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21 changes: 4 additions & 17 deletions README.md
Original file line number Diff line number Diff line change
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# MDRestraintsGenerator

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[![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)

Expand All @@ -12,17 +12,7 @@ with exporters for GROMACS. There is also experimental code for COM based
restraints (i.e. harmonic distance or hard wall), which export to the gromacs
pull code. These experimental implementations have yet to be completely tested.

In future implementations we aim to expand to other MD engines (notably OpenMM
support will be coming in the near future as part of efforts to support
the work done by OpenFE).

We also aim to eventually implement the following restraint types:

- Attach Pull Restraint style restraints
- Arbitrary multidimensional restraints (will require API overhaul)

Note: This is non-mature code, a lot is left to do and
major changes will happen at any time.
Note: This repository will be replaced by separate work done by OpenFE sphere in the near future.

## Installation

Expand Down Expand Up @@ -94,14 +84,11 @@ pytest -v MDRestraintsGenerator.tests

### Copyright

Copyright (c) 2020, Irfan Alibay
Copyright (c) 2025, Irfan Alibay

#### Acknowledgements

To cite this code, please refer the following:

- https://doi.org/10.26434/chemrxiv-2022-cw2kq-v3
- https://doi.org/10.1038/s42004-022-00721-4
- https://doi.org/10.5281/zenodo.6972482

Project based on the
[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.3.
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