I use babel to remove salts from smiles and I have encountered that babel changes heterocyclic compounds with nitrogens, see example below. Does anyone have any suggestions why this might happen?
input: C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F command: obabel -ismi file_in.smi -r -osmi -O file_out.smi output: C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1 thanks! Elisabet -- View this message in context: http://forums.openbabel.org/removing-salts-changes-the-structure-and-add-bonds-to-heterocyclic-compounds-with-nitrogen-tp4660003.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ 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
