MMTSB
Tool Set Documentation

Difference between revisions of "ensfiles.pl"

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used to specify the ensemble directory. If no further arguments are given
 
used to specify the ensemble directory. If no further arguments are given
 
it will list all ensemble files associated with the given tag.<BR>
 
it will list all ensemble files associated with the given tag.<BR>
 +
 
The option <B>-cluster</B> may be used to list only the files from
 
The option <B>-cluster</B> may be used to list only the files from
a specific cluster if <docmark>enscluster.pl</docmark> was run
+
a specific cluster if [[enscluster.pl]] was run
 
previously to perform the clustering. The utility
 
previously to perform the clustering. The utility
<docmark>showcluster.pl</docmark> is available to list all identified
+
[[showcluster.pl]] is available to list all identified
 
clusters. Normally cluster information is read for the tag for which the
 
clusters. Normally cluster information is read for the tag for which the
 
list of files is obtained. If clustering information is only available for
 
list of files is obtained. If clustering information is only available for
 
a different tag in the same ensemble of structures this tag may be given with
 
a different tag in the same ensemble of structures this tag may be given with
 
<B>-ctag</B> so that the corresponding cluster file is used instead.<BR>
 
<B>-ctag</B> so that the corresponding cluster file is used instead.<BR>
 +
 
The file list may be sorted according to values of
 
The file list may be sorted according to values of
 
an associated ensemble property if the property tag is given with <B>-sort</B>.<BR>
 
an associated ensemble property if the property tag is given with <B>-sort</B>.<BR>
 +
 
The option <B>-list</B> is available to provide a file with indices to
 
The option <B>-list</B> is available to provide a file with indices to
 
obtain file names for selected structures.<BR>
 
obtain file names for selected structures.<BR>
 +
 
Please note that by default the files are stored in compressed form
 
Please note that by default the files are stored in compressed form
 
(gzip). This script, however, always returns the file names in
 
(gzip). This script, however, always returns the file names in
uncompressed form without the <font color=#508060>.gz</font> extension, whether the
+
uncompressed form without the <font color=#508060>.gz</font> extension, whether the files are compressed or not.
files are compressed or not.
+
 
 
== Options ==
 
== Options ==
  

Revision as of 14:19, 30 July 2009

Usage

usage:   ensfiles.pl [options] tag
options: [-cluster level]
         [-ctag tag]
         [-dir workdir]
         [-list file]
         [-sort proptag]
         [-prop proptag]

Show source


Description

This script is used to extract a list of files from an ensemble structure. It requires an ensemble tag as argument and -dir may be used to specify the ensemble directory. If no further arguments are given it will list all ensemble files associated with the given tag.

The option -cluster may be used to list only the files from a specific cluster if enscluster.pl was run previously to perform the clustering. The utility showcluster.pl is available to list all identified clusters. Normally cluster information is read for the tag for which the list of files is obtained. If clustering information is only available for a different tag in the same ensemble of structures this tag may be given with -ctag so that the corresponding cluster file is used instead.

The file list may be sorted according to values of an associated ensemble property if the property tag is given with -sort.

The option -list is available to provide a file with indices to obtain file names for selected structures.

Please note that by default the files are stored in compressed form (gzip). This script, however, always returns the file names in uncompressed form without the .gz extension, whether the files are compressed or not.

Options

-help 
usage information


Examples

ensfiles.pl -dir data sample
extracts all ensemble structures associated with the sample tag.

data/0/1/sample.pdb
data/0/2/sample.pdb
data/0/3/sample.pdb
data/0/4/sample.pdb
data/0/5/sample.pdb
data/0/6/sample.pdb
data/0/7/sample.pdb
data/0/8/sample.pdb
data/0/9/sample.pdb
data/0/10/sample.pdb

...


ensfiles.pl -dir data -cluster t.2 sample
extracts the ensemble files in cluster t.2 from the sample set.

data/0/2/sample.pdb
data/0/4/sample.pdb
data/0/5/sample.pdb
data/0/6/sample.pdb
data/0/7/sample.pdb
data/0/9/sample.pdb
data/0/10/sample.pdb
data/0/13/sample.pdb
data/0/14/sample.pdb
data/0/15/sample.pdb

...


ensfiles.pl -dir data -list sel.file sample
extracts the file names from the ensemble structures belonging to the sample tag for the indices from sel.file.

data/0/1/sample.pdb
data/0/5/sample.pdb
data/0/6/sample.pdb
data/0/7/sample.pdb
data/0/9/sample.pdb