It's neither a bug nor a feature in this case, simply the specification of the
mdl format.
The SD in an sd file stands for "structured data" which are the properties you
are looking for plus the mol block.
A decent write up is here:
https://en.m.wikipedia.org/wiki/Chemical_table_file
If you see the dollar signs in your text block, it is indeed an sd record not
just a mol block.
----
Brian Kelley
> On Oct 2, 2016, at 3:46 PM, Maciek Wójcikowski <[email protected]> wrote:
>
> 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]
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