From b3b97872c129406257cebc25932d994deae2c6d6 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Wed, 9 Aug 2017 21:35:00 +0100
Subject: [PATCH] add methods to write out fitting to the two sections.
---
.../polynomialanalysis/polynomialplotting.py | 20 +++++++++++
.../polynomialplottingtest.py | 35 +++++++++++++++++++
.../test/resources/water_poly_fit_split.csv | 5 +++
3 files changed, 60 insertions(+)
create mode 100644 solventmapcreator/test/resources/water_poly_fit_split.csv
diff --git a/solventmapcreator/polynomialanalysis/polynomialplotting.py b/solventmapcreator/polynomialanalysis/polynomialplotting.py
index 9c4faab..083144f 100644
--- a/solventmapcreator/polynomialanalysis/polynomialplotting.py
+++ b/solventmapcreator/polynomialanalysis/polynomialplotting.py
@@ -31,6 +31,26 @@ def parse_energies_create_plot_input_data(free_energy_filename, polynomial_order
plot_data['figure_label'] = free_energy_filename.replace('.xml', '')
return plot_data
+def parse_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
+ 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 write_poly_data_to_file_split_fit(datapoints, order_list, filename,
+ pos_subset_list, neg_subset_list):
+ """This calculates the polynomial information for fitting to the 2 sub sets
+ and writes to file.
+ """
+ return polynomialdatawriter.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):
"""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.
diff --git a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
index 9c37b76..1a2a210 100644
--- a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
+++ b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
@@ -32,6 +32,8 @@ class PolynomialPlottingTestCase(unittest.TestCase):
os.remove("actual_water_poly_fit.csv")
if os.path.isfile("actual_water_poly_fit_subset.csv"):
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):
"""Test to see expected plot data is returned.
"""
@@ -71,6 +73,39 @@ class PolynomialPlottingTestCase(unittest.TestCase):
else:
LOGGER.debug("assert equal string")
self.assertEqual(actual_dict[key], expected_dict[key])
+ def test_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_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()
+ 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_split_fit(self):
+ """Test to see if expected_fit is done on the positive and negative subsets.
+ """
+ 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.write_poly_data_to_file_split_fit(self.expected_datapoints, [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_parse_energies_and_output_poly_data_subset(self):
"""Test to see if expected_fit is done on a smaller subset of points.
"""
diff --git a/solventmapcreator/test/resources/water_poly_fit_split.csv b/solventmapcreator/test/resources/water_poly_fit_split.csv
new file mode 100644
index 0000000..39d3f9a
--- /dev/null
+++ b/solventmapcreator/test/resources/water_poly_fit_split.csv
@@ -0,0 +1,5 @@
+Order Fit Range RMSE Covariance Coefficients
+2 positive 0.0000000 1.2077460 -0.8992891 -0.3969325
+2 negative 0.0188857 0.0017833 6.3245323 2.8927088 -0.0017566
+4 positive 0.0000000 1.3515748 -1.3179762 -0.1267861 -0.0151557 -0.0020380
+4 negative 0.0000000 5.0388427 2.2906276 -0.0985583 -0.0064807 -0.0001546
--
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