0 (lonepair), fixes vdw assingment for unknown elements (1.8 instead of 0.5)
* reimplement reading full sequence from mmCIF. Only with cif_use_auth=off and retain_order=off. Fill in missing CA atoms for polypeptides.
* new API function cmd.get_object_ttt()
* APBS Plugin: --whitespace argument for pdb2pqr
* fix scene next/previous, was broken on Windows 10
* fix split_states with non-unique titles
* fix "File > Run" fails if path has spaces
-------------------------------------------------------------------
Wed Sep 30 22:39:33 UTC 2015 - dhall@wustl.edu
- update to svnrev 4136
* cartoon_trace_atoms for sheets, fast connect_mode=4
* fix crash after headless ray tracing empty cartoon
* fix building on CentOS 6.3 / python2.6 / gcc 4.4.7
* cif_keepinmemory, pymol.querying.cif_get_array (experimental)
* ramp_update (new command)
* ramp objects now have "A > Range > ..." and "C > ..." menus
* mmCIF _chem_comp_atom: skip atoms with missing coordinates, prefer ideal over model coordinates
* cmd.set_key() decorator support
* fix isosurface all_states rendering
* pdb_hetatm_guess_valences for CIF loading
* mutagenesis wizard: improve "apply" performance
* fix measurement and alignment object partial PSE loading
* some load/save refactoring
* keep atom IDs when creating object from selection
* when renaming group "A" to "B", then also rename entry "A.X" to "B.X"
-------------------------------------------------------------------
Tue Jul 14 15:06:53 UTC 2015 - dhall@wustl.edu
- update to svnrev 4131
* fix handling of _pdbx_struct_assembly_gen with repeated asym_id
* create assembly for multi-state objects
* no pdb_insure_orthogonal for assemblies
* fix "File > Run"
* some "const correctness" refactoring
* experimental pymol.querying.get_object_ttt
* fix assemblies for cases like 4f3r which have multiple entries in the
_pdbx_struct_assembly_gen table
* fix ref counts in iterate/alter subscripts
* improve side_chain_helper and nucleic_adic_mode situation
* eliminate all "try/catch" blocks for std::map lookups
* clean up some MemoryDebug stuff and remove unused jenarix wrapper
* some mmCIF bonding fixes
* Experimental: cmd.get_assembly_ids
* mmCIF: support "_atom_site.pdbe_label_seq_id"
* mmCIF: set "ignore" flag for HETATMSs (no surface)
* improve memory usage and performance of components.cif parsing
* fix https://sf.net/p/pymol/bugs/169/
* fetch 'cif' by default
* fix 5-letter cif-fetch
* fix mutagenesis wizard for ignore_case=0
* add some documentation
* port selection macro parsing to C
* side-effects for settings min/max
* warn if selecting with lower-case arguments
* fix "File > Open" from drive root on Windows
* std::array replacement for pre-C++11
* define NOMINMAX, fmax -> std::max
* correct setting-level handling in presets
* unset: restore default for string/float3/color, warn for int/bool/float
* fix "Display > Sequence" needs redisplay
* migrate seq_view_label_color=white from old PSE
* remove machine generated code from web/pymolhttpd.py
* fix segfault in read_pdbx_struct_assembly
* use snprintf instead of to_string (for c++0x)
* https://sourceforge.net/p/pymol/patches/10/
* change default (!) of "ignore_case" setting to off. Case insensitve
identifier matching is not pctical anymore with large structures
which use upper and lower case chain identifiers.
* new setting "assembly" to load assemblies from mmCIF as multi-state
objects with all_states=1
* new setting "cif_use_auth" controls whether mmCIF "auth" identifiers
are used or not (on by default)
* mmCIF "CA/P ATOMS ONLY" chains: set atom-level cartoon_trace_atoms
and ribbon_trace_atoms
* CIF discrete and irregular multi-model loading support
* support "pdb_honor_model_number" setting for CIF
* load multiple objects ("data_" blocks) from one CIF file (multiplex=-1)
* don't store AtmToIdx, DiscreteAtmToIdx or DiscreteCSet to PSE
(unless pse_export_version <= 1.76)
* make python2.6 compatible
-------------------------------------------------------------------
Tue May 5 00:55:53 UTC 2015 - dhall@wustl.edu
- update to 1.7.6.0
* fix crash when loading malformed CIF file
* cif export fix for natoms = 0
* ignore SCALE matrices with negative determinant
* fix memory leaks with iterate/alter
* fix crash when saving PSE with deleted ramp
* VASP file support for: CHGCAR, OUTCAR, POSCAR, XDATCAR
* psf file support
* fix several memory leaks
* fix memory leak in get_global_components_bond_dict
* new setting: pse_export_version to save to old session formats
* change default: pdb_conect_nodup 0 -> 1
* sphere_mode=-1 -> 9 if shaders available else 0
* fix Tcl/Tk File menu unicode handling
* scenes: Restore the old behavior that when recalling a scene, all objects
which were not present when storing the scene are disabled.
* fix auto-complete for filenames with spaces
* fix an object menu panel group ordering problem
* remove unused variables (Partly applies https://sourceforge.net/p/pymol/bugs/166/)
* lots of: char* -> const char*
* remove inline Parse functions, simplify ParseFloat3List
* make functions static
* mmCIF: support CHEM_COMP_BOND from mmCIF file
* residue information for MOL2 export
* find > polar contacts > between chains
* keep initial scene when restoring legacy scenes
* remove static PFNGL* function declarations
https://sourceforge.net/p/pymol/bugs/165/
* removed obsolete code and settings: use_display_lists, simplify_display_lists, excl_display_lists_shaders
* rename _PYMOL_OPENGL_SHADERS -> _PYMOL_ARB_SHADERS
* SingletonPyMOLGlobalsNULL.patch
* https://sourceforge.net/p/pymol/bugs/162/
- Free ShaderMgr after Scene
- check (G != NULL) in MainOnExit
* https://sourceforge.net/p/pymol/bugs/161/
apply clang logical-op-parentheses suggestion
* more `const char *` arguments refactoring
* fixed roving density and roving detail demos (regression from last commit)
http://sourceforge.net/p/pymol/bugs/156
* fix "narrowing conversion" C++ errors
* removed unused code and preprocessors:
_PYMOL_GL_DRAWARRAYS
_PYMOL_GL_CALLLISTS
_PYMOL_CGO_DRAWARRAYS
_PYMOL_CGO_DRAWBUFFERS
OPENGL_ES_1
OPENGL_ES_2
* removed deprecated "register" specifier
* mmCIF _atom_sites.fract_transf support (SCALEn equivalent)
* Complete port of scenes to C++
* warn user if setting a setting on the wrong level
* cmd.extendaa: shortcut for cmd.extend with argument auto-completion
* reduced memory footprint of AtomInfoType
* expose "reps" to iterate/alter
* expose "protons" to iterate/alter
* adaptive cartoon quality and sampling, depending on number of atoms
* fix ring center color with cartoon_ring_color=default
* make SelectorGetTmp strictly molecular, fixes for example "dss" with group names
* fix "copy" can cause crash
* fix "custom" selection operator
* consider spec_count in shaders
* don't invalidate shaders for lighting settings
* don't disable shaders for all Intel chips
* don't touch sphere_mode when disabling shaders
* map_new buffer == -1 -> gaussian_resolution
* fix all_states picking
* remove cylinder_shader_ff_workaround and cylinders_shader_filter_faces
* remove unused gl_ambient setting
* fix Tcl/Tk menu settings logging
* fix: grid mode scales down label size incorrectly
* fix: no animate argument for cmd.origin
* fix side_chain_helper for hetatm polymer atoms
* fix .mmd export
* refactor many function to take "const" pointer arguments
-------------------------------------------------------------------
Thu Mar 12 17:30:12 UTC 2015 - dhall@wustl.edu
- update to svn rev 4108
* Fix error with multiple open "Save Molecule" dialogs
* https://sourceforge.net/p/pymol/mailman/message/33286949/
* fix windows build, PRIu64
* cmd.as -> cmd.show_as in old test files
* remove obsolete pymol2/make_cmd2.py
-------------------------------------------------------------------
Mon Jan 5 22:27:46 UTC 2015 - dhall@wustl.edu
- update to svn rev 4107
* elimination of more compiler warnings
* silence numpy deprecation warnings (NPY_1_7_API_VERSION)
* fix cif export with multiple objects
* glutLeaveFullScreen: fix for freeglut < 2.6 and < 2.8
-------------------------------------------------------------------
Thu Dec 4 14:43:13 UTC 2014 - dhall@wustl.edu
- update to pymol 1.7.4.0
* use COMPONENTS_CIF environment variable to look for components.cif
* update fetchHosts and hostPaths URLs
* change order of mmCIF _atom_site columns on export
* use _atom_site.label_asym_id as segi
* cif: read first_model_num
* fixed _foo?bar lookup could fail in mmCIF parsing
* deprecated full_screen setting (use full_screen command)
* fix collada_* settings in pymol.settings
* fix apbs_tools for tcl/tk 8.6
* fix fullscreen on OSX w/ GLUT
* silence compiler warnings
-------------------------------------------------------------------
Thu Oct 30 14:25:17 UTC 2014 - dhall@wustl.edu
- add libxml dependencies
-------------------------------------------------------------------
Mon Oct 20 20:37:41 UTC 2014 - dhall@wustl.edu
- update to svn rev 4098
* setup.py and plugin manager fixes
- thanks to Justin Lecher for the bug reports
* COLLADA (dae) export support
- Implemented by Jared Sampson as his POSF project.
* fast CIF loading, 1.7.3.1 (unstable/experimental)
* fast PDBx/mmCIF and core CIF loading in C++
* new connect_mode=4 does bonding with components.cif dictionary
(mmCIF only, components.cif needs to be present in current
directory)
* gray out residues in the sequence viewer that are missing from the
current state; Read missing residues from mmCIF files
(_pdbx_unobs_or_zero_occ_residues records) so that they show up in
the sequence viewer
* add spider map reading support
* load "map" as ccp4 instead of throwing "ambiguous" error
* xyz write support
* Improve right-button zoom: use origin instead of clipping slab
center as depth indicator, fixes zoom speed when far clipping plane
is very far away
* don't use dynamic_width for nonbonded rep
-------------------------------------------------------------------
Wed Oct 1 19:54:15 UTC 2014 - dhall@wustl.edu
- update to svnrev 4095
* delete obsolete layer*/Makefile.*
* ignore SCALEn if CRYST1 is 1x1x1 or invalid
* new/refactored API functions for accessing coordinates and maps as numpy arrays
* new API function: cmd.set_state_order
* Session file (PSE) support for callback objects
* fix/silence many compiler warnings
* fix bg_rgb_top/bg_rgb_bottom side effects
* revert "fix setting surface_circumscribe"
* delete some obsolete files
-------------------------------------------------------------------
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 (::)
-------------------------------------------------------------------
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"
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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
-------------------------------------------------------------------
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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