Fix API documentation
@@ -36,6 +36,14 @@ An inclusive "neighborhood" of thermodynamic states around this specified state
If all thermodynamic states are included in this neighborhood (the default), the MBAR scheme :cite:`Shirts2008statistically` can be used to optimally estimate free energies and uncertainties.
If a restricted neighborhood is used (in order to reduce the amount of time spent in the energy evaluation stage), a variant of the L-WHAM (local weighted histogram analysis method) :cite:`kumar1992weighted` is used to extract an estimate from all available information.
+.. currentmodule:: openmmtools.multistate
+.. autosummary::
+ :nosignatures:
+ :toctree: api/generated/
+
+ MultiStateSampler
+ MultiStateSamplerAnalyzer
+
``ReplicaExchangeSampler``: Replica exchange among thermodynamic states
-----------------------------------------------------------------------
@@ -56,6 +64,14 @@ where :math:`x` is the configuration of the subscripted states :math:`i` or :mat
While this scheme is typically carried out on neighboring states only, we also implement a much more efficient form of Gibbs sampling in which many swaps are attempted to generate an approximately uncorrelated sample of the state permutation over all :math:`K` :cite:`Chodera2011`.
This speeds up mixing and reduces the total number of samples needed to produce uncorrelated samples.
+.. currentmodule:: openmmtools.multistate
+.. autosummary::
+ :nosignatures:
+ :toctree: api/generated/
+
+ ReplicaExchangeSampler
+ ReplicaExchangeAnalyzer
+
``SAMSSampler``: Self-adjusted mixture sampling
-----------------------------------------------
@@ -101,26 +117,25 @@ The behavior of this first stage can be controlled by setting two parameters:
* ``gamma0`` controls the initial rate of weight adaptation. By default, this is 1.0, but can be set larger (e.g., 10.0) if the free energy differences between states are much larger.
* ``flatness_threshold`` controls the number of (fractional) visits to each thermodynamic state that must be accumulated before the asymptotically optimal weight adaptation scheme is used.
-Multistate Samplers
--------------------
-
.. currentmodule:: openmmtools.multistate
.. autosummary::
:nosignatures:
:toctree: api/generated/
- MultiStateSampler
- MultiStateSamplerAnalyzer
+ SAMSSampler
+ SAMSAnalyzer
- ReplicaExchangeSampler
- ReplicaExchangeAnalyzer
+Parallel tempering
+------------------
+
+.. currentmodule:: openmmtools.multistate
+.. autosummary::
+ :nosignatures:
+ :toctree: api/generated/
ParallelTemperingSampler
ParallelTemperingAnalyzer
- SAMSSampler
- SAMSAnalyzer
-
Multistate Reporters
--------------------
@@ -134,11 +149,21 @@ Multistate Reporters
Analysis of multiple thermodynamic transformations
--------------------------------------------------
+.. currentmodule:: openmmtools.multistate
+.. autosummary::
+ :nosignatures:
+ :toctree: api/generated/
+
MultiPhaseAnalyzer
Miscellaneous support classes
-----------------------------
+.. currentmodule:: openmmtools.multistate.multistateanalyzer
+.. autosummary::
+ :nosignatures:
+ :toctree: api/generated/
+
ObservablesRegistry
CachedProperty
InsufficientData
