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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. | |
| """The structure class, representing a macromolecular structure.""" | |
| from Bio.PDB.Entity import Entity | |
| class Structure(Entity): | |
| """The Structure class contains a collection of Model instances.""" | |
| def __init__(self, id): | |
| """Initialize the class.""" | |
| self.level = "S" | |
| Entity.__init__(self, id) | |
| def __repr__(self): | |
| """Return the structure identifier.""" | |
| return f"<Structure id={self.get_id()}>" | |
| def get_models(self): | |
| """Return models.""" | |
| yield from self | |
| def get_chains(self): | |
| """Return chains from models.""" | |
| for m in self.get_models(): | |
| yield from m | |
| def get_residues(self): | |
| """Return residues from chains.""" | |
| for c in self.get_chains(): | |
| yield from c | |
| def get_atoms(self): | |
| """Return atoms from residue.""" | |
| 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 .internal_coord attribute | |
| """ | |
| for chn in self.get_chains(): | |
| chn.internal_to_atom_coordinates(verbose) | |