adding scripts for struct params

meta_data_analysis/run_pdb_dssp.sh

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Sun Feb 16 11:21:44 2020
+
+@author: tanu
+"""
+#!/usr/bin/bash
+# Run dssp exe
+
+#%%
+# specify variables for input and output paths and filenames
+drug="pyrazinamide"
+#gene = "pnca"
+
+datadir="~git/Data"
+basedir=${datadir}"/"${drug}
+echo${basedir}
+
+# input
+inpath="/original"
+
+# uncomment as necessary
+in_filename="/3pl1.pdb"
+
+infile=${basedir}${inpath}${in_filename}
+echo${infile}
+
+# output file 
+outpath="/processed"
+outdir=${datadir}"/"${drug}${outpath}
+out_filename="/3pl1.dssp"
+outfile=${outdir}${out_filename}
+echo${outdir}
+
+if not os.path.exists(datadir):
+    print('Error!', datadir, 'does not exist. Please ensure it exists. Dir struc specified in README.md')
+    os.makedirs(datadir)
+    exit()
+
+if not os.path.exists(outdir):
+    print('Error!', outdir, 'does not exist.Please ensure it exists. Dir struc specified in README.md')
+    exit()
+    
+else:
+    print('Dir exists: Carrying on')
+# end of variable assignment for input and output files
+#%%
+# ommand line args
+dssp -i 3pl1.pdb -o 3pl1.dssp
+dssp -i