Thank you Matias and Dan.
td
On Tue, Oct 22, 2019 at 8:55 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You can load a pairwise distance file either via a 'readdata' command
> prior to cluster or by using the 'loadpairdist' option, e.g.
>
> readdata Cmatrix.cmatrix name PW
> runanalysis cluster crd1 pairdist PW ...
>
> or
>
> cluster C1 loadpairdist pairdist pw.out ...
>
> If you don't want to do any clustering you can use the 'readinfo'
> option to read the results of previous clustering.
>
> I guess it can be a bit annoying if you just want a summary that you
> have to specify something to cluster. I never really considered that
> case to be honest. If you want, you can "fool" cpptraj by creating a
> "fake" data set to cluster that has the same size as the data you
> want, then read that in and "cluster" on that after reading in your
> pairwise distance matrix. Here's an example where I've modified one of
> cpptraj's cluster test cases to do just that.
>
> Original:
>
> # Test loading PW distances from Cmatrix file
> cat > cluster.in <<EOF
> readdata Cmatrix.cmatrix name PW
> parm ../tz2.parm7
> loadtraj ../tz2.nc name MyTraj
> runanalysis cluster crd1 crdset MyTraj :2-10 clusters 3 epsilon 4.0
> summary summary2.dat \
> complete nofit pairdist PW \
> cpopvtime normpop.agr normpop
> EOF
> cpptraj -i cluster.in
>
> The trajectory tz2.nc is 101 frames. So I create a fake data set to
> cluster with 101 entries via something like:
>
> #!/bin/bash
> rm fakedata.dat
> for ((i=1; i<= 101; i++)) ; do
> echo "$i" >> fakedata.dat
> done
>
> Then you can use the following modified input: note the replacement of
> 'crdset' with 'nocoords' and 'data':
> # Test loading PW distances from Cmatrix file
> cat > cluster.in <<EOF
> readdata Cmatrix.cmatrix name PW
> parm ../tz2.parm7
> readdata fakedata.dat name MyData
> runanalysis cluster crd1 data MyData nocoords :2-10 clusters 3 epsilon
> 4.0 summary summary2.dat \
> complete nofit pairdist PW \
> cpopvtime normpop.agr normpop
> EOF
> cpptraj -i cluster.in
>
> That seems to work just fine. I'll add a feature request to cpptraj
> GitHub to make clustering on existing pairwise distance matrices
> easier. Thanks for the report!
>
> -Dan
>
> On Sat, Oct 19, 2019 at 6:27 PM Tim Davis <tdavis.2019a.gmail.com> wrote:
> >
> > Hi,
> > Is it possible to perform clustering using only the pairdist file?
> > Everything I've tried requires the trajectory file or a coord file to be
> > present. Why are these two files necessary if I only want the information
> > in the summary and info file. I don't want any PDB written. Thanks.
> > td
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Received on Tue Oct 22 2019 - 14:30:02 PDT
