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:
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_numpyAlternatively, you can install pdb_numpy from source:
git clone https://github.com/samuelmurail/pdb_numpy
cd pdb_numpy
python setup.py installDependencies
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:
`bash python setup.py build_ext --inplace `
License
This project is licensed under the GNU General Public License v2.0 - see the LICENSE file for details.
1 maintainer
Metadata
1 maintainer
Release files for pdb-numpy 0.0.12
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Release files / pdb_numpy-0.0.12.tar.gz
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