Пример #1
0
    def testSubgraphIsomorphismManyLabels(self):
        molecule = Molecule() # specific case (species)
        molecule.fromAdjacencyList("""
1 *1 C  1 {2,S} {3,S}
2    C  0 {1,S} {3,S}
3    C  0 {1,S} {2,S}
        """)

        pattern = MoleculePattern() # general case (functional group)
        pattern.fromAdjacencyList("""
1 *1 C 1 {2,S}, {3,S}
2    R 0 {1,S}
3    R 0 {1,S}
        """)

        labeled1 = molecule.getLabeledAtoms()
        labeled2 = pattern.getLabeledAtoms()
        initialMap = {}
        for label,atom1 in labeled1.iteritems():
            initialMap[atom1] = labeled2[label]
        self.assertTrue(molecule.isSubgraphIsomorphic(pattern, initialMap))

        match, mapping = molecule.findSubgraphIsomorphisms(pattern, initialMap)
        self.assertTrue(match)
        self.assertTrue(len(mapping) == 1)
        for map in mapping:
            self.assertTrue(len(map) == min(len(molecule.atoms), len(pattern.atoms)))
            for key, value in map.iteritems():
                self.assertTrue(key in molecule.atoms)
                self.assertTrue(value in pattern.atoms)
Пример #2
0
    def testSubgraphIsomorphismAgain(self):
        molecule = Molecule()
        molecule.fromAdjacencyList("""
        1 * C 0 {2,D} {7,S} {8,S}
        2 C 0 {1,D} {3,S} {9,S}
        3 C 0 {2,S} {4,D} {10,S}
        4 C 0 {3,D} {5,S} {11,S}
        5 C 0 {4,S} {6,S} {12,S} {13,S}
        6 C 0 {5,S} {14,S} {15,S} {16,S}
        7 H 0 {1,S}
        8 H 0 {1,S}
        9 H 0 {2,S}
        10 H 0 {3,S}
        11 H 0 {4,S}
        12 H 0 {5,S}
        13 H 0 {5,S}
        14 H 0 {6,S}
        15 H 0 {6,S}
        16 H 0 {6,S}
        """)

        pattern = MoleculePattern()
        pattern.fromAdjacencyList("""
        1 * C 0 {2,D} {3,S} {4,S}
        2   C 0 {1,D}
        3   H 0 {1,S}
        4   H 0 {1,S}
        """)

        molecule.makeHydrogensExplicit()

        labeled1 = molecule.getLabeledAtoms().values()[0]
        labeled2 = pattern.getLabeledAtoms().values()[0]

        initialMap = {labeled1: labeled2}
        self.assertTrue(molecule.isSubgraphIsomorphic(pattern, initialMap))

        initialMap = {labeled1: labeled2}
        match, mapping = molecule.findSubgraphIsomorphisms(pattern, initialMap)
        self.assertTrue(match)
        self.assertTrue(len(mapping) == 2,  "len(mapping) = %d, should be = 2" % (len(mapping)))
        for map in mapping:
            self.assertTrue(len(map) == min(len(molecule.atoms), len(pattern.atoms)))
            for key, value in map.iteritems():
                self.assertTrue(key in molecule.atoms)
                self.assertTrue(value in pattern.atoms)