* Tue Jan 16 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 2017 dhall@wustl.edu
- 1.9.0.0
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session
* Wed Sep 20 2017 dhall@wustl.edu
- update to svn rev 4177
* expose "oneletter" to label/iterate
* sequence viewer: MSE=M SEC=U
* wire/licorice rep aliases
* menu: A > copy to object
* new commands: copy_to, uniquify
* fix slow 'extract' performance
* Wed Aug 16 2017 dhall@wustl.edu
- obsolete and provide pymol
* Fri Aug 04 2017 dhall@wustl.edu
- move to python singlespec
* Fri Aug 04 2017 dhall@wustl.edu
- 1.8.7.0
* support "not ..." and "enabled" in name patterns (e.g.: delete not enabled)
* improve/fix unicode+utf-8 handling for labels
* iterate color settings: type int (e.g.: iterate all, print(s.sphere_color))
* fix cmd.load with contents https://sf.net/p/pymol/mailman/message/35966326/
* fix ray tracing of stick_ball + valence https://sf.net/p/pymol/mailman/message/35928857/
* web.pymolhttpd -> pymol.pymolhttpd
Generic "web" name conflicts with webpy
https://sf.net/p/pymol/bugs/148/
* make build reproducible
https://sf.net/p/pymol/patches/12/
* delete obsolete packaging files
* internal command line: consistent behavior across platforms
* new "label" selection operator
* alter_state: remove restriction on x/y/z/flags
* iterate/label: expose "state" for discrete atoms
* CTRL+L drag/click -> move/center in 3-Button-Viewing mode
* auto-detect $PREFIX/share/pymol as $PYMOL_PATH
* locale LC_NUMERIC=C float parsing/formatting
* Python 3: fix wrong PyCapsule_New destructor
* PSE compatibility between Python 2 and 3
* Fri May 05 2017 dhall@wustl.edu
- 1.8.6.1 fixes
* Python 3.6 fixes
* Python 3: fix builder bond order buttons (Red Hat Bug 1442127)
* fix MAE export PDB residue/atom names
* restored "scene_animation" setting (1.7.6 regression)
* restored "import cmd" prevention (1.8.6.0 regression)
* Mon Mar 13 2017 dhall@wustl.edu
- remove explicity library dependency
* Mon Mar 13 2017 dhall@wustl.edu
- require libmsgpack
* Mon Mar 13 2017 dhall@wustl.edu
- 1.8.6.0 release
* mmtf: "ignore" flag for hetatm
* mmtf: msgpack version check
* INSTALL: env variables documentation
* Tcl/Tk menu updates
* fast MMTF load support in C++ (adds msgpack-c dependency)
* extra_fit: report RMS for method=cealign; Thanks to Hongbo Zhu
* CTRL-L ligand zoom
* preset > classified (auto_show_classified equivalent)
* preset > interface (ported from Incentive PyMOL 1.8.0)
* set_key auto-completion
* command completion for selection language
* fix connect_mode=4 for N-H1 and N-H3
* fix CGO ALPHA and dup COLOR issue
* width/height arguments for movie export (mpng, movie.produce)
* fetch: support "fetch EMD-3489"
* auto_show_classified -1 => 3 for 500k+ atoms
* pick_shading => surface_color_smoothing off
* cleanup: eliminate pymol.pymol_launch variable
* update molfile plugins to VMD version 1.9.3
* fetch 2fofc/fofc: update URLs, EDS will retire in 2017
* fix sf#102 pseudoatom multi-state problem
* editor.attach_amino_acid: fix PRO/N geometry
* avoid selection keyword name conflicts, append underscore
* load: allow format=plugin (by extension) and format=plugin:PLUGIN (with PLUGIN being a molfile plugin identifier)
* load format "vdb": VIPERdb PDB variant with retain_order=1
* load/load_traj: guess trajectory object
* fetch
* new setting "fetch_type_default"
* type=mmtf: fetch MMTF format
* type=2fofc/fofc: get spacegroup from PDBe API
* update download URLs
* new setting: editor_auto_measure
* new default: ray_transparency_oblique_power=4.0
* "update" command: support "current state" (-1)
* alter elem -> update protons and vdw
* don't allow "import cmd" (corrupts PyMOL namespace)
* support "python -m pymol" to launch PyMOL
* Thu Dec 01 2016 dhall@wustl.edu
- 1.8.4.0 release
* Thu Sep 29 2016 dhall@wustl.edu
- update to svn rev 4161
* pse_export_version: legacy scenes support
* use ignore_case setting with set_name command
* setup.py: detect anaconda prefix
* Thu Sep 22 2016 dhall@wustl.edu
- update to svn rev 4160
* experimental MMTF load support
* map export in CCP4 format
* SDF V3000 import/export support
* refactor molecular file formats export: Unified handling of PDB, PQR, mmCIF, MOL2, SDF, XYZ, MAE
* PLY geometry import (as CGO)
* new command: unset_deep
* new setting: cartoon_all_alt: Create cartoon for every alt code
* stick_h_scale: default=1.0 (was: 0.4) but remove dependency on negative stick_radius
* auto_show_classified: Visualize small (< 50 atoms) polymer classified molecules like organic
* bymol selection operator: ignore zero-order bonds
* menu: isomesh/surface negative color
* improve alignment of residues with unknown resn (e.g. ligands):
give a match score of 5 to perfect matches of unknown residue codes.
Previously, those got match score -1.
* remove broken and obsolete "PMO" file support
* use "label_digits" setting with "label" command
* do not resize window when loading a session file
* fix ignored SCALE w/ identity rotation (e.g. 1WAP)
* fix "scene auto, clear" (Scene > Delete)
* new setting: pick_shading: do flat shading for programmable image color analysis
* experimental cmd.raw_image_callback: post cmd.draw() callback
* Mon Jun 20 2016 dhall@wustl.edu
- update to svn rev 4159
* fix crash with ray tracing very large images
- use size_t instead of int for ray trace image buffer size
- correct image buffer size for antialias (was oversampled twice)
* fix crash with "align" and atoms without coordinates
* fix mutagenesis wizard "No Mutation" (update and rms commands)
* experimental FreeBSD support
* fix/silence various compiler warnings
* partly fixes sf#177, sf#178
* fix crash when loading PSE with bg_image_filenamefix ray trace memory limit; fix align crash
* Tue Apr 19 2016 dhall@wustl.edu
- update to svnrev 4155
* experimental setting "pse_binary_dump"
* get_sasa_relative (command ported from Incentive PyMOL)
* Color menu uses util.color_deep (ported from Incentive PyMOL)
* C > by rep (ported from Incentive PyMOL)
* fix crash when saving mesh PSE without map
* fix isosurface invalidation when setting surface_negative_visible
* new setting: collada_background_box (by Jared Sampson)
* improve unicode filename loading
* fix "unset" of non-numeric settings
* Mon Mar 21 2016 dhall@wustl.edu
- update to svnrev 4153/1.8.1.2
* new setting: auto_show_classified
* cartoon/ribbon: auto-detect CA-only models
* fix selection macros with wildcards and colon (:) residue ranges (1.8.0 regression)
* mmCIF: load missing residues independent of cif_use_auth setting
* fix pdb_insure_orthogonal for multi-model PDBs
* Mon Feb 08 2016 dhall@wustl.edu
- update to svnrev 4149
* restore ignore_case=on default
* new setting: ignore_case_chain (default off)
* new setting: cartoon_gap_cutoff
* increase PYMOL_MAX_THREADS
* amber topology loading: bond order 1 for all bonds
* improve MOL2 file handling
* new grid_mode=3: grid per object-state
* distance mode=4: distance between centroids
* byring: new selection operator
* "Distances to Rings" mode in measurement wizard
* basic atom typing for MOL2 export
* cartoon dash: new dashed loop-like cartoon type
* object-level settings for measurements
* iterate: use Python exceptions
* iterate_state: ignore atomic=0 (fixes crash)
* format 'xyzstr': enable .gz and URL loading
* fix crash with object sele length >= 1024
* re-add -Wno-write-strings
* fix pmg_tk.skins.normal.encode()
* fix askopenfilename CANCEL case with multiple=0
* support segi, resn and name of arbitrary string length
* expose settings to iterate/alter via "s.<name>"
* Python 3 compatibility for champ module
* apbs_tools: apply fixes from Pymol-script-repo
* Tested with Python 2.6, 2.7, 3.4
* fix crash with empty alignment object from PSE
* fix cartoon ray tracing crash
* fix xyz export and emd fetch
* backport to pre-c++11 for OS X <= 10.8
* Tcl/Tk Settings GUI: feedback, radio buttons
* default alignment_as_cylinders changed to off
* fix restore legacy scenes with spaces
* fix invalid write in ObjectGadgetRampUpdate
* Thu Nov 05 2015 dhall@wustl.edu
- update to svnrev 4139
* color autocomplete for ramps, improve volume blending
* new default: scene_buttons=on
* normalize_ccp4_maps=2 -> use mean and stdev from file header
* fix alignment with atoms w/o coords in a state
* new filetypes: pdbml, pdbqt, cml
* cell/symmetry: accept alpha=beta=gamma=0.0 as 90.0
* leave unknown protons as -1 instead of 0 (lonepair), fixes vdw assingment for unknown elements (1.8 instead of 0.5)
* reimplement reading full sequence from mmCIF. Only with cif_use_auth=off and retain_order=off. Fill in missing CA atoms for polypeptides.
* new API function cmd.get_object_ttt()
* APBS Plugin: --whitespace argument for pdb2pqr
* fix scene next/previous, was broken on Windows 10
* fix split_states with non-unique titles
* fix "File > Run" fails if path has spaces
* Wed Sep 30 2015 dhall@wustl.edu
- update to svnrev 4136
* cartoon_trace_atoms for sheets, fast connect_mode=4
* fix crash after headless ray tracing empty cartoon
* fix building on CentOS 6.3 / python2.6 / gcc 4.4.7
* cif_keepinmemory, pymol.querying.cif_get_array (experimental)
* ramp_update (new command)
* ramp objects now have "A > Range > ..." and "C > ..." menus
* mmCIF _chem_comp_atom: skip atoms with missing coordinates, prefer ideal over model coordinates
* cmd.set_key() decorator support
* fix isosurface all_states rendering
* pdb_hetatm_guess_valences for CIF loading
* mutagenesis wizard: improve "apply" performance
* fix measurement and alignment object partial PSE loading
* some load/save refactoring
* keep atom IDs when creating object from selection
* when renaming group "A" to "B", then also rename entry "A.X" to "B.X"
* Tue Jul 14 2015 dhall@wustl.edu
- update to svnrev 4131
* fix handling of _pdbx_struct_assembly_gen with repeated asym_id
* create assembly for multi-state objects
* no pdb_insure_orthogonal for assemblies
* fix "File > Run"
* some "const correctness" refactoring
* experimental pymol.querying.get_object_ttt
* fix assemblies for cases like 4f3r which have multiple entries in the
_pdbx_struct_assembly_gen table
* fix ref counts in iterate/alter subscripts
* improve side_chain_helper and nucleic_adic_mode situation
* eliminate all "try/catch" blocks for std::map lookups
* clean up some MemoryDebug stuff and remove unused jenarix wrapper
* some mmCIF bonding fixes
* Experimental: cmd.get_assembly_ids
* mmCIF: support "_atom_site.pdbe_label_seq_id"
* mmCIF: set "ignore" flag for HETATMSs (no surface)
* improve memory usage and performance of components.cif parsing
* fix https://sf.net/p/pymol/bugs/169/
* fetch 'cif' by default
* fix 5-letter cif-fetch
* fix mutagenesis wizard for ignore_case=0
* add some documentation
* port selection macro parsing to C
* side-effects for settings min/max
* warn if selecting with lower-case arguments
* fix "File > Open" from drive root on Windows
* std::array replacement for pre-C++11
* define NOMINMAX, fmax -> std::max
* correct setting-level handling in presets
* unset: restore default for string/float3/color, warn for int/bool/float
* fix "Display > Sequence" needs redisplay
* migrate seq_view_label_color=white from old PSE
* remove machine generated code from web/pymolhttpd.py
* fix segfault in read_pdbx_struct_assembly
* use snprintf instead of to_string (for c++0x)
* https://sourceforge.net/p/pymol/patches/10/
* change default (!) of "ignore_case" setting to off. Case insensitve
identifier matching is not pctical anymore with large structures
which use upper and lower case chain identifiers.
* new setting "assembly" to load assemblies from mmCIF as multi-state
objects with all_states=1
* new setting "cif_use_auth" controls whether mmCIF "auth" identifiers
are used or not (on by default)
* mmCIF "CA/P ATOMS ONLY" chains: set atom-level cartoon_trace_atoms
and ribbon_trace_atoms
* CIF discrete and irregular multi-model loading support
* support "pdb_honor_model_number" setting for CIF
* load multiple objects ("data_" blocks) from one CIF file (multiplex=-1)
* don't store AtmToIdx, DiscreteAtmToIdx or DiscreteCSet to PSE
(unless pse_export_version <= 1.76)
* make python2.6 compatible