https://github.com/mdanalysis/pathsimanalysis
An MDAKit that calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff or Fréchet distances.
https://github.com/mdanalysis/pathsimanalysis
Last synced: 6 months ago
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An MDAKit that calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff or Fréchet distances.
- Host: GitHub
- URL: https://github.com/mdanalysis/pathsimanalysis
- Owner: MDAnalysis
- License: gpl-2.0
- Created: 2023-10-04T23:03:51.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-12T18:36:48.000Z (almost 2 years ago)
- Last Synced: 2024-10-29T17:36:07.062Z (over 1 year ago)
- Language: Python
- Homepage: https://mdanalysis.org/PathSimAnalysis
- Size: 7.4 MB
- Stars: 0
- Watchers: 7
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Authors: AUTHORS.md
Awesome Lists containing this project
README
PathSimAnalysis
==============================
[//]: # (Badges)
| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since] |
| :----------------- | :------- |
| **Status** | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
| **Community** | [![Powered by MDAnalysis][badge_mda]][url_mda]|
[badge_actions]: https://github.com/MDAnalysis/pathsimanalysis/actions/workflows/gh-ci.yaml/badge.svg
[badge_codecov]: https://codecov.io/gh/MDAnalysis/pathsimanalysis/branch/main/graph/badge.svg
[badge_commits_since]: https://img.shields.io/github/commits-since/MDAnalysis/pathsimanalysis/latest
[badge_docs]: https://readthedocs.org/projects/pathsimanalysis/badge/?version=latest
[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
[badge_release]: https://img.shields.io/github/release-pre/MDAnalysis/pathsimanalysis.svg
[url_actions]: https://github.com/MDAnalysis/pathsimanalysis/actions?query=branch%3Amain+workflow%3Agh-ci
[url_codecov]: https://codecov.io/gh/MDAnalysis/pathsimanalysis/branch/main
[url_docs]: https://pathsimanalysis.readthedocs.io/en/latest/?badge=latest
[url_latest_release]: https://github.com/MDAnalysis/pathsimanalysis/releases
[url_mda]: https://www.mdanalysis.org
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](https://github.com/MDAnalysis/pathsimanalysis/blob/main/CODE_OF_CONDUCT.md).
### Installation from packages
#### With conda from conda-forge
Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
You can install [pathsimanalysis from the conda-forge channel](https://anaconda.org/conda-forge/pathsimanalysis) 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](https://pypi.org/project/pathsimanalysis/) 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](https://docs.conda.io/en/latest/) as your package manager.
Below we provide instructions both for `conda` and
for `pip`.
#### With conda
Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) 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 Lesser GNU Public Licence, v2.1 or any higher version
(see the file [LICENSE](https://github.com/MDAnalysis/pathsimanalysis/blob/main/LICENSE)).
Copyright (c) 2023, MDAnalysis
#### 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 PathSimAnalysis in published work.