From 364e85d34866396800b1ea128ee489220e36601c Mon Sep 17 00:00:00 2001 From: Josh Allen Date: Sat, 11 Feb 2012 16:36:26 -0500 Subject: [PATCH] Added unit test suites for the TransitionState and Reaction classes. These suites focus on checking the setting of various attributes and properties, as well as reconstructing objects from pickled and repr() formats. --- tests/reactiontest.py | 181 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 181 insertions(+) create mode 100644 tests/reactiontest.py diff --git a/tests/reactiontest.py b/tests/reactiontest.py new file mode 100644 index 0000000..9d712f2 --- /dev/null +++ b/tests/reactiontest.py @@ -0,0 +1,181 @@ +#!/usr/bin/env python +# encoding: utf-8 + +################################################################################ +# +# PyRate - Python tools for computing chemical reaction rates +# +# Copyright (c) 2012 by Joshua W. Allen (jwallen@mit.edu) +# Yury V. Suleimanov (ysuleyma@mit.edu) +# William H. Green (whgreen@mit.edu) +# +# Permission is hereby granted, free of charge, to any person obtaining a +# copy of this software and associated documentation files (the "Software"), +# to deal in the Software without restriction, including without limitation +# the rights to use, copy, modify, merge, publish, distribute, sublicense, +# and/or sell copies of the Software, and to permit persons to whom the +# Software is furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. +# +################################################################################ + +""" +This script contains unit tests of the :mod:`pyrate.reaction` module. +""" + +import unittest +import math + +from pyrate.reaction import * +from pyrate.species import Species +from pyrate.kinetics import Arrhenius + +################################################################################ + +class TestTransitionState(unittest.TestCase): + """ + Contains unit tests of the :class:`TransitionState` class. + """ + + def setUp(self): + """ + A function run before each unit test in this class. + """ + self.label = 'TS1' + self.statmech = None + self.frequency = pq.Quantity(1000, "cm^-1") + self.transitionState = TransitionState( + label = self.label, + statmech = self.statmech, + frequency = self.frequency, + ) + + def test_label(self): + """ + Test that the TransitionState label property was properly set. + """ + self.assertEqual(self.transitionState.label, self.label) + + def test_frequency(self): + """ + Test that the TransitionState frequency property was properly set. + """ + self.assertAlmostEqual(self.transitionState.frequency / self.frequency, 1.0, 6, '{0} != {1} within 6 places'.format(self.transitionState.frequency, self.frequency)) + + def test_pickle(self): + """ + Test that a TransitionState object can be successfully pickled and + unpickled with no loss of information. + """ + import cPickle + transitionState = cPickle.loads(cPickle.dumps(self.transitionState)) + self.assertEqual(self.transitionState.label, transitionState.label) + self.assertEqual(self.transitionState.statmech, transitionState.statmech) + self.assertAlmostEqual(self.transitionState.frequency / transitionState.frequency, 1.0, 6, '{0} != {1} within 6 places'.format(self.transitionState.frequency, transitionState.frequency)) + + def test_repr(self): + """ + Test that a TransitionState object can be successfully reconstructed + from its repr() output with no loss of information. + """ + exec('transitionState = {0!r}'.format(self.transitionState)) + self.assertEqual(self.transitionState.label, transitionState.label) + self.assertEqual(self.transitionState.statmech, transitionState.statmech) + self.assertAlmostEqual(self.transitionState.frequency / transitionState.frequency, 1.0, 6, '{0} != {1} within 6 places'.format(self.transitionState.frequency, transitionState.frequency)) + +################################################################################ + +class TestReaction(unittest.TestCase): + """ + Contains unit tests of the :class:`Reaction` class. + """ + + def setUp(self): + """ + A function run before each unit test in this class. + """ + self.reactants = [Species(label='C2H4'), Species(label='H')] + self.products = [Species(label='C2H5')] + self.reversible = True + self.kinetics = Arrhenius(A=pq.Quantity(1.0e12,"cm^3/(mol*s)"), n=0.5, Ea=pq.Quantity(10.0,"kcal/mol"), T0=1*pq.K) + self.transitionState = None + self.reaction = Reaction( + reactants = self.reactants, + products = self.products, + reversible = self.reversible, + kinetics = self.kinetics, + transitionState = self.transitionState, + ) + + def test_reactants(self): + """ + Test that the Reaction reactants property was properly set. + """ + self.assertEqual(self.reaction.reactants, self.reactants) + + def test_reactants(self): + """ + Test that the Reaction products property was properly set. + """ + self.assertEqual(self.reaction.products, self.products) + + def test_reversible(self): + """ + Test that the Reaction reversible property was properly set. + """ + self.assertEqual(self.reaction.reversible, self.reversible) + + def test_kinetics(self): + """ + Test that the Reaction kinetics property was properly set. + """ + self.assertAlmostEqual(self.reaction.kinetics.A / self.kinetics.A, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.A, self.kinetics.A)) + self.assertAlmostEqual(self.reaction.kinetics.n / self.kinetics.n, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.n, self.kinetics.n)) + self.assertAlmostEqual(self.reaction.kinetics.Ea / self.kinetics.Ea, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.Ea, self.kinetics.Ea)) + self.assertAlmostEqual(self.reaction.kinetics.T0 / self.kinetics.T0, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.T0, self.kinetics.T0)) + + def test_pickle(self): + """ + Test that a TransitionState object can be successfully pickled and + unpickled with no loss of information. + """ + import cPickle + reaction = cPickle.loads(cPickle.dumps(self.reaction)) + self.assertEqual(self.reaction.reactants[0].label, reaction.reactants[0].label) + self.assertEqual(self.reaction.reactants[1].label, reaction.reactants[1].label) + self.assertEqual(self.reaction.products[0].label, reaction.products[0].label) + self.assertEqual(self.reaction.reversible, reaction.reversible) + self.assertAlmostEqual(self.reaction.kinetics.A / reaction.kinetics.A, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.A, reaction.kinetics.A)) + self.assertAlmostEqual(self.reaction.kinetics.n / reaction.kinetics.n, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.n, reaction.kinetics.n)) + self.assertAlmostEqual(self.reaction.kinetics.Ea / reaction.kinetics.Ea, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.Ea, reaction.kinetics.Ea)) + self.assertAlmostEqual(self.reaction.kinetics.T0 / reaction.kinetics.T0, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.T0, reaction.kinetics.T0)) + + def test_repr(self): + """ + Test that a TransitionState object can be successfully reconstructed + from its repr() output with no loss of information. + """ + exec('reaction = {0!r}'.format(self.reaction)) + self.assertEqual(self.reaction.reactants[0].label, reaction.reactants[0].label) + self.assertEqual(self.reaction.reactants[1].label, reaction.reactants[1].label) + self.assertEqual(self.reaction.products[0].label, reaction.products[0].label) + self.assertEqual(self.reaction.reversible, reaction.reversible) + self.assertAlmostEqual(self.reaction.kinetics.A / reaction.kinetics.A, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.A, reaction.kinetics.A)) + self.assertAlmostEqual(self.reaction.kinetics.n / reaction.kinetics.n, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.n, reaction.kinetics.n)) + self.assertAlmostEqual(self.reaction.kinetics.Ea / reaction.kinetics.Ea, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.Ea, reaction.kinetics.Ea)) + self.assertAlmostEqual(self.reaction.kinetics.T0 / reaction.kinetics.T0, 1.0, 6, '{0} != {1} within 6 places'.format(self.reaction.kinetics.T0, reaction.kinetics.T0)) + +################################################################################ + +if __name__ == '__main__': + unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))