API Documentation
=================

Public API
----------

.. automodule:: batter.api
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

Config Modules
--------------

.. automodule:: batter.config.run
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.config.simulation
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.config.utils
   :noindex:
   :members:
   :undoc-members:

RBFE Helpers
------------

.. automodule:: batter.rbfe
   :noindex:
   :members:
   :undoc-members:

Orchestrator Modules
--------------------

.. automodule:: batter.orchestrate.run
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.orchestrate.pipeline_utils
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.orchestrate.backend
   :noindex:
   :members:
   :undoc-members:

Execution Modules
-----------------

.. automodule:: batter.exec.base
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.local
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.slurm
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.slurm_mgr
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.amber.mdin
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.equil
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.equil_analysis
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.fe
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.fe_analysis
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.param_ligands
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.prepare_equil
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.prepare_fe
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.system_prep
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.exec.handlers.system_prep_masfe
   :noindex:
   :members:
   :undoc-members:

Parameterisation Modules
------------------------

.. automodule:: batter.param.ligand
   :noindex:
   :members:
   :undoc-members:

Pipeline Modules
----------------

.. automodule:: batter.pipeline.pipeline
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.pipeline.step
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.pipeline.payloads
   :noindex:
   :members:
   :undoc-members:

Runtime Modules
---------------

.. automodule:: batter.runtime.portable
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.runtime.fe_repo
   :noindex:
   :members:
   :undoc-members:

Systems Modules
---------------

.. automodule:: batter.systems.core
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.systems.mabfe
   :noindex:
   :members:
   :undoc-members:

.. automodule:: batter.systems.masfe
   :noindex:
   :members:
   :undoc-members:

Analysis Modules
----------------

.. automodule:: batter.analysis.analysis
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.analysis.cinnabar
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.analysis.cycle_closure
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.analysis.remd
   :noindex:
   :members:
   :undoc-members:
   :show-inheritance:

.. automodule:: batter.analysis.utils
   :noindex:
   :members:
   :undoc-members: