Clarify whether implicit solvent is supported for Absolute alchemical factory

[schuhmc]

From the documentation of AbsoluteAlchemicalFactory it seems like implicit solvent models are supported as one is used in the example:

openmmtools/openmmtools/alchemy/alchemy.py

Lines 496 to 620 in f3f355a

	class AbsoluteAlchemicalFactory(object):
	"""Factory of alchemically modified OpenMM Systems.
	The context parameters created are:
	- softcore_alpha: factor controlling softcore lengthscale for Lennard-Jones
	- softcore_beta: factor controlling softcore lengthscale for Coulomb
	- softcore_a: softcore Lennard-Jones parameter from Eq. 13 of Ref [1]
	- softcore_b: softcore Lennard-Jones parameter from Eq. 13 of Ref [1]
	- softcore_c: softcore Lennard-Jones parameter from Eq. 13 of Ref [1]
	- softcore_d: softcore electrostatics parameter
	- softcore_e: softcore electrostatics parameter
	- softcore_f: softcore electrostatics parameter
	Parameters
	----------
	consistent_exceptions : bool, optional, default = False
	If True, the same functional form of the System's nonbonded
	method will be use to determine the electrostatics contribution
	to the potential energy of 1,4 exceptions instead of the
	classical q1*q2/(4*epsilon*epsilon0*pi*r).
	switch_width : float, optional, default = 1.0 * angstroms
	Default switch width for electrostatics in periodic cutoff systems
	used in alchemical interactions only.
	alchemical_pme_treatment : str, optional, default = 'exact'
	Controls how alchemical region electrostatics are treated when PME is used.
	Options are ['direct-space', 'coulomb', 'exact'].
	- 'direct-space' only models the direct space contribution
	- 'coulomb' includes switched Coulomb interaction
	- 'exact' includes also the reciprocal space contribution, but it's
	only possible to annihilate the charges and the softcore parameters
	controlling the electrostatics are deactivated. Also, with this
	method, modifying the global variable `lambda_electrostatics` is
	not sufficient to control the charges. The recommended way to change
	them is through the `AlchemicalState` class.
	alchemical_rf_treatment : str, optional, default = 'switched'
	Controls how alchemical region electrostatics are treated when RF is used
	Options are ['switched', 'shifted']
	'switched' sets c_rf = 0 for all reaction-field interactions and ensures continuity with a switch
	'shifted' retains c_rf != 0 but can give erroneous results for hydration free energies
	disable_alchemical_dispersion_correction : bool, optional, default=False
	If True, the long-range dispersion correction will not be included for the alchemical
	region to avoid the need to recompute the correction (a CPU operation that takes ~ 0.5 s)
	every time 'lambda_sterics' is changed. If using nonequilibrium protocols, it is recommended
	that this be set to True since this can lead to enormous (100x) slowdowns if the correction
	must be recomputed every time step.
	split_alchemical_forces : bool, optional, default=True
	If True, forces that are altered to different alchemical variables
	will be split in different force groups. All non-alchemical forces
	will maintain their original force group. If more than 32 force
	groups are required, an error is thrown.
	Examples
	--------
	Create an alchemical factory to alchemically modify OpenMM System objects.
	>>> factory = AbsoluteAlchemicalFactory(consistent_exceptions=False)
	Create an alchemically modified version of p-xylene in T4 lysozyme L99A in GBSA.
	>>> # Create a reference system.
	>>> from openmmtools import testsystems
	>>> reference_system = testsystems.LysozymeImplicit().system
	>>> # Alchemically soften the pxylene atoms
	>>> pxylene_atoms = range(2603,2621) # p-xylene
	>>> alchemical_region = AlchemicalRegion(alchemical_atoms=pxylene_atoms)
	>>> alchemical_system = factory.create_alchemical_system(reference_system, alchemical_region)
	Alchemically modify one water in a water box.
	>>> reference_system = testsystems.WaterBox().system
	>>> alchemical_region = AlchemicalRegion(alchemical_atoms=[0, 1, 2])
	>>> alchemical_system = factory.create_alchemical_system(reference_system, alchemical_region)
	Alchemically modify some angles and torsions in alanine dipeptide and
	annihilate both sterics and electrostatics.
	>>> reference_system = testsystems.AlanineDipeptideVacuum().system
	>>> alchemical_region = AlchemicalRegion(alchemical_atoms=[0], alchemical_torsions=[0,1,2],
	... alchemical_angles=[0,1,2], annihilate_sterics=True,
	... annihilate_electrostatics=True)
	>>> alchemical_system = factory.create_alchemical_system(reference_system, alchemical_region)
	Alchemically modify a bond, angles, and torsions in toluene by automatically
	selecting bonds involving alchemical atoms.
	>>> toluene_implicit = testsystems.TolueneImplicit()
	>>> alchemical_region = AlchemicalRegion(alchemical_atoms=[0,1], alchemical_torsions=True,
	... alchemical_angles=True, annihilate_sterics=True)
	>>> alchemical_system = factory.create_alchemical_system(reference_system, alchemical_region)
	Once the alchemical system is created, you can modify its Hamiltonian
	through AlchemicalState
	>>> alchemical_state = AlchemicalState.from_system(alchemical_system)
	>>> alchemical_state.lambda_sterics
	1.0
	>>> alchemical_state.lambda_electrostatics = 0.5
	>>> alchemical_state.apply_to_system(alchemical_system)
	You can also modify its Hamiltonian directly into a context
	>>> import openmm
	>>> from openmm import unit
	>>> integrator = openmm.VerletIntegrator(1.0*unit.femtosecond)
	>>> context = openmm.Context(alchemical_system, integrator)
	>>> alchemical_state.set_alchemical_parameters(0.0) # Set all lambda to 0
	>>> alchemical_state.apply_to_context(context)
	Neglecting the long-range dispersion correction for the alchemical region
	(for nonequilibrium switching, for example) requires instantiating a factory
	with the appropriate options:
	>>> new_factory = AbsoluteAlchemicalFactory(consistent_exceptions=False, disable_alchemical_dispersion_correction=True)
	>>> reference_system = testsystems.WaterBox().system
	>>> alchemical_region = AlchemicalRegion(alchemical_atoms=[0, 1, 2])
	>>> alchemical_system = new_factory.create_alchemical_system(reference_system, alchemical_region)
	References
	----------
	[1] Pham TT and Shirts MR. Identifying low variance pathways for free
	energy calculations of molecular transformations in solution phase.
	JCP 135:034114, 2011. http://dx.doi.org/10.1063/1.3607597
	"""

However, in the beginning there is a TODO list containing an item:

openmmtools/openmmtools/alchemy/alchemy.py

Line 22 in f3f355a

# - Add support for other GBSA models.

Is this just a leftover from 7 yrs ago that never got removed? Which implicit solvent models are currently supported for use with AbsoluteAlchemicalFactory?

Thanks!