def test_ChainCollection_add_exception_2(self):
antibody_chothia = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='chothia',
show_progressbar=False,
verbose=False)
antibody_kabat = Chain(sequence=read_sequence(
'./tests/Data/chain_collection_fasta_test.fasta'),
numbering_scheme='kabat')
antibody_kabat.load()
self.assertRaises(ValueError, operator.add, antibody_chothia,
antibody_kabat)
def test_ChainCollection_add_exception_2(self):
# check if adding two ChainCollection objects with one sequence each
# results in a ChainCollection object with two sequences
antibody_chothia = ChainCollection(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='chothia')
antibody_chothia.load(show_progressbar=False, verbose=False)
antibody_kabat = Chain(sequence=read_sequence(
'./tests/Data/chain_collection_fasta_test.fasta'),
numbering_scheme='kabat')
antibody_kabat.load()
self.assertRaises(ValueError, operator.add, antibody_chothia,
antibody_kabat)
def test_ChainCollection_chain_2(self):
# checks if the chain type is read properly from a Chain object
test_chain = Chain(sequence=self.chain_test_sequence)
test_chain.load()
test_collection = ChainCollection(antibody_objects=[test_chain])
self.assertEqual(test_collection.chain, 'heavy')
def test_ChainCollection_input_2(self):
# instantiate ChainCollection with a loaded Chain object
test_chain = Chain(sequence=self.chain_test_sequence)
test_collection = ChainCollection(antibody_objects=[test_chain])
self.assertIsInstance(test_collection, ChainCollection)
def test_ChainCollection_input_1(self):
# instantiate ChainCollection with a Chain (empty) object
test_collection = ChainCollection(antibody_objects=[Chain()])
self.assertIsInstance(test_collection, ChainCollection)
def test_ChainCollection_input_exception_2(self):
# when ChainCollection.object_list is instantiated with
# a list with non Chain objects it throws an error
self.assertRaises(ValueError, ChainCollection, [Chain(), 0])
def test_Chain_unnumbered_sequene(self):
test_seq = Chain(sequence='TEST')
test_seq.load()
self.assertEqual(test_seq.status, 'Unnumbered')
def test_Chain_load(self):
chain = Chain(sequence=self.test_sequence)
chain.load()
self.assertIsInstance(chain, Chain)
def test_Chain_hydrophobicity_not_loaded(self):
test_sequence = read_sequence(
'./tests/Data/chain_collection_fasta_test.fasta')
obj = Chain(sequence=test_sequence, name="test")
self.assertAlmostEqual(
obj.ab_hydrophobicity_matrix(HYDROPHOBICITY_FLAGS.EW).sum(), -8.01)
def test_load_from_string(self):
test = Chain.load_from_string(sequence=self.test_sequence,
name="test",
numbering_scheme=NUMBERING_FLAGS.CHOTHIA)
self.assertEqual(test.ab_numbering()[82], "H82A")
def test_numbering_scheme_alignment_unknown_scheme(self):
test = Chain(sequence=self.test_sequence,
name="test",
numbering_scheme="MyNumberingScheme123")
self.assertRaises(ValueError, test.ab_numbering)
def test_numbering_scheme_alignment(self, name, input, expected):
test = Chain(sequence=self.test_sequence,
name="test",
numbering_scheme=input)
self.assertEqual(test.ab_numbering()[82], expected)
def test_ChainCollection_input_1(self):
# instantiate ChainCollection with a Chain (empty) object
# this doesn't make any sense and raises an error
self.assertRaises(ValueError, ChainCollection, [Chain(sequence="")])