def testSymmetryNumber(self):
"""Overall symmetry number"""
test_set = [('CC', 18), # ethane
('C=C=[C]C(C)(C)[C]=C=C', 'Who knows?'),
('C(=CC(c1ccccc1)C([CH]CCCCCC)C=Cc1ccccc1)[CH]CCCCCC', 1),
('[OH]', 1),#hydroxyl radical
('O=O', 2),#molecular oxygen
('[C]#[C]', 2),#C2
('[H][H]', 2),#H2
('C#C', 2),#acetylene
('C#CC#C', 2),#1,3-butadiyne
('C', 12),#methane
('C=O', 2),#formaldehyde
('[CH3]', 6),#methyl radical
('O', 2),#water
('C=C',4),#ethylene
('C1=C=C=1', '6?')#cyclic, cumulenic C3 species
]
fail_message = ''
for smile,should_be in test_set:
molecule = Molecule().fromSMILES(smile)
molecule.makeHydrogensExplicit()
symmetryNumber = molecule.calculateSymmetryNumber()
if symmetryNumber!=should_be:
fail_message+="Got total symmetry number of %s for %s (expected %s)\n"%(symmetryNumber,smile,should_be)
self.assertEqual(fail_message,'',fail_message)
def testAxisSymmetryNumber(self):
"""Axis symmetry number"""
test_set = [('C=C=C', 2), # ethane
('C=C=C=C', 2),
('C=C=C=[CH]', 2), # =C-H is straight
('C=C=[C]', 2),
('CC=C=[C]', 1),
('C=C=CC(CC)', 1),
('CC(C)=C=C(CC)CC', 2),
('C=C=C(C(C(C(C=C=C)=C=C)=C=C)=C=C)', 2),
('C=C=[C]C(C)(C)[C]=C=C', 1),
('C=C=C=O', 2),
('CC=C=C=O', 1),
('C=C=C=N', 1), # =N-H is bent
('C=C=C=[N]', 2)
]
# http://cactus.nci.nih.gov/chemical/structure/C=C=C(C(C(C(C=C=C)=C=C)=C=C)=C=C)/image
fail_message = ''
for smile,should_be in test_set:
molecule = Molecule().fromSMILES(smile)
molecule.makeHydrogensExplicit()
symmetryNumber = molecule.calculateAxisSymmetryNumber()
if symmetryNumber!=should_be:
fail_message+="Got axis symmetry number of %s for %s (expected %s)\n"%(symmetryNumber,smile,should_be)
self.assertEqual(fail_message,'',fail_message)
def testAdjacencyList(self):
"""
Check the adjacency list read/write functions for a full molecule.
"""
molecule1 = Molecule().fromAdjacencyList("""
1 C 0 {2,D}
2 C 0 {1,D} {3,S}
3 C 0 {2,S} {4,D}
4 C 0 {3,D} {5,S}
5 C 1 {4,S} {6,S}
6 C 0 {5,S}
""")
molecule2 = Molecule().fromSMILES('C=CC=C[CH]C')
molecule1.makeHydrogensExplicit()
molecule2.makeHydrogensExplicit()
self.assertTrue(molecule1.isIsomorphic(molecule2))
self.assertTrue(molecule2.isIsomorphic(molecule1))
molecule1.makeHydrogensImplicit()
molecule2.makeHydrogensImplicit()
self.assertTrue(molecule1.isIsomorphic(molecule2))
self.assertTrue(molecule2.isIsomorphic(molecule1))
molecule1.makeHydrogensExplicit()
molecule2.makeHydrogensImplicit()
self.assertTrue(molecule1.isIsomorphic(molecule2))
self.assertTrue(molecule2.isIsomorphic(molecule1))
molecule1.makeHydrogensImplicit()
molecule2.makeHydrogensExplicit()
self.assertTrue(molecule1.isIsomorphic(molecule2))
self.assertTrue(molecule2.isIsomorphic(molecule1))
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)
def testAtomSymmetryNumber(self):
testSet = [
['C', 12],
['[CH3]', 6],
['CC', 9],
['CCC', 18],
['CC(C)C', 81],
]
failMessage = ''
for SMILES, symmetry in testSet:
molecule = Molecule().fromSMILES(SMILES)
molecule.makeHydrogensExplicit()
symmetryNumber = 1
for atom in molecule.atoms:
if not molecule.isAtomInCycle(atom):
symmetryNumber *= molecule.calculateAtomSymmetryNumber(atom)
if symmetryNumber != symmetry:
failMessage += 'Expected symmetry number of %i for %s, got %i\n' % (symmetry, SMILES, symmetryNumber)
self.assertEqual(failMessage, '', failMessage)
def testBondSymmetryNumber(self):
testSet = [
['CC', 2],
['CCC', 1],
['CCCC', 2],
['C=C', 2],
['C#C', 2],
]
failMessage = ''
for SMILES, symmetry in testSet:
molecule = Molecule().fromSMILES(SMILES)
molecule.makeHydrogensExplicit()
symmetryNumber = 1
for atom1 in molecule.bonds:
for atom2 in molecule.bonds[atom1]:
if molecule.atoms.index(atom1) < molecule.atoms.index(atom2):
symmetryNumber *= molecule.calculateBondSymmetryNumber(atom1, atom2)
if symmetryNumber != symmetry:
failMessage += 'Expected symmetry number of %i for %s, got %i\n' % (symmetry, SMILES, symmetryNumber)
self.assertEqual(failMessage, '', failMessage)
