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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]
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