I will try to take a look in more detail this evening On Sat, 20 Apr 2019 at 07:55, Haris Hasic <haris-ha...@hotmail.com> wrote:
> Hello Greg, > > thank you for your quick reply. When I run AllChem.SanitizeMol(product) > the error increases and more bonds that shouldn't be there are added. For > all of them, the problem is the same, in the product they are marked as > SINGLE and in the reactants as AROMATIC. Picture is in the attachment. > > Note 1: I've also tried all the possible combination of sanitation (none, > just reactants, just products, everything) for this example just to be > sure, but the best result I get (the one in my previous question) is when I > don't run SanitizeMol on the product. > Note 2: It also happens to other examples (I added the pictures in the > examples and the SMARTS below for reproduction), it's not just this one. > Maybe I did something wrong in the code, but what I'm doing is pretty > straightforward. I display it as a picture, but I also print the raw > results just to be sure. I always get the same result, the SINGLE - > AROMATIC mismatch. > > Add. Ex. 1: " > Cl[CH2:1][C:2](=[O:3])[NH:4][c:5]1[c:6]([OH:7])[cH:8][cH:9][c:10]2[cH:11][cH:12][cH:13][cH:14][c:15]12>>[CH2:1]1[C:2](=[O:3])[NH:4][c:5]2[c:6]([cH:8][cH:9][c:10]3[cH:11][cH:12][cH:13][cH:14][c:15]23)[O:7]1" > > Add. Ex. 2: "Cl[C@H > :1]([C:2]([NH:3][c:4]1[c:5]([OH:6])[c:7]([CH3:8])[cH:9][c:10]([CH3:11])[cH:12]1)=[O:13])[CH2:14][CH:15]([CH3:16])[CH3:17]>>[C@ > @H:1]1([CH2:14][CH:15]([CH3:16])[CH3:17])[C:2](=[O:13])[NH:3][c:4]2[c:5]([c:7]([CH3:8])[cH:9][c:10]([CH3:11])[cH:12]2)[O:6]1 > " > > Add. Ex. 3: " > O[C:1](=[O:2])[c:3]1[cH:4][cH:5][c:6]([C:7]2([c:8]3[cH:9][cH:10][cH:11][cH:12][cH:13]3)[S:14][CH2:15][CH2:16][S:17]2)[cH:18][cH:19]1.[cH:20]1[cH:21][c:22]2[c:23]([o:24]1)[CH2:25][NH:26][CH2:27][CH2:28]2>>[C:1](=[O:2])([c:3]1[cH:4][cH:5][c:6]([C:7]2([c:8]3[cH:9][cH:10][cH:11][cH:12][cH:13]3)[S:14][CH2:15][CH2:16][S:17]2)[cH:18][cH:19]1)[N:26]1[CH2:25][c:23]2[c:22]([cH:21][cH:20][o:24]2)[CH2:28][CH2:27]1 > " > > Kind regards, > Hasic Haris, MSc > Tokyo Institute of Technology > ------------------------------ > *From:* Greg Landrum <greg.land...@gmail.com> > *Sent:* 20 April 2019 06:43 > *To:* Haris Hasic > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] Question about bond aromaticity change > detection > > 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 > >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
