mythos.observables.bond_distances
=================================

.. py:module:: mythos.observables.bond_distances

.. autoapi-nested-parse::

   Observable for computing bond distances from a Martini trajectory.



Classes
-------

.. autoapisummary::

   mythos.observables.bond_distances.BondDistances
   mythos.observables.bond_distances.BondDistancesMapped


Functions
---------

.. autoapisummary::

   mythos.observables.bond_distances._bond_distance


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

.. py:function:: _bond_distance(centers: jax.numpy.ndarray, pair: jax.numpy.ndarray, displacement_fn: collections.abc.Callable) -> float

   Compute the distance between a bonded pair of atoms.


.. py:class:: BondDistances

   Observable for computing bond distances for a single bond name.

   Given a :class:`MartiniTopology` and a bond name, this observable computes
   pairwise distances for all matching bonds across the trajectory.

   .. attribute:: topology

      The Martini topology containing bond information.

   .. attribute:: bond_name

      Bond name string to compute distances for.
      Has the form ``RESIDUE_BEAD1_BEAD2`` (e.g.
      ``"DMPC_GL1_GL2"``).  All bonds in the topology matching
      this name will be included in the output.

   .. attribute:: displacement_fn

      Factory that, given a box size vector, returns a
      displacement function respecting periodic boundary conditions.


   .. py:attribute:: topology
      :type:  mythos.energy.martini.base.MartiniTopology


   .. py:attribute:: bond_name
      :type:  str


   .. py:attribute:: displacement_fn
      :type:  collections.abc.Callable


   .. py:method:: _matching_pairs() -> jax.numpy.ndarray


   .. py:method:: __call__(trajectory: mythos.simulators.io.SimulatorTrajectory) -> jax.numpy.ndarray

      Compute bond distances for the requested bond name.

      :param trajectory: A :class:`SimulatorTrajectory` whose ``center`` has
                         shape ``(n_states, n_atoms, 3)`` and ``box_size`` has shape
                         ``(n_states, 3)``.

      :returns: Distance array of shape ``(n_states, n_matching_bonds)``.



.. py:class:: BondDistancesMapped

   Observable for computing bond distances for multiple bond names.

   Given a :class:`MartiniTopology` and a set of bond names, this observable
   computes pairwise distances for all matching bonds across the trajectory,
   returning a dictionary keyed by bond name.

   .. attribute:: topology

      The Martini topology containing bond information.

   .. attribute:: bond_names

      Tuple of bond name strings to compute distances for.
      Each name has the form ``RESIDUE_BEAD1_BEAD2`` (e.g.
      ``"DMPC_GL1_GL2"``).  All bonds in the topology matching a
      given name will be included in the output.

   .. attribute:: displacement_fn

      Factory that, given a box size vector, returns a
      displacement function respecting periodic boundary conditions.


   .. py:attribute:: topology
      :type:  mythos.energy.martini.base.MartiniTopology


   .. py:attribute:: bond_names
      :type:  tuple[str, Ellipsis]


   .. py:attribute:: displacement_fn
      :type:  collections.abc.Callable


   .. py:method:: __call__(trajectory: mythos.simulators.io.SimulatorTrajectory) -> dict[str, jax.numpy.ndarray]

      Compute bond distances for each requested bond name.

      :param trajectory: A :class:`SimulatorTrajectory` whose ``center`` has
                         shape ``(n_states, n_atoms, 3)`` and ``box_size`` has shape
                         ``(n_states, 3)``.

      :returns: Dictionary mapping each bond name to a distance array of shape
                ``(n_states, n_matching_bonds)``.