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)
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()
self.assertTrue(pos_compare)
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 rotmove_cuda(yaml_file):
# Parse a YAML configuration, return as Dict
cfg = Settings('rotmove_cuda.yaml').asDict()
structure = cfg['Structure']
#Select move type
ligand = RandomLigandRotationMove(structure, 'MOL')
#Iniitialize object that selects movestep
ligand_mover = MoveEngine(ligand)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, ligand.atom_indices, cfg['system'])
#Freeze atoms in the alchemical system to speed up alchemical calculation
cfg['freeze'] = { 'freeze_distance' : 12 ,
'freeze_center' : ':MOL',
'freeze_solvent': ':HOH,NA,CL'}
systems.alch = systems.freeze_radius(structure, systems.alch, **cfg['freeze'])
#Generate the OpenMM Simulations
simulations = SimulationFactory(systems, ligand_mover, cfg['simulation'], cfg['md_reporters'],
cfg['ncmc_reporters'])
# Run BLUES Simulation
blues = BLUESSimulation(simulations, cfg['simulation'])
blues.run()
def runNCMC(platform_name, nstepsNC, nprop, outfname):
#Generate the ParmEd Structure
prmtop = '../../complex_wat.prmtop'
inpcrd = '../../ligand1.equi.rst'
struct = parmed.load_file(prmtop, xyz=inpcrd)
print('Structure: %s' % struct.topology)
nstepsNC = 1000
#Define some options
opt = { 'temperature' : 300.0, 'friction' : 1, 'dt' : 0.002,
'nIter' : 5000, 'nstepsNC' : nstepsNC, 'nstepsMD' : 1000, 'nprop' : nprop,
'nonbondedMethod' : 'PME', 'nonbondedCutoff': 10,
'constraints': 'HBonds', 'freeze_distance' : 5.0,
'trajectory_interval' : 1000, 'reporter_interval' : 1000,
'ncmc_traj' : False, 'write_move' : False,
'platform' : platform_name,
'outfname' : 'gmx', 'NPT' : False,
'verbose' : False}
#Define the 'model' object we are perturbing here.
# Calculate particle masses of object to be moved
resname = "LIG"
dihedral_atoms = ["C10", "C9", "C3", "C2" ]
alch_list = ['C9', 'H92', 'H93', 'C1', 'C2', 'C3', 'C4', 'C5', 'C6', 'H1', 'H2', 'H4', 'H5', 'H6']
ligand = RotatableBondNoMove(struct, prmtop, inpcrd, dihedral_atoms, alch_list, resname)
# Initialize object that proposes moves.
ligand_mover = MoveEngine(ligand)
# Generate the MD, NCMC, ALCHEMICAL Simulation objects
simulations = SimulationFactory(struct, ligand_mover, **opt)
simulations.createSimulationSet()
# Add reporters to MD simulation.
#traj_reporter = openmm.app.DCDReporter(outfname+'-nc{}.dcd'.format(nstepsNC), opt['trajectory_interval'])
progress_reporter = openmm.app.StateDataReporter(sys.stdout, separator="\t",
reportInterval=opt['reporter_interval'],
step=True, totalSteps=opt['nIter']*opt['nstepsMD'],
time=True, speed=True, progress=True, remainingTime=True)
#simulations.md.reporters.append(traj_reporter)
simulations.md.reporters.append(progress_reporter)
netcdf_reporter = NetCDFReporter('gmx.nc', 500, crds=True)
simulations.md.reporters.append(netcdf_reporter)
# Run BLUES Simulation
blues = Simulation(simulations, ligand_mover, **opt)
blues.run(opt['nIter'])
# saving last restart
restrt = RestartReporter('blues.rst', 1, struct.ptr('natom') );
state = simulations.md.context.getState(getPositions=True, getEnergy=True, getVelocities=True, enforcePeriodicBox=True)
restrt.report(simulations.md, state)
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):
testsystem = testsystems.AlanineDipeptideVacuum(constraints=None)
self.structure = parmed.openmm.topsystem.load_topology(
topology=testsystem.topology,
system=testsystem.system,
xyz=testsystem.positions)
self.move = RandomLigandRotationMove(self.structure, 'ALA')
self.engine = MoveEngine(self.move)
system_cfg = {
'nonbondedMethod': app.NoCutoff,
'constraints': app.HBonds
}
self.systems = SystemFactory(self.structure, self.move.atom_indices,
system_cfg)
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_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 runNCMC(platform_name, relaxstepsNC, themdsteps):
#Define some options
opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.002,
'nIter': 50000,
'nstepsNC': relaxstepsNC,
'nstepsMD': themdsteps,
'nonbondedMethod': 'PME',
'nonbondedCutoff': 10,
'constraints': 'HBonds',
'trajectory_interval': 1000,
'reporter_interval': 1000,
'platform': platform_name,
'verbose': False,
'write_ncmc': False
}
#Generate the ParmEd Structure
#prmtop = utils.get_data_filename('blues', 'tests/data/eqToluene.prmtop')#
#inpcrd = utils.get_data_filename('blues', 'tests/data/eqToluene.inpcrd')
prmtop = '/home/burleyk/projects/sidechain/inputs/watDivaline.prmtop'
inpcrd = '/home/burleyk/projects/sidechain/inputs/watDivaline.inpcrd'
struct = parmed.load_file(prmtop, xyz=inpcrd)
#Define the 'model' object we are perturbing here.
# Calculate particle masses of object to be moved
ligand = SideChainMove(struct, [1])
ligand.atom_indices = ligand.rot_bond_atoms
# Initialize object that proposes moves.
ligand_mover = MoveEngine(ligand)
# Generate the MD, NCMC, ALCHEMICAL Simulation objects
simulations = SimulationFactory(struct, ligand_mover, **opt)
simulations.createSimulationSet()
blues = Simulation(simulations, ligand_mover, **opt)
#add the reporter here
blues.md_sim.reporters.append(
openmm.app.dcdreporter.DCDReporter('accept.dcd', 1000))
blues.runNCMC()
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.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, 'outfname' : 'vacDivaline',
'platform' : None,
'verbose' : False }
self.sidechain = SideChainMove(self.struct, [1])
self.mover = MoveEngine(self.sidechain)
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 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)
system_cfg = {
'nonbondedMethod': app.PME,
'nonbondedCutoff': 8.0 * unit.angstroms,
'constraints': app.HBonds
}
self.systems = SystemFactory(self.structure, self.atom_indices,
system_cfg)
move = RandomLigandRotationMove(self.structure, 'LIG')
self.engine = MoveEngine(move)
self.simulations = SimulationFactory(self.systems, self.engine)
self.system = self.simulations._system
def runNCMC(platform_name, nstepsNC, nprop, outfname):
#Generate the ParmEd Structure
prmtop = utils.get_data_filename('blues', 'tests/data/vacDivaline.prmtop')
inpcrd = utils.get_data_filename('blues', 'tests/data/vacDivaline.inpcrd')
struct = parmed.load_file(prmtop, xyz=inpcrd)
print('Structure: %s' % struct.topology)
#Define some options
opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.004,
'hydrogenMass': 3.024,
'nIter': 100,
'nstepsNC': nstepsNC,
'nstepsMD': 1000,
'nprop': nprop,
'nonbondedMethod': 'PME',
'nonbondedCutoff': 10,
'constraints': 'HBonds',
'trajectory_interval': 100,
'reporter_interval': 250,
'ncmc_traj': None,
'write_move': False,
'platform': platform_name,
'outfname': 'vacDivaline',
'verbose': False
}
#Define the 'model' object we are perturbing here.
# Calculate particle masses of object to be moved
ligand = SideChainMove(struct, [1])
# Initialize object that proposes moves.
ligand_mover = MoveEngine(ligand)
# Generate the MD, NCMC, ALCHEMICAL Simulation objects
simulations = SimulationFactory(struct, ligand_mover, **opt)
simulations.createSimulationSet()
# Add reporters to MD simulation.
trajfile = outfname + '-nc{}.dcd'.format(nstepsNC)
traj_reporter = openmm.app.DCDReporter(trajfile,
opt['trajectory_interval'])
progress_reporter = openmm.app.StateDataReporter(
sys.stdout,
separator="\t",
reportInterval=opt['reporter_interval'],
step=True,
totalSteps=opt['nIter'] * opt['nstepsMD'],
time=True,
speed=True,
progress=True,
elapsedTime=True,
remainingTime=True)
simulations.md.reporters.append(traj_reporter)
simulations.md.reporters.append(progress_reporter)
# Run BLUES Simulation
blues = Simulation(simulations, ligand_mover, **opt)
blues.run(opt['nIter'])
#Analysis
import mdtraj as md
import numpy as np
traj = md.load_dcd(trajfile, top='protein.pdb')
indicies = np.array([[0, 4, 6, 8]])
dihedraldata = md.compute_dihedrals(traj, indicies)
with open("dihedrals-%iNC.txt" % (nstepsNC), 'w') as output:
for value in dihedraldata:
output.write("%s\n" % str(value)[1:-1])
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]
self.assertEqual(len(vals), 11)
#Ensure it selects 1 rotatable bond in Valine
self.assertEqual(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()
self.assertTrue(pos_compare)
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 runNCMC(platform_name, nstepsNC, nprop, outfname):
#Generate the ParmEd Structure
prmtop = utils.get_data_filename('blues', 'tests/data/eqToluene.prmtop') #
inpcrd = utils.get_data_filename('blues', 'tests/data/eqToluene.inpcrd')
struct = parmed.load_file(prmtop, xyz=inpcrd)
#Define some options
opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.002,
'nIter': 100,
'nstepsNC': 10000,
'nstepsMD': 10000,
'nprop': 1,
'nonbondedMethod': 'PME',
'nonbondedCutoff': 10,
'constraints': 'HBonds',
'freeze_distance': 5.0,
'trajectory_interval': 2000,
'reporter_interval': 1000,
'write_move': False,
'platform': platform_name,
'outfname': 't4-toluene'
}
logger = init_logger(logging.getLogger(),
level=logging.INFO,
outfname=opt['outfname'])
opt['Logger'] = logger
#Define the 'model' object we are perturbing here.
# Calculate particle masses of object to be moved
ligand = RandomLigandRotationMove(struct, 'LIG')
ligand.calculateProperties()
# Initialize object that proposes moves.
ligand_mover = MoveEngine(ligand)
# Generate the MD, NCMC, ALCHEMICAL Simulation objects
simulations = SimulationFactory(struct, ligand_mover, **opt)
simulations.createSimulationSet()
# Add reporters to MD simulation.
traj_reporter = openmm.app.DCDReporter(
opt['outfname'] + '-nc{}.dcd'.format(nstepsNC),
opt['trajectory_interval'])
md_progress_reporter = BLUESStateDataReporter(
logger,
separator="\t",
title='md',
reportInterval=opt['reporter_interval'],
step=True,
totalSteps=opt['nIter'] * opt['nstepsMD'],
time=False,
speed=True,
progress=True,
remainingTime=True)
simulations.md.reporters.append(traj_reporter)
simulations.md.reporters.append(md_progress_reporter)
# Add reporters to NCMC simulation.
ncmc_reporter = BLUESHDF5Reporter(file=opt['outfname'] + '-pmoves.h5',
reportInterval=1,
coordinates=True,
frame_indices=[1, opt['nstepsNC']],
time=False,
cell=True,
temperature=False,
potentialEnergy=False,
kineticEnergy=False,
velocities=False,
atomSubset=None,
protocolWork=True,
alchemicalLambda=True,
parameters=opt,
environment=True)
ncmc_progress_reporter = BLUESStateDataReporter(
logger,
separator="\t",
title='ncmc',
reportInterval=opt['reporter_interval'],
step=True,
totalSteps=opt['nstepsNC'],
time=False,
speed=True,
progress=True,
remainingTime=True)
simulations.nc.reporters.append(ncmc_reporter)
simulations.nc.reporters.append(ncmc_progress_reporter)
# Run BLUES Simulation
blues = Simulation(simulations, ligand_mover, **opt)
blues.run(opt['nIter'])
from blues.moves import RandomLigandRotationMove
from blues.engine import MoveEngine
from blues.simulation import *
import json
from blues.settings import *
# Parse a YAML configuration, return as Dict
cfg = Settings('rotmove_cuda.yaml').asDict()
structure = cfg['Structure']
#Select move type
ligand = RandomLigandRotationMove(structure, 'LIG')
#Iniitialize object that selects movestep
ligand_mover = MoveEngine(ligand)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, ligand.atom_indices, cfg['system'])
#Freeze atoms in the alchemical system to speed up alchemical calculation
systems.alch = systems.freeze_radius(structure, systems.alch, **cfg['freeze'])
#Generate the OpenMM Simulations
simulations = SimulationFactory(systems, ligand_mover, cfg['simulation'],
cfg['md_reporters'], cfg['ncmc_reporters'])
# Run BLUES Simulation
blues = BLUESSimulation(simulations, cfg['simulation'])
blues.run()
def runNCMC(platform_name, nstepsNC, nprop, outfname):
#Generate the ParmEd Structure
prmtop = utils.get_data_filename('blues', 'tests/data/eqToluene.prmtop') #
inpcrd = utils.get_data_filename('blues', 'tests/data/eqToluene.inpcrd')
struct = parmed.load_file(prmtop, xyz=inpcrd)
print('Structure: %s' % struct.topology)
#Define some options
opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.002,
'nIter': 100,
'nstepsNC': nstepsNC,
'nstepsMD': 5000,
'nprop': nprop,
'nonbondedMethod': 'PME',
'nonbondedCutoff': 10,
'constraints': 'HBonds',
'freeze_distance': 5.0,
'trajectory_interval': 1000,
'reporter_interval': 1000,
'ncmc_traj': None,
'write_move': True,
'platform': platform_name,
'outfname': 't4-tol',
'verbose': False
}
#Define the 'model' object we are perturbing here.
# Calculate particle masses of object to be moved
ligand = RandomLigandRotationMove(struct, 'LIG')
ligand.calculateProperties()
# Initialize object that proposes moves.
ligand_mover = MoveEngine(ligand)
# Generate the MD, NCMC, ALCHEMICAL Simulation objects
simulations = SimulationFactory(struct, ligand_mover, **opt)
simulations.createSimulationSet()
# Add reporters to MD simulation.
traj_reporter = openmm.app.DCDReporter(
outfname + '-nc{}.dcd'.format(nstepsNC), opt['trajectory_interval'])
progress_reporter = openmm.app.StateDataReporter(
sys.stdout,
separator="\t",
reportInterval=opt['reporter_interval'],
step=True,
totalSteps=opt['nIter'] * opt['nstepsMD'],
time=True,
speed=True,
progress=True,
remainingTime=True)
simulations.md.reporters.append(traj_reporter)
simulations.md.reporters.append(progress_reporter)
# Run BLUES Simulation
blues = Simulation(simulations, ligand_mover, **opt)
blues.run(opt['nIter'])
from blues.moves import SideChainMove
from blues.engine import MoveEngine
from blues.simulation import *
import json
from blues.settings import *
# Parse a YAML configuration, return as Dict
cfg = Settings('sidechain_cuda.yaml').asDict()
structure = cfg['Structure']
#Select move type
sidechain = SideChainMove(structure, [1])
#Iniitialize object that selects movestep
sidechain_mover = MoveEngine(sidechain)
#Generate the openmm.Systems outside SimulationFactory to allow modifications
systems = SystemFactory(structure, sidechain.atom_indices, cfg['system'])
#Generate the OpenMM Simulations
simulations = SimulationFactory(systems, sidechain_mover, cfg['simulation'], cfg['md_reporters'],
cfg['ncmc_reporters'])
# Run BLUES Simulation
blues = BLUESSimulation(simulations, cfg['simulation'])
blues.run()
#Analysis
import mdtraj as md
import numpy as np
traj = md.load_netcdf('vacDivaline-test/vacDivaline.nc', top='tests/data/vacDivaline.prmtop')
def setUp(self):
prmtop = testsystems.get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.prmtop")
inpcrd = testsystems.get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.crd")
self.structure = parmed.load_file(prmtop, xyz=inpcrd)
class SetRotationMove(RandomLigandRotationMove):
def __init__(self, structure, resname='ALA'):
super(SetRotationMove, self).__init__(structure, resname)
def move(self, context):
"""Function that performs a random rotation about the
center of mass of the ligand. Define a set rotation
for reproducibility
"""
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]])
#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.move = SetRotationMove(self.structure, resname='ALA')
self.move.atom_indices = range(22)
self.move.topology = self.structure[self.move.atom_indices].topology
self.move.positions = self.structure[self.move.atom_indices].positions
self.move.calculateProperties()
self.engine = MoveEngine(self.move)
system_cfg = {
'nonbondedMethod': app.NoCutoff,
'constraints': app.HBonds
}
#self.systems = self.structure.createSystem(**system_cfg)
self.systems = SystemFactory(self.structure, self.move.atom_indices,
system_cfg)
mc_rep_cfg = {
'stream': {
'title': 'mc',
'reportInterval': 1,
'totalSteps': 4,
'step': True,
'speed': True,
'progress': True,
'remainingTime': True,
'currentIter': True
}
}
mc_reporters = ReporterConfig('ala-dipep-vac',
mc_rep_cfg).makeReporters()
cfg = {
'nprop': 1,
'dt': 0.000021 * unit.picoseconds,
'friction': 1 * 1 / unit.picoseconds,
'temperature': 300 * unit.kelvin,
'nIter': 2,
'nstepsMD': 1,
'mc_per_iter': 2
}
self.simulations = SimulationFactory(self.systems,
self.engine,
cfg,
md_reporters=mc_reporters)