forked from schrodinger/pymol-open-source
/
ChangeLog
5280 lines (2878 loc) · 247 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
=========================================================================
CHANGE LOG
=========================================================================
2021-05-10 Jarrett Johnson, Thomas Holder, Thomas Stewart
* 2.5.0
* File Import/Export
- DX binary map import (*dxbin)
- PDB/MMTF export: symmetry information now added
- Improved FASTA import
- Support for map.gz and mrc.gz extensions
* Builder & Panels
- Improved Fuse command (disallows hypervalent bonds, substitute monovalent atoms instead of attaching to them)
- Customizable keyboard shortcut menu
- Properties inspector now supports unsetting settings with “Delete” key
* Graphics & Visualization
- Ray interior colors now match primitives with `set ray_interior_color, atomic`
- Isomesh transparency support
- `sphere_mode` 5 removed (9 as replacement)
- Curved cartoon cylindrical helices
- Isosurface generation via marching cubes with setting `isosurface_algorithm, (0, 1)` (0 requires VTKm)
* PBC Handling
- Periodic boundary conditions supported in rebond, smooth, and intra_fit
* Python API
- Python 2 support removed
- pbc argument added to rebond, smooth, and intra_fit
- png(None) returns bytes
- scene_order() allows list for `names`
- pbc_wrap() and pbc_unwrap added
- matrix_reset() supports `state=0` for all states
- editing_ring() added
- unset now restores the default value for global settings
- load_traj now uses state=1 by default
- get_area command and dots representation: Exclude “flag ignore” atoms
2020-05-20 Thomas Holder, Jarrett Johnson
* 2.4.0
* load_traj
- support netcdf format
- support `selection` argument with all file formats
* CCP4/MRC Map Support
- Distinguish .ccp4 and .mrc extensions (regarding origin)
- .map extension: auto-detect the format
* New distance mode 8
* MMTF export: Consider `pdb_retain_ids` setting
* GLTF export (based on collada2gltf)
* New `internal_gui_name_color_mode` setting
* MPEG4 Movie export: Apply `movie_fps` setting to exported file
* Python API
- Improved error handling with exceptions
- New: cmd.rebond()
- New: cmd.get_capabilities()
- Fix: cmd.get_bonds() state off by one
- cmd.fit() et al.: raise on error
* Launch Options
- Restore `-V` launch argument for external GUI height
- macOS: `open` event opens new window
2019-02-11 Thomas Holder, Jarrett Johnson
* 2.3.0
* atom-level cartoon_transparency
* aln export for Nucleic Acids
* new API function: cmd.set_raw_alignment()
* fetch async=0 by default
2018-08-16 Thomas Holder, Jarrett Johnson
* fast MMTF export (requires mmtf-cpp)
* new setting: seq_view_gap_mode
* 2.3.0a0 (unstable/experimental)
2018-07-24 Thomas Holder, Jarrett Johnson
* 2.2.0
* Wizard > Mutagenesis > Nucleic Acids
* load format "pqr": retain_order=1
2018-07-03 Thomas Holder, Blaine Bell, Gabriel Marques
* Graphics refactoring, ported from Incentive PyMOL
Ported features:
- label improvements (multiline, connectors, background color)
- transparency_mode 3: Order-independent transparency
- bg_image_filename: Background image support
* new dependency (header-only): glm
2018-06-08 Thomas Holder <thomas.holder@schrodinger.com>
* fix selection wildcard (sf.net/p/pymol/bugs/209)
* fix PDB atom id > 99999 crash
* more robust PQR parsing
* pymol2.PyMOL() context manager
* new setting: cif_metalc_as_zero_order_bonds
* new setting: sdf_write_zero_order_bonds
* cif: accept _chem_comp_bond.type alias for _chem_comp_bond.value_order
2018-05-03 Thomas Holder <thomas.holder@schrodinger.com>
* fix anaglyph stereo in batch (headless) mode
* fix possible memory corruption with boolean settings
* measurement wizard: distances between states (all_states=on)
* get_fastastr: nucleic acid, by chain
* menu: A (Action) > group
* sequence viewer menu: ss (Secondary Structure)
* MAE export of groups (s_m_subgroupid)
* macOS: -O3 -fno-strict-aliasing (bugs/205)
2018-04-10 Thomas Holder <thomas.holder@schrodinger.com>
* sf.net/p/pymol/bugs/199 bash -> sh
* ignore zero-order bonds in neighbor lookup, this could cause
wrong bond order guessing in distance based bonding
* fix crash loading reduced 5ijo.mmtf
* volume panel: fix zoom (CTRL+R-Drag) and value input (R-Click)
* QOpenGLWidget support (not active by default)
* --gldebug -> backtrace on GL error
* 2.2.0a0 (unstable/experimental)
2018-03-13 Thomas Holder <thomas.holder@schrodinger.com>
* 2.1.0
* PyQt interface
2018-02-28 Thomas Holder <thomas.holder@schrodinger.com>
* stick_round_nub for COLLADA export
* UTF-8 in feedback
* display_scale_factor (ported from Incentive PyMOL)
* dx map import: support "type float" and skewed delta
2018-02-07 Thomas Holder <thomas.holder@schrodinger.com>
* new selection keywords: polymer.protein polymer.nucleic
* new command: multifilesave
* MMTF export (requires simplemmtf python module)
* select: present, state -1 -> current object state
* create: source_state = -1 -> current
(was: source_state = -1/0 -> all)
* cif: support quoted '?' and '.' as values
cif_get_array -> None instead of empty string for ? and .
* fix copy discrete object w/o coords
* fix loading pdbqr AutoDock 4 atom types
* fix get_model('none') and get_str('mol', 'none')
* h_add refactored: 5x faster, support discrete objects
2017-12-21 Thomas Holder, Piotr Rotkiewicz
* 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
2017-12-05 Thomas Holder, Piotr Rotkiewicz
* 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
2017-10-23 Thomas Holder <thomas.holder@schrodinger.com>
* pse_export_version support with Python 3 (experimental)
* fix setup.py --use-msgpackc=guess: catch EnvironmentError
2017-10-18 Thomas Holder <thomas.holder@schrodinger.com>
* 1.9.0.0
* use PyMOL 2.0 setting defaults
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session
2017-09-13 Thomas Holder, Piotr Rotkiewicz
* 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
2017-08-02 Thomas Holder <thomas.holder@schrodinger.com>
* 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/
* 1.8.7.0 (unstable/experimental)
2017-07-03 Thomas Holder <thomas.holder@schrodinger.com>
* web.pymolhttpd -> pymol.pymolhttpd
https://sf.net/p/pymol/bugs/148/
* make build reproducible
https://sf.net/p/pymol/patches/12/
2017-06-01 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2017-04-17 Thomas Holder <thomas.holder@schrodinger.com>
* 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)
* 1.8.6.1
2017-03-09 Thomas Holder, Piotr Rotkiewicz
* 1.8.6.0
2017-02-22 Thomas Holder <thomas.holder@schrodinger.com>
* fast MMTF load support in C++
* 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
* 1.8.5.1 (beta)
2017-01-19 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2016-12-14 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2016-12-05 Thomas Holder <thomas.holder@schrodinger.com>
* 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
* 1.8.5.0 (unstable/experimental)
2016-10-05 Thomas Holder <thomas.holder@schrodinger.com>
* 1.8.4.0
* setup.py: --no-launcher
2016-09-26 Thomas Holder <thomas.holder@schrodinger.com>
* pse_export_version: legacy scenes support
* use ignore_case setting with set_name command
* setup.py: detect anaconda prefix
* 1.8.3.3 (unstable/experimental)
2016-08-29 Thomas Holder <thomas.holder@schrodinger.com>
* 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
* 1.8.3.2 (unstable/experimental)
2016-05-26 Thomas Holder <thomas.holder@schrodinger.com>
* fix mutagenesis wizard "No Mutation" (update and rms commands)
* experimental FreeBSD support
* 1.8.2.1
2016-04-19 Thomas Holder <thomas.holder@schrodinger.com>
* 1.8.2.0
* 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
2016-03-27 Jared Sampson
* new setting: collada_background_box (default 0)
https://sourceforge.net/p/pymol/mailman/message/34961984/
2016-03-21 Thomas Holder, Gabriel Marques
* pse_export_version: save 1.7.6 compatible PSEs by default
* forward "set" to "set_bond" for bond-level settings
* fetch: use http instead of ftp with default host
* MOL2 export
- chain support (write substructure record)
* MOL2 import
- more reliable resn reconstruction
- hetatm=0 for subst_type=RESIDUE
- don't use root atom id for substructure mapping
* set_name w/ map: update dependents (mesh, surface, volume)
* skip mmCIF "CA ATOMS ONLY" detection (not needed anymore)
* fix COLLADA export crash with transparency
* fix load_traj crash w/ state-level settings
* 1.8.1.2 (beta)
2016-03-03 Thomas Holder <thomas.holder@schrodinger.com>
* new setting: auto_show_classified
* cartoon/ribbon: auto-detect CA-only models
* mmCIF reading of full sequence now independent of cif_use_auth
* mmCIF ss assignment to full residue, not only CA
* fix selection macros with wildcards and colon (:) residue ranges
(1.8.0 regression)
* fix SCALE coordinate transformation for multi-model PDBs (e.g. 1hho)
* fix logging of expressions which contain '''
2016-02-08 Thomas Holder <thomas.holder@schrodinger.com>
* restore ignore_case=on default
* new setting: ignore_case_chain (default off)
https://sourceforge.net/p/pymol/mailman/message/34815599/
* new setting: cartoon_gap_cutoff
* increase PYMOL_MAX_THREADS
https://sourceforge.net/p/pymol/mailman/message/34787473/
* amber topology loading: bond order 1 for all bonds
https://sourceforge.net/p/pymol/mailman/message/34812536/
* improve MOL2 file handling
* new grid_mode=3: grid per object-state
2016-01-11 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2015-12-14 Thomas Holder, Blaine Bell
* support segi, resn and name of arbitrary string length
* expose settings to iterate/alter via "s.<name>" (available
in Incentive PyMOL since 1.7.0)
* Python 3 compatibility for champ module
https://sf.net/p/pymol/bugs/172/
* apbs_tools: apply fixes from Pymol-script-repo
2015-12-09 Thomas Holder <thomas.holder@schrodinger.com>
* Python 3 compatibility, tested with Python 2.6, 2.7 and 3.4
* 1.8.1.0 (unstable/experimental)
2015-11-18 Thomas Holder, Blaine Bell, Gabriel Marques
* 1.8.0.0
* Tcl/Tk Settings GUI: feedback, radio buttons, font size dialog
* default alignment_as_cylinders changed to off
2015-10-15 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2015-10-06 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2015-08-30 Thomas Holder <thomas.holder@schrodinger.com>
* fix cartoon_trace_atoms for beta-sheets
* fast connect_mode=4: Add $PYMOL_DATA/chem_comp_bond-top100.cif
which is a subset of the components.cif dictionary and contains
only bond records for the 100 most frequent monomers in the PDB.
Download other monomers on-demand from PDBeChem.
2015-08-12 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2015-07-29 Thomas Holder <thomas.holder@schrodinger.com>
* 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"
2015-07-02 Thomas Holder <thomas.holder@schrodinger.com>
* mmcif: match pdb1, pdb2, ... files with assembly generation
- 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"
2015-06-23 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2015-06-17 Thomas Holder <thomas.holder@schrodinger.com>
* 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
2015-06-10 Thomas Holder <thomas.holder@schrodinger.com>
* fetch 'cif' by default (was: pdb)
* warn if selecting with lower-case arguments to help identifying
legacy selections which are incompatible with ignore_case=0
* port selection macro parsing from Python to C
* fix https://sf.net/p/pymol/bugs/169/ (cmd.fab() with existing object
name produces unexpected results and downstream segfault)
2015-05-20 Thomas Holder <thomas.holder@schrodinger.com>
* change default (!) of "ignore_case" setting to off. Case insensitve
identifier matching is not practical 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)
* 1.7.7.1 (unstable/experimental)
2015-05-04 Thomas Holder, Blaine Bell, Gabriel Marques
* 1.7.6.0
* VASP file support for: CHGCAR, OUTCAR, POSCAR, XDATCAR
* psf file support
* ignore SCALE matrices with negative determinant
* fix crash when loading malformed CIF file
* fix cif export for natoms = 0
* fix several memory leaks
* fix crash when saving PSE with deleted ramp
2015-04-20 Thomas Holder <thomas.holder@schrodinger.com>
* new setting: pse_export_version to save to old session formats
* fix memory leak in get_global_components_bond_dict
* change setting default: pdb_conect_nodup 0 -> 1
* fix Tcl/Tk File menu unicode handling
* fix auto-complete for filenames with spaces
* mmCIF: support CHEM_COMP_BOND from mmCIF file
* residue information for MOL2 export
2015-03-12 Thomas Holder, Blaine Bell, Gabriel Marques
* 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
* 1.7.5.0 (unstable/experimental)
2014-12-03 Thomas Holder, Blaine Bell, Gabriel Marques
* 1.7.4.0
2014-12-02 Thomas Holder <thomas.holder@schrodinger.com>
* use COMPONENTS_CIF environment variable to look for components.cif
* update fetchHosts and hostPaths URLs
* 1.7.3.6 (unstable/experimental)
2014-11-20 Thomas Holder <thomas.holder@schrodinger.com>
* cif: read first_model_num
* fixed _foo?bar lookup could fail in mmCIF parsing
* deprecated full_screen setting (use full_screen command)
* 1.7.3.4 (unstable/experimental)
2014-10-19 Jared Sampson, Thomas Holder
* COLLADA (dae) export support.
Implemented by Jared Sampson as his POSF project.
* 1.7.3.2 (unstable/experimental)
2014-10-16 Thomas Holder, Blaine Bell
* 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
* 1.7.3.1 (unstable/experimental)
2014-09-17 Thomas Holder, Blaine Bell
* ignore SCALEn if CRYST1 is 1x1x1 or invalid
* new/refactored API functions for accessing coordinates and maps
as numpy arrays:
* load_coords
* load_coordset (was: load_coords)
* get_coords
* get_coordset
* get_volume_field now returns numpy array
* 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
2014-09-08 Thomas Holder <thomas.holder@schrodinger.com>
* migrate all C files to C++ (rename c -> cpp)
* multi-letter chain support
* added missing function pymol.menu.measurement_color
* fix small regression bug in pymol.creating.unquote
2014-09-04 Thomas Holder, Blaine Bell
* 1.7.3.0 (unstable/experimental)
* sync various pieces of code with Incentive PyMOL
* faster iterate/alter implementation ported from Incentive PyMOL
* experimental mmCIF write support (atoms only)
* partial multi-letter chain support
* super: use guide instead of CA, enables nuc acid alignment
* fix movie panel not shown until resize
* eliminate some deprecated parsing modes
* python: convert some files to absolute_import
* --help and --version
* dynamic_measures refactoring, fixes duplicated IDs bug
* get_type returns object:alignment and object:ramp
* new "command" Wizard ported from Incentive PyMOL
2014-08-15 Thomas Holder, Blaine Bell
* 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"
* 1.7.2.1
2014-08-04 Thomas Holder, Blaine Bell, Gabriel Marques
* 1.7.2.0
* chempy.cif: fix symmetry loading
2014-07-31 Thomas Holder, Blaine Bell, Gabriel Marques
* Improve ObjectVolume rendering latency
* Improve label edge pixel rounding
* alter_state auto completion
* improve "Label" wizard
* re-implemented ObjectMoleculeSetDiscrete
* 1.7.1.9 (release candidate)
2014-07-09 Thomas Holder, Blaine Bell
* fix label_digits crash
* fixed get_angle3f to use doubles internally
* avoid ZeroDivisionError in Volume Panel
* support opaque_background with "draw"