用Python实现的PDB文件解析器和结构类。

PDB file parser and structure class implemented in Python.

作者信息

Hamelryck Thomas, Manderick Bernard

机构信息

Department of Cellular and Molecular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie and Computational Modeling Lab, Department of Computer Science, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.

出版信息

Bioinformatics. 2003 Nov 22;19(17):2308-10. doi: 10.1093/bioinformatics/btg299.

DOI:10.1093/bioinformatics/btg299

PMID:14630660

Abstract

UNLABELLED

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

摘要

未标注

Biopython项目提供了一组用Python实现的生物信息学工具。最近，Biopython通过一组处理大分子结构的模块得到了扩展。Biopython现在包含一个用于解析PDB文件的解析器，它能以一种易于使用但功能强大的数据结构提供原子信息。该解析器和数据结构处理的一些特征常常被其他软件包忽略或处理不当，例如原子和残基无序（如果晶体中存在点突变体）、各向异性B因子、多个模型和插入码。此外，该解析器会进行一些合理性检查以检测明显的错误。