19 Commits

Author SHA1 Message Date
Jarrett Johnson
7b10fa0e84 PYMOL-5089: MapType refactor 2025-09-26 12:07:26 -04:00
Jarrett Johnson
4e4b03c669 clang-format MapType module 2025-09-26 12:07:26 -04:00
Jarrett Johnson
8b17af434c PYMOL-4289: Fix MapNew crashes by removing bad verts from map 2025-09-26 12:07:26 -04:00
Jarrett Johnson
d46baf8943 Removed unused Memory cache 2025-09-26 12:07:26 -04:00
Jarrett Johnson
fbfda4a257 Replace NULL with nullptr 2024-05-20 09:07:33 -04:00
Jarrett Johnson
1180fec349 Replace makeshift C++17 with standard 2024-04-10 12:31:16 -04:00
Jarrett Johnson
65835f9991 Remove OOMac 2021-07-07 12:03:25 -04:00
Thomas Holder
e8936ad6f0 Refactor ExecutiveSymExp
Sets the coordset matrix, which fixes ANISOU rotation.
2020-12-03 18:11:05 +01:00
Thomas Holder
25340f76d4 Tetsurf API refactoring and documentation 2020-10-16 11:16:13 +02:00
Thomas Holder
21eb788f3d Refactor some MapType code
- Documentation for Map*Locus functions
- Make MapExclLocus* functions static (private)
- Remove unused MapInside
- Consolidate code
2020-06-22 11:20:45 +02:00
Thomas Holder
2e8dba6688 PYMOL-2281 pi_interactions stub 2020-04-09 15:12:03 +02:00
Thomas Holder
4f50d7568a eliminate pymol::vla non-const legacy VLA cast
Avoid assignment of pymol::vla<T> return values to T*.

Refactoring to facilitate this:
- const-correctness (const T* cast still works)
- .data()
- T* -> pymol::vla<T> function arguments
2019-09-23 15:56:55 +02:00
Thomas Holder
34d06bac7c PYMOL-3147 refactor: remove _MemoryDebug_ON
_MemoryDebug_ON
_MemoryCache_ON
2018-11-15 16:46:07 +01:00
Jarrett Johnson
53231a4553 PYMOL-3146 Remove C booleans macros 2018-11-15 16:36:18 +01:00
Thomas Holder
5acb6c4637 py37, align alt, flag 6+7
* Python 3.7 support (https://sf.net/p/pymol/bugs/197/)
* enable align with alt-codes
  - allow matching of non-alt-code to alt-code atoms in alignments
  - swap sorting priority of 'name' and 'alt' identifiers
  - sort empty 'alt' before non-empty 'alt'
* flags 6 and 7 for protein and nucleic acid
* mmCIF: read _atom_site.pdbx_formal_charge
* improve coordinate loading from mmcif chem_comp files
  - ignore columns with all ? (missing) values
  - select columns with "chem_comp_cartn_use" setting
* fix h_add: skip missing coordinates
2017-12-21 12:50:47 +00:00
Thomas Holder
999ceebbe8 1.8.3.2
* experimental MMTF load support
* map export in CCP4 format
* SDF V3000 import/export support
* refactor molecular file formats export: Unified handling of PDB, PQR, mmCIF, MOL2, SDF, XYZ, MAE
* PLY geometry import (as CGO)
* new command: unset_deep
* new setting: cartoon_all_alt: Create cartoon for every alt code
* stick_h_scale: default=1.0 (was: 0.4) but remove dependency on negative stick_radius
* auto_show_classified: Visualize small (< 50 atoms) polymer classified molecules like organic
* bymol selection operator: ignore zero-order bonds
* menu: isomesh/surface negative color
* improve alignment of residues with unknown resn (e.g. ligands):
  give a match score of 5 to perfect matches of unknown residue codes.
  Previously, those got match score -1.
* remove broken and obsolete "PMO" file support
* use "label_digits" setting with "label" command
* do not resize window when loading a session file
* fix ignored SCALE w/ identity rotation (e.g. 1WAP)
* fix "scene auto, clear" (Scene > Delete)
* new setting: pick_shading: do flat shading for programmable image color analysis
* experimental cmd.raw_image_callback: post cmd.draw() callback
2016-08-30 19:14:39 +00:00
Thomas Holder
22fdfe3e81 fixed roving detail/density demos, removed unused code
* fixed roving density and roving detail demos (regression from last commit)
  http://sourceforge.net/p/pymol/bugs/156
* fix "narrowing conversion" C++ errors
* removed unused code and preprocessors:
  _PYMOL_GL_DRAWARRAYS
  _PYMOL_GL_CALLLISTS
  _PYMOL_CGO_DRAWARRAYS
  _PYMOL_CGO_DRAWBUFFERS
  OPENGL_ES_1 
  OPENGL_ES_2
* removed deprecated "register" specifier
2015-03-13 22:19:47 +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