Sorry for the delayed reply.. my interpretation is certainly "aromatic OH" for phenolic H, which is certainly how the code is written. The implementation validates against the MMFF94 test set, which does not have an OH on a heterocyclic aromatic.
I think my question would be .. do you think there would be radically different results? Thanks, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ On Apr 14, 2014, at 9:00 AM, Toby Wright <toby.wri...@inhibox.com> wrote: > Hi, > > I'm attempting to use the MMFF94 forcefield to generate partial charges. I > noticed that the molecule whose smiles is Oc1ncccn1 (aka a phenol with two > carbons switched to nitrogens) gave the atom type 29 to the hydrogen attached > to the oxygen. > > Looking into the code in forcefields/forcefieldmmff94.cpp I see the pertinent > parts of the code path taken in atom typing goes: > > if (atom->GetAtomicNum() == 1) { > FOR_NBORS_OF_ATOM (nbr, atom) { > if (nbr->IsOxygen()) { > FOR_NBORS_OF_ATOM (nbrNbr, &*nbr) { > if (nbrNbr->IsCarbon()) { > if (nbrNbr->IsAromatic()) { > return 29; // phenol > } > > So the atom typing code states that any hydrogen neighbouring an oxygen which > in turn neighbours an aromatic carbon is the H in the HO of a phenol. But I > believe the existence of the nitrogen in the aromatic ring makes it not a > phenol. Am I wrong to think that or is this a bug? > > Yours, > > Toby Wright > > -- > InhibOx Ltd > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech_______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
