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 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))
