from rdkit import Chem tmp = """20346 RDKit 3D 36 38 0 0 0 0 0 0 0 0999 V2000 15.8390 -9.3370 68.8840 C 0 0 0 0 0 0 0 0 0 0 0 0 17.1400 -9.1830 69.5480 N 0 0 0 0 0 0 0 0 0 0 0 0 17.4030 -7.7570 69.7840 C 0 0 0 0 0 0 0 0 0 0 0 0 17.0930 -7.4160 71.2420 C 0 0 0 0 0 0 0 0 0 0 0 0 18.2300 -6.5720 71.8210 C 0 0 0 0 0 0 0 0 0 0 0 0 18.6770 -7.1570 73.0920 N 0 0 0 0 0 0 0 0 0 0 0 0 20.1430 -7.2290 73.1530 C 0 0 0 0 0 0 0 0 0 0 0 0 20.5650 -8.5770 73.7380 C 0 0 0 0 0 0 0 0 0 0 0 0 21.6390 -9.1530 72.9180 N 0 0 0 0 0 0 0 0 0 0 0 0 21.3560 -10.5710 72.6640 C 0 0 0 0 0 0 0 0 0 0 0 0 21.5940 -10.8820 71.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4320 -11.7190 70.6460 C 0 0 0 0 0 0 0 0 0 0 0 0 20.0430 -11.2190 69.3210 N 0 0 0 0 0 0 0 0 0 0 0 0 18.5820 -11.1310 69.1980 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1950 -9.7400 68.6920 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7370 -9.2360 69.9070 C 0 0 0 0 0 0 0 0 0 0 0 0 13.1700 -7.9140 71.1420 C 0 0 0 0 0 0 0 0 0 0 0 0 14.1800 -8.0060 70.2040 C 0 0 0 0 0 0 0 0 0 0 0 0 14.2840 -10.3730 70.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 13.2740 -10.2810 71.4890 C 0 0 0 0 0 0 0 0 0 0 0 0 12.7160 -9.0510 71.7840 C 0 0 0 0 0 0 0 0 0 0 0 0 11.6140 -8.9500 72.8070 C 0 0 0 0 0 0 0 0 0 0 0 0 11.8810 -7.8160 73.7040 N 0 0 0 0 0 0 0 0 0 0 0 0 12.9350 -8.1480 74.6710 C 0 0 0 0 0 0 0 0 0 0 0 0 14.2790 -7.6200 74.1620 C 0 0 0 0 0 0 0 0 0 0 0 0 14.9870 -6.8610 75.2860 C 0 0 0 0 0 0 0 0 0 0 0 0 15.4440 -5.5580 74.7840 N 0 0 0 0 0 0 0 0 0 0 0 0 15.1190 -4.5130 75.7650 C 0 0 0 0 0 0 0 0 0 0 0 0 14.5870 -3.2770 75.0370 C 0 0 0 0 0 0 0 0 0 0 0 0 13.3710 -2.7990 75.7080 N 0 0 0 0 0 0 0 0 0 0 0 0 12.3120 -2.5090 74.7330 C 0 0 0 0 0 0 0 0 0 0 0 0 10.9900 -3.1010 75.2260 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3040 -3.8450 74.0790 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7590 -5.1150 74.5740 N 0 0 0 0 0 0 0 0 0 0 0 0 10.0350 -6.2090 73.6340 C 0 0 0 0 0 0 0 0 0 0 0 0 10.6540 -7.3880 74.3890 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 3 2 1 0 4 3 1 0 5 4 1 0 6 5 1 0 7 6 1 0 8 7 1 0 9 8 1 0 10 9 1 0 11 10 1 0 12 11 1 0 13 12 1 0 14 13 1 0 15 14 1 0 15 2 1 0 16 1 1 0 18 16 1 0 18 17 2 0 19 16 2 0 20 19 1 0 21 20 2 0 21 17 1 0 22 21 1 0 23 22 1 0 24 23 1 0 25 24 1 0 26 25 1 0 27 26 1 0 28 27 1 0 29 28 1 0 30 29 1 0 31 30 1 0 32 31 1 0 33 32 1 0 34 33 1 0 35 34 1 0 36 35 1 0 36 23 1 0 M END > (1) 0.81 > (1) = $$$$ """ m = Chem.MolFromMolBlock(tmp) print m.GetPropsAsDict() from StringIO import StringIO m = Chem.ForwardSDMolSupplier(StringIO(tmp)).next() print m.GetPropsAsDict()