Dear Colleagues,
I noticed that when writing out molecules using SDWriter() , the properties
fields are followed by something like "(1)" , "(2)". I mean, the sdf looks
like:
propane
RDKit 3D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4280 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9040 1.3000 -0.3480 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
> <pKa> (1)
4.0999999
> <logP> (1)
2
$$$$
Just wonder what was the rationale behind this extra "(1)" on the property
field lines (pKa and logP in the above example)?
And is there a way to get rid of these? I am not sure if this extra "(1)"
is part of the standard sd format.
Thank you!
Regards,
Ling
---------------------------------------------------------------------------------------------------
To create an sdf, you can do something like:
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles("CCC")
>>> m.SetProp("pKa","3.3")
>>> with Chem.SDWriter("temp3.sdf") as o:
... o.write(m)
Or use Chem.SDMolSupplier() to get mols from another sdf.
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