Cluster.pm Show Source

The Cluster package provides functions to generate and manage cluster hierarchies for a set of structures. The actual clustering is done with the external programs jclust and kclust.

new([parameters])
creates a new Cluster object. Clustering parameters may given as hash-style key=>value pair arguments
setPar(parameters)
sets clustering parameters in hash-style key=>value format
 
setFileList(filelist)
resets the top level cluster from a list of files. This method needs to be called before clustering can be done.
 
runCluster([cluster][,method])
runs the jclust clustering program for the set of files in the top level cluster or in cluster if given as argument.
 
clusterHierarchy([level[,cluster]])
generates a cluster hierarchy beginning at the top level cluster or at a cluster given as argument by calling runCluster recursively. The level argument sets the maximum number of cluster levels that may be performed recursively
 
top()
returns the top level cluster
 
readFile(file)
reads cluster information from a file
 
writeFile(file[,centflag,centoutname])
writes the current cluster hierarchy to a file. Centroids are generated if centflag is set. The name used in the file template may be given through centoutname.
 
writeCentroids(centoutname)
writes the current cluster hierarchy to a file. Centroids are generated if centflag is set. The name used in the file template may be given through centoutname.
 
$list = allClusters()
return a list of all clusters
 
$list = clusterList(level)
return all clusters found at the given level
 
$list = fileList(level)
returns the list of files at a given level.
par -> { selmode, lsqfit, fraglist, fitfraglist,
         filetype, clustermode, contmaxdist,
         maxnum, minsize, method,
         radius, maxerr, iterate, mixfactor }
clustering paramters
 
topcl   -> { tag, level, 
             element[] -> { name, inx, dist },
             subcl[] -> { tag, level, element, subcl } }
cluster hierarchy data structure
 
allcl[] -> { tag, level, element, subcl }  
list of all clusters
GenUtil.pm  Molecule.pm  Analyze.pm
Michael Feig, Brooks group, TSRI