* 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
- 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
* ignore SCALEn if CRYST1 is 1x1x1 or invalid
* new/refactored API functions for accessing coordinates and maps as numpy arrays
* new API function: cmd.set_state_order
* Session file (PSE) support for callback objects
* fix/silence many compiler warnings
* fix bg_rgb_top/bg_rgb_bottom side effects
* revert "fix setting surface_circumscribe"
* delete some obsolete files
