Merge pull request #766 from OpenFreeEnergy/issue-742

Fixing API settings things

docs/reference/api/index.rst

@@ -14,3 +14,4 @@ OpenFE API Reference
     openmm_rfe
     openmm_solvation_afe
     openmm_md
+    openmm_protocol_settings

docs/reference/api/openmm_md.rst

@@ -1,12 +1,29 @@
-OpenMM Molecular Dynamics Protocol
-==================================
+OpenMM Molecular Dynamics (MD) Protocol
+=======================================
+
+.. _md protocol api:
+
+A Protocol for running MD simulation using OpenMM.
+
+
+Protocol API Specification
+--------------------------
+
+.. module:: openfe.protocols.openmm_md
+
+.. autosummary::
+   :nosignatures:
+   :toctree: generated/
+
+   PlainMDProtocol
+   PlainMDProtocolUnit
+   PlainMDProtocolResult
 
-This Protocol implements a standard MD execution for a solvated protein system.
 
 Protocol Settings
 -----------------
 
-.. module:: openfe.protocols.openmm_md
+.. module:: openfe.protocols.openmm_md.plain_md_settings
 
 .. autopydantic_model:: PlainMDProtocolSettings
    :model-show-json: False
@@ -19,3 +36,4 @@ Protocol Settings
    :inherited-members: SettingsBaseModel
    :exclude-members: get_defaults
    :member-order: bysource
+

docs/reference/api/openmm_protocol_settings.rst

@@ -0,0 +1,145 @@
+OpenMM Protocol Settings
+========================
+
+This page documents the Settings classes used by OpenMM-based Protocols.
+
+Details on which of these Settings classes are used by a given Protocol
+can be found on the individual Protocol API reference documentation pages:
+
+* :ref:`OpenMM Absolute Solvation Free Energy <afe solvation protocol api>`
+* :ref:`OpenMM Relative Free Energy <rfe protocol api>`
+* :ref:`OpenMM Molecular Dynamics Protocol <md protocol api>`
+
+
+Shared OpenMM Protocol Settings
+-------------------------------
+
+The following are Settings clases which are shared between multiple
+OpenMM-based Protocols. Please note that not all Protocols use these
+Settings classes.
+
+
+.. module:: openfe.protocols.openmm_utils.omm_settings
+
+.. 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
+
+.. autopydantic_model:: MDOutputSettings
+   :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
+
+.. autopydantic_model:: MDSimulationSettings
+   :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
+
+.. 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
+
+.. autopydantic_model:: OpenFFPartialChargeSettings
+   :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
+
+.. autopydantic_model:: OpenMMSolvationSettings
+   :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
+
+.. 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
+
+.. 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
+
+
+Shared MultiState OpenMM Protocol Settings
+------------------------------------------
+
+Protocol Settings shared between MultiState simulation protocols.
+
+These currently include the following Protocols:
+
+* :ref:`OpenMM Absolute Solvation Free Energy <afe solvation protocol api>`
+* :ref:`OpenMM Relative Free Energy <rfe protocol api>`
+
+
+.. autopydantic_model:: MultiStateOutputSettings
+   :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
+
+.. autopydantic_model:: MultiStateSimulationSettings
+   :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
+

docs/reference/api/openmm_rfe.rst

@@ -1,6 +1,8 @@
 OpenMM Relative Free Energy Protocol
 ====================================
 
+.. _rfe protocol api:
+
 This section provides details about the OpenMM Relative Free Energy Protocol
 implemented in OpenFE.
 
@@ -14,6 +16,7 @@ Protocol API specification
    :toctree: generated/
 
    RelativeHybridTopologyProtocol
+   RelativeHybridTopologyProtocolUnit
    RelativeHybridTopologyProtocolResult
 
 Protocol Settings
@@ -34,29 +37,13 @@ Below are the settings which can be tweaked in the protocol. The default setting
    :exclude-members: get_defaults
    :member-order: bysource
 
-.. module:: openfe.protocols.openmm_rfe.equil_rfe_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
+Protocol Specific Settings Classes
+----------------------------------
 
-.. 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
+Below are Settings classes which are unique to the `RelativeHybridTopologyProtocol`.
+
+.. module:: openfe.protocols.openmm_rfe.equil_rfe_settings
 
 .. autopydantic_model:: AlchemicalSettings
    :model-show-json: False
@@ -79,36 +66,3 @@ Below are the settings which can be tweaked in the protocol. The default setting
    :field-list-validators: False
    :inherited-members: SettingsBaseModel
    :member-order: bysource
-
-.. 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
-
-.. 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
-
-.. autopydantic_model:: MultiStateSimulationSettings
-   :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

docs/reference/api/openmm_solvation_afe.rst

@@ -1,6 +1,8 @@
 OpenMM Absolute Solvation Free Energy Protocol
 ==============================================
 
+.. _afe solvation protocol api:
+
 This section provides details about the OpenMM Absolute Solvation Free Energy Protocol
 implemented in OpenFE.
 
@@ -14,6 +16,8 @@ Protocol API specification
    :toctree: generated/
 
    AbsoluteSolvationProtocol
+   AbsoluteSolvationVacuumUnit
+   AbsoluteSolvationSolventUnit
    AbsoluteSolvationProtocolResult
 
 Protocol Settings
@@ -25,7 +29,7 @@ Below are the settings which can be tweaked in the protocol. The default setting
 
 .. module:: openfe.protocols.openmm_afe.equil_afe_settings
 
-.. autopydantic_model:: OpenMMSystemGeneratorFFSettings
+.. autopydantic_model:: AbsoluteSolvationSettings
    :model-show-json: False
    :model-show-field-summary: False
    :model-show-config-member: False
@@ -34,58 +38,17 @@ Below are the settings which can be tweaked in the protocol. The default setting
    :model-show-validator-summary: False
    :field-list-validators: False
    :inherited-members: SettingsBaseModel
+   :exclude-members: get_defaults
    :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:: 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:
+Protocol Specific Settings Classes
+----------------------------------
 
-.. autopydantic_model:: LambdaSettings
-   :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:
+Below are Settings classes which are unique to the `AbsoluteSolvationProtocol`.
 
-.. 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
+.. autopydantic_model:: AlchemicalSettings
    :model-show-json: False
    :model-show-field-summary: False
    :model-show-config-member: False
@@ -95,9 +58,8 @@ Below are the settings which can be tweaked in the protocol. The default setting
    :field-list-validators: False
    :inherited-members: SettingsBaseModel
    :member-order: bysource
-   :noindex:
 
-.. autopydantic_model:: MultiStateSimulationSettings
+.. autopydantic_model:: LambdaSettings
    :model-show-json: False
    :model-show-field-summary: False
    :model-show-config-member: False
@@ -107,4 +69,3 @@ Below are the settings which can be tweaked in the protocol. The default setting
    :field-list-validators: False
    :inherited-members: SettingsBaseModel
    :member-order: bysource
-   :noindex: