update LomapAtomMapper default settings to established best practices (#730)

* update LomapAtomMapper default settings to established best practices

* fixup tests for relative_alchemical_network_planner following lomap default change

make these tests use the legacy default settings for Lomap, they're just smoke testing and the actual mappings don't matter

* fixup regression tests for command line plan-rbfe

these are different now that the lomap defaults have been changed for 1.0

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py

@@ -74,8 +74,12 @@ class RelativeAlchemicalNetworkPlanner(
         if protocol is None:
             protocol = RelativeHybridTopologyProtocol(RelativeHybridTopologyProtocol.default_settings())
         if mappers is None:
-            mappers = [LomapAtomMapper(time=20, threed=True,
-                                       element_change=False, max3d=1)]
+            mappers = [LomapAtomMapper(time=20,
+                                       threed=True,
+                                       max3d=1.0,
+                                       element_change=True,
+                                       shift=False,
+                                       )]
 
         self.name = name
         self._mappers = mappers

openfe/tests/setup/alchemical_network_planner/test_relative_alchemical_network_planner.py

@@ -7,6 +7,7 @@ from ...conftest import atom_mapping_basic_test_files, T4_protein_component
 from gufe import SolventComponent, AlchemicalNetwork
 from openfe.setup.alchemical_network_planner import RHFEAlchemicalNetworkPlanner, RBFEAlchemicalNetworkPlanner
 from .edge_types import r_complex_edge, r_solvent_edge, r_vacuum_edge
+import openfe
 
 
 def test_rhfe_alchemical_network_planner_init():
@@ -22,7 +23,15 @@ def test_rbfe_alchemical_network_planner_init():
 
 
 def test_rbfe_alchemical_network_planner_call(atom_mapping_basic_test_files, T4_protein_component):
-    alchem_planner = RBFEAlchemicalNetworkPlanner()
+    alchem_planner = RBFEAlchemicalNetworkPlanner(
+        # these aren't default settings, but the test ligands aren't aligned
+        mappers=[openfe.LomapAtomMapper(
+            time=20,
+            element_change=False,
+            max3d=1,
+            shift=True,
+        )]
+    )
     alchem_network = alchem_planner(
         ligands=atom_mapping_basic_test_files.values(),
         solvent=SolventComponent(),
@@ -34,14 +43,20 @@ def test_rbfe_alchemical_network_planner_call(atom_mapping_basic_test_files, T4_
     edges = alchem_network.edges
     assert len(edges) == 14 # we build 2envs*8ligands-2startLigands = 14 relative edges. 
 
-    print(edges)
     assert sum([r_complex_edge(e) for e in edges]) == 7 # half of the transformations should be complex (they always are)!
     assert sum([r_solvent_edge(e) for e in edges]) == 7 # half of the transformations should be solvent!
     assert sum([r_vacuum_edge(e) for e in edges]) == 0 # no vacuum here!
 
 
 def test_rhfe_alchemical_network_planner_call_multigraph(atom_mapping_basic_test_files):
-    alchem_planner = RHFEAlchemicalNetworkPlanner()
+    alchem_planner = RHFEAlchemicalNetworkPlanner(
+        mappers=[openfe.LomapAtomMapper(
+            time=20,
+            element_change=False,
+            max3d=1,
+            shift=True,
+        )]
+    )
 
     ligand_network = alchem_planner._construct_ligand_network(atom_mapping_basic_test_files.values())
     ligand_network_edges = list(ligand_network.edges)
@@ -59,7 +74,14 @@ def test_rhfe_alchemical_network_planner_call_multigraph(atom_mapping_basic_test
 
 
 def test_rhfe_alchemical_network_planner_call(atom_mapping_basic_test_files):
-    alchem_planner = RHFEAlchemicalNetworkPlanner()
+    alchem_planner = RHFEAlchemicalNetworkPlanner(
+        mappers=[openfe.LomapAtomMapper(
+            time=20,
+            element_change=False,
+            max3d=1,
+            shift=True,
+        )]
+    )
     alchem_network = alchem_planner(ligands=atom_mapping_basic_test_files.values(), solvent=SolventComponent())
     
     assert isinstance(alchem_network, AlchemicalNetwork)

openfecli/parameters/plan_network_options.py

@@ -138,8 +138,13 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption
             raise KeyError(f"Bad mapper choice: '{opt.mapper.method}'")
         mapper_obj = cls(**opt.mapper.settings)
     else:
-        mapper_obj = LomapAtomMapper(time=20, threed=True, element_change=False,
-                                     max3d=1)
+        mapper_obj = LomapAtomMapper(
+            time=20,
+            threed=True,
+            max3d=1.0,
+            element_change=True,
+            shift=False
+        )
 
     # todo: choice of scorer goes here
     mapping_scorer = default_lomap_score

openfecli/tests/test_rbfe_tutorial.py

@@ -31,24 +31,24 @@ def tyk2_protein():
 
 @pytest.fixture
 def expected_transformations():
-    return ['easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json',
-            'easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json',
-            'easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json',
-            'easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json',
+    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_42_solvent_lig_ejm_43_solvent.json',
             'easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json',
-            'easy_rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json',
             'easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json',
-            'easy_rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json',
-            'easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json',
-            'easy_rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json',
             'easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json',
-            'easy_rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json',
             'easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json',
-            'easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json',
             'easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json',
-            'easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_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_complex_lig_jmc_27_complex.json',
+            'easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.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_27_complex_lig_jmc_28_complex.json',
+            'easy_rbfe_lig_jmc_27_solvent_lig_jmc_28_solvent.json']
 
 
 def test_plan_tyk2(tyk2_ligands, tyk2_protein, expected_transformations):
@@ -88,15 +88,15 @@ def mock_execute(expected_transformations):
 def ref_gather():
     return """\
 ligand_i\tligand_j\tDDG(i->j) (kcal/mol)\tuncertainty (kcal/mol)
-lig_ejm_31\tlig_ejm_42\t0.0\t0.0
 lig_ejm_31\tlig_ejm_46\t0.0\t0.0
 lig_ejm_31\tlig_ejm_47\t0.0\t0.0
 lig_ejm_31\tlig_ejm_48\t0.0\t0.0
 lig_ejm_31\tlig_ejm_50\t0.0\t0.0
 lig_ejm_42\tlig_ejm_43\t0.0\t0.0
-lig_ejm_46\tlig_jmc_23\t0.0\t0.0
+lig_ejm_42\tlig_ejm_50\t0.0\t0.0
 lig_ejm_46\tlig_jmc_27\t0.0\t0.0
-lig_ejm_46\tlig_jmc_28\t0.0\t0.0
+lig_jmc_23\tlig_jmc_27\t0.0\t0.0
+lig_jmc_27\tlig_jmc_28\t0.0\t0.0
 """