def gen(lig_idx): dests = [] ligs = [] proteins = [] lig_src = lig_src_base + str(lig_idx).zfill(4) + '.pk' with open(lig_src, 'rb') as f: lig_features, centers = pk.load(f) for pro_idx in idxs: dest = base_dest + '/' + str(pro_idx).zfill(4) + '_pro_' + str(lig_idx).zfill(4) + '_lig.npy' protein_path = protein_src_base +str(pro_idx).zfill(4)+'_pro_cg.pdb' if is_val: pro_features, _ = pdb_to_features(protein_path, centers) else: pro_features, _ = test_pdb_to_features(protein_path, centers) pro_features = pro_features[:,:,:,[0,7]] combined = np.concatenate((pro_features, lig_features), axis=3) combined = combined.astype(np.float32) np.save(dest, combined) dests.append(dest) ligs.append(lig_idx) proteins.append(pro_idx) return dests, ligs, proteins
score = [] for lig_idx in tqdm(idxs, file=sys.stdout): lig_src = './processed_data/eval/ligands_2/' + str(lig_idx).zfill( 4) + '.pk' with open(lig_src, 'rb') as f: lig_features, centers = pk.load(f) for pro_idx in tqdm(idxs, file=sys.stdout): dest = base_dest + '/' + str(pro_idx).zfill(4) + '_pro_' + str( lig_idx).zfill(4) + '_lig.npy' protein_path = './data/testing_data/' + str(pro_idx).zfill( 4) + '_pro_cg.pdb' pro_features, _ = test_pdb_to_features(protein_path, centers) pro_features = pro_features[:, :, :, [0, 7]] combined = np.concatenate((pro_features, lig_features), axis=3) combined = combined.astype(np.float32) np.save(dest, combined) dests.append(dest) ligs.append(lig_idx) proteins.append(pro_idx) csv_dest = f'./data/csv/test_acc10_2.csv' pro_lig_record = pd.DataFrame( { 'lig_id': ligs,
import sys ''' For generating ligands in test dataset Code is almost exactly the same as gen_ligand2_descriptors.py ''' ligands = [] ligand_root = './processed_data/eval/ligands_2' Path(ligand_root).mkdir(exist_ok=True, parents=True) ### Generate the ligands raw_ligand_paths = sorted( list(Path('./data/testing_data/').glob('*lig_cg.pdb'))) dests = [] idxs = [] idx = 0 for lig_path in tqdm(raw_ligand_paths, file=sys.stdout): features, centers = test_pdb_to_features(lig_path) features = features[:, :, :, [0, 7]] dest = ligand_root + '/' + str(idx + 1).zfill(4) + '.pk' with open(dest, 'wb') as f: pk.dump((features, centers), f) dests.append(dest) idxs.append(idx + 1) idx += 1 df = pd.DataFrame({'id': idxs, 'path': dests}) df.to_csv('./data/csv/ligand_2_data_eval.csv', index=None)