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| # Copyright (C) 2002, Thomas Hamelryck ([email protected]) | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Map residues of two structures to each other based on a FASTA alignment.""" | |
| from Bio.Data import PDBData | |
| from Bio.PDB import Selection | |
| from Bio.PDB.Polypeptide import is_aa | |
| class StructureAlignment: | |
| """Class to align two structures based on an alignment of their sequences.""" | |
| def __init__(self, fasta_align, m1, m2, si=0, sj=1): | |
| """Initialize. | |
| Attributes: | |
| - fasta_align - Alignment object | |
| - m1, m2 - two models | |
| - si, sj - the sequences in the Alignment object that | |
| correspond to the structures | |
| """ | |
| try: # MultipleSeqAlignment object | |
| ncolumns = fasta_align.get_alignment_length() | |
| except AttributeError: # Alignment object | |
| nrows, ncolumns = fasta_align.shape | |
| # Get the residues in the models | |
| rl1 = Selection.unfold_entities(m1, "R") | |
| rl2 = Selection.unfold_entities(m2, "R") | |
| # Residue positions | |
| p1 = 0 | |
| p2 = 0 | |
| # Map equivalent residues to each other | |
| map12 = {} | |
| map21 = {} | |
| # List of residue pairs (None if -) | |
| duos = [] | |
| for i in range(ncolumns): | |
| column = fasta_align[:, i] | |
| aa1 = column[si] | |
| aa2 = column[sj] | |
| if aa1 != "-": | |
| # Position in seq1 is not - | |
| while True: | |
| # Loop until an aa is found | |
| r1 = rl1[p1] | |
| p1 = p1 + 1 | |
| if is_aa(r1): | |
| break | |
| self._test_equivalence(r1, aa1) | |
| else: | |
| r1 = None | |
| if aa2 != "-": | |
| # Position in seq2 is not - | |
| while True: | |
| # Loop until an aa is found | |
| r2 = rl2[p2] | |
| p2 = p2 + 1 | |
| if is_aa(r2): | |
| break | |
| self._test_equivalence(r2, aa2) | |
| else: | |
| r2 = None | |
| if r1: | |
| # Map residue in seq1 to its equivalent in seq2 | |
| map12[r1] = r2 | |
| if r2: | |
| # Map residue in seq2 to its equivalent in seq1 | |
| map21[r2] = r1 | |
| # Append aligned pair (r is None if gap) | |
| duos.append((r1, r2)) | |
| self.map12 = map12 | |
| self.map21 = map21 | |
| self.duos = duos | |
| def _test_equivalence(self, r1, aa1): | |
| """Test if aa in sequence fits aa in structure (PRIVATE).""" | |
| resname = r1.get_resname() | |
| resname = PDBData.protein_letters_3to1_extended[resname] | |
| assert aa1 == resname | |
| def get_maps(self): | |
| """Map residues between the structures. | |
| Return two dictionaries that map a residue in one structure to | |
| the equivealent residue in the other structure. | |
| """ | |
| return self.map12, self.map21 | |
| def get_iterator(self): | |
| """Create an iterator over all residue pairs.""" | |
| for i in range(0, len(self.duos)): | |
| yield self.duos[i] | |