Biotite 0.31.0

Changelog

Additions

• New functionalities for sequence.SequenceProfile
  • Added method probability_matrix() to compute the symbol probabilities
    from total frequencies
  • Added method log_odds_matrix() to calculate a position weight matrix
  • Added methods sequence_probability() and sequence_score() to assess the
    adherence of a given sequence to a profile
• New functionalities for structure.BondList
  • New bond type structure.BondType.AROMATIC_TRIPLE to support triple bonds
    in aromatic systems
  • Added structure.BondList.without_aromaticity() to convert bonds with
    structure.BondType.AROMATIC_<order> to structure.BondType.<order>
• Added structure.info.bond_order()
  • Used to get the structure.BondType of the bond between two atoms in a
    residue
  • Replaces structure.info.bond_order()
  • Initial loading of bond dataset is much faster

Changes

• Deprecated structure.info.bond_order()

Fixes

• Fixed structure.io.pdb.PDBFile.get_structure() raising an exception,
  if the PDB file contains an invalid CRYST1 record, now a warning is printed
• Fixed CONECT records written by structure.io.pdb.PDBFile.set_structure()
  • Previously, an empty second CONECT record was created, if a atom has 4
    bond partners
• Fixed installation of Biotite source distribution with Python 3.10 (#356)
• Fixed running application.muscle.MuscleApp with nucleotide sequences