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27 Commits

Author SHA1 Message Date
Jarrett Johnson
07d7a790f0 Forward decls/Move headers to source 2021-08-20 11:24:10 -04:00
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
Thomas Holder
2dd9a34ded Refactor API: exporting, importing, viewing 
- Make `_self` a keyword-only argument
- Fix `get_viewport` logging
- Error propagation
- Remove unused `set_colorection_name`
 2020-06-22 13:15:48 +02:00
Thomas Holder
6f11b62566 PYMOL-3410 Remove Python 2 support 2020-06-05 09:13:06 +02:00
Thomas Holder
d080bbdb7b remove obsolete code 
Python module:

- pymol.embed

Preprocessor definitions:

- _PYMOL_ACTIVEX_OLD
- _PYMOL_MIN_GLUT
- _PYMOL_OLD_ACTIVEX
- _PYMOL_PRETEND_GLUT_FONT
- _PYMOL_SHARP3D
- _PYMOL_WX_GLUT
- PYMOL_ICC_LINUX
- HAVE_CONFIG_H
- aliased_int
- aliased_float
 2019-08-13 16:25:34 +02:00
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
5e04325863 cleanup (local/unused function declarations) 2019-02-06 15:43:14 +01:00
Jarrett Johnson
b5bc074b9b Replaced old Queue impl with std::queue 2018-12-06 08:51:23 +01:00
Thomas Holder
8bbe54e321 PyMOLGlobals for MainAsPyList/MainFromPyList 2018-11-16 12:20:28 +01:00
Thomas Holder
d0b3c70d0f fix --glut (remove MemoryDebugDump) 2018-11-16 12:18:18 +01:00
Jarrett Johnson
78021420a7 PYMOL-3095 Block Refactor 2018-11-15 15:48:32 +01:00
Thomas Holder
ac5a4c42d7 PYMOL-2173 fix wheel x/y on Windows 2018-09-06 17:12:14 +02:00
Thomas Holder
d402c26cb7 ScrollWheel action on Sequence Viewer 2018-09-06 17:09:54 +02:00
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
889cbb280f auto library mode 
* Python API: New "auto library mode". Automatically start a
  non-GUI PyMOL instance if the pymol.cmd API is used without
  running pymol.launch() first
* pdb_echo_tags for mmCIF and MMTF
* command parser: improve exception handling
* fix some PSE export memory leaks
* pymol2.cmd2: eliminate (non-weak) circular references
* movie making: reinterpolate after add_nutate/add_roll etc.
* support "module:callable" in loadfunctions/safefunctions
* yellow state indicator for discrete objects
* mpng modal draw improvements
 2017-12-05 18:37:16 +00:00
Thomas Holder
09fe0a5fbc 1.8.7.0 
* support "not ..." and "enabled" in name patterns (e.g.: delete not enabled)
* improve/fix unicode+utf-8 handling for labels
* iterate color settings: type int (e.g.: iterate all, print(s.sphere_color))
* fix cmd.load with contents https://sf.net/p/pymol/mailman/message/35966326/
* fix ray tracing of stick_ball + valence https://sf.net/p/pymol/mailman/message/35928857/
 2017-08-02 11:36:28 +00:00
Thomas Holder
0629165364 patches/12, bugs/148 
- web.pymolhttpd -> pymol.pymolhttpd
  Generic "web" name conflicts with webpy
  https://sf.net/p/pymol/bugs/148/
- make build reproducible
  https://sf.net/p/pymol/patches/12/
- delete obsolete packaging files
- internal command line: consistent behavior across platforms
 2017-07-03 13:10:23 +00:00
Thomas Holder
f6cfe9c55a mpng width/height, pick_shading/surface_color_smoothing, ... 
* width/height arguments for movie export (mpng, movie.produce)
* fetch: support "fetch EMD-3489"
* auto_show_classified -1 => 3 for 500k+ atoms
* pick_shading => surface_color_smoothing off
* cleanup: eliminate pymol.pymol_launch variable
 2017-01-19 15:45:50 +00:00
Thomas Holder
2d45a2d7ca Python 3 compatibility 
Tested with Python 2.6, 2.7, 3.4
 2015-12-09 17:01:32 +00:00
Thomas Holder
59d84a385b assembly fix, ref count fix, ... 
* fix assemblies for cases like 4f3r which have multiple entries in the _pdbx_struct_assembly_gen table
* fix ref counts in iterate/alter subscripts
* improve side_chain_helper and nucleic_adic_mode situation
* eliminate all "try/catch" blocks for std::map lookups
* clean up some MemoryDebug stuff and remove unused jenarix wrapper
 2015-06-23 14:07:26 +00:00
Thomas Holder
5cbfe6b0d4 fix invalid memory access during PyMOL_Stop 
- https://sourceforge.net/p/pymol/bugs/162/
  - Free ShaderMgr after Scene
  - check (G != NULL) in MainOnExit
- https://sourceforge.net/p/pymol/bugs/161/
  apply clang logical-op-parentheses suggestion
- more `const char *` arguments refactoring
 2015-03-16 18:58:36 +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
7c4b4dd38b cif fixes, deprecate full_screen setting, 1.7.3.4 
* cif: read first_model_num
* fixed _foo?bar lookup could fail in mmCIF parsing
* deprecated full_screen setting (use full_screen command)
 2014-11-20 19:38:53 +00:00
Thomas Holder
471f0dceee minor fixes 
- fix collada_* settings in pymol.settings
- fix apbs_tools for tcl/tk 8.6
- fix fullscreen on OSX w/ GLUT
- silence compiler warnings
 2014-11-04 14:58:32 +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