Yet Another Molecular Mechanics Benchmarking Suite (YAMMBS, pronounced like "yams") is a tool for benchmarking force fields.
YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accuracy of any results.
Use the file ./devtools/conda-envs/dev.yaml and also install yammbs 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 yammbs 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, TFD, etc.) analyses and save to results disk:
ddes = store.get_dde(force_field="openff-2.1.0.offxml")
ddes.to_csv(f"{force_field}-dde.csv")Note that the pattern in the script
from multiprocessing import freeze_support
def main():
# Your code here
if __name__ == "__main__":
freeze_support()
main()must be used for Python's multiprocessing module to behave well.
YAMMBS is open-source software distrubuted under the MIT license (see LICENSE). It derives from other open-source work that may be distributed under other licenses (see LICENSE-3RD-PARTY).
Copyright (c) 2022, Open Force Field Initiative