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 ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
