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

[theozh <th...@gm...>]

Hi Paolo,

thank you very much for your detailed answer.
I tried to reproduce your last suggestion (but I don't have Jupyter Notebook).
However, my bonds are still SINGLE and DOUBLE instead of UNSPECIFIED.
Does this maybe depend on the RDKit Version, I have 2019.03... ?

Maybe, I should update and need to investigate further.
Theo.


Am 19.05.2020 um 16:44 schrieb Paolo Tosco:
> 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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