Core workflow
=============

.. autoclass:: phenoms.SimulationSet
   :members:
   :inherited-members:

.. autoclass:: phenoms.ComparisonSet
   :members:
   :inherited-members:

.. autofunction:: phenoms.run_backbone_hbond_analysis
.. autofunction:: phenoms.simulation_set_from_dir
.. autofunction:: phenoms.comparison_sets_from_dirs
.. autofunction:: phenoms.detect_hbonds
.. autofunction:: phenoms.detect_hbonds_with_occupancy
.. autofunction:: phenoms.default_n_jobs
.. autofunction:: phenoms.default_output_root