Changelog

Additions

• Added application.muscle.Muscle5App to support the changed CLI of Muscle 5
• Added structure.orient_principal_components() to orient atom coordinates
  to the given axes
• biotite.structure.io.pdbx.get_structure() uses label_xxx or auth_xxx
  field as fallback, if the respective other one is not available
• Added default_bond_type parameter to
  biotite.structure.io.write_structure_to_ctab() and
  biotite.structure.connect_via_distances to allow the user to change the
  BondType in the generated BondList

Fixes

• sequence.io.gff.GFFFile.read() is now able to read GFF records with trailing
  tabs
• Fixed DeprecationWarning in structure.align_vectors() (#295)
• Fixed alignment in atom name column in
  structure.io.pdb.PDBFile.write()
• Fixed error handling in structure.index_xxx() functions, if invalid input
  shape is given
• Ensured quoted values in looped categories will not be truncated in
  structure.io.pdbx.PDBxFile.set_category()