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
Hi,
I want to insert a compound to table Substance. The table has id,
smiles(varchar) and structure(Mol). I used Mol class from
https://github.com/rvianello/razi repository.
When I try to execute SQL query using asyncpg:
insert into substance
(smiles, structure)
(select r.smiles,
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
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