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) atom_indices (CodeEntropy.levels.nodes.beads.UnitedAtomBead attribute) axes_manager (CodeEntropy.levels.forces.TorqueInputs attribute) AxesCalculator (class in CodeEntropy.levels.axes) B bin_width (CodeEntropy.levels.nodes.conformations.ConformationalStateConfig attribute) box (CodeEntropy.levels.forces.TorqueInputs attribute) build() (CodeEntropy.entropy.graph.EntropyGraph method) (CodeEntropy.levels.frame_dag.FrameGraph method) (CodeEntropy.levels.level_dag.LevelDAG method) build_conformational_states() (CodeEntropy.levels.dihedrals.ConformationStateBuilder method) build_parser() (CodeEntropy.config.argparse.ConfigResolver method) 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) 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.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.forces module CodeEntropy.levels.frame_dag module CodeEntropy.levels.hierarchy module CodeEntropy.levels.level_dag module CodeEntropy.levels.linalg module CodeEntropy.levels.neighbors module CodeEntropy.levels.nodes module CodeEntropy.levels.nodes.accumulators module CodeEntropy.levels.nodes.beads module CodeEntropy.levels.nodes.conformations module CodeEntropy.levels.nodes.covariance module CodeEntropy.levels.nodes.detect_levels module CodeEntropy.levels.nodes.detect_molecules module CodeEntropy.levels.nodes.find_neighbors 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) ComputeConformationalStatesNode (class in CodeEntropy.levels.nodes.conformations) ComputeNeighborsNode (class in CodeEntropy.levels.nodes.find_neighbors) 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) conformational_entropy_calculation() (CodeEntropy.entropy.configurational.ConformationalEntropy method) ConformationalEntropy (class in CodeEntropy.entropy.configurational) ConformationalStateConfig (class in CodeEntropy.levels.nodes.conformations) ConformationStateBuilder (class in CodeEntropy.levels.dihedrals) convert_lammps() (CodeEntropy.trajectory.mda.UniverseOperations method) CovarianceAccumulators (class in CodeEntropy.levels.nodes.accumulators) create_job_folder() (CodeEntropy.config.runtime.CodeEntropyRunner static method) create_submatrix() (CodeEntropy.levels.linalg.MatrixUtils method) D data (CodeEntropy.levels.frame_dag.FrameContext attribute) 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) E end (CodeEntropy.entropy.water.WaterEntropyInput attribute) (CodeEntropy.levels.nodes.find_neighbors.NeighborConfig 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.level_dag.LevelDAG method) execute_frame() (CodeEntropy.levels.frame_dag.FrameGraph method) export_console() (CodeEntropy.core.logging.LoggingConfig method) extract_fragment() (CodeEntropy.trajectory.mda.UniverseOperations method) F filter() (CodeEntropy.core.logging.ErrorFilter method) filter_zero_rows_columns() (CodeEntropy.levels.linalg.MatrixUtils method) find_bonded_atoms() (CodeEntropy.levels.axes.AxesCalculator method) force_covariances (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) force_partitioning (CodeEntropy.levels.forces.TorqueInputs attribute) forcetorque_counts (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) forcetorque_covariances (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) ForceTorqueCalculator (class in CodeEntropy.levels.forces) frame_counts (CodeEntropy.levels.nodes.accumulators.CovarianceAccumulators attribute) frame_covariance (CodeEntropy.levels.frame_dag.FrameContext attribute) frame_index (CodeEntropy.levels.frame_dag.FrameContext attribute) FrameContext (class in CodeEntropy.levels.frame_dag) FrameCovarianceNode (class in CodeEntropy.levels.nodes.covariance) FrameGraph (class in CodeEntropy.levels.frame_dag) 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_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_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_neighbors() (CodeEntropy.levels.neighbors.Neighbors method) get_RAD_neighbors() (CodeEntropy.levels.search.Search method) get_residue_axes() (CodeEntropy.levels.axes.AxesCalculator method) get_symmetry() (CodeEntropy.levels.neighbors.Neighbors method) get_UA_axes() (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) group_id (CodeEntropy.entropy.water.WaterEntropyInput 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 help (CodeEntropy.config.argparse.ArgSpec attribute) HierarchyBuilder (class in CodeEntropy.levels.hierarchy) I 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) 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.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) MatrixUtils (class in CodeEntropy.levels.linalg) merge_forces() (CodeEntropy.trajectory.mda.UniverseOperations method) module CodeEntropy CodeEntropy.cli CodeEntropy.config CodeEntropy.config.argparse CodeEntropy.config.runtime CodeEntropy.core 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.forces CodeEntropy.levels.frame_dag CodeEntropy.levels.hierarchy CodeEntropy.levels.level_dag CodeEntropy.levels.linalg CodeEntropy.levels.neighbors CodeEntropy.levels.nodes CodeEntropy.levels.nodes.accumulators CodeEntropy.levels.nodes.beads CodeEntropy.levels.nodes.conformations CodeEntropy.levels.nodes.covariance CodeEntropy.levels.nodes.detect_levels CodeEntropy.levels.nodes.detect_molecules CodeEntropy.levels.nodes.find_neighbors CodeEntropy.levels.search CodeEntropy.molecules CodeEntropy.molecules.grouping CodeEntropy.results CodeEntropy.results.reporter CodeEntropy.trajectory CodeEntropy.trajectory.frames CodeEntropy.trajectory.mda CodeEntropy.trajectory.source 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.levels.nodes.conformations.ConformationalStateConfig attribute) (CodeEntropy.trajectory.frames.FrameSelection property) n_modes (CodeEntropy.entropy.vibrational.VibrationalEntropyResult attribute) name (CodeEntropy.entropy.graph.NodeSpec attribute) nargs (CodeEntropy.config.argparse.ArgSpec attribute) NeighborConfig (class in CodeEntropy.levels.nodes.find_neighbors) Neighbors (class in CodeEntropy.levels.neighbors) node (CodeEntropy.entropy.graph.NodeSpec attribute) NodeSpec (class in CodeEntropy.entropy.graph) 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 print_args_table() (CodeEntropy.config.runtime.CodeEntropyRunner method) progress() (CodeEntropy.results.reporter.ResultsReporter method) R read_universe() (CodeEntropy.config.runtime.CodeEntropyRunner method) residue_id (CodeEntropy.levels.nodes.beads.UnitedAtomBead attribute) resolve() (CodeEntropy.config.argparse.ConfigResolver 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.beads.BuildBeadsNode method) (CodeEntropy.levels.nodes.conformations.ComputeConformationalStatesNode method) (CodeEntropy.levels.nodes.covariance.FrameCovarianceNode method) (CodeEntropy.levels.nodes.detect_levels.DetectLevelsNode method) (CodeEntropy.levels.nodes.detect_molecules.DetectMoleculesNode method) (CodeEntropy.levels.nodes.find_neighbors.ComputeNeighborsNode 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) shared (CodeEntropy.levels.frame_dag.FrameContext attribute) show_splash() (CodeEntropy.config.runtime.CodeEntropyRunner method) source_indices (CodeEntropy.trajectory.frames.FrameSelection property) source_start (CodeEntropy.trajectory.frames.FrameSelection property) source_stop_exclusive (CodeEntropy.trajectory.frames.FrameSelection property) start (CodeEntropy.entropy.water.WaterEntropyInput attribute) (CodeEntropy.levels.nodes.find_neighbors.NeighborConfig attribute) step (CodeEntropy.entropy.water.WaterEntropyInput attribute) (CodeEntropy.levels.nodes.find_neighbors.NeighborConfig attribute) str2bool() (CodeEntropy.config.argparse.ConfigResolver static method) strategy (CodeEntropy.molecules.grouping.GroupingConfig attribute) T temperature (CodeEntropy.entropy.water.WaterEntropyInput 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 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) write_universe() (CodeEntropy.config.runtime.CodeEntropyRunner method)