def test_mcsdr2(self):
# Disconnected
mol1 = smiles_to_compound("C1CCCC1CCCC(=O)O")
mol2 = reader.mol_from_text(MOL["CaAcO2"])
arr1 = mcsdr.DescriptorArray(mol1)
arr2 = mcsdr.DescriptorArray(mol2)
self.assertEqual(mcsdr.from_array(arr1, arr2).edge_count(), 3)
# No line graph
mol1 = smiles_to_compound("CO")
mol2 = smiles_to_compound("CC")
arr1 = mcsdr.DescriptorArray(mol1)
arr2 = mcsdr.DescriptorArray(mol2)
self.assertEqual(mcsdr.from_array(arr1, arr2).edge_count(), 0)
# TODO: minimum MCS edge size is 2
mol1 = smiles_to_compound("CCO")
mol2 = smiles_to_compound("CCC")
arr1 = mcsdr.DescriptorArray(mol1)
arr2 = mcsdr.DescriptorArray(mol2)
self.assertEqual(mcsdr.from_array(arr1, arr2).edge_count(), 0)
# This works well
mol1 = smiles_to_compound("CCCO")
mol2 = smiles_to_compound("CCCC")
arr1 = mcsdr.DescriptorArray(mol1)
arr2 = mcsdr.DescriptorArray(mol2)
self.assertEqual(mcsdr.from_array(arr1, arr2).edge_count(), 2)
# TODO: pitfall in line graph
mol1 = smiles_to_compound("CO(C)(C)C")
mol2 = smiles_to_compound("OC(O)(O)O")
arr1 = mcsdr.DescriptorArray(mol1)
arr2 = mcsdr.DescriptorArray(mol2)
def test_mcsdr1(self):
# TODO: pi mismatch is not acceptable
mol1 = reader.mol_from_text(MOL["Phe"])
mol2 = reader.mol_from_text(MOL["Arg"])
arr1 = mcsdr.DescriptorArray(mol1)
arr2 = mcsdr.DescriptorArray(mol2)
self.assertEqual(mcsdr.from_array(arr1, arr2).edge_count(), 5)
# Delta-y exchange will not occur due to distance descriptor
mol1 = smiles_to_compound("C1OC1CCC(=O)O")
mol2 = smiles_to_compound("CC(O)CCC(=O)O")
arr1 = mcsdr.DescriptorArray(mol1)
arr2 = mcsdr.DescriptorArray(mol2)
self.assertEqual(mcsdr.from_array(arr1, arr2).edge_count(), 7)
def test_timeout(self):
mol = reader.mol_from_text(MOL["Buckminsterfullerene"])
tout = mcsdr.DescriptorArray(mol, timeout=0.1)
self.assertFalse(tout.valid)
arr = mcsdr.DescriptorArray(mol, diameter=5, timeout=0.1)
sim = mcsdr.from_array(arr, arr, timeout=0.1)
self.assertGreater(sim.local_sim(), 0)
g1 = nx.read_gexf('temp_1.gexf')
g2 = nx.read_gexf('temp_2.gexf')
c1 = Compound()
c2 = Compound()
for node in g1.nodes():
c1.add_atom(node, Atom(g1.node[node]['type']))
for edge in g1.edges():
b = Bond()
b.order = int(g1[edge[0]][edge[1]]['valence'])
c1.add_bond(edge[0], edge[1], b)
for node in g2.nodes():
c2.add_atom(node, Atom(g2.node[node]['type']))
for edge in g2.edges():
b = Bond()
b.order = int(g2[edge[0]][edge[1]]['valence'])
c2.add_bond(edge[0], edge[1], b)
descriptor.assign_valence(c1)
descriptor.assign_valence(c2)
a1 = comparison_array(c1, ignore_hydrogen=False)
a2 = comparison_array(c2, ignore_hydrogen=False)
g = from_array(a1, a2)
f = open('mcs_result.txt', 'w')
f.write(str(g.edge_count()))
f.close()