Cli protocol settings via yaml input

docs/guide/cli/cli_yaml.rst

@@ -15,10 +15,12 @@ as an example, the settings file which re-specifies the default behaviour would
       threed: True
       max3d: 0.95
       element_change: True
+  protocol:
+    method: RelativeHybridTopologyProtocol
 
 The name of the algorithm is given behind the ``method:`` key and the arguments to the
 algorithm are then optionally given behind the ``settings:`` key.
-Both the `network:` and `mapper:` sections are optional.
+The ``network:``, ``mapper:``, and ``protocol:`` sections are all optional.
 
 This is then provided to the ``openfe plan-rbfe-network`` command as ::
 
@@ -76,3 +78,20 @@ settings file ::
     method: generate_radial_network
     settings:
       central_ligand: '0'
+
+Customising the Protocol
+-------------------------
+
+The Settings of a Protocol can be customised.  The settings variable names map directly between the Python API and
+yaml settings files.  For example, to customise the production length of
+the RFE Protocol, from Python would require a line of code such as::
+
+   settings.simulation_settings.production_length = '5.4 ns'
+
+This would be achieved via the yaml file as::
+
+  protocol:
+    method: RelativeHybridTopologyProtocol
+    settings:
+      simulation_settings:
+        production_length: 5.4 ns

openfe/setup/ligand_network_planning.py

@@ -88,12 +88,18 @@ def generate_radial_network(
     # handle central_ligand arg possibilities
     # after this, central_ligand is resolved to a SmallMoleculeComponent
     if isinstance(central_ligand, int):
+        central_ligand_index = central_ligand
         ligands = list(ligands)
         try:
-            central_ligand = ligands[central_ligand]
+            central_ligand = ligands[central_ligand_index]
         except IndexError:
             raise ValueError(f"index '{central_ligand}' out of bounds, there are "
                              f"{len(ligands)} ligands")
+        # you could do a list comprehension like:
+        # ligands = [l for l in ligands if l != central]
+        # but this wouldn't properly catch when multiple identical central ligands have been passed
+        # so instead slice out the central ligand
+        ligands = ligands[:central_ligand_index] + ligands[central_ligand_index + 1:]
     elif isinstance(central_ligand, str):
         ligands = list(ligands)
         possibles = [l for l in ligands if l.name == central_ligand]

openfecli/commands/plan_rbfe_network.py

@@ -18,6 +18,7 @@ def plan_rbfe_network_main(
     solvent,
     protein,
     cofactors,
+    protocol=None,
 ):
     """Utility method to plan a relative binding free energy network.
 
@@ -37,6 +38,8 @@ def plan_rbfe_network_main(
         protein component for complex simulations, to which the ligands are bound
     cofactors : Iterable[SmallMoleculeComponent]
         any cofactors alongisde the protein, can be empty list
+    protocol: Optional[Protocol]
+        fully set up Protocol to use
 
     Returns
     -------
@@ -53,6 +56,7 @@ def plan_rbfe_network_main(
         mappers=mapper,
         mapping_scorer=mapping_scorer,
         ligand_network_planner=ligand_network_planner,
+        protocol=protocol,
     )
     alchemical_network = network_planner(
         ligands=small_molecules, solvent=solvent, protein=protein,
@@ -145,6 +149,7 @@ def plan_rbfe_network(
     mapping_scorer = yaml_options.scorer
     ligand_network_planner = yaml_options.ligand_network_planner
     solvent = yaml_options.solvent
+    protocol = yaml_options.protocol
 
     write("\t\tSolvent: " + str(solvent))
     write("")
@@ -169,6 +174,7 @@ def plan_rbfe_network(
         solvent=solvent,
         protein=protein,
         cofactors=cofactors,
+        protocol=protocol,
     )
     write("\tDone")
     write("")

openfecli/commands/plan_rhfe_network.py

@@ -15,7 +15,7 @@
 
 def plan_rhfe_network_main(
     mapper, mapping_scorer, ligand_network_planner, small_molecules,
-    solvent,
+    solvent, protocol=None
 ):
     """Utility method to plan a relative hydration free energy network.
 
@@ -31,6 +31,7 @@ def plan_rhfe_network_main(
         molecules of the system
     solvent : SolventComponent
         Solvent component used for solvation
+    protocol : Optional[Protocol]
 
     Returns
     -------
@@ -46,6 +47,7 @@ def plan_rhfe_network_main(
         mappers=mapper,
         mapping_scorer=mapping_scorer,
         ligand_network_planner=ligand_network_planner,
+        protocol=protocol,
     )
     alchemical_network = network_planner(
         ligands=small_molecules, solvent=solvent
@@ -142,6 +144,7 @@ def plan_rhfe_network(molecules: List[str], yaml_settings: str, output_dir: str)
         ligand_network_planner=ligand_network_planner,
         small_molecules=small_molecules,
         solvent=solvent,
+        protocol=yaml_options.protocol,
     )
     write("\tDone")
     write("")