Tool Set Documentation

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usage: [options] tag [command]
options: [-new tag]
         [-set prop[:index][,prop[:index]]]
         [-natpdb pdbFile]
         [-dir workdir]
         [-update frq]
         [-run [from:]to]
         [-cmd file]
         [-log file]

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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 and 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 here


usage information
-new tag 
tag name for new set of structures to be added to ensemble
-set prop[:index][,...] 
property names (and column indices) for data to be added to ensemble
overwrite property data even if it already exists
do not pass PDB file as input to given command
-natpdb pdbFile 
provide reference structure for automatically calculating RMSD values
-dir workdir 
data directory
-update frq 
update frequency of property database during parallel calculation
(do not) compress new structures that are being created
-run [from:]to 
limit command to subset of ensemble
-cmd file 
provide script file to be executed
-log file 
output log file

Examples -dir data -set sasa lat -out sasa
obtains solvent accessible surface areas by executing -out sasa for each ensemble structure associated with the lat tag and stores them under the sasa property tag. -dir data -cpus 2 -new amber lat -par steps=100 -elog amber.elog
executes -par steps=100 -elog amber.elog for each structure associated with the lat tag to obtain new structures minimized with Amber. From the resulting structures a new ensemble set is created with the amber tag. The run is done in parallel on two CPUs.