def test_write_object():
"""Test writing of a object.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
#use names we might encounter in simulation
envname = 'vacuum'
modname = 'ExpandedEnsembleSampler'
varname = 'energy'
view = NetCDFStorageView(storage, envname, modname)
obj = {0: 0}
view.write_object('singleton', obj)
for iteration in range(10):
obj = {'iteration': iteration}
view.write_object(varname, obj, iteration=iteration)
for iteration in range(10):
obj = storage.get_object(envname,
modname,
varname,
iteration=iteration)
assert ('iteration' in obj)
assert (obj['iteration'] == iteration)
def test_write_object():
"""Test writing of a object.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
#use names we might encounter in simulation
envname = 'vacuum'
modname = 'ExpandedEnsembleSampler'
varname = 'energy'
view = NetCDFStorageView(storage, envname, modname)
obj = { 0 : 0 }
view.write_object('singleton', obj)
for iteration in range(10):
obj = { 'iteration' : iteration }
view.write_object(varname, obj, iteration=iteration)
for iteration in range(10):
obj = storage.get_object(envname, modname, varname, iteration=iteration)
assert ('iteration' in obj)
assert (obj['iteration'] == iteration)
def test_storage_append():
"""Test storage layer appending to a file.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
storage.close()
storage = NetCDFStorage(tmpfile.name, mode='a')
storage.close()
def test_write_object():
"""Test writing of a object.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
view = NetCDFStorageView(storage, 'envname', 'modname')
obj = { 0 : 0 }
view.write_object('singleton', obj)
for iteration in range(10):
obj = { 'iteration' : iteration }
view.write_object('varname', obj, iteration=iteration)
for iteration in range(10):
obj = storage.get_object('/envname/modname/varname', iteration=iteration)
assert ('iteration' in obj)
assert (obj['iteration'] == iteration)
def test_storage_view():
"""Test writing of a quantity.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
view1 = NetCDFStorageView(storage, envname='envname')
view2 = NetCDFStorageView(view1, modname='modname')
assert (view1._envname == 'envname')
assert (view2._envname == 'envname')
assert (view2._modname == 'modname')
def test_storage_append():
"""Test storage layer appending to a file.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
storage.close()
storage = NetCDFStorage(tmpfile.name, mode='a')
storage.close()
def test_write_quantity():
"""Test writing of a quantity.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
view = NetCDFStorageView(storage, 'envname', 'modname')
view.write_quantity('singleton', 1.0)
for iteration in range(10):
view.write_quantity('varname', float(iteration), iteration=iteration)
for iteration in range(10):
assert (storage._ncfile['/envname/modname/varname'][iteration] == float(iteration))
def test_write_array():
"""Test writing of a array.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
view1 = NetCDFStorageView(storage, 'envname1', 'modname')
view2 = NetCDFStorageView(storage, 'envname2', 'modname')
from numpy.random import random
shape = (10, 3)
array = random(shape)
view1.write_array('singleton', array)
for iteration in range(10):
array = random(shape)
view1.write_array('varname', array, iteration=iteration)
view2.write_array('varname', array, iteration=iteration)
for iteration in range(10):
array = storage._ncfile['/envname1/modname/varname'][iteration]
assert array.shape == shape
array = storage._ncfile['/envname2/modname/varname'][iteration]
assert array.shape == shape
def test_sync():
"""Test writing of a quantity.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
storage.sync()
def test_storage_create():
"""Test storage layer creating a new file.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
storage.close()
def test_sync():
"""Test writing of a quantity.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
storage.sync()
def test_storage_create():
"""Test storage layer creating a new file.
"""
tmpfile = tempfile.NamedTemporaryFile()
storage = NetCDFStorage(tmpfile.name, mode='w')
storage.close()
def __init__(self, molecules: List[str], output_filename: str, ncmc_switching_times: Dict[str, int], equilibrium_steps: Dict[str, int], timestep: unit.Quantity, initial_molecule: str=None, geometry_options: Dict=None):
self._molecules = [SmallMoleculeSetProposalEngine.canonicalize_smiles(molecule) for molecule in molecules]
environments = ['explicit', 'vacuum']
temperature = 298.15 * unit.kelvin
pressure = 1.0 * unit.atmospheres
constraints = app.HBonds
self._storage = NetCDFStorage(output_filename)
self._ncmc_switching_times = ncmc_switching_times
self._n_equilibrium_steps = equilibrium_steps
self._geometry_options = geometry_options
# Create a system generator for our desired forcefields.
from perses.rjmc.topology_proposal import SystemGenerator
system_generators = dict()
from pkg_resources import resource_filename
gaff_xml_filename = resource_filename('perses', 'data/gaff.xml')
barostat = openmm.MonteCarloBarostat(pressure, temperature)
system_generators['explicit'] = SystemGenerator([gaff_xml_filename, 'tip3p.xml'],
forcefield_kwargs={'nonbondedCutoff': 9.0 * unit.angstrom,
'implicitSolvent': None,
'constraints': constraints,
'ewaldErrorTolerance': 1e-5,
'hydrogenMass': 3.0*unit.amu}, periodic_forcefield_kwargs = {'nonbondedMethod': app.PME}
barostat=barostat)
system_generators['vacuum'] = SystemGenerator([gaff_xml_filename],
forcefield_kwargs={'implicitSolvent': None,
'constraints': constraints,
'hydrogenMass': 3.0*unit.amu}, nonperiodic_forcefield_kwargs = {'nonbondedMethod': app.NoCutoff})
#
# Create topologies and positions
#
topologies = dict()
positions = dict()
from openmoltools import forcefield_generators
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
# Create molecule in vacuum.
from perses.utils.openeye import extractPositionsFromOEMol
from openmoltools.openeye import smiles_to_oemol, generate_conformers
if initial_molecule:
smiles = initial_molecule
else:
smiles = np.random.choice(molecules)
molecule = smiles_to_oemol(smiles)
molecule = generate_conformers(molecule, max_confs=1)
topologies['vacuum'] = forcefield_generators.generateTopologyFromOEMol(molecule)
positions['vacuum'] = extractPositionsFromOEMol(molecule)
# Create molecule in solvent.
modeller = app.Modeller(topologies['vacuum'], positions['vacuum'])
modeller.addSolvent(forcefield, model='tip3p', padding=9.0 * unit.angstrom)
topologies['explicit'] = modeller.getTopology()
positions['explicit'] = modeller.getPositions()
# Set up the proposal engines.
proposal_metadata = {}
proposal_engines = dict()
for environment in environments:
proposal_engines[environment] = SmallMoleculeSetProposalEngine(self._molecules,
system_generators[environment])
# Generate systems
systems = dict()
for environment in environments:
systems[environment] = system_generators[environment].build_system(topologies[environment])
# Define thermodynamic state of interest.
thermodynamic_states = dict()
thermodynamic_states['explicit'] = states.ThermodynamicState(system=systems['explicit'],
temperature=temperature, pressure=pressure)
thermodynamic_states['vacuum'] = states.ThermodynamicState(system=systems['vacuum'], temperature=temperature)
# Create SAMS samplers
from perses.samplers.samplers import ExpandedEnsembleSampler, SAMSSampler
mcmc_samplers = dict()
exen_samplers = dict()
sams_samplers = dict()
for environment in environments:
storage = NetCDFStorageView(self._storage, envname=environment)
if self._geometry_options:
n_torsion_divisions = self._geometry_options['n_torsion_divsions'][environment]
use_sterics = self._geometry_options['use_sterics'][environment]
else:
n_torsion_divisions = 180
use_sterics = False
geometry_engine = geometry.FFAllAngleGeometryEngine(storage=storage, n_torsion_divisions=n_torsion_divisions, use_sterics=use_sterics)
move = mcmc.LangevinSplittingDynamicsMove(timestep=timestep, splitting="V R O R V",
n_restart_attempts=10)
chemical_state_key = proposal_engines[environment].compute_state_key(topologies[environment])
if environment == 'explicit':
sampler_state = states.SamplerState(positions=positions[environment],
box_vectors=systems[environment].getDefaultPeriodicBoxVectors())
else:
sampler_state = states.SamplerState(positions=positions[environment])
mcmc_samplers[environment] = mcmc.MCMCSampler(thermodynamic_states[environment], sampler_state, move)
exen_samplers[environment] = ExpandedEnsembleSampler(mcmc_samplers[environment], topologies[environment],
chemical_state_key, proposal_engines[environment],
geometry_engine,
options={'nsteps': self._ncmc_switching_times[environment]}, storage=storage, ncmc_write_interval=self._ncmc_switching_times[environment])
exen_samplers[environment].verbose = True
sams_samplers[environment] = SAMSSampler(exen_samplers[environment], storage=storage)
sams_samplers[environment].verbose = True
# Create test MultiTargetDesign sampler.
from perses.samplers.samplers import MultiTargetDesign
target_samplers = {sams_samplers['explicit']: 1.0, sams_samplers['vacuum']: -1.0}
designer = MultiTargetDesign(target_samplers, storage=self._storage)
# Store things.
self.molecules = molecules
self.environments = environments
self.topologies = topologies
self.positions = positions
self.system_generators = system_generators
self.proposal_engines = proposal_engines
self.thermodynamic_states = thermodynamic_states
self.mcmc_samplers = mcmc_samplers
self.exen_samplers = exen_samplers
self.sams_samplers = sams_samplers
self.designer = designer
