Hi Konrad,
You (and Peter later in the thread) make valid points about whether or not
particular functional groups are donors or acceptors. There are certainly
interesting discussions to be had about that - particularly when those
discussions are backed up by an analysis of experimental data - but that
doesn't really apply here.
The "Gobbi" pharmacophore definitions are taken from a publication and, as
such, shouldn't really be changed unless they differ from what's in that
publication.
As I said, discussions about a new set of definitions would be welcome.
They just need to have a different name. :-)
-greg
On Saturday, 30 April 2016, 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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