def test_singlet_vs_closed_shell(self):
adjlist_singlet = """
1 C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D} {3,S} {5,S}
3 C u0 p1 c0 {1,S} {2,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
"""
adjlist_closed_shell = """
1 C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D} {3,D}
3 C u0 p0 c0 {1,S} {2,D} {5,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {3,S}
"""
singlet = Species(molecule=[Molecule().fromAdjacencyList(adjlist_singlet)])
singlet.generateResonanceIsomers()
closed_shell = Species(molecule=[Molecule().fromAdjacencyList(adjlist_closed_shell)])
closed_shell.generateResonanceIsomers()
singlet_aug_inchi = singlet.getAugmentedInChI()
closed_shell_aug_inchi = closed_shell.getAugmentedInChI()
self.assertTrue(singlet_aug_inchi != closed_shell_aug_inchi)
def test_singlet_vs_closed_shell(self):
adjlist_singlet = """
1 C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D} {3,S} {5,S}
3 C u0 p1 c0 {1,S} {2,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
"""
adjlist_closed_shell = """
1 C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D} {3,D}
3 C u0 p0 c0 {1,S} {2,D} {5,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {3,S}
"""
singlet = Species(
molecule=[Molecule().fromAdjacencyList(adjlist_singlet)])
singlet.generateResonanceIsomers()
closed_shell = Species(
molecule=[Molecule().fromAdjacencyList(adjlist_closed_shell)])
closed_shell.generateResonanceIsomers()
singlet_aug_inchi = singlet.getAugmentedInChI()
closed_shell_aug_inchi = closed_shell.getAugmentedInChI()
self.assertTrue(singlet_aug_inchi != closed_shell_aug_inchi)
def compare(self, inchi, u_indices=None, p_indices=None):
u_layer = U_LAYER_PREFIX + U_LAYER_SEPARATOR.join(map(
str, u_indices)) if u_indices else None
p_layer = P_LAYER_PREFIX + P_LAYER_SEPARATOR.join(map(
str, p_indices)) if p_indices else None
aug_inchi = compose_aug_inchi(inchi, u_layer, p_layer)
mol = fromAugmentedInChI(Molecule(), aug_inchi)
ConsistencyChecker.check_multiplicity(mol.getRadicalCount(),
mol.multiplicity)
for at in mol.atoms:
ConsistencyChecker.check_partial_charge(at)
spc = Species(molecule=[mol])
spc.generateResonanceIsomers()
ignore_prefix = r"(InChI=1+)(S*)/"
aug_inchi_expected = re.split(ignore_prefix, aug_inchi)[-1]
aug_inchi_computed = re.split(ignore_prefix,
spc.getAugmentedInChI())[-1]
self.assertEquals(aug_inchi_expected, aug_inchi_computed)
return mol
def compare(self, adjlist, aug_inchi):
spc = Species(molecule=[Molecule().fromAdjacencyList(adjlist)])
spc.generateResonanceIsomers()
ignore_prefix = r"(InChI=1+)(S*)/"
exp = re.split(ignore_prefix, aug_inchi)[-1]
comp = re.split(ignore_prefix, spc.getAugmentedInChI())[-1]
self.assertEquals(exp, comp)
def compare(self, adjlist, aug_inchi):
spc = Species(molecule=[Molecule().fromAdjacencyList(adjlist)])
spc.generateResonanceIsomers()
ignore_prefix = r"(InChI=1+)(S*)/"
exp = re.split(ignore_prefix, aug_inchi)[-1]
comp = re.split(ignore_prefix, spc.getAugmentedInChI())[-1]
self.assertEquals(exp, comp)
def test_singlet_vs_triplet(self):
adjlist_singlet = """
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
"""
adjlist_triplet = """
multiplicity 3
1 C u2 p0 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
"""
singlet = Species(molecule=[Molecule().fromAdjacencyList(adjlist_singlet)])
triplet = Species(molecule=[Molecule().fromAdjacencyList(adjlist_triplet)])
singlet_aug_inchi = singlet.getAugmentedInChI()
triplet_aug_inchi = triplet.getAugmentedInChI()
self.assertTrue(singlet_aug_inchi != triplet_aug_inchi)
def test_singlet_vs_triplet(self):
adjlist_singlet = """
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
"""
adjlist_triplet = """
multiplicity 3
1 C u2 p0 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
"""
singlet = Species(molecule=[Molecule().fromAdjacencyList(adjlist_singlet)])
triplet = Species(molecule=[Molecule().fromAdjacencyList(adjlist_triplet)])
singlet_aug_inchi = singlet.getAugmentedInChI()
triplet_aug_inchi = triplet.getAugmentedInChI()
self.assertTrue(singlet_aug_inchi != triplet_aug_inchi)
def test_CO_triplet(self):
adjlist = """
multiplicity 3
1 C u2 p0 c0 {2,D}
2 O u0 p2 c0 {1,D}
"""
spc = Species(molecule=[Molecule().fromAdjacencyList(adjlist)])
aug_inchi = spc.getAugmentedInChI()
self.assertEqual(Species(molecule=[Molecule().fromAugmentedInChI(aug_inchi)]).isIsomorphic(spc), True)
def test_CO_triplet(self):
adjlist = """
multiplicity 3
1 C u2 p0 c0 {2,D}
2 O u0 p2 c0 {1,D}
"""
spc = Species(molecule=[Molecule().fromAdjacencyList(adjlist)])
aug_inchi = spc.getAugmentedInChI()
self.assertEqual(Species(molecule=[Molecule().fromAugmentedInChI(aug_inchi)]).isIsomorphic(spc), True)
def test_CCCO_triplet(self):
adjlist = """
multiplicity 3
1 C u0 p0 c0 {2,D} {5,S} {6,S}
2 C u0 p0 c0 {1,D} {3,S} {7,S}
3 C u1 p0 c0 {2,S} {4,S} {8,S}
4 O u1 p2 c0 {3,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
"""
mol = Molecule().fromAdjacencyList(adjlist)
spc = Species(molecule=[mol])
spc.generateResonanceIsomers()
aug_inchi = spc.getAugmentedInChI()
self.assertEqual(Species(molecule=[Molecule().fromAugmentedInChI(aug_inchi)]).isIsomorphic(spc), True)
def test_CCCO_triplet(self):
adjlist = """
multiplicity 3
1 C u0 p0 c0 {2,D} {5,S} {6,S}
2 C u0 p0 c0 {1,D} {3,S} {7,S}
3 C u1 p0 c0 {2,S} {4,S} {8,S}
4 O u1 p2 c0 {3,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
"""
mol = Molecule().fromAdjacencyList(adjlist)
spc = Species(molecule=[mol])
spc.generate_resonance_structures()
aug_inchi = spc.getAugmentedInChI()
self.assertEqual(Species(molecule=[Molecule().fromAugmentedInChI(aug_inchi)]).isIsomorphic(spc), True)
def compare(self, inchi, u_indices=[], p_indices = []):
u_layer = U_LAYER_PREFIX + U_LAYER_SEPARATOR.join(map(str, u_indices)) if u_indices else None
p_layer = P_LAYER_PREFIX + P_LAYER_SEPARATOR.join(map(str, p_indices)) if p_indices else None
aug_inchi = compose_aug_inchi(inchi, u_layer, p_layer)
mol = fromAugmentedInChI(Molecule(), aug_inchi)
ConsistencyChecker.check_multiplicity(mol.getRadicalCount(), mol.multiplicity)
for at in mol.atoms:
ConsistencyChecker.check_partial_charge(at)
spc = Species(molecule=[mol])
spc.generateResonanceIsomers()
ignore_prefix = r"(InChI=1+)(S*)/"
aug_inchi_expected = re.split(ignore_prefix, aug_inchi)[-1]
aug_inchi_computed = re.split(ignore_prefix, spc.getAugmentedInChI())[-1]
self.assertEquals(aug_inchi_expected, aug_inchi_computed)
return mol
