Biotite 0.25.0

Changelog

Additions

• New analysis capabilities for nucleic acid base pairs
  • Added structure.info.nucleotide_names()
  • Increased performance of structure.base_pairs()
  • Support for exotic nucleotides in structure.base_pairs() and
    structure.filter_nucleotides()
  • Added structure.base_pairs_edge() and
    structure.base_pairs_glycosidic_bond() for further
    characterization of base pairs
  • Added structure.base_stacking() for identification of pi-stacking
    of nucleobases
  • Added structure.pseudoknots() for identification of pseudoknots
    in a given list of base pairings
  • Added structure.dot_bracket(),
    structure.dot_bracket_from_structure() and
    structure.base_pairs_from_dot_bracket() for conversion of
    base pairs to dot-bracket-letter notation and vice versa
• New methods for structure.BondList:
  • Added get_all_bonds() for obtaining the bonds atoms for each atom
    in the structure
  • Added adjacency_matrix() and bond_type_matrix()
• Added structure.partial_charges() for partial charge calculation
  using the PEOE method
• Added structure.info.standardize_order(), that reorders atoms in
  residues into the PDB standard atom order for the respective residue
• Added structure.graphics.plot_ball_and_stick_model()
• Increased performance of residue level utilities
• Added structure.get_residue_positions()
• Added sequence.io.genbank.get_raw_sequence() which returns the
  sequence as string

Changes

• structure.hbond() raises a warning if an input structure without
  hydrogen atoms is given (#241)
• get_sequence() and get_sequences() of biotite.sequence.io.fasta
  and biotite.sequence.io.fastq convert selenocysteine to cysteine (#232)
• Changed order of sequence type biotite.sequence.io.fasta.get_sequence() and
  biotite.sequence.io.fasta.get_sequences() try to create (#232):
  • First: sequence.NucleotideSequence
  • If this fails: sequence.ProteinSequence
• Temporary files used by the application subpackage are removed via
  os.remove() due to issues on Windows (#243)

Fixes

• Fixed structure.base_pairs() for structures that contian residues,
  that are not in the PDB standard order (#237)
• Fixed slightly incorrect aspect ratio in molecular visualizations
  created via structure.graphics.plot_atoms()
• Fixed bounds check for input bonds the structure.BondList constructor
  (related to #252):
  • Previously, the bond type value was not allowed to exceed the number
    of atoms
• Fixed structure.BondList indexing with an unsorted index array (#238)
• Fixed the charge annotation of molecules obtained via
  structure.info.residue() (#254)