diff --git a/solventmapcreator/polynomialanalysis/polynomialplotting.py b/solventmapcreator/polynomialanalysis/polynomialplotting.py
new file mode 100644
index 0000000000000000000000000000000000000000..d7fdbd14fdd4191a260f0b1e6200b8de1f1a09ec
--- /dev/null
+++ b/solventmapcreator/polynomialanalysis/polynomialplotting.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for taking the datapoints for the solvation curve, and generating
+the polynomial fit data and also the plots.
+
+@author: mark
+"""
+
+import logging
+import resultsanalysis.resultsoutput.plottinginput as plottinginput
+import solventmapcreator.io.polynomialdatawriter as polynomialdatawriter
+import solventmapcreator.io.solvationenergyreader as solvationenergyreader
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def plot_energies_from_file(free_energy_filename, polynomial_order):
+ """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)
+ return plottinginput.create_scatter_graph_with_polynomial(plot_data)
+
+def parse_energies_create_plot_input_data(free_energy_filename, polynomial_order):
+ """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)
+ plot_data = datapoints.generateScatterPlotParameters(label_type='', polynomial_order=polynomial_order)
+ plot_data['figure_label'] = free_energy_filename.replace('.xml', '')
+ return plot_data
+
+def parse_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 write_poly_data_to_file(datapoints, order_list, filename):
+ """This calculates the polynomial information, and then outputs the
+ information to file.
+ """
+ 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)
diff --git a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
new file mode 100644
index 0000000000000000000000000000000000000000..3a50db705360bd51d50aee4ed6bd6a9841ebe0f0
--- /dev/null
+++ b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for testing the polynomialplotting script.
+
+@author: mark
+"""
+
+import logging
+import os
+import numpy as np
+import unittest
+import solventmapcreator.io.solvationenergyreader as solvationenergyreader
+import solventmapcreator.polynomialanalysis.polynomialplotting as polynomialplotting
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.DEBUG)
+
+class PolynomialPlottingTestCase(unittest.TestCase):
+ """Test case for polynomialplotting script
+ """
+ def setUp(self):
+ """Set up for tests
+ """
+ self.expected_datapoints = solvationenergyreader.parse_free_energy_from_file_with_data_arrays("resources/water.xml")
+ def tearDown(self):
+ """Clean up after tests.
+ """
+ del self.expected_datapoints
+ if os.path.isfile("actual_water_poly_fit.csv"):
+ os.remove("actual_water_poly_fit.csv")
+ def test_parse_energies_create_plot_input_data(self):
+ """Test to see expected plot data is returned.
+ """
+ expected_dict = {'figure_label': "resources/water",
+ '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",
+ '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': "/$kJmol^{-1}$"}
+ actual_dict = polynomialplotting.parse_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()))
+ 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])
+ def test_parse_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)
+ 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_write_poly_data_to_file(self):
+ """Test to see if expected polynomial fit data is written to file.
+ """
+ expected_file_name = "resources/water_poly_fit.csv"
+ actual_file_name = "actual_water_poly_fit.csv"
+ poly_file_out = polynomialplotting.write_poly_data_to_file(self.expected_datapoints,
+ [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_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.xml")
+ self.assertEqual(self.expected_datapoints, actual_datapoints)
+
diff --git a/solventmapcreator/test/resources/water_poly_fit.csv b/solventmapcreator/test/resources/water_poly_fit.csv
new file mode 100644
index 0000000000000000000000000000000000000000..0342fd8575a940e3f3ea75fd0cc8d82a911a87fa
--- /dev/null
+++ b/solventmapcreator/test/resources/water_poly_fit.csv
@@ -0,0 +1,3 @@
+Order RMSE Covariance Coefficients
+2 4.0483148 180.2773802 -3.5005663 -0.7862852 -0.2194883
+4 0.3415296 1.2830673 0.5181064 0.2546154 -0.3766517 -0.0206377 -0.0003760
diff --git a/solventmapcreator/test/solvationmapcreatortests.py b/solventmapcreator/test/solvationmapcreatortests.py
index 2655f1a3b59b3352294ebf01f5ff998ba247f49c..cedc2250c65320f9279b09207e66114399cf110b 100644
--- a/solventmapcreator/test/solvationmapcreatortests.py
+++ b/solventmapcreator/test/solvationmapcreatortests.py
@@ -18,7 +18,7 @@ from solventmapcreator.test.solvationcalculationtest.solvationplotinformationtes
from solventmapcreator.test.solvationcalculationtest.fractionaloccupancycalculatortest import FractionalOccupancyCalculatorTestCase
from solventmapcreator.test.polynomialanalysistest.polynomialdataanalysistest import PolynomialDataAnalysisTestCase
from solventmapcreator.test.polynomialanalysistest.polynomialcomparisontest import PolynomialComparisonTestCase
-
+from solventmapcreator.test.polynomialanalysistest.polynomialplottingtest import PolynomialPlottingTestCase
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
@@ -32,7 +32,8 @@ SOLVATION_CALCULATION_TEST_CASES = [SolvationCalculatorTestCase,
FractionalOccupancyCalculatorTestCase]
POLYNOMIAL_ANALYSIS_TEST_CASES = [PolynomialDataAnalysisTestCase,
- PolynomialComparisonTestCase]
+ PolynomialComparisonTestCase,
+ PolynomialPlottingTestCase]
def test_suite():
"""Function creates a test suite and then loads all the tests from the