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)
class DartLoaderTester(unittest.TestCase):
"""
Test if darts are made successfully
using SmartDartMove.dartsFromParmEd.
"""
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 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()
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,
'nIter': 10,
'nstepsMD': 50,
'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)'
}
}
sims = SimulationFactory(systems, self.engine, self.cfg)
self.ncmc_sim = sims.ncmc
self.initial_positions = self.ncmc_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
def test_dartsFromParmEd(self):
#load files to see if there are any errors
prmtop = utils.get_data_filename('blues', 'tests/data/TOL-parm.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/TOL-parm.inpcrd')
self.move.dartsFromParmEd(coord_files=[inpcrd], topology=prmtop)
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)
#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)
self.system_cfg = {
'nonbondedMethod': app.NoCutoff,
'constraints': app.HBonds
}
self.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,
'nIter': 10,
'nstepsMD': 50,
'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)'
}
}
sims = SimulationFactory(self.systems, self.move_engine, self.cfg)
self.ncmc_sim = sims.ncmc
self.move.calculateProperties()
self.initial_positions = self.ncmc_sim.context.getState(
getPositions=True).getPositions(asNumpy=True)
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)
class SmartDartTester(unittest.TestCase):
"""
Test the SmartDartMove.move() function.
"""
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_smart_dart(self):
"""Creates two darting regions, one at the center of mass origin,
and one displaced a little way from the center,
and checks to see if the alainine dipeptide correctly jumps between the two"""
orig_pos = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
com = self.move.getCenterOfMass(orig_pos[self.move.atom_indices], self.move.masses)
basis_part = self.move.basis_particles
com_new_coord = self.move._findNewCoord(orig_pos[basis_part[0]], orig_pos[basis_part[1]], orig_pos[basis_part[2]], com)
move_coord = com_new_coord[:] + np.array([1,1,1])*unit.nanometers
#standard_dart is the new positions of the center of mass if a move occurs
standard_dart = np.array([-0.0096823 , 0.50751791, 0.060064 ])
#dart_counter checks how many times darting to another dart occurs
#should be greater than 1
dart_counter = 0
#attempt the darting move 20 times
for i in range(20):
#set the new darts using the original settings
self.move.n_dartboard = [com_new_coord, move_coord]
nc_context = self.move.move(self.nc_sim.context)
pos_new = nc_context.getState(getPositions=True).getPositions(asNumpy=True)
for x in range(3):
#postions of the coordinates either should be the same, or displaced by the standard_dart value
if pos_new[0][x]._value - orig_pos[0][x]._value == 0:
np.testing.assert_almost_equal(pos_new[0][x]._value, orig_pos[0][x]._value, decimal=1)
else:
np.testing.assert_almost_equal(pos_new[0][x]._value, (orig_pos[0][x]._value + standard_dart[x]), decimal=1)
dart_counter = dart_counter+1
#reset and rerun
nc_context.setPositions(orig_pos)
#if the move worked, dart_counter should be greater than 0
assert dart_counter > 0
def test_self_dart(self):
"""same as test_smart_dart, but with self.self_dart=False, which should always cause
the com to jump to a different dart, as opposed to having a chance to stay where it is"""
self.move.self_dart=False
orig_pos = self.nc_sim.context.getState(getPositions=True).getPositions(asNumpy=True)
com = self.move.getCenterOfMass(orig_pos[self.move.atom_indices], self.move.masses)
basis_part = self.move.basis_particles
com_new_coord = self.move._findNewCoord(orig_pos[basis_part[0]], orig_pos[basis_part[1]], orig_pos[basis_part[2]], com)
move_coord = com_new_coord[:] + np.array([1,1,1])*unit.nanometers
standard_dart = np.array([-0.0096823 , 0.50751791, 0.060064 ])
#dart_counter checks how many times darting to another dart occurs
#should be greater than 1
dart_counter = 0
#attempt the darting move 20 times
for i in range(20):
#set the new darts using the original settings
self.move.n_dartboard = [com_new_coord, move_coord]
nc_context = self.move.move(self.nc_sim.context)
pos_new = nc_context.getState(getPositions=True).getPositions(asNumpy=True)
for x in range(3):
#postions of the coordinates either should be the same, or displaced by the standard_dart value
if pos_new[0][x]._value - orig_pos[0][x]._value == 0:
np.testing.assert_almost_equal(pos_new[0][x]._value, orig_pos[0][x]._value, decimal=1)
else:
np.testing.assert_almost_equal(pos_new[0][x]._value, (orig_pos[0][x]._value + standard_dart[x]), decimal=1)
dart_counter = dart_counter+1
#reset and rerun
nc_context.setPositions(orig_pos)
#if the move worked, dart_counter should equal 20*3
assert dart_counter == 60