create_vector

#  affinity vector is created and multiplied with gene expression values from receptors_contracted file
#  input param: target_dir
#  output: affinity vector in $target_dir
#  modification date: 09/03/2022

target_dir=$1
WORKDIR=$2

random_affinity=`cat $WORKDIR/random_affinity`
complexes=`cat $WORKDIR/complexes`
ONES=1

> $target_dir/vec

MD_engine=`cat $WORKDIR/MD_engine`   
if  [ $MD_engine == Vina ]
then
    for (( N=1; N<$((complexes+1)); N++ ))                  #create Vina vector
    do
        #printf -v n "%03d" $N
        printf -v log_index "%03d" $N
        
        if  [ -e ${target_dir}/log_${log_index}.txt ]
        then
            nolines=`wc -l < ${target_dir}/log_${log_index}.txt`
            if  [ $nolines -ne $ONES ]
            then
                lineno=`grep -n kcal ${target_dir}/log_${log_index}.txt | awk '{print $1}'` #get line nr with kcal string
                lineno=`echo $lineno | awk '{ print substr( $0, 1, length($0)-1 ) }'` #strip :
                let lineno=lineno+2        #read line with the best affinity and store in vec
                line=`head -$lineno ${target_dir}/log_${log_index}.txt | tail -1`
                echo $line | awk '{print $2}' >> ${target_dir}/vec
            else
                echo ${random_affinity} >> ${target_dir}/vec
            fi
        else
            echo ${random_affinity} >> ${target_dir}/vec
        fi
    done
else
    for (( N=1; N<$((complexes+1)); N++ ))                 #create Gromacs vector
    do
        printf -v comp_index "%03d" $N
        FBE=`cat ${target_dir}/log_${comp_index}.txt`
        echo $FBE >> $target_dir/vec
    done
    
fi
#cp ${target_dir}/vec ${target_dir}/vec.orig #for debug only


index=1
> $target_dir/vec.tmp
while read -r line
do
    genex=`echo $line | awk '{print $6}'`
    if  [ -z "$genex" ]                                    #set genex to 1 if unset or empty
    then
        genex=1
    fi
    affinity=`head -"$index" ${target_dir}/vec | tail -1`
    product=`echo $genex $affinity | awk '{print $1 * $2}'`
    echo $product >> ${target_dir}/vec.tmp
    let "index++"
done < $WORKDIR/receptors_contracted

mv $target_dir/vec.tmp ${target_dir}/vec