Hi Greg, basically I wanted to classify atomic interactions based on atom types as described by "Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints" (Marcou and Rognan). Most of the classifications were already in basefeatures.fdef except the weak hbond donor and acceptor definitions. The feature definitions were what I was looking for and I added some more features to implement the atom types described in the mentioned paper.
Cheers, Adrian On 10/16/07, Greg Landrum <[email protected]> wrote: > > Hi Adrian, > > If I understand the question properly, think you can do what you'd > like with recursive smarts, so the first case becomes: > [a,$(A=A),$(A#A),S+0] (a:a isn't necessary because in the RDKit an > aromatic atom always has an aromatic bond to another aromatic atom). > The second example doesn't need recursive smarts and could be something > like: > [!H0;c,CX3,CX2] > Though I'm not 100% sure what you're trying to accomplish with that one. > > If you would like to do more sophisticated queries, I'd recommend > looking into the feature definition capabilities described here: > > http://rdkit.svn.sourceforge.net/viewvc/*checkout*/rdkit/trunk/Docs/Programs/RDPharm3D/FDefFile.htm > > -greg > On 10/15/07, Adrian Schreyer <[email protected]> wrote: > > Is it somehow possible in RDKit to perform a boolean SMARTS query on > > individual atoms? For example I would like to identify possible weak > > hydrogen bond acceptors with a SMARTS query like this [a:a,A=A,A#A,S+0] > or > > weak donors with [c,CX3,CX2][H]. > > > > Adrian > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. > > Still grepping through log files to find problems? Stop. > > Now Search log events and configuration files using AJAX and a browser. > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > _______________________________________________ > > Rdkit-discuss mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > >
