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Biotite 0.40.0
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@padix-key padix-key released this 02 Apr 18:18
v0.40.0
4b0355a
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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  • structure.io.pdbx.PDBxFile is deprecated and superseded by CIFFile (#531)
  • structure.io.mmtf is deprecated and superseded by BinaryCIFFile (#531)

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
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