acellera-openff-interchange 0.5.1

A project (and object) for storing, manipulating, and converting molecular mechanics data.

OpenFF Interchange

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A project (and object) for storing, manipulating, and converting parametrized chemical systems.

Documentation

Documentation for Interchange, including examples, a brief user guide, release history, and API docs, is available on the OpenFF website. Example notebooks are rendered online among examples from other projects in the OpenFF ecosysytem docs.

How to cite

Please cite Interchange using the Zenodo record of the latest release or the version that was used. The BibTeX reference of the latest release can be found at this link.

Installation

Recent versions of the OpenFF Toolkit (0.11.0+, released August 2022) install Interchange by default through its Conda package.

Interchange can also be installed manually via mamba (or conda, etc.):

mamba install openff-interchange -c conda-forge

Getting started

The Interchange object serves primarily as a container object for parametrized chemical systems. Its key use case involves SMIRNOFF force fields and chemical topologies prepared via the OpenFF Toolkit. The resulting object stores parametrized chemical systems and provides APIs for export to common formats.

from openff.toolkit import ForceField, Molecule, Quantity

# Use the OpenFF Toolkit to generate a molecule object from a SMILES pattern
molecule = Molecule.from_smiles("CCO")

# Generate a conformer to be used as atomic coordinates
molecule.generate_conformers(n_conformers=1)

# Convert this molecule to a topology
topology = molecule.to_topology()

# Define periodicity via box vectors
topology.box_vectors = Quantity([4, 4, 4], "nanometer")

# Load OpenFF 2.0.0 "Sage"
sage = ForceField("openff-2.0.0.offxml")

# Create an Interchange object - can also use Interchange.from_smirnoff()
out = sage.create_interchange(force_field=sage, topology=topology)

# Convert the Interchnage object to an OpenMM System
system = out.to_openmm()

# or write to GROMACS files
out.to_gromacs(prefix="out")

# or write to Amber files
out.to_amber(prefix="out")

# or store as JSON
json_blob = out.json()

For more functionality, usage guidelines, and examples, please consult the full documentation

Developing

See the Development guide.

Copyright

Copyright (c) 2020, Open Force Field Initiative

License

The source code of Interchange is hosted on GitHub and is available under the MIT license (see the file LICENSE). Some parts inherit from code distributed under other licenses, as detailed in LICENSE-3RD-PARTY.

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.2.