address remaining failed tests

gmso/parameterization/topology_parameterizer.py

@@ -69,7 +69,7 @@ class TopologyParameterizationConfig(GMSOBase):
         default=False,
         description="A flag to determine whether or not to look at site.molecule "
         "to look parameterize each molecule only once. Will only be used if "
-        "identify_connected_components=False",
+        "speedup_by_molgraph=False",
     )
 
     ignore_params: list = Field(
@@ -114,7 +114,7 @@ def get_ff(self, key=None):
         else:
             return self.forcefields
 
-    def _parameterize_sites(self, sites, typemap, ff, use_molecule_info=None):
+    def _parameterize_sites(self, sites, typemap, ff, speedup_by_moltag=None):
         """Parameterize sites with appropriate atom-types from the forcefield."""
         for j, site in enumerate(sites):
             site.atom_type = ff.get_potential(
@@ -215,7 +215,7 @@ def _apply_connection_parameters(
                     )
 
     def _parameterize(
-        self, top, typemap, label_type=None, label=None, use_molecule_info=False
+        self, top, typemap, label_type=None, label=None, speedup_by_moltag=False
     ):
         """Parameterize a topology/subtopology based on an atomtype map."""
         if label and label_type:
@@ -226,7 +226,7 @@ def _parameterize(
             sites = top.sites
 
         self._parameterize_sites(
-            sites, typemap, forcefield, use_molecule_info=use_molecule_info
+            sites, typemap, forcefield, speedup_by_moltag=speedup_by_moltag
         )
         self._parameterize_connections(
             top,
@@ -337,27 +337,27 @@ def run_parameterization(self):
                         self.topology,
                         self.config.match_ff_by,
                         label,
-                        self.config.use_molecule_info,
-                        self.config.identify_connected_components,
+                        self.config.speedup_by_moltag,
+                        self.config.speedup_by_molgraph,
                     )
                     self._parameterize(
                         self.topology,
                         typemap,
                         label_type=self.config.match_ff_by,
                         label=label,
-                        use_molecule_info=self.config.use_molecule_info,  # This will be removed from the future iterations
+                        speedup_by_moltag=self.config.speedup_by_moltag,  # This will be removed from the future iterations
                     )
         else:
             typemap = self._get_atomtypes(
                 self.get_ff(),
                 self.topology,
-                use_molecule_info=self.config.use_molecule_info,
-                use_isomorphic_checks=self.config.identify_connected_components,
+                speedup_by_moltag=self.config.speedup_by_moltag,
+                use_isomorphic_checks=self.config.speedup_by_molgraph,
             )
             self._parameterize(
                 self.topology,
                 typemap,
-                use_molecule_info=self.config.use_molecule_info,
+                speedup_by_moltag=self.config.speedup_by_moltag,
             )
 
         self._set_scaling_factors()  # Set global or per molecule scaling factors
@@ -401,7 +401,7 @@ def _get_atomtypes(
         topology,
         label_type=None,
         label=None,
-        use_molecule_info=False,
+        speedup_by_moltag=False,
         use_isomorphic_checks=False,
     ):
         """Run atom-typing in foyer and return the typemap."""
@@ -412,7 +412,7 @@ def _get_atomtypes(
             label,
         )
 
-        if use_molecule_info:
+        if speedup_by_moltag:
             # Iterate through foyer_topology_graph, which is a subgraph of label_type
             typemap, reference = dict(), dict()
             for connected_component in nx.connected_components(

gmso/tests/parameterization/test_impropers_parameterization.py

@@ -17,7 +17,7 @@
 class TestImpropersParameterization(ParameterizationBaseTest):
     def test_improper_parameterization(self, fake_improper_ff_gmso, ethane):
         ethane.identify_connections()
-        apply(ethane, fake_improper_ff_gmso, assert_improper_params=True)
+        apply(ethane, fake_improper_ff_gmso, ignore_params=list())
 
         lib = PotentialTemplateLibrary()
         template_improper_type = lib["PeriodicImproperPotential"]
@@ -61,7 +61,7 @@ def test_improper_parameterization(self, fake_improper_ff_gmso, ethane):
 
     def test_improper_assertion_error(self, ethane_methane_top, oplsaa_gmso):
         with pytest.raises(ParameterizationError):
-            apply(ethane_methane_top, oplsaa_gmso, assert_improper_params=True)
+            apply(ethane_methane_top, oplsaa_gmso, ignore_params=list())
 
     @pytest.mark.parametrize(
         "mol2_loc",

gmso/tests/parameterization/test_opls_gmso.py

@@ -48,7 +48,7 @@ def test_foyer_oplsaa_files(
 
         gmso_top_from_pmd = from_parmed(struct, refer_type=True)
         gmso_top = from_parmed(struct, refer_type=False)
-        apply(gmso_top, oplsaa_gmso, identify_connected_components=False)
+        apply(gmso_top, oplsaa_gmso, speedup_by_molgraph=False)
 
         assert_same_atom_params(gmso_top, gmso_top_from_pmd)
         assert_same_connection_params(gmso_top, gmso_top_from_pmd)

gmso/tests/parameterization/test_parameterization_options.py

@@ -137,23 +137,23 @@ def test_empty_top_parameterization(self, oplsaa_gmso):
             apply(top=Topology(), forcefields=oplsaa_gmso)
 
     @pytest.mark.parametrize(
-        "identify_connected_components, use_molecule_info",
+        "speedup_by_molgraph, speedup_by_moltag",
         [(False, False), (True, False), (False, True), (True, True)],
     )
     def test_speedup_options(
         self,
         ethane_box_with_methane,
         oplsaa_gmso,
-        identify_connected_components,
-        use_molecule_info,
+        speedup_by_molgraph,
+        speedup_by_moltag,
     ):
         ethane_box_with_methane.identify_connections()
         apply(
             ethane_box_with_methane,
             oplsaa_gmso,
             identify_connections=False,
-            identify_connected_components=identify_connected_components,
-            use_molecule_info=use_molecule_info,
+            speedup_by_molgraph=speedup_by_molgraph,
+            speedup_by_moltag=speedup_by_moltag,
         )
 
         molecule_labels = ethane_box_with_methane.unique_site_labels("molecule")
@@ -214,8 +214,8 @@ def test_match_ff_by_molecule(self, ethane_box_with_methane, oplsaa_gmso):
             ff_dict,
             match_ff_by="molecule",
             identify_connections=False,
-            identify_connected_components=True,
-            use_molecule_info=True,
+            speedup_by_molgraph=True,
+            speedup_by_moltag=True,
         )
         assert ethane_box_with_methane.atom_types is not None
 
@@ -231,13 +231,13 @@ def test_match_ff_by_group(self, ethane_box_with_methane, oplsaa_gmso):
             ff_dict,
             match_ff_by="group",
             identify_connections=False,
-            identify_connected_components=True,
-            use_molecule_info=True,
+            speedup_by_molgraph=True,
+            speedup_by_moltag=True,
         )
         assert ethane_box_with_methane.atom_types is not None
 
     @pytest.mark.parametrize(
-        "identify_connected_components, use_molecule_info, match_ff_by",
+        "speedup_by_molgraph, speedup_by_moltag, match_ff_by",
         [
             (False, False, "group"),
             (True, False, "group"),
@@ -253,8 +253,8 @@ def test_hierarchical_mol_structure(
         self,
         oplsaa_gmso,
         hierarchical_top,
-        identify_connected_components,
-        use_molecule_info,
+        speedup_by_molgraph,
+        speedup_by_moltag,
         match_ff_by,
     ):
         top = deepcopy(hierarchical_top)
@@ -274,7 +274,7 @@ def test_hierarchical_mol_structure(
         apply(
             top,
             ff_dict,
-            identify_connected_components=identify_connected_components,
-            use_molecule_info=use_molecule_info,
+            speedup_by_molgraph=speedup_by_molgraph,
+            speedup_by_moltag=speedup_by_moltag,
             match_ff_by=match_ff_by,
         )

gmso/tests/parameterization/test_trappe_gmso.py

@@ -48,7 +48,7 @@ def test_foyer_trappe_files(
         apply(
             gmso_top,
             trappe_ua_gmso,
-            identify_connected_components=False,
+            speedup_by_molgraph=False,
             identify_connections=True,
         )
         gmso_top_from_parmeterized_pmd = from_parmed(struct_pmd)

gmso/utils/specific_ff_to_residue.py

@@ -284,10 +284,10 @@ def specific_ff_to_residue(
     gmso_apply(
         new_gmso_topology,
         gmso_compatible_forcefield_selection,
-        identify_connected_components=True,
+        speedup_by_molgraph=True,
         identify_connections=True,
         match_ff_by=gmso_match_ff_by,
-        use_molecule_info=True,
+        speedup_by_moltag=True,
         remove_untyped=True,
     )
     new_gmso_topology.update_topology()