tanu/LSHTM_analysis
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Merge branch 'embb_dev'

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This commit is contained in:
Tanushree Tunstall 2021-11-12 14:37:10 +00:00
commit c32de1bf0f
7 changed files with 238 additions and 116 deletions
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6
mcsm/run_mcsm.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', 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