Add alchemy section
.. _alchemy::
+
+Alchemical factories
+====================
+
+:mod:`openmmtools.alchemy` contains factories for generating `alchemically-modified <http://alchemistry.org>`_ versions of OpenMM ```System`` <http://docs.openmm.org/7.1.0/api-python/generated/simtk.openmm.openmm.System.html#simtk.openmm.openmm.System>`_ objects for use in alchemical free energy calculations.
+
+Absolute alchemical factories
+-----------------------------
+
+Absolute alchical factories modify the ``System`` object to allow part of the system to be alchemically annihilated or decoupled.
+This is useful for computing free energies of transfer, solvation, or binding for small molecules.
+
+.. currentmodule:: openmmtools.integrators
+.. autosummary::
+ :toctree: api/generated/
+
+ AlchemicalFunction
+ AlchemicalState
+ AlchemicalFactory
+
+Relative alchemical factories
+-----------------------------
+
+Coming soon!
