From 7f66d5d19e9d0eed5ad323de0faa2aa0075cb259 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 12 May 2020 12:50:49 +0100
Subject: [PATCH] adding commands for use of pdbtools

---
 scripts/data_extraction.py | 4 ++--
 scripts/pdbtools_commands  | 9 +++++++++
 2 files changed, 11 insertions(+), 2 deletions(-)
 create mode 100644 scripts/pdbtools_commands

diff --git a/scripts/data_extraction.py b/scripts/data_extraction.py
index a846b2b..259afa1 100755
--- a/scripts/data_extraction.py
+++ b/scripts/data_extraction.py
@@ -54,8 +54,8 @@ arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', defau
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output paths & filenames
-drug = 'cycloserine'
-gene = 'alr'
+#drug = 
+#gene = '
 
 drug = args.drug
 gene = args.gene
diff --git a/scripts/pdbtools_commands b/scripts/pdbtools_commands
new file mode 100644
index 0000000..d4986f7
--- /dev/null
+++ b/scripts/pdbtools_commands
@@ -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