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_freeze_radius(self, system_cfg):
print('Testing freeze_radius')
freeze_cfg = {'freeze_center': ':LIG', 'freeze_solvent': ':Cl-', 'freeze_distance': 3.0 * unit.angstroms}
# Setup toluene-T4 lysozyme system
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)
atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
system = SystemFactory.generateSystem(structure, **system_cfg)
# Freeze everything around the binding site
frzn_sys = SystemFactory.freeze_radius(structure, system, **freeze_cfg)
# Check that the ligand has NOT been frozen
lig_masses = [system.getParticleMass(i)._value for i in atom_indices]
assert all(m != 0 for m in lig_masses)
# Check that the binding site has NOT been frozen
selection = "({freeze_center}<:{freeze_distance._value})&!({freeze_solvent})".format(**freeze_cfg)
site_idx = SystemFactory.amber_selection_to_atomidx(structure, selection)
masses = [frzn_sys.getParticleMass(i)._value for i in site_idx]
assert all(m != 0 for m in masses)
# Check that the selection has been frozen
# Invert that selection to freeze everything but the binding site.
freeze_idx = set(range(system.getNumParticles())) - set(site_idx)
massless = [frzn_sys.getParticleMass(i)._value for i in freeze_idx]
assert all(m == 0 for m in massless)
def test_freeze_radius(self, system_cfg):
print('Testing freeze_radius')
freeze_cfg = {
'freeze_center': ':LIG',
'freeze_solvent': ':Cl-',
'freeze_distance': 3.0 * unit.angstroms
}
# Setup toluene-T4 lysozyme system
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)
atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
system = SystemFactory.generateSystem(structure, **system_cfg)
# Freeze everything around the binding site
frzn_sys = SystemFactory.freeze_radius(structure, system, **freeze_cfg)
# Check that the ligand has NOT been frozen
lig_masses = [system.getParticleMass(i)._value for i in atom_indices]
assert all(m != 0 for m in lig_masses)
# Check that the binding site has NOT been frozen
selection = "({freeze_center}<:{freeze_distance._value})&!({freeze_solvent})".format(
**freeze_cfg)
site_idx = SystemFactory.amber_selection_to_atomidx(
structure, selection)
masses = [frzn_sys.getParticleMass(i)._value for i in site_idx]
assert all(m != 0 for m in masses)
# Check that the selection has been frozen
# Invert that selection to freeze everything but the binding site.
freeze_idx = set(range(system.getNumParticles())) - set(site_idx)
massless = [frzn_sys.getParticleMass(i)._value for i in freeze_idx]
assert all(m == 0 for m in massless)
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 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 setUp(self):
# Load the waterbox with toluene into a structure.
self.prmtop = utils.get_data_filename('blues',
'tests/data/TOL-parm.prmtop')
self.inpcrd = utils.get_data_filename('blues',
'tests/data/TOL-parm.inpcrd')
self.structure = parmed.load_file(self.prmtop, xyz=self.inpcrd)
self.atom_indices = utils.atomIndexfromTop('LIG',
self.structure.topology)
self.system_cfg = {
'nonbondedMethod': app.PME,
'nonbondedCutoff': 8.0 * unit.angstroms,
'constraints': app.HBonds
}
self.systems = SystemFactory(self.structure, self.atom_indices,
self.system_cfg)
title='md',
step=True,
speed=True,
progress=True,
totalSteps=int(n_steps * nIter))
ncmc_state_reporter = BLUESStateDataStorage(reportInterval=reportInterval,
title='ncmc',
step=True,
speed=True,
progress=True,
remainingTime=True,
totalSteps=int(n_steps * nIter))
# Iniitialize our Move set
alchemical_atoms = utils.atomIndexfromTop('LIG', tol.topology)
rot_move = RandomLigandRotationMove(timestep=timestep,
n_steps=n_steps,
atom_subset=alchemical_atoms,
reporters=[ncmc_state_reporter])
langevin_move = ReportLangevinDynamicsMove(
timestep=timestep,
collision_rate=collision_rate,
n_steps=n_steps,
reassign_velocities=True,
reporters=[md_reporter, state_reporter])
sampler = BLUESSampler(thermodynamic_state=thermodynamic_state,
alch_thermodynamic_state=alch_thermodynamic_state,
sampler_state=sampler_state,
ncmc_move=rot_move,
dynamics_move=langevin_move,
def tol_atom_indices(structure):
atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
return atom_indices
def tol_atom_indices(structure):
atom_indices = utils.atomIndexfromTop('LIG', structure.topology)
return atom_indices
