Dear Greg,
this is VERY helpful, thanks a lot!
Nonetheless, I might come up with a few more questions...
Cheers,
Paul
>
> Dear Paul,
>
> On Mon, Nov 7, 2011 at 12:44 PM, <paul.czodrow...@merckgroup.com>
wrote:
> >
> > can anyone given an example how to use the acid/base pharmacophore
> > annotation using the Gobbi_Pharm2D fingerprints?
> >
>
> I guess this isn't what you want, but there's an explanation of how to
> generate the Gobbi_Pharm2D fingerprints in the online documentation
> here;
> http://www.rdkit.org/new_docs/GettingStartedInPython.html#chemical-
> features-and-pharmacophores
>
> If you're just interested in using the feature types as substructure
> queries you can do something like the following:
>
> Start by getting the feature definitions:
> In [17]: from rdkit.Chem.Pharm2D import Gobbi_Pharm2D
>
> In [18]: fds=Gobbi_Pharm2D.factory.featFactory.GetFeatureDefs()
>
> In [19]: fds
> Out[19]:
> {'AG.AcidicGroup': '[$([C,S](=[O,S,P])-[O;H1])]',
> 'AR.AromaticAttachment': '[$([a;D3](@*)(@*)*)]',
> 'BG.BasicGroup':
> '[$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C,a]);!$([C,
> a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O))])([C;!
> $(C(=O))])[C;!$(C(=O))]),$([N,n;X2;+0])]',
> 'HA.Acceptor':
> '[$([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]',
> 'HD.Donor':
'[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]',
> 'LH.Hydrophobic':
> '[$([C;H2,H1](!=*)[C;H2,H1][C;H2,H1][$([C;H1,H2,H3]);!$(C=*)]),
> $(C([C;H2,H3])([C;H2,H3])[C;H2,H3])]',
> 'RR.AliphaticAttachment': '[$([A;D3](@*)(@*)*)]',
> 'X.UnusualAtom': '[!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]'}
>
>
> Now build SMARTS pattern matchers for the acidic and basic groups:
>
> In [20]: acidPattern = Chem.MolFromSmarts(fds['AG.AcidicGroup'])
>
> In [21]: basePattern = Chem.MolFromSmarts(fds['BG.BasicGroup'])
>
>
> Now test those out:
>
> In [22]: Chem.MolFromSmiles('CCC(=O)O').HasSubstructMatch(acidPattern)
> Out[22]: True
>
> In [24]: Chem.MolFromSmiles('CCC(=O)O').HasSubstructMatch(basePattern)
> Out[24]: False
>
> In [25]: Chem.MolFromSmiles('CCCN').HasSubstructMatch(acidPattern)
> Out[25]: False
>
> In [26]: Chem.MolFromSmiles('CCCN').HasSubstructMatch(basePattern)
> Out[26]: True
>
>
> Does this get you closer to what you want?
>
> -greg
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