HI Hasic, The products of reactions are not sanitized, which means that aromaticity perception has not been run. Try calling Chem.SanitizeMol on the reaction products and see if that helps.
-greg On Fri, Apr 19, 2019 at 12:51 PM Haris Hasic <haris-ha...@hotmail.com> wrote: > Hello guys, > > I'm a artificial intelligence major, so I don't know a lot about > aromaticity definitions in chemistry but since I'm doing some research in > that field I run into a weird problem with identifying the aromatic bonds. > I initialize the reaction as follows: > > rxn = > "O[C:1](=[O:2])[c:3]1[cH:4][cH:5][c:6]([F:7])[c:8](-[c:9]2[c:10]([F:11])[cH:12][cH:13][cH:14][c:15]2[F:16])[n:17]1.[CH3:18][C@H > :19]1[CH2:20][N:21]([c:22]2[c:23]([NH2:24])[cH:25][n:26][c:27]3[c:28]2[CH2:29][CH2:30][O:31]3)[CH2:32][C@ > @H:33]([NH:34][C:35](=[O:36])[O:37][C:38]([CH3:39])([CH3:40])[CH3:41])[C@ > @H:42]1[O:43][Si:44]([CH3:45])([CH3:46])[C:47]([CH3:48])([CH3:49])[CH3:50]>>[C:1](=[O:2])([c:3]1[cH:4][cH:5][c:6]([F:7])[c:8](-[c:9]2[c:10]([F:11])[cH:12][cH:13][cH:14][c:15]2[F:16])[n:17]1)[NH:24][c:23]1[c:22]([N:21]2[CH2:20][C@H > :19]([CH3:18])[C@ > @H:42]([O:43][Si:44]([CH3:45])([CH3:46])[C:47]([CH3:48])([CH3:49])[CH3:50])[C@H > :33]([NH:34][C:35](=[O:36])[O:37][C:38]([CH3:39])([CH3:40])[CH3:41])[CH2:32]2)[c:28]2[c:27]([n:26][cH:25]1)[O:31][CH2:30][CH2:29]2" > > reaction = AllChem.ReactionFromSmarts(rxn) > AllChem.SanitizeRxn(reaction) > reaction.Initialize() > products = reaction.GetProducts() > reactants = reaction.GetReactants() > > The problem arises when I check whether the atom environments have > changed. That includes changes in neighborhood size, neighboring atom types > and bond types. But, for some reason, it detects different bond types in > the reactant molecule and product molecule, even if the structure does not > change at all. Pictures are in the links and in the attachment of the mail > The bond 26 - 27 should technically not be highlighted, but it is because > the bond types are different. In the reactant it says AROMATIC, but in the > product it is SINGLE. Is it correct, in a chemical sense, or is it a bug > in RDKit aromaticity calculation? How can I avoid adding this bond? > > Reactant 1: http://prntscr.com/ne3n44 > Reactant 2: http://prntscr.com/ne3p6x > Product: http://prntscr.com/ne3pfw > > This is the code I'm using to compare the bond types : > > product_mol.GetBondBetweenAtoms(product_atom_ind1, > product_atom_ind2).GetBondType() != > reactant_mol.GetBondBetweenAtoms(reactant_atom_ind1, reactant_atom_ind2 > ).GetBondType() > > if I print out the results, the output is: > > > >>> SINGLE - AROMATIC > > > Thank you for the help and if you need more background info, please let me > know. I apologize if the question was asked before. > > > Kind regards, > Hasic Haris, MSc > Tokyo Institute of Technology > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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