cluster.pl - Revision history

Edit: /* Options */

2009-07-28T03:27:48Z

Options

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2009-07-28T03:25:23Z

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2009-07-28T03:19:47Z

Description

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151.100.64.18: /* Options */ -mode rmsd

2008-06-30T08:41:26Z

Options: -mode rmsd

24.16.114.62: /* Description */

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Description

Feig at 14:10, 12 August 2006

2006-08-12T14:10:07Z

New page

__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="cluster.pl"></mmtsbToolUsage>

== Description ==

This script applies a clustering algorithm to a set
of files. The list of files can be passed either as the last arguments
on the command line or through standard input. The clustering result
is written to standard output. 
Two clustering methods are available. Hierarchical clustering
that uses automatic stopping criteria is used by default
or if the option -jclust is given.
With this cluster method the ideal number of
clusters is determined automatically up to a maximum number of clusters.
The default maximum is 4 clusters, it may be changed with -maxnum.
For each of these initially identified clusters the clustering procedure is
then reapplied to determine subclusters if the number
of elements in a cluster is larger than a given threshold. This
threshold is set to 400 structures by default and can be changed
with -minsize. The procedure is repeated recursively as long as there
are large enough subclusters or until a maximum recusion level is
reached. The level is set to 999 by default, which means practically
no limit, it can be changed with -maxlevel. 
An alternative clustering method employs a fixed cluster radius and
is selected with -kclust. Subclusters are not generated in this
case, and the resulting number of clusters cannot be limited with
-maxnum. The fixed cluster radius is given with -radius. 
Depending on the cluster method different cluster modes that
use different criteria for measuring distances between the
input structures are available. The cluster mode is selected with
-mode. Both cluster methods support clustering based on
cartesian coordinate RMSD between structures. With the hierarchical
clustering algorithm it is also possible to cluster based on similarities
in the contact map (contact).
In this case the option -contmaxdist determines the maximum distance
between residues for being counted in the comparison. The default
value is 12.0 A. 
The fixed radius clustering method supports dihedral based clustering
using RMSD values for phi angles (phi), psi angles (psi),
or both (phipsi). A mixing mode is also supported where the
distance measure is given by the sum of phi and psi RMSD values, divided by 20
and multiplied by a mixing factor, and the cartesian space RMSD multiplied
by 1 minus the mixing factor. This mode is selected with mix.
The mixing factor can be set with -mixfactor. 
In the default mode of operation the input structures are expected
to be in PDB format (option: -pdb). Alternatively, SICHO lattice
chains can be used as input if -sicho is given. 
For loop/fragment modeling it is possible to restrict the comparison
to a range of residues specified with the -l option. In this case
the fit between different structures before an RMSD value is calculated
may either be done based on the loop/fragment residues (default) or based
on the rest of protein excluding the loop/fragment if -fitxl is
specified. 
A log file can be requested if the option -log is used.
It is also possible to request output of the centroids of each cluster
with -centroid. The option -centout is used to provide
a template for the centroid file names. The centroids are written in PDB
format if the clustering is based on RMSD comparison. For contact map based
clustering the centroids are RGB maps with the contact map represented
as a bitmap.

== Options ==

; -help : usage information

== Examples ==

<mmtsbToolExample cmd="cluster.pl" set="/apps/mmtsb/bench/cluster.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="cluster.pl" set="/apps/mmtsb/bench/cluster.pl-test/test2"></mmtsbToolExample>

<mmtsbToolExample cmd="cluster.pl" set="/apps/mmtsb/bench/cluster.pl-test/test3"></mmtsbToolExample>

<mmtsbToolExample cmd="cluster.pl" set="/apps/mmtsb/bench/cluster.pl-test/test4"></mmtsbToolExample>

<mmtsbToolExample cmd="cluster.pl" set="/apps/mmtsb/bench/cluster.pl-test/test5"></mmtsbToolExample>

<mmtsbToolExample cmd="cluster.pl" set="/apps/mmtsb/bench/cluster.pl-test/test6"></mmtsbToolExample>

@@ Line 77: / Line 77: @@
 ; -help : usage information
 ; -jclust : invoke hierarchical clustering algorithm
-; -maxnum value : ?
+; -maxnum value : maximum number of clusters for hierarchical clustering
-; -minsize value : ?
+; -minsize value : minimum size of cluster to perform second level of hierarchical subclustering
-; -maxlevel value : ?
+; -maxlevel value : maximum number of clustering levels for hierarchical clustering
 ; -kclust : invoke K-means clustering algorithm
 ; -radius value : K-means clustering radius

@@ Line 93: / Line 93: @@
 ; -[no]lsqfit : superimpose structures before calculating RMSD values
 ; -centroid : write out centroid structures
-; -centout template : ?
+; -centout template : provide template for centroid file names
 ; -log file : generate log file

@@ Line 77: / Line 77: @@
 ; -help : usage information
 ; -jclust : invoke hierarchical clustering algorithm
 ; -kclust : invoke K-means clustering algorithm
 == Examples ==

←Older revision		Revision as of 03:18, 28 July 2009
Line 72:		Line 72:

	; -help : usage information		; -help : usage information
		+	; -jclust : invoke hierarchical clustering algorithm
		+	; -kclust : invoke K-means clustering algorithm

	== Examples ==		== Examples ==

←Older revision		Revision as of 08:41, 30 June 2008
Line 72:		Line 72:

	; -help : usage information		; -help : usage information
−

	== Examples ==		== Examples ==

@@ Line 68: / Line 68: @@
 clustering the centroids are RGB maps with the contact map represented
 as a bitmap.
 == Options ==

@@ Line 9: / Line 9: @@
 of files. The list of files can be passed either as the last arguments
 on the command line or through standard input. The clustering result
-is written to standard output.<BR>
+is written to standard output.
 Two clustering methods are available. Hierarchical clustering
 that uses automatic stopping criteria is used by default
@@ Line 23: / Line 24: @@
 are large enough subclusters or until a maximum recusion level is
 reached. The level is set to 999 by default, which means practically
-no limit, it can be changed with <B>-maxlevel</B>.<BR>
+no limit, it can be changed with <B>-maxlevel</B>.
 An alternative clustering method employs a fixed cluster radius and
 is selected with <B>-kclust</B>. Subclusters are not generated in this
 case, and the resulting number of clusters cannot be limited with
-<B>-maxnum</B>. The fixed cluster radius is given with <B>-radius</B>.<BR>
+<B>-maxnum</B>. The fixed cluster radius is given with <B>-radius</B>.
 Depending on the cluster method different cluster modes that
 use different criteria for measuring distances between the
@@ Line 37: / Line 40: @@
 In this case the option <B>-contmaxdist</B> determines the maximum distance
 between residues for being counted in the comparison. The default
-value is 12.0 A.<BR>
+value is 12.0 A.
 The fixed radius clustering method supports dihedral based clustering
 using RMSD values for phi angles (<font color=#508060>phi</font>), psi angles (<font color=#508060>psi</font>),
@@ Line 44: / Line 48: @@
 and multiplied by a mixing factor, and the cartesian space RMSD multiplied
 by 1 minus the mixing factor. This mode is selected with <font color=#508060>mix</font>.
-The mixing factor can be set with <B>-mixfactor</B>.<BR>
+The mixing factor can be set with <B>-mixfactor</B>.
 In the default mode of operation the input structures are expected
 to be in PDB format (option: <B>-pdb</B>). Alternatively, SICHO lattice
-chains can be used as input if <B>-sicho</B> is given.<BR>
+chains can be used as input if <B>-sicho</B> is given.
 For loop/fragment modeling it is possible to restrict the comparison
 to a range of residues specified with the <B>-l</B> option. In this case
@@ Line 53: / Line 59: @@
 may either be done based on the loop/fragment residues (default) or based
 on the rest of protein excluding the loop/fragment if <B>-fitxl</B> is
-specified.<BR>
+specified.
 A log file can be requested if the option <B>-log</B> is used.
 It is also possible to request output of the centroids of each cluster