def test_model_to_network():
assert_equal(model_to_network(TEST_MODEL).edges(), reactions_to_network(TEST_MODEL.reactions).edges())
network = model_to_network(TEST_MODEL)
assert_equal(len(network.nodes()), 1761)
assert_equal(len(network.edges()), 4924)
network = model_to_network(TEST_MODEL, max_distance=1.0)
# nodes = network.nodes()
# print(set(nodes).difference(set(TEST_MODEL.metabolites)))
# print(set(TEST_MODEL.metabolites).difference(set(nodes)))
assert_equal(len(network.nodes()), 1800)
assert_equal(len(network.edges()), 12853)
def test_model_to_network():
assert_equal(model_to_network(TEST_MODEL).edges(), reactions_to_network(TEST_MODEL.reactions).edges())
network = model_to_network(TEST_MODEL)
assert_equal(len(network.nodes()), 1761)
assert_equal(len(network.edges()), 4924)
network = model_to_network(TEST_MODEL, max_distance=1.)
# nodes = network.nodes()
# print(set(nodes).difference(set(TEST_MODEL.metabolites)))
# print(set(TEST_MODEL.metabolites).difference(set(nodes)))
assert_equal(len(network.nodes()), 1800)
assert_equal(len(network.edges()), 12853)
def test_model_to_network(salmonella):
assert model_to_network(salmonella).edges() == reactions_to_network(salmonella.reactions).edges()
network = model_to_network(salmonella)
assert len(network.nodes()) == 1761
assert len(network.edges()) == 4924
network = model_to_network(salmonella, max_distance=1.)
# nodes = network.nodes()
# print(set(nodes).difference(set(core_model_one.metabolites)))
# print(set(core_model_one.metabolites).difference(set(nodes)))
assert len(network.nodes()) == 1800
assert len(network.edges()) == 12853
def test_remove_highly_connected_nodes():
network = model_to_network(TEST_MODEL)
assert_in(TEST_MODEL.metabolites.atp_c, network.nodes())
assert_in(TEST_MODEL.metabolites.adp_c, network.nodes())
remove_highly_connected_nodes(network, max_degree=10, ignore=[TEST_MODEL.metabolites.atp_c])
assert_equal(len(network.nodes()), 1671)
assert_equal(len(network.edges()), 2342)
assert_in(TEST_MODEL.metabolites.atp_c, network.nodes())
assert_not_in(TEST_MODEL.metabolites.adp_c, network.nodes())
def test_remove_highly_connected_nodes():
network = model_to_network(TEST_MODEL)
assert_in(TEST_MODEL.metabolites.atp_c, network.nodes())
assert_in(TEST_MODEL.metabolites.adp_c, network.nodes())
remove_highly_connected_nodes(network, max_degree=10, ignore=[TEST_MODEL.metabolites.atp_c])
assert_equal(len(network.nodes()), 1671)
assert_equal(len(network.edges()), 2342)
assert_in(TEST_MODEL.metabolites.atp_c, network.nodes())
assert_not_in(TEST_MODEL.metabolites.adp_c, network.nodes())
def test_remove_highly_connected_nodes(salmonella):
network = model_to_network(salmonella)
assert salmonella.metabolites.atp_c in network.nodes()
assert salmonella.metabolites.adp_c in network.nodes()
remove_highly_connected_nodes(network, max_degree=10, ignore=[salmonella.metabolites.atp_c])
assert len(network.nodes()) == 1671
assert len(network.edges()) == 2342
assert salmonella.metabolites.atp_c in network.nodes()
assert salmonella.metabolites.adp_c not in network.nodes()
