def featurize_dude(dude_dir, target, pickle_dir, num_jobs):
"""Featurize DUD-E docked poses and write features to pickle_out.
Parameters
----------
dude_dir: string
Path to DUD-E directory
target: string
Name of DUD-E target.
pickle_dir: string
Path to directory to output pickles
"""
target_dir = os.path.join(dude_dir, target)
actives_dir = os.path.join(target_dir, "actives")
decoys_dir = os.path.join(target_dir, "decoys")
actives = [a for a in os.listdir(actives_dir)]
decoys = [a for a in os.listdir(decoys_dir)]
receptor = os.path.join(target_dir, "receptor.pdb")
pickle_out = os.path.join(target_dir, "out.pkl.gz")
# Just for debugging purposes
actives = actives[:1]
num_per_job = int(math.ceil(len(actives) / float(num_jobs)))
print "Number per job: %d" % num_per_job
protein_pdb_path = "/home/rbharath/DUD-E/aa2ar/receptor_hyd.pdb"
protein_pdbqt_path = "/home/rbharath/DUD-E/aa2ar/receptor_hyd.pdbqt"
print "About to load protein from input files"
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_path, protein_pdbqt_path)
binana = Binana()
feature_len = binana.num_features()
feature_vectors = {}
for compound in actives:
compound_name = compound.split(".")[0]
compound_pdbqt = compound_name + "_hyd_out.pdbqt"
compound_pdbqt = os.path.join(actives_dir, compound_pdbqt)
# Convert the pdbqt to pdb
pdbqt_to_pdb(compound_pdbqt, actives_dir)
compound_pdb = compound_name + "_hyd_out.pdb"
compound_pdb = os.path.join(actives_dir, compound_pdb)
structures = MultiStructure()
structures.load_from_files(compound_pdb, compound_pdbqt)
vectors = []
for key in sorted(structures.molecules.keys()):
structure = structures.molecules[key]
print "type(structure)"
print type(structure)
vectors.append(
binana.compute_input_vector(structure, protein_pdb_obj))
feature_vectors[compound_name] = vectors
with gzip.open(pickle_out, "wb") as f:
pickle.dump(feature_vectors, f)
decoys = decoys[:1]
def featurize_fingerprint(pdb_directories, pickle_out):
"""Featurize all pdbs in provided directories."""
# Instantiate copy of binana vector
binana = Binana()
# See features/tests/nnscore_test.py:TestBinana.testComputeInputVector
# for derivation.
feature_len = binana.num_features()
feature_vectors = {}
for count, pdb_dir in enumerate(pdb_directories):
print "\nprocessing %d-th pdb %s" % (count, dir)
print "About to extract ligand and protein input files"
ligand_pdb, ligand_pdbqt = None, None
protein_pdb, protein_pdbqt = None, None
for f in os.listdir(pdb_dir):
if re.search("_ligand_hyd.pdb$", f):
ligand_pdb = f
elif re.search("_ligand_hyd.pdbqt$", f):
ligand_pdbqt = f
elif re.search("_protein_hyd.pdb$", f):
protein_pdb = f
elif re.search("_protein_hyd.pdbqt$", f):
protein_pdbqt = f
print "Extracted Input Files:"
print (ligand_pdb, ligand_pdbqt, protein_pdb, protein_pdbqt)
if (not ligand_pdb or not ligand_pdbqt or not protein_pdb or not
protein_pdbqt):
raise ValueError("Required files not present for %s" % pdb_dir)
ligand_pdb_path = os.path.join(pdb_dir, ligand_pdb)
ligand_pdbqt_path = os.path.join(pdb_dir, ligand_pdbqt)
protein_pdb_path = os.path.join(pdb_dir, protein_pdb)
protein_pdbqt_path = os.path.join(pdb_dir, protein_pdbqt)
print "About to load ligand from input files"
ligand_pdb_obj = PDB()
ligand_pdb_obj.load_from_files(ligand_pdb_path, ligand_pdbqt_path)
print "About to load protein from input files"
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_path, protein_pdbqt_path)
print "About to generate feature vector."
features = binana.compute_input_vector(ligand_pdb_obj,
protein_pdb_obj)
if len(features) != feature_len:
raise ValueError("Feature length incorrect on %s" % pdb_dir)
print "Feature vector generated correctly."
print "About to compute ligand smiles string."
ligand_mol = Chem.MolFromPDBFile(ligand_pdb_path)
# TODO(rbharath): Why does this fail sometimes?
if ligand_mol is None:
continue
smiles = Chem.MolToSmiles(ligand_mol)
print "About to compute sequence."
protein = md.load(protein_pdb_path)
seq = [r.name for r in protein.top.residues]
# Write the computed quantities
feature_vectors[pdb_dir] = (features, smiles, seq)
print "About to write pickle to " + pickle_out
with open(pickle_out, "wb") as f:
pickle.dump(feature_vectors, f)
def featurize_fingerprint(pdb_directories, pickle_out):
"""Featurize all pdbs in provided directories."""
# Instantiate copy of binana vector
binana = Binana()
# See features/tests/nnscore_test.py:TestBinana.testComputeInputVector
# for derivation.
feature_len = binana.num_features()
feature_vectors = {}
for count, pdb_dir in enumerate(pdb_directories):
print "\nprocessing %d-th pdb %s" % (count, dir)
print "About to extract ligand and protein input files"
ligand_pdb, ligand_pdbqt = None, None
protein_pdb, protein_pdbqt = None, None
for f in os.listdir(pdb_dir):
if re.search("_ligand_hyd.pdb$", f):
ligand_pdb = f
elif re.search("_ligand_hyd.pdbqt$", f):
ligand_pdbqt = f
elif re.search("_protein_hyd.pdb$", f):
protein_pdb = f
elif re.search("_protein_hyd.pdbqt$", f):
protein_pdbqt = f
print "Extracted Input Files:"
print(ligand_pdb, ligand_pdbqt, protein_pdb, protein_pdbqt)
if (not ligand_pdb or not ligand_pdbqt or not protein_pdb
or not protein_pdbqt):
raise ValueError("Required files not present for %s" % pdb_dir)
ligand_pdb_path = os.path.join(pdb_dir, ligand_pdb)
ligand_pdbqt_path = os.path.join(pdb_dir, ligand_pdbqt)
protein_pdb_path = os.path.join(pdb_dir, protein_pdb)
protein_pdbqt_path = os.path.join(pdb_dir, protein_pdbqt)
print "About to load ligand from input files"
ligand_pdb_obj = PDB()
ligand_pdb_obj.load_from_files(ligand_pdb_path, ligand_pdbqt_path)
print "About to load protein from input files"
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_path, protein_pdbqt_path)
print "About to generate feature vector."
features = binana.compute_input_vector(ligand_pdb_obj, protein_pdb_obj)
if len(features) != feature_len:
raise ValueError("Feature length incorrect on %s" % pdb_dir)
print "Feature vector generated correctly."
print "About to compute ligand smiles string."
ligand_mol = Chem.MolFromPDBFile(ligand_pdb_path)
# TODO(rbharath): Why does this fail sometimes?
if ligand_mol is None:
continue
smiles = Chem.MolToSmiles(ligand_mol)
print "About to compute sequence."
protein = md.load(protein_pdb_path)
seq = [r.name for r in protein.top.residues]
# Write the computed quantities
feature_vectors[pdb_dir] = (features, smiles, seq)
print "About to write pickle to " + pickle_out
with gzip.open(pickle_out, "wb") as f:
pickle.dump(feature_vectors, f)
def featurize_dude(dude_dir, target, pickle_dir, num_jobs):
"""Featurize DUD-E docked poses and write features to pickle_out.
Parameters
----------
dude_dir: string
Path to DUD-E directory
target: string
Name of DUD-E target.
pickle_dir: string
Path to directory to output pickles
"""
target_dir = os.path.join(dude_dir, target)
actives_dir = os.path.join(target_dir, "actives")
decoys_dir = os.path.join(target_dir, "decoys")
actives = [a for a in os.listdir(actives_dir)]
decoys = [a for a in os.listdir(decoys_dir)]
receptor = os.path.join(target_dir, "receptor.pdb")
pickle_out = os.path.join(target_dir, "out.pkl.gz")
# Just for debugging purposes
actives = actives[:1]
num_per_job = int(math.ceil(len(actives)/float(num_jobs)))
print "Number per job: %d" % num_per_job
protein_pdb_path = "/home/rbharath/DUD-E/aa2ar/receptor_hyd.pdb"
protein_pdbqt_path = "/home/rbharath/DUD-E/aa2ar/receptor_hyd.pdbqt"
print "About to load protein from input files"
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_path, protein_pdbqt_path)
binana = Binana()
feature_len = binana.num_features()
feature_vectors = {}
for compound in actives:
compound_name = compound.split(".")[0]
compound_pdbqt = compound_name + "_hyd_out.pdbqt"
compound_pdbqt = os.path.join(actives_dir, compound_pdbqt)
# Convert the pdbqt to pdb
pdbqt_to_pdb(compound_pdbqt, actives_dir)
compound_pdb = compound_name + "_hyd_out.pdb"
compound_pdb = os.path.join(actives_dir, compound_pdb)
structures = MultiStructure()
structures.load_from_files(compound_pdb, compound_pdbqt)
vectors = []
for key in sorted(structures.molecules.keys()):
structure = structures.molecules[key]
print "type(structure)"
print type(structure)
vectors.append(binana.compute_input_vector(structure,
protein_pdb_obj))
feature_vectors[compound_name] = vectors
with gzip.open(pickle_out, "wb") as f:
pickle.dump(feature_vectors, f)
decoys = decoys[:1]
