Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W A action (CodeEntropy.config.argparse.ArgSpec attribute) add_group_label() (CodeEntropy.results.reporter.ResultsReporter method) add_residue_data() (CodeEntropy.results.reporter.ResultsReporter method) add_results_data() (CodeEntropy.results.reporter.ResultsReporter method) AggregateEntropyNode (class in CodeEntropy.entropy.nodes.aggregate) analysis_indices (CodeEntropy.trajectory.frames.FrameSelection property) ArgSpec (class in CodeEntropy.config.argparse) assign_peak_labels_and_count_flexible() (in module CodeEntropy.levels.dihedrals.kernels) atom_indices (CodeEntropy.levels.nodes.beads.UnitedAtomBead attribute) axes_manager (CodeEntropy.levels.forces.TorqueInputs attribute) AxesCalculator (class in CodeEntropy.levels.axes) AxesTopology (class in CodeEntropy.levels.nodes.axes_topology) B bonded_heavy_indices (CodeEntropy.levels.nodes.axes_topology.UAAxesTopology attribute) bonded_light_indices (CodeEntropy.levels.nodes.axes_topology.UAAxesTopology attribute) box (CodeEntropy.levels.forces.TorqueInputs attribute) build() (CodeEntropy.entropy.graph.EntropyGraph method) (CodeEntropy.levels.graph.conformation_dag.ConformationDAG method) (CodeEntropy.levels.graph.frame_dag.FrameGraph method) (CodeEntropy.levels.graph.level_dag.LevelDAG method) build_conformational_states() (CodeEntropy.levels.dihedrals.conformational_state_builder.ConformationStateBuilder method) build_parser() (CodeEntropy.config.argparse.ConfigResolver method) BuildAxesTopologyNode (class in CodeEntropy.levels.nodes.axes_topology) BuildBeadsNode (class in CodeEntropy.levels.nodes.beads) C calculate() (CodeEntropy.entropy.orientational.OrientationalEntropy method) calculate_and_log() (CodeEntropy.entropy.water.WaterEntropy method) center (CodeEntropy.levels.forces.TorqueInputs attribute) change_lambda_units() (CodeEntropy.config.runtime.CodeEntropyRunner method) check_slurm_env() (CodeEntropy.core.dask_clusters.HPCDaskManager method) chunk_frame_indices() (in module CodeEntropy.levels.execution.chunks) chunk_id (CodeEntropy.levels.dihedrals.angle_observations.ConformationChunkTask attribute) chunk_index (CodeEntropy.levels.execution.tasks.FrameChunkResult attribute) (CodeEntropy.levels.execution.tasks.FrameChunkTask attribute) clean_residue_name() (CodeEntropy.results.reporter.ResultsReporter static method) CodeEntropy module CodeEntropy.cli module CodeEntropy.config module CodeEntropy.config.argparse module CodeEntropy.config.runtime module CodeEntropy.core module CodeEntropy.core.dask_clusters module CodeEntropy.core.logging module CodeEntropy.entropy module CodeEntropy.entropy.configurational module CodeEntropy.entropy.graph module CodeEntropy.entropy.nodes module CodeEntropy.entropy.nodes.aggregate module CodeEntropy.entropy.nodes.configurational module CodeEntropy.entropy.nodes.orientational module CodeEntropy.entropy.nodes.vibrational module CodeEntropy.entropy.orientational module CodeEntropy.entropy.vibrational module CodeEntropy.entropy.water module CodeEntropy.entropy.workflow module CodeEntropy.levels module CodeEntropy.levels.axes module CodeEntropy.levels.dihedrals module CodeEntropy.levels.dihedrals.angle_observations module CodeEntropy.levels.dihedrals.conformational_state_builder module CodeEntropy.levels.dihedrals.kernels module CodeEntropy.levels.dihedrals.peak_detection module CodeEntropy.levels.dihedrals.state_assignment module CodeEntropy.levels.dihedrals.topology module CodeEntropy.levels.execution module CodeEntropy.levels.execution.chunks module CodeEntropy.levels.execution.policy module CodeEntropy.levels.execution.reducers module CodeEntropy.levels.execution.scheduler module CodeEntropy.levels.execution.tasks module CodeEntropy.levels.forces module CodeEntropy.levels.graph module CodeEntropy.levels.graph.conformation_dag module CodeEntropy.levels.graph.frame_dag module CodeEntropy.levels.graph.level_dag module CodeEntropy.levels.hierarchy module CodeEntropy.levels.linalg module CodeEntropy.levels.neighbors module CodeEntropy.levels.nodes module CodeEntropy.levels.nodes.accumulators module CodeEntropy.levels.nodes.axes_topology module CodeEntropy.levels.nodes.beads module CodeEntropy.levels.nodes.covariance module CodeEntropy.levels.nodes.detect_levels module CodeEntropy.levels.nodes.detect_molecules module CodeEntropy.levels.search module CodeEntropy.molecules module CodeEntropy.molecules.grouping module CodeEntropy.results module CodeEntropy.results.reporter module CodeEntropy.trajectory module CodeEntropy.trajectory.frames module CodeEntropy.trajectory.mda module CodeEntropy.trajectory.source module CodeEntropyRunner (class in CodeEntropy.config.runtime) compute_frame_covariance() (CodeEntropy.levels.forces.ForceTorqueCalculator method) ConfigResolver (class in CodeEntropy.config.argparse) configurational_key (CodeEntropy.entropy.nodes.aggregate.AggregateEntropyNode attribute) ConfigurationalEntropyNode (class in CodeEntropy.entropy.nodes.configurational) configure() (CodeEntropy.core.logging.LoggingConfig method) configure_cluster() (CodeEntropy.core.dask_clusters.HPCDaskManager method) conformational_entropy_calculation() (CodeEntropy.entropy.configurational.ConformationalEntropy method) ConformationalEntropy (class in CodeEntropy.entropy.configurational) ConformationChunkTask (class in CodeEntropy.levels.dihedrals.angle_observations) ConformationDAG (class in CodeEntropy.levels.graph.conformation_dag) ConformationPeakDetector (class in CodeEntropy.levels.dihedrals.peak_detection) ConformationStateAssigner (class in CodeEntropy.levels.dihedrals.state_assignment) ConformationStateBuilder (class in CodeEntropy.levels.dihedrals.conformational_state_builder) ConformationStateData (class in CodeEntropy.levels.dihedrals.state_assignment) ConformationStatePartial (class in CodeEntropy.levels.dihedrals.state_assignment) convert_lammps() (CodeEntropy.trajectory.mda.UniverseOperations method) covariance_partial (CodeEntropy.levels.execution.tasks.FrameChunkResult attribute) CovarianceAccumulators (class in CodeEntropy.levels.nodes.accumulators) CovarianceChunkPartial (class in CodeEntropy.levels.execution.tasks) CovarianceReducer (class in CodeEntropy.levels.execution.reducers) create_job_folder() (CodeEntropy.config.runtime.CodeEntropyRunner static method) create_submatrix() (CodeEntropy.levels.linalg.MatrixUtils method) D DEF_TEMPER (CodeEntropy.config.runtime.CodeEntropyRunner property) default (CodeEntropy.config.argparse.ArgSpec attribute) deps (CodeEntropy.entropy.graph.NodeSpec attribute) DetectLevelsNode (class in CodeEntropy.levels.nodes.detect_levels) DetectMoleculesNode (class in CodeEntropy.levels.nodes.detect_molecules) DihedralAngleCollector (class in CodeEntropy.levels.dihedrals.angle_observations) DihedralAngleObservable (class in CodeEntropy.levels.dihedrals.angle_observations) DihedralHistogramData (class in CodeEntropy.levels.dihedrals.peak_detection) DihedralPeakData (class in CodeEntropy.levels.dihedrals.peak_detection) DihedralTopologyDiscovery (class in CodeEntropy.levels.dihedrals.topology) E end (CodeEntropy.entropy.water.WaterEntropyInput attribute) EntropyGraph (class in CodeEntropy.entropy.graph) EntropyPair (class in CodeEntropy.entropy.nodes.vibrational) EntropyWorkflow (class in CodeEntropy.entropy.workflow) ErrorFilter (class in CodeEntropy.core.logging) execute() (CodeEntropy.entropy.graph.EntropyGraph method) (CodeEntropy.entropy.workflow.EntropyWorkflow method) (CodeEntropy.levels.execution.scheduler.FrameScheduler method) (CodeEntropy.levels.graph.conformation_dag.ConformationDAG method) (CodeEntropy.levels.graph.level_dag.LevelDAG method) execute_frame() (CodeEntropy.levels.graph.frame_dag.FrameGraph method) execute_frame_chunk_worker() (in module CodeEntropy.levels.execution.tasks) execute_frame_map_output() (in module CodeEntropy.levels.execution.tasks) ExecutionPolicy (class in CodeEntropy.levels.execution.policy) export_console() (CodeEntropy.core.logging.LoggingConfig method) extract_fragment() (CodeEntropy.trajectory.mda.UniverseOperations method) extract_fragment_atomgroup() (CodeEntropy.trajectory.mda.UniverseOperations method) F filter() (CodeEntropy.core.logging.ErrorFilter method) filter_zero_rows_columns() (CodeEntropy.levels.linalg.MatrixUtils method) finalise() (CodeEntropy.levels.execution.reducers.NeighborReducer static method) find_bonded_atoms() (CodeEntropy.levels.axes.AxesCalculator method) flex_res (CodeEntropy.levels.dihedrals.state_assignment.ConformationStateData attribute) (CodeEntropy.levels.dihedrals.state_assignment.ConformationStatePartial attribute) flexible_ua_updates (CodeEntropy.levels.dihedrals.state_assignment.ConformationStateData attribute) (CodeEntropy.levels.dihedrals.state_assignment.ConformationStatePartial attribute) force (CodeEntropy.levels.execution.tasks.CovarianceChunkPartial attribute) force_covariances (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) force_partitioning (CodeEntropy.levels.forces.TorqueInputs attribute) forcetorque (CodeEntropy.levels.execution.tasks.CovarianceChunkPartial attribute) forcetorque_counts (CodeEntropy.levels.execution.tasks.CovarianceChunkPartial attribute) (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) forcetorque_covariances (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) ForceTorqueCalculator (class in CodeEntropy.levels.forces) frame_chunk_size() (CodeEntropy.levels.execution.policy.ExecutionPolicy method) frame_counts (CodeEntropy.levels.execution.tasks.CovarianceChunkPartial attribute) (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) frame_indices (CodeEntropy.levels.dihedrals.angle_observations.ConformationChunkTask attribute) (CodeEntropy.levels.execution.tasks.FrameChunkResult attribute) (CodeEntropy.levels.execution.tasks.FrameChunkTask attribute) frame_selection (CodeEntropy.levels.dihedrals.angle_observations.ConformationChunkTask attribute) FrameChunkResult (class in CodeEntropy.levels.execution.tasks) FrameChunkTask (class in CodeEntropy.levels.execution.tasks) FrameCovarianceNode (class in CodeEntropy.levels.nodes.covariance) FrameGraph (class in CodeEntropy.levels.graph.frame_dag) FrameScheduler (class in CodeEntropy.levels.execution.scheduler) FrameSelection (class in CodeEntropy.trajectory.frames) FrameSource (class in CodeEntropy.trajectory.source) from_bounds() (CodeEntropy.trajectory.frames.FrameSelection class method) G get_beads() (CodeEntropy.levels.hierarchy.HierarchyBuilder method) get_bonded_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_bonded_axes_from_topology() (CodeEntropy.levels.axes.AxesCalculator method) get_console() (CodeEntropy.core.logging.LoggingConfig class method) get_custom_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_custom_moment_of_inertia() (CodeEntropy.levels.axes.AxesCalculator method) get_custom_principal_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_flipped_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_frame_neighbor_counts() (CodeEntropy.levels.neighbors.Neighbors method) get_grid_neighbors() (CodeEntropy.levels.search.Search method) get_KT2J() (CodeEntropy.config.runtime.CodeEntropyRunner method) get_moment_of_inertia_tensor() (CodeEntropy.levels.axes.AxesCalculator method) get_RAD_neighbors() (CodeEntropy.levels.search.Search method) get_residue_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_residue_axes_from_topology() (CodeEntropy.levels.axes.AxesCalculator method) get_symmetry() (CodeEntropy.levels.neighbors.Neighbors method) get_UA_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_UA_axes_from_topology() (CodeEntropy.levels.axes.AxesCalculator method) get_UA_masses() (CodeEntropy.levels.axes.AxesCalculator method) get_vanilla_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_vector() (CodeEntropy.levels.axes.AxesCalculator method) get_weighted_forces() (CodeEntropy.levels.forces.ForceTorqueCalculator method) get_weighted_torques() (CodeEntropy.levels.forces.ForceTorqueCalculator method) get_worker_frame_universe() (in module CodeEntropy.levels.execution.tasks) group_id (CodeEntropy.entropy.water.WaterEntropyInput attribute) (CodeEntropy.levels.dihedrals.angle_observations.ConformationChunkTask attribute) (CodeEntropy.levels.dihedrals.topology.MoleculeDihedralTopology attribute) group_id_to_index (CodeEntropy.levels.nodes.accumulators.GroupIndex attribute) GroupIndex (class in CodeEntropy.levels.nodes.accumulators) grouping_molecules() (CodeEntropy.molecules.grouping.MoleculeGrouper method) GroupingConfig (class in CodeEntropy.molecules.grouping) H has_neighbor_bonds (CodeEntropy.levels.nodes.axes_topology.ResidueAxesTopology attribute) heavy_atom_index (CodeEntropy.levels.nodes.axes_topology.UAAxesTopology attribute) help (CodeEntropy.config.argparse.ArgSpec attribute) HierarchyBuilder (class in CodeEntropy.levels.hierarchy) hist_res (CodeEntropy.levels.dihedrals.peak_detection.DihedralHistogramData attribute) hist_ua (CodeEntropy.levels.dihedrals.peak_detection.DihedralHistogramData attribute) histogram_counts_by_dihedral() (in module CodeEntropy.levels.dihedrals.kernels) HPCDaskManager (class in CodeEntropy.core.dask_clusters) I incremental_mean() (in module CodeEntropy.levels.execution.reducers) incremental_mean_value() (in module CodeEntropy.levels.execution.tasks) index_to_group_id (CodeEntropy.levels.nodes.accumulators.GroupIndex attribute) indices (CodeEntropy.trajectory.frames.FrameSelection attribute) infer_analysis_step() (CodeEntropy.trajectory.frames.FrameSelection method) infer_source_step() (CodeEntropy.trajectory.frames.FrameSelection method) infer_step() (CodeEntropy.trajectory.frames.FrameSelection method) InitCovarianceAccumulatorsNode (class in CodeEntropy.levels.nodes.accumulators) initialise() (CodeEntropy.levels.execution.reducers.NeighborReducer static method) iter_analysis_indices() (CodeEntropy.trajectory.frames.FrameSelection method) iter_indices() (CodeEntropy.trajectory.frames.FrameSelection method) (CodeEntropy.trajectory.source.FrameSource method) iter_pairs() (CodeEntropy.trajectory.frames.FrameSelection method) (CodeEntropy.trajectory.source.FrameSource method) iter_source_indices() (CodeEntropy.trajectory.frames.FrameSelection method) (CodeEntropy.trajectory.source.FrameSource method) L LevelDAG (class in CodeEntropy.levels.graph.level_dag) load_citation_data() (CodeEntropy.config.runtime.CodeEntropyRunner method) load_config() (CodeEntropy.config.argparse.ConfigResolver method) log_tables() (CodeEntropy.results.reporter.ResultsReporter method) LoggingConfig (class in CodeEntropy.core.logging) M main() (in module CodeEntropy.cli) make_frame_worker_shared_data() (in module CodeEntropy.levels.execution.tasks) MatrixUtils (class in CodeEntropy.levels.linalg) max_frame_chunk_size (CodeEntropy.levels.execution.policy.ExecutionPolicy attribute) max_frame_in_flight_multiplier (CodeEntropy.levels.execution.policy.ExecutionPolicy attribute) max_frame_in_flight_tasks() (CodeEntropy.levels.execution.policy.ExecutionPolicy method) merge_chunk_partial() (CodeEntropy.levels.execution.reducers.CovarianceReducer method) (CodeEntropy.levels.execution.reducers.NeighborReducer static method) merge_forces() (CodeEntropy.trajectory.mda.UniverseOperations method) merge_means() (in module CodeEntropy.levels.execution.reducers) min_frame_chunk_size (CodeEntropy.levels.execution.policy.ExecutionPolicy attribute) module CodeEntropy CodeEntropy.cli CodeEntropy.config CodeEntropy.config.argparse CodeEntropy.config.runtime CodeEntropy.core CodeEntropy.core.dask_clusters CodeEntropy.core.logging CodeEntropy.entropy CodeEntropy.entropy.configurational CodeEntropy.entropy.graph CodeEntropy.entropy.nodes CodeEntropy.entropy.nodes.aggregate CodeEntropy.entropy.nodes.configurational CodeEntropy.entropy.nodes.orientational CodeEntropy.entropy.nodes.vibrational CodeEntropy.entropy.orientational CodeEntropy.entropy.vibrational CodeEntropy.entropy.water CodeEntropy.entropy.workflow CodeEntropy.levels CodeEntropy.levels.axes CodeEntropy.levels.dihedrals CodeEntropy.levels.dihedrals.angle_observations CodeEntropy.levels.dihedrals.conformational_state_builder CodeEntropy.levels.dihedrals.kernels CodeEntropy.levels.dihedrals.peak_detection CodeEntropy.levels.dihedrals.state_assignment CodeEntropy.levels.dihedrals.topology CodeEntropy.levels.execution CodeEntropy.levels.execution.chunks CodeEntropy.levels.execution.policy CodeEntropy.levels.execution.reducers CodeEntropy.levels.execution.scheduler CodeEntropy.levels.execution.tasks CodeEntropy.levels.forces CodeEntropy.levels.graph CodeEntropy.levels.graph.conformation_dag CodeEntropy.levels.graph.frame_dag CodeEntropy.levels.graph.level_dag CodeEntropy.levels.hierarchy CodeEntropy.levels.linalg CodeEntropy.levels.neighbors CodeEntropy.levels.nodes CodeEntropy.levels.nodes.accumulators CodeEntropy.levels.nodes.axes_topology CodeEntropy.levels.nodes.beads CodeEntropy.levels.nodes.covariance CodeEntropy.levels.nodes.detect_levels CodeEntropy.levels.nodes.detect_molecules CodeEntropy.levels.search CodeEntropy.molecules CodeEntropy.molecules.grouping CodeEntropy.results CodeEntropy.results.reporter CodeEntropy.trajectory CodeEntropy.trajectory.frames CodeEntropy.trajectory.mda CodeEntropy.trajectory.source molecule_id (CodeEntropy.levels.dihedrals.angle_observations.ConformationChunkTask attribute) (CodeEntropy.levels.dihedrals.topology.MoleculeDihedralTopology attribute) molecule_order (CodeEntropy.levels.dihedrals.angle_observations.ConformationChunkTask attribute) (CodeEntropy.levels.dihedrals.topology.MoleculeDihedralTopology attribute) MoleculeDihedralTopology (class in CodeEntropy.levels.dihedrals.topology) MoleculeGrouper (class in CodeEntropy.molecules.grouping) moment_of_inertia (CodeEntropy.levels.forces.TorqueInputs attribute) N N_AVOGADRO (CodeEntropy.config.runtime.CodeEntropyRunner property) n_frames (CodeEntropy.trajectory.frames.FrameSelection property) n_modes (CodeEntropy.entropy.vibrational.VibrationalEntropyResult attribute) name (CodeEntropy.entropy.graph.NodeSpec attribute) nargs (CodeEntropy.config.argparse.ArgSpec attribute) neighbor_samples (CodeEntropy.levels.execution.tasks.FrameChunkResult attribute) neighbor_totals (CodeEntropy.levels.execution.tasks.FrameChunkResult attribute) NeighborReducer (class in CodeEntropy.levels.execution.reducers) Neighbors (class in CodeEntropy.levels.neighbors) node (CodeEntropy.entropy.graph.NodeSpec attribute) NodeSpec (class in CodeEntropy.entropy.graph) num_dihedrals_res (CodeEntropy.levels.dihedrals.peak_detection.DihedralHistogramData attribute) num_dihedrals_ua (CodeEntropy.levels.dihedrals.peak_detection.DihedralHistogramData attribute) num_residues (CodeEntropy.levels.dihedrals.angle_observations.DihedralAngleObservable attribute) (CodeEntropy.levels.dihedrals.peak_detection.DihedralHistogramData attribute) (CodeEntropy.levels.dihedrals.topology.MoleculeDihedralTopology attribute) O orientational_key (CodeEntropy.entropy.nodes.aggregate.AggregateEntropyNode attribute) OrientationalEntropy (class in CodeEntropy.entropy.orientational) OrientationalEntropyNode (class in CodeEntropy.entropy.nodes.orientational) OrientationalEntropyResult (class in CodeEntropy.entropy.orientational) output_key (CodeEntropy.entropy.nodes.aggregate.AggregateEntropyNode attribute) P peaks_res (CodeEntropy.levels.dihedrals.peak_detection.DihedralPeakData attribute) peaks_ua (CodeEntropy.levels.dihedrals.peak_detection.DihedralPeakData attribute) print_args_table() (CodeEntropy.config.runtime.CodeEntropyRunner method) progress() (CodeEntropy.results.reporter.ResultsReporter method) R read_universe() (CodeEntropy.config.runtime.CodeEntropyRunner method) reduce_frame_covariance_into_partial() (in module CodeEntropy.levels.execution.tasks) reduce_frame_map_output() (CodeEntropy.levels.execution.reducers.CovarianceReducer method) reduce_frame_output() (CodeEntropy.levels.execution.reducers.CovarianceReducer method) (CodeEntropy.levels.execution.reducers.NeighborReducer static method) requested_worker_count() (CodeEntropy.levels.execution.policy.ExecutionPolicy method) residue (CodeEntropy.levels.nodes.axes_topology.AxesTopology attribute) residue_angles (CodeEntropy.levels.dihedrals.angle_observations.DihedralAngleObservable attribute) residue_dihedrals (CodeEntropy.levels.dihedrals.topology.MoleculeDihedralTopology attribute) residue_heavy_indices (CodeEntropy.levels.nodes.axes_topology.ResidueAxesTopology attribute) (CodeEntropy.levels.nodes.axes_topology.UAAxesTopology attribute) residue_id (CodeEntropy.levels.nodes.beads.UnitedAtomBead attribute) residue_ua_masses (CodeEntropy.levels.nodes.axes_topology.ResidueAxesTopology attribute) (CodeEntropy.levels.nodes.axes_topology.UAAxesTopology attribute) ResidueAxesTopology (class in CodeEntropy.levels.nodes.axes_topology) resolve() (CodeEntropy.config.argparse.ConfigResolver method) resolve_conda_settings() (CodeEntropy.core.dask_clusters.HPCDaskManager method) ResultsReporter (class in CodeEntropy.results.reporter) rot (CodeEntropy.entropy.nodes.vibrational.EntropyPair attribute) rot_axes (CodeEntropy.levels.forces.TorqueInputs attribute) run() (CodeEntropy.entropy.nodes.aggregate.AggregateEntropyNode method) (CodeEntropy.entropy.nodes.configurational.ConfigurationalEntropyNode method) (CodeEntropy.entropy.nodes.orientational.OrientationalEntropyNode method) (CodeEntropy.entropy.nodes.vibrational.VibrationalEntropyNode method) (CodeEntropy.levels.nodes.accumulators.InitCovarianceAccumulatorsNode method) (CodeEntropy.levels.nodes.axes_topology.BuildAxesTopologyNode method) (CodeEntropy.levels.nodes.beads.BuildBeadsNode method) (CodeEntropy.levels.nodes.covariance.FrameCovarianceNode method) (CodeEntropy.levels.nodes.detect_levels.DetectLevelsNode method) (CodeEntropy.levels.nodes.detect_molecules.DetectMoleculesNode method) run_entropy_workflow() (CodeEntropy.config.runtime.CodeEntropyRunner method) S save_dataframes_as_json() (CodeEntropy.results.reporter.ResultsReporter method) Search (class in CodeEntropy.levels.search) seek() (CodeEntropy.trajectory.source.FrameSource method) select_atoms() (CodeEntropy.trajectory.mda.UniverseOperations method) select_frame_indices() (CodeEntropy.trajectory.mda.UniverseOperations method) select_frames() (CodeEntropy.trajectory.mda.UniverseOperations method) select_levels() (CodeEntropy.levels.hierarchy.HierarchyBuilder method) selection (CodeEntropy.trajectory.source.FrameSource attribute) set_level() (CodeEntropy.core.logging.LoggingConfig method) show_splash() (CodeEntropy.config.runtime.CodeEntropyRunner method) slurm_directives() (CodeEntropy.core.dask_clusters.HPCDaskManager method) slurm_prologues() (CodeEntropy.core.dask_clusters.HPCDaskManager method) source_indices (CodeEntropy.trajectory.frames.FrameSelection property) source_start (CodeEntropy.trajectory.frames.FrameSelection property) source_stop_exclusive (CodeEntropy.trajectory.frames.FrameSelection property) stable_keys() (in module CodeEntropy.levels.execution.reducers) start (CodeEntropy.entropy.water.WaterEntropyInput attribute) state_res (CodeEntropy.levels.dihedrals.state_assignment.ConformationStateData attribute) (CodeEntropy.levels.dihedrals.state_assignment.ConformationStatePartial attribute) states_ua_updates (CodeEntropy.levels.dihedrals.state_assignment.ConformationStateData attribute) (CodeEntropy.levels.dihedrals.state_assignment.ConformationStatePartial attribute) step (CodeEntropy.entropy.water.WaterEntropyInput attribute) str2bool() (CodeEntropy.config.argparse.ConfigResolver static method) strategy (CodeEntropy.molecules.grouping.GroupingConfig attribute) submit_master() (CodeEntropy.core.dask_clusters.HPCDaskManager method) system_network_interface() (CodeEntropy.core.dask_clusters.HPCDaskManager method) T target_frame_chunks_per_worker (CodeEntropy.levels.execution.policy.ExecutionPolicy attribute) task (CodeEntropy.levels.dihedrals.angle_observations.DihedralAngleObservable attribute) (CodeEntropy.levels.dihedrals.state_assignment.ConformationStatePartial attribute) temperature (CodeEntropy.entropy.water.WaterEntropyInput attribute) torque (CodeEntropy.levels.execution.tasks.CovarianceChunkPartial attribute) torque_covariances (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) TorqueInputs (class in CodeEntropy.levels.forces) total (CodeEntropy.entropy.orientational.OrientationalEntropyResult attribute) (CodeEntropy.entropy.vibrational.VibrationalEntropyResult attribute) trans (CodeEntropy.entropy.nodes.vibrational.EntropyPair attribute) type (CodeEntropy.config.argparse.ArgSpec attribute) U ua (CodeEntropy.levels.nodes.axes_topology.AxesTopology attribute) ua_all_atom_indices (CodeEntropy.levels.nodes.axes_topology.UAAxesTopology attribute) ua_angles_by_residue (CodeEntropy.levels.dihedrals.angle_observations.DihedralAngleObservable attribute) ua_atom_indices (CodeEntropy.levels.nodes.axes_topology.UAAxesTopology attribute) ua_dihedrals_by_residue (CodeEntropy.levels.dihedrals.topology.MoleculeDihedralTopology attribute) UAAxesTopology (class in CodeEntropy.levels.nodes.axes_topology) UnitedAtomBead (class in CodeEntropy.levels.nodes.beads) universe (CodeEntropy.entropy.water.WaterEntropyInput attribute) (CodeEntropy.trajectory.source.FrameSource attribute) UniverseOperations (class in CodeEntropy.trajectory.mda) V validate_inputs() (CodeEntropy.config.argparse.ConfigResolver method) vibrational_entropy_calculation() (CodeEntropy.entropy.vibrational.VibrationalEntropy method) vibrational_key (CodeEntropy.entropy.nodes.aggregate.AggregateEntropyNode attribute) VibrationalEntropy (class in CodeEntropy.entropy.vibrational) VibrationalEntropyNode (class in CodeEntropy.entropy.nodes.vibrational) VibrationalEntropyResult (class in CodeEntropy.entropy.vibrational) W WaterEntropy (class in CodeEntropy.entropy.water) WaterEntropyInput (class in CodeEntropy.entropy.water) wrap_degrees_positive() (in module CodeEntropy.levels.dihedrals.kernels) write_universe() (CodeEntropy.config.runtime.CodeEntropyRunner method)