add methods to deal with reading free energy information.

solventmapcreator/io/solvationenergyreader.py

@@ -13,6 +13,14 @@ logging.basicConfig()
 LOGGER = logging.getLogger(__name__)
 LOGGER.setLevel(logging.WARN)
 
+def parse_free_energy_from_file_with_data_arrays(filename):
+    """This reads in the information form file to a Datapoints object, and
+    creates the data arrays.
+    """
+    datapoints = parse_free_energy_from_file(filename)
+    datapoints.createDataArrays()
+    return datapoints
+
 def parse_binding_energy_from_file_with_data_arrays(filename):
     """This reads in the information form file to a Datapoints object, and
     creates the data arrays.
@@ -21,16 +29,33 @@ def parse_binding_energy_from_file_with_data_arrays(filename):
     datapoints.createDataArrays()
     return datapoints
 
+def parse_free_energy_from_file(filename):
+    """This parses the file and returns a datapoints representation of it.
+    """
+    solvation_energy_dict = parse_free_energy_info(filename)
+    return create_free_energy_datapoints_with_values(solvation_energy_dict)
+
 def parse_binding_energy_from_file(filename):
     """This parses the file and returns a datapoints representation of it.
     """
     solvation_energy_dict = parse_binding_energy_info(filename)
     return create_binding_datapoints_with_values(solvation_energy_dict)
+
+def create_free_energy_datapoints_with_values(solvation_energy_dict):
+    """This creates free energy datapoints.
+    """
+    return solvationreader.create_free_energy_datapoints_with_values(solvation_energy_dict)
+
 def create_binding_datapoints_with_values(solvation_energy_dict):
     """This creates binding datapoints
     """
     return solvationreader.create_binding_datapoints_with_values(solvation_energy_dict)
 
+def parse_free_energy_info(filename):
+    """This extracts the solvation information to a dictionary.
+    """
+    return solvationreader.parse_free_energy_info(filename)
+
 def parse_binding_energy_info(filename):
     """This extracts the solvation information to a dictionary.
     """

solventmapcreator/test/iotest/solvationenergyreadertest.py

@@ -25,20 +25,39 @@ class SolvationEnergyReaderTestCase(unittest.TestCase):
     def setUp(self):
         """Set up for tests
         """
-        self.solvation_info_dict = solvationenergyreader.parse_binding_energy_info("resources/energyvaluestest.xml")
+        self.solvation_binding_info_dict = solvationenergyreader.parse_binding_energy_info("resources/energyvaluestest.xml")
+        self.solvation_free_info_dict = solvationenergyreader.parse_free_energy_info("resources/energyvaluestest2.xml")
         self.expected_datapoints = Datapoints(("SSIP Value","Solvation Binding Energy"), (Units.dimensionless, Units.kj_per_mol))
         self.expected_datapoints.addDatapoint(Datapoint(Value(-14.100, "SSIP Value",
                                                               Units.dimensionless),
                                                         Value(-34.8195308084233,
                                                               "Solvation Binding Energy", Units.kj_per_mol),
                                                               "-14.100solute"))
+        self.expected_free_energy_datapoints = Datapoints(("SSIP Value","Solvation Free Energy"),
+                                                          (Units.dimensionless, Units.kj_per_mol))
+        self.expected_free_energy_datapoints.addDatapoint(Datapoint(Value(-14.100, "SSIP Value",
+                                                              Units.dimensionless),
+                                                          Value(-34.8195308084233,
+                                                                "Solvation Free Energy", Units.kj_per_mol),
+                                                                "-14.100solute"))
     def tearDown(self):
         """Tear down after tests.
         """
-        del self.solvation_info_dict
+        del self.solvation_binding_info_dict
+        del self.solvation_free_info_dict
         del self.expected_datapoints
+        del self.expected_free_energy_datapoints
+    def test_parse_free_energy_from_file_with_data_arrays(self):
+        """Test to see if expected datapoints and arrays are produced.
+        """
+        actual_datapoints = solvationenergyreader.parse_free_energy_from_file_with_data_arrays("resources/energyvaluestest2.xml")
+        self.assertEqual(self.expected_free_energy_datapoints, actual_datapoints)
+        np.testing.assert_array_almost_equal(np.array([[-14.100]]),
+                                             actual_datapoints.x_values)
+        np.testing.assert_array_almost_equal(np.array([[-34.8195308084233]]),
+                                             actual_datapoints.y_values)
     def test_parse_binding_energy_from_file_with_data_arrays(self):
-        """Test to see if 
+        """Test to see if expected datapoints and arrays are produced.
         """
         actual_datapoints = solvationenergyreader.parse_binding_energy_from_file_with_data_arrays("resources/energyvaluestest.xml")
         self.assertEqual(self.expected_datapoints, actual_datapoints)
@@ -46,24 +65,50 @@ class SolvationEnergyReaderTestCase(unittest.TestCase):
                                              actual_datapoints.x_values)
         np.testing.assert_array_almost_equal(np.array([[-34.8195308084233]]),
                                              actual_datapoints.y_values)
+    def test_parse_free_energy_from_file(self):
+        """Test to see if expected Datapoints object is created from reading of
+        a file.
+        """
+        actual_datapoints = solvationenergyreader.parse_free_energy_from_file("resources/energyvaluestest2.xml")
+        self.assertEqual(self.expected_free_energy_datapoints, actual_datapoints)
     def test_parse_binding_energy_from_file(self):
         """Test to see if expected Datapoints object is created from reading of
         a file.
         """
         actual_datapoints = solvationenergyreader.parse_binding_energy_from_file("resources/energyvaluestest.xml")
         self.assertEqual(self.expected_datapoints, actual_datapoints)
+    def test_create_free_energy_datapoints_with_values(self):
+        """Test to see if expected Datapoints object is created.
+        """
+        actual_datapoints = solvationenergyreader.create_free_energy_datapoints_with_values(self.solvation_free_info_dict)
+        self.assertEqual(self.expected_free_energy_datapoints, actual_datapoints)
     def test_create_binding_datapoints_with_values(self):
         """Test to see if expected Datapoints object is created.
         """
-        actual_datapoints = solvationenergyreader.create_binding_datapoints_with_values(self.solvation_info_dict)
+        actual_datapoints = solvationenergyreader.create_binding_datapoints_with_values(self.solvation_binding_info_dict)
         self.assertEqual(self.expected_datapoints, actual_datapoints)
+    def test_parse_free_energy_info(self):
+        """Test to see if expected free energy values are extracted from file.
+        """
+        expected_dict = {"total_energy": -34.8195308084233, "value_type":"MOLEFRACTION",
+                         "to_solvent_id":"water", "from_solvent_id":"",
+                         "stdinchikey":"-14.100solute"}
+        actual_dict_dict = self.solvation_free_info_dict
+        self.assertListEqual(["-14.100solute"], sorted(actual_dict_dict.keys()))
+        actual_dict = actual_dict_dict["-14.100solute"]
+        self.assertListEqual(sorted(expected_dict.keys()), sorted(actual_dict.keys()))
+        for key, value in expected_dict.items():
+            if key == "total_energy":
+                self.assertAlmostEqual(value, actual_dict[key])
+            else:
+                self.assertEqual(value, actual_dict[key])
     def test_parse_binding_energy_info(self):
         """Test to see if expected free energy values are extracted from file.
         """
         expected_dict = {"total_energy": -34.8195308084233, "value_type":"MOLEFRACTION",
                          "to_solvent_id":"water", "from_solvent_id":"",
                          "stdinchikey":"-14.100solute"}
-        actual_dict_dict = solvationenergyreader.parse_binding_energy_info("resources/energyvaluestest.xml")
+        actual_dict_dict = self.solvation_binding_info_dict
         self.assertListEqual(["-14.100solute"], sorted(actual_dict_dict.keys()))
         actual_dict = actual_dict_dict["-14.100solute"]
         self.assertListEqual(sorted(expected_dict.keys()), sorted(actual_dict.keys()))

solventmapcreator/test/resources/energyvaluestest2.xml

+<?xml version='1.0' encoding='UTF-8'?>
+<phase:EnergyValues xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema">
+  <phase:FreeEnergyCollection><phase:FreeEnergy phase:moleculeID="-14.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+        <phase:TotalEnergy>-34.8195308084233</phase:TotalEnergy>
+            <phase:EnergyContributions>
+                <phase:EnergyContribution phase:ssipID="1">-34.8195308084233</phase:EnergyContribution>
+            </phase:EnergyContributions>
+        </phase:FreeEnergy>
+  </phase:FreeEnergyCollection>
+</phase:EnergyValues>