Spaces:
No application file
No application file
| # 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) | |