-xh (see http://openbabel.org/docs/2.3.0/FileFormats/Overview.html)
On 24 March 2011 16:39, Douglas Houston <dhous...@staffmail.ed.ac.uk> wrote: > 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
