From d96c7086c0a5e0e28bcdae75aa0ef80aa7335b0f Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Wed, 19 Jul 2017 13:14:33 +0100
Subject: [PATCH] create method to calculate matrix.
---
.../solvationcalculation/solvationcalculator.py | 10 ++++++++++
.../solvationcalculatortest.py | 6 ++++++
2 files changed, 16 insertions(+)
diff --git a/solventmapcreator/solvationcalculation/solvationcalculator.py b/solventmapcreator/solvationcalculation/solvationcalculator.py
index 1ed157c..eba12c0 100644
--- a/solventmapcreator/solvationcalculation/solvationcalculator.py
+++ b/solventmapcreator/solvationcalculation/solvationcalculator.py
@@ -39,6 +39,16 @@ pairwise manner. As detailed in DOI: http://dx.doi.org/10.1039/c3sc22124e.
"""
EVDW = -5.6
+def calcluate_association_energy_matrix(epsilon_i_list, epsilon_j_list, temperature, theta, polynomial_coefficients):
+ """This iterates through and fills an array with all the solvation energies.
+ """
+ association_matrix = np.zeros((len(epsilon_i_list), len(epsilon_j_list)))
+ for i in range(len(epsilon_i_list)):
+ for j in range(len(epsilon_j_list)):
+ association_energy = calculate_association_energy(epsilon_i_list[i], epsilon_j_list[j], temperature, theta, polynomial_coefficients)
+ association_matrix[i][j] = association_energy
+ return association_matrix
+
def calculate_association_energy(epsilon_i, epsilon_j, temperature, theta, polynomial_coefficients):
"""This calculates the energy described above
"""
diff --git a/solventmapcreator/test/solvationcalculationtest/solvationcalculatortest.py b/solventmapcreator/test/solvationcalculationtest/solvationcalculatortest.py
index a479a06..e566d40 100644
--- a/solventmapcreator/test/solvationcalculationtest/solvationcalculatortest.py
+++ b/solventmapcreator/test/solvationcalculationtest/solvationcalculatortest.py
@@ -24,6 +24,12 @@ class SolvationCalculatorTestCase(unittest.TestCase):
def tearDown(self):
"""tear down after tests.
"""
+ def test_calcluate_association_energy_matrix(self):
+ """Test to see if expected matrix is produced.
+ """
+ expected_array = np.array([[-1.2500649680700651]])
+ actual_array = solvationcalculator.calcluate_association_energy_matrix([1.0],[1.0], 298.0, 1.0, np.array([0.5, 1.0]))
+ np.testing.assert_array_almost_equal(expected_array, actual_array)
def test_calculate_association_energy(self):
"""Test to see if expected_value is returned.
"""
--
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