Hi,
I've been using the MMFF94 forcefield and noticed an odd behaviour is a
couple of molecules.
> phenolish1 = Chem.MolFromSmiles('Oc1ncccn1')
> phenolish2 = Chem.MolFromSmiles('Oc1ncncc1')
> prop1 = AllChem.MMFFGetMoleculeProperties(Chem.AddHs(phenolish1))
> prop2 = AllChem.MMFFGetMoleculeProperties(Chem.AddHs(phenolish2))
> print prop1.GetMMFFAtomType(7) #Atom 7 is the H of the OH
21
> print prop2.GetMMFFAtomType(7) #Atom 7 is the H of the OH
29
Type 29 is a hydrogen attached to an oxygen in enols, phenols or HO-C=N
which is only sort of the case here (but perhaps pragmatically we should
consider phenol the closest option?)
Digging into the code in GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp we
see (between lines 2092 and 2133) that we consider an atom to hit the
phenol case if we have the oxygen attached to a carbon attached via an
aromatic bond to another carbon. We have this in phenolish2 but not in
phenolish1 hence the different outputs. If we change the test on line 2115
to:
if ((bond->getBondType() == Bond::AROMATIC) || ((nbr3Atom->getAtomicNum()
== 6) && (bond->getBondType() == Bond::DOUBLE))) {
then both cases above show the same behaviour, considering phenolish things
to be phenols for the sake of MMFF94 atom typing. Alternatively we could
consider phenolish things to be not phenols and implement atom type 21 for
the hydrogen in both cases. Any thoughts?
Yours,
Toby Wright
PS I'm aware that the tautomers above aren't ideal, these are fragments
snipped from more complex molecules to demonstrate the behaviour.
--
InhibOx Ltd
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