def test_from_string(self):
with self.subTest("single monomer example"):
self.assertEqual(Tbn({Monomer.from_string("a"): 1}), Tbn.from_string("a"))
with self.subTest("single monomer type, multiple monomer example"):
self.assertEqual(Tbn({Monomer.from_string("a"): 2}), Tbn.from_string("2[a]"))
with self.subTest("testing from_string with example from stablegen.net/help"):
example_text = \
"""
a*:b1 b*
a b:b2 >m1
a* >m2
b*
"""
example_tbn = Tbn({
Monomer.from_string("a* b*"): 1,
Monomer.from_string("a b", "m1"): 1,
Monomer.from_string("a*", "m2"): 1,
Monomer.from_string("b*"): 1,
})
self.assertEqual(example_tbn, Tbn.from_string(example_text))
with self.subTest("testing from_string with multisets"):
multiset_text = \
"""
2[ 3(a*) a b ]
[ c ]
5[ a a:favorite_a b >bob ]
7[ b a b b ]
b a b b b*
"""
multiset_tbn = Tbn({
Monomer.from_string("a* a* a* a b"): 2,
Monomer.from_string("c"): 1,
Monomer.from_string("2(a) b", "bob"): 5,
Monomer.from_string("3(b) a"): 7,
Monomer.from_string("b* 3(b) a"): 1,
})
self.assertEqual(multiset_tbn, Tbn.from_string(multiset_text))
with self.subTest("testing from_string with excess monomers"):
multiset_text = \
"""
2[ 3(a*) a b ]
inf[ c ]
5[ a a b >bob ]
inf[ b a b b ]
b a b b b*
"""
multiset_tbn = Tbn({
Monomer.from_string("a* a* a* a b"): 2,
Monomer.from_string("c"): infinity,
Monomer.from_string("2(a) b", "bob"): 5,
Monomer.from_string("3(b) a"): infinity,
Monomer.from_string("b* 3(b) a"): 1,
})
self.assertEqual(multiset_tbn, Tbn.from_string(multiset_text))
def test_configs_with_number_of_polymers(self):
test_cases = [
# second argument is a list of number of configurations expected for specific numbers of polymers:
# e.g. [a,b,c,d] => 'a' configurations with 1 polymer, 'b' configurations with 2 polymers, etc., up to 4
("a* b* \n a b \n a* \n b*", [1, 4, 1, 0], self.cp_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("a* b* \n a b \n a* \n b*", [1, 4, 1, 0], self.cp_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("a* b* \n a b \n a* \n b*", [1, 4, 1, 0], self.cp_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
# recall that POLYMER_UNBOUNDED_MATRIX does not allow spurious binding of polymers without limiting monomers
("a* b* \n a b \n a* \n b*", [1, 3, 1, 0], self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
# here VARIABLE_BOND_WEIGHT does not require saturation, hence more configurations
("a* b* \n a b \n a* \n b*", [1, 3, 3, 1], self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("2[a* b*] \n a b", [1, 2, 0, 0], self.cp_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("2[a* b*] \n a b", [1, 2, 0, 0], self.cp_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("2[a* b*] \n a b", [1, 1, 0, 0], self.cp_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("2[a* b*] \n a b", [1, 1, 0, 0], self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("2[a* b*] \n a b", [1, 1, 1, 0], self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", [1, 4, 0, 0],
self.cp_solver, SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", [1, 4, 0, 0],
self.cp_solver, SolverFormulation.POLYMER_BINARY_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", [1, 3, 0, 0],
self.cp_solver, SolverFormulation.POLYMER_INTEGER_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", [1, 3, 0, 0],
self.cp_solver, SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
]
for tbn_string, number_of_configs_with_polymer_count, solver, formulation in test_cases:
with self.subTest(tbn_string=tbn_string,
solver=solver,
formulation=formulation):
test_tbn = Tbn.from_string(tbn_string)
for polymer_count_minus_one, number_of_configs in enumerate(
number_of_configs_with_polymer_count):
polymer_count = polymer_count_minus_one + 1
constraints = Constraints().with_fixed_polymers(
polymer_count).with_unset_optimization_flag()
configurations = list(
solver.stable_configs(test_tbn,
constraints,
formulation=formulation))
self.assertEqual(number_of_configs, len(configurations))
for configuration in configurations:
self.assertEqual(polymer_count,
configuration.number_of_polymers())
def test_project_tbn_to_column_matrix(self):
with self.subTest("slack version"):
test_tbn = Tbn.from_string("a* b* \n a b \n a* \n b*")
actual_matrix = Formulation._project_tbn_to_column_matrix(test_tbn)
expected_matrix = np.array(
[
[-1, -1], # a b
[1, 1], # a* b*
[1, 0], # a*
[0, 1], # b*
],
np.int64).T
self.assertTrue(np.array_equal(expected_matrix, actual_matrix))
with self.subTest("no slack version"):
test_tbn = Tbn.from_string(
"a* b* \n a b"
) # no slack this time, should default to stars being limiting
actual_matrix = Formulation._project_tbn_to_column_matrix(test_tbn)
expected_matrix = np.array(
[
[1, 1], # a b
[-1, -1], # a* b*
],
np.int64).T
self.assertTrue(np.array_equal(expected_matrix, actual_matrix))
with self.subTest("second no slack version"):
test_tbn = Tbn.from_string("a \n a* b* \n a b")
actual_matrix = Formulation._project_tbn_to_column_matrix(test_tbn)
expected_matrix = np.array(
[
[1, 1], # a b
[-1, -1], # a* b*
[1, 0], # a
],
np.int64).T
self.assertTrue(np.array_equal(expected_matrix, actual_matrix))
def test_stable_configs(self):
test_cases = [
("a* b* \n a b \n a* \n b*", 1, 1, self.cp_solver,
SolverFormulation.BOND_AWARE_NETWORK),
("a* b* \n a b \n a* \n b*", 1, 1, self.cp_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("a* b* \n a b \n a* \n b*", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("a* b* \n a b \n a* \n b*", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("a* b* \n a b \n a* \n b*", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("a* b* \n a b \n a* \n b*", 1, 1, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("a* b* \n a b \n a* \n b*", 1, 1, self.cp_solver,
SolverFormulation.HILBERT_BASIS),
("a a \n a* a*", 2, 1, self.cp_solver,
SolverFormulation.BOND_AWARE_NETWORK),
("a a \n a* a*", 1, 1, self.cp_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("a a \n a* a*", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("a a \n a* a*", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("a a \n a* a*", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("a a \n a* a*", 1, 1, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("a a \n a* a*", 1, 1, self.cp_solver,
SolverFormulation.HILBERT_BASIS),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.BOND_AWARE_NETWORK),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("2[a* b*] \n a b", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("2[a* b*] \n a b", 1, 1, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("2[a* b*] \n a b", 1, 1, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("2[a* b*] \n a b", 1, 1, self.cp_solver,
SolverFormulation.HILBERT_BASIS),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 4, 5,
self.cp_solver, SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 4, 5,
self.cp_solver, SolverFormulation.POLYMER_BINARY_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 3, 5,
self.cp_solver, SolverFormulation.POLYMER_INTEGER_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 3, 5,
self.cp_solver, SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 3, 5,
self.cp_solver, SolverFormulation.VARIABLE_BOND_WEIGHT),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 3, 5,
self.cp_solver, SolverFormulation.HILBERT_BASIS),
("inf[a* b*] \n 2[a b]", 1, 2, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("inf[a* b*] \n 2[a b]", 1, 2, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", 2, 4, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", 2, 4, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
]
for tbn_string, number_of_configs, number_of_merges, solver, formulation in test_cases:
with self.subTest(tbn_string=tbn_string,
solver=solver,
formulation=formulation):
test_tbn = Tbn.from_string(tbn_string)
configurations = list(
solver.stable_configs(test_tbn,
formulation=formulation,
bond_weighting_factor=2.0))
self.assertEqual(number_of_configs, len(configurations))
for configuration in configurations:
self.assertEqual(number_of_merges,
configuration.number_of_merges())
low_w_test_cases = [
("a* b* \n a b \n a* \n b*", 1, 0.8, self.cp_solver, 0.4),
("a* b* \n a b \n a* \n b*", 1, 1.0, self.cp_solver, 0.6),
("2[a* b*] \n a b", 1, 0.8, self.cp_solver, 0.4),
("2[a* b*] \n a b", 1, 1.0, self.cp_solver, 0.6),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 1, 3.6,
self.cp_solver, 0.4),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 1, 4.2,
self.cp_solver, 0.6),
("inf[a* b*] \n 2[a b]", 1, 1.6, self.cp_solver, 0.4),
("inf[a* b*] \n 2[a b]", 1, 2.0, self.cp_solver, 0.6),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", 1, 3.6, self.cp_solver, 0.4),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", 2, 4.0, self.cp_solver, 0.6),
]
for tbn_string, number_of_configs, energy, solver, weight in low_w_test_cases:
with self.subTest("low w tests",
tbn_string=tbn_string,
solver=solver,
weight=weight):
test_tbn = Tbn.from_string(tbn_string)
configurations = list(
solver.stable_configs(
test_tbn,
formulation=SolverFormulation.VARIABLE_BOND_WEIGHT,
bond_weighting_factor=weight,
))
self.assertEqual(number_of_configs, len(configurations))
for configuration in configurations:
self.assertEqual(energy, configuration.energy(weight))
def test_stable_config(self):
test_cases = [
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver,
SolverFormulation.BOND_AWARE_NETWORK),
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver,
SolverFormulation.HILBERT_BASIS),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver,
SolverFormulation.BOND_AWARE_NETWORK),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver,
SolverFormulation.HILBERT_BASIS),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.BOND_AWARE_NETWORK),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("2[a* b*] \n a b", 2, 1, self.cp_solver,
SolverFormulation.HILBERT_BASIS),
("2[a* b*] \n a b", 2, 1, self.ip_solver,
SolverFormulation.BOND_AWARE_NETWORK),
("2[a* b*] \n a b", 2, 1, self.ip_solver,
SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("2[a* b*] \n a b", 2, 1, self.ip_solver,
SolverFormulation.POLYMER_BINARY_MATRIX),
("2[a* b*] \n a b", 2, 1, self.ip_solver,
SolverFormulation.POLYMER_INTEGER_MATRIX),
("2[a* b*] \n a b", 2, 1, self.ip_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("2[a* b*] \n a b", 2, 1, self.ip_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("2[a* b*] \n a b", 2, 1, self.ip_solver,
SolverFormulation.HILBERT_BASIS),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.cp_solver, SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.cp_solver, SolverFormulation.POLYMER_BINARY_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.cp_solver, SolverFormulation.POLYMER_INTEGER_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.cp_solver, SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.cp_solver, SolverFormulation.VARIABLE_BOND_WEIGHT),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.cp_solver, SolverFormulation.HILBERT_BASIS),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.ip_solver, SolverFormulation.BOND_OBLIVIOUS_NETWORK),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.ip_solver, SolverFormulation.POLYMER_BINARY_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.ip_solver, SolverFormulation.POLYMER_INTEGER_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.ip_solver, SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.ip_solver, SolverFormulation.VARIABLE_BOND_WEIGHT),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 2, 5,
self.ip_solver, SolverFormulation.HILBERT_BASIS),
("inf[a* b*] \n 2[a b]", infinity, 2, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("inf[a* b*] \n 2[a b]", infinity, 2, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("inf[a* b*] \n 2[a b]", infinity, 2, self.ip_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("inf[a* b*] \n 2[a b]", infinity, 2, self.ip_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 4, self.cp_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 4, self.cp_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 4, self.ip_solver,
SolverFormulation.POLYMER_UNBOUNDED_MATRIX),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 4, self.ip_solver,
SolverFormulation.VARIABLE_BOND_WEIGHT),
]
for tbn_string, number_of_polymers, number_of_merges, solver, formulation in test_cases:
with self.subTest(tbn_string=tbn_string,
solver=solver,
formulation=formulation):
test_tbn = Tbn.from_string(tbn_string)
configuration = solver.stable_config(test_tbn,
formulation=formulation,
bond_weighting_factor=2.0)
self.assertEqual(number_of_polymers,
configuration.number_of_polymers())
self.assertEqual(number_of_merges,
configuration.number_of_merges())
low_w_test_cases = [
("a* b* \n a b \n a* \n b*", 4, 0, self.cp_solver, 0.4),
("a* b* \n a b \n a* \n b*", 4, 0, self.ip_solver, 0.4),
("a* b* \n a b \n a* \n b*", 3, 1, self.cp_solver, 0.6),
("a* b* \n a b \n a* \n b*", 3, 1, self.ip_solver, 0.6),
("2[a* b*] \n a b", 3, 0, self.cp_solver, 0.4),
("2[a* b*] \n a b", 3, 0, self.ip_solver, 0.4),
("2[a* b*] \n a b", 2, 1, self.cp_solver, 0.6),
("2[a* b*] \n a b", 2, 1, self.ip_solver, 0.6),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 5, 2,
self.cp_solver, 0.4),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 5, 2,
self.ip_solver, 0.4),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 4, 3,
self.cp_solver, 0.6),
("6(a*) \n 2[3(a*)] \n a \n 5(a) \n 2(a) \n 4(a)", 4, 3,
self.ip_solver, 0.6),
("inf[a* b*] \n 2[a b]", infinity, 0, self.cp_solver, 0.4),
("inf[a* b*] \n 2[a b]", infinity, 0, self.ip_solver, 0.4),
("inf[a* b*] \n 2[a b]", infinity, 2, self.cp_solver, 0.6),
("inf[a* b*] \n 2[a b]", infinity, 2, self.ip_solver, 0.6),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 2, self.cp_solver,
0.4),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 2, self.ip_solver,
0.4),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 4, self.cp_solver,
0.6),
("inf[2(a*) 2(b*)] \n 2[3(a) 3(b)]", infinity, 4, self.ip_solver,
0.6),
]
for tbn_string, number_of_polymers, number_of_merges, solver, weight in low_w_test_cases:
with self.subTest("low w tests",
tbn_string=tbn_string,
solver=solver,
weight=weight):
test_tbn = Tbn.from_string(tbn_string)
configuration = solver.stable_config(
test_tbn,
formulation=SolverFormulation.VARIABLE_BOND_WEIGHT,
bond_weighting_factor=weight,
)
self.assertEqual(number_of_polymers,
configuration.number_of_polymers())
self.assertEqual(number_of_merges,
configuration.number_of_merges())
def get_tbn_from_filename(tbn_filename) -> Tbn:
with open(tbn_filename) as tbnFile:
tbn_as_string = tbnFile.read()
return Tbn.from_string(tbn_as_string)