v0.2.1: Configurable downloads and multiple matching

Highlights

• Pablo no longer automagically accesses the CCD by default; to enable the old behaviour, add STD_CCD_CACHE.auto_download = True
• Definitions in additional_definitions can now apply more than once to a PDB file

What's Changed

• Silence the dirty parts of the versioningit formats by @Yoshanuikabundi in #133
• Improve errors and handling of Maestro outputs by @Yoshanuikabundi in #134
• Prevent automatic downloads without user opt-in by @Yoshanuikabundi in #137
• Support multiple matches to additional definitions by @Yoshanuikabundi in #139

Full Changelog: v0.2.0...v0.2.1

v0.2.0: `additional_definitions` and docs!

Highlights

• additional_definitions argument can now perform substructure matches and re-use information from earlier stages
• Major documentation update - you can now read the Pablo book!
• Several API points have name changes for ergonomics - most notably, CCD_RESIDUE_DEFINITION_CACHE is now STD_CCD_CACHE

What's Changed

• Correct readme license type by @IAlibay in #71
• Fix typo in exception by @Yoshanuikabundi in #75
• Support large files produced by OpenMM and 4-character residue names by @Yoshanuikabundi in #93
• Protonation variant api by @Yoshanuikabundi in #94
• Improve docstrings and errors for CcdCache by @Yoshanuikabundi in #100
• Notebook cleanup by @Yoshanuikabundi in #102
• Begin writing PDB files that test residue and atom numbering by @Yoshanuikabundi in #64
• Matching refactor by @Yoshanuikabundi in #106
• Fix asymmetric crosslinks and add test by @Yoshanuikabundi in #113
• Support virtual sites by @Yoshanuikabundi in #112
• Match on CONECT records if atom names are incorrect by @Yoshanuikabundi in #110
• Add docstrings to _pdb_data.py by @Yoshanuikabundi in #114
• Parse CIF atom sites as PDB ATOM/HETATM records by @Yoshanuikabundi in #115
• Support PEP 639 by @mattwthompson in #124
• Additional substructures by @Yoshanuikabundi in #126
• Docs refresh by @Yoshanuikabundi in #122

New Contributors

• @IAlibay made their first contribution in #71
• @mattwthompson made their first contribution in #124

Full Changelog: v0.0.1a1...v0.2.0

PTM Prototype Alpha

This is an initial alpha release that supports loading proteins and custom amino acids from PDB files by matching atom names. It is being released to support the Post Translational Modification prototype:

https://github.com/openforcefield/ptm_prototype