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)