From ef4d25f62b4473cdca7cdfcba5f1a956a14e1251 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Mon, 24 Jul 2017 10:01:54 +0100
Subject: [PATCH] added method to do polynomial analysis on a subset of points.
---
.../polynomialanalysis/polynomialplotting.py | 10 ++++++++++
.../polynomialplottingtest.py | 15 +++++++++++++++
.../test/resources/water_poly_fit_subset.csv | 3 +++
3 files changed, 28 insertions(+)
create mode 100644 solventmapcreator/test/resources/water_poly_fit_subset.csv
diff --git a/solventmapcreator/polynomialanalysis/polynomialplotting.py b/solventmapcreator/polynomialanalysis/polynomialplotting.py
index d7fdbd1..9c4faab 100644
--- a/solventmapcreator/polynomialanalysis/polynomialplotting.py
+++ b/solventmapcreator/polynomialanalysis/polynomialplotting.py
@@ -31,6 +31,16 @@ 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_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_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.
diff --git a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
index 3a50db7..5b01f83 100644
--- a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
+++ b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
@@ -30,6 +30,8 @@ class PolynomialPlottingTestCase(unittest.TestCase):
del self.expected_datapoints
if os.path.isfile("actual_water_poly_fit.csv"):
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")
def test_parse_energies_create_plot_input_data(self):
"""Test to see expected plot data is returned.
"""
@@ -69,6 +71,19 @@ class PolynomialPlottingTestCase(unittest.TestCase):
else:
LOGGER.debug("assert equal string")
self.assertEqual(actual_dict[key], expected_dict[key])
+ def test_parse_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)
+ 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):
"""Test to see if expected polynomial fit information is outputted to file.
"""
diff --git a/solventmapcreator/test/resources/water_poly_fit_subset.csv b/solventmapcreator/test/resources/water_poly_fit_subset.csv
new file mode 100644
index 0000000..bd92d55
--- /dev/null
+++ b/solventmapcreator/test/resources/water_poly_fit_subset.csv
@@ -0,0 +1,3 @@
+Order RMSE Covariance Coefficients
+2 0.0188857 0.0017833 6.3245323 2.8927088 -0.0017566
+4 0.0000000 5.0388427 2.2906276 -0.0985583 -0.0064807 -0.0001546
--
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