Speaking from the peanut gallery, that seems to me to be a rather important
point, at least as far as pyrrole NH is concerned. I assume there is
widespread agreement that these are not acceptors.
I think thiophene S is usually regarded as a receptor, albeit a weak one,
but F is highly debatable. Some med chemists insist on F being regarded as
a receptor and others insist on F *not* being regarded as a receptor. In
the commercial world, the most important customer who gives a damn usually
wins. I'm not sure how much guidance this supplies to RDKit. :-)
Another question is whether aromatic CH is a donor; I'm not sure what RDKit
does here.
-P.
On Sat, Apr 30, 2016 at 9:37 AM, Konrad Koehler <konrad.koeh...@icloud.com>
wrote:
> Hi All,
>
> The following is a relatively minor point, but IMHO, the Gobbi hydrogen
> bond acceptor definition probably should be modified so that only aromatic
> nitrogen atoms with two and not three non-hydrogen attachments are
> considered as acceptors. For example, the aromatic nitrogen atom pyridine
> is an acceptor whereas the nitrogen in indole or N-methylindole is not.
> Also fluorine atoms (see https://doi.org/10.1016/0040-4020(96)00749-1
> <http://dx.doi.org/10.1016/0040-4020(96)00749-1>) do not appear to be
> good acceptors. In addition, thiophenes are very questionable acceptors.
>
> Hence in:
>
> in ~/envs/my-rdkit-env/lib/python2.7/site-packages/rdkit/Chem/Pharm2D/
> Gobbi_Pharm2D.py
>
> I have made the following modification:
>
> # Replaced the following line to the next line:
> # DefineFeature Acceptor
> [$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]
> DefineFeature Acceptor
> [$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n;D2;H0;+0]),$([o;+0]]
>
> Cheers,
>
> Konrad
>
> After modifying Gobbi_Pharm2D.py, the following test script gives:
>
> from rdkit import Chem, DataStructs
> from rdkit.Chem import ChemicalFeatures
> from rdkit.Chem.Pharm2D.SigFactory import SigFactory
> from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
>
> mol = Chem.MolFromSmiles('Cn1ccc2ccccc21’) # N-methylindole
>
> bi = {}
> fp = Generate.Gen2DFingerprint(mol,Gobbi_Pharm2D.factory,bitInfo=bi)
>
> onbits = fp.GetOnBits()
> for onbit in onbits:
> print onbit, Gobbi_Pharm2D.factory.GetBitDescription(onbit), bi[onbit]
>
> output:
>
> 77 AR HD |0 0|0 0| [[(3,), (0,)]]
>
> mol = Chem.MolFromSmiles('c1ncccc1C’) # 2-methylpyridine
>
> output:
>
> 63 AR BG |0 0|0 0| [[(5,), (1,)]]
> 70 AR HA |0 0|0 0| [[(5,), (1,)]]
>
>
>
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