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renamed extract chain file

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Tanushree Tunstall 2020-05-15 10:59:19 +01:00
parent 65db4a090e
commit 01a7cbf26e
2 changed files with 32 additions and 2 deletions
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4
scripts/pdb_chain_splitter.py
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@ -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()