Hi Greg,
Thanks a lot for the explanation.
It makes things clearer now.
Well the reason I'm doing SMARTS-SMARTS match is because I would like to
match functional groups with the reactants in reactions.
Regards,
Christos
Christos Kannas
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On 5 March 2014 04:44, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Christos,
>
>
> On Tue, Mar 4, 2014 at 3:46 PM, Christos Kannas <chriskan...@gmail.com>wrote:
>
>> Hi all,
>>
>> Why does the following happen?
>>
>> In [1]: from rdkit import Chem
>> In [2]: from rdkit.Chem import AllChem
>> In [3]: from rdkit.Chem import Draw
>>
>> In [4]: patt = Chem.MolFromSmarts("[CH;D2;!$(C-[!#6;!#1])]=O")
>>
>> In [5]: z2 = Chem.MolFromSmarts("[*]-C-C([H])(=O)", 1)
>> In [6]: print Chem.MolToSmiles(z2)
>> [*]CC=O
>> In [7]: print Chem.MolToSmarts(z2)
>> *-C-[C&!H0]=O
>> In [9]: z2.HasSubstructMatch(patt)
>> Out[9]: False
>>
>> In [10]: z3 = Chem.MolFromSmiles(Chem.MolToSmiles(z2))
>> In [11]: print Chem.MolToSmiles(z3)
>> [*]CC=O
>> In [12]: print Chem.MolToSmarts(z3)
>> [*]-[#6]-[#6]=[#8]
>> In [13]: z3.HasSubstructMatch(patt)
>> Out[13]: True
>>
>> Shouldn't be that z2 and z3 have the same information?
>>
>
> The way SMARTS/SMARTS matches is handled is different than the way
> SMARTS/SMILES matches works.
> The short answer is that when doing a SMARTS/SMARTS match, the RDKit
> compares the queries to each other; when doing a SMARTS/SMILES match, on
> the other hand, it checks to see if the atoms in the SMILES molecule match
> the queries in the SMARTS molecule.
>
> A bit longer answer:
> Molecules built using MolFromSmiles contain Atoms, molecules built using
> MolFromSmarts contain QueryAtoms. Both atoms and QueryAtoms have a Match()
> method that takes another Atom or QueryAtom as an argument and returns
> whether or not the two match.
> The substructure matching code makes heavy use of this Match() method.
> QueryAtom.Match(Atom) checks to see if the Atom satisfies the query.
> QueryAtom.Match(QueryAtom) checks to see if the queries on the atoms are
> the same. This uses a crude approach that is easy to fool, but I assume
> that a SMARTS-SMARTS match is not a frequent thing someone wants to do.
> query-query matching is also not a particularly easy problem to solve in a
> general way.
>
> -greg
>
>
>
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