From 4d42c4b52ee34289d3544502583766aea79fa350 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Mon, 3 Jul 2017 18:10:40 +0100
Subject: [PATCH] created test suite, and created script for the reading in of
information to a Datapoints object, with the arrays initialised.
---
solventmapcreator/io/solvationenergyreader.py | 38 ++++++++++
.../test/iotest/solvationenergyreadertest.py | 74 +++++++++++++++++++
.../test/solvationmapcreatortests.py | 35 +++++++++
3 files changed, 147 insertions(+)
create mode 100644 solventmapcreator/io/solvationenergyreader.py
create mode 100644 solventmapcreator/test/iotest/solvationenergyreadertest.py
create mode 100644 solventmapcreator/test/solvationmapcreatortests.py
diff --git a/solventmapcreator/io/solvationenergyreader.py b/solventmapcreator/io/solvationenergyreader.py
new file mode 100644
index 0000000..bda2ad6
--- /dev/null
+++ b/solventmapcreator/io/solvationenergyreader.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for the reading in of solvation energies for a given solvent.
+
+@author: mark
+"""
+
+import logging
+import resultsanalysis.fileparsing.xmlparsing.solvationreader as solvationreader
+
+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 Dapoints object, and
+ creates the data arrays.
+ """
+ datapoints = parse_free_energy_from_file(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_datapoints_with_values(solvation_energy_dict)
+
+def create_datapoints_with_values(solvation_energy_dict):
+ """
+ """
+ return solvationreader.create_datapoints_with_values(solvation_energy_dict)
+
+def parse_free_energy_info(filename):
+ """This extracts the slvation information to a dictionary.
+ """
+ return solvationreader.parse_free_energy_info(filename)
diff --git a/solventmapcreator/test/iotest/solvationenergyreadertest.py b/solventmapcreator/test/iotest/solvationenergyreadertest.py
new file mode 100644
index 0000000..6ed2665
--- /dev/null
+++ b/solventmapcreator/test/iotest/solvationenergyreadertest.py
@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script containing tests for the solvationenergyreader module.
+
+@author: mark
+"""
+
+import logging
+import unittest
+import numpy as np
+import solventmapcreator.io.solvationenergyreader as solvationenergyreader
+from resultsanalysis.dataclasses.datapoints import Datapoints
+from resultsanalysis.dataclasses.datapoint import Datapoint
+from resultsanalysis.dataclasses.units import Units
+from resultsanalysis.dataclasses.value import Value
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class SolvationEnergyReaderTestCase(unittest.TestCase):
+ """Test Case for the solvationenergyreader module.
+ """
+ def setUp(self):
+ """Set up for tests
+ """
+ self.solvation_info_dict = solvationenergyreader.parse_free_energy_info("resources/energyvaluestest.xml")
+ self.expected_datapoints = Datapoints(("ssip",""), (Units.dimensionless, Units.kj_per_mol))
+ self.expected_datapoints.addDatapoint(Datapoint(Value(-14.100, "ssip",
+ Units.dimensionless),
+ Value(-34.8195308084233,
+ "", Units.kj_per_mol),
+ "-14.100solute"))
+ def tearDown(self):
+ """Tear down after tests.
+ """
+ del self.solvation_info_dict
+ del self.expected_datapoints
+ def test_parse_free_energy_from_file_with_data_arrays(self):
+ """Test to see if
+ """
+ actual_datapoints = solvationenergyreader.parse_free_energy_from_file_with_data_arrays("resources/energyvaluestest.xml")
+ self.assertEqual(self.expected_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_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/energyvaluestest.xml")
+ self.assertEqual(self.expected_datapoints, actual_datapoints)
+ def test_create_datapoints_with_values(self):
+ """Test to see if expected Datapoints object is created.
+ """
+ actual_datapoints = solvationenergyreader.create_datapoints_with_values(self.solvation_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 = solvationenergyreader.parse_free_energy_info("resources/energyvaluestest.xml")
+ 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])
\ No newline at end of file
diff --git a/solventmapcreator/test/solvationmapcreatortests.py b/solventmapcreator/test/solvationmapcreatortests.py
new file mode 100644
index 0000000..6a71d92
--- /dev/null
+++ b/solventmapcreator/test/solvationmapcreatortests.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for running the tests.
+
+@author: mark
+"""
+
+import logging
+import unittest
+from solventmapcreator.test.iotest.solvationenergyreadertest import SolvationEnergyReaderTestCase
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+IO_TEST_CASES = [SolvationEnergyReaderTestCase]
+
+def test_suite():
+ """Function creates a test suite and then loads all the tests from the
+ different test cases.
+ """
+ LOGGER.info("setting up loader and test suite")
+ loader = unittest.TestLoader()
+ suite = unittest.TestSuite()
+ for test_case in IO_TEST_CASES:
+ LOGGER.debug("Adding %s", test_case)
+ suite.addTests(loader.loadTestsFromTestCase(test_case))
+ return suite
+
+if __name__ == '__main__':
+ LOGGER.info("calling test suite method")
+ SUITE = test_suite()
+ LOGGER.info("running test suite")
+ unittest.TextTestRunner(verbosity=2).run(SUITE)
--
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