vina-ssh

#! /usr/bin/env bash
ip=''
user=''

shift

payload_create() {
while true; do
  case $1 in
    receptor	) receptor=$(basename "$3"); vina_cache=$(dirname $3); shift 3;;
    ligand	) ligand=$(basename "$3"); shift 3;;
    center_x	) center_x="$3"; shift 3;;
    center_y	) center_y="$3"; shift 3;;
    center_z	) center_z="$3"; shift 3;;
    size_x	) size_x="$3"; shift 3;;
    size_y	) size_y="$3"; shift 3;;
    size_z	) size_z="$3"; shift 3;;
    out		) out=$(basename "$3"); shift 3;;
    log		) log=$(basename "$3"); shift 3;;
    num_modes	) num_modes="$3"; shift 3;;
    ''		) break;;
    *		) echo hi $1; shift 1;;
  esac
done
}

payload_create $(cat $@)
payload="receptor = $receptor
ligand = $ligand
center_x = $center_x
center_y = $center_y
center_z = $center_z
size_x = $size_x
size_y = $size_y
size_z = $size_z
out = $out
log = $log
num_modes = $num_modes"

scp $vina_cache/$receptor $vina_cache/$ligand $user@$ip:/tmp/

echo "$payload" | ssh $user@$ip "mkdir ~/.vina_ssh &> /dev/null
cd ~/.vina_ssh
cp /tmp/$receptor /tmp/$ligand . &> /dev/null
cat > ~/.vina_ssh/config_ssh.txt
vina --config ~/.vina_ssh/config_ssh.txt &> /dev/null
cat $out
rm -rf ~/.vina_ssh &> /dev/null
" > $vina_cache/$out