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Biotite 1.1.0

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@padix-key padix-key released this 24 Dec 12:44
v1.1.0
e76eb24
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Changelog

Additions

  • Support for Python 3.13 (#661).
  • Support for structural alphabets that encodes geometric information from structure.AtomArray objects in sequence.Sequence objects.
    • structure.alphabet.to_3di converts a structure into a 3Di sequence from Foldseek. (#665)
    • structure.alphabet.to_protein_blocks() converts a structure into a Protein Blocks sequence. (#676)
    • Added color schemes and defailt sequence.align.SubstitutionMatrix for these structural alphabets. (#682)
  • Support for positional substitution matrices. (#655)
    • sequence.PositionalSequence acts as a placeholder sequence for a sequence profile in alignment functions from sequence.align.
    • sequence.align.SubstitutionMatrix.as_positional() expands a substitution matrix into a positional substitution matrix.
  • New functionalities for structure.io.pdbx:
    • Custom annotations can be written with set_structure() with extra_fields=True. (#669)
    • Missing columns in atom_site category are now handled by using sensible default annotations. (#670)
    • Added compress() function that automatically finds optimal encodings for BinaryCIFFile, decreasing the file size by a factor of approx 8x. (#674)
    • get_assembly() now adds a sym_id annotation to better distinguish copies of the asymmetric unit. (#700)
  • Added PDBFile.get_space_group() and PDBFile.set_space_group() to read and write the space group information. (#707)
  • Added structure.concatenate(), which supports concatenating more than AtomArrayStack objects. (#712)
  • Performance improvements:
    • Doubled speed to parsing CIF files with structure.io.pdbx.CIFFile (#722).
    • Tripled speed of pickling sequence.align.KmerTable objects. (#664)
      • Speed of transferring sequence.align.KmerTable between processes improves likewise.

Changes

  • structure.io.pdbx.set_structure() does not write 'canonical' bonds to struct_conn category anymore. (#678)
  • The internal Chemical Component Dictionary is not version controlled anymore. (#687, #716)
    • For installations from local repository clones, it must be built with python -m biotite.setup_ccd.

Fixes

  • structure.io.pdbx can now handle atom_site categories with quoted values containing whitespaces. (#673)
  • nan values in structure.AtomArray now count as equal when comparing AtomArray objects. (#714)
  • Fixed wrong band calculation in sequence.align.align_banded() that occurred when the given band was outside the sequence bounds. (#723)
    • This lead to premature traceback termination in rare cases.
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