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Name: python312-pymol | Distribution: openSUSE Tumbleweed |
Version: 3.0.0 | Vendor: openSUSE |
Release: 1.1 | Build date: Tue Jun 18 17:42:12 2024 |
Group: Productivity/Scientific/Chemistry | Build host: reproducible |
Size: 23052527 | Source RPM: python-pymol-3.0.0-1.1.src.rpm |
Packager: http://bugs.opensuse.org | |
Url: https://pymol.org/ | |
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.
Python-2.0
* Tue Jun 18 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 * Fri Aug 11 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 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 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 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
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Fabrice Bellet, Sun Aug 18 01:11:36 2024