On 21/09/2018 16:53, Chris Earnshaw wrote:
Hi
I'm afraid I can't help with an RDkit solution to your question, but
there are a couple of issues which should be born in mind:
1) The centroid of a cluster is a vector mean of the fingerprints of
all the members of the cluster and probably will not
Dear Colin,
this is a specific problem I stumbled upon some time ago.[1]
I also mentioned it to the rDock mailing list.[2]
Maybe there is a better work-around, but in the meantime I wrote the
attached function.
It takes as input the Mol Block, which in my case are in a dataframe.
Hope that
On Sep 26, 2018, at 20:26, Peter S. Shenkin wrote:
> Ah, David, but how do you define a "real" singleton?
There can be many different definitions of what a '"real" singleton' might be,
but we are specifically talking about Butina clustering.
The Butina paper defines the term "false singleton",
Ah, David, but how do you define a "real" singleton?
-P.
On Wed, Sep 26, 2018 at 1:30 PM David Cosgrove
wrote:
> Slightly off topic, but a minor issue with the Taylor-Butina algorithm is
> that it generates “false singletons”. These are molecules just outside the
> clustering cutoff that are
Slightly off topic, but a minor issue with the Taylor-Butina algorithm is
that it generates “false singletons”. These are molecules just outside the
clustering cutoff that are stranded when their neighbours are put in a
different, larger cluster. We used to find it convenient to have a sweep of
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