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) analysis_particle_indices (yank.repex.Reporter attribute) analyze_directory() (in module yank.analyze)

analyze_phase() (yank.analyze.YankPhaseAnalyzer method) append() (yank.utils.CombinatorialLeaf method) apply_pdbfixer() (in module yank.pipeline) 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) compute_squared_distances() (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.repex.ParallelTempering.Status method) (yank.repex.ReplicaExchange.Status method) (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 class 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_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.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.repex.ParallelTempering.Status method) (yank.repex.ReplicaExchange.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.repex.ParallelTempering attribute) (yank.repex.ParallelTempering.Status attribute) (yank.repex.ReplicaExchange attribute) (yank.repex.ReplicaExchange.Status 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.ParallelTempering.Status attribute) (yank.repex.ReplicaExchange attribute) (yank.repex.ReplicaExchange.Status 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) ParallelTempering.Status (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_status() (yank.repex.ParallelTempering method) (yank.repex.ReplicaExchange class method) (yank.yank.AlchemicalPhase class method) (yank.yank.IMultiStateSampler class 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_region() (yank.yank.Topography method) remove_unequilibrated_data() (in module yank.analyze)

ReplicaExchange (class in yank.repex) ReplicaExchange.Status (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) round_charge() (yank.utils.Mol2File 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) 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.analyze.ReplicaExchangeAnalyzer method)

signs (yank.analyze.MultiPhaseAnalyzer attribute) SimulationNaNError 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) status() (yank.experiment.ExperimentBuilder method) 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

target_error (yank.repex.ParallelTempering.Status attribute) (yank.repex.ReplicaExchange.Status attribute) 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.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)

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) (yank.utils.SimulationNaNError 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)