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I'm writing a script to run AutoDock Vina. The script will look for all files with .pdbqt ending with ligand in front of it. When the script is run, it produces an output file with the same name of the file, but including _out.pdbqt on it. For example ligand_1.pdbqt becomes ligand_1_out.pdbqt. How can I prevent the ligand_1_out.pdbqt from being run in the script. The script is written below.

#!/bin/bash
for x in ligand_*.pdbqt;
do
./vina_1.2.3_mac_x86_64 --config conf.txt --ligand $x
done
Andy Lester
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Carlos Ventura
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  • I assume you want it to avoid trying to run output files on **subsequent** invocations after the first time through the loop... – Mark Setchell Feb 08 '22 at 19:58

1 Answers1

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You should be able to avoid files containing "out" with:

for x in ligand_*.pdbqt ; do
    [[ "$x" == *out** ]] && continue
    ./vina ...
done
Mark Setchell
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