various changes

foldx/mutrenamefiles.sh

@@ -2,7 +2,7 @@ PDB=$1
 n=$2
 OUTDIR=$3
 cd ${OUTDIR}
-logger "Running mutrenamefiles with PDB: ${PDB} n: ${n} OUTDIR: ${OUTDIR}"
+
 cp Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout Matrix_Hbonds_${PDB}_Repair_${n}_PN.txt
 sed -n '5,190p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_RR_${PDB}_Repair_${n}_PN.txt
 sed -n '194,379p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_MM_${PDB}_Repair_${n}_PN.txt
@@ -61,9 +61,3 @@ cp InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.fxout InteractingResidue
 sed -i '1,5d' InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt
 cp InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt
 sed -i '1,5d' InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt
-
-
-
-
-
-

foldx/mutrenamefiles_mac.sh

@@ -1,68 +0,0 @@
-PDB=$1
-n=$2
-#cd /home/tanu/git/LSHTM_analysis/foldx/
-logger "Running mutrenamefiles_mac"
-cp Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout Matrix_Hbonds_${PDB}_Repair_${n}_PN.txt
-sed -n '5,190p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_RR_${PDB}_Repair_${n}_PN.txt
-sed -n '194,379p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_MM_${PDB}_Repair_${n}_PN.txt
-sed -n '383,568p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_SM_${PDB}_Repair_${n}_PN.txt
-sed -n '572,757p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_SS_${PDB}_Repair_${n}_PN.txt
-cp Matrix_Distances_${PDB}_Repair_${n}_PN.fxout Matrix_Distances_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,4d Matrix_Distances_${PDB}_Repair_${n}_PN.txt
-cp Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout Matrix_Volumetric_${PDB}_Repair_${n}_PN.txt
-sed -n '5,190p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_RR_${PDB}_Repair_${n}_PN.txt
-sed -n '194,379p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_MM_${PDB}_Repair_${n}_PN.txt
-sed -n '383,568p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_SM_${PDB}_Repair_${n}_PN.txt
-sed -n '572,757p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_SS_${PDB}_Repair_${n}_PN.txt
-cp Matrix_Electro_${PDB}_Repair_${n}_PN.fxout Matrix_Electro_${PDB}_Repair_${n}_PN.txt
-sed -n '5,190p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_RR_${PDB}_Repair_${n}_PN.txt
-sed -n '194,379p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_MM_${PDB}_Repair_${n}_PN.txt
-sed -n '383,568p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_SM_${PDB}_Repair_${n}_PN.txt
-sed -n '572,757p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_SS_${PDB}_Repair_${n}_PN.txt
-cp Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout Matrix_Disulfide_${PDB}_Repair_${n}_PN.txt
-sed -n '5,190p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_RR_${PDB}_Repair_${n}_PN.txt
-sed -n '194,379p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_MM_${PDB}_Repair_${n}_PN.txt
-sed -n '383,568p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_SM_${PDB}_Repair_${n}_PN.txt
-sed -n '572,757p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_SS_${PDB}_Repair_${n}_PN.txt
-cp Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout Matrix_Partcov_${PDB}_Repair_${n}_PN.txt
-sed -n '5,190p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_RR_${PDB}_Repair_${n}_PN.txt
-sed -n '194,379p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_MM_${PDB}_Repair_${n}_PN.txt
-sed -n '383,568p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_SM_${PDB}_Repair_${n}_PN.txt
-sed -n '572,757p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_SS_${PDB}_Repair_${n}_PN.txt
-cp Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout Matrix_VdWClashes_${PDB}_Repair_${n}_PN.txt
-sed -n '5,190p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_RR_${PDB}_Repair_${n}_PN.txt
-sed -n '194,379p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_MM_${PDB}_Repair_${n}_PN.txt
-sed -n '383,568p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_SM_${PDB}_Repair_${n}_PN.txt
-sed -n '572,757p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_SS_${PDB}_Repair_${n}_PN.txt
-cp AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.fxout AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,2d AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.txt
-cp AllAtoms_Electro_${PDB}_Repair_${n}_PN.fxout AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,2d AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt
-cp AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,2d AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt
-cp AllAtoms_Partcov_${PDB}_Repair_${n}_PN.fxout AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,2d AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt
-cp AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,2d AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt
-cp AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,2d AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt
-cp InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,5d InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt
-cp InteractingResidues_Distances_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,5d InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt
-cp InteractingResidues_Electro_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,5d InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt
-cp InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,5d InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt
-cp InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,5d InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt
-cp InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,5d InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt
-cp InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt
-sed -i .bak -e 1,5d InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt
-
-
-
-
-
-

foldx/mutruncomplex.sh

@@ -1,10 +0,0 @@
-PDB=$1
-A=$2
-B=$3
-n=$4
-OUTDIR=$5
-cd ${OUTDIR}
-logger "Running mutruncomplex"
-foldx --command=AnalyseComplex --pdb="${PDB}_Repair_${n}.pdb" --analyseComplexChains=${A},${B} --water=PREDICT --vdwDesign=1
-cp ${OUTDIR}/Summary_${PDB}_Repair_${n}_AC.fxout ${OUTDIR}/Summary_${PDB}_Repair_${n}_AC.txt
-#sed -i .bak -e 1,8d ${OUTDIR}/Summary_${PDB}_Repair_${n}_AC.txt 

foldx/renamefiles.sh

@@ -1,7 +1,7 @@
 PDB=$1
 OUTDIR=$2
 cd ${OUTDIR}
-logger "Running renamefiles"
+
 cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt
 sed -i '1,8d' Dif_${PDB}_Repair.txt
 cp Matrix_Hbonds_${PDB}_Repair_PN.fxout Matrix_Hbonds_${PDB}_Repair_PN.txt
@@ -62,9 +62,3 @@ cp InteractingResidues_Volumetric_${PDB}_Repair_PN.fxout InteractingResidues_Vol
 sed -i '1,5d' InteractingResidues_Volumetric_${PDB}_Repair_PN.txt
 cp InteractingResidues_Disulfide_${PDB}_Repair_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_PN.txt
 sed -i '1,5d' InteractingResidues_Disulfide_${PDB}_Repair_PN.txt
-
-
-
-
-
-

foldx/renamefiles_mac.sh

@@ -1,68 +0,0 @@
-PDB=$1
-logger "Running renamefiles_mac"
-#cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt
-sed -i '.bak' -e 1,8d Dif_${PDB}_Repair.txt
-cp Matrix_Hbonds_${PDB}_Repair_PN.fxout Matrix_Hbonds_${PDB}_Repair_PN.txt
-sed -n '5,190p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_RR_${PDB}_Repair_PN.txt
-sed -n '194,379p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_MM_${PDB}_Repair_PN.txt
-sed -n '383,568p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_SM_${PDB}_Repair_PN.txt
-sed -n '572,757p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_SS_${PDB}_Repair_PN.txt
-cp Matrix_Distances_${PDB}_Repair_PN.fxout Matrix_Distances_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,4d Matrix_Distances_${PDB}_Repair_PN.txt
-cp Matrix_Volumetric_${PDB}_Repair_PN.fxout Matrix_Volumetric_${PDB}_Repair_PN.txt
-sed -n '5,190p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_RR_${PDB}_Repair_PN.txt
-sed -n '194,379p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_MM_${PDB}_Repair_PN.txt
-sed -n '383,568p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_SM_${PDB}_Repair_PN.txt
-sed -n '572,757p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_SS_${PDB}_Repair_PN.txt
-cp Matrix_Electro_${PDB}_Repair_PN.fxout Matrix_Electro_${PDB}_Repair_PN.txt
-sed -n '5,190p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_RR_${PDB}_Repair_PN.txt
-sed -n '194,379p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_MM_${PDB}_Repair_PN.txt
-sed -n '383,568p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_SM_${PDB}_Repair_PN.txt
-sed -n '572,757p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_SS_${PDB}_Repair_PN.txt
-cp Matrix_Disulfide_${PDB}_Repair_PN.fxout Matrix_Disulfide_${PDB}_Repair_PN.txt
-sed -n '5,190p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_RR_${PDB}_Repair_PN.txt
-sed -n '194,379p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_MM_${PDB}_Repair_PN.txt
-sed -n '383,568p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_SM_${PDB}_Repair_PN.txt
-sed -n '572,757p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_SS_${PDB}_Repair_PN.txt
-cp Matrix_Partcov_${PDB}_Repair_PN.fxout Matrix_Partcov_${PDB}_Repair_PN.txt
-sed -n '5,190p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_RR_${PDB}_Repair_PN.txt
-sed -n '194,379p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_MM_${PDB}_Repair_PN.txt
-sed -n '383,568p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_SM_${PDB}_Repair_PN.txt
-sed -n '572,757p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_SS_${PDB}_Repair_PN.txt
-cp Matrix_VdWClashes_${PDB}_Repair_PN.fxout Matrix_VdWClashes_${PDB}_Repair_PN.txt
-sed -n '5,190p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_RR_${PDB}_Repair_PN.txt
-sed -n '194,379p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_MM_${PDB}_Repair_PN.txt
-sed -n '383,568p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_SM_${PDB}_Repair_PN.txt
-sed -n '572,757p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_SS_${PDB}_Repair_PN.txt
-cp AllAtoms_Disulfide_${PDB}_Repair_PN.fxout AllAtoms_Disulfide_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,2d AllAtoms_Disulfide_${PDB}_Repair_PN.txt
-cp AllAtoms_Electro_${PDB}_Repair_PN.fxout AllAtoms_Electro_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,2d AllAtoms_Electro_${PDB}_Repair_PN.txt
-cp AllAtoms_Hbonds_${PDB}_Repair_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,2d AllAtoms_Hbonds_${PDB}_Repair_PN.txt
-cp AllAtoms_Partcov_${PDB}_Repair_PN.fxout AllAtoms_Partcov_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,2d AllAtoms_Partcov_${PDB}_Repair_PN.txt
-cp AllAtoms_VdWClashes_${PDB}_Repair_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,2d AllAtoms_VdWClashes_${PDB}_Repair_PN.txt
-cp AllAtoms_Volumetric_${PDB}_Repair_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,2d AllAtoms_Volumetric_${PDB}_Repair_PN.txt
-cp InteractingResidues_VdWClashes_${PDB}_Repair_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,5d InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt
-cp InteractingResidues_Distances_${PDB}_Repair_PN.fxout InteractingResidues_Distances_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,5d InteractingResidues_Distances_${PDB}_Repair_PN.txt
-cp InteractingResidues_Electro_${PDB}_Repair_PN.fxout InteractingResidues_Electro_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,5d InteractingResidues_Electro_${PDB}_Repair_PN.txt
-cp InteractingResidues_Hbonds_${PDB}_Repair_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,5d InteractingResidues_Hbonds_${PDB}_Repair_PN.txt
-cp InteractingResidues_Partcov_${PDB}_Repair_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,5d InteractingResidues_Partcov_${PDB}_Repair_PN.txt
-cp InteractingResidues_Volumetric_${PDB}_Repair_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,5d InteractingResidues_Volumetric_${PDB}_Repair_PN.txt
-cp InteractingResidues_Disulfide_${PDB}_Repair_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_PN.txt
-sed -i '.bak' -e 1,5d InteractingResidues_Disulfide_${PDB}_Repair_PN.txt
-
-
-
-
-
-

foldx/repairPDB.sh

@@ -1,9 +0,0 @@
-INDIR=$1
-PDB=$2
-OUTDIR=$3
-
-logger "Running repairPDB"
-
-#foldx --command=RepairPDB --pdb="${PDB}.pdb" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 outPDB=true --output-dir=${OUTDIR}
-
-foldx --command=RepairPDB --pdb-dir=${INDIR} --pdb=${PDB} --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 outPDB=true --output-dir=${OUTDIR}

foldx/runFoldx.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 import subprocess
 import os
+import sys
 import numpy as np
 import pandas as pd
 from contextlib import suppress
@@ -8,6 +9,8 @@ from pathlib import Path
 import re
 import csv
 import argparse
+import shutil
+import time
 #https://realpython.com/python-pathlib/
 
 # FIXME
@@ -22,8 +25,8 @@ homedir = os.path.expanduser('~')
 
 # set working dir
 os.getcwd()
-os.chdir(homedir + '/git/LSHTM_analysis/foldx/')
+#os.chdir(homedir + '/git/LSHTM_analysis/foldx/')
-os.getcwd()
+#os.getcwd()
 
 #=======================================================================
 #%% command line args
@@ -37,7 +40,7 @@ arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb fi
 arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
 arg_parser.add_argument('-p', '--process_dir', help = 'Temp processing dir for running foldX. By default, it assmes homedir + <drug> + processing. Make sure it is somewhere with LOTS of storage as it writes all output!') #FIXME
 
-arg_parser.add_argument('-pdb', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called <gene>_complex.pdb in input_dir')
+arg_parser.add_argument('-pdb', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called <gene>_complex.pdb in input_dir') # DO NOT specify an absolute path
 arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_mcsm_snps.csv exists')
 
 # FIXME: Doesn't work with 2 chains yet!
@@ -77,34 +80,45 @@ if not datadir:
     datadir = homedir + '/' + 'git/Data'
     
 if not indir:
-    indir = datadir + '/' + drug + '/input'
+    indir = 
+    datadir + '/' + drug + '/input'
     
 if not outdir:
     outdir = datadir + '/' + drug + '/output'
 
 #TODO: perhaps better handled by refactoring code to prevent generating lots of output files!
 if not process_dir:
-    process_dir = datadir + '/' + drug +'/' + 'processing'
+    process_dir = datadir + '/' + drug + '/processing'
+
+# Make all paths absolute in case the user forgot
+indir = os.path.abspath(indir)
+process_dir = os.path.abspath(process_dir)
+outdir = os.path.abspath(outdir)
+datadir = os.path.abspath(datadir)
 
 #=======
 # input
 #=======
 # FIXME
 if pdb_filename:
+    pdb_filename = os.path.abspath(pdb_filename)
     pdb_name = Path(pdb_filename).stem
+    infile_pdb = pdb_filename 
 else:
     pdb_filename = gene.lower() + '_complex.pdb'
     pdb_name = Path(pdb_filename).stem
-
     infile_pdb = indir + '/' + pdb_filename
+    
 actual_pdb_filename = Path(infile_pdb).name
 
 if mut_filename:
-    mutation_file = mut_filename
+    mutation_file = os.path.abspath(mut_filename)
+    infile_muts = mutation_file
+    print('User-provided mutation file in use:', infile_muts)
 else:
     mutation_file =  gene.lower() + '_mcsm_formatted_snps.csv'
-
     infile_muts = outdir + '/' + mutation_file
+    print('WARNING: Assuming default mutation file:', infile_muts)
 
 #=======
 # output 
@@ -116,6 +130,7 @@ print('Arguments being passed:'
 , '\nDrug:', args.drug
 , '\ngene:', args.gene
 , '\ninput dir:', indir
+, '\nprocess dir:', process_dir
 , '\noutput dir:', outdir
 , '\npdb file:', infile_pdb
 , '\npdb name:', pdb_name
@@ -124,6 +139,9 @@ print('Arguments being passed:'
 , '\nchain1:', args.chain1
 , '\noutput file:', outfile_foldx
 , '\n=============================================================')
+
+#### Delay for 10 seconds to check the params ####
+time.sleep(10)
 #=======================================================================
 
 def getInteractionEnergy(filename):
@@ -184,6 +202,19 @@ def loadFiles(df):
     f.close()
     return np.asarray(resultList, dtype=np.float32)
 
+# TODO: put the subprocess call in a 'def'
+#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
@@ -195,37 +226,128 @@ def main():
     nmuts = len(mutlist)
     print(nmuts)
     print(mutlist)
+    
     print('start')  
-    #subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
+    # some common parameters for foldX
-    subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
+    foldx_common=' --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 '
     
-    print('end')
+    print('\033[95mSTAGE: repair PDB (foldx subprocess) \033[0m')
-    output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
+    print('Running foldx RepairPDB for WT')
+    subprocess.call(['foldx' 
+    , '--command=RepairPDB'
+    , foldx_common
+    , '--pdb-dir=' + indir
+    ,  '--pdb=' + actual_pdb_filename 
+    , 'outPDB=true'
+    , '--output-dir=' + process_dir])
+    print('\033[95mCOMPLETED STAGE: repair PDB\033[0m')
+    print('\n==========================================================')
     
+    
+    print('\033[95mSTAGE: Foldx commands BM, PN and SD (foldx subprocess) for WT\033[0m')
+    print('Running foldx BuildModel for WT')
+    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 for WT')
+    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 for WT')
+    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[95mCOMPLETED STAGE: Foldx commands BM, PN and SD\033[0m')
+    print('\n==========================================================')
+    
+    
+    print('\033[95mSTAGE: Print Networks (foldx subprocess) for MT\033[0m')
     for n in range(1,nmuts+1):
-        print(n)
+        print('\033[95mNETWORK:\033[0m', n)
-        with suppress(Exception):
+        print('Running foldx PrintNetworks for mutation', n)
-            subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), process_dir])
+        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) 
+    print('\033[95mCOMPLETED STAGE: Print Networks (foldx subprocess) for MT\033[0m')
+    print('\n==========================================================')
     
+    
+    print('\033[95mSTAGE: Rename Mutation Files (shell)\033[0m')
     for n in range(1,nmuts+1):
-        print(n)
+        print('\033[95mMUTATION:\033[0m', n)
+        print('\033[96mCommand:\033[0m mutrenamefiles.sh %s %s %s' % (pdbname, str(n), process_dir ))    
+       #FIXME: 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[95mCOMPLETED STAGE: Rename Mutation Files (shell)\033[0m')
+    print('\n==========================================================')
     
+                
+    print('\033[95mSTAGE: Rename Files (shell) for WT\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[95mCOMPLETED STAGE: Rename Files (shell) for WT\033[0m')
+    print('\n==========================================================')
+    
     
     if comp=='y':
+        print('\033[95mSTAGE: Running foldx AnalyseComplex (foldx subprocess) for WT\033[0m')
         chain1=chainA
         chain2=chainB
-        with suppress(Exception):
+        subprocess.call(['foldx' 
-            subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
+        , '--command=AnalyseComplex'
-        for n in range(1,nmuts+1):
+        , '--pdb-dir=' + process_dir
-            with suppress(Exception):
+        ,  '--pdb=' + pdbname + '_Repair.pdb'
-                subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
+        , '--analyseComplexChains=' + chain1 + ',' + chain2
+        , '--water=PREDICT'
+        , '--vdwDesign=1'
+        , '--output-dir=' + process_dir], cwd=process_dir)
 
-    interactions = ['Distances','Electro_RR','Electro_MM','Electro_SM','Electro_SS','Disulfide_RR','Disulfide_MM','Disulfide_SM','Disulfide_SS',
+        # FIXME why would we ever need to do this?!? Cargo-culted from runcomplex.sh
-                    'Hbonds_RR','Hbonds_MM','Hbonds_SM','Hbonds_SS','Partcov_RR','Partcov_MM','Partcov_SM','Partcov_SS','VdWClashes_RR','VdWClashes_MM',
+        ac_source = process_dir + '/Summary_' + pdbname + '_Repair_AC.fxout'
-                    'VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS']
+        ac_dest = process_dir + '/Summary_' + pdbname + '_Repair_AC.txt'
+        shutil.copyfile(ac_source, ac_dest)
+        print('\033[95mCOMPLETED STAGE: foldx AnalyseComplex (subprocess) for WT:\033[0m', n)
+
+        for n in range(1,nmuts+1):
+            print('\033[95mSTAGE: Running foldx AnalyseComplex (foldx subprocess) for mutation:\033[0m', n)
+            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[95mCOMPLETED STAGE: foldx AnalyseComplex (subprocess) for mutation:\033[0m', n)
+        print('\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','VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS']
     
     dGdatafile = process_dir + '/Dif_' + pdbname + '_Repair.txt'
     dGdata = pd.read_csv(dGdatafile, sep = '\t')
@@ -267,8 +389,7 @@ def main():
         print(d)
         data[i+1] = d    
         
-    interactions = ['ddG', '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',
+    interactions = ['ddG', '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','VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS']   
-'VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS']   
 
     print(interactions)
 
@@ -292,8 +413,7 @@ def main():
         print(len(IE))
         data = np.append(data,[IE], axis = 0)
         print(data)
-        interactions = ['ddG','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',
+        interactions = ['ddG','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','VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS','Interaction Energy']  
-'VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS','Interaction Energy']  
 
     mut_file = process_dir + '/individual_list_' + pdbname + '.txt'
     with open(mut_file) as csvfile:
@@ -331,6 +451,7 @@ def main():
     #outputfilename = 'foldx_results_' + pdbname + '.csv'
     #results.to_csv(outputfilename)
     results2.to_csv(outputfilename, index = False)
+    print ('end')
     
 if __name__ == '__main__':
     main()

foldx/runPrintNetworks.sh

@@ -1,7 +0,0 @@
-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}

foldx/runcomplex.sh

@@ -1,9 +0,0 @@
-PDB=$1
-A=$2
-B=$3
-OUTDIR=$4
-cd ${OUTDIR}
-logger "Running runcomplex"
-foldx --command=AnalyseComplex --pdb="${PDB}_Repair.pdb" --analyseComplexChains=${A},${B} --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}
-cp ${OUTDIR}/Summary_${PDB}_Repair_AC.fxout ${OUTDIR}/Summary_${PDB}_Repair_AC.txt
-#sed -i .bak -e 1,8d ${OUTDIR}/Summary_${PDB}_Repair_AC.txt 

foldx/runfoldx.sh

@@ -1,9 +0,0 @@
-PDB=$1
-OUTDIR=$2
-cd ${OUTDIR}
-pwd
-ls
-logger "Running runfoldx"
-foldx --command=BuildModel --pdb="${PDB}_Repair.pdb" --mutant-file="individual_list_${PDB}.txt" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 --out-pdb=true --numberOfRuns=1 --output-dir=${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}

foldx/test2/mutrenamefiles.sh

@@ -2,7 +2,7 @@ PDB=$1
 n=$2
 OUTDIR=$3
 cd ${OUTDIR}
-
+#cd /home/git/LSHTM_analysis/foldx/test2
 cp Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout Matrix_Hbonds_${PDB}_Repair_${n}_PN.txt
 sed -n '5,190p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_RR_${PDB}_Repair_${n}_PN.txt
 sed -n '194,379p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_MM_${PDB}_Repair_${n}_PN.txt

foldx/test2/renamefiles.sh

@@ -1,8 +1,7 @@
 PDB=$1
 OUTDIR=$2
 cd ${OUTDIR}
-
+#cd /home/git/LSHTM_analysis/foldx/test2
-#cd /home/git/LSHTM_analysis/foldx/test
 cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt
 sed -i '1,8d' Dif_${PDB}_Repair.txt
 cp Matrix_Hbonds_${PDB}_Repair_PN.fxout Matrix_Hbonds_${PDB}_Repair_PN.txt