From 4fb86fb67f0787c48c636095995f2571a5364aaa Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Fri, 7 Jul 2017 20:45:40 +0100
Subject: [PATCH] added more functions to do it from a higher level, and rename
some input variables for greater clarity.
---
.../polynomialcomparison.py | 28 +++++++++++++------
.../polynomialcomparisontest.py | 24 ++++++++++++++--
2 files changed, 42 insertions(+), 10 deletions(-)
diff --git a/solventmapcreator/polynomialanalysis/polynomialcomparison.py b/solventmapcreator/polynomialanalysis/polynomialcomparison.py
index 9d2e813..f78446f 100644
--- a/solventmapcreator/polynomialanalysis/polynomialcomparison.py
+++ b/solventmapcreator/polynomialanalysis/polynomialcomparison.py
@@ -15,15 +15,21 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-def calculate_hausdorff_distance_matrix(x_values, polynomial_dict_by_solvent_id):
+def calculate_hausdorff_distance_matrix_from_poly_coeff(x_values, polynomial_order, poly_data_by_id):
+ """This first extracts and calculates the values, then returns the Hausdorff matrix.
+ """
+ polynomial_values_by_id = calculate_polynomial_values_all_solvents(x_values, polynomial_order, poly_data_by_id)
+ return calculate_hausdorff_distance_matrix(x_values, polynomial_values_by_id)
+
+def calculate_hausdorff_distance_matrix(x_values, polynomial_values_dict_by_solvent_id):
"""This calculates the hausdorff distance between all polynomial curves.
"""
- sorted_id_list = get_sorted_solvent_id_list(polynomial_dict_by_solvent_id)
+ sorted_id_list = get_sorted_solvent_id_list(polynomial_values_dict_by_solvent_id)
hausdorff_matrix = np.zeros((len(sorted_id_list), len(sorted_id_list)))
for i in range(len(sorted_id_list)):
- poly_values_i = polynomial_dict_by_solvent_id[sorted_id_list[i]]
+ poly_values_i = polynomial_values_dict_by_solvent_id[sorted_id_list[i]]
for j in range(i):
- poly_values_j = polynomial_dict_by_solvent_id[sorted_id_list[j]]
+ poly_values_j = polynomial_values_dict_by_solvent_id[sorted_id_list[j]]
hausdorff_value = calculate_hausdorff_distance(x_values, poly_values_i, poly_values_j)
if i == j:
hausdorff_matrix[i][i] = hausdorff_value
@@ -32,15 +38,21 @@ def calculate_hausdorff_distance_matrix(x_values, polynomial_dict_by_solvent_id)
hausdorff_matrix[j][i] = hausdorff_value
return hausdorff_matrix
-def calculate_rmsd_matrix(polynomial_dict_by_solvent_id):
+def calculate_rmsd_matrix_from_poly_coeff(x_values, polynomial_order, poly_data_by_id):
+ """This first extracts and calculates the values, then returns the RMSD matrix.
+ """
+ polynomial_values_by_id = calculate_polynomial_values_all_solvents(x_values, polynomial_order, poly_data_by_id)
+ return calculate_rmsd_matrix(polynomial_values_by_id)
+
+def calculate_rmsd_matrix(polynomial_values_dict_by_solvent_id):
"""This calculates the rmsd between all curves, and outputs a matrix.
"""
- sorted_id_list = get_sorted_solvent_id_list(polynomial_dict_by_solvent_id)
+ sorted_id_list = get_sorted_solvent_id_list(polynomial_values_dict_by_solvent_id)
rmsd_matrix = np.zeros((len(sorted_id_list), len(sorted_id_list)))
for i in range(len(sorted_id_list)):
- poly_values_i = polynomial_dict_by_solvent_id[sorted_id_list[i]]
+ poly_values_i = polynomial_values_dict_by_solvent_id[sorted_id_list[i]]
for j in range(i):
- poly_values_j = polynomial_dict_by_solvent_id[sorted_id_list[j]]
+ poly_values_j = polynomial_values_dict_by_solvent_id[sorted_id_list[j]]
rmsd_value = calculate_rmsd_between_curves(poly_values_i, poly_values_j)
#Noting that the matrix is symmetric
if i == j:
diff --git a/solventmapcreator/test/polynomialanalysistest/polynomialcomparisontest.py b/solventmapcreator/test/polynomialanalysistest/polynomialcomparisontest.py
index 1047d4c..3740157 100644
--- a/solventmapcreator/test/polynomialanalysistest/polynomialcomparisontest.py
+++ b/solventmapcreator/test/polynomialanalysistest/polynomialcomparisontest.py
@@ -46,8 +46,20 @@ class PolynomialComparisonTestCase(unittest.TestCase):
del self.poly_data_by_solvent_id
del self.x_values
del self.poly_values_dict
- def test_calculate_hausdorff_distance_matrix(self):
+ def test_(self):
+ """
"""
+ def test_calculate_hausdorff_distance_matrix_from_poly_coeff(self):
+ """Test tp see if expected matrix is produced.
+ """
+ expected_matrix = np.array([[0.0, 1.0, 4.0],
+ [1.0, 0.0, 3.0],
+ [4.0, 3.0, 0.0]])
+ actual_matrix = polynomialcomparison.calculate_hausdorff_distance_matrix_from_poly_coeff(self.x_values,
+ 2, self.poly_data_by_solvent_id)
+ np.testing.assert_array_almost_equal(expected_matrix, actual_matrix)
+ def test_calculate_hausdorff_distance_matrix(self):
+ """Test to see if expected matrix is produced.
"""
expected_matrix = np.array([[0.0, 1.0, 4.0],
[1.0, 0.0, 3.0],
@@ -55,6 +67,14 @@ class PolynomialComparisonTestCase(unittest.TestCase):
actual_matrix = polynomialcomparison.calculate_hausdorff_distance_matrix(self.x_values,
self.poly_values_dict)
np.testing.assert_array_almost_equal(expected_matrix, actual_matrix)
+ def test_calculate_rmsd_matrix_from_poly_coeff(self):
+ """Test to see if expected matrix is generated.
+ """
+ expected_matrix = np.array([[0.0, 1.0, 2.607681],
+ [1.0, 0.0, 1.949359],
+ [2.607681, 1.949359, 0.0]])
+ actual_matrix = polynomialcomparison.calculate_rmsd_matrix_from_poly_coeff(self.x_values, 2, self.poly_data_by_solvent_id)
+ np.testing.assert_array_almost_equal(expected_matrix, actual_matrix)
def test_calculate_rmsd_matrix(self):
"""Test to see if expected RMSD matrix is produced.
"""
@@ -115,4 +135,4 @@ class PolynomialComparisonTestCase(unittest.TestCase):
expected_values = np.array([4.0, 1.0, 0.0, 1.0, 4.0])
poly_coefficients = self.poly_data_by_solvent_id["poly_fit"][2]["coefficients"]
actual_values = polynomialcomparison.calculate_polynomial_values(self.x_values, poly_coefficients)
- np.testing.assert_array_almost_equal(expected_values, actual_values)
\ No newline at end of file
+ np.testing.assert_array_almost_equal(expected_values, actual_values)
--
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