def reduceToAlignable(struc1_allchains,
struc2_allchains,
seq1,
seq2,
subset1=None,
subset2=None,
atom_types=("N", "CA", "C", "O"),
modify_structures=True):
assert type(struc1_allchains) == type(struc2_allchains)
assert type(subset1) == type(subset2)
assert isinstance(struc1_allchains, Pdb)
assert None == subset1 or isinstance(subset1, Pdb)
if subset1 is None:
subset1 = struc1_allchains
if subset2 is None:
subset2 = struc2_allchains
if seq1 is None:
seq1 = subset1.get_seq()
if seq2 is None:
seq2 = subset2.get_seq()
if not (seq1 and seq2):
raise ValueError(
"Need to have non-empty sequence to align proteins:\nseq1:%s\nseq2:%s\n"
% (seq1, seq2))
## if structure has more than 1 chain, only use the first one
#if subset1.chaincount() > 1:
# subset1 = subset1.get_first_chain()
#if subset2.chaincount() > 1:
# subset2 = subset2.get_first_chain()
subset1_resbounds = subset1.residue_boundaries()
subset2_resbounds = subset2.residue_boundaries()
# residue count, according to the structure data
pdb1_rescount = len(subset1_resbounds)
pdb2_rescount = len(subset2_resbounds)
#print deGappify(seq1)
#print deGappify(subset1.get_seq())
#print deGappify(seq2)
#print deGappify(subset2.get_seq())
# Make sure the residue counts coincide in sequence and structure data
#
assert length_ungapped(
seq1
) == pdb1_rescount, "length_ungapped(seq1) = %d, pdb1_rescount = %d" % (
length_ungapped(seq1), pdb1_rescount)
assert length_ungapped(
seq2
) == pdb2_rescount, "length_ungapped(seq2) = %d, pdb2_rescount = %d" % (
length_ungapped(seq2), pdb2_rescount)
# Get the residue indeces of aligned residues
#
aligned_indeces1, aligned_indeces2 = find_aligned_residues(seq1, seq2)
assert len(aligned_indeces1) == len(aligned_indeces2)
if not aligned_indeces1:
raise ParsingError("No aligned residues?")
#
# Get the subset of backbone atoms corresponding to the aligned residues
#
#
#subset1_CA = subset1.get_CA()
#subset2_CA = subset2.get_CA()
aligned_pdb1 = Pdb(subset1, [])
aligned_pdb2 = Pdb(subset2, [])
for ix1, ix2 in zip(aligned_indeces1, aligned_indeces2):
#residue1 = subset1.get_residue(subset1_CA[ix1])
#residue2 = subset2.get_residue(subset2_CA[ix2])
#residue1 = residue1.get_atoms_by_type(atom_types)
#residue2 = residue2.get_atoms_by_type(atom_types)
residue1 = subset1.get_atoms(slice=subset1_resbounds[ix1],
atom_types=atom_types)
residue2 = subset2.get_atoms(slice=subset2_resbounds[ix2],
atom_types=atom_types)
if len(atom_types) != len(residue1) or len(atom_types) != len(
residue2):
residue1, residue2 = intersectAtomTypes(residue1, residue2)
assert len(residue1) == len(residue2)
aligned_pdb1.append_atoms(residue1)
aligned_pdb2.append_atoms(residue2)
assert len(aligned_pdb1) == len(aligned_pdb2)
return aligned_pdb1, aligned_pdb2
