o Rŀg @s:dZddlmZddlmZddlmZGdddZdS)zHMap residues of two structures to each other based on a FASTA alignment.)PDBData) Selection)is_aac@s2eZdZdZd ddZddZdd Zd d Zd S)StructureAlignmentzGClass to align two structures based on an alignment of their sequences.rcCs0z|}Wnty|j\}}Ynwt|d}t|d} d} d} i} i} g}t|D]]}|dd|f}||}||}|dkr[ || }| d} t|rSnqF|||nd}|dkrw | | }| d} t|ronqb|||nd}|r|| |<|r|| |<|||fq/| |_ | |_ ||_ dS)zInitialize. Attributes: - fasta_align - Alignment object - m1, m2 - two models - si, sj - the sequences in the Alignment object that correspond to the structures RrN-Tr) get_alignment_lengthAttributeErrorshaperunfold_entitiesranger_test_equivalenceappendmap12map21duos)self fasta_alignm1m2sisjncolumnsnrowsrl1rl2p1p2rrricolumnaa1aa2r1r2r%N/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/StructureAlignment.py__init__sT      zStructureAlignment.__init__cCs"|}tj|}||ksJdS)z6Test if aa in sequence fits aa in structure (PRIVATE).N) get_resnamerprotein_letters_3to1_extended)rr#r!resnamer%r%r&rQs z$StructureAlignment._test_equivalencecCs |j|jfS)zMap residues between the structures. Return two dictionaries that map a residue in one structure to the equivealent residue in the other structure. )rr)rr%r%r&get_mapsWs zStructureAlignment.get_mapsccs&tt|jD]}|j|VqdS)z*Create an iterator over all residue pairs.N)r lenr)rrr%r%r& get_iterator_szStructureAlignment.get_iteratorN)rr)__name__ __module__ __qualname____doc__r'rr+r-r%r%r%r&rs  ? rN)r1Bio.DatarBio.PDBrBio.PDB.Polypeptiderrr%r%r%r&s