Index

_

_abc_impl (wepy.util.kv.KV attribute) _add_field() (wepy.hdf5.WepyHDF5 method) _add_field_feature_dtype() (wepy.hdf5.WepyHDF5 method) _add_field_feature_shape() (wepy.hdf5.WepyHDF5 method) _add_init() (wepy.hdf5.WepyHDF5 method) _add_init_walkers() (wepy.hdf5.WepyHDF5 method) _add_run_field() (wepy.hdf5.WepyHDF5 method) _add_run_init() (wepy.hdf5.WepyHDF5 method) _add_run_record() (wepy.orchestration.orchestrator.Orchestrator method) _add_sparse_field_flag() (wepy.hdf5.WepyHDF5 method) _add_traj_field_data() (wepy.hdf5.WepyHDF5 method) _adj (wepy.resampling.resamplers.wexplore.RegionTree attribute) _adjust_disp_vector() (wepy.resampling.distances.distance.AtomPairDistance method) _after_fork() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess static method) (wepy.runners.openmm.OpenMMCPUWorker static method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess static method) (wepy.runners.openmm.OpenMMGPUWorker static method) (wepy.work_mapper.mapper.Worker static method) (wepy.work_mapper.task_mapper.WalkerTaskProcess static method) _all_to_all_distance() (wepy.resampling.resamplers.revo.REVOResampler method) _assignments_init() (wepy.analysis.network.BaseMacroStateNetwork method) _balance_children_shares() (wepy.resampling.resamplers.wexplore.RegionTree method) _bootstrap() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) _calc_max_num_clones() (wepy.resampling.resamplers.wexplore.RegionTree method) _calc_min_distance() (wepy.boundary_conditions.receptor.UnbindingBC method) _calc_share_donation() (wepy.resampling.resamplers.wexplore.RegionTree method) _calc_squashable_walkers() (wepy.resampling.resamplers.wexplore.RegionTree method) _calc_variation() (wepy.resampling.resamplers.revo.REVOResampler method) _calc_variation_loss() (wepy.resampling.resamplers.revo.REVOResampler method) _center_row() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) _check_clone_merge_specs() (wepy.resampling.resamplers.wexplore.RegionTree method) _check_closed() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) _check_resampled_walkers() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) _check_resampling_data() (wepy.resampling.resamplers.wexplore.WExploreResampler static method) _check_traj_field_consistency() (wepy.hdf5.WepyHDF5 method) _choose_rep_path() (wepy.hdf5.WepyHDF5 method) _contig_runs_to_continuations() (wepy.analysis.contig_tree.BaseContigTree class method) (wepy.analysis.contig_tree.Contig class method) (wepy.analysis.contig_tree.ContigTree class method) _contig_trace_to_contig_runs() (wepy.analysis.contig_tree.BaseContigTree class method) (wepy.analysis.contig_tree.Contig class method) (wepy.analysis.contig_tree.ContigTree class method) _continuations_to_contig_runs() (wepy.analysis.contig_tree.BaseContigTree class method) (wepy.analysis.contig_tree.Contig class method) (wepy.analysis.contig_tree.ContigTree class method) _convert_record_field_to_table_column() (wepy.hdf5.WepyHDF5 method) _convert_record_fields_to_table_columns() (wepy.hdf5.WepyHDF5 method) _create_init() (wepy.hdf5.WepyHDF5 method) _create_tree() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _decide_clone_leaf() (wepy.resampling.resamplers.wexplore.RegionTree method) _decide_merge_leaf() (wepy.resampling.resamplers.wexplore.RegionTree method) _decide_settle_balance() (wepy.resampling.resamplers.wexplore.RegionTree method) _delete_run_record() (wepy.orchestration.orchestrator.Orchestrator method) _dict_attr_to_compound_key_dict() (wepy.runners.openmm.OpenMMState method) _dispense_credit_shares() (wepy.resampling.resamplers.wexplore.RegionTree method) _dispense_debit_shares() (wepy.resampling.resamplers.wexplore.RegionTree method) _dispense_parental_shares() (wepy.resampling.resamplers.wexplore.RegionTree method) _execute() (wepy.util.kv.KV method) _extend_contiguous_traj_field() (wepy.hdf5.WepyHDF5 method) _extend_run_record_data_field() (wepy.hdf5.WepyHDF5 method) _extend_sparse_traj_field() (wepy.hdf5.WepyHDF5 method) _external_sigterm_shutdown() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) _find_best_donation_pair() (wepy.resampling.resamplers.wexplore.RegionTree method) _find_eligible_merge_pairs() (wepy.resampling.resamplers.revo.REVOResampler method) _gen_best_donation() (wepy.resampling.resamplers.wexplore.RegionTree method) _gen_reporters() (wepy.orchestration.configuration.Configuration method) _gen_work_mapper() (wepy.orchestration.configuration.Configuration method) _get_contiguous_traj_field() (wepy.hdf5.WepyHDF5 method) _get_field_path_grp() (wepy.hdf5.WepyHDF5 method) _get_ignore_trace() (wepy.analysis.profiles.ContigTreeProfiler class method) _get_nested_attr_from_compound_key() (wepy.runners.openmm.OpenMMState method) _get_sparse_traj_field() (wepy.hdf5.WepyHDF5 method) _init_checkpoint_db() (wepy.orchestration.orchestrator.Orchestrator method) _init_contiguous_traj_field() (wepy.hdf5.WepyHDF5 method) _init_continuations() (wepy.hdf5.WepyHDF5 method) _init_run_continual_record_grp() (wepy.hdf5.WepyHDF5 method) _init_run_records_field() (wepy.hdf5.WepyHDF5 method) _init_run_sporadic_record_grp() (wepy.hdf5.WepyHDF5 method) _init_sparse_traj_field() (wepy.hdf5.WepyHDF5 method) _init_traj_field() (wepy.hdf5.WepyHDF5 method) _init_traj_fields() (wepy.hdf5.WepyHDF5 method) _init_transition_counts() (wepy.analysis.network.BaseMacroStateNetwork method) _init_walker_actions() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) _initial_parent_distribution() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) _initialize_discontinuities() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _is_sporadic_records() (wepy.hdf5.WepyHDF5 method) _iter_field_paths() (in module wepy.hdf5) _key_init() (wepy.analysis.network.BaseMacroStateNetwork method) _layout_array() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) _leaf_regions_to_all_regions() (wepy.reporter.wexplore.dashboard.WExploreDashboardSection method) _make_child_parent_edges() (wepy.analysis.parents.ParentForest method) _make_record() (wepy.reporter.restree.ResTreeReporter static method) _make_records() (wepy.hdf5.WepyHDF5 method) _make_resampling_record() (wepy.reporter.restree.ResTreeReporter method) _make_task() (wepy.work_mapper.mapper.ABCWorkerMapper method) (wepy.work_mapper.mapper.WorkerMapper method) (wepy.work_mapper.task_mapper.TaskMapper method) _make_warping_record() (wepy.reporter.restree.ResTreeReporter method) _max_n_merges() (wepy.resampling.resamplers.wexplore.RegionTree class method) _new_json_to_mdtraj_topology() (in module wepy.util.mdtraj) _node (wepy.resampling.resamplers.wexplore.RegionTree attribute) _node_row_length() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) _novelty() (wepy.resampling.resamplers.revo.REVOResampler method) _overlaps() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) _percentage_cumulative_partitions() (in module wepy.analysis.profiles) _Popen() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess static method) (wepy.runners.openmm.OpenMMCPUWorker static method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess static method) (wepy.runners.openmm.OpenMMGPUWorker static method) (wepy.work_mapper.mapper.Worker static method) (wepy.work_mapper.task_mapper.WalkerTaskProcess static method)

_pred (wepy.resampling.resamplers.wexplore.RegionTree attribute) _progress() (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) _propagate_and_balance_shares() (wepy.resampling.resamplers.wexplore.RegionTree method) _read_init() (wepy.hdf5.WepyHDF5 method) _read_write_init() (wepy.hdf5.WepyHDF5 method) _rec_spanning_paths() (wepy.analysis.contig_tree.BaseContigTree class method) (wepy.analysis.contig_tree.Contig class method) (wepy.analysis.contig_tree.ContigTree class method) _report_bc() (wepy.reporter.hdf5.WepyHDF5Reporter method) _report_progress() (wepy.reporter.hdf5.WepyHDF5Reporter method) _report_resampler() (wepy.reporter.hdf5.WepyHDF5Reporter method) _report_resampling() (wepy.reporter.hdf5.WepyHDF5Reporter method) _report_warping() (wepy.reporter.hdf5.WepyHDF5Reporter method) _resample_cleanup() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) _resample_init() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) _resolve_platform() (wepy.runners.openmm.OpenMMRunner method) _root_spanning_contig_traces() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _run_cycle() (wepy.sim_manager.Manager method) _run_record_namedtuple() (wepy.hdf5.WepyHDF5 method) _run_records_continual() (wepy.hdf5.WepyHDF5 method) _run_records_sporadic() (wepy.hdf5.WepyHDF5 method) _run_task() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) _run_walker() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) _run_worker() (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) _save_checkpoint() (wepy.orchestration.orchestrator.Orchestrator method) _set_base_contigtree_to_self() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _set_base_network_to_self() (wepy.analysis.network.MacroStateNetwork method) _set_default_init_field_attributes() (wepy.hdf5.WepyHDF5 method) _set_discontinuities() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _set_field_feature_dtype() (wepy.hdf5.WepyHDF5 method) _set_field_feature_shape() (wepy.hdf5.WepyHDF5 method) _set_group_nodes_attribute() (wepy.analysis.network.BaseMacroStateNetwork method) _set_h5_mode() (wepy.hdf5.WepyHDF5 method) _set_parents() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _set_resampling_num_walkers() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) _set_resampling_panels() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _shutdown() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) _sigterm_shutdown() (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.mapper.WorkerMapper method) (wepy.work_mapper.task_mapper.TaskMapper method) _simple_gen_distribution() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) _simple_next_gen() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) _solve_merge_groupings() (wepy.resampling.resamplers.wexplore.RegionTree method) _spanning_paths() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _start_method (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess attribute) (wepy.runners.openmm.OpenMMCPUWorker attribute) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess attribute) (wepy.runners.openmm.OpenMMGPUWorker attribute) (wepy.work_mapper.mapper.Worker attribute) (wepy.work_mapper.task_mapper.WalkerTaskProcess attribute) _subtree_leaves() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _subtree_root() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _subtree_sliding_contig_windows() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) _succ (wepy.resampling.resamplers.wexplore.RegionTree attribute) _tranche_cumulative_partitions() (in module wepy.analysis.profiles) _tree_leaves() (wepy.analysis.contig_tree.BaseContigTree class method) (wepy.analysis.contig_tree.Contig class method) (wepy.analysis.contig_tree.ContigTree class method) _unaligned_image() (wepy.resampling.distances.receptor.RebindingDistance method) (wepy.resampling.distances.receptor.ReceptorDistance method) (wepy.resampling.distances.receptor.UnbindingDistance method) _unset_resampling_num_walkers() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) _update_bc() (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) _update_run_record() (wepy.orchestration.orchestrator.Orchestrator method) _validate_mode() (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.hdf5.WepyHDF5Reporter method) (wepy.reporter.reporter.FileReporter method) (wepy.reporter.reporter.ProgressiveFileReporter method) (wepy.reporter.restree.ResTreeReporter method) (wepy.reporter.walker.WalkerReporter method) _walk() (wepy.runners.randomwalk.RandomWalkRunner method) _warp() (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method)

A

ABCMapper (class in wepy.work_mapper.mapper) ABCWorkerMapper (class in wepy.work_mapper.mapper) action() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) add_child() (wepy.resampling.resamplers.wexplore.RegionTree method) add_configuration() (wepy.orchestration.orchestrator.Orchestrator method) add_continuation() (wepy.hdf5.WepyHDF5 method) add_edge() (wepy.resampling.resamplers.wexplore.RegionTree method) add_edges_from() (wepy.resampling.resamplers.wexplore.RegionTree method) add_metadata() (wepy.hdf5.WepyHDF5 method) add_node() (wepy.resampling.resamplers.wexplore.RegionTree method) add_nodes_from() (wepy.resampling.resamplers.wexplore.RegionTree method) add_observable() (wepy.hdf5.WepyHDF5 method) add_run_observable() (wepy.hdf5.WepyHDF5 method) add_run_record_query (wepy.orchestration.orchestrator.Orchestrator property) add_serial_configuration() (wepy.orchestration.orchestrator.Orchestrator method) add_serial_snapshot() (wepy.orchestration.orchestrator.Orchestrator method) add_snapshot() (wepy.orchestration.orchestrator.Orchestrator method) add_traj() (wepy.hdf5.WepyHDF5 method) add_traj_observable() (wepy.hdf5.WepyHDF5 method) add_weighted_edges_from() (wepy.resampling.resamplers.wexplore.RegionTree method) adj (wepy.resampling.resamplers.wexplore.RegionTree property) adjacency() (wepy.resampling.resamplers.wexplore.RegionTree method) adjlist_inner_dict_factory (wepy.resampling.resamplers.wexplore.RegionTree attribute) adjlist_outer_dict_factory (wepy.resampling.resamplers.wexplore.RegionTree attribute) ALL_ATOMS_REP_KEY (wepy.reporter.hdf5.WepyHDF5Reporter attribute) ALT_REPS (in module wepy.hdf5) alt_reps (wepy.hdf5.WepyHDF5 property) ALT_REPS_IDXS (in module wepy.hdf5) alt_reps_idxs (wepy.hdf5.WepyHDF5 property) ANCESTOR_DECISION_IDS (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision attribute) (wepy.resampling.decisions.decision.Decision attribute) (wepy.resampling.decisions.decision.NoDecision attribute) ancestors() (in module wepy.analysis.parents) apparatus (wepy.orchestration.snapshot.SimSnapshot property) apparatus_opts (wepy.orchestration.configuration.Configuration property) append_only (wepy.orchestration.orchestrator.Orchestrator property) (wepy.util.kv.KV property)

args (wepy.analysis.network.MacroStateNetworkError attribute) (wepy.analysis.network_layouts.layout.LayoutError attribute) (wepy.orchestration.orchestrator.OrchestratorError attribute) (wepy.reporter.reporter.ReporterError attribute) (wepy.resampling.resamplers.resampler.ResamplerError attribute) (wepy.resampling.resamplers.wexplore.RegionTreeError attribute) (wepy.work_mapper.mapper.TaskException attribute) (wepy.work_mapper.mapper.WorkerException attribute) (wepy.work_mapper.mapper.WorkerKilledError attribute) (wepy.work_mapper.mapper.WrapperException attribute) (wepy.work_mapper.task_mapper.TaskProcessException attribute) (wepy.work_mapper.task_mapper.TaskProcessKilledError attribute) assg_field_key (wepy.analysis.network.BaseMacroStateNetwork property) (wepy.analysis.network.MacroStateNetwork property) assign() (wepy.resampling.resamplers.wexplore.RegionTree method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) assign_clones() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) ASSIGNMENTS (wepy.analysis.network.BaseMacroStateNetwork attribute) AtomPairDistance (class in wepy.resampling.distances.distance) attributes (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.ABCMapper property) (wepy.work_mapper.mapper.ABCWorkerMapper property) (wepy.work_mapper.mapper.Mapper property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.mapper.WorkerMapper property) (wepy.work_mapper.task_mapper.TaskMapper property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property) authkey (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property)

B

balance_tree() (wepy.resampling.resamplers.wexplore.RegionTree method) base_contigtree (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) base_network (wepy.analysis.network.MacroStateNetwork property) BaseContigTree (class in wepy.analysis.contig_tree) BaseMacroStateNetwork (class in wepy.analysis.network) bc (boundary conditions) records BC (in module wepy.analysis.contig_tree) (in module wepy.hdf5) BC_DTYPES (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) bc_field_dtypes() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) bc_field_names() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) bc_field_shapes() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) BC_FIELDS (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) bc_fields() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method)

bc_grp() (wepy.hdf5.WepyHDF5 method) BC_IDX (wepy.orchestration.snapshot.WepySimApparatus attribute) bc_record_field_names() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) BC_RECORD_FIELDS (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) bc_records() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) bc_records_dataframe() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) BC_SECTION_TEMPLATE (wepy.reporter.dashboard.BCDashboardSection attribute) (wepy.reporter.receptor.dashboard.RebindingBCDashboardSection attribute) (wepy.reporter.receptor.dashboard.ReceptorBCDashboardSection attribute) (wepy.reporter.receptor.dashboard.UnbindingBCDashboardSection attribute) BC_SHAPES (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) BCDashboardSection (class in wepy.reporter.dashboard) bin_edges() (wepy.analysis.profiles.ContigTreeProfiler method) binding_site_idxs (wepy.boundary_conditions.receptor.RebindingBC property) boundary_condition_class (wepy.analysis.contig_tree.BaseContigTree property) (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) boundary_conditions (wepy.orchestration.snapshot.WepySimApparatus property) BoundaryConditions (class in wepy.boundary_conditions.boundary) BOX_VECTORS (in module wepy.hdf5) box_vectors (wepy.runners.openmm.OpenMMState property) box_vectors_to_lengths_angles() (in module wepy.util.util) box_vectors_unit (wepy.runners.openmm.OpenMMState property) box_vectors_values() (wepy.runners.openmm.OpenMMState method) BOX_VOLUME (in module wepy.hdf5) box_volume (wepy.runners.openmm.OpenMMState property) box_volume_unit (wepy.runners.openmm.OpenMMState property) box_volume_value() (wepy.runners.openmm.OpenMMState method) branch_tree() (wepy.resampling.resamplers.wexplore.RegionTree method)

C

calc_max_num_clones() (in module wepy.resampling.resamplers.wexplore) calc_progress_summary() (wepy.reporter.dashboard.BCDashboardSection method) (wepy.reporter.receptor.dashboard.RebindingBCDashboardSection method) (wepy.reporter.receptor.dashboard.ReceptorBCDashboardSection method) (wepy.reporter.receptor.dashboard.UnbindingBCDashboardSection method) calc_squashable_walkers_single_method() (in module wepy.resampling.resamplers.wexplore) calc_walker_summary() (wepy.reporter.dashboard.DashboardReporter method) calc_warp_rate() (in module wepy.analysis.rates) central_axis (wepy.analysis.network_layouts.tree.ResamplingTreeLayout attribute) characters_written (wepy.work_mapper.mapper.WorkerKilledError attribute) (wepy.work_mapper.task_mapper.TaskProcessKilledError attribute) children() (wepy.resampling.resamplers.wexplore.RegionTree method) cleanup() (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.hdf5.WepyHDF5Reporter method) (wepy.reporter.reporter.FileReporter method) (wepy.reporter.reporter.ProgressiveFileReporter method) (wepy.reporter.reporter.Reporter method) (wepy.reporter.restree.ResTreeReporter method) (wepy.reporter.walker.WalkerReporter method) (wepy.reporter.walker_pkl.WalkerPklReporter method) (wepy.sim_manager.Manager method) (wepy.work_mapper.mapper.ABCMapper method) (wepy.work_mapper.mapper.ABCWorkerMapper method) (wepy.work_mapper.mapper.Mapper method) (wepy.work_mapper.mapper.WorkerMapper method) (wepy.work_mapper.task_mapper.TaskMapper method) clear() (wepy.resampling.resamplers.wexplore.RegionTree method) (wepy.util.kv.KV method) clear_edges() (wepy.resampling.resamplers.wexplore.RegionTree method) clear_walkers() (wepy.resampling.resamplers.wexplore.RegionTree method) CLONE (wepy.resampling.decisions.clone_merge.CloneMergeDecisionEnum attribute) clone() (wepy.hdf5.WepyHDF5 method) (wepy.runners.openmm.OpenMMWalker method) (wepy.walker.Walker method) CloneMergeDecisionEnum (class in wepy.resampling.decisions.clone_merge) CloneMergeResampler (class in wepy.resampling.resamplers.clone_merge) close() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) (wepy.analysis.network.MacroStateNetwork method) (wepy.hdf5.WepyHDF5 method) (wepy.orchestration.orchestrator.Orchestrator method) (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.util.kv.KV method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) COLOR (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) combine_orch_wepy_hdf5s() (in module wepy.orchestration.cli) compute_observable() (wepy.hdf5.WepyHDF5 method) concat_traj_fields() (in module wepy.util.util) config_name (wepy.orchestration.configuration.Configuration property) Configuration (class in wepy.orchestration.configuration) configuration_hash_registered() (wepy.orchestration.orchestrator.Orchestrator method) configuration_hashes (wepy.orchestration.orchestrator.Orchestrator property) contig Contig (class in wepy.analysis.contig_tree) contig (wepy.analysis.parents.ParentForest property)

contig cycle idx contig trace contig tree contig walker trace contig_cycle_idx() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) contig_fields() (wepy.analysis.contig_tree.Contig method) contig_sliding_windows() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) contig_trace (wepy.analysis.contig_tree.Contig property) contig_trace_to_run_trace() (wepy.analysis.contig_tree.BaseContigTree static method) (wepy.analysis.contig_tree.Contig static method) (wepy.analysis.contig_tree.ContigTree static method) contig_tree (wepy.analysis.network.BaseMacroStateNetwork property) contig_warp_rates() (in module wepy.analysis.rates) ContigTree (class in wepy.analysis.contig_tree) contigtree (wepy.analysis.profiles.ContigTreeProfiler property) ContigTreeProfiler (class in wepy.analysis.profiles) contigtrees_bin_edges() (in module wepy.analysis.profiles) continual records continuation CONTINUATIONS (in module wepy.hdf5) continuations (wepy.analysis.contig_tree.BaseContigTree property) (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) (wepy.hdf5.WepyHDF5 property) continue_run_simulation() (wepy.sim_manager.Manager method) continue_run_simulation_by_time() (wepy.sim_manager.Manager method) CONTINUITY_VALUE (wepy.analysis.parents.ParentForest attribute) copy() (wepy.resampling.resamplers.wexplore.RegionTree method) copy_run_slice() (wepy.hdf5.WepyHDF5 method) counts_d_to_matrix() (in module wepy.analysis.transitions) create_run_table_query (wepy.orchestration.orchestrator.Orchestrator property) cumulative_partitions() (in module wepy.analysis.profiles) cutoff_distance (wepy.boundary_conditions.receptor.UnbindingBC property) cutoff_rmsd (wepy.boundary_conditions.receptor.RebindingBC property) CYCLE_DTYPES (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) CYCLE_FIELDS (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) CYCLE_IDX (in module wepy.hdf5) CYCLE_IDXS (in module wepy.hdf5) CYCLE_RECORD_FIELDS (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) CYCLE_SHAPES (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute)

D

daemon (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property) DASHBOARD_TEMPLATE (wepy.reporter.dashboard.DashboardReporter attribute) DashboardReporter (class in wepy.reporter.dashboard) DATA (in module wepy.hdf5) db (wepy.util.kv.KV property) db_uri (wepy.orchestration.orchestrator.Orchestrator property) (wepy.util.kv.KV property) DEBUG_MODES (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) debug_off() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) debug_on() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) decide() (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) decide_merge_groups_single_method() (in module wepy.resampling.resamplers.wexplore) Decision (class in wepy.resampling.decisions.decision) DECISION (in module wepy.hdf5) (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) decision (wepy.resampling.resamplers.clone_merge.CloneMergeResampler property) DECISION (wepy.resampling.resamplers.resampler.NoResampler attribute) decision (wepy.resampling.resamplers.resampler.NoResampler property) DECISION (wepy.resampling.resamplers.resampler.Resampler attribute) decision (wepy.resampling.resamplers.resampler.Resampler property) DECISION (wepy.resampling.resamplers.revo.REVOResampler attribute) decision (wepy.resampling.resamplers.revo.REVOResampler property) DECISION (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) decision (wepy.resampling.resamplers.wexplore.WExploreResampler property) decision instruction record decision record decision_class (wepy.analysis.contig_tree.BaseContigTree property) (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) decision_enum() (wepy.hdf5.WepyHDF5 method) decision_grp() (wepy.hdf5.WepyHDF5 method) decision_value_names() (wepy.hdf5.WepyHDF5 method) DEFAULT_CHECKPOINT_FILENAME (wepy.orchestration.orchestrator.Orchestrator attribute) DEFAULT_CONFIG_NAME (wepy.orchestration.configuration.Configuration attribute) (wepy.orchestration.orchestrator.Orchestrator attribute) DEFAULT_DECISION (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision attribute) (wepy.resampling.decisions.decision.Decision attribute) (wepy.resampling.decisions.decision.NoDecision attribute) default_decision() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method)

DEFAULT_MODE (wepy.orchestration.configuration.Configuration attribute) (wepy.orchestration.orchestrator.Orchestrator attribute) (wepy.reporter.dashboard.DashboardReporter attribute) (wepy.reporter.hdf5.WepyHDF5Reporter attribute) (wepy.reporter.reporter.FileReporter attribute) (wepy.reporter.reporter.ProgressiveFileReporter attribute) (wepy.reporter.restree.ResTreeReporter attribute) (wepy.reporter.walker.WalkerReporter attribute) DEFAULT_NARRATION (wepy.orchestration.configuration.Configuration attribute) (wepy.orchestration.orchestrator.Orchestrator attribute) DEFAULT_NODE_SHAPE (wepy.reporter.restree.ResTreeReporter attribute) DEFAULT_NUM_THREADS (wepy.runners.openmm.OpenMMCPUWorker attribute) DEFAULT_ORCHESTRATION_MODE (wepy.orchestration.orchestrator.Orchestrator attribute) DEFAULT_REPORTER_CLASS (wepy.orchestration.configuration.Configuration attribute) default_snapshot (wepy.orchestration.orchestrator.Orchestrator property) default_snapshot_hash (wepy.orchestration.orchestrator.Orchestrator property) DEFAULT_SUGGESTED_EXTENSION (wepy.reporter.dashboard.DashboardReporter attribute) (wepy.reporter.hdf5.WepyHDF5Reporter attribute) (wepy.reporter.reporter.FileReporter attribute) (wepy.reporter.reporter.ProgressiveFileReporter attribute) (wepy.reporter.restree.ResTreeReporter attribute) (wepy.reporter.walker.WalkerReporter attribute) DEFAULT_WORKDIR (wepy.orchestration.configuration.Configuration attribute) (wepy.orchestration.orchestrator.Orchestrator attribute) defined_traj_field_names (wepy.hdf5.WepyHDF5 property) degree (wepy.resampling.resamplers.wexplore.RegionTree property) del_in_tx() (wepy.util.kv.KV method) del_query (wepy.util.kv.KV property) delete_run_record_query (wepy.orchestration.orchestrator.Orchestrator property) deserialize() (wepy.orchestration.orchestrator.Orchestrator class method) dict() (wepy.runners.openmm.OpenMMState method) (wepy.walker.WalkerState method) DISCONTINUITY_KEY (wepy.analysis.contig_tree.BaseContigTree attribute) (wepy.analysis.contig_tree.Contig attribute) (wepy.analysis.contig_tree.ContigTree attribute) DISCONTINUITY_TARGET_IDXS (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) DISCONTINUITY_VALUE (in module wepy.analysis.parents) (wepy.analysis.parents.ParentForest attribute) DISCONTINUOUS_NODE_SHAPE (wepy.reporter.restree.ResTreeReporter attribute) Distance (class in wepy.resampling.distances.distance) distance (wepy.resampling.resamplers.wexplore.RegionTree property) distance() (wepy.resampling.distances.distance.AtomPairDistance method) (wepy.resampling.distances.distance.Distance method) (wepy.resampling.distances.distance.XYEuclideanDistance method) (wepy.resampling.distances.randomwalk.RandomWalkDistance method) (wepy.resampling.distances.receptor.RebindingDistance method) (wepy.resampling.distances.receptor.ReceptorDistance method) (wepy.resampling.distances.receptor.UnbindingDistance method) DTYPES (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision attribute) (wepy.resampling.decisions.decision.Decision attribute) (wepy.resampling.decisions.decision.NoDecision attribute)

E

edge_attr_dict_factory (wepy.resampling.resamplers.wexplore.RegionTree attribute) edge_attribute_to_matrix() (wepy.analysis.network.BaseMacroStateNetwork method) edge_subgraph() (wepy.resampling.resamplers.wexplore.RegionTree method) edges (wepy.resampling.resamplers.wexplore.RegionTree property) edges_to_dataframe() (wepy.analysis.network.BaseMacroStateNetwork method) edges_to_records() (wepy.analysis.network.BaseMacroStateNetwork method) ENUM (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision attribute) (wepy.resampling.decisions.decision.Decision attribute) (wepy.resampling.decisions.decision.NoDecision attribute) enum_by_name() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) enum_by_value() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) enum_dict_by_name() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) enum_dict_by_value() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method)

errno (wepy.work_mapper.mapper.WorkerKilledError attribute) (wepy.work_mapper.task_mapper.TaskProcessKilledError attribute) exitcode (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property) extend_cycle_bc_records() (wepy.hdf5.WepyHDF5 method) extend_cycle_progress_records() (wepy.hdf5.WepyHDF5 method) extend_cycle_resampler_records() (wepy.hdf5.WepyHDF5 method) extend_cycle_resampling_records() (wepy.hdf5.WepyHDF5 method) extend_cycle_run_group_records() (wepy.hdf5.WepyHDF5 method) extend_cycle_warping_records() (wepy.hdf5.WepyHDF5 method) extend_traj() (wepy.hdf5.WepyHDF5 method) extract_file_runs() (wepy.hdf5.WepyHDF5 method) extract_run() (wepy.hdf5.WepyHDF5 method)

F

fe_all_cumulative_profiles() (wepy.analysis.profiles.ContigTreeProfiler method) fe_cumulative_profiles() (wepy.analysis.profiles.ContigTreeProfiler method) fe_profile() (wepy.analysis.profiles.ContigTreeProfiler method) fe_profile_all() (wepy.analysis.profiles.ContigTreeProfiler method) fe_profile_trace() (wepy.analysis.profiles.ContigTreeProfiler method) feature_vector_to_gexf_viz_color_RGB() (wepy.analysis.network_layouts.layout_graph.LayoutGraph class method) feature_vector_to_gexf_viz_color_RGBA() (wepy.analysis.network_layouts.layout_graph.LayoutGraph class method) feature_vector_to_gexf_viz_position() (wepy.analysis.network_layouts.layout_graph.LayoutGraph class method) field_dtypes() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) FIELD_FEATURE_DTYPES (in module wepy.hdf5) field_feature_dtypes (wepy.hdf5.WepyHDF5 property) FIELD_FEATURE_DTYPES_STR (in module wepy.hdf5) FIELD_FEATURE_SHAPES (in module wepy.hdf5) field_feature_shapes (wepy.hdf5.WepyHDF5 property) FIELD_FEATURE_SHAPES_STR (in module wepy.hdf5) field_names() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) field_shapes() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) FIELDS (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision attribute) (wepy.resampling.decisions.decision.Decision attribute) (wepy.resampling.decisions.decision.NoDecision attribute) fields() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) FILE_ORDER (wepy.reporter.dashboard.DashboardReporter attribute) (wepy.reporter.hdf5.WepyHDF5Reporter attribute) (wepy.reporter.reporter.FileReporter attribute) (wepy.reporter.reporter.ProgressiveFileReporter attribute) (wepy.reporter.restree.ResTreeReporter attribute) (wepy.reporter.walker.WalkerReporter attribute)

file_path (wepy.reporter.dashboard.DashboardReporter property) (wepy.reporter.hdf5.WepyHDF5Reporter property) (wepy.reporter.reporter.FileReporter property) (wepy.reporter.reporter.ProgressiveFileReporter property) (wepy.reporter.restree.ResTreeReporter property) (wepy.reporter.walker.WalkerReporter property) file_paths (wepy.reporter.dashboard.DashboardReporter property) (wepy.reporter.hdf5.WepyHDF5Reporter property) (wepy.reporter.reporter.FileReporter property) (wepy.reporter.reporter.ProgressiveFileReporter property) (wepy.reporter.restree.ResTreeReporter property) (wepy.reporter.walker.WalkerReporter property) filename (wepy.hdf5.WepyHDF5 property) (wepy.work_mapper.mapper.WorkerKilledError attribute) (wepy.work_mapper.task_mapper.TaskProcessKilledError attribute) filename2 (wepy.work_mapper.mapper.WorkerKilledError attribute) (wepy.work_mapper.task_mapper.TaskProcessKilledError attribute) FileReporter (class in wepy.reporter.reporter) filters (wepy.orchestration.snapshot.SimApparatus property) (wepy.orchestration.snapshot.WepySimApparatus property) final_contig_trace() (wepy.analysis.contig_tree.Contig method) final_trace() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) force_shutdown() (wepy.work_mapper.mapper.WorkerMapper method) (wepy.work_mapper.task_mapper.TaskMapper method) FORCES (in module wepy.hdf5) forces (wepy.runners.openmm.OpenMMState property) forces_unit (wepy.runners.openmm.OpenMMState property) forces_values() (wepy.runners.openmm.OpenMMState method) FREE_ENERGY (wepy.analysis.parents.ParentForest attribute) free_energy_profile() (in module wepy.analysis.profiles)

G

gen_bc_section() (wepy.reporter.dashboard.BCDashboardSection method) (wepy.reporter.receptor.dashboard.RebindingBCDashboardSection method) (wepy.reporter.receptor.dashboard.ReceptorBCDashboardSection method) (wepy.reporter.receptor.dashboard.UnbindingBCDashboardSection method) gen_default_snapshot() (wepy.orchestration.orchestrator.Orchestrator method) gen_fields() (wepy.reporter.dashboard.BCDashboardSection method) (wepy.reporter.dashboard.ResamplerDashboardSection method) (wepy.reporter.dashboard.RunnerDashboardSection method) (wepy.reporter.openmm.OpenMMRunnerDashboardSection method) (wepy.reporter.receptor.dashboard.RebindingBCDashboardSection method) (wepy.reporter.receptor.dashboard.ReceptorBCDashboardSection method) (wepy.reporter.receptor.dashboard.UnbindingBCDashboardSection method) (wepy.reporter.revo.dashboard.REVODashboardSection method) (wepy.reporter.wexplore.dashboard.WExploreDashboardSection method) gen_performance_section() (wepy.reporter.dashboard.DashboardReporter method) gen_resampler_section() (wepy.reporter.dashboard.ResamplerDashboardSection method) (wepy.reporter.revo.dashboard.REVODashboardSection method) (wepy.reporter.wexplore.dashboard.WExploreDashboardSection method) gen_runner_section() (wepy.reporter.dashboard.RunnerDashboardSection method) (wepy.reporter.openmm.OpenMMRunnerDashboardSection method) gen_sim_manager() (wepy.orchestration.orchestrator.Orchestrator static method) gen_sim_section() (wepy.reporter.dashboard.DashboardReporter method) gen_sim_state() (in module wepy.runners.openmm) gen_start_snapshot() (wepy.orchestration.orchestrator.Orchestrator method) gen_uri() (in module wepy.util.kv) gen_walker_state() (in module wepy.runners.openmm) generate_state() (wepy.runners.openmm.OpenMMRunner method) get() (wepy.util.kv.KV method) get_branch_trace() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) get_configuration() (wepy.orchestration.orchestrator.Orchestrator method) get_contig_trace_fields() (wepy.hdf5.WepyHDF5 method) get_default_configuration() (wepy.orchestration.orchestrator.Orchestrator method) get_default_configuration_hash() (wepy.orchestration.orchestrator.Orchestrator method) get_default_init_walkers() (wepy.orchestration.orchestrator.Orchestrator method) get_default_sim_apparatus() (wepy.orchestration.orchestrator.Orchestrator method) get_default_snapshot() (wepy.orchestration.orchestrator.Orchestrator method) get_default_snapshot_hash() (wepy.orchestration.orchestrator.Orchestrator method) get_edge_attribute() (wepy.analysis.network.BaseMacroStateNetwork method) get_edge_attributes() (wepy.analysis.network.BaseMacroStateNetwork method) get_edge_data() (wepy.resampling.resamplers.wexplore.RegionTree method) get_edges_attribute() (wepy.analysis.network.BaseMacroStateNetwork method) get_mdtraj_topology() (wepy.hdf5.WepyHDF5 method) get_node_attribute() (wepy.analysis.network.BaseMacroStateNetwork method) get_node_attributes() (wepy.analysis.network.BaseMacroStateNetwork method) (wepy.analysis.network_layouts.layout_graph.LayoutGraph method)

get_node_colors() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) get_node_fields() (wepy.analysis.network.MacroStateNetwork method) get_node_positions() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) get_node_shapes() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) get_node_sizes() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) get_node_viz_attributes() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) get_nodes_attribute() (wepy.analysis.network.BaseMacroStateNetwork method) get_run_record() (wepy.orchestration.orchestrator.Orchestrator method) get_run_records() (wepy.orchestration.orchestrator.Orchestrator method) get_run_trace_fields() (wepy.hdf5.WepyHDF5 method) get_snapshot() (wepy.orchestration.orchestrator.Orchestrator method) get_state_fields_present() (in module wepy.runners.openmm) GET_STATE_KWARG_DEFAULTS (in module wepy.runners.openmm) get_subtree() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) get_topology() (wepy.hdf5.WepyHDF5 method) get_trace_fields() (wepy.hdf5.WepyHDF5 method) get_traj_field() (wepy.hdf5.WepyHDF5 method) get_traj_field_cycle_idxs() (wepy.hdf5.WepyHDF5 method) GEXF_EDGE_SHAPE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_EDGE_THICKNESS (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_COLOR (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_COLOR_ALPHA (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_COLOR_BLUE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_COLOR_GREEN (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_COLOR_RED (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_POSITION (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_POSITION_X (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_POSITION_Y (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_POSITION_Z (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_SHAPE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GEXF_VIZ_SIZE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) graph (wepy.analysis.contig_tree.BaseContigTree property) (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) (wepy.analysis.network.BaseMacroStateNetwork property) (wepy.analysis.network.MacroStateNetwork property) (wepy.analysis.network_layouts.layout_graph.LayoutGraph property) (wepy.analysis.parents.ParentForest property) graph_attr_dict_factory (wepy.resampling.resamplers.wexplore.RegionTree attribute) GRAPHVIZ_COLOR (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GRAPHVIZ_POSITION (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GRAPHVIZ_SHAPE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) GRAPHVIZ_SIZE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute)

H

h5 (wepy.hdf5.WepyHDF5 property) h5_mode (wepy.hdf5.WepyHDF5 property) has_edge() (wepy.resampling.resamplers.wexplore.RegionTree method) has_node() (wepy.resampling.resamplers.wexplore.RegionTree method)

has_predecessor() (wepy.resampling.resamplers.wexplore.RegionTree method) has_successor() (wepy.resampling.resamplers.wexplore.RegionTree method) hash_listing_formatter() (in module wepy.orchestration.cli) HASH_PICKLE_PROTOCOL (wepy.orchestration.orchestrator.Orchestrator attribute) hash_snapshot() (wepy.orchestration.orchestrator.Orchestrator class method)

I

ident (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property) idx idxs image() (wepy.resampling.distances.distance.AtomPairDistance method) (wepy.resampling.distances.distance.Distance method) (wepy.resampling.distances.distance.XYEuclideanDistance method) (wepy.resampling.distances.randomwalk.RandomWalkDistance method) (wepy.resampling.distances.receptor.RebindingDistance method) (wepy.resampling.distances.receptor.ReceptorDistance method) (wepy.resampling.distances.receptor.UnbindingDistance method) image_distance() (wepy.resampling.distances.distance.AtomPairDistance method) (wepy.resampling.distances.distance.Distance method) (wepy.resampling.distances.distance.XYEuclideanDistance method) (wepy.resampling.distances.randomwalk.RandomWalkDistance method) (wepy.resampling.distances.receptor.RebindingDistance method) (wepy.resampling.distances.receptor.ReceptorDistance method) (wepy.resampling.distances.receptor.UnbindingDistance method) images (wepy.resampling.resamplers.wexplore.RegionTree property) in_degree (wepy.resampling.resamplers.wexplore.RegionTree property) in_edges (wepy.resampling.resamplers.wexplore.RegionTree property) init() (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.hdf5.WepyHDF5Reporter method) (wepy.reporter.reporter.FileReporter method) (wepy.reporter.reporter.ProgressiveFileReporter method) (wepy.reporter.reporter.Reporter method) (wepy.reporter.restree.ResTreeReporter method) (wepy.reporter.walker.WalkerReporter method) (wepy.reporter.walker_pkl.WalkerPklReporter method) (wepy.sim_manager.Manager method) (wepy.work_mapper.mapper.ABCMapper method) (wepy.work_mapper.mapper.ABCWorkerMapper method) (wepy.work_mapper.mapper.Mapper method) (wepy.work_mapper.mapper.WorkerMapper method) (wepy.work_mapper.task_mapper.TaskMapper method) init_bc_record_fields() (wepy.hdf5.WepyHDF5 method) init_progress_record_fields() (wepy.hdf5.WepyHDF5 method) init_record_fields() (wepy.hdf5.WepyHDF5 method) init_resampler_record_fields() (wepy.hdf5.WepyHDF5 method) init_resampling_record_fields() (wepy.hdf5.WepyHDF5 method) init_run_bc() (wepy.hdf5.WepyHDF5 method) init_run_fields_bc() (wepy.hdf5.WepyHDF5 method)

init_run_fields_progress() (wepy.hdf5.WepyHDF5 method) init_run_fields_resampler() (wepy.hdf5.WepyHDF5 method) init_run_fields_resampling() (wepy.hdf5.WepyHDF5 method) init_run_fields_resampling_decision() (wepy.hdf5.WepyHDF5 method) init_run_fields_warping() (wepy.hdf5.WepyHDF5 method) init_run_progress() (wepy.hdf5.WepyHDF5 method) init_run_record_grp() (wepy.hdf5.WepyHDF5 method) init_run_resampler() (wepy.hdf5.WepyHDF5 method) init_run_resampling() (wepy.hdf5.WepyHDF5 method) init_run_resampling_decision() (wepy.hdf5.WepyHDF5 method) init_run_warping() (wepy.hdf5.WepyHDF5 method) INIT_WALKERS (in module wepy.hdf5) init_walkers_grp() (wepy.hdf5.WepyHDF5 method) init_warping_record_fields() (wepy.hdf5.WepyHDF5 method) initial_states (wepy.boundary_conditions.boundary.WarpBC property) (wepy.boundary_conditions.randomwalk.RandomWalkBC property) (wepy.boundary_conditions.receptor.RebindingBC property) (wepy.boundary_conditions.receptor.ReceptorBC property) (wepy.boundary_conditions.receptor.UnbindingBC property) initial_walker_fields() (wepy.hdf5.WepyHDF5 method) initial_walkers_to_mdtraj() (wepy.hdf5.WepyHDF5 method) initial_weights (wepy.boundary_conditions.boundary.WarpBC property) (wepy.boundary_conditions.randomwalk.RandomWalkBC property) (wepy.boundary_conditions.receptor.RebindingBC property) (wepy.boundary_conditions.receptor.ReceptorBC property) (wepy.boundary_conditions.receptor.UnbindingBC property) insert_query (wepy.util.kv.KV property) is_alive() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) is_debug_on (wepy.resampling.resamplers.clone_merge.CloneMergeResampler property) (wepy.resampling.resamplers.resampler.NoResampler property) (wepy.resampling.resamplers.resampler.Resampler property) (wepy.resampling.resamplers.revo.REVOResampler property) (wepy.resampling.resamplers.wexplore.WExploreResampler property) is_directed() (wepy.resampling.resamplers.wexplore.RegionTree method) is_multigraph() (wepy.resampling.resamplers.wexplore.RegionTree method) is_run_contig() (wepy.hdf5.WepyHDF5 method) items() (wepy.util.kv.KV method) iter_nodes_fields() (wepy.analysis.network.MacroStateNetwork method) iter_run_trajs() (wepy.hdf5.WepyHDF5 method) iter_runs() (wepy.hdf5.WepyHDF5 method) iter_trajs() (wepy.hdf5.WepyHDF5 method) iter_trajs_fields() (wepy.hdf5.WepyHDF5 method)

J

join() (wepy.hdf5.WepyHDF5 method) (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) json_to_mdtraj_topology() (in module wepy.util.mdtraj)

json_top_atom_count() (in module wepy.util.json_top) json_top_atom_df() (in module wepy.util.json_top) json_top_atom_fields() (in module wepy.util.json_top) json_top_chain_df() (in module wepy.util.json_top) json_top_chain_fields() (in module wepy.util.json_top) json_top_residue_df() (in module wepy.util.json_top) json_top_residue_fields() (in module wepy.util.json_top) json_top_subset() (in module wepy.util.json_top)

K

KEEP_MERGE (wepy.resampling.decisions.clone_merge.CloneMergeDecisionEnum attribute) keep_merge() (in module wepy.walker) KEYS (in module wepy.runners.openmm) (wepy.runners.openmm.OpenMMState attribute) keys() (wepy.util.kv.KV method) kill() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method)

KINETIC_ENERGY (in module wepy.hdf5) kinetic_energy (wepy.runners.openmm.OpenMMState property) kinetic_energy_unit (wepy.runners.openmm.OpenMMState property) kinetic_energy_value() (wepy.runners.openmm.OpenMMState method) KV (class in wepy.util.kv) KV_MODE (wepy.orchestration.orchestrator.Orchestrator attribute)

L

layout() (wepy.analysis.network_layouts.tree.ResamplingTreeLayout method) LayoutError LayoutGraph (class in wepy.analysis.network_layouts.layout_graph) layouts (wepy.analysis.network.BaseMacroStateNetwork property) leaf_nodes() (wepy.resampling.resamplers.wexplore.RegionTree method) leaves() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) lengths_and_angles_to_box_vectors() (in module wepy.util.util) level_nodes() (wepy.resampling.resamplers.wexplore.RegionTree method)

ligand_idxs (wepy.boundary_conditions.receptor.RebindingBC property) (wepy.boundary_conditions.receptor.ReceptorBC property) (wepy.boundary_conditions.receptor.UnbindingBC property) lineages() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) lineages_contig() (wepy.analysis.contig_tree.Contig method) link_file_runs() (wepy.hdf5.WepyHDF5 method) link_run() (wepy.hdf5.WepyHDF5 method) lock() (wepy.util.kv.KV method) lockless_set() (wepy.util.kv.KV method)

M

macrostate_weights() (wepy.analysis.network.MacroStateNetwork method) MacroStateNetwork (class in wepy.analysis.network) MacroStateNetworkError MAIN_REP_IDXS (in module wepy.hdf5) main_rep_idxs (wepy.hdf5.WepyHDF5 property) make_contig() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) Manager (class in wepy.sim_manager) map() (wepy.work_mapper.mapper.ABCMapper method) (wepy.work_mapper.mapper.ABCWorkerMapper method) (wepy.work_mapper.mapper.Mapper method) (wepy.work_mapper.mapper.WorkerMapper method) (wepy.work_mapper.task_mapper.TaskMapper method) Mapper (class in wepy.work_mapper.mapper) mapper_attributes (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) max_n_regions (wepy.resampling.resamplers.wexplore.RegionTree property) max_num_walkers (wepy.resampling.resamplers.wexplore.RegionTree property) max_num_walkers() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) max_num_walkers_setting (wepy.resampling.resamplers.clone_merge.CloneMergeResampler property) (wepy.resampling.resamplers.resampler.NoResampler property) (wepy.resampling.resamplers.resampler.Resampler property) (wepy.resampling.resamplers.revo.REVOResampler property) (wepy.resampling.resamplers.wexplore.WExploreResampler property) MAX_PROGRESS_NORM (wepy.reporter.restree.ResTreeReporter attribute) max_region_sizes (wepy.resampling.resamplers.wexplore.RegionTree property) mdtraj_to_json_topology() (in module wepy.util.mdtraj) merge() (in module wepy.walker) (wepy.runners.openmm.OpenMMWalker method) (wepy.walker.Walker method) merge_method (wepy.resampling.resamplers.wexplore.RegionTree property) MERGE_METHODS (wepy.resampling.resamplers.wexplore.RegionTree attribute) metadata (wepy.hdf5.WepyHDF5 property) microstate_weights() (wepy.analysis.network.MacroStateNetwork method) min_num_walkers (wepy.resampling.resamplers.wexplore.RegionTree property) min_num_walkers() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) min_num_walkers_setting (wepy.resampling.resamplers.clone_merge.CloneMergeResampler property) (wepy.resampling.resamplers.resampler.NoResampler property) (wepy.resampling.resamplers.resampler.Resampler property) (wepy.resampling.resamplers.revo.REVOResampler property) (wepy.resampling.resamplers.wexplore.WExploreResampler property) mode (wepy.hdf5.WepyHDF5 property) (wepy.orchestration.configuration.Configuration property) (wepy.orchestration.orchestrator.Orchestrator property) (wepy.reporter.dashboard.DashboardReporter property) (wepy.reporter.hdf5.WepyHDF5Reporter property) (wepy.reporter.reporter.FileReporter property) (wepy.reporter.reporter.ProgressiveFileReporter property) (wepy.reporter.restree.ResTreeReporter property) (wepy.reporter.walker.WalkerReporter property) (wepy.util.kv.KV property) MODES (wepy.hdf5.WepyHDF5 attribute) (wepy.reporter.dashboard.DashboardReporter attribute) modes (wepy.reporter.dashboard.DashboardReporter property) MODES (wepy.reporter.hdf5.WepyHDF5Reporter attribute) modes (wepy.reporter.hdf5.WepyHDF5Reporter property) MODES (wepy.reporter.reporter.FileReporter attribute) modes (wepy.reporter.reporter.FileReporter property) MODES (wepy.reporter.reporter.ProgressiveFileReporter attribute) modes (wepy.reporter.reporter.ProgressiveFileReporter property) MODES (wepy.reporter.restree.ResTreeReporter attribute) modes (wepy.reporter.restree.ResTreeReporter property) MODES (wepy.reporter.walker.WalkerReporter attribute) modes (wepy.reporter.walker.WalkerReporter property)

module wepy wepy.__about__ wepy.__main__ wepy._print_version wepy.analysis wepy.analysis.contig_tree wepy.analysis.network wepy.analysis.network_layouts wepy.analysis.network_layouts.layout wepy.analysis.network_layouts.layout_graph wepy.analysis.network_layouts.tree wepy.analysis.parents wepy.analysis.profiles wepy.analysis.rates wepy.analysis.transitions wepy.boundary_conditions wepy.boundary_conditions.boundary wepy.boundary_conditions.randomwalk wepy.boundary_conditions.receptor wepy.boundary_conditions.unbinding wepy.hdf5 wepy.orchestration wepy.orchestration.cli wepy.orchestration.configuration wepy.orchestration.orchestrator wepy.orchestration.snapshot wepy.reporter wepy.reporter.dashboard wepy.reporter.hdf5 wepy.reporter.openmm wepy.reporter.receptor wepy.reporter.receptor.dashboard wepy.reporter.reporter wepy.reporter.restree wepy.reporter.revo wepy.reporter.revo.dashboard wepy.reporter.walker wepy.reporter.walker_pkl wepy.reporter.wexplore wepy.reporter.wexplore.dashboard wepy.resampling wepy.resampling.decisions wepy.resampling.decisions.clone_merge wepy.resampling.decisions.decision wepy.resampling.distances wepy.resampling.distances.distance wepy.resampling.distances.randomwalk wepy.resampling.distances.receptor wepy.resampling.resamplers wepy.resampling.resamplers.clone_merge wepy.resampling.resamplers.resampler wepy.resampling.resamplers.revo wepy.resampling.resamplers.wexplore wepy.runners wepy.runners.openmm wepy.runners.randomwalk wepy.runners.runner wepy.sim_manager wepy.util wepy.util.json_top wepy.util.kv wepy.util.mdtraj wepy.util.util wepy.walker wepy.work_mapper wepy.work_mapper.mapper wepy.work_mapper.task_mapper wepy.work_mapper.worker monitor (wepy.orchestration.configuration.Configuration property) monitor_class (wepy.orchestration.configuration.Configuration property) monitor_partial_kwargs (wepy.orchestration.configuration.Configuration property) MultiCloneMergeDecision (class in wepy.resampling.decisions.clone_merge)

N

N_ATOMS (in module wepy.hdf5) N_DIMS (in module wepy.hdf5) N_DIMS_STR (in module wepy.hdf5) n_levels (wepy.resampling.resamplers.wexplore.RegionTree property) n_steps (wepy.analysis.parents.ParentForest property) name (wepy.resampling.resamplers.wexplore.RegionTree property) (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property) NAME_TEMPLATE (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess attribute) (wepy.runners.openmm.OpenMMCPUWorker attribute) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess attribute) (wepy.runners.openmm.OpenMMGPUWorker attribute) (wepy.work_mapper.mapper.Worker attribute) (wepy.work_mapper.task_mapper.WalkerTaskProcess attribute) narration (wepy.orchestration.configuration.Configuration property) native_state (wepy.boundary_conditions.receptor.RebindingBC property) nbunch_iter() (wepy.resampling.resamplers.wexplore.RegionTree method) neighbors() (wepy.resampling.resamplers.wexplore.RegionTree method) net_parent_table() (in module wepy.analysis.parents) new_run() (wepy.hdf5.WepyHDF5 method) next_run_idx() (wepy.hdf5.WepyHDF5 method) next_run_traj_idx() (wepy.hdf5.WepyHDF5 method) NoBC (class in wepy.boundary_conditions.boundary) node_assignments() (wepy.analysis.network.BaseMacroStateNetwork method) node_attr_dict_factory (wepy.resampling.resamplers.wexplore.RegionTree attribute) node_dict_factory (wepy.resampling.resamplers.wexplore.RegionTree attribute) node_fields_map() (wepy.analysis.network.MacroStateNetwork method) node_groups (wepy.analysis.network.BaseMacroStateNetwork property) node_id_to_idx() (wepy.analysis.network.BaseMacroStateNetwork method) node_id_to_idx_dict() (wepy.analysis.network.BaseMacroStateNetwork method) node_ids (wepy.analysis.network.BaseMacroStateNetwork property) (wepy.analysis.network.MacroStateNetwork property)

node_idx_to_id() (wepy.analysis.network.BaseMacroStateNetwork method) node_idx_to_id_dict() (wepy.analysis.network.BaseMacroStateNetwork method) node_layouts() (wepy.analysis.network.BaseMacroStateNetwork method) node_map() (wepy.analysis.network.BaseMacroStateNetwork method) node_observables() (wepy.analysis.network.BaseMacroStateNetwork method) node_radius (wepy.analysis.network_layouts.tree.ResamplingTreeLayout attribute) NoDecision (class in wepy.resampling.decisions.decision) nodes (wepy.resampling.resamplers.wexplore.RegionTree property) nodes_to_dataframe() (wepy.analysis.network.BaseMacroStateNetwork method) nodes_to_records() (wepy.analysis.network.BaseMacroStateNetwork method) NONE_STR (in module wepy.hdf5) NoResampler (class in wepy.resampling.resamplers.resampler) normalize_counts() (in module wepy.analysis.transitions) NoRunner (class in wepy.runners.runner) NOTHING (wepy.resampling.decisions.clone_merge.CloneMergeDecisionEnum attribute) (wepy.resampling.decisions.decision.NothingDecisionEnum attribute) NothingDecisionEnum (class in wepy.resampling.decisions.decision) num_atoms (wepy.hdf5.WepyHDF5 property) num_cycles (wepy.analysis.contig_tree.Contig property) num_dims (wepy.hdf5.WepyHDF5 property) num_init_walkers() (wepy.hdf5.WepyHDF5 method) num_run_cycles() (wepy.hdf5.WepyHDF5 method) num_run_trajs() (wepy.hdf5.WepyHDF5 method) num_runs (wepy.hdf5.WepyHDF5 property) num_states (wepy.analysis.network.BaseMacroStateNetwork property) (wepy.analysis.network.MacroStateNetwork property) num_traj_frames() (wepy.hdf5.WepyHDF5 method) num_trajs (wepy.hdf5.WepyHDF5 property) num_walkers() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) num_workers (wepy.work_mapper.mapper.ABCWorkerMapper property) (wepy.work_mapper.mapper.WorkerMapper property) (wepy.work_mapper.task_mapper.TaskMapper property) number_of_edges() (wepy.resampling.resamplers.wexplore.RegionTree method) number_of_nodes() (wepy.resampling.resamplers.wexplore.RegionTree method)

O

observable_field_names (wepy.hdf5.WepyHDF5 property) OBSERVABLES (in module wepy.hdf5) observables (wepy.analysis.network.BaseMacroStateNetwork property) omm_state_dict() (wepy.runners.openmm.OpenMMState method) open() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) (wepy.analysis.network.MacroStateNetwork method) (wepy.hdf5.WepyHDF5 method) OpenMMCPUWalkerTaskProcess (class in wepy.runners.openmm) OpenMMCPUWorker (class in wepy.runners.openmm) OpenMMGPUWalkerTaskProcess (class in wepy.runners.openmm) OpenMMGPUWorker (class in wepy.runners.openmm)

OpenMMRunner (class in wepy.runners.openmm) OpenMMRunnerDashboardSection (class in wepy.reporter.openmm) OpenMMState (class in wepy.runners.openmm) OpenMMWalker (class in wepy.runners.openmm) ORCH_FILENAME_TEMPLATE (wepy.orchestration.orchestrator.Orchestrator attribute) orch_path (wepy.orchestration.orchestrator.Orchestrator property) orchestrate_snapshot_run_by_time() (wepy.orchestration.orchestrator.Orchestrator method) Orchestrator (class in wepy.orchestration.orchestrator) OrchestratorError order() (wepy.resampling.resamplers.wexplore.RegionTree method) OTHER_KEY_TEMPLATE (wepy.runners.openmm.OpenMMState attribute) out_degree (wepy.resampling.resamplers.wexplore.RegionTree property) out_edges (wepy.resampling.resamplers.wexplore.RegionTree property)

P

PARAMETER_DERIVATIVES (in module wepy.hdf5) parameter_derivatives (wepy.runners.openmm.OpenMMState property) parameter_derivatives_features() (wepy.runners.openmm.OpenMMState method) parameter_derivatives_unit (wepy.runners.openmm.OpenMMState property) parameter_derivatives_values() (wepy.runners.openmm.OpenMMState method) PARAMETERS (in module wepy.hdf5) parameters (wepy.runners.openmm.OpenMMState property) parameters_features() (wepy.runners.openmm.OpenMMState method) parameters_unit (wepy.runners.openmm.OpenMMState property) parameters_values() (wepy.runners.openmm.OpenMMState method) parent panel parent table parent_cycle_discontinuities() (in module wepy.analysis.parents) parent_panel() (in module wepy.analysis.parents) parent_table (wepy.analysis.parents.ParentForest property) (wepy.reporter.restree.ResTreeReporter property) parent_table() (wepy.analysis.contig_tree.Contig method) parent_table_discontinuities() (in module wepy.analysis.parents) ParentForest (class in wepy.analysis.parents) parents() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) PARENTS_KEY (wepy.analysis.contig_tree.BaseContigTree attribute) (wepy.analysis.contig_tree.Contig attribute) (wepy.analysis.contig_tree.ContigTree attribute) PERFORMANCE_SECTION_TEMPLATE (wepy.reporter.dashboard.DashboardReporter attribute) pid (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property) place_walkers() (wepy.resampling.resamplers.wexplore.RegionTree method) pmax (wepy.resampling.resamplers.clone_merge.CloneMergeResampler property) (wepy.resampling.resamplers.revo.REVOResampler property) (wepy.resampling.resamplers.wexplore.RegionTree property) (wepy.resampling.resamplers.wexplore.WExploreResampler property) pmin (wepy.resampling.resamplers.clone_merge.CloneMergeResampler property) (wepy.resampling.resamplers.revo.REVOResampler property) (wepy.resampling.resamplers.wexplore.RegionTree property) (wepy.resampling.resamplers.wexplore.WExploreResampler property) pop() (wepy.util.kv.KV method) popitem() (wepy.util.kv.KV method) POSITION (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) POSITIONS (in module wepy.hdf5) positions (wepy.runners.openmm.OpenMMState property) POSITIONS_LIKE_FIELDS (in module wepy.hdf5) positions_unit (wepy.runners.openmm.OpenMMState property) positions_values() (wepy.runners.openmm.OpenMMState method) post_cycle() (wepy.runners.openmm.OpenMMRunner method) (wepy.runners.randomwalk.RandomWalkRunner method) (wepy.runners.runner.NoRunner method) (wepy.runners.runner.Runner method) POTENTIAL_ENERGY (in module wepy.hdf5) potential_energy (wepy.runners.openmm.OpenMMState property) potential_energy_unit (wepy.runners.openmm.OpenMMState property) potential_energy_value() (wepy.runners.openmm.OpenMMState method) pre_cycle() (wepy.runners.openmm.OpenMMRunner method) (wepy.runners.randomwalk.RandomWalkRunner method) (wepy.runners.runner.NoRunner method) (wepy.runners.runner.Runner method) pred (wepy.resampling.resamplers.wexplore.RegionTree property) predecessors() (wepy.resampling.resamplers.wexplore.RegionTree method) primary_key (wepy.util.kv.KV property) probability (wepy.runners.randomwalk.RandomWalkRunner property) PROGRESS (in module wepy.analysis.contig_tree) (in module wepy.hdf5) progress records PROGRESS_DTYPES (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute)

progress_field_dtypes() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) progress_field_names() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) progress_field_shapes() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) PROGRESS_FIELDS (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) progress_fields() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) progress_grp() (wepy.hdf5.WepyHDF5 method) progress_record_field_names() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) PROGRESS_RECORD_FIELDS (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) progress_records() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) progress_records_dataframe() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) PROGRESS_SHAPES (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) ProgressiveFileReporter (class in wepy.reporter.reporter)

R

RandomBC (class in wepy.boundary_conditions.boundary) RandomWalkBC (class in wepy.boundary_conditions.randomwalk) RandomWalkDistance (class in wepy.resampling.distances.randomwalk) RandomWalkRunner (class in wepy.runners.randomwalk) RebindingBC (class in wepy.boundary_conditions.receptor) RebindingBCDashboardSection (class in wepy.reporter.receptor.dashboard) RebindingDistance (class in wepy.resampling.distances.receptor) receptor_idxs (wepy.boundary_conditions.receptor.RebindingBC property) (wepy.boundary_conditions.receptor.ReceptorBC property) (wepy.boundary_conditions.receptor.UnbindingBC property) RECEPTOR_PARAMETERS (wepy.reporter.receptor.dashboard.RebindingBCDashboardSection attribute) (wepy.reporter.receptor.dashboard.UnbindingBCDashboardSection attribute) ReceptorBC (class in wepy.boundary_conditions.receptor) ReceptorBCDashboardSection (class in wepy.reporter.receptor.dashboard) ReceptorDistance (class in wepy.resampling.distances.receptor) reconcile_orchestrators() (in module wepy.orchestration.orchestrator) record() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) record_field_names() (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision class method) (wepy.resampling.decisions.decision.Decision class method) (wepy.resampling.decisions.decision.NoDecision class method) RECORD_FIELDS (in module wepy.hdf5) record_fields (wepy.hdf5.WepyHDF5 property) RECORD_FIELDS (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision attribute) (wepy.resampling.decisions.decision.Decision attribute) (wepy.resampling.decisions.decision.NoDecision attribute) records records() (wepy.analysis.contig_tree.Contig method) records_dataframe() (wepy.analysis.contig_tree.Contig method) records_grp() (wepy.hdf5.WepyHDF5 method) region_tree (wepy.resampling.resamplers.wexplore.WExploreResampler property) regions (wepy.resampling.resamplers.wexplore.RegionTree property) RegionTree (class in wepy.resampling.resamplers.wexplore) RegionTreeError register_run() (wepy.orchestration.orchestrator.Orchestrator method) remove_edge() (wepy.resampling.resamplers.wexplore.RegionTree method) remove_edges_from() (wepy.resampling.resamplers.wexplore.RegionTree method) remove_node() (wepy.resampling.resamplers.wexplore.RegionTree method) remove_nodes_from() (wepy.resampling.resamplers.wexplore.RegionTree method) reparametrize() (wepy.orchestration.configuration.Configuration method) (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.hdf5.WepyHDF5Reporter method) (wepy.reporter.reporter.FileReporter method) (wepy.reporter.reporter.ProgressiveFileReporter method) (wepy.reporter.restree.ResTreeReporter method) (wepy.reporter.walker.WalkerReporter method) report() (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.hdf5.WepyHDF5Reporter method) (wepy.reporter.reporter.FileReporter method) (wepy.reporter.reporter.ProgressiveFileReporter method) (wepy.reporter.reporter.Reporter method) (wepy.reporter.restree.ResTreeReporter method) (wepy.reporter.walker.WalkerReporter method) (wepy.reporter.walker_pkl.WalkerPklReporter method) REPORT_ITEM_KEYS (wepy.sim_manager.Manager attribute) reporter Reporter (class in wepy.reporter.reporter) REPORTER_CLASS_SEG_TEMPLATE (wepy.orchestration.configuration.Configuration attribute) reporter_classes (wepy.orchestration.configuration.Configuration property) reporter_partial_kwargs (wepy.orchestration.configuration.Configuration property) ReporterError reporters (wepy.orchestration.configuration.Configuration property) resample() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) resampler Resampler (class in wepy.resampling.resamplers.resampler) RESAMPLER (in module wepy.analysis.contig_tree) (in module wepy.hdf5) resampler (wepy.orchestration.snapshot.WepySimApparatus property) resampler records RESAMPLER_DTYPES (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) resampler_field_dtypes() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) resampler_field_names() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) resampler_field_shapes() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) RESAMPLER_FIELDS (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) resampler_fields() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) resampler_grp() (wepy.hdf5.WepyHDF5 method) RESAMPLER_IDX (wepy.orchestration.snapshot.WepySimApparatus attribute) resampler_record_field_names() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) RESAMPLER_RECORD_FIELDS (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) resampler_records() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) resampler_records_dataframe() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) RESAMPLER_SECTION_TEMPLATE (wepy.reporter.dashboard.ResamplerDashboardSection attribute) (wepy.reporter.revo.dashboard.REVODashboardSection attribute) (wepy.reporter.wexplore.dashboard.WExploreDashboardSection attribute) RESAMPLER_SHAPES (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) ResamplerDashboardSection (class in wepy.reporter.dashboard) ResamplerError RESAMPLING (in module wepy.analysis.contig_tree) (in module wepy.hdf5) resampling decision resampling panel resampling records resampling step resampling_contig_trace() (wepy.analysis.contig_tree.Contig method) RESAMPLING_DTYPES (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute)

resampling_field_dtypes() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) resampling_field_names() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) resampling_field_shapes() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) RESAMPLING_FIELDS (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) resampling_fields() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) resampling_grp() (wepy.hdf5.WepyHDF5 method) resampling_panel() (in module wepy.analysis.parents) (wepy.analysis.contig_tree.Contig method) RESAMPLING_PANEL_KEY (wepy.analysis.contig_tree.BaseContigTree attribute) (wepy.analysis.contig_tree.Contig attribute) (wepy.analysis.contig_tree.ContigTree attribute) resampling_record_field_names() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) RESAMPLING_RECORD_FIELDS (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) resampling_records() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) resampling_records_dataframe() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) RESAMPLING_SHAPES (wepy.resampling.resamplers.clone_merge.CloneMergeResampler attribute) (wepy.resampling.resamplers.resampler.NoResampler attribute) (wepy.resampling.resamplers.resampler.Resampler attribute) (wepy.resampling.resamplers.revo.REVOResampler attribute) (wepy.resampling.resamplers.wexplore.WExploreResampler attribute) resampling_trace() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) resampling_tree_layout_graph() (wepy.analysis.contig_tree.Contig method) ResamplingTreeLayout (class in wepy.analysis.network_layouts.tree) resolve_state_data_type_enum_values() (in module wepy.runners.openmm) ResTreeReporter (class in wepy.reporter.restree) reverse() (wepy.resampling.resamplers.wexplore.RegionTree method) REVODashboardSection (class in wepy.reporter.revo.dashboard) REVOResampler (class in wepy.resampling.resamplers.revo) RGBA_to_hex() (wepy.analysis.network_layouts.layout_graph.LayoutGraph class method) ROOT_CYCLE_IDX (wepy.analysis.parents.ParentForest attribute) root_leaves() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) ROOT_NODE (wepy.resampling.resamplers.wexplore.RegionTree attribute) roots (wepy.analysis.parents.ParentForest property) roots() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) row_spacing (wepy.analysis.network_layouts.tree.ResamplingTreeLayout attribute) run run contig run cycle idx run trace run() (wepy.hdf5.WepyHDF5 method) (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) run_configuration() (wepy.orchestration.orchestrator.Orchestrator method) run_configuration_hash() (wepy.orchestration.orchestrator.Orchestrator method) run_contig_records() (wepy.hdf5.WepyHDF5 method) run_contig_records_dataframe() (wepy.hdf5.WepyHDF5 method) run_contig_resampling_panel() (wepy.hdf5.WepyHDF5 method) run_continues() (wepy.orchestration.orchestrator.Orchestrator method) run_cycle() (wepy.sim_manager.Manager method) RUN_END_SNAPSHOT_HASH (in module wepy.hdf5) run_end_snapshot_hash() (wepy.hdf5.WepyHDF5 method) run_grp() (wepy.hdf5.WepyHDF5 method) run_hashes() (wepy.orchestration.orchestrator.Orchestrator method) RUN_IDX (in module wepy.hdf5) run_idxs (wepy.analysis.contig_tree.BaseContigTree property) (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) (wepy.hdf5.WepyHDF5 property) run_last_cycle_idx() (wepy.orchestration.orchestrator.Orchestrator method) run_records() (wepy.hdf5.WepyHDF5 method) run_records_dataframe() (wepy.hdf5.WepyHDF5 method) run_resampling_panel() (wepy.hdf5.WepyHDF5 method) run_segment() (wepy.runners.openmm.OpenMMRunner method) (wepy.runners.randomwalk.RandomWalkRunner method) (wepy.runners.runner.NoRunner method) (wepy.runners.runner.Runner method) (wepy.sim_manager.Manager method) RUN_SELECT_FIELDS (wepy.orchestration.orchestrator.Orchestrator attribute) run_simulation() (wepy.sim_manager.Manager method) run_simulation_by_time() (wepy.sim_manager.Manager method) run_snapshot_by_time() (wepy.orchestration.orchestrator.Orchestrator method) RUN_START_SNAPSHOT_HASH (in module wepy.hdf5) run_start_snapshot_hash() (wepy.hdf5.WepyHDF5 method) run_task() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) run_trace_to_contig_trace() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) run_trace_to_mdtraj() (wepy.hdf5.WepyHDF5 method) run_traj_idx_tuples() (wepy.hdf5.WepyHDF5 method) run_traj_idxs() (wepy.hdf5.WepyHDF5 method) run_trajs() (wepy.hdf5.WepyHDF5 method) run_transition_counts_matrix() (in module wepy.analysis.transitions) run_transition_probability_matrix() (in module wepy.analysis.transitions) runner Runner (class in wepy.runners.runner) runner (wepy.orchestration.snapshot.WepySimApparatus property) RUNNER_IDX (wepy.orchestration.snapshot.WepySimApparatus attribute) RUNNER_SECTION_TEMPLATE (wepy.reporter.dashboard.RunnerDashboardSection attribute) (wepy.reporter.openmm.OpenMMRunnerDashboardSection attribute) RunnerDashboardSection (class in wepy.reporter.dashboard) RUNS (in module wepy.hdf5) runs (wepy.hdf5.WepyHDF5 property)

S

segment_func (wepy.work_mapper.mapper.ABCMapper property) (wepy.work_mapper.mapper.ABCWorkerMapper property) (wepy.work_mapper.mapper.Mapper property) (wepy.work_mapper.mapper.WorkerMapper property) (wepy.work_mapper.task_mapper.TaskMapper property) sentinel (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) (wepy.work_mapper.task_mapper.WalkerTaskProcess property) serialize() (wepy.orchestration.orchestrator.Orchestrator class method) set_attrs_by_array() (wepy.analysis.parents.ParentForest method) set_debug_mode() (wepy.resampling.resamplers.clone_merge.CloneMergeResampler method) (wepy.resampling.resamplers.resampler.NoResampler method) (wepy.resampling.resamplers.resampler.Resampler method) (wepy.resampling.resamplers.revo.REVOResampler method) (wepy.resampling.resamplers.wexplore.WExploreResampler method) set_default_configuration() (wepy.orchestration.orchestrator.Orchestrator method) set_default_init_walkers() (wepy.orchestration.orchestrator.Orchestrator method) set_default_sim_apparatus() (wepy.orchestration.orchestrator.Orchestrator method) set_default_snapshot() (wepy.orchestration.orchestrator.Orchestrator method) set_in_tx() (wepy.util.kv.KV method) set_loglevel() (in module wepy.util.util) set_macrostate_weights() (wepy.analysis.network.MacroStateNetwork method) set_mode() (wepy.hdf5.WepyHDF5 method) (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.hdf5.WepyHDF5Reporter method) (wepy.reporter.reporter.FileReporter method) (wepy.reporter.reporter.ProgressiveFileReporter method) (wepy.reporter.restree.ResTreeReporter method) (wepy.reporter.walker.WalkerReporter method) set_node_attributes() (wepy.analysis.parents.ParentForest method) set_node_colors() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_gexf_colors_rgb() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_gexf_colors_rgba() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_gexf_positions() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_gexf_shape() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_gexf_sizes() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_gexf_viz() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_group() (wepy.analysis.network.BaseMacroStateNetwork method) set_node_positions() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_shapes() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_sizes() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_node_viz_attributes() (wepy.analysis.network_layouts.layout_graph.LayoutGraph method) set_nodes_attribute() (wepy.analysis.network.BaseMacroStateNetwork method) set_nodes_layout() (wepy.analysis.network.BaseMacroStateNetwork method) set_nodes_observable() (wepy.analysis.network.BaseMacroStateNetwork method) set_path() (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.hdf5.WepyHDF5Reporter method) (wepy.reporter.reporter.FileReporter method) (wepy.reporter.reporter.ProgressiveFileReporter method) (wepy.reporter.restree.ResTreeReporter method) (wepy.reporter.walker.WalkerReporter method) set_run_end_snapshot_hash() (wepy.hdf5.WepyHDF5 method) set_run_start_snapshot_hash() (wepy.hdf5.WepyHDF5 method) setdefault() (wepy.util.kv.KV method) SETTINGS (in module wepy.hdf5) settings_grp (wepy.hdf5.WepyHDF5 property) settle_run_options() (in module wepy.orchestration.cli) SHAPE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) SHAPES (wepy.resampling.decisions.clone_merge.MultiCloneMergeDecision attribute) (wepy.resampling.decisions.decision.Decision attribute) (wepy.resampling.decisions.decision.NoDecision attribute) sim_state (wepy.runners.openmm.OpenMMState property) SimApparatus (class in wepy.orchestration.snapshot)

SimSnapshot (class in wepy.orchestration.snapshot) SIMULATION_SECTION_TEMPLATE (wepy.reporter.dashboard.DashboardReporter attribute) SIZE (wepy.analysis.network_layouts.layout_graph.LayoutGraph attribute) size() (wepy.resampling.resamplers.wexplore.RegionTree method) sliding_contig_windows() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) sliding_window() (in module wepy.analysis.parents) sliding_windows() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) snapshot_hash_registered() (wepy.orchestration.orchestrator.Orchestrator method) snapshot_hashes (wepy.orchestration.orchestrator.Orchestrator property) snapshot_registered() (wepy.orchestration.orchestrator.Orchestrator method) span_contig() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) span_traces (wepy.analysis.contig_tree.BaseContigTree property) (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) spanning contig spanning_contig_traces() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) SPARSE_FIELDS (in module wepy.hdf5) sparse_fields (wepy.hdf5.WepyHDF5 property) SPARSE_IDXS (in module wepy.hdf5) split() (in module wepy.walker) sporadic records SPORADIC_RECORDS (in module wepy.hdf5) SQLITE3_DEFAULT_TIMEOUT (wepy.orchestration.orchestrator.Orchestrator attribute) SQUASH (wepy.resampling.decisions.clone_merge.CloneMergeDecisionEnum attribute) squash() (wepy.runners.openmm.OpenMMWalker method) (wepy.walker.Walker method) start() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) state_to_mdtraj() (wepy.analysis.network.MacroStateNetwork method) state_to_traj_fields() (wepy.analysis.network.MacroStateNetwork method) states_to_traj_fields() (wepy.analysis.network.MacroStateNetwork method) step() (wepy.analysis.parents.ParentForest method) step_spacing (wepy.analysis.network_layouts.tree.ResamplingTreeLayout attribute) steps() (wepy.analysis.parents.ParentForest method) strerror (wepy.work_mapper.mapper.WorkerKilledError attribute) (wepy.work_mapper.task_mapper.TaskProcessKilledError attribute) subgraph() (wepy.resampling.resamplers.wexplore.RegionTree method) subtrees() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) succ (wepy.resampling.resamplers.wexplore.RegionTree property) successors() (wepy.resampling.resamplers.wexplore.RegionTree method) SUGGESTED_EXTENSIONS (wepy.reporter.dashboard.DashboardReporter attribute) (wepy.reporter.hdf5.WepyHDF5Reporter attribute) (wepy.reporter.reporter.FileReporter attribute) (wepy.reporter.reporter.ProgressiveFileReporter attribute) (wepy.reporter.restree.ResTreeReporter attribute) (wepy.reporter.walker.WalkerReporter attribute) SUGGESTED_FILENAME_TEMPLATE (wepy.reporter.dashboard.DashboardReporter attribute) (wepy.reporter.hdf5.WepyHDF5Reporter attribute) (wepy.reporter.reporter.FileReporter attribute) (wepy.reporter.reporter.ProgressiveFileReporter attribute) (wepy.reporter.restree.ResTreeReporter attribute) (wepy.reporter.walker.WalkerReporter attribute) swmr_mode (wepy.hdf5.WepyHDF5 property)

T

table (wepy.util.kv.KV property) Task (class in wepy.work_mapper.mapper) TaskException TaskMapper (class in wepy.work_mapper.task_mapper) TaskProcessException TaskProcessKilledError terminate() (wepy.runners.openmm.OpenMMCPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMCPUWorker method) (wepy.runners.openmm.OpenMMGPUWalkerTaskProcess method) (wepy.runners.openmm.OpenMMGPUWorker method) (wepy.work_mapper.mapper.Worker method) (wepy.work_mapper.task_mapper.WalkerTaskProcess method) threshold (wepy.boundary_conditions.randomwalk.RandomWalkBC property) TIME (in module wepy.hdf5) time (wepy.runners.openmm.OpenMMState property) time_unit (wepy.runners.openmm.OpenMMState property) time_value() (wepy.runners.openmm.OpenMMState method) to_directed() (wepy.resampling.resamplers.wexplore.RegionTree method) to_directed_class() (wepy.resampling.resamplers.wexplore.RegionTree method) to_mdtraj() (wepy.hdf5.WepyHDF5 method) (wepy.runners.openmm.OpenMMState method) to_undirected() (wepy.resampling.resamplers.wexplore.RegionTree method)

to_undirected_class() (wepy.resampling.resamplers.wexplore.RegionTree method) TOPOLOGY (in module wepy.hdf5) topology (wepy.boundary_conditions.receptor.UnbindingBC property) (wepy.hdf5.WepyHDF5 property) trace trace_parent_table() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) trace_to_mdtraj() (wepy.hdf5.WepyHDF5 method) traj() (wepy.hdf5.WepyHDF5 method) traj_box_vectors_to_lengths_angles() (in module wepy.util.util) traj_fields_map() (wepy.hdf5.WepyHDF5 method) traj_fields_to_mdtraj() (in module wepy.util.mdtraj) (wepy.hdf5.WepyHDF5 method) TRAJ_IDX (in module wepy.hdf5) TRAJECTORIES (in module wepy.hdf5) trajectory trajectory fields transition_counts() (in module wepy.analysis.transitions) transition_counts_matrix() (in module wepy.analysis.transitions) transition_probability_matrix() (in module wepy.analysis.transitions) trees (wepy.analysis.parents.ParentForest property)

U

UnbindingBC (class in wepy.boundary_conditions.receptor) UnbindingBCDashboardSection (class in wepy.reporter.receptor.dashboard) UnbindingDistance (class in wepy.resampling.distances.receptor) UNIT_NAMES (in module wepy.runners.openmm) (in module wepy.runners.randomwalk) UNITS (in module wepy.hdf5) update() (wepy.resampling.resamplers.wexplore.RegionTree method) (wepy.util.kv.KV method) update_performance_values() (wepy.reporter.dashboard.DashboardReporter method) update_query (wepy.util.kv.KV property)

update_run_record_query (wepy.orchestration.orchestrator.Orchestrator property) update_values() (wepy.reporter.dashboard.BCDashboardSection method) (wepy.reporter.dashboard.DashboardReporter method) (wepy.reporter.dashboard.ResamplerDashboardSection method) (wepy.reporter.dashboard.RunnerDashboardSection method) (wepy.reporter.openmm.OpenMMRunnerDashboardSection method) (wepy.reporter.receptor.dashboard.RebindingBCDashboardSection method) (wepy.reporter.receptor.dashboard.ReceptorBCDashboardSection method) (wepy.reporter.receptor.dashboard.UnbindingBCDashboardSection method) (wepy.reporter.revo.dashboard.REVODashboardSection method) (wepy.reporter.wexplore.dashboard.WExploreDashboardSection method)

V

value_name (wepy.util.kv.KV property) value_types (wepy.util.kv.KV property) values() (wepy.util.kv.KV method) VELOCITIES (in module wepy.hdf5)

velocities (wepy.runners.openmm.OpenMMState property) velocities_unit (wepy.runners.openmm.OpenMMState property) velocities_values() (wepy.runners.openmm.OpenMMState method) viz_graph (wepy.analysis.network_layouts.layout_graph.LayoutGraph property)

W

walker Walker (class in wepy.walker) walker() (wepy.analysis.parents.ParentForest method) walker_assignments (wepy.resampling.resamplers.wexplore.RegionTree property) walker_task_type (wepy.work_mapper.task_mapper.TaskMapper property) walker_trace_to_run_trace() (wepy.analysis.contig_tree.BaseContigTree method) (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) walker_weights (wepy.resampling.resamplers.wexplore.RegionTree property) WalkerPklReporter (class in wepy.reporter.walker_pkl) WalkerReporter (class in wepy.reporter.walker) walkers (wepy.orchestration.snapshot.SimSnapshot property) WalkerState (class in wepy.walker) WalkerTaskProcess (class in wepy.work_mapper.task_mapper) warp_contig_trace() (wepy.analysis.contig_tree.Contig method) WARP_RECORD_COLNAMES (wepy.reporter.dashboard.BCDashboardSection attribute) (wepy.reporter.receptor.dashboard.RebindingBCDashboardSection attribute) (wepy.reporter.receptor.dashboard.ReceptorBCDashboardSection attribute) (wepy.reporter.receptor.dashboard.UnbindingBCDashboardSection attribute) warp_trace() (wepy.analysis.contig_tree.Contig method) (wepy.analysis.contig_tree.ContigTree method) warp_walkers() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) WarpBC (class in wepy.boundary_conditions.boundary) WARPING (in module wepy.analysis.contig_tree) (in module wepy.hdf5) warping records warping_discontinuity() (wepy.boundary_conditions.boundary.BoundaryConditions class method) (wepy.boundary_conditions.boundary.NoBC class method) (wepy.boundary_conditions.boundary.RandomBC class method) (wepy.boundary_conditions.boundary.WarpBC class method) (wepy.boundary_conditions.randomwalk.RandomWalkBC class method) (wepy.boundary_conditions.receptor.RebindingBC class method) (wepy.boundary_conditions.receptor.ReceptorBC class method) (wepy.boundary_conditions.receptor.UnbindingBC class method) WARPING_DTYPES (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) warping_field_dtypes() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) warping_field_names() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) warping_field_shapes() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) WARPING_FIELDS (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) warping_fields() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) warping_grp() (wepy.hdf5.WepyHDF5 method) warping_record_field_names() (wepy.boundary_conditions.boundary.BoundaryConditions method) (wepy.boundary_conditions.boundary.NoBC method) (wepy.boundary_conditions.boundary.RandomBC method) (wepy.boundary_conditions.boundary.WarpBC method) (wepy.boundary_conditions.randomwalk.RandomWalkBC method) (wepy.boundary_conditions.receptor.RebindingBC method) (wepy.boundary_conditions.receptor.ReceptorBC method) (wepy.boundary_conditions.receptor.UnbindingBC method) WARPING_RECORD_FIELDS (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) warping_records() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) warping_records_dataframe() (wepy.analysis.contig_tree.Contig method) (wepy.hdf5.WepyHDF5 method) WARPING_SHAPES (wepy.boundary_conditions.boundary.BoundaryConditions attribute) (wepy.boundary_conditions.boundary.NoBC attribute) (wepy.boundary_conditions.boundary.RandomBC attribute) (wepy.boundary_conditions.boundary.WarpBC attribute) (wepy.boundary_conditions.randomwalk.RandomWalkBC attribute) (wepy.boundary_conditions.receptor.RebindingBC attribute) (wepy.boundary_conditions.receptor.ReceptorBC attribute) (wepy.boundary_conditions.receptor.UnbindingBC attribute) WEIGHT (wepy.analysis.parents.ParentForest attribute) WEIGHT_DTYPE (in module wepy.hdf5) WEIGHT_SHAPE (in module wepy.hdf5) weighted ensemble WEIGHTS (in module wepy.hdf5) wepy module wepy.__about__ module wepy.__main__ module wepy._print_version module wepy.analysis module wepy.analysis.contig_tree module wepy.analysis.network module wepy.analysis.network_layouts module wepy.analysis.network_layouts.layout module wepy.analysis.network_layouts.layout_graph module wepy.analysis.network_layouts.tree module wepy.analysis.parents module wepy.analysis.profiles module

wepy.analysis.rates module wepy.analysis.transitions module wepy.boundary_conditions module wepy.boundary_conditions.boundary module wepy.boundary_conditions.randomwalk module wepy.boundary_conditions.receptor module wepy.boundary_conditions.unbinding module wepy.hdf5 module wepy.orchestration module wepy.orchestration.cli module wepy.orchestration.configuration module wepy.orchestration.orchestrator module wepy.orchestration.snapshot module wepy.reporter module wepy.reporter.dashboard module wepy.reporter.hdf5 module wepy.reporter.openmm module wepy.reporter.receptor module wepy.reporter.receptor.dashboard module wepy.reporter.reporter module wepy.reporter.restree module wepy.reporter.revo module wepy.reporter.revo.dashboard module wepy.reporter.walker module wepy.reporter.walker_pkl module wepy.reporter.wexplore module wepy.reporter.wexplore.dashboard module wepy.resampling module wepy.resampling.decisions module wepy.resampling.decisions.clone_merge module wepy.resampling.decisions.decision module wepy.resampling.distances module wepy.resampling.distances.distance module wepy.resampling.distances.randomwalk module wepy.resampling.distances.receptor module wepy.resampling.resamplers module wepy.resampling.resamplers.clone_merge module wepy.resampling.resamplers.resampler module wepy.resampling.resamplers.revo module wepy.resampling.resamplers.wexplore module wepy.runners module wepy.runners.openmm module wepy.runners.randomwalk module wepy.runners.runner module wepy.sim_manager module wepy.util module wepy.util.json_top module wepy.util.kv module wepy.util.mdtraj module wepy.util.util module wepy.walker module wepy.work_mapper module wepy.work_mapper.mapper module wepy.work_mapper.task_mapper module wepy.work_mapper.worker module wepy_h5 (wepy.analysis.contig_tree.Contig property) (wepy.analysis.contig_tree.ContigTree property) (wepy.analysis.network.MacroStateNetwork property) WepyHDF5 (class in wepy.hdf5) WepyHDF5Reporter (class in wepy.reporter.hdf5) WepySimApparatus (class in wepy.orchestration.snapshot) WExploreDashboardSection (class in wepy.reporter.wexplore.dashboard) WExploreResampler (class in wepy.resampling.resamplers.wexplore) with_traceback() (wepy.analysis.network.MacroStateNetworkError method) (wepy.analysis.network_layouts.layout.LayoutError method) (wepy.orchestration.orchestrator.OrchestratorError method) (wepy.reporter.reporter.ReporterError method) (wepy.resampling.resamplers.resampler.ResamplerError method) (wepy.resampling.resamplers.wexplore.RegionTreeError method) (wepy.work_mapper.mapper.TaskException method) (wepy.work_mapper.mapper.WorkerException method) (wepy.work_mapper.mapper.WorkerKilledError method) (wepy.work_mapper.mapper.WrapperException method) (wepy.work_mapper.task_mapper.TaskProcessException method) (wepy.work_mapper.task_mapper.TaskProcessKilledError method) work_dir (wepy.orchestration.configuration.Configuration property) work_mapper (wepy.orchestration.configuration.Configuration property) work_mapper_class (wepy.orchestration.configuration.Configuration property) work_mapper_partial_kwargs (wepy.orchestration.configuration.Configuration property) Worker (class in wepy.work_mapper.mapper) worker_idx (wepy.runners.openmm.OpenMMCPUWorker property) (wepy.runners.openmm.OpenMMGPUWorker property) (wepy.work_mapper.mapper.Worker property) worker_segment_times (wepy.work_mapper.mapper.ABCWorkerMapper property) (wepy.work_mapper.mapper.Mapper property) (wepy.work_mapper.mapper.WorkerMapper property) (wepy.work_mapper.task_mapper.TaskMapper property) worker_type (wepy.work_mapper.mapper.WorkerMapper property) WorkerException WorkerKilledError WorkerMapper (class in wepy.work_mapper.mapper) WrapperException write_dashboard() (wepy.reporter.dashboard.DashboardReporter method) write_gexf() (wepy.analysis.network.BaseMacroStateNetwork method) WRITE_MODES (wepy.hdf5.WepyHDF5 attribute)

X

XYEuclideanDistance (class in wepy.resampling.distances.distance)