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81 Commits

Author SHA1 Message Date
Jarrett Johnson
65835f9991 Remove OOMac 2021-07-07 12:03:25 -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
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
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
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
f84389f14f Refactor CCrystal and CSymmetry 
- Make members private
- Add getters and setters
- Remove CrystalUpdate, SymmetryUpdate, SymmetryFree
- Remove unused CCrystal members (Norm, RecipDim, UnitCellVolume)
- Add CCrystal unit test
 2020-12-11 13:57:26 +01:00
Thomas Holder
27385b023d Remove unneeded BondType members 
BondType::id
- was imported from MOL2 and ChemPy PKL
- was exported to ChemPy PKL
- had no API for querying or manipulation, other than IO with SDF/PKL

BondType::stereo
- was imported+exported from+to SDF and ChemPy PKL
- had no API for querying or manipulation, other than IO with SDF/PKL
- is a 2D projection property (but PyMOL doesn't do any 2D projection)

BondType::temp1
- Used in various places. Usage refactored to use local data structures.

Remove unused functions (leftovers from old undo system):
- BondTypeCompare
- AtomInfoCompareAll
 2020-12-03 18:13:22 +01:00
Thomas Holder
15b74a6062 Refactor: Remove fFree methods 
Also remove unused members:
- GadgetSet::P
- GadgetSet::Setting
 2020-10-16 11:14:05 +02:00
Thomas Holder
dc7572ede5 PYMOL-3541 Fix "show cell" for PDB files 
Regression of PYMOL-3216 dc3bdc4c7f41
 2020-10-16 11:13:58 +02:00
Jarrett Johnson
4431dd0ce2 Settings copied on object copy 2020-10-16 11:07:17 +02:00
Thomas Holder
60bafcace1 Remove _PYMOL_NO_UNDO stubs 2020-06-22 11:07:06 +02:00
Thomas Holder
32a318e8c5 PYMOL-3464 pse_binary_dump atom property support 2020-05-12 11:20:50 +02:00
Thomas Holder
dbaf3a379d pse_binary_dump: Allow forward compatibility 
Do not reject atom and bond lists which have additional list items.
 2020-05-12 11:20:17 +02:00
Thomas Holder
cc69c21605 refactor: use more atmToIdx() and coordPtr() 2020-03-13 09:16:52 +01:00
Thomas Holder
737cd4f65f CObject::getCurrentState refactoring 
fixes:
PYMOL-3388
PYMOL-3390
PYMOL-3391
 2020-03-13 09:09:38 +01:00
Jarrett Johnson
27938ac229 refactor pseudoatom 2020-03-13 09:01:45 +01:00
Thomas Holder
48a9994774 refactor: CoordSet CObjectState inheritance 2020-02-26 19:16:54 +01:00
Jarrett Johnson
af625b664f Set Geometry Result refactor 2020-02-26 19:04:24 +01:00
Thomas Holder
75f06a974e CObject function pointers -> virtual methods 2019-10-29 16:24:12 +01:00
Jarrett Johnson
6dafe8ca5b remove obsolete Debug files 2019-10-15 13:55:58 +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
Jarrett Johnson
00473b5656 C++ inheritance for Object classes 2019-09-04 18:18:01 +02:00
Nandini Naidu
673655e1ee Converted DiscreteCSet from C vla to C++ vla 2019-08-30 17:16:22 +02:00
Nandini Naidu
ceddc08d45 Changed DiscreteAtmtoIdx from C vla to C++ vla 2019-08-30 17:16:19 +02:00
Nandini Naidu
71f77b68ab Converted BondType Bond to a c vla 2019-08-30 17:12:59 +02:00
Nandini Naidu
3eea34803e changed Symmetry and PeriodicBox to unique pointers and changes other pointers to c++ vla's 2019-08-30 10:22:08 +02:00
Thomas Holder
5a4ab0eaa9 PYMOL-3272 remove obsolete metaphorics code 
cex files and m4x annotated PDB files don't exist anymore.
cex loading was broken for a long time, proof that nobody was using it.
 2019-08-19 22:07:24 +02:00
Nandini Naidu
79a6b1af5e changed AtmtoIdx and TmpBond to C++ vla's 2019-08-19 22:00:58 +02:00
Nandini Naidu
1d8d6c861a float Coord and int IdxtoAtm changed to C++ vlas 2019-08-13 17:06:49 +02:00
Nandini Naidu
1b017594ae symmetry class changes to make deep copyable 2019-08-13 16:20:41 +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
3807ca57a6 refactor: __func__ in feedback messages 2019-02-21 18:40:24 +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
0dcfcc8344 clang-tidy modernize-loop-convert 2019-01-18 10:03:28 +01:00
Thomas Holder
d38e621353 refactor: pymol::vla::operator->() usage 2018-12-14 13:33:10 +01:00
Thomas Holder
391034faa9 pymol::vla<AtomInfoType> 2018-12-10 18:05:08 +01:00
Thomas Holder
e414cc6dfe refactor: AtomInfoHistory lexidx_int_t 
pave the way for a non-primitive lexidx_t
 2018-11-15 16:09:57 +01:00
Thomas Holder
1eab612a45 refactor: lexidx_t -> const lexidx_t& 
pave the way for a non-primitive lexidx_t
 2018-11-15 16:09:44 +01:00
Thomas Holder
3b541d6bef lexidx_t cleanup 2018-11-15 16:08:29 +01:00
Thomas Holder
ea3917ba66 refactor: ObjectMoleculeMerge std::move 2018-11-15 16:07:16 +01:00
Thomas Holder
8f4cca5ee0 refactor: std::swap(atInfo, I->AtomInfo) 2018-11-15 16:06:53 +01:00
Thomas Holder
33937d8543 setup.py: drop --no-cxx11 option 2018-09-03 15:27:33 +02:00