def main(): p = enz.protein('../data/4key.pdb') p.mutate(44, 'Q') p.refold() print(p.df)
def main(): df = pd.read_csv('test_data/ManchesterSmiles.csv', index_col=0) p = enz.protein('../data/4key.pdb', seq=bm3_wt, key_sites=[82, 87, 330], cofactors=['HEM']) failures = [] for i in tqdm(df['Smiles']): try: p.dock(i, exhaustiveness=2) except Exception as e: failures.append(i) pd.Series(failures).to_csv('failures.csv')
def evaluate(gene): mutation_dictionary = dict(zip(TARGET_SITES, gene)) p = enz.protein( '4KEY.pdb', seq=BM3_DM, # my residue numbering system cofactors=['HEM']) # keep the heme for pos in mutation_dictionary: aa = mutation_dictionary[pos] p.mutate(pos, aa) p.refold() docking_results = p.dock( 'CCS(=O)(=O)C1=C(N2C=CC=CC2=N1)S(=O)(=O)NC(=O)NC3=NC(=CC(=N3)OC)OC', target_residues=TARGET_SITES, exhaustiveness=1) return score(p, docking_results)
def main(args): l = [] for i in tqdm(args): try: p = enz.protein(os.path.join(i, 'clean_receptor.pdb'), cofactors = ['HEM']) poses = [enz.mol(os.path.join(i, j)) for j in os.listdir(i) if 'vina' in j] scores = pd.read_csv(os.path.join(i, 'scores.csv'),index_col=0) scores['mode'] = scores['mode'].astype(int) x = get_info(p, poses, scores).reset_index() x['name'] = os.path.basename(i) l.append(x) except: print('error',i) df = pd.concat(l) df.reset_index(inplace=True,drop=True) df.to_csv('vina-info.csv') print(df)
def main(): p = enz.protein('4KEY.pdb', seq = BM3_DM, cofactors = ['HEM'], key_sites = [82, 87, 400, 49, 51, 181, 188, 263, 330]) r1 = p.dock(PIOGLITAZONE) r1.save('DM') p.mutate(75,'W') p.refold() r2 = p.dock(PIOGLITAZONE) r2.save('DM_L75W') p.mutate(188,'S') p.refold() r3 = p.dock(PIOGLITAZONE) r3.save('DM_L75W_L188S') p.mutate(75, 'L') p.refold() r4 = p.dock(PIOGLITAZONE) r4.save('DM_L188S')
def main(): p = enz.protein('../benchmark/data/2UWH.pdb', cofactors=['HEM', 'PLM']) print(p.df['residue_name'].unique()) p.save('test.pdb')
def main(): p = enz.protein('../data/1jme.pdb') enz.folds.init() pose = enz.folds.getpose(p.struc) print(enz.folds.fold_ccd(pose, {44:'Q'}))