class ComplexPrepTester(unittest.TestCase):
"""
Test the Complex Preparation cube
Example inputs from `openmm_orion/examples/data`
"""
def setUp(self):
self.cube = ComplexPrep('ComplexPrep')
self.runner = CubeTestRunner(self.cube)
self.runner.start()
def test_success(self):
print('Testing cube:', self.cube.name)
# File name
fn_protein = ommutils.get_data_filename('examples',
'data/Bace_solvated.oeb.gz')
fn_ligand = ommutils.get_data_filename('examples',
'data/lig_CAT13a_chg.oeb.gz')
# Read Protein molecule
protein = oechem.OEMol()
with oechem.oemolistream(fn_protein) as ifs:
oechem.OEReadMolecule(ifs, protein)
# Read Ligand molecule
ligand = oechem.OEMol()
with oechem.oemolistream(fn_ligand) as ifs:
oechem.OEReadMolecule(ifs, ligand)
# Process the molecules
self.cube.process(protein, self.cube.intake.name)
# Why do I have to manually set these on?
self.cube.check_system = True
self.cube.system = protein
self.cube.process(ligand, self.cube.system_port)
# 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)
complex = self.runner.outputs["success"].get()
self.assertEquals(complex.GetMaxAtomIdx(), 52312)
def tearDown(self):
self.runner.finalize()
def test_failure(self):
pass
def setUp(self):
self.cube = ComplexPrep('ComplexPrep')
self.runner = CubeTestRunner(self.cube)
self.runner.start()
# 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',
description="Protein Prefix")
splitter = Splitter("Splitter")
solvate = SolvationCube("Solvation")
# Complex Setting
complx = ComplexPrep("Complex")
ff = ForceFieldPrep("ForceField")
ofs = OEMolOStreamCube('ofs', title='OFS-Success')
ofs.set_parameters(backend='s3')
fail = OEMolOStreamCube('fail', title='OFS-Failure')
fail.set_parameters(backend='s3')
fail.set_parameters(data_out='fail.oeb.gz')
job.add_cubes(iprot, splitter, solvate, iligs, chargelig, complx, ff, ofs,
fail)
iprot.success.connect(splitter.intake)
splitter.success.connect(solvate.intake)
solvate.success.connect(complx.system_port)