It might be a good idea to sit down while you read this. You seem to have forgotten that Implicit Valence is not implicit valence, but rather the number of bonds to an atom. atomtyp.txt says 3 bonds to a boron. The =O and the OH is two bonds, so there's one missing. That's the reason for the two thousand different impval statements for nitrogen. Although three actual Implicit Valences would cover the lot, we go around the houses catching all the different possibilities of bond orders, etc.
So feel free to edit atomtyp.txt to patch it up for Boron. But better still, all in favor of replacing this impval business, say "aye". - Noel On 26 March 2013 21:50, Craig James <cja...@emolecules.com> wrote: > Anyone know what's going on with boron? The atomtyp.txt file looks right to > me. A double bond to oxygen seems to mess it up. I'm no chemist, but > everything I can find says this is just wrong. > > > $ echo "O=BO" | obabel -i smi -o smi > O=[BH]O > > Note the extra H on the boron atom. Here's the same thing as an SDF with > the "add H" option. Note that it adds TWO hydrogens, one for the -OH, and > an extra (incorrect) one for [BH]. > > $ echo "O=BO" | obabel -i smi -o sdf -h > > OpenBabel03261314442D > > 5 4 0 0 0 0 0 0 0 0999 V2000 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 2 0 0 0 0 > 2 3 1 0 0 0 0 > 2 4 1 0 0 0 0 > 3 5 1 0 0 0 0 > M END > $$$$ > > Thanks, > Craig > > > > ------------------------------------------------------------------------------ > Own the Future-Intel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
