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Bioinformatics. 2015 Dec 15;31(24):4017-9. doi: 10.1093/bioinformatics/btv482. Epub 2015 Aug 30.

BiopLib and BiopTools--a C programming library and toolset for manipulating protein structure.

Author information

1
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

Abstract

We describe BiopLib, a mature C programming library for manipulating protein structure, and BiopTools, a set of command-line tools which exploit BiopLib. The library also provides a small number of functions for handling protein sequence and general purpose programming and mathematics. BiopLib transparently handles PDBML (XML) format and standard PDB files. BiopTools provides facilities ranging from renumbering atoms and residues to calculation of solvent accessibility.

AVAILABILITY AND IMPLEMENTATION:

BiopLib and BiopTools are implemented in standard ANSI C. The core of the BiopLib library is a reliable PDB parser that handles alternate occupancies and deals with compressed PDB files and PDBML files automatically. The library is designed to be as flexible as possible, allowing users to handle PDB data as a simple list of atoms, or in a structured form using chains, residues and atoms. Many of the BiopTools command-line tools act as filters, taking a PDB (or PDBML) file as input and producing a PDB (or PDBML) file as output. All code is open source and documented using Doxygen. It is provided under the GNU Public Licence and is available from the authors' web site or from GitHub.

PMID:
26323716
PMCID:
PMC4673973
DOI:
10.1093/bioinformatics/btv482
[Indexed for MEDLINE]
Free PMC Article

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