From ddae107314681741ae66f434826678511c59daed Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Tue, 9 Nov 2021 12:44:11 +0000 Subject: [PATCH] saving work in LSHTM_analysis before combining data for targets --- mcsm/run_mcsm.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mcsm/run_mcsm.py b/mcsm/run_mcsm.py index 7e38543..dd0e150 100755 --- a/mcsm/run_mcsm.py +++ b/mcsm/run_mcsm.py @@ -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', default = None) -arg_parser.add_argument('-a','--affinity', help='Affinity in nM. REQUIRED only in "submit" stage', default = 0.99) +arg_parser.add_argument('-a','--affinity', help='Affinity in nM. REQUIRED only in "submit" stage', default = 10) #0.99 for pnca, gid, embb. For SP targets (alr,katg, rpob), use 10. arg_parser.add_argument('-pdb','--pdb_file', help = 'PDB File') arg_parser.add_argument('-m','--mutation_file', help = 'Mutation File, mcsm style') @@ -42,8 +42,8 @@ args = arg_parser.parse_args() #%% variables #host = "http://biosig.unimelb.edu.au" #prediction_url = f"{host}/mcsm_lig/prediction" -#drug = 'isoniazid' -#gene = 'KatG' +#drug = '' +#gene = '' #%%===================================================================== # Command line options gene = args.gene