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
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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