Re: [Rdkit-discuss] Substructure search issue with aliphatic/aromatic bonds

[Paolo T. <pao...@gm...>]

Hi Theo,

the lack of match is due to different aromaticity flags on atoms and 
bonds in the larger molecule.

This gist provides some explanation and a possible solution:

https://gist.github.com/ptosco/e410e45278b94e8f047ff224193d7788

Cheers,
p.

On 19/05/2020 14:13, theozh wrote:
> Dear RDKit-users,
>
> I would like to do a very simple substructure search.
> The chapter 3.5 "Substructure Searching" in RDKit Documentation (2019.09.1) is pretty short and doesn't point to a solution. So far, I've learned that you can create your search pattern via Chem.MolFromSmiles() or Chem.MolFromSmarts().
>
> In the below copy&paste minimal example, I want to use the first SMILES in the list as search pattern. I expect 2 matches but I get either 1 or 0 matches. So, I'm doing something wrong. What am I missing?
> Is it about implicit/explicit aromatic and aliphatic bonds or some explicit/implicit hydrogen?
> How to find the first structure in both SMILES?
>
> thank you for any hints,
> Theo.
>
> ### simple substructure search (but doesn't find what is expected)
> from rdkit import Chem
>
> smiles_strings = '''
> C12=CC=CN1NCCC2
> C12=CC=CC(C=C3)=C1N3NCC2
> '''
> smiles_list = smiles_strings.splitlines()[1:]
> print(smiles_list)
>
> pattern = Chem.MolFromSmiles(smiles_list[0])  # MolFromSmiles
> matches = [x for x in smiles_list if Chem.MolFromSmiles(x).HasSubstructMatch(pattern)]
> print(len(matches))   # result: 1, why not 2?
>
> pattern = Chem.MolFromSmarts(smiles_list[0])  # MolFromSmarts
> matches = [x for x in smiles_list if Chem.MolFromSmiles(x).HasSubstructMatch(pattern)]
> print(len(matches))   # result: 0, why not 2?
> ### end of code
>
>
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