def __init__(self, name='', label='', id=-1):
Vertex.__init__(self)
self.name = name # equivalent to Atom element symbol
self.label = label # equivalent to Atom label attribute
self.charge = 0
self.radicalElectrons = 0
self.lonePairs = 0
self.isotope = -1
self.id = id
self.mass = 0
def test_split(self):
"""
Test the graph split function to ensure a proper splitting of the graph
is being done.
"""
vertices = [Vertex() for i 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.addVertex(vertex)
for edge in edges:
graph.addEdge(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_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_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)
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 i 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.addVertex(vertex)
for edge in edges:
graph.addEdge(edge)
graph2 = graph.copy()
for vertex in graph.vertices:
self.assertTrue(graph2.hasVertex(vertex))
for v1 in graph.vertices:
for v2 in v1.edges:
self.assertTrue(graph2.hasEdge(v1, v2))
self.assertTrue(graph2.hasEdge(v2, v1))
self.assertTrue(graph2.isIsomorphic(graph))
self.assertTrue(graph.isIsomorphic(graph2))
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 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
def test_pickle(self):
"""
Test that a Graph object can be successfully pickled and unpickled
with no loss of information.
"""
vertices = [Vertex() for i 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.addVertex(vertex)
for edge in edges:
graph0.addEdge(edge)
graph0.updateConnectivityValues()
import cPickle
graph = cPickle.loads(cPickle.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.sortingLabel, v2.sortingLabel)
self.assertEqual(len(v1.edges), len(v2.edges))
self.assertTrue(graph0.isIsomorphic(graph))
self.assertTrue(graph.isIsomorphic(graph0))
def test_addVertex(self):
"""
Test the Graph.addVertex() method.
"""
vertex = Vertex()
self.graph.addVertex(vertex)
self.assertTrue(vertex in self.graph.vertices)
self.assertTrue(vertex.edges == {})
def test_hasVertex(self):
"""
Test the Graph.hasVertex() method.
"""
vertex = Vertex()
self.assertFalse(self.graph.hasVertex(vertex))
for v in self.graph.vertices:
self.assertTrue(self.graph.hasVertex(v))
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_merge(self):
"""
Test the graph merge function to ensure a proper merging of the graph
is being done.
"""
vertices1 = [Vertex() for i in range(4)]
edges1 = [
Edge(vertices1[0], vertices1[1]),
Edge(vertices1[1], vertices1[2]),
Edge(vertices1[2], vertices1[3]),
]
vertices2 = [Vertex() for i in range(3)]
edges2 = [
Edge(vertices2[0], vertices2[1]),
Edge(vertices2[1], vertices2[2]),
]
graph1 = Graph()
for vertex in vertices1:
graph1.addVertex(vertex)
for edge in edges1:
graph1.addEdge(edge)
graph2 = Graph()
for vertex in vertices2:
graph2.addVertex(vertex)
for edge in edges2:
graph2.addEdge(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_addEdge(self):
"""
Test the Graph.addEdge() method.
"""
vertex1 = Vertex()
vertex2 = Vertex()
edge = Edge(vertex1, vertex2)
try:
self.graph.addEdge(edge)
self.fail('Added edge between vertices not in graph to graph.')
except ValueError:
pass
self.graph.addVertex(vertex1)
self.graph.addVertex(vertex2)
self.graph.addEdge(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_subgraphIsomorphism(self):
"""
Check the subgraph isomorphism functions.
"""
vertices1 = [Vertex() for i 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 i in range(2)]
edges2 = [
Edge(vertices2[0], vertices2[1]),
]
graph1 = Graph()
for vertex in vertices1:
graph1.addVertex(vertex)
for edge in edges1:
graph1.addEdge(edge)
graph2 = Graph()
for vertex in vertices2:
graph2.addVertex(vertex)
for edge in edges2:
graph2.addEdge(edge)
self.assertFalse(graph1.isIsomorphic(graph2))
self.assertFalse(graph2.isIsomorphic(graph1))
self.assertTrue(graph1.isSubgraphIsomorphic(graph2))
mapList = graph1.findSubgraphIsomorphisms(graph2)
self.assertTrue(len(mapList) == 10)
for mapping in mapList:
self.assertTrue(graph1.isMappingValid(graph2, mapping))
self.assertTrue(graph1.isMappingValid(graph2, mapping))
def test_isomorphism(self):
"""
Check the graph isomorphism functions.
"""
vertices1 = [Vertex() for i 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 i 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.addVertex(vertex)
for edge in edges1:
graph1.addEdge(edge)
graph2 = Graph()
for vertex in vertices2:
graph2.addVertex(vertex)
for edge in edges2:
graph2.addEdge(edge)
self.assertTrue(graph1.isIsomorphic(graph2))
self.assertTrue(graph1.isSubgraphIsomorphic(graph2))
self.assertTrue(graph2.isIsomorphic(graph1))
self.assertTrue(graph2.isSubgraphIsomorphic(graph1))
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 i 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.addVertex(vertex)
for edge in edges:
graph.addEdge(edge)
graph.updateConnectivityValues()
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 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_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_getAllPolycylicVertices(self):
edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
self.graph.addEdge(edge) # To create a cycle
self.assertListEqual(self.graph.getAllPolycyclicVertices(), [])
edge2 = Edge(self.graph.vertices[0], self.graph.vertices[5])
self.graph.addEdge(
edge2) # Create another cycle to generate two fused cycles
self.assertEqual(len(self.graph.getAllPolycyclicVertices()), 2)
# Add new vertices and edges to generate a spirocyclic cycle
vertices = [Vertex() for i in range(2)]
for vertex in vertices:
self.graph.addVertex(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.addEdge(edge)
self.assertEqual(len(self.graph.getAllPolycyclicVertices()), 3)
