Dear Alexis,
as far as I know, this would be the SMARTS string with recursive pattern:
[$(C1=CN=[CH1][CH1]=N1),$(C1=[CH1]N=C[CH1]=N1),$(C1=[CH1]N=[CH1]C=N1),$(OC1=[CH1]C=NO1),$(OC1=NOC=[CH1]1),$(C1=CN=C([NX3])O1),$([#6X4]([#6X4](F)(F)(F))[NX3]),$(C(C#N)=NO),$(N1N=NN=C1),$(N1N=NC=[N]1),$(N1N=NC=[CH1]1),$(C1=NOC=N1),$(C1=NN=C[OX2]1),$(C1=NN=C[NH1]1),$([C]1(COC1)[OX2]),$([C]1(COC1)[NX3]),$(C([NX3H1])=N[CX4H3]),$([CX4]1([CX4][CX4]1)[NX3]),$([#16X4+2]([NX3])([OX1-])([OX1-])),$([#16X4]([NX3])(=[OX1])(=[OX1])),$([CX3](=[CX3])(F)),$([OX2][CX3](=[OX1])),$([NX3][CX3](=[OX1]))]
I don't know what you want to match specifically, but some of your pattern
won't match SMILES that are written as the aromatic form of the molecule
instead of the localized form.
Best wishes,
Emanuel
Alexis Parenty <alexis.parenty.h...@gmail.com> schrieb am Mo., 5. Feb. 2018
um 10:07 Uhr:
> Dear RDKiters,
>
> I would like to generate the bioisosters of amides from a large list of
> structures:
>
> The smarts patterns for the bioisosters of amides I am interested in is:
>
> smarts_path = ['C1=CN=[CH1][CH1]=N1', 'C1=[CH1]N=C[CH1]=N1',
> 'C1=[CH1]N=[CH1]C=N1', 'OC1=[CH1]C=NO1', 'OC1=NOC=[CH1]1',
> 'C1=CN=C([NX3])O1', '[#6X4]([#6X4](F)(F)(F))[NX3]', 'C(C#N)=NO',
> 'N1N=NN=C1', 'N1N=NC=[N]1', 'N1N=NC=[CH1]1', 'C1=NOC=N1', 'C1=NN=C[OX2]1',
> 'C1=NN=C[NH1]1', '[C]1(COC1)[OX2]', '[C]1(COC1)[NX3]',
> 'C([NX3H1])=N[CX4H3]', '[CX4]1([CX4][CX4]1)[NX3]',
> '[#16X4+2]([NX3])([OX1-])([OX1-])', '[#16X4]([NX3])(=[OX1])(=[OX1])',
> '[CX3](=[CX3])(F)', '[OX2][CX3](=[OX1])', '[NX3][CX3](=[OX1])']
>
> How would you best "disconnect the amide moiety" of a structure and
> "replace" it with the recursive smarts pattern of its bioisosters? The
> bioster matching patern above must be contained within a single smarts, so
> I think I need recursive smarts, right?
>
> Any directions would be very much appreciated.
>
> Best,
>
> Alexis
>
>
>
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