run_scan

#!/bin/bash

cwd=`pwd`
if [ -e setenv ]; then source setenv; else ./setenv.sh; source setenv; fi

if [ ! ${1} ] || [ ! ${2} ] || [ ! ${3} ] || [ ! ${4} ] || [ ! ${5} ] || [ ! ${6} ]; then
    printf "\n>>> Usage: ./run_scan <drude/c36> <resid> <atom1> <atom2> <atom3> <atom4>\n"
    printf "\ne.g. ./run_scan c36 buta c1 c2 c3 c4\n"
    printf "\nNeeds psf and crd files named: <resid>.<c36/drude>.psf & <resid>.<c36/drude>.crd\n\n"
    exit
fi

mkdir -p output
resid="${2}"
a1="${3}"
a2="${4}"
a3="${5}"
a4="${6}"
mkdir -p output/${resid}_dihe_${a1}_${a2}_${a3}_${a4}

rerun=1
if [ -e output/${resid}_dihe_${a1}_${a2}_${a3}_${a4}/psi4_ready ]; then
    printf "\n>>> Psi4 inputs already available! (Press ENTER to continue OR enter any key to re-run)"
    read -t 10 rep
    if [ $rep ]; then rerun=1; else rerun=0; fi
fi

if [ $rerun == 1 ]; then
    cd output/${resid}_dihe_${a1}_${a2}_${a3}_${a4}
    cp ../../scripts/0* ./
    cp ../../${resid}.${1}.* ./
    printf "\n>>> Generating coordinates..."
    $CHARMMDIR/charmm -i 01_generate_coordinates.inp method=$1 resid=$resid a1=$a1 a2=$a2 a3=$a3 a4=$a4 > 01_generate_coordinates.out
    flag=`tail -n 6 01_generate_coordinates.out | head -n 1 | awk '{print $1}'`
    if [ $flag == "ABNORMAL" ]; then
        printf " failed! Check 01_generate_coordinates.out for errors! \n"
        exit
    else
        printf " success!\n"
        sort -n fort.11 > mm_${resid}_dihe_${a1}_${a2}_${a3}_${a4}.txt
        rm fort.11
    fi

    printf "\n>>> Removing high energy conformations..."
    $PYTHONDIR/python 02_process_mme.py $resid $a1 $a2 $a3 $a4 > 02_process_mme.out
    if [ -e ${resid}_dihe_${a1}_${a2}_${a3}_${a4}.mme ]; then
        printf " success!\n"
    else
        printf " failed! Check 02_process_mme.out for errors! \n"
        exit
    fi

    printf "\n>>> Generating psi4 inputs...\n   "
    count=0
    for i in *psi4.pdb; do
        if [ $count != 5 ]; then printf "${i:2:4}... "; count=$((count+1))
        elif [ $count == 5 ]; then printf "${i:2:4}... \n   "; count=0; fi
        $PYTHONDIR/python 03_get_psi4_input.py $i $a1 $a2 $a3 $a4 > ${i:0:(-4)}.inp
    done
    printf " Done!\n"
    echo "Ready to run psi4" > psi4_ready
else
    cd output/${resid}_dihe_${a1}_${a2}_${a3}_${a4}
fi

printf "\n>>> Run psi4 now for all inputs one by one? (Press ENTER to continue OR enter any key to exit)"
read -t 30 rep
if [ $rep ]; then
    printf "\n>>> Now exiting...\n"
    exit
else
    printf "\n>>> Now running psi4 calculations >>>"
    echo 0 > status
    for i in *psi4.inp; do
	printf "\n    > ${i:0:(-4)} ..."
	if [ ! -e ${i}.dat ]; then
	    $PSI4DIR/psi4 -i ${i} -o ${i}.dat > /dev/null 2> /dev/null
	else
	    flag=`grep "Final energy is" ${i}.dat | wc -l`
	    if [ $flag == 0 ]; then
		$PSI4DIR/psi4 -i ${i} -o ${i}.dat > /dev/null 2> /dev/null
	    fi
	fi
	wait
	flag=`grep "Final energy is" ${i}.dat | wc -l`
	if [ $flag == 0 ]; then
	    echo 1 > status
	    printf " failed!"
	elif [ $flag == 1 ]; then
	    printf " done!"
	fi
    done
    if [ `cat status` == 0 ]; then
	printf "\n\n>>> Now extracting qm energies..."
	grep "Final energy is" d_*.dat | awk '{split($1,a,"_"); printf "%.2f %f %d\n",a[3],$5*627.5,a[2]}' > ${resid}_dihe_${a1}_${a2}_${a3}_${a4}.qme
	printf " done!\n"
	printf "\n>>> Now ploting the mm and qm energies..."
	$PYTHONDIR/python 04_plot_energy.py $resid $a1 $a2 $a3 $a4 > 04_plot_energy.out 2> 04_plot_energy.out
	if [ -e ${resid}_dihe_${a1}_${a2}_${a3}_${a4}.png ]; then
	    printf " done!\n\n"
	    printf "   ===================================================================================\n"
	    printf "   To view the results open: output/${resid}_dihe_${a1}_${a2}_${a3}_${a4}/${resid}_dihe_${a1}_${a2}_${a3}_${a4}.png\n"
	    printf "   ===================================================================================\n"
	    xdg-open ${resid}_dihe_${a1}_${a2}_${a3}_${a4}.png > /dev/null 2> /dev/null
	else
	    printf " failed! Check 04_plot_energy.out for errors!\n\n"
	    exit
	fi
    fi
    cd $cwd
fi

printf "\n>>> Want to make GIF (Press ENTER to continue OR enter any key to exit) : "
read -t 20 rep
if [ $rep ]; then
    printf "\n    Okay! to make GIF later just run : ./make_gif ${1} $resid $a1 $a2 $a3 $a4 \n"
    printf "\n    Now exiting... Cheers!\n\n"
else
    ./make_gif ${1} $resid $a1 $a2 $a3 $a4
fi
exit