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adding commands for use of pdbtools

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This commit is contained in:
Tanushree Tunstall 2020-05-12 12:50:49 +01:00
parent b28d866237
commit 7f66d5d19e
2 changed files with 11 additions and 2 deletions
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4
scripts/data_extraction.py
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@ -54,8 +54,8 @@ arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', defau
args = arg_parser.parse_args() args = arg_parser.parse_args()
#======================================================================= #=======================================================================
#%% variable assignment: input and output paths & filenames #%% variable assignment: input and output paths & filenames
drug = 'cycloserine' #drug =
gene = 'alr' #gene = '
drug = args.drug drug = args.drug
gene = args.gene gene = args.gene

9
scripts/pdbtools_commands Normal file
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@ -0,0 +1,9 @@
# renumber
home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/cycloserine/input/alr_complex_model.pdb -s 35 -r
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home/tanu/git/Data/rifampicin/input/rpob_complex_model.pdb -s 29 -r
# extract seq from structure
/home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_seq -a /home/tanu/git/Data/ethambutol/input/3byw.pdb > 3byw_seq.txt