- Use proper doxygen syntax for all function comments
- ObjectMoleculeUpdateNeighbors allow const argument
- Remove obsolete ObjectMolecule::BondCounter
- Make members private
- Add getters and setters
- Remove CrystalUpdate, SymmetryUpdate, SymmetryFree
- Remove unused CCrystal members (Norm, RecipDim, UnitCellVolume)
- Add CCrystal unit test
* 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
* fix assemblies for cases like 4f3r which have multiple entries in the _pdbx_struct_assembly_gen table
* fix ref counts in iterate/alter subscripts
* improve side_chain_helper and nucleic_adic_mode situation
* eliminate all "try/catch" blocks for std::map lookups
* clean up some MemoryDebug stuff and remove unused jenarix wrapper
* change default (!) of "ignore_case" setting to off. Case insensitve
identifier matching is not practical anymore with large structures
which use upper and lower case chain identifiers.
* new setting "assembly" to load assemblies from mmCIF as multi-state
objects with all_states=1
* new setting "cif_use_auth" controls whether mmCIF "auth" identifiers
are used or not (on by default)
* mmCIF "CA/P ATOMS ONLY" chains: set atom-level cartoon_trace_atoms
and ribbon_trace_atoms
* CIF discrete and irregular multi-model loading support
* support "pdb_honor_model_number" setting for CIF
* load multiple objects ("data_" blocks) from one CIF file (multiplex=-1)
* don't store AtmToIdx, DiscreteAtmToIdx or DiscreteCSet to PSE
(unless pse_export_version <= 1.76)
* 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
* fast PDBx/mmCIF and core CIF loading in C++
* new connect_mode=4 does bonding with components.cif dictionary
(mmCIF only, components.cif needs to be present in current
directory)
* gray out residues in the sequence viewer that are missing from the
current state; Read missing residues from mmCIF files
(_pdbx_unobs_or_zero_occ_residues records) so that they show up in
the sequence viewer
* add spider map reading support
* load "map" as ccp4 instead of throwing "ambiguous" error
* xyz write support
* Improve right-button zoom: use origin instead of clipping slab
center as depth indicator, fixes zoom speed when far clipping plane
is very far away
* don't use dynamic_width for nonbonded rep
