def testBranchCoeff4(self):
# this has 3 fragments: 2 dimers and a pentamer, which is branched
adj = dok_matrix((9, 9), dtype=np.float32)
adj_dict = {
(4, 8): 8.0,
(8, 4): 8.0,
(7, 3): 8.0,
(3, 7): 8.0,
(0, 2): 5.0,
(2, 0): 8.0,
(4, 2): 4.0,
(2, 4): 5.0,
(5, 6): 8.0,
(6, 5): 5.0,
(1, 2): 8.0,
(2, 1): 4.0
}
for key, val in adj_dict.items():
adj[key] = val
branch_degree = list(degree(adj))
good_branch_degree = [1, 1, 3, 1, 2, 1, 1, 1, 1]
self.assertTrue(branch_degree == good_branch_degree)
branch_coeff = overall_branching_coefficient(adj)
good_branch_coeff = 1 / 9
self.assertAlmostEqual(branch_coeff, good_branch_coeff)
def testBranchCoeff3(self):
adj = dok_matrix((10, 10), dtype=np.float32)
adj_dict = {
(0, 1): 8.0,
(1, 0): 8.0,
(1, 2): 4.0,
(2, 1): 8.0,
(2, 3): 4.0,
(3, 2): 8.0,
(3, 4): 5.0,
(4, 3): 8.0,
(5, 4): 8.0,
(4, 5): 5.0,
(5, 6): 4.0,
(6, 5): 8.0,
(7, 8): 8.0,
(8, 7): 8.0,
(0, 8): 4.0,
(8, 0): 5.0,
(8, 9): 4.0,
(9, 8): 8.0
}
for key, val in adj_dict.items():
adj[key] = val
branch_degree = list(degree(adj))
good_branch_degree = [2, 2, 2, 2, 2, 2, 1, 1, 3, 1]
self.assertTrue(branch_degree == good_branch_degree)
branch_coeff = overall_branching_coefficient(adj)
good_branch_coeff = 0.1
self.assertAlmostEqual(branch_coeff, good_branch_coeff)
def testBranchCoeff1(self):
# testing dimers and a monomer
adj = ADJ2
mono_degree = list(degree(adj))
good_mono_degree = [1, 1, 1, 1]
self.assertTrue(mono_degree == good_mono_degree)
branch_coeff = overall_branching_coefficient(adj)
self.assertTrue(branch_coeff == 0)
def testBranchCoeff2(self):
# testing timer and dimers
adj = ADJ3
branch_degree = list(degree(adj))
good_branch_degree = [2, 1, 1]
self.assertTrue(branch_degree == good_branch_degree)
branch_coeff = overall_branching_coefficient(adj)
self.assertTrue(branch_coeff == 0)
def testDegree0(self):
# Testing all monomers
adj = ADJ_ZEROS
mono_degree = list(degree(adj))
good_mono_degree = []
self.assertTrue(mono_degree == good_mono_degree)
branch_coeff = overall_branching_coefficient(adj)
self.assertTrue(branch_coeff == 0)