BESMARTS
BESMARTS: A toolkit for data-driven force field design using binary-encoded SMARTS - Published in JOSS (2025)
Science Score: 93.0%
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Published in Journal of Open Source Software
Keywords
Repository
A toolkit for data-driven force field design based on binary-encoded SMARTS
Basic Info
- Host: GitHub
- Owner: trevorgokey
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://besmarts.readthedocs.io
- Size: 1.19 MB
Statistics
- Stars: 5
- Watchers: 2
- Forks: 3
- Open Issues: 3
- Releases: 0
Topics
Metadata Files
README.md
BESMARTS
A toolkit for data-driven force field design based on binary-encoded SMARTS
Highlights of this package are:
- Map and perform bitwise operations between two molecular substructures of arbitrary size
- Search/iterate a substructure at the SMARTS-primitive level, using both numerical and analytic approaches
- Cluster molecular data by SMARTS using a SMARTS hierarchy
- Calculate energy and gradients using a classical force field based on (a basic implementation of) the SMIRNOFF format
- Geometry optimization
- Force field parameter optimization (under development)
See the ChemRxiv preprint for the theoretical unpinnings on which this package is based.
Installation
BESMARTS is on PyPI, but certain dependencies are not and only exist on conda
unless they are built from source. Currently, the best way to install all
functionality is to use conda to create a python environment with Ambertools:
conda create -n besmarts -c conda-forge python ambertools
conda activate besmarts
and then install BESMARTS via pip:
pip install 'besmarts[rdkit,scipy,openmm]'
For a more custom installation, one can install from git. If ambertools is not needed, one may set up an environment via ``` python -m venv besmarts . besmarts/bin/activate
```
followed by the actual install in develop mode:
git clone https://github.com/trevorgokey/besmarts besmarts-git
cd besmarts-git/besmarts-core/python
python -m pip install -e .
cd ../../besmarts-rdkit/python
python -m pip install -e .
cd ../../besmarts-mechanics/python
python -m pip install -e .
cd ../../besmarts-openmm/python
python -m pip install -e .
cd ../../besmarts-scipy/python
python -m pip install -e .
RDKit is needed to decode SMILES into graphs and offers a faster implementation of SMARTS matching when labeling from a SMARTS hierarchy.
Geometry optimization uses the SciPy minimizer and can be installed using
a similar process as above with besmarts-scipy. There is also an
interface to OpenMM and its molecule energy minimizer can be used instead after installing
besmarts-openmm. The OpenMM plugin is quite a bit faster and is recommended
if large or heavily numerical computations are needed. The native interface
to calculating energies and gradients is useful if novel functional forms are
needed and not in standard packages (e.g. OpenMM). We recommend using OpenMM if
it is supported and available on your system. The energies, hessians, and
gradients compared between the native and OpenMM implementations are nearly
exact; for energy/gradient down to 12 decimal places for linear terms, around 6
places for torsions, and between 4-12 places for Hessians. Included in the native
implementation is a very fast analytic MM hessian method that can produce the
entire matrix in the time it takes OpenMM to evalulate a single energy.
Molecular mechanics energy and gradient evaluations are implemented, but
require partial charges. By default, besmarts will try to charge molecules
with am1bcc using the sqm program from ambertools suite. Consequently,
make sure sqm is in your PATH by installing via conda or by other means.
Documentation
Documentation in this repository is hosted on RTD
Contributing
Contributions in the form of bug reports, enhancements, and general discussions are very welcome. See CONTRIBUTING.md for more details.
Owner
- Login: trevorgokey
- Kind: user
- Repositories: 1
- Profile: https://github.com/trevorgokey
JOSS Publication
BESMARTS: A toolkit for data-driven force field design using binary-encoded SMARTS
Authors
Department of Chemistry, University of California, Irvine, United States of America
Editor
Lucy Whalley
Tags
cheminformatics graphs forcefieldsGitHub Events
Total
- Issues event: 2
- Watch event: 2
- Issue comment event: 3
- Push event: 24
- Pull request event: 1
- Fork event: 1
- Create event: 2
Last Year
- Issues event: 2
- Watch event: 2
- Issue comment event: 3
- Push event: 24
- Pull request event: 1
- Fork event: 1
- Create event: 2
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 4
- Average time to close issues: 10 months
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 3.0
- Average comments per pull request: 0.75
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 3.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Yoshanuikabundi (1)
- AntObi (1)
Pull Request Authors
- Yoshanuikabundi (2)
- lilyminium (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 5
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Total downloads:
- pypi 126 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 6
- Total maintainers: 1
pypi.org: besmarts-scipy
BESMARTS SciPy plugin
- Homepage: https://github.com/trevorgokey/besmarts
- Documentation: https://besmarts-scipy.readthedocs.io/
- License: MIT
-
Latest release: 0.1.0
published 12 months ago
Rankings
Maintainers (1)
pypi.org: besmarts-mechanics
BESMARTS molecular mechanics force field fitting
- Homepage: https://github.com/trevorgokey/besmarts
- Documentation: https://besmarts-mechanics.readthedocs.io/
- License: MIT
-
Latest release: 0.1.1
published 12 months ago
Rankings
Maintainers (1)
pypi.org: besmarts
Binary Encoded SMARTS
- Homepage: https://github.com/trevorgokey/besmarts
- Documentation: https://besmarts.readthedocs.io/
- License: MIT
-
Latest release: 0.1.0
published 12 months ago
Rankings
Maintainers (1)
pypi.org: besmarts-openmm
BESMARTS OpenMM plugin
- Homepage: https://github.com/trevorgokey/besmarts
- Documentation: https://besmarts-openmm.readthedocs.io/
- License: MIT
-
Latest release: 0.1.0
published 12 months ago
Rankings
Maintainers (1)
pypi.org: besmarts-rdkit
BESMARTS RDKit plugin
- Homepage: https://github.com/trevorgokey/besmarts
- Documentation: https://besmarts-rdkit.readthedocs.io/
- License: MIT
-
Latest release: 0.1.0
published 12 months ago