def testCreateAndConnectAtom(self):
"""
Tests createAndConnectAtom method
"""
adjlist1 = """
1 *1 C u0 {2,S}
2 *2 C u0 {1,S}
"""
answer1 = """
1 *1 C u0 {2,S} {3,B}
2 *2 C u0 {1,S}
3 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
answer1 = Group().fromAdjacencyList(answer1)
atom1 = group1.getLabeledAtom("*1")
newAtom = group1.createAndConnectAtom(atomtypes = ["Cb"], connectingAtom = atom1, bondOrders = ["B"])
self.assertTrue(group1.isIsomorphic(answer1))
answer2 = """
1 *1 C u0 {2,S} {3,[S,D]}
2 *2 C u0 {1,S}
3 [Cs,Cd] u0 {1,[S,D]}
"""
#Test that wildcards work alright
group2 = Group().fromAdjacencyList(adjlist1)
answer2 = Group().fromAdjacencyList(answer2)
atom1 = group2.getLabeledAtom("*1")
newAtom = group2.createAndConnectAtom(atomtypes = ["Cs", "Cd"], connectingAtom = atom1, bondOrders = ["S","D"])
self.assertTrue(group2.isIsomorphic(answer2))
def testCreateAndConnectAtom(self):
"""
Tests createAndConnectAtom method
"""
adjlist1 = """
1 *1 C u0 {2,S}
2 *2 C u0 {1,S}
"""
answer1 = """
1 *1 C u0 {2,S} {3,B}
2 *2 C u0 {1,S}
3 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
answer1 = Group().fromAdjacencyList(answer1)
atom1 = group1.getLabeledAtom("*1")
newAtom = group1.createAndConnectAtom(atomtypes=["Cb"],
connectingAtom=atom1,
bondOrders=["B"])
self.assertTrue(group1.isIsomorphic(answer1))
answer2 = """
1 *1 C u0 {2,S} {3,[S,D]}
2 *2 C u0 {1,S}
3 [Cs,Cd] u0 {1,[S,D]}
"""
#Test that wildcards work alright
group2 = Group().fromAdjacencyList(adjlist1)
answer2 = Group().fromAdjacencyList(answer2)
atom1 = group2.getLabeledAtom("*1")
newAtom = group2.createAndConnectAtom(atomtypes=["Cs", "Cd"],
connectingAtom=atom1,
bondOrders=["S", "D"])
self.assertTrue(group2.isIsomorphic(answer2))
def testClassifyBenzeneCarbons(self):
"""
Tests the method classifyingBenzeneCarbons
"""
#This tests that we classify Cb atom types correctly
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group1.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 0)
for atom in group1.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we classify Cbf atomtypes correctly
adjlist2 = """
1 *1 Cbf u0
"""
group2 = Group().fromAdjacencyList(adjlist2)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group2.classifyBenzeneCarbons()
self.assertIn(group2.atoms[0], cbfAtomList)
self.assertIn(group2.atoms[0], cbfAtomList1)
#This tests that we can classify Cb atoms based on bonding and not just atomtype
adjlist3 = """
1 *1 C u0 {2,B}
2 *2 C u0 {1,B} {3,B}
3 *3 C u0 {2,B}
"""
group3 = Group().fromAdjacencyList(adjlist3)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group3.classifyBenzeneCarbons()
for atom in group3.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we can classify Cbf1 atoms based on bonding and not just atomtype
adjlist4 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B}
3 *3 C u0 {1,B}
4 *4 C u0 {1,B}
"""
group4 = Group().fromAdjacencyList(adjlist4)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group4.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 1)
self.assertEquals(len(cbfAtomList1), 1)
#This tests that we can classify Cbf2 atoms. In the following partial group, we should have:
#one Cbf2 atom, two Cbf1 atoms, and 5 Cb atoms
adjlist5 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B} {5,B} {6,B}
3 *3 C u0 {1,B} {7,B} {8,B}
4 *4 C u0 {1,B}
5 *5 C u0 {2,B}
6 *6 C u0 {2,B}
7 *7 C u0 {3,B}
8 *8 C u0 {3,B}
"""
group5 = Group().fromAdjacencyList(adjlist5)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group5.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList1), 2)
self.assertEquals(len(cbfAtomList2), 1)
self.assertEquals(len(cbAtomList), 5)
#Tests that we can classify connected Cbfs correctly. *1 should be connected to both *2 and *3
atom1 = group5.getLabeledAtom("*1")
atom2 = group5.getLabeledAtom("*2")
atom3 = group5.getLabeledAtom("*3")
self.assertIn(atom2, connectedCbfs[atom1])
self.assertIn(atom3, connectedCbfs[atom1])
self.assertIn(atom1, connectedCbfs[atom2])
self.assertIn(atom1, connectedCbfs[atom3])
class TestGroup(unittest.TestCase):
"""
Contains unit tests of the Graph class.
"""
def setUp(self):
self.adjlist = """
1 *2 [Cs,Cd] u0 {2,[S,D]} {3,S}
2 *1 [Os,Od] u0 {1,[S,D]}
3 R!H u0 {1,S}
"""
self.group = Group().fromAdjacencyList(self.adjlist)
def testClearLabeledAtoms(self):
"""
Test the Group.clearLabeledAtoms() method.
"""
self.group.clearLabeledAtoms()
for atom in self.group.atoms:
self.assertEqual(atom.label, '')
def testContainsLabeledAtom(self):
"""
Test the Group.containsLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(self.group.containsLabeledAtom(atom.label))
self.assertFalse(self.group.containsLabeledAtom('*3'))
self.assertFalse(self.group.containsLabeledAtom('*4'))
self.assertFalse(self.group.containsLabeledAtom('*5'))
self.assertFalse(self.group.containsLabeledAtom('*6'))
def testGetLabeledAtom(self):
"""
Test the Group.getLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertEqual(atom, self.group.getLabeledAtom(atom.label))
try:
self.group.getLabeledAtom('*3')
self.fail(
'Unexpected successful return from Group.getLabeledAtom() with invalid atom label.'
)
except ValueError:
pass
def testGetLabeledAtoms(self):
"""
Test the Group.getLabeledAtoms() method.
"""
labeled = self.group.getLabeledAtoms()
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(atom.label in labeled)
self.assertTrue(atom in labeled.values())
else:
self.assertFalse(atom.label in labeled)
self.assertFalse(atom in labeled.values())
def testFromAdjacencyList(self):
"""
Test the Group.fromAdjacencyList() method.
"""
atom1, atom2, atom3 = self.group.atoms
self.assertTrue(self.group.hasBond(atom1, atom2))
self.assertTrue(self.group.hasBond(atom1, atom3))
self.assertFalse(self.group.hasBond(atom2, atom3))
bond12 = atom1.bonds[atom2]
bond13 = atom1.bonds[atom3]
self.assertTrue(atom1.label == '*2')
self.assertTrue(atom1.atomType[0].label in ['Cs', 'Cd'])
self.assertTrue(atom1.atomType[1].label in ['Cs', 'Cd'])
self.assertTrue(atom1.radicalElectrons == [0])
self.assertTrue(atom2.label == '*1')
self.assertTrue(atom2.atomType[0].label in ['Os', 'Od'])
self.assertTrue(atom2.atomType[1].label in ['Os', 'Od'])
self.assertTrue(atom2.radicalElectrons == [0])
self.assertTrue(atom3.label == '')
self.assertTrue(atom3.atomType[0].label == 'R!H')
self.assertTrue(atom3.radicalElectrons == [0])
self.assertTrue(bond12.order == [1, 2])
self.assertTrue(bond13.isSingle())
def testToAdjacencyList(self):
"""
Test the Group.toAdjacencyList() method.
"""
adjlist = self.group.toAdjacencyList()
self.assertEqual(adjlist.strip(), self.adjlist.strip(), adjlist)
def testIsIsomorphic(self):
"""
Test the Group.isIsomorphic() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testFindIsomorphism(self):
"""
Test the Group.findIsomorphism() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findIsomorphism(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].items():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
for atom3 in atom1.bonds:
atom4 = result[0][atom3]
self.assertTrue(atom4 in atom2.bonds)
self.assertTrue(atom3.equivalent(atom4))
bond1 = atom1.bonds[atom3]
bond2 = atom2.bonds[atom4]
self.assertTrue(bond1.equivalent(bond2))
def testIsSubgraphIsomorphic(self):
"""
Test the Group.isSubgraphIsomorphic() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isSubgraphIsomorphic(group))
self.assertFalse(group.isIsomorphic(self.group))
def testFindSubgraphIsomorphisms(self):
"""
Test the Group.findSubgraphIsomorphisms() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findSubgraphIsomorphisms(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].iteritems():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
def testPickle(self):
"""
Test that a Group object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
group = cPickle.loads(cPickle.dumps(self.group))
self.assertEqual(len(self.group.atoms), len(group.atoms))
for atom0, atom in zip(group.atoms, self.group.atoms):
self.assertTrue(atom0.equivalent(atom))
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testCreateAndConnectAtom(self):
"""
Tests createAndConnectAtom method
"""
adjlist1 = """
1 *1 C u0 {2,S}
2 *2 C u0 {1,S}
"""
answer1 = """
1 *1 C u0 {2,S} {3,B}
2 *2 C u0 {1,S}
3 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
answer1 = Group().fromAdjacencyList(answer1)
atom1 = group1.getLabeledAtom("*1")
newAtom = group1.createAndConnectAtom(atomtypes=["Cb"],
connectingAtom=atom1,
bondOrders=["B"])
self.assertTrue(group1.isIsomorphic(answer1))
answer2 = """
1 *1 C u0 {2,S} {3,[S,D]}
2 *2 C u0 {1,S}
3 [Cs,Cd] u0 {1,[S,D]}
"""
#Test that wildcards work alright
group2 = Group().fromAdjacencyList(adjlist1)
answer2 = Group().fromAdjacencyList(answer2)
atom1 = group2.getLabeledAtom("*1")
newAtom = group2.createAndConnectAtom(atomtypes=["Cs", "Cd"],
connectingAtom=atom1,
bondOrders=["S", "D"])
self.assertTrue(group2.isIsomorphic(answer2))
def testAddImplicitAtomsFromAtomType(self):
"""
test Group.addImplicitAtomsFromAtomType() method
"""
#basic test adding oDouble
adjlist1 = """
1 *1 CO u0
"""
adjlist2 = """
1 *1 CO u0 {2,D}
2 O u0 {1,D}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
newGroup = group1.addImplicitAtomsFromAtomType()
self.assertTrue(group2.isIsomorphic(newGroup))
#testing the allDouble match (more complicated
adjlist3 = """
1 *1 Cdd u0
"""
adjlist4 = """
1 *1 Cdd u0 {2,D} {3,D}
2 C u0 {1,D}
3 C u0 {1,D}
"""
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
newGroup = group3.addImplicitAtomsFromAtomType()
self.assertTrue(group4.isIsomorphic(newGroup))
#test adding a triple bond
adjlist5 = """
1 *1 Ct u0
"""
adjlist6 = """
1 *1 Ct u0 {2,T}
2 C u0 {1,T}
"""
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
newGroup = group5.addImplicitAtomsFromAtomType()
self.assertTrue(group6.isIsomorphic(newGroup))
#test addition of lone pairs
adjlist7 = """
1 *1 N1d u0
"""
adjlist8 = """
1 *1 N1d u0 p2 {2,D}
2 C u0 {1,D}
"""
group7 = Group().fromAdjacencyList(adjlist7)
group8 = Group().fromAdjacencyList(adjlist8)
newGroup = group7.addImplicitAtomsFromAtomType()
self.assertTrue(group8.isIsomorphic(newGroup))
#test multiple implicit atoms at a time
adjlist9 = """
1 *1 Cd u0 {2,S}
2 Ct u0 {1,S}
"""
adjlist10 = """
1 *1 C u0 {2,S} {3,D}
2 Ct u0 {1,S} {4,T}
3 C u0 {1,D}
4 C u0 {2,T}
"""
group9 = Group().fromAdjacencyList(adjlist9)
group10 = Group().fromAdjacencyList(adjlist10)
newGroup = group9.addImplicitAtomsFromAtomType()
self.assertTrue(group10.isIsomorphic(newGroup))
def testClassifyBenzeneCarbons(self):
"""
Tests the method classifyingBenzeneCarbons
"""
#This tests that we classify Cb atom types correctly
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group1.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 0)
for atom in group1.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we classify Cbf atomtypes correctly
adjlist2 = """
1 *1 Cbf u0
"""
group2 = Group().fromAdjacencyList(adjlist2)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group2.classifyBenzeneCarbons()
self.assertIn(group2.atoms[0], cbfAtomList)
self.assertIn(group2.atoms[0], cbfAtomList1)
#This tests that we can classify Cb atoms based on bonding and not just atomtype
adjlist3 = """
1 *1 C u0 {2,B}
2 *2 C u0 {1,B} {3,B}
3 *3 C u0 {2,B}
"""
group3 = Group().fromAdjacencyList(adjlist3)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group3.classifyBenzeneCarbons()
for atom in group3.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we can classify Cbf1 atoms based on bonding and not just atomtype
adjlist4 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B}
3 *3 C u0 {1,B}
4 *4 C u0 {1,B}
"""
group4 = Group().fromAdjacencyList(adjlist4)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group4.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 1)
self.assertEquals(len(cbfAtomList1), 1)
#This tests that we can classify Cbf2 atoms. In the following partial group, we should have:
#one Cbf2 atom, two Cbf1 atoms, and 5 Cb atoms
adjlist5 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B} {5,B} {6,B}
3 *3 C u0 {1,B} {7,B} {8,B}
4 *4 C u0 {1,B}
5 *5 C u0 {2,B}
6 *6 C u0 {2,B}
7 *7 C u0 {3,B}
8 *8 C u0 {3,B}
"""
group5 = Group().fromAdjacencyList(adjlist5)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2,
connectedCbfs) = group5.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList1), 2)
self.assertEquals(len(cbfAtomList2), 1)
self.assertEquals(len(cbAtomList), 5)
#Tests that we can classify connected Cbfs correctly. *1 should be connected to both *2 and *3
atom1 = group5.getLabeledAtom("*1")
atom2 = group5.getLabeledAtom("*2")
atom3 = group5.getLabeledAtom("*3")
self.assertIn(atom2, connectedCbfs[atom1])
self.assertIn(atom3, connectedCbfs[atom1])
self.assertIn(atom1, connectedCbfs[atom2])
self.assertIn(atom1, connectedCbfs[atom3])
def testSortByConnectivity(self):
"""
Tests sortByConnectivity method
"""
#Basic test, we should get *1, *3 *2
adjlist1 = """
1 *1 C u0 {3,B}
2 *2 C u0 {3,B}
3 *3 C u0 {1,B} {2,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
orderedAtoms = group1.sortByConnectivity(group1.atoms)
self.assertEquals([x.label for x in orderedAtoms], ["*1", "*3", "*2"])
#Check a detached case, we should get *1, *3, *4, *2, *5
adjlist2 = """
1 *1 C u0 {3,B}
2 *2 C u0 {4,S} {5,B}
3 *3 C u0 {1,B} {4,B}
4 *4 C u0 {3,B} {2,S}
5 *5 C u0 {2,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
orderedAtoms = group2.sortByConnectivity(group2.atoms)
self.assertEquals([x.label for x in orderedAtoms],
["*1", "*3", "*4", "*2", "*5"])
def testAddImplicitBenzene(self):
"""
Test the Group.addImplicitBenzene method
"""
#tests it can make a benzene molecule
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
#tests it can make a bi-phenyl
adjlist2 = """
1 *1 Cb u0 {2,S}
2 *2 Cb u0 {1,S}
"""
#tests it can make a napthalene
adjlist3 = """
1 *1 Cbf u0
"""
#Test handling of Cbf2 atoms
adjlist4 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cbf u0 p0 c0 {1,B} {3,B}
3 *3 Cbf u0 p0 c0 {2,B}
"""
#test handling of heteroatoms and wildcards
adjlist5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B}
3 R!H u0 {1,B}
4 R!H u0 {1,B}
"""
adjlist6 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S}
4 *4 O u0 p0 c0 {3,S}
"""
adjlist7 = """
1 *1 Cb u0 {4,B}
2 *2 Cb u0 {3,B}
3 *3 Cb u0 {4,B} {2,B}
4 *4 Cb u0 {1,B} {3,B}
"""
benzene = """
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
biphenyl = """
1 C u0 {2,B} {6,B} {7,S}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
7 C u0 {8,B} {12,B} {1,S}
8 C u0 {7,B} {9,B}
9 C u0 {8,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {10,B} {12,B}
12 C u0 {11,B} {7,B}
"""
naphthalene = """
1 C u0 {2,B} {10,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B} {9,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {7,B}
7 C u0 {6,B} {8,B}
8 C u0 {7,B} {9,B}
9 C u0 {4,B} {8,B} {10,B}
10 C u0 {1,B} {9,B}
"""
phenanthrene = """
1 Cbf u0 p2 c0 {2,B} {7,B} {11,B}
2 Cbf u0 p0 c0 {1,B} {3,B} {5,B}
3 Cbf u0 p0 c0 {2,B} {4,B} {6,B}
4 C u0 {3,B} {8,B} {14,B}
5 C u0 {2,B} {9,B}
6 C u0 {3,B} {12,B}
7 C u0 {1,B} {8,B}
8 C u0 {4,B} {7,B}
9 C u0 {5,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {1,B} {10,B}
12 C u0 {6,B} {13,B}
13 C u0 {12,B} {14,B}
14 C u0 {4,B} {13,B}
"""
answer5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B} {5,B}
3 R!H u0 {1,B} {7,B} {10,B}
4 R!H u0 {1,B} {8,B}
5 Cb u0 {2,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {4,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {3,B} {9,B}
"""
answer6 = """
1 *1 Cbf u0 p2 c0 {2,B} {5,B} {8,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B} {11,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S} {7,B}
4 *4 O u0 p0 c0 {3,S}
5 Cb u0 {1,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {1,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {9,B} {11,B}
11 Cb u0 {2,B} {10,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
group7 = Group().fromAdjacencyList(adjlist7)
benzeneGroup = Group().fromAdjacencyList(benzene)
biphenylGroup = Group().fromAdjacencyList(biphenyl)
naphthaleneGroup = Group().fromAdjacencyList(naphthalene)
phenanthreneGroup = Group().fromAdjacencyList(phenanthrene)
answer5 = Group().fromAdjacencyList(answer5)
answer6 = Group().fromAdjacencyList(answer6)
group1 = group1.addImplicitBenzene()
self.assertTrue(benzeneGroup.isIsomorphic(group1))
group2 = group2.addImplicitBenzene()
self.assertTrue(biphenylGroup.isIsomorphic(group2))
group3 = group3.addImplicitBenzene()
self.assertTrue(naphthaleneGroup.isIsomorphic(group3))
group4 = group4.addImplicitBenzene()
self.assertTrue(phenanthreneGroup.isIsomorphic(group4))
group5 = group5.addImplicitBenzene()
self.assertTrue(answer5.isIsomorphic(group5))
group6 = group6.addImplicitBenzene()
self.assertTrue(answer6.isIsomorphic(group6))
group7 = group7.addImplicitBenzene()
self.assertTrue(benzeneGroup.isIsomorphic(group7))
def testMakeSampleMolecule(self):
"""
Test the Group.makeSampleMolecule method
"""
# result = self.group.makeSampleMolecule()
# print result.multiplicity
# self.assertTrue(result.isIsomorphic(Molecule().fromSMILES('OCC')))
#tests adding implicit atoms
adjlist1 = """
1 *1 Cd u0
"""
group1 = Group().fromAdjacencyList(adjlist1)
result1 = group1.makeSampleMolecule()
self.assertTrue(result1.isIsomorphic(Molecule().fromSMILES('C=C')))
#test creating implicit benzene atoms
adjlist2 = """
1 *1 Cbf u0 {2,B}
2 Cbf u0 {1,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
result2 = group2.makeSampleMolecule()
naphthaleneMolecule = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
resonanceList2 = naphthaleneMolecule.generateResonanceIsomers()
self.assertTrue(any([result2.isIsomorphic(x) for x in resonanceList2]))
#test the creation of a charged species
adjlist3 = """
1 *1 N5s u0
"""
group3 = Group().fromAdjacencyList(adjlist3)
result3 = group3.makeSampleMolecule()
self.assertTrue(result3.isIsomorphic(Molecule().fromSMILES('[NH4+]')))
#test creation of charged species when some single bonds present
adjlist4 = """
1 *2 [N5s,N5d] u0 {2,S} {3,S}
2 *3 R!H u1 {1,S}
3 *4 H u0 {1,S}
"""
group4 = Group().fromAdjacencyList(adjlist4)
result4 = group4.makeSampleMolecule()
self.assertTrue(
result4.isIsomorphic(Molecule().fromSMILES('[NH3+][CH2]')))
def testIsBenzeneExplicit(self):
"""
Test the Group.isBenzeneExplicit method
"""
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
self.assertFalse(group1.isBenzeneExplicit())
benzene = """
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
benzene = Group().fromAdjacencyList(benzene)
self.assertTrue(benzene.isBenzeneExplicit())
def test_repr_png(self):
"""Test that a png representation can be created."""
adjlist = """
1 *1 [C,Cd,Ct,CO,CS,Cb] u1 {2,[S,D,T,B]}
2 *2 [C,Cd,Ct,CO,CS,Cb] u0 {1,[S,D,T,B]} {3,[S,D,T,B]}
3 *3 [C,Cd,Ct,CO,CS,Cb] u0 {2,[S,D,T,B]} {4,[S,D,T,B]}
4 *4 [C,Cd,Ct,CO,CS,Cb] u0 {3,[S,D,T,B]}
"""
group = Group().fromAdjacencyList(adjlist)
result = group._repr_png_()
self.assertIsNotNone(result)
def testDrawGroup(self):
"""Test that the draw method returns the expected pydot graph."""
adjlist = """
1 *1 [C,Cd,Ct,CO,CS,Cb] u1 {2,[S,D,T,B]}
2 *2 [C,Cd,Ct,CO,CS,Cb] u0 {1,[S,D,T,B]} {3,[S,D,T,B]}
3 *3 [C,Cd,Ct,CO,CS,Cb] u0 {2,[S,D,T,B]} {4,[S,D,T,B]}
4 *4 [C,Cd,Ct,CO,CS,Cb] u0 {3,[S,D,T,B]}
"""
# Use of tabs in the expected string is intentional
expected = """
graph G {
graph [dpi=52];
node [label="\N"];
1 [fontname=Helvetica,
fontsize=16,
label="*1 C,Cd,Ct,CO,CS,Cb"];
2 [fontname=Helvetica,
fontsize=16,
label="*2 C,Cd,Ct,CO,CS,Cb"];
1 -- 2 [fontname=Helvetica,
fontsize=16,
label="S,D,T,B"];
3 [fontname=Helvetica,
fontsize=16,
label="*3 C,Cd,Ct,CO,CS,Cb"];
2 -- 3 [fontname=Helvetica,
fontsize=16,
label="S,D,T,B"];
4 [fontname=Helvetica,
fontsize=16,
label="*4 C,Cd,Ct,CO,CS,Cb"];
3 -- 4 [fontname=Helvetica,
fontsize=16,
label="S,D,T,B"];
}
"""
group = Group().fromAdjacencyList(adjlist)
result = group.draw('canon')
self.assertEqual(''.join(result.split()), ''.join(expected.split()))
class TestGroup(unittest.TestCase):
"""
Contains unit tests of the Graph class.
"""
def setUp(self):
self.adjlist = """
1 *2 [Cs,Cd] u0 {2,[S,D]} {3,S}
2 *1 [Os,Od] u0 {1,[S,D]}
3 R!H u0 {1,S}
"""
self.group = Group().fromAdjacencyList(self.adjlist)
def testClearLabeledAtoms(self):
"""
Test the Group.clearLabeledAtoms() method.
"""
self.group.clearLabeledAtoms()
for atom in self.group.atoms:
self.assertEqual(atom.label, '')
def testContainsLabeledAtom(self):
"""
Test the Group.containsLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(self.group.containsLabeledAtom(atom.label))
self.assertFalse(self.group.containsLabeledAtom('*3'))
self.assertFalse(self.group.containsLabeledAtom('*4'))
self.assertFalse(self.group.containsLabeledAtom('*5'))
self.assertFalse(self.group.containsLabeledAtom('*6'))
def testGetLabeledAtom(self):
"""
Test the Group.getLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertEqual(atom, self.group.getLabeledAtom(atom.label))
try:
self.group.getLabeledAtom('*3')
self.fail(
'Unexpected successful return from Group.getLabeledAtom() with invalid atom label.'
)
except ValueError:
pass
def testGetLabeledAtoms(self):
"""
Test the Group.getLabeledAtoms() method.
"""
labeled = self.group.getLabeledAtoms()
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(atom.label in labeled)
self.assertTrue(atom in labeled.values())
else:
self.assertFalse(atom.label in labeled)
self.assertFalse(atom in labeled.values())
def testFromAdjacencyList(self):
"""
Test the Group.fromAdjacencyList() method.
"""
atom1, atom2, atom3 = self.group.atoms
self.assertTrue(self.group.hasBond(atom1, atom2))
self.assertTrue(self.group.hasBond(atom1, atom3))
self.assertFalse(self.group.hasBond(atom2, atom3))
bond12 = atom1.bonds[atom2]
bond13 = atom1.bonds[atom3]
self.assertTrue(atom1.label == '*2')
self.assertTrue(atom1.atomType[0].label in ['Cs', 'Cd'])
self.assertTrue(atom1.atomType[1].label in ['Cs', 'Cd'])
self.assertTrue(atom1.radicalElectrons == [0])
self.assertTrue(atom2.label == '*1')
self.assertTrue(atom2.atomType[0].label in ['Os', 'Od'])
self.assertTrue(atom2.atomType[1].label in ['Os', 'Od'])
self.assertTrue(atom2.radicalElectrons == [0])
self.assertTrue(atom3.label == '')
self.assertTrue(atom3.atomType[0].label == 'R!H')
self.assertTrue(atom3.radicalElectrons == [0])
self.assertTrue(bond12.order == ['S', 'D'])
self.assertTrue(bond13.order == ['S'])
def testToAdjacencyList(self):
"""
Test the Group.toAdjacencyList() method.
"""
adjlist = self.group.toAdjacencyList()
self.assertEqual(adjlist.strip(), self.adjlist.strip(), adjlist)
def testIsIsomorphic(self):
"""
Test the Group.isIsomorphic() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testFindIsomorphism(self):
"""
Test the Group.findIsomorphism() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findIsomorphism(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].items():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
for atom3 in atom1.bonds:
atom4 = result[0][atom3]
self.assertTrue(atom4 in atom2.bonds)
self.assertTrue(atom3.equivalent(atom4))
bond1 = atom1.bonds[atom3]
bond2 = atom2.bonds[atom4]
self.assertTrue(bond1.equivalent(bond2))
def testIsSubgraphIsomorphic(self):
"""
Test the Group.isSubgraphIsomorphic() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isSubgraphIsomorphic(group))
self.assertFalse(group.isIsomorphic(self.group))
def testFindSubgraphIsomorphisms(self):
"""
Test the Group.findSubgraphIsomorphisms() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findSubgraphIsomorphisms(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].iteritems():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
def testPickle(self):
"""
Test that a Group object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
group = cPickle.loads(cPickle.dumps(self.group))
self.assertEqual(len(self.group.atoms), len(group.atoms))
for atom0, atom in zip(group.atoms, self.group.atoms):
self.assertTrue(atom0.equivalent(atom))
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testClassifyBenzeneCarbons(self):
"""
Tests the method classifyingBenzeneCarbons
"""
#This tests that we classify Cb atom types correctly
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group1.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 0)
for atom in group1.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we classify Cbf atomtypes correctly
adjlist2 = """
1 *1 Cbf u0
"""
group2 = Group().fromAdjacencyList(adjlist2)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group2.classifyBenzeneCarbons()
self.assertIn(group2.atoms[0], cbfAtomList)
self.assertIn(group2.atoms[0], cbfAtomList1)
#This tests that we can classify Cb atoms based on bonding and not just atomtype
adjlist3 = """
1 *1 C u0 {2,B}
2 *2 C u0 {1,B} {3,B}
3 *3 C u0 {2,B}
"""
group3 = Group().fromAdjacencyList(adjlist3)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group3.classifyBenzeneCarbons()
for atom in group3.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we can classify Cbf1 atoms based on bonding and not just atomtype
adjlist4 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B}
3 *3 C u0 {1,B}
4 *4 C u0 {1,B}
"""
group4 = Group().fromAdjacencyList(adjlist4)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group4.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 1)
self.assertEquals(len(cbfAtomList1), 1)
#This tests that we can classify Cbf2 atoms. In the following partial group, we should have:
#one Cbf2 atom, two Cbf1 atoms, and 5 Cb atoms
adjlist5 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B} {5,B} {6,B}
3 *3 C u0 {1,B} {7,B} {8,B}
4 *4 C u0 {1,B}
5 *5 C u0 {2,B}
6 *6 C u0 {2,B}
7 *7 C u0 {3,B}
8 *8 C u0 {3,B}
"""
group5 = Group().fromAdjacencyList(adjlist5)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group5.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList1), 2)
self.assertEquals(len(cbfAtomList2), 1)
self.assertEquals(len(cbAtomList), 5)
#Tests that we can classify connected Cbfs correctly. *1 should be connected to both *2 and *3
atom1 = group5.getLabeledAtom("*1")
atom2 = group5.getLabeledAtom("*2")
atom3 = group5.getLabeledAtom("*3")
self.assertIn(atom2, connectedCbfs[atom1])
self.assertIn(atom3, connectedCbfs[atom1])
self.assertIn(atom1, connectedCbfs[atom2])
self.assertIn(atom1, connectedCbfs[atom3])
class TestGroup(unittest.TestCase):
"""
Contains unit tests of the Graph class.
"""
def setUp(self):
self.adjlist = """
1 *2 [Cs,Cd] u0 {2,[S,D]} {3,S}
2 *1 [Os,Od] u0 {1,[S,D]}
3 R!H u0 {1,S}
"""
self.group = Group().fromAdjacencyList(self.adjlist)
def testClearLabeledAtoms(self):
"""
Test the Group.clearLabeledAtoms() method.
"""
self.group.clearLabeledAtoms()
for atom in self.group.atoms:
self.assertEqual(atom.label, '')
def testContainsLabeledAtom(self):
"""
Test the Group.containsLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(self.group.containsLabeledAtom(atom.label))
self.assertFalse(self.group.containsLabeledAtom('*3'))
self.assertFalse(self.group.containsLabeledAtom('*4'))
self.assertFalse(self.group.containsLabeledAtom('*5'))
self.assertFalse(self.group.containsLabeledAtom('*6'))
def testGetLabeledAtom(self):
"""
Test the Group.getLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertEqual(atom, self.group.getLabeledAtom(atom.label))
try:
self.group.getLabeledAtom('*3')
self.fail('Unexpected successful return from Group.getLabeledAtom() with invalid atom label.')
except ValueError:
pass
def testGetLabeledAtoms(self):
"""
Test the Group.getLabeledAtoms() method.
"""
labeled = self.group.getLabeledAtoms()
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(atom.label in labeled)
self.assertTrue(atom in labeled.values())
else:
self.assertFalse(atom.label in labeled)
self.assertFalse(atom in labeled.values())
def testFromAdjacencyList(self):
"""
Test the Group.fromAdjacencyList() method.
"""
atom1, atom2, atom3 = self.group.atoms
self.assertTrue(self.group.hasBond(atom1,atom2))
self.assertTrue(self.group.hasBond(atom1,atom3))
self.assertFalse(self.group.hasBond(atom2,atom3))
bond12 = atom1.bonds[atom2]
bond13 = atom1.bonds[atom3]
self.assertTrue(atom1.label == '*2')
self.assertTrue(atom1.atomType[0].label in ['Cs','Cd'])
self.assertTrue(atom1.atomType[1].label in ['Cs','Cd'])
self.assertTrue(atom1.radicalElectrons == [0])
self.assertTrue(atom2.label == '*1')
self.assertTrue(atom2.atomType[0].label in ['Os','Od'])
self.assertTrue(atom2.atomType[1].label in ['Os','Od'])
self.assertTrue(atom2.radicalElectrons == [0])
self.assertTrue(atom3.label == '')
self.assertTrue(atom3.atomType[0].label == 'R!H')
self.assertTrue(atom3.radicalElectrons == [0])
self.assertTrue(bond12.order == [1,2])
self.assertTrue(bond13.isSingle())
def testToAdjacencyList(self):
"""
Test the Group.toAdjacencyList() method.
"""
adjlist = self.group.toAdjacencyList()
self.assertEqual(adjlist.strip(), self.adjlist.strip(),adjlist)
def testIsIsomorphic(self):
"""
Test the Group.isIsomorphic() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testFindIsomorphism(self):
"""
Test the Group.findIsomorphism() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findIsomorphism(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].items():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
for atom3 in atom1.bonds:
atom4 = result[0][atom3]
self.assertTrue(atom4 in atom2.bonds)
self.assertTrue(atom3.equivalent(atom4))
bond1 = atom1.bonds[atom3]
bond2 = atom2.bonds[atom4]
self.assertTrue(bond1.equivalent(bond2))
def testIsSubgraphIsomorphic(self):
"""
Test the Group.isSubgraphIsomorphic() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isSubgraphIsomorphic(group))
self.assertFalse(group.isIsomorphic(self.group))
def testFindSubgraphIsomorphisms(self):
"""
Test the Group.findSubgraphIsomorphisms() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findSubgraphIsomorphisms(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].iteritems():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
def testPickle(self):
"""
Test that a Group object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
group = cPickle.loads(cPickle.dumps(self.group))
self.assertEqual(len(self.group.atoms), len(group.atoms))
for atom0, atom in zip(group.atoms, self.group.atoms):
self.assertTrue(atom0.equivalent(atom))
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testCreateAndConnectAtom(self):
"""
Tests createAndConnectAtom method
"""
adjlist1 = """
1 *1 C u0 {2,S}
2 *2 C u0 {1,S}
"""
answer1 = """
1 *1 C u0 {2,S} {3,B}
2 *2 C u0 {1,S}
3 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
answer1 = Group().fromAdjacencyList(answer1)
atom1 = group1.getLabeledAtom("*1")
newAtom = group1.createAndConnectAtom(atomtypes = ["Cb"], connectingAtom = atom1, bondOrders = ["B"])
self.assertTrue(group1.isIsomorphic(answer1))
answer2 = """
1 *1 C u0 {2,S} {3,[S,D]}
2 *2 C u0 {1,S}
3 [Cs,Cd] u0 {1,[S,D]}
"""
#Test that wildcards work alright
group2 = Group().fromAdjacencyList(adjlist1)
answer2 = Group().fromAdjacencyList(answer2)
atom1 = group2.getLabeledAtom("*1")
newAtom = group2.createAndConnectAtom(atomtypes = ["Cs", "Cd"], connectingAtom = atom1, bondOrders = ["S","D"])
self.assertTrue(group2.isIsomorphic(answer2))
def testAddImplicitAtomsFromAtomType(self):
"""
test Group.addImplicitAtomsFromAtomType() method
"""
#basic test adding oDouble
adjlist1 = """
1 *1 CO u0
"""
adjlist2 = """
1 *1 CO u0 {2,D}
2 O u0 {1,D}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
newGroup = group1.addImplicitAtomsFromAtomType()
self.assertTrue(group2.isIsomorphic(newGroup))
#testing the allDouble match (more complicated
adjlist3 = """
1 *1 Cdd u0
"""
adjlist4 = """
1 *1 Cdd u0 {2,D} {3,D}
2 C u0 {1,D}
3 C u0 {1,D}
"""
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
newGroup =group3.addImplicitAtomsFromAtomType()
self.assertTrue(group4.isIsomorphic(newGroup))
#test adding a triple bond
adjlist5 = """
1 *1 Ct u0
"""
adjlist6 = """
1 *1 Ct u0 {2,T}
2 C u0 {1,T}
"""
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
newGroup =group5.addImplicitAtomsFromAtomType()
self.assertTrue(group6.isIsomorphic(newGroup))
#test addition of lone pairs
adjlist7 = """
1 *1 N1d u0
"""
adjlist8 = """
1 *1 N1d u0 p2 {2,D}
2 C u0 {1,D}
"""
group7 = Group().fromAdjacencyList(adjlist7)
group8 = Group().fromAdjacencyList(adjlist8)
newGroup = group7.addImplicitAtomsFromAtomType()
self.assertTrue(group8.isIsomorphic(newGroup))
#test multiple implicit atoms at a time
adjlist9 = """
1 *1 Cd u0 {2,S}
2 Ct u0 {1,S}
"""
adjlist10 = """
1 *1 C u0 {2,S} {3,D}
2 Ct u0 {1,S} {4,T}
3 C u0 {1,D}
4 C u0 {2,T}
"""
group9 = Group().fromAdjacencyList(adjlist9)
group10 = Group().fromAdjacencyList(adjlist10)
newGroup =group9.addImplicitAtomsFromAtomType()
self.assertTrue(group10.isIsomorphic(newGroup))
def testClassifyBenzeneCarbons(self):
"""
Tests the method classifyingBenzeneCarbons
"""
#This tests that we classify Cb atom types correctly
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group1.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 0)
for atom in group1.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we classify Cbf atomtypes correctly
adjlist2 = """
1 *1 Cbf u0
"""
group2 = Group().fromAdjacencyList(adjlist2)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group2.classifyBenzeneCarbons()
self.assertIn(group2.atoms[0], cbfAtomList)
self.assertIn(group2.atoms[0], cbfAtomList1)
#This tests that we can classify Cb atoms based on bonding and not just atomtype
adjlist3 = """
1 *1 C u0 {2,B}
2 *2 C u0 {1,B} {3,B}
3 *3 C u0 {2,B}
"""
group3 = Group().fromAdjacencyList(adjlist3)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group3.classifyBenzeneCarbons()
for atom in group3.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we can classify Cbf1 atoms based on bonding and not just atomtype
adjlist4 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B}
3 *3 C u0 {1,B}
4 *4 C u0 {1,B}
"""
group4 = Group().fromAdjacencyList(adjlist4)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group4.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 1)
self.assertEquals(len(cbfAtomList1), 1)
#This tests that we can classify Cbf2 atoms. In the following partial group, we should have:
#one Cbf2 atom, two Cbf1 atoms, and 5 Cb atoms
adjlist5 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B} {5,B} {6,B}
3 *3 C u0 {1,B} {7,B} {8,B}
4 *4 C u0 {1,B}
5 *5 C u0 {2,B}
6 *6 C u0 {2,B}
7 *7 C u0 {3,B}
8 *8 C u0 {3,B}
"""
group5 = Group().fromAdjacencyList(adjlist5)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group5.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList1), 2)
self.assertEquals(len(cbfAtomList2), 1)
self.assertEquals(len(cbAtomList), 5)
#Tests that we can classify connected Cbfs correctly. *1 should be connected to both *2 and *3
atom1 = group5.getLabeledAtom("*1")
atom2 = group5.getLabeledAtom("*2")
atom3 = group5.getLabeledAtom("*3")
self.assertIn(atom2, connectedCbfs[atom1])
self.assertIn(atom3, connectedCbfs[atom1])
self.assertIn(atom1, connectedCbfs[atom2])
self.assertIn(atom1, connectedCbfs[atom3])
def testSortByConnectivity(self):
"""
Tests sortByConnectivity method
"""
#Basic test, we should get *1, *3 *2
adjlist1 = """
1 *1 C u0 {3,B}
2 *2 C u0 {3,B}
3 *3 C u0 {1,B} {2,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
orderedAtoms = group1.sortByConnectivity(group1.atoms)
self.assertEquals([x.label for x in orderedAtoms], ["*1", "*3", "*2"])
#Check a detached case, we should get *1, *3, *4, *2, *5
adjlist2 = """
1 *1 C u0 {3,B}
2 *2 C u0 {4,S} {5,B}
3 *3 C u0 {1,B} {4,B}
4 *4 C u0 {3,B} {2,S}
5 *5 C u0 {2,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
orderedAtoms = group2.sortByConnectivity(group2.atoms)
self.assertEquals([x.label for x in orderedAtoms], ["*1", "*3", "*4", "*2", "*5"])
def testAddImplicitBenzene(self):
"""
Test the Group.addImplicitBenzene method
"""
#tests it can make a benzene molecule
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
#tests it can make a bi-phenyl
adjlist2 = """
1 *1 Cb u0 {2,S}
2 *2 Cb u0 {1,S}
"""
#tests it can make a napthalene
adjlist3 = """
1 *1 Cbf u0
"""
#Test handling of Cbf2 atoms
adjlist4 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cbf u0 p0 c0 {1,B} {3,B}
3 *3 Cbf u0 p0 c0 {2,B}
"""
#test handling of heteroatoms and wildcards
adjlist5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B}
3 R!H u0 {1,B}
4 R!H u0 {1,B}
"""
adjlist6 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S}
4 *4 O u0 p0 c0 {3,S}
"""
adjlist7="""
1 *1 Cb u0 {4,B}
2 *2 Cb u0 {3,B}
3 *3 Cb u0 {4,B} {2,B}
4 *4 Cb u0 {1,B} {3,B}
"""
benzene ="""
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
biphenyl ="""
1 C u0 {2,B} {6,B} {7,S}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
7 C u0 {8,B} {12,B} {1,S}
8 C u0 {7,B} {9,B}
9 C u0 {8,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {10,B} {12,B}
12 C u0 {11,B} {7,B}
"""
naphthalene ="""
1 C u0 {2,B} {10,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B} {9,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {7,B}
7 C u0 {6,B} {8,B}
8 C u0 {7,B} {9,B}
9 C u0 {4,B} {8,B} {10,B}
10 C u0 {1,B} {9,B}
"""
phenanthrene = """
1 Cbf u0 p2 c0 {2,B} {7,B} {11,B}
2 Cbf u0 p0 c0 {1,B} {3,B} {5,B}
3 Cbf u0 p0 c0 {2,B} {4,B} {6,B}
4 C u0 {3,B} {8,B} {14,B}
5 C u0 {2,B} {9,B}
6 C u0 {3,B} {12,B}
7 C u0 {1,B} {8,B}
8 C u0 {4,B} {7,B}
9 C u0 {5,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {1,B} {10,B}
12 C u0 {6,B} {13,B}
13 C u0 {12,B} {14,B}
14 C u0 {4,B} {13,B}
"""
answer5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B} {5,B}
3 R!H u0 {1,B} {7,B} {10,B}
4 R!H u0 {1,B} {8,B}
5 Cb u0 {2,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {4,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {3,B} {9,B}
"""
answer6="""
1 *1 Cbf u0 p2 c0 {2,B} {5,B} {8,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B} {11,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S} {7,B}
4 *4 O u0 p0 c0 {3,S}
5 Cb u0 {1,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {1,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {9,B} {11,B}
11 Cb u0 {2,B} {10,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
group7 = Group().fromAdjacencyList(adjlist7)
benzeneGroup = Group().fromAdjacencyList(benzene)
biphenylGroup = Group().fromAdjacencyList(biphenyl)
naphthaleneGroup = Group().fromAdjacencyList(naphthalene)
phenanthreneGroup = Group().fromAdjacencyList(phenanthrene)
answer5 = Group().fromAdjacencyList(answer5)
answer6 = Group().fromAdjacencyList(answer6)
group1 = group1.addImplicitBenzene()
self.assertTrue(benzeneGroup.isIsomorphic(group1))
group2 = group2.addImplicitBenzene()
self.assertTrue(biphenylGroup.isIsomorphic(group2))
group3 = group3.addImplicitBenzene()
self.assertTrue(naphthaleneGroup.isIsomorphic(group3))
group4 = group4.addImplicitBenzene()
self.assertTrue(phenanthreneGroup.isIsomorphic(group4))
group5 = group5.addImplicitBenzene()
self.assertTrue(answer5.isIsomorphic(group5))
group6 = group6.addImplicitBenzene()
self.assertTrue(answer6.isIsomorphic(group6))
group7 = group7.addImplicitBenzene()
self.assertTrue(benzeneGroup.isIsomorphic(group7))
def testMakeSampleMolecule(self):
"""
Test the Group.makeSampleMolecule method
"""
# result = self.group.makeSampleMolecule()
# print result.multiplicity
# self.assertTrue(result.isIsomorphic(Molecule().fromSMILES('OCC')))
#tests adding implicit atoms
adjlist1 = """
1 *1 Cd u0
"""
group1 = Group().fromAdjacencyList(adjlist1)
result1 = group1.makeSampleMolecule()
self.assertTrue(result1.isIsomorphic(Molecule().fromSMILES('C=C')))
#test creating implicit benzene atoms
adjlist2 = """
1 *1 Cbf u0 {2,B}
2 Cbf u0 {1,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
result2 = group2.makeSampleMolecule()
naphthaleneMolecule = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
resonanceList2=naphthaleneMolecule.generateResonanceIsomers()
self.assertTrue(any([result2.isIsomorphic(x) for x in resonanceList2]))
#test the creation of a charged species
adjlist3 = """
1 *1 N5s u0
"""
group3 = Group().fromAdjacencyList(adjlist3)
result3 = group3.makeSampleMolecule()
self.assertTrue(result3.isIsomorphic(Molecule().fromSMILES('[NH4+]')))
#test creation of charged species when some single bonds present
adjlist4 = """
1 *2 [N5s,N5d] u0 {2,S} {3,S}
2 *3 R!H u1 {1,S}
3 *4 H u0 {1,S}
"""
group4 = Group().fromAdjacencyList(adjlist4)
result4 = group4.makeSampleMolecule()
self.assertTrue(result4.isIsomorphic(Molecule().fromSMILES('[NH3+][CH2]')))
def testIsBenzeneExplicit(self):
"""
Test the Group.isBenzeneExplicit method
"""
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
self.assertFalse(group1.isBenzeneExplicit())
benzene ="""
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
benzene = Group().fromAdjacencyList(benzene)
self.assertTrue(benzene.isBenzeneExplicit())
def test_repr_png(self):
"""Test that a png representation can be created."""
adjlist = """
1 *1 [C,Cd,Ct,CO,CS,Cb] u1 {2,[S,D,T,B]}
2 *2 [C,Cd,Ct,CO,CS,Cb] u0 {1,[S,D,T,B]} {3,[S,D,T,B]}
3 *3 [C,Cd,Ct,CO,CS,Cb] u0 {2,[S,D,T,B]} {4,[S,D,T,B]}
4 *4 [C,Cd,Ct,CO,CS,Cb] u0 {3,[S,D,T,B]}
"""
group = Group().fromAdjacencyList(adjlist)
result = group._repr_png_()
self.assertIsNotNone(result)
class TestGroup(unittest.TestCase):
"""
Contains unit tests of the Graph class.
"""
def setUp(self):
self.adjlist = """
1 *2 [Cs,Cd] u0 {2,[S,D]} {3,S}
2 *1 [Os,Od] u0 {1,[S,D]}
3 R!H u0 {1,S}
"""
self.group = Group().fromAdjacencyList(self.adjlist)
def testClearLabeledAtoms(self):
"""
Test the Group.clearLabeledAtoms() method.
"""
self.group.clearLabeledAtoms()
for atom in self.group.atoms:
self.assertEqual(atom.label, '')
def testContainsLabeledAtom(self):
"""
Test the Group.containsLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(self.group.containsLabeledAtom(atom.label))
self.assertFalse(self.group.containsLabeledAtom('*3'))
self.assertFalse(self.group.containsLabeledAtom('*4'))
self.assertFalse(self.group.containsLabeledAtom('*5'))
self.assertFalse(self.group.containsLabeledAtom('*6'))
def testGetLabeledAtom(self):
"""
Test the Group.getLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertEqual(atom, self.group.getLabeledAtom(atom.label))
try:
self.group.getLabeledAtom('*3')
self.fail('Unexpected successful return from Group.getLabeledAtom() with invalid atom label.')
except ValueError:
pass
def testGetLabeledAtoms(self):
"""
Test the Group.getLabeledAtoms() method.
"""
labeled = self.group.getLabeledAtoms()
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(atom.label in labeled)
self.assertTrue(atom in labeled.values())
else:
self.assertFalse(atom.label in labeled)
self.assertFalse(atom in labeled.values())
def testFromAdjacencyList(self):
"""
Test the Group.fromAdjacencyList() method.
"""
atom1, atom2, atom3 = self.group.atoms
self.assertTrue(self.group.hasBond(atom1,atom2))
self.assertTrue(self.group.hasBond(atom1,atom3))
self.assertFalse(self.group.hasBond(atom2,atom3))
bond12 = atom1.bonds[atom2]
bond13 = atom1.bonds[atom3]
self.assertTrue(atom1.label == '*2')
self.assertTrue(atom1.atomType[0].label in ['Cs','Cd'])
self.assertTrue(atom1.atomType[1].label in ['Cs','Cd'])
self.assertTrue(atom1.radicalElectrons == [0])
self.assertTrue(atom2.label == '*1')
self.assertTrue(atom2.atomType[0].label in ['Os','Od'])
self.assertTrue(atom2.atomType[1].label in ['Os','Od'])
self.assertTrue(atom2.radicalElectrons == [0])
self.assertTrue(atom3.label == '')
self.assertTrue(atom3.atomType[0].label == 'R!H')
self.assertTrue(atom3.radicalElectrons == [0])
self.assertTrue(bond12.order == ['S','D'])
self.assertTrue(bond13.order == ['S'])
def testToAdjacencyList(self):
"""
Test the Group.toAdjacencyList() method.
"""
adjlist = self.group.toAdjacencyList()
self.assertEqual(adjlist.strip(), self.adjlist.strip(),adjlist)
def testIsIsomorphic(self):
"""
Test the Group.isIsomorphic() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testFindIsomorphism(self):
"""
Test the Group.findIsomorphism() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findIsomorphism(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].items():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
for atom3 in atom1.bonds:
atom4 = result[0][atom3]
self.assertTrue(atom4 in atom2.bonds)
self.assertTrue(atom3.equivalent(atom4))
bond1 = atom1.bonds[atom3]
bond2 = atom2.bonds[atom4]
self.assertTrue(bond1.equivalent(bond2))
def testIsSubgraphIsomorphic(self):
"""
Test the Group.isSubgraphIsomorphic() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isSubgraphIsomorphic(group))
self.assertFalse(group.isIsomorphic(self.group))
def testFindSubgraphIsomorphisms(self):
"""
Test the Group.findSubgraphIsomorphisms() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findSubgraphIsomorphisms(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].iteritems():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
def testPickle(self):
"""
Test that a Group object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
group = cPickle.loads(cPickle.dumps(self.group))
self.assertEqual(len(self.group.atoms), len(group.atoms))
for atom0, atom in zip(group.atoms, self.group.atoms):
self.assertTrue(atom0.equivalent(atom))
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
class TestGroup(unittest.TestCase):
"""
Contains unit tests of the Graph class.
"""
def setUp(self):
self.adjlist = """
1 *2 [Cs,Cd] u0 {2,[S,D]} {3,S}
2 *1 [Os,Od] u0 {1,[S,D]}
3 R!H u0 {1,S}
"""
self.group = Group().fromAdjacencyList(self.adjlist)
def testClearLabeledAtoms(self):
"""
Test the Group.clearLabeledAtoms() method.
"""
self.group.clearLabeledAtoms()
for atom in self.group.atoms:
self.assertEqual(atom.label, '')
def testContainsLabeledAtom(self):
"""
Test the Group.containsLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(self.group.containsLabeledAtom(atom.label))
self.assertFalse(self.group.containsLabeledAtom('*3'))
self.assertFalse(self.group.containsLabeledAtom('*4'))
self.assertFalse(self.group.containsLabeledAtom('*5'))
self.assertFalse(self.group.containsLabeledAtom('*6'))
def testGetLabeledAtom(self):
"""
Test the Group.getLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertEqual(atom, self.group.getLabeledAtom(atom.label))
try:
self.group.getLabeledAtom('*3')
self.fail('Unexpected successful return from Group.getLabeledAtom() with invalid atom label.')
except ValueError:
pass
def testGetLabeledAtoms(self):
"""
Test the Group.getLabeledAtoms() method.
"""
labeled = self.group.getLabeledAtoms()
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(atom.label in labeled)
self.assertTrue(atom in labeled.values())
else:
self.assertFalse(atom.label in labeled)
self.assertFalse(atom in labeled.values())
def testFromAdjacencyList(self):
"""
Test the Group.fromAdjacencyList() method.
"""
atom1, atom2, atom3 = self.group.atoms
self.assertTrue(self.group.hasBond(atom1,atom2))
self.assertTrue(self.group.hasBond(atom1,atom3))
self.assertFalse(self.group.hasBond(atom2,atom3))
bond12 = atom1.bonds[atom2]
bond13 = atom1.bonds[atom3]
self.assertTrue(atom1.label == '*2')
self.assertTrue(atom1.atomType[0].label in ['Cs','Cd'])
self.assertTrue(atom1.atomType[1].label in ['Cs','Cd'])
self.assertTrue(atom1.radicalElectrons == [0])
self.assertTrue(atom2.label == '*1')
self.assertTrue(atom2.atomType[0].label in ['Os','Od'])
self.assertTrue(atom2.atomType[1].label in ['Os','Od'])
self.assertTrue(atom2.radicalElectrons == [0])
self.assertTrue(atom3.label == '')
self.assertTrue(atom3.atomType[0].label == 'R!H')
self.assertTrue(atom3.radicalElectrons == [0])
self.assertTrue(bond12.order == ['S','D'])
self.assertTrue(bond13.order == ['S'])
def testToAdjacencyList(self):
"""
Test the Group.toAdjacencyList() method.
"""
adjlist = self.group.toAdjacencyList()
self.assertEqual(adjlist.strip(), self.adjlist.strip(),adjlist)
def testIsIsomorphic(self):
"""
Test the Group.isIsomorphic() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testFindIsomorphism(self):
"""
Test the Group.findIsomorphism() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findIsomorphism(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].items():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
for atom3 in atom1.bonds:
atom4 = result[0][atom3]
self.assertTrue(atom4 in atom2.bonds)
self.assertTrue(atom3.equivalent(atom4))
bond1 = atom1.bonds[atom3]
bond2 = atom2.bonds[atom4]
self.assertTrue(bond1.equivalent(bond2))
def testIsSubgraphIsomorphic(self):
"""
Test the Group.isSubgraphIsomorphic() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isSubgraphIsomorphic(group))
self.assertFalse(group.isIsomorphic(self.group))
def testFindSubgraphIsomorphisms(self):
"""
Test the Group.findSubgraphIsomorphisms() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findSubgraphIsomorphisms(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].iteritems():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
def testPickle(self):
"""
Test that a Group object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
group = cPickle.loads(cPickle.dumps(self.group))
self.assertEqual(len(self.group.atoms), len(group.atoms))
for atom0, atom in zip(group.atoms, self.group.atoms):
self.assertTrue(atom0.equivalent(atom))
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testAddImplicitAtomsFromAtomType(self):
"""
test Group.addImplicitAtomsFromAtomType() method
"""
#basic test adding oDouble
adjlist1 = """
1 *1 CO u0
"""
adjlist2 = """
1 *1 CO u0 {2,D}
2 O u0 {1,D}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
newGroup = group1.addImplicitAtomsFromAtomType()
self.assertTrue(group2.isIsomorphic(newGroup))
#testing the allDouble match (more complicated
adjlist3 = """
1 *1 Cdd u0
"""
adjlist4 = """
1 *1 Cdd u0 {2,D} {3,D}
2 C u0 {1,D}
3 C u0 {1,D}
"""
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
newGroup =group3.addImplicitAtomsFromAtomType()
self.assertTrue(group4.isIsomorphic(newGroup))
#test adding a triple bond
adjlist5 = """
1 *1 Ct u0
"""
adjlist6 = """
1 *1 Ct u0 {2,T}
2 C u0 {1,T}
"""
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
newGroup =group5.addImplicitAtomsFromAtomType()
self.assertTrue(group6.isIsomorphic(newGroup))
#test addition of lone pairs
adjlist7 = """
1 *1 N1d u0
"""
adjlist8 = """
1 *1 N1d u0 p2 {2,D}
2 C u0 {1,D}
"""
group7 = Group().fromAdjacencyList(adjlist7)
group8 = Group().fromAdjacencyList(adjlist8)
newGroup = group7.addImplicitAtomsFromAtomType()
self.assertTrue(group8.isIsomorphic(newGroup))
#test multiple implicit atoms at a time
adjlist9 = """
1 *1 Cd u0 {2,S}
2 Ct u0 {1,S}
"""
adjlist10 = """
1 *1 C u0 {2,S} {3,D}
2 Ct u0 {1,S} {4,T}
3 C u0 {1,D}
4 C u0 {2,T}
"""
group9 = Group().fromAdjacencyList(adjlist9)
group10 = Group().fromAdjacencyList(adjlist10)
newGroup =group9.addImplicitAtomsFromAtomType()
self.assertTrue(group10.isIsomorphic(newGroup))
def testAddImplicitBenzene(self):
"""
Test the Group.addImplicitBenzene method
"""
#tests it can make a benzene molecule
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
#tests it can make a bi-phenyl
adjlist2 = """
1 *1 Cb u0 {2,S}
2 *2 Cb u0 {1,S}
"""
#tests it can make a napthalene
adjlist3 = """
1 *1 Cbf u0
"""
#Test handling of Cbf2 atoms
adjlist4 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cbf u0 p0 c0 {1,B} {3,B}
3 *3 Cbf u0 p0 c0 {2,B}
"""
#test handling of heteroatoms and wildcards
adjlist5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B}
3 R!H u0 {1,B}
4 R!H u0 {1,B}
"""
adjlist6 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S}
4 *4 O u0 p0 c0 {3,S}
"""
benzene ="""
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
biphenyl ="""
1 C u0 {2,B} {6,B} {7,S}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
7 C u0 {8,B} {12,B} {1,S}
8 C u0 {7,B} {9,B}
9 C u0 {8,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {10,B} {12,B}
12 C u0 {11,B} {7,B}
"""
naphthalene ="""
1 C u0 {2,B} {10,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B} {9,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {7,B}
7 C u0 {6,B} {8,B}
8 C u0 {7,B} {9,B}
9 C u0 {4,B} {8,B} {10,B}
10 C u0 {1,B} {9,B}
"""
phenanthrene = """
1 Cbf u0 p2 c0 {2,B} {7,B} {11,B}
2 Cbf u0 p0 c0 {1,B} {3,B} {5,B}
3 Cbf u0 p0 c0 {2,B} {4,B} {6,B}
4 C u0 {3,B} {8,B} {14,B}
5 C u0 {2,B} {9,B}
6 C u0 {3,B} {12,B}
7 C u0 {1,B} {8,B}
8 C u0 {4,B} {7,B}
9 C u0 {5,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {1,B} {10,B}
12 C u0 {6,B} {13,B}
13 C u0 {12,B} {14,B}
14 C u0 {4,B} {13,B}
"""
answer5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B} {5,B}
3 R!H u0 {1,B} {7,B} {10,B}
4 R!H u0 {1,B} {8,B}
5 Cb u0 {2,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {4,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {3,B} {9,B}
"""
answer6="""
1 *1 Cbf u0 p2 c0 {2,B} {5,B} {8,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B} {11,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S} {7,B}
4 *4 O u0 p0 c0 {3,S}
5 Cb u0 {1,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {1,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {9,B} {11,B}
11 Cb u0 {2,B} {10,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
benzeneGroup = Group().fromAdjacencyList(benzene)
biphenylGroup = Group().fromAdjacencyList(biphenyl)
naphthaleneGroup = Group().fromAdjacencyList(naphthalene)
phenanthreneGroup = Group().fromAdjacencyList(phenanthrene)
answer5 = Group().fromAdjacencyList(answer5)
answer6 = Group().fromAdjacencyList(answer6)
group1 = group1.addImplicitBenzene()
self.assertTrue(benzeneGroup.isIsomorphic(group1))
group2 = group2.addImplicitBenzene()
self.assertTrue(biphenylGroup.isIsomorphic(group2))
group3 = group3.addImplicitBenzene()
self.assertTrue(naphthaleneGroup.isIsomorphic(group3))
group4 = group4.addImplicitBenzene()
self.assertTrue(phenanthreneGroup.isIsomorphic(group4))
group5 = group5.addImplicitBenzene()
self.assertTrue(answer5.isIsomorphic(group5))
group6 = group6.addImplicitBenzene()
self.assertTrue(answer6.isIsomorphic(group6))
def testMakeSampleMolecule(self):
"""
Test the Group.makeSampleMolecule method
"""
# result = self.group.makeSampleMolecule()
# print result.multiplicity
# self.assertTrue(result.isIsomorphic(Molecule().fromSMILES('OCC')))
#tests adding implicit atoms
adjlist1 = """
1 *1 Cd u0
"""
group1 = Group().fromAdjacencyList(adjlist1)
result1 = group1.makeSampleMolecule()
self.assertTrue(result1.isIsomorphic(Molecule().fromSMILES('C=C')))
#test creating implicit benzene atoms
adjlist2 = """
1 *1 Cbf u0 {2,B}
2 Cbf u0 {1,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
result2 = group2.makeSampleMolecule()
naphthaleneMolecule = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
resonanceList2=naphthaleneMolecule.generateResonanceIsomers()
self.assertTrue(any([result2.isIsomorphic(x) for x in resonanceList2]))
#test the creation of a charged species
adjlist3 = """
1 *1 N5s u0
"""
group3 = Group().fromAdjacencyList(adjlist3)
result3 = group3.makeSampleMolecule()
self.assertTrue(result3.isIsomorphic(Molecule().fromSMILES('[NH4+]')))
def testIsBenzeneExplicit(self):
"""
Test the Group.isBenzeneExplicit method
"""
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
self.assertFalse(group1.isBenzeneExplicit())
benzene ="""
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
benzene = Group().fromAdjacencyList(benzene)
self.assertTrue(benzene.isBenzeneExplicit())
class TestGroup(unittest.TestCase):
"""
Contains unit tests of the Graph class.
"""
def setUp(self):
self.adjlist = """
1 *2 [Cs,Cd] u0 {2,[S,D]} {3,S}
2 *1 [Os,Od] u0 {1,[S,D]}
3 R!H u0 {1,S}
"""
self.group = Group().fromAdjacencyList(self.adjlist)
def testClearLabeledAtoms(self):
"""
Test the Group.clearLabeledAtoms() method.
"""
self.group.clearLabeledAtoms()
for atom in self.group.atoms:
self.assertEqual(atom.label, '')
def testContainsLabeledAtom(self):
"""
Test the Group.containsLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(self.group.containsLabeledAtom(atom.label))
self.assertFalse(self.group.containsLabeledAtom('*3'))
self.assertFalse(self.group.containsLabeledAtom('*4'))
self.assertFalse(self.group.containsLabeledAtom('*5'))
self.assertFalse(self.group.containsLabeledAtom('*6'))
def testGetLabeledAtom(self):
"""
Test the Group.getLabeledAtom() method.
"""
for atom in self.group.atoms:
if atom.label != '':
self.assertEqual(atom, self.group.getLabeledAtom(atom.label))
try:
self.group.getLabeledAtom('*3')
self.fail('Unexpected successful return from Group.getLabeledAtom() with invalid atom label.')
except ValueError:
pass
def testGetLabeledAtoms(self):
"""
Test the Group.getLabeledAtoms() method.
"""
labeled = self.group.getLabeledAtoms()
for atom in self.group.atoms:
if atom.label != '':
self.assertTrue(atom.label in labeled)
self.assertTrue(atom in labeled.values())
else:
self.assertFalse(atom.label in labeled)
self.assertFalse(atom in labeled.values())
def testFromAdjacencyList(self):
"""
Test the Group.fromAdjacencyList() method.
"""
atom1, atom2, atom3 = self.group.atoms
self.assertTrue(self.group.hasBond(atom1,atom2))
self.assertTrue(self.group.hasBond(atom1,atom3))
self.assertFalse(self.group.hasBond(atom2,atom3))
bond12 = atom1.bonds[atom2]
bond13 = atom1.bonds[atom3]
self.assertTrue(atom1.label == '*2')
self.assertTrue(atom1.atomType[0].label in ['Cs','Cd'])
self.assertTrue(atom1.atomType[1].label in ['Cs','Cd'])
self.assertTrue(atom1.radicalElectrons == [0])
self.assertTrue(atom2.label == '*1')
self.assertTrue(atom2.atomType[0].label in ['Os','Od'])
self.assertTrue(atom2.atomType[1].label in ['Os','Od'])
self.assertTrue(atom2.radicalElectrons == [0])
self.assertTrue(atom3.label == '')
self.assertTrue(atom3.atomType[0].label == 'R!H')
self.assertTrue(atom3.radicalElectrons == [0])
self.assertTrue(bond12.order == [1,2])
self.assertTrue(bond13.isSingle())
def testToAdjacencyList(self):
"""
Test the Group.toAdjacencyList() method.
"""
adjlist = self.group.toAdjacencyList()
self.assertEqual(adjlist.strip(), self.adjlist.strip(),adjlist)
def testIsIsomorphic(self):
"""
Test the Group.isIsomorphic() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testFindIsomorphism(self):
"""
Test the Group.findIsomorphism() method.
"""
adjlist = """
1 *1 [Os,Od] u0 {3,[S,D]}
2 R!H u0 {3,S}
3 *2 [Cs,Cd] u0 {1,[S,D]} {2,S}
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findIsomorphism(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].items():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
for atom3 in atom1.bonds:
atom4 = result[0][atom3]
self.assertTrue(atom4 in atom2.bonds)
self.assertTrue(atom3.equivalent(atom4))
bond1 = atom1.bonds[atom3]
bond2 = atom2.bonds[atom4]
self.assertTrue(bond1.equivalent(bond2))
def testIsSubgraphIsomorphic(self):
"""
Test the Group.isSubgraphIsomorphic() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
self.assertTrue(self.group.isSubgraphIsomorphic(group))
self.assertFalse(group.isIsomorphic(self.group))
def testFindSubgraphIsomorphisms(self):
"""
Test the Group.findSubgraphIsomorphisms() method.
"""
adjlist = """
1 *1 [Cs,Cd] u0
"""
group = Group().fromAdjacencyList(adjlist)
result = self.group.findSubgraphIsomorphisms(group)
self.assertEqual(len(result), 1)
for atom1, atom2 in result[0].iteritems():
self.assertTrue(atom1 in self.group.atoms)
self.assertTrue(atom2 in group.atoms)
self.assertTrue(atom1.equivalent(atom2))
def testPickle(self):
"""
Test that a Group object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
group = cPickle.loads(cPickle.dumps(self.group))
self.assertEqual(len(self.group.atoms), len(group.atoms))
for atom0, atom in zip(group.atoms, self.group.atoms):
self.assertTrue(atom0.equivalent(atom))
self.assertTrue(self.group.isIsomorphic(group))
self.assertTrue(group.isIsomorphic(self.group))
def testCreateAndConnectAtom(self):
"""
Tests createAndConnectAtom method
"""
adjlist1 = """
1 *1 C u0 {2,S}
2 *2 C u0 {1,S}
"""
answer1 = """
1 *1 C u0 {2,S} {3,B}
2 *2 C u0 {1,S}
3 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
answer1 = Group().fromAdjacencyList(answer1)
atom1 = group1.getLabeledAtom("*1")
newAtom = group1.createAndConnectAtom(atomtypes = ["Cb"], connectingAtom = atom1, bondOrders = ["B"])
self.assertTrue(group1.isIsomorphic(answer1))
answer2 = """
1 *1 C u0 {2,S} {3,[S,D]}
2 *2 C u0 {1,S}
3 [Cs,Cd] u0 {1,[S,D]}
"""
#Test that wildcards work alright
group2 = Group().fromAdjacencyList(adjlist1)
answer2 = Group().fromAdjacencyList(answer2)
atom1 = group2.getLabeledAtom("*1")
newAtom = group2.createAndConnectAtom(atomtypes = ["Cs", "Cd"], connectingAtom = atom1, bondOrders = ["S","D"])
self.assertTrue(group2.isIsomorphic(answer2))
def testAddImplicitAtomsFromAtomType(self):
"""
test Group.addImplicitAtomsFromAtomType() method
"""
#basic test adding oDouble
adjlist1 = """
1 *1 CO u0
"""
adjlist2 = """
1 *1 CO u0 {2,D}
2 O u0 {1,D}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
newGroup = group1.addImplicitAtomsFromAtomType()
self.assertTrue(group2.isIsomorphic(newGroup))
#testing the allDouble match (more complicated
adjlist3 = """
1 *1 Cdd u0
"""
adjlist4 = """
1 *1 Cdd u0 {2,D} {3,D}
2 C u0 {1,D}
3 C u0 {1,D}
"""
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
newGroup =group3.addImplicitAtomsFromAtomType()
self.assertTrue(group4.isIsomorphic(newGroup))
#test adding a triple bond
adjlist5 = """
1 *1 Ct u0
"""
adjlist6 = """
1 *1 Ct u0 {2,T}
2 C u0 {1,T}
"""
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
newGroup =group5.addImplicitAtomsFromAtomType()
self.assertTrue(group6.isIsomorphic(newGroup))
#test addition of lone pairs
adjlist7 = """
1 *1 N1d u0
"""
adjlist8 = """
1 *1 N1d u0 p2 {2,D}
2 C u0 {1,D}
"""
group7 = Group().fromAdjacencyList(adjlist7)
group8 = Group().fromAdjacencyList(adjlist8)
newGroup = group7.addImplicitAtomsFromAtomType()
self.assertTrue(group8.isIsomorphic(newGroup))
#test multiple implicit atoms at a time
adjlist9 = """
1 *1 Cd u0 {2,S}
2 Ct u0 {1,S}
"""
adjlist10 = """
1 *1 C u0 {2,S} {3,D}
2 Ct u0 {1,S} {4,T}
3 C u0 {1,D}
4 C u0 {2,T}
"""
group9 = Group().fromAdjacencyList(adjlist9)
group10 = Group().fromAdjacencyList(adjlist10)
newGroup =group9.addImplicitAtomsFromAtomType()
self.assertTrue(group10.isIsomorphic(newGroup))
def testClassifyBenzeneCarbons(self):
"""
Tests the method classifyingBenzeneCarbons
"""
#This tests that we classify Cb atom types correctly
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group1.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 0)
for atom in group1.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we classify Cbf atomtypes correctly
adjlist2 = """
1 *1 Cbf u0
"""
group2 = Group().fromAdjacencyList(adjlist2)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group2.classifyBenzeneCarbons()
self.assertIn(group2.atoms[0], cbfAtomList)
self.assertIn(group2.atoms[0], cbfAtomList1)
#This tests that we can classify Cb atoms based on bonding and not just atomtype
adjlist3 = """
1 *1 C u0 {2,B}
2 *2 C u0 {1,B} {3,B}
3 *3 C u0 {2,B}
"""
group3 = Group().fromAdjacencyList(adjlist3)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group3.classifyBenzeneCarbons()
for atom in group3.atoms:
self.assertIn(atom, cbAtomList)
#This tests that we can classify Cbf1 atoms based on bonding and not just atomtype
adjlist4 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B}
3 *3 C u0 {1,B}
4 *4 C u0 {1,B}
"""
group4 = Group().fromAdjacencyList(adjlist4)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group4.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList), 1)
self.assertEquals(len(cbfAtomList1), 1)
#This tests that we can classify Cbf2 atoms. In the following partial group, we should have:
#one Cbf2 atom, two Cbf1 atoms, and 5 Cb atoms
adjlist5 = """
1 *1 C u0 {2,B} {3,B} {4,B}
2 *2 C u0 {1,B} {5,B} {6,B}
3 *3 C u0 {1,B} {7,B} {8,B}
4 *4 C u0 {1,B}
5 *5 C u0 {2,B}
6 *6 C u0 {2,B}
7 *7 C u0 {3,B}
8 *8 C u0 {3,B}
"""
group5 = Group().fromAdjacencyList(adjlist5)
(cbAtomList, cbfAtomList, cbfAtomList1, cbfAtomList2, connectedCbfs)=group5.classifyBenzeneCarbons()
self.assertEquals(len(cbfAtomList1), 2)
self.assertEquals(len(cbfAtomList2), 1)
self.assertEquals(len(cbAtomList), 5)
#Tests that we can classify connected Cbfs correctly. *1 should be connected to both *2 and *3
atom1 = group5.getLabeledAtom("*1")
atom2 = group5.getLabeledAtom("*2")
atom3 = group5.getLabeledAtom("*3")
self.assertIn(atom2, connectedCbfs[atom1])
self.assertIn(atom3, connectedCbfs[atom1])
self.assertIn(atom1, connectedCbfs[atom2])
self.assertIn(atom1, connectedCbfs[atom3])
def testSortByConnectivity(self):
"""
Tests sortByConnectivity method
"""
#Basic test, we should get *1, *3 *2
adjlist1 = """
1 *1 C u0 {3,B}
2 *2 C u0 {3,B}
3 *3 C u0 {1,B} {2,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
orderedAtoms = group1.sortByConnectivity(group1.atoms)
self.assertEquals([x.label for x in orderedAtoms], ["*1", "*3", "*2"])
#Check a detached case, we should get *1, *3, *4, *2, *5
adjlist2 = """
1 *1 C u0 {3,B}
2 *2 C u0 {4,S} {5,B}
3 *3 C u0 {1,B} {4,B}
4 *4 C u0 {3,B} {2,S}
5 *5 C u0 {2,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
orderedAtoms = group2.sortByConnectivity(group2.atoms)
self.assertEquals([x.label for x in orderedAtoms], ["*1", "*3", "*4", "*2", "*5"])
def testAddImplicitBenzene(self):
"""
Test the Group.addImplicitBenzene method
"""
#tests it can make a benzene molecule
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
#tests it can make a bi-phenyl
adjlist2 = """
1 *1 Cb u0 {2,S}
2 *2 Cb u0 {1,S}
"""
#tests it can make a napthalene
adjlist3 = """
1 *1 Cbf u0
"""
#Test handling of Cbf2 atoms
adjlist4 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cbf u0 p0 c0 {1,B} {3,B}
3 *3 Cbf u0 p0 c0 {2,B}
"""
#test handling of heteroatoms and wildcards
adjlist5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B}
3 R!H u0 {1,B}
4 R!H u0 {1,B}
"""
adjlist6 = """
1 *1 Cbf u0 p2 c0 {2,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S}
4 *4 O u0 p0 c0 {3,S}
"""
adjlist7="""
1 *1 Cb u0 {4,B}
2 *2 Cb u0 {3,B}
3 *3 Cb u0 {4,B} {2,B}
4 *4 Cb u0 {1,B} {3,B}
"""
benzene ="""
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
biphenyl ="""
1 C u0 {2,B} {6,B} {7,S}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
7 C u0 {8,B} {12,B} {1,S}
8 C u0 {7,B} {9,B}
9 C u0 {8,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {10,B} {12,B}
12 C u0 {11,B} {7,B}
"""
naphthalene ="""
1 C u0 {2,B} {10,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B} {9,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {7,B}
7 C u0 {6,B} {8,B}
8 C u0 {7,B} {9,B}
9 C u0 {4,B} {8,B} {10,B}
10 C u0 {1,B} {9,B}
"""
phenanthrene = """
1 Cbf u0 p2 c0 {2,B} {7,B} {11,B}
2 Cbf u0 p0 c0 {1,B} {3,B} {5,B}
3 Cbf u0 p0 c0 {2,B} {4,B} {6,B}
4 C u0 {3,B} {8,B} {14,B}
5 C u0 {2,B} {9,B}
6 C u0 {3,B} {12,B}
7 C u0 {1,B} {8,B}
8 C u0 {4,B} {7,B}
9 C u0 {5,B} {10,B}
10 C u0 {9,B} {11,B}
11 C u0 {1,B} {10,B}
12 C u0 {6,B} {13,B}
13 C u0 {12,B} {14,B}
14 C u0 {4,B} {13,B}
"""
answer5 = """
1 *1 Cbf u0 {2,B} {3,B} {4,B}
2 R!H u0 {1,B} {5,B}
3 R!H u0 {1,B} {7,B} {10,B}
4 R!H u0 {1,B} {8,B}
5 Cb u0 {2,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {4,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {3,B} {9,B}
"""
answer6="""
1 *1 Cbf u0 p2 c0 {2,B} {5,B} {8,B}
2 *2 Cb u0 p0 c0 {1,B} {3,B} {11,B}
3 *3 Cb u0 p0 c0 {2,B} {4,S} {7,B}
4 *4 O u0 p0 c0 {3,S}
5 Cb u0 {1,B} {6,B}
6 Cb u0 {5,B} {7,B}
7 Cb u0 {3,B} {6,B}
8 Cb u0 {1,B} {9,B}
9 Cb u0 {8,B} {10,B}
10 Cb u0 {9,B} {11,B}
11 Cb u0 {2,B} {10,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group2 = Group().fromAdjacencyList(adjlist2)
group3 = Group().fromAdjacencyList(adjlist3)
group4 = Group().fromAdjacencyList(adjlist4)
group5 = Group().fromAdjacencyList(adjlist5)
group6 = Group().fromAdjacencyList(adjlist6)
group7 = Group().fromAdjacencyList(adjlist7)
benzeneGroup = Group().fromAdjacencyList(benzene)
biphenylGroup = Group().fromAdjacencyList(biphenyl)
naphthaleneGroup = Group().fromAdjacencyList(naphthalene)
phenanthreneGroup = Group().fromAdjacencyList(phenanthrene)
answer5 = Group().fromAdjacencyList(answer5)
answer6 = Group().fromAdjacencyList(answer6)
group1 = group1.addImplicitBenzene()
self.assertTrue(benzeneGroup.isIsomorphic(group1))
group2 = group2.addImplicitBenzene()
self.assertTrue(biphenylGroup.isIsomorphic(group2))
group3 = group3.addImplicitBenzene()
self.assertTrue(naphthaleneGroup.isIsomorphic(group3))
group4 = group4.addImplicitBenzene()
self.assertTrue(phenanthreneGroup.isIsomorphic(group4))
group5 = group5.addImplicitBenzene()
self.assertTrue(answer5.isIsomorphic(group5))
group6 = group6.addImplicitBenzene()
self.assertTrue(answer6.isIsomorphic(group6))
group7 = group7.addImplicitBenzene()
self.assertTrue(benzeneGroup.isIsomorphic(group7))
def testPickWildcards(self):
"""
Test the Group.pickWildCards function
"""
#The following tests are for picking optimal bond orders when there are bond wilcards
#test that Cb/Cbf atoms with [D,B] chooses [B] instead of [D] bonds
adjlist1 = """
1 *1 R!H u1 {2,[D,B]}
2 *2 [Cbf,Cdd] u0 {1,[D,B]} {3,[D,B]}
3 *3 [Cb,Cd] u0 {2,[D,B]} {4,S}
4 *4 R!H u0 {3,S} {5,S}
5 *5 H u0 {4,S}
"""
group1 = Group().fromAdjacencyList(adjlist1)
group1.pickWildcards()
atoms = group1.atoms
self.assertTrue(atoms[0].bonds[atoms[1]].isBenzene())
self.assertTrue(atoms[1].bonds[atoms[2]].isBenzene())
adjlist2 = """
1 *1 R!H u1 {2,[S,D]} {4,[S,D]}
2 *2 [CO,Cdd] u0 {1,[S,D]} {3,[S,D]}
3 *3 [Od,Cd] u0 {2,[S,D]}
4 *4 [Cdd,Cd] u0 {1,[S,D]}
"""
group2 = Group().fromAdjacencyList(adjlist2)
group2.pickWildcards()
atoms = group2.atoms
self.assertTrue(atoms[1].bonds[atoms[2]].isDouble)
self.assertTrue(atoms[0].bonds[atoms[3]].isDouble)
def testMakeSampleMolecule(self):
"""
Test the Group.makeSampleMolecule method
"""
def performSampMoleComparison(adjlist, answer_smiles):
"""
Creates a sample molecule from the adjlist and returns if it is isomorphic to a molecule created from
the inputted smiles
"""
group = Group().fromAdjacencyList(adjlist)
result = group.makeSampleMolecule()
return (result.isIsomorphic(Molecule().fromSMILES(answer_smiles)))
########################################################################################################################
#tests adding implicit atoms
adjlist = """
1 *1 Cd u0
"""
answer_smiles = 'C=C'
self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
#test creating implicit benzene atoms
adjlist2 = """
1 *1 Cbf u0 {2,B}
2 Cbf u0 {1,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
result2 = group2.makeSampleMolecule()
naphthaleneMolecule = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
resonanceList2=naphthaleneMolecule.generateResonanceIsomers()
self.assertTrue(any([result2.isIsomorphic(x) for x in resonanceList2]))
#test the creation of a positively charged species
adjlist = """
1 *1 N5s u0
"""
answer_smiles = '[NH4+]'
self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
#test the creation of a negatively charged species
#commented out until new nitrogen atom types added in
# adjlist = """
# 1 *1 N2s u0
# """
# answer_smiles = '[NH2-]'
# self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
#test creation of charged species when some single bonds present
adjlist = """
1 *2 [N5s,N5d] u0 {2,S} {3,S}
2 *3 R!H u1 {1,S}
3 *4 H u0 {1,S}
"""
answer_smiles = '[NH3+][CH2]'
self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
def testIsBenzeneExplicit(self):
"""
Test the Group.isBenzeneExplicit method
"""
adjlist1 = """
1 *1 Cb u0 {2,B}
2 *2 Cb u0 {1,B}
"""
group1 = Group().fromAdjacencyList(adjlist1)
self.assertFalse(group1.isBenzeneExplicit())
benzene ="""
1 C u0 {2,B} {6,B}
2 C u0 {1,B} {3,B}
3 C u0 {2,B} {4,B}
4 C u0 {3,B} {5,B}
5 C u0 {4,B} {6,B}
6 C u0 {5,B} {1,B}
"""
benzene = Group().fromAdjacencyList(benzene)
self.assertTrue(benzene.isBenzeneExplicit())
def test_repr_png(self):
"""Test that a png representation can be created."""
adjlist = """
1 *1 [C,Cd,Ct,CO,CS,Cb] u1 {2,[S,D,T,B]}
2 *2 [C,Cd,Ct,CO,CS,Cb] u0 {1,[S,D,T,B]} {3,[S,D,T,B]}
3 *3 [C,Cd,Ct,CO,CS,Cb] u0 {2,[S,D,T,B]} {4,[S,D,T,B]}
4 *4 [C,Cd,Ct,CO,CS,Cb] u0 {3,[S,D,T,B]}
"""
group = Group().fromAdjacencyList(adjlist)
result = group._repr_png_()
self.assertIsNotNone(result)
def testDrawGroup(self):
"""Test that the draw method returns the expected pydot graph."""
adjlist = """
1 *1 [C,Cd,Ct,CO,CS,Cb] u1 {2,[S,D,T,B]}
2 *2 [C,Cd,Ct,CO,CS,Cb] u0 {1,[S,D,T,B]} {3,[S,D,T,B]}
3 *3 [C,Cd,Ct,CO,CS,Cb] u0 {2,[S,D,T,B]} {4,[S,D,T,B]}
4 *4 [C,Cd,Ct,CO,CS,Cb] u0 {3,[S,D,T,B]}
"""
# Use of tabs in the expected string is intentional
expected = """
graph G {
graph [dpi=52];
node [label="\N"];
1 [fontname=Helvetica,
fontsize=16,
label="*1 C,Cd,Ct,CO,CS,Cb"];
2 [fontname=Helvetica,
fontsize=16,
label="*2 C,Cd,Ct,CO,CS,Cb"];
1 -- 2 [fontname=Helvetica,
fontsize=16,
label="S,D,T,B"];
3 [fontname=Helvetica,
fontsize=16,
label="*3 C,Cd,Ct,CO,CS,Cb"];
2 -- 3 [fontname=Helvetica,
fontsize=16,
label="S,D,T,B"];
4 [fontname=Helvetica,
fontsize=16,
label="*4 C,Cd,Ct,CO,CS,Cb"];
3 -- 4 [fontname=Helvetica,
fontsize=16,
label="S,D,T,B"];
}
"""
group = Group().fromAdjacencyList(adjlist)
result = group.draw('canon')
self.assertEqual(''.join(result.split()), ''.join(expected.split()))
def testMergeGroups(self):
"""
Test the mergeGroups() function
"""
#basic test of merging a backbone and end group
backbone1 = Group().fromAdjacencyList("""
1 *1 R!H u1 {2,S}
2 *4 R!H u0 {1,S} {3,S}
3 *6 R!H u0 {2,S} {4,S}
4 *5 R!H u0 {3,S} {5,S}
5 *2 R!H u0 {4,S} {6,S}
6 *3 H u0 {5,S}
""")
end1 = Group().fromAdjacencyList("""
1 *2 Cs u0 {2,S} {3,S}
2 *3 H u0 {1,S}
3 S u0 {1,S}
""")
desiredMerge1 = Group().fromAdjacencyList("""
1 *1 R!H u1 {2,S}
2 *4 R!H u0 {1,S} {3,S}
3 *6 R!H u0 {2,S} {4,S}
4 *5 R!H u0 {3,S} {5,S}
5 *2 Cs u0 {4,S} {6,S} {7,S}
6 *3 H u0 {5,S}
7 S u0 {5,S}
""")
mergedGroup = backbone1.mergeGroups(end1)
self.assertTrue(mergedGroup.isIdentical(desiredMerge1))
#test it works when there is a cyclical structure to the backbone
backbone2 = Group().fromAdjacencyList("""
1 *1 R!H u1 {2,S} {4,S}
2 *4 R!H u0 {1,S} {3,S}
3 *2 R!H u0 {2,S} {4,S}
4 *3 R!H u0 {3,S} {1,S}
""")
end2 = Group().fromAdjacencyList("""
1 *2 Os u0 {2,S}
2 *3 Cs u0 {1,S}
""")
desiredMerge2 = Group().fromAdjacencyList("""
1 *1 R!H u1 {2,S} {4,S}
2 *4 R!H u0 {1,S} {3,S}
3 *2 Os u0 {2,S} {4,S}
4 *3 Cs u0 {3,S} {1,S}
""")
mergedGroup = backbone2.mergeGroups(end2)
self.assertTrue(mergedGroup.isIdentical(desiredMerge2))
