Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
Bioinformatics. 2020 May 1;36(9):2750-2754. doi: 10.1093/bioinformatics/btaa072.
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.
结构生物学依赖于特定的文件格式来传递关于大分子结构的信息。传统上，这一直是 PDB 格式，但越来越多的新格式，如 PDBML、mmCIF 和 MMTF，也在被使用。在这里，我们介绍了 atomium，这是一个用于解析、操作和保存 PDB、mmCIF 和 MMTF 文件格式的现代、轻量级的 Python 库。此外，我们还提供了一个 Web 服务 pdb2json，它使用 atomium 为整个蛋白质数据库提供一致的 JSON 表示。
atomium 是用 Python 实现的，其性能与现有的 BioPython 库相当。然而，它在功能和 API 设计方面具有显著的优势。atomium 可从 atomium.bioinf.org.uk 获取，pdb2json 可在 pdb2json.bioinf.org.uk 访问。
补充数据可在“Bioinformatics”在线获取。
