Hi Quoc-Tuan
both those mols match the smarts pattern in my python3 version of rdkit
(2019.03.3 – hmm, it might be time for an upgrade)
>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2019.03.3'
>>> from rdkit import Chem
>>> patt =
>>> Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c2cccc3.c1ccc(cc1)C~C2NC~Cc3c2cccc3')
>>> mol =
>>> Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C2)NCCc5cc4Oc1c(c3)OC')
>>> mol.HasSubstructMatch(patt)
True
>>> mol =
>>> Chem.MolFromSmiles('COc1ccc7cc1Oc2ccc(cc2)CC3N(C)CCc4c3cc(c(c4)OC)Oc5ccc6c(c5)CCNC6C7')
>>> mol.HasSubstructMatch(patt)
True
do you have an older version – your print statements look like python2?
Best wishes
Richard
From: Quoc-Tuan DO <[email protected]>
Sent: 21 July 2020 13:09
To: [email protected]
Subject: [EXTERNAL] [Rdkit-discuss] substructure matching
Hello,
I am not very familiar with smiles/smarts and find the following results quite
puzzling:
>>> patt =
>>> Chem.MolFromSmiles('c1ccc(cc1)C~C2NC~Cc3c2cccc3.c1ccc(cc1)C~C2NC~Cc3c2cccc3')
>>> mol =
>>> Chem.MolFromSmiles('COc1ccc2cc1Oc1ccc(cc1)CC1N(C)CCc3c1c1Oc4cc5C(C2)NCCc5cc4Oc1c(c3)OC')
>>> print mol.HasSubstructMatch(patt)
False
>>> mol =
>>> Chem.MolFromSmiles('COc1ccc7cc1Oc2ccc(cc2)CC3N(C)CCc4c3cc(c(c4)OC)Oc5ccc6c(c5)CCNC6C7')
>>> print mol.HasSubstructMatch(patt)
True
It seems that a presence of an extra Ph - O - Ph makes the difference but I am
not sure why. How should the smarts be to have positive results for both smiles
?
Thank you in advance for your help.
Best regards,
Quoc-Tuan
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