Source code for gmso.core.bond

"""Module for 2-partner connections between sites."""

from typing import Callable, ClassVar, Optional, Tuple

from pydantic import ConfigDict, Field

from gmso.abc.abstract_connection import Connection
from gmso.core.atom import Atom
from gmso.core.bond_type import BondType


[docs] class Bond(Connection): """A 2-partner connection between sites. This is a subclass of the gmso.abc.Connection superclass. This class has strictly 2 members in its connection_members. The connection_type in this class corresponds to gmso.BondType. Notes ----- Inherits some methods from Connection: __eq__, __repr__, _validate methods. Additional _validate methods are presented. """ __members_creator__: ClassVar[Callable] = Atom.model_validate connection_members_: Tuple[Atom, Atom] = Field( ..., description="The 2 atoms involved in the bond.", alias="connection_members", ) bond_type_: Optional[BondType] = Field( default=None, description="BondType of this bond.", alias="bond_type", ) restraint_: Optional[dict] = Field( default=None, description=""" Restraint for this bond, must be a dict with the following keys: 'b0' (unit of length), 'kb' (unit of energy/(mol * length**2)). Refer to https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html for more information. """, alias="restraint", ) model_config = ConfigDict( alias_to_fields=dict( **Connection.model_config["alias_to_fields"], **{ "bond_type": "bond_type_", "restraint": "restraint_", } ) ) @property def bond_type(self): """Return parameters of the potential type.""" return self.__dict__.get("bond_type_") @property def connection_type(self): """Return parameters of the potential type.""" return self.__dict__.get("bond_type_") @property def restraint(self): """Return the restraint of this bond.""" return self.__dict__.get("restraint_")
[docs] def equivalent_members(self): """Get a set of the equivalent connection member tuples. Returns ------- frozenset A unique set of tuples of equivalent connection members Notes ----- For a bond: i, j == j, i where i and j are the connection members. """ return frozenset( [self.connection_members, tuple(reversed(self.connection_members))] )
def __setattr__(self, key, value): """Handle attribute assignment.""" if key == "connection_type": super(Bond, self).__setattr__("bond_type", value) else: super(Bond, self).__setattr__(key, value)