diff --git a/solventmapcreator/io/solventxmlreader.py b/solventmapcreator/io/solventxmlreader.py
index 8b3798987d65a5f0879482646fd1653fc7d3c4e4..eac539d4c0a90509c505cde0d5682c4ba7408a4b 100644
--- a/solventmapcreator/io/solventxmlreader.py
+++ b/solventmapcreator/io/solventxmlreader.py
@@ -21,14 +21,26 @@ PHASE_NAMESPACE_DICT = {"phase":"http://www-hunter.ch.cam.ac.uk/PhaseSchema",
"ssip":"http://www-hunter.ch.cam.ac.uk/SSIP",
'cml':'http://www.xml-cml.org/schema'}
-def calculate_freactional_occupancy_for_solvent(solvent_element):
- """
+IDEAL_MAX_SSIP_CONCENTRATION_MOLAR = 300.0
+
+def calculate_fractional_occupancy_for_solvent(solvent_element):
+ """This calculates the contribution to the fractional occupancy from the solvent.
"""
+ xpath_expression = "phase:Molecule"
+ molecule_element_list = solvent_element.xpath(xpath_expression, namespaces=PHASE_NAMESPACE_DICT)
+ solvent_fractional_occupancy = 0.0
+ for molecule_element in molecule_element_list:
+ fractional_occupancy_contribution = calculate_fractional_occupancy_contribution(molecule_element)
+ solvent_fractional_occupancy += fractional_occupancy_contribution
+ return solvent_fractional_occupancy
def calculate_fractional_occupancy_contribution(molecule_element):
+ """This calculates the contribution to the fractional occupancy for this species.
"""
- """
-
+ concentration_value = get_concentration_value(molecule_element)
+ number_of_ssips = get_number_of_ssips_in_molecule(molecule_element)
+ return (concentration_value * number_of_ssips)/IDEAL_MAX_SSIP_CONCENTRATION_MOLAR
+
def get_concentration_value(molecule_element):
"""This extracts the concentration.
"""
@@ -38,14 +50,14 @@ def get_concentration_value(molecule_element):
return float(concentration_element_list[0].text)
else:
LOGGER.debug("len:")
- LOGGER.debug(len(solvent_element_list))
- LOGGER.debug(solvent_element_list)
+ LOGGER.debug(len(concentration_element_list))
+ LOGGER.debug(concentration_element_list)
raise ValueError("Wrong number of Concentration Elements.")
def get_number_of_ssips_in_molecule(molecule_element):
"""This extracts the SSIP elements and return the number.
"""
- xpath_expression = "ssip:SSIP"
+ xpath_expression = "ssip:SSIPList/ssip:SSIP"
ssip_element_list = molecule_element.xpath(xpath_expression, namespaces=PHASE_NAMESPACE_DICT)
return len(ssip_element_list)
@@ -66,7 +78,7 @@ def create_solvent_xpath_expression(solvent_id):
"""This creates the xpath expression to extract the solvent Element based
on solventID.
"""
- return "phase:Solvent[@phase:solventID={:s}]".format(solvent_id)
+ return 'phase:Solvent[@phase:solventID="{:s}"]'.format(solvent_id)
def read_element_tree(filename):
"""This reads in an xml file to an element tree.
diff --git a/solventmapcreator/test/iotest/solventxmlreadertest.py b/solventmapcreator/test/iotest/solventxmlreadertest.py
new file mode 100644
index 0000000000000000000000000000000000000000..e88530e571a723228911516be5a039f44c286ba1
--- /dev/null
+++ b/solventmapcreator/test/iotest/solventxmlreadertest.py
@@ -0,0 +1,114 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script containing tests for the solventxmlreader.
+
+@author: mark
+"""
+
+import logging
+import unittest
+from lxml import etree
+import solventmapcreator.io.solventxmlreader as solventxmlreader
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class SolventXMLReaderTestCase(unittest.TestCase):
+ """Test case for solventxmlreader script tests.
+ """
+ def setUp(self):
+ """Set up for tests.
+ """
+ self.solvent_list_xml = solventxmlreader.read_element_tree("resources/watersolvent.xml")
+ self.water_solvent_element = self.solvent_list_xml.xpath("phase:Solvent", namespaces=solventxmlreader.PHASE_NAMESPACE_DICT)[0]
+ self.water_molecule_element = self.water_solvent_element.xpath("phase:Molecule", namespaces=solventxmlreader.PHASE_NAMESPACE_DICT)[0]
+ self.maxDiff=None
+ def tearDown(self):
+ """Tear down after tests.
+ """
+ del self.solvent_list_xml
+ del self.water_solvent_element
+ del self.water_molecule_element
+ def test_calculate_fractional_occupancy_for_solvent(self):
+ """Test to see if expected value is returned for the fractional
+ occupancy.
+ """
+ expected_value = 55.35 * 4.0 /300.0
+ actual_value = solventxmlreader.calculate_fractional_occupancy_for_solvent(self.water_solvent_element)
+ self.assertAlmostEqual(expected_value, actual_value)
+ def test_calculate_fractional_occupancy_contribution(self):
+ """Test to see if expected contribution to fractional occupancy is returned.
+ """
+ expected_value = 55.35* 4.0 / 300.0
+ actual_value = solventxmlreader.calculate_fractional_occupancy_contribution(self.water_molecule_element)
+ self.assertAlmostEqual(expected_value, actual_value)
+ def test_get_concentration_value(self):
+ """Test to see if expected concentration is returned
+ """
+ expected_value = 55.3500
+ actual_value = solventxmlreader.get_concentration_value(self.water_molecule_element)
+ self.assertAlmostEqual(expected_value, actual_value)
+ def test_get_number_of_ssips_in_molecule(self):
+ """Test to see if expected number of SSIPs is returned.
+ """
+ expected_value = 4
+ actual_value = solventxmlreader.get_number_of_ssips_in_molecule(self.water_molecule_element)
+ self.assertEqual(expected_value, actual_value)
+ def test_get_solvent_element_by_id(self):
+ """Test to see if expected solvent element is returned.
+ """
+ expected_xml = ('<phase:Solvent xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:cml="http://www.xml-cml.org/schema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" phase:solventID="water" phase:solven' +
+ 'tName="water" phase:numberOfMolecules="1">\n' +
+ ' <phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N">\n' +
+ ' <ssip:SSIPList>\n' +
+ '\t\t\t<ssip:SurfaceInformation numberOfPoints="1000">\n' +
+ '\t\t\t\t<ssip:IsosurfaceDensity>0.002</ssip:IsosurfaceDensity>\n' +
+ '\t\t\t\t<ssip:TotalSurfaceArea>10.0</ssip:TotalSurfaceArea>\n' +
+ '\t\t\t\t<ssip:NegativeSurfaceArea>5.0</ssip:NegativeSurfaceArea>\n' +
+ '\t\t\t\t<ssip:PositiveSurfaceArea>5.0</ssip:PositiveSurfaceArea>\n' +
+ '\t\t\t</ssip:SurfaceInformation>\n' +
+ '\t\t\t<ssip:SSIP x3="1.0" y3="0.0" z3="0.0" nearestAtomID="a1">2.8</ssip:SSIP>\n' +
+ '\t\t\t<ssip:SSIP x3="1.0" y3="1.0" z3="1.0" nearestAtomID="a1">2.8</ssip:SSIP>\n' +
+ '\t\t\t<ssip:SSIP x3="0.0" y3="1.0" z3="1.0" nearestAtomID="a1">-4.5</ssip:SSIP>\n' +
+ '\t\t\t<ssip:SSIP x3="0.0" y3="1.0" z3="0.0" nearestAtomID="a1">-4.5</ssip:SSIP>\n' +
+ '\t\t</ssip:SSIPList>\n' +
+ ' <phase:Concentration phase:units="MOLAR">55.350000</phase:Concentration>\n' +
+ ' </phase:Molecule>\n' +
+ ' </phase:Solvent>\n')
+ actual_xml = solventxmlreader.get_solvent_element_by_id(self.solvent_list_xml, "water")
+ self.assertEqual(expected_xml, etree.tounicode(actual_xml))
+ def test_create_solvent_xpath_expression(self):
+ """Test to seeif expected xpath expression is created.
+ """
+ expected_expression = 'phase:Solvent[@phase:solventID="water"]'
+ actual_expression = solventxmlreader.create_solvent_xpath_expression("water")
+ self.assertEqual(expected_expression, actual_expression)
+ def test_read_element_tree(self):
+ """Test to see if expected file is read in.
+ """
+ expected_xml = ('<phase:SolventList xmlns:cml="http://www.xml-cml.org/sch' +
+ 'ema" xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSc' +
+ 'hema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP">' +
+ '\n <phase:Solvent phase:solventID="water" phase:solven' +
+ 'tName="water" phase:numberOfMolecules="1">\n' +
+ ' <phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N">\n' +
+ ' <ssip:SSIPList>\n' +
+ '\t\t\t<ssip:SurfaceInformation numberOfPoints="1000">\n' +
+ '\t\t\t\t<ssip:IsosurfaceDensity>0.002</ssip:IsosurfaceDensity>\n' +
+ '\t\t\t\t<ssip:TotalSurfaceArea>10.0</ssip:TotalSurfaceArea>\n' +
+ '\t\t\t\t<ssip:NegativeSurfaceArea>5.0</ssip:NegativeSurfaceArea>\n' +
+ '\t\t\t\t<ssip:PositiveSurfaceArea>5.0</ssip:PositiveSurfaceArea>\n' +
+ '\t\t\t</ssip:SurfaceInformation>\n' +
+ '\t\t\t<ssip:SSIP x3="1.0" y3="0.0" z3="0.0" nearestAtomID="a1">2.8</ssip:SSIP>\n' +
+ '\t\t\t<ssip:SSIP x3="1.0" y3="1.0" z3="1.0" nearestAtomID="a1">2.8</ssip:SSIP>\n' +
+ '\t\t\t<ssip:SSIP x3="0.0" y3="1.0" z3="1.0" nearestAtomID="a1">-4.5</ssip:SSIP>\n' +
+ '\t\t\t<ssip:SSIP x3="0.0" y3="1.0" z3="0.0" nearestAtomID="a1">-4.5</ssip:SSIP>\n' +
+ '\t\t</ssip:SSIPList>\n' +
+ ' <phase:Concentration phase:units="MOLAR">55.350000</phase:Concentration>\n' +
+ ' </phase:Molecule>\n' +
+ ' </phase:Solvent>\n' +
+ '</phase:SolventList>')
+ actual_xml = solventxmlreader.read_element_tree("resources/watersolvent.xml")
+ self.assertEqual(expected_xml, etree.tounicode(actual_xml))
diff --git a/solventmapcreator/test/solvationmapcreatortests.py b/solventmapcreator/test/solvationmapcreatortests.py
index 3b64ce011c1059b050c68584f0be3318d144e9bf..9f274dc6b15477900713bedb29c7789dc99dcc40 100644
--- a/solventmapcreator/test/solvationmapcreatortests.py
+++ b/solventmapcreator/test/solvationmapcreatortests.py
@@ -9,6 +9,7 @@ Script for running the tests.
import logging
import unittest
from solventmapcreator.test.iotest.solvationenergyreadertest import SolvationEnergyReaderTestCase
+from solventmapcreator.test.iotest.solventxmlreadertest import SolventXMLReaderTestCase
from solventmapcreator.test.iotest.polynomialdatawritertest import PolynomialDataWriterTestCase
from solventmapcreator.test.iotest.polynomialdatareadertest import PolynomialDataReaderTestCase
from solventmapcreator.test.solvationcalculationtest.solvationcalculatortest import SolvationCalculatorTestCase
@@ -19,8 +20,8 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-IO_TEST_CASES = [SolvationEnergyReaderTestCase, PolynomialDataWriterTestCase,
- PolynomialDataReaderTestCase]
+IO_TEST_CASES = [SolvationEnergyReaderTestCase, SolventXMLReaderTestCase,
+ PolynomialDataWriterTestCase, PolynomialDataReaderTestCase]
SOLVATION_CALCULATION_TEST_CASES = [SolvationCalculatorTestCase]