I must be missing something really obvious. I tried the -h option but there are no hydrogens in the output.
This is the command I'm using: babel -ipdb hydroxymate.pdb -osmi -h The help page says: Write Options e.g. -xt h Output explicit hydrogens as such How else do you use the h option? Quoting Noel O'Boyle <baoille...@gmail.com>: > babel -H smi gives the "h" output option. See the docs for more info. > > - Noel > > On 24 March 2011 16:10, Douglas Houston <dhous...@staffmail.ed.ac.uk> wrote: >> Hi, >> >> Can anyone tell if if there's a way to get OpenBabel to output >> explicit hydrogens in smiles strings? >> >> I'm trying to define a hydroxymate group, which has a hydroxyl group, >> but the smiles I'm getting from OB at the moment doesn't seem to >> differentiate between a hydroxyl and an ether, i.e. it gives ONC=O >> when I need [OH]NC=O. I thought using -h might do it but no luck. >> >> Regards, >> >> Doug >> >> _____________________________________________________ >> Dr. Douglas R. Houston >> Scientific Programme Coordinator / Research Associate >> Room 3.23 >> Institute of Structural and Molecular Biology >> Michael Swann Building >> King's Buildings >> University of Edinburgh >> Edinburgh, EH9 3JR, UK >> Tel. 0131 650 7358 >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> >> ------------------------------------------------------------------------------ >> Enable your software for Intel(R) Active Management Technology to meet the >> growing manageability and security demands of your customers. Businesses >> are taking advantage of Intel(R) vPro (TM) technology - will your software >> be a part of the solution? Download the Intel(R) Manageability Checker >> today! http://p.sf.net/sfu/intel-dev2devmar >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > _____________________________________________________ Dr. Douglas R. Houston Scientific Programme Coordinator / Research Associate Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
