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 setUp(self):
p = protein.ProteinMoleculeFromSequence("NALA ALA CALA")
b = builder.SystemBuilder(explicit_solvent=True,
explicit_ions=True,
p_ioncount=3,
n_ioncount=3)
self.system = b.build_system_from_molecules([p])
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):
with in_temp_dir():
with open("pdb.pdb", "w") as outfile:
outfile.write(pdb_string)
p = subsystem.SubSystemFromPdbFile("pdb.pdb")
b = builder.SystemBuilder(explicit_solvent=True)
self.system = b.build_system([p])
def setUp(self):
# create a tri-ala molecule
p = protein.ProteinMoleculeFromSequence('NALA ALA CALA')
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([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.system.openmm_runner.cmap.openmm.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 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 setUp(self):
# create a tri-ala molecule
p = protein.ProteinMoleculeFromSequence("NALA ALA CALA")
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
# create eight 24x24 maps filled with 0, 1, ..7
self.maps = [np.zeros((24, 24)) + i for i in range(8)]
# 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.system.openmm_runner.cmap.openmm.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 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)
def make_system(self, restype):
sequence = f"NALA {restype} CALA"
p = subsystem.SubSystemFromSequence(sequence)
b = builder.SystemBuilder()
self.system = b.build_system([p])
def make_system(self, restype):
sequence = f"NALA {restype} CALA"
p = protein.ProteinMoleculeFromSequence(sequence)
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
def setUp(self):
p = protein.ProteinMoleculeFromSequence('NALA ALA CALA')
b = builder.SystemBuilder()
sys = b.build_system_from_molecules([p])
self.bonds = ParmTopReader(sys.top_string).get_bonds()
def setUp(self):
p = protein.ProteinMoleculeFromSequence('NALA ALA CALA')
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
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 make_system(self, restype):
sequence = 'NALA {0} CALA'.format(restype)
p = protein.ProteinMoleculeFromSequence(sequence)
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
def setUp(self):
p = protein.ProteinMoleculeFromSequence("NALA ALA CALA")
b = builder.SystemBuilder()
self.system = b.build_system_from_molecules([p])
self.system.temperature_scaler = ConstantTemperatureScaler(300.)
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 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 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)
