def test_gather_features(self):
"""Test gather_features() function"""
def mocked_get_cnc(apo):
residues = {}
for i, res in enumerate(
('ALA', 'MET', 'GLU', 'ASN', 'PHE', 'GLN', 'LYS', 'VAL', 'GLU',
'LYS', 'ILE', 'GLY')):
residues[(res, i + 1, 'A')] = 42.
return residues, ('1', '1')
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'pm_XXX.pdb'),
'XXX_mdl.pdb')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdlA.sqc'),
'.')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdlA.hcs'),
'.')
with utils.mocked_object(bmi_feature_parser, 'get_cnc',
mocked_get_cnc):
bmi_feature_parser.gather_features('XXX_mdl', ['A'])
with open('XXX_mdlA.feat') as fh:
data = fh.readlines()
self.assertEqual(len(data), 96)
self.assertEqual(
data[0][:116],
'ATOM 1 N ALA A 1 -17.647 -2.542 37.435 '
'1.00 25.00 N'
'\t12.16\t11.0\t42.0\t18.98\t-\t0.17\t0.0\t2.00')
def test_gather_features(self):
"""Test gather_features() function"""
def mocked_get_cnc(apo):
residues = {}
for i, res in enumerate(('ALA', 'MET', 'GLU', 'ASN', 'PHE', 'GLN',
'LYS', 'VAL', 'GLU', 'LYS', 'ILE', 'GLY')):
residues[(res, i + 1, 'A')] = 42.
return residues, ('1', '1')
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'pm_XXX.pdb'),
'XXX_mdl.pdb')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdlA.sqc'),
'.')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'XXX_mdlA.hcs'),
'.')
with utils.mocked_object(bmi_feature_parser, 'get_cnc',
mocked_get_cnc):
bmi_feature_parser.gather_features('XXX_mdl', ['A'])
with open('XXX_mdlA.feat') as fh:
data = fh.readlines()
self.assertEqual(len(data), 96)
self.assertEqual(data[0][:116],
'ATOM 1 N ALA A 1 -17.647 -2.542 37.435 '
'1.00 25.00 N'
'\t12.16\t11.0\t42.0\t18.98\t-\t0.17\t0.0\t2.00')
def test_build_model_gaps(self):
"""Test build_model() with gaps"""
import modeller.automodel
def mocked_loopmodel_make(self):
self.loop.outputs.append({
'failure': None,
'name': 'input.pdb',
'Normalized DOPE score': -1.
})
with utils.temporary_working_directory() as tmpdir:
with open('alignment.pir', 'w') as fh:
fh.write(">P1;XXX\n")
fh.write("structureX:input.pdb:1:A:2:A::::\n")
fh.write("A--A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("AAAA*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
fh.write(pdb_line[:25] + '2' + pdb_line[26:] + '\n')
with utils.mocked_object(modeller.automodel.loopmodel, 'make',
mocked_loopmodel_make):
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
def test_main(self):
"""Test complete run of predict"""
indir = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_working_directory():
shutil.copy(os.path.join(indir, 'XXX.features'), '.')
shutil.copy(os.path.join(indir, 'XXX_mdl.pdb'), '.')
with utils.mocked_object(pickle, 'load', mock_pickle_load):
cryptosite.predict.predict('XXX.features', model='final')
os.unlink('XXX.pol.pred')
os.unlink('XXX.pol.pred.pdb')
def test_main(self):
"""Test complete run of predict"""
indir = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(indir, 'XXX.features'), '.')
shutil.copy(os.path.join(indir, 'XXX_mdl.pdb'), '.')
with utils.mocked_object(pickle, 'load', mock_pickle_load):
cryptosite.predict.predict('XXX.features', model='final')
os.unlink('XXX.pol.pred')
os.unlink('XXX.pol.pred.pdb')
def test_get_cnc_pockets(self):
"""Test get_cnc() parsing of pocket information"""
with utils.temporary_working_directory() as tmpdir:
os.mkdir('test_out')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test_out.pdb'),
'test_out')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test_info.txt'),
'test_out')
with utils.mocked_object(subprocess, 'check_call', mock_check_call):
res, num = bmi_feature_parser.get_cnc('test')
self.assertAlmostEqual(res[('ALA', 2, 'A')], 0.0, places=1)
self.assertAlmostEqual(res[('ALA', 1, 'A')], 0.8, places=1)
def test_get_cnc_pockets(self):
"""Test get_cnc() parsing of pocket information"""
with utils.temporary_working_directory() as tmpdir:
os.mkdir('test_out')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test_out.pdb'),
'test_out')
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test_info.txt'),
'test_out')
with utils.mocked_object(subprocess, 'check_call',
mock_check_call):
res, num = bmi_feature_parser.get_cnc('test')
self.assertAlmostEqual(res[('ALA', 2, 'A')], 0.0, places=1)
self.assertAlmostEqual(res[('ALA', 1, 'A')], 0.8, places=1)
def test_parse_blast(self):
"""Test parse_blast() function"""
blast_out = os.path.join(TOPDIR, 'test', 'input', 'XXXA.blast')
with utils.temporary_working_directory() as tmpdir:
with utils.mocked_object(cryptosite.seq_conservation, 'ucluster',
mock_ucluster):
# Should get a ValueError if the sequences don't match
self.assertRaises(ValueError,
cryptosite.seq_conservation.parse_blast,
blast_out, 'XXX', 'CC')
cryptosite.seq_conservation.parse_blast(blast_out, 'XXX',
'AMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL')
os.unlink('XXX.ali')
os.unlink('XXX.sqc')
def test_soap_module(self):
"""Test soap script as a module"""
with utils.temporary_working_directory() as tmpdir:
for pdb in ('test.pdb', 'pm.pdb0.pdb', 'pm.pdb1.pdb',
'pm.pdb2.pdb', 'pm.pdb.B10010002.pdb'):
fname = os.path.join(tmpdir, pdb)
with open(fname, 'w') as fh:
fh.write("""
ATOM 1 N CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
""")
with utils.mocked_object(soap_protein_od, 'Scorer', MockScorer):
cryptosite.soap.soap_score()
with open('SnapList.txt') as fh:
data = fh.readlines()
# don't know glob order
self.assertEqual(len(data), 2)
self.assertTrue(re.match('pm\.pdb\d\.pdb\t10\.0', data[0]))
self.assertTrue(re.match('pm\.pdb\d\.pdb\t20\.0', data[1]))
def test_soap_module(self):
"""Test soap script as a module"""
with utils.temporary_working_directory() as tmpdir:
for pdb in ('test.pdb', 'pm.pdb0.pdb', 'pm.pdb1.pdb',
'pm.pdb2.pdb', 'pm.pdb.B10010002.pdb'):
fname = os.path.join(tmpdir, pdb)
with open(fname, 'w') as fh:
fh.write("""
ATOM 1 N CYS A 1 18.511 -1.416 15.632 1.00 6.84 C
""")
with utils.mocked_object(soap_protein_od, 'Scorer', MockScorer):
cryptosite.soap.soap_score()
with open('SnapList.txt') as fh:
data = fh.readlines()
# don't know glob order
self.assertEqual(len(data), 2)
self.assertTrue(re.match('pm\.pdb\d\.pdb\t10\.0', data[0]))
self.assertTrue(re.match('pm\.pdb\d\.pdb\t20\.0', data[1]))
def test_build_model_gaps(self):
"""Test build_model() with gaps"""
import modeller.automodel
def mocked_loopmodel_make(self):
self.loop.outputs.append({'failure':None, 'name':'input.pdb',
'Normalized DOPE score':-1.})
with utils.temporary_working_directory() as tmpdir:
with open('alignment.pir', 'w') as fh:
fh.write(">P1;XXX\n")
fh.write("structureX:input.pdb:1:A:2:A::::\n")
fh.write("A--A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("AAAA*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
fh.write(pdb_line[:25] + '2' + pdb_line[26:] + '\n')
with utils.mocked_object(modeller.automodel.loopmodel, 'make',
mocked_loopmodel_make):
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
def test_run_blast(self):
"""Test run_blast() function"""
with utils.mocked_object(subprocess, 'check_call', mock_check_call):
cryptosite.seq_conservation.run_blast('test')
