def check_range(start, end, protein):
# Observe what positions of each protein in the gonnet alignment and the
# bbtm alignment correspond to a given range in the pdb sequence.
# Positions ocrresponding to gaps in the pdb sequence not shown.
print('name then seq distance then bbtm segment then gonnet segment')
pdb_seq_name = 'chaina_' + protein.lower()
for name in bbtm_alignments[protein].keys():
print(name)
print(matrices.compare(bbtm_alignments[protein][name],
bbtm_alignments[protein][pdb_seq_name],
id_matrix))
print(matrices.compare(gonnet_alignments[protein][name],
gonnet_alignments[protein][pdb_seq_name],
id_matrix))
print(bbtm_alignments[protein][name][start: end])
print(gonnet_alignments[protein][name][start:end])
print()
# Calculate the family moments, that is, the moments for all
# sequences in the alignments
family_moments = CIDict((pdbid, list()) for pdbid in alignments.keys())
for pdbid in family_moments.keys():
for seq_index in range(len(oracles[pdbid].get_alignment())):
# Calculate the moment
family_moment = moment(structure_dict[pdbid], resi_lists[pdbid],
centers[pdbid],
partial(calculator_adapter, calc),
oracles[pdbid].sequence(seq_index))
# Calculate the %identity with the pdb sequence
pdb_sequence = oracles[pdbid].get_pdb_seq_record().seq
sequence = oracles[pdbid].get_alignment()[seq_index].seq
normalized_distance = matrices.compare(pdb_sequence, sequence,
identity)
seq_id = oracles[pdbid].get_alignment()[seq_index].id
family_moments[pdbid].append((seq_id, normalized_distance,
family_moment))
# If this is the pdb sequence, then calculating the moment using
# only structural information, without using the MSA, should give
# the same result. If it doesn't, something went wrong!
if 'chaina' in seq_id:
no_seq_moment = moment(structure_dict[pdbid], resi_lists[pdbid],
centers[pdbid],
partial(no_seq_calculator_adapter, calc),
None)
assert (no_seq_moment == family_moment).all(), \
