2021-06-16 Wagner/Mitchell Check-in

openff-sphinx-theme

• JM: Got demonstration prepared

  • Demo site: https://openforcefield.github.io/openff-sphinx-theme/

  • Toolkit PR:

  • Toolkit RTD preview: https://open-forcefield-toolkit--979.org.readthedocs.build/en/979/

  • JW – Looks good. I’m inclined to approve, but to make sure it’s compatible with Interchange and Evaluator, could you open similar PRs to those repos as well?

    • – Give toolkit colors? Or default logo+colors

Next week

• Cookbook of “all the different ways to make a molecule”

  • In notebook format

    • Can we link to this from the Molecule class docstring? Should this be IN the molecule class docstring?

  • “Molecules should have explicit hydrogens, bond orders, formal charges, stereochemistry (defined on GRAPH, not just 3D)”

  • Molecule.add_atom and Molecule.add_bond

  • from_file

  • from_file_obj

  • from_object, which really delegates to:

    • from_rdkit

    • from_openeye

  • from_smiles

  • from_mapped_smiles

  • from_qcschema

  • offmol.remap (instance method)

  • from_topology

  • from_inchi – “InChI is not intended to be an interchange format” NOTE THAT THIS DOESN’T PRESERVE ATOM ORDER!!

  • from_iupac (requires OpenEye)

  • Things that go through Topology, and you actually need to know the GRAPH of the molecule ahead of time (they require a unique_molecules keyword argument with the full identity of the molecules to run). This really just reorders the atoms to be in the other object’s order:

    • Topology.from_openmm (add’l step mol=topology.reference_molecules[0])

      • Maybe make a new method for Molecule.from_openmm which returns a list of Molecules?

    • Topology.from_mdtraj (add’l step mol=topology.reference_molecules[0])

  • Molecule.from_pdb_and_smiles

  • Molecule.from_dict() (which underlies from_ bson, json, toml, messagepack, yaml, pickle, etc)