def test_missing_fasta_file(self):
mm = AddSequenceToMmcif(input_mmcif='input.cif',
output_mmcif='output.cif',
fasta_file='missing_file.fasta')
data = mm.process_input_sequences()
self.assertEqual(data, dict())
self.assertTrue(len(data.keys()) == 0)
def test_invalid_fasta_file(self):
mm = AddSequenceToMmcif(
input_mmcif='input.cif',
output_mmcif='output.cif',
fasta_file=self.test_files.TEST_INVALID_FASTA_ONE_SEQUENCE)
data = mm.process_input_sequences()
self.assertEqual(data, dict())
self.assertTrue(len(data.keys()) == 0)
def test_get_data_from_3zt9_via_AddSequenceToMmcif_process_data(self):
self.test_files.one_sequence()
test_dir = tempfile.mkdtemp()
output_cif = os.path.join(test_dir, 'output.cif')
mm = AddSequenceToMmcif(input_mmcif=self.test_files.cif,
output_mmcif=output_cif,
fasta_file=self.test_files.fasta)
worked = mm.process_data()
self.assertTrue(worked)
shutil.rmtree(test_dir)
def test_process_fasta_five_chains(self):
self.test_files.five_sequences()
expected_result = self.test_files.sample_seq
mm = AddSequenceToMmcif(input_mmcif='input.cif',
output_mmcif='output.cif',
fasta_file=self.test_files.fasta)
data = mm.process_input_sequences()
self.assertTrue(len(data.keys()) == 5)
for key in data:
self.assertTrue(key in expected_result)
self.assertTrue(data[key] == expected_result[key])
def test_get_data_from_3zt9_via_AddSequenceToMmcif_get_best_match(self):
self.test_files.one_sequence()
expected_result = self.test_files.sample_seq['pdb|3zt9|A']
entity_dict = self.test_files.observed_seq
mm = AddSequenceToMmcif(input_mmcif=self.test_files.cif,
output_mmcif='output.cif',
fasta_file=self.test_files.fasta)
mm.process_input_sequences()
best_seq, best_score = mm.get_best_match(
mmcif_sequence=entity_dict['1']['sequence'])
self.assertTrue(best_seq == expected_result)
self.assertTrue(best_score > 0)
def test_process_sequence_two_chains(self):
sequence = 'MEKLEVGIYTRAREGEIACGDACLVKRVEGVIFLAVGDGIGHGPEAARAAEIAIASMESSMNTGLVNIFQLCHRELRGTRGAVAALCRVDRRQGLWQAAIVGNIHVKILSAKGIITPLATPGILGYNYPHQLLIAKGSYQEGDLFLIHSDGIQEGAVPLALLANYRLTAEELVRLIGEKYGRRDDDVAVIVAR'
chains = 'A,B'
mm = AddSequenceToMmcif(input_mmcif='input.cif',
output_mmcif='output.cif',
input_chainids=chains,
input_sequence=sequence)
data = mm.process_input_sequences()
self.assertTrue(len(data.keys()) == 2)
for key in data:
self.assertTrue(key in chains.split(','))
self.assertTrue(data[key] == sequence)
def test_get_data_from_5liz_via_AddSequenceToMmcif(self):
self.test_files.five_sequences()
mm = AddSequenceToMmcif(input_mmcif=self.test_files.cif,
output_mmcif='output.cif')
entity_dict = self.test_files.observed_seq
sequence_dict = mm.process_mmcif()
self.assertFalse(sequence_dict == dict())
for entity_id in entity_dict:
chains = sequence_dict.get(entity_id, {}).get('chains', [])
self.assertTrue(
sequence_dict.get(entity_id, {}).get('sequence', '') ==
entity_dict[entity_id]['sequence'])
self.assertTrue(
sorted(chains) == sorted(entity_dict[entity_id]['chains']))
def common_function(self):
sample_seq = self.test_files.sample_seq
temp_dir = tempfile.mkdtemp()
output_cif = os.path.join(temp_dir, 'output.cif')
mm = AddSequenceToMmcif(input_mmcif=self.test_files.cif,
output_mmcif=output_cif,
fasta_file=self.test_files.fasta)
worked = mm.process_data()
self.assertTrue(worked)
self.assertTrue(os.path.exists(output_cif))
om = mmcifHandling()
if om.parse_mmcif(fileName=output_cif):
entity_poly = om.getCategory('entity_poly')
for cat in entity_poly:
for instance, entity_id in enumerate(
entity_poly[cat]['entity_id']):
sequence = entity_poly[cat]['pdbx_seq_one_letter_code'][
instance]
sample_seq_key = self.test_files.sample_seq_to_obs_remapping[
entity_id]
self.assertTrue(sequence == sample_seq[sample_seq_key])
shutil.rmtree(temp_dir)