def test_get_traj():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 300.0 * unit.kelvin
T_i = [T_min, T_min * 1.01, T_min * 1.1]
n_replicas = len(T_i)
ho = testsystems.AlanineDipeptideExplicit()
system = ho.system
positions = ho.positions
states = [ ThermodynamicState(system=system, temperature=T_i[i]) for i in range(n_replicas) ]
coordinates = [positions] * n_replicas
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations":3}
replica_exchange = ReplicaExchange.create(states, coordinates, nc_filename, mpicomm=mpicomm, parameters=parameters)
replica_exchange.run()
db = replica_exchange.database
prmtop_filename = testsystems.get_data_filename("data/alanine-dipeptide-explicit/alanine-dipeptide.prmtop")
crd_filename = testsystems.get_data_filename("data/alanine-dipeptide-explicit/alanine-dipeptide.crd")
trj0 = md.load_restrt(crd_filename, top=prmtop_filename)
db.set_traj(trj0)
trj1 = db.get_traj(state_index=0)
trj2 = db.get_traj(replica_index=0)
def test_alchemy():
import os
import simtk.unit as unit
import simtk.openmm as openmm
import numpy as np
import simtk.openmm.app as app
import alchemy
# Create SystemBuilder objects.
from openmmtools import testsystems
receptor_pdb_filename = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit/receptor.pdb")
ligand_mol2_filename = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit/ligand.tripos.mol2")
receptor = BiopolymerPDBSystemBuilder(receptor_pdb_filename, pH=7.0)
ligand = Mol2SystemBuilder(ligand_mol2_filename, charge=0)
complex = ComplexSystemBuilder(ligand, receptor, remove_ligand_overlap=True)
timestep = 2 * unit.femtoseconds # timestep
temperature = 300.0 * unit.kelvin # simulation temperature
collision_rate = 20.0 / unit.picoseconds # Langevin collision rate
minimization_tolerance = 10.0 * unit.kilojoules_per_mole / unit.nanometer
minimization_steps = 20
plat = "CPU"
i = 2
platform = openmm.Platform.getPlatformByName(plat)
forcefield = app.ForceField
systembuilders = [ligand, receptor, complex]
receptor_atoms = complex.receptor_atoms
ligand_atoms = complex.ligand_atoms
factory = alchemy.AbsoluteAlchemicalFactory(systembuilders[i].system, ligand_atoms=ligand_atoms)
protocol = factory.defaultComplexProtocolImplicit()
systems = factory.createPerturbedSystems(protocol)
integrator_interacting = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
# test an alchemical intermediate and an unperturbed system:
fully_interacting = app.Simulation(systembuilders[i].topology, systems[0], integrator_interacting, platform=plat)
fully_interacting.context.setPositions(systembuilders[i].positions)
fully_interacting.minimizeEnergy(tolerance=10 * unit.kilojoule_per_mole)
fully_interacting.reporters.append(app.PDBReporter("fully_interacting.pdb", 10))
for j in range(10):
print str(j)
fully_interacting.step(100)
del fully_interacting
for p in range(1, len(systems)):
print "now simulating " + str(p)
integrator_partialinteracting = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
partially_interacting = app.Simulation(
systembuilders[i].topology, systems[p], integrator_partialinteracting, platform=plat
)
partially_interacting.context.setPositions(systembuilders[i].positions)
partially_interacting.minimizeEnergy(tolerance=10 * unit.kilojoule_per_mole)
partially_interacting.reporters.append(app.PDBReporter("partial_interacting" + str(p) + ".pdb", 10))
for k in range(10):
print str(k)
partially_interacting.step(100)
del partially_interacting
def test_alchemy():
import os
import simtk.unit as unit
import simtk.openmm as openmm
import numpy as np
import simtk.openmm.app as app
import alchemy
# Create SystemBuilder objects.
from openmmtools import testsystems
receptor_pdb_filename = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit/receptor.pdb")
ligand_mol2_filename = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit/ligand.tripos.mol2")
receptor = BiopolymerPDBSystemBuilder(receptor_pdb_filename, pH=7.0)
ligand = Mol2SystemBuilder(ligand_mol2_filename, charge=0)
complex = ComplexSystemBuilder(ligand, receptor, remove_ligand_overlap=True)
timestep = 2 * unit.femtoseconds # timestep
temperature = 300.0 * unit.kelvin # simulation temperature
collision_rate = 20.0 / unit.picoseconds # Langevin collision rate
minimization_tolerance = 10.0 * unit.kilojoules_per_mole / unit.nanometer
minimization_steps = 20
plat = "CPU"
i=2
platform = openmm.Platform.getPlatformByName(plat)
forcefield = app.ForceField
systembuilders = [ligand, receptor, complex]
receptor_atoms = complex.receptor_atoms
ligand_atoms = complex.ligand_atoms
factory = alchemy.AbsoluteAlchemicalFactory(systembuilders[i].system, ligand_atoms=ligand_atoms)
protocol = factory.defaultComplexProtocolImplicit()
systems = factory.createPerturbedSystems(protocol)
integrator_interacting = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
#test an alchemical intermediate and an unperturbed system:
fully_interacting = app.Simulation(systembuilders[i].topology, systems[0], integrator_interacting, platform=plat)
fully_interacting.context.setPositions(systembuilders[i].positions)
fully_interacting.minimizeEnergy(tolerance=10*unit.kilojoule_per_mole)
fully_interacting.reporters.append(app.PDBReporter('fully_interacting.pdb', 10))
for j in range(10):
logger.info(str(j))
fully_interacting.step(100)
del fully_interacting
for p in range(1, len(systems)):
logger.info("now simulating " + str(p))
integrator_partialinteracting = openmm.LangevinIntegrator(temperature, collision_rate, timestep)
partially_interacting = app.Simulation(systembuilders[i].topology, systems[p], integrator_partialinteracting, platform=plat)
partially_interacting.context.setPositions(systembuilders[i].positions)
partially_interacting.minimizeEnergy(tolerance=10*unit.kilojoule_per_mole)
partially_interacting.reporters.append(app.PDBReporter('partial_interacting'+str(p)+'.pdb', 10))
for k in range(10):
logger.info(str(k))
partially_interacting.step(100)
del partially_interacting
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 test_get_data_filename():
"""Testing retrieval of data files shipped with distro.
"""
relative_path = 'data/alanine-dipeptide-gbsa/alanine-dipeptide.prmtop'
filename = testsystems.get_data_filename(relative_path)
if not os.path.exists(filename):
raise Exception("Could not locate data files. Expected %s" % relative_path)
def test_get_data_filename():
"""Testing retrieval of data files shipped with distro.
"""
relative_path = 'data/alanine-dipeptide-gbsa/alanine-dipeptide.prmtop'
filename = testsystems.get_data_filename(relative_path)
if not os.path.exists(filename):
raise Exception("Could not locate data files. Expected %s" % relative_path)
def test_systembuilder_lysozyme_pdb_mol2():
# TODO: Ensure we have some way to skip these when OpenEye tools are not installed.
raise SkipTest
logger.info("====================================================================")
logger.info("Creating T4 lysozyme L99A in OBC GBSA from PDB and mol2 with SystemBuilder...")
# Retrieve receptor and ligand file paths.
receptor_pdb_filename = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit/receptor.pdb")
ligand_mol2_filename = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit/ligand.tripos.mol2")
# Use systembuilder
from yank.systembuilder import Mol2SystemBuilder, BiopolymerPDBSystemBuilder, ComplexSystemBuilder
ligand = Mol2SystemBuilder(ligand_mol2_filename)
receptor = BiopolymerPDBSystemBuilder(receptor_pdb_filename)
complex = ComplexSystemBuilder(ligand, receptor, remove_ligand_overlap=True)
# Test alchemically modified systems.
receptor_atoms = range(0,2603) # T4 lysozyme L99A
ligand_atoms = range(2603,2621) # p-xylene
alchemical_factory_check(complex.system, complex.positions, receptor_atoms, ligand_atoms)
logger.info("====================================================================")
logger.info("")
def test_get_traj():
nc_filename = tempfile.mkdtemp() + "/out.nc"
T_min = 300.0 * unit.kelvin
T_i = [T_min, T_min * 1.01, T_min * 1.1]
n_replicas = len(T_i)
ho = testsystems.AlanineDipeptideExplicit()
system = ho.system
positions = ho.positions
states = [
ThermodynamicState(system=system, temperature=T_i[i])
for i in range(n_replicas)
]
coordinates = [positions] * n_replicas
mpicomm = dummympi.DummyMPIComm()
parameters = {"number_of_iterations": 3}
replica_exchange = ReplicaExchange.create(states,
coordinates,
nc_filename,
mpicomm=mpicomm,
parameters=parameters)
replica_exchange.run()
db = replica_exchange.database
prmtop_filename = testsystems.get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.prmtop")
crd_filename = testsystems.get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.crd")
trj0 = md.load_restrt(crd_filename, top=prmtop_filename)
db.set_traj(trj0)
trj1 = db.get_traj(state_index=0)
trj2 = db.get_traj(replica_index=0)
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 = get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.prmtop")
self.inpcrd = get_data_filename(
"data/alanine-dipeptide-explicit/alanine-dipeptide.crd")
self.full_struct = parmed.load_file(self.prmtop, xyz=self.inpcrd)
self.opt = {
'temperature': 300.0,
'friction': 1,
'dt': 0.00002,
'nIter': 2,
'nstepsNC': 4,
'nstepsMD': 2,
'nprop': 1,
'nonbondedMethod': 'PME',
'nonbondedCutoff': 10,
'constraints': 'HBonds',
'trajectory_interval': 1,
'reporter_interval': 1,
'outfname': 'mc-test',
'platform': None
}
def test_setup_binding():
dirname = testsystems.get_data_filename("data/T4-lysozyme-L99A-implicit")
storedir = tempfile.mkdtemp()
run_cli('setup binding amber --setupdir=%(dirname)s --ligname MOL --store %(storedir)s' % vars())
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)