# Bio.PDB.StructureAlignment module

Map residues of two structures to each other based on a FASTA alignment.

class Bio.PDB.StructureAlignment.StructureAlignment(fasta_align: MultipleSeqAlignment | Alignment | None = None, m1: Model | None = None, m2: Model | None = None, si: int = 0, sj: int = 1, aligner: PairwiseAligner | None = None)

  Bases: `object`

  Class to align two structures based on an alignment of their sequences.

  __init__(fasta_align: MultipleSeqAlignment | Alignment | None = None, m1: Model | None = None, m2: Model | None = None, si: int = 0, sj: int = 1, aligner: PairwiseAligner | None = None) → None

    Initialize.

    Attributes:

      - fasta_align - Alignment object / MSA object or None (if None, one will be generated automatically)

      - m1, m2 - two models (Bio.PDB.Model.Model objects). Their default values are set to None to maintain legacy code, but they CANNOT be None

      - si, sj - the sequences in the Alignment object that correspond to the structures

      - aligner - Optional aligner, mutually exclusive with fasta_align, allows for customization of automatic alignment, otherwise blastp defaults will be used

  get_maps()

    Map residues between the structures.

    Return two dictionaries that map a residue in one structure to the equivealent residue in the other structure.

  get_iterator()

    Create an iterator over all residue pairs.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 23
  __static_attributes__ = ('aligner', 'duos', 'map12', 'map21')

Biopython v: 1.86

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