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Top Forums Shell Programming and Scripting For loop to run external program Post 302557592 by Corona688 on Wednesday 21st of September 2011 04:29:07 PM
Old 09-21-2011
You nearly had it! Smilie You didn't put a ; or newline before the 'do', though.

You don't need to put the filenames in a variable. That could actually be bad -- $FILES will split "file name.pdbgt file2.pdbgt" into "file", "name.pdbgt", "file2.pdbgt". "for FILE in *" won't.

You also don't need to put the ".pdbgt" back on the end, it never left Smilie

Code:
#!/bin/bash
for f in /home/afalk/Desktop/battest/*.pdbqt
do
        vina --config /home/afalk/Desktop/A.txt --ligand "$f"
done

 

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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 input is in the form accepted by f77(1) -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. -tn Make the nonzero integer n the lowest valued label in the output program (default 10). -cn Increment successive labels in the output program by the nonzero integer n (default 1). -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 a small code segments to a loop if otherwise the loop would have exits to several places including the segment, and the segment can be reached only from the loop. `Small' is close to, but not equal to, the number of statements in the code segment. Values of n under 10 are suggested. FILES
/tmp/struct* /usr/libexec/struct/* SEE ALSO
f77(1) BUGS
Struct knows Fortran 66 syntax, but not full Fortran 77. 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. The labels generated cannot go above 32767. If you get a goto without a target, try -e . 7th Edition October 22, 1996 STRUCT(1)
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