#!/bin/bash
#just skip reading this blah-blah in the beginning of the script
if [ -z "$OSTYPE" ]; then
      if which cygpath 1>/dev/null 2>/dev/null; then
              OSTYPE=cygwin
      fi
fi
mypath=$0
while [ -h "$mypath" ]; do  # Resolve symlinks
        ls=`ls -ld "$mypath"`
        link=`expr "$ls" : '.*-> \(.*\)$'`
        if expr "$link" : '\/' > /dev/null; then
                mypath="$link"
        else
                mypath=`dirname "$mypath"`/"$link"
        fi
done

if expr "$mypath" : '[^\/]' > /dev/null; then
	mypath="`pwd`/$mypath"
fi

case "$OSTYPE" in
cygwin*)
	dir="`dirname $mypath`"
	dir="`cygpath -w $dir`"
        JCHEMHOME="$dir\\..\\.."
        ;;
*)
        dir=`dirname $mypath`
        JCHEMHOME="$dir/../.."
        ;;
esac

# continue reading here, this is the real thing
echo
echo
echo
echo "Usage: optimize <target file> <actives file>"
echo "Target and actives can be chosen from the directory"
echo "'examples/molecule', e.g.:"
echo "optimize nci500.smiles beta2_adrenoceptor_antagonists.smiles"
echo
echo 
echo "This example generates one set of molecular files for parameter" 
echo "optimization and evaluation of different parametrized metrics of two"
echo "molecular descriptors (pharmacophore fingerprints and chemical"
echo "fingerprints). Then it performs the optimization of parameters and"
echo "evaluation of the performance of the generated parametrized metrics."
echo "These metrics are used in screening a set of molecules against a set of"
echo "known actives."
echo
echo 
echo "Results are written into the file example_statistics.stat."
echo
echo
##### 
#!/bin/bash
############################
#Generate random test files
############################
   $JCHEMHOME/examples/bin/randomms $1 opt-target hit-target -n 50 -v
   $JCHEMHOME/examples/bin/randomms $2 hit-test opt-actives -p 35 -v
   $JCHEMHOME/examples/bin/randomms opt-actives opt-test opt-query -p 50 -v
##########################
# Optimize for Enrichment
##########################
   $JCHEMHOME/bin/optimizemetrics \
   opt-target opt-test opt-query -e 3 -H Median -v -f Enrichment \
     -k CF -c cfp.xml -o opt-CF.xml \
       -M Tanimotot Tanimoto \
       -M Tanimotoa Tanimoto -a \
       -M Euclideant Euclidean \
       -M Euclideann Euclidean -n \
       -M Euclideana Euclidean -a \
     -k PF -o opt-PF.xml -c pharma-frag.xml \
       -M Tanimotot Tanimoto \
       -M Tanimotos Tanimoto -s \
       -M Tanimotoa Tanimoto -a \
       -M Tanimotosa Tanimoto -s -a \
       -M Euclideant Euclidean \
       -M Euclideann Euclidean -n \
       -M Euclideanwn Euclidean -w -n \
       -M Euclideana Euclidean -a \
       -M Euclideanwa Euclidean -w -a \
       -M Euclideanan Euclidean -a -n \
       -M Euclideanwan Euclidean -w -a -n \
     -k PF -o opt-PF-z0.7.xml -c pharma-fuzzy.xml \
       -M Tanimotot0.7 Tanimoto \
       -M Tanimotos0.7 Tanimoto -s \
       -M Tanimotoa0.7 Tanimoto -a \
       -M Tanimotosa0.7 Tanimoto -s -a \
       -M Euclideant0.7 Euclidean \
       -M Euclideann0.7 Euclidean -n \
       -M Euclideanwn0.7 Euclidean -w -n \
       -M Euclideana0.7 Euclidean -a \
       -M Euclideanwa0.7 Euclidean -w -a \
       -M Euclideanan0.7 Euclidean -a -n \
       -M Euclideanwan0.7 Euclidean -w -a -n \
#
   $JCHEMHOME/bin/hitstatistics \
   hit-target hit-test opt-query -o example_statistics.stat -e 3 -g -v -H Median -b \
     -k PF -c opt-PF.xml \
     -k PF -c opt-PF-z0.7.xml \
     -k CF -c opt-CF.xml

echo
echo "Now the output text file example_statistics.stat"
echo "containing statistics about the performance of screening with the"
echo "parametrized metrics is displayed."
echo

less example_statistics.stat