def test_from_adjacency_list3(self):
"""
adjlist: Test the Molecule.from_adjacency_list() method 3.
"""
# molecule 3
adjlist = """
1 *1 C u1 {2,S} {3,S} {4,S}
2 H u0 {1,S}
3 H u0 {1,S}
4 *2 N u0 p0 c+1 {1,S} {5,S} {6,D}
5 O u0 p3 c-1 {4,S}
6 O u0 p2 {4,D}
"""
molecule = Molecule().from_adjacency_list(adjlist)
self.assertTrue(molecule.multiplicity == 2)
atom1 = molecule.atoms[0]
atom2 = molecule.atoms[3]
atom3 = molecule.atoms[4]
atom4 = molecule.atoms[5]
self.assertTrue(molecule.has_bond(atom2, atom1))
self.assertTrue(molecule.has_bond(atom2, atom3))
self.assertTrue(molecule.has_bond(atom2, atom4))
self.assertFalse(molecule.has_bond(atom1, atom3))
self.assertFalse(molecule.has_bond(atom1, atom4))
bond21 = atom2.bonds[atom1]
bond23 = atom2.bonds[atom3]
bond24 = atom2.bonds[atom4]
self.assertTrue(atom1.label == '*1')
self.assertTrue(atom1.element.symbol == 'C')
self.assertTrue(atom1.radical_electrons == 1)
self.assertTrue(atom1.charge == 0)
self.assertTrue(atom2.label == '*2')
self.assertTrue(atom2.element.symbol == 'N')
self.assertTrue(atom2.radical_electrons == 0)
self.assertTrue(atom2.charge == 1)
self.assertTrue(atom3.label == '')
self.assertTrue(atom3.element.symbol == 'O')
self.assertTrue(atom3.radical_electrons == 0)
self.assertTrue(atom3.charge == -1)
self.assertTrue(atom4.label == '')
self.assertTrue(atom4.element.symbol == 'O')
self.assertTrue(atom4.radical_electrons == 0)
self.assertTrue(atom4.charge == 0)
self.assertTrue(bond21.is_single())
self.assertTrue(bond23.is_single())
self.assertTrue(bond24.is_double())
def test_atom_mapping_2(self):
"""Test that to_rdkit_mol returns correct indices and atom mappings when hydrogens are removed."""
adjlist = """
1 H u0 p0 c0 {2,S}
2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {2,S}
5 O u0 p2 c0 {2,S} {6,S}
6 H u0 p0 c0 {5,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
rdkitmol, rd_atom_indices = to_rdkit_mol(mol,
remove_h=True,
return_mapping=True)
heavy_atoms = [at for at in mol.atoms if at.number != 1]
for at1 in heavy_atoms:
for at2 in heavy_atoms:
if mol.has_bond(at1, at2):
try:
rdkitmol.GetBondBetweenAtoms(rd_atom_indices[at1],
rd_atom_indices[at2])
except RuntimeError:
self.fail(
"RDKit failed in finding the bond in the original atom!"
)