Add lomap network generator

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 <https://docs.openfree.energy/en/stable/guide/cli/cli_yaml.html>`_
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

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``

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()