PathSimAnalysis

Latest release
Status
Community

Calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff and Fréchet distances.

PathSimAnalysis is bound by a Code of Conduct.

Installation from packages

With conda from conda-forge

Ensure that you have conda installed.

You can install pathsimanalysis from the conda-forge channel with

conda install -c conda-forge pathsimanalysis

or alternatively with mamba if you have it installed:

mamba install -c conda-forge pathsimanalysis

Install from PyPI

The latest release of PathSimAnalysis is available on PyPI and can be installed with:

pip install pathsimanalysis

Installation from source

To build PathSimAnalysis 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 pathsimanalysis
conda activate pathsimanalysis

Install the development and documentation dependencies:

conda env update --name pathsimanalysis --file devtools/conda-envs/test_env.yaml
conda env update --name pathsimanalysis --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]"

Copyright

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

Copyright (c) 2023, MDAnalysis

Acknowledgements

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