class TestGraph(unittest.TestCase):
"""
Contains unit tests of the Vertex, Edge, and Graph classes. Most of the
functionality of Vertex and Edge is only meaningful when part of a graph,
so we test them all together instead of having separate unit test classes
for each.
"""
def setUp(self):
"""
A function run before each unit test in this class.
"""
vertices = [Vertex() for _ in range(6)]
edges = [
Edge(vertices[0], vertices[1]),
Edge(vertices[1], vertices[2]),
Edge(vertices[2], vertices[3]),
Edge(vertices[3], vertices[4]),
Edge(vertices[4], vertices[5]),
]
self.graph = Graph(vertices)
for edge in edges:
self.graph.add_edge(edge)
def test_vertices(self):
"""
Test that the vertices attribute can be accessed.
"""
vertices = self.graph.vertices
self.assertTrue(isinstance(vertices, list))
self.assertEqual(len(vertices), 6)
def test_add_vertex(self):
"""
Test the Graph.add_vertex() method.
"""
vertex = Vertex()
self.graph.add_vertex(vertex)
self.assertTrue(vertex in self.graph.vertices)
self.assertTrue(vertex.edges == {})
def test_add_edge(self):
"""
Test the Graph.add_edge() method.
"""
vertex1 = Vertex()
vertex2 = Vertex()
edge = Edge(vertex1, vertex2)
try:
self.graph.add_edge(edge)
self.fail('Added edge between vertices not in graph to graph.')
except ValueError:
pass
self.graph.add_vertex(vertex1)
self.graph.add_vertex(vertex2)
self.graph.add_edge(edge)
self.assertTrue(vertex1 in self.graph.vertices)
self.assertTrue(vertex1 in vertex2.edges)
self.assertTrue(vertex2 in self.graph.vertices)
self.assertTrue(vertex2 in vertex1.edges)
self.assertTrue(vertex1.edges[vertex2] is edge)
self.assertTrue(vertex2.edges[vertex1] is edge)
def test_get_edge(self):
"""
Test the Graph.get_edge() method.
"""
vertex1 = self.graph.vertices[2]
vertex2 = self.graph.vertices[4]
try:
self.graph.get_edge(vertex1, vertex2)
self.fail(
'Returned an edge between vertices that should not be connected in graph.'
)
except ValueError:
pass
vertex1 = self.graph.vertices[2]
vertex2 = self.graph.vertices[3]
edge = self.graph.get_edge(vertex1, vertex2)
self.assertNotEqual(edge, None)
self.assertTrue(isinstance(edge, Edge))
self.assertTrue(vertex1.edges[vertex2] is edge)
self.assertTrue(vertex2.edges[vertex1] is edge)
def test_get_edges(self):
"""
Test the Graph.get_edges() method.
"""
vertex1 = self.graph.vertices[2]
edges = self.graph.get_edges(vertex1)
self.assertTrue(isinstance(edges, dict))
self.assertEqual(len(edges), 2)
self.assertTrue(self.graph.vertices[1] in edges)
self.assertTrue(self.graph.vertices[3] in edges)
def test_get_all_edges(self):
"""
Test the Graph.get_all_edges() method.
"""
edges = self.graph.get_all_edges()
self.assertTrue(isinstance(edges, list))
self.assertEqual(len(edges), 5)
def test_has_vertex(self):
"""
Test the Graph.has_vertex() method.
"""
vertex = Vertex()
self.assertFalse(self.graph.has_vertex(vertex))
for v in self.graph.vertices:
self.assertTrue(self.graph.has_vertex(v))
def test_has_edge(self):
"""
Test the Graph.has_edge() method.
"""
vertex1 = self.graph.vertices[2]
vertex2 = self.graph.vertices[4]
self.assertFalse(self.graph.has_edge(vertex1, vertex2))
vertex1 = self.graph.vertices[2]
vertex2 = self.graph.vertices[3]
self.assertTrue(self.graph.has_edge(vertex1, vertex2))
def test_remove_vertex(self):
"""
Test the Graph.remove_vertex() method.
"""
vertex = self.graph.vertices[2]
self.assertTrue(self.graph.has_vertex(vertex))
self.graph.remove_vertex(vertex)
self.assertFalse(self.graph.has_vertex(vertex))
for v in self.graph.vertices:
self.assertFalse(vertex in v.edges)
def test_remove_edge(self):
"""
Test the Graph.remove_edge() method.
"""
vertex1 = self.graph.vertices[2]
vertex2 = self.graph.vertices[3]
self.assertTrue(self.graph.has_edge(vertex1, vertex2))
edge = self.graph.get_edge(vertex1, vertex2)
self.graph.remove_edge(edge)
self.assertFalse(vertex1 in vertex2.edges)
self.assertFalse(vertex2 in vertex1.edges)
def test_copy(self):
"""
Test the graph copy function to ensure a complete copy of the graph is
made while preserving vertices and edges.
"""
vertices = [Vertex() for _ in range(6)]
edges = [
Edge(vertices[0], vertices[1]),
Edge(vertices[1], vertices[2]),
Edge(vertices[2], vertices[3]),
Edge(vertices[3], vertices[4]),
Edge(vertices[4], vertices[5]),
]
graph = Graph()
for vertex in vertices:
graph.add_vertex(vertex)
for edge in edges:
graph.add_edge(edge)
graph2 = graph.copy()
for vertex in graph.vertices:
self.assertTrue(graph2.has_vertex(vertex))
for v1 in graph.vertices:
for v2 in v1.edges:
self.assertTrue(graph2.has_edge(v1, v2))
self.assertTrue(graph2.has_edge(v2, v1))
self.assertTrue(graph2.is_isomorphic(graph))
self.assertTrue(graph.is_isomorphic(graph2))
def test_copy_and_map(self):
"""
Test the returned dictionary points toward equivaalent vertices and edges
"""
vertices = [Vertex() for _ in range(6)]
edges = [
Edge(vertices[0], vertices[1]),
Edge(vertices[1], vertices[2]),
Edge(vertices[2], vertices[3]),
Edge(vertices[3], vertices[4]),
Edge(vertices[4], vertices[5]),
]
graph = Graph()
for vertex in vertices:
graph.add_vertex(vertex)
for edge in edges:
graph.add_edge(edge)
graph_dict = graph.copy_and_map()
graph2 = Graph(vertices=list(graph_dict.values()))
for vertex in graph.vertices:
self.assertTrue(graph2.has_vertex(graph_dict[vertex]))
for v1 in graph.vertices:
for v2 in v1.edges:
self.assertTrue(graph2.has_edge(graph_dict[v1],
graph_dict[v2]))
self.assertTrue(graph2.has_edge(graph_dict[v2],
graph_dict[v1]))
self.assertTrue(graph2.is_isomorphic(graph))
self.assertTrue(graph.is_isomorphic(graph2))
def test_split(self):
"""
Test the graph split function to ensure a proper splitting of the graph
is being done.
"""
vertices = [Vertex() for _ in range(6)]
edges = [
Edge(vertices[0], vertices[1]),
Edge(vertices[1], vertices[2]),
Edge(vertices[2], vertices[3]),
Edge(vertices[4], vertices[5]),
]
graph = Graph()
for vertex in vertices:
graph.add_vertex(vertex)
for edge in edges:
graph.add_edge(edge)
graphs = graph.split()
self.assertTrue(len(graphs) == 2)
self.assertTrue(
len(graphs[0].vertices) == 4 or len(graphs[0].vertices) == 2)
self.assertTrue(
len(graphs[0].vertices) +
len(graphs[1].vertices) == len(graph.vertices))
def test_merge(self):
"""
Test the graph merge function to ensure a proper merging of the graph
is being done.
"""
vertices1 = [Vertex() for _ in range(4)]
edges1 = [
Edge(vertices1[0], vertices1[1]),
Edge(vertices1[1], vertices1[2]),
Edge(vertices1[2], vertices1[3]),
]
vertices2 = [Vertex() for _ in range(3)]
edges2 = [
Edge(vertices2[0], vertices2[1]),
Edge(vertices2[1], vertices2[2]),
]
graph1 = Graph()
for vertex in vertices1:
graph1.add_vertex(vertex)
for edge in edges1:
graph1.add_edge(edge)
graph2 = Graph()
for vertex in vertices2:
graph2.add_vertex(vertex)
for edge in edges2:
graph2.add_edge(edge)
graph = graph1.merge(graph2)
self.assertTrue(
len(graph1.vertices) + len(graph2.vertices) == len(graph.vertices))
for vertex1 in vertices1:
self.assertTrue(vertex1 in graph.vertices)
for vertex2 in vertex1.edges:
self.assertTrue(vertex2 in graph.vertices)
for vertex2 in vertices2:
self.assertTrue(vertex2 in graph.vertices)
for vertex1 in vertex2.edges:
self.assertTrue(vertex1 in vertex2.edges)
def test_reset_connectivity_values(self):
"""
Test the Graph.reset_connectivity_values() method.
"""
self.graph.reset_connectivity_values()
for vertex in self.graph.vertices:
self.assertEqual(vertex.connectivity1, -1)
self.assertEqual(vertex.connectivity2, -1)
self.assertEqual(vertex.connectivity3, -1)
self.assertEqual(vertex.sorting_label, -1)
def test_update_connectivity_values(self):
"""
Test the Graph.update_connectivity_values() method.
"""
self.graph.update_connectivity_values()
self.assertEqual(self.graph.vertices[0].connectivity1, 1)
self.assertEqual(self.graph.vertices[0].connectivity2, 2)
self.assertEqual(self.graph.vertices[0].connectivity3, 3)
self.assertEqual(self.graph.vertices[0].sorting_label, -1)
self.assertEqual(self.graph.vertices[1].connectivity1, 2)
self.assertEqual(self.graph.vertices[1].connectivity2, 3)
self.assertEqual(self.graph.vertices[1].connectivity3, 6)
self.assertEqual(self.graph.vertices[1].sorting_label, -1)
self.assertEqual(self.graph.vertices[2].connectivity1, 2)
self.assertEqual(self.graph.vertices[2].connectivity2, 4)
self.assertEqual(self.graph.vertices[2].connectivity3, 7)
self.assertEqual(self.graph.vertices[2].sorting_label, -1)
self.assertEqual(self.graph.vertices[3].connectivity1, 2)
self.assertEqual(self.graph.vertices[3].connectivity2, 4)
self.assertEqual(self.graph.vertices[3].connectivity3, 7)
self.assertEqual(self.graph.vertices[3].sorting_label, -1)
self.assertEqual(self.graph.vertices[4].connectivity1, 2)
self.assertEqual(self.graph.vertices[4].connectivity2, 3)
self.assertEqual(self.graph.vertices[4].connectivity3, 6)
self.assertEqual(self.graph.vertices[4].sorting_label, -1)
self.assertEqual(self.graph.vertices[5].connectivity1, 1)
self.assertEqual(self.graph.vertices[5].connectivity2, 2)
self.assertEqual(self.graph.vertices[5].connectivity3, 3)
self.assertEqual(self.graph.vertices[5].sorting_label, -1)
def test_sort_vertices(self):
"""
Test the Graph.sort_vertices() method.
"""
self.graph.update_connectivity_values()
self.graph.sort_vertices()
for vertex1, vertex2 in zip(self.graph.vertices[:-1],
self.graph.vertices[1:]):
self.assertTrue(vertex1.sorting_label < vertex2.sorting_label)
self.assertTrue(vertex1.connectivity3 >= vertex2.connectivity3)
self.assertTrue(vertex1.connectivity2 >= vertex2.connectivity2)
self.assertTrue(vertex1.connectivity1 >= vertex2.connectivity1)
def test_vertex_connectivity_values(self):
"""
Tests the vertex connectivity values as introduced by Morgan (1965).
First CV1 is the number of neighbours
CV2 is the sum of neighbouring CV1 values
CV3 is the sum of neighbouring CV2 values
Graph: Expected (and tested) values:
0-1-2-3-4 1-3-2-2-1 3-4-5-3-2 4-11-7-7-3
| | | |
5 1 3 4
"""
vertices = [Vertex() for _ in range(6)]
edges = [
Edge(vertices[0], vertices[1]),
Edge(vertices[1], vertices[2]),
Edge(vertices[2], vertices[3]),
Edge(vertices[3], vertices[4]),
Edge(vertices[1], vertices[5]),
]
graph = Graph()
for vertex in vertices:
graph.add_vertex(vertex)
for edge in edges:
graph.add_edge(edge)
graph.update_connectivity_values()
for i, cv_ in enumerate([1, 3, 2, 2, 1, 1]):
cv = vertices[i].connectivity1
self.assertEqual(
cv, cv_,
"On vertex {0:d} got connectivity[0]={1:d} but expected {2:d}".
format(i, cv, cv_))
for i, cv_ in enumerate([3, 4, 5, 3, 2, 3]):
cv = vertices[i].connectivity2
self.assertEqual(
cv, cv_,
"On vertex {0:d} got connectivity[0]={1:d} but expected {2:d}".
format(i, cv, cv_))
for i, cv_ in enumerate([4, 11, 7, 7, 3, 4]):
cv = vertices[i].connectivity3
self.assertEqual(
cv, cv_,
"On vertex {0:d} got connectivity[0]={1:d} but expected {2:d}".
format(i, cv, cv_))
def test_isomorphism(self):
"""
Check the graph isomorphism functions.
"""
vertices1 = [Vertex() for _ in range(6)]
edges1 = [
Edge(vertices1[0], vertices1[1]),
Edge(vertices1[1], vertices1[2]),
Edge(vertices1[2], vertices1[3]),
Edge(vertices1[3], vertices1[4]),
Edge(vertices1[4], vertices1[5]),
]
vertices2 = [Vertex() for _ in range(6)]
edges2 = [
Edge(vertices2[0], vertices2[1]),
Edge(vertices2[1], vertices2[2]),
Edge(vertices2[2], vertices2[3]),
Edge(vertices2[3], vertices2[4]),
Edge(vertices2[4], vertices2[5]),
]
graph1 = Graph()
for vertex in vertices1:
graph1.add_vertex(vertex)
for edge in edges1:
graph1.add_edge(edge)
graph2 = Graph()
for vertex in vertices2:
graph2.add_vertex(vertex)
for edge in edges2:
graph2.add_edge(edge)
self.assertTrue(graph1.is_isomorphic(graph2))
self.assertTrue(graph1.is_subgraph_isomorphic(graph2))
self.assertTrue(graph2.is_isomorphic(graph1))
self.assertTrue(graph2.is_subgraph_isomorphic(graph1))
def test_isomorphism_disconnected(self):
"""
Check the graph isomorphism for broken graphs.
This tries to match graphs with a missing bond,
eg. [ 0-1-2-3-4 5 ] should match [ 0-1-2-3-4 5 ]
"""
vertices1 = [Vertex() for _ in range(6)]
edges1 = [
Edge(vertices1[0], vertices1[1]),
Edge(vertices1[1], vertices1[2]),
Edge(vertices1[2], vertices1[3]),
Edge(vertices1[3], vertices1[4]),
# Edge(vertices1[4], vertices1[5]),
]
vertices2 = [Vertex() for _ in range(6)]
edges2 = [
Edge(vertices2[0], vertices2[1]),
Edge(vertices2[1], vertices2[2]),
Edge(vertices2[2], vertices2[3]),
Edge(vertices2[3], vertices2[4]),
# Edge(vertices2[4], vertices2[5]),
]
graph1 = Graph()
for vertex in vertices1:
graph1.add_vertex(vertex)
for edge in edges1:
graph1.add_edge(edge)
graph2 = Graph()
for vertex in vertices2:
graph2.add_vertex(vertex)
for edge in edges2:
graph2.add_edge(edge)
self.assertTrue(graph1.is_isomorphic(graph2))
self.assertTrue(graph1.is_subgraph_isomorphic(graph2))
self.assertTrue(graph2.is_isomorphic(graph1))
self.assertTrue(graph2.is_subgraph_isomorphic(graph1))
self.assertTrue(len(graph1.find_subgraph_isomorphisms(graph2)) > 0)
def test_subgraph_isomorphism(self):
"""
Check the subgraph isomorphism functions.
"""
vertices1 = [Vertex() for _ in range(6)]
edges1 = [
Edge(vertices1[0], vertices1[1]),
Edge(vertices1[1], vertices1[2]),
Edge(vertices1[2], vertices1[3]),
Edge(vertices1[3], vertices1[4]),
Edge(vertices1[4], vertices1[5]),
]
vertices2 = [Vertex() for _ in range(2)]
edges2 = [
Edge(vertices2[0], vertices2[1]),
]
graph1 = Graph()
for vertex in vertices1:
graph1.add_vertex(vertex)
for edge in edges1:
graph1.add_edge(edge)
graph2 = Graph()
for vertex in vertices2:
graph2.add_vertex(vertex)
for edge in edges2:
graph2.add_edge(edge)
self.assertFalse(graph1.is_isomorphic(graph2))
self.assertFalse(graph2.is_isomorphic(graph1))
self.assertTrue(graph1.is_subgraph_isomorphic(graph2))
map_list = graph1.find_subgraph_isomorphisms(graph2)
self.assertTrue(len(map_list) == 10)
for mapping in map_list:
self.assertTrue(graph1.is_mapping_valid(graph2, mapping))
self.assertTrue(graph1.is_mapping_valid(graph2, mapping))
def test_pickle(self):
"""
Test that a Graph object can be successfully pickled and unpickled
with no loss of information.
"""
vertices = [Vertex() for _ in range(6)]
edges = [
Edge(vertices[0], vertices[1]),
Edge(vertices[1], vertices[2]),
Edge(vertices[2], vertices[3]),
Edge(vertices[3], vertices[4]),
Edge(vertices[4], vertices[5]),
]
graph0 = Graph()
for vertex in vertices:
graph0.add_vertex(vertex)
for edge in edges:
graph0.add_edge(edge)
graph0.update_connectivity_values()
import pickle
graph = pickle.loads(pickle.dumps(graph0))
self.assertEqual(len(graph0.vertices), len(graph.vertices))
for v1, v2 in zip(graph0.vertices, graph.vertices):
self.assertEqual(v1.connectivity1, v2.connectivity1)
self.assertEqual(v1.connectivity2, v2.connectivity2)
self.assertEqual(v1.connectivity3, v2.connectivity3)
self.assertEqual(v1.sorting_label, v2.sorting_label)
self.assertEqual(len(v1.edges), len(v2.edges))
self.assertTrue(graph0.is_isomorphic(graph))
self.assertTrue(graph.is_isomorphic(graph0))
def test_is_cyclic(self):
"""
Test the Graph.is_cyclic() method.
"""
self.assertFalse(self.graph.is_cyclic())
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle
self.assertTrue(self.graph.is_cyclic())
def test_is_vertex_in_cycle(self):
"""
Test the Graph.is_vertex_in_cycle() method.
"""
for vertex in self.graph.vertices:
self.assertFalse(self.graph.is_vertex_in_cycle(vertex))
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle
for vertex in self.graph.vertices[0:4]:
self.assertTrue(self.graph.is_vertex_in_cycle(vertex))
for vertex in self.graph.vertices[4:]:
self.assertFalse(self.graph.is_vertex_in_cycle(vertex))
def test_is_edge_in_cycle(self):
"""
Test the Graph.is_edge_in_cycle() method.
"""
for vertex1 in self.graph.vertices:
for vertex2, edge in vertex1.edges.items():
self.assertFalse(self.graph.is_edge_in_cycle(edge))
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle
for vertex1 in self.graph.vertices:
for vertex2, edge in vertex1.edges.items():
if self.graph.vertices.index(
vertex1) < 4 and self.graph.vertices.index(
vertex2) < 4:
self.assertTrue(self.graph.is_edge_in_cycle(edge))
else:
self.assertFalse(self.graph.is_edge_in_cycle(edge))
def test_get_all_cyclic_vertices(self):
self.assertListEqual(self.graph.get_all_cyclic_vertices(), [])
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle
self.assertEqual(len(self.graph.get_all_cyclic_vertices()), 4)
def test_get_all_polycylic_vertices(self):
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle
self.assertListEqual(self.graph.get_all_polycyclic_vertices(), [])
edge2 = Edge(self.graph.vertices[0], self.graph.vertices[5])
self.graph.add_edge(
edge2) # Create another cycle to generate two fused cycles
self.assertEqual(len(self.graph.get_all_polycyclic_vertices()), 2)
# Add new vertices and edges to generate a spirocyclic cycle
vertices = [Vertex() for _ in range(2)]
for vertex in vertices:
self.graph.add_vertex(vertex)
edges = [
Edge(self.graph.vertices[5], self.graph.vertices[6]),
Edge(self.graph.vertices[6], self.graph.vertices[7]),
Edge(self.graph.vertices[5], self.graph.vertices[7]),
]
for edge in edges:
self.graph.add_edge(edge)
self.assertEqual(len(self.graph.get_all_polycyclic_vertices()), 3)
def test_get_all_cycles(self):
"""
Test the Graph.get_all_cycles() method.
"""
cycle_list = self.graph.get_all_cycles(self.graph.vertices[0])
self.assertEqual(len(cycle_list), 0)
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle
cycle_list = self.graph.get_all_cycles(self.graph.vertices[0])
self.assertEqual(len(cycle_list), 2)
self.assertEqual(len(cycle_list[0]), 4)
self.assertEqual(len(cycle_list[1]), 4)
def test_get_all_cycles_of_size(self):
"""
Test the Graph.getRingsOfSize() method
"""
cycle_list = self.graph.get_all_cycles_of_size(6)
self.assertEqual(len(cycle_list), 0)
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle of length 4
edge = Edge(self.graph.vertices[0], self.graph.vertices[5])
self.graph.add_edge(
edge
) # To create a cycle of length 6 and another cycle of length 4
cycle_list = self.graph.get_all_cycles_of_size(4)
self.assertEqual(len(cycle_list), 2)
self.assertEqual(len(cycle_list[0]), 4)
self.assertEqual(len(cycle_list[1]), 4)
def test_get_all_simple_cycles_of_size(self):
"""
Test the Graph.get_all_simple_cycles_of_size() method.
"""
cycle_list = self.graph.get_all_cycles_of_size(6)
self.assertEqual(len(cycle_list), 0)
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle of length 4
edge = Edge(self.graph.vertices[0], self.graph.vertices[5])
self.graph.add_edge(
edge
) # To create a cycle of length 6 and another cycle of length 4
cycle_list = self.graph.get_all_simple_cycles_of_size(4)
self.assertEqual(len(cycle_list), 2)
self.assertEqual(len(cycle_list[0]), 4)
self.assertEqual(len(cycle_list[1]), 4)
cycle_list = self.graph.get_all_simple_cycles_of_size(6)
self.assertEqual(len(cycle_list), 0)
def test_get_smallest_set_of_smallest_rings(self):
"""
Test the Graph.get_smallest_set_of_smallest_rings() method.
"""
cycle_list = self.graph.get_smallest_set_of_smallest_rings()
self.assertEqual(len(cycle_list), 0)
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge) # To create a cycle
cycle_list = self.graph.get_smallest_set_of_smallest_rings()
self.assertEqual(len(cycle_list), 1)
self.assertEqual(len(cycle_list[0]), 4)
def test_get_relevant_cycles(self):
"""
Test the Graph.get_relevant_cycles() method.
"""
cycle_list = self.graph.get_relevant_cycles()
self.assertEqual(len(cycle_list), 0)
# Create a cycle of length 4
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.add_edge(edge)
# Create a second cycle of length 4
edge = Edge(self.graph.vertices[0], self.graph.vertices[5])
self.graph.add_edge(edge)
# Create a bridge forming multiple cycles of length 4
edge = Edge(self.graph.vertices[1], self.graph.vertices[4])
self.graph.add_edge(edge)
# SSSR should be 3 cycles of length 4
cycle_list = self.graph.get_smallest_set_of_smallest_rings()
self.assertEqual(len(cycle_list), 3)
size_list = sorted([len(cycle) for cycle in cycle_list])
self.assertEqual(size_list, [4, 4, 4])
# RC should be 5 cycles of length 4
cycle_list = self.graph.get_relevant_cycles()
self.assertEqual(len(cycle_list), 5)
size_list = sorted([len(cycle) for cycle in cycle_list])
self.assertEqual(size_list, [4, 4, 4, 4, 4])
def test_cycle_list_order_sssr(self):
"""
Test that get_smallest_set_of_smallest_rings return vertices in the proper order.
There are methods such as symmetry and molecule drawing which rely
on the fact that subsequent list entries are connected.
"""
# Create a cycle of length 5
edge = Edge(self.graph.vertices[0], self.graph.vertices[4])
self.graph.add_edge(edge)
# Test SSSR
sssr = self.graph.get_smallest_set_of_smallest_rings()
self.assertEqual(len(sssr), 1)
self.assertEqual(len(sssr[0]), 5)
for i in range(5):
self.assertTrue(self.graph.has_edge(sssr[0][i], sssr[0][i - 1]))
def test_cycle_list_order_relevant_cycles(self):
"""
Test that get_relevant_cycles return vertices in the proper order.
There are methods such as symmetry and molecule drawing which rely
on the fact that subsequent list entries are connected.
"""
# Create a cycle of length 5
edge = Edge(self.graph.vertices[0], self.graph.vertices[4])
self.graph.add_edge(edge)
# Test RC
rc = self.graph.get_relevant_cycles()
self.assertEqual(len(rc), 1)
self.assertEqual(len(rc[0]), 5)
for i in range(5):
self.assertTrue(self.graph.has_edge(rc[0][i], rc[0][i - 1]))
def test_get_polycyclic_rings(self):
"""
Test that the Graph.get_polycycles() method returns only polycyclic rings.
"""
vertices = [Vertex() for _ in range(27)]
bonds = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6),
(6, 7), (7, 8), (8, 9), (9, 10), (10, 11), (11, 12), (12, 13),
(13, 14), (14, 15), (14, 12), (12, 16), (16, 10), (10, 17),
(17, 18), (18, 19), (9, 20), (20, 21), (21, 7), (6, 22),
(22, 23), (22, 4), (23, 3), (23, 24), (24, 25), (25, 1)]
edges = []
for bond in bonds:
edges.append(Edge(vertices[bond[0]], vertices[bond[1]]))
graph = Graph()
for vertex in vertices:
graph.add_vertex(vertex)
for edge in edges:
graph.add_edge(edge)
graph.update_connectivity_values()
sssr = graph.get_smallest_set_of_smallest_rings()
self.assertEqual(len(sssr), 6)
polycyclic_vertices = set(graph.get_all_polycyclic_vertices())
expected_polycyclic_vertices = set(
[vertices[index] for index in [3, 23, 4, 22, 12]])
self.assertEqual(polycyclic_vertices, expected_polycyclic_vertices)
continuous_rings = graph.get_polycycles()
expected_continuous_rings = [
[vertices[index] for index in [1, 2, 3, 4, 5, 6, 22, 23, 24, 25]],
# [vertices[index] for index in [7,8,9,21,20]], # This is a nonpolycyclic ring
[vertices[index] for index in [10, 11, 12, 13, 14, 16]],
]
# Convert to sets for comparison purposes
continuous_rings = [set(ring) for ring in continuous_rings]
expected_continuous_rings = [
set(ring) for ring in expected_continuous_rings
]
for ring in expected_continuous_rings:
self.assertTrue(ring in continuous_rings)
def test_get_max_cycle_overlap(self):
"""
Test that get_max_cycle_overlap returns the correct overlap numbers
for different graphs.
"""
def make_graph(edge_inds):
nvert = max(max(inds) for inds in edge_inds) + 1
vertices = [Vertex() for _ in range(nvert)]
graph = Graph(vertices)
for idx1, idx2 in edge_inds:
graph.add_edge(Edge(vertices[idx1], vertices[idx2]))
return graph
linear = make_graph([(0, 1), (1, 2)])
mono = make_graph([(0, 1), (0, 2), (1, 2), (2, 3), (3, 4), (3, 5),
(4, 5)])
spiro = make_graph([(0, 1), (0, 2), (1, 2), (2, 3), (2, 4), (3, 4)])
fused = make_graph([(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)])
bridged = make_graph([(0, 1), (0, 2), (1, 3), (1, 4), (2, 3), (2, 5),
(4, 5)])
cube = make_graph([(0, 1), (0, 2), (0, 4), (1, 3), (1, 5), (2, 3),
(2, 6), (3, 7), (4, 5), (4, 6), (5, 7), (6, 7)])
self.assertEqual(linear.get_max_cycle_overlap(), 0)
self.assertEqual(mono.get_max_cycle_overlap(), 0)
self.assertEqual(spiro.get_max_cycle_overlap(), 1)
self.assertEqual(fused.get_max_cycle_overlap(), 2)
self.assertEqual(bridged.get_max_cycle_overlap(), 3)
# With the current algorithm for maximum overlap determination, a cube
# only has an overlap of 2, because the set of relevant cycles
# contains the six four-membered faces. This could be changed in the
# future.
self.assertEqual(cube.get_max_cycle_overlap(), 2)
def test_get_largest_ring(self):
"""
Test that the Graph.get_polycycles() method returns only polycyclic rings.
"""
vertices = [Vertex() for _ in range(27)]
bonds = [(0, 1), (1, 2),
(2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (9, 10), (10, 11),
(11, 12), (12, 13), (13, 14), (14, 15), (12, 16), (10, 17),
(17, 18), (18, 19), (9, 20), (20, 21), (6, 22), (22, 23),
(22, 8), (8, 4), (23, 3), (23, 24), (24, 25), (25, 1)]
edges = []
for bond in bonds:
edges.append(Edge(vertices[bond[0]], vertices[bond[1]]))
graph = Graph()
for vertex in vertices:
graph.add_vertex(vertex)
for edge in edges:
graph.add_edge(edge)
graph.update_connectivity_values()
rings = graph.get_polycycles()
self.assertEqual(len(rings), 1)
# ensure the last ring doesn't include vertex 8, since it isn't in the
# longest ring. Try two different items since one might contain the vertex 8
long_ring = graph.get_largest_ring(rings[0][0])
long_ring2 = graph.get_largest_ring(rings[0][1])
if len(long_ring) > len(long_ring2):
longest_ring = long_ring
else:
longest_ring = long_ring2
self.assertEqual(len(longest_ring), len(rings[0]) - 1)
def test_sort_cyclic_vertices(self):
"""Test that sort_cyclic_vertices works properly for a valid input."""
edge = Edge(self.graph.vertices[0], self.graph.vertices[5])
self.graph.add_edge(edge) # To create a cycle
# Sort the vertices
original = list(self.graph.vertices)
ordered = self.graph.sort_cyclic_vertices(original)
# Check that we didn't lose any vertices
self.assertEqual(len(self.graph.vertices), len(ordered),
'Sorting changed the number of vertices.')
# Check that the order is different
self.assertNotEqual(self.graph.vertices, ordered,
'Sorting did not change the order of vertices.')
# Check that subsequent vertices are connected
for i in range(5):
self.assertTrue(self.graph.has_edge(ordered[i], ordered[i - 1]))
def test_sort_cyclic_vertices_invalid(self):
"""Test that sort_cyclic_vertices raises an error for an invalid input."""
edge = Edge(self.graph.vertices[0], self.graph.vertices[4])
self.graph.add_edge(edge) # To create a cycle
original = list(self.graph.vertices)
with self.assertRaisesRegexp(RuntimeError,
'do not comprise a single cycle'):
self.graph.sort_cyclic_vertices(original)
def test_sort_cyclic_vertices_noncyclic(self):
"""Test that sort_cyclic_vertices raises an error for a noncyclic input."""
original = list(self.graph.vertices)
with self.assertRaisesRegexp(RuntimeError,
'do not comprise a single cycle'):
self.graph.sort_cyclic_vertices(original)
def test_sort_cyclic_vertices_unconnected(self):
"""Test that sort_cyclic_vertices raises an error for an unconnected input."""
self.graph.add_vertex(Vertex())
original = list(self.graph.vertices)
with self.assertRaisesRegexp(RuntimeError,
'not all vertices are connected'):
self.graph.sort_cyclic_vertices(original)
