Pdb_Numpy is a python library allowing simple operations on pdb coor files.
Project description
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About PDB-numpy
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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
cython
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.
To build locally the extension module, you can run the following command:
python setup.py build_ext --inplace
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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