Merge branch 'master' into deregister-toolkit

docs/releasehistory.rst

@@ -7,6 +7,28 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+0.7.1 - Current development
+---------------------------
+
+Bugfixes
+""""""""
+- `PR #634 <https://github.com/openforcefield/openforcefield/pull/634>`_: Fixes a bug in which calling 
+  :py:meth:`RDKitToolkitWrapper.from_file <openforcefield.utils.toolkits.RDKitToolkitWrapper.from_file>` directly
+  would not load files correctly if passed lowercase `file_format`. Note that this bug did not occur when calling
+  :`Molecule.from_file` <openforcefield.topology.molecule.Molecule.from_file>`.
+- `PR #631 <https://github.com/openforcefield/openforcefield/pull/631>`_: Fixes a bug in which calling
+  :py:meth:`openforcefield.utils.utils.utils.unit_to_string <openforcefield.utils.utils.unit_to_string>` returned
+  ``None`` when the unit is dimensionless. Now ``"dimensionless"`` is returned.
+- `PR #630 <https://github.com/openforcefield/openforcefield/pull/630>`_: Closes issue `Issue #629 
+  <https://github.com/openforcefield/openforcefield/issues/629>`_ in which the wrong exception is raised when
+  attempting to instantiate a ``ForceField`` from an unparsable string.
+
+New features
+""""""""""""
+- `PR #632 <https://github.com/openforcefield/openforcefield/pull/632>`_: Adds
+  :py:meth:`ForceField.registered_parameter_handlers 
+  <openforcefield.typing.engines.smirnoff.forcefield.ForceField.registered_parameter_handlers>`
+
 0.7.0 - Charge Increment Model, Proper Torsion interpolation, and new Molecule methods
 --------------------------------------------------------------------------------------
 

openforcefield/tests/test_forcefield.py

@@ -617,6 +617,12 @@ def test_create_forcefield_from_file(self):
         assert len(forcefield._parameter_handlers['ImproperTorsions']._parameters) == 4
         assert len(forcefield._parameter_handlers['vdW']._parameters) == 35
 
+    def test_load_bad_string(self):
+        with pytest.raises(IOError) as exception_info:
+            ForceField('1234')
+        assert 'Source 1234 could not be read.' in str(exception_info.value)
+        assert 'syntax error' in str(exception_info.value)
+
     @pytest.mark.skip(reason='Needs to be updated for 0.2.0 syntax')
     def test_create_forcefield_from_file_list(self):
         # These offxml files are located in package data path, which is automatically installed and searched
@@ -1211,6 +1217,26 @@ def test_nonbonded_method_resolution(self,
                 forcefield.get_parameter_handler('Electrostatics', {}).method = electrostatics_method
                 omm_system = forcefield.create_openmm_system(topology)
 
+    def test_registered_parameter_handlers(self):
+        """Test registered_parameter_handlers property"""
+        forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')
+        registered_handlers = forcefield.registered_parameter_handlers
+
+        expected_handlers = [
+            'Bonds',
+            'Angles',
+            'ProperTorsions',
+            'ImproperTorsions',
+            'vdW',
+            'Electrostatics',
+            'ToolkitAM1BCC',
+        ]
+
+        for expected_handler in expected_handlers:
+            assert expected_handler in registered_handlers
+
+        assert 'LibraryChrages' not in registered_handlers
+
     def test_parameter_handler_lookup(self):
         """Ensure __getitem__ lookups work"""
         forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')

openforcefield/tests/test_toolkits.py

@@ -469,6 +469,21 @@ def test_load_multiconformer_sdf_as_separate_molecules_properties(self):
         np.testing.assert_allclose(molecules[1].partial_charges / unit.elementary_charge,
                                    [0.027170, 0.027170, 0.027170, 0.027170, -0.108680])
 
+    @pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), reason='OpenEye Toolkit not available')
+    def test_file_extension_case(self):
+        """
+        Test round-trips of some file extensions when called directly from the toolkit wrappers,
+        including lower- and uppercase file extensions. Note that this test does not ensure
+        accuracy, it only tests that reading/writing without raising an exception.
+        """
+        mols_in = OpenEyeToolkitWrapper().from_file(file_path=get_data_file_path('molecules/ethanol.sdf'), file_format='sdf')
+
+        assert len(mols_in) > 0
+
+        mols_in = OpenEyeToolkitWrapper().from_file(file_path=get_data_file_path('molecules/ethanol.sdf'), file_format='SDF')
+
+        assert len(mols_in) > 0
+
     @pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), reason='OpenEye Toolkit not available')
     def test_write_sdf_charges(self):
         """Test OpenEyeToolkitWrapper for writing partial charges to a sdf file"""
@@ -1397,7 +1412,22 @@ def test_to_from_rdkit_core_props_unset(self):
         assert molecule2.partial_charges is None
 
         assert molecule2.to_smiles(toolkit_registry=toolkit_wrapper) == expected_output_smiles
-
+
+    @pytest.mark.skipif(not RDKitToolkitWrapper.is_available(), reason='RDKit Toolkit not available')
+    def test_file_extension_case(self):
+        """
+        Test round-trips of some file extensions when called directly from the toolkit wrappers,
+        including lower- and uppercase file extensions. Note that this test does not ensure
+        accuracy, it only tests that reading/writing without raising an exception.
+        """
+        mols_in = RDKitToolkitWrapper().from_file(file_path=get_data_file_path('molecules/ethanol.sdf'), file_format='sdf')
+
+        assert len(mols_in) > 0
+
+        mols_in = RDKitToolkitWrapper().from_file(file_path=get_data_file_path('molecules/ethanol.sdf'), file_format='SDF')
+
+        assert len(mols_in) > 0
+
     @pytest.mark.skipif(not RDKitToolkitWrapper.is_available(), reason='RDKit Toolkit not available')
     def test_get_sdf_coordinates(self):
         """Test RDKitToolkitWrapper for importing a single set of coordinates from a sdf file"""

openforcefield/tests/test_utils.py

@@ -71,3 +71,11 @@ def test_ast_eval(unit_string, expected_unit):
     ast_root_node = ast.parse(unit_string, mode='eval').body
     parsed_units = _ast_eval(ast_root_node)
     assert parsed_units == expected_unit
+
+def test_dimensionless_units():
+    assert utils.string_to_unit('dimensionless') == unit.dimensionless
+
+    unit_string = utils.unit_to_string(unit.dimensionless)
+    unit_value = utils.string_to_unit(unit_string)
+
+    assert unit_value == unit.dimensionless

openforcefield/typing/engines/smirnoff/forcefield.py

@@ -556,6 +556,19 @@ def register_parameter_io_handler(self, parameter_io_handler):
                     self._parameter_io_handlers[io_format]))
         self._parameter_io_handlers[io_format] = parameter_io_handler
 
+    @property
+    def registered_parameter_handlers(self):
+        """
+        Return the list of registered parameter handlers by name
+
+        .. warning :: This API is experimental and subject to change.
+
+        Returns
+        -------
+            registered_parameter_handlers: iterable of names of ParameterHandler objects in this ForceField
+
+        """
+        return [*self._parameter_handlers.keys()]
 
     # TODO: Do we want to make this optional?
 
@@ -970,14 +983,14 @@ def parse_smirnoff_from_source(self, source):
                 smirnoff_data = parameter_io_handler.parse_file(source)
                 return smirnoff_data
             except ParseError as e:
-                exception_msg = str(e)
+                exception_msg = e.msg
             except (FileNotFoundError, OSError):
                 # If this is not a file path or a file handle, attempt parsing as a string.
                 try:
                     smirnoff_data = parameter_io_handler.parse_string(source)
                     return smirnoff_data
                 except ParseError as e:
-                    exception_msg = str(e)
+                    exception_msg = e.msg
 
         # If we haven't returned by now, the parsing was unsuccessful
         valid_formats = [

openforcefield/typing/engines/smirnoff/io.py

@@ -204,7 +204,7 @@ def parse_string(self, data):
             smirnoff_data = xmltodict.parse(data, attr_prefix='')
             return smirnoff_data
         except ExpatError as e:
-            raise ParseError(e)
+            raise ParseError(str(e))
 
     def to_file(self, file_path, smirnoff_data):
         """Write the current forcefield parameter set to a file.

openforcefield/utils/toolkits.py

@@ -677,7 +677,7 @@ def to_file(self, molecule, file_path, file_format):
         from openeye import oechem
         oemol = self.to_openeye(molecule)
         ofs = oechem.oemolostream(file_path)
-        openeye_format = getattr(oechem, 'OEFormat_' + file_format)
+        openeye_format = getattr(oechem, 'OEFormat_' + file_format.upper())
         ofs.SetFormat(openeye_format)
 
         # OFFTK strictly treats SDF as a single-conformer format.
@@ -2364,6 +2364,9 @@ def from_file(self,
 
         """
         from rdkit import Chem
+
+        file_format = file_format.upper()
+
         mols = list()
         if (file_format == 'MOL') or (file_format == 'SDF'):
             for rdmol in Chem.SupplierFromFilename(file_path, removeHs=False, sanitize=False, strictParsing=True):

openforcefield/utils/utils.py

@@ -146,6 +146,8 @@ def unit_to_string(input_unit):
         The serialized unit.
     """
 
+    if input_unit == unit.dimensionless:
+        return "dimensionless"
 
     # Decompose output_unit into a tuples of (base_dimension_unit, exponent)
     unit_string = None