added scratch/

scripts/scratch/chain_splitter_template.py

@@ -0,0 +1,49 @@
+#!/usr/bin/python3
+
+#=======================================================================
+# TASK: extract chain from pdb and save each chain as a separate file
+
+# link for saving each chain as a separate file
+# https://stackoverflow.com/questions/11685716/how-to-extract-chains-from-a-pdb-file
+# command line args
+# https://stackoverflow.com/questions/15753701/how-can-i-pass-a-list-as-a-command-line-argument-with-argparse
+#=======================================================================   
+
+#%%
+import os, sys
+from Bio.PDB import Select, PDBIO
+from Bio.PDB.PDBParser import PDBParser
+#%% homdir and curr dir and local imports
+homedir = os.path.expanduser('~') 
+# set working dir
+os.getcwd()
+os.chdir(homedir + '/git/LSHTM_analysis/scripts')
+os.getcwd()
+#%%
+class ChainSelect(Select):
+    def __init__(self, chain):
+        self.chain = chain
+
+    def accept_chain(self, chain):
+        if chain.get_id() == self.chain:
+            return 1
+        else:          
+            return 0
+
+def main(): 
+    chains = ['A','B','C','F']
+    p = PDBParser(PERMISSIVE=1)       
+    #structure = p.get_structure(pdb_file, pdb_file)
+    structure = p.get_structure('/home/tanu/git/Data/ethambutol/input/3byw', '/home/tanu/git/Data/ethambutol/input/3byw.pdb')
+    #print('STRUCTURE:', structure.get_id())
+#    pdb_filename = print()
+    for chain in chains:
+        pdb_chain_file = 'pdb_file_chain_{}.pdb'.format(chain)         
+                        
+        io = PDBIO()               
+        io.set_structure(structure)
+        io.save('{}'.format(pdb_chain_file), ChainSelect(chain))
+
+# If run from command line...
+if __name__ == "__main__":
+    main()