def setUp(self):
self.cube = ForceFieldPrep('ForceFieldPrep')
self.runner = CubeTestRunner(self.cube)
self.runner.start()
class ForceFieldPrepTester(unittest.TestCase):
"""
Test the Complex Preparation cube
Example inputs from `openmm_orion/examples/data`
"""
def setUp(self):
self.cube = ForceFieldPrep('ForceFieldPrep')
self.runner = CubeTestRunner(self.cube)
self.runner.start()
def test_excipient_successGaff2(self):
print('Testing cube:', self.cube.name)
# File name
fn_complex = ommutils.get_data_filename(
'examples', 'data/pbace_lcat13a_solvated_complex.oeb.gz')
# Read Protein molecule
complex = oechem.OEMol()
with oechem.oemolistream(fn_complex) as ifs:
oechem.OEReadMolecule(ifs, complex)
# Selecting ligand and excipient parametrization
self.cube.args.ligand_forcefield = 'GAFF2'
self.cube.args.other_forcefield = 'GAFF2'
# Process the molecules
self.cube.process(complex, 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)
complex = self.runner.outputs["success"].get()
def test_excipient_successSmirnoff(self):
print('Testing cube:', self.cube.name)
# File name
fn_complex = ommutils.get_data_filename(
'examples', 'data/pbace_lcat13a_solvated_complex.oeb.gz')
# Read Protein molecule
complex = oechem.OEMol()
with oechem.oemolistream(fn_complex) as ifs:
oechem.OEReadMolecule(ifs, complex)
# Selecting ligand and excipient parametrization
self.cube.args.ligand_forcefield = 'SMIRNOFF'
self.cube.args.other_forcefield = 'SMIRNOFF'
# Process the molecules
self.cube.process(complex, 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)
#complex = self.runner.outputs["success"].get()
def test_protein_non_std_residue(self):
print('Testing cube:', self.cube.name)
# File name
fn_complex = ommutils.get_data_filename(
'examples', 'data/pCDK2_l1h1q_solvated_complex.oeb.gz')
# Read Protein molecule
complex = oechem.OEMol()
with oechem.oemolistream(fn_complex) as ifs:
oechem.OEReadMolecule(ifs, complex)
# Process the molecules
self.cube.process(complex, 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)
def tearDown(self):
self.runner.finalize()
def test_failure(self):
pass
default=1.25,
description="Solution density in g/ml")
solvate.promote_parameter(
'close_solvent',
promoted_name='close_solvent',
default=True,
description='The solvent molecules will be placed very close to the solute'
)
solvate.promote_parameter(
'salt_concentration',
promoted_name='salt_concentration',
default=50.0,
description='Salt concentration (Na+, Cl-) in millimolar')
# Force Field Application
ff = ForceFieldPrep("ForceField")
ff.promote_parameter('protein_forcefield',
promoted_name='protein_ff',
default='amber99sbildn.xml')
ff.promote_parameter('solvent_forcefield',
promoted_name='solvent_ff',
default='tip3p.xml')
ff.promote_parameter('ligand_forcefield',
promoted_name='ligand_ff',
default='GAFF2')
ff.promote_parameter('other_forcefield',
promoted_name='other_ff',
default='GAFF2')
# Output the prepared systems
complex_prep_ofs = OEMolOStreamCube('complex_prep_ofs',
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)
iligs.success.connect(chargelig.intake)
description="Protein file name")
iprot.promote_parameter("protein_prefix",
promoted_name="protein_prefix",
default='PRT',
description="Protein prefix")
# COMPLEX SETTING
# Complex cube used to assemble the ligands and the solvated protein
complx = ComplexPrep("Complex")
# The solvation cube is used to solvate the system and define the ionic strength of the solution
solvateComplex = HydrationCube("HydrationComplex", title="HydrationComplex")
# Complex Force Field Application
ffComplex = ForceFieldPrep("ForceFieldComplex", title="ForceFieldComplex")
ffComplex.promote_parameter('protein_forcefield',
promoted_name='protein_ff',
default='amber99sbildn.xml')
ffComplex.promote_parameter('solvent_forcefield',
promoted_name='solvent_ff',
default='tip3p.xml')
ffComplex.promote_parameter('ligand_forcefield',
promoted_name='ligand_ff',
default='GAFF2')
ffComplex.promote_parameter('other_forcefield',
promoted_name='other_ff',
default='GAFF2')
# Minimization
minComplex = OpenMMminimizeCube('minComplex', title='MinimizeComplex')