On 01/02/2011 07:12, Andrew Dalke wrote: > On Jan 31, 2011, at 8:15 PM, chakravar...@ncbs.res.in wrote: >> I noticed that molecules such as Myristic acid and Palmitic acid have same >> similarity score of 1, > ... >> I am thinking of modifying Tanimoto score to other coefficient's like >> Kulczynski >> index or Russel index. > The only way to get a Tanimoto score of 1 is if the two fingerprints are > identical. In that case there is no scoring method can tell the difference > between the two because they are identical. > > To get what you want you'll need to come up with a new fingerprinting scheme, > not a new scoring method. None of OpenBabel's fingerprints provide a complete description of a molecule. They are really intended as part of a fast screening method to exclude molecules that, compared with a target molecule, are too dissimilar (or too similar) or which are not a superstructure of it. None of the current fingerprint types include stereochemistry and the FP2 fingerprint has a built-in lack of certainty because different fragments can be assigned to the the same bit. It also indexes by the presence or absence of fragments of up to 7 atoms, so does not discriminate well for long chains of carbon atoms, like fatty acids or normal hydrocarbons. It is possible make specialized FP3 fingerprints to handle this type of structure, by including the number of times a substructure occurs. Further description is in the code, although recompilation is not necessary to make a new fingerprint type. However I guess this is probably further than you want to go.
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