Hi Geoffrey,
The calculation of DBI when DME is used is same as the calculation of DBI
when rmsd is used. The DBI is defined as the average, for all clusters X, of
fred, where fred(X) = max, across other clusters Y, of (Cx + Cy)/dXY. Here
Cx is the average distance from points in X to the centroid, similarly Cy,
and dXY is
the distance between cluster centroids:
DBI = average(fred(X))
fred(X) = max((C(X)+C(Y))/distance(X,Y))
C(X) = average(distance(x, x-centroid))
C(Y) = average(distance(y, y-centroid))
distance(X,Y) = distance(x-centroid, y-centroid)
Since you can reproduce the DBI value with rmsd metric, I guess the problem
does not lie in the DBI calculation. Here I found two possible causes that
DME might go wrong.
1. The centroid of a cluster using rmsd metric will implicitly aligned.
There is no alignment before calculating the centroid when DME metric is
used.
2. When calculating DME, we used formula:
DME = sqrt(sum((distance(X,i,j)-distance(Y,i,j))^2)/C(N,2)), in which
distance(X,i,j) is the distance between atom i and atom j in structure X.
C(N,2) is N*(N-1)/2. But I've also seen formulas like this:
DME = sqrt(sum(distance(X,i,j)-distance(Y,i,j))/C(N,2)) (sum up the
distance error, not the square of distance error) or
DME = sqrt(sum((distance(X,i,j)-distance(Y,i,j))^2)/N^2) (sum up all the
pairs, including (i,i), which should be 0, then divided by the number of
total pairs, N^2)
I don't know how you calculate the DME. Hope this explanation helps.
Best,
Jianyin Shao
On Mon, May 3, 2010 at 2:48 PM, Geoffrey Wood <ge.ffw.d.gmail.com> wrote:
> Dear Amber Users,
>
> I have been looking carefully at the clustering tools in ptraj in
> particular
> the cluster validity testing using the davies bouldin index (DBI). If my
> set measure is RMSD then I am able to reproduce the DBI when I calculate it
> "by hand" using ptraj... i.e taking the RMSD of each centroid with the
> others and applying the DBI formula. However, when I take the set measure
> to be the DME then I am unable to reproduce the values that ptraj
> calculates. In this case ptraj doesn't have a DME command but it is easy
> enough to use the distance command and calculate this matrix by hand. My
> question is: how is ptraj calculating the DBI when the set measure is DME?
>
> Thanks in advance, Geoffrey Wood
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Received on Mon May 10 2010 - 16:30:04 PDT
