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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.
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
The latest release of PathSimAnalysis is available on PyPI and can be installed with:
pip install pathsimanalysis
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.
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
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]"
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
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using PathSimAnalysis in published work.