Index

A

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

analyze_phase() (yank.analyze.YankPhaseAnalyzer method) append() (yank.utils.CombinatorialLeaf method) apply_to_context() (yank.restraints.RestraintState method) apply_to_system() (yank.restraints.RestraintState method) available_restraint_classes() (in module yank.restraints) available_restraint_types() (in module yank.restraints)

B

Boresch (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.utils.CombinatorialLeaf method) (yank.utils.CombinatorialTree method) close() (yank.repex.Reporter 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) config_root_logger() (in module yank.utils) convert_if_quantity() (in module yank.experiment) copy() (yank.utils.CombinatorialLeaf method) count() (yank.utils.CombinatorialLeaf method) create() (yank.repex.ParallelTempering method) (yank.repex.ReplicaExchange 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

delay_termination() (in module yank.mpi) delayed_termination() (in module yank.mpi) determine_missing_parameters() (yank.restraints.Boresch method) (yank.restraints.FlatBottom method) (yank.restraints.Harmonic method) (yank.restraints.RadiallySymmetricRestraint method) (yank.restraints.ReceptorLigandRestraint method)

distribute() (in module yank.mpi)

E

equilibrate() (yank.repex.ParallelTempering method) (yank.repex.ReplicaExchange method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method) expand_id_nodes() (yank.utils.CombinatorialTree method) Experiment (class in yank.experiment) ExperimentBuilder (class in yank.experiment)

export_script() (yank.utils.TLeap method) extend() (yank.repex.ParallelTempering method) (yank.repex.ReplicaExchange 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

filepath (yank.repex.Reporter attribute) find_alchemical_counterions() (in module yank.pipeline) find_phases_in_store_directory() (in module yank.utils)

FlatBottom (class in yank.restraints) from_storage() (yank.repex.ParallelTempering method) (yank.repex.ReplicaExchange class method) (yank.yank.AlchemicalPhase static method)

G

generate_mixing_statistics() (yank.analyze.ReplicaExchangeAnalyzer method) generate_phase_name() (in module yank.analyze) generate_signature_schema() (in module yank.utils) get() (yank.utils.CombinatorialTree method) get_analyzer() (in module yank.analyze) get_data_filename() (in module yank.utils) get_decorrelation_time() (in module yank.analyze) get_enthalpy() (yank.analyze.ReplicaExchangeAnalyzer method) get_entropy() (yank.analyze.ReplicaExchangeAnalyzer method) get_equilibration_data() (in module yank.analyze) get_equilibration_data_per_sample() (in module yank.analyze) get_free_energy() (yank.analyze.ReplicaExchangeAnalyzer method) get_keyword_args() (in module yank.utils) get_leap_recommended_pbradii() (in module yank.pipeline)

get_molecule_dir() (yank.pipeline.SetupDatabase method) get_mpicomm() (in module yank.mpi) get_oe_mol_positions() (in module yank.utils) get_standard_state_correction() (yank.analyze.ReplicaExchangeAnalyzer method) (yank.restraints.Boresch method) (yank.restraints.FlatBottom method) (yank.restraints.Harmonic method) (yank.restraints.RadiallySymmetricRestraint method) (yank.restraints.ReceptorLigandRestraint method) get_states_energies() (yank.analyze.ReplicaExchangeAnalyzer method) (yank.analyze.YankPhaseAnalyzer method) get_system() (yank.pipeline.SetupDatabase method) get_system_files_paths() (yank.pipeline.SetupDatabase method) get_timeseries() (yank.analyze.ReplicaExchangeAnalyzer static method) (yank.analyze.YankPhaseAnalyzer static method)

H

Harmonic (class in yank.restraints)

I

IMultiStateSampler (class in yank.yank) index() (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.repex.ParallelTempering attribute) (yank.repex.ReplicaExchange attribute) (yank.yank.AlchemicalPhase attribute) is_molecule_setup() (yank.pipeline.SetupDatabase method)

is_open() (yank.repex.Reporter method) is_openeye_installed() (in module yank.utils) 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.repex.ParallelTempering attribute) (yank.repex.ReplicaExchange attribute) (yank.yank.AlchemicalPhase attribute) (yank.yank.IMultiStateSampler attribute)

K

keys() (yank.utils.CombinatorialTree method)

kT (yank.analyze.ReplicaExchangeAnalyzer attribute) (yank.analyze.YankPhaseAnalyzer 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

mbar (yank.analyze.ReplicaExchangeAnalyzer attribute) (yank.analyze.YankPhaseAnalyzer attribute) mcmc_moves (yank.repex.ParallelTempering attribute) (yank.repex.ReplicaExchange attribute) merge_dict() (in module yank.utils) metadata (yank.repex.ParallelTempering attribute) (yank.repex.ReplicaExchange attribute) (yank.yank.IMultiStateSampler attribute)

minimize() (yank.repex.ParallelTempering method) (yank.repex.ReplicaExchange method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method) Mol2File (class in yank.utils) MOLECULES_DIR (yank.pipeline.SetupDatabase attribute) MultiPhaseAnalyzer (class in yank.analyze)

N

n_replicas (yank.repex.ParallelTempering attribute) (yank.repex.ReplicaExchange attribute) name (yank.analyze.ReplicaExchangeAnalyzer attribute) (yank.analyze.YankPhaseAnalyzer attribute) named_combinations() (yank.utils.CombinatorialTree method)

names (yank.analyze.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.analyze.MultiPhaseAnalyzer attribute) (yank.analyze.ReplicaExchangeAnalyzer attribute) (yank.analyze.YankPhaseAnalyzer attribute) on_single_node() (in module yank.mpi)

online_analysis_interval (yank.repex.ReplicaExchange attribute) open() (yank.repex.Reporter method) 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) ParallelTempering (class in yank.repex) parse() (yank.experiment.ExperimentBuilder method) phases (yank.analyze.MultiPhaseAnalyzer attribute)

pop() (yank.utils.CombinatorialLeaf method) (yank.utils.CombinatorialTree method) popitem() (yank.utils.CombinatorialTree method) process_unit_bearing_str() (in module yank.utils) 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_dict() (yank.repex.Reporter method) read_energies() (yank.repex.Reporter method) read_last_iteration() (yank.repex.Reporter method) read_mbar_free_energies() (yank.repex.Reporter method) read_mcmc_moves() (yank.repex.Reporter method) read_mixing_statistics() (yank.repex.Reporter method) read_replica_thermodynamic_states() (yank.repex.Reporter method) read_sampler_states() (yank.repex.Reporter method) read_system_files() (in module yank.pipeline) read_thermodynamic_states() (yank.repex.Reporter method) read_timestamp() (yank.repex.Reporter method) receptor_atoms (yank.yank.Topography attribute) ReceptorLigandRestraint (class in yank.restraints) reference_states (yank.analyze.ReplicaExchangeAnalyzer attribute) (yank.analyze.YankPhaseAnalyzer attribute) remove() (yank.utils.CombinatorialLeaf method) remove_overlap() (in module yank.pipeline) remove_unequilibrated_data() (in module yank.analyze) ReplicaExchange (class in yank.repex)

ReplicaExchangeAnalyzer (class in yank.analyze) Reporter (class in yank.repex) reporter (yank.analyze.ReplicaExchangeAnalyzer attribute) (yank.analyze.YankPhaseAnalyzer attribute) resname (yank.utils.Mol2File attribute) resnames (yank.utils.Mol2File attribute) restrain_state() (yank.restraints.Boresch method) (yank.restraints.FlatBottom method) (yank.restraints.Harmonic method) (yank.restraints.RadiallySymmetricRestraint method) (yank.restraints.ReceptorLigandRestraint method) RestraintParameterError RestraintState (class in yank.restraints) RestraintStateError reverse() (yank.utils.CombinatorialLeaf method) run() (yank.experiment.Experiment method) (yank.repex.ParallelTempering method) (yank.repex.ReplicaExchange method) (yank.utils.TLeap method) (yank.yank.AlchemicalPhase method) (yank.yank.IMultiStateSampler method) run_experiments() (yank.experiment.ExperimentBuilder method) run_single_node() (in module yank.mpi)

S

sampler_states (yank.repex.ParallelTempering attribute) (yank.repex.ReplicaExchange attribute) (yank.yank.IMultiStateSampler attribute) save_unit() (yank.utils.TLeap method) script (yank.utils.TLeap attribute) setdefault() (yank.utils.CombinatorialTree method) setup_dir (yank.experiment.ExperimentBuilder attribute) setup_experiments() (yank.experiment.ExperimentBuilder method) SetupDatabase (class in yank.pipeline) show_mixing_statistics() (yank.analyze.ReplicaExchangeAnalyzer method)

signs (yank.analyze.MultiPhaseAnalyzer attribute) solute_atoms (yank.yank.Topography attribute) solvate() (yank.utils.TLeap method) solvent_atoms (yank.yank.Topography attribute) sort() (yank.utils.CombinatorialLeaf method) standard_state_correction_method (yank.restraints.Boresch attribute) storage_exists() (yank.repex.Reporter method) strip_protons() (in module yank.pipeline) subsample_data_along_axis() (in module yank.analyze) sync() (yank.repex.Reporter method) SYSTEMS_DIR (yank.pipeline.SetupDatabase attribute)

T

TLeap (class in yank.utils) to_openmm_app() (in module yank.experiment) to_unit_validator() (in module yank.utils) Topography (class in yank.yank) topology (yank.restraints.FlatBottom attribute) (yank.restraints.Harmonic attribute) (yank.restraints.RadiallySymmetricRestraint attribute) (yank.yank.Topography attribute)

trailblaze_alchemical_protocol() (in module yank.pipeline) transform() (yank.utils.TLeap method) typename() (in module yank.utils)

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)

V

validate_parameters() (in module yank.utils)

values() (yank.utils.CombinatorialTree method)

W

with_traceback() (yank.experiment.YamlParseError method) (yank.restraints.RestraintParameterError method) (yank.restraints.RestraintStateError method) write_dict() (yank.repex.Reporter method) write_energies() (yank.repex.Reporter method) write_last_iteration() (yank.repex.Reporter method) write_mbar_free_energies() (yank.repex.Reporter method)

write_mcmc_moves() (yank.repex.Reporter method) write_mixing_statistics() (yank.repex.Reporter method) write_oe_molecule() (in module yank.utils) write_replica_thermodynamic_states() (yank.repex.Reporter method) write_sampler_states() (yank.repex.Reporter method) write_thermodynamic_states() (yank.repex.Reporter method) write_timestamp() (yank.repex.Reporter method)

Y

YamlParseError yank.analyze (module) yank.experiment (module) yank.mpi (module) yank.pipeline (module) yank.repex (module)

yank.restraints (module) yank.utils (module) yank.yank (module) YankDumper (class in yank.experiment) YankLoader (class in yank.experiment) YankPhaseAnalyzer (class in yank.analyze)