tanu/LSHTM_analysis
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Tanushree Tunstall 2021-02-08 16:16:53 +00:00
parent fa25a30dcf
commit 99b77434b5
3 changed files with 7 additions and 4 deletions
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2
foldx/test2/repairPDB.sh
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@ -1,7 +1,7 @@
INDIR=$1
PDB=$2
OUTDIR=$3
cd ${OUTDIR}
logger "Running repairPDB"
#foldx --command=RepairPDB --pdb="${PDB}.pdb" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 outPDB=true --output-dir=${OUTDIR}

3
foldx/test2/runFoldx.py
View file

@ -105,6 +105,7 @@ else:
infile_pdb = indir + '/' + pdb_filename
actual_pdb_filename = Path(infile_pdb).name
#actual_pdb_filename = os.path.abspath(infile_pdb)
if mut_filename:
mutation_file = os.path.abspath(mut_filename)
@ -208,9 +209,11 @@ def main():
print('start')
#subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
print('\033[95mSTAGE: repair PDB\033[0m')
print('EXECUTING: repairPDB.sh %s %s %s' % (indir, actual_pdb_filename, process_dir))
subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
print('\033[95mCOMPLETE: repair PDB\033[0m')
print('\033[95mSTAGE: run FoldX (shell)\033[0m')
print('EXECUTING: runfoldx.sh %s %s ' % (pdbname, process_dir))
output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
print('\033[95mCOMPLETE: run FoldX (shell)\033[0m')

6
foldx/test2/runfoldx.sh
View file

@ -4,6 +4,6 @@ cd ${OUTDIR}
pwd
ls -l
logger "Running runfoldx"
foldx --command=BuildModel --pdb="${PDB}_Repair.pdb" --mutant-file="individual_list_${PDB}.txt" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 --out-pdb=true --numberOfRuns=1 --output-dir=.
foldx --command=PrintNetworks --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=.
foldx --command=SequenceDetail --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=.
foldx --command=BuildModel --pdb="${PDB}_Repair.pdb" --mutant-file="individual_list_${PDB}.txt" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 --out-pdb=true --numberOfRuns=1 --output-dir=${OUTDIR}
foldx --command=PrintNetworks --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}
foldx --command=SequenceDetail --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}