#!/usr/bin/env python import rdkit from rdkit import Chem mol_block="""na RDKit 3D 43 43 0 0 0 0 0 0 0 0999 V2000 -0.7077 -3.1561 2.8013 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0608 -3.2163 3.2632 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1477 -4.0293 3.2485 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3211 -2.1193 1.8322 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9388 -2.0034 1.3877 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3403 -0.9550 0.3857 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3696 0.2396 0.3569 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6808 1.0987 -0.8014 N 0 0 0 0 0 0 0 0 0 0 0 0 1.1909 2.4443 -0.6923 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5137 2.9331 0.4707 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6552 3.1530 -1.9200 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0827 -0.2733 0.2951 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3451 -1.1851 1.4224 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1382 0.8516 0.2827 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0117 1.6298 1.4942 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6023 0.3892 0.1299 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0034 -0.3945 1.2754 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8843 -0.3803 -1.1651 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3059 -0.5335 -1.3500 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7046 -0.4812 0.6894 N 0 0 0 0 0 0 0 0 0 0 0 0 3.8261 -0.4692 -0.2282 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6383 -0.6253 -1.6505 N 0 0 0 0 0 0 0 0 0 0 0 0 5.0348 -0.2815 0.2377 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6975 -2.7206 1.6911 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3033 -1.4820 -0.5943 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4884 0.7994 1.3151 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5411 0.6903 -1.7745 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6866 4.2530 -1.7493 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6744 2.7962 -2.1902 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9635 2.9565 -2.7698 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1774 -0.8635 -0.6464 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9155 1.5113 -0.5913 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3915 2.5777 1.3209 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2192 1.3211 0.0969 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0345 -0.3582 1.3622 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4118 -1.3892 -1.1260 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4669 0.1734 -2.0385 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4435 -1.1005 -2.2050 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8781 -0.1399 1.6831 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4725 -0.6561 -2.3094 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6811 -0.6060 -2.1091 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8801 -0.2504 -0.4078 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2161 -0.1487 1.2771 H 0 0 0 0 0 0 0 0 0 0 0 0 1 4 1 0 1 3 2 0 1 2 1 0 4 13 1 0 4 5 2 0 5 6 1 0 6 20 1 1 6 7 1 0 7 12 1 0 7 8 1 6 8 9 1 0 9 11 1 0 9 10 2 0 12 14 1 6 12 13 1 0 14 16 1 6 14 15 1 0 16 18 1 6 16 17 1 0 18 19 1 0 20 21 1 0 21 23 2 3 21 22 1 0 5 24 1 0 6 25 1 0 7 26 1 0 8 27 1 0 11 28 1 0 11 29 1 0 11 30 1 0 12 31 1 0 14 32 1 0 15 33 1 0 16 34 1 0 17 35 1 0 18 36 1 0 18 37 1 0 19 38 1 0 20 39 1 0 22 40 1 0 22 41 1 0 23 42 1 0 23 43 1 0 M CHG 2 2 -1 23 1 M END > <_TriposChargeType> (1) GASTEIGER $$$$""" print Chem.MolFromMolBlock(mol_block) m = Chem.MolFromMolBlock(mol_block, sanitize=False) Chem.AddHs(m, addCoords=True)