Python Graph.getAllPolycyclicVertices方法代碼示例

本文整理匯總了Python中rmgpy.molecule.graph.Graph.getAllPolycyclicVertices方法的典型用法代碼示例。如果您正苦於以下問題：Python Graph.getAllPolycyclicVertices方法的具體用法？Python Graph.getAllPolycyclicVertices怎麽用？Python Graph.getAllPolycyclicVertices使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類rmgpy.molecule.graph.Graph的用法示例。

在下文中一共展示了Graph.getAllPolycyclicVertices方法的4個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。

示例1: TestGraph

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

#.........這裏部分代碼省略.........
            self.assertFalse(self.graph.isVertexInCycle(vertex))
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge) # To create a cycle
        for vertex in self.graph.vertices[0:4]:
            self.assertTrue(self.graph.isVertexInCycle(vertex))
        for vertex in self.graph.vertices[4:]:
            self.assertFalse(self.graph.isVertexInCycle(vertex))
        
    def test_isEdgeInCycle(self):
        """
        Test the Graph.isEdgeInCycle() method.
        """
        for vertex1 in self.graph.vertices:
            for vertex2, edge in vertex1.edges.items():
                self.assertFalse(self.graph.isEdgeInCycle(edge))
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(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.isEdgeInCycle(edge))
                else:
                    self.assertFalse(self.graph.isEdgeInCycle(edge))
                    
    def test_getAllCyclicVertices(self):
        self.assertListEqual(self.graph.getAllCyclicVertices(), [])
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge) # To create a cycle
        self.assertEqual(len(self.graph.getAllCyclicVertices()), 4)
        
    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)
                      
    def test_getAllCycles(self):
        """
        Test the Graph.getAllCycles() method.
        """
        cycleList = self.graph.getAllCycles(self.graph.vertices[0])
        self.assertEqual(len(cycleList), 0)
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge) # To create a cycle
        cycleList = self.graph.getAllCycles(self.graph.vertices[0])
        self.assertEqual(len(cycleList), 2)
        self.assertEqual(len(cycleList[0]), 4)
        self.assertEqual(len(cycleList[1]), 4)

    def test_getAllCyclesOfSize(self):
        """
        Test the Graph.getRingsOfSize() method
        """
        cycleList = self.graph.getAllCyclesOfSize(6)

開發者ID:connie，項目名稱:RMG-Py，代碼行數:70，代碼來源:graphTest.py

示例2: TestGraph

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

#.........這裏部分代碼省略.........
        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.connectivity, v2.connectivity)
            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_isCyclic(self):
        """
        Test the Graph.isCyclic() method.
        """
        self.assertFalse(self.graph.isCyclic())
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge)  # To create a cycle
        self.assertTrue(self.graph.isCyclic())

    def test_isVertexInCycle(self):
        """
        Test the Graph.isVertexInCycle() method.
        """
        for vertex in self.graph.vertices:
            self.assertFalse(self.graph.isVertexInCycle(vertex))
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge)  # To create a cycle
        for vertex in self.graph.vertices[0:4]:
            self.assertTrue(self.graph.isVertexInCycle(vertex))
        for vertex in self.graph.vertices[4:]:
            self.assertFalse(self.graph.isVertexInCycle(vertex))

    def test_isEdgeInCycle(self):
        """
        Test the Graph.isEdgeInCycle() method.
        """
        for vertex1 in self.graph.vertices:
            for vertex2, edge in vertex1.edges.items():
                self.assertFalse(self.graph.isEdgeInCycle(edge))
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(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.isEdgeInCycle(edge))
                else:
                    self.assertFalse(self.graph.isEdgeInCycle(edge))

    def test_getAllCyclicVertices(self):
        self.assertListEqual(self.graph.getAllCyclicVertices(), [])
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge)  # To create a cycle
        self.assertEqual(len(self.graph.getAllCyclicVertices()), 4)

    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)

    def test_getAllCycles(self):
        """
        Test the Graph.getAllCycles() method.
        """
        cycleList = self.graph.getAllCycles(self.graph.vertices[0])
        self.assertEqual(len(cycleList), 0)
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge)  # To create a cycle
        cycleList = self.graph.getAllCycles(self.graph.vertices[0])
        self.assertEqual(len(cycleList), 2)
        self.assertEqual(len(cycleList[0]), 4)
        self.assertEqual(len(cycleList[1]), 4)

    def test_getSmallestSetOfSmallestRings(self):
        """
        Test the Graph.getSmallestSetOfSmallestRings() method.
        """
        cycleList = self.graph.getSmallestSetOfSmallestRings()
        self.assertEqual(len(cycleList), 0)
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge)  # To create a cycle
        cycleList = self.graph.getSmallestSetOfSmallestRings()
        self.assertEqual(len(cycleList), 1)
        self.assertEqual(len(cycleList[0]), 4)

開發者ID:QuinlanofCork，項目名稱:RMG-Py，代碼行數:104，代碼來源:graphTest.py

示例3: test_getPolycyclicRings

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

開發者ID:connie，項目名稱:RMG-Py，代碼行數:67，代碼來源:graphTest.py

示例4: TestGraph

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

#.........這裏部分代碼省略.........
            self.assertFalse(self.graph.isVertexInCycle(vertex))
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge) # To create a cycle
        for vertex in self.graph.vertices[0:4]:
            self.assertTrue(self.graph.isVertexInCycle(vertex))
        for vertex in self.graph.vertices[4:]:
            self.assertFalse(self.graph.isVertexInCycle(vertex))
        
    def test_isEdgeInCycle(self):
        """
        Test the Graph.isEdgeInCycle() method.
        """
        for vertex1 in self.graph.vertices:
            for vertex2, edge in vertex1.edges.items():
                self.assertFalse(self.graph.isEdgeInCycle(edge))
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(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.isEdgeInCycle(edge))
                else:
                    self.assertFalse(self.graph.isEdgeInCycle(edge))
                    
    def test_getAllCyclicVertices(self):
        self.assertListEqual(self.graph.getAllCyclicVertices(), [])
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge) # To create a cycle
        self.assertEqual(len(self.graph.getAllCyclicVertices()), 4)
        
    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)
                      
    def test_getAllCycles(self):
        """
        Test the Graph.getAllCycles() method.
        """
        cycleList = self.graph.getAllCycles(self.graph.vertices[0])
        self.assertEqual(len(cycleList), 0)
        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
        self.graph.addEdge(edge) # To create a cycle
        cycleList = self.graph.getAllCycles(self.graph.vertices[0])
        self.assertEqual(len(cycleList), 2)
        self.assertEqual(len(cycleList[0]), 4)
        self.assertEqual(len(cycleList[1]), 4)

    def test_getAllCyclesOfSize(self):
        """
        Test the Graph.getRingsOfSize() method
        """
        cycleList = self.graph.getAllCyclesOfSize(6)

開發者ID:ReactionMechanismGenerator，項目名稱:RMG-Py，代碼行數:70，代碼來源:graphTest.py

注：本文中的rmgpy.molecule.graph.Graph.getAllPolycyclicVertices方法示例由純淨天空整理自Github/MSDocs等開源代碼及文檔管理平台，相關代碼片段篩選自各路編程大神貢獻的開源項目，源碼版權歸原作者所有，傳播和使用請參考對應項目的License；未經允許，請勿轉載。