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dont break when the pdb file is in a weird place with a weird name

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Tanushree Tunstall 2021-02-09 15:20:55 +00:00
parent 73b705a563
commit b5b54c7658
1 changed files with 2 additions and 2 deletions
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4
foldx/runFoldx.py
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@ -40,7 +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('-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('-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') # DO NOT specify an absolute path 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') 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! # FIXME: Doesn't work with 2 chains yet!
@ -244,7 +244,7 @@ def main():
subprocess.call(['foldx' subprocess.call(['foldx'
, '--command=RepairPDB' , '--command=RepairPDB'
, foldx_common , foldx_common
, '--pdb-dir=' + indir , '--pdb-dir=' + os.path.dirname(pdb_filename)
, '--pdb=' + actual_pdb_filename , '--pdb=' + actual_pdb_filename
, 'outPDB=true' , 'outPDB=true'
, '--output-dir=' + process_dir]) , '--output-dir=' + process_dir])