def _featurize_complex(self, mol_pdb, protein_pdb):
"""
Compute Binana fingerprint for complex.
"""
mol_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
with open(mol_pdb_file.name, "w") as mol_f:
mol_f.writelines(mol_pdb)
protein_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
with open(protein_pdb_file.name, "w") as protein_f:
protein_f.writelines(protein_pdb)
mol_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
mol_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
hydrogenate_and_compute_partial_charges(
mol_pdb_file.name, "pdb", mol_hyd_file.name,
mol_pdbqt_file.name)
protein_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
protein_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
hydrogenate_and_compute_partial_charges(
protein_pdb_file.name, "pdb", protein_hyd_file.name,
protein_pdbqt_file.name)
mol_pdb_obj = PDB()
mol_pdb_obj.load_from_files(mol_pdb_file.name, mol_pdbqt_file.name)
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(
protein_pdb_file.name, protein_pdbqt_file.name)
features = self.binana.compute_input_vector(mol_pdb_obj, protein_pdb_obj)
return features
def prepare_ligand(mol_name, save_dir):
# print("Preparing ligand %s" % mol_name)
outfile = "/home/enf/deep-docking/shallow/test_output.txt"
filename = str(mol_name) + ".mol2"
filename = os.path.join(save_dir, filename)
prepared_filename = os.path.join(save_dir, "%s_prepared.pdb" % mol_name)
prepared_pdbqt = os.path.join(save_dir, "%s_prepared.pdbqt" % mol_name)
if os.path.exists(prepared_pdbqt):
return
hydrogenate_and_compute_partial_charges(
filename, "mol2", hyd_output=prepared_filename, pdbqt_output=prepared_pdbqt, verbose=False, protein=False
)
def prepare_ligand(mol_name, save_dir):
#print("Preparing ligand %s" % mol_name)
outfile = "/home/enf/deep-docking/shallow/test_output.txt"
filename = str(mol_name) + ".mol2"
filename = os.path.join(save_dir, filename)
prepared_filename = os.path.join(save_dir, "%s_prepared.pdb" %mol_name)
prepared_pdbqt = os.path.join(save_dir, "%s_prepared.pdbqt" %mol_name)
if os.path.exists(prepared_pdbqt):
return
hydrogenate_and_compute_partial_charges(filename, "mol2",
hyd_output=prepared_filename,
pdbqt_output=prepared_pdbqt,
verbose=False, protein=False)
def prepare_receptors(dude_dir, new_dir):
for subdir, dirs, files in os.walk(dude_dir):
receptor_name = os.path.basename(subdir)
print("Currently examining receptor %s " % receptor_name)
save_dir = os.path.join(new_dir, receptor_name)
if not os.path.exists(save_dir):
os.makedirs(save_dir)
receptor_filename = os.path.join(subdir, "receptor.pdb")
if not os.path.exists(receptor_filename):
continue
prepared_filename = os.path.join(save_dir, "%s.pdb" % receptor_name)
prepared_pdbqt = os.path.join(save_dir, "%s.pdbqt" % receptor_name)
if os.path.exists(prepared_pdbqt):
continue
hydrogenate_and_compute_partial_charges(
receptor_filename, ".pdb", hyd_output=prepared_filename, pdbqt_output=prepared_pdbqt, verbose=False
)
def prepare_receptors(dude_dir, new_dir):
for subdir, dirs, files in os.walk(dude_dir):
receptor_name = os.path.basename(subdir)
print("Currently examining receptor %s " % receptor_name)
save_dir = os.path.join(new_dir, receptor_name)
if not os.path.exists(save_dir):
os.makedirs(save_dir)
receptor_filename = os.path.join(subdir, "receptor.pdb")
if not os.path.exists(receptor_filename):
continue
prepared_filename = os.path.join(save_dir, "%s.pdb" % receptor_name)
prepared_pdbqt = os.path.join(save_dir, "%s.pdbqt" % receptor_name)
if os.path.exists(prepared_pdbqt):
continue
hydrogenate_and_compute_partial_charges(receptor_filename, ".pdb",
hyd_output=prepared_filename,
pdbqt_output=prepared_pdbqt,
verbose=False)
