Index

A

add_commands() (yank.utils.TLeap method) add_ions() (yank.utils.TLeap method) add_region() (yank.yank.Topography method) AlchemicalPhase (class in yank.yank) AlchemicalPhaseFactory (class in yank.experiment) analyze_directory() (in module yank.analyze) append() (yank.utils.CombinatorialLeaf method)

apply_modeller() (in module yank.pipeline) apply_pdbfixer() (in module yank.pipeline) apply_to_context() (yank.restraints.RestraintState method) apply_to_system() (yank.restraints.RestraintState method) auto_analyze() (yank.analyze.ExperimentAnalyzer method) available_restraint_classes() (in module yank.restraints) available_restraint_types() (in module yank.restraints)

B

Boresch (class in yank.restraints)

BoreschLike (class in yank.restraints) build_experiments() (yank.experiment.ExperimentBuilder method)

C

camelcase_to_underscore() (in module yank.utils) check_system_consistency() (yank.restraints.RestraintState method) CLASH_THRESHOLD (yank.pipeline.SetupDatabase attribute) clear() (yank.multistate.multistateanalyzer.MultiPhaseAnalyzer method) (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.multistateanalyzer.PhaseAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) (yank.utils.CombinatorialLeaf method) (yank.utils.CombinatorialTree method) combinatorial_constructor() (yank.experiment.YankLoader static method) combinatorial_representer() (yank.experiment.YankDumper static method) CombinatorialLeaf (class in yank.utils) CombinatorialTree (class in yank.utils) combine() (yank.utils.TLeap method) compute_min_dist() (in module yank.pipeline) compute_min_max_dist() (in module yank.pipeline)

compute_net_charge() (in module yank.pipeline) compute_radius_of_gyration() (in module yank.pipeline) compute_squared_distances() (in module yank.pipeline) config_root_logger() (in module yank.utils) copy() (yank.utils.CombinatorialLeaf method) count() (yank.multistate.multistatesampler.MultiStateSampler.Status method) (yank.multistate.paralleltempering.ParallelTemperingSampler.Status method) (yank.multistate.replicaexchange.ReplicaExchangeSampler.Status method) (yank.multistate.sams.SAMSSampler.Status method) (yank.utils.CombinatorialLeaf method) create() (yank.multistate.multistatesampler.MultiStateSampler method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method) create_alchemical_phase() (yank.experiment.AlchemicalPhaseFactory method) create_restraint() (in module yank.restraints) create_system() (in module yank.pipeline)

D

default_options() (yank.multistate.multistatesampler.MultiStateSampler class method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) delay_termination() (in module yank.mpi) delayed_termination() (in module yank.mpi) determine_missing_parameters() (yank.restraints.Boresch method) (yank.restraints.BoreschLike method) (yank.restraints.FlatBottom method) (yank.restraints.Harmonic method) (yank.restraints.PeriodicTorsionBoresch method) (yank.restraints.RMSD method) (yank.restraints.RadiallySymmetricRestraint method) (yank.restraints.ReceptorLigandRestraint method)

dev_validation() (yank.restraints.RMSD method) distribute() (in module yank.mpi) dump_serial_data() (yank.analyze.ExperimentAnalyzer method)

E

equilibrate() (yank.multistate.multistatesampler.MultiStateSampler method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method) expand_id_nodes() (yank.utils.CombinatorialTree method) Experiment (class in yank.experiment) ExperimentAnalyzer (class in yank.analyze) ExperimentBuilder (class in yank.experiment)

export_script() (yank.utils.TLeap method) extend() (yank.multistate.multistatesampler.MultiStateSampler method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) (yank.utils.CombinatorialLeaf method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method) extract_trajectory() (in module yank.analyze) extract_u_n() (in module yank.analyze)

F

find_alchemical_counterions() (in module yank.pipeline) find_phases_in_store_directory() (in module yank.utils) FlatBottom (class in yank.restraints) from_storage() (yank.multistate.multistatesampler.MultiStateSampler class method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) (yank.yank.AlchemicalPhase class method)

G

generate_development_feature() (in module yank.utils) generate_mixing_statistics() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) get() (yank.utils.CombinatorialTree method) get_analyzer() (in module yank.analyze) get_data_filename() (in module yank.utils) get_effective_energy_timeseries() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.multistateanalyzer.PhaseAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) get_enthalpy() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) get_entropy() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) get_equilibration_data() (yank.analyze.ExperimentAnalyzer method) get_experiment_directories() (yank.experiment.ExperimentBuilder method) get_experiment_free_energy_data() (yank.analyze.ExperimentAnalyzer method)

get_free_energy() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) get_general_simulation_data() (yank.analyze.ExperimentAnalyzer method) get_keyword_args() (in module yank.utils) get_leap_recommended_pbradii() (in module yank.pipeline) get_mixing_data() (yank.analyze.ExperimentAnalyzer method) get_molecule_dir() (yank.pipeline.SetupDatabase method) get_mpicomm() (in module yank.mpi) get_oe_mol_positions() (in module yank.utils) get_openmm_explicit_nb_method_strings() (in module yank.experiment) get_openmm_implicit_nb_method_strings() (in module yank.experiment) get_openmm_nonbonded_methods_strings() (in module yank.experiment) get_region() (yank.yank.Topography method) get_standard_state_correction() (yank.restraints.Boresch method) (yank.restraints.BoreschLike method) (yank.restraints.FlatBottom method) (yank.restraints.Harmonic method) (yank.restraints.PeriodicTorsionBoresch method) (yank.restraints.RMSD method) (yank.restraints.RadiallySymmetricRestraint method) (yank.restraints.ReceptorLigandRestraint method) get_system() (yank.pipeline.SetupDatabase method) get_system_files_paths() (yank.pipeline.SetupDatabase method)

H

Harmonic (class in yank.restraints) has_log_weights (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute)

I

IMultiStateSampler (class in yank.yank) index() (yank.multistate.multistatesampler.MultiStateSampler.Status method) (yank.multistate.paralleltempering.ParallelTemperingSampler.Status method) (yank.multistate.replicaexchange.ReplicaExchangeSampler.Status method) (yank.multistate.sams.SAMSSampler.Status method) (yank.utils.CombinatorialLeaf method) initialize_alchemical_phase() (yank.experiment.AlchemicalPhaseFactory method) insert() (yank.utils.CombinatorialLeaf method) ions_atoms (yank.yank.Topography attribute) is_completed (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.multistatesampler.MultiStateSampler.Status attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler.Status attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler.Status attribute) (yank.multistate.sams.SAMSSampler attribute) (yank.multistate.sams.SAMSSampler.Status attribute) (yank.yank.AlchemicalPhase attribute) is_modeller_installed() (in module yank.utils)

is_molecule_setup() (yank.pipeline.SetupDatabase method) is_openeye_installed() (in module yank.utils) is_periodic (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.sams.SAMSSampler attribute) is_system_setup() (yank.pipeline.SetupDatabase method) is_terminal_verbose() (in module yank.utils) items() (yank.utils.CombinatorialTree method) iteration (yank.experiment.Experiment attribute) (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.multistatesampler.MultiStateSampler.Status attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler.Status attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler.Status attribute) (yank.multistate.sams.SAMSSampler attribute) (yank.multistate.sams.SAMSSampler.Status attribute) (yank.yank.AlchemicalPhase attribute) (yank.yank.IMultiStateSampler attribute)

K

keys() (yank.utils.CombinatorialTree method) kT (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute)

L

lambda_restraints (yank.restraints.RestraintState attribute) ligand_atoms (yank.yank.Topography attribute)

load_oe_molecules() (in module yank.utils) load_parameters() (yank.utils.TLeap method) load_unit() (yank.utils.TLeap method)

M

mcmc_moves (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.sams.SAMSSampler attribute) metadata (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.sams.SAMSSampler attribute) (yank.yank.IMultiStateSampler attribute) minimize() (yank.multistate.multistatesampler.MultiStateSampler method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method)

Mol2File (class in yank.utils) MOLECULES_DIR (yank.pipeline.SetupDatabase attribute) MultiExperimentAnalyzer (class in yank.analyze) MultiPhaseAnalyzer (class in yank.multistate.multistateanalyzer) MultiStateSampler (class in yank.multistate.multistatesampler) MultiStateSampler.Status (class in yank.multistate.multistatesampler) MultiStateSamplerAnalyzer (class in yank.multistate.multistateanalyzer)

N

n_equilibration_iterations (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute) n_iterations (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute) n_replicas (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.sams.SAMSAnalyzer attribute) (yank.multistate.sams.SAMSSampler attribute) n_states (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.sams.SAMSAnalyzer attribute) (yank.multistate.sams.SAMSSampler attribute)

name (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute) named_combinations() (yank.utils.CombinatorialTree method) names (yank.multistate.multistateanalyzer.MultiPhaseAnalyzer attribute) net_charge (yank.utils.Mol2File attribute) new_section() (yank.utils.TLeap method) number_of_iterations (yank.yank.AlchemicalPhase attribute) (yank.yank.IMultiStateSampler attribute)

O

observables (yank.multistate.multistateanalyzer.MultiPhaseAnalyzer attribute) (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.ObservablesRegistry attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute) observables_defined_by_phase (yank.multistate.multistateanalyzer.ObservablesRegistry attribute) observables_defined_by_single_state (yank.multistate.multistateanalyzer.ObservablesRegistry attribute) observables_defined_by_two_states (yank.multistate.multistateanalyzer.ObservablesRegistry attribute) observables_with_error (yank.multistate.multistateanalyzer.ObservablesRegistry attribute)

observables_with_error_adding_linear (yank.multistate.multistateanalyzer.ObservablesRegistry attribute) observables_with_error_adding_quadrature (yank.multistate.multistateanalyzer.ObservablesRegistry attribute) ObservablesRegistry (class in yank.multistate.multistateanalyzer) on_single_node() (in module yank.mpi) online_analysis_interval (yank.multistate.multistatesampler.MultiStateSampler attribute) options (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.sams.SAMSSampler attribute) ordered_constructor() (yank.experiment.YankLoader static method) ordered_representer() (yank.experiment.YankDumper static method) output_dir (yank.experiment.ExperimentBuilder attribute)

P

pack_transformation() (in module yank.pipeline) ParallelTemperingAnalyzer (class in yank.multistate.paralleltempering) ParallelTemperingSampler (class in yank.multistate.paralleltempering) ParallelTemperingSampler.Status (class in yank.multistate.paralleltempering) parse() (yank.experiment.ExperimentBuilder method) PeriodicTorsionBoresch (class in yank.restraints) PhaseAnalyzer (class in yank.multistate.multistateanalyzer)

phases (yank.multistate.multistateanalyzer.MultiPhaseAnalyzer attribute) pop() (yank.utils.CombinatorialLeaf method) (yank.utils.CombinatorialTree method) popitem() (yank.utils.CombinatorialTree method) print_analysis_data() (in module yank.analyze) process_tool_directive() (in module yank.pipeline) pull_close() (in module yank.pipeline)

Q

quantity_from_string() (in module yank.utils)

R

RadiallySymmetricRestraint (class in yank.restraints) randomize_ligand() (yank.yank.AlchemicalPhase method) read_csv_lines() (in module yank.pipeline) read_energies() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.multistateanalyzer.PhaseAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) read_log_weights() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.multistateanalyzer.PhaseAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) read_logZ() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.multistateanalyzer.PhaseAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) read_status() (yank.multistate.multistatesampler.MultiStateSampler class method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) (yank.yank.AlchemicalPhase class method) (yank.yank.IMultiStateSampler class method) read_system_files() (in module yank.pipeline) receptor_atoms (yank.yank.Topography attribute) ReceptorLigandRestraint (class in yank.restraints) reference_states (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute) reformat_energies_for_mbar() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.multistateanalyzer.PhaseAnalyzer static method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) register_one_state_observable() (yank.multistate.multistateanalyzer.ObservablesRegistry method) register_phase_observable() (yank.multistate.multistateanalyzer.ObservablesRegistry method)

register_two_state_observable() (yank.multistate.multistateanalyzer.ObservablesRegistry method) remove() (yank.utils.CombinatorialLeaf method) remove_overlap() (in module yank.pipeline) remove_region() (yank.yank.Topography method) ReplicaExchangeAnalyzer (class in yank.multistate.replicaexchange) ReplicaExchangeSampler (class in yank.multistate.replicaexchange) ReplicaExchangeSampler.Status (class in yank.multistate.replicaexchange) reporter (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute) resname (yank.utils.Mol2File attribute) resnames (yank.utils.Mol2File attribute) restrain_state() (yank.restraints.Boresch method) (yank.restraints.BoreschLike method) (yank.restraints.FlatBottom method) (yank.restraints.Harmonic method) (yank.restraints.PeriodicTorsionBoresch method) (yank.restraints.RMSD method) (yank.restraints.RadiallySymmetricRestraint method) (yank.restraints.ReceptorLigandRestraint method) RestraintParameterError RestraintState (class in yank.restraints) RestraintStateError reverse() (yank.utils.CombinatorialLeaf method) RMSD (class in yank.restraints) round_charge() (yank.utils.Mol2File method) run() (yank.experiment.Experiment method) (yank.multistate.multistatesampler.MultiStateSampler method) (yank.multistate.paralleltempering.ParallelTemperingSampler method) (yank.multistate.replicaexchange.ReplicaExchangeSampler method) (yank.multistate.sams.SAMSSampler method) (yank.utils.TLeap method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method) run_all_analysis() (yank.analyze.MultiExperimentAnalyzer method) run_experiments() (yank.experiment.ExperimentBuilder method) run_single_node() (in module yank.mpi)

S

sampler_states (yank.multistate.multistatesampler.MultiStateSampler attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler attribute) (yank.multistate.sams.SAMSSampler attribute) (yank.yank.IMultiStateSampler attribute) SAMSAnalyzer (class in yank.multistate.sams) SAMSSampler (class in yank.multistate.sams) SAMSSampler.Status (class in yank.multistate.sams) save_unit() (yank.utils.TLeap method) script (yank.utils.TLeap attribute) select() (yank.yank.Topography method) setdefault() (yank.utils.CombinatorialTree method) setup_all_systems() (yank.pipeline.SetupDatabase method) setup_dir (yank.experiment.ExperimentBuilder attribute) setup_experiments() (yank.experiment.ExperimentBuilder method) SetupDatabase (class in yank.pipeline)

show_mixing_statistics() (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer method) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer method) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer method) (yank.multistate.sams.SAMSAnalyzer method) signs (yank.multistate.multistateanalyzer.MultiPhaseAnalyzer attribute) solute_atoms (yank.yank.Topography attribute) solvate() (yank.utils.TLeap method) solvent_atoms (yank.yank.Topography attribute) sort() (yank.utils.CombinatorialLeaf method) statistical_inefficiency (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute) status() (yank.experiment.ExperimentBuilder method) strip_protons() (in module yank.pipeline) SYSTEMS_DIR (yank.pipeline.SetupDatabase attribute)

T

target_error (yank.multistate.multistatesampler.MultiStateSampler.Status attribute) (yank.multistate.paralleltempering.ParallelTemperingSampler.Status attribute) (yank.multistate.replicaexchange.ReplicaExchangeSampler.Status attribute) (yank.multistate.sams.SAMSSampler.Status attribute) TLeap (class in yank.utils)

to_openmm_app() (in module yank.experiment) Topography (class in yank.yank) topology (yank.yank.Topography attribute) trailblaze_alchemical_protocol() (in module yank.pipeline) transform() (yank.utils.TLeap method)

U

underscore_to_camelcase() (in module yank.utils) update() (yank.utils.CombinatorialTree method) update_nested_dict() (in module yank.utils) update_yaml() (yank.experiment.ExperimentBuilder method)

use_online_data (yank.multistate.multistateanalyzer.MultiStateSamplerAnalyzer attribute) (yank.multistate.multistateanalyzer.PhaseAnalyzer attribute) (yank.multistate.paralleltempering.ParallelTemperingAnalyzer attribute) (yank.multistate.replicaexchange.ReplicaExchangeAnalyzer attribute) (yank.multistate.sams.SAMSAnalyzer attribute)

V

validate_parameters() (in module yank.utils)

values() (yank.utils.CombinatorialTree method) verbose (yank.experiment.ExperimentBuilder attribute)

W

with_traceback() (yank.experiment.YamlParseError method) (yank.restraints.RestraintParameterError method) (yank.restraints.RestraintStateError method)

write_oe_molecule() (in module yank.utils)

Y

YamlParseError yank.analyze (module) yank.experiment (module) yank.mpi (module) yank.multistate (module) yank.multistate.multistateanalyzer (module) yank.multistate.multistatesampler (module) yank.multistate.paralleltempering (module)

yank.multistate.replicaexchange (module) yank.multistate.sams (module) yank.pipeline (module) yank.restraints (module) yank.utils (module) yank.yank (module) YankDumper (class in yank.experiment) YankLoader (class in yank.experiment)