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.