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image:: https://img.shields.io/badge/Python-3.6%203.8-brightgreen.svg\n    :alt: Python version\n    :target: https://pypi.python.org/pypi/pbxplore\n\n.. image:: https://badge.fury.io/py/pbxplore.svg\n    :alt: PyPI PBxplore version\n    :target: https://pypi.python.org/pypi/pbxplore\n\n.. image:: https://github.com/pierrepo/PBxplore/workflows/GitHub%20CI%20code/badge.svg\n    :alt: GitHub Actions build status\n    :target: https://github.com/pierrepo/PBxplore/actions?query=workflow%3A%22GitHub+CI+code%22\n\n.. image:: https://github.com/pierrepo/PBxplore/workflows/GitHub%20CI%20doc/badge.svg\n    :alt: GitHub Actions build documentation status\n    :target: https://github.com/HubLot/PBxplore/actions?query=workflow%3A%22GitHub+CI+doc%22\n\n.. image:: https://readthedocs.org/projects/pbxplore/badge/?version=latest\n    :alt: PBxplore documentation\n    :target: https://pbxplore.readthedocs.org/en/latest/\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.598132.svg\n   :alt: Zenodo badge\n   :target: https://doi.org/10.5281/zenodo.598132\n\n\n**PBxplore** is a suite of tools dedicated to Protein Block (PB) analysis.\nProtein Blocks are structural prototypes defined by\n`de Brevern et al \u003chttps://www.ncbi.nlm.nih.gov/pubmed/11025540\u003e`_. The 3-dimensional local\nstructure of a protein backbone can be modelized as an 1-dimensional sequence of PBs.\nIn principle, any conformation of any amino acid could be represented by one of\nthe sixteen available Protein Blocks (see Figure 1).\n\n.. image:: https://raw.githubusercontent.com/pierrepo/PBxplore/master/doc/source/img/PBs.jpg\n    :alt: PBs\n\n**Figure 1.** Schematic representation of the sixteen protein blocks,\nlabeled from *a* to *p* (`Creative commons 4.0 CC-BY \u003chttps://creativecommons.org/licenses/by/4.0/\u003e`_).\n\n\nPBxplore provides both a Python library and command-line tools. Basically, PBxplore can:\n\n* **assign PBs** from a single PDB, many PDBs or a molecular dynamics simulation trajectory.\n* use analysis tools to perform **statistical analysis** on PBs.\n* use analysis tools to **study protein flexibility and deformability**.\n\n\nRequirements\n------------\n\nPBxplore requires:\n\n* Python 3.x (\u003e= 3.6)\n* Python modules: `NumPy \u003chttp://numpy.scipy.org/\u003e`_, `Matplotlib \u003chttp://matplotlib.org/\u003e`_, `MDAnalysis \u003chttps://code.google.com/p/mdanalysis/\u003e`_ (version \u003e= 0.11).\n\nOptionally, PBxplore can use:\n\n* `WebLogo 3 \u003chttp://weblogo.threeplusone.com/\u003e`_ to create logo from PB sequences.\n\n\nInstallation\n------------\n\nOnce dependencies installed, the most straightforward way is to use `pip`:\n\n.. code-block:: bash\n\n    $ pip install pbxplore\n\n\nPBxplore can also be installed for the current user only:\n\n.. code-block:: bash\n\n    $ pip install --user pbxplore\n\n\nDocumentation\n-------------\n\nAll documentation are hosted by Read The Docs and can be found `here \u003chttps://pbxplore.readthedocs.org/en/latest/\u003e`_.\n\n\nCitation\n--------\n\nIf you use PBxplore, please cite this tool as:\n\n| Barnoud J, Santuz H, Craveur P, Joseph AP, Jallu V, de Brevern AG, Poulain P,\n| PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks\n| *PeerJ*  5:e4013 `\u003chttps://doi.org/10.7717/peerj.4013\u003e`_ (2017).\n|\n\nThe published version (1.3.8) is archived in Zenodo |zenodo-badge|\n\n.. |zenodo-badge| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1016257.svg\n   :alt: Zenodo badge\n   :target: https://doi.org/10.5281/zenodo.1016257\n\nand Software Heritage |SWH-badge|\n\n.. |SWH-badge| image:: https://archive.softwareheritage.org/badge/swh:1:dir:4260527877ab457f65eb1299437cf022301a4788/\n    :alt: Software Heritage badge\n    :target: https://archive.softwareheritage.org/swh:1:dir:4260527877ab457f65eb1299437cf022301a4788;origin=https://github.com/pierrepo/PBxplore;visit=swh:1:snp:fb4066f408260c44decc7cac3624b56747a3de69;anchor=swh:1:rev:ba1290912cd65c86a01f70716e1d3133778bba75/\n\n\nContact \u0026 Support\n-----------------\n\nPBxplore is a research software and has been developped by:\n\n* Pierre Poulain, \"Mitochondria, Metals and Oxidative Stress\" group, Institut Jacques Monod, UMR 7592, Univ. Paris, CNRS, France.\n* Jonathan Barnoud, University of Groningen, Groningen, The Netherlands.\n* Hubert Santuz, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France.\n* Alexandre G. de Brevern \u0026 Gabriel Cretin, DSIMB, INSERM, UMR_S 1134, INTS, Univ Paris, Paris, France.\n\nIf you want to report a bug, request a feature,\nuse the `GitHub issue system \u003chttps://github.com/pierrepo/PBxplore/issues\u003e`_.\n\n\nLicense\n-------\n\nPBxplore is licensed under `The MIT License \u003chttps://github.com/pierrepo/PBxplore/blob/master/LICENSE\u003e`_.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpierrepo%2Fpbxplore","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpierrepo%2Fpbxplore","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpierrepo%2Fpbxplore/lists"}