Add bond/angle wildcard handling

gmso/core/forcefield.py

@@ -351,6 +351,33 @@ def _get_bond_type(self, atom_types, return_match_order=False, warn=False):
         if reverse in self.bond_types:
             match = self.bond_types[reverse], (1, 0)
 
+        if match:
+            if return_match_order:
+                return match
+            else:
+                return match[0]
+
+        for i in range(1, 3):
+            forward_patterns = mask_with(atom_types, i)
+            reverse_patterns = mask_with(reversed(atom_types), i)
+
+            for forward_pattern, reverse_pattern in zip(
+                forward_patterns, reverse_patterns
+            ):
+                forward_match_key = FF_TOKENS_SEPARATOR.join(forward_pattern)
+                reverse_match_key = FF_TOKENS_SEPARATOR.join(reverse_pattern)
+
+                if forward_match_key in self.bond_types:
+                    match = self.bond_types[forward_match_key], (0, 1)
+                    break
+
+                if reverse_match_key in self.bond_types:
+                    match = self.bond_types[reverse_match_key], (1, 0)
+                    break
+
+            if match:
+                break
+
         msg = (
             f"BondType between atoms {atom_types[0]} and {atom_types[1]} "
             f"is missing from the ForceField"
@@ -382,6 +409,33 @@ def _get_angle_type(self, atom_types, return_match_order=False, warn=False):
         if reverse in self.angle_types:
             match = self.angle_types[reverse], (2, 1, 0)
 
+        if match:
+            if return_match_order:
+                return match
+            else:
+                return match[0]
+
+        for i in range(1, 4):
+            forward_patterns = mask_with(atom_types, i)
+            reverse_patterns = mask_with(reversed(atom_types), i)
+
+            for forward_pattern, reverse_pattern in zip(
+                forward_patterns, reverse_patterns
+            ):
+                forward_match_key = FF_TOKENS_SEPARATOR.join(forward_pattern)
+                reverse_match_key = FF_TOKENS_SEPARATOR.join(reverse_pattern)
+
+                if forward_match_key in self.angle_types:
+                    match = self.angle_types[forward_match_key], (0, 1, 2)
+                    break
+
+                if reverse_match_key in self.angle_types:
+                    match = self.angle_types[reverse_match_key], (2, 1, 0)
+                    break
+
+            if match:
+                break
+
         msg = (
             f"AngleType between atoms {atom_types[0]}, {atom_types[1]} "
             f"and {atom_types[2]} is missing from the ForceField"

gmso/tests/files/alkanes_wildcards.xml

@@ -46,38 +46,32 @@
   <BondTypes expression="0.5*k*(r - r_eq)**2">
     <ParametersUnitDef parameter="k" unit="kJ/(mol*nm**2)"/>
     <ParametersUnitDef parameter="r_eq" unit="nm"/>
-    <BondType name="BondType-Harmonic-1" type1="CT" type2="HC">
+    <BondType name="BondType-Harmonic-wildcard" type1="*" type2="*">
       <Parameters>
-        <Parameter name="k" value="284512.0"/>
-        <Parameter name="r_eq" value="0.109"/>
+        <Parameter name="k" value="1"/>
+        <Parameter name="r_eq" value="1"/>
       </Parameters>
     </BondType>
-    <BondType name="BondType-Harmonic-2" type1="CT" type2="CT">
+    <BondType name="BondType-Harmonic-135" type1="*" type2="opls_135">
       <Parameters>
-        <Parameter name="k" value="224262.4"/>
-        <Parameter name="r_eq" value="0.1529"/>
+        <Parameter name="k" value="2"/>
+        <Parameter name="r_eq" value="1"/>
       </Parameters>
     </BondType>
   </BondTypes>
   <AngleTypes expression="0.5*k*(theta - theta_eq)**2">
     <ParametersUnitDef parameter="k" unit="kJ/(mol*rad**2)"/>
     <ParametersUnitDef parameter="theta_eq" unit="rad"/>
-    <AngleType name="AngleType-Harmonic-1" type1="HC" type2="CT" type3="HC">
+    <AngleType name="AngleType-Harmonic-wildcard" type1="*" type2="*" type3="*">
       <Parameters>
-        <Parameter name="k" value="276.144"/>
-        <Parameter name="theta_eq" value="1.88146493365"/>
+        <Parameter name="k" value="1"/>
+        <Parameter name="theta_eq" value="1"/>
       </Parameters>
     </AngleType>
-    <AngleType name="AngleType-Harmonic-2" type1="CT" type2="CT" type3="HC">
+    <AngleType name="AngleType-Harmonic-opls_135" type1="*" type2="*" type3="opls_135">
       <Parameters>
-        <Parameter name="k" value="313.8"/>
-        <Parameter name="theta_eq" value="1.93207948196"/>
-      </Parameters>
-    </AngleType>
-    <AngleType name="AngleType-Harmonic-3" type1="CT" type2="CT" type3="CT">
-      <Parameters>
-        <Parameter name="k" value="488.273"/>
-        <Parameter name="theta_eq" value="1.966986067"/>
+        <Parameter name="k" value="1"/>
+        <Parameter name="theta_eq" value="1"/>
       </Parameters>
     </AngleType>
   </AngleTypes>
@@ -88,24 +82,14 @@
     <ParametersUnitDef parameter="c3" unit="kJ/mol"/>
     <ParametersUnitDef parameter="c4" unit="kJ/mol"/>
     <ParametersUnitDef parameter="c5" unit="kJ/mol"/>
-    <DihedralType name="RyckaertBellemansTorsionPotential-1" type1="HC" type2="CT" type3="CT" type4="">
-        <Parameters>
-        <Parameter name="c0" value="0.6276"/>
-        <Parameter name="c1" value="1.8828"/>
-        <Parameter name="c2" value="0.0"/>
-        <Parameter name="c3" value="-2.5104"/>
-        <Parameter name="c4" value="0.0"/>
-        <Parameter name="c5" value="0.0"/>
-      </Parameters>
-    </DihedralType>
-    <DihedralType name="RyckaertBellemansTorsionPotential-3" type1="CT" type2="CT" type3="CT" type4="CT">
+    <DihedralType name="RyckaertBellemansTorsionPotential-1" type1="*" type2="*" type3="*" type4="">
         <Parameters>
-        <Parameter name="c0" value="2.9288"/>
-        <Parameter name="c1" value="-1.4644"/>
-        <Parameter name="c2" value="0.2092"/>
-        <Parameter name="c3" value="-1.6736"/>
-        <Parameter name="c4" value="0.0"/>
-        <Parameter name="c5" value="0.0"/>
+        <Parameter name="c0" value="1"/>
+        <Parameter name="c1" value="1"/>
+        <Parameter name="c2" value="1"/>
+        <Parameter name="c3" value="1"/>
+        <Parameter name="c4" value="1"/>
+        <Parameter name="c5" value="0"/>
       </Parameters>
     </DihedralType>
   </DihedralTypes>

gmso/tests/parameterization/test_opls_gmso.py → gmso/tests/parameterization/test_parameterizations.py

@@ -4,11 +4,13 @@
 import parmed as pmd
 import pytest
 
+from gmso import ForceField
 from gmso.external.convert_parmed import from_parmed
 from gmso.parameterization.parameterize import apply
 from gmso.tests.parameterization.parameterization_base_test import (
     ParameterizationBaseTest,
 )
+from gmso.tests.utils import get_path
 
 
 def get_foyer_opls_test_dirs():
@@ -56,3 +58,25 @@ def test_foyer_oplsaa_files(
         assert_same_connection_params(gmso_top, gmso_top_from_pmd)
         assert_same_connection_params(gmso_top, gmso_top_from_pmd, "angles")
         assert_same_connection_params(gmso_top, gmso_top_from_pmd, "dihedrals")
+
+
+class TestGeneralParameterizations(ParameterizationBaseTest):
+    def test_wildcards(self, ethane_methane_top):
+        from gmso.core.views import PotentialFilters
+
+        ff = ForceField(get_path("alkanes_wildcards.xml"))
+        ptop = apply(ethane_methane_top, ff, identify_connections=True)
+        assert ptop.is_fully_typed()
+        assert len(ptop.bond_types) == 11
+        assert len(ptop.bond_types(PotentialFilters.UNIQUE_NAME_CLASS)) == 2
+        assert ptop.bonds[0].bond_type.member_types == ("*", "opls_135")  # ethane
+        assert ptop.bonds[8].bond_type.member_types == ("*", "*")  # methane
+
+        assert len(ptop.angle_types) == 12 + 6  # ethane + methane
+        assert len(ptop.angle_types(PotentialFilters.UNIQUE_NAME_CLASS)) == 2
+        assert ptop.angles[0].angle_type.member_types == ("*", "*", "*")
+        assert ptop.angles[2].angle_type.member_types == ("*", "*", "opls_135")
+
+        assert len(ptop.dihedral_types) == 9
+        assert len(ptop.dihedral_types(PotentialFilters.UNIQUE_NAME_CLASS)) == 1
+        assert ptop.dihedrals[0].dihedral_type.member_types == ("*", "*", "*", "*")