OpenFF CLI

Command line utilities for the Open Force Field software stack

Please note that this software in an early and experimental state and unsuitable for production.

Installation

Currently, the only available installation method is a local build

git clone https://github.com/openforcefield/openff-cli
cd openff-cli
python -m pip install .

Usage

check_versions.py

A simple utility to print the OpenFF packages found to be installed, and their versions

$ python openff/cli/check_versions.py
Found the following packages installed
Package name        	Version
------------            -------
OpenFF Toolkit      	0.7.2
Openforcefields     	1.2.1
OpenFF Evaluator    	Not found
OpenFF System       	Not found
OpenFF CLI          	Not found
CMILES              	0.1.5

generate_conformers.py

Generate conformers from a starting structure, and minimize them using an OpenFF force field. Toolkit wrappers in the OpenFF Toolkit is used to call either The RDKit or OpenEye Omega to generate conformers, which are then energy-minimized with OpenMM.

This requires OpenFF Toolkit version 0.7.1 or newer.

$ python openff/cli/generate_conformers.py --help
usage: generate_conformers.py [-h] -t TOOLKIT -f FORCEFIELD -m MOLECULE
                              [-r RMS_CUTOFF] [-p PREFIX]
                              [--constrained CONSTRAINED]

Generate conformers with cheminformatics toolkits

required arguments:
  -t TOOLKIT, --toolkit TOOLKIT
                        Name of the underlying cheminformatics toolkit to use.
                        Accepted values are openeye and rdkit
  -f FORCEFIELD, --forcefield FORCEFIELD
                        Name of the force field to use, i.e. openff-1.0.0
  -m MOLECULE, --molecule MOLECULE
                        Path to an input file containing a molecule(s)

optional arguments:
  -r RMS_CUTOFF, --rms-cutoff RMS_CUTOFF
                        The redundancy cutoff between pre-minimized conformers
  -p PREFIX, --prefix PREFIX
                        The prefix for filenames of output molecules
  --constrained CONSTRAINED
                        Whether or not to use a constrained version of the
                        force field

Examples:

Generate conformers from a molecule in an SDF file, using The RDKit to sample conformers, and minimizing with OpenFF 1.2.0 "Parsley":

$ python openff/cli/generate_conformers.py --molecule x.sdf --toolkit rdkit --forcefield openff-1.2.0

This produces many files named molecule_N.sdf where N begins at 0 for the lowest-energy conformer and increases with increasing conformer energy. In this case, 97 conformers were generated:

$ ls molecule_*.sdf | wc -l

Do the same, but with OpenEye Omega, OpenFF 1.0 "Parsley," and a save the conformers in files starting with coolmol:

$ python openff/cli/generate_conformers.py --molecule molecule.sdf --toolkit openeye --forcefield openff-1.0.0 --prefix coolmol

In this case, 101 conformers were generated, following the same naming scheme:

$ ls coolmol_*.sdf | wc -l
     101

Copyright

Copyright (c) 2020, Open Force Field Initiative

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.3.