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.