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859 Commits

Author SHA1 Message Date
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
2d132b7c1e PYMOL-5001: (Part Five) OrthoMakeSizedImage and Composite 2025-01-04 21:08:08 -05:00
Jarrett Johnson
279ce3f870 PYMOL-5001: (Part Four) SceneMakeSizedImage Refactor 2025-01-04 20:58:58 -05:00
Jarrett Johnson
b52b6f2174 Port code changes from incentive (06/2023) 2025-01-04 12:09:32 -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
Jarrett Johnson
83f11bc317 More Replace NULL with nullptr 2024-06-02 20:44:43 -04:00
Jarrett Johnson
fbfda4a257 Replace NULL with nullptr 2024-05-20 09:07:33 -04:00
Jarrett Johnson
74ffc07ea7 Replace monkeypatch distutils with CMake setuptools Extensions 2024-05-20 08:37:33 -04:00
Jarrett Johnson
1e9d81d6d2 Fix GIL for CmdGetCCP4Str 2024-05-11 10:32:33 -04:00
Jarrett Johnson
f55d3f18e7 PYMOL-4512: Move camera on curve 2024-01-30 16:43:47 -05:00
Jarrett Johnson
54720cbff4 PYMOL-4452: PNGs not saving on deferred png draw 2024-01-30 16:25:42 -05:00
Jarrett Johnson
b9491abb93 PYMOL-4102: CmdScene should take quiet arg 2024-01-30 16:24:47 -05:00
Jarrett Johnson
e35caa651a PYMOL-4343: load_coordset quiet 2024-01-30 16:14:20 -05:00
Jarrett Johnson
c4420ca364 PYMOL-4075 new command: look_at 2024-01-30 15:30:52 -05:00
Jarrett Johnson
6bfc590446 PYMOL-4025 ObjectCurve 2024-01-30 15:30:40 -05:00
Jarrett Johnson
9e2ca7d92c Move GetRawAlignment to ExecutivePython 2024-01-30 12:53:05 -05:00
Thomas Holder
af77ece88c Fix GIL for get_unused_name (#324) 
Fixes https://github.com/schrodinger/pymol-open-source/issues/320
 2023-12-20 10:38:11 -05:00
Jarrett Johnson
9333da43b2 Specify color ramp for volume state 
Fixes #289
 2023-07-20 12:07:03 -04:00
Thomas Holder
a3f3dd16c2 Fix GIL for get_object_ttt and friends (#285) 
The following functions were releasing the GIL and then calling Python
functions:

- CmdCombineObjectTTT
- CmdTransformObject
- CmdTransformSelection
- CmdGetObjectTTT

Fixed by either moving the Python calls outside the unblocked API
context, or by using a blocked API context.
 2023-04-15 13:38:59 -04:00
Thomas Holder
b8a7bae98b Fix crash in find_molfile_plugin (#233) 
Was calling Python function with unblocked interpreter.
 2022-04-25 11:25:03 -04:00
Jarrett Johnson
eea082966b Remove orthoCGO defines; fix warnings 2022-03-08 15:31:11 -05:00
Jarrett Johnson
910329a903 New clip API modes and get_clip 2022-02-22 16:30:32 -05:00
Jarrett Johnson
a96fd64cc2 Add Feedback/Block headers 2021-08-20 11:29:12 -04:00
Jarrett Johnson
07d7a790f0 Forward decls/Move headers to source 2021-08-20 11:24:10 -04:00
Thomas Stewart
0d2f6b6c72 PYMOL-3717 Get/Set Commands for Scene Messages 2021-08-20 10:46:39 -04:00
Thomas Stewart
cfba0c2755 PYMOL-3705 Fix quiet for png 2021-07-07 12:31:26 -04:00
Thomas Stewart
cb277dfd86 PYMOL-3694 Scene Refactor to Store Thumbnail 
- Adding a pymol::Image thumbnail to MovieScene
    - This allows the thumbnail to be directly
      tied to the Scene when it's stored
- Adding set and get methods to Image.h
 2021-07-07 12:27:02 -04:00
Jarrett Johnson
65835f9991 Remove OOMac 2021-07-07 12:03:25 -04:00
Jarrett Johnson
d34b5b20fc Destroy Temp selector before APIExit 2021-07-07 11:43:26 -04:00
Jarrett Johnson
108e698242 InternalGUIMode enum class 2021-04-28 05:31:23 -04:00
Thomas Holder
3355efcf6f PYMOL-3176 draw/png/mpng/refresh: cmd._call_with_opengl_context 
When running with a GUI, always run these functions in the main thread
and call makeCurrent() for the OpenGL context.

Reverts workarounds from these commits:
- fabcd9b8 "QOpenGLWidget: fix "png foo.png"" (`glReadBuffer(G->DRAW_BUFFER0)`)
- 8dcce851 "prepare for QOpenGLWidget support" ("refresh" before "draw")

Fixes https://github.com/schrodinger/pymol-open-source/issues/25
Fixes https://github.com/schrodinger/pymol-open-source/issues/150
 2021-04-28 04:39:04 -04:00
Thomas Holder
305894124e cmd.png(None) -> bytes 2021-04-28 04:38:33 -04:00
Jarrett Johnson
974195df2b Restore Cmd API block for CmdMSet 2021-04-28 04:05:14 -04:00
Jarrett Johnson
f06526198b Backport Cmd.cpp cleanup from undo 2021-04-28 04:04:41 -04:00
Jarrett Johnson
a529575bd6 Backport SceneClip refactor 2021-04-28 03:57:49 -04:00
Jarrett Johnson
3d5b08e162 MovieScene refactor undo backport 2021-04-28 03:57:43 -04:00
Jarrett Johnson
f3c15a29cc Backport Executive additions from undo 2021-04-28 03:57:31 -04:00
Thomas Holder
3ab08be830 memory usage info 
- pymol::memory_usage()
- pymol::memory_available()
- Replace iOS-only function get_free_memory() with pymol::memory_available()
 2021-04-06 10:23:24 -04:00
Jarrett Johnson
f6dd412e7d Symop strings from 'bond' never nullptr 2021-03-26 14:29:52 +01:00
Thomas Holder
3049a8f580 PYMOL-3621 File > Open > CMS 2021-03-26 14:16:02 +01:00
Thomas Holder
07435800fc pbc_wrap/pbc_unwrap, smooth+intra_fit pbc support 
- new `pbc_wrap` and `pbc_unwrap` commands
- `intra_fit pbc=1` (default) automatically unwraps and rewraps
- `smooth pbc=1` (default) automatically unwraps and rewraps
- Changes CoordSetRealToFrac/CoordSetFracToReal to take the
  premultiplied state matrix into account
 2021-03-26 14:04:35 +01:00
Thomas Holder
ba78bd90e8 PYMOL-3595 smooth cutoff 
- Add a cutoff argument to the smooth command
 2021-03-26 13:53:01 +01:00
Thomas Holder
4893bdd1bd PYMOL-3618 scene_order with spaces in names 
Allow passing an actual list to cmd.scene_order() so that we don't have
to split a string by spaces.
 2021-03-26 13:49:09 +01:00
Thomas Holder
ddcc931077 Graceful error message for "label all, stereo" 
... if rdkit and SCHRODINGER are not available.
 2021-03-26 13:48:21 +01:00
Thomas Holder
9154ce95a4 defer_builds_mode 3: Don't purge object-level caches 
`cRepInvPurge` will only purge reps, but will not invalidate object data
like nonbonded atoms, neighbors, selections, or sculpting.
 2021-02-18 19:32:11 +01:00
Jarrett Johnson
a32a6d05e0 init_cmd func adds pymol._cmd to global modules 2021-02-11 19:14:14 +01:00
Jarrett Johnson
355c45d229 Place CObject in pymol namespace 2021-02-11 19:14:06 +01:00
Thomas Holder
f3c0419654 rebond pbc=1 
- Add `pbc` argument to cmd.rebond()
- Refactor ObjectMoleculeConnect
- Add support for OpenMP
 2021-02-11 19:05:08 +01:00
Thomas Holder
1142e3ab22 PYMOL-3570 Bonds to crystal symmetry mates 2021-02-11 18:58:26 +01:00