Biotite 0.14.0

Changelog

Additions

• Added convenience functions for chains, similar to the functions for residues
  • Added get_chain_starts()
  • Added get_chains()
  • Added get_chain_count()
  • Added chain_iter()
• Revamped interface for GenBank files
  • sequence.io.genbank.GenBankFile provides a low-level API for obtaining field names and the corresponding lines and subfields
  • sequence.io.genbank.GenBankFile is now used for both GenBank and GenPept files
  • High level objects are obtained via module-level functions
    • get_locus(), get_definition(), get_accession(), get_version(), get_gi(), get_source(), get_db_link(), get_annotation(), get_sequence() and get_annotated_sequence() are now functions sequence.io.genbank
  • Added set_locus(), set_annotation(), set_sequence(), set_annotated_sequence(), to sequence.io.genbank for creating and editing GenBank files

Changes

• structure.dihedral_backbone() does not require a chain ID anymore
  • The dihedrals are automatically calculated over all chains
  • Dihedrals at the transition of one chain to the next one are NaN
• Completely changed usage of sequence.io.genbank.GenBankFile (see above)

Fixes

• Atom IDs above 99999 and residue IDs above 9999 do not break writing structure.io.gro.GROFile
  • In case of overflow, the ID restarts at 1
• Dummy boxes in .gro files are not converted into a real box attribute of a structure.AtomArray anymore
• When creating a sequence.Alignment from strings, it is checked whether at least to strings (sequences) are given
• Fixed annotation equality checks when setting an structure.AtomArrayStack element with an structure.AtomArray
• Fixed indexing a sequence.AnnotatedSequence with a sequence.Feature containing multiple locations
  • Previously the locations were merged in a random order resulting in wrong sequence.Sequence objects