def test_mdprep(self):
protein_path = utils.get_data_filename('examples', 'data/Bace_protein.pdb')
ligand_path = utils.get_data_filename('examples', 'data/lig_CAT13a.oeb.gz')
run_args = [
'--protein', protein_path,
'--ligands', ligand_path,
'--max_conformers', '800',
'--protein_prefix', 'Bace',
'--solvent_padding', '10',
'--salt_conc', '100',
'--protein_ff', 'amber99sbildn.xml',
'--solvent_ff', 'tip3p.xml',
'--ligand_ff', 'GAFF2',
'--other_ff', 'GAFF2',
'--min_steps', '30000',
'--m_restraints', 'noh (ligand or protein)',
'--m_restraintWt', '5.0',
'--warm_psec', '10.0',
'--w_restraints', 'noh (ligand or protein)',
'--w_restraintWt', '2.0',
'--w_trajectory_interval', '1000',
'--w_reporter_interval', '10000',
'--w_outfname', 'warmup',
'--eq1_psec', '10.0',
'--eq1_restraints', 'noh (ligand or protein)',
'--eq1_restraintWt', '2.0',
'--eq1_trajectory_interval', '1000',
'--eq1_reporter_interval', '10000',
'--eq1_outfname', 'equil1',
'--eq2_psec', '10.0',
'--eq2_restraints', 'noh (ligand or protein)',
'--eq2_restraintWt', '0.5',
'--eq2_trajectory_interval', '1000',
'--eq2_reporter_interval', '10000',
'--eq2_outfname', 'equil2',
'--eq3_psec', '10.0',
'--eq3_restraints', 'ca_protein or (noh ligand)',
'--eq3_restraintWt', '0.1',
'--eq3_trajectory_interval', '1000',
'--eq3_reporter_interval', '10000',
'--eq3_outfname', 'equil3',
'--ofs-data_out', 'success.oeb',
'--fail-data_out', 'fail.oeb',
]
self.assertFalse(floe.run(args=run_args))
def test_npt(self):
complex_path = utils.get_data_filename(
'examples', 'data/pP38_lp38a_2x_complex.oeb.gz')
run_args = [
'--complex',
complex_path,
'--picosec',
'10',
'--temperature',
'300',
'--pressure',
'1',
'--restraints',
'noh (ligand or protein)',
'--restraintWt',
'2.0',
'--trajectory_interval',
'10',
'--reporter_interval',
'100',
'--suffix',
'npt',
'--ofs-data_out',
'success.oeb',
'--fail-data_out',
'fail.oeb',
]
self.assertFalse(floe.run(args=run_args))
def _test_success(self):
print('Testing cube:', self.cube.name)
# Complex file name
complex_fname = utils.get_data_filename('examples', 'data/pbace_lcat13a_complex.oeb.gz')
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(complex_fname) as ifs:
oechem.OEReadMolecule(ifs, mol)
# Calculate starting potential energy
eng_i = self.calculate_eng(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()
# Calculate final potential energy
eng_f = self.calculate_eng(outmol)
self.assertLess(eng_f, eng_i)
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_minimization(self):
complex_path = utils.get_data_filename('examples', 'data/pbace_lcat13a_complex.oeb.gz')
run_args = [
'--complex', complex_path,
'--ofs-data_out', 'success.oeb',
'--fail-data_out', 'fail.oeb',
'--steps', '30000',
]
self.assertFalse(floe.run(args=run_args))
def test_complex_prep(self):
protein_path = utils.get_data_filename('examples',
'data/Bace_protein.pdb')
ligand_path = utils.get_data_filename('examples',
'data/lig_CAT13a.oeb.gz')
run_args = [
'--protein',
protein_path,
'--ligands',
ligand_path,
'--max_conformers',
'800',
'--ofs-data_out',
'success.oeb',
'--fail-data_out',
'fail.oeb',
]
self.assertFalse(floe.run(args=run_args))
def applyffProtein(protein, opt):
"""
This function applies the selected force field to the
protein
Parameters:
-----------
protein: OEMol molecule
The protein to parametrize
opt: python dictionary
The options used to parametrize the protein
Return:
-------
protein_structure: Parmed structure instance
The parametrized protein parmed structure
"""
topology, positions = oeommutils.oemol_to_openmmTop(protein)
forcefield = app.ForceField(opt['protein_forcefield'])
unmatched_residues = forcefield.getUnmatchedResidues(topology)
if unmatched_residues:
# Extended ff99SBildn force field
oechem.OEThrow.Info("The following protein residues are not recognized "
"by the selected FF: {} - {}"
"\n...Extended FF is in use".format(opt['protein_forcefield'], unmatched_residues))
ffext_fname = utils.get_data_filename('ComplexPrepCubes', 'ffext/amber99SBildn_ext.xml')
forcefield = app.ForceField()
forcefield.loadFile(ffext_fname)
unmatched_residues = forcefield.getUnmatchedResidues(topology)
if unmatched_residues:
oechem.OEThrow.Fatal("Error. The following protein residues are not recognized "
"by the extended force field {}".format(unmatched_residues))
omm_system = forcefield.createSystem(topology, rigidWater=False)
protein_structure = parmed.openmm.load_topology(topology, omm_system, xyz=positions)
return protein_structure
def _test_success(self):
print('Testing cube:', self.cube.name)
# Complex file name
complex_fname = utils.get_data_filename(
'examples', 'data/pP38_lp38a_2x_complex.oeb.gz')
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(complex_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()
# Calculate final volume and temperature
vol_f, temp_f = self.calculate_VT(outmol)
# Check 3*std volume
# Average volume and its standard deviation (in nm^3) measured along
# one 10ns run for the selected system
avg_volume = 683.6 * (unit.nanometers**3)
std_volume = 1.3
self.assertAlmostEqual(avg_volume / (unit.nanometers**3),
vol_f.in_units_of(unit.nanometers**3) /
(unit.nanometers**3),
delta=3 * std_volume)
# Check 3*std temperature
# Average temperature and its standard deviation (in K) measured along
# one 10ns run for the selected system
avg_temperature = 300.0 * unit.kelvin
std_temperature = 1.1
self.assertAlmostEqual(avg_temperature / unit.kelvin,
temp_f.in_units_of(unit.kelvin) / unit.kelvin,
delta=3 * std_temperature)
def test_success(self):
print('Testing cube:', self.cube.name)
# Read a molecule
mol = oechem.OEMol()
ifs = oechem.oemolistream(utils.get_data_filename('examples', 'data/TOL-smnf.oeb.gz'))
if not oechem.OEReadMolecule(ifs, mol):
raise Exception('Cannot read molecule')
ifs.close()
# 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)
# Get the output molecule, check that it has score.
outmol = self.runner.outputs["success"].get()
self.assertTrue(oechem.OEHasSDData(outmol, 'Chemgauss4'))
def setUp(self):
self.cube = FREDDocking('fred')
self.cube.args.receptor = utils.get_data_filename('examples','data/T4-receptor.oeb.gz')
self.runner = CubeTestRunner(self.cube)
self.runner.start()
def test_restraints():
lig_fname = utils.get_data_filename('examples',
'data/pP38_lp38a_2x_complex.oeb.gz')
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(lig_fname) as ifs:
oechem.OEReadMolecule(ifs, mol)
res_dic = {}
mask = 'protein'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'ligand'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'water'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'ions'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'cofactors'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'ca_protein'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'protein or ligand'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'noh (protein or ligand)'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'ca_protein or (noh ligand)'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
mask = 'resid A:4 A:5 A:6 A:7'
ind_set = restraints(mol, mask=mask)
res_dic[mask] = ind_set
dic_fname = utils.get_data_filename(
'examples', 'data/restraint_test_P38_lp38a_2x.pickle')
file = open(dic_fname, 'rb')
res_dic_loaded = pickle.load(file)
for k in res_dic_loaded:
if res_dic[k] == res_dic_loaded[k]:
pass
else:
raise ValueError(
"Restraints checking Errors on mask: {}".format(k))
