diff --git a/foldx/test2/mutruncomplex.sh b/foldx/test2/deprecated_shell/mutruncomplex.sh
similarity index 100%
rename from foldx/test2/mutruncomplex.sh
rename to foldx/test2/deprecated_shell/mutruncomplex.sh
diff --git a/foldx/test2/repairPDB.sh b/foldx/test2/deprecated_shell/repairPDB.sh
similarity index 100%
rename from foldx/test2/repairPDB.sh
rename to foldx/test2/deprecated_shell/repairPDB.sh
diff --git a/foldx/test2/runPrintNetworks.sh b/foldx/test2/deprecated_shell/runPrintNetworks.sh
similarity index 100%
rename from foldx/test2/runPrintNetworks.sh
rename to foldx/test2/deprecated_shell/runPrintNetworks.sh
diff --git a/foldx/test2/runcomplex.sh b/foldx/test2/deprecated_shell/runcomplex.sh
similarity index 100%
rename from foldx/test2/runcomplex.sh
rename to foldx/test2/deprecated_shell/runcomplex.sh
diff --git a/foldx/test2/runfoldx.sh b/foldx/test2/deprecated_shell/runfoldx.sh
similarity index 100%
rename from foldx/test2/runfoldx.sh
rename to foldx/test2/deprecated_shell/runfoldx.sh
diff --git a/foldx/test2/runFoldx.py b/foldx/test2/runFoldx.py
index 2ba784d..0e0fab6 100755
--- a/foldx/test2/runFoldx.py
+++ b/foldx/test2/runFoldx.py
@@ -9,6 +9,7 @@ from pathlib import Path
 import re
 import csv
 import argparse
+import shutil
 #https://realpython.com/python-pathlib/
 
 # FIXME
@@ -226,55 +227,123 @@ def main():
     #subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
     # once you decide to use the function
     # repairPDB(pdbname)
+    
+    # FIXME: put this hack elsewhere
+    foldx_common=' --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 '
+    
     subprocess.call(['foldx' 
     , '--command=RepairPDB'
+    , foldx_common
     , '--pdb-dir=' + indir
     ,  '--pdb=' + actual_pdb_filename 
-    , '--ionStrength=0.05'#
-    , '--pH=7'
-    , '--water=PREDICT'
-    , '--vdwDesign=1'
     , 'outPDB=true'
     , '--output-dir=' + process_dir])
     print('\033[95mCOMPLETE: repair PDB\033[0m')
-    print('\033[95mSTAGE: run FoldX (shell)\033[0m')
+    print('\033[95mSTAGE: run FoldX (subprocess)\033[0m')
     print('EXECUTING: runfoldx.sh %s %s ' % (pdbname, process_dir))
-    output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
-    print('\033[95mCOMPLETE: run FoldX (shell)\033[0m')
+    #output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
+    
+    print('Running foldx BuildModel')
+    subprocess.call(['foldx' 
+    , '--command=BuildModel'
+    , foldx_common
+    , '--pdb-dir=' + process_dir
+    ,  '--pdb=' + pdbname + '_Repair.pdb'
+    , '--mutant-file="individual_list_' + pdbname +'.txt"'
+    , 'outPDB=true'
+    , '--numberOfRuns=1'
+    , '--output-dir=' + process_dir], cwd=process_dir)
+
+    print('Running foldx PrintNetworks')
+    subprocess.call(['foldx' 
+    , '--command=PrintNetworks'
+    , '--pdb-dir=' + process_dir
+    ,  '--pdb=' + pdbname + '_Repair.pdb'
+    , '--water=PREDICT'
+    , '--vdwDesign=1'
+    , '--output-dir=' + process_dir], cwd=process_dir)
+
+    print('Running foldx SequenceDetail')
+    subprocess.call(['foldx' 
+    , '--command=SequenceDetail'
+    , '--pdb-dir=' + process_dir
+    ,  '--pdb=' + pdbname + '_Repair.pdb'
+    , '--water=PREDICT'
+    , '--vdwDesign=1'
+    , '--output-dir=' + process_dir], cwd=process_dir)
+
+    
+    print('\033[95mCOMPLETE: run FoldX (subprocess)\033[0m')
     
     print('\033[95mSTAGE: Print Networks (shell)\033[0m')
     for n in range(1,nmuts+1):
         print('\033[95mNETWORK:\033[0m', n)
-        print('\033[96mCommand:\033[0m runPrintNetworks.sh %s %s %s' % (pdbname, str(n), process_dir ))
-        with suppress(Exception):
-            subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), process_dir])
+        #print('\033[96mCommand:\033[0m runPrintNetworks.sh %s %s %s' % (pdbname, str(n), process_dir ))
+        #with suppress(Exception):
+        #foldx --command=PrintNetworks --pdb="${PDB}_Repair_${n}.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}
+        print('Running foldx PrintNetworks for mutation', n)
+        subprocess.call(['foldx' 
+        , '--command=PrintNetworks'
+        , '--pdb-dir=' + process_dir
+        ,  '--pdb=' + pdbname + '_Repair_' + str(n) + '.pdb'
+        , '--water=PREDICT'
+        , '--vdwDesign=1'
+        , '--output-dir=' + process_dir], cwd=process_dir)
+            #subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), process_dir])
     print('\033[95mCOMPLETE: Print Networks (shell)\033[0m')
 
     print('\033[95mSTAGE: Rename Mutation Files (shell)\033[0m')
     for n in range(1,nmuts+1):
         print('\033[95mMUTATION:\033[0m', n)
         print('\033[96mCommand:\033[0m mutrenamefiles.sh %s %s %s' % (pdbname, str(n), process_dir ))
+        # FIXME: this is bad design and needs to be done in a pythonic way
         with suppress(Exception):
             subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname, str(n), process_dir])
     print('\033[95mCOMPLETE: Rename Mutation Files (shell)\033[0m')
             
     print('\033[95mSTAGE: Rename Files (shell)\033[0m')
+    # FIXME: this is bad design and needs to be done in a pythonic way
     out = subprocess.check_output(['bash','renamefiles.sh', pdbname, process_dir])
     print('\033[95mCOMPLETE: Rename Files (shell)\033[0m')
 
     if comp=='y':
-        print('\033[95mSTAGE: Run Complex (shell)\033[0m')
+        print('\033[95mSTAGE: Running foldx AnalyseComplex (subprocess)\033[0m')
         chain1=chainA
         chain2=chainB
-        with suppress(Exception):
+        #with suppress(Exception):
             #subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
-            subprocess(['foldx --command=AnalyseComplex --pdb="%s_Repair.pdb" --analyseComplexChains=%s,%s --water=PREDICT --vdwDesign=1 --output-dir=%s'] % (pdbname, chain1, chain2, process_dir))
+        subprocess.call(['foldx' 
+        , '--command=AnalyseComplex'
+        , '--pdb-dir=' + process_dir
+        ,  '--pdb=' + pdbname + '_Repair.pdb'
+        , '--analyseComplexChains=' + chain1 + ',' + chain2
+        , '--water=PREDICT'
+        , '--vdwDesign=1'
+        , '--output-dir=' + process_dir], cwd=process_dir)
+
+        # FIXME why would we ever need to do this?!? Cargo-culted from runcomplex.sh
+        ac_source = process_dir + '/Summary_' + pdbname + '_Repair_AC.fxout'
+        ac_dest = process_dir + '/Summary_' + pdbname + '_Repair_AC.txt'
+        shutil.copyfile(ac_source, ac_dest)
 
         for n in range(1,nmuts+1):
-            print('\033[95mSTAGE: Run Mutation Complex (shell) for mutation:\033[0m', n)
-            with suppress(Exception):
-                subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
-        print('\033[95mCOMPLETE: Run Complex (shell)\033[0m')
+            print('\033[95mSTAGE: Running foldx AnalyseComplex (subprocess) for mutation:\033[0m', n)
+            #with suppress(Exception):
+            #    subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
+            subprocess.call(['foldx' 
+            , '--command=AnalyseComplex'
+            , '--pdb-dir=' + process_dir
+            ,  '--pdb=' + pdbname + '_Repair_' + str(n) + '.pdb'
+            , '--analyseComplexChains=' + chain1 + ',' + chain2
+            , '--water=PREDICT'
+            , '--vdwDesign=1'
+            , '--output-dir=' + process_dir], cwd=process_dir)
+
+            # FIXME why would we ever need to do this?!? Cargo-culted from runcomplex.sh
+            ac_mut_source = process_dir + '/Summary_' + pdbname + '_Repair_' + str(n) +'_AC.fxout'
+            ac_mut_dest = process_dir + '/Summary_' + pdbname + '_Repair)' + str(n) +'_AC.txt'
+            shutil.copyfile(ac_mut_source, ac_mut_dest)
+        print('\033[95mCOMPLETE: foldx AnalyseComplex (subprocess) for mutation:\033[0m', n)
 
     interactions = ['Distances','Electro_RR','Electro_MM','Electro_SM','Electro_SS','Disulfide_RR','Disulfide_MM','Disulfide_SM','Disulfide_SS',
                     'Hbonds_RR','Hbonds_MM','Hbonds_SM','Hbonds_SS','Partcov_RR','Partcov_MM','Partcov_SM','Partcov_SS','VdWClashes_RR','VdWClashes_MM',