From a0c87679e615878731bbec9221399f6ef2854fce Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Tue, 18 Jul 2017 17:06:27 +0100
Subject: [PATCH] added function and corresponding test for getting fractional
occupancy from file.
---
solventmapcreator/io/solventxmlreader.py | 7 +++++++
solventmapcreator/test/iotest/solventxmlreadertest.py | 6 ++++++
2 files changed, 13 insertions(+)
diff --git a/solventmapcreator/io/solventxmlreader.py b/solventmapcreator/io/solventxmlreader.py
index c4adb70..1ef1bec 100644
--- a/solventmapcreator/io/solventxmlreader.py
+++ b/solventmapcreator/io/solventxmlreader.py
@@ -23,6 +23,13 @@ PHASE_NAMESPACE_DICT = {"phase":"http://www-hunter.ch.cam.ac.uk/PhaseSchema",
IDEAL_MAX_SSIP_CONCENTRATION_MOLAR = 300.0
+def get_fractional_occupancy_for_solvent_from_file(solvent_filename, solvent_id):
+ """This reads inthe file and extracts the solvent information, and returns
+ the fractional occupancy contribution from the solvent.
+ """
+ solvent_list_element = read_element_tree(solvent_filename)
+ return get_fractional_occupancy_for_solvent(solvent_list_element, solvent_id)
+
def get_fractional_occupancy_for_solvent(solvent_list_element, solvent_id):
"""This extracts the solvent XML, and calculates the fractional occupancy
contribution for the solvent.
diff --git a/solventmapcreator/test/iotest/solventxmlreadertest.py b/solventmapcreator/test/iotest/solventxmlreadertest.py
index 2b900a7..bb685f4 100644
--- a/solventmapcreator/test/iotest/solventxmlreadertest.py
+++ b/solventmapcreator/test/iotest/solventxmlreadertest.py
@@ -31,6 +31,12 @@ class SolventXMLReaderTestCase(unittest.TestCase):
del self.solvent_list_xml
del self.water_solvent_element
del self.water_molecule_element
+ def test_get_fractional_occupancy_for_solvent_from_file(self):
+ """Test to see if expected value is returned.
+ """
+ expected_value = 55.35 * 4.0 /300.0
+ actual_value = solventxmlreader.get_fractional_occupancy_for_solvent_from_file("resources/watersolvent.xml", "water")
+ self.assertAlmostEqual(expected_value, actual_value)
def test_get_fractional_occupancy_for_solvent(self):
"""Test to see if expected fractional occupancy is returned.
"""
--
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