From d4a7e3b6356403a0bf082dbf99252df72f949773 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 8 Feb 2021 16:59:42 +0000
Subject: [PATCH] modifying script to avoid invoking bash as a subprocess

---
 foldx/test2/runFoldx.py | 31 +++++++++++++++++++++++++++++--
 1 file changed, 29 insertions(+), 2 deletions(-)

diff --git a/foldx/test2/runFoldx.py b/foldx/test2/runFoldx.py
index 23bed97..2ba784d 100755
--- a/foldx/test2/runFoldx.py
+++ b/foldx/test2/runFoldx.py
@@ -195,6 +195,19 @@ def loadFiles(df):
     f.close()
     return np.asarray(resultList, dtype=np.float32)
 
+# TODO: use this code pattern rather than invoking bash
+#def repairPDB():
+#    subprocess.call(['foldx' 
+#    , '--command=RepairPDB'
+#    , '--pdb-dir=' + indir
+#    ,  '--pdb=' + actual_pdb_filename 
+#    , '--ionStrength=0.05'#
+#   , '--pH=7'
+#    , '--water=PREDICT'
+#    , '--vdwDesign=1'
+#    , 'outPDB=true'
+#    , '--output-dir=' + process_dir])
+
 #=======================================================================    
 def main():
     pdbname = pdb_name
@@ -210,7 +223,19 @@ def main():
     #subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
     print('\033[95mSTAGE: repair PDB\033[0m')
     print('EXECUTING: repairPDB.sh %s %s %s' % (indir, actual_pdb_filename, process_dir))
-    subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
+    #subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
+    # once you decide to use the function
+    # repairPDB(pdbname)
+    subprocess.call(['foldx' 
+    , '--command=RepairPDB'
+    , '--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('EXECUTING: runfoldx.sh %s %s ' % (pdbname, process_dir))
@@ -242,7 +267,9 @@ def main():
         chain1=chainA
         chain2=chainB
         with suppress(Exception):
-            subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
+            #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))
+
         for n in range(1,nmuts+1):
             print('\033[95mSTAGE: Run Mutation Complex (shell) for mutation:\033[0m', n)
             with suppress(Exception):