seamm-ff-util 2024.6.27

seamm_ff_util

SEAMM Forcefield Utilities

The SEAMM Forcefield Utilities read and write forcefields, assigns them to molecules, and creates energy expressions.

• Free software: BSD license

• Documentation: https://seamm_ff_util.readthedocs.io.

Features

• TODO

Credits

This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award OAC-1547580 and CHE-2136142.

History

2024.6.27 – Support for local forcefield files

• Added support for local forcefields files which can either be used directly or included by existing files.

• Added URI handler to support local files

• Added support for BibTex references in forcefield files, and automatically adding citations to the Reference Handler.

• Add ‘fragments’ section to forcefields for atom-typing via a fragment or entire molecule. This supports using LigParGen for OPLS-AA forcefields.

2023.8.27 – Added support for tabulated angle potentials

2023.4.6 – Added support for Buckingham potentials

• Also improved unit handling across all terms in forcefields.

2023.3.5 – Added molecule numbers for LAMMPS input

• Added the molecule number for each atom for when using LAMMPS

2023.2.6 – Added handling of OPLS-AA forcefield

• Added handling of the OPLS-AA forcefield

• Moved documentation to new MolSSI theme and diátaxis layout

• Cleaned up internal dependencies and workflows for GitHub

2022.5.29 – Fixed bug typing larger systems

• Fixed bug with atom typing due to limit in matches. by @paulsaxe in #59

2022.2.3 – Fixed bug due to changing ordering of atoms.

• Fixed bug with atom type assignment due to changed order of atoms. In the process, switch to using RDKit directly, which is both more direct and avoids the ordering problem.

0.1.0 – (2017-12-05)

• First release on PyPI.