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Jeffrey Wagner

Jeffrey Wagner

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Notes

First week retrospective

  • Meeting frequency?

    • IP – It’s been good so far.

  • Are tasks well specified enough?

    • IP – Tasks right now are small and well-specified. They will probably get bigger in the future.

  • JW – After another week or two of one-on-one meetings, we’ll move to one one-on-one each week, and some general design meeting.

  • IP – I lacked context for VU meeting and MoSDeF

    • JW – It’s partly to introduce you to a group that we’ll be gathering requirements from, and partly to show how a major inter-ecosystem interoperability project actually happens.

Development environment issues

  • networkx 2.3 + py3.9 dependency problem

  • Conda – can we specify development dependencies?

    • (General) – We should change the development build instructions to run (something like) conda env create -n openff-dev -f test_env.yaml

    • IP will open a PR for this change (and add a Documentation updated section to releasehistory pointing out the change) , JW will review

Pydantic Atom class review

  • IP – Had to install pydantic and pint manually – How do I ensure that a consistent version of these is being used? Can I modify test_env?

    • JW – Yes, do feel free to modify test_env in your environment

  • (Discussed why we might need different unit registries/CODATAs)

  • JW – If we can let people set formal charge using either int or quantity, but always store it as quantity

  • Stereochemistry is complicated. Long story short, we may want to support

    • Stereocenters being “R”. “S”, or “undefined”

    • Stereochemistry defined as clockwise/counterclockwise

  • Will it be possible to do a gradual replacement of current functionality using pydantic models, or will we get in trouble with circular references?

Next steps

  • Replace all Atom functionality with pydantic?

  • Begin formalizing requirements

  • Search for RDKit/AmberTools functionality to go from PDB to SDF/something with bond orders

    • JW – One non-optimal strategy would be ambpdb → antechamber (see first and last lines of

      Github link macro
      linkhttps://github.com/openforcefield/amber-ff-porting/blob/cbe0eda246d89265bd7dccd1e0d8f93ebb6b7d51/GenerateDipeptides.sh#L129-L139
      )

  • (need to contact Matt) Start studying AtomTypedTopology vs. normal topology and design common API.

    • An openFF system contains

      • A topology

      • a forcefield / list of parameters

      • A mapping of how the parameters have been assigned to the topology

      • coordinates + box vectors

    • Will need to support

    • Code Block
      mol = Molecule.from_smiles('CCO')
ff = ForceField('openff-1.3.0.offxml')
off_sys1 = ff.create_openFF_system(mol)
off_sys2 = openff.System.from_gromacs('something.gro', something.top')
combined_off_sys = off_sys1 + off_sys2

  • We will eventually want to be able to combine topologies (both Cheminformatics-based and atom-type-based). Combining cheminformatics topologies will look something like this:

  • Code Block
    from openff.toolkit.topology import Molecule, Topology
smileses = [('ethanol', 'CCO'), 
            ('reversed_ethanol', 'OCC'),
            ('cyclohexane', 'C1CCCCC1'),
            ('benzene', 'c1ccccc1'),
            ('acetate', 'CC(=O)[O-]'),
            ('chlorine', '[Cl-]'),
            ('methane', 'C'),
            ('adamantane', 'C1C2CC3CC1CC(C2)C3')
           ]
mols = []
for name, smiles in smileses:
    mol = Molecule.from_smiles(smiles)
    mols.append(mol)


topology1 = Topology.from_molecules(mols[:4])
topology1.add_molecule(mols[0])
topology1.add_molecule(mols[1])
topology2 = Topology.from_molecules(mols[3:])
topology2.add_molecule(mols[0])
topology2.add_molecule(mols[1])

print(topology1.n_topology_molecules, topology2.n_topology_molecules)

def combine_topologies(topology1, topology2):
    import copy
    topology1 = copy.deepcopy(topology1)
    topology2 = copy.deepcopy(topology2)
    for topology_molecule in topology2.topology_molecules:
        new_mol = topology_molecule.reference_molecule.remap(topology_molecule._ref_to_top_index)
        topology1.add_molecule(new_mol)
    return topology1

combined_top = combine_topologies(topology1, topology2)

# If we successfuly maintained the atom orders 
combined_top.topology_molecules[-1].atom(0)

    • Code Block
      class MoleculeBase:
    def __init__():
        ...
    def atoms
      ...
    def bonds
       ...

class AtomBase:
    def name
    
class CheminformaticsAtom(AtomBase):
    def formal_charge
    def stereochemistry
    
class AtomtypedAtom(AtomBase)
    def atom_type
    def atom_name
  
class BondBase
class CheminformaticsBond
class AtomTypedBond

class MoleculeBase
    (most of the functionality will be defined here)
class CheminformaticsMoleucle
    (only a few weird things will be here)
    def total_charge
class AtomTypedMolecule


class Topology:
    def

Action items

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Decisions