Biotite 0.17.0

Changelog

Additions

• Support for hybrid-36 encoding in structure.io.pdb.PDBFile
• Added get_coord() method in structure.io.pdb.PDBFile for efficiently reading only the coordinates from a file
• structure.CellList can be configured to put only a subset of atoms into the cells via the selection parameter
• Improved functionalities in database subpackage.
  • A lot of new query types in database.rcsb
  • The min and max parameter of some database.rcsb queries are now optional
  • database.rcsb.fetch() and database.entrez.fetch() are able to write the downloaded files into a file-like object instead of writing the file to hard drive
  • database.entrez.fetch() properly checks for invalid responses from server based on https://github.com/kblin/ncbi-entrez-error-messages
  • database.entrez.fetch() also supports common database names
  • database.entrez.SimpleQuery also supports abbreviated field names
• structure.io.load_structure() and structure.io.save_structure() support keyword arguments that are forwarded to the respective read() or get_structure() method.

Changes

• database subpackage raises database.RequestError objects when the server gives an invalid response

Fixes

• Fixed cross references in the API reference
• sequence.io.genbank.GenBankFile raises a warning instead of an exception if the feature's location identifier is not understood and skips the feature
• structure.io.pdb.PDBFile properly checks whether all models have the same amount of atoms, when building a structure.AtomArrayStack