Merge pull request #573 from OpenFreeEnergy/ahfe-refactor

Absolute solvation free energies + base things for ABFEs

.gitignore

@@ -161,5 +161,8 @@ cython_debug/
 # vim
 *.swp
 
+# vscode
+.vscode/
+
 # Example notebooks
-docs/ExampleNotebooks/
+docs/ExampleNotebooks/

docs/reference/api/index.rst

@@ -12,3 +12,4 @@ OpenFE API Reference
     alchemical_network_planning
     defining_and_executing_simulations
     openmm_rfe
+    openmm_solvation_afe

docs/reference/api/openmm_solvation_afe.rst

@@ -0,0 +1,146 @@
+OpenMM Absolute Solvation Free Energy Protocol
+==============================================
+
+This section provides details about the OpenMM Absolute Solvation Free Energy Protocol
+implemented in OpenFE.
+
+Protocol API specification
+--------------------------
+
+.. module:: openfe.protocols.openmm_afe.equil_solvation_afe_method
+
+.. autosummary::
+   :nosignatures:
+   :toctree: generated/
+
+   AbsoluteSolvationProtocol
+   AbsoluteSolvationProtocolResult
+
+Protocol Settings
+-----------------
+
+
+Below are the settings which can be tweaked in the protocol. The default settings (accessed using :meth:`AbsoluteSolvationProtocol.default_settings`) will automatically populate settings which we have found to be useful for running solvation free energy calculations. There will however be some cases (such as when calculating difficult to converge systems) where you will need to tweak some of the following settings.
+
+.. autopydantic_model:: AbsoluteSolvationSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :exclude-members: get_defaults
+   :member-order: bysource
+   :noindex:
+
+.. module:: openfe.protocols.openmm_afe.equil_afe_settings
+
+.. autopydantic_model:: OpenMMSystemGeneratorFFSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: ThermoSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: AlchemicalSamplerSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: AlchemicalSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: OpenMMEngineSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: IntegratorSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: SimulationSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: SolvationSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:
+
+.. autopydantic_model:: SystemSettings
+   :model-show-json: False
+   :model-show-field-summary: False
+   :model-show-config-member: False
+   :model-show-config-summary: False
+   :model-show-validator-members: False
+   :model-show-validator-summary: False
+   :field-list-validators: False
+   :inherited-members: SettingsBaseModel
+   :member-order: bysource
+   :noindex:

openfe/protocols/openmm_afe/__init__.py

@@ -0,0 +1,22 @@
+# This code is part of OpenFE and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/openfe
+"""
+Run absolute free energy calculations using OpenMM and OpenMMTools.
+
+"""
+
+from .equil_solvation_afe_method import (
+    AbsoluteSolvationProtocol,
+    AbsoluteSolvationSettings,
+    AbsoluteSolvationProtocolResult,
+    AbsoluteSolvationVacuumUnit,
+    AbsoluteSolvationSolventUnit,
+)
+
+__all__ = [
+    "AbsoluteSolvationProtocol",
+    "AbsoluteSolvationSettings",
+    "AbsoluteSolvationProtocolResult",
+    "AbsoluteVacuumUnit",
+    "AbsoluteSolventUnit",
+]