On 30/06/2011 01:23, A. Heifets wrote: > When I use FastSearch, the numbers added by addinindex seem to always > start from 1, unlike searching the original SDF. Am I doing it wrong? > > $ obabel -isdf ./small_db.sdf -osmi --addoutindex --addinindex -s"n1ccccc1" > c12ccccc2[n+](c(cc1)/*=*/C=c/1\ccc2ccccc2n1CC)CC 0261.cdx#1 49 1 > [n+]1(CC)ccc(/*=*/C=c/2\ccn(CC)c3ccccc23)c2ccccc12 0260.cdx#1 51 2 > 2 molecules converted > > $ obabel -ifs ./small_db.fs -osmi --addoutindex --addinindex -s"n1ccccc1" > 2 candidates from fingerprint search phase > c12ccccc2[n+](c(cc1)/*=*/C=c/1\ccc2ccccc2n1CC)CC 0261.cdx#1 1 1 > [n+]1(CC)ccc(/*=*/C=c/2\ccn(CC)c3ccccc23)c2ccccc12 0260.cdx#1 2 2 > 2 molecules converted >
It is gratifying that you are using these features and finding dark corners like this. Normally OBConversion controls the conversion process and addinindex simply reports the number it has already processed. FastSearchFormat's input is not a normal conversion - it is a single read of the .fs index for the fingerprint stage. The input index reported is that from the second stage, which is a normal SMARTS filtering. If there were false positives in the fingerprint stage, I expect the input and output indices reported from the second stage would be different. FastsearchFormat does not record the index of its fingerprint matches; the position of the molecule in the original datafile is used instead. So it would be more complicated to provide a meaningful input index for fastsearches, although not impossible. However, from a philosophical point of view I prefer an ID like a title, which is aimed at humans and can have a rich content, rather than an index which is a restrictive computer-centric concept. Chris ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
