On Wed, Oct 10, 2012 at 10:23:49AM -0400, Geoff Hutchison wrote: > > And ChemSpyder seems to agree with this second one. Was this > > really intended to be caffein? And which of these then is > > correct for it? > > The test structure was originally drawn with Ghemical ages ago > (maybe 2001?). You're correct that the other bonding is > better. If you want to edit it, please be sure to let me know > so we can reset the energies / gradients for the tests.
It changes also the number of electrons for the molecule. Actually a good test for too greedy kekulization :) Geoff, feel free to update the SDF file together with the energies and gradients. Related quiestion. The N atoms are still considered aromatic, right? So the question is about canonstable test SMILES and N atom aromacity there, since my attempt to fix wrong bond order perception led to that test failing. Basically which should be considered correct? 4: ref = CCN(CCNc1ccc2c3c1c(=O)c1c(n3NN2)ccc(c1)[N+](=O)[O-])CC 4: can = CCN(CCNc1ccc2c3c1c(=O)c1cc(ccc1n3[nH][nH]2)[N+](=O)[O-])CC Reinis ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
