atomium-a Python structure parser.
basic_science · Level V
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- Record sourced from PubMed, PMID 32044951.
- Also identified by DOI 10.1093/bioinformatics/btaa072 and PMC identifier 7203745.
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Abstract
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. 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 data are available at Bioinformatics online.
Medical subject headings
- Software