"""Module for 2-partner connections between sites."""
from typing import Callable, ClassVar, Optional, Tuple
from gmso.abc.abstract_connection import Connection
from gmso.core.atom import Atom
from gmso.core.bond_type import BondType
try:
from pydantic.v1 import Field
except ImportError:
from pydantic import Field
[docs]
class Bond(Connection):
__base_doc__ = """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.parse_obj
connection_members_: Tuple[Atom, Atom] = Field(
..., description="The 2 atoms involved in the bond."
)
bond_type_: Optional[BondType] = Field(
default=None, description="BondType of this bond."
)
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.
""",
)
@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."""
# ToDo: Deprecate this?
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)
[docs]
class Config:
"""Pydantic configuration for Bond."""
fields = {
"bond_type_": "bond_type",
"connection_members_": "connection_members",
"restraint_": "restraint",
}
alias_to_fields = {
"bond_type": "bond_type_",
"connection_members": "connection_members_",
"restraint": "restraint_",
}