Hi Sebastian,
I'm a bit mystified by this and am going to have to dig around a bit to see
if I can figure out what's going on.
-greg
On Wed, May 9, 2018 at 9:59 PM Sebastian Wandernoth <s_wandern...@gmx.de>
wrote:
> Hey guys,
>
> any chance to get an answer on my issue? Even if the answer is that this
> feature is currently not included in RDKit, it would still be helpful :-)
>
> Best regards
> Sebastian
>
> *Gesendet:* Dienstag, 24. April 2018 um 09:33 Uhr
> *Von:* "Sebastian Wandernoth" <s_wandern...@gmx.de>
> *An:* rdkit-discuss@lists.sourceforge.net
> *Betreff:* [Rdkit-discuss] atom mapping in reaction searches
> Hey guys,
>
> I'm still working on my search engine for reactions and I'm a bit puzzled
> as to what RDKit does with atom mapping information.
> I'm still working with the PostgreSQL cartridge version 0.73.0, which
> should correspond to the release 2017.9.3.
>
> I'm starting off with this example reaction which is fully mapped
> ([S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1)
>
> If I'm using a completely unmapped reaction as query I expect to find this
> one. So the following should return TRUE:
>
> SELECT
> reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1')
> @> reaction_from_smarts('S1C(Cl)=NC=C1>>S(=O)(=O)1OCC(C2SC(Cl)=NC=2)=N1');
>
> ... which it does
>
>
> Next step is to map one atom correctly in the query and try again. I still
> expect this to return TRUE:
>
> SELECT
> reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1')
> @>
> reaction_from_smarts('[S:1]1C(Cl)=NC=C1>>S(=O)(=O)1OCC(C2[S:1]C(Cl)=NC=2)=N1');
>
> ... which it doesn't
>
>
> With two atoms mapped correctly in the query, I wouldn't expect to get
> different results from the previous try:
>
> SELECT
> reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1')
> @>
> reaction_from_smarts('[S:1]1C(Cl)=NC=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1]C(Cl)=NC=2)=N1');
>
> ... this one however returns TRUE again
>
>
> Final try I did was to include a wrong mapping in the query. I definitely
> would expect to get back FALSE here (I'm mapping one sulfur atom to a
> carbon atom and a nitrogen to an oxygen):
>
> SELECT
> reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1')
> @>
> reaction_from_smarts('[S:1]1C(Cl)=[N:2]C=C1>>S(=[O:2])(=O)1O[CH2:1]C(C2SC(Cl)=NC=2)=N1');
>
> ... however this returns TRUE yet again.
>
> Playing around with it a bit more I found that whatever single atom I map
> in the query, I always get back FALSE and if I map more than one atom, I
> always get back TRUE...
> Does this have something to do with the parameter 'rdkit.
> threshold_unmapped_reactant_atoms'? My suspicion is that RDKit only
> counts how many atoms are mapped and not compare them to the correct
> mapping. Can you confirm this?
> Is there any way at all to include atom mapping in the query to filter the
> reactions the way I want to?
>
>
> I hope you guys can help me here. Sorry for the lengthy question, but I
> wanted to include as much information as possible for you to pinpoint the
> issue.
>
> Best regards
> Sebastian
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