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
- 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.
pdb_numpy is available on PyPI and can be installed using pip:
pip install pdb_numpyAlternatively, you can install pdb_numpy from source:
git clone https://github.com/samuelmurail/pdb_numpy
cd pdb_numpy
python setup.py installpdb_numpy requires the following dependencies:
numpycython
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:
`bash
python setup.py build_ext --inplace
`
- Samuel Murail, Associate Professor - Université Paris Cité, CMPLI.
See also the list of contributors who participated in this project.
This project is licensed under the GNU General Public License v2.0 - see the LICENSE file for details.