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2346 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
ce1fb16bde halogen-bond detection and display (PYMOL-3466) 2024-01-30 12:46:06 -05:00
Jarrett Johnson
c3e298356a Fix pep8 W605 warnings 2023-12-21 12:20:41 -05:00
Thomas Holder
5622d7616d Fix volume editor for Python 3.10 (#301) 
Related to https://github.com/Pymol-Scripts/Pymol-script-repo/issues/136
 2023-07-28 02:08:20 -04:00
Jarrett Johnson
26d795fe92 Remove PLY scaling factor 
Fixes #286
 2023-07-20 12:13:23 -04:00
Jarrett Johnson
9333da43b2 Specify color ramp for volume state 
Fixes #289
 2023-07-20 12:07:03 -04:00
Jarrett Johnson
d24468af04 Provide warning for comma-separated delete args 
Fixes #255
 2022-10-25 01:32:01 -04:00
Jarrett Johnson
666beb1bd0 PYMOL-3857 failing load cmd with quoted backslashes 2022-08-17 15:02:49 -04:00
ys_song
ecc93c9806 correct plugin install behavior (#236) 2022-06-13 12:14:01 -04:00
Daniel Farrell
c28e663085 Use XDG_CONFIG_HOME for pymolrc (#235) 
* Update invocation.py
 2022-06-06 06:22:03 -04:00
Thomas Holder
abc307745d iterate: Add explicit_valence and explicit_degree (#227) 2022-03-11 17:37:26 -05:00
Kris Janssen
7cbe883b42 Fix for missing scene panel dialog in Tk GUI (#228) 
Co-authored-by: Kris Janssen <kris.janssen@ucb.com>
 2022-03-11 17:34:18 -05:00
Thomas Holder
d589382ffc Fix fallback MMTF loader (#226) 
* Fix fallback MMTF loader

`msgpack-python` 1.0 uses `raw=False` by default, which means that data
(including dictionary keys) are `str` instead of `bytes`.

Also works with `u-msgpack-python` 2.7, which uses `str` as well with
Python 3 and ignores the `raw` argument.

Fixes https://github.com/schrodinger/pymol-open-source/issues/225

* Fix tests for chempy.mmtf

- testLoadMMTFMissingOptionalGroupTypeFields
- testLoadMMTFStr
- testLoadRawMMTF
 2022-03-08 16:36:56 -05:00
Jarrett Johnson
1e47c52424 set new clip modes 2022-02-22 16:32:38 -05:00
Jarrett Johnson
910329a903 New clip API modes and get_clip 2022-02-22 16:30:32 -05:00
Thomas Holder
f92440b5dd get_sasa_relative: Add subsele argument 2021-11-10 02:22:41 -05:00
Thomas Stewart
0d2f6b6c72 PYMOL-3717 Get/Set Commands for Scene Messages 2021-08-20 10:46:39 -04:00
Jarrett Johnson
f81ce44908 CGO Builder API 2021-08-20 10:38:33 -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
99db4653ab Update BioMSA 1.79 API usage 2021-07-07 12:11:42 -04:00
Thomas Stewart
5e3c6564b7 PYMOL-3693 Reordering scenes, double click recall 2021-07-07 12:11:27 -04:00
Thomas Stewart
8354e26abd PYMOL-3692 Basic buttons for scene panel 2021-07-07 12:11:23 -04:00
Thomas Stewart
f7a572c060 PYMOL-3691 Creating a table for viewing scenes 2021-07-07 12:11:08 -04:00
Jarrett Johnson
2c98f66df7 Update isosurface help docstring 2021-07-07 12:10:24 -04:00
Jarrett Johnson
817ba934c9 PYMOL-3684 Allow parsing of decorated functions 2021-07-07 12:09:40 -04:00
Thomas Stewart
6b2382da4e PYMOL-3664 Using Bio.Align instead of Bio.SubsMat 
- Bio.SubsMat.MatrixInfo is depricated
- Now trying to import substitution_matrices
  from Bio.Align first
 2021-07-07 11:54:44 -04:00
Thomas Stewart
47f14eb9b3 PYMOL-3590 Shortcut manual reset detection 
- Added logic for when user manually assigns default
- Unlocking sizing on column width
 2021-04-28 05:23:31 -04:00
Thomas Stewart
ae1d4146c1 PYMOL-3636 Making props a dialog to fix showing 
- conda-forge caused issue showing/hiding
- Only opened once when floating
- Issue fixed but no longer dockable
 2021-04-28 05:23:28 -04:00
Thomas Stewart
a30c11bc5a PYMOL-3590 Shortcut menu Create/Confirm fixes 
- Fixed previous assignment being called
- Create/confirm are now QDialog
- Create/confirm no longer dockable
- Improved key recognition in create
- Replacing _weakrefproxy with _
 2021-04-28 05:19:12 -04:00
Thomas Holder
32b43f8d53 Plugins: Remove obsolete legacy Tk initialization 
Fixes `pymol.plugins.plugin_load` in headless mode.

https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg16060.html
 2021-04-28 05:05:23 -04:00
Thomas Holder
d69aceee1a Make all fetch URLs HTTPS 
Starting May 10 2021, RCSB will be enforcing https for all access to the
rcsb.org APIs.
 2021-04-28 05:05:13 -04:00
Thomas Stewart
704e79ca7b PYMOL 3590 Shortcuts Reset All and Create New fix 
- Reset all was not properly removing user defined shortcuts
    - Create new shortcut menu now can edit existing
    - Confirmation menu added
 2021-04-28 05:05:07 -04:00
Thomas Stewart
6987a121ef PYMOL 3597 Props class refactor and unset with del 
Able to unset:
    - Object level settings
    - Object-state-level settings and props
    - Atom level settings and user properties
    - TTT and ostate matrices to identity
 2021-04-28 05:04:18 -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
af00ac3892 PYMOL_USE_QOPENGLWIDGET 2021-04-28 04:38:56 -04:00
Thomas Holder
305894124e cmd.png(None) -> bytes 2021-04-28 04:38:33 -04:00
Thomas Stewart
6a2168c335 Removed Qt import from shortcut_manager 2021-04-28 04:35:55 -04:00
Thomas Stewart
8906681b30 PYMOL-3590 Keyboard Shortcut Menu 
- Adds menu to view, edit, and reset keyboard shortcuts
- Stores default shortcuts in new file, shortcut_dict
- Save shortcuts to file and load on launch
 2021-04-28 04:35:38 -04:00
Thomas Holder
6a6134bb53 Better warning message for GLUT/Tk fallback 2021-04-20 09:18:32 +02:00
Thomas Holder
b067c54380 pymol -p: Error handling, docstring, code cleanup 
- RuntimeError instead of AttributeError for sys.stdin = None
- With "keep alive" (-K), stop attempting to read from STDIN after EOF
 2021-03-26 14:53:10 +01:00
Thomas Holder
bfffdd2c8a PYMOL-3176 Fix "draw" with QOpenGLWidget 
Fixes https://github.com/schrodinger/pymol-open-source/issues/25
 2021-03-26 14:52:37 +01:00
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
30ac2d263f auto-completion for sculpt_iterate command 2021-03-26 14:20:24 +01:00
Jarrett Johnson
fd0716d5c8 PYMOL-3623: Prevent deletion of phosphate oxygens 2021-03-26 14:20:18 +01:00
Thomas Holder
3049a8f580 PYMOL-3621 File > Open > CMS 2021-03-26 14:16:02 +01:00
Thomas Holder
da45c0dafa MAE import dialog: discrete states 2021-03-26 14:08:07 +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
1f7bc7bccf PYMOL-3620 load_traj state=1 by default 2021-03-26 13:49:13 +01:00