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
5,847 Commits 10 Branches 6 Tags
master
Commit Graph

39 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
Jarrett Johnson
8c232d149d Remove unused headers 2024-01-30 15:51:55 -05:00
Jarrett Johnson
74894e01da Generic CGO Render 2022-03-08 15:16:16 -05:00
Jarrett Johnson
40a54a1c91 Replace OV (ObjectAlignment) 2021-07-07 12:19:16 -04:00
Jarrett Johnson
65835f9991 Remove OOMac 2021-07-07 12:03:25 -04:00
Jarrett Johnson
7d392b852c Backport Seq refactor from undo 2021-04-28 04:05:21 -04:00
Jarrett Johnson
355c45d229 Place CObject in pymol namespace 2021-02-11 19:14:06 +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
Jarrett Johnson
4431dd0ce2 Settings copied on object copy 2020-10-16 11:07:17 +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
8b9efcc028 refactor: use more pymol::Result 2020-04-23 14:11:17 +02:00
Thomas Holder
737cd4f65f CObject::getCurrentState refactoring 
fixes:
PYMOL-3388
PYMOL-3390
PYMOL-3391
 2020-03-13 09:09:38 +01:00
Thomas Holder
75f06a974e CObject function pointers -> virtual methods 2019-10-29 16:24:12 +01:00
Thomas Holder
ceb77d1144 invalidate ObjectAlignment when merging 2019-10-29 16:03:47 +01:00
Jarrett Johnson
0affe77a1a ObjectAlignment refactor 2019-10-29 16:03:32 +01:00
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
Jarrett Johnson
00473b5656 C++ inheritance for Object classes 2019-09-04 18:18:01 +02:00
Thomas Holder
035d6fe611 C++ inheritance for all CObject subclasses 2019-03-29 13:36:14 +01:00
Jarrett Johnson
37f95ef227 ObjectMolecule proper C++ inheritance 2019-03-29 13:04:12 +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
b2e049a3ef rewrite "get_raw_alignment" 
new: 1:1 dump of the ObjectAlignment
old: reinterpetation of the derived selection

Note: (model,index) element order withing columns might differ between
old and new implementation.
 2018-12-14 13:33:17 +01:00
Jarrett Johnson
fde67f2d9b PYMOL-3098 ScenePickVLA Refactor 2018-11-15 16:44:02 +01:00
Thomas Holder
0f48252978 PYMOL-3141 cmd.set_raw_alignment() 2018-11-15 16:33:51 +01:00
Thomas Holder
7722d1bc4c PYMOL-3111 aln export for Nucleic Acids 2018-09-03 15:32:06 +02:00
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
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
520bf2a72a 1.9.0.0 
* use PyMOL 2.0 setting defaults
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session
 2017-10-18 17:21:19 +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
9f53f30e47 segi, resn, name of arbitrary length; settings in iterate/alter 
* support segi, resn and name of arbitrary string length
* expose settings to iterate/alter via "s.<name>"
* Python 3 compatibility for champ module
* apbs_tools: apply fixes from Pymol-script-repo
 2015-12-14 19:11:12 +00:00
Thomas Holder
57ae658ef3 fix crash with empty alignment object from PSE 2015-12-04 00:28:20 +00:00
Thomas Holder
f9f76fed07 scene_buttons=on, ... 
* new default: scene_buttons=on
* normalize_ccp4_maps=2 -> use mean and stdev from file header
* fix alignment with atoms w/o coords in a state
 2015-10-15 17:43:51 +00:00
Thomas Holder
8bf29abf88 post sf.net downtime update 
* fix isosurface all_states rendering
* pdb_hetatm_guess_valences for CIF loading
* mutagenesis wizard: improve "apply" performance
* fix measurement and alignment object partial PSE loading
* some load/save refactoring
* keep atom IDs when creating object from selection
* when renaming group "A" to "B", then also rename entry "A.X" to "B.X"
 2015-07-29 14:25:52 +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
f42840260b c++ for all PyMOL c files 
- renaming files c -> cpp
- c++ specific syntax (::)
 2014-09-08 13:42:11 +00:00