Hi Susan,
adding explicit hydrogens is an expensive operation that you normally try
to avoid unless you have to (e.g., because you need to deal with 3D
molecule coordinates).
I would rather change the query in order to use implicit H queries, e.g.
something like:
q =
Sorry I replied too soon, just another quick question.
I am trying to use the postgres cartridge. Is there any function to add
hydrogens to the molecules once in the database? Or should this be done as
a preprocessing step beforehand? E.g. I have a .smi or .sdf should all the
molecules already
Ah, great thanks Paolo!
On Fri, Jul 22, 2022 at 11:44 AM Paolo Tosco
wrote:
> Hi Susan,
>
> If you use [#1] in your SMARTS query, for your molecule to match there
> should be a real hydrogen atom in your molecule graph, while in your
> molecule you only have implicit hydrogens, unless you
Hi Susan,
If you use [#1] in your SMARTS query, for your molecule to match there
should be a real hydrogen atom in your molecule graph, while in your
molecule you only have implicit hydrogens, unless you explicitly add them
calling Chem.AddHs():
print(Chem.AddHs(m).HasSubstructMatch(q))
True
Hi all,
I am trying to do substructure search using query atom lists, but I am
seeing unexpected behaviour when I have hydrogen in my query atom list…
import rdkit
print(rdkit.__version__)
from rdkit import Chem
>>2022.03.2
## having carbon in the query atom list seems to work as
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