Hi Noel, Many thanks for your answer which is exactly what I'm looking for. However, for some reason the hydrogens are still not being added when I use the command. I've attached the CIF file in case I have missed something.
Thanks, Scott On 10 September 2012 22:46, Noel O'Boyle <baoille...@gmail.com> wrote: > (Forgot to cc to the list) > > Hi Scott, > > The missing information is what bonds connect the heavy atoms as > without this it's not possible to deduce where (and how many) the > hydrogens are. But there should be no need to worry about this. Just > use Open Babel to convert the cif file and add hydrogens: > > obabel myfile.cif -O myfile.xyz -h > > Behind the scenes, OB determines (i.e. wise guesses) the bond orders > (i.e. single, double, etc.), and then "-h" tells it to add hydrogens. > These are added in 3D space based on the coodinates of the > neighbouring atoms. > > > On 8 September 2012 18:01, scott_m <js...@cam.ac.uk> wrote: > > 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 > >
ACEOXM.cif
Description: Binary data
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