#!/bin/sh
#
# extracts a .pdb-file from a pcp config file and includes shielding measurements from .csv files

if [ -z "$1" ]; then
	echo "Usage: $0 <config> [output.xyz]"
else
	config=$1
	pfad=`dirname $1`
	if [ ! -z "$2" ]; then
		outputname=$2
	else
		outputname="$pfad/"`basename $1`
	fi
fi


echo -n "Retrieving Ion types ..."
# Note [\t ] finds tabs AND spaces as separators
ions=(`grep '^Ion_Type.[^_]' $config | awk -F"[\t ]" {'print $9'}`)
elements=(`grep '^Ion_Type.[^_]' $config | awk -F"[\t ]" {'print $8'}`)
ionnumber=(`grep '^Ion_Type.[^_]' $config | awk -F"[\t ]" {'print $2'}`)
echo "done"

level=0
while [ ! -z "`find $pfad -name pcp.chi.L${level}.csv`" ]; do
	output="${outputname}.L${level}.pdb"
	echo "Converting $config to $output...done"
	let level=$level+1
	# Schreibe Kopf
	echo -e "COMPND\t$config" >$output
	echo -e "AUTHOR\tgenerated with meas2pdb" >>$output
	# Fuege Ionen dran
	nr=1
	j=1
	#echo "         1         2         3         4         5         6         7         8" >>$output
	#echo "12345678901234567890123456789012345678901234567890123456789012345678901234567890" >>$output
	while [ $j -le ${#ions[*]} ]; do
		k=0
		ions_per_type=(`grep ^Ion_Type${j}_ $config | sed -e "s#\.#,#g" | awk -F"[\t ]" '{print $2" "$3" "$4}'`)
		step=3
		#echo "Step size for Ion type $j is $step"
		while [ $k -lt ${ionnumber[$j-1]} ]; do
			serial=`echo $nr | awk -F"\n" '{printf "% 5d",$1}'`
			name=`echo ${ions[$j-1]} | awk -F"\n" '{printf "%2.2s",$1}'`
			nmr=`tail -n $level $pfad/*sigma_i${k}_${ions[$j-1]}_PAS.csv | head -n 1 | sed -e "s#\.#,#g" | awk -F"[\t ]" '{printf ("%6.2f", (($5*1e+6)))}' | sed -e "s#,#\.#g"`
			coords=`echo -e "${ions_per_type[(($k*$step))]}\t${ions_per_type[(($k*$step+1))]}\t${ions_per_type[(($k*$step+2))]}" | awk -F"[\t ]" '{printf "%8.3f%8.3f%8.3f",$1,$2,$3}' | sed -e "s#,#\.#g"`
			echo -e "ATOM  ${serial} ${name}   UNK A   1    ${coords}${nmr}  1.00          ${name}" >>$output
			let k=$k+1
			let nr=$nr+1
		done
		let j=$j+1
	done
	# Schliesse mit Fuss
	echo "END" >>$output

done

exit 0