Source code for stk.molecular.atoms.atom



from __future__ import annotations

[docs]class Atom: """ An abstract base class for atoms. A subclass is made for each element. The name of each subclass is the periodic table symbol of that element. Atoms of a particular element can be made with this class or with the subclass representing that element. Examples: *Initialization.* Initialization of an :class:`.Atom` can happen in one of two ways. The atom can be initialized through the :class:`.Atom` class or through the class representing the element. .. testcode:: initialization import stk # h0 is an instance of the H class. h0 = stk.Atom(id=0, atomic_number=1) # h1 is also an instance of the H class. h1 = stk.H(id=1) When the class corresponding to the element is used directly, the ``atomic_number`` is not provided. Here are a few more examples. .. testcode:: initialization # Both he0 and he1 are instances of the He class. he0 = stk.Atom(id=2, atomic_number=2) he1 = stk.He(id=3) # Both c0 and c1 are instances of the # C class. c0 = stk.Atom(id=4, atomic_number=6) c1 = stk.C(id=5) """ # Maps each atomic number (int) to the relevant Atom subclass. _elements: dict[int, type[Atom]] = {}
[docs] def __init__( self, id: int, atomic_number: int, charge: int = 0, ) -> None: """ Initialize an :class:`Atom`. Parameters: id: The id of the atom. atomic_number: The atomic number. charge: The formal charge. """ self._elements[atomic_number].__init__(self, id, charge) self.__class__ = self._elements[atomic_number]
[docs] def get_id(self) -> int: """ Get the id of the atom. Returns: The id. """ raise NotImplementedError()
[docs] def with_id(self, id: int) -> Atom: """ Get a clone but with a different id. Parameters: id: The id of the clone. Returns: A clone with a new id. """ raise NotImplementedError()
[docs] def get_atomic_number(self) -> int: """ Get the atomic number of the atom. Returns: The atomic number. """ raise NotImplementedError()
[docs] def get_charge(self) -> int: """ Get the charge of the atom. Returns: The charge. """ raise NotImplementedError()
[docs] def clone(self) -> Atom: """ Return a clone. Returns: The clone. """ raise NotImplementedError()