I think I'm using the latter and other hydrogens are added, but not the one I mentioned. Using version 2.3.
Best Regards, James -----Original Message----- From: Chris Morley [mailto:c.mor...@gaseq.co.uk] Sent: 13 July 2012 14:52 To: James Jack Cc: openbabel-disc...@lists.sf.net Subject: Re: [Open Babel] (no subject) On 11/07/2012 18:51, James Jack wrote: > > When I convert this to a 3D molfile with "add explicit H" checked in > the OpenBabel GUI or I try the same in code the OH seems to become O- > (O with a negative charge). > In the GUI you need to check "Add hydrogens (make explicit)" but have the editbox labelled "Add hydrogens appropriate for this pH" on the next line empty. In code something like pMol->AddHydrogens(false, false); But this may not be necessary. If you use "Generate 3D coordinates" in the GUI or something like OBOp* pOp = OBOp::FindType("gen3D"); if(pOp) pOp->Do(pMol); in code, explicit hydrogens are added automatically. Chris Accelrys Limited (http://accelrys.com) Registered office: 334 Cambridge Science Park, Cambridge, CB4 0WN, UK Registered in England: 2326316 ------------------------------------------------------------------------------ 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
