Hello,
I am running rdkit version 2017.09.3.
I read an sdf with
supplier = SDMolSupplier('try/try.sdf')
I then took the first mol from supplier and named it mol. I then performed
fragmented = Recap.RecapDecompose(mol, minFragmentSize=3). I looped through its children with:
fragmented_children_smiles = []
for key in list(fragmented_children):
fragmented_children_smiles.append(fragmented.GetAllChildren()[key].smiles)
smile = fragmented_children_smiles[0]
for key in list(fragmented_children):
fragmented_children_smiles.append(fragmented.GetAllChildren()[key].smiles)
smile = fragmented_children_smiles[0]
Now, smile is '[*]Nc1ccc(OC)cc1C([*])=O' . Theoretically, smile should of course be a substructure of mol. But if I check this like this:
smile = MolFromSmiles(smile)
if mol.HasSubstructMatch(smile):
print('match smile!!!!')
nothing gets printed. Apparently, this is because of the [*], if I delete them, there is a match. But why are they there in the first place? Why does HasSubstructMatch not work when they are included? And, most importantly, can I solve this problem, without going trough the code and deleting all '[*]'? First of all, I do not know if the smiles would still make sense if I did that and also, there are some structures like '([*])' and '()' is of course not valid, so deleting them for a large number of smiles would be really bothersome...
Thank you for your help!
Regards,
Larissa Pusch
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