modelarchive documentation

This is the ModelArchive Python package, providing the core functionality used by the ModelArchive team to handle, refine, and produce ModelCIF files. We may also add userland tooling for the database itself, in the future.

For real-world usage examples, browse our modelcif-converters repository. /projects contains a list of “modelling project to ModelCIF files” conversions from the past. The latter ones should use this package.

Contents:

• Reference databases (modelarchive.databases)
  • NCBI (modelarchive.databases.ncbi)
  • UniProtKB (modelarchive.databases.uniprotkb)
• Handling ModelCIF (modelarchive.modelcif)
  • Accessing ModelCIF (modelarchive.modelcif.access)
  • Editing ModelCIF (modelarchive.modelcif.edit)
  • Fixing AlphaFold 2 ModelCIF files (modelarchive.modelcif.fix_af2)
  • Fixing AlphaFold 3 ModelCIF files (modelarchive.modelcif.fix_af3)
  • ModelCif as dict (modelarchive.modelcif.ma_dict)

Credit

While at ModelArchive, we develop the ModelCIF mmCIF extension (alongside other contributors), key functionality underlying our Python package comes from external developments: the python-modelcif and the gemmi packages.

• python-modelcif is brilliant in creating ModelCIF files from scratch

• gemmi is our go-to package for refining and updating existing ModelCIF files