def general_restraint_run(options):
"""
Generalized restraint simulation run to test free energy = standard state correction.
options : Dict. A dictionary of substitutions for restraint_test_yaml
"""
with mmtools.utils.temporary_directory() as output_directory:
# TODO refactor this to use AlchemicalPhase API rather than a YAML script.
options['output_directory'] = output_directory
# run both setup and experiment
yaml_builder = experiment.ExperimentBuilder(restraint_test_yaml %
options)
yaml_builder.run_experiments()
# Estimate Free Energies
ncfile_path = os.path.join(output_directory, 'experiments',
'complex.nc')
ncfile = netcdf.Dataset(ncfile_path, 'r')
Deltaf_ij, dDeltaf_ij = analyze.estimate_free_energies(ncfile)
# Correct the sign for the fact that we are adding vs removing the restraints
DeltaF_simulated = Deltaf_ij[-1, 0]
dDeltaF_simulated = dDeltaf_ij[-1, 0]
DeltaF_restraints = ncfile.groups['metadata'].variables[
'standard_state_correction'][0]
ncfile.close()
# Check if they are close
assert np.allclose(DeltaF_restraints,
DeltaF_simulated,
rtol=dDeltaF_simulated)
def general_restraint_run(options):
"""
Generalized restraint simulation run to test free energy = standard state correction.
options : Dict. A dictionary of substitutions for restraint_test_yaml
"""
with mmtools.utils.temporary_directory() as output_directory:
# TODO refactor this to use AlchemicalPhase API rather than a YAML script.
options['input_directory'] = get_data_filename(
os.path.join('tests', 'data'))
options['output_directory'] = output_directory
# run both setup and experiment
yaml_builder = experiment.ExperimentBuilder(restraint_test_yaml %
options)
yaml_builder.run_experiments()
# Estimate Free Energies
ncfile_path = os.path.join(output_directory, 'experiments',
'complex.nc')
reporter = multistate.MultiStateReporter(ncfile_path, open_mode='r')
#analyzer = multistate.MultiStateSamplerAnalyzer(reporter)
analyzer = YankMultiStateSamplerAnalyzer(reporter)
Deltaf_ij, dDeltaf_ij = analyzer.get_free_energy()
# Correct the sign for the fact that we are adding vs removing the restraints
DeltaF_simulated = Deltaf_ij[-1, 0]
dDeltaF_simulated = dDeltaf_ij[-1, 0]
print('Standard state correction:')
#ncfile = netcdf.Dataset(ncfile_path, 'r')
#print(ncfile.groups['metadata'].variables['standard_state_correction'][:])
#print(float(ncfile.groups['metadata'].variables['standard_state_correction'][:]))
#ncfile.close()
DeltaF_restraints = analyzer.get_standard_state_correction()
# Check if they are close
msg = ''
msg += 'Computed: %8.3f kT\n' % (DeltaF_restraints)
msg += 'Actual: %8.3f +- %8.3f kT\n' % (DeltaF_simulated,
dDeltaF_simulated)
msg += 'ERROR: %8.3f +- %8.3f kT\n' % (
DeltaF_restraints - DeltaF_simulated, dDeltaF_simulated)
# DEBUG
print(msg)
assert np.allclose(
DeltaF_restraints, DeltaF_simulated, rtol=2 *
dDeltaF_simulated), 'Standard state correction is inaccurate.\n' + msg