diff --git a/news/add_lomap_network_generator_to_cli.rst b/news/add_lomap_network_generator_to_cli.rst new file mode 100644 index 000000000..9cf0564fc --- /dev/null +++ b/news/add_lomap_network_generator_to_cli.rst @@ -0,0 +1,23 @@ +**Added:** + +* Added CLI support for ``generate_lomap_network``. This option can be specified as a `YAML-defined setting `_ + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/openfecli/parameters/plan_network_options.py b/openfecli/parameters/plan_network_options.py index 19c2ed03e..02d7622df 100644 --- a/openfecli/parameters/plan_network_options.py +++ b/openfecli/parameters/plan_network_options.py @@ -123,6 +123,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption generate_minimal_spanning_network, generate_maximal_network, generate_minimal_redundant_network, + generate_lomap_network, ) from openfe.setup import ( LomapAtomMapper, @@ -179,6 +180,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption 'mst': generate_minimal_spanning_network, 'generate_minimal_redundant_network': generate_minimal_redundant_network, 'generate_maximal_network': generate_maximal_network, + 'generate_lomap_network': generate_lomap_network, } try: @@ -225,6 +227,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption - `generate_minimal_spanning_tree` - `generate_minimal_redundant_network` - `generate_radial_network` + - `generate_lomap_network` Supported partial charge method choices are: - ``am1bcc`` diff --git a/openfecli/tests/commands/test_plan_rbfe_network.py b/openfecli/tests/commands/test_plan_rbfe_network.py index ca2b3c407..b8cdd569e 100644 --- a/openfecli/tests/commands/test_plan_rbfe_network.py +++ b/openfecli/tests/commands/test_plan_rbfe_network.py @@ -338,39 +338,37 @@ def test_plan_rbfe_network_charge_changes(cdk8_files): @pytest.fixture -def custom_yaml_settings(): +def lomap_yaml_settings(): return """\ network: - method: generate_minimal_redundant_network + method: generate_lomap_network settings: - mst_num: 2 + max_path_length: 6 mapper: method: LomapAtomMapper settings: time: 45 element_change: True - + partial_charge: method: nagl settings: nagl_model: openff-gnn-am1bcc-0.1.0-rc.3.pt """ -@pytest.mark.xfail(HAS_OPENEYE, reason="openff-nagl#177") -def test_custom_yaml_plan_rbfe_smoke_test(custom_yaml_settings, eg5_files, tmpdir): - protein, ligand, cofactor = eg5_files +def test_lomap_yaml_plan_rbfe_smoke_test(lomap_yaml_settings, cdk8_files, tmpdir): + protein, ligand = cdk8_files settings_path = tmpdir / "settings.yaml" with open(settings_path, "w") as f: - f.write(custom_yaml_settings) + f.write(lomap_yaml_settings) assert settings_path.exists() args = [ '-p', protein, '-M', ligand, - '-C', cofactor, - '-s', settings_path, + '-s', settings_path ] runner = CliRunner()