https://github.com/becksteinlab/mdpow-molconfgen
torsional sampler
https://github.com/becksteinlab/mdpow-molconfgen
Last synced: 11 months ago
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torsional sampler
- Host: GitHub
- URL: https://github.com/becksteinlab/mdpow-molconfgen
- Owner: Becksteinlab
- License: gpl-2.0
- Created: 2023-06-21T05:11:57.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-07-11T01:03:19.000Z (12 months ago)
- Last Synced: 2025-07-11T05:31:03.582Z (12 months ago)
- Language: Jupyter Notebook
- Size: 3.36 MB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Authors: AUTHORS.md
Awesome Lists containing this project
README
# mdpow-molconfgen #
[//]: # (Badges)
| **Latest release** | [](https://github.com/becksteinlab/mdpow-molconfgen/releases)  [](https://mdpow-molconfgen.readthedocs.io/en/latest/?badge=latest)|
| :------ | :------- |
| **Status** | [](https://github.com/becksteinlab/mdpow-molconfgen/actions?query=branch%3Amain+workflow%3Agh-ci) [](https://codecov.io/gh/becksteinlab/mdpow-molconfgen/branch/main) |
| **Community** | [](https://www.gnu.org/licenses/gpl-2.0) [](https://www.mdanalysis.org)|
Generation of conformers of small molecules.
## Background ##
1. find all N major torsions
2. generate all conformers by rotating all torsions in increments
delta for a total of (2π/delta)^N conformers
3. write to a trajectory
4. evaluate the force field energy with `gmx mdrun -rerun`.
5. find minima in the N-dimensional energy landscape
### Implementation notes ###
1. Load molecules with MDAnalysis.
2. Convert to RDKit molecule.
3. Perform torsion drive with [rdkit.Chem.rdMolTransforms](https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html)
### Initial testing systems ###
From the [COW dataset](https://github.com/Becksteinlab/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](https://github.com/becksteinlab/mdpow-molconfgen/blob/main/CODE_OF_CONDUCT.md).
### Installation
To build mdpow-molconfgen from source,
we highly recommend using virtual environments.
If possible, we strongly recommend that you use
[mamba](https://mamba.readthedocs.io/en/latest/index.html) 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](https://www.gromacs.org) installation.
#### With pip from PyPi
You can directly install the [mdpow-molconfgen package](https://pypi.org/project/mdpow-molconfgen/) PyPi package with
```
pip install mdpow-molconfgen
```
This will install all dependencies (except GROMACS).
#### With mamba from source
Ensure that you have [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) 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](https://github.com/becksteinlab/mdpow-molconfgen/blob/main/LICENSE)).
Copyright (c) 2023, Oliver Beckstein
#### Acknowledgements
Project based on the
[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using mdpow-molconfgen in published work.