source: util/meas2pdb.sh@ 725869

#!/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