script for saving pdb chains in single file

scripts/chain_extract.py

@@ -10,21 +10,15 @@
 
 from Bio.PDB import PDBParser, PDBIO, Select
 
-io = PDBIO()
-pdb = PDBParser().get_structure("3byw", "3byw.pdb")
-
 
 # Select() Method to return True for every chain in 'chains'
-class ChainSelect(Select):
+class ChainExtract(Select):
-   def accept_chain(self, chain):
+    def __init__(self, chain):
-       #print dir(chain)
+        self.chain = chain
-       if chain.id in chains:
+    
-           return 1
+    def accept_chain(self, chain):
-       else:
+        #print(dir(chain))
-           return 0
+        if chain.id in self.chain:
-
+            return 1
-if __name__ == '__main__':
+        else:
-    chains = ['G', 'H'] # specify selected chains
+            return 0
-    io.set_structure(pdb)
-    io.save(pdb.get_id() + "_crop.pdb", ChainSelect())
-

scripts/pdb_chain_extract.py

@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+
+# Copyright 2020, Tanushree Tunstall
+# This program is distributed under General Public License v. 3.  See the file
+# COPYING for a copy of the license.
+
+__description__ = \
+"""
+chain_extract.py
+
+extract chain/s from pdb and saves each chain as a separate file
+"""
+__author__ = "Tanushree Tunstall"
+__date__ = ""
+#=======================================================================
+import os, shutil, sys
+#from pdbtools.helper import cmdline
+from chain_extract import ChainExtract
+from Bio.PDB import PDBParser, PDBIO, Select
+#from Bio.PDB.PDBParser import PDBParser
+
+#io = PDBIO()
+import argparse
+#=======================================================================
+
+def main():
+    """
+    Function to call if run from command line.
+
+    Example use:
+    pdb_chain_extract.py -f <your_pdb_file> -c <chainid1><chainid2>
+    Extracts chain 'A' by default.
+    FIXME: extract all chains from the given pdb and write them out individually
+    """
+    arg_parser = argparse.ArgumentParser()
+    arg_parser.add_argument('-i', '--pdb_file', help='provide pdb file', default = 'None')
+    arg_parser.add_argument('-c', '--chain', help='chain/s to extract without spaces.', nargs = '+',  default = 'A', type = list)
+    arg_parser.add_argument('-p', '--out_path', help='specify output path',  default = '.', type = str)
+    arg_parser.add_argument('-o', '--out_file', help='specify output filename. Will be used as a prefix to append chain id and pdb file extension',  default = 'pdbfile', type = str)
+    args = arg_parser.parse_args()
+
+    # Extract chains and write each chain as a separate file
+    pdb_file = args.pdb_file
+    print('input pdb file:', pdb_file)
+    
+    # type = list, makes it a list of lists. Hence extracting the list of chains.
+    chains = args.chain[0]
+    #chains = ['A','B','C']
+    print ('user supplied chain:', chains)
+    
+    # output filename and path
+    outpath = args.out_path
+    outfile = args.out_file
+
+    # get structure
+    p = PDBParser(PERMISSIVE=1)       
+    structure = p.get_structure(pdb_file, pdb_file)
+    print('input pdb filename:', structure.get_id())
+
+    my_chains = chains
+    #my_chains = ['G', 'H'] 
+    c_names = ''.join(my_chains)
+    print('Extracting chains:', my_chains)
+    pdb_chains_file = outpath + '/' + outfile + '_' + c_names + '.pdb'
+    io = PDBIO()
+    io.set_structure(structure)
+    #io.save(structure.get_id() + "_crop.structure", ChainExtract())
+    #io.save("_crop.pdb", ChainExtract(my_chains))
+    #io.save('{}'.format(pdb_chains_file), ChainExtract(my_chains))
+    io.save(pdb_chains_file, ChainExtract(my_chains))
+
+if __name__ == "__main__":
+    main()
+

scripts/pdb_chain_splitter.py

@@ -40,7 +40,7 @@ def main():
 
     # Extract chains and write each chain as a separate file
     pdb_file = args.pdb_file
-    print('inpput pdb file:', pdb_file)
+    print('input pdb file:', pdb_file)
     
     # type = list, makes it a list of lists. Hence extracting the list of chains.
     chains = args.chain[0]

scripts/pdbtools_commands

@@ -23,3 +23,21 @@ home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_residue_renumber /home
 /home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/ethambutol/input/3byw.pdb
 
 /home/tanu/git/LSHTM_analysis/scripts/pdbtools/scripts/pdb_ligand /home/tanu/git/Data/cycloserine/input/alr_complex_model.pdb
+
+
+
+
+#^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+# my pdb tools
+
+#======================================================
+# save specifed chains as individual pdbs
+#======================================================
+./pdb_chain_splitter.py -i /home/tanu/git/Data/ethambutol/input/3byw.pdb -c DF -p /home/tanu/git/Data/ethambutol/input -o 3byw
+
+#======================================================
+# save specifed chains as one pdb
+#======================================================
+./pdb_chain_extract.py -i /home/tanu/git/Data/ethambutol/input/3byw.pdb -c DF -p /home/tanu/git/Data/ethambutol/input -o 3byw^C
+