PyMOL Molecular Graphics System Code

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"

pse_export_version support with Python 3

(svn propdel svn:executable)

1.9.0.0

* use PyMOL 2.0 setting defaults
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session

oneletter, wire/licorice, copy_to

* expose "oneletter" to label/iterate
* sequence viewer: MSE=M SEC=U
* wire/licorice rep aliases
* menu: A > copy to object
* new commands: copy_to, uniquify
* fix slow 'extract' performance

1.8.7.0

* support "not ..." and "enabled" in name patterns (e.g.: delete not enabled)
* improve/fix unicode+utf-8 handling for labels
* iterate color settings: type int (e.g.: iterate all, print(s.sphere_color))
* fix cmd.load with contents https://sf.net/p/pymol/mailman/message/35966326/
* fix ray tracing of stick_ball + valence https://sf.net/p/pymol/mailman/message/35928857/

patches/12, bugs/148

- web.pymolhttpd -> pymol.pymolhttpd
Generic "web" name conflicts with webpy
https://sf.net/p/pymol/bugs/148/
- make build reproducible
https://sf.net/p/pymol/patches/12/
- delete obsolete packaging files
- internal command line: consistent behavior across platforms