diff --git a/solventmapcreator/polynomialanalysis/polynomialplotting.py b/solventmapcreator/polynomialanalysis/polynomialplotting.py
index 964efbf7e1aa58658859c68f5e331fa00f65c25c..e4eb7aaeb9fd6debdc9523787f4816aa426e1b8e 100644
--- a/solventmapcreator/polynomialanalysis/polynomialplotting.py
+++ b/solventmapcreator/polynomialanalysis/polynomialplotting.py
@@ -18,10 +18,24 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-def plot_binding_energies_from_file(free_energy_filename, polynomial_order, **kwargs):
+def plot_free_energies_from_file(free_energy_filename, polynomial_order, **kwargs):
"""This creates in the plotting information, and outputs a plot to file.
"""
- plot_data = parse_binding_energies_create_plot_input_data(free_energy_filename,
+ plot_data = parse_free_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:
+ return plottinginput.create_scatter_graph_with_polynomial(plot_data)
+
+def plot_binding_energies_from_file(binding_energy_filename, polynomial_order, **kwargs):
+ """This creates in the plotting information, and outputs a plot to file.
+ """
+ plot_data = parse_binding_energies_create_plot_input_data(binding_energy_filename,
polynomial_order,
kwargs.get("pos_subset_list",
None),
@@ -51,18 +65,32 @@ def create_scatter_with_split_poly(input_data, **kwargs):
plottinginput.plt.close(scatter_plot)
return 0
-def parse_binding_energies_create_plot_input_data(free_energy_filename, polynomial_order,
+def parse_free_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_binding_energy_from_file_with_data_arrays(free_energy_filename)
+ datapoints = parse_free_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,
+ pos_subset_list, neg_subset_list)
+ plot_data['polynomial coefficients'] = poly_coeff_dict
+ plot_data['figure_label'] = free_energy_filename.replace('.xml', '_fe')
+ return plot_data
+
+def parse_binding_energies_create_plot_input_data(binding_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_binding_energy_from_file_with_data_arrays(binding_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,
pos_subset_list, neg_subset_list)
plot_data['polynomial coefficients'] = poly_coeff_dict
- plot_data['figure_label'] = free_energy_filename.replace('.xml', '')
+ plot_data['figure_label'] = binding_energy_filename.replace('.xml', '_be')
return plot_data
def generate_poly_pos_neg_separate_fit(datapoints, order, pos_subset_list, neg_subset_list):
@@ -76,9 +104,18 @@ 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(binding_energy_filename, order_list, poly_filename,
+def parse_free_energy_poly_data_to_file_split_fit(free_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
+ """This reads in the binding 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)
+ return write_poly_data_to_file_split_fit(datapoints, order_list, poly_filename,
+ pos_subset_list, neg_subset_list)
+
+def parse_binding_energy_poly_data_to_file_split_fit(binding_energy_filename, order_list, poly_filename,
+ pos_subset_list, neg_subset_list):
+ """This reads in the binding energy information, and then performs the fits on the
two separate subsets, and outputs to file.
"""
datapoints = parse_binding_energy_from_file_with_data_arrays(binding_energy_filename)
@@ -96,21 +133,37 @@ def write_poly_data_to_file_split_fit(datapoints, order_list, filename,
pos_subset_list,
neg_subset_list)
-def parse_binding_energies_and_output_poly_data_subset(free_energy_filename, order_list, poly_filename, subset_list):
+
+def parse_free_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_subset = datapoints.createDatapointsSubGroup(subset_list)
+ datapoints_subset.createDataArrays()
+ return write_poly_data_to_file(datapoints_subset, order_list, poly_filename)
+
+def parse_binding_energies_and_output_poly_data_subset(binding_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_binding_energy_from_file_with_data_arrays(free_energy_filename)
+ datapoints = parse_binding_energy_from_file_with_data_arrays(binding_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_free_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)
+ return write_poly_data_to_file(datapoints, order_list, poly_filename)
-def parse_binding_energies_and_output_poly_data(free_energy_filename, order_list, poly_filename):
+def parse_binding_energies_and_output_poly_data(binding_energy_filename, order_list, poly_filename):
"""This reads in the energy information, and then outputs the polynomial
information to file.
"""
- datapoints = parse_binding_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(datapoints, order_list, poly_filename)
def write_poly_data_to_file(datapoints, order_list, filename):
@@ -119,6 +172,12 @@ 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):
+ """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)
+
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.
diff --git a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
index 0dea4c9b4683bccdff4af2534177b3995b133f02..56f27b32692c5d2b330eec431d084e433b2630d8 100644
--- a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
+++ b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
@@ -24,6 +24,7 @@ class PolynomialPlottingTestCase(unittest.TestCase):
"""Set up for tests
"""
self.expected_datapoints = solvationenergyreader.parse_binding_energy_from_file_with_data_arrays("resources/water.xml")
+ self.expected_free_energydatapoints = solvationenergyreader.parse_free_energy_from_file_with_data_arrays("resources/water_freeenergy.xml")
def tearDown(self):
"""Clean up after tests.
"""
@@ -34,10 +35,78 @@ 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_free_energies_create_plot_input_data(self):
+ """Test to see expected plot data is returned.
+ """
+ expected_dict = {'figure_label': "resources/water_freeenergy_fe",
+ 'plot_axis_range':[-15.4 , 7.2 , -38.635444, 0.918583],
+ 'polynomial coefficients': np.array([5.18106356e-01,
+ 2.54615444e-01,
+ -3.76651666e-01,
+ -2.06376692e-02,
+ -3.76010096e-04]),
+ 'polynomial order': 4,
+ 'x_axis_range':[-15.4, 7.2000000000000002],
+ 'x_data': np.array([[-0.1, -11.1, -14.1, -15.4, -2.4,
+ -4.3, -5.4, -9.1, 0.5, 1.2, 7.2]]),
+ 'x_label': "SSIP Value",
+ 'y_axis_range': [-38.635444, 0.918583],
+ 'y_data': np.array([[0.9185830776018105, -26.013780093398356,
+ -34.8195308084233, -38.635444108544405,
+ -1.4082598726557432, -6.170784422419204,
+ -9.315464914185585, -20.143787975013183,
+ 0.6588682955012527, -0.4429837300591526,
+ -25.844114335864262]]),
+ 'y_label': "Solvation Free Energy/$kJmol^{-1}$"}
+ actual_dict = polynomialplotting.parse_free_energies_create_plot_input_data("resources/water_freeenergy.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()))
+ for key in actual_dict.keys():
+ LOGGER.debug("Key: %s", key)
+ if key == 'y_data' or key == 'x_data' or key == 'polynomial coefficients':
+ LOGGER.debug("assert equal array x and y data")
+ np.testing.assert_array_almost_equal(actual_dict[key],
+ expected_dict[key])
+ elif key == 'plot_axis_range' or key == 'x_axis_range' or key == 'y_axis_range':
+ np.testing.assert_array_almost_equal(np.array(actual_dict[key]),
+ np.array(expected_dict[key]))
+ else:
+ LOGGER.debug("assert equal string")
+ self.assertEqual(actual_dict[key], expected_dict[key])
+ #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_free_energies_create_plot_input_data("resources/water_freeenergy.xml", 4,
+ pos_set_list, neg_set_list)
+ self.assertListEqual(sorted(actual_dict2.keys()), sorted(expected_dict.keys()))
+ for key in actual_dict.keys():
+ LOGGER.debug("Key: %s", key)
+ if key == 'y_data' or key == 'x_data':
+ LOGGER.debug("assert equal array x and y data")
+ np.testing.assert_array_almost_equal(actual_dict2[key],
+ expected_dict[key])
+ elif key == 'polynomial coefficients':
+ self.assertListEqual(["negative", "positive"],
+ sorted(actual_dict2['polynomial coefficients'].keys()))
+ negative_coeffs = np.array([5.038843e+00, 2.290628e+00, -9.855830e-02,
+ -6.480660e-03, -1.545673e-04])
+ positive_coeffs = np.array([1.351575, -1.317976, -0.126786,
+ -0.015156, -0.002038])
+ np.testing.assert_array_almost_equal(negative_coeffs,
+ actual_dict2['polynomial coefficients']["negative"])
+ np.testing.assert_array_almost_equal(positive_coeffs,
+ actual_dict2['polynomial coefficients']["positive"])
+ elif key == 'plot_axis_range' or key == 'x_axis_range' or key == 'y_axis_range':
+ np.testing.assert_array_almost_equal(np.array(actual_dict2[key]),
+ np.array(expected_dict[key]))
+ else:
+ LOGGER.debug("assert equal string")
+ self.assertEqual(expected_dict[key], actual_dict2[key])
def test_parse_binding_energies_create_plot_input_data(self):
"""Test to see expected plot data is returned.
"""
- expected_dict = {'figure_label': "resources/water",
+ expected_dict = {'figure_label': "resources/water_be",
'plot_axis_range':[-15.4 , 7.2 , -38.635444, 0.918583],
'polynomial coefficients': np.array([5.18106356e-01,
2.54615444e-01,
@@ -122,7 +191,7 @@ class PolynomialPlottingTestCase(unittest.TestCase):
actual_dict["negative"])
np.testing.assert_array_almost_equal(positive_coeffs,
actual_dict["positive"])
- def test_parse_poly_data_to_file_split_fit(self):
+ def test_free_energy_parse_poly_data_to_file_split_fit(self):
"""Test to see if expected fit is done on the positive and negative subsets
after the file was read in.
"""
@@ -130,9 +199,26 @@ class PolynomialPlottingTestCase(unittest.TestCase):
actual_file_name = "actual_water_poly_fit_split.csv"
neg_set_list = ["-5.400solute", "-4.300solute", "-9.100solute", "-11.100solute", "-15.400solute"]
pos_set_list = ["0.500solute", "1.200solute", "7.200solute"]
- poly_file_out = polynomialplotting.parse_poly_data_to_file_split_fit("resources/water.xml", [2, 4],
- actual_file_name, pos_set_list,
- neg_set_list)
+ poly_file_out = polynomialplotting.parse_free_energy_poly_data_to_file_split_fit("resources/water_freeenergy.xml", [2, 4],
+ actual_file_name, pos_set_list,
+ neg_set_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_binding_energy_parse_poly_data_to_file_split_fit(self):
+ """Test to see if expected fit is done on the positive and negative subsets
+ after the file was read in.
+ """
+ expected_file_name = "resources/water_poly_fit_split.csv"
+ actual_file_name = "actual_water_poly_fit_split.csv"
+ neg_set_list = ["-5.400solute", "-4.300solute", "-9.100solute", "-11.100solute", "-15.400solute"]
+ pos_set_list = ["0.500solute", "1.200solute", "7.200solute"]
+ poly_file_out = polynomialplotting.parse_binding_energy_poly_data_to_file_split_fit("resources/water.xml", [2, 4],
+ actual_file_name, pos_set_list,
+ neg_set_list)
self.assertEqual(0, poly_file_out)
with open(expected_file_name, 'r') as exp_file:
exp_file_lines = exp_file.readlines()
@@ -155,6 +241,20 @@ 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_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_free_energies_and_output_poly_data_subset("resources/water_freeenergy.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_binding_energies_and_output_poly_data_subset(self):
"""Test to see if expected_fit is done on a smaller subset of points.
"""
@@ -168,6 +268,19 @@ 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_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_free_energies_and_output_poly_data("resources/water_freeenergy.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()
+ 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_binding_energies_and_output_poly_data(self):
"""Test to see if expected polynomial fit information is outputted to file.
"""
@@ -193,6 +306,11 @@ 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):
+ """Test to see if expected datapoints are read in.
+ """
+ actual_datapoints = polynomialplotting.parse_free_energy_from_file_with_data_arrays("resources/water_freeenergy.xml")
+ self.assertEqual(self.expected_free_energydatapoints, actual_datapoints)
def test_parse_binding_energy_from_file_with_data_arrays(self):
"""Test to see if expected datapoints are read in.
"""
diff --git a/solventmapcreator/test/resources/water_freeenergy.xml b/solventmapcreator/test/resources/water_freeenergy.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bb8c15910d6d7452d2e01e8ced7ce16808991082
--- /dev/null
+++ b/solventmapcreator/test/resources/water_freeenergy.xml
@@ -0,0 +1,48 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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:FreeEnergy phase:moleculeID="-5.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-9.315464914185585</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-9.315464914185585</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="-4.300solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-6.170784422419204</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-6.170784422419204</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="7.200solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-25.844114335864262</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-25.844114335864262</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="0.500solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>0.6588682955012527</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">0.6588682955012527</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="-0.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>0.9185830776018105</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">0.9185830776018105</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="-2.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-1.4082598726557432</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-1.4082598726557432</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="1.200solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-0.4429837300591526</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-0.4429837300591526</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="-9.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-20.143787975013183</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-20.143787975013183</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="-11.100solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-26.013780093398356</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-26.013780093398356</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ <phase:FreeEnergy phase:moleculeID="-15.400solute" phase:fromSolventID="" phase:toSolventID="water" phase:valueType="MOLEFRACTION">
+ <phase:TotalEnergy>-38.635444108544405</phase:TotalEnergy>
+ <phase:EnergyContributions><phase:EnergyContribution phase:ssipID="1">-38.635444108544405</phase:EnergyContribution></phase:EnergyContributions>
+ </phase:FreeEnergy>
+ </phase:FreeEnergyCollection>
+</phase:EnergyValues>