Hi Alexis,

If you have substructures with substitutions at a single atom, it tends to
be simpler to use Chem.ReplaceSubstructs to do this. This is, however, not
the case here (or in general for bioisosteric replacement)

The most flexible way to do what you're looking for is to use the RDKit's
chemical reaction functionality and create one reaction per isosteric
replacement you want to make. Here's a simple example showing the "amide ->
1,2,3 triazole" replacement:

In [11]: triazoleRxn = AllChem.ReactionFromSmarts('[*
:1]C(=O)N[*:2]>>[*:1]c1cn([*:2])nn1')


And here's how you'd use that to perform a replacement:

In [12]: ps = triazoleRxn.RunReactants((Chem.MolFromSmiles('C1CC1C(=O)
Nc1ccccc1'),))

In [13]: Chem.MolToSmiles(ps[0][0])
Out[13]: 'c1ccc(-n2cc(C3CC3)nn2)cc1'


Notice that I added the bioisostere itself to the products of the reaction
as SMILES. You don't want query features there.

I hope this helps,
-greg




On Mon, Feb 5, 2018 at 10:07 AM, Alexis Parenty <
alexis.parenty.h...@gmail.com> wrote:

> 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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