[DRAFT] PR for interfacing out parameterization #12
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Nice! |
| @@ -226,17 +226,13 @@ def get_input_set( | |||
| openff_topology = get_openff_topology(openff_counts) | |||
| openmm_topology = openff_topology.to_openmm() | |||
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| assert np.all(ffs == ffs[0]), "All Molecules must use the same force field" | |||
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This is what I had previously implemented but this isn't generally true.
- We might want to parameterize water differently than everything else.
- We might need to include a few custom parameters from another force field.
You don't need to implement either, but it'd be good to stay flexible so we can add these later on.
| INTERCHANGE_PARAMETERIZER: dict[str,str] = { | ||
| "sage": ["openff_unconstrained-2.0.0.offxml"] | ||
| } | ||
| DEFAULT_PARAMETERIZER: dict[str,str] = { |
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Interchange should probably be the default parameterizer.
| force_field = ForceField(*(self.parameterizer_type.value.get(self.force_field))) | ||
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| system = force_field.createSystem(topology=self.topology, nonbondedMethod=NoCutoff, polarization='mutual', mutualInducedTargetEpsilon=0.00001,constraints=None, rigidWater=False) |
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Nice! This is so straightforward!
| @@ -192,6 +193,7 @@ def get_coordinates( | |||
| ] | |||
| coords = Molecule.from_sites(sites) | |||
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When I first implemented this I used a raw Molecule call to pymatgen.core.structure.Molecule but in hindsight that was a mistake. In the codebase, there is also a openff.toolkit.Molecule, an Openbabel Molecule, and an RDkit Molecule. For openff, I import openff.toolkit as tk and then call tk.Molecule. Let's replicate that for the pymatgen object too.
A few options:
import pymatgen.core.structure.Molecule as pmg_Molecule
import pymatgen.core.structure # then use structure.Molecule
import pymatgen.core.structure as pmg # then use pmg.MoleculeI'll make a pass through the rest of the codebase to ferret this out.
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