On 20/11/2012 08:03, Visvaldas K. wrote: > Dear all, > > I am trying to look for certain molecules in the sdf/fs database > containing certain fragments as substructure. The problem is my > fragments can be small (I am running a script to do multiple searches), > so I can get "too many candidates in the fingerprint search phase". The > simple solution is to filter out the big molecules before doing > substructure search, but openbabel does the substructure search first, i.e. > > obabel dbase.sdf -d --filter "atoms < 20" -O results.sdf -s trial.smi > -al 9000 -ifs > > gives the identical "too many candidates" message. Of course, I can keep > increasing "-al 9000" but that's a workaround and not the real solution. > It is possible to do filtering while making the .fs file, so only a subset of the molecules in the dataset are indexed.
obabel dbase.sdf -O filtered.fs -d --filter "atoms<20" This will help to reduce the number of hits in the fingerprint search. > For some reason, piping > > obabel dbase.fs -d --filter "atoms < 20" -ocopy | obabel -ifs -O > results.sdf -s trial.smi -al 9000 > > stalls even at the first step --- it seems that one cannot filter "fs" > database, but I am not sure if I am using the correct syntax. The .fs file is a list of fingerprints and the position of the corresponding molecule in the datafile. So a fastsearch needs to be on a data file which has been indexed. This piping attempt does not work because the molecules you are hoping to search are in a stream not a file and they have not been indexed. Incidentally, the FastsearchFormat in the development code now allows substructure searching with multiple molecules in the target file (your trial.smi), which may save some scripting. Chris ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
