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run.sh
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run.sh
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#!/bin/bash
ligand_library=$1
box_center=$( echo $2 | sed 's/ //g' )
box_size=$( echo $3 | sed 's/ //g' )
top_n_scores=$4
force_field=$5
docking_method=$6
flexible_sidechains='Empty'
receptor=$(find * -type f | grep -v 'tapisjob')
# set flexible sidechains, if any
#FLEX=${flexible_sidechains}
#if [ -z $FLEX ]; then
# FLEX='Empty'
#fi
# Log commands, timing, run job
echo -n "starting: "
date
echo "================================================================"
echo "python3 /autodock-src/autodock.py \\"
echo " --receptor ${receptor} \\"
echo " --ligand_library ${ligand_library} \\"
echo " --center=\"${box_center}\" \\"
echo " --size \"${box_size}\" \\"
echo " --number ${top_n_scores} \\"
echo " --forcefield ${force_field} \\"
echo " --docking ${docking_method} \\"
echo " --sidechains ${flexible_sidechains} "
echo "================================================================"
MV2_ENABLE_AFFINITY=0 MV2_SMP_USE_CMA=0 \
python3 /autodock-src/autodock.py \
--receptor ${receptor} \
--ligand_library ${ligand_library} \
--center="${box_center}" \
--size "${box_size}" \
--number ${top_n_scores} \
--forcefield ${force_field} \
--docking ${docking_method} \
--sidechains ${flexible_sidechains}
echo -n "ending: "
date