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# Copyright (C) 2002, Thomas Hamelryck ([email protected])
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code for chopping up (dicing) a structure.
This module is used internally by the Bio.PDB.extract() function.
"""
import re
import warnings
from Bio.PDB.PDBIO import PDBIO
from Bio import BiopythonWarning
_hydrogen = re.compile("[123 ]*H.*")
class ChainSelector:
"""Only accepts residues with right chainid, 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):
"""Initialize the class."""
self.chain_id = chain_id
self.start = start
self.end = end
self.model_id = model_id
def accept_model(self, model):
"""Verify if model match the model identifier."""
# model - only keep model 0
if model.get_id() == self.model_id:
return 1
return 0
def accept_chain(self, chain):
"""Verify if chain match chain identifier."""
if chain.get_id() == self.chain_id:
return 1
return 0
def accept_residue(self, residue):
"""Verify if a residue sequence is between the start and end sequence."""
# residue - between start and end
hetatm_flag, resseq, icode = residue.get_id()
if hetatm_flag != " ":
# skip HETATMS
return 0
if icode != " ":
warnings.warn(
f"WARNING: Icode {icode} at position {resseq}", BiopythonWarning
)
if self.start <= resseq <= self.end:
return 1
return 0
def accept_atom(self, atom):
"""Verify if atoms are not Hydrogen."""
# 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)
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