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.. _API_analysis: | ||
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.. automodule:: yank.analyze | ||
:members: | ||
:inherited-members: |
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.. _API_experiment: | ||
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.. automodule:: yank.experiment | ||
:members: | ||
:inherited-members: |
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.. _API: | ||
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############# | ||
API Reference | ||
############# | ||
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YANK's API allows users to setup and run their own simulations in programmatic ways. If you would rather run YANK with | ||
YAML input files, please see the command line interface and the YAML options. | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
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analysis_api | ||
experiment_api | ||
mpi_api | ||
multistate_api/index | ||
pipeline_api | ||
restraints_api | ||
utils_api | ||
yank_api | ||
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UML class diagram | ||
================= | ||
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This UML diagram is a minimal representation of YANK's structure. This is not meant to be a comprehensive and accurate | ||
representation of the API, but only to provide a visual overview of the relationships between the available classes | ||
available, their role, and the way the interact with the OpenMMTools framework. | ||
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.. figure:: site-resources/images/YANKUMLClassDiagram.png |
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.. _API_mpi: | ||
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.. automodule:: yank.mpi | ||
:members: | ||
:inherited-members: |
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.. _API_analyzer: | ||
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.. automodule:: yank.multistate.multistateanalyzer | ||
:members: | ||
:inherited-members: |
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.. _API_multistate: | ||
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################# | ||
MultiState Module | ||
################# | ||
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This is the API for the Multi State sub-module and its classes. | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
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analyzers_api | ||
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.. _API_multistate_head: | ||
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.. automodule:: yank.multistate | ||
:members: | ||
:inherited-members: | ||
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.. automodule:: yank.multistate.multistatesampler | ||
:members: | ||
:inherited-members: | ||
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.. automodule:: yank.multistate.replicaexchange | ||
:members: | ||
:inherited-members: | ||
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.. automodule:: yank.multistate.paralleltempering | ||
:members: | ||
:inherited-members: | ||
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.. automodule:: yank.multistate.sams | ||
:members: | ||
:inherited-members: |
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.. _API_pipeline: | ||
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.. automodule:: yank.pipeline | ||
:members: | ||
:inherited-members: |
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.. _API_restraints: | ||
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.. automodule:: yank.restraints | ||
:members: | ||
:inherited-members: |
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.. _API_utils: | ||
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.. automodule:: yank.utils | ||
:members: | ||
:inherited-members: |
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.. _API_yank: | ||
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.. automodule:: yank.yank | ||
:members: | ||
:inherited-members: |