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)
def testAdjacencyListPattern(self):
"""
Check the adjacency list read/write functions for a molecular
substructure.
"""
pattern1 = MoleculePattern().fromAdjacencyList("""
1 {Cs,Os} 0 {2,S}
2 R!H 0 {1,S}
""")
pattern1.toAdjacencyList()
def __init__(self, chemgraph):
chemgraph = chemgraph.strip()
self.name = chemgraph.splitlines()[0]
self.node_name = None
if not chemgraph.splitlines()[1].strip().startswith('1'):
#logging.debug("I think this is a compound structure: %s"%chemgraph)
self.compound_structure=True
self.chemgraph = chemgraph
return
else:
self.compound_structure=False
s = MoleculePattern()
s.fromAdjacencyList(chemgraph.strip(), withLabel=True)
self._structure = s
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)
