I have a problem with the following smiles [O][N][C]([C])[C] and related smiles. When I try to add hydrogens nothing happens. The correct formula is C3H7NO. It looks to be some problem with the square brackets but I don't know how to automatically adjust the smiles so that it will add the right amount of H's to match the chemical formula.
Background: I have a number of CIF files and I want to extract the 3D coordinate information of the molecules but the H's are not always listed in the coordinate section (despite being in the formula). To fix this I was hoping to add hydrogens with openbabel. Thanks, Scott -- View this message in context: http://forums.openbabel.org/Adding-Hydrogens-not-working-tp4655446.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
