#!/usr/bin/env bash

#######################################################################################
## ADJUSTABLE PARAMETERS                                                             ##
#######################################################################################

# set folder name that contains the jobs
job_folder="4-new_jobs"

#######################################################################################
## CLUSTER ANALYSIS                                                                  ##
#######################################################################################

out_dir="$(basename ${0})"
out_dir="${out_dir%%.*}"

# create array of systems

function get_systems() {
  systems=()
  all_systems=()
  _jobs=( $(ls -d ../${job_folder}/*/*/) )
  for _job in ${_jobs[@]}; do
    all_systems+=( $(basename ${_job}) )
  done
  systems+=( $(for _system in ${all_systems[@]}; do echo ${_system}; done | sort -u) )
}
get_systems

for system in ${systems[@]}; do
    mkdir -p ${out_dir}/median/${system}
    mkdir -p ${out_dir}/average/${system}

    # median clusters

    # on SrtA
    ( echo 'chA_&_CA_&_r_66-205' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/median/${system}/${system}.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/median/${system}/${system}.xpm -dist ${out_dir}/median/${system}/${system}.xvg -cl ${out_dir}/median/${system}/${system}.pdb ) &
	
    # on ligand
    ( echo 'chB' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/median/${system}/${system}_ligand.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/median/${system}/${system}_ligand.xpm -dist ${out_dir}/median/${system}/${system}_ligand.xvg -cl ${out_dir}/median/${system}/${system}_ligand.pdb ) &

    # average clusters

    # on SrtA
    ( echo 'chA_&_CA_&_r_66-205' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/average/${system}/${system}_av.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/average/${system}/${system}_av.xpm -dist ${out_dir}/average/${system}/${system}_av.xvg -av -cl ${out_dir}/average/${system}/${system}_av.pdb ) &
	
    # on ligand
    ( echo 'chB' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/average/${system}/${system}_ligand_av.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/average/${system}/${system}_ligand_av.xpm -dist ${out_dir}/average/${system}/${system}_ligand_av.xvg -av -cl ${out_dir}/average/${system}/${system}_ligand_av.pdb ) &

  wait

done