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36 Commits

Author SHA1 Message Date
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
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
65835f9991 Remove OOMac 2021-07-07 12:03:25 -04:00
Jarrett Johnson
355c45d229 Place CObject in pymol namespace 2021-02-11 19:14:06 +01:00
Jarrett Johnson
5ac8328ec2 PYMOL-3573 fix angle measurement load crash 2020-12-03 18:16:11 +01:00
Jarrett Johnson
5459465e36 ObjectDist copy/assign fix 2020-11-11 16:53:55 +01:00
Jarrett Johnson
4431dd0ce2 Settings copied on object copy 2020-10-16 11:07:17 +02:00
Jarrett Johnson
465a8bd1d8 ObjectDist refactor backport 2020-10-05 11:46:12 +02:00
Thomas Holder
08c9dff871 PYMOL-3533 Refactor Rep as polymorphic type (2) 
Part 2: virtual member functions
 2020-09-30 09:46:26 +02:00
Jarrett Johnson
1c26a96739 Named Renderpasses 2020-07-03 15:00:38 +02:00
Thomas Holder
2e8dba6688 PYMOL-2281 pi_interactions stub 2020-04-09 15:12:03 +02:00
Thomas Holder
7847fe6014 refactor: C++ify DistSet 2020-02-26 19:08:34 +01:00
Thomas Holder
75f06a974e CObject function pointers -> virtual methods 2019-10-29 16:24:12 +01:00
Jarrett Johnson
00473b5656 C++ inheritance for Object classes 2019-09-04 18:18:01 +02:00
Thomas Holder
5a4ab0eaa9 PYMOL-3272 remove obsolete metaphorics code 
cex files and m4x annotated PDB files don't exist anymore.
cex loading was broken for a long time, proof that nobody was using it.
 2019-08-19 22:07:24 +02:00
Nandini Naidu
a41ee95dbb Used min_max_element function for range determination. 2019-08-13 15:16:15 +02:00
Thomas Holder
035d6fe611 C++ inheritance for all CObject subclasses 2019-03-29 13:36:14 +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
5e04325863 cleanup (local/unused function declarations) 2019-02-06 15:43:14 +01:00
Jarrett Johnson
fde67f2d9b PYMOL-3098 ScenePickVLA Refactor 2018-11-15 16:44:02 +01:00
Thomas Holder
4f3c781a74 cleanup: compiler warnings 
-Wdangling-else
-Wmisleading-indentation
-Wmismatched-tags
-Wparentheses
-Wsometimes-uninitialized
-Wunused-but-set-variable
-Wunused-function
-Wunused-label
-Wunused-variable
 2018-08-16 19:00:17 +02:00
Thomas Holder
148e2df4e2 (fix compiling mobile) 2018-07-23 11:37:01 +02:00
Thomas Holder
f21c61958e Graphics refactoring, ported from Incentive PyMOL 2018-07-03 20:19:12 +02:00
Thomas Holder
5faa72b373 call SceneObjectDel in ObjectPurge 
Some object types did not call SceneObjectDel (e.g. ObjectGroup) which
could cause segmentation fault in ExecutiveFree
 2018-06-19 17:29:02 -04:00
Thomas Holder
1742d75d13 anaglyph batch mode, all_states measurements, ... 
* fix anaglyph stereo in batch (headless) mode
* fix possible memory corruption with boolean settings
* measurement wizard: distances between states (all_states=on)
* get_fastastr: nucleic acid, by chain
* menu: A (Action) > group
* sequence viewer menu: ss (Secondary Structure)
* MAE export of groups (s_m_subgroupid)
* macOS: -O3 -fno-strict-aliasing (bugs/205)
 2018-05-03 14:46:44 +00:00
Thomas Holder
4bbe42513c stick_round_nub, UTF-8, display_scale_factor, ... 
* stick_round_nub for COLLADA export
* UTF-8 in feedback
* display_scale_factor (ported from Incentive PyMOL)
* dx map import: support "type float" and skewed delta
 2018-02-28 13:16:16 +00:00
Thomas Holder
2930efa152 1.8.5.0 (unstable/experimental) 
* avoid selection keyword name conflicts, append underscore
* load: allow format=plugin (by extension) and format=plugin:PLUGIN (with PLUGIN being a molfile plugin identifier)
* load format "vdb": VIPERdb PDB variant with retain_order=1
* load/load_traj: guess trajectory object
* fetch
    * new setting "fetch_type_default"
    * type=mmtf: fetch MMTF format
    * type=2fofc/fofc: get spacegroup from PDBe API
    * update download URLs
* new setting: editor_auto_measure
* new default: ray_transparency_oblique_power=4.0
* "update" command: support "current state" (-1)
* alter elem -> update protons and vdw
* don't allow "import cmd" (corrupts PyMOL namespace)
* support "python -m pymol" to launch PyMOL
 2016-12-05 19:04:04 +00:00
Thomas Holder
6f78f0d567 1.8.3.3 (unstable/experimental) 
* pse_export_version: legacy scenes support
* use ignore_case setting with set_name command
* setup.py: detect anaconda prefix
 2016-09-26 19:49:55 +00:00
Thomas Holder
d0d46b9a42 PyMOL 1.8.2.0 
- fix/silence various compiler warnings
- partly fixes sf#177, sf#178
- fix crash when loading PSE with bg_image_filename
 2016-04-19 22:02:24 +00:00
Thomas Holder
2787af79fc byring, distance mode=4, cartoon dash, ... 
* distance mode=4: distance between centroids
* byring: new selection operator
* "Distances to Rings" mode in measurement wizard
* basic atom typing for MOL2 export
* cartoon dash: new dashed loop-like cartoon type
* object-level settings for measurements
* iterate: use Python exceptions
* iterate_state: ignore atomic=0 (fixes crash)
* format 'xyzstr': enable .gz and URL loading
* fix crash with object sele length >= 1024
* re-add -Wno-write-strings
* fix pmg_tk.skins.normal.encode()
* fix askopenfilename CANCEL case with multiple=0
 2016-01-11 16:56:37 +00:00
Thomas Holder
dad194ad0f Restore scenes "disable" recall behavior... 
- scenes: Restore the old behavior that when recalling a scene, all objects
  which were not present when storing the scene are disabled.
- fix auto-complete for filenames with spaces
- fix an object menu panel group ordering problem

Refactoring:
- remove unused variables (Partly applies https://sourceforge.net/p/pymol/bugs/166/)
- lots of: char* -> const char*
- remove inline Parse functions, simplify ParseFloat3List
- make functions static
 2015-04-09 21:35:38 +00:00
Thomas Holder
e274a46085 fast CIF loading, 1.7.3.1 (unstable/experimental) 
* fast PDBx/mmCIF and core CIF loading in C++
* new connect_mode=4 does bonding with components.cif dictionary
  (mmCIF only, components.cif needs to be present in current
  directory)
* gray out residues in the sequence viewer that are missing from the
  current state; Read missing residues from mmCIF files
  (_pdbx_unobs_or_zero_occ_residues records) so that they show up in
  the sequence viewer
* add spider map reading support
* load "map" as ccp4 instead of throwing "ambiguous" error
* xyz write support
* Improve right-button zoom: use origin instead of clipping slab
  center as depth indicator, fixes zoom speed when far clipping plane
  is very far away
* don't use dynamic_width for nonbonded rep
 2014-10-16 20:14:27 +00:00
Thomas Holder
4dd7c7ffd4 SCALEn, numpy, set_state_order, ... 
* ignore SCALEn if CRYST1 is 1x1x1 or invalid
* new/refactored API functions for accessing coordinates and maps as numpy arrays
* new API function: cmd.set_state_order
* Session file (PSE) support for callback objects
* fix/silence many compiler warnings
* fix bg_rgb_top/bg_rgb_bottom side effects
* revert "fix setting surface_circumscribe"
* delete some obsolete files
 2014-09-17 19:17:56 +00:00
Thomas Holder
f42840260b c++ for all PyMOL c files 
- renaming files c -> cpp
- c++ specific syntax (::)
 2014-09-08 13:42:11 +00:00