From fcea2c825bfb1ad24682ef7a2b7a1e85e7250cc6 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Mon, 26 Mar 2018 20:49:34 +0100
Subject: [PATCH] added methods for writing to file after extracting the
required values, and updated tests.
---
.../io/solvationenergyextraction.py | 27 +++++++++
.../iotest/solvationenergyextractiontest.py | 55 ++++++++++++++++---
2 files changed, 74 insertions(+), 8 deletions(-)
diff --git a/solventmapcreator/io/solvationenergyextraction.py b/solventmapcreator/io/solvationenergyextraction.py
index 0291cc8..25606ee 100644
--- a/solventmapcreator/io/solvationenergyextraction.py
+++ b/solventmapcreator/io/solvationenergyextraction.py
@@ -35,6 +35,33 @@ def get_solvent_id_list(solvent_list_element_tree):
LOGGER.info("Solvent IDs found %i", len(solvent_ids))
return solvent_ids
+def extract_and_write_energy_values_for_solvent_list(solvent_id_list, energy_xml, energy_type, directory):
+ """This extracts the energies for each solvent and writes the energies found to a new file per solvent.
+ """
+ for solvent_id in solvent_id_list:
+ extract_and_write_energy_values_for_solvent(solvent_id, energy_xml,
+ energy_type, directory)
+
+def extract_and_write_energy_values_for_solvent(solvent_id, energy_xml, energy_type, directory):
+ """This extracts the elements and writes the energies found ot a new file.
+ """
+ energy_values_element = generate_energy_values_element_for_solvent(solvent_id, energy_xml, energy_type)
+ element_tree = create_element_tree(energy_values_element)
+ outfilename = directory + create_output_filename(solvent_id, energy_type)
+ write_element_tree_to_file(element_tree, outfilename)
+
+def generate_energy_values_element_for_solvent(solvent_id, energy_xml, energy_type):
+ """This extracts the elements for the solvents and creates a new EnergyValues element.
+ """
+ if energy_type == "binding":
+ xpath_expression = generate_binding_energy_xpath_expression(solvent_id)
+ energy_elements = get_energy_elements(energy_xml, xpath_expression)
+ return generate_energy_values_element(energy_elements, energy_type)
+ elif energy_type == "free":
+ xpath_expression = generate_free_energy_xpath_expression(solvent_id)
+ energy_elements = get_energy_elements(energy_xml, xpath_expression)
+ return generate_energy_values_element(energy_elements, energy_type)
+
def create_output_filename(to_solvent_id, energy_type):
"""This creates an output filename based on the solvent id and energy type.
"""
diff --git a/solventmapcreator/test/iotest/solvationenergyextractiontest.py b/solventmapcreator/test/iotest/solvationenergyextractiontest.py
index 0119d9b..ab31087 100644
--- a/solventmapcreator/test/iotest/solvationenergyextractiontest.py
+++ b/solventmapcreator/test/iotest/solvationenergyextractiontest.py
@@ -22,13 +22,14 @@ class SolvationEnergyExtractionTestCase(unittest.TestCase):
def setUp(self):
"""Set up for tests
"""
+ self.maxDiff=None
self.solvent_filename = "resources/watersolvent.xml"
self.solvent_xml = solvationenergyextraction.read_xml_file(self.solvent_filename)
self.binding_energy_filename = "resources/energyvaluestest.xml"
self.free_energy_filename = "resources/energyvaluestest2.xml"
self.actual_output_filename = "resources/watersolvation.xml"
- self.actual_output_filename2 = "water.xml"
- self.actual_output_filename3 = "water.xml"
+ self.actual_output_filename2 = "waterfree.xml"
+ self.actual_output_filename3 = "waterbinding.xml"
self.binding_energy_xml = solvationenergyextraction.read_xml_file(self.binding_energy_filename)
self.free_energy_xml = solvationenergyextraction.read_xml_file(self.free_energy_filename)
def tearDown(self):
@@ -46,11 +47,6 @@ class SolvationEnergyExtractionTestCase(unittest.TestCase):
if os.path.isfile(self.actual_output_filename3):
os.remove(self.actual_output_filename3)
del self.actual_output_filename3
-
- def test_(self):
- """
- """
- self.fail("not implemented")
def test_read_in_solvent_id_list(self):
"""Test to see if expected solvent ID list is returned.
"""
@@ -63,6 +59,39 @@ class SolvationEnergyExtractionTestCase(unittest.TestCase):
expected_solvent_list = ["water"]
actual_list = solvationenergyextraction.get_solvent_id_list(self.solvent_xml)
self.assertListEqual(expected_solvent_list, actual_list)
+ def test_extract_and_write_energy_values_for_solvent_list(self):
+ """Test to see if expected files is produced.
+ """
+ solvationenergyextraction.extract_and_write_energy_values_for_solvent_list(["water"], self.binding_energy_xml, "binding", "")
+ with open(self.actual_output_filename3, "r") as actual_file:
+ actual_xml = actual_file.read()
+ with open("resources/energyvaluestest.xml") as expected_file:
+ expected_xml = expected_file.read()
+ self.assertEqual(expected_xml, actual_xml)
+ def test_extract_and_write_energy_values_for_solvent(self):
+ """Test to see if expected file is produced.
+ """
+ solvationenergyextraction.extract_and_write_energy_values_for_solvent("water", self.free_energy_xml, "free", "")
+ with open(self.actual_output_filename2, "r") as actual_file:
+ actual_xml = actual_file.read()
+ with open("resources/energyvaluestest2.xml") as expected_file:
+ expected_xml = expected_file.read()
+ self.assertEqual(expected_xml, actual_xml)
+ def test_generate_energy_values_element_for_solvent(self):
+ """Test to see expected energy values is produced.
+ """
+ expected_xml = """<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>
+"""
+ actual_element = solvationenergyextraction.generate_energy_values_element_for_solvent("water", self.free_energy_xml, "free")
+ self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_element, pretty_print=True))
def test_create_output_filename(self):
"""Test to see if expected filename is produced.
"""
@@ -72,7 +101,17 @@ class SolvationEnergyExtractionTestCase(unittest.TestCase):
def test_write_element_tree_to_file(self):
"""Test to see if expecetd file is written.
"""
- self.fail("not implemented")
+ xpath_expression = solvationenergyextraction.generate_free_energy_xpath_expression("water")
+ free_elements = solvationenergyextraction.get_energy_elements(self.free_energy_xml,
+ xpath_expression)
+ energy_values_element = solvationenergyextraction.generate_energy_values_element(free_elements, "free")
+ energy_values_tree = solvationenergyextraction.create_element_tree(energy_values_element)
+ solvationenergyextraction.write_element_tree_to_file(energy_values_tree, self.actual_output_filename)
+ with open(self.actual_output_filename, "r") as actual_file:
+ actual_xml = actual_file.read()
+ with open("resources/energyvaluestest2.xml") as expected_file:
+ expected_xml = expected_file.read()
+ self.assertEqual(expected_xml, actual_xml)
def test_create_element_tree(self):
"""Test to see if expected element tree is produced.
"""
--
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