From 99b77434b5210f65db3c61a3f54001d559c46906 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 8 Feb 2021 16:16:53 +0000
Subject: [PATCH] more debug

---
 foldx/test2/repairPDB.sh | 2 +-
 foldx/test2/runFoldx.py  | 3 +++
 foldx/test2/runfoldx.sh  | 6 +++---
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/foldx/test2/repairPDB.sh b/foldx/test2/repairPDB.sh
index ee1a13c..8db843c 100755
--- a/foldx/test2/repairPDB.sh
+++ b/foldx/test2/repairPDB.sh
@@ -1,7 +1,7 @@
 INDIR=$1
 PDB=$2
 OUTDIR=$3
-
+cd ${OUTDIR}
 logger "Running repairPDB"
 
 #foldx --command=RepairPDB --pdb="${PDB}.pdb" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 outPDB=true --output-dir=${OUTDIR}
diff --git a/foldx/test2/runFoldx.py b/foldx/test2/runFoldx.py
index 42db217..23bed97 100755
--- a/foldx/test2/runFoldx.py
+++ b/foldx/test2/runFoldx.py
@@ -105,6 +105,7 @@ else:
 
 infile_pdb = indir + '/' + pdb_filename
 actual_pdb_filename = Path(infile_pdb).name
+#actual_pdb_filename = os.path.abspath(infile_pdb)
 
 if mut_filename:
     mutation_file = os.path.abspath(mut_filename)
@@ -208,9 +209,11 @@ def main():
     print('start')
     #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])
     print('\033[95mCOMPLETE: repair PDB\033[0m')
     print('\033[95mSTAGE: run FoldX (shell)\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')
     
diff --git a/foldx/test2/runfoldx.sh b/foldx/test2/runfoldx.sh
index fa7ba84..4f86033 100755
--- a/foldx/test2/runfoldx.sh
+++ b/foldx/test2/runfoldx.sh
@@ -4,6 +4,6 @@ cd ${OUTDIR}
 pwd
 ls -l
 logger "Running runfoldx"
-foldx --command=BuildModel --pdb="${PDB}_Repair.pdb" --mutant-file="individual_list_${PDB}.txt" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 --out-pdb=true --numberOfRuns=1 --output-dir=.
-foldx --command=PrintNetworks --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=.
-foldx --command=SequenceDetail --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=.
+foldx --command=BuildModel --pdb="${PDB}_Repair.pdb" --mutant-file="individual_list_${PDB}.txt" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 --out-pdb=true --numberOfRuns=1 --output-dir=${OUTDIR}
+foldx --command=PrintNetworks --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}
+foldx --command=SequenceDetail --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}