atomium—a Python structure parser | Zendy

Sam M Ireland | Zendy; Andrew C.R. Martin | Zendy

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atomium—a Python structure parser

Author(s) -

Sam M Ireland,

Andrew C.R. Martin

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa072

Subject(s) - python (programming language) , json , parsing , computer science , programming language , file format , protein data bank (rcsb pdb) , world wide web , protein data bank , biology , protein structure , biochemistry

Structural biology relies on specific file formats to convey information about macromolecular structures. Traditionally this has been the PDB format, but increasingly newer formats, such as PDBML, mmCIF and MMTF are being used. Here we present atomium, a modern, lightweight, Python library for parsing, manipulating and saving PDB, mmCIF and MMTF file formats. In addition, we provide a web service, pdb2json, which uses atomium to give a consistent JSON representation to the entire Protein Data Bank.

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