William Gilpin1. 1. Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
Abstract
SUMMARY: We have created a Python programming interface for the RCSB Protein Data Bank (PDB) that allows search and data retrieval for a wide range of result types, including BLAST and sequence motif queries. The API relies on the existing XML-based API and operates by creating custom XML requests from native Python types, allowing extensibility and straightforward modification. The package has the ability to perform many types of advanced search of the PDB that are otherwise only available through the PDB website. AVAILABILITY AND IMPLEMENTATION: PyPDB is implemented exclusively in Python 3 using standard libraries for maximal compatibility. The most up-to-date version, including iPython notebooks containing usage tutorials, is available free-of-charge under an open-source MIT license via GitHub at https://github.com/williamgilpin/pypdb, and the full API reference is at http://williamgilpin.github.io/pypdb_docs/html/. The latest stable release is also available on PyPI. CONTACT: wgilpin@stanford.edu.
SUMMARY: We have created a Python programming interface for the RCSB Protein Data Bank (PDB) that allows search and data retrieval for a wide range of result types, including BLAST and sequence motif queries. The API relies on the existing XML-based API and operates by creating custom XML requests from native Python types, allowing extensibility and straightforward modification. The package has the ability to perform many types of advanced search of the PDB that are otherwise only available through the PDB website. AVAILABILITY AND IMPLEMENTATION: PyPDB is implemented exclusively in Python 3 using standard libraries for maximal compatibility. The most up-to-date version, including iPython notebooks containing usage tutorials, is available free-of-charge under an open-source MIT license via GitHub at https://github.com/williamgilpin/pypdb, and the full API reference is at http://williamgilpin.github.io/pypdb_docs/html/. The latest stable release is also available on PyPI. CONTACT: wgilpin@stanford.edu.
Authors: Pietro Boccaletto; Marcin Magnus; Catarina Almeida; Adriana Zyla; Astha Astha; Radoslaw Pluta; Blazej Baginski; Elzbieta Jankowska; Stanislaw Dunin-Horkawicz; Tomasz K Wirecki; Michal J Boniecki; Filip Stefaniak; Janusz M Bujnicki Journal: Nucleic Acids Res Date: 2018-01-04 Impact factor: 16.971