2021-09-28 Pulido/Wagner check-in

Updates

• JW

  • HierarchySchemes and Elements prototyped

  • Working on TopologyMolecule deprecation

• IP

  • Checked out CCTBX, this DOES apply residue names and stuff, but it DOESN’T apply bondorders + formal charges. Largely aimed at crystallographers with messy data. So one module handles PDB, another handles MMCIF.

    • IP – Kinda tricky because it pulls in a bunch of dependencies

    • JW – Licensing issues?

      • (General) – It’s MIT or BSD3 licensed

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Next steps

• What loading pathways do we WANT to offer?

  • Load from Element + bond existence

    • Element PDB w/ CONECT

    • mmcif w/ bonds

  • Load from atomtyped representation with atom names matching a known typing scheme

    • Atomtyped PDB w/o CONECT (Perses entry point)

    • mmcif w/o bonds

• What loading pathways CAN we offer?

  • (slow) Molecule.from_pdb (matching to residue templates)

    • Element PDB w/ CONECT → OFFMol

    • (would require more work) mmcif with bonds → OFFMol

  • CCTBX

    • Element PDB → Atomtyped PDB w/ CONECT

• What prep method will people have used beforehand?

  • AMBER tleap protein prep → SDF that can probably be fixed

  • Schrodinger protein prep → ?

  • Chimera protein prep → ?

  • CCTBX cleanup →

  • PDBFixer → Atomtyped PDB w/ CONECT

  • Pymol mutagenesis wizard output → Atomtyped PDB w/ sometimes-messy CONECT

• IP – We could speed up subgraph matching by splitting at peptide bonds.

  • JW – Agree. But how do we empower users to handle their own corner cases?

  • IP – Could let users add new residue SMILES

  • IP – Could let people match only a range of atoms for complex molecules

    • JW – This could work well, but then we may end up with partially-annotated molecules, and that could get really messy if people try to assign chemical information in different steps – When they try to convert to a full OFFMol, it’ll be hard to communicate which parts didn’t get bonds+formal charges.

• JW will plan to have TypedMolecules optionally hold element, formal charge, stereo, and bond info, and potentially let them be upscaled to OFFMols if all info is present.

• IP will try to speed up subgraph matching by splitting at peptide bonds. This will provide a prototype and early users to start providing feedback and finding corner cases.

• IP – I spoke with DHahn the other day. I’ll be contributing a bit to the PLBenchmarks repo, and will probably also be involved in the continuous benchmarking efforts. I’m thinking about making a PLBenchmarks conda package.

• JW – PLBenchmarks has a bunch of protein structures prepared in Schrodinger, so that will be a great source of example input data.

  • IP – CCTBX refused to read these, they probably violate the PDB spec in some way.

• JW – I don’t think the biopolymer stuff will be in a major OpenFF Toolkit release in 2021. Instead, we should either direct people to do development builds from the branch, or I can make omnia conda packages from the topology-refactor branch