Bugs item #3423054, was opened at 2011-10-13 13:02 Message generated for change (Tracker Item Submitted) made by cmayne You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3423054&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Command-line Tools Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chris (cmayne) Assigned to: Nobody/Anonymous (nobody) Summary: inconsistent fingerprint generation Initial Comment: I have come across a problem with certain smiles strings with regard to generating a fs index and probing against that index. Consider the file test.smi c1cccc(c1[N+](=O)[O-])Sc1ccc(cc1)C chem001 build a fs index $ babel -ismi test.smi -ofs test.fs build properly, converting 1 molecule probing against the fs with the exact same input smiles: $ babel test.fs hitlist.smi -s'c1cccc(c1[N+](=O)[O-])Sc1ccc(cc1)C' -at0.85 yields 0 molecules converted Rerunning the same probe but with a lower tanimoto threshold results in a hit: $ babel test.fs hitlist.smi -s'c1cccc(c1[N+](=O)[O-])Sc1ccc(cc1)C' -at0.80 yields 1 molecule converted Direct comparison works: $ obabel -:'c1cccc(c1[N+](=O)[O-])Sc1ccc(cc1)C' -:'c1cccc(c1[N+](=O)[O-])Sc1ccc(cc1)C' -ofpt yields a tanimoto of 1 and probing directly against the original .smi file: $ babel test.smi hitlist.smi -s'c1cccc(c1[N+](=O)[O-])Sc1ccc(cc1)C' -at0.85 yields 1 molecule converted In my tests using ~85 probe molecules against a 160,000-entry database this last method (direct comparison to the smi file) doesn't always work. However, the molecules that give problems when probing against the fs index are different from the molecules that give problems when probing directly against the smi file. My OS is Mac OSX 10.6.8 This error reproduces on Open Babel 2.3.0 and 2.3.9 (dev version) Christopher Mayne cgma...@gmail.com ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3423054&group_id=40728 ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
