Add some trajectory analysis scripts

trajectory_analysis/7-contacts2.sh

@@ -0,0 +1,148 @@
+#!/usr/bin/env bash
+export VMDNOCUDA=1
+#export VMDNOOPTIX=1
+export VMDNOOSPRAY=1
+
+#######################################################################################
+## ADJUSTABLE PARAMETERS                                                             ##
+#######################################################################################
+
+# set sel1 and sel1 name
+sel1=("resid 171" "acceptor")
+# set sel2 and sel2 name
+#sel2=("chain B and resname PHQ" "{/Arial-Italic Boc}")
+sel2=("resid 140 204" "donor")
+# job folder
+job_folder="4-jobs"
+# cutoff
+cutoff=3.0
+
+
+#######################################################################################
+## FUNCTIONS                                                                         ##
+#######################################################################################
+
+# set folder name for output files
+out_dir="$(basename ${0})"
+out_dir="${out_dir%%.*}"
+
+# set output suffix
+suffix="${sel1[0]}_vs_${sel2[0]}"
+suffix="${suffix// /_}"
+
+# create array of systems
+
+function get_systems() {
+  systems=()
+  all_systems=()
+  _jobs=( $(ls -d 1-concat/combined/*.pdb) )
+  for _job in ${_jobs[@]}; do
+    all_systems+=( $( basename ${_job%-*.pdb} ) )
+  done
+  systems+=( $(for _system in ${all_systems[@]}; do echo ${_system}; done | sort -u) )
+}
+get_systems
+
+
+#######################################################################################
+## CALC CONTACTS                                                                     ##
+#######################################################################################
+
+function calc_contacts_num() {
+  
+  mkdir -p ${out_dir}
+  echo ${systems[@]}
+  
+  for system in ${systems[@]}; do
+    
+    psf=$(ls 1-concat/combined/${system}-*.psf)
+    dcd=$(ls 1-concat/combined/${system}-*.dcd)
+  
+    echo 'set n [molinfo top get numframes]' > temp.tcl
+    echo "set sel1 [atomselect top \""${sel1[0]}"\"]" >> temp.tcl
+    echo "set sel2 [atomselect top \""${sel2[0]}"\"]" >> temp.tcl
+    echo "set fp [open "${out_dir}/${system}-${suffix}.csv" w]" >> temp.tcl
+    
+    # cycle over the trajectory
+    echo 'for {set i 0} {$i <= $n} {incr i} {' >> temp.tcl
+    echo '  $sel1 frame $i' >> temp.tcl
+    echo '  $sel2 frame $i' >> temp.tcl
+    echo "  set contacts [measure contacts ${cutoff} \$sel1 \$sel2]" >> temp.tcl
+    echo '  set count [llength [lindex $contacts 0]]' >> temp.tcl
+    echo '  puts $fp "${i} ${count}"' >> temp.tcl
+    echo '}'  >> temp.tcl
+    echo 'close $fp'  >> temp.tcl
+    
+    vmd -dispdev text -eofexit ${psf} ${dcd} < "temp.tcl"
+    sync
+    rm "temp.tcl"
+    
+  done
+  
+}
+  
+  
+calc_contacts_num
+  
+function plot_contacts_num() {
+
+  systems=()
+  names=()
+  
+  for (( i = 0 ; i < ${#systems_names[@]} ; i+=2 )); do
+    systems+=(${systems_names[${i}]})
+  done
+  
+  for (( i = 1 ; i < ${#systems_names[@]} ; i+=2 )); do
+    names+=("${systems_names[${i}]}")
+  done
+
+  echo 'set terminal pngcairo enhanced size 1600,1200 font "arial,24" linewidth 2' > temp
+  echo "set output \"${out_dir}/combined-${suffix}.png\"" >> temp
+  echo 'set autoscale' >> temp
+  echo "set title \"${sel1[1]}-${sel2[1]} contacts\" font \"arial,40\"" >> temp
+  echo 'set xlabel "ns" font "arial,32"' >> temp
+  echo 'set ylabel "# Contacts" font "arial,32"' >> temp
+  echo 'set border 1+2' >> temp
+  echo 'set xtics nomirror out' >> temp
+  echo 'set ytics nomirror' >> temp
+  echo 'set grid' >> temp
+  echo 'set grid noxtics' >> temp
+  echo 'set key box top right' >> temp
+  echo '#set yrange [-25:0]' >> temp
+  echo '#set format y "%+-2.f"' >> temp
+  echo 'set style data lines' >> temp
+  echo '#set xzeroaxis ls 8' >> temp
+  
+  # linetypes
+  echo '#set style line 1 pi 0 lw 1 ps 1 pt 0 lc rgb "black"' >> temp
+  echo 'set style line 1 pi 0 lw 1 ps 1 pt 0 lc rgb "red"' >> temp
+  echo 'set style line 2 pi 0 lw 1 ps 1 pt 0 lc rgb "green"' >> temp
+  echo 'set style line 3 pi 0 lw 1 ps 1 pt 0 lc rgb "blue"' >> temp
+  echo 'set style line 4 pi 0 lw 1 ps 1 pt 0 lc rgb "orange"' >> temp
+  
+  # plot
+  echo 'plot \' >> temp
+  
+  for (( i = 0 ; i < ${#systems[@]} ; i++ )); do
+    if [ $i -eq $((${#systems[@]} - 1)) ]; then
+      echo "\"${out_dir}/${systems[$i]}-${suffix}.csv\" using 1:2 with linespoints ls $((${i} + 1)) title \""${names[$i]}"\"" >> temp
+    else
+      echo "\"${out_dir}/${systems[$i]}-${suffix}.csv\" using 1:2 with linespoints ls $((${i} + 1)) title \""${names[$i]}"\", \\" >> temp
+    fi
+  done
+  
+  echo 'exit' >> temp
+
+  gnuplot temp
+  #rm temp
+}
+  
+  
+  
+  
+  
+  
+  
+  
+