tests for added functions

Author: Oliver Scott

tests/test_network.py

@@ -15,6 +15,12 @@ def test_network(sdf_file):
     return network
 
 
+@pytest.fixture(name='network')
+def long_test_network():
+    network = sg.ScaffoldNetwork.from_smiles_file('tests/test_smiles.smi')
+    return network
+
+
 def test_network_from_sdf(sdf_file):
     network = sg.ScaffoldNetwork.from_sdf(sdf_file)
     assert network.num_scaffold_nodes == 8
@@ -33,5 +39,47 @@ def test_hiers(sdf_file):
     assert network.num_molecule_nodes == 2
 
 
+def test_hierarchy_functions(network):
+    hierarchy_sizes = network.get_hierarchy_sizes()
+    assert hierarchy_sizes[1] == 7
+    assert hierarchy_sizes[2] == 10
+    assert hierarchy_sizes[3] == 7
+    assert hierarchy_sizes[4] == 1
+    assert network.max_hierarchy() == 4
+    assert network.min_hierarchy() == 1
+    s_in_h2 = {
+        'C1=Cn2cnnc2CN=C1', 'O=C1CN=C(c2ccccn2)C=CN1', 'O=C1CN=Cc2ccccc2N1',
+        'C1=CC(c2ccccc2)=[NH+]CC=N1', 'C1=Nc2ccccc2C=[NH+]C1',
+        'O=C1CC(=O)N(c2ccccc2)C=CN1', 'O=C1CC(=O)Nc2ccccc2N1',
+        'O=C1CN=C(c2ccccc2)C=CN1', 'O=C1C[NH+]=Cc2ccccc2N1',
+        'O=C1C[NH+]=C(c2ccccc2)C=CN1'
+    }
+    assert s_in_h2 == set(network.get_scaffolds_in_hierarchy(2))
+
+
+def test_simple_functions(network):
+    assert network.scaffold_in_graph('C1=Cn2cnnc2CN=C1') is True
+    # Below is the non-canonical SMILES of the above
+    assert network.scaffold_in_graph('C1=C-n2:c:n:n:c:2-C-N=C-1') is True
+    assert network.scaffold_in_graph('c1ccccc1CCNc2ccccc2') is False
+    assert network.molecule_in_graph('Adinazolam') is True
+    assert network.molecule_in_graph('Citalopram') is False
+
+
+def test_traversal(network):
+    s_for_adinazolam = {
+        'c1ccc(C2=NCc3nncn3-c3ccccc32)cc1', 'C1=NCc2nncn2-c2ccccc21',
+        'C1=Cn2cnnc2CN=C1c1ccccc1', 'C1=Cn2cnnc2CN=C1', 'c1nnc[nH]1'
+    }
+    assert set(network.get_scaffolds_for_molecule('Adinazolam')) == s_for_adinazolam
+    m_for_scaffold = {'Adinazolam', 'Alprazolam'}
+    assert set(network.get_molecules_for_scaffold('c1nnc[nH]1')) == m_for_scaffold
+
+
+def test_separate_disconnected(network):
+    assert len(network.separate_disconnected_components()) == 2
+    assert type(network.separate_disconnected_components()[0]) == type(network)
+
+
 def test_repr(test_net):
     assert repr(test_net) == '<ScaffoldNetwork at {}>'.format(hex(id(test_net)))

tests/test_smiles.smi

@@ -0,0 +1,10 @@
+CN(C)Cc1n-2c(nn1)CN=C(c1ccccc1)c1cc(Cl)ccc12 Adinazolam
+Cc1n-2c(nn1)CN=C(c1ccccc1)c1cc(Cl)ccc12 Alprazolam
+Brc1cc2c(cc1)NC(=O)CN=C2c1ncccc1 Bromazepam
+CNC1=Nc2c(cc(Cl)cc2)C(c2ccccc2)=[N+]([O-])C1 Chlordiazepoxide
+CN1c2ccc(Cl)cc2N(c2ccccc2)C(=O)CC1=O Clobazam
+[O-][N+](=O)c1cc2c(cc1)NC(=O)CN=C2c1c(Cl)cccc1 Clonazepam
+OC(=O)C1N=C(c2ccccc2)c2cc(Cl)ccc2NC1=O Clorazepate
+Clc1cc2c(cc1)NC(=O)CN=C2c1c(Cl)cccc1 Delorazepam
+[O-][N+]1=C(c2ccccc2)c2cc(Cl)ccc2NC(=O)C1 Demoxepam
+Clc1cc2c(cc1)NC(=O)CC(=O)N2c1ccccc1 Desmethylclobazam