added scratch/

scripts/scratch/chain_extract_template.py

@@ -0,0 +1,52 @@
+#!/usr/bin/python3
+
+#=======================================================================
+# TASK: select specified chains from the structure & save a cropped structure with
+# the selected chains. Useful for dimer, etc modelling.
+
+# link for saving each chain as a separate file
+# https://stackoverflow.com/questions/11685716/how-to-extract-chains-from-a-structure-file
+#=======================================================================
+#%%
+import os, sys
+from Bio.PDB import PDBParser, PDBIO, Select
+#%% homdir and curr dir and local imports
+homedir = os.path.expanduser('~') 
+# set working dir
+os.getcwd()
+os.chdir(homedir + '/git/Data/ethambutol/input/')
+os.getcwd()
+#%%
+# Select() Method to return True for every chain in 'chains'
+class ChainExtract(Select):
+    def __init__(self, chain):
+        self.chain = chain
+        
+    def accept_chain(self, chain):
+        #print dir(chain)
+        if chain.id in self.chain:
+            return 1
+        else:
+            return 0
+             
+def main():
+    p = PDBParser(PERMISSIVE=1)  
+    structure = p.get_structure("3byw", "3byw.pdb")
+    
+    my_chains = ['G', 'H'] # specify selected chains
+    c_names = ''.join(my_chains)
+   
+    pdb_chains_file = 'pdb_crop_' + c_names + '.pdb'
+    
+    io = PDBIO()
+    io.set_structure(structure)
+    #io.save(structure.get_id() + "_crop.structure", ChainExtract(my_chains))
+    io.save(pdb_chains_file, ChainExtract(my_chains))
+    
+if __name__ == '__main__':
+    main()
+#%%
+# test
+#my_chains = ['G', 'H'] # specify selected chains
+#foo = ''.join(my_chains) # to append to file name
+#pdb_chains_file = '_{}.pdb'.format(my_chains)