I note in passing that the development code has an option to preserve the aromaticity as read in SMILES, but Geoff's point stands that the structures are identicial and should be read identically by any toolkit.
- Noel On 7 June 2017 at 04:16, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: > I use babel to remove salts from smiles and I have encountered that babel > changes heterocyclic compounds with nitrogens, see example below. > > > This will trigger aromaticity perception, but the structure is unchanged. > > input: > C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F > > vs. > > output: C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1 > > > If I depict these, e.g. > https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5%5BnH%5D4.OC(=O)C(F)(F)F/image > https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)n1c(=O)%5BnH%5Dc2cc(Cl)ccc12)NC(=O)c1cc2ccccc2%5BnH%5D1/image > > There is no difference. What's happened is that in the Open Babel > aromaticity model, the [nH]c(=O)n motif is aromatic. In your input, it's > marked as aliphatic. > > The bond orders are otherwise identical. What bonds are added? > > -Geoff > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
