Add alchemical network creation userguide page #808
Conversation
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #808 +/- ##
==========================================
- Coverage 94.12% 92.31% -1.82%
==========================================
Files 133 133
Lines 9767 9767
==========================================
- Hits 9193 9016 -177
- Misses 574 751 +177
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
| @@ -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. | |||
|
|
|||
| A :class:`.ChemicalSystem` is made up of one or more ``ChemicalComponent``\ | |||
There was a problem hiding this comment.
Removing these bits because they are duplicates of other setup pages.
There was a problem hiding this comment.
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` | ||
|
|
||
| The `Relative Alchemical Network Planners cookbook <../../cookbook/rfe_alchemical_planners>`_ |
There was a problem hiding this comment.
PR for cookbook is here: OpenFreeEnergy/ExampleNotebooks#124
IAlibay
changed the title
| 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. | ||
|
|
||
| .. todo: link to appropriate CLI page in the userguide? |
There was a problem hiding this comment.
is this this one?
.. _guide-introduction:
|
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
richardjgowers
force-pushed
the
userguide-alchemical-networks
branch
from
88ca0ce to
8a362fa
Compare
Fixes #805 #790
Checklist
newsentryDevelopers certificate of origin