def test_magic_copy():
c = CRN()
c.r("A + B <> 2C", [1, 1])
c2 = copy(c)
assert(id(c2) != id(c))
assert(id(c2.reactions[0]) != id(c.reactions[0]))
assert(c2.reactions[0] == c.reactions[0])
def test_magic_copy():
c = CRN()
c.r("A + B <> 2C", [1, 1])
c2 = copy(c)
assert (id(c2) != id(c))
assert (id(c2.reactions[0]) != id(c.reactions[0]))
assert (c2.reactions[0] == c.reactions[0])
def test_copy_reaction():
c = CRN()
c.r("2A + B > C", 1.0)
reaction = c.reactions[0]
r2 = reaction.copy(1)
print(r2)
def test_copy_reaction():
c = CRN()
c.r("2A + B > C", 1.0)
reaction = c.reactions[0]
r2 = reaction.copy(1)
print(r2)
def test_add_reaction_shoud_maintain_state():
c1 = CRN()
c1.r("A + B > C", 1)
c1['A'] = 1.0
c1.r('B > C', 2)
assert(c1['A'] == 1)
def test_add_reaction_shoud_maintain_state():
c1 = CRN()
c1.r("A + B > C", 1)
c1['A'] = 1.0
c1.r('B > C', 2)
assert (c1['A'] == 1)
def test_bidirectional(reactants, products, direction, rates, num_rxns):
rxn = reactants + direction + products
c = CRN()
if 0 in rates:
with pytest.raises(CRNException):
c.r(rxn, rates)
else:
for i in range(num_rxns):
c.r(rxn, rates)
assert (2 * num_rxns == len(c.reactions))
def test_bidirectional(reactants, products, direction, rates, num_rxns):
rxn = reactants + direction + products
c = CRN()
if 0 in rates:
with pytest.raises(CRNException):
c.r(rxn, rates)
else:
for i in range(num_rxns):
c.r(rxn, rates)
assert(2*num_rxns == len(c.reactions))
def test_magic_add():
c1 = CRN()
c1.r("2A + B > C", 1.0)
c2 = CRN()
c1.r("3A + B <> C", [1.0, 3.0])
c3 = c1 + c2
assert (len(c3.reactions) == 3)
for r in c3.reactions:
print(r)
def test_magic_add():
c1 = CRN()
c1.r("2A + B > C", 1.0)
c2 = CRN()
c1.r("3A + B <> C", [1.0, 3.0])
c3 = c1 + c2
assert(len(c3.reactions) == 3)
for r in c3.reactions:
print(r)
def test_merge_maintains_part():
c = CRN()
c.r("A + B > 2C", 1, part='part1')
c2 = CRN()
c2.r("AB > BC", 1, part='part2')
c3 = CRN.merge_all([c, c2])
for r in c3.reactions:
print(r)
assert c3.reactions[0].part == 'part1'
assert c3.reactions[1].part == 'part2'
print(c3)
def test_merge_maintains_part():
c = CRN()
c.r("A + B > 2C", 1, part='part1')
c2 = CRN()
c2.r("AB > BC", 1, part='part2')
c3 = CRN.merge_all([c, c2])
for r in c3.reactions:
print(r)
assert c3.reactions[0].part == 'part1'
assert c3.reactions[1].part == 'part2'
print(c3)
def test_add_operator():
"""Expect to remove duplicates"""
eqn1 = "A + B > C"
eqn2 = "C <> A + B"
c1 = CRN()
c1.r(eqn1, 0.01)
c2 = CRN()
c2.r(eqn2, [1, 0.01])
c3 = c1 + c2
assert(len(c3.reactions) == 3)
c3.remove_duplicates()
assert(len(c3.reactions) == 2)
def test_add_operator():
"""Expect to remove duplicates"""
eqn1 = "A + B > C"
eqn2 = "C <> A + B"
c1 = CRN()
c1.r(eqn1, 0.01)
c2 = CRN()
c2.r(eqn2, [1, 0.01])
c3 = c1 + c2
assert (len(c3.reactions) == 3)
c3.remove_duplicates()
assert (len(c3.reactions) == 2)
def test_merge_all():
c1 = CRN()
c1.r("A + B <> 2C", [1, 1])
c1['A'] = 2
c2 = copy(c1)
c2['A'] = 4
c2['B'] = 1
assert(c1['A'] == 2)
assert(c1['B'] == 0)
assert(c1['C'] == 0)
c3 = CRN.merge_all([c1, c2])
assert(c3['A'] == 4)
assert(c3['B'] == 1)
assert(c3['C'] == 0)
def test_reduce():
"""Expect to remove duplicates"""
eqn1 = "A + B > C"
eqn2 = "C <> A + B"
c1 = CRN()
c1.r(eqn1, 0.01)
c2 = CRN()
c2.r(eqn2, [1, 0.01])
c3 = c1 + c2
assert (len(c3.reactions) == 3)
c3.reduce()
assert (len(c3.reactions) == 2)
assert (c3.reactions[0].rate == 0.02)
def test_reduce():
"""Expect to remove duplicates"""
eqn1 = "A + B > C"
eqn2 = "C <> A + B"
c1 = CRN()
c1.r(eqn1, 0.01)
c2 = CRN()
c2.r(eqn2, [1, 0.01])
c3 = c1 + c2
assert(len(c3.reactions) == 3)
c3.reduce()
assert(len(c3.reactions) == 2)
assert(c3.reactions[0].rate == 0.02)
def test_N():
c = CRN()
c.r("A + 2B <> C", [1.0, 2.0])
print(c.E)
print(c.N)
print(c.R)
print(c.P)
c.set_state(dict(C=55))
print(c.x)
print("v(x)")
x = np.ones((3,1))*5
print(c.v(x))
d = c.run(0.001, 20)
print(d)
def test_N():
c = CRN()
c.r("A + 2B <> C", [1.0, 2.0])
print(c.E)
print(c.N)
print(c.R)
print(c.P)
c.set_state(dict(C=55))
print(c.x)
print("v(x)")
x = np.ones((3, 1)) * 5
print(c.v(x))
d = c.run(0.001, 20)
print(d)
def test_merge_all():
c1 = CRN()
c1.r("A + B <> 2C", [1, 1])
c1['A'] = 2
c2 = copy(c1)
c2['A'] = 4
c2['B'] = 1
assert (c1['A'] == 2)
assert (c1['B'] == 0)
assert (c1['C'] == 0)
c3 = CRN.merge_all([c1, c2])
assert (c3['A'] == 4)
assert (c3['B'] == 1)
assert (c3['C'] == 0)
def test_get_part():
c = CRN()
c.r("A + B > 2C", 1, part='part1')
c2 = CRN()
c2.r("AB <> BC", [1, 1], part='part2')
c3 = CRN.merge_all([c, c2])
c4 = c3.get_part('part1')
c5 = c3.get_part('part2')
c6 = c3.get_part('part1', 'part2')
assert len(c3.reactions) == 3
assert len(c4.reactions) == 1
assert len(c5.reactions) == 2
assert len(c6.reactions) == 3
def test_get_part():
c = CRN()
c.r("A + B > 2C", 1, part='part1')
c2 = CRN()
c2.r("AB <> BC", [1,1], part='part2')
c3 = CRN.merge_all([c, c2])
c4 = c3.get_part('part1')
c5 = c3.get_part('part2')
c6 = c3.get_part('part1', 'part2')
assert len(c3.reactions) == 3
assert len(c4.reactions) == 1
assert len(c5.reactions) == 2
assert len(c6.reactions) == 3
def test_merge():
c1 = CRN()
c1.r("A + B <> 2C", [1, 1])
c1['A'] = 2
c2 = copy(c1)
c2['A'] = 4
c2['B'] = 1
assert(c1['A'] == 2)
assert(c1['B'] == 0)
assert(c1['C'] == 0)
c1.merge(c2)
assert(c1['A'] == 4)
assert(c1['B'] == 1)
assert(c1['C'] == 0)
def test_merge_with_add():
c1 = CRN()
c1.r("A + B <> 2C", [1, 1])
c1['A'] = 2
c2 = copy(c1)
c2['A'] = 4
c2['B'] = 1
assert (c1['A'] == 2)
assert (c1['B'] == 0)
assert (c1['C'] == 0)
print(c1.x)
c1.merge(c2, lambda a, b: a + b)
assert (c1['A'] == 6)
assert (c1['B'] == 1)
assert (c1['C'] == 0)
def test_merge_with_add():
c1 = CRN()
c1.r("A + B <> 2C", [1, 1])
c1['A'] = 2
c2 = copy(c1)
c2['A'] = 4
c2['B'] = 1
assert(c1['A'] == 2)
assert(c1['B'] == 0)
assert(c1['C'] == 0)
print(c1.x)
c1.merge(c2, lambda a, b: a+b)
assert(c1['A'] == 6)
assert(c1['B'] == 1)
assert(c1['C'] == 0)
def test_merge():
c1 = CRN()
c1.r("A + B <> 2C", [1, 1])
c1['A'] = 2
c2 = copy(c1)
c2['A'] = 4
c2['B'] = 1
assert (c1['A'] == 2)
assert (c1['B'] == 0)
assert (c1['C'] == 0)
c1.merge(c2)
assert (c1['A'] == 4)
assert (c1['B'] == 1)
assert (c1['C'] == 0)
def test_run():
c = CRN()
c.r("P1 > m1 + P1", 0.01)
c.r("m1 > ", 0.01)
c.r("P1 + m2 <> PR1", [0.001, 0.001])
c.set_state({"P1": 1})
df = c.run(750)
gradient(df, 'time', 1)
gradient(df, 'time', 2)
plot(df, 'time', c.E)
def test_run():
c = CRN()
c.r("P1 > m1 + P1", 0.01)
c.r("m1 > ", 0.01)
c.r("P1 + m2 <> PR1", [0.001, 0.001])
c.set_state({"P1": 1})
df = c.run(750)
gradient(df, 'time', 1)
gradient(df, 'time', 2)
plot(df, 'time', c.E)
def nor_gate(i, j, k):
c = CRN()
prom = "P{}{}".format(i, j)
txn = "{0} > {0} + {1}".format(prom, k)
deg = "{0} > ".format(k)
r1 = "{0} + {1} <> {0}{1}".format(prom, i)
r2 = "{0} + {1} <> {0}{1}".format(prom, j)
c.r(txn, 1.0, 'txn')
c.r(deg, 0.1, 'deg')
c.r(r1, [0.01, 0.05], 'repr')
c.r(r2, [0.01, 0.0005], 'repr')
c[prom] = 1
return c
def test_basic():
c = CRN()
c.r("A + 2B <> C", [1.0, 2.0])
assert (2 == len(c.reactions))
def test_basic2():
c = CRN()
c.r("A + 2B > 3C", 1.0)
assert(1 ==len(c.reactions))
def test_basic2():
c = CRN()
c.r("A + 2B > 3C", 1.0)
assert (1 == len(c.reactions))
def test_set_operator():
c = CRN()
c.r("A + B <> 2C", [1, 1])
c['A'] = 1.1
assert(list(c.x.flatten()) == [1.1, 0, 0])
def test_set_operator():
c = CRN()
c.r("A + B <> 2C", [1, 1])
c['A'] = 1.1
assert (list(c.x.flatten()) == [1.1, 0, 0])
def test_basic():
c = CRN()
c.r("A + 2B <> C", [1.0, 2.0])
assert(2 == len(c.reactions))