Changelog for python3-pymol-2.4.0-bp156.3.5.x86_64.rpm :

* Wed May 19 2021 Steve Kowalik - Remove the execute bit from some test scripts to remove a spurious requirement.
* Sun Feb 21 2021 andy great - 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 - 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 Brüns - 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 - 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-packagingAATTopensuse.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 tchvatalAATTsuse.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 tchvatalAATTsuse.com- Fix fdupes call- Install license and docu files
* Wed Jun 06 2018 jengelhAATTinai.de- Trim marketing words from description.
* Wed May 02 2018 tchvatalAATTsuse.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.edu- obsolete and provide pymol
* Fri Aug 04 2017 dhallAATTwustl.edu- move to python singlespec
* Fri Aug 04 2017 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.edu- remove explicity library dependency
* Mon Mar 13 2017 dhallAATTwustl.edu- require libmsgpack
* Mon Mar 13 2017 dhallAATTwustl.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 dhallAATTwustl.edu- 1.8.4.0 release
* Thu Sep 29 2016 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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.\"
* 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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.edu- add libxml dependencies
* Mon Oct 20 2014 dhallAATTwustl.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