def test_run_dock(self):
orig_dir = os.getcwd()
temp_dir = tempfile.mkdtemp()
temp_dir_abs = os.path.abspath(temp_dir)
prot_sci_prep_dir = os.path.join(temp_dir, 'prot_sci_prep_dir')
lig_sci_prep_dir = os.path.join(temp_dir, 'lig_sci_prep_dir')
dock_dir = os.path.join(temp_dir, 'dock_dir')
try:
os.mkdir(prot_sci_prep_dir)
sample_prot_dir = os.path.join(prot_sci_prep_dir, '1fcz')
os.mkdir(sample_prot_dir)
sample_prot_file = os.path.join(
sample_prot_dir, 'hiResHolo-1fcz_1fcy_prepared.pdb')
with open(sample_prot_file, 'wb') as of:
of.write('test')
sample_center_file = os.path.join(sample_prot_dir, 'center.txt')
with open(sample_center_file, 'wb') as of:
of.write('1,2,3')
sample_cand_targinfo_file = os.path.join(sample_prot_dir,
'1fcz.txt')
with open(sample_cand_targinfo_file, 'wb') as of:
of.write('query, 1fcz')
os.mkdir(lig_sci_prep_dir)
sample_lig_dir = os.path.join(lig_sci_prep_dir, '1fcz')
os.mkdir(sample_lig_dir)
sample_lig_file = os.path.join(sample_lig_dir,
'lig_156_prepared.sdf')
with open(sample_lig_file, 'wb') as of:
of.write('test')
sample_lig_targinfo_file = os.path.join(sample_lig_dir, '1fcz.txt')
with open(sample_lig_targinfo_file, 'wb') as of:
of.write('query, 1fcz')
os.mkdir(dock_dir)
d = Dock()
d.run_dock(prot_sci_prep_dir, lig_sci_prep_dir, dock_dir)
dock_targ_dir = os.path.join(dock_dir, '1fcz')
self.assertEqual(os.path.isdir(dock_targ_dir), True)
dock_cand_prep_dir = os.path.join(dock_targ_dir,
'hiResHolo_1fcy_tech_prep')
self.assertEqual(os.path.isdir(dock_cand_prep_dir), True)
dock_lig_prep_dir = os.path.join(dock_targ_dir,
'lig_156_tech_prep')
self.assertEqual(os.path.isdir(dock_lig_prep_dir), True)
dock_cand_dock_dir = os.path.join(dock_targ_dir,
'hiResHolo_1fcy_docking')
self.assertEqual(os.path.isdir(dock_cand_dock_dir), True)
dock_lig_file = os.path.join(dock_cand_dock_dir,
'lig_156_prepared.sdf')
self.assertEqual(os.path.exists(dock_lig_file), True)
dock_cand_file = os.path.join(dock_cand_dock_dir,
'hiResHolo-1fcz_1fcy_prepared.pdb')
self.assertEqual(os.path.exists(dock_cand_file), True)
finally:
os.chdir(orig_dir)
shutil.rmtree(temp_dir_abs)
def test_parse_cand_name(self):
d = Dock()
# Blank name
self.assertEqual(d.parse_cand_name(''), False)
# Good name
candfile = os.path.join(
'some_directory',
'hiResHolo-1fcz_1fcy' + d.SCI_PREPPED_PROT_SUFFIX)
self.assertEqual(d.parse_cand_name(candfile),
('hiResHolo', '1fcz', '1fcy'))
# Good name, but in list
self.assertEqual(d.parse_cand_name([candfile]), False)
# Wrong suffix
candfile = os.path.join('some_directory',
'hiResHolo-1fcz_1fcy_prepared.xxx')
self.assertEqual(d.parse_cand_name(candfile), False)
# Change to be right suffix
d.SCI_PREPPED_PROT_SUFFIX = '_prepared.xxx'
self.assertEqual(d.parse_cand_name(candfile),
('hiResHolo', '1fcz', '1fcy'))
def test_parse_lig_filename(self):
d = Dock()
# Blank name
self.assertEqual(d.parse_lig_filename(''), False)
# Good name
ligfile = os.path.join('some_directory',
'lig_TST' + d.SCI_PREPPED_LIG_SUFFIX)
self.assertEqual(d.parse_lig_filename(ligfile), 'TST')
# Good name, but in list
self.assertEqual(d.parse_lig_filename([ligfile]), False)
# Wrong suffix
ligfile = os.path.join('some_directory', 'lig_TST_prepared.xxx')
self.assertEqual(d.parse_lig_filename(ligfile), False)
# Change expected suffix to "_prepared.xxx"
d.SCI_PREPPED_LIG_SUFFIX = '_prepared.xxx'
self.assertEqual(d.parse_lig_filename(ligfile), 'TST')
def test_get_sci_prepped_lig(self):
# test where file does not exist
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
self.assertEqual(
d.get_sci_prepped_lig(temp_dir, d.SCI_PREPPED_LIG_SUFFIX),
False)
finally:
shutil.rmtree(temp_dir)
# Test where correct file exists
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
ligfile = os.path.join(temp_dir,
'lig_TST' + d.SCI_PREPPED_LIG_SUFFIX)
f = open(ligfile, 'w')
f.write(
'There is no test to ensure the contents are valid. This string should pass though.'
)
f.flush()
f.close()
self.assertEqual(
d.get_sci_prepped_lig(temp_dir, d.SCI_PREPPED_LIG_SUFFIX),
ligfile)
finally:
shutil.rmtree(temp_dir)
# Test where file has wrong suffix
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
ligfile = os.path.join(temp_dir, 'lig_TST_prepared.xxx')
f = open(ligfile, 'w')
f.write(
'There is no test to ensure the contents are valid. This string should pass though.'
)
f.flush()
f.close()
self.assertEqual(
d.get_sci_prepped_lig(temp_dir, d.SCI_PREPPED_LIG_SUFFIX),
False)
finally:
shutil.rmtree(temp_dir)
# Test where multiple correct files exist
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
ligfile = os.path.join(temp_dir,
'lig_TST' + d.SCI_PREPPED_LIG_SUFFIX)
f = open(ligfile, 'w')
f.write(
'There is no test to ensure the contents are valid. This string should pass though.'
)
f.flush()
f.close()
ligfile = os.path.join(temp_dir,
'lig_TS2' + d.SCI_PREPPED_LIG_SUFFIX)
f = open(ligfile, 'w')
f.write(
'There is no test to ensure the contents are valid. This string should pass though.'
)
f.flush()
f.close()
self.assertEqual(
d.get_sci_prepped_lig(temp_dir, d.SCI_PREPPED_LIG_SUFFIX),
False)
finally:
shutil.rmtree(temp_dir)
def test_get_pocket_center(self):
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
# test where file does not exist
self.assertEqual(d.get_pocket_center(temp_dir), False)
finally:
shutil.rmtree(temp_dir)
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
# test with valid center.txt file
pcfile = os.path.join(temp_dir, 'center.txt')
f = open(pcfile, 'w')
f.write('1,2')
f.flush()
f.close()
self.assertEqual(d.get_pocket_center(temp_dir), False)
finally:
shutil.rmtree(temp_dir)
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
# test where file does not exist
self.assertEqual(d.get_pocket_center(temp_dir), False)
pcfile = os.path.join(temp_dir, 'center.txt')
f = open(pcfile, 'w')
f.write('1,2,3')
f.flush()
f.close()
self.assertEqual(d.get_pocket_center(temp_dir), [1.0, 2.0, 3.0])
finally:
shutil.rmtree(temp_dir)
temp_dir = tempfile.mkdtemp()
try:
d = Dock()
# test where file does not exist
self.assertEqual(d.get_pocket_center(temp_dir), False)
pcfile = os.path.join(temp_dir, 'center.txt')
f = open(pcfile, 'w')
f.write('a,b,c')
f.flush()
f.close()
self.assertEqual(d.get_pocket_center(temp_dir), False)
finally:
shutil.rmtree(temp_dir)
def test_receptor_technical_prep(self):
"""Test where we run receptor_technical_prep() with fake arguments
to verify we always get back the 1st argument as an array
"""
d = Dock()
self.assertEqual(d.receptor_technical_prep('hi', 'foo'), ['hi'])
def test_ligand_technical_prep(self):
"""Test where we run ligand_technical_prep() with fake argument
to verify we always get back the argument as an array
"""
d = Dock()
self.assertEqual(d.ligand_technical_prep('hi'), ['hi'])
def test_dock(self):
"""Test where we run dock() with fake arguments
to verify we always get False
"""
d = Dock()
self.assertEqual(d.dock(1, 2, 3, 4), False)
def __init__(self, gnina_args=''):
self.args = gnina_args
Dock.__init__(self)