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

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

.. autoapi-nested-parse::

   Bond potential energy function for Martini 2.



Attributes
----------

.. autoapisummary::

   mythos.energy.martini.m2.bond.BOND_K_PREFIX
   mythos.energy.martini.m2.bond.BOND_R0_PREFIX


Classes
-------

.. autoapisummary::

   mythos.energy.martini.m2.bond.BondConfiguration
   mythos.energy.martini.m2.bond.Bond


Functions
---------

.. autoapisummary::

   mythos.energy.martini.m2.bond.pair_bond


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

.. py:data:: BOND_K_PREFIX
   :value: 'bond_k_'


.. py:data:: BOND_R0_PREFIX
   :value: 'bond_r0_'


.. 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:function:: pair_bond(centers: mythos.utils.types.Arr_States_3, pair: mythos.utils.types.Vector2D, k_bond: float, r0_bond: float, displacement_fn: callable) -> float

   Calculate bond energy for a given pair of particles.


.. 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.