On 14/07/2012 12:41, Geoffrey Hutchison wrote: > >> I think I'm using the latter and other hydrogens are added, but not the one >> I mentioned. Using version 2.3. > > Ah. I just looked through the gen3d code to see why this is happening: > >> pmol->AddHydrogens(false, true); // Add some hydrogens before running MMFF > > So if you're using code, you want to run gen3d and *then* add hydrogens again > to re-protonate the OH with existing versions of libopenbabel. I'm not sure > if this is the appropriate default for gen3d, since it might violate the > principle of least surprise. (Certainly it surprised you.) > > Thoughts? Should the default gen3d use the pH model corrections for adding > hydrogens?
I also was surprised to see that the hydrogen added in gen3D was pH dependent. Not every body using gen3D works in solution. I think there should be no adjustment for pH, especially as the pH code may not be entirely reliable. Chris ------------------------------------------------------------------------------ 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
