Python Graph.updateConnectivityValues方法代碼示例

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]
    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))

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]
    def test_vertex_connectivity_values(self):
        """
        Tests the vertex connectivity values as introduced by Morgan (1965).
        
        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
        
                                # = 3     # = 4         # = 4
                                         *selected*
        """
        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([11, 15, 18, 10, 7, 11]):
            cv = vertices[i].connectivity
            self.assertEqual(cv, cv_, "On vertex {0:d} got connectivity[0]={1:d} but expected {2:d}".format(i, cv, cv_))

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]
    def test_getLargestRing(self):
        """
        Test that the Graph.getPolycyclicRings() method returns only polycyclic rings.
        """
        vertices = [Vertex() for i 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.addVertex(vertex)
        for edge in edges: graph.addEdge(edge)
        graph.updateConnectivityValues()
        
        rings = graph.getPolycyclicRings()
        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.getLargestRing(rings[0][0])
        long_ring2 = graph.getLargestRing(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)

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]
    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_))

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]

#.........這裏部分代碼省略.........
        ]

        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_resetConnectivityValues(self):
        """
        Test the Graph.resetConnectivityValues() method.
        """
        self.graph.resetConnectivityValues()
        for vertex in self.graph.vertices:
            self.assertEqual(vertex.connectivity1, -1)
            self.assertEqual(vertex.connectivity2, -1)
            self.assertEqual(vertex.connectivity3, -1)
            self.assertEqual(vertex.sortingLabel, -1)
    
    def test_updateConnectivityValues(self):
        """
        Test the Graph.updateConnectivityValues() method.
        """
        self.graph.updateConnectivityValues()
        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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -1)
    
    def test_sortVertices(self):
        """
        Test the Graph.sortVertices() method.

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]
    def test_getPolycyclicRings(self):
        """
        Test that the Graph.getPolycyclicRings() method returns only polycyclic rings.
        """
        vertices = [Vertex() for i 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.addVertex(vertex)
        for edge in edges: graph.addEdge(edge)
        graph.updateConnectivityValues()
        
        SSSR = graph.getSmallestSetOfSmallestRings()
        self.assertEqual(len(SSSR),6)
        polycyclicVertices = set(graph.getAllPolycyclicVertices())
        expectedPolycyclicVertices = set([vertices[index] for index in [3,23,4,22,12]])
        
        self.assertEqual(polycyclicVertices, expectedPolycyclicVertices)
        
        continuousRings = graph.getPolycyclicRings()
        expectedContinuousRings = [[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
        continuousRings = [set(ring) for ring in continuousRings]
        expectedContinuousRings = [set(ring) for ring in expectedContinuousRings]
        for ring in expectedContinuousRings:
            self.assertTrue(ring in continuousRings)

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]

#.........這裏部分代碼省略.........
        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_resetConnectivityValues(self):
        """
        Test the Graph.resetConnectivityValues() method.
        """
        self.graph.resetConnectivityValues()
        for vertex in self.graph.vertices:
            self.assertEqual(vertex.connectivity, -1)
            self.assertEqual(vertex.sortingLabel, -1)

    def test_updateConnectivityValues(self):
        """
        Test the Graph.updateConnectivityValues() method.
        """
        self.graph.updateConnectivityValues()
        self.assertEqual(self.graph.vertices[0].connectivity, 10)
        self.assertEqual(self.graph.vertices[0].sortingLabel, -1)
        self.assertEqual(self.graph.vertices[1].connectivity, 19)
        self.assertEqual(self.graph.vertices[1].sortingLabel, -1)
        self.assertEqual(self.graph.vertices[2].connectivity, 23)
        self.assertEqual(self.graph.vertices[2].sortingLabel, -1)
        self.assertEqual(self.graph.vertices[3].connectivity, 23)
        self.assertEqual(self.graph.vertices[3].sortingLabel, -1)
        self.assertEqual(self.graph.vertices[4].connectivity, 19)
        self.assertEqual(self.graph.vertices[4].sortingLabel, -1)
        self.assertEqual(self.graph.vertices[5].connectivity, 10)
        self.assertEqual(self.graph.vertices[5].sortingLabel, -1)

    def test_sortVertices(self):
        """
        Test the Graph.sortVertices() method.
        """
        self.graph.updateConnectivityValues()
        self.graph.sortVertices()
        for vertex1, vertex2 in zip(self.graph.vertices[:-1], self.graph.vertices[1:]):
            self.assertTrue(vertex1.sortingLabel < vertex2.sortingLabel)
            self.assertTrue(vertex1.connectivity >= vertex2.connectivity)

    def test_vertex_connectivity_values(self):
        """
        Tests the vertex connectivity values as introduced by Morgan (1965).
        
        Graph:     Expected (and tested) values:

# 需要導入模塊: from rmgpy.molecule.graph import Graph [as 別名]
# 或者: from rmgpy.molecule.graph.Graph import updateConnectivityValues [as 別名]

#.........這裏部分代碼省略.........
        ]

        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_resetConnectivityValues(self):
        """
        Test the Graph.resetConnectivityValues() method.
        """
        self.graph.resetConnectivityValues()
        for vertex in self.graph.vertices:
            self.assertEqual(vertex.connectivity1, -1)
            self.assertEqual(vertex.connectivity2, -1)
            self.assertEqual(vertex.connectivity3, -1)
            self.assertEqual(vertex.sortingLabel, -1)
    
    def test_updateConnectivityValues(self):
        """
        Test the Graph.updateConnectivityValues() method.
        """
        self.graph.updateConnectivityValues()
        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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -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].sortingLabel, -1)
    
    def test_sortVertices(self):
        """
        Test the Graph.sortVertices() method.