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5,127 Commits 10 Branches 6 Tags
cpp11
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1320 Commits

Author SHA1 Message Date
Anton Butsev
442d7ca981 View/color salt-bridge interactions differently from hydrogen bonds (PYMOL-3846) 2024-01-30 12:57:54 -05:00
Anton Butsev
465a28182e halogen-bond detection and display (PYMOL-3466) 2024-01-30 12:53:41 -05:00
Jarrett Johnson
9e2ca7d92c Move GetRawAlignment to ExecutivePython 2024-01-30 12:53:05 -05:00
Anton Butsev
ce1fb16bde halogen-bond detection and display (PYMOL-3466) 2024-01-30 12:46:06 -05:00
Thomas Holder
125054d936 Fix SelectorTmp::getAtomCount() w/ selection name (#323) 
Fixes https://github.com/schrodinger/pymol-open-source/issues/322
 2023-12-20 10:41:54 -05:00
Thomas Holder
d59041b68c enum cAtomProtected_* (#316) 2023-09-25 12:18:38 -04:00
Thomas Holder
18d7e33c20 Fix mouse_selection_mode=3 (segments) (#315) 
PyMOL 2.4 regression

Fixes https://github.com/schrodinger/pymol-open-source/issues/313
 2023-09-25 11:35:42 -04:00
Jarrett Johnson
9333da43b2 Specify color ramp for volume state 
Fixes #289
 2023-07-20 12:07:03 -04:00
Jarrett Johnson
53f1d78106 Abstract many C++ viewport calls 2022-08-17 15:02:29 -04:00
Jarrett Johnson
1f94226f5f PYMOL-3726 Update surface color on ramp rename 2022-05-04 15:54:40 -04:00
Jarrett Johnson
37b36d97aa Fix broken group parenting 2022-03-08 15:32:35 -05:00
Jarrett Johnson
eea082966b Remove orthoCGO defines; fix warnings 2022-03-08 15:31:11 -05:00
Jarrett Johnson
74894e01da Generic CGO Render 2022-03-08 15:16:16 -05:00
Thomas Holder
54b187c6aa More consistent cmd.load_model discrete behavior 
- Allow discrete=0 for multi-state objects
- Keep existing discrete flag with discrete=-1

Fixes https://github.com/schrodinger/pymol-open-source/issues/212
 2021-12-15 15:05:35 -05:00
Thomas Holder
9d5b1f07ea Fix guide selector bug 
Closes https://github.com/schrodinger/pymol-open-source/issues/198
 2021-11-05 11:49:56 -04:00
Jarrett Johnson
fceae6fe66 PlugIOManager: use vector over VLA 2021-08-20 11:45:09 -04:00
Jarrett Johnson
07d7a790f0 Forward decls/Move headers to source 2021-08-20 11:24:10 -04:00
Jarrett Johnson
03ceb6fb41 PYMOL-3712 Reshape GUI after loading object 2021-08-20 10:48:25 -04:00
Thomas Stewart
0d2f6b6c72 PYMOL-3717 Get/Set Commands for Scene Messages 2021-08-20 10:46:39 -04:00
Thomas Stewart
2d7159dc07 PYMOL-3718 Fix MyPNG crash from MovieSceneStore 2021-08-20 10:45:41 -04:00
Thomas Stewart
5aa9f59275 PYMOL-3694 Thumbnail using SceneUpdate 
- Fixes double recalling of scenes
- Fixes crash when using middle mouse
  switching between scenes
 2021-08-20 10:37:40 -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
40a54a1c91 Replace OV (ObjectAlignment) 2021-07-07 12:19:16 -04:00
Jarrett Johnson
a2b642dc16 Replace OV/VLA (Setting) 2021-07-07 12:14:54 -04:00
Jarrett Johnson
8b249db7b6 Replace OV/VLA (Executive) 2021-07-07 12:12:28 -04:00
Jarrett Johnson
c55494cc86 Don't allow overwrite of objs for new iso/volumes 2021-07-07 12:07:22 -04:00
Jarrett Johnson
65835f9991 Remove OOMac 2021-07-07 12:03:25 -04:00
Jarrett Johnson
108e698242 InternalGUIMode enum class 2021-04-28 05:31:23 -04:00
Jarrett Johnson
30405aad60 Backport algos and refactor from undo 2021-04-28 05:26:26 -04:00
Jarrett Johnson
8738ad5af8 OrthoRenderMode enum class 2021-04-28 05:23:10 -04:00
Thomas Holder
6f77e5efb0 GIL pre-conditions 2021-04-28 05:15:35 -04:00
Thomas Stewart
66ef180467 PYMOL-3615 Display Seq hide_underscore_names 
- Exposing hide_underscore_names settings to seq viewer
- Added a SettingGet overload for pymol::CObject
 2021-04-28 04:35:48 -04:00
Thomas Holder
10af8bd0b9 Refactor ObjectMolecule::Neighbor access 
- Make ObjectMolecule::Neighbor private
- Use AtomNeighbors or ObjectMolecule::getNeighborArray
- Eliminate ObjectMoleculeUpdateNeighbors
 2021-04-28 04:34:33 -04:00
Thomas Holder
b3f1ffefb5 Refactor CExecutive::Panel 2021-04-28 04:11:59 -04:00
Jarrett Johnson
46646c10ff CSelector copyable (undo backport) 2021-04-28 04:10:16 -04:00
Jarrett Johnson
7d392b852c Backport Seq refactor from undo 2021-04-28 04:05:21 -04:00
Jarrett Johnson
f06526198b Backport Cmd.cpp cleanup from undo 2021-04-28 04:04:41 -04:00
Jarrett Johnson
976e038f35 Removed unused Executive member 2021-04-28 04:02:30 -04:00
Jarrett Johnson
2a8d306a6d Add missing ExecutiveDef.h 2021-04-28 03:57:52 -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
d5d05f19c9 PYMOL-3624 Handle map.gz and mrc.gz extensions 2021-03-26 14:30:12 +01:00
Jarrett Johnson
f6dd412e7d Symop strings from 'bond' never nullptr 2021-03-26 14:29:52 +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
afe911d212 matrix_reset: Support state=0 (all states) 2021-03-26 13:49:33 +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
91c7692a05 Fix group dragging crash (+cleanup) 
- Fix crash when dragging a group over a a second-level child
- Eliminate `SpecRec::is_hidden` (not 100% functional and unnecessarily
  complicated, use `SpecRec::isHidden()` instead)
- Remove unnecessary underscore checks for `I->Panel` iterations
 2021-03-26 13:47:49 +01:00
Thomas Holder
491e9c5a4d load_raw dx support 2021-02-18 19:33:11 +01:00
Thomas Holder
0851e8122f smooth: PYMOL_OPENMP and refactoring 
- Clean up ExecutiveSmooth
- Run the state for-loop in parallel with OpenMP
 2021-02-18 19:32:33 +01:00