from typing import Callable, ClassVar, Optional, Tuple
from pydantic import ConfigDict, Field, model_validator
from gmso.abc.abstract_connection import Connection
from gmso.core.atom import Atom
from gmso.core.bond import Bond
from gmso.core.dihedral_type import DihedralType
[docs]
class Dihedral(Connection):
"""A 4-partner connection between sites.
This is a subclass of the gmso.Connection superclass.
This class has strictly 4 members in its connection_members.
The connection_type in this class corresponds to gmso.DihedralType.
The connectivity of a dihedral is:
m1–m2–m3–m4
where m1, m2, m3, and m4 are connection members 1-4, respectively.
Notes
-----
Inherits some methods from Connection:
__eq__, __repr__, _validate methods
Additional _validate methods are presented.
"""
__members_creator__: ClassVar[Callable] = Atom.model_validate
connectivity: ClassVar[Tuple[Tuple[int]]] = ((0, 1), (1, 2), (2, 3))
connection_members_: Tuple[Atom, Atom, Atom, Atom] = Field(
...,
description="The 4 atoms involved in the dihedral.",
alias="connection_members",
)
bonds_: Tuple[Bond, Bond, Bond] = Field(
default=None,
description="""
List of connection bonds.
Ordered to align with connection_members, such that self.bonds_[0] is
the bond between (self.connection_members[0], self.connection_members[1]).
""",
alias="bonds",
)
dihedral_type_: Optional[DihedralType] = Field(
default=None,
description="DihedralType of this dihedral.",
alias="dihedral_type",
)
restraint_: Optional[dict] = Field(
default=None,
description="""
Restraint for this dihedral, must be a dict with the following keys:
'k' (unit of energy/(mol * angle**2)), 'phi_eq' (unit of angle), 'delta_phi' (unit of angle).
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"],
**{
"dihedral_type": "dihedral_type_",
"restraint": "restraint_",
},
)
)
@property
def dihedral_type(self):
return self.__dict__.get("dihedral_type_")
@property
def connection_type(self):
# ToDo: Deprecate this?
return self.__dict__.get("dihedral_type_")
@property
def restraint(self):
"""Return the restraint of this dihedral."""
return self.__dict__.get("restraint_")
@property
def bonds(self):
"""Return the bonds that makeup this dihedral.
Connectivity is ((0,1), (1,2), (2,3))
"""
return self.__dict__.get("bonds_")
@property
def bonds_orders(self):
"""Return the bond_order strings of this dihedral."""
return "".join([b.bond_order for b in self.bonds])
[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 dihedral:
i, j, k, l == l, k, j, i
where i, j, k, and l are the connection members.
"""
return frozenset(
[self.connection_members, tuple(reversed(self.connection_members))]
)
def __setattr__(self, key, value):
if key == "connection_type":
super(Dihedral, self).__setattr__("dihedral_type_", value)
else:
super(Dihedral, self).__setattr__(key, value)
[docs]
@model_validator(mode="before")
@classmethod
def set_dependent_value_default(cls, data):
"""Automatically set bonds for this dihedral if connection_members is defined."""
if "bonds" not in data and "connection_members" in data:
atoms = data["connection_members"]
data["bonds"] = (
Bond(connection_members=(atoms[0], atoms[1])),
Bond(connection_members=(atoms[1], atoms[2])),
Bond(connection_members=(atoms[2], atoms[3])),
)
return data