Hi Eduardo,
If I'm understanding what you want to do correctly, then you could try
extending your SMARTS pattern to include a ring bond to a neighbor from
each atom in the ring:
*@*~1~*(@*)~*(@*)~*(@*)~*(@*)~*~1@*
If you only want the indices of the ring atoms, you can then just pick
those out
The above solution with !r4 doesn't work because for sssr reasons these
atoms are considered to be in a 4 membered ring also if the 4 membered ring
is "exo" to the central 6 membered one. AFAIK there is no good way to do a
general ring size filter in an atom definition using SMARTS. Below is a
> Nevermind, x3 won't exclude the fused 4-atom rings from your first example.
> I'll let you know if I think of some other way. :-)
I think you'd want something like this, perhaps - to exclude atoms in ring size
4?
[*;R2!r4]~1~[*;R2!r4]~[*;R2!r4]~[*;R2!r4]~[*;R2!r4]~[*;R2!r4]~1
I also don't
On Tue, Jun 7, 2022 at 1:39 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> Perhaps using x3 instead (means "number of ring bonds") would work for
> your purposes?
>
Nevermind, x3 won't exclude the fused 4-atom rings from your first example.
I'll let you know if I think of
Hi Eduardo,
I believe the problem is that r6 means "in *smallest* SSSR ring of size
", where "smallest" in this context means that, for example, for an atom
at the ring fusion between a 5-member ring and a 6-member ring, r5 would
match that atom but r6 wouldn't.
Perhaps using x3 instead (means
Greetings!!
I hope this email finds you well.
I need a SMARTS pattern that matches this molecule fragment
[image: image.png]
The first pattern I used was:
[*;R2]~1~[*;R2]~[*;R2]~[*;R2]~[*;R2]~[*;R2]~1
However, it also matches this fragment. This is not the expected behavior
but it agrees with
On 12/01/2021 15:10, Fiorella Ruggiu wrote:
Hi Francois,
not sure if you have solved this yet. I believe it won't be possible
to use AllChem.ReplaceSubstructs without breaking the rings or
enumerating them. You can however use reactions for this problem.
Here's an example based on yours:
mol =
Hi Francois,
not sure if you have solved this yet. I believe it won't be possible to use
AllChem.ReplaceSubstructs without breaking the rings or enumerating them.
You can however use reactions for this problem. Here's an example based on
yours:
mol = Chem.MolFromSmiles('O=c1[nH]1')
rxn =
Dear list,
I have been trying to replace this SMARTS pattern in a ring:
'c(=O)[nH]'
By this SMILES fragment:
'c(O)n'
My trials using a single SMARTS pattern search then replace
break open the ring, which is not what I want.
My not working trial code:
---
mol =
Dear Colin,
you might specify the number of implicit Hs that you want on the carbons
of the indazole nucleus, e.g.:
'[#7]1:[#6]:[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2:[#7]:1-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1'
This would rule out substituted indazoles.
HTH, cheers
p.
On 02/05/18 09:26, Colin
Hello everyone,
I have trouble finding what I want using smarts pattern :
Let's say I have for example these molecules :
smis
=('n2cc1c1n2Cc1c1CC','n2cc1c1n2Cc1c(CC)cc(CCl)cc1','n2cc1c(CC)1n2Cc1c1CC','n2cc1cc(CF)ccc1n2Cc1cc(CC)ccc1CC')
ms = [Chem.MolFromSmiles(x) for x in
Start with your benzene molecule
m = Chem.MolFromSmiles('c1c1')
make a pattern using Peter's example, with three aromatic atoms connected
by three aromatic bonds
patt = Chem.MolFromSmarts('a:a:a')
and it's a match:
m.HasSubstructMatch(patt)
>True
Kekulize your mol, and the pattern
Hi,
In SMARTS, 'a' matches an aromatic atom. So you would match your molecule
with the pattern 'aaa', or if you wanted to restrict yourself to carbons,
'ccc'.
This would match whether you created the molecule from a Kekulized or an
aromatic SMILES. Remember that it's the molecular recognition
Hello,
Suppose I read in the SMILES of an aromatic molecule e.g., for
benzene
c1c1
I then want to convert the molecule to a Kekule representation and
then perform various SMARTS pattern recognition e.g.
[C]=[C]-[C]
I have tried various Kekule commands in
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