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import re
from Bio.PDB.PDBIO import PDBIO
_hydrogen=re.compile("[123 ]*H.*")
class ChainSelector:
"""
Only accepts residues with right chainid
and between start and end. Remove hydrogens, waters and ligands.
Only use model 0 by default.
"""
def __init__(self, chain_id, start, end, model_id=0):
self.chain_id=chain_id
self.start=start
self.end=end
self.model_id=0
def accept_model(self, model):
# model - only keep model 0
if model.get_id()==self.model_id:
return 1
return 0
def accept_chain(self, chain):
if chain.get_id()==self.chain_id:
return 1
return 0
def accept_residue(self, residue):
# residue - between start and end
hetatm_flag, resseq, icode=residue.get_id()
if hetatm_flag!=" ":
# skip HETATMS
return 0
if icode!=" ":
print "WARNING: Icode at ", residue.get_id()
if self.start<=resseq<=self.end:
return 1
return 0
def accept_atom(self, atom):
# atoms - get rid of hydrogens
name=atom.get_id()
if _hydrogen.match(name):
return 0
else:
return 1
def extract(structure, chain_id, start, end, filename):
"""
Write out selected portion to filename.
"""
sel=ChainSelector(chain_id, start, end)
io=PDBIO()
io.set_structure(structure)
io.save(filename, sel)
if __name__=="__main__":
from Bio.PDB.PDBParser import PDBParser
import sys
p=PDBParser()
s=p.get_structure("scr", sys.argv[1])
extract(s, "A", 1, 100, "out.pdb")
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