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About PDB-numpy
===============
``pdb_numpy`` is a python library designed to facilitate working with PDB files
in the context of structural bioinformatics. The library builds upon the
powerful ``numpy`` library to provide efficient and easy-to-use tools for
reading, manipulating, and analyzing PDB files.
The library includes a number of functions for working with PDB files,
including functions for parsing PDB files and extracting relevant information,
such as atomic coordinates, residue identities, and structural information.
Additionally, ``pdb_numpy`` provides a range of functions for performing common
manipulations on PDB structures, such as aligning structures, superimposing
structures, and calculating RMSD values.
* Source code repository:
https://github.com/samuelmurail/pdb_numpy
Main features:
--------------
- Reading and writing PDB/MMCIF files
- Selecting atoms
- Superimposing structures using sequences alignment
- RMSD calculation
- DockQ calculation
- Secondary Structure calculation (pseudo DSSP)
For more examples and documentation, see the ``pdb_numpy`` documentation at
https://pdb-numpy.readthedocs.io/en/latest/readme.html.
Installation
------------
``pdb_numpy`` is available on PyPI and can be installed using ``pip``:
.. code-block:: bash
pip install pdb_numpy
Alternatively, you can install ``pdb_numpy`` from source:
.. code-block:: bash
git clone https://github.com/samuelmurail/pdb_numpy
cd pdb_numpy
python setup.py install
Dependencies
------------
``pdb_numpy`` requires the following dependencies:
- ``numpy``
- ``scipy``
Contributing
------------
``pdb_numpy`` is an open-source project and contributions are welcome. If
you find a bug or have a feature request, please open an issue on the GitHub
repository at https://github.com/samuelmurail/pdb_numpy. If you would like
to contribute code, please fork the repository and submit a pull request.
Author
--------------
* `Samuel Murail <https://samuelmurail.github.io/PersonalPage/>`_, Associate Professor - `Université Paris Cité <https://u-paris.fr>`_, `CMPLI <http://bfa.univ-paris-diderot.fr/equipe-8/>`_.
See also the list of `contributors <https://github.com/samuelmurail/pdb_numpy/contributors>`_ who participated in this project.
License
--------------
This project is licensed under the GNU General Public License v2.0 - see the ``LICENSE`` file for details.
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