def align_conserved(self, start=0, stop=None):
"""
Try all possible conserved alignments, or optionally a slice of the
total possibilities for use with multiprocessing. Does not preserve
residue order, and not all atoms can be matched so it will typical
exclude many atoms.
Note: ignores local_segment.
"""
# It's inefficient to calculate this separately for each
# process, but reduces the data that needs to be sent via IPC
# and this is not a significant portion of the total work for
# soups of typical size.
total, it = iter_residues_for_conserved_alignment(self.atoms1, self.atoms2)
if start > 0 or stop is not None:
it = itertools.islice(it, start, stop)
local_best = None
for res1bytype, res2bytype in it:
# flatten tuples, they are list of list by type
res1 = [r for rstype in res1bytype for r in rstype]
res2 = [r for rstype in res2bytype for r in rstype]
s = self._rmsd_rot_res(res1, res2)
if local_best is None or s.score < local_best.score:
s.strategy = ("conserved", start, stop)
local_best = s
if self.best is None or local_best.score < self.best.score:
self.best = local_best
return local_best
def _main():
args = parse_args()
pdb1_path = _pdbpath(args.pdb1)
pdb2_path = _pdbpath(args.pdb2)
download_pdbs(pdb1_path, pdb2_path)
soup1 = pdbatoms.Soup(pdb1_path)
soup2 = pdbatoms.Soup(pdb2_path)
sa = StructuralAlign(soup1, soup2, args.local_segment)
best_contiguous = sa.align_contiguous()
best_contiguous.print_multiline()
if args.random_attempts:
best_random = sa.align_random(args.random_attempts)
best_random.print_multiline()
if args.conserved:
ncpus = multiprocessing.cpu_count()
total, it = iter_residues_for_conserved_alignment(sa.atoms1, sa.atoms2)
per_job = int(math.ceil(float(total) / ncpus))
jobs = [(sa, start, start + per_job) for start in xrange(0, total, per_job)]
assert len(jobs) == ncpus
pool = multiprocessing.Pool(ncpus)
results = pool.map(_job_align_conserved, jobs)
best_conserved = None
for result in results:
result.print_multiline()
if best_conserved is None or result.score < best_conserved.score:
best_conserved = result
if best_conserved.score < sa.best.score:
sa.best = best_conserved
print "======== best =========="
sa.best.print_multiline()
if args.pdb1_transform_out:
soup1x = sa.get_transformed_soup1()
pdb1_outpath = _pdbpath(args.pdb1_transform_out)
soup1x.write_pdb(pdb1_outpath)
if args.png_out:
pymol_cartoon(pdb1_outpath, pdb2_path, args.png_out)
elif args.pdb2_transform_out:
soup2x = sa.get_transformed_soup2()
pdb2_outpath = _pdbpath(args.pdb2_transform_out)
soup2x.write_pdb(pdb2_outpath)
if args.png_out:
pymol_cartoon(pdb1_path, pdb2_outpath, args.png_out)
