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

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

Hi Theo,

I don't think the RDKit version should make a difference; did you notice 
that rdmolops.AdjustQueryProperties() does not modify the molecule in 
place, but rather returns a modified copy?

pattern_generic_bonds  =  Chem.AdjustQueryProperties(pattern,  query_params)

That might be the reason. Also, only pattern_generic_bonds will have 
UNSPECIFIED bonds, the mols will still have SINGLE and DOUBLE bonds.

Feel free to contact me off-list if you need help with the above.

Cheers,
p.

On 19/05/2020 17:01, theozh wrote:
> 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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