menger-curvature 0.3.0

This project aims to provide a simple MDAkit for JIT accelerated Menger curvature calculation

Menger_Curvature

Latest release
Status
Community

This project aims to provide a simple MDAkit for JIT accelerated Menger curvature calculation

Menger_Curvature is bound by a Code of Conduct.

Installation

User

With pypi project

The easiest way to install Menger_Curvature is through pip:

pip install menger-curvature

This will install the latest stable release from PyPI.

Developper

Clone the repository and enter it:

git clone https://github.com/EtienneReboul/menger_curvature.git
cd menger_curvature

To build Menger_Curvature 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.

With conda

Ensure that you have conda installed.

Create a virtual environment and activate it:

conda create --name menger_curvature
conda activate menger_curvature

Install the development and documentation dependencies:

conda env update --name menger_curvature --file devtools/conda-envs/test_env.yaml
conda env update --name menger_curvature --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

With pip

To build the package from source, run:

pip install .

If you want to create a development environment, install the dependencies required for tests and docs with:

pip install ".[test,doc]"

Examples

Calculate Menger curvature for the chain A of a tubulin protein trajectory in serial mode:

>>> import MDAnalysis as mda
>>> from menger.analysis.mengercurvature import MengerCurvature
>>> from menger.tests.utils import make_universe
>>> md_name = "tubulin_chain_a"
>>> u = make_universe(
...     topology_name=f"{md_name}.pdb",
...     trajectory_name=f"{md_name}.dcd",
... )
>>> menger_analyser = MengerCurvature(
...     u,
...     select="name CA and chainID A",
...     spacing=2
... )
>>> menger_analyser.run()
>>> average_curvature = menger_analyser.results.local_curvatures
>>> flexibility = menger_analyser.results.local_flexibilities
>>> menger_curvature = menger_analyser.results.curvature_array

Calculate Menger curvature for the chain A of a tubulin protein trajectory in parallel mode:

>>> import MDAnalysis as mda
>>> from menger.analysis.mengercurvature import MengerCurvature
>>> from menger.tests.utils import make_universe
>>> md_name = "tubulin_chain_a"
>>> u = make_universe(
...     topology_name=f"{md_name}.pdb",
...     trajectory_name=f"{md_name}.dcd",
... )
>>> menger_analyser = MengerCurvature(
...     u,
...     select="name CA and chainID A",
...     spacing=2,
...     n_workers=4
... )
>>> menger_analyser.run_parallel()
>>> average_curvature = menger_analyser.results.local_curvatures
>>> flexibility = menger_analyser.results.local_flexibilities
>>> menger_curvature = menger_analyser.results.curvature_array

Copyright

The Menger_Curvature source code is hosted at https://github.com/EtienneReboul/menger_curvature and is available under the GNU General Public License, version 2 (see the file LICENSE).

Copyright (c) 2025, LBT

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using Menger_Curvature in published work.