Biotite 0.36.0

Changelog

Additions

• Added Python 3.11 build
• Better support for macromolecular assemblies and symmetry mates (#450)
  • biotite.structure.io.pdb and biotite.structure.io.mmtf now support parsing of assemblies via list_assemblies() and get_assembly()
  • biotite.structure.io.pdb is able to parse all atoms within a single unit cell via get_symmetry_mates()
• Added structure.rmspd() to compute the root-mean-square-pairwise-deviation
  • This is a method to determine deviations between to models without the need of prior structure superimposition
• Refactored structure.annotate_sse() (#448)
  • Higher performance due to more vectorization
  • Multiple chains can be processed at once
• More granular macromolecule filters in structure subpackage (#436)
  • Added filter_peptide_backbone() and filter_phosphate_backbone() to filter backbone atoms of proteins and nucleotides, respectively
  • Added filter_linear_bond_continuity() that filters atoms that are within distance boundaries to the next atom
  • Added filter_polymer() that filters biomacromolecules of the given type (peptide, nucleotide, carbohydrate) and minimum length
• More integrity checks in structure subpackage (#436)
  • check_linear_continuity() gives positions in a structure where atoms are not within distance boundaries to the next atom
  • check_backbone_continuity() does the same exclusively for peptide/nucleotide backbone atoms
• Added sequence.common_alphabet() to determine the Alphabet from a list of alphabets that extends all other alphabets from this list (#446)
• sequence.phylo.Tree.to_newick() and sequence.phylo.TreeNode.to_newick() allow rounding of distance labels (#439)
• application.TantanApp is able to process multiple sequences in a single call (#446)
  • This significantly improves the performance especially for short sequences

Changes

• structure.filter_backbone() is deprecated and replaced by filter_peptide_backbone() (#436)
• structure.check_bond_continuity() is deprecated and replaced by check_backbone_continuity() (#436)
• Deprecated chain_id parameter in structure.annotate_sse(), multiple chains can now be processed at once (#448)

Fixes

• structure.CellList accepts empty query coordinates in get_atoms() and get_atoms_in_cells() (#448)
• Fixed padding of CRYST1 records to 80 instead of 70 characters (#453)
• Fixed issue, where application.dssp.DSSPApp did not give correct number of secondary structure elements for multi-chain structures (#444)
• Resolved MemoryError in structure.repeat_box() (#450)