Add alchemical network creation userguide page#808
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| @@ -29,20 +29,18 @@ calculate the free energy differences between the two | |||
| :class:`.ChemicalSystem`\ s that are the nodes for that edge. In addition to | |||
| containing the information for each :class:`.ChemicalSystem`, the | |||
| :class:`.Transformation` also contains a :class:`.Protocol` and, when | |||
| relevant, atom mapping information for alchemical transformations. | |||
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| A :class:`.ChemicalSystem` is made up of one or more ``ChemicalComponent``\ | |||
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Removing these bits because they are duplicates of other setup pages.
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This is very much just a draft image - any ideas on a better one would be greatly appreciated!
| * :class:`.RBFEAlchemicalNetworkPlanner`: creating relative binding free energy networks using :class:`.RelativeHybridTopologyProtocol` | ||
| * :class:`.RHFEAlchemicalNetworkPlanner`: creating relative hydration free energy networks using :class:`.RelativeHybridTopologyProtocol` | ||
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| The `Relative Alchemical Network Planners cookbook <../../cookbook/rfe_alchemical_planners>`_ |
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PR for cookbook is here: OpenFreeEnergy/ExampleNotebooks#124
| Please see the :ref:`RBFE CLI tutorial <rbfe_cli_tutorial.html>` | ||
| for an example on how to use the CLI to run an RBFE campaign. | ||
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| .. todo: link to appropriate CLI page in the userguide? |
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is this this one?
.. _guide-introduction:
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Something's up with the cookbooks, for some reason the references aren't working. I suspect I won't have much time to hunt this one down, can someone else look into this? |
this adds a reference anchor in the nbsphinx prolog for each nblink included cookbook include rfe_alchemical_planners in cookbook list
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Fixes #805 #790
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