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Top Forums Shell Programming and Scripting For loop to run external program Post 302557587 by oldmanwinter on Wednesday 21st of September 2011 04:18:33 PM
Old 09-21-2011
Question For loop to run external program

Hi, I was hoping for help with a for loop to run a program (vina) repeatedly using all the files in a folder as input. Currently my code looks like this:
Code:
#!/bin/bash
FILES=/home/afalk/Desktop/battest/*.pdbqt
for f in $FILES do
vina --config /home/afalk/Desktop/A.txt --ligand "$f".pdbqt
done

vina simply runs as "vina" in the terminal and this code is my attempt at translating a working batch file I had for windows. Whenever I try to run this, and after endless changes to the syntax all I get is "line 4: syntax error near unexpected token `vina'". Can anyone see what I'm doing wrong?
 

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for(n)							       Tcl Built-In Commands							    for(n)

__________________________________________________________________________________________________________________________________________________

NAME
for - 'For' loop SYNOPSIS
for start test next body _________________________________________________________________ DESCRIPTION
For is a looping command, similar in structure to the C for statement. The start, next, and body arguments must be Tcl command strings, and test is an expression string. The for command first invokes the Tcl interpreter to execute start. Then it repeatedly evaluates test as an expression; if the result is non-zero it invokes the Tcl interpreter on body, then invokes the Tcl interpreter on next, then repeats the loop. The command terminates when test evaluates to 0. If a continue command is invoked within body then any remaining commands in the current execution of body are skipped; processing continues by invoking the Tcl interpreter on next, then evaluating test, and so on. If a break command is invoked within body or next, then the for command will return immediately. The operation of break and continue are similar to the corresponding statements in C. For returns an empty string. Note: test should almost always be enclosed in braces. If not, variable substitutions will be made before the for command starts execut- ing, which means that variable changes made by the loop body will not be considered in the expression. This is likely to result in an infinite loop. If test is enclosed in braces, variable substitutions are delayed until the expression is evaluated (before each loop iter- ation), so changes in the variables will be visible. See below for an example: EXAMPLES
Print a line for each of the integers from 0 to 10: for {set x 0} {$x<10} {incr x} { puts "x is $x" } Either loop infinitely or not at all because the expression being evaluated is actually the constant, or even generate an error! The actual behaviour will depend on whether the variable x exists before the for command is run and whether its value is a value that is less than or greater than/equal to ten, and this is because the expression will be substituted before the for command is executed. for {set x 0} $x<10 {incr x} { puts "x is $x" } Print out the powers of two from 1 to 1024: for {set x 1} {$x<=1024} {set x [expr {$x * 2}]} { puts "x is $x" } SEE ALSO
break, continue, foreach, while KEYWORDS
for, iteration, looping Tcl for(n)
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