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Generation of conformers of small molecules.
- 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
- Load molecules with MDAnalysis.
- Convert to RDKit molecule.
- Perform torsion drive with rdkit.Chem.rdMolTransforms
From the COW dataset:
- V36-methylacetate : 1 dihedral
- V46-2-methyl-1-nitrobenzene : steric hindrance
- V39-butylacetate : 4 dihedrals
mdpow-molconfgen is bound by a Code of Conduct.
To build mdpow-molconfgen from source,
we highly recommend using virtual environments.
If possible, we strongly recommend that you use
Anaconda as your package manager.
Below we provide instructions both for conda and
for pip.
Ensure that you have conda installed.
Create a virtual environment and activate it:
conda create --name mdpow-molconfgen
conda activate mdpow-molconfgen
Install the development and documentation dependencies:
conda env update --name mdpow-molconfgen --file devtools/conda-envs/test_env.yaml
conda 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:
conda update --all
And when you are finished, you can exit the virtual environment with:
conda deactivate
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]"
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
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdpow-molconfgen in published work.