I've noticed that GMail might have mess up spaces in the text, so I included the example as an attachment.
---- Pozdrawiam, | Best regards, Maciek Wójcikowski [email protected] 2016-10-02 21:46 GMT+02:00 Maciek Wójcikowski <[email protected]>: > Hi RDKitters, > > Is it a bug or a feature? When using Chem.MolFromMolBlock there is no > properties from SD file. There is a bit of code to replicate that issue: > > 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 >> > <act> (1) >> 0.81 >> > <act_rel> (1) >> = >> > <act_type> (1) >> IC50 >> > <chembl_id> (1) >> CHEMBL18442 >> $$$$ >> """ >> m = Chem.MolFromMolBlock(tmp) >> print m.GetPropsAsDict() >> from StringIO import StringIO >> m = Chem.ForwardSDMolSupplier(StringIO(tmp)).next() >> print m.GetPropsAsDict() > > > > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > [email protected] >
rdkit_molprops.py
Description: application/chimera
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