I think this will do it
pattern = Chem.MolFromSmarts('C1~C~C2~C~C~C~C~C~2~C~C~1')
you need to ring closure bonds to be set to any as well
hope that helps
Rich
From: Jean-Marc Nuzillard <[email protected]>
Sent: 17 January 2020 09:54
To: RDKit Discuss <[email protected]>
Subject: [EXTERNAL] [Rdkit-discuss] SMARTS and ring closure
Dear all,
I would like to write a SMARTS chain that matches any compound with a decalin
ring system,
whatever bond multiplicity.
I wrote it as 'C1~C~C2~C~C~C~C~C2~C~C1' with ~ standing for "any bond".
The C1-C1 and C2-C2 bonds have the "default type", which is single or aromatic.
The code
m1 = Chem.MolFromSmiles('C1CCCC(=C12)CCCC2')
m2 = Chem.MolFromSmiles('C1CCC=C(C12)CCCC2')
pattern = Chem.MolFromSmarts('C1~C~C2~C~C~C~C~C2~C~C1')
print(m1.HasSubstructMatch(pattern))
print(m2.HasSubstructMatch(pattern))
prints False for m1 and True for m2 because the double bond in m1 is located
at the place of one of the ring closure bonds in pattern.
My question is how to write a SMARTS chain that fits in all cases for decalin
or any other ring system and is more related to SMARTS-writing than to RDKit, I
admit.
Best,
Jean-Marc
--
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry, CNRS UMR 7312
Faculté des Sciences Exactes et Naturelles, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax : 33 3 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
ORCID: 0000-0002-5120-2556
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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