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

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)

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