Hi I don't think the reaction SMARTS does specify a change in the charges. The N and O have to be charged in order to match the reactant pattern but they won't be altered by the transformation. If you specify that the product atoms are explicitly neutral I think you'll get the result you want - [#8-:2]-[#7+:1]=[O:3]>>[O+0:2]=[N+0:1]=[O:3]
Chris Earnshaw On 9 October 2017 at 15:57, Chris Murphy <chris.mur...@schrodinger.com> wrote: > Hi, > > I am using rdChemReactions to perform substructure transformations as > defined by configurable reaction smarts. When I create the reaction and run > a mol through it that I expect to be transformed by the indicated reaction > smarts, I see that the bonds have been changed according to the smarts, but > the charges are not changed. > > I am using the following smarts to define the transformation: > [#8-:2]-[#7+:1]=[O:3]>>[O:2]=[N:1]=[O:3] > > The input molecule is as follows: > > Mrv16c5 10061718252D > > 9 9 0 0 0 0 999 V2000 > -0.5916 -0.0678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3060 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3060 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.5916 -1.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.1229 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.1229 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.5916 0.7572 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 > -1.3061 1.1697 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 > 0.1229 1.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 2 0 0 0 0 > 2 3 1 0 0 0 0 > 3 4 2 0 0 0 0 > 4 5 1 0 0 0 0 > 5 6 2 0 0 0 0 > 6 1 1 0 0 0 0 > 1 7 1 0 0 0 0 > 7 8 1 0 0 0 0 > 7 9 2 0 0 0 0 > M END > $$$$ > > and the output ends up being: > > RDKit 2D > > 9 9 0 0 0 0 0 0 0 0999 V2000 > -1.3061 1.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -0.5916 0.7572 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > 0.1229 1.1697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > -0.5916 -0.0678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3060 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.1229 -0.4803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3060 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.1229 -1.3054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -0.5916 -1.7179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 2 0 > 2 3 2 0 > 4 2 1 0 > 4 5 2 0 > 6 4 1 0 > 5 7 1 0 > 8 6 2 0 > 7 9 2 0 > 9 8 1 0 > M CHG 2 1 -1 2 1 > M END > > It seems the that NO bond is successfully converted to a double bond, but > the charges have not been changed, even though the reaction smarts indicates > that they N and O should be changed to neutral. Are there any glaring issues > with using reactions to do transformations like this? > > Thanks! > > -Chris > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
