Core
====

Data model
----------

.. automodule:: rbfenetmap.core.models

Options
-------

.. automodule:: rbfenetmap.core.options

Soft-core repair
----------------

.. automodule:: rbfenetmap.core.softcore

.. automodule:: rbfenetmap.core.coreprune

Molecular graphs
----------------

.. automodule:: rbfenetmap.core.molgraph

.. automodule:: rbfenetmap.core.kabsch

.. automodule:: rbfenetmap.core.align

Pipeline
--------

.. automodule:: rbfenetmap.core.pipeline

.. automodule:: rbfenetmap.core.pairs

.. automodule:: rbfenetmap.core.descriptors

.. automodule:: rbfenetmap.core.mcs

.. automodule:: rbfenetmap.core.cbfe

Diagnostics and cost
--------------------

.. automodule:: rbfenetmap.core.diagnostics

.. automodule:: rbfenetmap.core.cost

.. automodule:: rbfenetmap.core.clustering

Optimal design
--------------

.. automodule:: rbfenetmap.core.design

.. automodule:: rbfenetmap.core.consistency

Surgery and diagnostics
-----------------------

.. automodule:: rbfenetmap.core.surgery

.. automodule:: rbfenetmap.core.replanning

Intermediate ligands
--------------------

.. automodule:: rbfenetmap.core.intermediates

.. automodule:: rbfenetmap.core.posing

Plugin registry
---------------

.. automodule:: rbfenetmap.core.pluginregistry

Contracts
---------

.. automodule:: rbfenetmap.core.meta.mappers

.. automodule:: rbfenetmap.core.meta.scorers

.. automodule:: rbfenetmap.core.meta.planners

.. automodule:: rbfenetmap.core.meta.exporters

.. automodule:: rbfenetmap.core.meta.intermediates

Validation and errors
---------------------

.. automodule:: rbfenetmap.core.validate

.. automodule:: rbfenetmap.core.exceptions