def setUp(self): self.compound1 = compounds.Compound({ "a1": "H", "a2": "O" }, {"b1": ("a1", "a2", { 'order': 1, 'chirality': None })}, {"id": "Hydroxide"}) self.compound2 = compounds.Compound( { "a1": "H", "a2": "H", "a3": "O", "a4": "H" }, { "b1": ("a1", "a3", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }), "b3": ("a3", "a4", { 'order': 1, 'chirality': None }) }, {"id": "Hydronium"}) self.acid1 = Acid(self.compound2, 'a1', -1.74) self.base1 = Base(self.compound1, 'a2', 15.7) self.conditions1 = Conditions({}) self.acidbase1 = AcidBase(self.acid1, self.base1, self.conditions1)
def test_negative_charge(self): compound = compounds.Compound({ "a1": "H", "a2": "O" }, {"b1": ("a1", "a2", { "order": 1 })}, {}) self.assertEqual(compound.charge, -1)
def setUp(self): self.compound1 = compounds.Compound({ "a1": "H", "a2": "O" }, {"b1": ("a1", "a2", { 'order': 1, 'chirality': None })}, {"id": "Hydroxide"}) self.compound2 = compounds.Compound( { "a1": "H", "a2": "H", "a3": "O", "a4": "H" }, { "b1": ("a1", "a3", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }), "b3": ("a3", "a4", { 'order': 1, 'chirality': None }) }, {"id": "Hydronium"}) self.compound3 = compounds.Compound({ 'a1': 'H', 'a2': 'O', 'a3': 'H' }, { 'b1': ('a1', 'a2', { 'order': 1, 'chirality': None }), 'b2': ('a2', 'a3', { 'order': 1, 'chirality': None }) }, {'id': "Water"}) self.acid = Acid(self.compound2, 'a1', -1.74) self.base = Base(self.compound1, 'a2', 16) self.conj_acid = Acid(self.compound3, 'a3', 16) self.conditions = Conditions({})
def test_hydroxide_hydronium(self): self.maxDiff = None parts = self.acidbase1.react() majors, minors = parts.major, parts.minor major = (Product( compounds.Compound({ "a1": "H", "a2": "O", "a3": "H" }, { "b1": ("a1", "a2", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }) }, {"id": "Conjugate acid of Hydroxide"}), 50), Product( compounds.Compound({ "a1": "H", "a2": "O", "a3": "H" }, { "b1": ("a1", "a2", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }) }, {"id": "Conjugate base of Hydronium"}), 50)) minor = () expected = Products(major, minor) exp_majors, exp_minors = expected.major, expected.minor self.assertEqual(exp_minors, minors) self.assertEqual(exp_majors, majors)
def setUp(self): self.compound1 = compounds.Compound({ "a1": "H", "a2": "H", "a3": "O" }, { "b1": ("a1", "a3", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }) }, {"id": "Water"})
def test_isomorphism2(self): self.compound4 = compounds.Compound({ 'a1': 'H', 'a3': 'O', 'a2': 'H' }, { 'b1': ('a1', 'a3', { 'order': 1, 'chirality': None }), 'b2': ('a2', 'a3', { 'order': 1, 'chirality': None }) }) self.assertEquals(self.compound3, self.compound4)
def test_positive_charge(self): compound = compounds.Compound( { "a1": "H", "a2": "H", "a3": "H", "a4": "O" }, { "b1": ("a1", "a4", { "order": 1 }), "b2": ("a2", "a4", { "order": 1 }), "b3": ("a3", "a4", { "order": 1 }) }, {}) self.assertEqual(compound.charge, 1)
def _calculate_products(self): """Determines the expected products of the reaction. Returns ------- tuple A tuple of tuples. The form is something like (Major Product, Minor Product) which can be further broken down into ((Conj. Acid, Conj. Base, Salt), (Empty Product)) Notes ----- This will generally be the conjugate acid and base, as well as some salt (or other byproduct). This method is still incomplete - it lacks support for generating the salt from ionic compounds. """ conjugate_acid = None conjugate_base = None salt = None # NYI acid, base = deepcopy(self.acid[0]), deepcopy(self.base[0]) conjugate_acid = base.to_conjugate_acid() other = acid.other_info try: other['id'] = "Conjugate base of {}".format(acid.other_info['id']) except KeyError: other['id'] = "Unknown Base" conjugate_base = compounds.Compound( *self._remove_node(acid, self.acid[1]), other_info=other) return ((Product(conjugate_acid, 50), Product(conjugate_base, 50), Product(salt, 0)), (Product(None, 0),))
def setUp(self): self.compound1 = compounds.Compound({ "a1": "H", "a2": "H", "a3": "O" }, { "b1": ("a1", "a3", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }) }, {"id": "Water"}) self.compound2 = compounds.Compound( { "a1": "H", "a2": "H", "a3": "O", "a4": "H" }, { "b1": ("a1", "a3", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }), "b3": ("a3", "a4", { 'order': 1, 'chirality': None }) }, {"id": "Hydronium"}) self.acid1 = Acid(self.compound2, 'a1', -1.74) self.base1 = Base(self.compound1, 'a2', -1.74) self.conditions1 = Conditions({}) self.acidbase1 = AcidBase(self.acid1, self.base1, self.conditions1) self.hydroiodic = Acid( compounds.Compound({ "a1": "H", "a2": "I" }, {"b1": ("a1", "a2", { 'order': 1, 'chirality': None })}, {"id": "Hydroiodic acid"}), 'a1', -10) self.conditions2 = Conditions({ 'pka': -10, 'acidic': True, 'pka_molecule': self.hydroiodic, 'pka_location': 'a1' }) self.acidbase2 = AcidBase(self.acid1, self.base1, self.conditions2) self.hydroxide = Base( compounds.Compound({ "a1": "H", "a2": "O", "a3": "Na" }, { "b1": ("a1", "a2", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }) }, {"id": "Sodium Hydroxide"}), 'a2', 15.7) self.conditions3 = Conditions({ 'pka': 15.7, 'basic': True, 'pka_molecule': self.hydroxide, 'pka_location': 'a2' }) self.acidbase3 = AcidBase(self.acid1, self.base1, self.conditions3)
def test_repr(self): assert repr(compounds._CompoundWrapper(compounds.Compound({}, {}, {})))
def test_string(self): assert str(compounds._CompoundWrapper(compounds.Compound({}, {}, {})))
def setUp(self): # Water self.compound1 = compounds.Compound({ "a1": "H", "a2": "H", "a3": "O" }, { "b1": ("a1", "a3", { 'order': 1, 'chirality': None }), "b2": ("a2", "a3", { 'order': 1, 'chirality': None }) }, {"id": "Water"}) # Ketone self.compound2 = compounds.Compound( { "a1": "H", "a2": "H", "a3": "H", "a4": "H", "a5": "H", "a6": "H", "a7": "C", "a8": "C", "a9": "C", "a10": "O" }, { "b0": ("a1", "a7", { 'order': 1, 'chirality': None }), "b1": ("a2", "a7", { 'order': 1, 'chirality': None }), "b2": ("a3", "a7", { 'order': 1, 'chirality': None }), "b3": ("a4", "a9", { 'order': 1, 'chirality': None }), "b4": ("a5", "a9", { 'order': 1, 'chirality': None }), "b5": ("a6", "a9", { 'order': 1, 'chirality': None }), "b6": ("a7", "a8", { 'order': 1, 'chirality': None }), "b7": ("a9", "a8", { 'order': 1, 'chirality': None }), "b8": ("a8", "a10", { 'order': 2, 'chirality': None }) }, {})