Hi everyone,
I am new to rdkit but I am already impressed by its vibrant community. I
have a question regarding deleting substructure. In the RDKIT
documentation, this is a snippet of code describing how to delete
substructure:
>>>m = Chem.MolFromSmiles("CC(=O)O")
>>>patt =
Hi Chenyang,
If you're really interested in counting the number of times the
substructure appears, you can do that much quicker with
`GetSubstructMatches()`:
In [2]: m = Chem.MolFromSmiles('CC(C)CCO')
In [3]: len(m.GetSubstructMatches(Chem.MolFromSmarts('[CH3;X4]')))
Out[3]: 2
Is that
Hi Greg,
Thanks for a prompt reply. I did try "GetSubstructMatches()" and it returns
correct numbers of substructures for CH3COOH. The potential problem with
this approach is that if the molecule is getting complicated, it will
possibly generate duplicate numbers for certain functional groups.
The solution that Hongbin proposes to the double-counting problem is a good
one. Just be sure to sort your substructure queries in the right order so
that the more complex ones come first.
Another thing you might think about is making your queries more specific.
For example, as you pointed out
Hi, Chenyang, You don't need to delete the substructure from the molecule.
Just check whehter the mapped atoms have been matched. For example:
m = Chem.MolFromSmiles('CC(=O)O')OH = Chem.MolFromSmarts('[OH]')COOH =
Chem.MolFromSmarts('C(O)=O')
m.GetSubstructMatches(OH)>>
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