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84 Commits

Author SHA1 Message Date
Jarrett Johnson
e0378ecd6d Remove properties #ifdefs 2026-02-20 16:46:25 -05:00
Jarrett Johnson
92eeb4867f Port properties feature from incentive 2026-02-20 16:46:25 -05:00
Jarrett Johnson
ec17f65a7f PYMOL-5161: Update screen after bg color change 2025-09-26 12:07:30 -04:00
Jarrett Johnson
d188d36b11 PYMOL-5001: (Part Three) Further DrawBuffer refactor 2025-01-04 20:51:19 -05:00
Jarrett Johnson
545e0444bc Fix selection zooming for libcmol 2025-01-04 13:35:30 -05:00
Jarrett Johnson
414c418515 Combine default_frame_bufferID and DRAWBUFFER0 into GLFramebufferConfig 2025-01-04 13:11:45 -05:00
Jarrett Johnson
fbfda4a257 Replace NULL with nullptr 2024-05-20 09:07:33 -04:00
Jarrett Johnson
1d9e93d52f PYMOL-3919: Remove OVOneToOne uses 2024-01-30 15:48:01 -05:00
Jarrett Johnson
53f1d78106 Abstract many C++ viewport calls 2022-08-17 15:02:29 -04:00
Thomas Holder
abc307745d iterate: Add explicit_valence and explicit_degree (#227) 2022-03-11 17:37:26 -05:00
Jarrett Johnson
34e39904c8 PYMOL-3766 Move GL code out of CGO.cpp 
API-specific behavior is now done in separate files
 2022-03-08 15:07:49 -05:00
Jarrett Johnson
07d7a790f0 Forward decls/Move headers to source 2021-08-20 11:24:10 -04:00
Jarrett Johnson
a529575bd6 Backport SceneClip refactor 2021-04-28 03:57:49 -04:00
Thomas Holder
d5d05f19c9 PYMOL-3624 Handle map.gz and mrc.gz extensions 2021-03-26 14:30:12 +01:00
Thomas Holder
491e9c5a4d load_raw dx support 2021-02-18 19:33:11 +01:00
Thomas Holder
dc2aff4133 Refactor: Doxygen comments, ObjectMoleculeUpdateNeighbors 
- Use proper doxygen syntax for all function comments
- ObjectMoleculeUpdateNeighbors allow const argument
- Remove obsolete ObjectMolecule::BondCounter
 2021-01-14 15:23:06 +01:00
Thomas Holder
6cb2b6f05f Some library mode cleanup 
- Remove message "PyMOL not running, entering library mode"
- Disable library mode when non-singleton instances are created
- Remove `_cmd._del` and use a capsule destructor instead, this fixes
  `pymol2.PyMOL().__del__` with Python 3.8 (`_cmd` is `None`).
- Clean up `Cmd_New` and `PyMOL_New`
 2020-11-19 13:49:30 +01:00
Jarrett Johnson
af9630b95b Remove PyMOLGlobals typedef 2020-10-16 11:18:59 +02:00
Jarrett Johnson
e2cd8a3558 CmdColor to call ExecutiveColorFromSele 2020-09-22 11:01:38 +02:00
Thomas Holder
09413be126 Refactor cmd.select_list() 2020-07-15 17:42:00 +02:00
Thomas Holder
5ff04c04f4 fix PyMOL_CmdEnable/PyMOL_CmdDisable by sele 2020-07-03 15:24:38 +02:00
Thomas Holder
b9de9957b1 Properties dialog: flags, label, cartoon, oneletter 
- Expose additional fields
- Use binary or hex formatting if applicable
 2020-07-03 15:24:34 +02:00
Thomas Holder
82881264bc get_click_string: support any object type 
- report `type` and `index` for non-molecular objects
- report `bond`
- expose to Python
 2020-07-03 14:54:43 +02:00
Thomas Holder
6f11b62566 PYMOL-3410 Remove Python 2 support 2020-06-05 09:13:06 +02:00
Thomas Holder
d3ec17c692 Restore PyMOL_CmdEnable status reporting 
Regression of 22b19c80c575
 2020-05-12 11:42:15 +02:00
Jarrett Johnson
6aad8574c4 pymol::Result color; remove_picked; move, map_trim, map_set, origin 2020-05-05 07:59:59 +02:00
Thomas Holder
15b899622c Propagate errors from the selector engine 2020-04-23 14:19:17 +02:00
Thomas Holder
8b9efcc028 refactor: use more pymol::Result 2020-04-23 14:11:17 +02:00
Jarrett Johnson
27938ac229 refactor pseudoatom 2020-03-13 09:01:45 +01:00
Thomas Holder
9ff3a3ddb8 PYMOL-3356 fix distance reset argument 
- Make "reset" argument consistent for all measurement commands
- Improve error handling for all measurement commands
 2020-02-20 12:01:19 +01:00
Thomas Holder
6337b36d83 isosurface/isomesh/volume error handling 
- reject state < -2
- don't create empty surface for invalid selection
- don't delete surf_name if early error detected
 2020-01-22 11:52:20 +01:00
Thomas Holder
a0e7b6541f add fname argument to ExecutiveLoad 2020-01-22 11:52:17 +01:00
Jarrett Johnson
3d18fe3783 use standard containers in CSelector; CSelector split 2020-01-10 16:52:28 +01:00
Thomas Holder
b57f131940 -Wunused-variable 2019-11-27 13:18:08 +01:00
Thomas Holder
276640cd29 Port EPAM's VR fork to PyMOL 2.4 
Porting the essential parts of EPAM System's "openvr" branch to the
master branch.

Original authors:
Natalia Smirnova, EPAM Systems, Inc.
Pavel Smirnov, EPAM Systems, Inc.

Original fork:
https://github.com/epam/pymol-open-source/tree/openvr

Adjustments:
- Make feature optional with "--openvr" compile option
- Python 3 support
- Remove C++11 workarounds
- Exclude build system changes

Co-authored-by: Natalia Smirnova <Natalia_Smirnova@epam.com>
Co-authored-by: Pavel Smirnov <pavel_smirnov1@epam.com>
 2019-11-11 00:50:01 -08:00
Jarrett Johnson
6d8d4d89df movie class refactor 2019-10-15 14:00:11 +02:00
Thomas Holder
698d3cebff refactor pymol.querying 
- use with _self.lockcm: pattern
- use API_SETUP_ARGS and related patterns
- use APIEnter instead of APIEnterNotModal
- propagate errors as much as possible (using pymol::Error or PyErr_XXX)
- add doxygen-style documentation for C++ functions
 2019-10-15 13:54:54 +02:00
Jarrett Johnson
ce0bb0d734 remove and replace dead ExecutiveDistance 2019-06-07 15:48:02 +02:00
Jarrett Johnson
05a0604186 Feedback Refactor 2019-05-08 16:41:33 +02:00
Thomas Holder
723166140a PYMOL-3219 eliminate _PYMOL_INLINE 2019-03-29 13:37:41 +01:00
Thomas Holder
d2b93e011f remove MacPyMOL 2019-03-29 13:17:35 +01:00
Thomas Holder
b59ce09d8a refactor: pymol::malloc<T> 
- use typed/namespaced malloc wrapper
- remove Alloc et al.
- remove mmalloc et al.
- remove CINTERFACE define
 2019-02-21 17:41:58 +01:00
Thomas Holder
3956270b6e cleanup: remove _sgi_stereo 2019-01-29 20:43:44 +01:00
Jarrett Johnson
7960f0db30 PYMOL-3102 pymol::Image 2018-12-10 21:15:17 +01:00
Thomas Holder
34d06bac7c PYMOL-3147 refactor: remove _MemoryDebug_ON 
_MemoryDebug_ON
_MemoryCache_ON
 2018-11-15 16:46:07 +01:00
Thomas Holder
46b52c0a5f define -> enum: cObject_t, cLoadType_t 2018-11-15 16:32:40 +01:00
Jarrett Johnson
78021420a7 PYMOL-3095 Block Refactor 2018-11-15 15:48:32 +01:00
Thomas Holder
90939028a3 const correctness for Color.cpp 2018-07-03 20:31:13 +02:00
Thomas Holder
f21c61958e Graphics refactoring, ported from Incentive PyMOL 2018-07-03 20:19:12 +02:00
Thomas Holder
665aa6884a fix wildcard, fix PDB 99999 crash, PQR parsing... 
* 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
* better support for mingwpy compiler (Christoph Gohlke)
 2018-06-08 10:52:36 +00:00