openfe.protocols#
Descriptions and implementations of free energy calculation protocols.
A Protocol describes a methodology for computing a free energy from a
pair of chemical systems. It produces a number of ProtocolDAG objects,
which are directed acyclic graphs describing the dependencies between
individual units of work that can otherwise be run in parallel. Each unit of
work is described and implemented by a ProtocolUnit. The results of a
ProtocolUnit are described by a ProtocolUnitResult when successful
or else a ProtocolUnitFailure; these types are then collected into a
ProtocolDAGResult to describe the result of a protocol DAG, and
multiple DAGs from different transformations in the same campaign can be
collected into a ProtocolResult.
Protocol instances are configured by Pydantic models describing their
settings.. Base classes and a number of implemented building blocks for complex
configurations are found in the settings module.
Other submodules in this module represent individual implementations of protocols.
Modules
Settings models for Protocols. |
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Run relative free energy calculations on hybrid topologies with OpenMM. |
Classes
A protocol that implements an alchemical transformation. |
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An executable directed acyclic graph (DAG) of |
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A unit of work within a ProtocolDAG. |
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Successful result of a single |
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Failed result of a single |
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Result for a single execution of an entire |
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Container for all results for a single |