Merge branch 'main' into 748-remove-gmso-xml-conversions

gmso/parameterization/parameterize.py

@@ -12,63 +12,52 @@ def apply(
     forcefields,
     match_ff_by="molecule",
     identify_connections=False,
-    identify_connected_components=True,
-    use_molecule_info=False,
-    assert_bond_params=True,
-    assert_angle_params=True,
-    assert_dihedral_params=True,
-    assert_improper_params=False,
+    speedup_by_molgraph=False,
+    speedup_by_moltag=False,
+    ignore_params=["improper"],
     remove_untyped=False,
     fast_copy=True,
 ):
     """Set Topology parameter types from GMSO ForceFields.
 
     Parameters
     ----------
-    top: gmso.core.topology.Topology, required
+    top : gmso.core.topology.Topology, required
         The GMSO topology on which to apply forcefields
 
-    forcefields: ForceField or dict, required
+    forcefields : ForceField or dict, required
         The forcefield to apply. If a dictionary is used the keys are labels that match
         the molecule name (specified as a label of site), and the values are gmso ForceField objects that gets applied
         to the specified molecule.
         Note: if a Topology with no molecule is provided, this option will only take
         a ForceField object. If a dictionary of ForceFields is provided, this method will
         fail.
 
-    match_ff_by: str, optional, default="molecule"
+    match_ff_by : str, optional, default="molecule"
         They site's tag used to match the forcefields provided above to the Topology.
         Options include "molecule" and "group". This option is only valid if forcefields are provided
         as a dict.
 
-    identify_connections: bool, optional, default=False
+    identify_connections : bool, optional, default=False
         If true, add connections identified using networkx graph matching to match
         the topology's bonding graph to smaller sub-graphs that correspond to an angle,
         dihedral, improper etc
 
-    identify_connected_components: bool, optional, default=True
+    speedup_by_molgraph: bool, optional, default=False
         A flag to determine whether or not to search the topology for repeated disconnected
         structures, otherwise known as molecules and type each molecule only once.
+        This option will be usefult to handle systems with many repeated small molecules,
+        but may slow down system with large molecule, e.g., monolayer.
 
-    use_molecule_info: bool, optional, default=False
-        A flag to determine whether or not to look at site.residue_name to look parameterize
-        each molecule only once. Currently unused.
+    speedup_by_moltag : bool, optional, default=False
+        A flag to determine whether or not to look at site.molecule_name to try to parameterize
+        each molecule only once. This option provides speedup for topologies with properly
+        assigned molecule and residue labels.
 
-    assert_bond_params : bool, optional, default=True
-        If True, an error is raised if parameters are not found for all system
-        bonds.
-
-    assert_angle_params : bool, optional, default=True
-        If True, an error is raised if parameters are not found for all system
-        angles.
-
-    assert_dihedral_params : bool, optional, default=True
-        If True, an error is raised if parameters are not found for all system
-        proper dihedrals.
-
-    assert_improper_params : bool, optional, default=False
-        If True, an error is raised if parameters are not found for all system
-        improper dihedrals.
+    ignore_params : set or list or tuple, optional, default=["impropers"]
+        Skipping the checks that make sure all connections (in the list) have a connection types.
+        Available options includes "bonds", "angles", "dihedrals", and "impropers".
+        If you wish to have all connection types checks, provides an empty set/list/tuple.
 
     remove_untyped : bool, optional, default=False
         If True, after the atomtyping and parameterization step, remove all connection
@@ -83,16 +72,14 @@ def apply(
         this should be changed to False if further modification of expressions are
         necessary post parameterization.
     """
+    ignore_params = set([option.lower() for option in ignore_params])
     config = TopologyParameterizationConfig.parse_obj(
         dict(
             match_ff_by=match_ff_by,
             identify_connections=identify_connections,
-            identify_connected_components=identify_connected_components,
-            use_molecule_info=use_molecule_info,
-            assert_bond_params=assert_bond_params,
-            assert_angle_params=assert_angle_params,
-            assert_dihedral_params=assert_dihedral_params,
-            assert_improper_params=assert_improper_params,
+            speedup_by_molgraph=speedup_by_molgraph,
+            speedup_by_moltag=speedup_by_moltag,
+            ignore_params=ignore_params,
             remove_untyped=remove_untyped,
             fast_copy=fast_copy,
         )

gmso/parameterization/topology_parameterizer.py

@@ -58,44 +58,24 @@ class TopologyParameterizationConfig(GMSOBase):
         "angle, dihedral, improper etc",
     )
 
-    identify_connected_components: bool = Field(
+    speedup_by_molgraph: bool = Field(
         default=False,
         description="A flag to determine whether or not to search the topology"
         " for repeated disconnected structures, otherwise known as "
         "molecules and type each molecule only once.",
     )
 
-    use_molecule_info: bool = Field(
+    speedup_by_moltag: bool = Field(
         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",
-    )  # Unused
-
-    assert_bond_params: bool = Field(
-        default=True,
-        description="If True, an error is raised if parameters are not found for "
-        "all system bonds.",
+        "speedup_by_molgraph=True",
     )
 
-    assert_angle_params: bool = Field(
-        default=True,
-        description="If True, an error is raised if parameters are not found for "
-        "all system angles",
-    )
-
-    assert_dihedral_params: bool = (
-        Field(
-            default=True,
-            description="If True, an error is raised if parameters are not found for "
-            "all system dihedrals.",
-        ),
-    )
-
-    assert_improper_params: bool = Field(
-        default=False,
-        description="If True, an error is raised if parameters are not found for "
-        "all system impropers.",
+    ignore_params: list = Field(
+        default=[],
+        description="Skipping the checks that make sure all connections (in the list) "
+        "have a connection types.",
     )
 
     remove_untyped: bool = Field(
@@ -134,7 +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(
@@ -170,16 +150,20 @@ def _parameterize_connections(
             impropers = top.impropers
 
         self._apply_connection_parameters(
-            bonds, ff, self.config.assert_bond_params
+            bonds, ff, False if "bond" in self.config.ignore_params else True
         )
         self._apply_connection_parameters(
-            angles, ff, self.config.assert_angle_params
+            angles, ff, False if "angle" in self.config.ignore_params else True
         )
         self._apply_connection_parameters(
-            dihedrals, ff, self.config.assert_dihedral_params
+            dihedrals,
+            ff,
+            False if "dihedral" in self.config.ignore_params else True,
         )
         self._apply_connection_parameters(
-            impropers, ff, self.config.assert_improper_params
+            impropers,
+            ff,
+            False if "improper" in self.config.ignore_params else True,
         )
 
     def _apply_connection_parameters(
@@ -231,7 +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:
@@ -242,7 +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,
@@ -353,27 +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
@@ -417,7 +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."""
@@ -428,7 +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()