spyrmsdkit

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MDAnalysis Kit (MDAKit) for SPyRMSD.

SPyRMSD is a lightwaght Python package for the calculation of symmetry-corrected RMSD using graph isomorphism. This MDAKit brings the capabiliry of SPyRMSD to MDAnalysis, for the calculation of symmetry-corrected RMSD over molecular dynamics trajectories.

spyrmsdkit is bound by a Code of Conduct.

If you are using spyrmsdkit, please cite the following paper:

@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 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 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).

Acknowledgements

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

RMeli / spyrmsdkit