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refactor foldx pipeline to include:

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* command-line args
* creating necessary dirs automagically
* code cleanup, syntax errors, etc etc
This commit is contained in:
Tanushree Tunstall 2020-06-30 17:14:30 +01:00
parent e8a66a7a94
commit 973a1a33da
12 changed files with 700 additions and 56 deletions
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9
foldx/runfoldx.sh Executable file
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@ -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}