> Since OpenBabel is designating aromatic bonds, we have to go along with that > for use in our program. (If we knew the original bond -- from Avogadro input > -- between the pertinent atoms, we could just use that info but OpenBabel > rearranges the atom sequences ----- which we don't really need to have done, > either!)
There's absolutely no way that's happening. Sorry to sound so emphatic, but Avogadro v1 directly uses Open Babel. Unless you're removing hydrogens, there's never any atom reordering occurring inside the Open Babel code. And if you're deleting hydrogens - you don't need to do that to depict 2D diagrams, since they can ignore hydrogens themselves. > I have attached 4 screen shots of our graphics showing examples of molecules > where aromatic bonds (double dashed bonds) should not occur. It appears the > program thinks that the electron pairs on oxygen and nitrogen (also > phosphorus) should be combined with the double bonds or aromatic ring to make > delocalized "aromatic" structures. The heteroatoms don't have to be > adjacent (e.g. a similar case occurs with P in the 1,3 positions of the > cyclobutane ring). If you get X chemists in a room, chances are that you'll have X+1 definitions of "what is aromatic" after not too long. As Noel indicated, an aromaticity model for cheminformatics (Daylight, previous Open Babel aromaticity models, etc.) may not match your intuition. If you have MOL and CML formats from Avogadro or other programs, these will have 1, 2, 3 bond orders without aromaticity. You're done. PDB is a whole different ball of wax and I'd suggest you avoid that format as much as you can. Hope that helps, -Geoff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
