Index A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V | W A ACTUAL_TIME (prolint.config.enums.NormalizationMethod attribute), [1] (prolint.config.NormalizationMethod attribute), [1] add() (prolint.core.ExtendedAtomGroup method) (prolint.core.groups.ExtendedAtomGroup method) (prolint.core.groups.PLAtomGroupBase method) AMINO_ACID_COLORS (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) AMINO_ACID_ONE_LETTER (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) AnalysisRegistry (class in prolint.analysis) (class in prolint.analysis.base) AnalysisResult (class in prolint.analysis) (class in prolint.analysis.base) analyze() (prolint.core.contact_provider.ComputedContacts method) apply_function() (prolint.contacts.base.BaseContactStore method) (prolint.contacts.BaseContactStore method) (prolint.contacts.exact_contacts.ExactContacts method) (prolint.contacts.ExactContacts method) (prolint.core.contact_provider.ComputedContacts method) apply_prolint_style() (in module prolint.plotting) (in module prolint.plotting.theme) AtomDistancesAnalysis (class in prolint.analysis) (class in prolint.analysis.distances) available() (prolint.analysis.AnalysisRegistry class method) (prolint.analysis.base.AnalysisRegistry class method) (prolint.plotting.base.PlottingRegistry class method) (prolint.plotting.PlottingRegistry class method) B BaseAnalysis (class in prolint.analysis) (class in prolint.analysis.base) BaseContactStore (class in prolint.contacts) (class in prolint.contacts.base) BasePlotter (class in prolint.plotting) (class in prolint.plotting.base) C COLOR_SCALES (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) color_to_tuple() (in module prolint.config) (in module prolint.config.colors) COLORS (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) compute() (prolint.contacts.base.BaseContactStore method) (prolint.contacts.BaseContactStore method) (prolint.core.contact_provider.ContactsProvider method) (prolint.core.ContactsProvider method) compute_contacts() (prolint.core.Universe method) (prolint.core.universe.Universe method) (prolint.Universe method) compute_database_durations() (prolint.contacts.exact_contacts.ExactContacts method) (prolint.contacts.ExactContacts method) compute_metric() (prolint.contacts.base.BaseContactStore method) (prolint.contacts.BaseContactStore method) (prolint.contacts.exact_contacts.ExactContacts method) (prolint.contacts.ExactContacts method) (prolint.core.contact_provider.ComputedContacts method) ComputedContacts (class in prolint.core.contact_provider) contact_frames (prolint.computers.contacts.SerialContacts attribute) (prolint.computers.SerialContacts attribute) (prolint.contacts.base.BaseContactStore attribute) (prolint.contacts.BaseContactStore attribute) (prolint.contacts.exact_contacts.ExactContacts attribute) (prolint.contacts.ExactContacts attribute) (prolint.core.contact_provider.ComputedContacts property) ContactComputerBase (class in prolint.computers) (class in prolint.computers.base) ContactEventsPlotter (class in prolint.plotting) (class in prolint.plotting.timeseries) contacts (prolint.analysis.base.BaseAnalysis attribute) (prolint.analysis.BaseAnalysis attribute) (prolint.computers.contacts.SerialContacts attribute) (prolint.computers.SerialContacts attribute) (prolint.contacts.base.BaseContactStore property) (prolint.contacts.BaseContactStore property) (prolint.contacts.exact_contacts.ExactContacts attribute) (prolint.contacts.ExactContacts attribute) (prolint.core.contact_provider.ComputedContacts property) ContactsProvider (class in prolint.core) (class in prolint.core.contact_provider) COUNTS (prolint.config.enums.NormalizationMethod attribute), [1] (prolint.config.NormalizationMethod attribute), [1] create() (prolint.analysis.AnalysisRegistry class method) (prolint.analysis.base.AnalysisRegistry class method) cutoff (prolint.computers.contacts.SerialContacts attribute) (prolint.computers.SerialContacts attribute) D data (prolint.analysis.AnalysisResult attribute) (prolint.analysis.base.AnalysisResult attribute) database (prolint.computers.contacts.SerialContacts attribute) (prolint.computers.SerialContacts attribute) (prolint.core.contact_provider.ContactsProvider attribute) (prolint.core.ContactsProvider attribute) (prolint.core.Universe property) (prolint.core.universe.Universe property) (prolint.Universe property) DatabaseContactsAnalysis (class in prolint.analysis) (class in prolint.analysis.timeseries) DatabaseContactsHeatmapPlotter (class in prolint.plotting) (class in prolint.plotting.heatmap) DEFAULT_FORMAT (in module prolint.config.logging) DEFAULT_SIM_PARAMS (in module prolint.config.units) DensityMapAnalysis (class in prolint.analysis) (class in prolint.analysis.density) DensityMapPlotter (class in prolint.plotting) (class in prolint.plotting.density) description (prolint.analysis.AtomDistancesAnalysis attribute) (prolint.analysis.base.BaseAnalysis attribute) (prolint.analysis.BaseAnalysis attribute) (prolint.analysis.DatabaseContactsAnalysis attribute) (prolint.analysis.density.DensityMapAnalysis attribute) (prolint.analysis.density.RadialDensityAnalysis attribute) (prolint.analysis.DensityMapAnalysis attribute) (prolint.analysis.DistanceAnalysis attribute) (prolint.analysis.distances.AtomDistancesAnalysis attribute) (prolint.analysis.distances.DistanceAnalysis attribute) (prolint.analysis.kinetics.KineticsAnalysis attribute) (prolint.analysis.KineticsAnalysis attribute) (prolint.analysis.metrics.MetricsAnalysis attribute) (prolint.analysis.MetricsAnalysis attribute) (prolint.analysis.RadialDensityAnalysis attribute) (prolint.analysis.shared_contacts.SharedContactsAnalysis attribute) (prolint.analysis.SharedContactsAnalysis attribute) (prolint.analysis.timeseries.DatabaseContactsAnalysis attribute) (prolint.analysis.timeseries.TimeSeriesAnalysis attribute) (prolint.analysis.TimeSeriesAnalysis attribute) (prolint.plotting.base.BasePlotter attribute), [1] (prolint.plotting.BasePlotter attribute), [1] (prolint.plotting.ContactEventsPlotter attribute) (prolint.plotting.DatabaseContactsHeatmapPlotter attribute) (prolint.plotting.density.DensityMapPlotter attribute) (prolint.plotting.density.RadialDensityPlotter attribute) (prolint.plotting.DensityMapPlotter attribute) (prolint.plotting.DistanceHeatmapPlotter attribute) (prolint.plotting.DistanceTimeSeriesPlotter attribute) (prolint.plotting.heatmap.DatabaseContactsHeatmapPlotter attribute) (prolint.plotting.heatmap.DistanceHeatmapPlotter attribute) (prolint.plotting.heatmap.HeatmapPlotter attribute) (prolint.plotting.HeatmapPlotter attribute) (prolint.plotting.kinetics.ResidenceDistributionPlotter attribute) (prolint.plotting.kinetics.SurvivalCurvePlotter attribute) (prolint.plotting.LogoGridPlotter attribute) (prolint.plotting.network.NetworkPlotter attribute) (prolint.plotting.NetworkPlotter attribute) (prolint.plotting.RadialDensityPlotter attribute) (prolint.plotting.ResidenceDistributionPlotter attribute) (prolint.plotting.ResidueMetricsPlotter attribute) (prolint.plotting.residues.LogoGridPlotter attribute) (prolint.plotting.residues.ResidueMetricsPlotter attribute) (prolint.plotting.SurvivalCurvePlotter attribute) (prolint.plotting.timeseries.ContactEventsPlotter attribute) (prolint.plotting.timeseries.DistanceTimeSeriesPlotter attribute) (prolint.plotting.timeseries.TimeSeriesPlotter attribute) (prolint.plotting.TimeSeriesPlotter attribute) detect_replicas() (in module prolint.core.replica_detection) detection_method (prolint.core.replica_detection.ReplicaDetectionResult attribute) difference() (prolint.core.contact_provider.ComputedContacts method) DistanceAnalysis (class in prolint.analysis) (class in prolint.analysis.distances) DistanceHeatmapPlotter (class in prolint.plotting) (class in prolint.plotting.heatmap) DistanceTimeSeriesPlotter (class in prolint.plotting) (class in prolint.plotting.timeseries) E ExactContacts (class in prolint.contacts) (class in prolint.contacts.exact_contacts) ExtendedAtomGroup (class in prolint.core) (class in prolint.core.groups) F fast_contiguous_segment_lengths() (in module prolint.utils) (in module prolint.utils.utils) fast_unique_comparison() (in module prolint.utils) (in module prolint.utils.utils) FEMTOSECOND (prolint.config.enums.TimeUnit attribute), [1] (prolint.config.TimeUnit attribute), [1] filter_resids_by_resname() (prolint.core.ExtendedAtomGroup method) (prolint.core.groups.ExtendedAtomGroup method) (prolint.core.groups.PLAtomGroupBase method) first_resid (prolint.core.replica_detection.ReplicaInfo attribute) fragments (prolint.core.replica_detection.ReplicaDetectionResult attribute) fs (prolint.config.UnitConversionFactor attribute), [1] (prolint.config.units.UnitConversionFactor attribute), [1] G get_all_resids() (prolint.core.ExtendedAtomGroup method) (prolint.core.groups.ExtendedAtomGroup method) (prolint.core.groups.PLAtomGroupBase method) get_class() (prolint.analysis.AnalysisRegistry class method) (prolint.analysis.base.AnalysisRegistry class method) (prolint.plotting.base.PlottingRegistry class method) (prolint.plotting.PlottingRegistry class method) get_color_for_value() (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) get_colormap() (in module prolint.plotting) (in module prolint.plotting.theme) get_info() (prolint.plotting.base.PlottingRegistry class method) (prolint.plotting.PlottingRegistry class method) get_logger() (in module prolint) (in module prolint.config) (in module prolint.config.logging) get_replica_atoms() (in module prolint.core.replica_detection) get_resids() (prolint.core.ExtendedAtomGroup method) (prolint.core.groups.ExtendedAtomGroup method) (prolint.core.groups.PLAtomGroupBase method) get_resnames() (prolint.core.ExtendedAtomGroup method) (prolint.core.groups.ExtendedAtomGroup method) (prolint.core.groups.PLAtomGroupBase method) get_unit_label() (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) GRADIENTS (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) H has_repeated_resids (prolint.core.replica_detection.ReplicaDetectionResult attribute) HeatmapPlotter (class in prolint.plotting) (class in prolint.plotting.heatmap) hex_to_rgb() (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) I interpolate_color() (in module prolint.plotting) (in module prolint.plotting.theme) interpolate_gradient() (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) intersection() (prolint.computers.base.ContactComputerBase method) (prolint.computers.ContactComputerBase method) (prolint.core.contact_provider.ComputedContacts method) K KineticsAnalysis (class in prolint.analysis) (class in prolint.analysis.kinetics) L last_resid (prolint.core.replica_detection.ReplicaInfo attribute) list_plotters() (prolint.plotting.base.PlottingRegistry class method) (prolint.plotting.PlottingRegistry class method) load_theme() (in module prolint.config) (in module prolint.config.colors) logger (in module prolint.analysis.density) (in module prolint.analysis.kinetics) (in module prolint.analysis.timeseries) (in module prolint.computers.contacts) (in module prolint.contacts.exact_contacts) (in module prolint.core.contact_provider) (in module prolint.core.replica_detection) (in module prolint.core.universe) LogoGridPlotter (class in prolint.plotting) (class in prolint.plotting.residues) M MAX_NETWORK_RESIDUES (in module prolint.plotting) (in module prolint.plotting.network) metadata (prolint.analysis.AnalysisResult attribute) (prolint.analysis.base.AnalysisResult attribute) MetricsAnalysis (class in prolint.analysis) (class in prolint.analysis.metrics) MICROSECOND (prolint.config.enums.TimeUnit attribute), [1] (prolint.config.TimeUnit attribute), [1] MILLISECOND (prolint.config.enums.TimeUnit attribute), [1] (prolint.config.TimeUnit attribute), [1] MIN_EVENTS_BI (prolint.analysis.kinetics.KineticsAnalysis attribute), [1] (prolint.analysis.KineticsAnalysis attribute), [1] MIN_EVENTS_MONO (prolint.analysis.kinetics.KineticsAnalysis attribute), [1] (prolint.analysis.KineticsAnalysis attribute), [1] module prolint prolint.analysis prolint.analysis.base prolint.analysis.density prolint.analysis.distances prolint.analysis.kinetics prolint.analysis.metrics prolint.analysis.shared_contacts prolint.analysis.timeseries prolint.computers prolint.computers.base prolint.computers.contacts prolint.config prolint.config.colors prolint.config.enums prolint.config.logging prolint.config.units prolint.contacts prolint.contacts.base prolint.contacts.exact_contacts prolint.core prolint.core.contact_provider prolint.core.groups prolint.core.replica_detection prolint.core.universe prolint.plotting prolint.plotting.base prolint.plotting.density prolint.plotting.heatmap prolint.plotting.kinetics prolint.plotting.network prolint.plotting.residues prolint.plotting.structure prolint.plotting.theme prolint.plotting.timeseries prolint.utils prolint.utils.utils ms (prolint.config.UnitConversionFactor attribute), [1] (prolint.config.units.UnitConversionFactor attribute), [1] N n_replicas (prolint.core.replica_detection.ReplicaDetectionResult attribute) n_residues (prolint.core.replica_detection.ReplicaInfo attribute) name (prolint.analysis.AtomDistancesAnalysis attribute) (prolint.analysis.base.BaseAnalysis attribute) (prolint.analysis.BaseAnalysis attribute) (prolint.analysis.DatabaseContactsAnalysis attribute) (prolint.analysis.density.DensityMapAnalysis attribute) (prolint.analysis.density.RadialDensityAnalysis attribute) (prolint.analysis.DensityMapAnalysis attribute) (prolint.analysis.DistanceAnalysis attribute) (prolint.analysis.distances.AtomDistancesAnalysis attribute) (prolint.analysis.distances.DistanceAnalysis attribute) (prolint.analysis.kinetics.KineticsAnalysis attribute) (prolint.analysis.KineticsAnalysis attribute) (prolint.analysis.metrics.MetricsAnalysis attribute) (prolint.analysis.MetricsAnalysis attribute) (prolint.analysis.RadialDensityAnalysis attribute) (prolint.analysis.shared_contacts.SharedContactsAnalysis attribute) (prolint.analysis.SharedContactsAnalysis attribute) (prolint.analysis.timeseries.DatabaseContactsAnalysis attribute) (prolint.analysis.timeseries.TimeSeriesAnalysis attribute) (prolint.analysis.TimeSeriesAnalysis attribute) (prolint.plotting.base.BasePlotter attribute), [1] (prolint.plotting.BasePlotter attribute), [1] (prolint.plotting.ContactEventsPlotter attribute) (prolint.plotting.DatabaseContactsHeatmapPlotter attribute) (prolint.plotting.density.DensityMapPlotter attribute) (prolint.plotting.density.RadialDensityPlotter attribute) (prolint.plotting.DensityMapPlotter attribute) (prolint.plotting.DistanceHeatmapPlotter attribute) (prolint.plotting.DistanceTimeSeriesPlotter attribute) (prolint.plotting.heatmap.DatabaseContactsHeatmapPlotter attribute) (prolint.plotting.heatmap.DistanceHeatmapPlotter attribute) (prolint.plotting.heatmap.HeatmapPlotter attribute) (prolint.plotting.HeatmapPlotter attribute) (prolint.plotting.kinetics.ResidenceDistributionPlotter attribute) (prolint.plotting.kinetics.SurvivalCurvePlotter attribute) (prolint.plotting.LogoGridPlotter attribute) (prolint.plotting.network.NetworkPlotter attribute) (prolint.plotting.NetworkPlotter attribute) (prolint.plotting.RadialDensityPlotter attribute) (prolint.plotting.ResidenceDistributionPlotter attribute) (prolint.plotting.ResidueMetricsPlotter attribute) (prolint.plotting.residues.LogoGridPlotter attribute) (prolint.plotting.residues.ResidueMetricsPlotter attribute) (prolint.plotting.SurvivalCurvePlotter attribute) (prolint.plotting.timeseries.ContactEventsPlotter attribute) (prolint.plotting.timeseries.DistanceTimeSeriesPlotter attribute) (prolint.plotting.timeseries.TimeSeriesPlotter attribute) (prolint.plotting.TimeSeriesPlotter attribute) NANOSECOND (prolint.config.enums.TimeUnit attribute), [1] (prolint.config.TimeUnit attribute), [1] NetworkPlotter (class in prolint.plotting) (class in prolint.plotting.network) norm_factor (prolint.config.SimulationParams attribute), [1] (prolint.config.units.SimulationParams attribute), [1] (prolint.contacts.base.BaseContactStore attribute) (prolint.contacts.BaseContactStore attribute) (prolint.core.contact_provider.ComputedContacts property) NormalizationLiteral (in module prolint.core.universe) NormalizationMethod (class in prolint.config) (class in prolint.config.enums) normalize_by (prolint.core.Universe property) (prolint.core.universe.Universe property) (prolint.Universe property) normalizer (prolint.config.SimulationParams attribute), [1] (prolint.config.units.SimulationParams attribute), [1] ns (prolint.config.UnitConversionFactor attribute), [1] (prolint.config.units.UnitConversionFactor attribute), [1] P params (prolint.core.contact_provider.ContactsProvider attribute) (prolint.core.ContactsProvider attribute) (prolint.core.Universe attribute) (prolint.core.universe.Universe attribute) (prolint.Universe attribute) PICOSECOND (prolint.config.enums.TimeUnit attribute), [1] (prolint.config.TimeUnit attribute), [1] PLAtomGroupBase (class in prolint.core.groups) plot() (in module prolint.plotting) (in module prolint.plotting.base) (prolint.plotting.base.BasePlotter class method) (prolint.plotting.base.PlottingRegistry class method) (prolint.plotting.BasePlotter class method) (prolint.plotting.ContactEventsPlotter class method) (prolint.plotting.DatabaseContactsHeatmapPlotter class method) (prolint.plotting.density.DensityMapPlotter class method) (prolint.plotting.density.RadialDensityPlotter class method) (prolint.plotting.DensityMapPlotter class method) (prolint.plotting.DistanceHeatmapPlotter class method) (prolint.plotting.DistanceTimeSeriesPlotter class method) (prolint.plotting.heatmap.DatabaseContactsHeatmapPlotter class method) (prolint.plotting.heatmap.DistanceHeatmapPlotter class method) (prolint.plotting.heatmap.HeatmapPlotter class method) (prolint.plotting.HeatmapPlotter class method) (prolint.plotting.kinetics.ResidenceDistributionPlotter class method) (prolint.plotting.kinetics.SurvivalCurvePlotter class method) (prolint.plotting.LogoGridPlotter class method) (prolint.plotting.network.NetworkPlotter class method) (prolint.plotting.NetworkPlotter class method) (prolint.plotting.PlottingRegistry class method) (prolint.plotting.RadialDensityPlotter class method) (prolint.plotting.ResidenceDistributionPlotter class method) (prolint.plotting.ResidueMetricsPlotter class method) (prolint.plotting.residues.LogoGridPlotter class method) (prolint.plotting.residues.ResidueMetricsPlotter class method) (prolint.plotting.SurvivalCurvePlotter class method) (prolint.plotting.timeseries.ContactEventsPlotter class method) (prolint.plotting.timeseries.DistanceTimeSeriesPlotter class method) (prolint.plotting.timeseries.TimeSeriesPlotter class method) (prolint.plotting.TimeSeriesPlotter class method) PLOT_STYLE (in module prolint.plotting.theme) PlottingRegistry (class in prolint.plotting) (class in prolint.plotting.base) prolint module prolint.analysis module prolint.analysis.base module prolint.analysis.density module prolint.analysis.distances module prolint.analysis.kinetics module prolint.analysis.metrics module prolint.analysis.shared_contacts module prolint.analysis.timeseries module prolint.computers module prolint.computers.base module prolint.computers.contacts module prolint.config module prolint.config.colors module prolint.config.enums module prolint.config.logging module prolint.config.units module prolint.contacts module prolint.contacts.base module prolint.contacts.exact_contacts module prolint.core module prolint.core.contact_provider module prolint.core.groups module prolint.core.replica_detection module prolint.core.universe module prolint.plotting module prolint.plotting.base module prolint.plotting.density module prolint.plotting.heatmap module prolint.plotting.kinetics module prolint.plotting.network module prolint.plotting.residues module prolint.plotting.structure module prolint.plotting.theme module prolint.plotting.timeseries module prolint.utils module prolint.utils.utils module provider (prolint.core.contact_provider.ComputedContacts attribute) ps (prolint.config.UnitConversionFactor attribute), [1] (prolint.config.units.UnitConversionFactor attribute), [1] Q query (prolint.computers.contacts.SerialContacts attribute) (prolint.computers.SerialContacts attribute) (prolint.core.contact_provider.ContactsProvider attribute) (prolint.core.ContactsProvider attribute) (prolint.core.Universe property) (prolint.core.universe.Universe property) (prolint.Universe property) R RadialDensityAnalysis (class in prolint.analysis) (class in prolint.analysis.density) RadialDensityPlotter (class in prolint.plotting) (class in prolint.plotting.density) register() (prolint.analysis.AnalysisRegistry class method) (prolint.analysis.base.AnalysisRegistry class method) (prolint.plotting.base.PlottingRegistry class method) (prolint.plotting.PlottingRegistry class method) remove() (prolint.core.ExtendedAtomGroup method) (prolint.core.groups.ExtendedAtomGroup method) (prolint.core.groups.PLAtomGroupBase method) replica_id (prolint.core.replica_detection.ReplicaInfo attribute) replica_info (prolint.core.replica_detection.ReplicaDetectionResult attribute) ReplicaDetectionResult (class in prolint.core.replica_detection) ReplicaInfo (class in prolint.core.replica_detection) required_analysis (prolint.plotting.base.BasePlotter attribute), [1] (prolint.plotting.BasePlotter attribute), [1] (prolint.plotting.ContactEventsPlotter attribute) (prolint.plotting.DatabaseContactsHeatmapPlotter attribute) (prolint.plotting.density.DensityMapPlotter attribute) (prolint.plotting.density.RadialDensityPlotter attribute) (prolint.plotting.DensityMapPlotter attribute) (prolint.plotting.DistanceHeatmapPlotter attribute) (prolint.plotting.DistanceTimeSeriesPlotter attribute) (prolint.plotting.heatmap.DatabaseContactsHeatmapPlotter attribute) (prolint.plotting.heatmap.DistanceHeatmapPlotter attribute) (prolint.plotting.heatmap.HeatmapPlotter attribute) (prolint.plotting.HeatmapPlotter attribute) (prolint.plotting.kinetics.ResidenceDistributionPlotter attribute) (prolint.plotting.kinetics.SurvivalCurvePlotter attribute) (prolint.plotting.LogoGridPlotter attribute) (prolint.plotting.network.NetworkPlotter attribute) (prolint.plotting.NetworkPlotter attribute) (prolint.plotting.RadialDensityPlotter attribute) (prolint.plotting.ResidenceDistributionPlotter attribute) (prolint.plotting.ResidueMetricsPlotter attribute) (prolint.plotting.residues.LogoGridPlotter attribute) (prolint.plotting.residues.ResidueMetricsPlotter attribute) (prolint.plotting.SurvivalCurvePlotter attribute) (prolint.plotting.timeseries.ContactEventsPlotter attribute) (prolint.plotting.timeseries.DistanceTimeSeriesPlotter attribute) (prolint.plotting.timeseries.TimeSeriesPlotter attribute) (prolint.plotting.TimeSeriesPlotter attribute) ResidenceDistributionPlotter (class in prolint.plotting) (class in prolint.plotting.kinetics) ResidueMetricsPlotter (class in prolint.plotting) (class in prolint.plotting.residues) resname_counts (prolint.core.ExtendedAtomGroup property) (prolint.core.groups.ExtendedAtomGroup property) (prolint.core.groups.PLAtomGroupBase property) run() (prolint.analysis.AtomDistancesAnalysis method) (prolint.analysis.base.BaseAnalysis method) (prolint.analysis.BaseAnalysis method) (prolint.analysis.DatabaseContactsAnalysis method) (prolint.analysis.density.DensityMapAnalysis method) (prolint.analysis.density.RadialDensityAnalysis method) (prolint.analysis.DensityMapAnalysis method) (prolint.analysis.DistanceAnalysis method) (prolint.analysis.distances.AtomDistancesAnalysis method) (prolint.analysis.distances.DistanceAnalysis method) (prolint.analysis.kinetics.KineticsAnalysis method) (prolint.analysis.KineticsAnalysis method) (prolint.analysis.metrics.MetricsAnalysis method) (prolint.analysis.MetricsAnalysis method) (prolint.analysis.RadialDensityAnalysis method) (prolint.analysis.shared_contacts.SharedContactsAnalysis method) (prolint.analysis.SharedContactsAnalysis method) (prolint.analysis.timeseries.DatabaseContactsAnalysis method) (prolint.analysis.timeseries.TimeSeriesAnalysis method) (prolint.analysis.TimeSeriesAnalysis method) (prolint.contacts.base.BaseContactStore method) (prolint.contacts.BaseContactStore method) (prolint.contacts.exact_contacts.ExactContacts method) (prolint.contacts.ExactContacts method) S s (prolint.config.UnitConversionFactor attribute), [1] (prolint.config.units.UnitConversionFactor attribute), [1] SECOND (prolint.config.enums.TimeUnit attribute), [1] (prolint.config.TimeUnit attribute), [1] SEGMENT_IDS (in module prolint.core.replica_detection) SerialContacts (class in prolint.computers) (class in prolint.computers.contacts) setup_logging() (in module prolint) (in module prolint.config) (in module prolint.config.logging) SharedContactsAnalysis (class in prolint.analysis) (class in prolint.analysis.shared_contacts) SIMPLE_FORMAT (in module prolint.config.logging) SimulationParams (class in prolint.config) (class in prolint.config.units) SurvivalCurvePlotter (class in prolint.plotting) (class in prolint.plotting.kinetics) T TimeSeriesAnalysis (class in prolint.analysis) (class in prolint.analysis.timeseries) TimeSeriesPlotter (class in prolint.plotting) (class in prolint.plotting.timeseries) TimeUnit (class in prolint.config) (class in prolint.config.enums) TimeUnitLiteral (in module prolint.core.universe) U union() (prolint.computers.base.ContactComputerBase method) (prolint.computers.ContactComputerBase method) unique_resnames (prolint.core.ExtendedAtomGroup property) (prolint.core.groups.ExtendedAtomGroup property) (prolint.core.groups.PLAtomGroupBase property) unit_conversion_factor (prolint.config.SimulationParams attribute), [1] (prolint.config.units.SimulationParams attribute), [1] UNIT_LABELS (in module prolint.config) (in module prolint.config.colors) (in module prolint.plotting) (in module prolint.plotting.theme) UnitConversionFactor (class in prolint.config) (class in prolint.config.units) units (prolint.config.SimulationParams attribute), [1] (prolint.config.units.SimulationParams attribute), [1] (prolint.core.Universe property) (prolint.core.universe.Universe property) (prolint.Universe property) Universe (class in prolint) (class in prolint.core) (class in prolint.core.universe) universe (prolint.analysis.base.BaseAnalysis attribute) (prolint.analysis.BaseAnalysis attribute) update_database() (prolint.core.Universe method) (prolint.core.universe.Universe method) (prolint.Universe method) update_query() (prolint.core.Universe method) (prolint.core.universe.Universe method) (prolint.Universe method) us (prolint.config.UnitConversionFactor attribute), [1] (prolint.config.units.UnitConversionFactor attribute), [1] V VALID_UNITS (in module prolint.core.universe) validate_result() (prolint.plotting.base.BasePlotter class method) (prolint.plotting.BasePlotter class method) (prolint.plotting.ContactEventsPlotter class method) (prolint.plotting.DatabaseContactsHeatmapPlotter class method) (prolint.plotting.density.DensityMapPlotter class method) (prolint.plotting.density.RadialDensityPlotter class method) (prolint.plotting.DensityMapPlotter class method) (prolint.plotting.DistanceHeatmapPlotter class method) (prolint.plotting.DistanceTimeSeriesPlotter class method) (prolint.plotting.heatmap.DatabaseContactsHeatmapPlotter class method) (prolint.plotting.heatmap.DistanceHeatmapPlotter class method) (prolint.plotting.heatmap.HeatmapPlotter class method) (prolint.plotting.HeatmapPlotter class method) (prolint.plotting.kinetics.ResidenceDistributionPlotter class method) (prolint.plotting.kinetics.SurvivalCurvePlotter class method) (prolint.plotting.LogoGridPlotter class method) (prolint.plotting.network.NetworkPlotter class method) (prolint.plotting.NetworkPlotter class method) (prolint.plotting.RadialDensityPlotter class method) (prolint.plotting.ResidenceDistributionPlotter class method) (prolint.plotting.ResidueMetricsPlotter class method) (prolint.plotting.residues.LogoGridPlotter class method) (prolint.plotting.residues.ResidueMetricsPlotter class method) (prolint.plotting.SurvivalCurvePlotter class method) (prolint.plotting.timeseries.ContactEventsPlotter class method) (prolint.plotting.timeseries.DistanceTimeSeriesPlotter class method) (prolint.plotting.timeseries.TimeSeriesPlotter class method) (prolint.plotting.TimeSeriesPlotter class method) W write_pdb() (in module prolint.plotting) (in module prolint.plotting.structure)