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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) | |