From ada8220f874aaf5df63e441ee3d021deae2cb1a3 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Mon, 19 Mar 2018 19:10:05 +0000
Subject: [PATCH] update to make use of validation of XML, and also rename of
methods to make clear the existing functions operate on binding energies.
---
solventmapcreator/io/solvationenergyreader.py | 21 ++-
solventmapcreator/io/solventxmlreader.py | 29 ++---
.../polynomialanalysis/polynomialplotting.py | 34 ++---
.../test/iotest/solvationenergyreadertest.py | 22 ++--
.../test/iotest/solventxmlreadertest.py | 123 +++++++++++-------
.../polynomialplottingtest.py | 22 ++--
.../test/resources/energyvaluestest.xml | 6 +-
solventmapcreator/test/resources/water.xml | 44 +++----
.../test/resources/watersolvent.xml | 48 ++++---
9 files changed, 194 insertions(+), 155 deletions(-)
diff --git a/solventmapcreator/io/solvationenergyreader.py b/solventmapcreator/io/solvationenergyreader.py
index 437f231..2e116fc 100644
--- a/solventmapcreator/io/solvationenergyreader.py
+++ b/solventmapcreator/io/solvationenergyreader.py
@@ -13,26 +13,25 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-def parse_free_energy_from_file_with_data_arrays(filename):
+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.
"""
- datapoints = parse_free_energy_from_file(filename)
+ datapoints = parse_binding_energy_from_file(filename)
datapoints.createDataArrays()
return datapoints
-def parse_free_energy_from_file(filename):
+def parse_binding_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):
- """
+ solvation_energy_dict = parse_binding_energy_info(filename)
+ return create_binding_datapoints_with_values(solvation_energy_dict)
+def create_binding_datapoints_with_values(solvation_energy_dict):
+ """This creates binding datapoints
"""
- return solvationreader.create_datapoints_with_values(solvation_energy_dict)
+ return solvationreader.create_binding_datapoints_with_values(solvation_energy_dict)
-def parse_free_energy_info(filename):
+def parse_binding_energy_info(filename):
"""This extracts the solvation information to a dictionary.
"""
- return solvationreader.parse_free_energy_info(filename)
+ return solvationreader.parse_binding_energy_info(filename)
diff --git a/solventmapcreator/io/solventxmlreader.py b/solventmapcreator/io/solventxmlreader.py
index b9395ba..414062a 100644
--- a/solventmapcreator/io/solventxmlreader.py
+++ b/solventmapcreator/io/solventxmlreader.py
@@ -12,6 +12,7 @@ This allows the calculation of the fractional occupancy of the phase.
import logging
from lxml import etree
+import resultsanalysis.fileparsing.xmlparsing.xmlvalidation as xmlvalidation
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
@@ -40,7 +41,7 @@ def get_fractional_occupancy_for_solvent(solvent_list_element, solvent_id):
def calculate_fractional_occupancy_for_solvent(solvent_element):
"""This calculates the contribution to the fractional occupancy from the solvent.
"""
- xpath_expression = "phase:Molecule"
+ xpath_expression = "phase:Molecules/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:
@@ -51,27 +52,23 @@ def calculate_fractional_occupancy_for_solvent(solvent_element):
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
+ concentration_sum_value = get_concentration_value_sum(molecule_element)
+ return (concentration_sum_value)/IDEAL_MAX_SSIP_CONCENTRATION_MOLAR
-def get_concentration_value(molecule_element):
+def get_concentration_value_sum(molecule_element):
"""This extracts the concentration.
"""
- xpath_expression = "phase:Concentration"
+ xpath_expression = "phase:SSIPs/phase:SSIP/phase:TotalConcentration"
concentration_element_list = molecule_element.xpath(xpath_expression, namespaces=PHASE_NAMESPACE_DICT)
- if len(concentration_element_list) == 1:
- return float(concentration_element_list[0].text)
- else:
- LOGGER.debug("len:")
- LOGGER.debug(len(concentration_element_list))
- LOGGER.debug(concentration_element_list)
- raise ValueError("Wrong number of Concentration Elements.")
+ total_concentration = 0.0
+ for i in range(len(concentration_element_list)):
+ total_concentration += float(concentration_element_list[0].text)
+ return total_concentration
def get_number_of_ssips_in_molecule(molecule_element):
"""This extracts the SSIP elements and return the number.
"""
- xpath_expression = "ssip:SSIPList/ssip:SSIP"
+ xpath_expression = "phase:SSIPs/phase:SSIP"
ssip_element_list = molecule_element.xpath(xpath_expression, namespaces=PHASE_NAMESPACE_DICT)
return len(ssip_element_list)
@@ -92,9 +89,9 @@ 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:Solvents/phase:Solvent[@phase:solventID="{:s}"]'.format(solvent_id)
def read_element_tree(filename):
"""This reads in an xml file to an element tree.
"""
- return etree.parse(filename)
+ return xmlvalidation.validate_and_read_xml_file(filename, xmlvalidation.PHASE_SCHEMA)
diff --git a/solventmapcreator/polynomialanalysis/polynomialplotting.py b/solventmapcreator/polynomialanalysis/polynomialplotting.py
index 9272bdd..964efbf 100644
--- a/solventmapcreator/polynomialanalysis/polynomialplotting.py
+++ b/solventmapcreator/polynomialanalysis/polynomialplotting.py
@@ -18,13 +18,15 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-def plot_energies_from_file(free_energy_filename, polynomial_order, **kwargs):
+def plot_binding_energies_from_file(free_energy_filename, polynomial_order, **kwargs):
"""This creates in the plotting information, and outputs a plot to file.
"""
- plot_data = parse_energies_create_plot_input_data(free_energy_filename,
- polynomial_order,
- kwargs.get("pos_subset_list", None),
- kwargs.get("neg_subset_list", None))
+ plot_data = parse_binding_energies_create_plot_input_data(free_energy_filename,
+ polynomial_order,
+ kwargs.get("pos_subset_list",
+ None),
+ kwargs.get("neg_subset_list",
+ None))
if type(plot_data['polynomial coefficients']) is dict:
return create_scatter_with_split_poly(plot_data, **kwargs)
else:
@@ -49,12 +51,12 @@ def create_scatter_with_split_poly(input_data, **kwargs):
plottinginput.plt.close(scatter_plot)
return 0
-def parse_energies_create_plot_input_data(free_energy_filename, polynomial_order,
- pos_subset_list=None, neg_subset_list=None):
+def parse_binding_energies_create_plot_input_data(free_energy_filename, polynomial_order,
+ pos_subset_list=None, neg_subset_list=None):
"""This creates the input data for a plot. This overrides the default figure
label, so that the figures can be distinguished based on the solvent.
"""
- datapoints = parse_free_energy_from_file_with_data_arrays(free_energy_filename)
+ datapoints = parse_binding_energy_from_file_with_data_arrays(free_energy_filename)
plot_data = datapoints.generateScatterPlotParameters(label_type='', polynomial_order=polynomial_order)
if pos_subset_list != None and neg_subset_list != None:
poly_coeff_dict = generate_poly_pos_neg_separate_fit(datapoints, polynomial_order,
@@ -74,12 +76,12 @@ def generate_poly_pos_neg_separate_fit(datapoints, order, pos_subset_list, neg_s
return {"positive":poly_dict["positive"]["coefficients"],
"negative":poly_dict["negative"]["coefficients"]}
-def parse_poly_data_to_file_split_fit(free_energy_filename, order_list, poly_filename,
+def parse_poly_data_to_file_split_fit(binding_energy_filename, order_list, poly_filename,
pos_subset_list, neg_subset_list):
"""This reads in the energy information, and then performs the fits on the
two separate subsets, and outputs to file.
"""
- datapoints = parse_free_energy_from_file_with_data_arrays(free_energy_filename)
+ datapoints = parse_binding_energy_from_file_with_data_arrays(binding_energy_filename)
return write_poly_data_to_file_split_fit(datapoints, order_list, poly_filename,
pos_subset_list, neg_subset_list)
@@ -94,21 +96,21 @@ def write_poly_data_to_file_split_fit(datapoints, order_list, filename,
pos_subset_list,
neg_subset_list)
-def parse_energies_and_output_poly_data_subset(free_energy_filename, order_list, poly_filename, subset_list):
+def parse_binding_energies_and_output_poly_data_subset(free_energy_filename, order_list, poly_filename, subset_list):
"""This reads in the energy information, and then selects teh subset of
points to carry out the analysis on, outputs the polynomial information to file.
"""
- datapoints = parse_free_energy_from_file_with_data_arrays(free_energy_filename)
+ datapoints = parse_binding_energy_from_file_with_data_arrays(free_energy_filename)
datapoints_subset = datapoints.createDatapointsSubGroup(subset_list)
datapoints_subset.createDataArrays()
return write_poly_data_to_file(datapoints_subset, order_list, poly_filename)
-def parse_energies_and_output_poly_data(free_energy_filename, order_list, poly_filename):
+def parse_binding_energies_and_output_poly_data(free_energy_filename, order_list, poly_filename):
"""This reads in the energy information, and then outputs the polynomial
information to file.
"""
- datapoints = parse_free_energy_from_file_with_data_arrays(free_energy_filename)
+ datapoints = parse_binding_energy_from_file_with_data_arrays(free_energy_filename)
return write_poly_data_to_file(datapoints, order_list, poly_filename)
def write_poly_data_to_file(datapoints, order_list, filename):
@@ -117,8 +119,8 @@ def write_poly_data_to_file(datapoints, order_list, filename):
"""
return polynomialdatawriter.write_poly_data_to_file(datapoints, order_list, filename)
-def parse_free_energy_from_file_with_data_arrays(filename):
+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.
"""
- return solvationenergyreader.parse_free_energy_from_file_with_data_arrays(filename)
+ return solvationenergyreader.parse_binding_energy_from_file_with_data_arrays(filename)
diff --git a/solventmapcreator/test/iotest/solvationenergyreadertest.py b/solventmapcreator/test/iotest/solvationenergyreadertest.py
index 3bc05ee..f908f87 100644
--- a/solventmapcreator/test/iotest/solvationenergyreadertest.py
+++ b/solventmapcreator/test/iotest/solvationenergyreadertest.py
@@ -25,45 +25,45 @@ class SolvationEnergyReaderTestCase(unittest.TestCase):
def setUp(self):
"""Set up for tests
"""
- self.solvation_info_dict = solvationenergyreader.parse_free_energy_info("resources/energyvaluestest.xml")
- self.expected_datapoints = Datapoints(("SSIP Value","Solvation Energy"), (Units.dimensionless, Units.kj_per_mol))
+ self.solvation_info_dict = solvationenergyreader.parse_binding_energy_info("resources/energyvaluestest.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 Energy", Units.kj_per_mol),
+ "Solvation Binding Energy", 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):
+ def test_parse_binding_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")
+ actual_datapoints = solvationenergyreader.parse_binding_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):
+ 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_free_energy_from_file("resources/energyvaluestest.xml")
+ actual_datapoints = solvationenergyreader.parse_binding_energy_from_file("resources/energyvaluestest.xml")
self.assertEqual(self.expected_datapoints, actual_datapoints)
- def test_create_datapoints_with_values(self):
+ def test_create_binding_datapoints_with_values(self):
"""Test to see if expected Datapoints object is created.
"""
- actual_datapoints = solvationenergyreader.create_datapoints_with_values(self.solvation_info_dict)
+ actual_datapoints = solvationenergyreader.create_binding_datapoints_with_values(self.solvation_info_dict)
self.assertEqual(self.expected_datapoints, actual_datapoints)
- def test_parse_free_energy_info(self):
+ 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_free_energy_info("resources/energyvaluestest.xml")
+ actual_dict_dict = solvationenergyreader.parse_binding_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()))
diff --git a/solventmapcreator/test/iotest/solventxmlreadertest.py b/solventmapcreator/test/iotest/solventxmlreadertest.py
index bb685f4..aacf439 100644
--- a/solventmapcreator/test/iotest/solventxmlreadertest.py
+++ b/solventmapcreator/test/iotest/solventxmlreadertest.py
@@ -22,8 +22,8 @@ class SolventXMLReaderTestCase(unittest.TestCase):
"""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.water_solvent_element = self.solvent_list_xml.xpath("phase:Solvents/phase:Solvent", namespaces=solventxmlreader.PHASE_NAMESPACE_DICT)[0]
+ self.water_molecule_element = self.water_solvent_element.xpath("phase:Molecules/phase:Molecule", namespaces=solventxmlreader.PHASE_NAMESPACE_DICT)[0]
self.maxDiff=None
def tearDown(self):
"""Tear down after tests.
@@ -56,11 +56,11 @@ class SolventXMLReaderTestCase(unittest.TestCase):
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):
+ def test_get_concentration_value_sum(self):
"""Test to see if expected concentration is returned
"""
- expected_value = 55.3500
- actual_value = solventxmlreader.get_concentration_value(self.water_molecule_element)
+ expected_value = 55.3500 * 4
+ actual_value = solventxmlreader.get_concentration_value_sum(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.
@@ -71,56 +71,81 @@ class SolventXMLReaderTestCase(unittest.TestCase):
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')
+ 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:solventName="water">
+ <phase:Molecules>
+ <phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N"><cml:molecule ssip:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" cml:id="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="O" cml:id="a1" cml:x3="0.0569236794019" cml:y3="0.53497425302" cml:z3="-9.99862395488E-5"/>
+ <cml:atom cml:elementType="H" cml:id="a2" cml:x3="-0.735721920018" cml:y3="-0.0219270863225" cml:z3="-1.029173866E-4"/>
+ <cml:atom cml:elementType="H" cml:id="a3" cml:x3="0.785198240616" cml:y3="-0.103847166698" cml:z3="-1.97096373822E-4"/>
+ </cml:atomArray>
+ <cml:bondArray>
+ <cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a3" cml:order="1"/>
+ </cml:bondArray>
+ </cml:molecule>
+ <ssip:SurfaceInformation>
+ <ssip:TotalSurfaceArea>37.48483410829331</ssip:TotalSurfaceArea>
+ <ssip:NegativeSurfaceArea>18.664358683092974</ssip:NegativeSurfaceArea>
+ <ssip:PositiveSurfaceArea>18.82047542519977</ssip:PositiveSurfaceArea>
+ <ssip:ElectronDensityIsosurface>0.002</ssip:ElectronDensityIsosurface>
+ <ssip:NumberOFMEPSPoints>2286</ssip:NumberOFMEPSPoints>
+ </ssip:SurfaceInformation>
+ <phase:SSIPs phase:units="MOLAR">
+ <phase:SSIP ssip:value="2.9387503903833574" ssip:nearestAtomID="a3" cml:x3="1.509794550767402" cml:y3="-0.8784982637871289" cml:z3="-1.6986589692899999E-4" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="2.9275582734233065" ssip:nearestAtomID="a2" cml:x3="-1.4603207114038939" cml:y3="-0.790973405157027" cml:z3="0.12362427220238399" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="-6.263074063139137" ssip:nearestAtomID="a1" cml:x3="0.156188781751346" cml:y3="1.6969169177862917" cml:z3="1.172598045109361" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="-6.607684490829715" ssip:nearestAtomID="a1" cml:x3="0.06855491260794999" cml:y3="1.9788577934582507" cml:z3="-0.77762067563301" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ </phase:SSIPs>
+</phase:Molecule>
+ </phase:Molecules>
+ </phase:Solvent>
+
+'''
actual_xml = solventxmlreader.get_solvent_element_by_id(self.solvent_list_xml, "water")
- self.assertEqual(expected_xml, etree.tounicode(actual_xml))
+ self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
def test_create_solvent_xpath_expression(self):
- """Test to seeif expected xpath expression is created.
+ """Test to see if expected xpath expression is created.
"""
- expected_expression = 'phase:Solvent[@phase:solventID="water"]'
+ expected_expression = 'phase:Solvents/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>')
+ expected_xml = '''<phase:SolventList xmlns:cml="http://www.xml-cml.org/schema" xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP">
+ <phase:Solvents>
+ <phase:Solvent phase:solventID="water" phase:solventName="water">
+ <phase:Molecules>
+ <phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N"><cml:molecule ssip:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" cml:id="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="O" cml:id="a1" cml:x3="0.0569236794019" cml:y3="0.53497425302" cml:z3="-9.99862395488E-5"/>
+ <cml:atom cml:elementType="H" cml:id="a2" cml:x3="-0.735721920018" cml:y3="-0.0219270863225" cml:z3="-1.029173866E-4"/>
+ <cml:atom cml:elementType="H" cml:id="a3" cml:x3="0.785198240616" cml:y3="-0.103847166698" cml:z3="-1.97096373822E-4"/>
+ </cml:atomArray>
+ <cml:bondArray>
+ <cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a3" cml:order="1"/>
+ </cml:bondArray>
+ </cml:molecule>
+ <ssip:SurfaceInformation>
+ <ssip:TotalSurfaceArea>37.48483410829331</ssip:TotalSurfaceArea>
+ <ssip:NegativeSurfaceArea>18.664358683092974</ssip:NegativeSurfaceArea>
+ <ssip:PositiveSurfaceArea>18.82047542519977</ssip:PositiveSurfaceArea>
+ <ssip:ElectronDensityIsosurface>0.002</ssip:ElectronDensityIsosurface>
+ <ssip:NumberOFMEPSPoints>2286</ssip:NumberOFMEPSPoints>
+ </ssip:SurfaceInformation>
+ <phase:SSIPs phase:units="MOLAR">
+ <phase:SSIP ssip:value="2.9387503903833574" ssip:nearestAtomID="a3" cml:x3="1.509794550767402" cml:y3="-0.8784982637871289" cml:z3="-1.6986589692899999E-4" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="2.9275582734233065" ssip:nearestAtomID="a2" cml:x3="-1.4603207114038939" cml:y3="-0.790973405157027" cml:z3="0.12362427220238399" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="-6.263074063139137" ssip:nearestAtomID="a1" cml:x3="0.156188781751346" cml:y3="1.6969169177862917" cml:z3="1.172598045109361" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="-6.607684490829715" ssip:nearestAtomID="a1" cml:x3="0.06855491260794999" cml:y3="1.9788577934582507" cml:z3="-0.77762067563301" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ </phase:SSIPs>
+</phase:Molecule>
+ </phase:Molecules>
+ </phase:Solvent>
+ </phase:Solvents>
+</phase:SolventList>
+'''
actual_xml = solventxmlreader.read_element_tree("resources/watersolvent.xml")
- self.assertEqual(expected_xml, etree.tounicode(actual_xml))
+ self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
diff --git a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
index 70c65a4..0dea4c9 100644
--- a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
+++ b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
@@ -23,7 +23,7 @@ class PolynomialPlottingTestCase(unittest.TestCase):
def setUp(self):
"""Set up for tests
"""
- self.expected_datapoints = solvationenergyreader.parse_free_energy_from_file_with_data_arrays("resources/water.xml")
+ self.expected_datapoints = solvationenergyreader.parse_binding_energy_from_file_with_data_arrays("resources/water.xml")
def tearDown(self):
"""Clean up after tests.
"""
@@ -34,7 +34,7 @@ class PolynomialPlottingTestCase(unittest.TestCase):
os.remove("actual_water_poly_fit_subset.csv")
if os.path.isfile("actual_water_poly_fit_split.csv"):
os.remove("actual_water_poly_fit_split.csv")
- def test_parse_energies_create_plot_input_data(self):
+ def test_parse_binding_energies_create_plot_input_data(self):
"""Test to see expected plot data is returned.
"""
expected_dict = {'figure_label': "resources/water",
@@ -56,8 +56,8 @@ class PolynomialPlottingTestCase(unittest.TestCase):
-9.315464914185585, -20.143787975013183,
0.6588682955012527, -0.4429837300591526,
-25.844114335864262]]),
- 'y_label': "Solvation Energy/$kJmol^{-1}$"}
- actual_dict = polynomialplotting.parse_energies_create_plot_input_data("resources/water.xml", 4)
+ 'y_label': "Solvation Binding Energy/$kJmol^{-1}$"}
+ actual_dict = polynomialplotting.parse_binding_energies_create_plot_input_data("resources/water.xml", 4)
LOGGER.debug(actual_dict["x_data"].tolist())
LOGGER.debug(actual_dict["y_data"].tolist())
self.assertListEqual(sorted(actual_dict.keys()), sorted(expected_dict.keys()))
@@ -76,7 +76,7 @@ class PolynomialPlottingTestCase(unittest.TestCase):
#test to see if new functionality is supported
neg_set_list = ["-5.400solute", "-4.300solute", "-9.100solute", "-11.100solute", "-15.400solute"]
pos_set_list = ["0.500solute", "1.200solute", "7.200solute"]
- actual_dict2 = polynomialplotting.parse_energies_create_plot_input_data("resources/water.xml", 4,
+ actual_dict2 = polynomialplotting.parse_binding_energies_create_plot_input_data("resources/water.xml", 4,
pos_set_list, neg_set_list)
self.assertListEqual(sorted(actual_dict2.keys()), sorted(expected_dict.keys()))
for key in actual_dict.keys():
@@ -155,25 +155,25 @@ class PolynomialPlottingTestCase(unittest.TestCase):
with open(actual_file_name, 'r') as act_file:
act_file_lines = act_file.readlines()
self.assertListEqual(act_file_lines, exp_file_lines)
- def test_parse_energies_and_output_poly_data_subset(self):
+ def test_parse_binding_energies_and_output_poly_data_subset(self):
"""Test to see if expected_fit is done on a smaller subset of points.
"""
expected_file_name = "resources/water_poly_fit_subset.csv"
actual_file_name = "actual_water_poly_fit_subset.csv"
subset_list = ["-5.400solute", "-4.300solute", "-9.100solute", "-11.100solute", "-15.400solute"]
- poly_file_out = polynomialplotting.parse_energies_and_output_poly_data_subset("resources/water.xml", [2, 4], actual_file_name, subset_list)
+ poly_file_out = polynomialplotting.parse_binding_energies_and_output_poly_data_subset("resources/water.xml", [2, 4], actual_file_name, subset_list)
self.assertEqual(0, poly_file_out)
with open(expected_file_name, 'r') as exp_file:
exp_file_lines = exp_file.readlines()
with open(actual_file_name, 'r') as act_file:
act_file_lines = act_file.readlines()
self.assertListEqual(act_file_lines, exp_file_lines)
- def test_parse_energies_and_output_poly_data(self):
+ def test_parse_binding_energies_and_output_poly_data(self):
"""Test to see if expected polynomial fit information is outputted to file.
"""
expected_file_name = "resources/water_poly_fit.csv"
actual_file_name = "actual_water_poly_fit.csv"
- poly_file_out = polynomialplotting.parse_energies_and_output_poly_data("resources/water.xml", [2, 4], actual_file_name)
+ poly_file_out = polynomialplotting.parse_binding_energies_and_output_poly_data("resources/water.xml", [2, 4], actual_file_name)
self.assertEqual(0, poly_file_out)
with open(expected_file_name, 'r') as exp_file:
exp_file_lines = exp_file.readlines()
@@ -193,9 +193,9 @@ class PolynomialPlottingTestCase(unittest.TestCase):
with open(actual_file_name, 'r') as act_file:
act_file_lines = act_file.readlines()
self.assertListEqual(act_file_lines, exp_file_lines)
- def test_parse_free_energy_from_file_with_data_arrays(self):
+ def test_parse_binding_energy_from_file_with_data_arrays(self):
"""Test to see if expected datapoints are read in.
"""
- actual_datapoints = polynomialplotting.parse_free_energy_from_file_with_data_arrays("resources/water.xml")
+ actual_datapoints = polynomialplotting.parse_binding_energy_from_file_with_data_arrays("resources/water.xml")
self.assertEqual(self.expected_datapoints, actual_datapoints)
diff --git a/solventmapcreator/test/resources/energyvaluestest.xml b/solventmapcreator/test/resources/energyvaluestest.xml
index af814c6..08a2759 100644
--- a/solventmapcreator/test/resources/energyvaluestest.xml
+++ b/solventmapcreator/test/resources/energyvaluestest.xml
@@ -1,8 +1,10 @@
<?xml version='1.0' encoding='UTF-8'?>
<phase:EnergyValues xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema">
- <phase:BindingEnergyCollection><phase:BindingEnergy phase:stdInChIKey="-14.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergyCollection><phase:BindingEnergy phase:moleculeID="-14.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-34.8195308084233</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-34.8195308084233</phase:EnergyContribution>
+ <phase:EnergyContributions>
+ <phase:EnergyContribution phase:ssipID="1">-34.8195308084233</phase:EnergyContribution>
+ </phase:EnergyContributions>
</phase:BindingEnergy>
</phase:BindingEnergyCollection>
</phase:EnergyValues>
diff --git a/solventmapcreator/test/resources/water.xml b/solventmapcreator/test/resources/water.xml
index 249e029..db2736f 100644
--- a/solventmapcreator/test/resources/water.xml
+++ b/solventmapcreator/test/resources/water.xml
@@ -1,48 +1,48 @@
<?xml version='1.0' encoding='UTF-8'?>
<phase:EnergyValues xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema">
- <phase:BindingEnergyCollection><phase:BindingEnergy phase:stdInChIKey="-14.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergyCollection><phase:BindingEnergy phase:moleculeID="-14.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-34.8195308084233</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-34.8195308084233</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-34.8195308084233</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="-5.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="-5.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-9.315464914185585</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-9.315464914185585</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-9.315464914185585</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="-4.300solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="-4.300solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-6.170784422419204</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-6.170784422419204</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-6.170784422419204</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="7.200solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="7.200solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-25.844114335864262</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-25.844114335864262</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-25.844114335864262</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="0.500solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="0.500solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>0.6588682955012527</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">0.6588682955012527</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">0.6588682955012527</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="-0.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="-0.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>0.9185830776018105</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">0.9185830776018105</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">0.9185830776018105</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="-2.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="-2.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-1.4082598726557432</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-1.4082598726557432</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-1.4082598726557432</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="1.200solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="1.200solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-0.4429837300591526</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-0.4429837300591526</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-0.4429837300591526</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="-9.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="-9.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-20.143787975013183</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-20.143787975013183</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-20.143787975013183</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="-11.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="-11.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-26.013780093398356</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-26.013780093398356</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-26.013780093398356</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
- <phase:BindingEnergy phase:stdInChIKey="-15.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:BindingEnergy phase:moleculeID="-15.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
<phase:TotalEnergy>-38.635444108544405</phase:TotalEnergy>
- <phase:EnergyContribution phase:ssipID1="1">-38.635444108544405</phase:EnergyContribution>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-38.635444108544405</phase:EnergyContribution></phase:EnergyContributions>
</phase:BindingEnergy>
</phase:BindingEnergyCollection>
</phase:EnergyValues>
diff --git a/solventmapcreator/test/resources/watersolvent.xml b/solventmapcreator/test/resources/watersolvent.xml
index 4fb26bd..68fbabf 100644
--- a/solventmapcreator/test/resources/watersolvent.xml
+++ b/solventmapcreator/test/resources/watersolvent.xml
@@ -1,20 +1,34 @@
<?xml version='1.0' encoding='UTF-8'?>
<phase:SolventList xmlns:cml="http://www.xml-cml.org/schema" xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP">
- <phase:Solvent phase:solventID="water" phase:solventName="water" phase:numberOfMolecules="1">
- <phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
- <ssip:SSIPList>
- <ssip:SurfaceInformation numberOfPoints="1000">
- <ssip:IsosurfaceDensity>0.002</ssip:IsosurfaceDensity>
- <ssip:TotalSurfaceArea>10.0</ssip:TotalSurfaceArea>
- <ssip:NegativeSurfaceArea>5.0</ssip:NegativeSurfaceArea>
- <ssip:PositiveSurfaceArea>5.0</ssip:PositiveSurfaceArea>
- </ssip:SurfaceInformation>
- <ssip:SSIP x3="1.0" y3="0.0" z3="0.0" nearestAtomID="a1">2.8</ssip:SSIP>
- <ssip:SSIP x3="1.0" y3="1.0" z3="1.0" nearestAtomID="a1">2.8</ssip:SSIP>
- <ssip:SSIP x3="0.0" y3="1.0" z3="1.0" nearestAtomID="a1">-4.5</ssip:SSIP>
- <ssip:SSIP x3="0.0" y3="1.0" z3="0.0" nearestAtomID="a1">-4.5</ssip:SSIP>
- </ssip:SSIPList>
- <phase:Concentration phase:units="MOLAR">55.350000</phase:Concentration>
- </phase:Molecule>
- </phase:Solvent>
+ <phase:Solvents>
+ <phase:Solvent phase:solventID="water" phase:solventName="water">
+ <phase:Molecules>
+ <phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N"><cml:molecule ssip:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" cml:id="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="O" cml:id="a1" cml:x3="0.0569236794019" cml:y3="0.53497425302" cml:z3="-9.99862395488E-5"/>
+ <cml:atom cml:elementType="H" cml:id="a2" cml:x3="-0.735721920018" cml:y3="-0.0219270863225" cml:z3="-1.029173866E-4"/>
+ <cml:atom cml:elementType="H" cml:id="a3" cml:x3="0.785198240616" cml:y3="-0.103847166698" cml:z3="-1.97096373822E-4"/>
+ </cml:atomArray>
+ <cml:bondArray>
+ <cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a3" cml:order="1"/>
+ </cml:bondArray>
+ </cml:molecule>
+ <ssip:SurfaceInformation>
+ <ssip:TotalSurfaceArea>37.48483410829331</ssip:TotalSurfaceArea>
+ <ssip:NegativeSurfaceArea>18.664358683092974</ssip:NegativeSurfaceArea>
+ <ssip:PositiveSurfaceArea>18.82047542519977</ssip:PositiveSurfaceArea>
+ <ssip:ElectronDensityIsosurface>0.002</ssip:ElectronDensityIsosurface>
+ <ssip:NumberOFMEPSPoints>2286</ssip:NumberOFMEPSPoints>
+ </ssip:SurfaceInformation>
+ <phase:SSIPs phase:units="MOLAR">
+ <phase:SSIP ssip:value="2.9387503903833574" ssip:nearestAtomID="a3" cml:x3="1.509794550767402" cml:y3="-0.8784982637871289" cml:z3="-1.6986589692899999E-4" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="2.9275582734233065" ssip:nearestAtomID="a2" cml:x3="-1.4603207114038939" cml:y3="-0.790973405157027" cml:z3="0.12362427220238399" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="-6.263074063139137" ssip:nearestAtomID="a1" cml:x3="0.156188781751346" cml:y3="1.6969169177862917" cml:z3="1.172598045109361" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ <phase:SSIP ssip:value="-6.607684490829715" ssip:nearestAtomID="a1" cml:x3="0.06855491260794999" cml:y3="1.9788577934582507" cml:z3="-0.77762067563301" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.350000</phase:TotalConcentration></phase:SSIP>
+ </phase:SSIPs>
+</phase:Molecule>
+ </phase:Molecules>
+ </phase:Solvent>
+ </phase:Solvents>
</phase:SolventList>
--
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