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* Add an Analysis unit to SepTopProtocol. * Update PDB writing via MDTraj in AFE and SepTop Protocols to account for box dimensions with mdtraj_from_openmm utility. * Split up some SepTop tests into different files. * Updated the CLI gathering to account for post openfe v1.11 Analysis units --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
86 lines
2.7 KiB
ReStructuredText
86 lines
2.7 KiB
ReStructuredText
OpenMM Separated Topologies Protocol
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====================================
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.. _septop protocol api:
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This section provides details about the OpenMM Separated Topologies Protocol
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implemented in OpenFE.
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Protocol API specification
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--------------------------
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.. module:: openfe.protocols.openmm_septop.equil_septop_method
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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SepTopProtocol
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SepTopComplexSetupUnit
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SepTopComplexRunUnit
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SepTopComplexAnalysisUnit
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SepTopSolventSetupUnit
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SepTopSolventRunUnit
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SepTopSolventAnalysisUnit
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SepTopProtocolResult
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Protocol Settings
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-----------------
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Below are the settings which can be tweaked in the protocol. The default settings (accessed using :meth:`SepTopProtocol.default_settings`) will automatically populate settings which we have found to be useful for running a Separated Topologies free energy calculation. 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.
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.. module:: openfe.protocols.openmm_septop.equil_septop_settings
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.. autopydantic_model:: SepTopSettings
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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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:exclude-members: get_defaults
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:member-order: bysource
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Protocol Specific Settings Classes
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----------------------------------
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Below are Settings classes which are unique to the `SepTopProtocol`.
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.. autopydantic_model:: AlchemicalSettings
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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:: LambdaSettings
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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:: SepTopEquilOutputSettings
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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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