execute_experiments.sh

#!/bin/bash

# check the input parameters ($1 path of proteins | $2 initial number of bits | $3 final number of bits)
if [ "$1" == "" ] || [ "$2" == "" ] || [ "$3" == "" ]; then
    echo "Any parameter is missing"
    echo "Parameter 1 (proteins path): " $1
    echo "Parameter 2 (initial number bits): " $2
    echo "Parameter 3 (final number bits): " $3

    exit 1
fi

# read all lines of the file
lines=()
while read line; do
    lines+=("$line")
done <$1


for index in $(seq $2 $3); do
    
    for line in "${lines[@]}"; do

        proteinline="$(tr -s ' ' <<< "$line")"
        protein="$(cut -d' ' -f1 <<<"$proteinline")"
        aa="$(cut -d' ' -f2 <<<"$proteinline")"
        id="$(cut -d' ' -f3 <<<"$proteinline")"
        id=${id/"("/""}
        id=${id/")"/""}

        if [[ $id == *"#"* ]]; then

            for init in minifold random; do
                python3 main.py $protein $aa $index $init simulation
            done
    else       
            for init in minifold random; do
                python3 main.py $protein $aa $index $init simulation -i $id
            done
        fi
    done
done