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 create_group(element, u1, c1):
adjlist = get_group_string(element, u1, c1)
return Group().from_adjacency_list(adjlist), adjlist
