Hi RDKitters,
I have (yet another) question about the handling of SMARTS. I have a set of
SMARTS (http://www.macinchem.org/reviews/pains/painsFilter.php) which I have
been using to perform PAINS filters but I've just discovered some strange
behaviour, I would expect a match to happen in the example below.
>>> p = Chem.MolFromSmarts('[#6]-[#6](=[#16])-[#1]')
>>> m = Chem.MolFromSmiles('CC=S')
>>> m.HasSubstructMatch(p)
False
This can be fixed using the alternative form of the SMARTS
>>> p2 = Chem.MolFromSmarts('[#6]-[#6H](=[#16])')
>>> m.HasSubstructMatch(p2)
True
Doing some research (which I can no longer find the link for) it seems that
[#1] seems to be reserved for more 'interesting' cases of hydrogen, for example:
>>> m = Chem.MolFromSmiles('CC(=S)[H]')
>>> m.HasSubstructMatch(p)
False
>>> m = Chem.MolFromSmiles('CC(=S)[2H]')
>>> m.HasSubstructMatch(p)
True
Also this seems to be changing the examples which greg posted in
http://sourceforge.net/p/rdkit/mailman/message/31650578/
>>> p1=Chem.MolFromSmarts('c2sccc2[#1]')
>>> mol=Chem.MolFromSmiles('Clc2sccc2[H]')
>>> mol.HasSubstructMatch(p1)
False
Firstly is this expected behaviour? Because it's different to what I would
expect, and different to how Pipeline Pilot behaves with SMARTS matching. And
secondly, does anyone know how to get the expected behaviour without rewriting
all the SMARTS.?
Thanks in advance. Apologies for the long read.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
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