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)
self.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.opt = { 'temperature' : 300.0, 'friction' : 1, 'dt' : 0.002,
'nIter' : 10, 'nstepsNC' : 10, 'nstepsMD' : 50,
'nonbondedMethod' : 'PME', 'nonbondedCutoff': 10, 'constraints': 'HBonds',
'trajectory_interval' : 10, 'reporter_interval' : 10,
'platform' : None, 'outfname' : 'smartdart-test',
'verbose' : False }
#Initialize the SmartDartMove object
self.move = SmartDartMove(structure,
basis_particles=[100, 110, 150],
coord_files = [inpcrd, inpcrd], topology=prmtop,
self_dart=False, resname='LIG', )
self.engine = MoveEngine(self.move)
self.engine.selectMove()
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.engine, **self.opt)
system = sims.generateSystem(structure, **self.opt)
alch_system = sims.generateAlchSystem(system, self.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure, self.engine, alch_system, ncmc=True, **self.opt)
self.initial_positions = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
def test_generateSimFromStruct(self):
print('Generating Simulation from parmed.Structure')
integrator = openmm.LangevinIntegrator(100 * unit.kelvin, 1,
0.002 * unit.picoseconds)
simulation = SimulationFactory.generateSimFromStruct(
self.structure, self.system, integrator)
#Check that we've made a Simulation object
self.assertIsInstance(simulation, app.Simulation)
state = simulation.context.getState(getPositions=True)
positions = state.getPositions(asNumpy=True) / unit.nanometers
box_vectors = state.getPeriodicBoxVectors(
asNumpy=True) / unit.nanometers
struct_box = np.array(
self.structure.box_vectors.value_in_unit(unit.nanometers))
struct_pos = np.array(
self.structure.positions.value_in_unit(unit.nanometers))
#Check that the box_vectors/positions in the Simulation
# have been set from the parmed.Structure
np.testing.assert_array_almost_equal(positions, struct_pos)
np.testing.assert_array_equal(box_vectors, struct_box)
print('Attaching Reporter')
reporters = [app.StateDataReporter('test.log', 5)]
self.assertEqual(len(simulation.reporters), 0)
simulation = SimulationFactory.attachReporters(simulation, reporters)
self.assertEqual(len(simulation.reporters), 1)
os.remove('test.log')
def test_simulationRun(self):
"""Tests the Simulation.runNCMC() function"""
self.opt = { 'temperature' : 300.0, 'friction' : 1, 'dt' : 0.002,
'nIter' : 2, 'nstepsNC' : 100, 'nstepsMD' : 2, 'nprop' : 1,
'nonbondedMethod' : 'NoCutoff', 'constraints': 'HBonds',
'trajectory_interval' : 1, 'reporter_interval' : 1, 'outfname' : 'blues-test',
'platform' : None, 'write_move' : False}
testsystem = testsystems.AlanineDipeptideVacuum(constraints=None)
structure = parmed.openmm.topsystem.load_topology(topology=testsystem.topology,
system=testsystem.system,
xyz=testsystem.positions,
)
self.model = RandomLigandRotationMove(structure, resname='ALA')
self.model.atom_indices = range(22)
self.model.topology = structure.topology
self.model.positions = structure.positions
self.model.calculateProperties()
self.mover = MoveEngine(self.model)
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.mover, **self.opt)
#print(sims)
system = sims.generateSystem(structure, **self.opt)
simdict = sims.createSimulationSet()
alch_system = sims.generateAlchSystem(system, self.model.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure, self.mover, alch_system, ncmc=True, **self.opt)
self.model.calculateProperties()
self.initial_positions = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
asim = Simulation(sims, self.mover, **self.opt)
asim.run(self.opt['nIter'])
def test_simulationfactory(self):
#Initialize the SimulationFactory object
move = RandomLigandRotationMove(self.full_struct, 'LIG')
engine = MoveEngine(move)
sims = SimulationFactory(self.full_struct, engine, **self.opt)
system = sims.generateSystem(self.full_struct, **self.opt)
self.assertIsInstance(system, openmm.System)
alch_system = sims.generateAlchSystem(system, move.atom_indices)
self.assertIsInstance(alch_system, openmm.System)
md_sim = sims.generateSimFromStruct(self.full_struct, engine, system, **self.opt)
self.assertIsInstance(md_sim, openmm.app.simulation.Simulation)
nc_sim = sims.generateSimFromStruct(self.full_struct, engine, alch_system, ncmc=True, **self.opt)
self.assertIsInstance(nc_sim, openmm.app.simulation.Simulation)
def setUp(self):
# Obtain topologies/positions
prmtop = testsystems.get_data_filename("data/alanine-dipeptide-gbsa/alanine-dipeptide.prmtop")
inpcrd = testsystems.get_data_filename("data/alanine-dipeptide-gbsa/alanine-dipeptide.crd")
testsystem = testsystems.AlanineDipeptideVacuum(constraints=None)
structure = parmed.openmm.topsystem.load_topology(topology=testsystem.topology,
system=testsystem.system,
xyz=testsystem.positions,
)
#self.atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
self.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.opt = { 'temperature' : 300.0, 'friction' : 1, 'dt' : 0.002,
'nIter' : 10, 'nstepsNC' : 10, 'nstepsMD' : 50,
'nonbondedMethod' : 'NoCutoff', 'nonbondedCutoff': 10, 'constraints': 'HBonds',
'trajectory_interval' : 10, 'reporter_interval' : 10, 'outfname' : 'smartdart-test',
'platform' : None,
'verbose' : False }
#Initialize the Model object
basis_particles = [0,2,7]
self.move = SmartDartMove(structure, basis_particles=basis_particles,
coord_files=[inpcrd, inpcrd],
topology=prmtop,
resname='ALA', self_dart=True)
self.move.atom_indices = range(22)
self.move.topology = structure.topology
self.move.positions = structure.positions
self.move_engine = MoveEngine(self.move)
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.move_engine, **self.opt)
system = sims.generateSystem(structure, **self.opt)
alch_system = sims.generateAlchSystem(system, self.move.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure, self.move_engine, alch_system, ncmc=True, **self.opt)
self.move.calculateProperties()
self.initial_positions = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
def test_generateSimFromStruct(self, structure, system, tmpdir):
print('Generating Simulation from parmed.Structure')
integrator = openmm.LangevinIntegrator(100 * unit.kelvin, 1, 0.002 * unit.picoseconds)
simulation = SimulationFactory.generateSimFromStruct(structure, system, integrator)
#Check that we've made a Simulation object
assert isinstance(simulation, app.Simulation)
state = simulation.context.getState(getPositions=True)
positions = state.getPositions(asNumpy=True) / unit.nanometers
box_vectors = state.getPeriodicBoxVectors(asNumpy=True) / unit.nanometers
struct_box = np.array(structure.box_vectors.value_in_unit(unit.nanometers))
struct_pos = np.array(structure.positions.value_in_unit(unit.nanometers))
#Check that the box_vectors/positions in the Simulation
# have been set from the parmed.Structure
np.testing.assert_array_almost_equal(positions, struct_pos)
np.testing.assert_array_equal(box_vectors, struct_box)
print('Attaching Reporter')
reporters = [app.StateDataReporter(tmpdir.join('test.log'), 5)]
assert len(simulation.reporters) == 0
simulation = SimulationFactory.attachReporters(simulation, reporters)
assert len(simulation.reporters) == 1
def runEthyleneTest(N):
filename = 'ethylene-test_%s' % N
print('Running %s...' % filename)
seed = np.random.randint(low=1, high=5000)
#print('Seed', seed)
# filename = 'ethylene-test_%s' % N
# print(filename)
# Set Simulation parameters
sim_cfg = {
'platform': 'CPU',
'nprop': 1,
'propLambda': 0.3,
'dt': 1 * unit.femtoseconds,
'friction': 1 / unit.picoseconds,
'temperature': 200 * unit.kelvin,
'nIter': 100,
'nstepsMD': 20,
'nstepsNC': 20,
'propSteps': 20,
'moveStep': 10
}
totalSteps = int(sim_cfg['nIter'] * sim_cfg['nstepsMD'])
reportInterval = 5
alchemical_atoms = [2, 3, 4, 5, 6, 7]
alchemical_functions = {
'lambda_sterics':
'min(1, (1/0.3)*abs(lambda-0.5))',
'lambda_electrostatics':
'step(0.2-lambda) - 1/0.2*lambda*step(0.2-lambda) + 1/0.2*(lambda-0.8)*step(lambda-0.8)'
}
md_reporters = {'traj_netcdf': {'reportInterval': reportInterval}}
# Load a Parmed Structure for the Topology and create our openmm.Simulation
structure_pdb = utils.get_data_filename(
'blues', 'tests/data/ethylene_structure.pdb')
structure = parmed.load_file(structure_pdb)
# Initialize our move proposal class
rot_move = RandomLigandRotationMove(structure, 'LIG')
mover = MoveEngine(rot_move)
# Load our OpenMM System and create Integrator
system_xml = utils.get_data_filename('blues',
'tests/data/ethylene_system.xml')
with open(system_xml, 'r') as infile:
xml = infile.read()
system = openmm.XmlSerializer.deserialize(xml)
integrator = openmm.LangevinIntegrator(sim_cfg['temperature'],
sim_cfg['friction'], sim_cfg['dt'])
integrator.setRandomNumberSeed(seed)
alch_integrator = openmm.LangevinIntegrator(sim_cfg['temperature'],
sim_cfg['friction'],
sim_cfg['dt'])
alch_integrator.setRandomNumberSeed(seed)
alch_system = SystemFactory.generateAlchSystem(system, alchemical_atoms)
ncmc_integrator = AlchemicalExternalLangevinIntegrator(
nsteps_neq=sim_cfg['nstepsNC'],
alchemical_functions=alchemical_functions,
splitting="H V R O R V H",
temperature=sim_cfg['temperature'],
timestep=sim_cfg['dt'])
# ncmc_integrator.setRandomNumberSeed(seed)
# Pack our systems into a single object
systems = SystemFactory(structure, alchemical_atoms)
systems.md = system
systems.alch = alch_system
# Make our reporters
md_reporter_cfg = ReporterConfig(filename, md_reporters)
md_reporters_list = md_reporter_cfg.makeReporters()
# Pack our simulations into a single object
simulations = SimulationFactory(systems, mover)
simulations.md = SimulationFactory.generateSimFromStruct(
structure, system, integrator, 'CPU')
simulations.md = SimulationFactory.attachReporters(simulations.md,
md_reporters_list)
simulations.alch = SimulationFactory.generateSimFromStruct(
structure, system, alch_integrator, 'CPU')
simulations.ncmc = SimulationFactory.generateSimFromStruct(
structure, alch_system, ncmc_integrator, 'CPU')
ethylene_sim = BLUESSimulation(simulations, sim_cfg)
ethylene_sim.run()
def test_simulationRun(self):
"""Tests the Simulation.runMC() function"""
self.opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.00002,
'nIter': 2,
'nstepsNC': 2,
'nstepsMD': 1,
'nprop': 1,
'nonbondedMethod': 'NoCutoff',
'constraints': 'HBonds',
'trajectory_interval': 1,
'reporter_interval': 1,
'outfname': 'mc-test',
'platform': None,
'constraints': 'HBonds',
'mc_per_iter': 2
}
structure = self.full_struct
class SetRotationMove(RandomLigandRotationMove):
def __init__(self, structure, resname='LIG'):
super(SetRotationMove, self).__init__(structure, resname)
def move(self, context):
"""Function that performs a random rotation about the
center of mass of the ligand.
"""
#TODO: check if we need to deepcopy
positions = context.getState(getPositions=True).getPositions(
asNumpy=True)
self.positions = positions[self.atom_indices]
self.center_of_mass = self.getCenterOfMass(
self.positions, self.masses)
reduced_pos = self.positions - self.center_of_mass
# Define random rotational move on the ligand
#set rotation so that test is reproducible
set_rotation_matrix = np.array(
[[-0.62297988, -0.17349253, 0.7627558],
[0.55082352, -0.78964857, 0.27027502],
[0.55541834, 0.58851973, 0.58749893]])
#set_rotation_matrix = np.array([[1, 0, 0],
# [0, 1, 0],
# [0, 0, 1]])
#multiply lig coordinates by rot matrix and add back COM translation from origin
rot_move = np.dot(reduced_pos, set_rotation_matrix
) * positions.unit + self.center_of_mass
# Update ligand positions in nc_sim
for index, atomidx in enumerate(self.atom_indices):
positions[atomidx] = rot_move[index]
context.setPositions(positions)
positions = context.getState(getPositions=True).getPositions(
asNumpy=True)
self.positions = positions[self.atom_indices]
return context
self.model = SetRotationMove(structure, resname='ALA')
#self.model = RandomLigandRotationMove(structure, resname='ALA')
self.model.atom_indices = range(22)
self.model.topology = structure[self.model.atom_indices].topology
self.model.positions = structure[self.model.atom_indices].positions
self.model.calculateProperties()
self.mover = MoveEngine(self.model)
#Initialize the SimulationFactory object
sims = SimulationFactory(structure, self.mover, **self.opt)
#print(sims)
system = sims.generateSystem(structure, **self.opt)
simdict = sims.createSimulationSet()
alch_system = sims.generateAlchSystem(system, self.model.atom_indices)
self.nc_sim = sims.generateSimFromStruct(structure,
self.mover,
alch_system,
ncmc=True,
**self.opt)
self.model.calculateProperties()
self.initial_positions = self.nc_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
mc_sim = Simulation(sims, self.mover, **self.opt)
#monkeypatch to access acceptance value
def nacceptRejectMC(self, temperature=300, **opt):
"""Function that chooses to accept or reject the proposed move.
"""
md_state0 = self.current_state['md']['state0']
md_state1 = self.current_state['md']['state1']
log_mc = (md_state1['potential_energy'] -
md_state0['potential_energy']) * (
-1.0 / self.nc_sim.context._integrator.kT)
randnum = math.log(np.random.random())
if log_mc > randnum:
self.accept += 1
print('MC MOVE ACCEPTED: log_mc {} > randnum {}'.format(
log_mc, randnum))
self.md_sim.context.setPositions(md_state1['positions'])
else:
self.reject += 1
print('MC MOVE REJECTED: log_mc {} < {}'.format(
log_mc, randnum))
self.md_sim.context.setPositions(md_state0['positions'])
self.log_mc = log_mc
self.md_sim.context.setVelocitiesToTemperature(
self.opt['temperature'])
mc_sim.acceptRejectMC = nacceptRejectMC
nacceptRejectMC.__get__(mc_sim)
mc_sim.acceptRejectMC = types.MethodType(nacceptRejectMC, mc_sim)
mc_sim.runMC(self.opt['nIter'])
#get log acceptance
print(mc_sim.log_mc)
#if mc is working, should be around -24.1
assert mc_sim.log_mc <= -23.8 and mc_sim.log_mc >= -24.3
def md_sim(structure, system):
integrator = openmm.LangevinIntegrator(100 * unit.kelvin, 1, 0.002 * unit.picoseconds)
md_sim = SimulationFactory.generateSimFromStruct(structure, system, integrator)
return md_sim
def md_sim(structure, system):
integrator = openmm.LangevinIntegrator(100 * unit.kelvin, 1,
0.002 * unit.picoseconds)
md_sim = SimulationFactory.generateSimFromStruct(structure, system,
integrator)
return md_sim
