diff --git a/docs/guide/execution/quickrun_execution.rst b/docs/guide/execution/quickrun_execution.rst index f306696d6..23ebe51dc 100644 --- a/docs/guide/execution/quickrun_execution.rst +++ b/docs/guide/execution/quickrun_execution.rst @@ -86,23 +86,23 @@ This should result in the following file structure after execution: results_parallel/ ├── results_0 - │   ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex + │   ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex │   │   └── shared_RelativeHybridTopologyProtocolUnit-79c279f04ec84218b7935bc0447539a9_attempt_0 │   │   ├── checkpoint.nc │   │   ├── simulation.nc - │   ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json + │   ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json ├── results_1 - │   ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex + │   ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex │   │   └── shared_RelativeHybridTopologyProtocolUnit-a3cef34132aa4e9cbb824fcbcd043b0e_attempt_0 │   │   ├── checkpoint.nc │   │   ├── simulation.nc - │   ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json + │   ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json └── results_2 - ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex + ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex │   └── shared_RelativeHybridTopologyProtocolUnit-abb2b104151c45fc8b0993fa0a7ee0af_attempt_0 │   ├── checkpoint.nc │   ├── simulation.nc - └── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json + └── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json The results of which can be gathered from the CLI using the ``openfe gather`` command, in this case you should direct it to the root directory which includes the repeat results and it will automatically collate the information diff --git a/docs/guide/troubleshooting.rst b/docs/guide/troubleshooting.rst index d408ef807..35303c847 100644 --- a/docs/guide/troubleshooting.rst +++ b/docs/guide/troubleshooting.rst @@ -53,7 +53,7 @@ Save this configuration file as ``debug_logging.conf`` and then run ``openfe qui .. code-block:: bash - $ openfe --log debug_logging.conf quickrun -d results/ -o results/result_lig_ejm_31_solvent_lig_ejm_42_solvent.json transformations/easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json + $ openfe --log debug_logging.conf quickrun -d results/ -o results/result_lig_ejm_31_solvent_lig_ejm_42_solvent.json transformations/rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json Note that the ``--log debug_logging.conf`` argument goes between ``openfe`` and ``quickrun`` on the command line. diff --git a/news/remove_easy_prefix.rst b/news/remove_easy_prefix.rst new file mode 100644 index 000000000..ca27cac0c --- /dev/null +++ b/news/remove_easy_prefix.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* CLI network planners' default names use prefixes `rbfe_` or `rhfe_` , instead of `easy_rbfe` or `easy_rhfe`, to simplify default transformation names. + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py b/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py index cf79b2f3b..748e46f70 100644 --- a/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py +++ b/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py @@ -241,7 +241,7 @@ class RHFEAlchemicalNetworkPlanner(RelativeAlchemicalNetworkPlanner): def __init__( self, - name: str = "easy_rhfe", + name: str = "rhfe", mappers: Optional[Iterable[LigandAtomMapper]] = None, mapping_scorer: Callable[[LigandAtomMapping], float] = default_lomap_score, ligand_network_planner: Callable = generate_minimal_spanning_network, @@ -303,7 +303,7 @@ class RBFEAlchemicalNetworkPlanner(RelativeAlchemicalNetworkPlanner): """ def __init__( self, - name: str = "easy_rbfe", # TODO: change this default to "" in 2.0 + name: str = "rbfe", mappers: Optional[Iterable[LigandAtomMapper]] = None, mapping_scorer: Callable[[LigandAtomMapping], float] = default_lomap_score, ligand_network_planner: Callable = generate_minimal_spanning_network, diff --git a/openfe/tests/setup/alchemical_network_planner/test_relative_alchemical_network_planner.py b/openfe/tests/setup/alchemical_network_planner/test_relative_alchemical_network_planner.py index 6f4166d41..484da6099 100644 --- a/openfe/tests/setup/alchemical_network_planner/test_relative_alchemical_network_planner.py +++ b/openfe/tests/setup/alchemical_network_planner/test_relative_alchemical_network_planner.py @@ -13,13 +13,13 @@ def test_rhfe_alchemical_network_planner_init(): alchem_planner = RHFEAlchemicalNetworkPlanner() - assert alchem_planner.name == "easy_rhfe" + assert alchem_planner.name == "rhfe" def test_rbfe_alchemical_network_planner_init(): alchem_planner = RBFEAlchemicalNetworkPlanner() - assert alchem_planner.name == "easy_rbfe" + assert alchem_planner.name == "rbfe" def test_rbfe_alchemical_network_planner_call(atom_mapping_basic_test_files, T4_protein_component): diff --git a/openfecli/tests/commands/test_gather.py b/openfecli/tests/commands/test_gather.py index ef83d2d5c..f6c067cd9 100644 --- a/openfecli/tests/commands/test_gather.py +++ b/openfecli/tests/commands/test_gather.py @@ -189,8 +189,8 @@ def results_dir_serial_missing_legs(self, tmpdir)->str: tar.extractall('.') results_dir_path = os.path.abspath(tar.getnames()[0]) - files_to_remove = ["easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json", - "easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json" + files_to_remove = ["rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json", + "rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json" ] for fname in files_to_remove: (pathlib.Path(results_dir_path)/ fname).unlink() diff --git a/openfecli/tests/commands/test_plan_rbfe_network.py b/openfecli/tests/commands/test_plan_rbfe_network.py index b8cdd569e..d70f7ebae 100644 --- a/openfecli/tests/commands/test_plan_rbfe_network.py +++ b/openfecli/tests/commands/test_plan_rbfe_network.py @@ -147,13 +147,13 @@ def test_plan_rbfe_network(mol_dir_args, protein_args, tmpdir, yaml_nagl_setting # we can get these in either order: 22 first or 55 first expected_output_1 = [ "Small Molecules: SmallMoleculeComponent(name=ligand_23) SmallMoleculeComponent(name=ligand_55)", - "- easy_rbfe_ligand_23_complex_ligand_55_complex.json", - "- easy_rbfe_ligand_23_solvent_ligand_55_solvent.json", + "- rbfe_ligand_23_complex_ligand_55_complex.json", + "- rbfe_ligand_23_solvent_ligand_55_solvent.json", ] expected_output_2 = [ "Small Molecules: SmallMoleculeComponent(name=ligand_55) SmallMoleculeComponent(name=ligand_23)", - "- easy_rbfe_ligand_55_complex_ligand_23_complex.json", - "- easy_rbfe_ligand_55_solvent_ligand_23_solvent.json", + "- rbfe_ligand_55_complex_ligand_23_complex.json", + "- rbfe_ligand_55_solvent_ligand_23_solvent.json", ] patch_base = ( diff --git a/openfecli/tests/commands/test_plan_rhfe_network.py b/openfecli/tests/commands/test_plan_rhfe_network.py index 7f6d80fbd..5e9d8acae 100644 --- a/openfecli/tests/commands/test_plan_rhfe_network.py +++ b/openfecli/tests/commands/test_plan_rhfe_network.py @@ -123,13 +123,13 @@ def test_plan_rhfe_network(mol_dir_args, tmpdir, yaml_nagl_settings): # we can get these in either order: 22 then 55 or 55 then 22 expected_output_1 = [ "Small Molecules: SmallMoleculeComponent(name=ligand_23) SmallMoleculeComponent(name=ligand_55)", - "- easy_rhfe_ligand_23_vacuum_ligand_55_vacuum.json", - "- easy_rhfe_ligand_23_solvent_ligand_55_solvent.json", + "- rhfe_ligand_23_vacuum_ligand_55_vacuum.json", + "- rhfe_ligand_23_solvent_ligand_55_solvent.json", ] expected_output_2 = [ "Small Molecules: SmallMoleculeComponent(name=ligand_55) SmallMoleculeComponent(name=ligand_23)", - "- easy_rhfe_ligand_55_vacuum_ligand_23_vacuum.json", - "- easy_rhfe_ligand_55_solvent_ligand_23_solvent.json", + "- rhfe_ligand_55_vacuum_ligand_23_vacuum.json", + "- rhfe_ligand_55_solvent_ligand_23_solvent.json", ] patch_base = ( diff --git a/openfecli/tests/data/rbfe_results.tar.gz b/openfecli/tests/data/rbfe_results.tar.gz index db690020a..7be120c40 100644 Binary files a/openfecli/tests/data/rbfe_results.tar.gz and b/openfecli/tests/data/rbfe_results.tar.gz differ diff --git a/openfecli/tests/test_rbfe_tutorial.py b/openfecli/tests/test_rbfe_tutorial.py index 7e77dc500..680c28383 100644 --- a/openfecli/tests/test_rbfe_tutorial.py +++ b/openfecli/tests/test_rbfe_tutorial.py @@ -32,24 +32,24 @@ def tyk2_protein(): @pytest.fixture def expected_transformations(): - return ['easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json', - 'easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json', - 'easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json', - 'easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json', - 'easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json', - 'easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json', - 'easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json', - 'easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json', - 'easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json', - 'easy_rbfe_lig_ejm_42_complex_lig_ejm_50_complex.json', - 'easy_rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json', - 'easy_rbfe_lig_ejm_42_solvent_lig_ejm_50_solvent.json', - 'easy_rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json', - 'easy_rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json', - 'easy_rbfe_lig_jmc_23_complex_lig_jmc_27_complex.json', - 'easy_rbfe_lig_jmc_23_solvent_lig_jmc_27_solvent.json', - 'easy_rbfe_lig_jmc_23_solvent_lig_jmc_28_solvent.json', - 'easy_rbfe_lig_jmc_23_complex_lig_jmc_28_complex.json'] + return ['rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json', + 'rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json', + 'rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json', + 'rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json', + 'rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json', + 'rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json', + 'rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json', + 'rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json', + 'rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json', + 'rbfe_lig_ejm_42_complex_lig_ejm_50_complex.json', + 'rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json', + 'rbfe_lig_ejm_42_solvent_lig_ejm_50_solvent.json', + 'rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json', + 'rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json', + 'rbfe_lig_jmc_23_complex_lig_jmc_27_complex.json', + 'rbfe_lig_jmc_23_solvent_lig_jmc_27_solvent.json', + 'rbfe_lig_jmc_23_solvent_lig_jmc_28_solvent.json', + 'rbfe_lig_jmc_23_complex_lig_jmc_28_complex.json'] def test_plan_tyk2(tyk2_ligands, tyk2_protein, expected_transformations):