Add some trajectory analysis scripts
This commit is contained in:
cryobry
210
trajectory_analysis/7-contacts.sh
Executable file
210
trajectory_analysis/7-contacts.sh
Executable file
@@ -0,0 +1,210 @@
|
||||
#!/usr/bin/env bash
|
||||
export VMDNOCUDA=1
|
||||
#export VMDNOOPTIX=1
|
||||
export VMDNOOSPRAY=1
|
||||
|
||||
#######################################################################################
|
||||
## ADJUSTABLE PARAMETERS ##
|
||||
#######################################################################################
|
||||
|
||||
# set sel1 and sel1 name
|
||||
sel1=("chain A and name CA" "SrtA")
|
||||
# set sel2 and sel2 name
|
||||
#sel2=("chain B and resname PHQ" "{/Arial-Italic Boc}")
|
||||
sel2=("chain B" "SS")
|
||||
# only run specific systems
|
||||
#my_systems=("ALL")
|
||||
systems_names=('ALL' '+{/Arial-Italic Boc} +Ca^{2+}' 'no_CA' '+{/Arial-Italic Boc} −Ca^{2+}' 'no_PHQ' '−{/Arial-Italic Boc} +Ca^{2+}' 'no_PHQ_no_CA' '−{/Arial-Italic Boc} −Ca^{2+}')
|
||||
# cutoff
|
||||
cutoff=3.0
|
||||
# combine?
|
||||
combine=1
|
||||
|
||||
#######################################################################################
|
||||
## 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// /_}"
|
||||
|
||||
|
||||
#######################################################################################
|
||||
## CALC CONTACTS ##
|
||||
#######################################################################################
|
||||
|
||||
function calc_contacts() {
|
||||
|
||||
systems=()
|
||||
|
||||
for (( i = 0 ; i < ${#systems_names[@]} ; i+=2 )); do
|
||||
systems+=(${systems_names[i]})
|
||||
done
|
||||
|
||||
mkdir -p ${out_dir}
|
||||
|
||||
for system in ${systems[@]}; do
|
||||
|
||||
psf=$(ls 1-concat/combined/${system}-*.psf)
|
||||
dcd=$(ls 1-concat/combined/${system}-*.dcd)
|
||||
|
||||
echo 'set numframes [expr {[molinfo top get numframes] - 1}]' > temp.tcl
|
||||
echo 'set totframes [expr $numframes + 1]' >> temp.tcl
|
||||
echo "set A [atomselect top \""${sel1[0]}"\"]" >> temp.tcl
|
||||
echo "set B [atomselect top \""${sel2[0]}"\"]" >> temp.tcl
|
||||
|
||||
# cycle over the trajectory
|
||||
echo 'for {set i 0} {$i <= $numframes} {incr i} {' >> temp.tcl
|
||||
echo ' foreach resID [$A get resid] {' >> temp.tcl
|
||||
echo ' set A_temp [atomselect top "resid $resID"]' >> temp.tcl
|
||||
echo ' $A_temp frame $i' >> temp.tcl
|
||||
echo ' $B frame $i' >> temp.tcl
|
||||
echo ' $A_temp update' >> temp.tcl
|
||||
echo ' $B update' >> temp.tcl
|
||||
echo " foreach {listA tmp} [measure contacts ${cutoff} \$A_temp \$B] break" >> temp.tcl
|
||||
echo ' if {[llength $listA] > 0} {' >> temp.tcl
|
||||
echo ' lappend contactTable($resID) $i' >> temp.tcl
|
||||
echo ' } else {' >> temp.tcl
|
||||
echo ' lappend contactTable($resID)' >> temp.tcl
|
||||
echo ' }' >> temp.tcl
|
||||
echo ' $A_temp delete' >> temp.tcl
|
||||
echo ' }' >> temp.tcl
|
||||
echo ' puts $i' >> temp.tcl
|
||||
echo '}' >> temp.tcl
|
||||
|
||||
# open output file for writing
|
||||
echo "set fContAB \""${out_dir}/${system}-${suffix}-contacts.csv"\"" >> temp.tcl
|
||||
echo 'set fcAB [open $fContAB w]' >> temp.tcl
|
||||
# calculate percentage
|
||||
echo 'foreach resID [lsort -integer [array names contactTable]] {' >> temp.tcl
|
||||
echo ' set frames [llength $contactTable($resID)]' >> temp.tcl
|
||||
echo ' set percentage [expr 100.0 * $frames / $totframes]' >> temp.tcl
|
||||
# write to file
|
||||
echo ' puts $fcAB "$resID $percentage"' >> temp.tcl
|
||||
echo ' flush $fcAB' >> temp.tcl
|
||||
# set user values
|
||||
echo ' set sel1 [atomselect top "resid $resID"]' >> temp.tcl
|
||||
echo ' for {set i 0} {$i <= $numframes} {incr i} {' >> temp.tcl
|
||||
echo ' $sel1 frame $i' >> temp.tcl
|
||||
echo ' $sel1 set user $percentage' >> temp.tcl
|
||||
echo ' }' >> temp.tcl
|
||||
echo ' $sel1 delete' >> temp.tcl
|
||||
echo '}' >> temp.tcl
|
||||
# close output files
|
||||
echo 'close $fcAB' >> temp.tcl
|
||||
echo 'exit' >> temp.tcl
|
||||
|
||||
vmd -dispdev text -eofexit ${psf} ${dcd} < "temp.tcl"
|
||||
sync
|
||||
rm "temp.tcl"
|
||||
|
||||
plot_contacts "${system}"
|
||||
|
||||
done
|
||||
|
||||
if (( ${combine} != 0 )); then
|
||||
plot_combined_contacts "${systems_names[@]}"
|
||||
fi
|
||||
|
||||
}
|
||||
|
||||
function plot_contacts() {
|
||||
|
||||
echo 'set terminal pngcairo enhanced size 1600,1200 font "arial,24" linewidth 2' > temp
|
||||
echo "set output \"${out_dir}/${1}-${suffix}-contacts.png\"" >> temp
|
||||
echo 'set autoscale' >> temp
|
||||
echo "set title \"${sel1[1]}-${sel2[1]} contacts\" font \"arial,40\"" >> temp
|
||||
echo 'set xlabel "Residue" font "arial,32"' >> temp
|
||||
echo 'set ylabel "% Contacts" font "arial,32"' >> temp
|
||||
echo 'set border 1+2' >> temp
|
||||
echo 'set xtics nomirror out' >> temp
|
||||
echo 'set ytics nomirror' >> temp
|
||||
echo 'set grid' >> temp
|
||||
echo 'set grid noxtics' >> temp
|
||||
echo 'set key box off' >> temp
|
||||
echo '#set yrange [-25:0]' >> temp
|
||||
echo '#set format y "%+-2.f"' >> temp
|
||||
echo 'set style data lines' >> temp
|
||||
echo 'set xzeroaxis ls 8' >> temp
|
||||
|
||||
echo "plot "${out_dir}/${1}-${suffix}-contacts.csv" using 1:2 with impulses ls 8" >> temp
|
||||
|
||||
echo 'exit' >> temp
|
||||
|
||||
gnuplot temp
|
||||
rm temp
|
||||
}
|
||||
|
||||
|
||||
# probably want to handle this one manually
|
||||
function plot_combined_contacts() {
|
||||
|
||||
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[${i}]}")
|
||||
done
|
||||
|
||||
echo 'set terminal pngcairo enhanced size 2400,1200 font "arial,24" linewidth 2' > temp
|
||||
echo "set output \"${out_dir}/combined-${suffix}-contacts.png\"" >> temp
|
||||
echo 'set autoscale' >> temp
|
||||
echo "set title \"${sel1[1]}-${sel2[1]} contacts\" font \"arial,40\"" >> temp
|
||||
echo 'set xlabel "Residue" font "arial,32"' >> temp
|
||||
echo 'set ylabel "% Contacts" font "arial,32"' >> temp
|
||||
echo 'set border 1+2' >> temp
|
||||
echo 'set xtics nomirror out rotate' >> temp
|
||||
echo 'set ytics nomirror' >> temp
|
||||
echo 'set grid' >> temp
|
||||
echo 'set grid noxtics' >> temp
|
||||
echo 'set key box top center' >> temp
|
||||
echo '#set style data histogram' >> temp
|
||||
echo 'set style fill solid border' >> 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
|
||||
|
||||
# thin out xtic labels
|
||||
echo 'every(col) = (int(column(col))%10 ==0)?stringcolumn(1):""' >> temp
|
||||
|
||||
# plot
|
||||
echo 'plot \' >> temp
|
||||
|
||||
for (( i = 0 ; i < ${#systems[@]} ; i++ )); do
|
||||
if [ $i -eq $((${#systems[@]} - 1)) ]; then
|
||||
echo "\"${out_dir}/${systems[$i]}-${suffix}-contacts.csv\" using 2:xticlabels(every(1)) with histogram ls $((${i} + 1)) title \""${names[$i]}"\"" >> temp
|
||||
else
|
||||
echo "\"${out_dir}/${systems[$i]}-${suffix}-contacts.csv\" using 2:xticlabels(every(1)) with histogram ls $((${i} + 1)) title \""${names[$i]}"\", \\" >> temp
|
||||
fi
|
||||
done
|
||||
|
||||
echo 'exit' >> temp
|
||||
|
||||
gnuplot temp
|
||||
#rm temp
|
||||
|
||||
}
|
||||
|
||||
|
||||
calc_contacts
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user