A full example to compute and measure pairwise similarity with FuzCav. It assumes that the progarm is installed in a sourced directory ($FuzCav)

Step1: Tagging Calpha atoms of cavity-lining residues
	$FuzCav/utils/CaTagger.pl site1.mol2 > site1_Tagged.mol2
	$FuzCav/utils/CaTagger.pl site2.mol2 > site2_Tagged.mol2
	
Step2: Computinf FuzCav fingerprints
	java -jar $FuzCav/dist/3pointPharCav.jar -d $FuzCav/utils/resDef/tableDefCA.txt -t $FuzCav/utils/triplCav/interval.txt -l listCavTagged -o FPCount.txt -c
	-d [file]: table of CA properties definition
	-t [file]: table of FP definition (intervals anf properties arrangement)
	-l [file]: list of cavity file
	-o [file]: file to store the FP
	-c : flag to set FP in count mode
	
Step3: Computing pairwise simialrities
	$FuzCav/utils/simC++/simCalc  FPCount.txt listComp
	first argument : the FP generated by the java program
	second argument : a file containing the list of pair to compute similarity
