Noel O'Boyle wrote: > 2009/11/18 Craig A. James <cja...@emolecules.com>: >> Tim, >> >> I've run into a problem: OpenBabel add a hydrogen to any potentially-chiral >> carbon that doesn't have four bonds, for example, when it parses "ClC(Br)I" >> (but not "ClC(Cl)Br" since it can't be chiral). I'm pretty sure it's the >> new stereo code that's doing this, but I haven't dug into it yet. > > I don't think this is right: > >>>> mol = pybel.readstring("smi", "ClC(Br)I") >>>> mol.OBMol.NumAtoms() > 4 > > No hydrogen present. ?? Do I misunderstand?
echo "C(Cl)(Br)I" | /usr/local/openbabel/bin/babel -i smi -o can -xh Cl[CH](Br)I It's the "-xh" option, if you do "babel -Hcan" you'll see this: h explict hydrogen form, e.g. [CH3][CH3] We added this specifically so that you can carry hydrogens through from a user's drawing to a SMARTS expression. It's a hack, for sure, but incredibly useful in real life. In Python, you'd have to set the "-xh" option for the SMILES writer, using whatever function pybel offers for that. Craig ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel