MolSSI / mmic_openff

Tactic MMIC translator for OpenFF/MMSchema

OpenFF translator for MMSchema

This is part of the MolSSI Molecular Mechanics Interoperable Components (MMIC) project. This package provides translators between MMSchema and OpenFF toolkit.

mmic_openff provides 2 classes of translators for: molecules and forcefields.

Models

from mmic_openff.models import OpenFFMol

# Convert MMSchema to OpenFF molecule
off_mol = OpenFFMol.from_schema(mm_mol) -> 

# Convert OpenFF to MMSchema molecule
mm_mol = OpenFFMol.to_schema(off_mol) -> mmelemental.models.Molecule

One could do similar conversions for the ForceField model as well.

Components

The from_schema and to_schema methods in the OpenFFMol model use translation components provided by mmic_openff and MMElemental to convert between MMSchema and OpenFF representations.

from mmic_openff.components import OpenFFToMolComponent, MolToOpenFFComponent
from mmic_openff.models.import OpenFFMol
from mmelemental.models import Molecule

MMSchema to OpenFF molecule

# Create MMSchema molecule
mm_mol = Molecule.from_file(path_to_file)

# Create translation input
inp = {
    "schema_object": mm_mol,
    "schema_version": 1,
    "schema_name": "mmschema",
}

# Run translator compute
outp = MolToOpenFFComponent.compute(inp)

# Extract OpenFF molecule object
mol = outp.data_object.data

OpenFF to MMSchema molecule

from simtk.openmm import app

# Create OpenFF input

...

# Create translation input
inp = {
    "data_object": ommol,
    "schema_version": 1,
    "schema_name": "mmschema",
}

# Running translator compute
outp = Translator.compute(inp)

# Extract MMSchema molecule
mm_mol = outp.schema_object

One could do similar conversions with the force field component as well.

Copyright

Copyright (c) 2021, MolSSI

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.5.