| Name | mdpow-molconfgen JSON |
| Version |
0.3.0a1
JSON |
| download |
| home_page | None |
| Summary | Generation of conformers of small molecules. |
| upload_time | 2025-07-11 00:46:49 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | None |
| keywords |
molecular
simulations
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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/sampl5-distribution-water-cyclohexane/tree/master/11_validation_dataset92):
- 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`.
#### With mamba
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
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.
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"description": "# mdpow-molconfgen #\n\n[//]: # (Badges)\n\n| **Latest release** | [](https://github.com/becksteinlab/mdpow-molconfgen/releases)  [](https://mdpow-molconfgen.readthedocs.io/en/latest/?badge=latest)|\n| :------ | :------- |\n| **Status** | [](https://github.com/becksteinlab/mdpow-molconfgen/actions?query=branch%3Amain+workflow%3Agh-ci) [](https://codecov.io/gh/becksteinlab/mdpow-molconfgen/branch/main) |\n| **Community** | [](https://www.gnu.org/licenses/gpl-2.0) [](https://www.mdanalysis.org)|\n\nGeneration of conformers of small molecules.\n\n## Background ##\n\n1. find all N major torsions\n2. generate all conformers by rotating all torsions in increments\n delta for a total of (2\u03c0/delta)^N conformers\n3. write to a trajectory\n4. evaluate the force field energy with `gmx mdrun -rerun`. \n5. find minima in the N-dimensional energy landscape\n\n### Implementation notes ###\n\n1. Load molecules with MDAnalysis.\n2. Convert to RDKit molecule.\n3. Perform torsion drive with [rdkit.Chem.rdMolTransforms](https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html)\n\n\n### Initial testing systems ###\nFrom the [COW dataset](https://github.com/Becksteinlab/sampl5-distribution-water-cyclohexane/tree/master/11_validation_dataset92): \n\n- V36-methylacetate : 1 dihedral\n- V46-2-methyl-1-nitrobenzene : steric hindrance\n- V39-butylacetate : 4 dihedrals\n\n## First steps\n\n### Community\n\nmdpow-molconfgen is bound by a [Code of Conduct](https://github.com/becksteinlab/mdpow-molconfgen/blob/main/CODE_OF_CONDUCT.md).\n\n### Installation\n\nTo build mdpow-molconfgen from source,\nwe highly recommend using virtual environments.\nIf possible, we strongly recommend that you use \n[mamba](https://mamba.readthedocs.io/en/latest/index.html) as your package manager.\nBelow we provide instructions both for `mamba` and\nfor `pip`.\n\n#### With mamba\n\nEnsure that you have [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) installed.\n\nCreate a virtual environment and activate it:\n\n```\nmamba create --name mdpow-molconfgen\nmamba activate mdpow-molconfgen\n```\n\nInstall the development and documentation dependencies:\n\n```\nmamba env update --name mdpow-molconfgen --file devtools/conda-envs/test_env.yaml\nmamba env update --name mdpow-molconfgen --file docs/requirements.yaml\n```\n\nBuild this package from source:\n\n```\npip install -e .\n```\n\nIf you want to update your dependencies (which can be risky!), run:\n\n```\nmamba update --all\n```\n\nAnd when you are finished, you can exit the virtual environment with:\n\n```\nmamba deactivate\n```\n\n#### With pip\n\nTo build the package from source, run:\n\n```\npip install -e .\n```\n\nIf you want to create a development environment, install\nthe dependencies required for tests and docs with:\n\n```\npip install -e \".[test,doc]\"\n```\n\n### Copyright\n\nThe mdpow-molconfgen source code is hosted at https://github.com/becksteinlab/mdpow-molconfgen\nand is available under the GNU General Public License, version 2 (see the file [LICENSE](https://github.com/becksteinlab/mdpow-molconfgen/blob/main/LICENSE)).\n\nCopyright (c) 2023, Oliver Beckstein\n\n\n#### Acknowledgements\n \nProject based on the \n[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.\nPlease cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using mdpow-molconfgen in published work.\n\n",
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