pub_soft/pymol-open-source
3
0
Fork 0
mirror of https://github.com/schrodinger/pymol-open-source.git synced 2026-06-04 20:04:21 +08:00
Code Issues Packages Projects Releases Wiki Activity
5,127 Commits 10 Branches 6 Tags
cpp11
Commit Graph

15 Commits

Author SHA1 Message Date
Jarrett Johnson
65835f9991 Remove OOMac 2021-07-07 12:03:25 -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
7ad3b9d11b CField refactoring 
New member functions to replace data access macros:

- CField::get
- CField::ptr

New CFieldTyped derived class with typed accessors.
 2020-10-16 11:15:55 +02:00
Jarrett Johnson
e7a2919f68 field refactor 2019-11-27 13:15:15 +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
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
c2731f62ef molfile plugins, fetch URLs, ... 
* update molfile plugins to VMD version 1.9.3
* fetch 2fofc/fofc: update URLs, EDS will retire in 2017
* fix sf#102 pseudoatom multi-state problem
* editor.attach_amino_acid: fix PRO/N geometry
 2016-12-14 19:07:39 +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
f4582bbfcb pse_binary_dump, get_sasa_relative, color_deep, ... 
- experimental setting "pse_binary_dump"
- get_sasa_relative (command ported from Incentive PyMOL)
- Color menu uses util.color_deep (ported from Incentive PyMOL)
- C > by rep (ported from Incentive PyMOL)
- fix crash when saving mesh PSE without map
- fix isosurface invalidation when setting surface_negative_visible
 2016-04-17 02:00:50 +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
9bb5c2d971 1.7.5.0 (unstable/experimental) 
* mmCIF _atom_sites.fract_transf support (SCALEn equivalent)
* Complete port of scenes to C++
* warn user if setting a setting on the wrong level
* cmd.extendaa: shortcut for cmd.extend with argument auto-completion
* reduced memory footprint of AtomInfoType
* expose "reps" to iterate/alter
* expose "protons" to iterate/alter
* adaptive cartoon quality and sampling, depending on number of atoms
* fix ring center color with cartoon_ring_color=default
* make SelectorGetTmp strictly molecular, fixes for example "dss" with group names
* fix "copy" can cause crash
* fix "custom" selection operator
* consider spec_count in shaders
* don't invalidate shaders for lighting settings
* don't disable shaders for all Intel chips
* don't touch sphere_mode when disabling shaders
* map_new buffer == -1 -> gaussian_resolution
* fix all_states picking
* remove cylinder_shader_ff_workaround and cylinders_shader_filter_faces
* remove unused gl_ambient setting
* fix Tcl/Tk menu settings logging
* fix: grid mode scales down label size incorrectly
* fix: no animate argument for cmd.origin
* fix side_chain_helper for hetatm polymer atoms
* fix .mmd export
* refactor many function to take "const" pointer arguments
 2015-03-12 17:44:19 +00:00
Thomas Holder
238694b266 silence numpy deprecation warnings (NPY_1_7_API_VERSION) 
Thanks Jack Howarth for the patch.   
https://sourceforge.net/p/pymol/patches/7/
 2014-12-11 23:09:41 +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
4f28b77336 multi-letter chain support 2014-09-08 15:52:34 +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