def test_fragments_by_id__usingwebservice_withsomebadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?fragment_ids=2n2k_MTN_frag1,foo-bar'
# TODO use value mol
fragments = [{
'nr_r_groups': 0, 'smiles': 'CC1(C)C=C(C[S-])C(C)(C)[NH+]1O', 'pdb_code': '2n2k',
'atom_codes': 'O1,N1,C1,C2,C3,C4,S1,C5,C6,C7,C8,C9', 'het_code': 'MTN', 'hash_code': 'd491952cd7c9dc30',
'frag_nr': 1, 'frag_id': '2n2k_MTN_frag1', 'rowid': 175992, 'het_chain': 'A', 'het_seq_nr': 101,
'prot_chain': 'A', 'uniprot_acc': 'P0CG48', 'uniprot_name': 'Polyubiquitin-C', 'prot_name': 'ubiquitin',
'ec_number': None, 'mol': None,
'pdb_title': 'Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand',
}]
body = {
'detail': "Fragment with identifier 'foo-bar' not found",
'absent_identifiers': ['foo-bar'],
'fragments': fragments,
'status': 404,
'title': 'Not Found',
'type': 'about:blank'
}
m.get(url, json=body, status_code=404, headers={'Content-Type': 'application/problem+json'})
with pytest.raises(IncompleteFragments) as e:
frag_ids = pd.Series(['2n2k_MTN_frag1', 'foo-bar'])
fragments_by_id(frag_ids, base_url)
assert_frame_equal(pd.DataFrame(fragments), e.value.fragments)
assert e.value.absent_identifiers == ['foo-bar']
def test_fragments_by_id__withbadid():
frag_ids = pd.Series(['foo-bar'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_id(frag_ids, 'data/fragments.sqlite')
assert_frame_equal(e.value.fragments, pd.DataFrame())
assert e.value.absent_identifiers == ['foo-bar']
def test_fragments_by_id__withbadid():
frag_ids = pd.Series(['foo-bar'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_id(frag_ids, 'data/fragments.sqlite')
assert_frame_equal(e.value.fragments, pd.DataFrame())
assert e.value.absent_identifiers == ['foo-bar']
def test_fragments_by_id__withsomebadid():
frag_ids = pd.Series(['2n2k_MTN_frag1', 'foo-bar'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_id(frag_ids, 'data/fragments.sqlite')
fragments = [{
'nr_r_groups':
0,
'smiles':
'CC1(C)C=C(C[S-])C(C)(C)[NH+]1O',
'pdb_code':
'2n2k',
'atom_codes':
'O1,N1,C1,C2,C3,C4,S1,C5,C6,C7,C8,C9',
'het_code':
'MTN',
'hash_code':
'd491952cd7c9dc30',
'frag_nr':
1,
'frag_id':
'2n2k_MTN_frag1',
'rowid':
175992,
'het_chain':
'A',
'het_seq_nr':
101,
'prot_chain':
'A',
'uniprot_acc':
'P0CG48',
'uniprot_name':
'Polyubiquitin-C',
'prot_name':
'ubiquitin',
'ec_number':
None,
'pdb_title':
'Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand',
}]
# ignoring molecules
e.value.fragments.drop('mol', axis=1, inplace=True, errors='ignore')
assert_frame_equal(e.value.fragments, pd.DataFrame(fragments))
assert e.value.absent_identifiers == ['foo-bar']
def test_fragments_by_id__withsomebadid():
frag_ids = pd.Series(['2n2k_MTN_frag1', 'foo-bar'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_id(frag_ids, 'data/fragments.sqlite')
fragments = [{
'nr_r_groups': 0, 'smiles': 'CC1(C)C=C(C[S-])C(C)(C)[NH+]1O', 'pdb_code': '2n2k',
'atom_codes': 'O1,N1,C1,C2,C3,C4,S1,C5,C6,C7,C8,C9', 'het_code': 'MTN', 'hash_code': 'd491952cd7c9dc30',
'frag_nr': 1, 'frag_id': '2n2k_MTN_frag1', 'rowid': 175992, 'het_chain': 'A', 'het_seq_nr': 101,
'prot_chain': 'A', 'uniprot_acc': 'P0CG48', 'uniprot_name': 'Polyubiquitin-C', 'prot_name': 'ubiquitin',
'ec_number': None,
'pdb_title': 'Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand',
}]
# ignoring molecules
e.value.fragments.drop('mol', axis=1, inplace=True, errors='ignore')
assert_frame_equal(e.value.fragments, pd.DataFrame(fragments))
assert e.value.absent_identifiers == ['foo-bar']
def test_fragments_by_id__usingwebservice_withbadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?fragment_ids=foo-bar'
body = {
'detail': "Fragment with identifier 'foo-bar' not found",
'absent_identifiers': ['foo-bar'],
'fragments': [],
'status': 404,
'title': 'Not Found',
'type': 'about:blank'
}
m.get(url, json=body, status_code=404, headers={'Content-Type': 'application/problem+json'})
with pytest.raises(IncompleteFragments) as e:
frag_ids = pd.Series(['foo-bar'])
fragments_by_id(frag_ids, base_url)
assert e.value.fragments.empty
assert e.value.absent_identifiers == ['foo-bar']
def test_fragments_by_id__usingwebservice_withbadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?fragment_ids=foo-bar'
body = {
'detail': "Fragment with identifier 'foo-bar' not found",
'absent_identifiers': ['foo-bar'],
'fragments': [],
'status': 404,
'title': 'Not Found',
'type': 'about:blank'
}
m.get(url,
json=body,
status_code=404,
headers={'Content-Type': 'application/problem+json'})
with pytest.raises(IncompleteFragments) as e:
frag_ids = pd.Series(['foo-bar'])
fragments_by_id(frag_ids, base_url)
assert e.value.fragments.empty
assert e.value.absent_identifiers == ['foo-bar']
def test_fragments_by_id():
frag_ids = pd.Series(['2n2k_MTN_frag1'])
result = fragments_by_id(frag_ids, 'data/fragments.sqlite')
# ignoring molecules
result.drop('mol', axis=1, inplace=True)
expected = [{
'nr_r_groups': 0, 'smiles': 'CC1(C)C=C(C[S-])C(C)(C)[NH+]1O', 'pdb_code': '2n2k',
'atom_codes': 'O1,N1,C1,C2,C3,C4,S1,C5,C6,C7,C8,C9', 'het_code': 'MTN', 'hash_code': 'd491952cd7c9dc30',
'frag_nr': 1, 'frag_id': '2n2k_MTN_frag1', 'rowid': 175992, 'het_chain': 'A', 'het_seq_nr': 101,
'prot_chain': 'A', 'uniprot_acc': 'P0CG48', 'uniprot_name': 'Polyubiquitin-C', 'prot_name': 'ubiquitin',
'ec_number': None,
'pdb_title': 'Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand',
}]
assert_frame_equal(result, pd.DataFrame(expected))
def test_fragments_by_id_with_prefix():
frag_ids = pd.Series(['2n2k_MTN_frag1'])
result = fragments_by_id(frag_ids, 'data/fragments.sqlite', 'prefix_')
# ignoring molecules
result.drop('prefix_mol', axis=1, inplace=True)
expected = [{
'prefix_nr_r_groups':
0,
'prefix_smiles':
'CC1(C)C=C(C[S-])C(C)(C)[NH+]1O',
'prefix_pdb_code':
'2n2k',
'prefix_atom_codes':
'O1,N1,C1,C2,C3,C4,S1,C5,C6,C7,C8,C9',
'prefix_het_code':
'MTN',
'prefix_hash_code':
'd491952cd7c9dc30',
'prefix_frag_nr':
1,
'prefix_frag_id':
'2n2k_MTN_frag1',
'prefix_rowid':
175992,
'prefix_het_chain':
'A',
'prefix_het_seq_nr':
101,
'prefix_prot_chain':
'A',
'prefix_uniprot_acc':
'P0CG48',
'prefix_uniprot_name':
'Polyubiquitin-C',
'prefix_prot_name':
'ubiquitin',
'prefix_ec_number':
None,
'prefix_pdb_title':
'Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand',
}]
assert_frame_equal(result, pd.DataFrame(expected))
from kripodb.canned import fragments_by_pdb_codes, fragments_by_id
# Map options to kripo arguments
id_column = options['id_column']
fragments_db_filename = options['fragmentsdb']
id_type = options['id_type']
# Select input column
queries = input_table[id_column]
# Fetch fragments
if id_type == 'pdb':
output_table = fragments_by_pdb_codes(queries, fragments_db_filename)
elif id_type == 'fragment':
output_table = fragments_by_id(queries, fragments_db_filename)
else:
raise NotImplementedError('Type of identifier unknown')
def test_fragments_by_id__usingwebservice_withsomebadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?fragment_ids=2n2k_MTN_frag1,foo-bar'
# TODO use value mol
fragments = [{
'nr_r_groups':
0,
'smiles':
'CC1(C)C=C(C[S-])C(C)(C)[NH+]1O',
'pdb_code':
'2n2k',
'atom_codes':
'O1,N1,C1,C2,C3,C4,S1,C5,C6,C7,C8,C9',
'het_code':
'MTN',
'hash_code':
'd491952cd7c9dc30',
'frag_nr':
1,
'frag_id':
'2n2k_MTN_frag1',
'rowid':
175992,
'het_chain':
'A',
'het_seq_nr':
101,
'prot_chain':
'A',
'uniprot_acc':
'P0CG48',
'uniprot_name':
'Polyubiquitin-C',
'prot_name':
'ubiquitin',
'ec_number':
None,
'mol':
None,
'pdb_title':
'Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand',
}]
body = {
'detail': "Fragment with identifier 'foo-bar' not found",
'absent_identifiers': ['foo-bar'],
'fragments': fragments,
'status': 404,
'title': 'Not Found',
'type': 'about:blank'
}
m.get(url,
json=body,
status_code=404,
headers={'Content-Type': 'application/problem+json'})
with pytest.raises(IncompleteFragments) as e:
frag_ids = pd.Series(['2n2k_MTN_frag1', 'foo-bar'])
fragments_by_id(frag_ids, base_url)
assert_frame_equal(pd.DataFrame(fragments), e.value.fragments)
assert e.value.absent_identifiers == ['foo-bar']