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# Copyright (C) 2002, Thomas Hamelryck ([email protected])
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Model class, used in Structure objects."""
from Bio.PDB.Entity import Entity
from Bio.PDB.internal_coords import IC_Chain
class Model(Entity):
"""The object representing a model in a structure.
In a structure derived from an X-ray crystallography experiment,
only a single model will be present (with some exceptions). NMR
structures normally contain many different models.
"""
def __init__(self, id, serial_num=None):
"""Initialize.
Arguments:
- id - int
- serial_num - int
"""
self.level = "M"
if serial_num is None:
self.serial_num = id
else:
self.serial_num = serial_num
Entity.__init__(self, id)
def __repr__(self):
"""Return model identifier."""
return f"<Model id={self.get_id()}>"
def get_chains(self):
"""Return chains."""
yield from self
def get_residues(self):
"""Return residues."""
for c in self.get_chains():
yield from c
def get_atoms(self):
"""Return atoms."""
for r in self.get_residues():
yield from r
def atom_to_internal_coordinates(self, verbose: bool = False) -> None:
"""Create/update internal coordinates from Atom X,Y,Z coordinates.
Internal coordinates are bond length, angle and dihedral angles.
:param verbose bool: default False
describe runtime problems
"""
for chn in self.get_chains():
chn.atom_to_internal_coordinates(verbose)
def internal_to_atom_coordinates(self, verbose: bool = False) -> None:
"""Create/update atom coordinates from internal coordinates.
:param verbose bool: default False
describe runtime problems
:raises Exception: if any chain does not have .pic attribute
"""
for chn in self.get_chains():
chn.internal_to_atom_coordinates(verbose)
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