From b5b54c7658867cadf2c5a34f2f63170dc6e2ccae Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Tue, 9 Feb 2021 15:20:55 +0000 Subject: [PATCH] dont break when the pdb file is in a weird place with a weird name --- foldx/runFoldx.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/foldx/runFoldx.py b/foldx/runFoldx.py index b5a4e69..d54d507 100755 --- a/foldx/runFoldx.py +++ b/foldx/runFoldx.py @@ -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 + + output') arg_parser.add_argument('-p', '--process_dir', help = 'Temp processing dir for running foldX. By default, it assmes homedir + + 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 _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 _complex.pdb in input_dir') arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called _mcsm_snps.csv exists') # FIXME: Doesn't work with 2 chains yet! @@ -244,7 +244,7 @@ def main(): subprocess.call(['foldx' , '--command=RepairPDB' , foldx_common - , '--pdb-dir=' + indir + , '--pdb-dir=' + os.path.dirname(pdb_filename) , '--pdb=' + actual_pdb_filename , 'outPDB=true' , '--output-dir=' + process_dir])