Thanks very much Paulo.
Yours,
Toby
--
InhibOx Ltd
On 15 April 2014 00:25, Paolo Tosco <paolo.to...@unito.it> wrote:
> Dear Toby,
>
> I checked the MMFF literature and indeed that hydrogen must be type 29; I
> just submitted a pull request with the bug fix. Apparently the test case
> that you presented is not covered by the validation suite and so I missed
> that bug until today: thank you very much for reporting it!
>
> Cheers,
> p.
>
>
> On 04/14/2014 03:42 PM, Toby Wright wrote:
>
> 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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> --
> ==========================================================
> Paolo Tosco, Ph.D.
> Department of Drug Science and Technology
> Via Pietro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
> Fax: +39 011 670 7687 | E-mail: paolo.tosco@unito.ithttp://open3dqsar.org |
> http://open3dalign.org
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