:>"^œ ã@s`dZddlmZddlmZddlmZddlmZGdd„de ƒZ dS) zHMap residues of two structures to each other based on a FASTA alignment.é)Úprint_function)ÚSCOPData)Ú Selection)Úis_aac@sLeZdZdZdddd„Zdd„Zdd „Zd d „Zd S) ÚStructureAlignmentzGClass to align two structures based on an alignment of their sequences.récCs{|jƒ}tj|dƒ}tj|dƒ}d} d} i} i} g} x t|ƒD]ý}|dd…|f}||}||}|dkrÒx%|| }| d} t|ƒršPqšW|j||ƒnd}|dkrx%|| }| d} t|ƒrçPqçW|j||ƒnd}|r5|| |<|rE|| |<| j||fƒq[W| |_| |_| |_ dS)zÚInitialize. Attributes: - fasta_align - Alignment object - m1, m2 - two models - si, sj - the sequences in the Alignment object that correspond to the structures ÚRrNú-r) Zget_alignment_lengthrZunfold_entitiesÚrangerÚ_test_equivalenceÚappendÚmap12Úmap21Úduos)ÚselfZ fasta_alignÚm1Úm2ÚsiZsjÚlengthZrl1Zrl2Úp1Úp2r rrÚiÚcolumnÚaa1Zaa2Úr1Zr2©rú?/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/StructureAlignment.pyÚ__init__sH               zStructureAlignment.__init__cCs/|jƒ}tj|}||ks+t‚dS)z6Test if aa in sequence fits aa in structure (PRIVATE).N)Z get_resnamerZprotein_letters_3to1ÚAssertionError)rrrÚresnamerrrr Qs  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. )r r)rrrrÚget_mapsWszStructureAlignment.get_mapsccs3x,tdt|jƒƒD]}|j|VqWdS)z*Create an iterator over all residue pairs.rN)r Úlenr)rrrrrÚ get_iterator_szStructureAlignment.get_iteratorN)Ú__name__Ú __module__Ú __qualname__Ú__doc__rr r r"rrrrrs <  rN) r&Ú __future__rZBio.DatarZBio.PDBrZBio.PDB.PolypeptiderÚobjectrrrrrÚs