Dear all,
Thanks a lot for the suggestions. I am trying the FastSearch class now and
hope it will be faster a bit.
Rob
On Fri, Jun 25, 2010 at 8:49 AM, Igor Filippov <igor.v.filip...@gmail.com>wrote:
>
> > > I have two lists of molecules. The first list contains testing
> molecules
> > > (test.sdf) and the second contains training molecules (train.sdf).
> > >
> > > I would like to compare each test molecule to all the training molecule
> and
> > > calculate a corresponding Tanimoto similarity score. (I implemented it
> in my
> > > code and it is super slow as it is O(n^2) ). I use GetFingerprint() and
> > > Tanimoto() functions for such purpose. After the comparison, I picked
> up the
> > > kth most similar molecules to the test molecule and predict something
> for
> > > the test molecule. I am trying to make things a bit faster.
> >
> > There is no way to speed this up - if it's O(N^2) it's O(N^2).
> >
>
> There are clever ways to pre-screen your set if you are looking for
> molecules above a certain Tanimoto threshold from the other set of
> molecules. See for example:
> An Intersection Inequality Sharper than the Tanimoto Triangle Inequality
> for Efficiently Searching Large Databases
> Pierre Baldi and Daniel S. Hirschberg
> J. Chem. Inf. Model., 2009, 49 (8), pp 1866–1870
> Publication Date (Web): July 14, 2009 (Article)
> DOI: 10.1021/ci900133j
>
>
> If all you want is a list of all Tanimoto coefficients between two sets
> then it's indeed O(N^2), I don't see any way around it.
> Why would you want such an all-encompassing list though?
> It's all how you formulate the problem...
>
> Best regards,
> Igor
>
>
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