cpptraj
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Add option to read in generic ASCII files as a pairwise distance matrix
This allows non-standard, user-defined distance metric in clustering analysis.
This should be possible now as of #915 (may have also been possible before but I'm certain it works now). The ASCII file just needs to have a header with the format:
#F1 F2 <name> [nframes <#>]
Where F1 and F2 are the frame numbers, nframes <#> specifies the total number of frames (in case this is a "sieved" matrix, i.e. it is missing certain frames). This file can be read in with the readdata command and then given to the cluster command via the pairdist keyword.