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Difference between revisions of "enscluster.pl"
Line 35: | Line 35: | ||
; -jclust : hierarchical clustering | ; -jclust : hierarchical clustering | ||
; -kclust : K-means clustering | ; -kclust : K-means clustering | ||
− | ; -maxnum value : maximum number of | + | ; -maxnum value : maximum number of clusters for hierarchical clustering |
; -minsize value : minimum cluster size to generate subclusters in hierarchical clustering | ; -minsize value : minimum cluster size to generate subclusters in hierarchical clustering | ||
; -maxlevel value : maximum levels for hierarchical clustering | ; -maxlevel value : maximum levels for hierarchical clustering |
Revision as of 14:33, 30 July 2009
Usage
usage: enscluster.pl [options] tag options: [-jclust] [-kclust] [-maxnum value] [-minsize value] [-maxlevel value] [-radius value] [-[no]iterate] [-maxerr value] [-mode rmsd|contact|phi|psi|phipsi|mix] [-contmaxdist value] [-mixfactor value] [-l min:max[=min:max ...]] [-fit min:max[=min:max] | -fitxl] [-selmode ca|cb|cab|heavy|all] [-[no]lsqfit] [-dir workdir] [-opt file[:file]]
Description
This script applies a clustering algorithm to ensemble
structures. The options and functionality is very similar to
cluster.pl. The differences are that instead
of a list of files an ensemble tag is expected and the output is
stored in a file tag.cluster in the ensemble
data directory. The clustering options are also stored in and read
from the options file associated with the ensemble tag.
In addition to the parameters from cluster.pl
the parameter -dir is used to specify the ensemble directory.
With -opt other options files (other than the default one) can
be read in.
For fragment/loop modeling the residue range may be specified as
in cluster.pl, but if a residue range has been
stored in the ensemble configuration file previously clustering
will also only be based on the corresponding residue subset even
if -l is not explicitly given. Fitting for RMSD based clustering
is always done for the protein template surrounding the selected
residues.
The centroid output options are not supported in the ensemble clustering script.
Options
- -help
- usage information
- -jclust
- hierarchical clustering
- -kclust
- K-means clustering
- -maxnum value
- maximum number of clusters for hierarchical clustering
- -minsize value
- minimum cluster size to generate subclusters in hierarchical clustering
- -maxlevel value
- maximum levels for hierarchical clustering
- -radius value
- define cluster radius for K-means clustering
- -[no]iterate
- (do not) iterate during K-means clustering
- -mode rmsd|contact|phi|psi|phipsi|mix
- measure for comparing structures during clustering
- -contmaxdist value
- contact distance threshold if clustering based on contact map
- -mixfactor value
- weight factor if clustering both on RMSD and contact map
- -l min:max[=min:max ..]
- compare only specified residue range when clustering
- -selmode ca|cb|cab|heavy|all
- atoms used for comparing structures during clustering
- -[no]lsqfit
- (do not) superimpose structures before comparing
- -dir workdir
- data directory
- -opt file[:file]
- provide file with clustering options