MMTSB
Tool Set Documentation

Difference between revisions of "rexanalysis.pl"

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== Description ==
 
== Description ==
This script is used to extract and process replica exchange simulation information from the server output files.
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This script is used to extract and process replica exchange simulation information from the server output files.<BR>
With the option -clients a list of all client IDs is selected, with -conds all replica conditions are selected.
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The option -byclient selects simulation information at each step for a given client. The output consists of <add information here>
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The option <TT>-byclient</TT> selects simulation information at each step for a specific client. With <TT>-bytemp</TT> and <TT>-bycond</TT> the same information is selected at each step for different replicas at specific temperatures or conditions.<BR>
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).
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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.
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The option <TT>-apply</TT> can be used to apply an external command to each conformation, with <TT>-function</TT> an internal perl function is applied
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(see [[analyze.pl]] for more details).<BR>
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It is also possible to carry out WHAM analysis through the external ptWHAM
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program by using the <TT>-wham</TT> option.<BR>
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When it is desirable to deal with trajectory files rather than archive files, <TT>-out</TT> can be used to specify a CHARMM-compatible trajectory output file where structures will be written.  This option for generating a DCD file is useful when dealing with large structures, for visualization, and for analysis. A subset of coordinates can be written to the trajectory file via the <TT>-atoms</TT> or <TT>-nsel</TT> options.
  
 
== Options ==
 
== Options ==
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; -bytemp temp : show information for specific temperature
 
; -bytemp temp : show information for specific temperature
 
; -bycond condindex : show information for specific condition
 
; -bycond condindex : show information for specific condition
; -order client|temp :
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; -order client|temp : when showing information for all clients order either by client or by temperature
 
; -apply cmd : apply a custom command for analysis
 
; -apply cmd : apply a custom command for analysis
 
; -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&#58;fname&#58;from&#58;to&#58;nbins[=...] : WHAM analysis
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; -wham prop&#58;fname&#58;from&#58;to&#58;nbins[=...] : request WHAM analysis
; -whamtemp temp[&#58;temp2...] : Temperature-WHAM analysis
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; -whamtemp temp[&#58;temp2...] : specify temperature(s) for WHAM analysis
; -whamener file :  
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; -whamener file : output file name for WHAM energies
 
; -out dcdfile : convert a any archive file to trajectory file
 
; -out dcdfile : convert a any archive file to trajectory file
 
; -atoms from&#58;to : specify an atom selection range for output trajectory file
 
; -atoms from&#58;to : specify an atom selection range for output trajectory file
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== Examples ==
 
== Examples ==
  
<small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -bytemp 310 -apply "convpdb.pl -chain A |  centerOfMass.pl " > centerOfMass-A-temp310.data</span></small>
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<mmtsbToolExample cmd="rexanalysis.pl" set="test1"></mmtsbToolExample>
<br>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:<br>
 
<small>awk '{print $5,$6,$7}' centerOfMass-A-temp310.data > centerOfMass-A-temp310.data.dat</small>
 
 
 
 
 
<small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -best -apply "convpdb.pl -chain A |  centerOfMass.pl " > centerOfMass-A-cond0.data</span></small>
 
<br>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
 
 
 
 
 
<small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -bycond 2 -apply "convpdb.pl -chain B |  rgyr.pl " > rgyr-cond2-B.data</span></small>
 
<br>This command computes the radius of gyration for a series of pdb files, based on condition 2 from replica exchange simulations.
 
  
  add output
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<mmtsbToolExample cmd="rexanalysis.pl" set="test2"></mmtsbToolExample>
  
The data in the output file can be pulled out by:<br>
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<mmtsbToolExample cmd="rexanalysis.pl" set="test3"></mmtsbToolExample>
<small>awk '{print $5}' rgyr-cond2-B.data >rgyr-cond2-B.data.dat</small>
 

Latest revision as of 01:52, 31 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.

The option -byclient selects simulation information at each step for a specific client. With -bytemp and -bycond the same information is selected at each step for different replicas at specific temperatures or conditions.

The option -apply can be used to apply an external command to each conformation, with -function an internal perl function is applied (see analyze.pl for more details).

It is also possible to carry out WHAM analysis through the external ptWHAM program by using the -wham option.

When it is desirable to deal with trajectory files rather than archive files, -out can be used to specify a CHARMM-compatible trajectory output file where structures will be written. This option for generating a DCD file is useful when dealing with large structures, for visualization, and for analysis. A subset of coordinates can be written to the trajectory file via the -atoms or -nsel options.

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 
when showing information for all clients order either by client or by temperature
-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[=...] 
request WHAM analysis
-whamtemp temp[:temp2...] 
specify temperature(s) for WHAM analysis
-whamener file 
output file name for WHAM energies
-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 1:4 -bytemp 300 -apply centerOfMass.pl -dir rex
computes the center of mass for the first 4 cycles at 300K from a replica exchange simulation

1 0 298.000000 aa1 0.765086 0.601017 1.998906
2 0 298.000000 aa2 0.763471 0.364911 2.078037
3 0 298.000000 aa2 0.767218 0.393992 2.071549
4 0 298.000000 aa2 0.753049 0.413178 2.076809


rexanalysis.pl -inx 1:4 -order temp -function end2end.distance -dir rex
computes the end-to-end distance with the given function for all replicas and writes them out sorted by the temperature of the replica at each cycle

48.3714121150086 9.18275149396955 32.2333772043824 32.9814352174068 
8.95924567137212 48.5532828447264 31.8888307248792 33.1154562704487 
8.2763734207683 31.9335954912691 48.592404128629 32.5800590238876 
8.0443633682225 31.2211429323143 48.5883151179376 32.1646963144377 


rexanalysis.pl -bycond 2 -nsel 1-25 -out traj.dcd -dir rex
generates a trajectory from the replica exchange conformations at condition 2 for residues 1 through 25