MMTSB
Tool Set Documentation

ensfiles.pl

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Usage

usage:   ensfiles.pl [options] tag
options: [-cluster level]
         [-ctag tag]
         [-dir workdir]
         [-list file]
         [-sort proptag]
         [-prop proptag]
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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
-cluster level 
clustering level for hierarchical clusters
-ctag alttag 
read clustering info from alttag.clusters
-dir directory 
data directory
-list file 
read index file of file names to be returned from file
-sort tag 
sort file list by given property
-prop tag 
write out property value along with file name

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