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 of the match results you get back
-greg
On Tue, Jun 7, 2022 at 7:23 PM Eduardo Mayo <eduardomayoya...@gmail.com>
wrote:
> 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 the pattern, so I tried adding the ring size constrain.
> [image: image.png]
> Now the pattern I am using is this:
> [*;R2r6]~1~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~1
>
> It worked quite well but now it fail to find matches in this molecule
> [image: image.png]
>
> Does anyone know what I am doing wrong??
>
> Code:
> -------
>
> m1 = Chem.MolFromSmiles(
> "c1ccc2cc3c(ccc4c5ccccc5c5cc6c7cc8c(cc7c6cc5c34)c3cccnc38)cc2c1")
> m2 = Chem.MolFromSmiles(
> "b1cccc2c1c1c(c3ccc4ccc4c3c3c4c5cc[nH]c5c4c13)c1ncc3ccccc3c21")
> m3 = Chem.MolFromSmiles(
> "b1ccbc2c1c1ccoc1c1c2c2ccsc2c2[nH]c3ncc4c(c3c21)=c1ncccc1=4")
>
> p = Chem.MolFromSmarts("[*;R2]~1~[*;R2]~[*;R2]~[*;R2]~[*;R2]~[*;R2]~1")
> for m, expected_value in zip([m1,m2,m3],[1,2,2]):
> print(len(m.GetSubstructMatches(p)) == expected_value)
>
>
> p = Chem.MolFromSmarts(
> "[*;R2r6]~1~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~[*;R2r6]~1")
> for m, expected_value in zip([m1,m2,m3],[1,2,2]):
> print(len(m.GetSubstructMatches(p)) == expected_value)
>
> All the best,
> Eduardo
>
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