- 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
- Make members private
- Add getters and setters
- Remove CrystalUpdate, SymmetryUpdate, SymmetryFree
- Remove unused CCrystal members (Norm, RecipDim, UnitCellVolume)
- Add CCrystal unit test
Add some custom PyMOL atom site columns, matching "iterate" variables:
_atom_site.pymol_label
_atom_site.pymol_vdw
_atom_site.pymol_elec_radius
_atom_site.pymol_partial_charge
- put in "pymol" namespace
- modernize memory management (C++11)
- make cif_array API more STL like (get_nrow() -> size(),
row -> pos, etc.)
- as<> and to_vector<> with default
- cif_file::datablocks() preserves order (map -> vector)
* 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)
* 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
* Python 3.7 support (https://sf.net/p/pymol/bugs/197/)
* enable align with alt-codes
- allow matching of non-alt-code to alt-code atoms in alignments
- swap sorting priority of 'name' and 'alt' identifiers
- sort empty 'alt' before non-empty 'alt'
* flags 6 and 7 for protein and nucleic acid
* mmCIF: read _atom_site.pdbx_formal_charge
* improve coordinate loading from mmcif chem_comp files
- ignore columns with all ? (missing) values
- select columns with "chem_comp_cartn_use" setting
* fix h_add: skip missing coordinates
* Python API: New "auto library mode". Automatically start a
non-GUI PyMOL instance if the pymol.cmd API is used without
running pymol.launch() first
* pdb_echo_tags for mmCIF and MMTF
* command parser: improve exception handling
* fix some PSE export memory leaks
* pymol2.cmd2: eliminate (non-weak) circular references
* movie making: reinterpolate after add_nutate/add_roll etc.
* support "module:callable" in loadfunctions/safefunctions
* yellow state indicator for discrete objects
* mpng modal draw improvements
* fast MMTF load support in C++ (adds msgpack-c dependency)
* extra_fit: report RMS for method=cealign; Thanks to Hongbo Zhu
* CTRL-L ligand zoom
* preset > classified (auto_show_classified equivalent)
* preset > interface (ported from Incentive PyMOL 1.8.0)
* set_key auto-completion
* command completion for selection language
* fix connect_mode=4 for N-H1 and N-H3
* fix CGO ALPHA and dup COLOR issue
* experimental MMTF load support
* map export in CCP4 format
* SDF V3000 import/export support
* refactor molecular file formats export: Unified handling of PDB, PQR, mmCIF, MOL2, SDF, XYZ, MAE
* PLY geometry import (as CGO)
* new command: unset_deep
* new setting: cartoon_all_alt: Create cartoon for every alt code
* stick_h_scale: default=1.0 (was: 0.4) but remove dependency on negative stick_radius
* auto_show_classified: Visualize small (< 50 atoms) polymer classified molecules like organic
* bymol selection operator: ignore zero-order bonds
* menu: isomesh/surface negative color
* improve alignment of residues with unknown resn (e.g. ligands):
give a match score of 5 to perfect matches of unknown residue codes.
Previously, those got match score -1.
* remove broken and obsolete "PMO" file support
* use "label_digits" setting with "label" command
* do not resize window when loading a session file
* fix ignored SCALE w/ identity rotation (e.g. 1WAP)
* fix "scene auto, clear" (Scene > Delete)
* new setting: pick_shading: do flat shading for programmable image color analysis
* experimental cmd.raw_image_callback: post cmd.draw() callback
