Source code for gmso.core.atom

"""Represent general atomic information in GMSO."""
import warnings
from typing import Optional, Union

import unyt as u
from pydantic import Field, validator

from import Site
from gmso.core.atom_type import AtomType
from gmso.core.element import Element
from gmso.utils._constants import UNIT_WARNING_STRING
from gmso.utils.misc import ensure_valid_dimensions

[docs]class Atom(Site): __base_doc__ = """An atom represents a single element association in a topology. Atoms are the representation of an element within `gmso` that describes any general atom in a molecular simulation. Atoms also contain information that are unique to elements vs other types of interaction sites in molecular simulations. For example, charge, mass, and periodic table information. Notes ----- Atoms have all the attributes inherited from the base Site class, The order of precedence when attaining properties `charge` and `mass` is: 1. atom.charge > atom.atom_type.charge 2. atom.mass > atom.atom_type.mass Examples -------- >>> from gmso.core.atom import Atom >>> atom1 = Atom(name='lithium') See Also -------- An Abstract Base class for implementing site objects in GMSO. The class Atom bases from the site class """ charge_: Optional[Union[u.unyt_quantity, float]] = Field( None, description="Charge of the atom", ) mass_: Optional[Union[u.unyt_quantity, float]] = Field( None, description="Mass of the atom" ) element_: Optional[Element] = Field( None, description="Element associated with the atom" ) atom_type_: Optional[AtomType] = Field( None, description="AtomType associated with the atom" ) @property def charge(self) -> Union[u.unyt_quantity, None]: """Return the charge of the atom.""" charge = self.__dict__.get("charge_", None) atom_type = self.__dict__.get("atom_type_", None) if charge is not None: return charge elif atom_type is not None: return atom_type.charge else: return None @property def mass(self) -> Union[u.unyt_quantity, None]: """Return the mass of the atom.""" mass = self.__dict__.get("mass_", None) atom_type = self.__dict__.get("atom_type_", None) if mass is not None: return mass elif atom_type is not None: return atom_type.mass else: return None @property def element(self) -> Union[Element, None]: """Return the element associated with the atom.""" return self.__dict__.get("element_", None) @property def atom_type(self) -> Union[AtomType, None]: """Return the atom_type associated with the atom.""" return self.__dict__.get("atom_type_", None)
[docs] def clone(self): """Clone this atom.""" return Atom(, label=self.label,, molecule=self.molecule, residue=self.residue, position=self.position, charge=self.charge_, mass=self.mass_, element=self.element_, atom_type=None if not self.atom_type else self.atom_type.clone(), )
def __le__(self, other): """Less than or equal to operator.""" if isinstance(other, Atom): return hash(self) <= hash(other) else: raise TypeError( f"Cannot compare equality between {type(self)} and {type(other)}" ) def __lt__(self, other): """Less than operator.""" if isinstance(other, Atom): return hash(self) < hash(other) else: raise TypeError( f"Cannot compare equality between {type(self)} and {type(other)}" )
[docs] @validator("charge_") def is_valid_charge(cls, charge): """Ensure that the charge is physically meaningful.""" if charge is None: return None if not isinstance(charge, u.unyt_array): warnings.warn( UNIT_WARNING_STRING.format("Charges", "elementary charge") ) charge *= u.elementary_charge else: ensure_valid_dimensions(charge, u.elementary_charge) return charge
[docs] @validator("mass_") def is_valid_mass(cls, mass): """Ensure that the mass is physically meaningful.""" if mass is None: return None default_mass_units = u.gram / u.mol if not isinstance(mass, u.unyt_array): warnings.warn(UNIT_WARNING_STRING.format("Masses", "g/mol")) mass *= default_mass_units else: ensure_valid_dimensions(mass, default_mass_units) return mass
[docs] class Config: """Pydantic configuration for the atom class.""" extra = "forbid" fields = { "charge_": "charge", "mass_": "mass", "element_": "element", "atom_type_": "atom_type", } alias_to_fields = { "charge": "charge_", "mass": "mass_", "element": "element_", "atom_type": "atom_type_", } validate_assignment = True