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71 lines
2.1 KiB
Python
71 lines
2.1 KiB
Python
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
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#
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""The structure class, representing a macromolecular structure."""
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from Bio.PDB.Entity import Entity
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from typing import TYPE_CHECKING
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if TYPE_CHECKING:
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from Bio.PDB.Model import Model
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class Structure(Entity[None, "Model"]):
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"""The Structure class contains a collection of Model instances."""
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def __init__(self, id):
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"""Initialize the class."""
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self.level = "S"
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Entity.__init__(self, id)
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def __repr__(self):
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"""Return the structure identifier."""
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return f"<Structure id={self.get_id()}>"
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def get_models(self):
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"""Return models."""
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yield from self
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def get_chains(self):
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"""Return chains from models."""
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for m in self.get_models():
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yield from m
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def get_residues(self):
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"""Return residues from chains."""
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for c in self.get_chains():
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yield from c
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def get_atoms(self):
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"""Return atoms from residue."""
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for r in self.get_residues():
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yield from r
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def atom_to_internal_coordinates(self, verbose: bool = False) -> None:
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"""Create/update internal coordinates from Atom X,Y,Z coordinates.
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Internal coordinates are bond length, angle and dihedral angles.
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:param verbose bool: default False
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describe runtime problems
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"""
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for chn in self.get_chains():
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chn.atom_to_internal_coordinates(verbose)
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def internal_to_atom_coordinates(self, verbose: bool = False) -> None:
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"""Create/update atom coordinates from internal coordinates.
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:param verbose bool: default False
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describe runtime problems
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:raises Exception: if any chain does not have .internal_coord attribute
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"""
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for chn in self.get_chains():
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chn.internal_to_atom_coordinates(verbose)
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