MMTSB
Tool Set Documentation

Difference between revisions of "rexanalysis.pl"

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; -help : usage information
 
; -help : usage information
 
; -dir workdir : replica exchange directory
 
; -dir workdir : replica exchange directory
; -inx from:to : specify replica exchange cycle(s)
+
; -inx from:to : specify replica exchange cycle(s)
 
; -step value : skip replica exchange cycles according to the given value
 
; -step value : skip replica exchange cycles according to the given value
 
; -byclient client : show information for specific client
 
; -byclient client : show information for specific client
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; -function file : apply a custom function for analysis
 
; -function file : apply a custom function for analysis
 
; -nanvalue value : replace all NAN values with the given value
 
; -nanvalue value : replace all NAN values with the given value
; -wham prop:fname:from:to:nbins[=...] : WHAM analysis
+
; -wham prop:fname:from:to:nbins[=...] : WHAM analysis
; -whamtemp temp[:temp2...] : Temperature-WHAM analysis
+
; -whamtemp temp[:temp2...] : Temperature-WHAM analysis
; -whemener file :  
+
; -whamener file :  
 
; -out dcdfile : convert a any archive file to trajectory file
 
; -out dcdfile : convert a any archive file to trajectory file
; -atoms from:to : specify an atom selection range for output trajectory file
+
; -atoms from:to : specify an atom selection range for output trajectory file
 
; -nsel Selection : specify a selection for output trajectory file
 
; -nsel Selection : specify a selection for output trajectory file
 
; -verbose : outputs periodic notifications while generating output trajectory file
 
; -verbose : outputs periodic notifications while generating output trajectory file

Revision as of 04:58, 29 July 2009

Usage

usage:   rexanalysis.pl [options]
options: [-dir workdir]
         [-inx from:to] [-step value]
         [-byclient clientid]
         [-bytemp temp]
         [-bycond condindex]
         [-order client|temp]
         [-apply cmd]
         [-function file]
         [-nanvalue value]
         [-wham prop:fname:from:to:nbins[=...]]
         [-whamtemp temp[:temp2...]
         [-whamener file]
         [-out dcdfile]
         [-atoms from:to]  [-nsel Selection]
         [-verbose]

Show source


Description

This script is used to extract and process replica exchange simulation information from the server output files. With the option -clients a list of all client IDs is selected, with -conds all replica conditions are selected. The option -byclient selects simulation information at each step for a given client. The output consists of <add information here> With -bytemp and -bycond the same information is selected at each step for the client at the given temperature or with the given condition. -best is available as a shortcut notation for the first condition (usually corresponding to the lowest temperature). The option -apply can be used to request additional processing with other MMTSB tools. The option -function can be used to further process the data with user-defined functions.

Options

-help 
usage information
-dir workdir 
replica exchange directory
-inx from:to 
specify replica exchange cycle(s)
-step value 
skip replica exchange cycles according to the given value
-byclient client 
show information for specific client
-bytemp temp 
show information for specific temperature
-bycond condindex 
show information for specific condition
-order client|temp 
-apply cmd 
apply a custom command for analysis
-function file 
apply a custom function for analysis
-nanvalue value 
replace all NAN values with the given value
-wham prop:fname:from:to:nbins[=...] 
WHAM analysis
-whamtemp temp[:temp2...] 
Temperature-WHAM analysis
-whamener file 
-out dcdfile 
convert a any archive file to trajectory file
-atoms from:to 
specify an atom selection range for output trajectory file
-nsel Selection 
specify a selection for output trajectory file
-verbose 
outputs periodic notifications while generating output trajectory file

Examples

rexanalysis.pl -inx 1500:2000 -bytemp 310 -apply "convpdb.pl -chain A | centerOfMass.pl " > centerOfMass-A-temp310.data
This command computes the center of mass for a series of pdb files (in this case, the last 500 structures of 2000), based on temperature from replica exchange simulations. Note how multiple MMTSB toolset commands are invoked in this one line.

 add output

The data in the output file can be pulled out by:
awk '{print $5,$6,$7}' centerOfMass-A-temp310.data > centerOfMass-A-temp310.data.dat


rexanalysis.pl -inx 1500:2000 -best -apply "convpdb.pl -chain A | centerOfMass.pl " > centerOfMass-A-cond0.data
This command computes the center of mass for a series of pdb files, based on first condition from replica exchange simulations ("-best" is the shortcut for "-bycond 0" and usually corresponds to the lowest temperature).

 add output


rexanalysis.pl -inx 1500:2000 -bycond 2 -apply "convpdb.pl -chain B | rgyr.pl " > rgyr-cond2-B.data
This command computes the radius of gyration for a series of pdb files, based on condition 2 from replica exchange simulations.

 add output

The data in the output file can be pulled out by:
awk '{print $5}' rgyr-cond2-B.data >rgyr-cond2-B.data.dat