* use gufe.SmallMoleculeComponent in place of LigandMolecule
* thought this would fix the serialization test but it doesn't :(
* fix network serialization
Co-authored-by: David W.H. Swenson <david.swenson@omsf.io>
* API renames
To try thinking bigger and be more future proof, label everything currently designed for Ligands as for ligands. i.e.
- Molecule -> LigandMolecule
- AtomMapper -> LigandAtomMapper
- AtomMapping -> LigandAtomMapping
- Network -> LigandNetwork
* fixup
* revert change to Network name
* fixup fixtures to use AddHs
* update pep8 and mypy
* missed one
Co-authored-by: IAlibay <ialibay@mdanalysis.org>
Co-authored-by: David W.H. Swenson <david.swenson@omsf.io>
* Initial skeleton for the CLI
Currently requires the OPS CLI to be installed as well; next steps:
1. Add parameter core classes to infrastructure
2. Fully separate infrastructure into its own package
* switch to using plugcli
* tests for CLI
* helps if you add the tests...
* pep8 and deps cleanup
* add test_plugins
* Start of CLI atommapping report
* Add tests for parameters
* Almost-working atommapping command
* add hack to work-around lomap issue
* fix test
* pep8; docstrings; add header comments
* Add tests for commands/atommapping
* docstrings
* add init to command to stop circular import error
* remove init and it still works?
Co-authored-by: richard <richard@nextmovesoftware.com>
