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

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

.. autoapi-nested-parse::

   Martini2 energy functions.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/mythos/energy/martini/m2/angle/index
   /autoapi/mythos/energy/martini/m2/bond/index
   /autoapi/mythos/energy/martini/m2/lj/index


Classes
-------

.. autoapisummary::

   mythos.energy.martini.m2.Angle
   mythos.energy.martini.m2.AngleConfiguration
   mythos.energy.martini.m2.Bond
   mythos.energy.martini.m2.BondConfiguration
   mythos.energy.martini.m2.LJ
   mythos.energy.martini.m2.LJConfiguration


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

.. 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.



.. 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:: LJ

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


   Lennard-Jones potential energy function for Martini 2.


   .. py:attribute:: params
      :type:  LJConfiguration


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

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


   "Configuration for Martini Lennard-Jones energy function.

   All parameters provided must be of the form "lj_sigma_A_B" or "lj_epsilon_A_B",
   where A and B are bead types. Pair order is ignored unless both orderings
   are provided. It is required that sigma and epsilon parameters are provided
   for any bead type pairs present in the system.

   Couplings are supported (see :class:`MartiniEnergyConfiguration` for details).


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

      Hook for additional initialization in subclasses.