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# MDRestraintsGenerator
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![GH Actions CI](https://github.com/IAlibay/MDRestraintsGenerator/actions/workflows/ci.yaml/badge.svg)
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[![codecov](https://codecov.io/gh/IAlibay/MDRestraintsGenerator/branch/master/graph/badge.svg)](https://codecov.io/gh/Bigginlab/MDRestraintsGenerator/branch/master)
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[![codecov](https://codecov.io/gh/IAlibay/MDRestraintsGenerator/branch/master/graph/badge.svg)](https://codecov.io/gh/IAlibay/MDRestraintsGenerator/branch/master)
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[![DOI](https://zenodo.org/badge/185426662.svg)](https://zenodo.org/badge/latestdoi/185426662)
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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)
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restraints (i.e. harmonic distance or hard wall), which export to the gromacs
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pull code. These experimental implementations have yet to be completely tested.
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In future implementations we aim to expand to other MD engines (notably OpenMM
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support will be coming in the near future as part of efforts to support
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the work done by OpenFE).
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We also aim to eventually implement the following restraint types:
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- Attach Pull Restraint style restraints
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- Arbitrary multidimensional restraints (will require API overhaul)
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Note: This is non-mature code, a lot is left to do and
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major changes will happen at any time.
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Note: This repository will be replaced by separate work done by OpenFE sphere in the near future.
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## Installation
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### Copyright
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Copyright (c) 2020, Irfan Alibay
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Copyright (c) 2025, Irfan Alibay
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#### Acknowledgements
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To cite this code, please refer the following:
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- https://doi.org/10.26434/chemrxiv-2022-cw2kq-v3
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- https://doi.org/10.1038/s42004-022-00721-4
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- https://doi.org/10.5281/zenodo.6972482
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Project based on the
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[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.3.

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