Dear Brice and Richard,
for some reason, I missed your answers.
Many thanks !
I also checked your solution (inserting a ~ between C and n)
with SMARTSviewer, https://smartsview.zbh.uni-hamburg.de/ ,
for which I am pleased to advertise.
Best,
Jean-Marc
Le 17/01/2020 à 11:21, Brice Hoffmann a écrit :
Dear Jean-Marc,
adding '~' between C and ring number seems to work:
'm1 = Chem.MolFromSmiles('C1CCCC(=C12)CCCC2')
m2 = Chem.MolFromSmiles('C1CCC=C(C12)CCCC2')
pattern = Chem.MolFromSmarts('C~1~C~C~2~C~C~C~C~C~2~C~C~1')
print(m1.HasSubstructMatch(pattern))
print(m2.HasSubstructMatch(pattern))
return True and True
Best regards,
Brice
Le ven. 17 janv. 2020 à 10:55, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> a écrit :
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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--
Brice HOFFMANN
Senior Scientist,
Molecular Modeling & Computational Chemistry
iktos.ai <http://iktos.ai/>
24 rue chaptal 75009 Paris
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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