Re: [Rdkit-discuss] SMARTS and ring closure
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('C1(=C12)2')
m2 = Chem.MolFromSmiles('C1CCC=C(C12)2')
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
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('C1(=C12)2')
m2 = Chem.MolFromSmiles('C1CCC=C(C12)2')
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: -0002-5120-2556
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
Brice HOFFMANN
Senior Scientist,
Molecular Modeling & Computational Chemistry
iktos.ai
Re: [Rdkit-discuss] SMARTS and ring closure
Dear Jean-Marc,
adding '~' between C and ring number seems to work:
'm1 = Chem.MolFromSmiles('C1(=C12)2')
m2 = Chem.MolFromSmiles('C1CCC=C(C12)2')
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> 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('C1(=C12)2')
> m2 = Chem.MolFromSmiles('C1CCC=C(C12)2')
> 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
> 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html
>
> ORCID:
> -0002-5120-2556http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
Brice HOFFMANN
Senior Scientist,
Molecular Modeling & Computational Chemistry
iktos.ai
24 rue chaptal 75009 Paris
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[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('C1(=C12)2')
m2 = Chem.MolFromSmiles('C1CCC=C(C12)2')
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: -0002-5120-2556
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
