findClusters
This script clusters structures by their positional RMSD, using the given atom selection.
Usage: findClusters [option] <pdb files>
where options are zero or more of:
-psf=<psf file> -selection=<atoms to consider for clustering [name CA]> -fitSelection=<atoms to use for fitting [defauts to -selection]> -noFit -tolerance=<distance tol used to exit algorithm [1.000000]>If -noFit is specified, then the structures are not fit before being clustered.
Initially, each structure is in a separate cluster. The algorithm to combine these clusters is as follows:
- find closest two clusters, combine these
- generate a new distance matrix, where now distance between clusters is the shortest structure-structure distance of the clusters
- repeat until the shortest distance is larger than the tolerance
The result is printed to stdout.
If the -psf option is not given, PSF information is automatically generated from the input PDB. All input structures must have the same PSF.