Hi Toby and Greg,
Thanks a lot for your answers.
I'll use Toby's solution as it fits my situation better, as I'll have to do
this only for the compounds that will be used, and not on the reactants.
Best,
Christos
On 19 February 2014 10:40, Toby Wright <toby.wri...@inhibox.com> wrote:
> Hi Christos,
>
> If you add hydrogens to m3 after creating it in RDKit then both m1 and m2
> are recognised as substructures of m3. See below for how I achieved this:
>
> >>> from rdkit import Chem
> >>> m1 = Chem.MolFromSmarts("[C:3][C:4](=[O:5])[O:6]([H:100])")
> >>> m2 = Chem.MolFromSmarts("[C:3][C:4](=[O:5])[O;H:6]")
> >>> m3 = Chem.MolFromSmiles("CCCCCCCCCCCCCC(=O)O")
> >>> m3H = Chem.AddHs(m3)
> >>> m3.HasSubstructMatch(m1)
> False
> >>> m3H.HasSubstructMatch(m1)
> True
> >>> m3.HasSubstructMatch(m2)
> True
> >>> m3H.HasSubstructMatch(m2)
> True
>
> Hope that helps.
>
> Yours,
>
> Toby Wright
>
> --
> InhibOx Ltd, Oxford
>
>
>
> On 19 February 2014 10:25, Christos Kannas <chriskan...@gmail.com> wrote:
>
>> Hi all,
>>
>> At my current project I'm working on reaction based multiobjective de
>> novo design.
>> And I have a set of reactions that I have converted into SMIRKS and
>> reaction SMARTS..
>>
>> The problem I have is that when I have a reactant pattern in SSMARTS, as
>> required by SMIRKS, that has explicit mapped Hydrogens that play a role in
>> reaction, and I request a substructure search matching to a compound that
>> has the substructure in question it can not find a match. But when I change
>> the pattern to not have explicit mapped hydrogens the substructure matching
>> search is successful.
>>
>> To help you understand I've created this small IPython Notebook
>> http://nbviewer.ipython.org/gist/CKannas/9089271
>>
>> Can you give me the reasons why this happens?
>>
>> Best,
>> Christos
>>
>> --
>>
>> Christos Kannas
>> Researcher
>> Ph.D Student
>>
>> Mob (UK): +44 (0) 7447700937
>> Mob (Cyprus): +357 99530608
>>
>> [image: View Christos Kannas's profile on
>> LinkedIn]<http://cy.linkedin.com/in/christoskannas>
>>
>>
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>
--
Christos Kannas
Researcher
Ph.D Student
Mob (UK): +44 (0) 7447700937
Mob (Cyprus): +357 99530608
[image: View Christos Kannas's profile on
LinkedIn]<http://cy.linkedin.com/in/christoskannas>
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