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:

pip install pdb_numpy

Alternatively, you can install pdb_numpy from source:

git clone https://github.com/samuelmurail/pdb_numpy
cd pdb_numpy
python setup.py install

Or you can install last version from the github repo:

pip install git+https://github.com/samuelmurail/pdb_numpy.git@main

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, Associate Professor - Université Paris Cité, CMPLI.

See also the list of 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.