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

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structure.io.pdbx.PDBxFile is deprecated and superseded by CIFFile (#531)
structure.io.mmtf is deprecated and superseded by BinaryCIFFile (#531)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

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