Ejemplo n.º 1
0
    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))
Ejemplo n.º 2
0
    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 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))
        self.assertTrue(len(graph1.findSubgraphIsomorphisms(graph2)) > 0)
Ejemplo n.º 3
0
    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))
Ejemplo n.º 4
0
    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 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))
        self.assertTrue(len(graph1.findSubgraphIsomorphisms(graph2)) > 0)
Ejemplo n.º 5
0
    def isSubgraphIsomorphic(self, other, initialMap=None):
        """
        Fragment's subgraph isomorphism check is done by first creating 
        a representative molecule of fragment, and then following same procedure
        of subgraph isomorphism check of `Molecule` object aganist `Group` object
        """
        if not isinstance(other, gr.Group):
            raise TypeError(
                'Got a {0} object for parameter "other", when a Molecule object is required.'
                .format(other.__class__))
        group = other

        mapping = self.assign_representative_molecule()

        # Check multiplicity
        if group.multiplicity:
            if self.mol_repr.multiplicity not in group.multiplicity:
                return False

        # Compare radical counts
        if self.mol_repr.getRadicalCount() < group.radicalCount:
            return False

        # Compare element counts
        element_count = self.mol_repr.get_element_count()
        for element, count in group.elementCount.iteritems():
            if element not in element_count:
                return False
            elif element_count[element] < count:
                return False

        # Do the isomorphism comparison
        new_initial_map = None
        if initialMap:
            new_initial_map = {}
            for fragment_vertex in initialMap:
                repr_mol_vertex = mapping[fragment_vertex]
                new_initial_map[repr_mol_vertex] = initialMap[fragment_vertex]

        result = Graph.isSubgraphIsomorphic(self.mol_repr, other,
                                            new_initial_map)
        return result
Ejemplo n.º 6
0
    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))
Ejemplo n.º 7
0
    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))