class RandomRotationTester(unittest.TestCase):
"""
Test the RandomLigandRotationMove class.
"""
def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues', 'tests/data/TOL-parm.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/TOL-parm.inpcrd')
structure = parmed.load_file(prmtop, xyz=inpcrd)
self.atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
#Initialize the Move object
self.move = RandomLigandRotationMove(structure, 'LIG', 3134)
self.engine = MoveEngine(self.move)
self.engine.selectMove()
self.system_cfg = {
'nonbondedMethod': app.NoCutoff,
'constraints': app.HBonds
}
systems = SystemFactory(structure, self.move.atom_indices,
self.system_cfg)
#Initialize the SimulationFactory object
self.cfg = {
'dt': 0.002 * unit.picoseconds,
'friction': 1 * 1 / unit.picoseconds,
'temperature': 300 * unit.kelvin,
'nprop': 1,
'nIter': 1,
'nstepsMD': 1,
'nstepsNC': 10,
'alchemical_functions': {
'lambda_sterics':
'step(0.199999-lambda) + step(lambda-0.2)*step(0.8-lambda)*abs(lambda-0.5)*1/0.3 + step(lambda-0.800001)',
'lambda_electrostatics':
'step(0.2-lambda)- 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)'
}
}
self.simulations = SimulationFactory(systems, self.engine, self.cfg)
self.ncmc_sim = self.simulations.ncmc
self.initial_positions = self.ncmc_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
def test_random_rotation(self):
before_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[self.atom_indices, :]
self.simulations.ncmc.context = self.engine.runEngine(
self.simulations.ncmc.context)
after_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[self.atom_indices, :]
#Check that the ligand has been rotated
pos_compare = np.not_equal(before_move, after_move).all()
assert pos_compare
class RandomRotationTester(unittest.TestCase):
"""
Test the RandomLigandRotationMove class.
"""
def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues', 'tests/data/TOL-parm.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/TOL-parm.inpcrd')
structure = parmed.load_file(prmtop, xyz=inpcrd)
self.atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
#Initialize the Move object
self.move = RandomLigandRotationMove(structure, 'LIG', 3134)
self.engine = MoveEngine(self.move)
self.engine.selectMove()
self.system_cfg = {'nonbondedMethod': app.NoCutoff, 'constraints': app.HBonds}
systems = SystemFactory(structure, self.move.atom_indices, self.system_cfg)
#Initialize the SimulationFactory object
self.cfg = {
'dt': 0.002 * unit.picoseconds,
'friction': 1 * 1 / unit.picoseconds,
'temperature': 300 * unit.kelvin,
'nprop': 1,
'nIter': 1,
'nstepsMD': 1,
'nstepsNC': 10,
'alchemical_functions': {
'lambda_sterics':
'step(0.199999-lambda) + step(lambda-0.2)*step(0.8-lambda)*abs(lambda-0.5)*1/0.3 + step(lambda-0.800001)',
'lambda_electrostatics':
'step(0.2-lambda)- 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)'
}
}
self.simulations = SimulationFactory(systems, self.engine, self.cfg)
self.ncmc_sim = self.simulations.ncmc
self.initial_positions = self.ncmc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
def test_random_rotation(self):
before_move = self.simulations.ncmc.context.getState(getPositions=True).getPositions(
asNumpy=True)[self.atom_indices, :]
self.simulations.ncmc.context = self.engine.runEngine(self.simulations.ncmc.context)
after_move = self.simulations.ncmc.context.getState(getPositions=True).getPositions(
asNumpy=True)[self.atom_indices, :]
#Check that the ligand has been rotated
pos_compare = np.not_equal(before_move, after_move).all()
assert pos_compare
class WaterTranslationTester(unittest.TestCase):
"""
Test the RandomLigandRotationMove class.
"""
def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues',
'tests/data/eqToluene.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/eqToluene.pdb')
structure = parmed.load_file(prmtop, xyz=inpcrd)
#Initialize the Move object
self.move = WaterTranslationMove(
structure,
protein_selection='(index 1656) or (index 1657)',
radius=0.9 * unit.nanometer)
self.atom_indices = self.move.atom_indices
self.engine = MoveEngine(self.move)
self.engine.selectMove()
self.system_cfg = {
'nonbondedMethod': app.NoCutoff,
'constraints': app.HBonds
}
systems = SystemFactory(structure, self.move.atom_indices,
self.system_cfg)
#Initialize the SimulationFactory object
self.cfg = {
'dt': 0.002 * unit.picoseconds,
'friction': 1 * 1 / unit.picoseconds,
'temperature': 300 * unit.kelvin,
'nprop': 1,
'nIter': 1,
'nstepsMD': 1,
'nstepsNC': 100,
'alchemical_functions': {
'lambda_sterics':
'step(0.199999-lambda) + step(lambda-0.2)*step(0.8-lambda)*abs(lambda-0.5)*1/0.3 + step(lambda-0.800001)',
'lambda_electrostatics':
'step(0.2-lambda)- 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)'
}
}
self.simulations = SimulationFactory(systems, self.engine, self.cfg)
self.ncmc_sim = self.simulations.ncmc
self.initial_positions = self.ncmc_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
def test_water_translation_before(self):
self.original_com_position = self.move.traj.xyz[0][
self.move.protein_atoms[0]]
before_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[self.atom_indices, :]
#new_context = self.engine.runEngine(self.simulations.ncmc.context)
new_context = self.move.beforeMove(self.simulations.ncmc.context)
after_move = new_context.getState(getPositions=True).getPositions(
asNumpy=True)[self.atom_indices, :]
#Check that the ligand has been rotated
pos_compare = np.not_equal(before_move, after_move).all()
self.move.traj.xyz[0][
self.move.protein_atoms[0]] = self.original_com_position
assert pos_compare
def test_water_translation_move(self):
#before_move = self.simulations.ncmc.context.getState(getPositions=True).getPositions(
# asNumpy=True)[self.atom_indices, :]
self.original_com_position = self.ncmc_sim.context.getState(
getPositions=True).getPositions(
asNumpy=True)[self.move.protein_atoms[0]]
com_protein_before = self.move.traj.xyz[0,
self.move.protein_atoms[0], :]
self.simulations.ncmc.context = self.move.beforeMove(
self.simulations.ncmc.context)
before_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[self.atom_indices, :]
self.simulations.ncmc.context = self.engine.runEngine(
self.simulations.ncmc.context)
after_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[self.atom_indices, :]
#Check that the ligand has been rotated
pos_compare = np.not_equal(before_move, after_move).all()
assert pos_compare
#check distance
com_protein_after = self.move.traj.xyz[0,
self.move.protein_atoms[0], :]
#check that the center of mass refereence has changed
assert np.not_equal(self.original_com_position,
com_protein_after).all()
#check that the new water position is within the specified radius
pairs = self.move.traj.topology.select_pairs(
np.array(self.move.atom_indices[0]).flatten(),
np.array(self.move.protein_atoms[0]).flatten())
water_distance = md.compute_distances(self.move.traj,
pairs,
periodic=True)
water_dist = np.linalg.norm(water_distance)
assert np.less_equal(water_dist, self.move.radius._value)
self.move.traj.xyz[0][
self.move.protein_atoms[0]] = self.original_com_position
def test_water_translation_after(self):
before_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[self.atom_indices, :]
self.simulations.ncmc.context = self.engine.runEngine(
self.simulations.ncmc.context)
new_context = self.move.beforeMove(self.simulations.ncmc.context)
new_context = self.move.move(self.simulations.ncmc.context)
after_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)
#Check that the move treats inbound water correctly
assert self.simulations.ncmc.context._integrator.getGlobalVariableByName(
'protocol_work') == 0
after_move[self.move.atom_indices] = after_move[
self.move.atom_indices] + [self.move.radius._value, 0, 0
] * self.move.radius.unit
self.simulations.ncmc.context.setPositions(after_move)
new_context = self.move.afterMove(self.simulations.ncmc.context)
#Check that the move would be rejected in case it's out of bounds
assert self.simulations.ncmc.context._integrator.getGlobalVariableByName(
'protocol_work') >= 999999
class SideChainTester(unittest.TestCase):
"""
Test the SmartDartMove.move() function.
"""
def setUp(self):
# Obtain topologies/positions
prmtop = utils.get_data_filename('blues',
'tests/data/vacDivaline.prmtop')
inpcrd = utils.get_data_filename('blues',
'tests/data/vacDivaline.inpcrd')
self.struct = parmed.load_file(prmtop, xyz=inpcrd)
self.sidechain = SideChainMove(self.struct, [1])
self.engine = MoveEngine(self.sidechain)
self.engine.selectMove()
self.system_cfg = {
'nonbondedMethod': app.NoCutoff,
'constraints': app.HBonds
}
self.systems = SystemFactory(self.struct, self.sidechain.atom_indices,
self.system_cfg)
self.cfg = {
'dt': 0.002 * unit.picoseconds,
'friction': 1 * 1 / unit.picoseconds,
'temperature': 300 * unit.kelvin,
'nIter': 1,
'nstepsMD': 1,
'nstepsNC': 4,
'alchemical_functions': {
'lambda_sterics':
'step(0.199999-lambda) + step(lambda-0.2)*step(0.8-lambda)*abs(lambda-0.5)*1/0.3 + step(lambda-0.800001)',
'lambda_electrostatics':
'step(0.2-lambda)- 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)'
}
}
self.simulations = SimulationFactory(self.systems, self.engine,
self.cfg)
def test_getRotBondAtoms(self):
vals = [v for v in self.sidechain.rot_atoms[1].values()][0]
assert len(vals) == 11
#Ensure it selects 1 rotatable bond in Valine
assert len(self.sidechain.rot_bonds) == 1
def test_sidechain_move(self):
atom_indices = [v for v in self.sidechain.rot_atoms[1].values()][0]
before_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[atom_indices, :]
self.simulations.ncmc.context = self.engine.runEngine(
self.simulations.ncmc.context)
after_move = self.simulations.ncmc.context.getState(
getPositions=True).getPositions(asNumpy=True)[atom_indices, :]
#Check that our system has run dynamics
# Integrator must step for context to update positions
# Remove the first two atoms in check as these are the anchor atoms and are not rotated.
pos_compare = np.not_equal(before_move, after_move)[2:, :].all()
assert pos_compare