Biotite 1.0.0

Changelog

Additions

• Support for Numpy 2.0 (#529)
  • 1.x versions are still compatible.
• Trajectory file interfaces in structure.io do not require mdtraj as extra dependency anymore (#627).
  • Instead the much smaller biotraj package is now a mandatory dependency of Biotite.
• New documentation website (#552).
• Improved performance of multiple auxiliary methods in sequence.Alphabet.

Changes

• sequence.graphics uses flower color scheme as default instead of rainbow. (#617).
  • It represents similarity of amino acids better.
• structure.io.pdbx.get_sequence() returns dict mapping chain IDs to sequences (#611).
• Previously deprecated functionality was removed. (#624)
  • read() instance method of File classes: Use read() class method instead.
  • temp_file() and temp_dir(): Use corresponding functionality from tempfile instead.
  • application.viennarna.RNAfoldApp.get_mfe(): Use application.viennarna.RNAfoldApp.get_free_energy() instead.
  • atom_mask parameter of structure.connect_via_distances() and structure.connect_via_residue_names(): Filter the atoms before instead.
  • Support for Alignment objects as input to sequence.graphics.plot_sequence_logo(): Input a Profile instead.
  • sequence.io.fastq.FastqFile.get_sequence(): Use sequence.io.fastq.FastqFile.get_seq_string() or sequence.io.fastq.get_sequence() instead.
  • structure.filter_backbone(): Use structure.filter_peptide_backbone() instead.
  • structure.check_id_continuity(): Use structure.check_res_id_continuity() instead.
  • structure.check_bond_continuity(): Use structure.check_backbone_continuity() instead.
  • structure.renumber_atom_ids(): Set the atom_id annotation with numpy.arange() instead.
  • structure.renumber_res_ids(): Use structure.create_continuous_res_ids() instead.
  • chain_id parameter of structure.annotate_sse(): Filter the AtomArray before instead.
  • structure.superimpose_apply(): Use structure.AffineTransformation.apply() instead.
  • structure.io.read_structure_from_ctab() and structure.io.write_structure_to_ctab(): Use corresponding functions from structure.io.mol.
  • structure.io.mol.MolFile.get_header() and structure.io.mol.MolFile.set_header(): Use the header attribute instead.
  • structure.io.npz: Internal .npz format is not used anymore.
  • structure.io.pdbx.PDBxFile: Use structure.io.pdbx.CIFFile instead.
  • structure.io.mmtf: .mmtf was superseded by .bcif accessible with structure.io.pdbx.BinaryCIFFile.

Fixes

• Fixed compilation warnings about deprecated NumPy API. (#626)
• Fixed structure.BondList sometime discarding bonds after merging to bond lists (#618).
• Fixed incorrect handling of quotes when reading and writing a structure.io.pdbx.CIFFile (#619).