def test_centralmoments_using_MM_model(self):
"""
Given the MM model hard codded bellow,the result of central moment should match exactly the expected one
:return:
"""
counter_nvecs = [[0, 0], [0, 2], [1, 1], [2, 0]]
mcounter_nvecs = [[0, 0], [0, 1], [1, 0], [0, 2], [1, 1], [2, 0]]
counter = [Moment(c,sympy.Symbol("YU{0}".format(i))) for i,c in enumerate(counter_nvecs)]
mcounter = [Moment(c,sympy.Symbol("y_{0}".format(i))) for i,c in enumerate(mcounter_nvecs)]
m = to_sympy_matrix([
['-c_0*y_0*(y_0 + y_1 - 181) + c_1*(-y_0 - y_1 + 301)',
0,
'-c_0',
'-c_0'],
[
'c_2*(-y_0 - y_1 + 301)',
0,
0,
0]
])
species = sympy.Matrix(map(sympy.var, ['y_0', 'y_1']))
propensities = to_sympy_matrix(['c_0*y_0*(y_0 + y_1 - 181)',
'c_1*(-y_0 - y_1 + 301)',
'c_2*(-y_0 - y_1 + 301)'])
stoichiometry_matrix = sympy.Matrix([[-1, 1, 0],
[0, 0, 1]])
expected = to_sympy_matrix([
["c_2*(-y_0 - y_1 + 301)"," -2*c_2"," -2*c_2"," 0"],
["-c_0*y_0*y_1*(y_0 + y_1 - 181) + c_1*y_1*(-y_0 - y_1 + 301) + c_2*y_0*(-y_0 - y_1 + 301) - c_2*y_2*(-y_0 - y_1 + 301) - y_1*(-c_0*y_0*(y_0 + y_1 - 181) + c_1*(-y_0 - y_1 + 301))"," -c_0*y_0 - c_1"," -c_0*y_0 - c_0*(y_0 + y_1 - 181) - c_1 - c_2"," -c_2"],
["-2*c_0*y_0**2*(y_0 + y_1 - 181) + c_0*y_0*(y_0 + y_1 - 181) + 2*c_1*y_0*(-y_0 - y_1 + 301) + c_1*(-y_0 - y_1 + 301) - 2*y_2*(-c_0*y_0*(y_0 + y_1 - 181) + c_1*(-y_0 - y_1 + 301))"," 0"," -4*c_0*y_0 + 2*c_0*y_2 + c_0 - 2*c_1"," -4*c_0*y_0 + 2*c_0*y_2 - 2*c_0*(y_0 + y_1 - 181) + c_0 - 2*c_1"]
])
answer = eq_central_moments(counter, mcounter, m, species, propensities, stoichiometry_matrix, 2)
assert_sympy_expressions_equal(answer, expected)
def test_centralmoments_using_p53model(self):
"""
Given the p53 model hard codded bellow,the result of central moment should match exactly the expected one
:return:
"""
counter_nvecs = [[0, 0, 0], [0, 0, 2], [0, 1, 1], [0, 2, 0], [1, 0, 1], [1, 1, 0], [2, 0, 0]]
mcounter_nvecs = [[0, 0, 0], [0, 0, 1], [0, 1, 0], [1, 0, 0], [0, 0, 2], [0, 1, 1], [0, 2, 0],
[1, 0, 1], [1, 1, 0], [2, 0, 0]]
counter = [Moment(c,sympy.Symbol("YU{0}".format(i))) for i,c in enumerate(counter_nvecs)]
mcounter = [Moment(c,sympy.Symbol("y_{0}".format(i))) for i,c in enumerate(mcounter_nvecs)]
m = to_sympy_matrix([
['c_0 - c_1*y_0 - c_2*y_0*y_2/(c_6 + y_0)',
0,
0,
0,
'c_2*y_0/(c_6 + y_0)**2 - c_2/(c_6 + y_0)',
0,
'-c_2*y_0*y_2/(c_6 + y_0)**3 + c_2*y_2/(c_6 + y_0)**2'],
[
'c_3*y_0 - c_4*y_1',
0,
0,
0,
0,
0,
0],
[
'c_4*y_1 - c_5*y_2',
0,
0,
0,
0,
0,
0
]])
species = to_sympy_matrix(['y_0', 'y_1', 'y_2'])
propensities = to_sympy_matrix(['c_0',
'c_1 * y_0',
'c_2*y_0*y_2/(c_6 + y_0)',
'c_3*y_0',
'c_4*y_1',
'c_5*y_2'])
stoichiometry_matrix = to_sympy_matrix([[1, -1, -1, 0, 0, 0],
[0, 0, 0, 1, -1, 0],
[0, 0, 0, 0, 1, -1]])
answer = eq_central_moments(counter, mcounter, m, species, propensities, stoichiometry_matrix, 2)
expected = to_sympy_matrix([
[" 2*c_4*y_1*y_2 + c_4*y_1 - 2*c_5*y_2**2 + c_5*y_2 - 2*y_1*(c_4*y_1 - c_5*y_2)"," -2*c_5"," 2*c_4"," 0"," 0"," 0"," 0"],
["c_3*y_0*y_2 + c_4*y_1**2 - c_4*y_1*y_2 - c_4*y_1 - c_5*y_1*y_2 - y_1*(c_3*y_0 - c_4*y_1) - y_2*(c_4*y_1 - c_5*y_2)"," 0"," -c_4 - c_5"," c_4"," c_3"," 0"," 0"],
["2*c_3*y_0*y_1 + c_3*y_0 - 2*c_4*y_1**2 + c_4*y_1 - 2*y_2*(c_3*y_0 - c_4*y_1)"," 0"," 0"," -2*c_4"," 0"," 2*c_3","0"],
["c_0*y_2 - c_1*y_0*y_2 - c_2*y_0*y_2**2/(c_6 + y_0) + c_4*y_0*y_1 - c_5*y_0*y_2 - y_1*(c_0 - c_1*y_0 - c_2*y_0*y_2/(c_6 + y_0)) - y_3*(c_4*y_1 - c_5*y_2)"," -c_2*y_0/(c_6 + y_0)"," 0"," 0"," -c_1 + 2*c_2*y_0*y_2/(c_6 + y_0)**2 - 2*c_2*y_2/(c_6 + y_0) - c_5 - y_1*(c_2*y_0/(c_6 + y_0)**2 - c_2/(c_6 + y_0))","c_4"," -c_2*y_0*y_2**2/(c_6 + y_0)**3 + c_2*y_2**2/(c_6 + y_0)**2 - y_1*(-c_2*y_0*y_2/(c_6 + y_0)**3 + c_2*y_2/(c_6 + y_0)**2)"],
["c_0*y_1 - c_1*y_0*y_1 - c_2*y_0*y_1*y_2/(c_6 + y_0) + c_3*y_0**2 - c_4*y_0*y_1 - y_2*(c_0 - c_1*y_0 - c_2*y_0*y_2/(c_6 + y_0)) - y_3*(c_3*y_0 - c_4*y_1)"," 0"," -c_2*y_0/(c_6 + y_0)"," 0"," c_2*y_0*y_1/(c_6 + y_0)**2 - c_2*y_1/(c_6 + y_0) - y_2*(c_2*y_0/(c_6 + y_0)**2 - c_2/(c_6 + y_0))"," -c_1 + c_2*y_0*y_2/(c_6 + y_0)**2 - c_2*y_2/(c_6 + y_0) - c_4"," -c_2*y_0*y_1*y_2/(c_6 + y_0)**3 + c_2*y_1*y_2/(c_6 + y_0)**2 + c_3 - y_2*(-c_2*y_0*y_2/(c_6 + y_0)**3 + c_2*y_2/(c_6 + y_0)**2)"],
["2*c_0*y_0 + c_0 - 2*c_1*y_0**2 + c_1*y_0 - 2*c_2*y_0**2*y_2/(c_6 + y_0) + c_2*y_0*y_2/(c_6 + y_0) - 2*y_3*(c_0 - c_1*y_0 - c_2*y_0*y_2/(c_6 + y_0))"," 0"," 0"," 0"," 2*c_2*y_0**2/(c_6 + y_0)**2 - 4*c_2*y_0/(c_6 + y_0) - c_2*y_0/(c_6 + y_0)**2 + c_2/(c_6 + y_0) - 2*y_3*(c_2*y_0/(c_6 + y_0)**2 - c_2/(c_6 + y_0))"," 0"," -2*c_1 - 2*c_2*y_0**2*y_2/(c_6 + y_0)**3 + 4*c_2*y_0*y_2/(c_6 + y_0)**2 + c_2*y_0*y_2/(c_6 + y_0)**3 - 2*c_2*y_2/(c_6 + y_0) - c_2*y_2/(c_6 + y_0)**2 - 2*y_3*(-c_2*y_0*y_2/(c_6 + y_0)**3 + c_2*y_2/(c_6 + y_0)**2)"]
])
assert_sympy_expressions_equal(answer, expected)
