- 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
- Use proper doxygen syntax for all function comments
- ObjectMoleculeUpdateNeighbors allow const argument
- Remove obsolete ObjectMolecule::BondCounter
- 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
- Remove obsolete CoordSet::LabPos
- Fix AppendAtomVertex (HydrogenAdder): It was not resizing
has_atom_state_settings, atom_state_setting_id, and RefPos
- Make members private
- Add getters and setters
- Remove CrystalUpdate, SymmetryUpdate, SymmetryFree
- Remove unused CCrystal members (Norm, RecipDim, UnitCellVolume)
- Add CCrystal unit test
CGOOptimizeToVBONotIndexed and CGOOptimizeToVBOIndexed will
automatically call CGOCombineBeginEnd if the input CGO has Begin/End
operations. They will also set `use_shader` on the CGO.
Fixes `set cgo_debug; wizard demo, raster3d`
Eliminate various CGOFree calls by using unique_ptr.
Track the "rep has transparency" information with a flag which is set
during CGO building. Fixes CoordSet::render() which was trying to get
this information from the object-state-level setting.
Porting the essential parts of EPAM System's "openvr" branch to the
master branch.
Original authors:
Natalia Smirnova, EPAM Systems, Inc.
Pavel Smirnov, EPAM Systems, Inc.
Original fork:
https://github.com/epam/pymol-open-source/tree/openvr
Adjustments:
- Make feature optional with "--openvr" compile option
- Python 3 support
- Remove C++11 workarounds
- Exclude build system changes
Co-authored-by: Natalia Smirnova <Natalia_Smirnova@epam.com>
Co-authored-by: Pavel Smirnov <pavel_smirnov1@epam.com>
* fix selection wildcard (sf.net/p/pymol/bugs/209)
* fix PDB atom id > 99999 crash
* more robust PQR parsing
* pymol2.PyMOL() context manager
* new setting: cif_metalc_as_zero_order_bonds
* new setting sdf_write_zero_order_bonds
* cif: accept _chem_comp_bond.type alias for _chem_comp_bond.value_order
* better support for mingwpy compiler (Christoph Gohlke)
