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File pymol.changes of Package pymol
------------------------------------------------------------------- Tue Jan 16 16:35:27 UTC 2018 - dhall@wustl.edu - update to svn rev 4194 * 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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