Chris,
Wow! Your recursive SMARTS expression works as needed!
Hmmm... Help me understand this better ... it looks like you "walk around" the
ring of the substructure we want to exclude and employ a slightly different
recursive SMARTS beginning at that atom. Is that correct?
Also, since my situation is likely to get more complicated with respect to
exclusions, suppose I still wanted to utilize the general aromatic expression
for a 6-membered ring i.e. [a]1:[a]:[a]:[a][a]:[a]1, and I wanted to exclude
the structures we have been discussing, and I also wanted to exclude
pyridine i.e., [n]1:[c]:[c]:[c]:[c]:[c]1.
Is there a SMARTS expression that would capture 2 exclusions?
Perhaps this is getting too clumsy! It might be better to have one or more
inclusion SMARTS and one or more exclusion SMARTS, and write code
to remove those groups of atoms that are coming from the exclusion SMARTS.
Any ideas for PYTHON/RDkit code? Something like
test_smiles = 'c1ccccc1'
inclusion_pattern = '[a]1:[a]:[a]:[a]:[a]:[a]1'
exclusion_pattern = '[n]1:[c]:[c]:[c]:[c]:[c]1'
etc...
Hmmm... any other ideas, suggestions, comments?
Thanks again.
Regards,
Jim Metz
-----Original Message-----
From: Chris Earnshaw <cgearns...@gmail.com>
To: James T. Metz <jamestm...@aol.com>
Cc: Rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net>
Sent: Sun, Sep 24, 2017 4:01 am
Subject: Re: [Rdkit-discuss] need SMARTS query with a specific exclusion
Hi Jim
It can be done with recursive SMARTS, though the syntax is a bit
painful This may do what you want -
[$(a);!$(n1(C)ccc(=O)nc1=O);!$(c1cc(=O)nc(=O)n1C);!$(c1c(=O)nc(=O)n(C)c1);!$(c(=O)1nc(=O)n(C)cc1);!$(n1c(=O)n(C)ccc1=O);!$(c(=O)1n(C)ccc(=O)n1)]:1:a:a:a:a:a:1
Its basically the general 6-ring aromatic pattern a:1:a:a:a:a:a:1,
with recursive SMARTS applied to the first atom to ensure that this
can't match any of the 6 ring atoms in your undesired system.
Regards,
Chris Earnshaw
On 24 September 2017 at 05:04, James T. Metz via Rdkit-discuss
<rdkit-discuss@lists.sourceforge.net> wrote:
> Hello,
>
> Suppose I have the following molecule
>
> m = 'CN1C=CC(=O)NC1=O'
>
> I would like to be able to use a SMARTS pattern
>
> pattern = '[a]1:[a][a]:[a]:[a]:a]1'
>
> to recognize the 6 atoms in a typical aromatic ring, but
> I do not want to recognize the 6 atoms in the molecule,
> m, as aromatic. In other words, I am trying to write
> a specific exclusion.
>
> Is it possible to modify the SMARTS pattern to
> exclude the above molecule? I have tried using
> recursive SMARTS, but I can't get the syntax to
> work.
>
> Any ideas? Thank you.
>
> Regards,
> Jim Metz
>
>
>
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