def test_get_sas(self):
"""Test get_sas() function"""
with utils.temporary_working_directory():
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'),
'1abc.pdb')
out = cryptosite.am_bmi.get_sas('1abc', 1.4)
self.assertEqual(len(out), 60)
def test_read_ligand_data(self):
"""Test read_ligand_data() function"""
with utils.temporary_working_directory() as tmpdir:
cryptosite.patch_mapper.make_ligand_file('ligands.ids')
xyz, ligands = cryptosite.patch_mapper.read_ligand_data()
self.assertEqual(len(xyz), 16)
self.assertEqual(len(ligands), 16)
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_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_read_ligand_data(self):
"""Test read_ligand_data() function"""
with utils.temporary_working_directory():
cryptosite.patch_mapper.make_ligand_file('ligands.ids')
xyz, ligands = cryptosite.patch_mapper.read_ligand_data()
self.assertEqual(len(xyz), 16)
self.assertEqual(len(ligands), 16)
def test_get_sas(self):
"""Test get_sas() function"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'),
'1abc.pdb')
out = cryptosite.am_bmi.get_sas('1abc', 1.4)
self.assertEqual(len(out), 60)
def test_get_cnc(self):
"""Test get_cnc() function"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'),
'1abc.pdb')
res, num = bmi_feature_parser.get_cnc('1abc')
self.assertEqual(len(res), 8)
self.assertEqual(num, ('1', '1'))
def test_get_cnc(self):
"""Test get_cnc() function"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'),
'1abc.pdb')
res, num = bmi_feature_parser.get_cnc('1abc')
self.assertEqual(len(res), 8)
self.assertEqual(num, ('1', '1'))
def test_extract_chains(self):
"""Test extract_chains()"""
fname = os.path.join(TOPDIR, 'test', 'input', 'test.pdb')
with utils.temporary_working_directory() as tmpdir:
tmp_pdb = os.path.join(tmpdir, 'test.pdb')
shutil.copy(fname, tmp_pdb)
chains = cryptosite.setup.extract_chains(tmp_pdb, ['B', 'A'])
self.assertEqual(chains, ['A', 'B'])
def test_patchmap_feature(self):
"""Test patchmap_feature() function"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'), '.')
with mock_patch_dock_lig_score():
cryptosite.patch_mapper.patchmap_feature('test')
with open('test.pdb.ptm') as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 8)
def test_patchmap_feature(self):
"""Test patchmap_feature() function"""
with utils.temporary_working_directory():
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'), '.')
with mock_patch_dock_lig_score():
cryptosite.patch_mapper.patchmap_feature('test')
with open('test.pdb.ptm') as fh:
contents = fh.readlines()
self.assertEqual(len(contents), 8)
def test_process_directory(self):
"""Test process_directory() function"""
indir = os.path.join(TOPDIR, 'test', 'input', 'gather-inputs')
inputs = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(inputs, 'XXX_mdl.bmiftr'), '.')
cryptosite.gather.process_directory(indir)
os.unlink('XXX.features')
os.unlink('XXX.am')
def test_extract_chains_missing(self):
"""Test extract_chains() with missing chains"""
fname = os.path.join(TOPDIR, 'test', 'input', 'test.pdb')
with utils.temporary_working_directory() as tmpdir:
tmp_pdb = os.path.join(tmpdir, 'test.pdb')
shutil.copy(fname, tmp_pdb)
self.assertRaises(cryptosite.setup.MissingChainsError,
cryptosite.setup.extract_chains, tmp_pdb,
['A', 'C', 'D'])
def test_process_directory(self):
"""Test process_directory() function"""
indir = os.path.join(TOPDIR, 'test', 'input', 'gather-inputs')
inputs = os.path.join(TOPDIR, 'test', 'input')
with utils.temporary_working_directory():
shutil.copy(os.path.join(inputs, 'XXX_mdl.bmiftr'), '.')
cryptosite.gather.process_directory(indir)
os.unlink('XXX.features')
os.unlink('XXX.am')
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_main(self):
"""Test simple complete run of am_bmi"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input',
'pm.pdb.B10010001.pdb'), '.')
with open('SnapList.txt', 'w') as fh:
fh.write("pm.pdb.B10010001.pdb -100.0\n")
fh.write("high-energy.pdb -10.0\n")
subprocess.check_call(['cryptosite', 'am_bmi'])
with open('am_features.out') as fh:
lines = sorted(fh.readlines())
self.assertEqual(len(lines), 12)
self.assertEqual(lines[0], 'ALA\t1\tA\t17.328\t12.02\t32.6\t48.0\n')
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_main(self):
"""Test simple complete run of am_bmi"""
with utils.temporary_working_directory():
shutil.copy(
os.path.join(TOPDIR, 'test', 'input', 'pm.pdb.B10010001.pdb'),
'.')
with open('SnapList.txt', 'w') as fh:
fh.write("pm.pdb.B10010001.pdb -100.0\n")
fh.write("high-energy.pdb -10.0\n")
subprocess.check_call(['cryptosite', 'am_bmi'])
with open('am_features.out') as fh:
lines = sorted(fh.readlines())
self.assertEqual(len(lines), 12)
self.assertEqual(lines[0], 'ALA\t1\tA\t17.328\t12.02\t32.6\t48.0\n')
def test_build_model_no_gaps(self):
"""Test build_model() with no gaps"""
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:1:A::::\n")
fh.write("A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("A*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
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_build_model_no_gaps(self):
"""Test build_model() with no gaps"""
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:1:A::::\n")
fh.write("A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("A*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
def test_res_parser(self):
"""Test res_parser() function"""
with utils.temporary_working_directory():
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'pm_XXX.pdb'),
'XXX_mdl.pdb')
for inp in ('XXX_mdlA.feat', 'XXX_mdlA.sqc', 'XXX_mdl.sas',
'XXX_mdl.pdb.ptm'):
shutil.copy(os.path.join(TOPDIR, 'test', 'input', inp), '.')
res_parser_bmi.res_parser('XXX_mdl')
with open('XXX_mdl.bmiftr') as fh:
data = sorted(fh.readlines())
self.assertEqual(len(data), 3)
self.assertEqual(
data[1][:50], 'XXX_mdl\tALA\t1\tA\t2.298\t106.4\t-10.77\t0.0\t'
'U\t0.17\t0.0\t')
def test_main(self):
"""Test simple complete run of pockets"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(
os.path.join(TOPDIR, 'test', 'input', 'pm.pdb.B10010001.pdb'),
'.')
with open('SnapList.txt', 'w') as fh:
fh.write("pm.pdb.B10010001.pdb -100.0\n")
fh.write("high-energy.pdb -10.0\n")
subprocess.check_call(['cryptosite', 'pockets'])
with open('pockets.out') as fh:
lines = fh.readlines()
self.assertEqual(len(lines), 13)
self.assertEqual(lines[1], 'ALA\t1\tA\t0.0\n')
self.assertEqual(lines[2], 'MET\t2\tA\t0.092\n')
def test_res_parser(self):
"""Test res_parser() function"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'pm_XXX.pdb'),
'XXX_mdl.pdb')
for inp in ('XXX_mdlA.feat', 'XXX_mdlA.sqc', 'XXX_mdl.sas',
'XXX_mdl.pdb.ptm'):
shutil.copy(os.path.join(TOPDIR, 'test', 'input', inp), '.')
res_parser_bmi.res_parser('XXX_mdl')
with open('XXX_mdl.bmiftr') as fh:
data = sorted(fh.readlines())
self.assertEqual(len(data), 3)
self.assertEqual(data[1][:50],
'XXX_mdl\tALA\t1\tA\t2.298\t106.4\t-10.77\t0.0\t'
'U\t0.17\t0.0\t')
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_HydChrSSE(self):
"""Test HydChrSSE() function"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'),
'1abc.pdb')
hyd_chr_sse.HydChrSSE('1abc', 'A')
with open('1ab_mdlA.hcs') as fh:
data = fh.read()
self.assertEqual(
data, """ 1 \tA\t-\t0.17\t0
2 \tY\t-\t-0.94\t0
3 \tV\t-\t0.07\t0
4 \tI\t-\t-0.31\t0
5 \tT\t-\t0.14\t0
6 \tE\tS\t2.02\t-1
7 \tP\tT\t0.45\t0
8 \tC\tT\t-0.24\t0
9 \tI\t-\t-0.31\t0
""")
def test_HydChrSSE(self):
"""Test HydChrSSE() function"""
with utils.temporary_working_directory() as tmpdir:
shutil.copy(os.path.join(TOPDIR, 'test', 'input', 'test.pdb'),
'1abc.pdb')
hyd_chr_sse.HydChrSSE('1abc', 'A')
with open('1ab_mdlA.hcs') as fh:
data = fh.read()
self.assertEqual(data,
""" 1 \tA\t-\t0.17\t0
2 \tY\t-\t-0.94\t0
3 \tV\t-\t0.07\t0
4 \tI\t-\t-0.31\t0
5 \tT\t-\t0.14\t0
6 \tE\tS\t2.02\t-1
7 \tP\tT\t0.45\t0
8 \tC\tT\t-0.24\t0
9 \tI\t-\t-0.31\t0
""")
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 of complete run of setup"""
with utils.temporary_working_directory() as tmpdir:
fname = os.path.join(TOPDIR, 'test', 'input', 'test.pdb')
with utils.mocked_objects([
(cryptosite.cleaning, 'muscleAlign', mock_muscle_align),
(cryptosite.seq_conservation, 'run_blast', mock_run_blast),
(cryptosite.seq_conservation, 'parse_blast', mock_parse_blast),
(cryptosite.cleaning, 'build_model', mock_build_model),
(cryptosite.hyd_chr_sse, 'HydChrSSE', mock_HydChrSSE),
(cryptosite.patch_mapper, 'patchmap_feature',
mock_patchmap_feature),
(cryptosite.bmi_feature_parser, 'gather_features',
mock_gather_features),
(cryptosite.res_parser_bmi, 'res_parser', mock_res_parser)
]):
cryptosite.setup.setup(fname, ['A'], short=True)
# Verify that AllosMod inputs were created
os.unlink('XXX/align.ali')
os.unlink('XXX/XXX.pdb')
os.unlink('XXX/input.dat')
os.unlink('XXX/list')
def test_main(self):
"""Test of complete run of setup"""
with utils.temporary_working_directory() as tmpdir:
fname = os.path.join(TOPDIR, 'test', 'input', 'test.pdb')
with utils.mocked_objects(
[(cryptosite.cleaning, 'muscleAlign', mock_muscle_align),
(cryptosite.seq_conservation, 'run_blast', mock_run_blast),
(cryptosite.seq_conservation, 'parse_blast',
mock_parse_blast),
(cryptosite.cleaning, 'build_model', mock_build_model),
(cryptosite.hyd_chr_sse, 'HydChrSSE', mock_HydChrSSE),
(cryptosite.patch_mapper, 'patchmap_feature',
mock_patchmap_feature),
(cryptosite.bmi_feature_parser, 'gather_features',
mock_gather_features),
(cryptosite.res_parser_bmi, 'res_parser',
mock_res_parser)]):
cryptosite.setup.setup(fname, ['A'], short=True)
# Verify that AllosMod inputs were created
os.unlink('XXX/align.ali')
os.unlink('XXX/XXX.pdb')
os.unlink('XXX/input.dat')
os.unlink('XXX/list')
def test_ucluster(self):
"""Test ucluster() function"""
with utils.temporary_working_directory():
with mock_usearch():
clusters = cryptosite.seq_conservation.ucluster('dummy.ali')
self.assertEqual(len(clusters), 4)
