diff --git a/foldx/mutrenamefiles.sh b/foldx/mutrenamefiles.sh
new file mode 100755
index 0000000..88a5d03
--- /dev/null
+++ b/foldx/mutrenamefiles.sh
@@ -0,0 +1,69 @@
+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_${n}_PN.txt
+sed -n '383,568p' Matrix_Hbonds_${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_${n}_PN.txt
+sed -i '1,4d' Matrix_Distances_${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_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Electro_${PDB}_Repair_${n}_PN.fxout AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Partcov_${PDB}_Repair_${n}_PN.fxout AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Distances_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Electro_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Volumetric_${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
+
+
+
+
+
+
diff --git a/foldx/mutrenamefiles_mac.sh b/foldx/mutrenamefiles_mac.sh
new file mode 100755
index 0000000..b0e2fe9
--- /dev/null
+++ b/foldx/mutrenamefiles_mac.sh
@@ -0,0 +1,68 @@
+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
+
+
+
+
+
+
diff --git a/foldx/mutruncomplex.sh b/foldx/mutruncomplex.sh
new file mode 100755
index 0000000..2b2c4e1
--- /dev/null
+++ b/foldx/mutruncomplex.sh
@@ -0,0 +1,10 @@
+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 
diff --git a/foldx/renamefiles.sh b/foldx/renamefiles.sh
new file mode 100755
index 0000000..553ba5f
--- /dev/null
+++ b/foldx/renamefiles.sh
@@ -0,0 +1,70 @@
+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
+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 '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_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Disulfide_${PDB}_Repair_PN.txt
+cp AllAtoms_Electro_${PDB}_Repair_PN.fxout AllAtoms_Electro_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Electro_${PDB}_Repair_PN.txt
+cp AllAtoms_Hbonds_${PDB}_Repair_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Hbonds_${PDB}_Repair_PN.txt
+cp AllAtoms_Partcov_${PDB}_Repair_PN.fxout AllAtoms_Partcov_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Partcov_${PDB}_Repair_PN.txt
+cp AllAtoms_VdWClashes_${PDB}_Repair_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_VdWClashes_${PDB}_Repair_PN.txt
+cp AllAtoms_Volumetric_${PDB}_Repair_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Volumetric_${PDB}_Repair_PN.txt
+cp InteractingResidues_VdWClashes_${PDB}_Repair_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt
+cp InteractingResidues_Distances_${PDB}_Repair_PN.fxout InteractingResidues_Distances_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Distances_${PDB}_Repair_PN.txt
+cp InteractingResidues_Electro_${PDB}_Repair_PN.fxout InteractingResidues_Electro_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Electro_${PDB}_Repair_PN.txt
+cp InteractingResidues_Hbonds_${PDB}_Repair_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Hbonds_${PDB}_Repair_PN.txt
+cp InteractingResidues_Partcov_${PDB}_Repair_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Partcov_${PDB}_Repair_PN.txt
+cp InteractingResidues_Volumetric_${PDB}_Repair_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_PN.txt
+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
+
+
+
+
+
+
diff --git a/foldx/renamefiles_mac.sh b/foldx/renamefiles_mac.sh
new file mode 100755
index 0000000..ea517bc
--- /dev/null
+++ b/foldx/renamefiles_mac.sh
@@ -0,0 +1,68 @@
+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
+
+
+
+
+
+
diff --git a/foldx/repairPDB.sh b/foldx/repairPDB.sh
new file mode 100755
index 0000000..ee1a13c
--- /dev/null
+++ b/foldx/repairPDB.sh
@@ -0,0 +1,9 @@
+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}
diff --git a/foldx/runFoldx.py b/foldx/runFoldx.py
new file mode 100755
index 0000000..b1bbcd4
--- /dev/null
+++ b/foldx/runFoldx.py
@@ -0,0 +1,332 @@
+#!/usr/bin/env python3
+import subprocess
+import os
+import numpy as np
+import pandas as pd
+from contextlib import suppress
+from pathlib import Path
+import re
+import csv
+import argparse
+#https://realpython.com/python-pathlib/
+
+# FIXME
+#strong dependency of file and path names
+#cannot pass file with path. Need to pass them separately
+#assumptions made for dir struc as standard
+#datadir + drug + input
+
+#=======================================================================
+#%% specify input and curr dir
+homedir = os.path.expanduser('~')
+
+# set working dir
+os.getcwd()
+os.chdir(homedir + '/git/LSHTM_analysis/foldx/')
+os.getcwd()
+
+#=======================================================================
+#%% command line args
+arg_parser = argparse.ArgumentParser()
+
+arg_parser.add_argument('-d', '--drug',     help = 'drug name', default = 'pyrazinamide')
+arg_parser.add_argument('-g', '--gene',     help = 'gene name', default = 'pncA') # case sensitive
+
+
+arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + drug + input', default = None)
+arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + drug + output', default = None)
+
+
+arg_parser.add_argument('-f', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called gene_complex.pdb', default = None)
+arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called gene_test_snps.csv exists', default = None)
+
+arg_parser.add_argument('-c1', '--chain1',    help = 'Chain1 ID', default = 'A') # case sensitive
+arg_parser.add_argument('-c2', '--chain2',    help = 'Chain2 ID', default = 'B') # case sensitive
+
+args = arg_parser.parse_args()
+#=======================================================================
+#%% variable assignment: input and output 
+#drug = 'pyrazinamide'
+#gene = 'pncA'
+#gene_match = gene + '_p.'
+#%%=====================================================================
+# Command Line Options
+drug            = args.drug
+gene            = args.gene
+indir           = args.input_dir
+outdir          = args.output_dir
+mut_filename    = args.mutation_file
+chainA          = args.chain1
+chainB          = args.chain2
+pdb_filename    = args.pdb_file
+
+# os.path.splitext will fail interestingly with file.pdb.txt.zip
+#pdb_name = os.path.splitext(pdb_file)[0]
+# Just the filename, thanks
+#pdb_name = Path(in_filename_pdb).stem
+
+#==========
+# dir
+#==========
+datadir = homedir + '/' + 'git/Data'
+
+if not indir:
+    indir = datadir + '/' + drug + '/' + 'input'
+
+if not outdir:
+    outdir = datadir + '/' + drug + '/' + 'output'
+# FIXME: 
+process_dir = datadir + '/' + drug +'/' + 'processing'
+# FIXME: this is a temporary directory and should be correctly handled
+os.mkdir(process_dir)
+#=======
+# input
+#=======
+# FIXME
+
+
+if pdb_filename:
+    pdb_name = Path(pdb_filename).stem
+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
+else:
+    #mutation_file =  gene.lower() + '_mcsm_snps.csv' #real
+    mutation_file =  gene.lower() + '_test_snps.csv' #test
+
+infile_muts = outdir + '/' + mutation_file
+
+#=======
+# output 
+#=======
+out_filename = gene.lower() + '_foldx_results.csv'
+outfile_foldx =  outdir + '/' + out_filename
+
+print('Arguments being passed:'
+, '\nDrug:', args.drug
+, '\ngene:', args.gene
+, '\ninput dir:', indir
+, '\noutput dir:', outdir
+, '\npdb file:', infile_pdb
+, '\npdb name:', pdb_name
+, '\nactual pdb name:', actual_pdb_filename
+, '\nmutation file:', infile_muts
+, '\nchain1:', args.chain1
+, '\noutput file:', outfile_foldx
+, '\n=============================================================')
+#=======================================================================
+
+def getInteractionEnergy(filename):
+    data = pd.read_csv(filename,sep = '\t')
+    return data['Interaction Energy'].loc[0]
+
+def getInteractions(filename):
+    data = pd.read_csv(filename, index_col = 0, header = 0, sep = '\t')
+    contactList = getIndexes(data,1)
+    number = len(contactList)
+    return number
+
+def formatMuts(mut_file,pdbname):
+    with open(mut_file) as csvfile:
+        readCSV = csv.reader(csvfile)
+        muts = []
+        for row in readCSV:
+                mut = row[0]
+                muts.append(mut)
+        
+    mut_list = []
+    outfile = process_dir + '/individual_list_' + pdbname + '.txt'
+    with open(outfile, 'w') as output:
+        for m in muts:
+                print(m)
+                mut = m[:1] + chainA+ m[1:] 
+                mut_list.append(mut)
+                mut = mut + ';'
+                print(mut)
+                output.write(mut)
+                output.write('\n')
+    return mut_list
+
+def getIndexes(data, value):
+    colnames = data.columns.values
+    listOfPos = list()
+    result = data.isin([value])
+    result.columns = colnames
+    seriesdata = result.any()
+    columnNames = list(seriesdata[seriesdata==True].index)
+    for col in columnNames:
+        rows = list(result[col][result[col]==True].index)
+        
+        for row in rows:
+            listOfPos.append((row,col))
+    
+    return listOfPos
+
+def loadFiles(df):
+    # load a text file in to np matrix
+    resultList = []
+    f = open(df,'r')
+    for line in f:
+        line = line.rstrip('\n')
+        aVals = line.split('\t')
+        fVals = list(map(np.float32, sVals))
+        resultList.append(fVals)
+    f.close()
+    return np.asarray(resultList, dtype=np.float32)
+
+#=======================================================================    
+def main():
+    pdbname = pdb_name
+    comp = '' # for complex only
+    mut_filename = infile_muts #pnca_test_snps.csv
+    mutlist = formatMuts(mut_filename, pdbname)
+
+    print(mutlist)
+    nmuts = len(mutlist)
+    print(nmuts)
+    print(mutlist)
+    print('start')
+    #subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
+    subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
+    
+    print('end')
+    output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
+    
+    for n in range(1,nmuts+1):
+        print(n)
+        with suppress(Exception):
+            subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), process_dir])
+        
+    for n in range(1,nmuts+1):
+        print(n)
+        with suppress(Exception):
+            subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname, str(n), process_dir])
+            
+    out = subprocess.check_output(['bash','renamefiles.sh', pdbname, process_dir])
+
+    if comp=='y':
+        chain1=chainA
+        chain2=chainB
+        with suppress(Exception):
+            subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
+        for n in range(1,nmuts+1):
+            with suppress(Exception):
+                subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
+
+    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')
+    
+    ddG=[]
+    print('ddG')
+    print(len(dGdata))
+    for i in range(0,len(dGdata)):
+        ddG.append(dGdata['total energy'].loc[i])
+    
+
+    nint = len(interactions)
+    wt_int = []
+
+    for i in interactions:
+        filename = process_dir + '/Matrix_' + i + '_'+ pdbname + '_Repair_PN.txt'
+        wt_int.append(getInteractions(filename))
+    print('wt')
+    print(wt_int)
+    
+    ntotal = nint+1
+    print(ntotal)
+    print(nmuts)
+    data = np.empty((ntotal,nmuts))
+    data[0] = ddG
+    print(data)
+    for i in range(0,len(interactions)):
+        d=[]
+        p=0
+        for n in range(1, nmuts+1):
+            print(i)
+            filename = process_dir + '/Matrix_' + interactions[i] + '_' + pdbname + '_Repair_' + str(n) + '_PN.txt'
+            mut = getInteractions(filename)
+            diff = wt_int[i] - mut
+            print(diff)
+            print(wt_int[i])
+            print(mut)
+            d.append(diff)
+        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',
+'VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS']   
+
+    print(interactions)
+
+    IE = []
+    if comp=='y':
+        wtfilename = process_dir + '/Summary_' + pdbname + '_Repair_AC.txt'
+        wtE = getInteractionEnergy(wtfilename)
+        print(wtE)
+        for n in range(1,nmuts+1):
+            print(n)
+            filename = process_dir + '/Summary_' + pdbname + '_Repair_' + str(n) + '_AC.txt'
+            mutE = getInteractionEnergy(filename)
+            print(mutE)
+            diff = wtE - mutE
+            print(diff)
+            IE.append(diff)
+        print(IE)
+        IEresults = pd.DataFrame(IE,columns = ['Interaction Energy'], index = mutlist)
+        IEfilename = 'foldx_complexresults_'+pdbname+'.csv'
+        IEresults.to_csv(IEfilename)
+        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',
+'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:
+        readCSV = csv.reader(csvfile)
+        mutlist = []
+        for row in readCSV:
+                mut = row[0]
+                mutlist.append(mut)
+    print(mutlist)
+    print(len(mutlist))
+    print(data)
+    results = pd.DataFrame(data, columns = mutlist, index = interactions)
+    results.append(ddG)
+    #print(results.head())
+    
+    # my style formatted results
+    results2 = results.T # transpose df
+    results2.index.name = 'mutationinformation' # assign name to index
+    results2 = results2.reset_index() # turn it into a columns
+  
+    results2['mutationinformation'] = results2['mutationinformation'].replace({r'([A-Z]{1})[A-Z]{1}([0-9]+[A-Z]{1});' : r'\1 \2'}, regex = True) # capture mcsm style muts (i.e not the chain id)
+    results2['mutationinformation'] = results2['mutationinformation'].str.replace(' ', '') # remove empty space
+    
+    results2.rename(columns = {'Distances': 'Contacts'}, inplace = True)
+        
+    # lower case columns
+    results2.columns = results2.columns.str.lower()
+    
+    print('Writing file in the format below:\n'
+        , results2.head()
+        , '\nNo. of rows:', len(results2)
+        , '\nNo. of cols:', len(results2.columns))
+    
+    outputfilename = outfile_foldx   
+    #outputfilename = 'foldx_results_' + pdbname + '.csv'
+    #results.to_csv(outputfilename)
+    results2.to_csv(outputfilename, index = False)
+    
+if __name__ == '__main__':
+    main()
diff --git a/foldx/runPrintNetworks.sh b/foldx/runPrintNetworks.sh
new file mode 100755
index 0000000..c2bebab
--- /dev/null
+++ b/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}
diff --git a/foldx/runcomplex.sh b/foldx/runcomplex.sh
new file mode 100755
index 0000000..9cfd32a
--- /dev/null
+++ b/foldx/runcomplex.sh
@@ -0,0 +1,10 @@
+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 
+
diff --git a/foldx/runfoldx.sh b/foldx/runfoldx.sh
new file mode 100755
index 0000000..5a929ce
--- /dev/null
+++ b/foldx/runfoldx.sh
@@ -0,0 +1,9 @@
+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}
diff --git a/mcsm/mcsm.py b/mcsm/mcsm.py
index c9a84eb..9eb0e56 100644
--- a/mcsm/mcsm.py
+++ b/mcsm/mcsm.py
@@ -14,8 +14,6 @@ import numpy as np
 from mcsm import *
 #==============================
 #%% global variables for defs
-
-
 #==============================
 #%% 
 
@@ -194,9 +192,9 @@ def format_mcsm_output(mcsm_outputcsv):
     #############
     # format colnames: all lowercase, remove spaces and use '_' to join 
     print('Assigning meaningful colnames i.e without spaces and hyphen and reflecting units'
-            , '\n===================================================================')
+            , '\n=======================================================')
     my_colnames_dict = {'Predicted Affinity Change': 'PredAffLog' # relevant info from this col will be extracted and the column discarded
-        , 'Mutation information': 'mutation_information' # {wild_type}<position>{mutant_type}
+        , 'Mutation information': 'mutationinformation' # {wild_type}<position>{mutant_type}
         , 'Wild-type': 'wild_type' # one letter amino acid code
         , 'Position': 'position' # number
         , 'Mutant-type': 'mutant_type' # one letter amino acid code
@@ -206,41 +204,41 @@ def format_mcsm_output(mcsm_outputcsv):
         , 'DUET stability change': 'duet_stability_change'} # in kcal/mol
 
     mcsm_data.rename(columns = my_colnames_dict, inplace = True)
-#%%===========================================================================
+#%%=====================================================================
     #################################
-    # populate mutation_information 
+    # populate mutationinformation 
     # col which is currently blank
     #################################
-    # populate mutation_information column:mcsm style  muts {WT}<POS>{MUT}
-    print('Populating column : mutation_information which is currently empty\n', mcsm_data['mutation_information'])
-    mcsm_data['mutation_information'] = mcsm_data['wild_type'] +  mcsm_data['position'].astype(str) + mcsm_data['mutant_type']
-    print('checking after populating:\n', mcsm_data['mutation_information']
-            , '\n===================================================================')
+    # populate mutationinformation column:mcsm style  muts {WT}<POS>{MUT}
+    print('Populating column : mutationinformation which is currently empty\n', mcsm_data['mutationinformation'])
+    mcsm_data['mutationinformation'] = mcsm_data['wild_type'] +  mcsm_data['position'].astype(str) + mcsm_data['mutant_type']
+    print('checking after populating:\n', mcsm_data['mutationinformation']
+            , '\n=======================================================')
 
     # Remove spaces b/w pasted columns
-    print('removing white space within column: \mutation_information')
-    mcsm_data['mutation_information'] = mcsm_data['mutation_information'].str.replace(' ', '')
-    print('Correctly formatted column: mutation_information\n', mcsm_data['mutation_information']
-            , '\n===================================================================')
-#%%===========================================================================
+    print('removing white space within column: \mutationinformation')
+    mcsm_data['mutationinformation'] = mcsm_data['mutationinformation'].str.replace(' ', '')
+    print('Correctly formatted column: mutationinformation\n', mcsm_data['mutationinformation']
+            , '\n=======================================================')
+#%%=====================================================================
     #############
     # sanity check: drop dupliate muts
     #############
     # shouldn't exist as this should be eliminated at the time of running mcsm
     print('Sanity check:'
             , '\nChecking duplicate mutations')
-    if mcsm_data['mutation_information'].duplicated().sum() == 0:
+    if mcsm_data['mutationinformation'].duplicated().sum() == 0:
         print('PASS: No duplicate mutations detected (as expected)'
                 , '\nDim of data:', mcsm_data.shape
-                , '\n===============================================================')
+                , '\n===================================================')
     else:
         print('WARNING: Duplicate mutations detected'
                 , '\nDim of df with duplicates:', mcsm_data.shape
                 , 'Removing duplicate entries')
-        mcsm_data = mcsm_data.drop_duplicates(['mutation_information'])
+        mcsm_data = mcsm_data.drop_duplicates(['mutationinformation'])
         print('Dim of data after removing duplicate muts:', mcsm_data.shape
-        , '\n===============================================================')
-#%%=========================================================================== 
+        , '\n===========================================================')
+#%%===================================================================== 
     #############
     # Create col: duet_outcome
     #############
@@ -259,8 +257,8 @@ def format_mcsm_output(mcsm_outputcsv):
     #    print('FAIL: DUET outcome assigned incorrectly'
     #        , '\nExpected no. of stabilising mutations:', DUET_pos
     #        , '\nGot no. of stabilising mutations', mcsm_data['duet_outcome'].value_counts()['Stabilising']
-    #        , '\n===============================================================')
-#%%===========================================================================
+    #        , '\n======================================================')
+#%%=====================================================================
     #############
     # Extract numeric
     # part of ligand_distance col
@@ -271,7 +269,7 @@ def format_mcsm_output(mcsm_outputcsv):
     print('extracting numeric part of col: ligand_distance')
     mcsm_data['ligand_distance'] = mcsm_data['ligand_distance'].str.extract('(\d+\.?\d*)')
     print('Ligand Distance:',mcsm_data['ligand_distance'])
-#%%===========================================================================
+#%%=====================================================================
     #############
     # Create 2 columns:
     # ligand_affinity_change and ligand_outcome
@@ -282,7 +280,7 @@ def format_mcsm_output(mcsm_outputcsv):
     # categorocal part: '\b(\w+ing)\b'
     print('Extracting numerical and categorical parts from the col: PredAffLog')
     print('to create two columns: ligand_affinity_change and ligand_outcome'
-            , '\n===================================================================')
+            , '\n=======================================================')
 
     # 1) Extracting the predicted affinity change (numerical part)
     mcsm_data['ligand_affinity_change'] = mcsm_data['PredAffLog'].str.extract('(-?\d+\.?\d*)', expand = True)
@@ -308,24 +306,24 @@ def format_mcsm_output(mcsm_outputcsv):
     if check.all():
         print('PASS: spelling change successfull'
                 , '\nNo. of predicted affinity changes:\n', british_spl
-                , '\n===============================================================')
+                , '\n===================================================')
     else:
         sys.exit('FAIL: spelling change unsucessfull'
                 , '\nExpected:\n', american_spl
                 , '\nGot:\n', british_spl
-                , '\n===============================================================')
-#%%===========================================================================
+                , '\n===================================================')
+#%%=====================================================================
     #############
     # ensuring corrrect dtype for numeric columns
     #############
     # check dtype in cols
     print('Checking dtypes in all columns:\n', mcsm_data.dtypes
-            , '\n===================================================================')
+            , '\n=======================================================')
     print('Converting the following cols to numeric:'
             , '\nligand_distance'
             , '\nduet_stability_change'
             , '\nligand_affinity_change'
-            , '\n===================================================================')
+            , '\n=======================================================')
 
     # using apply method  to change stabilty and affinity values to numeric
     numeric_cols = ['duet_stability_change', 'ligand_affinity_change', 'ligand_distance']
@@ -336,12 +334,12 @@ def format_mcsm_output(mcsm_outputcsv):
     if cols_check.all():
         print('PASS: dtypes for selected cols:', numeric_cols
                 , '\nchanged to numeric'
-                , '\n===============================================================')
+                , '\n===================================================')
     else:
         sys.exit('FAIL:dtype change to numeric for selected cols unsuccessful'
-                , '\n===============================================================')
+                , '\n===================================================')
         print(mcsm_data.dtypes)
-#%%===========================================================================
+#%%=====================================================================
     #############
     # scale duet values
     #############
@@ -357,7 +355,7 @@ def format_mcsm_output(mcsm_outputcsv):
             , '\n---------------------------------------------------------------'
             , '\nScaled duet scores:\n', mcsm_data['duet_scaled'])
 
-#%%===========================================================================
+#%%=====================================================================
     #############
     # scale affinity values
     #############
@@ -373,7 +371,7 @@ def format_mcsm_output(mcsm_outputcsv):
             , '\n---------------------------------------------------------------'
             , '\nScaled affinity scores:\n', mcsm_data['affinity_scaled'])
             
-#%%===========================================================================
+#%%=====================================================================
     #############
     # adding column: wild_position
     # useful for plots and db
@@ -385,33 +383,33 @@ def format_mcsm_output(mcsm_outputcsv):
     print('removing white space within column: wild_position')
     mcsm_data['wild_position'] = mcsm_data['wild_position'].str.replace(' ', '')
     print('Correctly formatted column: wild_position\n', mcsm_data['wild_position'].head()
-          , '\n===================================================================')
+          , '\n=========================================================')
     
-#%%===========================================================================    
+#%%=====================================================================    
     
     #############
     # ensuring corrrect dtype in non-numeric cols
     #############
     
     #) char cols
-    char_cols = ['PredAffLog', 'mutation_information', 'wild_type', 'mutant_type', 'chain', 'ligand_id', 'duet_outcome', 'ligand_outcome', 'wild_position']
+    char_cols = ['PredAffLog', 'mutationinformation', 'wild_type', 'mutant_type', 'chain', 'ligand_id', 'duet_outcome', 'ligand_outcome', 'wild_position']
 
     #mcsm_data[char_cols] = mcsm_data[char_cols].astype(str)
     cols_check_char = mcsm_data.select_dtypes(include = 'object').columns.isin(char_cols)
     
     if cols_check_char.all():
         print('PASS: dtypes for char cols:', char_cols, 'are indeed string'
-                , '\n===============================================================')
+                , '\n===================================================')
     else:
         sys.exit('FAIL:dtype change to numeric for selected cols unsuccessful'
-                , '\n===============================================================')
+                , '\n===================================================')
     #mcsm_data['ligand_distance', 'ligand_affinity_change'].apply(is_numeric_dtype(mcsm_data['ligand_distance', 'ligand_affinity_change']))
     print(mcsm_data.dtypes)
-#%%=============================================================================
+#%%=====================================================================
     # Removing PredAff log column as it is not needed?
     print('Removing col: PredAffLog since relevant info has been extracted from it')
     mcsm_dataf = mcsm_data.drop(columns = ['PredAffLog'])
-#%%===========================================================================
+#%%=====================================================================
     #############
     # sanity check before writing file
     #############
@@ -421,14 +419,14 @@ def format_mcsm_output(mcsm_outputcsv):
     if len(mcsm_dataf.columns) == expected_cols:
         print('PASS: formatting successful'
                 , '\nformatted df has expected no. of cols:', expected_cols
-                , '\n---------------------------------------------------------------'
+                , '\n---------------------------------------------------'
                 , '\ncolnames:', mcsm_dataf.columns
-                , '\n----------------------------------------------------------------'
+                , '\n---------------------------------------------------'
                 , '\ndtypes in cols:', mcsm_dataf.dtypes
-                , '\n----------------------------------------------------------------'
+                , '\n---------------------------------------------------'
                 , '\norig data shape:', dforig_shape
                 , '\nformatted df shape:', mcsm_dataf.shape
-                , '\n===============================================================')
+                , '\n===================================================')
     else: 
         sys.exit('FAIL: something went wrong in formatting df'
                 , '\nLen of orig df:', dforig_len
@@ -438,7 +436,7 @@ def format_mcsm_output(mcsm_outputcsv):
                 , '\nCheck formatting:'
                 , '\ncheck hardcoded value:', expected_ncols_toadd
                 , '\nis', expected_ncols_toadd, 'the no. of expected cols to add?'
-                , '\n===============================================================')
+                , '\n===================================================')
                 
                 
     return mcsm_dataf
diff --git a/scripts/combine_afs_ors.py b/scripts/combine_afs_ors.py
index fb21980..2fb0f8f 100755
--- a/scripts/combine_afs_ors.py
+++ b/scripts/combine_afs_ors.py
@@ -71,7 +71,7 @@ infile2 = outdir + '/' + in_filename_afor_kin
 print('Input file0:', infile0
       , '\nInput file1:', infile1
       , '\nInput file2:', infile2
-      , '\n===================================================================')
+      , '\n=============================================================')
 
 #=======
 # output 
@@ -79,7 +79,7 @@ print('Input file0:', infile0
 out_filename = gene.lower() + '_metadata_afs_ors.csv'
 outfile =  outdir + '/' + out_filename
 print('Output file:', outfile
-      , '\n===================================================================')
+      , '\n=============================================================')
 
 
 del(in_filename_afor, in_filename_afor_kin, datadir, indir, outdir)
@@ -217,13 +217,7 @@ if fail:
 del(left_df, right_df, common_cols, merging_cols, nmerging_cols, my_join, ndiff1, ndiff2, missing_mutinfo
     , expected_rows, expected_cols, fail)
 del(afor_df, snpinfo_df)
-
-
-
-
-
-
-
+#=======================================================================
 
 #%% Second merge: combined_df1 and afor_kin_df