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
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