PyMOL Molecular Graphics System Code

fix wildcard, fix PDB 99999 crash, PQR parsing...

* 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)

anaglyph batch mode, all_states measurements, ...

* fix anaglyph stereo in batch (headless) mode
* fix possible memory corruption with boolean settings
* measurement wizard: distances between states (all_states=on)
* get_fastastr: nucleic acid, by chain
* menu: A (Action) > group
* sequence viewer menu: ss (Secondary Structure)
* MAE export of groups (s_m_subgroupid)
* macOS: -O3 -fno-strict-aliasing (bugs/205)

restore r4188

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

PyQt interface (2.1.0)

stick_round_nub, UTF-8, display_scale_factor, ...

* 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

polymer.protein polymer.nucleic multifilesave ...

* new selection keywords: polymer.protein polymer.nucleic
* new command: multifilesave
* MMTF export (requires simplemmtf python module)
* select: present, state -1 -> current object state
* create: source_state = -1 -> current
(was: source_state = -1/0 -> all)
* cif: support quoted '?' and '.' as values
cif_get_array -> None instead of empty string for ? and .
* fix copy discrete object w/o coords
* fix loading pdbqr AutoDock 4 atom types
* fix get_model('none') and get_str('mol', 'none')
* h_add refactored: 5x faster, support discrete objects

py37, align alt, flag 6+7

* 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

auto library mode

* 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

pymol/bugs/196, pmw/bugs/47

* fix elements from .gro files (pymol/bugs/196, r4181 regression)
* save .mtl: raise exception
* Python 3:
- fix "GUI Font Size" dialog (pmw/bugs/47)
- fix COLLADA export

some elements wrong from SDF and XYZ

Reported by Xin Wu: "Si" element from XYZ file loaded as "S"