From 01a7cbf26eb5b252fce2a7c2aa237e67e5aea8d2 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 15 May 2020 10:59:19 +0100
Subject: [PATCH] renamed extract chain file

---
 scripts/chain_extract.py      | 30 ++++++++++++++++++++++++++++++
 scripts/pdb_chain_splitter.py |  4 ++--
 2 files changed, 32 insertions(+), 2 deletions(-)
 create mode 100644 scripts/chain_extract.py

diff --git a/scripts/chain_extract.py b/scripts/chain_extract.py
new file mode 100644
index 0000000..657f460
--- /dev/null
+++ b/scripts/chain_extract.py
@@ -0,0 +1,30 @@
+#!/usr/bin/python3
+
+#=======================================================================
+# TASK: select specified chains from the pdb & save a cropped PDB 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-pdb-file
+#=======================================================================
+
+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):
+   def accept_chain(self, chain):
+       #print dir(chain)
+       if chain.id in chains:
+           return 1
+       else:
+           return 0
+
+if __name__ == '__main__':
+    chains = ['G', 'H'] # specify selected chains
+    io.set_structure(pdb)
+    io.save(pdb.get_id() + "_crop.pdb", ChainSelect())
+
diff --git a/scripts/pdb_chain_splitter.py b/scripts/pdb_chain_splitter.py
index a0d7e70..9a163b2 100755
--- a/scripts/pdb_chain_splitter.py
+++ b/scripts/pdb_chain_splitter.py
@@ -27,13 +27,13 @@ def main():
     Function to call if run from command line.
 
     Example use:
-    pdb_chain_splitter.py -f <your_pdb_file> -c aB
+    pdb_chain_splitter.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. Case insensitive.', nargs = '+',  default = 'A', type = list)
+    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 = 'pdb_file_chain', type = str)
     args = arg_parser.parse_args()