#!/bin/bash
#The script runs c2s_rmsd_analysis.py script which evaluates produced models by comparing them to the native structure given in $1
#The evaluation can be focused on a certain part of the structure give the start and end of this part in $2 and $3. The residue nubers in target.pdb 
# and model.pdb can be shifted. give the offset in $4. Finally, in $5 give the main part of output files names.


target=$1
focus1=$2
focus2=$3
offset=$4
temp_name=$5

EXPECTED_ARGS=5
BAD_ARGS=2

if [ $# -lt ${EXPECTED_ARGS} ]
then
        echo "USAGE: c2s_model_analysis <target.pdb> <focus_res1> <focus_res2> <offset> <temp_name> "
        exit $BAD_ARGS
fi




ls *.pdb | while read model; do
c2s_rmsd_analysis.py $model ${target} $focus1 $focus2 $offset
c2s_measure_dist.py $model $offset $target
done
c2s_measure_dist.py $target 0 $target

echo -e "\nGeneral rmsd" > tmp_${temp_name}_rmsd_gen
echo -e "\nRMSD of resiudes - general alignment" > tmp_${temp_name}_rmsd_res
echo -e "\nRMSD of residues - filter alignment" > tmp_${temp_name}_rmsd_filt
echo -e "\nRMSD of filter center residues - filter center alignment" > tmp_${temp_name}_rmsd_filt_centr
echo -e "\nDistances within the selectivity filter" > tmp_${temp_name}_pore_width
echo -e "\nDistances from ions in the pore and displacements from native positions" > tmp_${temp_name}_at_dist

rm tmp_${temp_name}
cat *_rmsd_analysis.txt | sed -e '1!{/Model/d}' >> tmp_${temp_name}_rmsd_gen
cat *_residues_rmsd.txt | sed -e '1!{/Model/d}' >> tmp_${temp_name}_rmsd_res 
cat *_res_filt_rmsd.txt | sed -e '1!{/Model/d}' >> tmp_${temp_name}_rmsd_filt
cat *_res_filt_centr_rmsd.txt | sed -e '1!{/Model/d}' >> tmp_${temp_name}_rmsd_filt_centr
cat *pore_width.txt | sed -e '1!{/Model/d}' >> tmp_${temp_name}_pore_width
cat *at_dist.txt | sed -e '1!{/Model/d}' >> tmp_${temp_name}_at_dist


cat tmp_${temp_name}* > tmp_${temp_name}

