diff --git a/ippisite/ippidb/tests.py b/ippisite/ippidb/tests.py
index f9720708e183042e27b29b246c635c8bd5fd4585..ed1a17904e24745f18af1a925a7b71991ffd8fa4 100644
--- a/ippisite/ippidb/tests.py
+++ b/ippisite/ippidb/tests.py
@@ -13,7 +13,8 @@ from openbabel import vectorUnsignedInt, OBFingerprint
from ippidb import ws, models
from ippidb.ws import get_uniprot_info
-from .models import Compound, CompoundTanimoto, create_tanimoto, update_compound_cached_properties, Symmetry
+from .models import Compound, CompoundTanimoto, create_tanimoto, \
+ update_compound_cached_properties, Symmetry
from .models import DrugBankCompound
from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey
@@ -24,15 +25,18 @@ class MolSmiTestCase(TestCase):
"""
def setUp(self):
- self.smiles_str = "C"
- # the MOL version is also a valid regexp to validate arbitrary name in the openbabel-generated version
- self.mol_str = "\n OpenBabel[0-9]{11}D\n\n 1 0 0 0 0 0 0 0 0 0999 V2000\n 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\nM END\n"
+ self.smiles = "C"
+ # the MOL version is also a valid regexp to validate arbitrary name in
+ # the openbabel-generated version
+ self.mol = "\n OpenBabel[0-9]{11}D\n\n 1 0 0 0 0 0 0 0 " \
+ " 0 0999 V2000\n 1.0000 0.0000 0.0000 C 0 0 0 0 " \
+ " 0 0 0 0 0 0 0 0\nM END\n"
def test_mol2smi(self):
- self.assertEqual(mol2smi(self.mol_str), self.smiles_str)
+ self.assertEqual(mol2smi(self.mol), self.smiles)
def test_smi2mol2smi(self):
- self.assertTrue(re.compile(self.mol_str).match(smi2mol(self.smiles_str)))
+ self.assertTrue(re.compile(self.mol).match(smi2mol(self.smiles)))
class SmiInchi(TestCase):
@@ -41,8 +45,11 @@ class SmiInchi(TestCase):
"""
def setUp(self):
- self.smiles_str = "CC(C)C(=O)C1=C(C(=C(C(=C1)C(=O)C2=CC=C(C=C2)OC3=CC=CC=C3)O)O)O"
- self.inchi_str = "InChI=1S/C23H20O6/c1-13(2)19(24)17-12-18(22(27)23(28)21(17)26)20(25)14-8-10-16(11-9-14)29-15-6-4-3-5-7-15/h3-13,26-28H,1-2H3"
+ self.smiles_str = "CC(C)C(=O)C1=C(C(=C(C(=C1)C(=O)C2=CC=C(C=C2)" \
+ "OC3=CC=CC=C3)O)O)O"
+ self.inchi_str = "InChI=1S/C23H20O6/c1-13(2)19(24)17-12-18(22" \
+ "(27)23(28)21(17)26)20(25)14-8-10-16(11-9-14)29-15-6-4-3-" \
+ "5-7-15/h3-13,26-28H,1-2H3"
self.inchikey_str = "CVVQMBDTMYUWTR-UHFFFAOYSA-N"
def test_smi2inchi(self):
@@ -60,10 +67,14 @@ class FingerPrinterTestCase(TestCase):
def setUp(self):
self.fingerprinter = FingerPrinter("FP4")
self.smiles = "CC"
- self.fp = vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
+ self.fp = vectorUnsignedInt([
+ 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
self.smiles_dict = {1: "CC", 2: "CCC"}
- self.fp_dict = {1: vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
- 2: vectorUnsignedInt([3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])}
+ self.fp_dict = {
+ 1: vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0]),
+ 2: vectorUnsignedInt([3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0])}
self.tanimoto_dict = {1: 1.0, 2: 0.5}
def test_fingerprints_available(self):
@@ -84,13 +95,18 @@ class FingerPrinterTestCase(TestCase):
self.assertEqualVUI(self.fingerprinter.fp(self.smiles), self.fp)
def test_fp_dict(self):
- self.assertEqualVUIdict(self.fingerprinter.fp_dict(self.smiles_dict), self.fp_dict)
+ self.assertEqualVUIdict(self.fingerprinter.fp_dict(self.smiles_dict),
+ self.fp_dict)
def test_tanimoto_fps(self):
- self.assertEqual(self.fingerprinter.tanimoto_fps(self.smiles, self.fp_dict), self.tanimoto_dict)
+ self.assertEqual(self.fingerprinter.tanimoto_fps(self.smiles,
+ self.fp_dict),
+ self.tanimoto_dict)
def test_tanimoto_smiles(self):
- self.assertEqual(self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict), self.tanimoto_dict)
+ self.assertEqual(self.fingerprinter.tanimoto_smiles(self.smiles,
+ self.smiles_dict),
+ self.tanimoto_dict)
class FingerPrinterTestCaseCompound1ECFP4(TestCase):
@@ -98,11 +114,14 @@ class FingerPrinterTestCaseCompound1ECFP4(TestCase):
def setUp(self):
self.fingerprinter = FingerPrinter("ECFP4")
self.smiles = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
- self.smiles_dict = {1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"}
+ self.smiles_dict = {1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)"
+ "c(O)c1O"}
self.tanimoto_dict = {1: 1.0}
def test_tanimoto_smiles(self):
- self.assertEqual(self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict), self.tanimoto_dict)
+ self.assertEqual(self.fingerprinter.tanimoto_smiles(self.smiles,
+ self.smiles_dict),
+ self.tanimoto_dict)
def create_dummy_compound(id_, smiles):
@@ -169,31 +188,33 @@ class CompoundTanimotoTestCase(TestCase):
def setUp(self):
self.smiles_dict = {1: "CC", 2: "CCC"}
- self.smiles_query = "CC"
+ self.query = "CC"
for id_, smiles in self.smiles_dict.items():
create_dummy_compound(id_, smiles)
def test_create(self):
- create_tanimoto(self.smiles_query, "FP4")
- ct = CompoundTanimoto.objects.get(id=1, canonical_smiles=self.smiles_query)
+ create_tanimoto(self.query, "FP4")
+ ct = CompoundTanimoto.objects.get(id=1, canonical_smiles=self.query)
self.assertEqual(ct.tanimoto, 1.0)
- ct = CompoundTanimoto.objects.get(id=2, canonical_smiles=self.smiles_query)
+ ct = CompoundTanimoto.objects.get(id=2, canonical_smiles=self.query)
self.assertEqual(ct.tanimoto, 0.5)
class CompoundTanimotoTestCaseCompound1ECFP4(TestCase):
def setUp(self):
- self.smiles_dict = {1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O",
- 2: "NC(=N)N[C@H](C1CCCCC1)C(=O)NCC(=O)N1CCC(CC1)c1cc(n[nH]1)-c1ccc(Cl)cc1Cl"}
- self.smiles_query = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
+ self.smiles_dict = {
+ 1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O",
+ 2: "NC(=N)N[C@H](C1CCCCC1)C(=O)NCC(=O)N1CCC(CC1)c1cc(n[nH]1)"
+ "-c1ccc(Cl)cc1Cl"}
+ self.query = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
for id_, smiles in self.smiles_dict.items():
create_dummy_compound(id_, smiles)
def test_create(self):
- create_tanimoto(self.smiles_query, "ECFP4")
- ct = CompoundTanimoto.objects.get(id=1, canonical_smiles=self.smiles_query)
- ct2 = CompoundTanimoto.objects.get(id=2, canonical_smiles=self.smiles_query)
+ create_tanimoto(self.query, "ECFP4")
+ ct = CompoundTanimoto.objects.get(id=1, canonical_smiles=self.query)
+ ct2 = CompoundTanimoto.objects.get(id=2, canonical_smiles=self.query)
self.assertEqual(ct.tanimoto, 1.0)
self.assertEqual(float(ct2.tanimoto), 0.0971)
@@ -341,6 +362,7 @@ class QueryCompoundViewsTestCase(TestCase):
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
+
class TestGetDoiInfo(TestCase):
"""
Test retrieving information for a DOI entry
@@ -348,8 +370,10 @@ class TestGetDoiInfo(TestCase):
def test_get_doi_info(self):
resp = ws.get_doi_info('10.1073/pnas.0805139105')
- self.assertEqual(resp['title'], 'A quantitative atlas of mitotic phosphorylation')
- self.assertEqual(resp['journal_name'], 'Proceedings of the National Academy of Sciences')
+ self.assertEqual(resp['title'], 'A quantitative atlas of mitotic'
+ ' phosphorylation')
+ self.assertEqual(resp['journal_name'], 'Proceedings of the National'
+ ' Academy of Sciences')
self.assertEqual(resp['biblio_year'], 2008)
self.assertEqual(resp['authors_list'],
'Dephoure N., Zhou C., Villen J., Beausoleil S. A., '
@@ -365,24 +389,29 @@ class TestGetPfamInfo(TestCase):
class TestGetGooglePatentInfo(TestCase):
def test_it(self):
- target = {'title': 'Secure virtual machine bootstrap in untrusted cloud infrastructures',
+ target = {'title': 'Secure virtual machine bootstrap in untrusted'
+ ' cloud infrastructures',
'journal_name': None,
'biblio_year': '2010',
- 'authors_list': 'Fabio R. Maino, Pere Monclus, David A. McGrew, Robert T. Bell, '
+ 'authors_list': 'Fabio R. Maino, Pere Monclus, David A.'
+ ' McGrew, Robert T. Bell, '
'Steven Joseph Rich, Cisco Technology Inc'}
resp = ws.get_google_patent_info('US8856504')
self.assertEqual(resp, target)
def test_entry_not_found(self):
- self.assertRaises(ws.PatentNotFound, ws.get_google_patent_info, 'US8856504US8856504US885US8856504US8856504')
+ self.assertRaises(ws.PatentNotFound, ws.get_google_patent_info,
+ 'US8856504US8856504US885US8856504US8856504')
class TestGetPubMEDIdInfo(TestCase):
def test_create_protein(self):
- target = {'title': 'Gene List significance at-a-glance with GeneValorization.',
+ target = {'title': 'Gene List significance at-a-glance with'
+ ' GeneValorization.',
'journal_name': 'Bioinformatics (Oxford, England)',
'biblio_year': '2011',
- 'authors_list': 'Brancotte B, Biton A, Bernard-Pierrot I, Radvanyi F, Reyal F, Cohen-Boulakia S'}
+ 'authors_list': 'Brancotte B, Biton A, Bernard-Pierrot I, '
+ 'Radvanyi F, Reyal F, Cohen-Boulakia S'}
resp = ws.get_pubmed_info('21349868')
self.assertEqual(resp, target)
@@ -394,27 +423,37 @@ class TestGetUniprotInfo(TestCase):
def test_get_uniprot_info(self):
resp = get_uniprot_info('Q15286')
- self.assertEqual(resp['recommended_name'], 'Ras-related protein Rab-35')
+ self.assertEqual(resp['recommended_name'],
+ 'Ras-related protein Rab-35')
self.assertEqual(resp['organism'], 9606)
self.assertEqual(resp['gene_id'], 11021)
- exp_gene_names = [{'name': 'RAB35', 'type': 'primary'}, {'name': 'RAB1C', 'type': 'synonym'},
+ exp_gene_names = [{'name': 'RAB35', 'type': 'primary'},
+ {'name': 'RAB1C', 'type': 'synonym'},
{'name': 'RAY', 'type': 'synonym'}]
self.assertEqual(sorted(resp['gene_names'], key=lambda k: k['name']),
sorted(exp_gene_names, key=lambda k: k['name']))
self.assertEqual(resp['entry_name'], 'RAB35_HUMAN')
self.assertEqual(resp['short_name'], 'RAB35')
- exp_molecular_functions = ['GO_0003924', 'GO_0005525', 'GO_0005546', 'GO_0019003']
- self.assertEqual(sorted(resp['molecular_functions']), sorted(exp_molecular_functions))
- exp_cellular_localisations = ['GO_0000139', 'GO_0005829', 'GO_0005886', 'GO_0005905', 'GO_0010008',
- 'GO_0030665', 'GO_0031253', 'GO_0042470', 'GO_0045171', 'GO_0045334',
- 'GO_0055038', 'GO_0070062', 'GO_0098993']
- self.assertEqual(sorted(resp['cellular_localisations']), sorted(exp_cellular_localisations))
- exp_biological_processes = ['GO_0000281', 'GO_0006886', 'GO_0008104', 'GO_0016197',
- 'GO_0019882', 'GO_0031175', 'GO_0032456', 'GO_0032482',
- 'GO_0036010', 'GO_0048227', 'GO_1990090']
- self.assertEqual(sorted(resp['biological_processes']), sorted(exp_biological_processes))
+ exp_molecular_functions = ['GO_0003924', 'GO_0005525', 'GO_0005546',
+ 'GO_0019003']
+ self.assertEqual(sorted(resp['molecular_functions']),
+ sorted(exp_molecular_functions))
+ exp_cellular_localisations = ['GO_0000139', 'GO_0005829', 'GO_0005886',
+ 'GO_0005905', 'GO_0010008', 'GO_0030665',
+ 'GO_0031253', 'GO_0042470', 'GO_0045171',
+ 'GO_0045334', 'GO_0055038', 'GO_0070062',
+ 'GO_0098993']
+ self.assertEqual(sorted(resp['cellular_localisations']),
+ sorted(exp_cellular_localisations))
+ exp_biological_processes = ['GO_0000281', 'GO_0006886', 'GO_0008104',
+ 'GO_0016197', 'GO_0019882', 'GO_0031175',
+ 'GO_0032456', 'GO_0032482', 'GO_0036010',
+ 'GO_0048227', 'GO_1990090']
+ self.assertEqual(sorted(resp['biological_processes']),
+ sorted(exp_biological_processes))
exp_accessions = ['Q15286', 'B2R6E0', 'B4E390']
- self.assertEqual(sorted(resp['accessions']), sorted(exp_accessions))
+ self.assertEqual(sorted(resp['accessions']),
+ sorted(exp_accessions))
exp_citations = [
{'doi': '10.1006/bbrc.1994.2889', 'pmid': '7811277'},
{'doi': '10.1038/ng1285', 'pmid': '14702039'},
@@ -433,9 +472,11 @@ class TestGetUniprotInfo(TestCase):
]
self.assertEqual(sorted(exp_citations, key=lambda k: k['pmid']),
sorted(resp['citations'], key=lambda k: k['pmid']))
- exp_alternative_names = [{'full': 'GTP-binding protein RAY'}, {'full': 'Ras-related protein Rab-1C'}]
- self.assertEqual(sorted(exp_alternative_names, key=lambda k: k['full']),
- sorted(resp['alternative_names'], key=lambda k: k['full']))
+ exp_alternative_names = [{'full': 'GTP-binding protein RAY'},
+ {'full': 'Ras-related protein Rab-1C'}]
+ self.assertEqual(
+ sorted(exp_alternative_names, key=lambda k: k['full']),
+ sorted(resp['alternative_names'], key=lambda k: k['full']))
def test_get_uniprot_info_domains(self):
resp = get_uniprot_info('O00255')
@@ -456,7 +497,8 @@ class TestGetPDBUniProtMapping(TestCase):
self.assertEqual(len(resp), len(set(resp)))
def test_entry_not_found(self):
- self.assertRaises(ws.EntryNotFoundError, ws.get_pdb_uniprot_mapping, 'Xu85')
+ self.assertRaises(ws.EntryNotFoundError, ws.get_pdb_uniprot_mapping,
+ 'Xu85')
class TestConvertIUPACToSMILESAndMore(TestCase):
@@ -469,17 +511,27 @@ class TestConvertIUPACToSMILESAndMore(TestCase):
(
'2,4,6-trinitrotoluene',
{
- "inchi": "InChI=1/C7H5N3O6/c1-4-6(9(13)14)2-5(8(11)12)3-7(4)10(15)16/h2-3H,1H3",
- "stdinchi": "InChI=1S/C7H5N3O6/c1-4-6(9(13)14)2-5(8(11)12)3-7(4)10(15)16/h2-3H,1H3",
+ "inchi": "InChI=1/C7H5N3O6/c1-4-6(9(13)14)2-5(8(11)12)"
+ "3-7(4)10(15)16/h2-3H,1H3",
+ "stdinchi": "InChI=1S/C7H5N3O6/c1-4-6(9(13)14)2-5(8(11)"
+ "12)3-7(4)10(15)16/h2-3H,1H3",
"stdinchikey": "SPSSULHKWOKEEL-UHFFFAOYSA-N",
- "smiles": "[N+](=O)([O-])C1=C(C)C(=CC(=C1)[N+](=O)[O-])[N+](=O)[O-]",
+ "smiles": "[N+](=O)([O-])C1=C(C)C(=CC(=C1)[N+](=O)[O-])"
+ "[N+](=O)[O-]",
}
),
(
- '3-{1-oxo-6-[4-(piperidin-4-yl)butanamido]-2,3-dihydro-1H-isoindol-2-yl}propanoic acid',
+ '3-{1-oxo-6-[4-(piperidin-4-yl)butanamido]-2,3-dihydro-1H-'
+ 'isoindol-2-yl}propanoic acid',
{
- "inchi": "InChI=1/C20H27N3O4/c24-18(3-1-2-14-6-9-21-10-7-14)22-16-5-4-15-13-23(11-8-19(25)26)20(27)17(15)12-16/h4-5,12,14,21H,1-3,6-11,13H2,(H,22,24)(H,25,26)/f/h22,25H",
- "stdinchi": "InChI=1S/C20H27N3O4/c24-18(3-1-2-14-6-9-21-10-7-14)22-16-5-4-15-13-23(11-8-19(25)26)20(27)17(15)12-16/h4-5,12,14,21H,1-3,6-11,13H2,(H,22,24)(H,25,26)",
+ "inchi": "InChI=1/C20H27N3O4/c24-18(3-1-2-14-6-9-21-10-"
+ "7-14)22-16-5-4-15-13-23(11-8-19(25)26)20(27)17"
+ "(15)12-16/h4-5,12,14,21H,1-3,6-11,13H2,(H,22,"
+ "24)(H,25,26)/f/h22,25H",
+ "stdinchi": "InChI=1S/C20H27N3O4/c24-18(3-1-2-14-6-9-21"
+ "-10-7-14)22-16-5-4-15-13-23(11-8-19(25)26)"
+ "20(27)17(15)12-16/h4-5,12,14,21H,1-3,6-11,"
+ "13H2,(H,22,24)(H,25,26)",
"stdinchikey": "HWRXVANHVCXVHA-UHFFFAOYSA-N",
"smiles": "O=C1N(CC2=CC=C(C=C12)NC(CCCC1CCNCC1)=O)CCC(=O)O"
}
@@ -490,16 +542,21 @@ class TestConvertIUPACToSMILESAndMore(TestCase):
dict_returned = ws.convert_iupac_to_smiles_and_inchi(iupac)
self.assertEqual(dict_expected["smiles"], dict_returned["smiles"])
self.assertEqual(dict_expected["inchi"], dict_returned["inchi"])
- self.assertEqual(dict_expected["stdinchi"], dict_returned["stdinchi"])
- self.assertEqual(dict_expected["stdinchikey"], dict_returned["stdinchikey"])
+ self.assertEqual(dict_expected["stdinchi"],
+ dict_returned["stdinchi"])
+ self.assertEqual(dict_expected["stdinchikey"],
+ dict_returned["stdinchikey"])
def test_invalid_entry(self):
- self.assertRaises(ws.EntryNotFoundError, ws.convert_iupac_to_smiles_and_inchi, '3-{1-oxo-6-[4-(piperid')
- self.assertRaises(ws.EntryNotFoundError, ws.convert_iupac_to_smiles_and_inchi, None)
+ self.assertRaises(ws.EntryNotFoundError,
+ ws.convert_iupac_to_smiles_and_inchi,
+ '3-{1-oxo-6-[4-(piperid')
+ self.assertRaises(ws.EntryNotFoundError,
+ ws.convert_iupac_to_smiles_and_inchi, None)
class DuplicateGeneNameTestCase(TestCase):
def test_works(self):
models.Protein.objects.get_or_create(uniprot_id='P12497')
- models.Protein.objects.get_or_create(uniprot_id='P0C6F2')
\ No newline at end of file
+ models.Protein.objects.get_or_create(uniprot_id='P0C6F2')