149 lines
4.4 KiB
Bash
Executable File
149 lines
4.4 KiB
Bash
Executable File
#!/usr/bin/env bash
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export VMDNOCUDA=1
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#export VMDNOOPTIX=1
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export VMDNOOSPRAY=1
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#######################################################################################
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## ADJUSTABLE PARAMETERS ##
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#######################################################################################
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# set sel1 and sel1 name
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sel1=("resid 171" "acceptor")
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# set sel2 and sel2 name
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#sel2=("chain B and resname PHQ" "{/Arial-Italic Boc}")
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sel2=("resid 140 204" "donor")
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# job folder
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job_folder="4-jobs"
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# cutoff
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cutoff=3.0
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#######################################################################################
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## FUNCTIONS ##
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#######################################################################################
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# set folder name for output files
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out_dir="$(basename ${0})"
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out_dir="${out_dir%%.*}"
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# set output suffix
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suffix="${sel1[0]}_vs_${sel2[0]}"
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suffix="${suffix// /_}"
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# create array of systems
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function get_systems() {
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systems=()
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all_systems=()
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_jobs=( $(ls -d 1-concat/combined/*.pdb) )
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for _job in ${_jobs[@]}; do
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all_systems+=( $( basename ${_job%-*.pdb} ) )
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done
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systems+=( $(for _system in ${all_systems[@]}; do echo ${_system}; done | sort -u) )
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}
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get_systems
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#######################################################################################
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## CALC CONTACTS ##
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#######################################################################################
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function calc_contacts_num() {
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mkdir -p ${out_dir}
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echo ${systems[@]}
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for system in ${systems[@]}; do
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psf=$(ls 1-concat/combined/${system}-*.psf)
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dcd=$(ls 1-concat/combined/${system}-*.dcd)
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echo 'set n [molinfo top get numframes]' > temp.tcl
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echo "set sel1 [atomselect top \""${sel1[0]}"\"]" >> temp.tcl
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echo "set sel2 [atomselect top \""${sel2[0]}"\"]" >> temp.tcl
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echo "set fp [open "${out_dir}/${system}-${suffix}.csv" w]" >> temp.tcl
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# cycle over the trajectory
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echo 'for {set i 0} {$i <= $n} {incr i} {' >> temp.tcl
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echo ' $sel1 frame $i' >> temp.tcl
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echo ' $sel2 frame $i' >> temp.tcl
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echo " set contacts [measure contacts ${cutoff} \$sel1 \$sel2]" >> temp.tcl
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echo ' set count [llength [lindex $contacts 0]]' >> temp.tcl
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echo ' puts $fp "${i} ${count}"' >> temp.tcl
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echo '}' >> temp.tcl
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echo 'close $fp' >> temp.tcl
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vmd -dispdev text -eofexit ${psf} ${dcd} < "temp.tcl"
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sync
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rm "temp.tcl"
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done
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}
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calc_contacts_num
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function plot_contacts_num() {
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systems=()
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names=()
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for (( i = 0 ; i < ${#systems_names[@]} ; i+=2 )); do
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systems+=(${systems_names[${i}]})
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done
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for (( i = 1 ; i < ${#systems_names[@]} ; i+=2 )); do
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names+=("${systems_names[${i}]}")
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done
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echo 'set terminal pngcairo enhanced size 1600,1200 font "arial,24" linewidth 2' > temp
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echo "set output \"${out_dir}/combined-${suffix}.png\"" >> temp
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echo 'set autoscale' >> temp
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echo "set title \"${sel1[1]}-${sel2[1]} contacts\" font \"arial,40\"" >> temp
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echo 'set xlabel "ns" font "arial,32"' >> temp
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echo 'set ylabel "# Contacts" font "arial,32"' >> temp
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echo 'set border 1+2' >> temp
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echo 'set xtics nomirror out' >> temp
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echo 'set ytics nomirror' >> temp
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echo 'set grid' >> temp
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echo 'set grid noxtics' >> temp
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echo 'set key box top right' >> temp
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echo '#set yrange [-25:0]' >> temp
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echo '#set format y "%+-2.f"' >> temp
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echo 'set style data lines' >> temp
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echo '#set xzeroaxis ls 8' >> temp
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# linetypes
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echo '#set style line 1 pi 0 lw 1 ps 1 pt 0 lc rgb "black"' >> temp
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echo 'set style line 1 pi 0 lw 1 ps 1 pt 0 lc rgb "red"' >> temp
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echo 'set style line 2 pi 0 lw 1 ps 1 pt 0 lc rgb "green"' >> temp
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echo 'set style line 3 pi 0 lw 1 ps 1 pt 0 lc rgb "blue"' >> temp
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echo 'set style line 4 pi 0 lw 1 ps 1 pt 0 lc rgb "orange"' >> temp
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# plot
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echo 'plot \' >> temp
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for (( i = 0 ; i < ${#systems[@]} ; i++ )); do
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if [ $i -eq $((${#systems[@]} - 1)) ]; then
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echo "\"${out_dir}/${systems[$i]}-${suffix}.csv\" using 1:2 with linespoints ls $((${i} + 1)) title \""${names[$i]}"\"" >> temp
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else
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echo "\"${out_dir}/${systems[$i]}-${suffix}.csv\" using 1:2 with linespoints ls $((${i} + 1)) title \""${names[$i]}"\", \\" >> temp
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fi
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done
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echo 'exit' >> temp
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gnuplot temp
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#rm temp
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}
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