mythos.energy.martini.m2.angle
==============================

.. py:module:: mythos.energy.martini.m2.angle

.. autoapi-nested-parse::

   Angle potential energy function for Martini 2.



Attributes
----------

.. autoapisummary::

   mythos.energy.martini.m2.angle.ANGLE_K_PREFIX
   mythos.energy.martini.m2.angle.ANGLE_THETA0_PREFIX


Classes
-------

.. autoapisummary::

   mythos.energy.martini.m2.angle.AngleConfiguration
   mythos.energy.martini.m2.angle.Angle


Functions
---------

.. autoapisummary::

   mythos.energy.martini.m2.angle.compute_angle
   mythos.energy.martini.m2.angle.triplet_angle


Module Contents
---------------

.. py:data:: ANGLE_K_PREFIX
   :value: 'angle_k_'


.. py:data:: ANGLE_THETA0_PREFIX
   :value: 'angle_theta0_'


.. py:class:: AngleConfiguration(couplings: dict[str, list[str]] | None = None, **kwargs)

   Bases: :py:obj:`mythos.energy.martini.base.MartiniEnergyConfiguration`


   Configuration for Martini angle energy function.

   Angle params must be provided as "angle_k_I_J_K" and "angle_theta0_I_J_K" in
   corresponding pairs for each angle name in the system. NAME should be in the
   format of "MOLTYPE_ATOMNAME1_ATOMNAME2_ATOMNAME3", e.g., "DMPC_NC3_PO4_GL1".


   .. py:method:: __post_init__() -> None

      Hook for additional initialization in subclasses.



.. py:function:: compute_angle(r_ij: mythos.utils.types.Vector3D, r_kj: mythos.utils.types.Vector3D) -> float

   Compute the angle between three particles (angle at j).

   :param r_ij: Displacement vector from j to i.
   :param r_kj: Displacement vector from j to k.

   :returns: The angle theta_ijk in radians.


.. py:function:: triplet_angle(centers: mythos.utils.types.Arr_States_3, triplet: mythos.utils.types.Vector3D, k_angle: float, theta0_angle: float, displacement_fn: callable, use_G96: bool) -> float

   Calculate angle energy for a given triplet of particles.

   :param centers: Positions of all particles.
   :param triplet: Indices [i, j, k] of the three particles forming the angle.
   :param k_angle: Force constant for the angle.
   :param theta0_angle: Equilibrium angle in radians.
   :param displacement_fn: Function to compute displacement between particles.
   :param use_G96: Whether to use Gromacs 1996 cosine-based angle potential (as in
                   Martini 2) or standard harmonic angle potential.

   :returns: 0.5 * k * (theta - theta0)^2
   :rtype: Harmonic angle energy


.. py:class:: Angle

   Bases: :py:obj:`mythos.energy.martini.base.MartiniEnergyFunction`


   Angle potential energy function for Martini 2.


   .. py:attribute:: params
      :type:  AngleConfiguration


   .. py:attribute:: use_G96
      :type:  ClassVar[bool]
      :value: True



   .. py:method:: __post_init__(topology: None = None) -> None


   .. py:method:: compute_energy(trajectory: mythos.simulators.io.SimulatorTrajectory) -> float

      Compute the energy of the system given the nucleotide.