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 have explicit hydrogens?
Thanks,
Susan
On Fri, Jul 22, 2022 at 11:51 AM Susan Leung <susanhle...@gmail.com> wrote:
> Ah, great thanks Paolo!
>
> On Fri, Jul 22, 2022 at 11:44 AM Paolo Tosco <paolo.tosco.m...@gmail.com>
> 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 explicitly add them
>> calling Chem.AddHs():
>>
>> print(Chem.AddHs(m).HasSubstructMatch(q))
>> True
>>
>> Cheers,
>> p.
>>
>> On Fri, Jul 22, 2022 at 12:13 PM Susan Leung <susanhle...@gmail.com>
>> wrote:
>>
>>> 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 expected
>>>
>>> q = Chem.MolFromSmarts('[#17,#6]-[#6]-[#17]')
>>>
>>> m = Chem.MolFromSmiles('ClCCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>> m = Chem.MolFromSmiles('CCCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>>
>>>
>>> >>True
>>>
>>> >>True
>>>
>>>
>>>
>>> ## having hydrogen in the query atom list doesn't work as expected
>>>
>>> q = Chem.MolFromSmarts('[#17,#1]-[#6]-[#17]')
>>>
>>> m = Chem.MolFromSmiles('ClCCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>> m = Chem.MolFromSmiles('CCl')
>>>
>>> print(m.HasSubstructMatch(q))
>>>
>>>
>>>
>>> >>True
>>> >>False
>>>
>>>
>>>
>>> Best wishes,
>>>
>>>
>>>
>>> Susan
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
