class LigChargeTester(unittest.TestCase):
"""
Test ELF10 charge cube
Example inputs from `openmm_orion/examples/data`
"""
def setUp(self):
self.cube = LigChargeCube('elf10charge')
self.cube.args.max_conforms = 800
self.runner = CubeTestRunner(self.cube)
self.runner.start()
def test_success(self):
print('Testing cube:', self.cube.name)
# File name of a charged ligand
lig_fname = utils.get_data_filename('examples', 'data/lig_CAT13a_chg.oeb.gz')
# Read OEMol molecule
mol = oechem.OEMol()
ifs = oechem.oemolistream(lig_fname)
if not oechem.OEReadMolecule(ifs, mol):
raise Exception('Cannot read molecule from %s' % lig_fname)
ifs.close()
mol_copy = mol.CreateCopy()
# Set the partial charge to zero
for at in mol_copy.GetAtoms():
at.SetPartialCharge(0.0)
# Process the molecules
self.cube.process(mol_copy, 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 outmol
outmol = self.runner.outputs["success"].get()
# Loop through atoms and make sure partial charges were set
for iat, oat in zip(mol.GetAtoms(), outmol.GetAtoms()):
self.assertNotEqual(iat.GetPartialCharge(), oat.GetPartialCharge)
def test_failure(self):
pass
def tearDown(self):
self.runner.finalize()
Outputs:
--------
ofs: Output file
"""
job.classification = [['Simulation']]
job.tags = [tag for lists in job.classification for tag in lists]
# Ligand setting
iligs = OEMolIStreamCube("Ligands", title="Ligand Reader")
iligs.promote_parameter("data_in",
promoted_name="ligands",
title="Ligand Input File",
description="Ligand file name")
chargelig = LigChargeCube("LigCharge")
chargelig.promote_parameter(
'max_conformers',
promoted_name='max_conformers',
description="Set the max number of conformers per ligand",
default=800)
# Protein Setting
iprot = ProteinReader("ProteinReader")
iprot.promote_parameter("data_in",
promoted_name="protein",
title="Protein Input File",
description="Protein file name")
iprot.promote_parameter("protein_prefix",
promoted_name="protein_prefix",
default='PRT',
def setUp(self):
self.cube = LigChargeCube('elf10charge')
self.cube.args.max_conforms = 800
self.runner = CubeTestRunner(self.cube)
self.runner.start()