* Fix fallback MMTF loader
`msgpack-python` 1.0 uses `raw=False` by default, which means that data
(including dictionary keys) are `str` instead of `bytes`.
Also works with `u-msgpack-python` 2.7, which uses `str` as well with
Python 3 and ignores the `raw` argument.
Fixes https://github.com/schrodinger/pymol-open-source/issues/225
* Fix tests for chempy.mmtf
- testLoadMMTFMissingOptionalGroupTypeFields
- testLoadMMTFStr
- testLoadRawMMTF
- Use proper doxygen syntax for all function comments
- ObjectMoleculeUpdateNeighbors allow const argument
- Remove obsolete ObjectMolecule::BondCounter
- Remove message "PyMOL not running, entering library mode"
- Disable library mode when non-singleton instances are created
- Remove `_cmd._del` and use a capsule destructor instead, this fixes
`pymol2.PyMOL().__del__` with Python 3.8 (`_cmd` is `None`).
- Clean up `Cmd_New` and `PyMOL_New`
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>
- use context managers
- remove `lock_api_c` (not needed)
- add progress bar to GUI (only visible while `cmd.get_progress() >= 0`)
- make `_cmd._draw`, `_cmd._getRedisplay`, etc. non-blocking to make
progress bar possible
* 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)
r4188 was published on 2018-04-10 but lost after a sourceforge storage problem.
See for example https://sourceforge.net/p/forge/site-support/17420/
2.2.0a0 (unstable/experimental)
* sf.net/p/pymol/bugs/199 bash -> sh
* ignore zero-order bonds in neighbor lookup
* fix crash loading reduced 5ijo.mmtf
* volume panel: fix zoom (CTRL+R-Drag) and value input (R-Click)
* QOpenGLWidget support (not active by default)
* --gldebug -> backtrace on GL error
* 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
