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5,127 Commits 10 Branches 6 Tags
cpp11
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1530 Commits

Author SHA1 Message Date
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
9c82294fab PYMOL-4014 Respect quiet argument for cif load 2024-01-30 12:06:24 -05:00
Thomas Holder
d59041b68c enum cAtomProtected_* (#316) 2023-09-25 12:18:38 -04:00
Jarrett Johnson
9333da43b2 Specify color ramp for volume state 
Fixes #289
 2023-07-20 12:07:03 -04:00
Thomas Holder
b034d5c3e6 MMTF loader: Use entityList for HETATM flag (#296) 
Fixes https://github.com/schrodinger/pymol-open-source/issues/295
 2023-07-18 11:51:18 -04:00
Thomas Holder
006645fad5 Fix crash when loading discrete object (#261) 
Follow-up on "PYMOL-3840 Fix cartoon rep memory init"
682572b978
 2022-10-05 21:41:48 -04:00
Thomas Holder
85b6ce440a New setting: cell_centered (#259) 
Closes https://github.com/schrodinger/pymol-open-source/issues/258
 2022-10-05 11:15:15 -04:00
Jarrett Johnson
682572b978 PYMOL-3840 Fix cartoon rep memory init 
Fix #234

Commit that introduced bug: e4856c2fe4026d69b768190a3ff144873a199189
 2022-05-04 15:54:44 -04:00
Thomas Stewart
07d9206379 PYMOL-3823: Fix for misleading h-bonds 2022-05-04 15:54:43 -04:00
Thomas Holder
abc307745d iterate: Add explicit_valence and explicit_degree (#227) 2022-03-11 17:37:26 -05:00
Jarrett Johnson
74894e01da Generic CGO Render 2022-03-08 15:16:16 -05:00
Jarrett Johnson
2cc253782b PYMOL-3168 Remove dashes when cartoon hidden 2022-02-22 16:32:57 -05:00
Thomas Holder
54b187c6aa More consistent cmd.load_model discrete behavior 
- Allow discrete=0 for multi-state objects
- Keep existing discrete flag with discrete=-1

Fixes https://github.com/schrodinger/pymol-open-source/issues/212
 2021-12-15 15:05:35 -05:00
Jarrett Johnson
9aa79d7538 fix #191 correct CGO state resizing 2021-09-10 12:46:49 -04:00
Jarrett Johnson
66de86cb52 SceneView encapsulation 2021-08-20 12:10:22 -04:00
Jarrett Johnson
07d7a790f0 Forward decls/Move headers to source 2021-08-20 11:24:10 -04:00
Jarrett Johnson
9742359bc0 Replace OV (AtomInfo) 2021-07-07 12:19:24 -04:00
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
Guillaume Bouvier
6bdd7f5d2f Fixing SYBYL atom types for Sulphoxide sulphur (S.o) and Sulphone sulphur (S.o2) in layer2/Mol2Typing.cpp 
The SYBYL atom typing for Sulphoxide sulphur (S.o) and Sulphone sulphur (S.o2) doesn't match the SYBYL typing (https://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html)
 2021-04-28 07:02:32 -04:00
Thomas Holder
b85270bc30 PYMOL-3528 isosurface with VTKm 
New setting: isosurface_algorithm
 2021-04-28 05:17:34 -04:00
Thomas Holder
6f77e5efb0 GIL pre-conditions 2021-04-28 05:15:35 -04:00
Jarrett Johnson
b184f73cce RenderContext enum class 2021-04-28 05:13:30 -04:00
Thomas Holder
10af8bd0b9 Refactor ObjectMolecule::Neighbor access 
- Make ObjectMolecule::Neighbor private
- Use AtomNeighbors or ObjectMolecule::getNeighborArray
- Eliminate ObjectMoleculeUpdateNeighbors
 2021-04-28 04:34:33 -04:00
Jarrett Johnson
7d392b852c Backport Seq refactor from undo 2021-04-28 04:05:21 -04:00
Thomas Holder
d5d05f19c9 PYMOL-3624 Handle map.gz and mrc.gz extensions 2021-03-26 14:30:12 +01:00
Jarrett Johnson
f6dd412e7d Symop strings from 'bond' never nullptr 2021-03-26 14:29:52 +01:00
Thomas Holder
07435800fc pbc_wrap/pbc_unwrap, smooth+intra_fit pbc support 
- new `pbc_wrap` and `pbc_unwrap` commands
- `intra_fit pbc=1` (default) automatically unwraps and rewraps
- `smooth pbc=1` (default) automatically unwraps and rewraps
- Changes CoordSetRealToFrac/CoordSetFracToReal to take the
  premultiplied state matrix into account
 2021-03-26 14:04:35 +01:00
Thomas Holder
8b0a5d4156 PYMOL-2851 surface for all-ignored objects 
If all atoms in a coordinate set have "flag ignore", then don't use
the flag. This should allow showing ligand surface after extracting a
ligand to a new object.
 2021-03-26 13:48:57 +01:00
Thomas Holder
14cffe226e Fix PYMOL-3012 fix_chemistry C-O bond 2021-03-26 13:48:52 +01:00
Thomas Holder
8598bbcfc4 Refactor: Make assign_pdb_known_residue more readable 2021-03-26 13:48:46 +01:00
Thomas Holder
e0f39aa6d4 Fix crash with solvent_radius=0 
Closes https://github.com/schrodinger/pymol-open-source/issues/169
 2021-02-18 19:33:33 +01:00
Thomas Holder
491e9c5a4d load_raw dx support 2021-02-18 19:33:11 +01:00
Thomas Holder
9154ce95a4 defer_builds_mode 3: Don't purge object-level caches 
`cRepInvPurge` will only purge reps, but will not invalidate object data
like nonbonded atoms, neighbors, selections, or sculpting.
 2021-02-18 19:32:11 +01:00
Thomas Holder
9e5b765e60 sculpt_iterate: state=0 for all states 2021-02-11 19:14:45 +01:00
Jarrett Johnson
355c45d229 Place CObject in pymol namespace 2021-02-11 19:14:06 +01:00
Thomas Holder
f3c0419654 rebond pbc=1 
- Add `pbc` argument to cmd.rebond()
- Refactor ObjectMoleculeConnect
- Add support for OpenMP
 2021-02-11 19:05:08 +01:00
Thomas Holder
1142e3ab22 PYMOL-3570 Bonds to crystal symmetry mates 2021-02-11 18:58:26 +01:00
Thomas Holder
0562e1ec18 Fix GCC 4.8 and Intel Compiler support 
- Fix `pymol::string_format` with `pymol::zstring_view`
- Skip `std::is_trivially_copyable` for GCC 4.8
- Eliminate some compiler warnings

Closes https://github.com/schrodinger/pymol-open-source/issues/163
 2021-02-01 12:38:43 +01:00
Thomas Holder
8919b9cdd6 Fix mesh_negative_color with carved meshes 
Fixes https://github.com/schrodinger/pymol-open-source/issues/157
 2021-01-18 19:29:19 +01:00
Thomas Holder
6818037bb8 symexp: Symmetry operation as title 2021-01-18 19:29:11 +01:00
Thomas Stewart
23cd55c02c PYMOL-3585 ObjectCGO copyable, cmd.copy on all obj 
- Refactored ObjectCGO
    - cache_ptr for state CGO's
    - State now stored as std::vector
- noexcept added for cache_ptr move
- cmd.copy will now work with all objects
    - Uses clone() method
 2021-01-14 15:42:24 +01:00
Thomas Holder
63c1796bc0 StateIndex_t, StateIndexPython_t 2021-01-14 15:36:48 +01:00
Thomas Holder
4578d0145e Improve fuse command 
- Allow mixed hydrogen/non-hydrogen input
- Treat all "single geometry" atoms like hydrogens
- Attaching to an atom with no free valence is an error
 2021-01-14 15:36:29 +01:00
Thomas Holder
5308f66381 Refactor: ITERNEIGHBORATOMS -> AtomNeighbors 2021-01-14 15:31:38 +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
Thomas Holder
68a18a3e09 CoordSet refactoring/cleanup 
- Remove unused CoordSet::appendIndices()
- Simplify ObjectMoleculeDummyNew
- Simplify ObjectMoleculeSort
- Turn atom_state_setting_id into a method
- Consolidate CoordSetAdjustAtmIdx and CoordSetPurge
- Convert IdxToAtm and AtmToIdx to std::vector
- Eliminate CoordSet::NAtIndex
- Use setNIndex() where possible
 2021-01-14 14:15:44 +01:00
Thomas Holder
f0a7c72e3c Fix PYMOL-3583 Removing atoms removes properties 2021-01-14 14:08:12 +01:00
Thomas Holder
b1d9cee8aa Fix PYMOL-3582 Crash in CoordSetPurge 
- Remove obsolete CoordSet::LabPos
- Fix AppendAtomVertex (HydrogenAdder): It was not resizing
  has_atom_state_settings, atom_state_setting_id, and RefPos
 2021-01-14 14:07:22 +01:00