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Bioinformatics Vol. 19 no. 17 2003
pages 2308-2310
© 2003 Oxford University Press

Applications Note

PDB file parser and structure class implemented in Python

Thomas Hamelryck 1,2,* and Bernard Manderick 2

1 Department of Cellular and Molecular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) and 2 Computational Modeling Lab (COMO), Department of Computer Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium

Received on January 21, 2003 ; revised on March 3, 2003 ; accepted on May 10, 2003

Summary: The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors.

Availability: The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

Contact: thamelry{at}vub.ac.be

* To whom correspondence should be addressed.


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