Merge branch 'master' into 561-layered-dihedrals

Author: justinGilmer

azure-pipelines.yml

@@ -83,9 +83,13 @@ stages:
 
           - bash: |
               source activate gmso-dev
-              bash <(curl -s https://codecov.io/bash) -C $(Build.SourceVersion)
-            condition: and( eq( variables['Agent.OS'], 'Linux' ), eq( variables['python.version'], '3.7' ) )
+              curl -Os https://uploader.codecov.io/latest/linux/codecov
+              chmod +x codecov
+              ./codecov -t ${CODECOV_UPLOAD_TOKEN} -C $(Build.SourceVersion)
+            condition: and( eq( variables['Agent.OS'], 'Linux'  ), eq( variables['python.version'], '3.7'  )  )
             displayName: Upload coverage report to codecov.io
+            env:
+              CODECOV_UPLOAD_TOKEN: $(codecovUploadToken)
 
           - task: PublishCodeCoverageResults@1
             inputs:

gmso/abc/abstract_connection.py

@@ -31,6 +31,40 @@ def connection_members(self):
     def name(self):
         return self.__dict__.get("name_")
 
+    @property
+    def member_types(self):
+        """Return the atomtype of the connection members as a list of string."""
+        return self._get_members_types_or_classes("member_types_")
+
+    @property
+    def member_classes(self):
+        """Return the class of the connection members as a list of string."""
+        return self._get_members_types_or_classes("member_classes_")
+
+    def _has_typed_members(self):
+        """Check if all the members of this connection are typed."""
+        return all(
+            member.atom_type
+            for member in self.__dict__.get("connection_members_")
+        )
+
+    def _get_members_types_or_classes(self, to_return):
+        """Return types or classes for connection members if they exist."""
+        assert to_return in {"member_types_", "member_classes_"}
+        ctype = getattr(self, "connection_type")
+        ctype_attr = getattr(ctype, to_return) if ctype else None
+
+        if ctype_attr:
+            return list(ctype_attr)
+        elif self._has_typed_members():
+            tc = [
+                member.atom_type.name
+                if to_return == "member_types_"
+                else member.atom_type.atomclass
+                for member in self.__dict__.get("connection_members_")
+            ]
+            return tc if all(tc) else None
+
     @root_validator(pre=True)
     def validate_fields(cls, values):
         connection_members = values.get("connection_members", [])

gmso/core/angle_type.py

@@ -26,7 +26,13 @@ class AngleType(ParametricPotential):
 
     member_types_: Optional[Tuple[str, str, str]] = Field(
         None,
-        description="List-like of gmso.AtomType.name or gmso.AtomType.atomclass "
+        description="List-like of gmso.AtomType.name "
+        "defining the members of this angle type",
+    )
+
+    member_classes_: Optional[Tuple[str, str, str]] = Field(
+        None,
+        description="List-like of gmso.AtomType.atomclass "
         "defining the members of this angle type",
     )
 
@@ -38,6 +44,7 @@ def __init__(
         independent_variables=None,
         potential_expression=None,
         member_types=None,
+        member_classes=None,
         topology=None,
         tags=None,
     ):
@@ -61,6 +68,7 @@ def __init__(
             potential_expression=potential_expression,
             topology=topology,
             member_types=member_types,
+            member_classes=member_classes,
             set_ref=ANGLE_TYPE_DICT,
             tags=tags,
         )
@@ -69,7 +77,17 @@ def __init__(
     def member_types(self):
         return self.__dict__.get("member_types_")
 
+    @property
+    def member_classes(self):
+        return self.__dict__.get("member_classes_")
+
     class Config:
-        fields = {"member_types_": "member_types"}
+        fields = {
+            "member_types_": "member_types",
+            "member_classes_": "member_classes",
+        }
 
-        alias_to_fields = {"member_types": "member_types_"}
+        alias_to_fields = {
+            "member_types": "member_types_",
+            "member_classes": "member_classes_",
+        }

gmso/core/bond_type.py

@@ -27,7 +27,13 @@ class BondType(ParametricPotential):
 
     member_types_: Optional[Tuple[str, str]] = Field(
         None,
-        description="List-like of of gmso.AtomType.name or gmso.AtomType.atomclass "
+        description="List-like of of gmso.AtomType.name "
+        "defining the members of this bond type",
+    )
+
+    member_classes_: Optional[Tuple[str, str]] = Field(
+        None,
+        description="List-like of of gmso.AtomType.atomclass "
         "defining the members of this bond type",
     )
 
@@ -39,6 +45,7 @@ def __init__(
         independent_variables=None,
         potential_expression=None,
         member_types=None,
+        member_classes=None,
         topology=None,
         tags=None,
     ):
@@ -62,6 +69,7 @@ def __init__(
             potential_expression=potential_expression,
             topology=topology,
             member_types=member_types,
+            member_classes=member_classes,
             set_ref=BOND_TYPE_DICT,
             tags=tags,
         )
@@ -71,9 +79,19 @@ def member_types(self):
         """Return the members involved in this bondtype."""
         return self.__dict__.get("member_types_")
 
+    @property
+    def member_classes(self):
+        return self.__dict__.get("member_classes_")
+
     class Config:
         """Pydantic configuration for class attributes."""
 
-        fields = {"member_types_": "member_types"}
+        fields = {
+            "member_types_": "member_types",
+            "member_classes_": "member_classes",
+        }
 
-        alias_to_fields = {"member_types": "member_types_"}
+        alias_to_fields = {
+            "member_types": "member_types_",
+            "member_classes": "member_classes_",
+        }

gmso/core/dihedral_type.py

@@ -32,10 +32,16 @@ class DihedralType(ParametricPotential):
 
     member_types_: Optional[Tuple[str, str, str, str]] = Field(
         None,
-        description="List-like of of gmso.AtomType.name or gmso.AtomType.atomclass "
+        description="List-like of of gmso.AtomType.name "
         "defining the members of this dihedral type",
     )
 
+    member_classes_: Optional[Tuple[str, str, str, str]] = Field(
+        None,
+        description="List-like of of gmso.AtomType.atomclass defining the "
+        "members of this dihedral type",
+    )
+
     def __init__(
         self,
         name="DihedralType",
@@ -44,6 +50,7 @@ def __init__(
         independent_variables=None,
         potential_expression=None,
         member_types=None,
+        member_classes=None,
         topology=None,
         tags=None,
     ):
@@ -68,6 +75,7 @@ def __init__(
             potential_expression=potential_expression,
             topology=topology,
             member_types=member_types,
+            member_classes=member_classes,
             set_ref=DIHEDRAL_TYPE_DICT,
             tags=tags,
         )
@@ -76,7 +84,17 @@ def __init__(
     def member_types(self):
         return self.__dict__.get("member_types_")
 
-    class Config:
-        fields = {"member_types_": "member_types"}
+    @property
+    def member_classes(self):
+        return self.__dict__.get("member_classes_")
 
-        alias_to_fields = {"member_types": "member_types_"}
+    class Config:
+        fields = {
+            "member_types_": "member_types",
+            "member_classes_": "member_classes",
+        }
+
+        alias_to_fields = {
+            "member_types": "member_types_",
+            "member_classes": "member_classes_",
+        }

gmso/core/improper_type.py

@@ -38,7 +38,13 @@ class ImproperType(ParametricPotential):
 
     member_types_: Optional[Tuple[str, str, str, str]] = Field(
         None,
-        description="List-like of of gmso.AtomType.name or gmso.AtomType.atomclass "
+        description="List-like of gmso.AtomType.name "
+        "defining the members of this improper type",
+    )
+
+    member_classes_: Optional[Tuple[str, str, str, str]] = Field(
+        None,
+        description="List-like of gmso.AtomType.atomclass "
         "defining the members of this improper type",
     )
 
@@ -50,6 +56,7 @@ def __init__(
         independent_variables=None,
         potential_expression=None,
         member_types=None,
+        member_classes=None,
         topology=None,
         tags=None,
     ):
@@ -74,6 +81,7 @@ def __init__(
             potential_expression=potential_expression,
             topology=topology,
             member_types=member_types,
+            member_classes=member_classes,
             set_ref=IMPROPER_TYPE_DICT,
             tags=tags,
         )
@@ -83,9 +91,19 @@ def member_types(self):
         """Return member information for this ImproperType."""
         return self.__dict__.get("member_types_")
 
+    @property
+    def member_classes(self):
+        return self.__dict__.get("member_classes_")
+
     class Config:
         """Pydantic configuration for attributes."""
 
-        fields = {"member_types_": "member_types"}
+        fields = {
+            "member_types_": "member_types",
+            "member_classes_": "member_classes",
+        }
 
-        alias_to_fields = {"member_types": "member_types_"}
+        alias_to_fields = {
+            "member_types": "member_types_",
+            "member_classes": "member_classes_",
+        }

gmso/exceptions.py

@@ -26,5 +26,9 @@ class MissingAtomTypesError(ForceFieldParseError):
     """Error for missing AtomTypes when creating a ForceField from an XML file."""
 
 
+class MixedClassAndTypesError(ForceFieldParseError):
+    """Error for missing AtomTypes when creating a ForceField from an XML file."""
+
+
 class MissingPotentialError(ForceFieldError):
     """Error for missing Potential when searching for Potentials in a ForceField."""

gmso/tests/files/ff-example0.xml

@@ -31,13 +31,13 @@
     <BondTypes expression="0.5 * k * (r-r_eq)**2">
         <ParametersUnitDef parameter="r_eq" unit="nm"/>
         <ParametersUnitDef parameter="k" unit="kJ/mol"/>
-        <BondType name="BondType1" class1='Ar' type2='Ar'>
+        <BondType name="BondType1" type1='Ar' type2='Ar'>
             <Parameters>
                 <Parameter name='r_eq' value="10.0"/>
                 <Parameter name='k' value="10000"/>
             </Parameters>
         </BondType>
-        <BondType name="BondType2" type1='Xe' class2="Xe">
+        <BondType name="BondType2" type1='Xe' type2="Xe">
             <Parameters>
                 <Parameter name='r_eq' value="10"/>
                 <Parameter name='k' value="20000"/>
@@ -65,7 +65,7 @@
     <DihedralTypes expression="0.5 * z * (r-r_eq)**2">
         <ParametersUnitDef parameter="r_eq" unit="nm"/>
         <ParametersUnitDef parameter="z" unit="kJ/mol"/>
-        <DihedralType name="DihedralType1" class1='Ar' class2='Ar' type3="Ar" type4="Ar">
+        <DihedralType name="DihedralType1" class1='Ar' class2='Ar' class3="Ar" class4="Ar">
             <Parameters>
                 <Parameter name='r_eq' value="10.0"/>
                 <Parameter name='z' value="100"/>

gmso/tests/test_bond.py

@@ -100,3 +100,36 @@ def test_equivalent_members_set(self):
 
         assert tuple(bond_eq.connection_members) in bond.equivalent_members()
         assert tuple(bond.connection_members) in bond_eq.equivalent_members()
+
+    def test_bond_member_classes_none(self, typed_ethane):
+        bonds = typed_ethane.bonds
+        assert bonds[0].member_classes is None
+
+    def test_bond_member_types(self, typed_ethane):
+        bonds = typed_ethane.bonds
+        assert set(bonds[0].member_types) == set(["opls_135", "opls_140"])
+
+    def test_bond_member_classes_from_connection_members(self):
+        atype1 = AtomType(atomclass="CT", name="t1")
+
+        atype2 = AtomType(atomclass="CK", name="t2")
+
+        bond = Bond(
+            connection_members=[Atom(atom_type=atype1), Atom(atom_type=atype2)]
+        )
+        assert set(bond.member_classes) == set(["CT", "CK"])
+        assert set(bond.member_types) == set(["t1", "t2"])
+
+    def test_bond_member_types_classes_from_bond_type(self):
+        atom_type = AtomType()
+        atom1 = Atom(atom_type=atom_type)
+        atom2 = Atom(atom_type=atom_type)
+
+        btype = BondType(
+            name="atom1-atom2-bond",
+            member_types=["at1", "at2"],
+            member_classes=["XE", "XE"],
+        )
+        bond = Bond(connection_members=[atom1, atom2], bond_type=btype)
+        assert set(bond.member_classes) == set(["XE", "XE"])
+        assert set(bond.member_types) == set(["at1", "at2"])

gmso/tests/test_forcefield.py

@@ -137,7 +137,7 @@ def test_ff_angletypes_from_xml(self, ff):
         assert ff.angle_types["Xe~Xe~Xe"].parameters["z"] == u.unyt_quantity(
             20, u.kJ / u.mol
         )
-        assert ff.angle_types["Xe~Xe~Xe"].member_types == ("Xe", "Xe", "Xe")
+        assert ff.angle_types["Xe~Xe~Xe"].member_classes == ("Xe", "Xe", "Xe")
 
     def test_ff_dihedraltypes_from_xml(self, ff):
         assert len(ff.dihedral_types) == 2
@@ -154,7 +154,7 @@ def test_ff_dihedraltypes_from_xml(self, ff):
         assert ff.dihedral_types["Ar~Ar~Ar~Ar"].parameters[
             "z"
         ] == u.unyt_quantity(100, u.kJ / u.mol)
-        assert ff.dihedral_types["Ar~Ar~Ar~Ar"].member_types == (
+        assert ff.dihedral_types["Ar~Ar~Ar~Ar"].member_classes == (
             "Ar",
             "Ar",
             "Ar",
@@ -171,7 +171,7 @@ def test_ff_dihedraltypes_from_xml(self, ff):
         assert ff.dihedral_types["Xe~Xe~Xe~Xe"].parameters[
             "z"
         ] == u.unyt_quantity(20, u.kJ / u.mol)
-        assert ff.dihedral_types["Xe~Xe~Xe~Xe"].member_types == (
+        assert ff.dihedral_types["Xe~Xe~Xe~Xe"].member_classes == (
             "Xe",
             "Xe",
             "Xe",