2021-05-19 Wagner/Mitchell Check in

Owned by Jeffrey Wagner, created
May 20, 2021
2 min read

Participants

  • @Jeffrey Wagner

  • @Josh Mitchell

Discussion topics

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Notes

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Notes

Recap

  • latest tag got merged + made

  • Toolkit showcase merged

  • Examples helper merged, package will be made at next release.

Working on

    • Spurious test failures – Re-kicked during meeting

  • Working on FF modification example

    • JM – Seems like toolkit showcase is cleaner. I’ll port it over to use more of that in the main package example

    • JM – Thinking about whether to use the same molecule for the whole thing.

    • JW – This is tricky because the molecules fromt eh sowcase were carefully selected to show differences based on one parameter (that doesn’t cancel itself out)

    • JM – Could make a hydroxyl angle straight. Thinking of an example where we add a new term to a FF, and it overrides singe it’s the most specific.

    • JW – good idea. If this explodes, it may be because torsions get unhappy when they get linear.

    • JW: Code to generate a SMARTS for a whole molecule, and then capturing just eg. a torsion of interest

from openff.toolkit.topology import Molecule, Topology mol = Molecule.from_smiles('C=CO') print(mol.to_smiles(mapped=True)) mol.properties['atom_map'] = {0:1, 1:2, 2:3, 6:4} print(mol.to_smiles(mapped=True))
[C:1](=[C:2]([O:3][H:7])[H:6])([H:4])[H:5] [H][C:1]([H])=[C:2]([H])[O:3][H:4]

Opened

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