Changelog for python2-pymol-1.9.0.0.svn4184-bp150.2.4.x86_64.rpm :

* Tue Jan 16 2018 dhallAATTwustl.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 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
* Wed Oct 01 2014 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 drhallAATTbu.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.edu- Add no-build-date.patch : eliminates build date in executable
* Mon Nov 11 2013 dhallAATTwustl.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 dhallAATTwustl.edu- Drop setup.patch: upstream fixed bug- update to svn rev 4045
* fix setup.py sys.argv
* Sat Oct 05 2013 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dimstarAATTopensuse.org- Add freetype2-devel: the source #includes ft2build.h, so it\'s only correct to build require it.
* Sun Mar 24 2013 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.edu- Adding checks for Quadro cards- Improved Plugin Manager; Thomas Holder\'s PyMOL OSFP project
* Fri Apr 13 2012 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 cfarrellAATTsuse.com- license update: Python-2.0 Use the SPDX identifier (http://www.spdx.org/licenses)
* Wed Jan 04 2012 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.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 dhallAATTwustl.edu- update to svn rev 3962:
* code cleanup
* fix opengl from python
* read and importing fixes
* Thu Jul 07 2011 dhallAATTwustl.edu- Small state bugfix- Feedback bugfix- Updated TNT to 3.0b
* Sun Jul 03 2011 saschpeAATTgmx.de- Spec file cleanup:
* Added proper license header
* Removed authors from description
* Fri Jun 17 2011 dhallAATTwustl.edu- have just one package rather than pymol+python-pymol, maybe chempy will split out later
* Thu Jun 16 2011 dhallAATTwustl.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 dhallAATTwustl.edu- update to svn version 3951- fix clipped group names- much faster ribbons
* Tue May 10 2011 dhallAATTwustl.edu- move pymol_path stuff into python module
* Tue May 10 2011 dhallAATTwustl.edu- fix dependencies- mark file as executable
* Tue May 10 2011 dhallAATTwustl.educorrect separation between pymol and python-pymol-
* Tue May 10 2011 dhallAATTwustl.eduInitial checkin of pymol 1.4.1-