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 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])
