- 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
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.
When using `ribbon_sampling > 1`, use color and pick information from
the correct atom.
Refactoring side effect: Support `ribbon_color` setting special colors
like ramp names, "back", and "front".
* 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
* restore ignore_case=on default
* new setting: ignore_case_chain (default off)
* new setting: cartoon_gap_cutoff
* increase PYMOL_MAX_THREADS
* amber topology loading: bond order 1 for all bonds
* improve MOL2 file handling
* new grid_mode=3: grid per object-state
* 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
* 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)
- scenes: Restore the old behavior that when recalling a scene, all objects
which were not present when storing the scene are disabled.
- fix auto-complete for filenames with spaces
- fix an object menu panel group ordering problem
Refactoring:
- remove unused variables (Partly applies https://sourceforge.net/p/pymol/bugs/166/)
- lots of: char* -> const char*
- remove inline Parse functions, simplify ParseFloat3List
- make functions static
* 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
