def pdb_atom_names(self):
"""
"""
session = Session()
query = session.query(
chem_comp_fragment_atoms.c.hit,
func.array_agg(chem_comp_fragment_atoms.c.pdb_name))
query = query.filter(chem_comp_fragment_atoms.c.chem_comp_fragment_id
== self.chem_comp_fragment_id)
query = query.group_by(chem_comp_fragment_atoms.c.hit)
return query.all()
def do(controller):
"""
"""
# timer to clock functions and parts of the program
timer = Timer()
timer.start("app")
# get the controller command
cmd = controller.command
# get the command line arguments and options
args = controller.pargs
insert = binding_site_fuzcav.insert()
tracker = fuzcav.get_tracker()
# get the fuzcav side chain representative table from the credoscript metadata
metadata.reflect(schema='bio', only=('fuzcav_rep_sc_atoms', ))
fuzcav_rep_sc_atoms = Table('bio.fuzcav_rep_sc_atoms',
metadata,
autoload=True)
timer.start()
session = Session()
# get all ligands that have more than 7 heavy atoms and no clashes
query = session.query(Ligand.ligand_id, Ligand.biomolecule_id)
query = query.filter(
and_(Ligand.num_hvy_atoms >= 7, Ligand.is_clashing == False))
if args.incremental:
# subquery to get the current max ligand_id from the binding_site_fuzcav table
sq = session.query(
func.max(binding_site_fuzcav.c.ligand_id).label(
'ligand_id')).subquery('sq')
# only include new ligands
query = query.filter(Ligand.ligand_id > sq.c.ligand_id)
ligand_ids = query.order_by(Ligand.ligand_id).all()
# debug how much time it took to get all contacts
app.log.debug(
"all new ligand identifiers retrieved in {0:.2f} seconds.".format(
timer.elapsed()))
#
query = BindingSiteResidue.query.join('Peptide', 'Atoms')
#query = query.join(Peptide, Peptide.residue_id==BindingSiteResidue.residue_id)
#query = query.join(Atom, Atom.residue_id==Peptide.residue_id)
query = query.outerjoin(
fuzcav_rep_sc_atoms,
and_(fuzcav_rep_sc_atoms.c.res_name == Peptide.res_name,
fuzcav_rep_sc_atoms.c.atom_name == Atom.atom_name))
query = query.filter(
and_(
Peptide.is_non_std == False,
or_(Atom.atom_name == 'CA',
fuzcav_rep_sc_atoms.c.atom_name != None)))
query = query.with_entities(Peptide.res_name, Atom)
if args.progressbar:
bar = ProgressBar(widgets=[
'Binding Sites: ',
SimpleProgress(), ' ',
Percentage(),
Bar()
],
maxval=len(ligand_ids)).start()
# iterate through ligands
for counter, row in enumerate(ligand_ids, 1):
if args.progressbar: bar.update(counter)
ligand_id, biomolecule_id = row.ligand_id, row.biomolecule_id
timer.start()
# get all the fuzcav atoms (either CA or representative)
# important to use the proper atom partition!
atoms = query.filter(
and_(BindingSiteResidue.ligand_id == ligand_id,
Atom.biomolecule_id == biomolecule_id)).all()
# debug how much time it took to get all contacts
app.log.debug("all FuzCav atoms retrieved in {0:.2f} seconds.".format(
timer.elapsed()))
# ignore hits with too few peptides
if len(atoms) < 14:
app.log.debug("Ligand {} has only {} FuzCav atoms and will be "
"ignored.".format(ligand_id, len(atoms)))
continue
# get the calpha atom and its features for each residue
calphas = ((np.array(atom.coords,
dtype=float), (fuzcav.FEATURES[res_name]))
for res_name, atom in atoms if atom.atom_name == 'CA')
# get the representative atom and its features for each residue
representatives = (
(np.array(atom.coords, dtype=float), (fuzcav.FEATURES[res_name]))
for res_name, atom in atoms
if atom.atom_name == fuzcav.REPRESENTATIVES[res_name])
timer.start()
calphafp = fuzcav.make_fp(calphas, tracker)
repfp = fuzcav.make_fp(representatives, tracker)
# debug how much time it took to get all contacts
app.log.debug("fingerprints generated in {0:.2f} seconds.".format(
timer.elapsed()))
# insert the fingerprints into the table
if not args.dry_run:
engine.execute(insert,
ligand_id=ligand_id,
calphafp=calphafp.tolist(),
repfp=repfp.tolist())
# finish the optional progress bar
if args.progressbar: bar.finish()
session.close()