When there are only a small number of molecules, fpt format will give you what you want; you are nearly there.
In the GUI, select sdf for the input format and ftp for the output. Open the sdf file with the pattern molecule, then open the sdf file with all the other molecules you want to compare to it, holding CTRL as you leave the open dialog (which allows more than one input file). Click Convert, and you will get a list of the Tanimoto coefficients between the first molecule and each of the rest, using the default FP2 fingerprint. On the command line (Windows or Linux): obabel patternmol.sdf othermols.sdf -ofpt Chris On 24/01/2011 06:30, chakravar...@ncbs.res.in wrote: > Hi, > > I am new to openbabel. I came to know of open babel recently and want to use > it for > my academic work. > > Here is my Query: > > I want to calculate tanimoto coefficient (similarity score) of two lipid > molecules > but could not find step-by-step procedure to do so in open babel > documentation. > > What I have done so far: > > I converted .sdf files of two lipids into SMILES string and obtained > fingerprints > (FP2) of SMILES string. FP2 of one of the molecules looks like this - > > 00000000 01000000 00000000 00000400 00080000 00000000 > 00000000 00000000 00000000 00000080 00000000 40010000 > 00000000 00800000 00000000 00080008 00000000 00000000 > 01402000 00000001 00000000 10000010 03000000 00000010 > 00000000 00000000 00000000 00000000 00000000 00040000 > 00020000 00000000 > > Now, I would like to compare two such fingerprints (actually more than two) > and > calculate their similarity score. Can someone advice me how to do it ? > > Thanks in Advance > Chak > > PS: I am new to openbabel and Linux. Till now, I used openbabel GUI in > windows. > Even though I have installed openbabel in my ubuntu, I have not used it. > > > > ------------------------------------------------------------------------------ > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! > Finally, a world-class log management solution at an even better price-free! > Download using promo code Free_Logger_4_Dev2Dev. Offer expires > February 28th, so secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsight-sfd2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
