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 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_success(self):
print('Testing cube:', self.cube.name)
# File name
fname = ommutils.get_data_filename('examples', 'data/Bace_protein.pdb')
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(fname) as ifs:
oechem.OEReadMolecule(ifs, mol)
# Process the molecules
self.cube.process(mol, 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)
outmol = self.runner.outputs["success"].get()
prot, lig, wat, other = utils.split(outmol)
npa = prot.GetMaxAtomIdx()
nla = lig.GetMaxAtomIdx()
noa = other.GetMaxAtomIdx()
nwa = wat.GetMaxAtomIdx()
self.assertEquals(npa, 6044)
self.assertEquals(nla, 0)
# Ions added to excipients
self.assertEquals(noa, 80)
# Water molecules added
self.assertEquals(nwa, 46152)
# Check Box vectors
box_vectors = outmol.GetData('box_vectors')
box_vectors = ommutils.PackageOEMol.decodePyObj(box_vectors)
box_vectors = box_vectors.in_units_of(unit.nanometers)
self.assertAlmostEqual(box_vectors[0][0] / unit.nanometers,
8.23,
delta=0.01)
self.assertEqual(box_vectors[0][1] / unit.nanometers, 0.0)
self.assertEqual(box_vectors[0][2] / unit.nanometers, 0.0)
self.assertAlmostEqual(box_vectors[1][1] / unit.nanometers,
8.23,
delta=0.01)
self.assertEqual(box_vectors[1][0] / unit.nanometers, 0.0)
self.assertEqual(box_vectors[1][2] / unit.nanometers, 0.0)
self.assertAlmostEqual(box_vectors[2][2] / unit.nanometers,
8.23,
delta=0.01)
self.assertEqual(box_vectors[2][0] / unit.nanometers, 0.0)
self.assertEqual(box_vectors[2][1] / unit.nanometers, 0.0)
def test_openmmTop_to_oemol(self):
protein = ommutils.get_data_filename('examples', 'data/T4-protein.pdb')
pdb = app.PDBFile(protein)
oe_mol = oeommtools.openmmTop_to_oemol(pdb.topology, pdb.positions)
# Assert
self.assertEqual(pdb.topology.getNumAtoms(), oe_mol.NumAtoms())
for (op_at, oe_at) in zip(pdb.topology.atoms(), oe_mol.GetAtoms()):
self.assertEqual(op_at.index, oe_at.GetIdx())
oe_pos = [v for k, v in oe_mol.GetCoords().items()]
np.testing.assert_almost_equal(
pdb.getPositions(asNumpy=True).in_units_of(unit.angstrom) /
unit.angstrom,
np.array(oe_pos),
decimal=2)
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 test_oemol_to_openmmTop(self):
protein = ommutils.get_data_filename('examples', 'data/T4-protein.pdb')
mol = oechem.OEMol()
ifs = oechem.oemolistream(protein)
oechem.OEReadMolecule(ifs, mol)
top, omm_pos = oeommtools.oemol_to_openmmTop(mol)
# Assert Atom numbers
self.assertEqual(top.getNumAtoms(), mol.NumAtoms())
for (op_at, oe_at) in zip(top.atoms(), mol.GetAtoms()):
# Assert atom indexes
self.assertEqual(op_at.index, oe_at.GetIdx())
oe_pos = [v for k, v in mol.GetCoords().items()]
# Assert atom positions
self.assertEqual(oe_pos,
omm_pos.in_units_of(unit.angstrom) / unit.angstrom)
# Assert bond order
dic_bond_openmm = {}
for bond in top.bonds():
# OpenMM atoms
at0_idx = bond[0].index
at1_idx = bond[1].index
if at0_idx < at1_idx:
dic_bond_openmm[(at0_idx, at1_idx)] = bond.order
else:
dic_bond_openmm[(at1_idx, at0_idx)] = bond.order
dic_bond_oe = {}
for bond in mol.GetBonds():
# OE atoms
at0_idx = bond.GetBgnIdx()
at1_idx = bond.GetEndIdx()
if at0_idx < at1_idx:
dic_bond_oe[(at0_idx, at1_idx)] = bond.GetOrder()
else:
dic_bond_oe[(at1_idx, at0_idx)] = bond.GetOrder()
self.assertEqual(dic_bond_openmm, dic_bond_oe)
def test_success(self):
print('Testing cube:', self.cube.name)
# File name
fname = ommutils.get_data_filename('examples', 'data/Bace_protein.pdb')
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(fname) as ifs:
oechem.OEReadMolecule(ifs, mol)
atom_i = mol.GetMaxAtomIdx()
# Process the molecules
self.cube.process(mol, 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)
outmol = self.runner.outputs["success"].get()
atom_f = outmol.GetMaxAtomIdx()
self.assertEquals(atom_i, atom_f)
# Check Total number of atoms
prot, lig, wat, other = utils.split(outmol)
# Check protein, ligand, excipients and water number of atoms
npa = prot.GetMaxAtomIdx()
nla = lig.GetMaxAtomIdx()
noa = other.GetMaxAtomIdx()
nwa = wat.GetMaxAtomIdx()
self.assertEquals(npa, 6044)
self.assertEquals(nla, 0)
self.assertEquals(noa, 14)
self.assertEquals(nwa, 57)