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6.figures.sh
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6.figures.sh
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show=0
return_dir=`pwd`
echo 'main location:' $return_dir
oligomer='dimer'
oligomer_s='d'
ls | grep "average_curves" > list_av
line=$(ls | grep "average_curves" | wc -l)
copy_file(){
#cp $return_dir/6.contributions.py .
#cp $return_dir/6.contributions.par .
cp $return_dir/6.virus.par .
cp $return_dir/6.line.dat .
}
# Function
make_figure1(){
copy_file
for ((v=1; v<=4 ; v+=1)) do
if [ $v -eq 1 ]; then
virus=ZIKV-UG
fi
if [ $v -eq 2 ]; then
virus=ZIKV-BR
fi
if [ $v -eq 3 ]; then
virus=DENV2
fi
if [ $v -eq 4 ]; then
virus=WNV
fi
echo $virus
sed 's/##show##/'${show}'/g' 6.contributions.py | sed 's/##virus##/'${virus}'/g' | sed 's/##ext##/'${ext}'/g' | sed 's/##bin##/'${bin_size}'/g' | sed 's/##number##/'${number}'/g' | sed 's/##line##/'${line_f}'/g' > 666 ; mv 666 6.contributions.$virus.py
python 6.contributions.$virus.py
sed 's/##virus##/'${virus}'/g' 6.contributions.par > 6.contributions_$virus.par
gracebat ${virus}_dimer_pH7.0${line_f}${bin_size}.pmf ${virus}_${oligomer_s}_vdw_pH7.0${line_f}${bin_size}.pmf ${virus}_fixed_charges_pH7.0${line_f}${bin_size}.pmf ${virus}_ch_dip_pH7.0${line_f}${bin_size}.pmf ${virus}_ch_reg_pH7.0${line_f}${bin_size}.pmf ${virus}_charge_central_pH7.0${line_f}${bin_size}.pmf ${virus}_charge_distributed_pH7.0${line_f}${bin_size}.pmf 6.line.dat -p 6.contributions_$virus.par -autoscale xy -saveall ${virus}_contributions.xvg
echo ${virus} >> command_figure.txt
echo "gracebat ${virus}_dimer_pH7.0${line_f}${bin_size}.pmf ${virus}_${oligomer_s}_vdw_pH7.0${line_f}${bin_size}.pmf ${virus}_fixed_charges_pH7.0${line_f}${bin_size}.pmf ${virus}_ch_dip_pH7.0${line_f}${bin_size}.pmf ${virus}_ch_reg_pH7.0.pmf ${virus}_charge_central_pH7.0${line_f}${bin_size}.pmf ${virus}_charge_distributed_pH7.0${line_f}${bin_size}.pmf 6.line.dat -p 6.contributions_$virus.par -autoscale xy -saveall ${virus}_contributions.xvg" >> command_figure.txt
echo >> command_figure.txt
gracebat ${virus}_dimer_pH7.0${line_f}${bin_size}.pmf ${virus}_${oligomer_s}_vdw_pH7.0${line_f}${bin_size}.pmf ${virus}_fixed_charges_pH7.0${line_f}${bin_size}.pmf ${virus}_ch_dip_pH7.0${line_f}${bin_size}.pmf ${virus}_ch_reg_pH7.0${line_f}${bin_size}.pmf ${virus}_charge_central_pH7.0${line_f}${bin_size}.pmf ${virus}_charge_distributed_pH7.0${line_f}${bin_size}.pmf 6.line.dat -p 6.contributions_$virus.par -autoscale xy -hdevice PNG -saveall ${virus}_contributions.png
mv ${virus}_contributions.ps figures_contributions/
mv ${virus}_contributions.xvg figures_contributions/
mv ${virus}_contributions.png figures_contributions/
mv 6.contributions_$virus.par figures_contributions
done
mv command_figure.txt figures_contributions
cp 6.line.dat figures_contributions
}
make_figure2(){
copy_file
for ((con=4 ; con <= 5; con+=1)) do
if [ $con -eq 1 ]; then
condition=monomer
fi
if [ $con -eq 2 ]; then
condition=dimer
fi
if [ $con -eq 3 ]; then
condition=dimer_0.005M
fi
if [ $con -eq 4 ]; then
condition=dimer
fi
if [ $con -eq 5 ]; then
condition=d_vdw
fi
if [ $con -eq 6 ]; then
condition=fixed_charges
fi
if [ $con -eq 7 ]; then
condition=ch_dip
fi
if [ $con -eq 8 ]; then
condition=ch_reg
fi
if [ $con -eq 9 ]; then
condition=charge_central
fi
if [ $con -eq 10 ]; then
condition=charge_distributed
fi
sed 's/##contribution##/'${condition}'/g' 6.virus.par > virus_${condition}.par
gracebat ZIKV-UG_${condition}_pH7.0${line_f}${bin_size}.pmf ZIKV-BR_${condition}_pH7.0${line_f}${bin_size}.pmf DENV2_${condition}_pH7.0${line_f}${bin_size}.pmf WNV_${condition}_pH7.0${line_f}${bin_size}.pmf 6.line.dat -p virus_${condition}.par -autoscale xy -saveall virus_${condition}.xvg
gracebat ZIKV-UG_${condition}_pH7.0${line_f}${bin_size}.pmf ZIKV-BR_${condition}_pH7.0${line_f}${bin_size}.pmf DENV2_${condition}_pH7.0${line_f}${bin_size}.pmf WNV_${condition}_pH7.0${line_f}${bin_size}.pmf 6.line.dat -p virus_${condition}.par -autoscale xy -hdevice PNG -saveall virus_${condition}.png
echo ${condition} >> command_figure.txt
echo "gracebat ZIKV-UG_${condition}_pH7.0${line_f}${bin_size}.pmf ZIKV-BR_${condition}_pH7.0${line_f}${bin_size}.pmf DENV2_${condition}_pH7.0${line_f}${bin_size}.pmf WNV_${condition}_pH7.0${line_f}${bin_size}.pmf 6.line.dat -p virus_${condition}.par -autoscale xy -saveall virus_${condition}.xvg" >> command_figure.txt
echo >> command_figure.txt
mv virus_$condition.ps figures_virus/
mv virus_$condition.xvg figures_virus/
mv virus_$condition.png figures_virus/
mv virus_${condition}.par figures_virus/
done
mv command_figure.txt figures_virus/
mv 6.line.dat figures_virus/
}
#line=1
for ((i=1 ; i<=$line ; i +=1)) do
dir_ave=$(head -n$i list_av | tail -n1)
bin_size=$(head -n$i list_av | tail -n1 | cut -d "_" -f3)
if echo $dir_ave | grep -q "bin"; then
number=-2
ext=''
line_f='_'
rm -r $dir_ave/figures_virus
mkdir -p $dir_ave/figures_virus
#rm -r $dir_ave/figures_contributions
#mkdir -p $dir_ave/figures_contributions
cd $dir_ave/
pwd
#make_figure1 # figure contributions
make_figure2 # figure viruses
rm *par
cd $return_dir
else
number=-1
ext='.pmf'
line_f=''
rm -r $dir_ave/figures_virus
mkdir -p $dir_ave/figures_virus
#rm -r $dir_ave/figures_contributions
#mkdir -p $dir_ave/figures_contributions
cd $dir_ave/
pwd
#make_figure1 # figure contributions
make_figure2 # figure viruses
rm *par
cd $return_dir
fi
done
rm list_av
#