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358 Commits

Author SHA1 Message Date
Jarrett Johnson
46530027e6 Fix cell color for ray/png 
Fixes #505
 2026-05-04 10:58:05 -04:00
Jarrett Johnson
f1fa2ed417 Empty chain selections should be quoted 
Fixes #502
 2026-03-25 03:13:49 -04:00
Jarrett Johnson
fafebb56d3 Improve peptide nucleic acid visualization 
Fixes #187
 2026-03-10 22:28:14 -04:00
Jarrett Johnson
5456a6768b PYMOL-5436: Add new command 'protonate' for chemically-aware protonation 2026-03-10 22:27:49 -04:00
Jarrett Johnson
4769e62c02 PYMOL-5418: Add USAlign implementation for structural alignment 2026-03-01 00:10:16 -05:00
Jarrett Johnson
841c094393 Adjust test for autoerr missing key 2026-02-24 01:55:05 -05:00
Jarrett Johnson
d30a289129 Fix dropped residues with cif_use_auth and inscodes 2026-02-21 01:16:36 -05:00
Jarrett Johnson
ede1553a9c PYMOL-5422: Fix matrix_copy pointer alias 2026-02-20 18:06:28 -05:00
Jarrett Johnson
bc0943cb7d Improve validation coefficient import 2026-02-20 17:04:57 -05:00
Jarrett Johnson
92eeb4867f Port properties feature from incentive 2026-02-20 16:46:25 -05:00
Jarrett Johnson
4a2da35286 Support multiobject bcif exporting 2026-02-19 14:17:59 -05:00
Jarrett Johnson
9eb37e002c PYMOL-5409: Fix partial esp maps covering entire surface (#373) 
Fixes #445
 2026-02-10 15:18:00 -05:00
Pedro Sousa Lacerda
0a53de09b0 Add support for >=, <=, == operators in selections 2025-12-08 09:32:07 -05:00
Pedro Sousa Lacerda
796d84edec Small refactor to accommodate support for >=, <= and == operators in selections 2025-12-08 09:32:07 -05:00
pslacerda1
9c92399973 Add new_command and improved type inference (#470) 2025-11-28 12:42:41 -05:00
Jarrett Johnson
7b40e3e5fe PYMOL-5361: export BCIF implementation 2025-11-25 14:56:27 -05:00
Thomas Holder
9375fd24c0 get_object_list('') -> [] 
Closes https://github.com/schrodinger/pymol-open-source/issues/478
 2025-11-11 13:29:33 -05:00
Thomas Holder
c8e2a1b724 Error propagation for cmd.get_object_list() 2025-11-11 13:29:33 -05:00
Jarrett Johnson
33c5c7c36a Support CIF structure factors to Density Map (#455) 2025-05-13 01:10:54 -04:00
Pedro Lacerda
8f957b847e Attempt to detect delocalized atoms (#439) 2025-05-04 13:27:23 -04:00
Pedro Lacerda
f31e79fae8 Support cmd.iterate expression as a decorated function (#449) 2025-05-04 12:38:36 -04:00
ye11owSub
17c6cbd96d Fix ci pipeline for python3.9 and python3.13 (#435) 2025-04-05 12:47:18 -04:00
ye11owSub
fef4a02642 refactoring shortcut.py script (#391) 2025-01-24 23:34:53 -05:00
Thomas Stewart
e2d5bf30b2 Pymol 4944: Drag reordering for groups 2025-01-04 21:15:46 -05:00
Jarrett Johnson
c5e32bdb73 update CI 2025-01-04 19:43:14 -05:00
Jarrett Johnson
4d2ef6d3d2 PYMOL-5019: Fix chemistry fix 2025-01-04 13:36:50 -05:00
Jarrett Johnson
d82b626b60 New command: delete_states 
Delete states from multistate objects. Currently only supports
non-discrete molecular objects.
 2024-08-30 11:26:51 -04:00
Pedro Lacerda
d6b4762021 Add atom object name on the cmd.get_model() returned model (#380) 2024-08-07 10:35:54 -04:00
Jarrett Johnson
5c0bfd98b7 Add conftest to tests/api to reinitialize 2024-06-10 20:28:18 -04:00
Thomas Holder
9d01072cac Fix test_utils.compatible_with (#372) 
Fixes https://github.com/schrodinger/pymol-open-source/issues/370
 2024-06-10 11:31:59 -04:00
Jarrett Johnson
6731589c9b BinaryCIF Import Implementation (#353) 2024-06-05 00:01:49 -04:00
Pedro Lacerda
6a7e094a0d declare_command cmd extension API (#349) 2024-05-20 08:28:17 -04:00
Jarrett Johnson
a4cc70c2ff Add CI for Windows and Mac 2024-05-12 12:20:12 -04:00
Branch Vincent
3d3c896379 replace distutils for python 3.12 (#362) 
Co-authored-by: Jarrett Johnson <jarrett.johnson@schrodinger.com>
 2024-05-11 01:12:58 -04:00
Jarrett Johnson
246e0a4c2d Nucleic Acid builder and general improvements (#354) 
Fixes #102 #351 

Migrating support from Incentive for the following:

- Nucleic Acid builder in the Builder panel (Jarrett Johnson @JarrettSJohnson)
- `fnab` command to build nucleic acid chains by sequence (Jarrett Johnson @JarrettSJohnson)
- Improvements to nucleic acid building from native structures (Thomas Stewart @TstewDev)
- highlight attachment points for improved usability (Thomas Holder @speleo3)

Co-authored-by: Jarrett Johnson <jarrett.johnson@schrodinger.com>
Co-authored-by: Thomas Stewart <thomas.stewart@schrodinger.com>
Co-authored-by: Thomas Holder <thomas@thomas-holder.de>
 2024-04-08 09:55:18 -04:00
Thomas Holder
9dcb2091cd Support running all tests with pytest, make --no-mmlibs --no-undo the default (#333) 
* Support running all tests with pytest

* Make --no-mmlibs --no-undo the default

These tests seem unsupported by modern PyMOL versions (like 2.5.6), see
https://github.com/schrodinger/pymol-testing/issues/9

Add `--with-mmlibs` and `--with-undo` options to enable these tests.

* Require PyMOL 2.6 for testLoadPLY
 2024-01-31 03:10:03 -05:00
Thomas Holder
6c0da3bd59 MMTF loader HETATM test (#8) 
See https://github.com/schrodinger/pymol-open-source/issues/295
 2023-07-20 13:22:36 -04:00
Jarrett Johnson
45e8f366ff Fix testLoadPLY test 2023-07-20 12:28:33 -04:00
Thomas Holder
b160c5861c Don't use a hard-coded port for testLoadPWG (#7) 2023-05-19 12:51:33 -04:00
Jarrett Johnson
666ce10b82 Improve pytest tests support 2023-04-15 15:47:44 -04:00
Jarrett Johnson
41b6bcad1c tests: look_at, clip: near_set, far_set 2023-04-14 15:23:59 -04:00
Jarrett Johnson
4945cad8fb undo tests with pytest 2023-04-14 14:30:28 -04:00
Jarrett Johnson
0187397a75 Merge branch 'master' of https://github.com/schrodinger/pymol-testing 2022-09-09 15:45:15 -04:00
Thomas Holder
2daee149ca Tests for explicit_valence and explicit_degree (#5) 
Tests for https://github.com/schrodinger/pymol-open-source/pull/227
 2022-03-14 11:44:05 -04:00
Thomas Holder
d58aa97899 Test for get_sasa_relative with subsele 
Test for https://github.com/schrodinger/pymol-open-source/pull/202
 2021-11-10 03:11:31 -05:00
Thomas Holder
3847fcde48 Test for guide selector bug 
Test for https://github.com/schrodinger/pymol-open-source/issues/198
 2021-11-05 16:26:12 +01:00
Thomas Stewart
e5dcbbc60b Test for Scene Message get/set 2021-07-08 16:10:36 -04:00
Thomas Holder
eedfb6bac2 isosurface_algorithm for PYMOL-3494 test 2021-04-20 15:26:13 +02:00
Thomas Holder
b732d44335 Fix ray_color_ramps test for PYMOL-3528 2021-04-19 12:09:03 +02:00
Thomas Holder
2a0a13b074 test for cmd.png(None) 2021-04-09 14:28:12 +02:00