def test_fragments_by_pdb_codes__withsomebadid():
pdb_codes = pd.Series(['2n2k', '0000'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_pdb_codes(pdb_codes, 'data/fragments.sqlite')
# ignoring molecules
e.value.fragments.drop('mol', axis=1, inplace=True, errors='ignore')
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',
}, {
'nr_r_groups': 1, 'smiles': '[*]C[S-]', 'pdb_code': '2n2k', 'atom_codes': 'C4,S1', 'het_code': 'MTN',
'hash_code': '8b8dc32f7e8a9db3', 'frag_nr': 2, 'frag_id': '2n2k_MTN_frag2', 'rowid': 175950, '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',
}, {
'nr_r_groups': 1, 'smiles': '[*]C1=CC(C)(C)[NH+](O)C1(C)C', 'pdb_code': '2n2k',
'atom_codes': 'O1,N1,C1,C2,C3,C5,C6,C7,C8,C9', 'het_code': 'MTN', 'hash_code': '17c58abf7bdf33ba',
'frag_nr': 3, 'frag_id': '2n2k_MTN_frag3', 'rowid': 175971, '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(pd.DataFrame(expected), e.value.fragments)
assert e.value.absent_identifiers == ['0000']
def test_fragments_by_pdb_codes__usingwebservice_withsomebadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?pdb_codes=2n2k,0000'
# 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 '0000' not found",
'absent_identifiers': ['0000'],
'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:
pdb_codes = pd.Series(['2n2k', '0000'])
fragments_by_pdb_codes(pdb_codes, base_url)
assert_frame_equal(pd.DataFrame(fragments), e.value.fragments)
assert e.value.absent_identifiers == ['0000']
def test_fragments_by_pdb_codes__withbadid():
pdb_codes = pd.Series(['0000'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_pdb_codes(pdb_codes, 'data/fragments.sqlite')
assert_frame_equal(e.value.fragments, pd.DataFrame())
assert e.value.absent_identifiers == ['0000']
def test_fragments_by_pdb_codes__withbadid():
pdb_codes = pd.Series(['0000'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_pdb_codes(pdb_codes, 'data/fragments.sqlite')
assert_frame_equal(e.value.fragments, pd.DataFrame())
assert e.value.absent_identifiers == ['0000']
def test_fragments_by_pdb_codes__usingwebservice_withbadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?pdb_codes=0000'
body = {
'detail': "Fragment with identifier '0000' not found",
'absent_identifiers': ['0000'],
'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:
pdb_codes = pd.Series(['0000'])
fragments_by_pdb_codes(pdb_codes, base_url)
assert e.value.fragments.empty
assert e.value.absent_identifiers == ['0000']
def test_fragments_by_pdb_codes__usingwebservice_withbadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?pdb_codes=0000'
body = {
'detail': "Fragment with identifier '0000' not found",
'absent_identifiers': ['0000'],
'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:
pdb_codes = pd.Series(['0000'])
fragments_by_pdb_codes(pdb_codes, base_url)
assert e.value.fragments.empty
assert e.value.absent_identifiers == ['0000']
def test_fragments_by_pdb_codes_with_prefix():
pdb_codes = pd.Series(['3wxj'])
result = fragments_by_pdb_codes(pdb_codes, 'data/fragments.sqlite', 'prefix_')
# ignoring molecules
result.drop('prefix_mol', axis=1, inplace=True, errors='ignore')
expected = [{
'prefix_nr_r_groups': 0, 'prefix_smiles': 'O=P([O-])([O-])OCC(O)CO', 'prefix_pdb_code': '3wxj',
'prefix_atom_codes': 'O1,C1,C2,O2,C3,O1P,O4P,O2P,O3P,P', 'prefix_het_code': 'G3P', 'prefix_hash_code': 'ee9013689ff298d4',
'prefix_frag_nr': 1, 'prefix_frag_id': '3wxj_G3P_frag1', 'prefix_rowid': 352104, 'prefix_het_chain': 'B', 'prefix_het_seq_nr': 601,
'prefix_prot_chain': 'B', 'prefix_uniprot_acc': 'D3KVM3', 'prefix_uniprot_name': None, 'prefix_prot_name': 'Glycerol kinase',
'prefix_ec_number': '2.7.1.30',
'prefix_pdb_title': 'Crystal structure of trypanosoma brucei gambiense glycerol kinase in complex with glycerol 3-phosphate',
}]
assert_frame_equal(result, pd.DataFrame(expected))
def test_fragments_by_pdb_codes_with_prefix():
pdb_codes = pd.Series(['3wxj'])
result = fragments_by_pdb_codes(pdb_codes, 'data/fragments.sqlite',
'prefix_')
# ignoring molecules
result.drop('prefix_mol', axis=1, inplace=True, errors='ignore')
expected = [{
'prefix_nr_r_groups':
0,
'prefix_smiles':
'O=P([O-])([O-])OCC(O)CO',
'prefix_pdb_code':
'3wxj',
'prefix_atom_codes':
'O1,C1,C2,O2,C3,O1P,O4P,O2P,O3P,P',
'prefix_het_code':
'G3P',
'prefix_hash_code':
'ee9013689ff298d4',
'prefix_frag_nr':
1,
'prefix_frag_id':
'3wxj_G3P_frag1',
'prefix_rowid':
352104,
'prefix_het_chain':
'B',
'prefix_het_seq_nr':
601,
'prefix_prot_chain':
'B',
'prefix_uniprot_acc':
'D3KVM3',
'prefix_uniprot_name':
None,
'prefix_prot_name':
'Glycerol kinase',
'prefix_ec_number':
'2.7.1.30',
'prefix_pdb_title':
'Crystal structure of trypanosoma brucei gambiense glycerol kinase in complex with glycerol 3-phosphate',
}]
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_pdb_codes__usingwebservice_withsomebadid(base_url):
with requests_mock.mock() as m:
url = base_url + '/fragments?pdb_codes=2n2k,0000'
# 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 '0000' not found",
'absent_identifiers': ['0000'],
'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:
pdb_codes = pd.Series(['2n2k', '0000'])
fragments_by_pdb_codes(pdb_codes, base_url)
assert_frame_equal(pd.DataFrame(fragments), e.value.fragments)
assert e.value.absent_identifiers == ['0000']
def test_fragments_by_pdb_codes__withsomebadid():
pdb_codes = pd.Series(['2n2k', '0000'])
with pytest.raises(IncompleteFragments) as e:
fragments_by_pdb_codes(pdb_codes, 'data/fragments.sqlite')
# ignoring molecules
e.value.fragments.drop('mol', axis=1, inplace=True, errors='ignore')
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',
}, {
'nr_r_groups':
1,
'smiles':
'[*]C[S-]',
'pdb_code':
'2n2k',
'atom_codes':
'C4,S1',
'het_code':
'MTN',
'hash_code':
'8b8dc32f7e8a9db3',
'frag_nr':
2,
'frag_id':
'2n2k_MTN_frag2',
'rowid':
175950,
'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',
}, {
'nr_r_groups':
1,
'smiles':
'[*]C1=CC(C)(C)[NH+](O)C1(C)C',
'pdb_code':
'2n2k',
'atom_codes':
'O1,N1,C1,C2,C3,C5,C6,C7,C8,C9',
'het_code':
'MTN',
'hash_code':
'17c58abf7bdf33ba',
'frag_nr':
3,
'frag_id':
'2n2k_MTN_frag3',
'rowid':
175971,
'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(pd.DataFrame(expected), e.value.fragments)
assert e.value.absent_identifiers == ['0000']
