Merge pull request #183 from umesh-timalsina/175-core-equality-checks

Rework equality checks and representation of core types

azure-pipelines.yml

@@ -0,0 +1,35 @@
+trigger:
+  - 175-core-equality-checks
+pr:
+  - master
+
+jobs:
+  - job: TestsForTopology
+    pool:
+      vmImage: 'ubuntu-latest'
+    steps:
+      - bash: echo "##vso[task.prependpath]$CONDA/bin"
+        displayName: Add conta to path
+
+      - bash: |
+          conda config --set always_yes yes --set changeps1 no
+          conda config --add channels omnia
+          conda config --add channels janschulz
+          conda config --add channels conda-forge
+          conda config --add channels mosdef
+        displayName: Add relavent channels
+
+      - bash: |
+          conda create -n test-environment
+          source activate test-environment
+          conda install --yes --file requirements.txt
+          conda install pytest
+          pip install -e .
+        displayName: Install requirements, Install branch
+
+      - bash: |
+          source activate test-environment
+          python -m pytest -v topology
+        displayName: Run Tests
+
+

topology/core/angle.py

@@ -30,22 +30,6 @@ def __init__(self, connection_members=[], connection_type=None, name="Angle"):
         super(Angle, self).__init__(connection_members=connection_members,
                 connection_type=connection_type, name=name)
 
-    def __eq__(self, other):
-        return hash(self) == hash(other)
-
-    def __hash__(self):
-        if self.connection_type:
-            return hash(
-                tuple(
-                    (
-                        self.name,
-                        self.connection_type,
-                        tuple(self.connection_members),
-                    )
-                )
-            )
-        return hash(tuple(self.connection_members))
-
 
 def _validate_three_partners(connection_members):
     """Ensure 3 partners are involved in Angle"""

topology/core/angle_type.py

@@ -3,6 +3,8 @@
 
 from topology.core.potential import Potential
 from topology.exceptions import TopologyError
+from topology.utils.decorators import confirm_dict_existence
+from topology.utils._constants import ANGLE_TYPE_DICT
 
 
 class AngleType(Potential):
@@ -18,6 +20,8 @@ class AngleType(Potential):
     independent vars : set of str
         See `Potential` documentation for more information
     member_types : list of topology.AtomType.name (str)
+    topology: topology.core.Topology, the topology of which this angle_type is a part of, default=None
+    set_ref: (str), the string name of the bookkeeping set in topology class.
 
     Notes
     ----
@@ -30,45 +34,51 @@ def __init__(self,
                  expression='0.5 * k * (theta-theta_eq)**2',
                  parameters=None,
                  independent_variables=None,
-                 member_types=None):
+                 member_types=None,
+                 topology=None):
         if parameters is None:
             parameters = {
-                     'k': 1000 * u.Unit('kJ / (deg**2)'),
-                     'theta_eq': 180 * u.deg
-                 }
+                'k': 1000 * u.Unit('kJ / (deg**2)'),
+                'theta_eq': 180 * u.deg
+            }
         if independent_variables is None:
             independent_variables = {'theta'}
 
         if member_types is None:
             member_types = list()
-
         super(AngleType, self).__init__(name=name, expression=expression,
-                parameters=parameters, independent_variables=independent_variables)
-
+                                        parameters=parameters, independent_variables=independent_variables,
+                                        topology=topology)
         self._member_types = _validate_three_member_type_names(member_types)
+        self._set_ref = ANGLE_TYPE_DICT
+
+    @property
+    def set_ref(self):
+        return self._set_ref
 
     @property
     def member_types(self):
         return self._member_types
 
     @member_types.setter
+    @confirm_dict_existence
     def member_types(self, val):
         if self.member_types != val:
             warnings.warn("Changing an AngleType's constituent "
-                    "member types: {} to {}".format(self.member_types, val))
+                          "member types: {} to {}".format(self.member_types, val))
         self._member_types = _validate_three_member_type_names(val)
 
     def __repr__(self):
         return "<AngleType {}, id {}>".format(self.name, id(self))
 
+
 def _validate_three_member_type_names(types):
     """Ensure 3 partners are involved in AngleType"""
     if len(types) != 3 and len(types) != 0:
         raise TopologyError("Trying to create an AngleType "
-                "with {} constituent types". format(len(types)))
+                            "with {} constituent types".format(len(types)))
     if not all([isinstance(t, str) for t in types]):
         raise TopologyError("Types passed to AngleType "
                             "need to be strings corresponding to AtomType names")
 
     return types
-

topology/core/atom_type.py

@@ -1,9 +1,10 @@
 import warnings
 import unyt as u
 
-from topology.utils.testing import allclose
 from topology.core.potential import Potential
 from topology.utils.misc import unyt_to_hashable
+from topology.utils.decorators import confirm_dict_existence
+from topology.utils._constants import ATOM_TYPE_DICT
 
 
 class AtomType(Potential):
@@ -45,6 +46,8 @@ class AtomType(Potential):
         Set of other atom types that this atom type overrides
     definition : str
         SMARTS string defining this atom type
+    topology: topology.core.Topology, the topology of which this atom_type is a part of, default=None
+    set_ref: (str), the string name of the bookkeeping set in topology class.
 
     """
 
@@ -56,7 +59,8 @@ def __init__(self,
                  parameters=None,
                  independent_variables=None,
                  atomclass='', doi='', overrides=None, definition='',
-                 description=''):
+                 description='',
+                 topology=None):
         if parameters is None:
             parameters = {'sigma': 0.3 * u.nm,
                           'epsilon': 0.3 * u.Unit('kJ')}
@@ -70,22 +74,28 @@ def __init__(self,
             name=name,
             expression=expression,
             parameters=parameters,
-            independent_variables=independent_variables)
+            independent_variables=independent_variables,
+            topology=topology)
         self._mass = _validate_mass(mass)
         self._charge = _validate_charge(charge)
         self._atomclass = _validate_str(atomclass)
         self._doi = _validate_str(doi)
         self._overrides = _validate_set(overrides)
         self._description = _validate_str(description)
         self._definition = _validate_str(definition)
-
+        self._set_ref = ATOM_TYPE_DICT
         self._validate_expression_parameters()
 
+    @property
+    def set_ref(self):
+        return self._set_ref
+
     @property
     def charge(self):
         return self._charge
 
     @charge.setter
+    @confirm_dict_existence
     def charge(self, val):
         self._charge = _validate_charge(val)
 
@@ -94,6 +104,7 @@ def mass(self):
         return self._mass
 
     @mass.setter
+    @confirm_dict_existence
     def mass(self, val):
         self._mass = _validate_mass(val)
 
@@ -102,6 +113,7 @@ def atomclass(self):
         return self._atomclass
 
     @atomclass.setter
+    @confirm_dict_existence
     def atomclass(self, val):
         self._atomclass = val
 
@@ -110,6 +122,7 @@ def doi(self):
         return self._doi
 
     @doi.setter
+    @confirm_dict_existence
     def doi(self, doi):
         self._doi = _validate_str(doi)
 
@@ -118,6 +131,7 @@ def overrides(self):
         return self._overrides
 
     @overrides.setter
+    @confirm_dict_existence
     def overrides(self, overrides):
         self._overrides = _validate_set(overrides)
 
@@ -126,6 +140,7 @@ def description(self):
         return self._description
 
     @description.setter
+    @confirm_dict_existence
     def description(self, description):
         self._description = _validate_str(description)
 
@@ -134,6 +149,7 @@ def definition(self):
         return self._definition
 
     @definition.setter
+    @confirm_dict_existence
     def definition(self, definition):
         self._definition = _validate_str(definition)
 
@@ -185,11 +201,13 @@ def _validate_mass(mass):
 
     return mass
 
+
 def _validate_str(val):
     if not isinstance(val, str):
         raise ValueError("Passed value {} is not a string".format(val))
     return val
 
+
 def _validate_set(val):
     if not isinstance(val, set):
         raise ValueError("Passed value {} is not a set".format(val))

topology/core/bond.py

@@ -23,35 +23,19 @@ class Bond(Connection):
 
     def __init__(self, connection_members=None, connection_type=None, name="Bond"):
         if connection_members is None:
-            connection_members = list()
+            connection_members = tuple()
         connection_members = _validate_two_partners(connection_members)
         connection_type = _validate_bondtype(connection_type)
 
         super(Bond, self).__init__(connection_members=connection_members,
                 connection_type=connection_type, name=name)
 
-    def __eq__(self, other):
-        return hash(self) == hash(other)
-
-    def __hash__(self):
-        if self.connection_type:
-            return hash(
-                tuple(
-                    (
-                        self.name,
-                        self.connection_type,
-                        tuple(self.connection_members),
-                    )
-                )
-            )
-        return hash(tuple(self.connection_members))
 
 def _validate_two_partners(connection_members):
     """Ensure 2 partners are involved in Bond"""
     if len(connection_members) != 2:
         raise TopologyError("Trying to create a Bond "
                 "with {} connection members". format(len(connection_members)))
-
     return connection_members
 
 

topology/core/bond_type.py

@@ -1,7 +1,10 @@
 import unyt as u
+import warnings
 
 from topology.core.potential import Potential
+from topology.utils.decorators import confirm_dict_existence
 from topology.exceptions import TopologyError
+from topology.utils._constants import BOND_TYPE_DICT
 
 
 class BondType(Potential):
@@ -29,45 +32,53 @@ def __init__(self,
                  expression='0.5 * k * (r-r_eq)**2',
                  parameters=None,
                  independent_variables=None,
-                 member_types=None):
+                 member_types=None,
+                 topology=None,
+                 set_ref='bond_type_set'):
         if parameters is None:
             parameters = {
-                     'k': 1000 * u.Unit('kJ / (nm**2)'),
-                     'r_eq': 0.14 * u.nm
-                 }
+                'k': 1000 * u.Unit('kJ / (nm**2)'),
+                'r_eq': 0.14 * u.nm
+            }
         if independent_variables is None:
             independent_variables = {'r'}
 
         if member_types is None:
             member_types = list()
 
         super(BondType, self).__init__(name=name, expression=expression,
-                parameters=parameters, independent_variables=independent_variables)
-
+                                       parameters=parameters, independent_variables=independent_variables,
+                                       topology=topology)
+        self._set_ref = BOND_TYPE_DICT
         self._member_types = _validate_two_member_type_names(member_types)
 
+    @property
+    def set_ref(self):
+        return self._set_ref
+
     @property
     def member_types(self):
         return self._member_types
 
     @member_types.setter
+    @confirm_dict_existence
     def member_types(self, val):
         if self.member_types != val:
             warnings.warn("Changing a BondType's constituent "
-                    "member types: {} to {}".format(self.member_types, val))
+                          "member types: {} to {}".format(self.member_types, val))
         self._member_types = _validate_two_member_type_names(val)
 
     def __repr__(self):
         return "<BondType {}, id {}>".format(self.name, id(self))
 
+
 def _validate_two_member_type_names(types):
     """Ensure 2 partners are involved in BondType"""
     if len(types) != 2 and len(types) != 0:
         raise TopologyError("Trying to create a BondType "
-                "with {} constituent types". format(len(types)))
+                            "with {} constituent types".format(len(types)))
     if not all([isinstance(t, str) for t in types]):
         raise TopologyError("Types passed to BondType "
                             "need to be strings corresponding to AtomType names")
 
     return types
-