Porter Craig T, Martin Andrew C R
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
Bioinformatics. 2015 Dec 15;31(24):4017-9. doi: 10.1093/bioinformatics/btv482. Epub 2015 Aug 30.
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.
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.
我们描述了BiopLib，一个用于操纵蛋白质结构的成熟C编程语言库，以及BiopTools，一组利用BiopLib的命令行工具。该库还提供了少量用于处理蛋白质序列以及通用编程和数学的函数。BiopLib透明地处理PDBML（XML）格式和标准PDB文件。BiopTools提供了从原子和残基重新编号到溶剂可及性计算等一系列功能。
BiopLib和BiopTools是用标准ANSI C实现的。BiopLib库的核心是一个可靠的PDB解析器，它能处理交替占据情况，并自动处理压缩的PDB文件和PDBML文件。该库设计得尽可能灵活，允许用户将PDB数据作为简单的原子列表来处理，或者以使用链、残基和原子的结构化形式来处理。许多BiopTools命令行工具充当过滤器，以PDB（或PDBML）文件作为输入，并生成一个PDB（或PDBML）文件作为输出。所有代码都是开源的，并使用Doxygen进行了文档记录。它是在GNU公共许可证下提供的，可以从作者的网站或GitHub上获取。
