Hi
Dot-disconnected fragments are not going to work for this, as you describe.
You need to use recursive SMARTS (see
https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html section
4.4). Something like:
Clc[$(cBr);$(ccBr);$(cccBr)]
should (I hope!) be a reasonable starting point.
Chris Earnshaw
On Wed, 29 Jan 2020 at 11:12, Alexis Parenty <alexis.parenty.h...@gmail.com>
wrote:
> Hi everyone,
>
>
>
> Is there a way to get a substructure match of regioisomers using a smarts
> by separating the fragments with “.”:
>
>
>
> The following approach works but is too permissive since it will also
> match structures with a bromide or a chloride linked to a aliphatic
> carbon...
>
>
> [image: image.png]
>
>
>
> mol_smiles_structure = Chem.MolFromSmiles("Clc1cc(Br)ccc1")
>
> mol_smarts_fragment = Chem.MolFromSmarts("c1ccccc1.[Cl].[Br]")
>
> print(mol_smiles_structure.HasSubstructMatch(mol_smarts_fragment))
>
> ð True
>
>
>
>
>
> mol_smiles_structure = Chem.MolFromSmiles("ClCc1cc(Br)ccc1")
>
> print(mol_smiles_structure.HasSubstructMatch(mol_smarts_fragment))
>
> ð True
>
>
>
> If I specify that the Br and the Cl need to be attached to an aromatic to
> make it less permissive, it no longer match because I cannot specify that
> the two general aromatics [a] also belong to the benzene ring... (i,e. it
> tries to look for 8 aromatics instead of six...)
>
> mol_smiles_structure = Chem.MolFromSmiles("Clc1cc(Br)ccc1")
>
> mol_smarts_fragment = Chem.MolFromSmarts("c1ccccc1.[a][Cl].[a][Br]")
>
> print(mol_smiles_structure.HasSubstructMatch(mol_smarts_fragment))
>
> ð False
>
>
>
> Thanks!
>
> Alexis
>
>
>
>
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