Thanks Noel When do you think this fix will get into the public version? I found a not-soelegant workaround using the Cactus server, so no great hurry.
Sorry about the title :) I hit send before I was done typing Best regards, Jan > On 22 Mar 2017, at 21:24, Noel O'Boyle <baoille...@gmail.com> wrote: > > This is already fixed in my development code, where I have changed the > handling of implicit hydrogens throughout the library: > >> obabel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF | obabel -iinchi -osmi > ============================== > *** Open Babel Warning in InChI code > #1 :Proton(s) added/removed > 1 molecule converted > CCOC(=O)c1ccc(cc1)[NH3+] > 1 molecule converted > > The problem is that the current code just gives the InChI a charged > nitrogen and tells it to guess the number of hydrogens (aka apply the > InChI implicit valence model). The new code gives it the number of > implicit hydrogens. > > BTW, consider a less general subject line in future. :-) > > Regards, > - Noel > > > On 18 March 2017 at 15:00, Jan Halborg Jensen <jhjen...@chem.ku.dk> wrote: >> Hi all >> >> babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF >> >> gives >> >> InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1 >> >> but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+] >> >> I use obabel -oinchi temp3.inchi -osmi >> >> Any help appreciated >> >> Best regards, Jan >> >> ------------------------------------------------------------------------------ >> 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
