Biotite 0.28.0

Changelog

Additions

• Most classes support now the repr() function (#290)
• Add equality comparison for sequence.CodonTable
• Added structure.info.all_residues(), that gives all residue names from the
  Chemical Component Dictionary
• Updated resources from Chemical Component Dictionary in structure.info
• Add structure.io.mol.MOLFile to support MOL and SDF files for
  small molecule structure data
• Add database.uniprot for UniProt database support
  • database.uniprot.search() searches for Uniprot IDs that match a given
    database.uniprot.Query
  • database.uniprot.fetch() downloads the file corresponding to the given
    Uniprot ID.
• Increase performance of structure.pseudoknots() by using NetworkX
  to identify conflicting regions (#289)

Changes

• Changed structure.BondType enum values for more precise description of
  aromatic bonds
  • BondType.AROMATIC is replaced by
    BondType.AROMATIC_SINGLE and BondType.AROMATIC_DOUBLE
  • New method structure.BondList.remove_aromaticity() converts
    BondType.AROMATIC_SINGLE to BondType.SINGLE and
    BondType.AROMATIC_DOUBLE to BondType.DOUBLE in-place

Fixes

• Fixed error, when reading a single model from a structure.io.PDBFile,
  if the MODEL line is missing in the file
• Fixed the format of formal charges written to structure.io.PDBFile
  • Previously it was e.g. '+2' instead of the correct 2+
• Fixed atom_i parameter when reading a trajectory via
  structure.io.load_structure() (#308)
• Fixed performance issue of structure.CellList
  • Previously the number of evaluated cells was too large, if the radius
    parameter of structure.CellList.get_atoms() was equal to the
    cell_size parameter of the constructor (#311)
• Setting an existing annotation array in structure.AtomArray and
  structure.AtomArrayStack preserves the NumPy dtype