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python39-pymol-2.4.0-3.3 RPM for armv6hl

From OpenSuSE Ports Tumbleweed for armv6hl

Name: python39-pymol Distribution: openSUSE Tumbleweed
Version: 2.4.0 Vendor: openSUSE
Release: 3.3 Build date: Fri Jul 9 04:47:15 2021
Group: Productivity/Scientific/Chemistry Build host: obs-arm-11
Size: 21370900 Source RPM: python-pymol-2.4.0-3.3.src.rpm
Packager: http://bugs.opensuse.org
Url: https://pymol.org/2/
Summary: A Molecular Viewer
PyMOL is a molecular graphics system targetted at medium to large
biomolecules like proteins. It can generate molecular graphics
images and animations.

Features include:

* Visualization of molecules, molecular trajectories and surfaces
  of crystallography data or orbitals
* Molecular builder and sculptor
* Internal raytracer and movie generator
* Fully extensible and scriptable via a python interface

The file formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile,
ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps.

Provides

Requires

License

Python-2.0

Changelog

* Wed May 19 2021 Steve Kowalik <steven.kowalik@suse.com>
  - Remove the execute bit from some test scripts to remove a spurious
    requirement.
* Sun Feb 21 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 01 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 01 2020 Stefan BrĂ¼ns <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 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 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 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 2018 tchvatal@suse.com
  - Fix fdupes call
  - Install license and docu files
* Wed Jun 06 2018 jengelh@inai.de
  - Trim marketing words from description.
* Wed May 02 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 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 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 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 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 2017 dhall@wustl.edu
  - obsolete and provide pymol
* Fri Aug 04 2017 dhall@wustl.edu
  - move to python singlespec
* Fri Aug 04 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 05 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 2017 dhall@wustl.edu
  - remove explicity library dependency
* Mon Mar 13 2017 dhall@wustl.edu
  - require libmsgpack
* Mon Mar 13 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 01 2016 dhall@wustl.edu
  - 1.8.4.0 release
* Thu Sep 29 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 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 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 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 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 08 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 05 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 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 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 05 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 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 05 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 04 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 2014 dhall@wustl.edu
  - add libxml dependencies
* Mon Oct 20 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 01 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 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 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 08 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 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 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 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 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 04 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 06 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 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 2013 dhall@wustl.edu
  - Add no-build-date.patch : eliminates build date in executable
* Mon Nov 11 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 07 2013 dhall@wustl.edu
  - Drop setup.patch: upstream fixed bug
  - update to svn rev 4045
    * fix setup.py sys.argv
* Sat Oct 05 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 09 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 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 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 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 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 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 04 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 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 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 2013 dimstar@opensuse.org
  - Add freetype2-devel: the source #includes ft2build.h, so it's
    only correct to build require it.
* Sun Mar 24 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 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 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 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 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 05 2012 dhall@wustl.edu
  - Adding checks for Quadro cards
  - Improved Plugin Manager; Thomas Holder's PyMOL OSFP project
* Fri Apr 13 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 06 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 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 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 2012 cfarrell@suse.com
  - license update: Python-2.0
    Use the SPDX identifier (http://www.spdx.org/licenses)
* Wed Jan 04 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 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 03 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 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 05 2011 dhall@wustl.edu
  - update to svn rev 3962:
    * code cleanup
    * fix opengl from python
    * read and importing fixes
* Thu Jul 07 2011 dhall@wustl.edu
  - Small state bugfix
  - Feedback bugfix
  - Updated TNT to 3.0b
* Sun Jul 03 2011 saschpe@gmx.de
  - Spec file cleanup:
    * Added proper license header
    * Removed authors from description
* Fri Jun 17 2011 dhall@wustl.edu
  - have just one package rather than pymol+python-pymol, maybe chempy
    will split out later
* Thu Jun 16 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 02 2011 dhall@wustl.edu
  - update to svn version 3951
  - fix clipped group names
  - much faster ribbons
* Tue May 10 2011 dhall@wustl.edu
  - move pymol_path stuff into python module
* Tue May 10 2011 dhall@wustl.edu
  - fix dependencies
  - mark file as executable
* Tue May 10 2011 dhall@wustl.edu
  correct separation between pymol and python-pymol-
* Tue May 10 2011 dhall@wustl.edu
  Initial checkin of pymol 1.4.1-

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Fabrice Bellet, Fri Nov 19 23:23:55 2021