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* Playing around with codespell * revert some things --------- Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
150 lines
4.8 KiB
ReStructuredText
150 lines
4.8 KiB
ReStructuredText
OpenMM Protocol Settings
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========================
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.. _openmm protocol settings api:
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This page documents the Settings classes used by OpenMM-based Protocols.
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Details on which of these Settings classes are used by a given Protocol
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can be found on the individual Protocol API reference documentation pages:
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* :ref:`OpenMM Absolute Solvation Free Energy <afe solvation protocol api>`
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* :ref:`OpenMM Relative Free Energy <rfe protocol api>`
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* :ref:`OpenMM Relative Free Energy using SepTop <septop protocol api>`
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* :ref:`OpenMM Molecular Dynamics Protocol <md protocol api>`
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Shared OpenMM Protocol Settings
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-------------------------------
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The following are Settings classes which are shared between multiple
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OpenMM-based Protocols. Please note that not all Protocols use these
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Settings classes.
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.. module:: openfe.protocols.openmm_utils.omm_settings
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.. autopydantic_model:: IntegratorSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: MDOutputSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: MDSimulationSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: OpenMMEngineSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: OpenFFPartialChargeSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: OpenMMSolvationSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: OpenMMSystemGeneratorFFSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: ThermoSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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Shared MultiState OpenMM Protocol Settings
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------------------------------------------
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Protocol Settings shared between MultiState simulation protocols.
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These currently include the following Protocols:
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* :ref:`OpenMM Absolute Solvation Free Energy <afe solvation protocol api>`
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* :ref:`OpenMM Relative Free Energy <rfe protocol api>`
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* :ref:`OpenMM Relative Free Energy using SepTop <septop protocol api>`
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.. autopydantic_model:: MultiStateOutputSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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.. autopydantic_model:: MultiStateSimulationSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:member-order: bysource
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