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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