Biotite 0.40.0

Changelog

Additions

• Refactored struc.superimpose() (#526)
  • Multiple fixed models are allowed
  • Increased performance for multiple models
• Support for BinaryCIF file format (#531)
  • Added 'bcif' format to database.rcsb.fetch()
  • Added structure.io.pdbx.BinaryCIFFile to parse BinaryCIF files
  • Added structure.io.pdbx.CIFFile to parse CIF files with analogous API to BinaryCIFFile
  • High-level PDBx API (get_structure(), get_assembly(), etc.) supports these new file classes
  • Added include_bondsparameter to structure.io.pdbx.get_structure() and structure.io.pdbx.get_assembly() to parse bond information from file
• Refactored structure.info subpackage (#540)
  • Decreased initial loading time when package is imported
  • The component dataset is now stored as compressed BinaryCIF decreasing the Biotite package size
  • The component dataset is updated to the current version, i.e. the latest chemical components from the wwPDB are included
  • The project now contains the setup_ccd.py script, enabling the user to get an up-to-date version of the component dataset

Changes

• Removed structure.info.bond_order() and structure.info.bond_dataset (#540)
• struc.superimpose returns now an AffineTransformation object instead of a transformation tuple (#526)
  • superimpose_apply() is deprecated in favor of AffineTransformation.apply()
• structure.io.pdbx.PDBxFile is deprecated and superseded by CIFFile (#531)
• structure.io.mmtf is deprecated and superseded by BinaryCIFFile (#531)
  • This is reflected by the RCSB announcement to deprecate MMTF

Fixes

• Handle invalid CRYST1 records in PDB files correctly (#523)
• Ensure that NumPy 1.x is used (#537)
  • Support for 2.x will be added in the future