def test_implicit_runner_amap(self): p = subsystem.SubSystemFromSequence("NALA ALA CALA") b = builder.SystemBuilder() sys = b.build_system([p]) sys.temperature_scaler = temperature.ConstantTemperatureScaler(300.0 * u.kelvin) opt = options.RunOptions() opt.timesteps = 20 opt.use_amap = True opt.amap_beta_bias = 10 runner = openmm_runner.OpenMMRunner(sys, opt, platform="Reference") runner.prepare_for_timestep(sys.get_state_template(), 0.0, 1) pos = sys._coordinates.copy() vel = np.zeros_like(pos) alpha = 0.0 energy = 0.0 box_vectors = np.zeros(3) s = state.SystemState(pos, vel, alpha, energy, box_vectors) s = runner.minimize_then_run(s) s = runner.run(s) assert s
def test_explicit_runner_scaler(self): p = subsystem.SubSystemFromSequence("NALA ALA CALA") b = builder.SystemBuilder(explicit_solvent=True) sys = b.build_system([p]) sys.temperature_scaler = temperature.ConstantTemperatureScaler(300.0 * u.kelvin) rest2_scaler = temperature.GeometricTemperatureScaler( 0, 1, 300.0 * u.kelvin, 350.0 * u.kelvin ) opt = options.RunOptions(solvation="explicit") opt.rest2_scaler = temperature.REST2Scaler(300.0 * u.kelvin, rest2_scaler) opt.minimize_steps = 100 opt.timesteps = 2 opt.use_rest2 = True runner = openmm_runner.OpenMMRunner(sys, opt, platform="Reference") runner.prepare_for_timestep(sys.get_state_template(), 0.0, 1) pos = sys._coordinates.copy() vel = np.zeros_like(pos) alpha = 0.0 energy = 0.0 box_vectors = sys._box_vectors s = state.SystemState(pos, vel, alpha, energy, box_vectors) s = runner.minimize_then_run(s) s = runner.run(s) assert s
def test_lyn_should_match_lys(self): p = subsystem.SubSystemFromSequence("NCYX ALA CCYX") p.add_disulfide(ResidueIndex(0), ResidueIndex(2)) b = builder.SystemBuilder() system = b.build_system([p]) system.index.residue(0, expected_resname="CYS", one_based=False) system.index.residue(2, expected_resname="CYS", one_based=False)
def setUp(self): # create a tri-ala molecule p = subsystem.SubSystemFromSequence("NALA ALA CALA") b = builder.SystemBuilder() self.system = b.build_system([p, p]) # mock openmm system to recieve the new cmap torsion force self.mock_openmm_system = mock.Mock(spec=openmm.System) # patch out CMAPTorsionForce so we can see how it is called self.patcher = mock.patch( "meld.runner.transform.cmap.mm.CMAPTorsionForce", spec=openmm.CMAPTorsionForce, ) self.MockCMAP = self.patcher.start() self.mock_cmap = mock.Mock(spec=openmm.CMAPTorsionForce) self.MockCMAP.return_value = self.mock_cmap
def make_system(self, restype): sequence = f"NALA {restype} CALA" p = subsystem.SubSystemFromSequence(sequence) b = builder.SystemBuilder() self.system = b.build_system([p])
def test_lyn_should_match_lys(self): p1 = subsystem.SubSystemFromSequence("NALA LYN CLYS") b = builder.SystemBuilder() system = b.build_system([p1]) system.index.residue(1, expected_resname="LYS", one_based=False)
def setUp(self): p1 = subsystem.SubSystemFromSequence("NALA CYS CLYS") p2 = subsystem.SubSystemFromSequence("NARG TRP CTYR") b = builder.SystemBuilder() self.system = b.build_system([p1, p2])
def setUp(self): p1 = subsystem.SubSystemFromSequence("NALA ALA CALA") p2 = subsystem.SubSystemFromSequence("NALA ALA CALA") b = builder.SystemBuilder() self.system = b.build_system([p1, p2])
def test_ash_should_match_asp(self): p1 = subsystem.SubSystemFromSequence("NALA GLH CLYS") b = builder.SystemBuilder() system = b.build_system([p1]) system.index.atom(1, "CA", expected_resname="GLU", one_based=False)
def test_hip_should_match_his(self): p1 = subsystem.SubSystemFromSequence("NALA HIP CLYS") b = builder.SystemBuilder() system = b.build_system([p1]) system.index.atom(1, "CA", expected_resname="HIS", one_based=False)
def setUp(self): p = subsystem.SubSystemFromSequence("NALA ALA CALA") b = builder.SystemBuilder() self.system = b.build_system([p]) self.system.temperature_scaler = temperature.ConstantTemperatureScaler( 300.0 * kelvin)