#!/bin/sh

/bin/rm -f md?_cpout.pH_2.00.gz

EXE=../../bin/cphstats

NFAIL=0

if [ ! -z "$1" -a "$1" = "clean" ]; then
   /bin/rm -f md?_cpout.pH_?.??
   /bin/rm -f *.dat
   /bin/rm -f *.calcpka
   /bin/rm -f *.txt
   exit 0
fi

if [ ! -x $EXE ]; then
   echo "Could not find cphstats in the previous directory."
   echo "Re-install, then test again."
   exit 1
fi

# First unpack the REMD files

$EXE -O --fix-remd md2_cpout pH*/1AKI.dry.md2.cpout
$EXE -O --fix-remd md3_cpout pH*/1AKI.dry.md3.cpout

# Diff some of them

../dacdif md2_cpout.pH_2.00.save md2_cpout.pH_2.00
../dacdif md3_cpout.pH_4.50.save md3_cpout.pH_4.50

# Check the calcpka output
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_2.00 -o pH_2.00.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_2.50 -o pH_2.50.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_3.00 -o pH_3.00.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_3.50 -o pH_3.50.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 -o pH_4.00.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.50 -o pH_4.50.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_5.00 -o pH_5.00.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_5.50 -o pH_5.50.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_6.00 -o pH_6.00.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_6.50 -o pH_6.50.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_7.00 -o pH_7.00.calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_7.50 -o pH_7.50.calcpka

../dacdif -r 5e-1 pH_2.00.calcpka.save pH_2.00.calcpka
../dacdif -r 5e-1 pH_2.50.calcpka.save pH_2.50.calcpka
../dacdif -r 5e-1 pH_3.00.calcpka.save pH_3.00.calcpka
../dacdif -r 5e-1 pH_3.50.calcpka.save pH_3.50.calcpka
../dacdif -r 5e-1 pH_4.00.calcpka.save pH_4.00.calcpka
../dacdif -r 5e-1 pH_4.50.calcpka.save pH_4.50.calcpka
../dacdif -r 5e-1 pH_5.00.calcpka.save pH_5.00.calcpka
../dacdif -r 5e-1 pH_5.50.calcpka.save pH_5.50.calcpka
../dacdif -r 5e-1 pH_6.00.calcpka.save pH_6.00.calcpka
../dacdif -r 5e-1 pH_6.50.calcpka.save pH_6.50.calcpka
../dacdif -r 5e-1 pH_7.00.calcpka.save pH_7.00.calcpka
../dacdif -r 5e-1 pH_7.50.calcpka.save pH_7.50.calcpka

# Check reading of gzipped cpouts
for cpout in md?_cpout.pH_2.00; do
   gzip -9 $cpout
done
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_2.00.gz -o pH_2.00.calcpka \
     --debug > cphstats_output.txt

../dacdif -r 5e-1 pH_2.00.calcpka.save pH_2.00.calcpka
../dacdif -r 5e-1 cphstats_output.txt.save cphstats_output.txt

# Check running averages
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     -r 100000 --no-calcpka -n 100
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     -r 100000 -R running_avg.dat -d --no-calcpka -n 1000
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     -r 100000 -R running_pKa.dat -a --no-calcpka -n 5000

../dacdif -r 5e-1 running_avgs.dat.save running_avgs.dat
../dacdif -r 5e-1 running_avg.dat.save running_avg.dat
../dacdif -r 5e-1 running_pKa.dat.save running_pKa.dat

# Check chunk averages
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --chunk 1000000 --no-calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --chunk 1000000 --chunk-out chunk_deprot.dat --no-calcpka -d
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --chunk 1000000 --chunk-out chunk_pka.dat --no-calcpka -a

../dacdif -r 5e-1 chunk.dat.save chunk.dat
../dacdif -r 5e-1 chunk_deprot.dat.save chunk_deprot.dat
../dacdif -r 5e-1 chunk_pka.dat.save chunk_pka.dat

# Check cumulative output
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --cumulative --no-calcpka -n 1000 --no-calcpka
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --cumulative --no-calcpka -n 1000 -d --no-calcpka \
     --cumulative-out cumulative_deprot.dat
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --cumulative --no-calcpka -n 1000 -a --no-calcpka \
     --cumulative-out cumulative_pka.dat

../dacdif -r 5e-1 cumulative.dat.save cumulative.dat
../dacdif -r 5e-1 cumulative_deprot.dat.save cumulative_deprot.dat
../dacdif -r 5e-1 cumulative_pka.dat.save cumulative_pka.dat

# Check the population output
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --population pop.dat --no-calcpka

../dacdif -r 5e-1 pop.dat.save pop.dat

# Check the conditional probability output
$EXE -O -i 1AKI.dry.equil.cpin md?_cpout.pH_4.00 \
     --no-calcpka -c 35:prot,52:0 -c 66:D,48:P \
     --conditional-output conditional.dat \
     --chunk-conditional conditional_chunks.dat

../dacdif -r 5e-1 conditional.dat.save conditional.dat
../dacdif -r 5e-1 conditional_chunks.dat.save conditional_chunks.dat