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test2 bugfixes

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This commit is contained in:
Tanushree Tunstall 2021-02-08 15:24:22 +00:00
parent 4d03a43c4a
commit a67156bc87
13 changed files with 851 additions and 69 deletions
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61
foldx/test2/mutrenamefiles.sh Executable file
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PDB=$1
n=$2
#cd /home/git/LSHTM_analysis/foldx/test/
cp Matrix_Hbonds_${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

10
foldx/test2/mutruncomplex.sh Executable file
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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

62
foldx/test2/renamefiles.sh Executable file
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PDB=$1
#cd /home/git/LSHTM_analysis/foldx/test
cp Dif_${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
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

9
foldx/test2/repairPDB.sh Executable file
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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}

344
foldx/test2/runFoldx.py Executable file
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#!/usr/bin/env python3
import subprocess
import os
import sys
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 = None)
arg_parser.add_argument('-g', '--gene', help = 'gene name (case sensitive)', default = None)
arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
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('-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!
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
datadir = args.datadir
indir = args.input_dir
outdir = args.output_dir
process_dir = args.process_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
#==============
# directories
#==============
if not datadir:
datadir = homedir + '/' + 'git/Data'
if not indir:
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'
# 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_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 = 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
#=======
out_filename = gene.lower() + '_foldx.csv'
outfile_foldx = outdir + '/' + out_filename
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
, '\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_mcsm_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()

250
foldx/test2/runFoldx_test.py Executable file
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#!/usr/bin/env python3
import subprocess
import os
import numpy as np
import pandas as pd
from contextlib import suppress
import re
import csv
def getInteractions(filename):
data = pd.read_csv(filename, index_col=0, header =0, sep="\t")
contactList = getIndexes(data,1)
print(contactList)
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 = "/home/tanu/git/LSHTM_analysis/foldx/test2/individual_list_"+pdbname+".txt"
with open(outfile, "w") as output:
for m in muts:
print(m)
mut = m[:1]+'A'+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 = '3pl1'
mut_filename = "pnca_muts_sample.csv"
mutlist = formatMuts(mut_filename, pdbname)
print(mutlist)
nmuts = len(mutlist)+1
print(nmuts)
print(mutlist)
print("start")
output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname])
print("end")
for n in range(1,nmuts):
print(n)
with suppress(Exception):
subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname,str(n)])
for n in range(1,nmuts):
print(n)
with suppress(Exception):
subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname,str(n)])
out = subprocess.check_output(['bash','renamefiles.sh',pdbname])
dGdatafile = "/home/tanu/git/LSHTM_analysis/foldx/test2/Dif_"+pdbname+"_Repair.txt"
dGdata = pd.read_csv(dGdatafile, sep="\t")
print(dGdata)
ddG=[]
for i in range(0,len(dGdata)):
ddG.append(dGdata['total energy'].loc[i])
print(ddG)
distfile = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Distances_"+pdbname+"_Repair_PN.txt"
wt_nc = getInteractions(distfile)
elecfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_RR_"+pdbname+"_Repair_PN.txt"
wt_neRR = getInteractions(elecfileRR)
elecfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_MM_"+pdbname+"_Repair_PN.txt"
wt_neMM = getInteractions(elecfileMM)
elecfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_SM_"+pdbname+"_Repair_PN.txt"
wt_neSM = getInteractions(elecfileSM)
elecfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_SS_"+pdbname+"_Repair_PN.txt"
wt_neSS = getInteractions(elecfileSS)
disufileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_RR_"+pdbname+"_Repair_PN.txt"
wt_ndRR = getInteractions(disufileRR)
disufileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_MM_"+pdbname+"_Repair_PN.txt"
wt_ndMM = getInteractions(disufileMM)
disufileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_SM_"+pdbname+"_Repair_PN.txt"
wt_ndSM = getInteractions(disufileSM)
disufileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_SS_"+pdbname+"_Repair_PN.txt"
wt_ndSS = getInteractions(disufileSS)
hbndfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_RR_"+pdbname+"_Repair_PN.txt"
wt_nhRR = getInteractions(hbndfileRR)
hbndfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_MM_"+pdbname+"_Repair_PN.txt"
wt_nhMM = getInteractions(hbndfileMM)
hbndfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_SM_"+pdbname+"_Repair_PN.txt"
wt_nhSM = getInteractions(hbndfileSM)
hbndfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_SS_"+pdbname+"_Repair_PN.txt"
wt_nhSS = getInteractions(hbndfileSS)
partfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_RR_"+pdbname+"_Repair_PN.txt"
wt_npRR = getInteractions(partfileRR)
partfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_MM_"+pdbname+"_Repair_PN.txt"
wt_npMM = getInteractions(partfileMM)
partfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_SM_"+pdbname+"_Repair_PN.txt"
wt_npSM = getInteractions(partfileSM)
partfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_SS_"+pdbname+"_Repair_PN.txt"
wt_npSS = getInteractions(partfileSS)
vdwcfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_RR_"+pdbname+"_Repair_PN.txt"
wt_nvRR = getInteractions(vdwcfileRR)
vdwcfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_MM_"+pdbname+"_Repair_PN.txt"
wt_nvMM = getInteractions(vdwcfileMM)
vdwcfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_SM_"+pdbname+"_Repair_PN.txt"
wt_nvSM = getInteractions(vdwcfileSM)
vdwcfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_SS_"+pdbname+"_Repair_PN.txt"
wt_nvSS = getInteractions(vdwcfileSS)
volufileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_RR_"+pdbname+"_Repair_PN.txt"
wt_nvoRR = getInteractions(volufileRR)
volufileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_MM_"+pdbname+"_Repair_PN.txt"
wt_nvoMM = getInteractions(volufileMM)
volufileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_SM_"+pdbname+"_Repair_PN.txt"
wt_nvoSM = getInteractions(volufileSM)
volufileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_SS_"+pdbname+"_Repair_PN.txt"
wt_nvoSS = getInteractions(volufileSS)
dnc = []
dneRR = []
dneMM = []
dneSM = []
dneSS = []
dndRR = []
dndMM = []
dndSM = []
dndSS = []
dnhRR = []
dnhMM = []
dnhSM = []
dnhSS = []
dnpRR = []
dnpMM = []
dnpSM = []
dnpSS = []
dnvRR = []
dnvMM = []
dnvSM = []
dnvSS = []
dnvoRR = []
dnvoMM = []
dnvoSM = []
dnvoSS = []
for n in range(1, nmuts):
filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Distances_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
mut_nc = getInteractions(filename)
diffc = wt_nc - mut_nc
dnc.append(diffc)
filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
mut_neRR = getInteractions(filename)
diffeRR = wt_neRR - mut_neRR
dneRR.append(diffeRR)
filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
mut_ndRR = getInteractions(filename)
diffdRR = wt_ndRR - mut_ndRR
dndRR.append(diffdRR)
filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
mut_nhRR = getInteractions(filename)
diffhRR = wt_nhRR - mut_nhRR
dnhRR.append(diffhRR)
filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
mut_npRR = getInteractions(filename)
diffpRR = wt_npRR - mut_npRR
dnpRR.append(diffpRR)
filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
mut_nvRR = getInteractions(filename)
diffvRR = wt_nvRR - mut_nvRR
dnvRR.append(diffvRR)
filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
mut_nvoRR = getInteractions(filename)
diffvoRR = wt_nvoRR - mut_nvoRR
dnvoRR.append(diffvoRR)
print(dnc)
print(dneRR)
print(dndRR)
print(dnhRR)
print(dnpRR)
print(dnvRR)
print(dnvoRR)
results = pd.DataFrame([(ddG),(dnc),(dneRR),(dndRR),(dnhRR),(dnpRR),(dnvRR),(dnvoRR)], columns=mutlist, index=["ddG","contacts","electro","disulfide","hbonds","partcov","VdWClashes","volumetric"])
results.append(ddG)
print(results)
results2 = results.T # transpose df
outputfilename = "foldx_results_"+pdbname+".csv"
# results.to_csv(outputfilename)
results2.to_csv(outputfilename)
if __name__ == "__main__":
main()

7
foldx/test2/runPrintNetworks.sh Executable file
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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}

9
foldx/test2/runcomplex.sh Executable file
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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

9
foldx/test2/runfoldx.sh Executable file
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PDB=$1
OUTDIR=$2
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=.