def test_second_neighbor(self):
"""
Tests that Pauli operators for 2nd neighbor interactions are created correctly.
"""
main_chain_residue_seq = "SAASS"
side_chain_residue_sequences = ["", "", "A", "", ""]
mj_interaction = MiyazawaJerniganInteraction()
pair_energies = mj_interaction.calculate_energy_matrix(
main_chain_residue_seq)
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
lambda_1 = 2
lower_main_bead_index = 1
upper_main_bead_index = 4
side_chain_lower_main_bead = 0
side_chain_upper_main_bead = 0
distance_map = DistanceMap(peptide)
second_neighbor = distance_map._second_neighbor(
peptide,
lower_main_bead_index,
side_chain_upper_main_bead,
upper_main_bead_index,
side_chain_lower_main_bead,
lambda_1,
pair_energies,
)
expected_path = self.get_resource_path(
"test_second_neighbor",
PATH,
)
expected = read_expected_file(expected_path)
self.assertEqual(second_neighbor, expected)
def test_calc_total_distances(self):
"""
Tests that total distances for all beads are calculated correctly.
"""
distance_map = DistanceMap(self.peptide)
upper_bead_1 = self.peptide.get_main_chain[2].side_chain[0]
lower_bead_1 = self.peptide.get_main_chain[1]
upper_bead_2 = self.peptide.get_main_chain[2].side_chain[0]
lower_bead_2 = self.peptide.get_main_chain[0]
expected_path = self.get_resource_path(
"test_calc_total_distances_1",
PATH,
)
expected_1 = read_expected_file(expected_path)
expected_path = self.get_resource_path(
"test_calc_total_distances_2",
PATH,
)
expected_2 = read_expected_file(expected_path)
self.assertEqual(distance_map[lower_bead_1, upper_bead_1], expected_1)
self.assertEqual(distance_map[lower_bead_2, upper_bead_2], expected_2)