ensrun.pl - Revision history

Edit: /* Description */

2009-07-30T12:25:08Z

Description

Edit: /* Options */

2009-07-30T12:24:25Z

Options

Edit: /* Description */

2009-07-30T12:14:00Z

Description

Edit: /* Description */

2009-07-30T12:11:04Z

Description

Feig at 14:28, 12 August 2006

2006-08-12T14:28:52Z

New page

__NOTOC__
== Usage ==

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

== Description ==

This script is used to execute user commands for ensemble structures.
Required is the tag of the strucutures for which the command is applied.
A single command may follow as the last parameter on the command line.
Alternatively, one or more commands can be provided through standard input.
 
For each ensemble structure the command is then executed with the
PDB structure passed through standard input/output. For a list of
commands, the PDB structure is only passed to the first command.
The command has to be setup appropriately to be able to read the PDB
structure from standard input unless -noinp is given. In this
case no data is passed to the command through standard input/output.
 
Three modes are available to treat the
command output. In the first mode (if neither of the options -set or
-new are given) the output is ignored. In the second mode
the output is used to set one or more property values within
the ensemble under property tags given with the -set option.
One or more property tag names may be appended with an index specifying the
field within the command output line where the respective value is located.
Values that have been set already they will not be recomputed
and overwritten unless -overwrite is specified.
In the third mode the command output is assumed to be a new PDB structure
and used to generate a new ensemble structure set. In this case the
corresponding tag of the new ensemble has to be set with -new. The
new structures are then automatically checked in and analyzed if
a reference structure is available or supplied with -natpdb.
 
As in <docmark>ensmin.pl</docmark> and <docmark>enslatsim.pl</docmark>
the options -dir, -run are available to select the
ensemble directory and specify a subset of ensemble structures.
The options for parallel execution are listed <A HREF="http://mmtsb.scripps.edu/cgi-bin/parallelopt">here.</A> 

== Options ==

; -help : usage information

== Examples ==

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

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

@@ Line 33: / Line 33: @@
 a reference structure is available or supplied with <B>-natpdb</B>.
 <BR><BR>
-As in <docmark>ensmin.pl</docmark> and <docmark>enslatsim.pl</docmark>
+As in [[ensmin.pl]] and [[enslatsim.pl]]
 the options <B>-dir</B>, <B>-run</B> are available to select the
 ensemble directory and specify a subset of ensemble structures.

@@ Line 36: / Line 36: @@
 the options <B>-dir</B>, <B>-run</B> are available to select the
 ensemble directory and specify a subset of ensemble structures.
-The options for parallel execution are listed [http://feig.bch.msu.edu/cgi-bin/parallelopt here]<BR>
+The options for parallel execution are listed [http://feig.bch.msu.edu/mmtsb/PARALLELoptions here]<BR>
 == Options ==

@@ Line 36: / Line 36: @@
 the options <B>-dir</B>, <B>-run</B> are available to select the
 ensemble directory and specify a subset of ensemble structures.
-The options for parallel execution are listed <A HREF="http://mmtsb.scripps.edu/cgi-bin/parallelopt">here.</A><BR>
+The options for parallel execution are listed [http://feig.bch.msu.edu/cgi-bin/parallelopt here]<BR>
 == Options ==

@@ Line 41: / Line 41: @@
 ; -help : usage information
+; -new tag : tag name for new set of structures to be added to ensemble
 == Examples ==