https://github.com/rmeli/spyrmsdkit
MDAnalysis Kit (MDAKit) for SPyRMSD
https://github.com/rmeli/spyrmsdkit
Last synced: 2 months ago
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MDAnalysis Kit (MDAKit) for SPyRMSD
- Host: GitHub
- URL: https://github.com/rmeli/spyrmsdkit
- Owner: RMeli
- License: gpl-2.0
- Created: 2023-05-19T09:10:11.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-05-31T20:58:01.000Z (about 1 year ago)
- Last Synced: 2025-02-01T05:26:02.316Z (4 months ago)
- Language: Python
- Size: 92.8 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
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
spyrmsdkit
==============================
[//]: # (Badges)
| **Latest release** | [](https://github.com/RMeli/spyrmsdkit/releases)  [](https://spyrmsdkit.readthedocs.io/en/latest/?badge=latest)|
| :------ | :------- |
| **Status** | [](https://github.com/RMeli/spyrmsdkit/actions?query=branch%3Amain+workflow%3Agh-ci) [](https://codecov.io/gh/RMeli/spyrmsdkit/branch/main) |
| **Community** | [](https://www.gnu.org/licenses/gpl-2.0) [](https://www.mdanalysis.org)|
MDAnalysis Kit (MDAKit) for SPyRMSD.
[SPyRMSD](https://github.com/RMeli/spyrmsd) is a lightwaght Python package for the calculation of symmetry-corrected RMSD using graph isomorphism. This MDAKit brings the capabiliry of [SPyRMSD](https://github.com/RMeli/spyrmsd) to MDAnalysis, for the calculation of symmetry-corrected RMSD over molecular dynamics trajectories.
spyrmsdkit is bound by a [Code of Conduct](https://github.com/RMeli/spyrmsdkit/blob/main/CODE_OF_CONDUCT.md).
*If you are using `spyrmsdkit`, please cite the following paper:*
```text
@article{spyrmsd2020,
Author = {Meli, Rocco and Biggin, Philip C.},
Journal = {Journal of Cheminformatics},
Number = {1},
Pages = {49},
Title = {spyrmsd: symmetry-corrected RMSD calculations in Python},
Volume = {12},
Year = {2020}
}
```
**Note on license**: MDAnalysis is in the process of changing license. The licence of this repo will change in the future to a compatible, more permissive one.
### Installation
To build spyrmsdkit 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 spyrmsdkit
conda activate spyrmsdkit
```
Install the development and documentation dependencies:
```
conda env update --name spyrmsdkit --file devtools/conda-envs/test_env.yaml
conda env update --name spyrmsdkit --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 -e .
```
If you want to create a development environment, install
the dependencies required for tests and docs with:
```
pip install -e ".[test,doc]"
```
### Copyright
The spyrmsdkit source code is hosted at https://github.com/RMeli/spyrmsdkit
and is available under the GNU General Public License, version 2 (see the file [LICENSE](https://github.com/RMeli/spyrmsdkit/blob/main/LICENSE)).
Copyright (c) 2023, Rocco Meli
#### 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 spyrmsdkit in published work.