def test_inspect_synonyms(self):
dopamine = resolve('dopamine')[0]
self.assertTrue(inspect_synonyms(dopamine, 'Intropin'))
self.assertTrue(inspect_synonyms(dopamine, 'parcopa'))
self.assertTrue(inspect_synonyms(dopamine, 'SINEMET'))
self.assertFalse(inspect_synonyms(dopamine, 'viagra'))
self.assertFalse(inspect_synonyms(dopamine, ''))
def test_inchi_serialiser(self):
serialiser = get_serializer('inchi')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'Name:\tInChI:\n')
self.assertEqual(
serialiser.serialize_line(mols),
'InChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11'
'-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1\tInChI=1S/C21'
'H24FN3O4.ClH/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11-3-2-6-2'
'3-16(11)10-24;/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28);1H/t11-,16+;/m0./s1\n'
)
self.assertEqual(
serialiser.serialize_line(mols, human=True),
'InChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11'
'-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1\tInChI=1S/C21'
'H24FN3O4.ClH/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11-3-2-6-2'
'3-16(11)10-24;/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28);1H/t11-,16+;/m0./s1\n'
)
self.assertEqual(
serialiser.serialize_line(mols, human=True, name='Vigamox'),
'Vigamox\tInChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(2'
'0)24-8-11-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1\tInC'
'hI=1S/C21H24FN3O4.ClH/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-1'
'1-3-2-6-23-16(11)10-24;/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28);1H/t11-,16+;/m0./s1\n'
)
def test_mols_to_targets(self):
ret = mols_to_targets(['CHEMBL819'], organism='Escherichia coli')
serialiser = get_serializer('uniprot')
self.assertEqual(set(serialiser.serialize_line(ret).strip().split(',')), {'A1E3K9', 'P62593', 'P35695'})
ret = mols_to_targets(['CHEMBL819'], organism='Escherichia coli', include_parents=True)
serialiser = get_serializer('uniprot')
self.assertEqual(set(serialiser.serialize_line(ret).strip().split(',')),
{'A1E3K9', 'P62593', 'P35695', 'P00811'})
ret = mols_to_targets(['CHEMBL25', 'CHEMBL1'])
serialiser = get_serializer('gene_name')
self.assertTrue({'POLK', 'ADRA2RL2', 'CCR2', 'CHRM5', 'ADRA2L1', 'CMKAR1', 'PTPRC', 'HADH2', 'ITGAB', 'VIPR1'
}.issubset(set(serialiser.serialize_line(ret).strip().split(','))))
ret = mols_to_targets(['CHEMBL2', 'CHEMBL1737'])
serialiser = get_serializer('chembl_id')
targets_a = set(serialiser.serialize_line(ret).strip().split(','))
self.assertTrue({'CHEMBL213', 'CHEMBL1916', 'CHEMBL205', 'CHEMBL4071', 'CHEMBL1909043', 'CHEMBL2622',
}.issubset(targets_a))
ret = mols_to_targets(['CHEMBL2', 'CHEMBL1737'], only_ids=True)
serialiser = get_serializer('chembl_id')
targets_b = set(serialiser.serialize_line(ret).strip().split(','))
self.assertTrue({'CHEMBL213', 'CHEMBL1916', 'CHEMBL205', 'CHEMBL4071', 'CHEMBL1909043', 'CHEMBL2622',
}.issubset(targets_b))
self.assertEqual(targets_a, targets_b)
drugs = ['Viagra', 'Gleevec']
ret = mols_to_targets([resolve(x)[0]['molecule_chembl_id'] for x in drugs])
serialiser = get_serializer('uniprot')
self.assertTrue({'Q9BQI3', 'P00523', 'O15111', 'P22612', 'P25021', 'P16591', 'Q13153', 'Q8WXR4', 'P28564',
}.issubset(set(serialiser.serialize_line(ret).strip().split(','))))
def main():
options = get_options()
with open(options.input) if options.input else sys.stdin as in_f, \
open(options.output, 'w') if options.output else sys.stdout as out_f:
serializer_cls = get_serializer(options.format)
if not serializer_cls:
sys.stderr.write('Unsupported format', options.format)
return
if options.human:
serializer_cls.write_header(out_f)
for line in in_f:
name = line.strip()
if not name:
continue
resolved = None
try:
resolved = resolve(name, options.single)
except Exception as e:
pass
if options.parent:
resolved = get_parents(resolved)
out_f.write(
serializer_cls.serialize_line(resolved,
human=options.human,
name=name))
def test_inspect_synonyms(self):
dopamine = resolve('dopamine')[0]
self.assertTrue(inspect_synonyms(dopamine, 'Intropin'))
self.assertTrue(inspect_synonyms(dopamine, 'parcopa'))
self.assertTrue(inspect_synonyms(dopamine, 'SINEMET'))
self.assertFalse(inspect_synonyms(dopamine, 'viagra'))
self.assertFalse(inspect_synonyms(dopamine, ''))
def main():
options = get_options()
with open(options.input) if options.input else sys.stdin as in_f, \
open(options.output, 'w') if options.output else sys.stdout as out_f:
serializer_cls = get_serializer(options.format)
if not serializer_cls:
sys.stderr.write('Unsupported format', options.format)
return
if options.human:
serializer_cls.write_header(out_f)
for line in in_f:
name = line.strip()
if not name:
continue
resolved = None
try:
resolved = resolve(name, options.single)
except Exception as e:
pass
if options.parent:
resolved = get_parents(resolved)
out_f.write(serializer_cls.serialize_line(resolved, human=options.human, name=name))
def test_chembl_id_serialiser(self):
serialiser = get_serializer('chembl_id')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'Name:\tChEMBL ID:\n')
self.assertEqual(serialiser.serialize_line(mols), 'CHEMBL32,CHEMBL1200735\n')
self.assertEqual(serialiser.serialize_line(mols, human=True), 'CHEMBL32,CHEMBL1200735\n')
self.assertEqual(serialiser.serialize_line(mols, human=True, name='Vigamox'),
'Vigamox\tCHEMBL32,CHEMBL1200735\n')
def test_sdf_serialiser(self):
serialiser = get_serializer('sdf')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), '')
self.assertEqual(serialiser.serialize_line(mols), sdf, serialiser.serialize_line(mols))
self.assertEqual(serialiser.serialize_line(mols, human=True), sdf)
self.assertEqual(serialiser.serialize_line(mols, human=True, name='Vigamox'), sdf)
serialiser = get_serializer('mol')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), '')
self.assertEqual(serialiser.serialize_line(mols), sdf, serialiser.serialize_line(mols))
self.assertEqual(serialiser.serialize_line(mols, human=True), sdf)
self.assertEqual(serialiser.serialize_line(mols, human=True, name='Vigamox'), sdf)
def test_chembl_key_serialiser(self):
serialiser = get_serializer('inchi_key')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'Name:\tInChI Key:\n')
self.assertEqual(serialiser.serialize_line(mols), 'FABPRXSRWADJSP-MEDUHNTESA-N,IDIIJJHBXUESQI-DFIJPDEKSA-N\n')
self.assertEqual(serialiser.serialize_line(mols, human=True),
'FABPRXSRWADJSP-MEDUHNTESA-N,IDIIJJHBXUESQI-DFIJPDEKSA-N\n')
self.assertEqual(serialiser.serialize_line(mols, human=True, name='Vigamox'),
'Vigamox\tFABPRXSRWADJSP-MEDUHNTESA-N,IDIIJJHBXUESQI-DFIJPDEKSA-N\n')
def test_chembl_id_serialiser(self):
serialiser = get_serializer('chembl_id')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'Name:\tChEMBL ID:\n')
self.assertEqual(serialiser.serialize_line(mols),
'CHEMBL32,CHEMBL1200735\n')
self.assertEqual(serialiser.serialize_line(mols, human=True),
'CHEMBL32,CHEMBL1200735\n')
self.assertEqual(
serialiser.serialize_line(mols, human=True, name='Vigamox'),
'Vigamox\tCHEMBL32,CHEMBL1200735\n')
def test_sdf_serialiser(self):
serialiser = get_serializer('sdf')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), '')
self.assertEqual(serialiser.serialize_line(mols), sdf,
serialiser.serialize_line(mols))
self.assertEqual(serialiser.serialize_line(mols, human=True), sdf)
self.assertEqual(
serialiser.serialize_line(mols, human=True, name='Vigamox'), sdf)
serialiser = get_serializer('mol')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), '')
self.assertEqual(serialiser.serialize_line(mols), sdf,
serialiser.serialize_line(mols))
self.assertEqual(serialiser.serialize_line(mols, human=True), sdf)
self.assertEqual(
serialiser.serialize_line(mols, human=True, name='Vigamox'), sdf)
def test_smiles_serialiser(self):
serialiser = get_serializer('smi')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'SMILES Name\n')
self.assertEqual(serialiser.serialize_line(mols),
'COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n'
'Cl.COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n')
self.assertEqual(serialiser.serialize_line(mols, human=True),
'COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n'
'Cl.COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n')
self.assertEqual(serialiser.serialize_line(mols, human=True, name='Vigamox'),
'COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O Vigamox\n'
'Cl.COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O Vigamox\n')
def test_chembl_key_serialiser(self):
serialiser = get_serializer('inchi_key')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'Name:\tInChI Key:\n')
self.assertEqual(
serialiser.serialize_line(mols),
'FABPRXSRWADJSP-MEDUHNTESA-N,IDIIJJHBXUESQI-DFIJPDEKSA-N\n')
self.assertEqual(
serialiser.serialize_line(mols, human=True),
'FABPRXSRWADJSP-MEDUHNTESA-N,IDIIJJHBXUESQI-DFIJPDEKSA-N\n')
self.assertEqual(
serialiser.serialize_line(mols, human=True, name='Vigamox'),
'Vigamox\tFABPRXSRWADJSP-MEDUHNTESA-N,IDIIJJHBXUESQI-DFIJPDEKSA-N\n'
)
def main():
options = get_options()
source_format = options.source_format.lower()
if source_format not in AVAILABLE_SOURCE_FORMATS:
sys.stderr.write('Unsupported source format', options.source_format)
return
inp = sys.stdin
if source_format == 'sdf':
with open(options.input) if options.input else sys.stdin as in_f:
options.input = None
inp = convert_to_smiles(in_f)
with open(options.input) if options.input else inp as in_f, \
open(options.output, 'w') if options.output else sys.stdout as out_f:
serializer_cls = get_serializer(options.dest_format)
if not serializer_cls:
sys.stderr.write('Unsupported format', options.dest_format)
return
if options.human:
serializer_cls.write_header(out_f)
for line in in_f:
if not line or line.lower().startswith('smiles'):
continue
chunk = line.strip().split()[0]
identifiers = chunk.strip().split(',')
valid_identifiers = list()
for identifier in identifiers:
if chembl_id_regex.match(identifier):
valid_identifiers.append(identifier)
elif smiles_regex.match(identifier):
valid_identifiers.extend([x['molecule_chembl_id'] for x in resolve(identifier)])
targets = mols_to_targets(valid_identifiers,
organism=options.organism,
only_ids=(options.dest_format == 'chembl_id'),
include_parents=options.parent,
chunk_size=int(options.chunk))
out_f.write(serializer_cls.serialize_line(targets, human=options.human, name=','.join(valid_identifiers)))
def test_smiles_serialiser(self):
serialiser = get_serializer('smi')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'SMILES Name\n')
self.assertEqual(
serialiser.serialize_line(mols),
'COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n'
'Cl.COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n'
)
self.assertEqual(
serialiser.serialize_line(mols, human=True),
'COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n'
'Cl.COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O\n'
)
self.assertEqual(
serialiser.serialize_line(mols, human=True, name='Vigamox'),
'COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O Vigamox\n'
'Cl.COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)C(=O)O Vigamox\n'
)
def test_inchi_serialiser(self):
serialiser = get_serializer('inchi')
mols = resolve('Vigamox')
buf = StringIO()
serialiser.write_header(buf)
buf.seek(0)
self.assertEqual(buf.read(), 'Name:\tInChI:\n')
self.assertEqual(serialiser.serialize_line(mols),
'InChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11'
'-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1\tInChI=1S/C21'
'H24FN3O4.ClH/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11-3-2-6-2'
'3-16(11)10-24;/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28);1H/t11-,16+;/m0./s1\n')
self.assertEqual(serialiser.serialize_line(mols, human=True),
'InChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11'
'-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1\tInChI=1S/C21'
'H24FN3O4.ClH/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-11-3-2-6-2'
'3-16(11)10-24;/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28);1H/t11-,16+;/m0./s1\n')
self.assertEqual(serialiser.serialize_line(mols, human=True, name='Vigamox'),
'Vigamox\tInChI=1S/C21H24FN3O4/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(2'
'0)24-8-11-3-2-6-23-16(11)10-24/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28)/t11-,16+/m0/s1\tInC'
'hI=1S/C21H24FN3O4.ClH/c1-29-20-17-13(19(26)14(21(27)28)9-25(17)12-4-5-12)7-15(22)18(20)24-8-1'
'1-3-2-6-23-16(11)10-24;/h7,9,11-12,16,23H,2-6,8,10H2,1H3,(H,27,28);1H/t11-,16+;/m0./s1\n')
def test_get_parents(self):
parents = get_parents(resolve('CHEMBL1642'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL941')
parents = get_parents(resolve('CHEMBL941'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL941')
parents = get_parents(resolve('CHEMBL1200735'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL32')
parents = get_parents(resolve('CHEMBL32'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL32')
parents = get_parents(resolve('CHEMBL1642') + resolve('CHEMBL1200735'))
self.assertEqual(len(parents), 2)
self.assertEqual(parents[1]['molecule_chembl_id'], 'CHEMBL941')
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL32')
def test_get_parents(self):
parents = get_parents(resolve('CHEMBL1642'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL941')
parents = get_parents(resolve('CHEMBL941'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL941')
parents = get_parents(resolve('CHEMBL1200735'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL32')
parents = get_parents(resolve('CHEMBL32'))
self.assertEqual(len(parents), 1)
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL32')
parents = get_parents(resolve('CHEMBL1642') + resolve('CHEMBL1200735'))
self.assertEqual(len(parents), 2)
self.assertEqual(parents[1]['molecule_chembl_id'], 'CHEMBL941')
self.assertEqual(parents[0]['molecule_chembl_id'], 'CHEMBL32')
def test_resolve(self):
ret = resolve('viagra')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL1737')
ret = resolve('gleevec')
self.assertEqual(len(ret), 2)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL941')
self.assertEqual(ret[1]['molecule_chembl_id'], 'CHEMBL1642')
ret = resolve('gleevec', single_result=True)
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL941')
ret = resolve('aspirin')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL25')
ret = resolve('chembl59')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL59')
ret = resolve('OLEOYL')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL191896')
ret = resolve('Fc1ccc2[nH]c3CCN(CCc4ccncc4)Cc3c2c1')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL300443')
ret = resolve('VYFYYTLLBUKUHU-WTJCDBBSSA-N')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL3247442')
ret = resolve('Vigamox')
self.assertEqual(len(ret), 2)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL32')
self.assertEqual(ret[1]['molecule_chembl_id'], 'CHEMBL1200735')
ret = resolve('Vigamox', single_result=True)
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL32')
ret = resolve(
'InChI=1S/C8H12N4O5/c9-6(16)7-10-2-12(11-7)8-5(15)4(14)3(1-13)17-8/h2-5,8,13-15H,1H2,(H2,9,16)'
)
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL34')
def test_enhance_mols_with_parents(self):
enhanced = [x['molecule_chembl_id'] for x in enhance_mols_with_parents(resolve('CHEMBL1642'))]
self.assertEqual(enhanced, ['CHEMBL941', 'CHEMBL1642'])
def test_resolve(self):
ret = resolve('viagra')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL1737')
ret = resolve('gleevec')
self.assertEqual(len(ret), 2)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL941')
self.assertEqual(ret[1]['molecule_chembl_id'], 'CHEMBL1642')
ret = resolve('gleevec', single_result=True)
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL941')
ret = resolve('aspirin')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL25')
ret = resolve('chembl59')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL59')
ret = resolve('OLEOYL')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL191896')
ret = resolve('Fc1ccc2[nH]c3CCN(CCc4ccncc4)Cc3c2c1')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL300443')
ret = resolve('VYFYYTLLBUKUHU-WTJCDBBSSA-N')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL3247442')
ret = resolve('Vigamox')
self.assertEqual(len(ret), 2)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL32')
self.assertEqual(ret[1]['molecule_chembl_id'], 'CHEMBL1200735')
ret = resolve('Vigamox', single_result=True)
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL32')
ret = resolve('InChI=1S/C8H12N4O5/c9-6(16)7-10-2-12(11-7)8-5(15)4(14)3(1-13)17-8/h2-5,8,13-15H,1H2,(H2,9,16)')
self.assertEqual(len(ret), 1)
self.assertEqual(ret[0]['molecule_chembl_id'], 'CHEMBL34')
def test_mols_to_targets(self):
ret = mols_to_targets(['CHEMBL819'], organism='Escherichia coli')
serialiser = get_serializer('uniprot')
self.assertEqual(
set(serialiser.serialize_line(ret).strip().split(',')),
{'A1E3K9', 'P62593', 'P35695'})
ret = mols_to_targets(['CHEMBL819'],
organism='Escherichia coli',
include_parents=True)
serialiser = get_serializer('uniprot')
self.assertEqual(
set(serialiser.serialize_line(ret).strip().split(',')),
{'A1E3K9', 'P62593', 'P35695', 'P00811'})
ret = mols_to_targets(['CHEMBL25', 'CHEMBL1'])
serialiser = get_serializer('gene_name')
self.assertTrue({
'POLK', 'ADRA2RL2', 'CCR2', 'CHRM5', 'ADRA2L1', 'CMKAR1', 'PTPRC',
'HADH2', 'ITGAB', 'VIPR1'
}.issubset(set(serialiser.serialize_line(ret).strip().split(','))))
ret = mols_to_targets(['CHEMBL2', 'CHEMBL1737'])
serialiser = get_serializer('chembl_id')
targets_a = set(serialiser.serialize_line(ret).strip().split(','))
self.assertTrue({
'CHEMBL213',
'CHEMBL1916',
'CHEMBL205',
'CHEMBL4071',
'CHEMBL1909043',
'CHEMBL2622',
}.issubset(targets_a))
ret = mols_to_targets(['CHEMBL2', 'CHEMBL1737'], only_ids=True)
serialiser = get_serializer('chembl_id')
targets_b = set(serialiser.serialize_line(ret).strip().split(','))
self.assertTrue({
'CHEMBL213',
'CHEMBL1916',
'CHEMBL205',
'CHEMBL4071',
'CHEMBL1909043',
'CHEMBL2622',
}.issubset(targets_b))
self.assertEqual(targets_a, targets_b)
drugs = ['Viagra', 'Gleevec']
ret = mols_to_targets(
[resolve(x)[0]['molecule_chembl_id'] for x in drugs])
serialiser = get_serializer('uniprot')
self.assertTrue({
'Q9BQI3',
'P00523',
'O15111',
'P22612',
'P25021',
'P16591',
'Q13153',
'Q8WXR4',
'P28564',
}.issubset(set(serialiser.serialize_line(ret).strip().split(','))))
def test_enhance_mols_with_parents(self):
enhanced = [
x['molecule_chembl_id']
for x in enhance_mols_with_parents(resolve('CHEMBL1642'))
]
self.assertEqual(enhanced, ['CHEMBL941', 'CHEMBL1642'])