https://github.com/becksteinlab/mdpow-molconfgen
torsional sampler
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: acs.org -
✓Committers with academic emails
1 of 2 committers (50.0%) from academic institutions -
✓Institutional organization owner
Organization becksteinlab has institutional domain (becksteinlab.physics.asu.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.5%) to scientific vocabulary
Repository
torsional sampler
Basic Info
- Host: GitHub
- Owner: Becksteinlab
- License: gpl-2.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 3.36 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 3
- Releases: 5
Metadata Files
README.md
mdpow-molconfgen
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Generation of conformers of small molecules.
Background
- find all N major torsions
- generate all conformers by rotating all torsions in increments delta for a total of (2π/delta)^N conformers
- write to a trajectory
- evaluate the force field energy with
gmx mdrun -rerun. - find minima in the N-dimensional energy landscape
Implementation notes
- Load molecules with MDAnalysis.
- Convert to RDKit molecule.
- Perform torsion drive with rdkit.Chem.rdMolTransforms
Initial testing systems
From the COW dataset:
- V36-methylacetate : 1 dihedral
- V46-2-methyl-1-nitrobenzene : steric hindrance
- V39-butylacetate : 4 dihedrals
First steps
Community
mdpow-molconfgen is bound by a Code of Conduct.
Installation
To build mdpow-molconfgen from source,
we highly recommend using virtual environments.
If possible, we strongly recommend that you use
mamba as your package manager.
Below we provide instructions both for mamba and
for pip.
Note that for some functionality you also need a working GROMACS installation.
With pip from PyPi
You can directly install the mdpow-molconfgen package PyPi package with
pip install mdpow-molconfgen
This will install all dependencies (except GROMACS).
With mamba from source
Ensure that you have mamba installed.
Create a virtual environment and activate it:
mamba create --name mdpow-molconfgen
mamba activate mdpow-molconfgen
Install the development and documentation dependencies:
mamba env update --name mdpow-molconfgen --file devtools/conda-envs/test_env.yaml
mamba env update --name mdpow-molconfgen --file docs/requirements.yaml
Build this package from source:
pip install -e .
If you want to update your dependencies (which can be risky!), run:
mamba update --all
And when you are finished, you can exit the virtual environment with:
mamba deactivate
With pip from source
To build the package from source, run:
pip install -e .
If you want to create a development environment, install the dependencies required for tests and docs with:
pip install -e ".[test,doc]"
Copyright
The mdpow-molconfgen source code is hosted at https://github.com/becksteinlab/mdpow-molconfgen and is available under the GNU General Public License, version 2 (see the file LICENSE).
Copyright (c) 2023, Oliver Beckstein
Acknowledgements
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdpow-molconfgen in published work.
Owner
- Name: Becksteinlab
- Login: Becksteinlab
- Kind: organization
- Email: obeckste@asu.edu
- Location: Tempe, AZ
- Website: https://becksteinlab.physics.asu.edu
- Repositories: 56
- Profile: https://github.com/Becksteinlab
Computational Biophysics at Arizona State University
GitHub Events
Total
- Create event: 6
- Release event: 1
- Issues event: 5
- Delete event: 1
- Issue comment event: 3
- Push event: 23
- Pull request review comment event: 20
- Pull request review event: 4
- Pull request event: 5
- Fork event: 1
Last Year
- Create event: 6
- Release event: 1
- Issues event: 5
- Delete event: 1
- Issue comment event: 3
- Push event: 23
- Pull request review comment event: 20
- Pull request review event: 4
- Pull request event: 5
- Fork event: 1
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Oliver Beckstein | o****t@g****m | 64 |
| Richard Richardson | r****4@a****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 6
- Total pull requests: 6
- Average time to close issues: 6 months
- Average time to close pull requests: 3 months
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.17
- Average comments per pull request: 0.5
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 6
- Average time to close issues: 6 months
- Average time to close pull requests: 3 months
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.17
- Average comments per pull request: 0.5
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- orbeckst (6)
- rich-squared (1)
Pull Request Authors
- orbeckst (4)
- rich-squared (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: mdpow-molconfgen
Generation of conformers of small molecules.
- Documentation: https://mdpow-molconfgen.readthedocs.io/
- License: gpl-2.0
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Latest release: 0.3.0a1
published 9 months ago