Bio.PDB.StructureAlignment module

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

class Bio.PDB.StructureAlignment.StructureAlignment(fasta_align, m1, m2, si=0, sj=1)

Bases: object

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

__init__(self, fasta_align, m1, m2, si=0, sj=1)


  • fasta_align - Alignment object

  • m1, m2 - two models

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


Map residues between the structures.

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


Create an iterator over all residue pairs.