def test_complex_bookkeeping(self):
# n1 molecules of A-X
# n2 molecules of A-X2
# n3 molecules of A-X3
# n4 molecules of A-X-bnd-X-A
# number of complexes = n1 + n2 + n3 + n4
# number matches to pattern A-X = n1 + 2*n2 + 3*n3 + 2*n4
pAx = Pattern('pAx').add_node(A(id='a').add_sites(X(id='x')))
m = Matcher()
m.add_pattern(pAx)
n1,n2,n3,n4 = 0,0,0,0
# n1 molecules of A-X
n1 = 100
for i in range(n1):
a,x = A(),X()
m.send_tokens([token_add_node(a),token_add_node(x)])
x.molecule = a
m.send_tokens([token_add_edge(a,'sites','molecule',x)])
# n2 molecules of A-X2
n2 = 50
for i in range(n2):
a,x1,x2 = A(), X(), X()
m.send_tokens([token_add_node(a),token_add_node(x1),token_add_node(x2)])
x1.molecule = a
x2.molecule = a
m.send_tokens([token_add_edge(a,'sites','molecule',x1),token_add_edge(a,'sites','molecule',x2)])
# n3 molecules of A-X3
n3 = 25
for i in range(n3):
a,x1,x2,x3 = A(), X(), X(), X()
m.send_tokens([token_add_node(a),token_add_node(x1),token_add_node(x2),token_add_node(x3)])
x1.molecule = a
x2.molecule = a
x3.molecule = a
m.send_tokens([token_add_edge(a,'sites','molecule',x1),token_add_edge(a,'sites','molecule',x2),token_add_edge(a,'sites','molecule',x3)])
# n4 molecules of A-X-bnd-X-A
n4 = 10
for i in range(n4):
a1,a2,x1,x2 = A(), A(), X(), X()
m.send_tokens([token_add_node(a1),token_add_node(x1)])
m.send_tokens([token_add_node(a2),token_add_node(x2)])
x1.molecule = a1
x2.molecule = a2
m.send_tokens([token_add_edge(a1,'sites','molecule',x1)])
m.send_tokens([token_add_edge(a2,'sites','molecule',x2)])
bnd = Bond()
m.send_tokens([token_add_node(bnd)])
bnd.add_sites(x1,x2)
m.send_tokens([token_add_edge(bnd,'sites','bond',x1)])
m.send_tokens([token_add_edge(bnd,'sites','bond',x2)])
c1 = m.count_complexes()
c2 = m.count('pAx')
self.assertEqual(c1,n1 + n2 + n3 + n4)
self.assertEqual(c2,n1 + 2*n2 + 3*n3 + 2*n4)
def test_token_passing_10(self):
# testing loops formed by A(x!0,x!1)
n = 10
A_list = []
x_right_list = []
x_left_list = []
for i in range(n):
a1, xL, xR = A(), X(), X()
a1.add_sites(xL, xR)
A_list.append(a1)
x_left_list.append(xL)
x_right_list.append(xR)
for i in range(n):
bnd = Bond()
x1 = x_left_list[i]
x2 = x_right_list[i - 1]
bnd.add_sites(x1, x2)
#pattern
p = Pattern('loop').add_node(A_list[0])
self.assertEqual(len(p), 4 * n)
m = Matcher()
m.add_pattern(p)
# tokens
tokens = []
left = []
right = []
for i in range(n):
a, xL, xR = A(), X(), X()
left.append(xL)
right.append(xR)
tokens = [token_add_node(x) for x in [a, xL, xR]]
m.send_tokens(tokens)
a.add_sites(xL, xR)
tokens = [
token_add_edge(a, 'sites', 'molecule', x) for x in [xL, xR]
]
m.send_tokens(tokens)
for i in range(n):
bnd = Bond()
tokens = [token_add_node(bnd)]
m.send_tokens(tokens)
bnd.add_sites(left[i], right[i - 1])
tokens = [
token_add_edge(bnd, 'sites', 'bond', x)
for x in [left[i], right[i - 1]]
]
m.send_tokens(tokens)
self.assertEqual(m.count('loop'), 2 * n)
def test_token_passing_05(self):
# Test pattern Ax:A(x[id=x]), X:X[id=x] with condition Ax.x in X.x
p_X = Pattern('X').add_node( X('x',ph=True) )
p_Ax = Pattern('Ax').add_node( A('a').add_sites(X('x') ) ) \
.add_expression('x in X.x')
m = Matcher()
with self.assertRaises(BuildError):
for p in reversed([p_X, p_Ax]):
m.add_pattern(p)
m = Matcher()
for p in [p_X, p_Ax]:
m.add_pattern(p)
#
x001 = X(ph=True)
a001 = A()
tokens = [token_add_node(a001),token_add_node(x001)]
m.send_tokens(tokens)
x001.set_molecule(a001)
tokens = [token_add_edge(a001,'sites','molecule',x001)]
m.send_tokens(tokens)
self.assertEqual(m.count('X'),1)
self.assertEqual(m.count('Ax'),1)
#
x001.ph = False
tokens = [
token_edit_attrs(x001,['ph'])
]
m.send_tokens(tokens)
self.assertEqual(m.count('X'),0)
self.assertEqual(m.count('Ax'),0)
def test_token_passing_09(self):
# multiple var matching
# Test AxT:A[id=a](X[id=X,ph=True])
# Ax:A[id=a](X[id=x])
# with joint condition Ax.[a,x] in AxT.[a,x]
p_AxT = Pattern('AxT').add_node( A('a').add_sites( X('x',ph=True) ) )
p_Ax = Pattern('Ax').add_node( A('a').add_sites(X('x')) ) \
.add_expression('[a,x] in AxT.[a,x]')
m = Matcher()
for p in [p_AxT,p_Ax]:
m.add_pattern(p)
n=25
for i in range(n):
a001,x001 = A(),X(ph=True)
tokens = [token_add_node(a001),token_add_node(x001)]
m.send_tokens(tokens)
x001.set_molecule(a001)
tokens = [token_add_edge(a001,'sites','molecule',x001)]
m.send_tokens(tokens)
self.assertEqual(m.count('Ax'),n)
n=25
for i in range(n):
a001,x001 = A(),X(ph=False)
tokens = [token_add_node(a001),token_add_node(x001)]
m.send_tokens(tokens)
x001.set_molecule(a001)
tokens = [token_add_edge(a001,'sites','molecule',x001)]
m.send_tokens(tokens)
self.assertEqual(m.count('Ax'),n)
n=25
for i in range(n):
x001 = X(ph=True)
tokens = [token_add_node(x001)]
m.send_tokens(tokens)
self.assertEqual(m.count('Ax'),n)
def test_token_passing_07(self):
# Test A(<empty>)
p1 = Pattern('p1').add_node( A('a') )
p1.add_expression('a.sites empty')
p2 = Pattern('p2').add_node( A('a') )
m = Matcher()
for p in [p1,p2]:
m.add_pattern(p)
self.assertEqual(m.count('p1'),0)
self.assertEqual(m.count('p2'),0)
# Add new A:
a001 = A()
tok = token_add_node(a001)
m.send_token(tok)
self.assertEqual(m.count('p1'),1)
self.assertEqual(m.count('p2'),1)
# Add new X
x001 = X()
tok = token_add_node(x001)
m.send_token(tok)
self.assertEqual(m.count('p1'),1)
self.assertEqual(m.count('p2'),1)
# X.set_molecule(A)
x001.set_molecule(a001)
tok = token_add_edge(a001,'sites','molecule',x001)
m.send_token(tok)
self.assertEqual(m.count('p1'),0)
self.assertEqual(m.count('p2'),1)
# X.unset_molecule()
x001.unset_molecule()
tok = token_remove_edge(a001,'sites','molecule',x001)
m.send_token(tok)
self.assertEqual(m.count('p1'),1)
self.assertEqual(m.count('p2'),1)
# Remove A
tok = token_remove_node(a001)
m.send_token(tok)
self.assertEqual(m.count('p1'),0)
self.assertEqual(m.count('p2'),0)
def test_token_passing_06(self):
# Test Ax:A(X[id=x]), X:X[id=x,ph=True] with condition A.x not in X.x
p_X = Pattern('X').add_node(X('x', ph=True))
p_Ax = Pattern('Ax').add_node( A('a').add_sites(X('x') ) ) \
.add_expression('x not in X.x')
m = Matcher()
for p in [p_X, p_Ax]:
m.add_pattern(p)
#
a001 = A()
x001 = X(ph=True)
tokens = [token_add_node(a001), token_add_node(x001)]
m.send_tokens(tokens)
x001.set_molecule(a001)
tokens = [
token_add_edge(a001, 'sites', 'molecule', x001),
]
m.send_tokens(tokens)
self.assertEqual(m.count('X'), 1)
self.assertEqual(m.count('Ax'), 0)
#
x001.ph = False
tokens = [token_edit_attrs(x001, ['ph'])]
m.send_tokens(tokens)
self.assertEqual(m.count('X'), 0)
self.assertEqual(m.count('Ax'), 1)
#
x001.ph = True
tokens = [token_edit_attrs(x001, ['ph'])]
m.send_tokens(tokens)
self.assertEqual(m.count('X'), 1)
self.assertEqual(m.count('Ax'), 0)
def test_token_passing_08(self):
# Test A(x)
# One-edge
p_Ax = Pattern('Ax').add_node( A('a').add_sites(X('x') ) )
m = Matcher()
for p in [p_Ax]:
m.add_pattern(p)
a001 = A()
tokens = [token_add_node(a001)]
m.send_tokens(tokens)
n = 100
for i in range(n):
x = X()
tokens = [token_add_node(x)]
m.send_tokens(tokens)
x.set_molecule(a001)
tokens = [token_add_edge(x,'molecule','sites',a001)]
m.send_tokens(tokens)
self.assertEqual(m.count('Ax'),n)
# Test A(x,x)
# Two edges
p_Axx = Pattern('Axx').add_node( A('a').add_sites( X('x1'),X('x2') ) )
m = Matcher()
for p in [p_Axx]:
m.add_pattern(p)
a001 = A()
tokens = [token_add_node(a001)]
m.send_tokens(tokens)
n = 25
for i in range(n):
x = X()
tokens = [token_add_node(x)]
m.send_tokens(tokens)
x.set_molecule(a001)
tokens = [token_add_edge(x,'molecule','sites',a001)]
m.send_tokens(tokens)
self.assertEqual(m.count('Axx'),n*(n-1))
# Three edges
# Test A(x,x,x)
p_Axxx = Pattern('Axxx').add_node( A('a').add_sites( X('x1'),X('x2'),X('x3') ) )
m = Matcher()
for p in [p_Axxx]:
m.add_pattern(p)
a001 = A()
tokens = [token_add_node(a001)]
m.send_tokens(tokens)
n = 25
for i in range(n):
x = X()
tokens = [token_add_node(x)]
m.send_tokens(tokens)
x.set_molecule(a001)
tokens = [token_add_edge(x,'molecule','sites',a001)]
m.send_tokens(tokens)
self.assertEqual(m.count('Axxx'),n*(n-1)*(n-2))