mythos.energy.martini.m3
========================

.. py:module:: mythos.energy.martini.m3

.. autoapi-nested-parse::

   Martini2 energy functions.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/mythos/energy/martini/m3/angle/index


Classes
-------

.. autoapisummary::

   mythos.energy.martini.m3.AngleConfiguration
   mythos.energy.martini.m3.Bond
   mythos.energy.martini.m3.BondConfiguration
   mythos.energy.martini.m3.Angle


Package Contents
----------------

.. 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:class:: Bond

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


   Bond potential energy function for Martini 2.


   .. py:attribute:: params
      :type:  BondConfiguration


   .. 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.



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

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


   Configuration for Martini bond energy function.

   Bond params must be provided as "bond_k_NAME" and "bond_r0_NAME" in
   corresponding pairs for each bond name in the system. NAME should be in the
   format of "MOLTYPE_ATOMNAME1_ATOMNAME2", e.g., "DMPC_NC3_PO4".


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

      Hook for additional initialization in subclasses.



.. py:class:: Angle

   Bases: :py:obj:`mythos.energy.martini.m2.angle.Angle`


   Angle energy function for Martini3.


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