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ran foldx and mcsm (get) for 33k dataset

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This commit is contained in:
Tanushree Tunstall 2020-07-08 20:30:32 +01:00
parent 172fa18420
commit 8931441fa5
3 changed files with 14 additions and 15 deletions
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6
mcsm/mcsm_wrapper.py
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@ -16,7 +16,7 @@ arg_parser.add_argument('-H', '--host', help='mCSM Server', default = 'http:/
arg_parser.add_argument('-U', '--url', help='mCSM Server URL', default = 'http://biosig.unimelb.edu.au/mcsm_lig/prediction')
arg_parser.add_argument('-c', '--chain', help='Chain ID as per PDB, Case sensitive', default = 'A')
arg_parser.add_argument('-l','--ligand', help='Ligand ID as per PDB, Case sensitive. REQUIRED only in "submit" stage')
arg_parser.add_argument('-a','--affinity', help='Affinity in nM', default = 10)
arg_parser.add_argument('-a','--affinity', help='Affinity in nM', default = 0.99)
#arg_parser.add_argument('-p','--pdb_file', help = 'PDB File')
arg_parser.add_argument('--datadir', help = 'Data Directory')
arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode')
@ -60,8 +60,8 @@ in_filename_pdb = gene.lower() + '_complex.pdb'
infile_pdb = indir + '/' + in_filename_pdb
#in_filename_snps = gene.lower() + '_mcsm_snps_test.csv' #(outfile2, from data_extraction.py)
in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile2, from data_extraction.py)
#in_filename_snps = gene.lower() + '_mcsm_snps_test.csv'
in_filename_snps = gene.lower() + '_mcsm_snps.csv' #(outfile_mcsm_snps, from data_extraction.py)
infile_snps = outdir + '/' + in_filename_snps
# mcsm_results globals