class LigChargeTester(unittest.TestCase):
"""
Test ELF10 charge cube
"""
def setUp(self):
self.cube = ParallelLigandChargeCube('elf10charge')
self.cube.args.max_conforms = 800
self.runner = CubeTestRunner(self.cube)
self.runner.start()
@pytest.mark.travis
@pytest.mark.local
def test_success(self):
print('Testing cube:', self.cube.name)
# File name of a charged ligand
lig_fname = os.path.join(FILE_DIR, "lig_CAT13a_chg.oeb.gz")
# Read OEMol molecule
ligand = oechem.OEMol()
with oechem.oemolistream(lig_fname) as ifs:
oechem.OEReadMolecule(ifs, ligand)
ligand_copy = ligand.CreateCopy()
# Set the partial charge to zero
for at in ligand_copy.GetAtoms():
at.SetPartialCharge(0.0)
ligand_record = OERecord()
ligand_record.set_value(Fields.primary_molecule, ligand_copy)
ligand_record.set_value(Fields.flaskid, 0)
ligand_record.set_value(Fields.title, ligand_copy.GetTitle())
# Process the molecules
self.cube.process(ligand_record, self.cube.intake.name)
# Assert that one molecule was emitted on the success port
self.assertEqual(self.runner.outputs['success'].qsize(), 1)
# Assert that zero molecules were emitted on the failure port
self.assertEqual(self.runner.outputs['failure'].qsize(), 0)
# Check out ligand
out_record = self.runner.outputs["success"].get()
out_ligand = out_record.get_value(Fields.primary_molecule)
# Loop through atoms and make sure partial charges were set
for iat, oat in zip(ligand.GetAtoms(), out_ligand.GetAtoms()):
self.assertNotEqual(iat.GetPartialCharge(), oat.GetPartialCharge)
job.classification = [['Molecular Dynamics']]
# job.uuid = "372e1890-d053-4027-970a-85b209e4676f"
job.tags = [tag for lists in job.classification for tag in lists]
# Ligand setting
iligs = DatasetReaderCube("LigandReader", title="Ligand Reader")
iligs.promote_parameter("data_in",
promoted_name="ligands",
title="Ligand Input Dataset",
description="Ligand Dataset")
ligset = LigandSetting("LigandSetting", title="Ligand Setting")
ligset.set_parameters(lig_res_name='LIG')
chargelig = ParallelLigandChargeCube("LigCharge", title="Ligand Charge")
chargelig.promote_parameter('charge_ligands',
promoted_name='charge_ligands',
description="Charge the ligand or not",
default=True)
ligid = IDSettingCube("Ligand Ids")
# Protein Reading cube. The protein prefix parameter is used to select a name for the
# output system files
iprot = DatasetReaderCube("ProteinReader", title="Protein Reader")
iprot.promote_parameter("data_in",
promoted_name="protein",
title='Protein Input Dataset',
description="Protein Dataset")
def setUp(self):
self.cube = ParallelLigandChargeCube('elf10charge')
self.cube.args.max_conforms = 800
self.runner = CubeTestRunner(self.cube)
self.runner.start()