Use the file ../devtools/conda-envs/dev.yaml and also install ibstore with something like python -m pip install -e ..

It is assumed that the input molecules are stored in a openff-qcsubmit model like OptimizationResultCollection.

See the file run.py for a start-to-finish example.

Load a molecule dataset into the used representation:

from ibstore import MoleculeStore

store = MoleculeStore.from_qcsubmit_collection(
    collection=my_collection,
    database_name="my_database.sqlite",
)

Run MM optimizations of all molecules using a particular force field

store.optimize_mm(force_field="openff-2.1.0.offxml")

Run DDE or RMSD analysis and save to disk:

ddes = store.get_dde(force_field="openff-2.1.0.offxml")
ddes.to_csv(f"{force_field}-dde.csv")

rmsds = store.get_rmsd(force_field="openff-2.1.0.offxml")
rmsds.to_csv(f"{force_field}-rmsd.csv")

Note that the pattern

def main():
    # Your code here

if __name__ == "__main__":
    freeze_support()
    main()

must be used for Python's multiprocessing module to behave well.

Copyright (c) 2022, Open Force Field Initiative