The PairwiseDistances is a binary file of n*n floating numbers. If you read
them out sequentially, you will get (1,1), (1,2), ..., (1,n), (2,1), ...,
(n,n).
Best,
Jianyin
On Fri, Oct 29, 2010 at 11:03 AM, Yannick Spill <yannick.spill.pasteur.fr>wrote:
> Thanks Jianyin!
>
> Is the format of PairwiseDistances something standard that I could
> read/convert with another tool, or is there a description of it somewhere?
>
> Yannick
>
> > Hi Yannick,
> >
> > It is hard coded. So if you want smaller bins, you need to modify the
> > source
> > code and recompile the ptraj.
> > In cluster.c, search
> > "SymmetricMatrixDistribution(This->PairwiseDistances,20,File)", then
> > replace
> > 20 with a larger number you want, say 100. Recompile, and you will get
> 100
> > bins.
> >
> > Best,
> >
> > Jianyin Shao
> >
> > On Fri, Oct 29, 2010 at 8:57 AM, Yannick SPILL
> > <Yannick.Spill.pasteur.fr>wrote:
> >
> >> Hi,
> >>
> >> is there a way to extract the distribution of distances from the
> >> PairwiseDistances file after performing a (average linkage) clustering
> >> using ptraj from amber 11 ? I'm not satisfied with the distribution it
> >> outputs during the process, as I'd like a smaller binning.
> >>
> >> thanks!
> >>
> >> Yannick
> >>
> >>
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Received on Fri Oct 29 2010 - 12:00:02 PDT
