I need to extract specific chains from PDB files( Sometiems more than one chain). How to extract chains from a PDB file? . It's the same question and "marked" answer, answers my problem. But it does not work in python 3. It gives errors one after the other. Does anybody knows how can i work this in python 3?
Or any other code for the same kind of problem
Thank you in advance.
import os
from Bio import PDB
class ChainSplitter:
def __init__(self, out_dir=None):
""" Create parsing and writing objects, specify output directory. """
self.parser = PDB.PDBParser()
self.writer = PDB.PDBIO()
if out_dir is None:
out_dir = os.path.join(os.getcwd(), "chain_PDBs")
self.out_dir = out_dir
def make_pdb(self, pdb_path, chain_letters, overwrite=False, struct=None):
""" Create a new PDB file containing only the specified chains.
Returns the path to the created file.
:param pdb_path: full path to the crystal structure
:param chain_letters: iterable of chain characters (case insensitive)
:param overwrite: write over the output file if it exists
"""
chain_letters = [chain.upper() for chain in chain_letters]
# Input/output files
(pdb_dir, pdb_fn) = os.path.split(pdb_path)
pdb_id = pdb_fn[3:7]
out_name = "pdb%s_%s.ent" % (pdb_id, "".join(chain_letters))
out_path = os.path.join(self.out_dir, out_name)
print ("OUT PATH:",out_path)
plural = "s" if (len(chain_letters) > 1) else "" # for printing
# Skip PDB generation if the file already exists
if (not overwrite) and (os.path.isfile(out_path)):
print("Chain%s %s of '%s' already extracted to '%s'." %
(plural, ", ".join(chain_letters), pdb_id, out_name))
return out_path
print("Extracting chain%s %s from %s..." % (plural,
", ".join(chain_letters), pdb_fn))
# Get structure, write new file with only given chains
if struct is None:
struct = self.parser.get_structure(pdb_id, pdb_path)
self.writer.set_structure(struct)
self.writer.save(out_path, select=SelectChains(chain_letters))
return out_path
class SelectChains(PDB.Select):
""" Only accept the specified chains when saving. """
def __init__(self, chain_letters):
self.chain_letters = chain_letters
def accept_chain(self, chain):
return (chain.get_id() in self.chain_letters)
if __name__ == "__main__":
""" Parses PDB id's desired chains, and creates new PDB structures. """
import sys
if not len(sys.argv) == 2:
print ("Usage: $ python %s 'pdb.txt'" % __file__)
sys.exit()
pdb_textfn = sys.argv[1]
pdbList = PDB.PDBList()
splitter = ChainSplitter("/home/patrick/Desktop/chain_splitting")
with open(pdb_textfn) as pdb_textfile:
for line in pdb_textfile:
pdb_id = line[:4].lower()
chain = line[4]
pdb_fn = pdbList.retrieve_pdb_file(pdb_id)
splitter.make_pdb(pdb_fn, chain)
retrieve_pdb_file
has the optional parameter file_format
. When no information is provided, the PDB server returns cif files. Biopython's parser expects a PDB file.
You can change the line to
pdbList.retrieve_pdb_file(pdb_id, file_format='pdb')
and you should get a PDB file and the rest of the code runs through..
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