def test_chain_instantiation(self):
structure = biostructmap.Structure(self.test_file)
test_chain = structure[0]['A']
self.assertEqual(test_chain.get_id(),'A')
self.assertTrue(isinstance(test_chain.chain, Bio.PDB.Chain.Chain))
self.assertEqual(test_chain.parent(), structure[0])
for residue in test_chain:
#Test iteration
self.assertTrue(isinstance(residue, Bio.PDB.Residue.Residue))
#test _getitem__ method work to return a model object
self.assertTrue(isinstance(test_chain[residue.get_id()], Bio.PDB.Residue.Residue))
def test_model_instantiation(self):
structure = biostructmap.Structure(self.test_file)
test_model = structure[0]
self.assertEqual(test_model.get_id(),0)
self.assertTrue(isinstance(test_model.model, Bio.PDB.Model.Model))
self.assertEqual(test_model.parent(), structure)
for chain in test_model:
#Test iteration
self.assertTrue(isinstance(chain, biostructmap.Chain))
#test _getitem__ method work to return a model object
self.assertTrue(isinstance(test_model[chain.get_id()], biostructmap.Chain))
def test_structure_object_instantiation_with_file_like_object(self):
with open(self.test_file, 'r') as f:
test_filelike = io.StringIO(f.read())
structure = biostructmap.Structure(test_filelike)
for model in structure:
#Test iteration
self.assertTrue(isinstance(model, biostructmap.Model))
#test _getitem__ method work to return a model object
self.assertTrue(isinstance(structure[model.get_id()], biostructmap.Model))
self.assertTrue(isinstance(structure.structure, Bio.PDB.Structure.Structure))
self.assertTrue(isinstance(structure.sequences, dict))
def test_rsa_filtering_procedure(self):
data = {'A': [x for x in range(0, 25)]}
structure = biostructmap.Structure(self.test_file)
mapping = structure.map(data)
filtered_mapping = structure.map(data, rsa_range=[0.2, 1])
self.assertEqual(filtered_mapping[('A', (' ', 13, ' '))], None)
self.assertEqual(
set(mapping.keys()) - set([
x for x in filtered_mapping.keys()
if filtered_mapping[x] is not None
]),
set([('A', (' ', 4, ' ')), ('A', (' ', 13, ' ')),
('A', (' ', 16, ' '))]))
def test_structure_object_instantiation(self):
structure = biostructmap.Structure(self.test_file)
for model in structure:
#Test iteration
self.assertTrue(isinstance(model, biostructmap.Model))
#test _getitem__ method work to return a model object
self.assertTrue(
isinstance(structure[model.get_id()], biostructmap.Model))
self.assertTrue(
isinstance(structure.structure, Bio.PDB.Structure.Structure))
self.assertTrue(
isinstance(structure.structure[0]['A'], Bio.PDB.Chain.Chain))
self.assertTrue(isinstance(structure.sequences, dict))
def setUp(self):
self.test_file = './tests/pdb/4nuv.cif'
self.test_pdb = './tests/pdb/4nuv.pdb'
self.structure = biostructmap.Structure(self.test_file, mmcif=True)
self.structure_pdb = biostructmap.Structure(self.test_pdb)
self.ref_seq = ('ASNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDT'
'NFHRDITFRKLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDF'
'GDIIMGTDMEGIGYSKVVENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAM'
'MYSVKKRLKGNFIWICKLNVAVNIEPQIYRWIREWGRDYVSELPTEVQKLK'
'EKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQWDVLSNKFISVKNA'
'EKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCSVEEAKK'
'NTQEVVTNVDN')
reference_seqs = {'A': self.ref_seq, 'B': self.ref_seq}
data = {('A', 'B'): range(500)}
self.mapped = self.structure.map(data=None,
method='count_residues',
ref=reference_seqs,
radius=3)
self.mapped_pdb = self.structure_pdb.map(data=None,
method='count_residues',
ref=reference_seqs,
radius=3)
def setUp(self):
self.test_file = './tests/pdb/1zrl.pdb'
self.structure = biostructmap.Structure(self.test_file)
self.test_align = './tests/msa/protein_MSA_1zrl.fsa'
self.msa = biostructmap.SequenceAlignment(self.test_align)
ref_seq = ('MKCNISIYFFASFFVLYFAKARNEYDIKENEKFLDVYKEKFNELDKKKYGNVQKTDKKIFTFIENKLDILNNSKFNKRWK'
'SYGTPDNIDKNMSLINKHNNEEMFNNNYQSFLSTSSLIKQNKYVPINAVRVSRILSFLDSRINNGRNTSSNNEVLSNCRE'
'KRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLSIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFL'
'DYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQI'
'TQWIKEWHGEFLLERDNRSKLPKSKCKNNTLYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIK'
'ISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPY'
'KLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYW'
'NDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQD'
'KTKMIETLKVECKEKPCEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSN'
'LNFEDEFKEELHSDYKNKCTMCPEVKDVPISIIRNNEQTS')
self.reference_seqs = {'A': ref_seq}
def test_secondary_structure_dictionary_creation(self):
chain = biostructmap.Structure(self.test_file)[0]['A']
ss_dict_numeric = {1: 7, 2: 7, 3: 7, 4: 6, 5: 6, 6: 6,
7: 5, 8: 5, 9: 7, 10: 7, 11: 7, 12: 7,
13: 7, 14: 5, 15: 5, 16: 7, 17: 5, 18: 5,
19: 7, 20: 7, 21: 7, 22: 6, 23: 7, 24: 7}
ss_dict = {1: '-', 2: '-', 3: '-', 4: 'S', 5: 'S',
6: 'S', 7: 'T', 8: 'T', 9: '-', 10: '-',
11: '-', 12: '-', 13: '-', 14: 'T', 15: 'T',
16: '-', 17: 'T', 18: 'T', 19: '-', 20: '-',
21: '-', 22: 'S', 23: '-', 24: '-'}
_ss_dict_numeric = {(' ', x, ' '): y for x, y in ss_dict_numeric.items()}
_ss_dict = {(' ', x, ' '): y for x, y in ss_dict.items()}
self.assertDictEqual(_ss_dict, chain.secondary_structure())
self.assertDictEqual(_ss_dict_numeric,
chain.secondary_structure(numeric_ss_code=True))
def setUp(self):
self.test_file = './tests/pdb/4nuv.cif'
self.structure = biostructmap.Structure(self.test_file, mmcif=True)
def setUp(self):
self.test_file = './tests/pdb/1as5.cif'
self.test_align = './tests/msa/MSA_small.fsa'
self.structure = biostructmap.Structure(self.test_file, mmcif=True)
def test_residue_number_to_atom_number_function(self):
structure = biostructmap.Structure(self.test_file)
mapping = structure[0]['A'].residue_to_atom_map()
self.assertEqual(len(mapping), 25)
first_residue_atoms = list(range(1,21))
self.assertEqual(sorted(mapping[1]), first_residue_atoms)
def test_rsa_determination(self):
chain = biostructmap.Structure(self.test_file)[0]['A']
result = chain.rel_solvent_access()
for residue in [residues for residues in chain if residues.get_id()[0] == ' ']:
self.assertTrue(isinstance(result[residue.get_id()], float))
def test_structure_nearby_function(self):
structure = biostructmap.Structure(self.test_file)
result = structure.nearby()
self.assertTrue(isinstance(result, dict))
for i in result.values():
self.assertTrue(isinstance(i, set))