From ea4f59393dec0e4ac32685d3de6acef99e0cb705 Mon Sep 17 00:00:00 2001 From: richard gowers Date: Fri, 8 Mar 2024 14:54:30 +0000 Subject: [PATCH] cli: use yaml specified Protocol in plan-rbfe-network --- openfecli/commands/plan_rbfe_network.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/openfecli/commands/plan_rbfe_network.py b/openfecli/commands/plan_rbfe_network.py index 2c2d13fdd..495c35ea9 100644 --- a/openfecli/commands/plan_rbfe_network.py +++ b/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("")