Index

_

__init__() (meld.comm.HostInfo method) (meld.comm.MPICommunicator method) (meld.helpers.REMDInfo method) (meld.interfaces.ExtraAngleParam method) (meld.interfaces.ExtraBondParam method) (meld.interfaces.ExtraTorsParam method) (meld.interfaces.ICommunicator method) (meld.interfaces.IRunner method) (meld.interfaces.IState method) (meld.interfaces.ISystem method) (meld.remd.adaptor.AdaptationPolicy method) (meld.remd.adaptor.AdaptationRequired method) (meld.remd.adaptor.EqualAcceptanceAdaptor method) (meld.remd.adaptor.NullAdaptor method) (meld.remd.adaptor.SwitchingCompositeAdaptor method) (meld.remd.ladder.NearestNeighborLadder method) (meld.remd.leader.LeaderReplicaExchangeRunner method) (meld.remd.worker.WorkerReplicaExchangeRunner method) (meld.runner.fake_runner.FakeSystemRunner method) (meld.runner.openmm_runner.OpenMMRunner method) (meld.runner.transform.rest2.REST2Transformer method) (meld.runner.transform.restraints.cartesian.CartesianRestraintTransformer method) (meld.runner.transform.restraints.cartesian.YZCartesianTransformer method) (meld.runner.transform.restraints.com.AbsoluteCOMRestraintTransformer method) (meld.runner.transform.restraints.com.COMRestraintTransformer method) (meld.runner.transform.restraints.confinement.ConfinementRestraintTransformer method) (meld.runner.transform.restraints.meld.meld.MeldRestraintTransformer method) (meld.runner.transform.restraints.meld.tracker.RestraintTracker method) (meld.runner.transform.TransformerBase method) (meld.system.amber.CrdReader method) (meld.system.amber.ParmTopReader method) (meld.system.builders.amber.amap.CMAPResidue method) (meld.system.builders.amber.builder.AmberOptions method) (meld.system.builders.amber.builder.AmberSystemBuilder method) (meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile method) (meld.system.builders.amber.subsystem.AmberSubSystemFromSequence method) (meld.system.builders.spec.SystemSpec method) (meld.system.density.DensityManager method) (meld.system.density.DensityMap method) (meld.system.indexing.AtomIndex method) (meld.system.indexing.Indexer method) (meld.system.indexing.ResidueIndex method) (meld.system.mapping.PeakMapManager method) (meld.system.mapping.PeakMapper method) (meld.system.mapping.PeakMapping method) (meld.system.meld_system.System method) (meld.system.montecarlo.DoubleTorsionMover method) (meld.system.montecarlo.MonteCarloScheduler method) (meld.system.montecarlo.Mover method) (meld.system.montecarlo.RandomTorsionMover method) (meld.system.montecarlo.TranslationMover method) (meld.system.options.RunOptions method) (meld.system.param_sampling.ContinuousParameter method) (meld.system.param_sampling.ContinuousPrior method) (meld.system.param_sampling.ContinuousSampler method) (meld.system.param_sampling.DiscreteParameter method) (meld.system.param_sampling.DiscretePrior method) (meld.system.param_sampling.DiscreteSampler method) (meld.system.param_sampling.ExponentialContinuousPrior method) (meld.system.param_sampling.ExponentialDiscretePrior method) (meld.system.param_sampling.Parameter method) (meld.system.param_sampling.ParameterManager method) (meld.system.param_sampling.ParameterState method) (meld.system.param_sampling.Prior method) (meld.system.param_sampling.Sampler method) (meld.system.param_sampling.ScaledExponentialDiscretePrior method) (meld.system.param_sampling.UniformContinuousPrior method) (meld.system.param_sampling.UniformDiscretePrior method) (meld.system.patchers.rdc_integrator.CustomRDCIntegrator method) (meld.system.pdb_writer.PDBWriter method) (meld.system.restraints.AbsoluteCOMRestraint method) (meld.system.restraints.AlwaysActiveCollection method) (meld.system.restraints.CartesianRestraint method) (meld.system.restraints.COMRestraint method) (meld.system.restraints.ConfinementRestraint method) (meld.system.restraints.DensityRestraint method) (meld.system.restraints.DistanceRestraint method) (meld.system.restraints.DistProfileRestraint method) (meld.system.restraints.GMMDistanceRestraint method) (meld.system.restraints.GMMParams method) (meld.system.restraints.HyperbolicDistanceRestraint method) (meld.system.restraints.NonSelectableRestraint method) (meld.system.restraints.RdcRestraint method) (meld.system.restraints.Restraint method) (meld.system.restraints.RestraintGroup method) (meld.system.restraints.RestraintManager method) (meld.system.restraints.SelectableRestraint method) (meld.system.restraints.SelectivelyActiveCollection method) (meld.system.restraints.TorsionRestraint method) (meld.system.restraints.TorsProfileRestraint method) (meld.system.restraints.YZCartesianRestraint method) (meld.system.scalers.AlphaMapper method) (meld.system.scalers.BlurScaler method) (meld.system.scalers.ConstantBlurScaler method) (meld.system.scalers.ConstantPositioner method) (meld.system.scalers.ConstantRamp method) (meld.system.scalers.ConstantScaler method) (meld.system.scalers.GeometricScaler method) (meld.system.scalers.LinearBlurScaler method) (meld.system.scalers.LinearPositioner method) (meld.system.scalers.LinearRamp method) (meld.system.scalers.LinearScaler method) (meld.system.scalers.NonLinearRamp method) (meld.system.scalers.NonLinearScaler method) (meld.system.scalers.PlateauLinearScaler method) (meld.system.scalers.PlateauNonLinearScaler method) (meld.system.scalers.PlateauSmoothScaler method) (meld.system.scalers.Positioner method) (meld.system.scalers.RestraintScaler method) (meld.system.scalers.ScalerRegistry method) (meld.system.scalers.TimeRamp method) (meld.system.scalers.TimeRampSwitcher method) (meld.system.state.SystemState method) (meld.system.temperature.ConstantTemperatureScaler method) (meld.system.temperature.GeometricTemperatureScaler method) (meld.system.temperature.LinearTemperatureScaler method) (meld.system.temperature.REST2Scaler method) (meld.system.temperature.TemperatureScaler method) (meld.util.HostNameContextFilter method) (meld.vault.DataStore method)

A

AbsoluteCOMRestraint (class in meld.system.restraints) AbsoluteCOMRestraintTransformer (class in meld.runner.transform.restraints.com) adapt() (meld.remd.adaptor.EqualAcceptanceAdaptor method) (meld.remd.adaptor.SwitchingCompositeAdaptor method) adapt_now (meld.remd.adaptor.AdaptationRequired attribute) AdaptationPolicy (class in meld.remd.adaptor) AdaptationRequired (class in meld.remd.adaptor) add_amap() (in module meld.system.builders.amber.amap) add_as_always_active() (meld.system.restraints.RestraintManager method) add_as_always_active_list() (meld.system.restraints.RestraintManager method) add_elastic_network_restraints() (in module meld.system.builders.build_elastic_network_restraints) add_extra_angle() (meld.interfaces.ISystem method) (meld.system.meld_system.System method) add_extra_bond() (meld.interfaces.ISystem method) (meld.system.meld_system.System method) add_extra_torsion() (meld.interfaces.ISystem method) (meld.system.meld_system.System method) add_interactions() (meld.runner.transform.restraints.cartesian.CartesianRestraintTransformer method) (meld.runner.transform.restraints.cartesian.YZCartesianTransformer method) (meld.runner.transform.restraints.com.AbsoluteCOMRestraintTransformer method) (meld.runner.transform.restraints.com.COMRestraintTransformer method) (meld.runner.transform.restraints.confinement.ConfinementRestraintTransformer method) (meld.runner.transform.restraints.meld.meld.MeldRestraintTransformer method) (meld.runner.transform.TransformerBase method)

add_rdc_alignment() (in module meld.system.patchers.rdc_alignment) add_restraint() (meld.system.restraints.AlwaysActiveCollection method) add_selectively_active_collection() (meld.system.restraints.RestraintManager method) add_virtual_spin_label() (in module meld.system.patchers.spin_label) AlphaMapper (class in meld.system.scalers) alphas (meld.remd.leader.LeaderReplicaExchangeRunner property) always_active (meld.system.restraints.RestraintManager property) AlwaysActiveCollection (class in meld.system.restraints) AmberOptions (class in meld.system.builders.amber.builder) AmberSubSystemFromPdbFile (class in meld.system.builders.amber.subsystem) AmberSubSystemFromSequence (class in meld.system.builders.amber.subsystem) AmberSystemBuilder (class in meld.system.builders.amber.builder) angle (meld.interfaces.ExtraAngleParam attribute) append_traj() (meld.vault.DataStore method) atom() (meld.system.indexing.Indexer method) atom_name (meld.system.mapping.PeakMapping attribute) atom_names (meld.interfaces.ISystem property) (meld.system.meld_system.System property) AtomIndex (class in meld.system.indexing) atoms (meld.system.restraints.GMMParams attribute)

B

backup() (meld.vault.DataStore method) barostat (meld.interfaces.ISystem property) (meld.system.builders.spec.SystemSpec attribute) (meld.system.meld_system.System property) barrier() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method)

BlurScaler (class in meld.system.scalers) box_vectors (meld.system.builders.spec.SystemSpec attribute) broadcast_all_states_to_workers() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) build_system() (meld.system.builders.amber.builder.AmberSystemBuilder method) builder_info (meld.system.builders.spec.SystemSpec attribute)

C

C (meld.system.builders.amber.amap.CMAPResidue attribute) CA (meld.system.builders.amber.amap.CMAPResidue attribute) CartesianRestraint (class in meld.system.restraints) CartesianRestraintTransformer (class in meld.runner.transform.restraints.cartesian) close() (meld.vault.DataStore method) CMAPResidue (class in meld.system.builders.amber.amap) communicator (meld.helpers.REMDInfo attribute) compute_exchanges() (meld.remd.ladder.NearestNeighborLadder method) COMRestraint (class in meld.system.restraints) COMRestraintTransformer (class in meld.runner.transform.restraints.com) ConfinementRestraint (class in meld.system.restraints) ConfinementRestraintTransformer (class in meld.runner.transform.restraints.confinement) ConstantBlurScaler (class in meld.system.scalers) ConstantPositioner (class in meld.system.scalers)

ConstantRamp (class in meld.system.scalers) ConstantScaler (class in meld.system.scalers) ConstantTemperatureScaler (class in meld.system.temperature) continuous (meld.system.param_sampling.ParameterState attribute) ContinuousParameter (class in meld.system.param_sampling) ContinuousPrior (class in meld.system.param_sampling) ContinuousSampler (class in meld.system.param_sampling) coordinates (meld.system.builders.spec.SystemSpec attribute) CrdReader (class in meld.system.amber) create_elastic_network_restraints() (in module meld.system.builders.build_elastic_network_restraints) create_restraint() (meld.system.restraints.RestraintManager method) create_restraint_group() (meld.system.restraints.RestraintManager method) create_scaler() (meld.system.restraints.RestraintManager method) CustomRDCIntegrator (class in meld.system.patchers.rdc_integrator)

D

DataStore (class in meld.vault) density (meld.system.meld_system.System attribute) DensityManager (class in meld.system.density) DensityMap (class in meld.system.density) DensityRestraint (class in meld.system.restraints) devices (meld.comm.HostInfo attribute) discrete (meld.system.param_sampling.ParameterState attribute) DiscreteParameter (class in meld.system.param_sampling)

DiscretePrior (class in meld.system.param_sampling) DiscreteSampler (class in meld.system.param_sampling) DistanceRestraint (class in meld.system.restraints) DistProfileRestraint (class in meld.system.restraints) distribute_alphas_to_workers() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) distribute_states_to_workers() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) DoubleTorsionMover (class in meld.system.montecarlo)

E

energy (meld.interfaces.ExtraTorsParam attribute) EqualAcceptanceAdaptor (class in meld.remd.adaptor) ExponentialContinuousPrior (class in meld.system.param_sampling)

ExponentialDiscretePrior (class in meld.system.param_sampling) ExtraAngleParam (class in meld.interfaces) ExtraBondParam (class in meld.interfaces) ExtraTorsParam (class in meld.interfaces)

F

FakeSystemRunner (class in meld.runner.fake_runner) filter() (meld.util.HostNameContextFilter method) finalize() (meld.runner.transform.rest2.REST2Transformer method) (meld.runner.transform.TransformerBase method) (meld.system.builders.spec.SystemSpec method)

force_constant (meld.interfaces.ExtraAngleParam attribute) (meld.interfaces.ExtraBondParam attribute) freeze_atoms() (in module meld.system.patchers.freeze) from_params() (meld.system.restraints.GMMDistanceRestraint class method)

G

gather_energies_from_workers() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) gather_states_from_workers() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) generate_tleap_input() (meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile method) (meld.system.builders.amber.subsystem.AmberSubSystemFromSequence method) GeometricScaler (class in meld.system.scalers) GeometricTemperatureScaler (class in meld.system.temperature) get_atom_map() (meld.system.amber.ParmTopReader method) get_atom_names() (meld.system.amber.ParmTopReader method) get_bonds() (meld.system.amber.ParmTopReader method) get_box_vectors() (meld.system.amber.CrdReader method) get_constructor_for_key() (meld.system.scalers.ScalerRegistry class method) get_coordinates() (meld.system.amber.CrdReader method)

get_pdb_string() (meld.system.pdb_writer.PDBWriter method) get_pdb_writer() (meld.interfaces.ISystem method) (meld.system.meld_system.System method) get_rdc_restraints() (in module meld.parse) get_residue_names() (meld.system.amber.ParmTopReader method) get_residue_numbers() (meld.system.amber.ParmTopReader method) get_runner() (in module meld.runner) get_secondary_structure_restraints() (in module meld.parse) get_sequence_from_AA1() (in module meld.parse) get_sequence_from_AA3() (in module meld.parse) get_state_template() (meld.interfaces.ISystem method) (meld.system.meld_system.System method) GMMDistanceRestraint (class in meld.system.restraints) GMMParams (class in meld.system.restraints) groups (meld.system.restraints.SelectivelyActiveCollection property)

H

host_name (meld.comm.HostInfo attribute) HostInfo (class in meld.comm)

HostNameContextFilter (class in meld.util) HyperbolicDistanceRestraint (class in meld.system.restraints)

I

i (meld.interfaces.ExtraAngleParam attribute) (meld.interfaces.ExtraBondParam attribute) (meld.interfaces.ExtraTorsParam attribute) ICommunicator (class in meld.interfaces) in_temp_dir() (in module meld.util) index (meld.system.meld_system.System attribute) Indexer (class in meld.system.indexing) initialize() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) (meld.vault.DataStore method)

integrator (meld.interfaces.ISystem property) (meld.system.builders.spec.SystemSpec attribute) (meld.system.meld_system.System property) IRunner (class in meld.interfaces) is_leader() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) IState (class in meld.interfaces) ISystem (class in meld.interfaces) iterate_box_vectors() (meld.vault.DataStore method) iterate_permutation_vectors() (meld.vault.DataStore method) iterate_positions() (meld.vault.DataStore method)

J

j (meld.interfaces.ExtraAngleParam attribute) (meld.interfaces.ExtraBondParam attribute) (meld.interfaces.ExtraTorsParam attribute)

K

k (meld.interfaces.ExtraAngleParam attribute) (meld.interfaces.ExtraTorsParam attribute)

L

l (meld.interfaces.ExtraTorsParam attribute) launch() (in module meld.remd.launch) LeaderReplicaExchangeRunner (class in meld.remd.leader) length (meld.interfaces.ExtraBondParam attribute) LinearBlurScaler (class in meld.system.scalers) LinearPositioner (class in meld.system.scalers) LinearRamp (class in meld.system.scalers) LinearScaler (class in meld.system.scalers) LinearTemperatureScaler (class in meld.system.temperature) load_acceptance_probabilities() (meld.vault.DataStore method) load_all_acceptance_probabilities() (meld.vault.DataStore method) load_all_alphas() (meld.vault.DataStore method) load_all_box_vectors() (meld.vault.DataStore method) load_all_energies() (meld.vault.DataStore method) load_all_energy_matrices() (meld.vault.DataStore method) load_all_permutation_vectors() (meld.vault.DataStore method) load_all_positions() (meld.vault.DataStore method)

load_all_velocities() (meld.vault.DataStore method) load_alphas() (meld.vault.DataStore method) load_box_vectors() (meld.vault.DataStore method) load_communicator() (meld.vault.DataStore method) load_data_store() (meld.vault.DataStore class method) load_energies() (meld.vault.DataStore method) load_energy_matrix() (meld.vault.DataStore method) load_permutation_vector() (meld.vault.DataStore method) load_positions() (meld.vault.DataStore method) load_positions_random_access() (meld.vault.DataStore method) load_remd_runner() (meld.vault.DataStore method) load_run_options() (meld.vault.DataStore method) load_states() (meld.vault.DataStore method) load_system() (meld.vault.DataStore method) load_velocities() (meld.vault.DataStore method) log_dir (meld.vault.DataStore attribute) log_timing() (in module meld.util) log_versions() (in module meld.remd.launch)

M

map_name (meld.system.mapping.PeakMapping attribute) mapper (meld.system.meld_system.System attribute) max_safe_block (meld.vault.DataStore property) max_safe_frame (meld.vault.DataStore property) max_steps (meld.remd.leader.LeaderReplicaExchangeRunner property) (meld.remd.worker.WorkerReplicaExchangeRunner property) means (meld.system.restraints.GMMParams attribute) meld.comm module meld.helpers module meld.interfaces module meld.parse module meld.remd module meld.remd.adaptor module meld.remd.ladder module meld.remd.launch module meld.remd.leader module meld.remd.permute module meld.remd.worker module meld.runner module meld.runner.fake_runner module meld.runner.openmm_runner module meld.runner.transform module meld.runner.transform.rest2 module meld.runner.transform.restraints module meld.runner.transform.restraints.cartesian module meld.runner.transform.restraints.com module meld.runner.transform.restraints.confinement module meld.runner.transform.restraints.meld module meld.runner.transform.restraints.meld.meld module meld.runner.transform.restraints.meld.tracker module meld.runner.transform.restraints.util module meld.system module meld.system.amber module meld.system.builders module meld.system.builders.amber module meld.system.builders.amber.amap module meld.system.builders.amber.builder module meld.system.builders.amber.subsystem module meld.system.builders.build_elastic_network_restraints module meld.system.builders.martini module meld.system.builders.spec module meld.system.density module meld.system.indexing module meld.system.mapping module meld.system.meld_system module meld.system.montecarlo module meld.system.options module meld.system.param_sampling module meld.system.patchers module meld.system.patchers.freeze module meld.system.patchers.potential module meld.system.patchers.rdc_alignment module meld.system.patchers.rdc_integrator module meld.system.patchers.spin_label module meld.system.pdb_writer module meld.system.restraints module meld.system.scalers module meld.system.state module meld.system.temperature module meld.test_install module meld.util module meld.vault module MeldPlugin (C++ type) MeldPlugin::CalcMeldForceKernel (C++ class) MeldPlugin::CalcMeldForceKernel::CalcMeldForceKernel (C++ function) MeldPlugin::CalcMeldForceKernel::copyParametersToContext (C++ function) MeldPlugin::CalcMeldForceKernel::execute (C++ function) MeldPlugin::CalcMeldForceKernel::initialize (C++ function) MeldPlugin::CalcMeldForceKernel::Name (C++ function) MeldPlugin::MeldForce (C++ class) MeldPlugin::MeldForce::addCollection (C++ function) MeldPlugin::MeldForce::addDistanceRestraint (C++ function) MeldPlugin::MeldForce::addDistProfileRestraint (C++ function) MeldPlugin::MeldForce::addGMMRestraint (C++ function) MeldPlugin::MeldForce::addGridPotential (C++ function) MeldPlugin::MeldForce::addGridPotentialRestraint (C++ function) MeldPlugin::MeldForce::addGroup (C++ function) MeldPlugin::MeldForce::addHyperbolicDistanceRestraint (C++ function) MeldPlugin::MeldForce::addRDCRestraint (C++ function) MeldPlugin::MeldForce::addTorsionRestraint (C++ function) MeldPlugin::MeldForce::addTorsProfileRestraint (C++ function) MeldPlugin::MeldForce::CollectionInfo (C++ class) MeldPlugin::MeldForce::CollectionInfo::CollectionInfo (C++ function), [1] MeldPlugin::MeldForce::CollectionInfo::group_indices (C++ member) MeldPlugin::MeldForce::CollectionInfo::n_active (C++ member) MeldPlugin::MeldForce::collections (C++ member) MeldPlugin::MeldForce::containsParticle (C++ function) MeldPlugin::MeldForce::createImpl (C++ function) MeldPlugin::MeldForce::DistanceRestraintInfo (C++ class) MeldPlugin::MeldForce::DistanceRestraintInfo::DistanceRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::DistanceRestraintInfo::force_constant (C++ member) MeldPlugin::MeldForce::DistanceRestraintInfo::global_index (C++ member) MeldPlugin::MeldForce::DistanceRestraintInfo::particle1 (C++ member) MeldPlugin::MeldForce::DistanceRestraintInfo::particle2 (C++ member) MeldPlugin::MeldForce::DistanceRestraintInfo::r1 (C++ member) MeldPlugin::MeldForce::DistanceRestraintInfo::r2 (C++ member) MeldPlugin::MeldForce::DistanceRestraintInfo::r3 (C++ member) MeldPlugin::MeldForce::DistanceRestraintInfo::r4 (C++ member) MeldPlugin::MeldForce::distanceRestraints (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo (C++ class) MeldPlugin::MeldForce::DistProfileRestraintInfo::a0 (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::a1 (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::a2 (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::a3 (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::atom1 (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::atom2 (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::DistProfileRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::DistProfileRestraintInfo::globalIndex (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::nBins (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::rMax (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::rMin (C++ member) MeldPlugin::MeldForce::DistProfileRestraintInfo::scaleFactor (C++ member) MeldPlugin::MeldForce::distProfileRestraints (C++ member) MeldPlugin::MeldForce::getBondedParticles (C++ function) MeldPlugin::MeldForce::getCollectionParams (C++ function) MeldPlugin::MeldForce::getDistanceRestraintParams (C++ function) MeldPlugin::MeldForce::getDistProfileRestraintParams (C++ function) MeldPlugin::MeldForce::getGMMRestraintParams (C++ function) MeldPlugin::MeldForce::getGridPotentialParams (C++ function) MeldPlugin::MeldForce::getGridPotentialRestraintParams (C++ function) MeldPlugin::MeldForce::getGroupParams (C++ function) MeldPlugin::MeldForce::getHyperbolicDistanceRestraintParams (C++ function) MeldPlugin::MeldForce::getNumCollections (C++ function) MeldPlugin::MeldForce::getNumDistProfileRestParams (C++ function) MeldPlugin::MeldForce::getNumDistProfileRestraints (C++ function) MeldPlugin::MeldForce::getNumDistRestraints (C++ function) MeldPlugin::MeldForce::getNumGMMRestraints (C++ function) MeldPlugin::MeldForce::getNumGridPotentialRestraints (C++ function) MeldPlugin::MeldForce::getNumGridPotentials (C++ function) MeldPlugin::MeldForce::getNumGroups (C++ function) MeldPlugin::MeldForce::getNumHyperbolicDistRestraints (C++ function) MeldPlugin::MeldForce::getNumRDCAlignments (C++ function) MeldPlugin::MeldForce::getNumRDCRestraints (C++ function) MeldPlugin::MeldForce::getNumTorsionRestraints (C++ function) MeldPlugin::MeldForce::getNumTorsProfileRestParams (C++ function) MeldPlugin::MeldForce::getNumTorsProfileRestraints (C++ function) MeldPlugin::MeldForce::getNumTotalRestraints (C++ function) MeldPlugin::MeldForce::getRDCRestraintParameters (C++ function) MeldPlugin::MeldForce::getRDCScaleFactor (C++ function) MeldPlugin::MeldForce::getTorsionRestraintParams (C++ function) MeldPlugin::MeldForce::getTorsProfileRestraintParams (C++ function) MeldPlugin::MeldForce::GMMRestraintInfo (C++ class)

MeldPlugin::MeldForce::GMMRestraintInfo::atomIndices (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::globalIndex (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::GMMRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::GMMRestraintInfo::means (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::nComponents (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::nPairs (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::precisionOffDiagonal (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::precisionOnDiagonal (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::scale (C++ member) MeldPlugin::MeldForce::GMMRestraintInfo::weights (C++ member) MeldPlugin::MeldForce::gmmRestraints (C++ member) MeldPlugin::MeldForce::GridPotentialInfo (C++ class) MeldPlugin::MeldForce::GridPotentialInfo::density_index (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::GridPotentialInfo (C++ function), [1] MeldPlugin::MeldForce::GridPotentialInfo::gridx (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::gridy (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::gridz (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::nx (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::ny (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::nz (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::originx (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::originy (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::originz (C++ member) MeldPlugin::MeldForce::GridPotentialInfo::potential (C++ member) MeldPlugin::MeldForce::GridPotentialRestraintInfo (C++ class) MeldPlugin::MeldForce::GridPotentialRestraintInfo::globalIndex (C++ member) MeldPlugin::MeldForce::GridPotentialRestraintInfo::gridpos_x (C++ member) MeldPlugin::MeldForce::GridPotentialRestraintInfo::gridpos_y (C++ member) MeldPlugin::MeldForce::GridPotentialRestraintInfo::gridpos_z (C++ member) MeldPlugin::MeldForce::GridPotentialRestraintInfo::GridPotentialRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::GridPotentialRestraintInfo::mu (C++ member) MeldPlugin::MeldForce::GridPotentialRestraintInfo::particle (C++ member) MeldPlugin::MeldForce::gridPotentialRestraints (C++ member) MeldPlugin::MeldForce::gridPotentials (C++ member) MeldPlugin::MeldForce::GroupInfo (C++ class) MeldPlugin::MeldForce::GroupInfo::GroupInfo (C++ function), [1] MeldPlugin::MeldForce::GroupInfo::n_active (C++ member) MeldPlugin::MeldForce::GroupInfo::restraint_indices (C++ member) MeldPlugin::MeldForce::groups (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo (C++ class) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::asymptote (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::force_constant (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::global_index (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::HyperbolicDistanceRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::particle1 (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::particle2 (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::r1 (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::r2 (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::r3 (C++ member) MeldPlugin::MeldForce::HyperbolicDistanceRestraintInfo::r4 (C++ member) MeldPlugin::MeldForce::hyperbolicDistanceRestraints (C++ member) MeldPlugin::MeldForce::isDirty (C++ member) MeldPlugin::MeldForce::MeldForce (C++ function), [1] MeldPlugin::MeldForce::meldParticleSet (C++ member) MeldPlugin::MeldForce::modifyCollectionNumActive (C++ function) MeldPlugin::MeldForce::modifyDistanceRestraint (C++ function) MeldPlugin::MeldForce::modifyDistProfileRestraint (C++ function) MeldPlugin::MeldForce::modifyGMMRestraint (C++ function) MeldPlugin::MeldForce::modifyGridPotential (C++ function) MeldPlugin::MeldForce::modifyGridPotentialRestraint (C++ function) MeldPlugin::MeldForce::modifyGroupNumActive (C++ function) MeldPlugin::MeldForce::modifyHyperbolicDistanceRestraint (C++ function) MeldPlugin::MeldForce::modifyRDCRestraint (C++ function) MeldPlugin::MeldForce::modifyTorsionRestraint (C++ function) MeldPlugin::MeldForce::modifyTorsProfileRestraint (C++ function) MeldPlugin::MeldForce::n_rdc_alignments (C++ member) MeldPlugin::MeldForce::n_restraints (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo (C++ class) MeldPlugin::MeldForce::RDCRestraintInfo::alignment (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::force_constant (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::global_index (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::kappa (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::obs (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::particle1 (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::particle2 (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::quad_cut (C++ member) MeldPlugin::MeldForce::RDCRestraintInfo::RDCRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::RDCRestraintInfo::tol (C++ member) MeldPlugin::MeldForce::rdcRestraints (C++ member) MeldPlugin::MeldForce::rdcScaleFactor (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo (C++ class) MeldPlugin::MeldForce::TorsionRestraintInfo::atom1 (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::atom2 (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::atom3 (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::atom4 (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::deltaPhi (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::forceConstant (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::globalIndex (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::phi (C++ member) MeldPlugin::MeldForce::TorsionRestraintInfo::TorsionRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::torsions (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo (C++ class) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a0 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a1 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a10 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a11 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a12 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a13 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a14 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a15 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a2 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a3 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a4 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a5 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a6 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a7 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a8 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::a9 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom1 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom2 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom3 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom4 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom5 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom6 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom7 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::atom8 (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::globalIndex (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::nBins (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::scaleFactor (C++ member) MeldPlugin::MeldForce::TorsProfileRestraintInfo::TorsProfileRestraintInfo (C++ function), [1] MeldPlugin::MeldForce::torsProfileRestraints (C++ member) MeldPlugin::MeldForce::updateMeldParticleSet (C++ function) MeldPlugin::MeldForce::updateParametersInContext (C++ function) MeldPlugin::MeldForce::usesPeriodicBoundaryConditions (C++ function) MeldPlugin::MeldForceImpl (C++ class) MeldPlugin::MeldForceImpl::calcForcesAndEnergy (C++ function) MeldPlugin::MeldForceImpl::getBondedParticles (C++ function) MeldPlugin::MeldForceImpl::getDefaultParameters (C++ function) MeldPlugin::MeldForceImpl::getKernelNames (C++ function) MeldPlugin::MeldForceImpl::getOwner (C++ function) MeldPlugin::MeldForceImpl::initialize (C++ function) MeldPlugin::MeldForceImpl::kernel (C++ member) MeldPlugin::MeldForceImpl::MeldForceImpl (C++ function) MeldPlugin::MeldForceImpl::owner (C++ member) MeldPlugin::MeldForceImpl::updateContextState (C++ function) MeldPlugin::MeldForceImpl::updateParametersInContext (C++ function) MeldPlugin::MeldForceImpl::~MeldForceImpl (C++ function) MeldRestraintTransformer (class in meld.runner.transform.restraints.meld.meld) module meld.comm meld.helpers meld.interfaces meld.parse meld.remd meld.remd.adaptor meld.remd.ladder meld.remd.launch meld.remd.leader meld.remd.permute meld.remd.worker meld.runner meld.runner.fake_runner meld.runner.openmm_runner meld.runner.transform meld.runner.transform.rest2 meld.runner.transform.restraints meld.runner.transform.restraints.cartesian meld.runner.transform.restraints.com meld.runner.transform.restraints.confinement meld.runner.transform.restraints.meld meld.runner.transform.restraints.meld.meld meld.runner.transform.restraints.meld.tracker meld.runner.transform.restraints.util meld.system meld.system.amber meld.system.builders meld.system.builders.amber meld.system.builders.amber.amap meld.system.builders.amber.builder meld.system.builders.amber.subsystem meld.system.builders.build_elastic_network_restraints meld.system.builders.martini meld.system.builders.spec meld.system.density meld.system.indexing meld.system.mapping meld.system.meld_system meld.system.montecarlo meld.system.options meld.system.param_sampling meld.system.patchers meld.system.patchers.freeze meld.system.patchers.potential meld.system.patchers.rdc_alignment meld.system.patchers.rdc_integrator meld.system.patchers.spin_label meld.system.pdb_writer meld.system.restraints meld.system.scalers meld.system.state meld.system.temperature meld.test_install meld.util meld.vault MonteCarloScheduler (class in meld.system.montecarlo) Mover (class in meld.system.montecarlo) MPICommunicator (class in meld.comm) multiplicity (meld.interfaces.ExtraTorsParam attribute)

N

N (meld.system.builders.amber.amap.CMAPResidue attribute) n_atoms (meld.comm.MPICommunicator property) (meld.interfaces.ICommunicator property) (meld.interfaces.ISystem property) (meld.system.meld_system.System property) (meld.vault.DataStore property) n_components (meld.system.restraints.GMMParams attribute) n_distances (meld.system.restraints.GMMParams attribute) n_replicas (meld.comm.MPICommunicator property) (meld.helpers.REMDInfo attribute) (meld.interfaces.ICommunicator property) (meld.remd.leader.LeaderReplicaExchangeRunner property) (meld.vault.DataStore property)

n_workers (meld.comm.MPICommunicator property) (meld.interfaces.ICommunicator property) NearestNeighborLadder (class in meld.remd.ladder) negotiate_device_id() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) NonLinearRamp (class in meld.system.scalers) NonLinearScaler (class in meld.system.scalers) NonSelectableRestraint (class in meld.system.restraints) NullAdaptor (class in meld.remd.adaptor) num_active (meld.system.restraints.RestraintGroup property) (meld.system.restraints.SelectivelyActiveCollection property) num_alignments (meld.interfaces.ISystem property) (meld.system.meld_system.System property)

O

omm_system (meld.interfaces.ISystem property) (meld.system.meld_system.System property) OpenMM (C++ type) OpenMM::MeldForceProxy (C++ class)

OpenMM::MeldForceProxy::deserialize (C++ function) OpenMM::MeldForceProxy::MeldForceProxy (C++ function) OpenMM::MeldForceProxy::serialize (C++ function) OPENMM_EXPORT_MELD (C macro) OpenMMRunner (class in meld.runner.openmm_runner)

P

param_sampler (meld.system.meld_system.System attribute) Parameter (class in meld.system.param_sampling) ParameterManager (class in meld.system.param_sampling) ParameterState (class in meld.system.param_sampling) ParmTopReader (class in meld.system.amber) PDBWriter (class in meld.system.pdb_writer) peak_id (meld.system.mapping.PeakMapping attribute) PeakMapManager (class in meld.system.mapping) PeakMapper (class in meld.system.mapping) PeakMapping (class in meld.system.mapping)

permute_states() (in module meld.remd.permute) phase (meld.interfaces.ExtraTorsParam attribute) PlateauLinearScaler (class in meld.system.scalers) PlateauNonLinearScaler (class in meld.system.scalers) PlateauSmoothScaler (class in meld.system.scalers) Positioner (class in meld.system.scalers) precisions (meld.system.restraints.GMMParams attribute) prepare_for_tleap() (meld.system.builders.amber.subsystem.AmberSubSystemFromPdbFile method) (meld.system.builders.amber.subsystem.AmberSubSystemFromSequence method) Prior (class in meld.system.param_sampling)

R

RandomTorsionMover (class in meld.system.montecarlo) rank (meld.comm.MPICommunicator property) (meld.interfaces.ICommunicator property) RdcRestraint (class in meld.system.restraints) receive_all_states_from_leader() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) receive_alphas_from_leader() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) receive_states_from_leader() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) remd_runner (meld.helpers.REMDInfo attribute) REMDInfo (class in meld.helpers) remove_potential() (in module meld.system.patchers.potential) res_name (meld.system.builders.amber.amap.CMAPResidue attribute) res_num (meld.system.builders.amber.amap.CMAPResidue attribute) reset() (meld.remd.adaptor.EqualAcceptanceAdaptor method) (meld.remd.adaptor.NullAdaptor method) (meld.remd.adaptor.SwitchingCompositeAdaptor method) reset_now (meld.remd.adaptor.AdaptationRequired attribute)

residue (meld.system.builders.amber.amap.CMAPResidue attribute) residue() (meld.system.indexing.Indexer method) residue_names (meld.interfaces.ISystem property) (meld.system.meld_system.System property) residue_numbers (meld.interfaces.ISystem property) (meld.system.meld_system.System property) ResidueIndex (class in meld.system.indexing) REST2Scaler (class in meld.system.temperature) REST2Transformer (class in meld.runner.transform.rest2) Restraint (class in meld.system.restraints) RestraintGroup (class in meld.system.restraints) RestraintManager (class in meld.system.restraints) restraints (meld.system.meld_system.System attribute) (meld.system.restraints.RestraintGroup property) RestraintScaler (class in meld.system.scalers) RestraintTracker (class in meld.runner.transform.restraints.meld.tracker) run() (meld.remd.leader.LeaderReplicaExchangeRunner method) (meld.remd.worker.WorkerReplicaExchangeRunner method) RunOptions (class in meld.system.options)

S

Sampler (class in meld.system.param_sampling) save_acceptance_probabilities() (meld.vault.DataStore method) save_alphas() (meld.vault.DataStore method) save_box_vectors() (meld.vault.DataStore method) save_communicator() (meld.vault.DataStore method) save_data_store() (meld.vault.DataStore method) save_energies() (meld.vault.DataStore method) save_energy_matrix() (meld.vault.DataStore method) save_permutation_vector() (meld.vault.DataStore method) save_positions() (meld.vault.DataStore method) save_remd_runner() (meld.vault.DataStore method) save_run_options() (meld.vault.DataStore method) save_states() (meld.vault.DataStore method) save_system() (meld.vault.DataStore method) save_velocities() (meld.vault.DataStore method) ScaledExponentialDiscretePrior (class in meld.system.param_sampling) ScalerRegistry (class in meld.system.scalers) SelectableRestraint (class in meld.system.restraints) selectively_active_collections (meld.system.restraints.RestraintManager property)

SelectivelyActiveCollection (class in meld.system.restraints) send_energies_to_leader() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) send_states_to_leader() (meld.comm.MPICommunicator method) (meld.interfaces.ICommunicator method) setup_data_store() (in module meld.helpers) setup_indexing() (in module meld.system.indexing) setup_replica_exchange() (in module meld.helpers) should_adapt() (meld.remd.adaptor.AdaptationPolicy method) solvation (meld.interfaces.ISystem property) (meld.system.builders.spec.SystemSpec attribute) (meld.system.meld_system.System property) step (meld.remd.leader.LeaderReplicaExchangeRunner property) (meld.remd.worker.WorkerReplicaExchangeRunner property) strip_unit() (in module meld.util) SwitchingCompositeAdaptor (class in meld.remd.adaptor) System (class in meld.system.meld_system) system (meld.system.builders.spec.SystemSpec attribute) SystemSpec (class in meld.system.builders.spec) SystemState (class in meld.system.state)

T

temperature_scaler (meld.system.meld_system.System attribute) TemperatureScaler (class in meld.system.temperature) template_box_vectors (meld.interfaces.ISystem property) (meld.system.meld_system.System property) template_coordinates (meld.interfaces.ISystem property) (meld.system.meld_system.System property) template_velocities (meld.interfaces.ISystem property) (meld.system.meld_system.System property) test_install() (in module meld.test_install) TimeRamp (class in meld.system.scalers) TimeRampSwitcher (class in meld.system.scalers)

to_worker() (meld.remd.leader.LeaderReplicaExchangeRunner method) topology (meld.interfaces.ISystem property) (meld.system.builders.spec.SystemSpec attribute) (meld.system.meld_system.System property) TorsionRestraint (class in meld.system.restraints) TorsProfileRestraint (class in meld.system.restraints) TransformerBase (class in meld.runner.transform) TranslationMover (class in meld.system.montecarlo) trial() (meld.system.montecarlo.DoubleTorsionMover method) (meld.system.montecarlo.RandomTorsionMover method) (meld.system.montecarlo.TranslationMover method)

U

UniformContinuousPrior (class in meld.system.param_sampling) UniformDiscretePrior (class in meld.system.param_sampling) update() (meld.remd.adaptor.EqualAcceptanceAdaptor method) (meld.remd.adaptor.NullAdaptor method) (meld.remd.adaptor.SwitchingCompositeAdaptor method) (meld.runner.transform.rest2.REST2Transformer method) (meld.runner.transform.restraints.cartesian.CartesianRestraintTransformer method) (meld.runner.transform.restraints.cartesian.YZCartesianTransformer method) (meld.runner.transform.restraints.com.AbsoluteCOMRestraintTransformer method) (meld.runner.transform.restraints.com.COMRestraintTransformer method) (meld.runner.transform.restraints.confinement.ConfinementRestraintTransformer method) (meld.runner.transform.restraints.meld.meld.MeldRestraintTransformer method) (meld.runner.transform.TransformerBase method) (meld.system.montecarlo.MonteCarloScheduler method)

V

velocities (meld.system.builders.spec.SystemSpec attribute)

W

weights (meld.system.restraints.GMMParams attribute)

WorkerReplicaExchangeRunner (class in meld.remd.worker)

Y

YZCartesianRestraint (class in meld.system.restraints)

YZCartesianTransformer (class in meld.runner.transform.restraints.cartesian)