Hi all, I am attempting to match some SMILE strings against a SMART pattern. In essence, attempting to get results identical to what one gets using the Daylight Depict match (http://www.daylight.com/daycgi_tutorials/depictmatch.cgi). I have used obgrep, the python api through pybel, and babel itself, and seem to give similar results, which makes me suspect that my queries might not be well formed.
Case 1) Consider matching the SMILE string "C[C@H](C(=O)O)O" against the smart "*C(*)(O)C*". The daylight server says that there is no match, while if I run "obgrep -f "*C(*)(O)C*" smiles.smi" with smiles.smi containing the above SMILE string, then openbabel says the match succeeds. On the other hand, if I run with no "-f" flag then I get an barrage of incorrect matches against other molecules. Case 2) Sometimes the matches succeed. For instance we can match the SMILES "CC(=O)O", "C(=O)(N)O", and "C(=O)([O-])O" against the SMART "*C(*)(=O)" correctly, i.e., the daylight depict match and openbabel agree. What am I missing? saurabh ------------------------------------------------------------------------------ Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Discover what all the cheering's about. Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
