Merge pull request #750 from openforcefield/rmin-half-sigma

Fix missing sigma/rmin_half attrs

.github/workflows/CI.yml

@@ -134,7 +134,7 @@ jobs:
         if: ${{ matrix.cfg.rdkit == 'true' && matrix.cfg.openeye == 'TRUE' }}
         continue-on-error: true
         run: |
-          pytest -r fE -tb=short openforcefield/tests/test_links.py
+          pytest -r fE --tb=short openforcefield/tests/test_links.py
 
       - name: Run unit tests
         shell: bash -l {0}

docs/releasehistory.rst

@@ -22,7 +22,6 @@ API-breaking changes
   there are no special behaviors that are accessed in the case of partially-licensed OpenEye backends. The
   new behavior of this method is the same as if the default value above is always provided.
 
-
 New features
 """"""""""""
 - `PR #751 <https://github.com/openforcefield/openforcefield/pull/751>`_: Adds
@@ -40,21 +39,24 @@ New features
   to look up individual :py:class:`ParameterType <openforcefield.typing.engines.smirnoff.parameters.ParameterType>`
   objects.
 
-Behavior changed
-""""""""""""""""
-- `PR #753 <https://github.com/openforcefield/openforcefield/pull/753>`_: ``ParameterLookupError``
-  is now raised when passing to
-  :py:meth:`ParameterList.index <openforcefield.typing.engines.smirnoff.parameters.ParameterList>`
-  a SMIRKS pattern not found in the parameter list.
-
 Bugfixes
 """"""""
 - `PR #745 <https://github.com/openforcefield/openforcefield/pull/745>`_: Fixes bug when
   serializing molecule with conformers to JSON.
+- `PR #750 <https://github.com/openforcefield/openforcefield/pull/750>`_: Fixes a bug causing either
+  ``sigma`` or ``rmin_half`` to sometimes be missing on
+  :py:class:`vdWHandler.vdWType <openforcefield.typing.engines.smirnoff.parameters.vdWHandler>`
+  objects.
 - `PR #756 <https://github.com/openforcefield/openforcefield/pull/756>`_: Fixes bug when running
   :py:meth:`vdWHandler.create_force <openforcefield.typing.engines.smirnoff.parameters.vdWHandler.create_force>`
   using a ``vdWHandler`` that was initialized using the API.
 
+Behavior changed
+""""""""""""""""
+- `PR #753 <https://github.com/openforcefield/openforcefield/pull/753>`_: ``ParameterLookupError``
+  is now raised when passing to
+  :py:meth:`ParameterList.index <openforcefield.typing.engines.smirnoff.parameters.ParameterList>`
+  a SMIRKS pattern not found in the parameter list.
 
 
 0.8.0 - Virtual Sites

openforcefield/tests/test_parameters.py

@@ -1728,6 +1728,41 @@ def test_create_force_defaults(self):
         vdw_handler.create_force(omm_sys, topology)
 
 
+class TestvdWType:
+    """
+    Test the behavior of vdWType
+    """
+
+    def test_sigma_rmin_half(self):
+        """Test the setter/getter behavior or sigma and rmin_half"""
+        from openforcefield.typing.engines.smirnoff.parameters import vdWHandler
+
+        data = {
+            "smirks": "[*:1]",
+            "sigma": 0.5 * unit.angstrom,
+            "epsilon": 0.5 * unit.kilocalorie_per_mole,
+        }
+        param = vdWHandler.vdWType(**data)
+
+        assert param.sigma is not None
+        assert param.rmin_half is not None
+        assert param.sigma == param.rmin_half / 2 ** (1 / 6)
+        assert "sigma" in param.to_dict()
+        assert "rmin_half" not in param.to_dict()
+
+        param.sigma = 0.8 * unit.angstrom
+
+        assert param.sigma == param.rmin_half / 2 ** (1 / 6)
+        assert "sigma" in param.to_dict()
+        assert "rmin_half" not in param.to_dict()
+
+        param.rmin_half = 0.8 * unit.angstrom
+
+        assert param.sigma == param.rmin_half / 2 ** (1 / 6)
+        assert "sigma" not in param.to_dict()
+        assert "rmin_half" in param.to_dict()
+
+
 class TestVirtualSiteHandler:
     """
     Test the creation of a VirtualSiteHandler and the implemented VirtualSiteTypes

openforcefield/typing/engines/smirnoff/parameters.py

@@ -1066,7 +1066,7 @@ def _process_indexed_attributes(self, smirnoff_data, indexed_attr_lengths=None):
 
         return smirnoff_data
 
-    def to_dict(self, discard_cosmetic_attributes=False):
+    def to_dict(self, discard_cosmetic_attributes=False, duplicate_attributes=None):
         """
         Convert this object to dict format.
 
@@ -1078,6 +1078,9 @@ def to_dict(self, discard_cosmetic_attributes=False):
         ----------
         discard_cosmetic_attributes : bool, optional. Default = False
             Whether to discard non-spec attributes of this object
+        duplicate_attributes : list of string, optional. Default = None
+            A list of names of attributes that redundantly decsribe
+            data and should be discarded during serializaiton
 
         Returns
         -------
@@ -1090,6 +1093,10 @@ def to_dict(self, discard_cosmetic_attributes=False):
         # optional attributes that are set to None defaults.
         attribs_to_return = list(self._get_defined_parameter_attributes().keys())
 
+        if duplicate_attributes is not None:
+            for duplicate in duplicate_attributes:
+                attribs_to_return.pop(attribs_to_return.index(duplicate))
+
         # Start populating a dict of the attribs.
         indexed_attribs = set(self._get_indexed_parameter_attributes().keys())
         mapped_attribs = set(self._get_mapped_parameter_attributes().keys())
@@ -3496,6 +3503,31 @@ def __init__(self, **kwargs):
 
             super().__init__(**kwargs)
 
+            if sigma:
+                self._extra_nb_var = "rmin_half"
+            if rmin_half:
+                self._extra_nb_var = "sigma"
+
+        def __setattr__(self, name, value):
+            super().__setattr__(key=name, value=value)
+            if name == "rmin_half":
+                super().__setattr__("sigma", value / 2 ** (1 / 6))
+                self._extra_nb_var = "sigma"
+
+            if name == "sigma":
+                super().__setattr__("rmin_half", value * 2 ** (1 / 6))
+                self._extra_nb_var = "rmin_half"
+
+        def to_dict(
+            self,
+            discard_cosmetic_attributes=False,
+            duplicate_attributes=None,
+        ):
+            return super().to_dict(
+                discard_cosmetic_attributes=discard_cosmetic_attributes,
+                duplicate_attributes=[self._extra_nb_var],
+            )
+
     _TAGNAME = "vdW"  # SMIRNOFF tag name to process
     _INFOTYPE = vdWType  # info type to store
     # _KWARGS = ['ewaldErrorTolerance',
@@ -5066,6 +5098,11 @@ def __init__(self, **kwargs):
 
             super().__init__(**kwargs)
 
+            if sigma:
+                self._extra_nb_var = "rmin_half"
+            if rmin_half:
+                self._extra_nb_var = "sigma"
+
         # @type.converter
         # def type(self, attr, vsite_type):
         #     """
@@ -5203,6 +5240,7 @@ def _add_virtual_site(self, fn, atoms, orientations, *args, **kwargs):
                 "replace": kwargs.pop("replace", False),
             }
             kwargs.update(base_args)
+            kwargs.pop(self._extra_nb_var)
 
             return fn(*args, **kwargs)