def generate_poses(self,
protein_file,
ligand_file,
centroid=None,
box_dims=None,
dry_run=False,
out_dir=None):
"""Generates the docked complex and outputs files for docked complex."""
if out_dir is None:
out_dir = tempfile.mkdtemp()
# Prepare receptor
receptor_name = os.path.basename(protein_file).split(".")[0]
protein_hyd = os.path.join(out_dir, "%s.pdb" % receptor_name)
protein_pdbqt = os.path.join(out_dir, "%s.pdbqt" % receptor_name)
hydrogenate_and_compute_partial_charges(protein_file,
"pdb",
hyd_output=protein_hyd,
pdbqt_output=protein_pdbqt,
protein=True)
# Get protein centroid and range
# TODO(rbharath): Need to add some way to identify binding pocket, or this is
# going to be extremely slow!
if centroid is not None and box_dims is not None:
protein_centroid = centroid
else:
if not self.detect_pockets:
receptor_mol = rdkit_util.load_molecule(protein_hyd,
calc_charges=False,
add_hydrogens=False)
protein_centroid = mol_xyz_util.get_molecule_centroid(
receptor_mol[0])
protein_range = mol_xyz_util.get_molecule_range(
receptor_mol[0])
box_dims = protein_range + 5.0
else:
logger.info("About to find putative binding pockets")
pockets, pocket_atoms_maps, pocket_coords = self.pocket_finder.find_pockets(
protein_file, ligand_file)
# TODO(rbharath): Handle multiple pockets instead of arbitrarily selecting
# first pocket.
logger.info("Computing centroid and size of proposed pocket.")
pocket_coord = pocket_coords[0]
protein_centroid = np.mean(pocket_coord, axis=1)
pocket = pockets[0]
(x_min, x_max), (y_min, y_max), (z_min, z_max) = pocket
x_box = (x_max - x_min) / 2.
y_box = (y_max - y_min) / 2.
z_box = (z_max - z_min) / 2.
box_dims = (x_box, y_box, z_box)
# Prepare receptor
ligand_name = os.path.basename(ligand_file).split(".")[0]
ligand_hyd = os.path.join(out_dir, "%s.pdb" % ligand_name)
ligand_pdbqt = os.path.join(out_dir, "%s.pdbqt" % ligand_name)
# TODO(rbharath): Generalize this so can support mol2 files as well.
hydrogenate_and_compute_partial_charges(ligand_file,
"sdf",
hyd_output=ligand_hyd,
pdbqt_output=ligand_pdbqt,
protein=False)
# Write Vina conf file
conf_file = os.path.join(out_dir, "conf.txt")
write_conf(protein_pdbqt,
ligand_pdbqt,
protein_centroid,
box_dims,
conf_file,
exhaustiveness=self.exhaustiveness)
# Define locations of log and output files
log_file = os.path.join(out_dir, "%s_log.txt" % ligand_name)
out_pdbqt = os.path.join(out_dir, "%s_docked.pdbqt" % ligand_name)
# TODO(rbharath): Let user specify the number of poses required.
if not dry_run:
logger.info("About to call Vina")
call("%s --config %s --log %s --out %s" %
(self.vina_cmd, conf_file, log_file, out_pdbqt),
shell=True)
# TODO(rbharath): Convert the output pdbqt to a pdb file.
# Return docked files
return protein_hyd, out_pdbqt
def generate_poses(self,
protein_file,
ligand_file,
centroid=None,
box_dims=None,
dry_run=False,
out_dir=None):
"""Generates the docked complex and outputs files for docked complex."""
if out_dir is None:
out_dir = tempfile.mkdtemp()
# Prepare receptor
receptor_name = os.path.basename(protein_file).split(".")[0]
protein_hyd = os.path.join(out_dir, "%s.pdb" % receptor_name)
protein_pdbqt = os.path.join(out_dir, "%s.pdbqt" % receptor_name)
hydrogenate_and_compute_partial_charges(
protein_file,
"pdb",
hyd_output=protein_hyd,
pdbqt_output=protein_pdbqt,
protein=True)
# Get protein centroid and range
# TODO(rbharath): Need to add some way to identify binding pocket, or this is
# going to be extremely slow!
if centroid is not None and box_dims is not None:
protein_centroid = centroid
else:
if not self.detect_pockets:
receptor_mol = rdkit_util.load_molecule(
protein_hyd, calc_charges=False, add_hydrogens=False)
protein_centroid = mol_xyz_util.get_molecule_centroid(receptor_mol[0])
protein_range = mol_xyz_util.get_molecule_range(receptor_mol[0])
box_dims = protein_range + 5.0
else:
logger.info("About to find putative binding pockets")
pockets, pocket_atoms_maps, pocket_coords = self.pocket_finder.find_pockets(
protein_file, ligand_file)
# TODO(rbharath): Handle multiple pockets instead of arbitrarily selecting
# first pocket.
logger.info("Computing centroid and size of proposed pocket.")
pocket_coord = pocket_coords[0]
protein_centroid = np.mean(pocket_coord, axis=1)
pocket = pockets[0]
(x_min, x_max), (y_min, y_max), (z_min, z_max) = pocket
x_box = (x_max - x_min) / 2.
y_box = (y_max - y_min) / 2.
z_box = (z_max - z_min) / 2.
box_dims = (x_box, y_box, z_box)
# Prepare receptor
ligand_name = os.path.basename(ligand_file).split(".")[0]
ligand_hyd = os.path.join(out_dir, "%s.pdb" % ligand_name)
ligand_pdbqt = os.path.join(out_dir, "%s.pdbqt" % ligand_name)
# TODO(rbharath): Generalize this so can support mol2 files as well.
hydrogenate_and_compute_partial_charges(
ligand_file,
"sdf",
hyd_output=ligand_hyd,
pdbqt_output=ligand_pdbqt,
protein=False)
# Write Vina conf file
conf_file = os.path.join(out_dir, "conf.txt")
write_conf(
protein_pdbqt,
ligand_pdbqt,
protein_centroid,
box_dims,
conf_file,
exhaustiveness=self.exhaustiveness)
# Define locations of log and output files
log_file = os.path.join(out_dir, "%s_log.txt" % ligand_name)
out_pdbqt = os.path.join(out_dir, "%s_docked.pdbqt" % ligand_name)
# TODO(rbharath): Let user specify the number of poses required.
if not dry_run:
logger.info("About to call Vina")
call(
"%s --config %s --log %s --out %s" % (self.vina_cmd, conf_file,
log_file, out_pdbqt),
shell=True)
# TODO(rbharath): Convert the output pdbqt to a pdb file.
# Return docked files
return protein_hyd, out_pdbqt