refactor foldx pipeline to include:

* command-line args
* creating necessary dirs automagically
* code cleanup, syntax errors, etc etc

foldx/runPrintNetworks.sh

@@ -0,0 +1,7 @@
+PDB=$1
+n=$2
+OUTDIR=$3
+logger "Running runPrintNetworks"
+cd ${OUTDIR}
+ 
+foldx --command=PrintNetworks --pdb="${PDB}_Repair_${n}.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}