def testSubgraphIsomorphismManyLabels(self):
molecule = Molecule() # specific case (species)
molecule.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S}
3 C u0 p0 c0 {1,S} {2,S} {7,S} {8,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {3,S}
8 H u0 p0 c0 {3,S}
""")
group = Group() # general case (functional group)
group.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S}, {3,S}
2 R!H u0 p0 c0 {1,S}
3 R!H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms()
labeled2 = group.getLabeledAtoms()
initialMap = {}
for label,atom1 in labeled1.iteritems():
initialMap[atom1] = labeled2[label]
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
self.assertEqual(len(mapping), 2)
for map in mapping:
self.assertTrue(len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def testSubgraphIsomorphismManyLabels(self):
molecule = Molecule() # specific case (species)
molecule.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 C u0 p0 c0 {1,S} {3,S} {5,S} {6,S}
3 C u0 p0 c0 {1,S} {2,S} {7,S} {8,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {3,S}
8 H u0 p0 c0 {3,S}
""")
group = Group() # general case (functional group)
group.fromAdjacencyList("""
1 *1 C u1 p0 c0 {2,S}, {3,S}
2 R!H u0 p0 c0 {1,S}
3 R!H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms()
labeled2 = group.getLabeledAtoms()
initialMap = {}
for label, atom1 in labeled1.iteritems():
initialMap[atom1] = labeled2[label]
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
self.assertEqual(len(mapping), 2)
for map in mapping:
self.assertTrue(
len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def methyl_in_ethane():
"""
12 possible ways to put CH3 in H3C-CH3:
2 possibilities for the carbon atom
3! possibilities to organize the 3 H-atoms.
total = 2 * 3! = 12
"""
adjlist_mol = """
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
"""
#mol = Group().fromAdjacencyList(adjlist_mol)
mol= Molecule().fromAdjacencyList(adjlist_mol)
adjlist_group = """
1 C ux p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
"""
group = Group().fromAdjacencyList(adjlist_group)
K= np.zeros((4,8))
R= np.zeros((8,4))
result = mol.findSubgraphIsomorphisms(group)
for i, match in enumerate(result):
print 'Match no: {}'.format(i)
for k,v in match.iteritems():
molatno = mol.atoms.index(k)
gratno = group.atoms.index(v)
print 'Mol atom number: {}, Group atom number: {}'.format(molatno, gratno)
K[gratno,molatno]= K[gratno,molatno]+1
R[molatno,gratno]= R[molatno,gratno]+1
K= K / (len(result))
R= R / (len(result))
print K
print R
return result
def test_isomorphism_R():
mol = Molecule().fromAdjacencyList("""
1 C u0 p0 c0
""", saturateH=True)
gp = Group().fromAdjacencyList("""
1 R u0 p0 c0
""")
assert_true(len(mol.findSubgraphIsomorphisms(gp)) > 0)
def test_isomorphism_R():
mol = Molecule().fromAdjacencyList("""
1 C u0 p0 c0
""", saturateH=True)
gp = Group().fromAdjacencyList("""
1 R u0 p0 c0
""")
assert_true(len(mol.findSubgraphIsomorphisms(gp)) > 0)
def test_isomorphism_mol_group_not_identical():
"""
Testing multiplicities in mol and group that don't match
"""
mol = Molecule().fromAdjacencyList("""
1 C u0 p0 c0
""", saturateH=True)
gp = Group().fromAdjacencyList("""
multiplicity [2]
1 R u0 p0 c0
""")
assert_false(mol.isSubgraphIsomorphic(gp))
assert_false(len(mol.findSubgraphIsomorphisms(gp)) > 0)
def test_isomorphism_mol_group_not_identical():
"""
Testing multiplicities in mol and group that don't match
"""
mol = Molecule().fromAdjacencyList("""
1 C u0 p0 c0
""", saturateH=True)
gp = Group().fromAdjacencyList("""
multiplicity [2]
1 R u0 p0 c0
""")
assert_false(mol.isSubgraphIsomorphic(gp))
assert_false(len(mol.findSubgraphIsomorphisms(gp)) > 0)
def testSubgraphIsomorphismAgain(self):
molecule = Molecule()
molecule.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {7,S} {8,S}
2 C u0 p0 c0 {1,D} {3,S} {9,S}
3 C u0 p0 c0 {2,S} {4,D} {10,S}
4 C u0 p0 c0 {3,D} {5,S} {11,S}
5 C u0 p0 c0 {4,S} {6,S} {12,S} {13,S}
6 C u0 p0 c0 {5,S} {14,S} {15,S} {16,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {2,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {4,S}
12 H u0 p0 c0 {5,S}
13 H u0 p0 c0 {5,S}
14 H u0 p0 c0 {6,S}
15 H u0 p0 c0 {6,S}
16 H u0 p0 c0 {6,S}
""")
group = Group()
group.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms().values()[0]
labeled2 = group.getLabeledAtoms().values()[0]
initialMap = {labeled1: labeled2}
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
initialMap = {labeled1: labeled2}
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
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(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def testSubgraphIsomorphism(self):
"""
Check the graph isomorphism functions.
"""
molecule = Molecule().fromSMILES('C=CC=C[CH]C')
group = Group().fromAdjacencyList("""
1 Cd u0 p0 c0 {2,D}
2 Cd u0 p0 c0 {1,D}
""")
self.assertTrue(molecule.isSubgraphIsomorphic(group))
mapping = molecule.findSubgraphIsomorphisms(group)
self.assertTrue(len(mapping) == 4, "len(mapping) = %d, should be = 4" % (len(mapping)))
for map in mapping:
self.assertTrue(len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def testSubgraphIsomorphismAgain(self):
molecule = Molecule()
molecule.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {7,S} {8,S}
2 C u0 p0 c0 {1,D} {3,S} {9,S}
3 C u0 p0 c0 {2,S} {4,D} {10,S}
4 C u0 p0 c0 {3,D} {5,S} {11,S}
5 C u0 p0 c0 {4,S} {6,S} {12,S} {13,S}
6 C u0 p0 c0 {5,S} {14,S} {15,S} {16,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
9 H u0 p0 c0 {2,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {4,S}
12 H u0 p0 c0 {5,S}
13 H u0 p0 c0 {5,S}
14 H u0 p0 c0 {6,S}
15 H u0 p0 c0 {6,S}
16 H u0 p0 c0 {6,S}
""")
group = Group()
group.fromAdjacencyList("""
1 * C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
""")
labeled1 = molecule.getLabeledAtoms().values()[0]
labeled2 = group.getLabeledAtoms().values()[0]
initialMap = {labeled1: labeled2}
self.assertTrue(molecule.isSubgraphIsomorphic(group, initialMap))
initialMap = {labeled1: labeled2}
mapping = molecule.findSubgraphIsomorphisms(group, initialMap)
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(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
def testSubgraphIsomorphism(self):
"""
Check the graph isomorphism functions.
"""
molecule = Molecule().fromSMILES('C=CC=C[CH]C')
group = Group().fromAdjacencyList("""
1 Cd u0 p0 c0 {2,D}
2 Cd u0 p0 c0 {1,D}
""")
self.assertTrue(molecule.isSubgraphIsomorphic(group))
mapping = molecule.findSubgraphIsomorphisms(group)
self.assertTrue(
len(mapping) == 4,
"len(mapping) = %d, should be = 4" % (len(mapping)))
for map in mapping:
self.assertTrue(
len(map) == min(len(molecule.atoms), len(group.atoms)))
for key, value in map.iteritems():
self.assertTrue(key in molecule.atoms)
self.assertTrue(value in group.atoms)
