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Top Forums Shell Programming and Scripting For loop to run external program Post 302557615 by cfajohnson on Wednesday 21st of September 2011 05:12:46 PM
Old 09-21-2011
Quote:
Originally Posted by oldmanwinter
Thank you, except now it says "line 5: vina: command not found" if I change the code to
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

it returns "line 5: --config: command not found" config is an internal command for vina.

It is trying to run the command, --config, because $vina is empty.
 

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STRUCT(1)						      General Commands Manual							 STRUCT(1)

NAME
struct - structure Fortran programs SYNOPSIS
struct [ option ] ... file DESCRIPTION
Struct translates the Fortran program specified by file (standard input default) into a Ratfor program. Wherever possible, Ratfor control constructs replace the original Fortran. Statement numbers appear only where still necessary. Cosmetic changes are made, including chang- ing Hollerith strings into quoted strings and relational operators into symbols (.e.g. `.GT.' into `>'). The output is appropriately indented. The following options may occur in any order. -s Input is accepted in standard format, i.e. comments are specified by a c, C, or * in column 1, and continuation lines are specified by a nonzero, nonblank character in column 6. Normally, a statement whose first nonblank character is not alphanumeric is treated as a continuation. -i Do not turn computed goto statements into switches. (Ratfor does not turn switches back into computed goto statements.) -a Turn sequences of else ifs into a non-Ratfor switch of the form switch { case pred1: code case pred2: code case pred3: code default: code } The case predicates are tested in order; the code appropriate to only one case is executed. This generalized form of switch state- ment does not occur in Ratfor. -b Generate goto's instead of multilevel break statements. -n Generate goto's instead of multilevel next statements. -en If n is 0 (default), place code within a loop only if it can lead to an iteration of the loop. If n is nonzero, admit code segments with fewer than n statements to a loop if otherwise the loop would have exits to several places including the segment, and the seg- ment can be reached only from the loop. FILES
/tmp/struct* /usr/lib/struct/* SEE ALSO
f77(1) BUGS
Struct knows Fortran 66 syntax, but not full Fortran 77 (alternate returns, IF...THEN...ELSE, etc.) If an input Fortran program contains identifiers which are reserved words in Ratfor, the structured version of the program will not be a valid Ratfor program. Extended range DO's generate cryptic errors. Columns 73-80 are not special even when -s is in effect. Will not generate Ratfor FOR statements. STRUCT(1)
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