atomium—a Python structure parser

atomium—a Python structure parser

Abstract Summary 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...

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Veröffentlicht in:Bioinformatics 2020-05, Vol.36 (9), p.2750-2754
Hauptverfasser: Ireland, Sam M, Martin, Andrew C R
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Databases, Protein
Molecular Structure
Original Papers
Software
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creator Ireland, Sam M
Martin, Andrew C R
description Abstract Summary 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. Availability and implementation atomium is implemented in Python and its performance is equivalent to the existing library BioPython. However, it has significant advantages in features and API design. atomium is available from atomium.bioinf.org.uk and pdb2json can be accessed at pdb2json.bioinf.org.uk Supplementary information Supplementary data are available at Bioinformatics online.
doi_str_mv 10.1093/bioinformatics/btaa072
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subjects Databases, Protein
Molecular Structure
Original Papers
Software
title atomium—a Python structure parser
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