mllf API
=========

File Handling
-------------

For detailed documentation on file formats and usage examples, see :doc:`file_handling`.

.. autosummary::
   :toctree: api

   mllf.file_handling.read_bias_coeff
   mllf.file_handling.read_rtf
   mllf.file_handling.read_pdb
   mllf.file_handling.write_bias_coeff
   mllf.file_handling.read_output
   mllf.file_handling.generate_combinations

DeepSet Modules
---------------

For detailed documentation on DeepSet pretraining, see :doc:`deepset_pretraining`.

.. autosummary::
   :toctree: api

   mllf.cb.deepset_autoencoder
   mllf.cb.deepset_pretraining_dataset
   mllf.cb.train_deepset_autoencoder
   mllf.cb.aev_processor

Graph and CB Modules
--------------------

For detailed documentation on CB architecture, see :doc:`cb_setup`.

.. autosummary::
   :toctree: api

   mllf.cb.graph
   mllf.cb.policy
   mllf.cb.value_net
   mllf.cb.rgcn
   mllf.cb.graph_utils

Workflow Utilities
------------------

For detailed documentation on the workflow system, see :doc:`workflow`.

.. autosummary::
   :toctree: api

   mllf.cli.workflow