def test_create_pauli_for_contacts_2(self):
"""
Tests that Pauli operators for contact qubits are created correctly.
"""
main_chain_residue_seq = "SAASSS"
side_chain_residue_sequences = ["", "", "A", "A", "S", ""]
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
(
lower_main_upper_main,
lower_side_upper_main,
lower_main_upper_side,
lower_side_upper_side,
r_contact,
) = contact_map_builder._create_contact_qubits(peptide)
expected_path = self.get_resource_path(
"test_create_pauli_for_contacts_2_expected_1",
PATH,
)
expected_1 = read_expected_file(expected_path)
expected_path = self.get_resource_path(
"test_create_pauli_for_contacts_2_expected_2",
PATH,
)
expected_2 = read_expected_file(expected_path)
self.assertEqual(lower_main_upper_main[1][6], expected_1)
self.assertEqual(lower_main_upper_side[1][5], expected_2)
self.assertEqual(lower_side_upper_main, {})
self.assertEqual(lower_side_upper_side, {})
self.assertEqual(r_contact, 2)
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)
def test_calc_distances_main_chain(self):
"""
Tests that distances for all beads on the main chain are calculated correctly.
"""
self.distance_map_builder._calc_distances_main_chain(self.peptide)
expected_path = self.get_resource_path(
"test_calc_distances_main_chain_1",
PATH,
)
expected_1 = read_expected_file(expected_path)
expected_path = self.get_resource_path(
"test_calc_distances_main_chain_2",
PATH,
)
expected_2 = read_expected_file(expected_path)
expected_path = self.get_resource_path(
"test_calc_distances_main_chain_3",
PATH,
)
expected_3 = read_expected_file(expected_path)
expected_path = self.get_resource_path(
"test_calc_distances_main_chain_4",
PATH,
)
expected_4 = read_expected_file(expected_path)
lower_main_bead_0 = self.peptide.get_main_chain[0]
upper_main_bead_4 = self.peptide.get_main_chain[4]
lower_main_bead_1 = self.peptide.get_main_chain[1]
upper_main_bead_3 = self.peptide.get_main_chain[3]
# checking only some of the entries
self.assertEqual(
self.distance_map_builder._distance_map_axes[0][lower_main_bead_0]
[upper_main_bead_4],
expected_1,
)
self.assertEqual(
self.distance_map_builder._distance_map_axes[0][lower_main_bead_1]
[upper_main_bead_4],
expected_2,
)
self.assertEqual(
self.distance_map_builder._distance_map_axes[1][lower_main_bead_0]
[upper_main_bead_3],
expected_3,
)
self.assertEqual(
self.distance_map_builder._distance_map_axes[1][lower_main_bead_0]
[upper_main_bead_4],
expected_4,
)
def test_check_turns(self):
"""
Tests that check turns operators are generate correctly.
"""
main_chain_residue_seq = "SAASSA"
side_chain_residue_sequences = ["", "", "A", "A", "A", ""]
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
bead_2 = peptide.get_main_chain[2]
bead_3 = peptide.get_main_chain[3]
bead_4 = peptide.get_main_chain[4]
side_bead_2 = bead_2.side_chain[0]
side_bead_3 = bead_3.side_chain[0]
side_bead_4 = bead_4.side_chain[0]
lambda_back = 10
lambda_chiral = 10
lambda_1 = 10
penalty_params = PenaltyParameters(lambda_chiral, lambda_back, lambda_1)
mj_interaction = MiyazawaJerniganInteraction()
pair_energies = mj_interaction.calculate_energy_matrix(main_chain_residue_seq)
qubit_op_builder = QubitOpBuilder(peptide, pair_energies, penalty_params)
t_23 = qubit_op_builder._create_turn_operators(bead_2, bead_3)
t_34 = qubit_op_builder._create_turn_operators(bead_3, bead_4)
t_2s3 = qubit_op_builder._create_turn_operators(side_bead_2, bead_3)
t_3s4s = qubit_op_builder._create_turn_operators(side_bead_3, side_bead_4)
expected_path_t23 = self.get_resource_path(
"test_check_turns_expected_t23",
PATH,
)
expected_t23 = read_expected_file(expected_path_t23)
expected_path_t34 = self.get_resource_path(
"test_check_turns_expected_t34",
PATH,
)
expected_t34 = read_expected_file(expected_path_t34)
expected_path_t2s3 = self.get_resource_path(
"test_check_turns_expected_t2s3",
PATH,
)
expected_t_2s3 = read_expected_file(expected_path_t2s3)
expected_path_t3s4s = self.get_resource_path(
"test_check_turns_expected_t3s4s",
PATH,
)
expected_t_3s4s = read_expected_file(expected_path_t3s4s)
self.assertEqual(t_23, expected_t23)
self.assertEqual(t_34, expected_t34)
self.assertEqual(t_2s3, expected_t_2s3)
self.assertEqual(t_3s4s, expected_t_3s4s)
def test_main_bead_constructor(self):
"""Tests that a MainBead is created."""
main_chain_len = 4
num_turn_qubits = 2 * (main_chain_len - 1)
main_bead_id = 3
residue_type = "S"
turn_qubits = (
0.5 * _build_full_identity(num_turn_qubits) - 0.5 *
(I ^ Z ^ I ^ I ^ I ^ I),
0.5 * _build_full_identity(num_turn_qubits) - 0.5 *
(Z ^ I ^ I ^ I ^ I ^ I),
)
side_chain_residue_sequences = ["S"]
side_chain = SideChain(main_chain_len, main_bead_id,
side_chain_residue_sequences)
main_bead = MainBead(main_bead_id, residue_type, turn_qubits,
side_chain)
self.assertEqual(main_bead.side_chain, side_chain)
indic_0, indic_1, indic_2, indic_3 = main_bead.indicator_functions
expected_path_indic_0 = self.get_resource_path(
"test_main_bead_constructor_expected_indic_0",
PATH,
)
expected_indic_0 = read_expected_file(expected_path_indic_0)
expected_path_indic_1 = self.get_resource_path(
"test_main_bead_constructor_expected_indic_1",
PATH,
)
expected_indic_1 = read_expected_file(expected_path_indic_1)
expected_path_indic_2 = self.get_resource_path(
"test_main_bead_constructor_expected_indic_2",
PATH,
)
expected_indic_2 = read_expected_file(expected_path_indic_2)
expected_path_indic_3 = self.get_resource_path(
"test_main_bead_constructor_expected_indic_3",
PATH,
)
expected_indic_3 = read_expected_file(expected_path_indic_3)
self.assertEqual(indic_0, expected_indic_0)
self.assertEqual(indic_1, expected_indic_1)
self.assertEqual(indic_2, expected_indic_2)
self.assertEqual(indic_3, expected_indic_3)
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_protein_folding_problem_2_second_bead_side_chain(self):
"""Tests if a protein folding problem is created and returns a correct qubit operator if
a second main bead has a side chain."""
lambda_back = 10
lambda_chiral = 10
lambda_1 = 10
penalty_terms = PenaltyParameters(lambda_chiral, lambda_back, lambda_1)
main_chain_residue_seq = "SAAS"
side_chain_residue_sequences = ["", "A", "A", ""]
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
mj_interaction = MiyazawaJerniganInteraction()
protein_folding_problem = ProteinFoldingProblem(
peptide, mj_interaction, penalty_terms)
qubit_op = protein_folding_problem._qubit_op_full()
expected_path = self.get_resource_path(
"test_protein_folding_problem_2_second_bead_side_chain",
PATH,
)
expected = read_expected_file(expected_path)
self.assertEqual(qubit_op, expected)
def test_side_bead_constructor(self):
"""Tests that a SideBead is created."""
residue_type = "S"
main_chain_len = 4
num_turn_qubits = 2 * (main_chain_len - 1)
main_chain_id = 3
side_bead_id = 3
turn_qubits = (
0.5 * _build_full_identity(num_turn_qubits) - 0.5 *
(I ^ I ^ I ^ I ^ I ^ Z),
0.5 * _build_full_identity(num_turn_qubits) - 0.5 *
(I ^ I ^ I ^ I ^ Z ^ I),
)
side_bead = SideBead(main_chain_id, side_bead_id, residue_type,
turn_qubits)
indic_0, indic_1, indic_2, indic_3 = side_bead.indicator_functions
expected_path_indic_0 = self.get_resource_path(
"test_side_bead_constructor_expected_indic_0",
PATH,
)
expected_indic_0 = read_expected_file(expected_path_indic_0)
expected_path_indic_1 = self.get_resource_path(
"test_side_bead_constructor_expected_indic_1",
PATH,
)
expected_indic_1 = read_expected_file(expected_path_indic_1)
expected_path_indic_2 = self.get_resource_path(
"test_side_bead_constructor_expected_indic_2",
PATH,
)
expected_indic_2 = read_expected_file(expected_path_indic_2)
expected_path_indic_3 = self.get_resource_path(
"test_side_bead_constructor_expected_indic_3",
PATH,
)
expected_indic_3 = read_expected_file(expected_path_indic_3)
self.assertEqual(indic_0, expected_indic_0)
self.assertEqual(indic_1, expected_indic_1)
self.assertEqual(indic_2, expected_indic_2)
self.assertEqual(indic_3, expected_indic_3)
def test_create_h_bbsc_and_h_scbb(self):
"""Tests if H_BBSC and H_SCBB Hamiltonians qubit operators are built correctly."""
main_chain_residue_seq = "APRLAAA"
side_chain_residue_sequences = ["", "", "A", "", "", "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)
penalty_params = PenaltyParameters()
qubit_op_builder = QubitOpBuilder(peptide, pair_energies, penalty_params)
h_bbsc, h_scbb = qubit_op_builder._create_h_bbsc_and_h_scbb()
expected_path_h_bbsc = self.get_resource_path(
"test_create_h_bbsc_and_h_scbb_expected_h_bbsc",
PATH,
)
expected_path_h_scbb = self.get_resource_path(
"test_create_h_bbsc_and_h_scbb_expected_h_scbb",
PATH,
)
expected_h_bbsc = read_expected_file(expected_path_h_bbsc)
expected_h_scbb = read_expected_file(expected_path_h_scbb)
self.assertEqual(h_bbsc, expected_h_bbsc)
self.assertEqual(h_scbb, expected_h_scbb)
def test_create_h_bbbb(self):
"""Tests if H_BBBB Hamiltonian qubit operator is built correctly."""
main_chain_residue_seq = "SAASSASA"
side_chain_residue_sequences = ["", "", "A", "", "", "A", "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)
penalty_params = PenaltyParameters()
qubit_op_builder = QubitOpBuilder(peptide, pair_energies, penalty_params)
h_bbbb = qubit_op_builder._create_h_bbbb()
expected_path = self.get_resource_path(
"test_create_h_bbbb_expected",
PATH,
)
expected = read_expected_file(expected_path)
self.assertEqual(h_bbbb, expected)
def test_add_distances_side_chain(self):
"""
Tests that distances for all beads on side chains are calculated correctly.
"""
self.distance_map_builder._calc_distances_main_chain(self.peptide)
self.distance_map_builder._add_distances_side_chain(self.peptide)
expected_path = self.get_resource_path(
"test_add_distances_side_chain",
PATH,
)
expected = read_expected_file(expected_path)
lower_main_bead = self.peptide.get_main_chain[0]
upper_side_bead = self.peptide.get_main_chain[2].side_chain[0]
# checking only some of the entries
self.assertEqual(
self.distance_map_builder._distance_map_axes[0][lower_main_bead][upper_side_bead],
expected,
)
def test_create_h_chiral_2(self):
"""
Tests that the Hamiltonian chirality constraints is created correctly.
"""
main_chain_residue_seq = "SAACS"
side_chain_residue_sequences = ["", "", "A", "A", ""]
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
mj_interaction = MiyazawaJerniganInteraction()
pair_energies = mj_interaction.calculate_energy_matrix(main_chain_residue_seq)
penalty_params = PenaltyParameters()
qubit_op_builder = QubitOpBuilder(peptide, pair_energies, penalty_params)
h_chiral = qubit_op_builder._create_h_chiral()
expected_path = self.get_resource_path(
"test_create_h_chiral_2_expected",
PATH,
)
expected = read_expected_file(expected_path)
self.assertEqual(h_chiral, expected)
def test_build_qubit_op(self):
"""Tests if a total Hamiltonian qubit operator is built correctly."""
lambda_back = 10
lambda_chiral = 10
lambda_1 = 10
main_chain_residue_seq = "SAASSASAA"
side_chain_residue_sequences = ["", "", "A", "A", "A", "A", "A", "A", ""]
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
mj_interaction = MiyazawaJerniganInteraction()
penalty_params = PenaltyParameters(lambda_chiral, lambda_back, lambda_1)
pair_energies = mj_interaction.calculate_energy_matrix(main_chain_residue_seq)
qubit_op_builder = QubitOpBuilder(peptide, pair_energies, penalty_params)
qubit_op = qubit_op_builder._build_qubit_op()
expected_path = self.get_resource_path(
"test_build_qubit_op_expected",
PATH,
)
expected = read_expected_file(expected_path)
self.assertEqual(qubit_op, expected)
def test_create_h_back_side_chains(self):
"""
Tests that the Hamiltonian to back-overlaps is created correctly in the presence of side
chains which should not have any influence in this case.
"""
main_chain_residue_seq = "SAASS"
side_chain_residue_sequences = ["", "", "A", "A", ""]
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
mj_interaction = MiyazawaJerniganInteraction()
pair_energies = mj_interaction.calculate_energy_matrix(main_chain_residue_seq)
penalty_params = PenaltyParameters()
qubit_op_builder = QubitOpBuilder(peptide, pair_energies, penalty_params)
h_back = qubit_op_builder._create_h_back()
expected_path = self.get_resource_path(
"test_create_h_back_side_chains_expected",
PATH,
)
expected = read_expected_file(expected_path)
self.assertEqual(h_back, expected)
