Index

_

__getattr__() (polyzymd.compare.config.PlotSettings method) __init__() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.solvent.CoSolvent method) (polyzymd.builders.solvent.SolvationCounts method) (polyzymd.builders.solvent.SolventBuilder method) (polyzymd.builders.solvent.SolventComposition method) (polyzymd.builders.substrate.SubstrateBuilder method) (polyzymd.builders.system_builder.SystemBuilder method) (polyzymd.compare.comparators.binding_free_energy.BindingFreeEnergyComparator method) (polyzymd.compare.comparators.contacts.ContactsComparator method) (polyzymd.compare.comparators.distances.DistancesComparator method) (polyzymd.compare.comparators.exposure.ExposureDynamicsComparator method) (polyzymd.compare.comparators.polymer_affinity.PolymerAffinityScoreComparator method) (polyzymd.compare.comparators.rmsf.RMSFComparator method) (polyzymd.compare.comparators.triad.TriadComparator method) (polyzymd.compare.config.AnalysisSettingsContainer method) (polyzymd.compare.config.ComparisonSettingsContainer method) (polyzymd.compare.config.PlotSettings method) (polyzymd.compare.core.base.BaseComparator method) (polyzymd.compare.statistics.ANOVAResult method) (polyzymd.compare.statistics.EffectSize method) (polyzymd.compare.statistics.TTestResult method) (polyzymd.config.loader.ConfigLoader method) (polyzymd.core.parameters.BarostatParameters method) (polyzymd.core.parameters.IntegratorParameters method) (polyzymd.core.parameters.ReporterParameters method) (polyzymd.core.parameters.SimulationParameters method) (polyzymd.core.parameters.SimulationPhase method) (polyzymd.core.parameters.ThermoParameters method) (polyzymd.core.parameters.ThermostatParameters method) (polyzymd.core.restraints.AtomSelection method) (polyzymd.core.restraints.RestraintDefinition method) (polyzymd.simulation.continuation.ContinuationManager method) (polyzymd.simulation.runner.SimulationRunner method) (polyzymd.workflow.daisy_chain.DaisyChainConfig method) (polyzymd.workflow.daisy_chain.DaisyChainSubmitter method) (polyzymd.workflow.daisy_chain.SubmissionResult method) (polyzymd.workflow.slurm.JobContext method) (polyzymd.workflow.slurm.SlurmConfig method) (polyzymd.workflow.slurm.SlurmScriptGenerator method)

__post_init__() (polyzymd.builders.solvent.CoSolvent method)

A

aa_groups (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] above_label (polyzymd.compare.settings.DistancePairSettings attribute), [1] account (polyzymd.workflow.slurm.SlurmConfig attribute), [1] affinity_score (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] affinity_score_per_replicate (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] affinity_score_uncertainty (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] AffinityGroupBarPlotter (class in polyzymd.compare.plotters.polymer_affinity) AffinityPlotSettings (class in polyzymd.compare.config) AffinityScoreConditionSummary (class in polyzymd.compare.results.polymer_affinity) AffinityScoreEntry (class in polyzymd.compare.results.polymer_affinity) AffinityScorePairwiseEntry (class in polyzymd.compare.results.polymer_affinity) AffinityStackedBarPlotter (class in polyzymd.compare.plotters.polymer_affinity) align_trajectory (polyzymd.compare.settings.DistancesAnalysisSettings attribute), [1] alignment_frame (polyzymd.compare.settings.DistancesAnalysisSettings attribute), [1] alignment_mode (polyzymd.compare.settings.DistancesAnalysisSettings attribute), [1] alignment_selection (polyzymd.compare.settings.DistancesAnalysisSettings attribute), [1] all_conformers (polyzymd.builders.substrate.SubstrateBuilder property) AM1BCC (polyzymd.config.schema.ChargeMethod attribute) analysis_settings (polyzymd.compare.config.ComparisonConfig attribute), [1] analysis_type() (polyzymd.compare.settings.BindingFreeEnergyAnalysisSettings class method) (polyzymd.compare.settings.BindingFreeEnergyComparisonSettings class method) (polyzymd.compare.settings.BindingPreferenceFieldsMixin class method) (polyzymd.compare.settings.CatalyticTriadAnalysisSettings class method) (polyzymd.compare.settings.CatalyticTriadComparisonSettings class method) (polyzymd.compare.settings.ContactsAnalysisSettings class method) (polyzymd.compare.settings.ContactsComparisonSettings class method) (polyzymd.compare.settings.DistancePairSettings class method) (polyzymd.compare.settings.DistancesAnalysisSettings class method) (polyzymd.compare.settings.DistancesComparisonSettings class method) (polyzymd.compare.settings.ExposureAnalysisSettings class method) (polyzymd.compare.settings.ExposureComparisonSettings class method) (polyzymd.compare.settings.PolymerAffinityScoreComparisonSettings class method) (polyzymd.compare.settings.PolymerAffinityScoreSettings class method) (polyzymd.compare.settings.RMSFAnalysisSettings class method) (polyzymd.compare.settings.RMSFComparisonSettings class method) (polyzymd.compare.settings.SecondaryStructureAnalysisSettings class method) (polyzymd.compare.settings.SecondaryStructureComparisonSettings class method) (polyzymd.compare.settings.TriadPairSettings class method)

AnalysisSettingsContainer (class in polyzymd.compare.config) ANDERSEN (polyzymd.config.schema.ThermostatType attribute) annotate_heatmap (polyzymd.compare.config.BFEPlotSettings attribute), [1] annotation_fontsize (polyzymd.compare.config.PlotTheme attribute) anova (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute) ANOVAResult (class in polyzymd.compare.statistics) ANOVASummary (class in polyzymd.compare.core.base) apply() (polyzymd.core.restraints.RestraintDefinition method) apply_restraints() (in module polyzymd.core.restraints) atom1 (polyzymd.config.schema.RestraintConfig attribute), [1] (polyzymd.core.restraints.RestraintDefinition attribute), [1] atom2 (polyzymd.config.schema.RestraintConfig attribute), [1] (polyzymd.core.restraints.RestraintDefinition attribute), [1] AtomSelection (class in polyzymd.core.restraints) AtomSelectionConfig (class in polyzymd.config.schema) auto_generate_residue_name() (polyzymd.config.schema.MonomerSpec method)

B

bar_alpha (polyzymd.compare.config.PlotTheme attribute) bar_capsize (polyzymd.compare.config.PlotTheme attribute) bar_edgecolor (polyzymd.compare.config.PlotTheme attribute) bar_linewidth (polyzymd.compare.config.PlotTheme attribute) barostat (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] (polyzymd.core.parameters.BarostatParameters attribute), [1] barostat_frequency (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] barostat_params (polyzymd.core.parameters.ThermoParameters attribute), [1] BarostatParameters (class in polyzymd.core.parameters) BarostatType (class in polyzymd.config.schema) base_directory (polyzymd.config.schema.OutputConfig attribute) BaseComparator (class in polyzymd.compare.core.base) BaseComparisonResult (class in polyzymd.compare.core.base), [1], [2], [3], [4] BaseConditionSummary (class in polyzymd.compare.core.base) below_label (polyzymd.compare.settings.DistancePairSettings attribute), [1] BFEBarPlotter (class in polyzymd.compare.plotters.binding_free_energy) BFEHeatmapPlotter (class in polyzymd.compare.plotters.binding_free_energy) BFEPlotSettings (class in polyzymd.compare.config)

BindingFreeEnergyAnalysisSettings (class in polyzymd.compare.settings) BindingFreeEnergyComparator (class in polyzymd.compare.comparators.binding_free_energy) BindingFreeEnergyComparisonSettings (class in polyzymd.compare.settings) BindingFreeEnergyResult (class in polyzymd.compare.results.binding_free_energy) BindingPreferenceFieldsMixin (class in polyzymd.compare.settings) box (polyzymd.config.schema.SolventConfig attribute), [1] box_vectors (polyzymd.builders.solvent.SolventBuilder property) (polyzymd.config.schema.PolymerPackingConfig attribute), [1] BoxConfig (class in polyzymd.config.schema) BoxShape (class in polyzymd.config.schema) build() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.substrate.SubstrateBuilder method) build_enzyme() (polyzymd.builders.system_builder.SystemBuilder method) build_from_config() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.substrate.SubstrateBuilder method) (polyzymd.builders.system_builder.SystemBuilder method) build_polymers() (polyzymd.builders.system_builder.SystemBuilder method) build_substrate() (polyzymd.builders.system_builder.SystemBuilder method)

C

cache_directory (polyzymd.config.schema.PolymerConfig attribute), [1] CACHED (polyzymd.config.schema.PolymerGenerationMode attribute) can_plot() (polyzymd.compare.plotters.binding_free_energy.BFEBarPlotter method) (polyzymd.compare.plotters.binding_free_energy.BFEHeatmapPlotter method) (polyzymd.compare.plotters.exposure.ExposureChaperoneFractionPlotter method) (polyzymd.compare.plotters.exposure.ExposureEnrichmentHeatmapPlotter method) (polyzymd.compare.plotters.polymer_affinity.AffinityGroupBarPlotter method) (polyzymd.compare.plotters.polymer_affinity.AffinityStackedBarPlotter method) canonical_sequence() (in module polyzymd.builders.polymer) CatalyticTriadAnalysisSettings (class in polyzymd.compare.settings) CatalyticTriadComparisonSettings (class in polyzymd.compare.settings) chain_id (polyzymd.compare.settings.SecondaryStructureAnalysisSettings attribute), [1] characters (polyzymd.builders.polymer.PolymerBuilder property) charge_method (polyzymd.config.schema.SubstrateConfig attribute), [1] ChargeMethod (class in polyzymd.config.schema) charger (polyzymd.config.schema.PolymerConfig attribute), [1] check_existing_slurm_jobs() (in module polyzymd.workflow.daisy_chain) checkpoint_interval (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] cl (polyzymd.builders.solvent.SolvationCounts attribute), [1] clear() (polyzymd.compare.core.registry.ComparatorRegistry class method) co_solvents (polyzymd.builders.solvent.SolvationCounts attribute), [1] (polyzymd.builders.solvent.SolventComposition attribute), [1] (polyzymd.config.schema.SolventConfig attribute), [1] cohens_d (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.statistics.EffectSize attribute), [1] cohens_d() (in module polyzymd.compare.statistics) color_palette (polyzymd.compare.config.PlotSettings attribute), [1] colormap (polyzymd.compare.config.BFEPlotSettings attribute), [1] combine_solutes() (polyzymd.builders.system_builder.SystemBuilder method) ComparatorRegistry (class in polyzymd.compare.core.registry) compare() (polyzymd.compare.comparators.binding_free_energy.BindingFreeEnergyComparator method) (polyzymd.compare.comparators.contacts.ContactsComparator method) (polyzymd.compare.comparators.distances.DistancesComparator method) (polyzymd.compare.comparators.exposure.ExposureDynamicsComparator method) (polyzymd.compare.comparators.polymer_affinity.PolymerAffinityScoreComparator method) (polyzymd.compare.core.base.BaseComparator method) comparison_settings (polyzymd.compare.config.ComparisonConfig attribute), [1] comparison_type (polyzymd.compare.comparators.binding_free_energy.BindingFreeEnergyComparator attribute) (polyzymd.compare.comparators.contacts.ContactsComparator attribute) (polyzymd.compare.comparators.distances.DistancesComparator attribute) (polyzymd.compare.comparators.exposure.ExposureDynamicsComparator attribute) (polyzymd.compare.comparators.polymer_affinity.PolymerAffinityScoreComparator attribute) (polyzymd.compare.comparators.rmsf.RMSFComparator attribute) (polyzymd.compare.comparators.triad.TriadComparator attribute) (polyzymd.compare.core.base.BaseComparator attribute) (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute) comparison_type_name() (polyzymd.compare.comparators.binding_free_energy.BindingFreeEnergyComparator class method) (polyzymd.compare.comparators.contacts.ContactsComparator class method) (polyzymd.compare.comparators.distances.DistancesComparator class method) (polyzymd.compare.comparators.exposure.ExposureDynamicsComparator class method) (polyzymd.compare.comparators.polymer_affinity.PolymerAffinityScoreComparator class method) (polyzymd.compare.comparators.rmsf.RMSFComparator class method) (polyzymd.compare.comparators.triad.TriadComparator class method) (polyzymd.compare.core.base.BaseComparator class method) ComparisonConfig (class in polyzymd.compare.config) ComparisonSettingsContainer (class in polyzymd.compare.config)

compute_binding_preference (polyzymd.compare.settings.BindingFreeEnergyAnalysisSettings attribute), [1] (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1] (polyzymd.compare.settings.PolymerAffinityScoreSettings attribute), [1] compute_residence_times (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1] concentration (polyzymd.builders.solvent.CoSolvent attribute), [1] (polyzymd.config.schema.CoSolventSpec attribute), [1] condition_a (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] condition_b (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] ConditionConfig (class in polyzymd.compare.config) conditions (polyzymd.compare.config.ComparisonConfig attribute), [1] (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] config (polyzymd.compare.config.ConditionConfig attribute), [1] (polyzymd.workflow.slurm.SlurmScriptGenerator property) config_path (polyzymd.compare.core.base.BaseConditionSummary attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.exposure.ExposureConditionSummary attribute) (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] ConfigLoader (class in polyzymd.config.loader) conformer_index (polyzymd.builders.substrate.SubstrateBuilder property) (polyzymd.config.schema.SubstrateConfig attribute), [1] contact_fraction_profile_threshold (polyzymd.compare.config.ContactsPlotSettings attribute), [1] contact_share (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] ContactsAnalysisSettings (class in polyzymd.compare.settings) ContactsComparator (class in polyzymd.compare.comparators.contacts) ContactsComparisonSettings (class in polyzymd.compare.settings) ContactsPlotSettings (class in polyzymd.compare.config) ContinuationManager (class in polyzymd.simulation.continuation) control (polyzymd.compare.config.ComparisonConfig attribute), [1] control_label (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute) CoSolvent (class in polyzymd.builders.solvent) CoSolventSpec (class in polyzymd.config.schema) count (polyzymd.config.schema.PolymerConfig attribute), [1] create() (polyzymd.compare.core.registry.ComparatorRegistry class method) create_flat_bottom() (polyzymd.core.restraints.RestraintFactory static method) create_harmonic() (polyzymd.core.restraints.RestraintFactory static method) create_interchange() (polyzymd.builders.system_builder.SystemBuilder method) create_job_name() (in module polyzymd.workflow.daisy_chain) create_npt_parameters() (in module polyzymd.core.parameters) create_nvt_parameters() (in module polyzymd.core.parameters) created_at (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] cross_temperature (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] CUBE (polyzymd.config.schema.BoxShape attribute) cutoff (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1]

D

DaisyChainConfig (class in polyzymd.workflow.daisy_chain) DaisyChainSubmitter (class in polyzymd.workflow.daisy_chain) dc_config (polyzymd.workflow.daisy_chain.DaisyChainSubmitter property) defaults (polyzymd.compare.config.ComparisonConfig attribute), [1] delta_delta_G (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] delta_G (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] delta_G_a (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] delta_G_b (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] delta_G_per_contact (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] delta_G_per_replicate (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] delta_G_uncertainty (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] delta_score (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] density (polyzymd.builders.solvent.CoSolvent attribute), [1] (polyzymd.config.schema.CoSolventSpec attribute), [1] description (polyzymd.compare.config.ComparisonConfig attribute), [1] (polyzymd.compare.settings.CatalyticTriadAnalysisSettings attribute), [1] (polyzymd.config.schema.AtomSelectionConfig attribute), [1] (polyzymd.config.schema.EnzymeConfig attribute), [1] (polyzymd.config.schema.SimulationConfig attribute), [1] (polyzymd.core.restraints.AtomSelection attribute), [1]

diff_colormap (polyzymd.compare.config.SSPlotSettings attribute), [1] direction (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.statistics.EffectSize attribute), [1] discover_replicate_dirs() (polyzymd.config.schema.SimulationConfig method) distance (polyzymd.config.schema.RestraintConfig attribute), [1] (polyzymd.core.restraints.RestraintDefinition attribute), [1] DistancePairSettings (class in polyzymd.compare.settings) DistancesAnalysisSettings (class in polyzymd.compare.settings) DistancesComparator (class in polyzymd.compare.comparators.distances) DistancesComparisonSettings (class in polyzymd.compare.settings) DistancesPlotSettings (class in polyzymd.compare.config) dot_alpha (polyzymd.compare.config.PlotTheme attribute) dot_color (polyzymd.compare.config.PlotTheme attribute) dot_size (polyzymd.compare.config.PlotTheme attribute) dpi (polyzymd.compare.config.PlotSettings attribute), [1] dry_run (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] duration (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] DYNAMIC (polyzymd.config.schema.PolymerGenerationMode attribute)

E

effect_size_interpretation (polyzymd.compare.core.base.PairwiseComparison attribute), [1] effective_scratch_directory (polyzymd.config.schema.OutputConfig property) EffectSize (class in polyzymd.compare.statistics) email (polyzymd.workflow.slurm.SlurmConfig attribute), [1] enabled (polyzymd.config.schema.PolymerConfig attribute), [1] (polyzymd.config.schema.RestraintConfig attribute), [1] (polyzymd.core.restraints.RestraintDefinition attribute), [1] enrichment_by_polymer_type (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] enrichment_colormap (polyzymd.compare.config.ContactsPlotSettings attribute), [1] enrichment_normalization (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1] enrichment_ratio (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] Ensemble (class in polyzymd.config.schema) ensemble (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] (polyzymd.core.parameters.ThermoParameters property) ensure_list() (polyzymd.compare.config.ConditionConfig class method) entries (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] enzyme (polyzymd.config.schema.SimulationConfig attribute), [1] enzyme_pdb_for_sasa (polyzymd.compare.settings.BindingPreferenceFieldsMixin attribute), [1] EnzymeBuilder (class in polyzymd.builders.enzyme) EnzymeConfig (class in polyzymd.config.schema) equilibration_stages (polyzymd.config.schema.SimulationPhasesConfig attribute), [1]

equilibration_time (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] equilibration_time_ns (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] EquilibrationStageConfig (class in polyzymd.config.schema) ESPALOMA (polyzymd.config.schema.ChargeMethod attribute) exclude (polyzymd.workflow.slurm.SlurmConfig attribute), [1] excluded_conditions (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] expand_env_vars_in_paths() (polyzymd.config.schema.OutputConfig class method) expand_path() (in module polyzymd.config.schema) expected_share (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] export_to_gromacs() (polyzymd.builders.system_builder.SystemBuilder method) exposure_threshold (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] ExposureAnalysisSettings (class in polyzymd.compare.settings) ExposureChaperoneFractionPlotter (class in polyzymd.compare.plotters.exposure) ExposureComparisonResult (class in polyzymd.compare.results.exposure) ExposureComparisonSettings (class in polyzymd.compare.settings) ExposureConditionSummary (class in polyzymd.compare.results.exposure) ExposureDynamicsComparator (class in polyzymd.compare.comparators.exposure) ExposureEnrichmentHeatmapPlotter (class in polyzymd.compare.plotters.exposure) extra_vars (polyzymd.workflow.slurm.JobContext attribute), [1]

F

f_statistic (polyzymd.compare.core.base.ANOVASummary attribute), [1] (polyzymd.compare.statistics.ANOVAResult attribute), [1] fdr_alpha (polyzymd.compare.settings.BindingFreeEnergyComparisonSettings attribute), [1] (polyzymd.compare.settings.ContactsComparisonSettings attribute), [1] (polyzymd.compare.settings.PolymerAffinityScoreComparisonSettings attribute), [1] figsize (polyzymd.compare.config.ContactsPlotSettings attribute), [1] (polyzymd.compare.config.DistancesPlotSettings attribute), [1] figsize_bars (polyzymd.compare.config.BFEPlotSettings attribute), [1] (polyzymd.compare.config.TriadPlotSettings attribute), [1] figsize_cf_by_aa_class_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_cf_by_partition_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_comparison (polyzymd.compare.config.RMSFPlotSettings attribute), [1] figsize_contact_fraction_profile (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_content_bars (polyzymd.compare.config.SSPlotSettings attribute), [1] figsize_diff_heatmap (polyzymd.compare.config.SSPlotSettings attribute), [1] figsize_enrichment_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_enrichment_heatmap (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_group_bars (polyzymd.compare.config.AffinityPlotSettings attribute), [1] figsize_heatmap (polyzymd.compare.config.BFEPlotSettings attribute), [1] figsize_kde_panel (polyzymd.compare.config.TriadPlotSettings attribute), [1] figsize_profile (polyzymd.compare.config.RMSFPlotSettings attribute), [1] figsize_residence_time_profile (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_rt_by_aa_class_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_rt_by_partition_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_stacked (polyzymd.compare.config.AffinityPlotSettings attribute), [1] figsize_system_coverage_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_system_coverage_heatmap (polyzymd.compare.config.ContactsPlotSettings attribute), [1] figsize_timeline (polyzymd.compare.config.SSPlotSettings attribute), [1] figsize_user_partition_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] fill_alpha (polyzymd.compare.config.PlotTheme attribute) FLAT_BOTTOM (polyzymd.config.schema.RestraintType attribute) (polyzymd.core.restraints.RestraintType attribute) force (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1]

force_constant (polyzymd.config.schema.PositionRestraintConfig attribute), [1] (polyzymd.config.schema.RestraintConfig attribute), [1] (polyzymd.core.restraints.RestraintDefinition attribute), [1] force_field (polyzymd.config.schema.SimulationConfig attribute), [1] ForceFieldConfig (class in polyzymd.config.schema) format (polyzymd.compare.config.PlotSettings attribute), [1] format_affinity_console_table() (in module polyzymd.compare.polymer_affinity_formatters) format_affinity_json() (in module polyzymd.compare.polymer_affinity_formatters) format_affinity_markdown() (in module polyzymd.compare.polymer_affinity_formatters) format_affinity_result() (in module polyzymd.compare.polymer_affinity_formatters) format_bfe_console_table() (in module polyzymd.compare.binding_free_energy_formatters) format_bfe_json() (in module polyzymd.compare.binding_free_energy_formatters) format_bfe_markdown() (in module polyzymd.compare.binding_free_energy_formatters) format_bfe_result() (in module polyzymd.compare.binding_free_energy_formatters) format_directory_name() (polyzymd.config.schema.OutputConfig method) formula (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] FreeEnergyConditionSummary (class in polyzymd.compare.results.binding_free_energy) FreeEnergyEntry (class in polyzymd.compare.results.binding_free_energy) FreeEnergyPairwiseEntry (class in polyzymd.compare.results.binding_free_energy) from_config() (polyzymd.builders.system_builder.SystemBuilder class method) (polyzymd.core.restraints.RestraintFactory static method) from_dict() (polyzymd.core.parameters.BarostatParameters class method) (polyzymd.core.parameters.IntegratorParameters class method) (polyzymd.core.parameters.ReporterParameters class method) (polyzymd.core.parameters.SimulationParameters class method) (polyzymd.core.parameters.SimulationPhase class method) (polyzymd.core.parameters.ThermoParameters class method) (polyzymd.core.parameters.ThermostatParameters class method) from_json() (polyzymd.core.parameters.SimulationParameters class method) from_preset() (polyzymd.workflow.slurm.SlurmConfig class method) from_simulation_config() (polyzymd.workflow.daisy_chain.DaisyChainConfig class method) from_yaml() (polyzymd.compare.config.ComparisonConfig class method) (polyzymd.config.schema.SimulationConfig class method)

G

generate_2d_kde (polyzymd.compare.config.TriadPlotSettings attribute), [1] generate_analysis_yaml() (polyzymd.compare.config.ComparisonConfig method) generate_analysis_yaml_for_all() (polyzymd.compare.config.ComparisonConfig method) generate_bars (polyzymd.compare.config.BFEPlotSettings attribute), [1] (polyzymd.compare.config.TriadPlotSettings attribute), [1] generate_cf_by_aa_class_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_cf_by_partition_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_comparison_template() (in module polyzymd.compare.config) generate_contact_fraction_profile (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_content_bars (polyzymd.compare.config.SSPlotSettings attribute), [1] generate_diff_heatmap (polyzymd.compare.config.SSPlotSettings attribute), [1] generate_enrichment_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_enrichment_heatmap (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_group_bars (polyzymd.compare.config.AffinityPlotSettings attribute), [1] generate_heatmap (polyzymd.compare.config.BFEPlotSettings attribute), [1] generate_individual_bars (polyzymd.compare.config.SSPlotSettings attribute), [1] generate_job_script() (polyzymd.workflow.daisy_chain.DaisyChainSubmitter method) (polyzymd.workflow.slurm.SlurmScriptGenerator method) generate_kde_panel (polyzymd.compare.config.TriadPlotSettings attribute), [1] generate_random_sequence() (in module polyzymd.builders.polymer) generate_residence_time_profile (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_rt_by_aa_class_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_rt_by_partition_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_stacked_bars (polyzymd.compare.config.AffinityPlotSettings attribute), [1] generate_state_bars (polyzymd.compare.config.DistancesPlotSettings attribute), [1] generate_system_coverage_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_system_coverage_heatmap (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generate_timeline (polyzymd.compare.config.SSPlotSettings attribute), [1] generate_user_partition_bars (polyzymd.compare.config.ContactsPlotSettings attribute), [1] generation_mode (polyzymd.config.schema.PolymerConfig attribute), [1] get() (polyzymd.compare.config.AnalysisSettingsContainer method) (polyzymd.compare.config.ComparisonSettingsContainer method) (polyzymd.compare.core.registry.ComparatorRegistry class method)

get_alignment_config() (polyzymd.compare.settings.DistancesAnalysisSettings method) get_all_analysis_types() (in module polyzymd.compare.settings) get_all_comparison_types() (in module polyzymd.compare.settings) get_comparison() (polyzymd.compare.core.base.BaseComparisonResult method), [1], [2], [3], [4] get_component_info() (polyzymd.builders.system_builder.SystemBuilder method) get_condition() (polyzymd.compare.config.ComparisonConfig method) (polyzymd.compare.core.base.BaseComparisonResult method), [1], [2], [3], [4] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult method) (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult method) get_enabled_analyses() (polyzymd.compare.config.AnalysisSettingsContainer method) get_enabled_comparisons() (polyzymd.compare.config.ComparisonSettingsContainer method) get_entry() (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary method) get_final_temperature() (polyzymd.config.schema.EquilibrationStageConfig method) get_job_scripts_directory() (polyzymd.config.schema.OutputConfig method) get_molecule() (polyzymd.builders.enzyme.EnzymeBuilder method) get_n_conformers() (polyzymd.builders.substrate.SubstrateBuilder method) get_openmm_components() (polyzymd.builders.system_builder.SystemBuilder method) get_packing_info() (polyzymd.builders.polymer.PolymerBuilder method) get_pair_labels() (polyzymd.compare.settings.CatalyticTriadAnalysisSettings method) (polyzymd.compare.settings.DistancesAnalysisSettings method) get_pair_selections() (polyzymd.compare.settings.CatalyticTriadAnalysisSettings method) (polyzymd.compare.settings.DistancesAnalysisSettings method) get_pair_thresholds() (polyzymd.compare.settings.DistancesAnalysisSettings method) get_projects_directory() (polyzymd.config.schema.SimulationConfig method) get_ranking() (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult method) get_slurm_logs_directory() (polyzymd.config.schema.OutputConfig method) get_start_temperature() (polyzymd.config.schema.EquilibrationStageConfig method) get_working_directory() (polyzymd.config.schema.SimulationConfig method) gpu_directive_style (polyzymd.workflow.slurm.SlurmConfig attribute), [1] gpu_type (polyzymd.workflow.slurm.SlurmConfig attribute), [1] gpus (polyzymd.workflow.slurm.SlurmConfig attribute), [1] group (polyzymd.config.schema.PositionRestraintConfig attribute), [1] group_contributions (polyzymd.compare.results.polymer_affinity.PolymerTypeScore attribute), [1] grouping (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1]

H

handle_legacy_base_directory() (polyzymd.config.schema.OutputConfig method) HARMONIC (polyzymd.config.schema.RestraintType attribute) (polyzymd.core.restraints.RestraintType attribute) hide_right_spine (polyzymd.compare.config.PlotTheme attribute)

hide_top_spine (polyzymd.compare.config.PlotTheme attribute) highlight_line_alpha (polyzymd.compare.config.PlotTheme attribute) highlight_residues (polyzymd.compare.config.ContactsPlotSettings attribute), [1] (polyzymd.compare.config.RMSFPlotSettings attribute), [1] history (polyzymd.simulation.runner.SimulationRunner property)

I

include_default_aa_groups (polyzymd.compare.settings.BindingPreferenceFieldsMixin attribute), [1] independent_ttest() (in module polyzymd.compare.statistics) initiation (polyzymd.config.schema.ReactionConfig attribute), [1] integ_params (polyzymd.core.parameters.SimulationParameters attribute), [1] IntegratorParameters (class in polyzymd.core.parameters) interchange (polyzymd.builders.system_builder.SystemBuilder property)

interpretation (polyzymd.compare.statistics.EffectSize attribute), [1] IonConfig (class in polyzymd.config.schema) ions (polyzymd.config.schema.SolventConfig attribute), [1] is_dry_run (polyzymd.workflow.daisy_chain.SubmissionResult attribute), [1] is_registered() (polyzymd.compare.core.registry.ComparatorRegistry class method) is_temperature_ramping (polyzymd.config.schema.EquilibrationStageConfig property)

J

job_chains (polyzymd.workflow.daisy_chain.DaisyChainSubmitter property) job_id (polyzymd.workflow.daisy_chain.SubmissionResult attribute), [1] job_name (polyzymd.workflow.slurm.JobContext attribute), [1]

job_scripts_subdir (polyzymd.config.schema.OutputConfig attribute), [1] JOB_TEMPLATE (polyzymd.workflow.slurm.SlurmScriptGenerator attribute) JobContext (class in polyzymd.workflow.slurm)

K

k_b() (polyzymd.compare.settings.BindingFreeEnergyAnalysisSettings method) kcl_concentration (polyzymd.builders.solvent.SolventComposition attribute), [1] (polyzymd.config.schema.IonConfig attribute), [1]

kde_fill_alpha (polyzymd.compare.config.TriadPlotSettings attribute), [1] kde_xlim (polyzymd.compare.config.TriadPlotSettings attribute), [1]

L

label (polyzymd.compare.config.ConditionConfig attribute), [1] (polyzymd.compare.core.base.BaseConditionSummary attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.exposure.ExposureConditionSummary attribute) (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.settings.DistancePairSettings attribute), [1] (polyzymd.compare.settings.TriadPairSettings attribute), [1] (polyzymd.config.schema.MonomerSpec attribute), [1] label_fontsize (polyzymd.compare.config.PlotTheme attribute) LANGEVIN (polyzymd.config.schema.ThermostatType attribute) LANGEVIN_MIDDLE (polyzymd.config.schema.ThermostatType attribute) legend_bbox (polyzymd.compare.config.PlotTheme attribute) legend_fontsize (polyzymd.compare.config.PlotTheme attribute) legend_loc (polyzymd.compare.config.PlotTheme attribute)

length (polyzymd.builders.polymer.PolymerBuilder property) (polyzymd.config.schema.PolymerConfig attribute), [1] line_alpha (polyzymd.compare.config.PlotTheme attribute) list_available() (polyzymd.compare.core.registry.ComparatorRegistry class method) load() (polyzymd.compare.core.base.BaseComparisonResult class method), [1], [2], [3], [4] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult class method) (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult class method) (polyzymd.config.loader.ConfigLoader method) load_checkpoint() (polyzymd.simulation.runner.SimulationRunner method) load_config() (in module polyzymd.config.loader) load_config_dict() (in module polyzymd.config.loader) load_previous_state() (polyzymd.simulation.continuation.ContinuationManager method) loaded_molecules (polyzymd.builders.polymer.PolymerBuilder property) LOWER_WALL (polyzymd.config.schema.RestraintType attribute) (polyzymd.core.restraints.RestraintType attribute)

M

max_retries (polyzymd.config.schema.PolymerConfig attribute), [1] mean_chaperone_fraction (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] mean_contact_fraction (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] mean_n_transient (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] mean_total_chaperone_events (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] mean_total_unassisted_events (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] mean_transient_fraction (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] memory (polyzymd.workflow.slurm.SlurmConfig attribute), [1] methodology (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] metric (polyzymd.compare.core.base.ANOVASummary attribute), [1] (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] metric_type (polyzymd.compare.comparators.binding_free_energy.BindingFreeEnergyComparator property) (polyzymd.compare.comparators.contacts.ContactsComparator property) (polyzymd.compare.comparators.distances.DistancesComparator property) (polyzymd.compare.comparators.exposure.ExposureDynamicsComparator property) (polyzymd.compare.comparators.polymer_affinity.PolymerAffinityScoreComparator property) (polyzymd.compare.comparators.rmsf.RMSFComparator property) (polyzymd.compare.comparators.triad.TriadComparator property) (polyzymd.compare.core.base.BaseComparator property) mgcl2_concentration (polyzymd.builders.solvent.SolventComposition attribute), [1] (polyzymd.config.schema.IonConfig attribute), [1] min_effect_size (polyzymd.compare.settings.ContactsComparisonSettings attribute), [1] min_event_length (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] minimal() (polyzymd.compare.config.PlotTheme class method) minimize() (polyzymd.simulation.runner.SimulationRunner method) mixed_temperatures (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] model (polyzymd.config.schema.PrimarySolventConfig attribute), [1] model_config (polyzymd.compare.config.AffinityPlotSettings attribute) (polyzymd.compare.config.AnalysisSettingsContainer attribute) (polyzymd.compare.config.BFEPlotSettings attribute) (polyzymd.compare.config.ComparisonConfig attribute) (polyzymd.compare.config.ComparisonSettingsContainer attribute) (polyzymd.compare.config.ConditionConfig attribute) (polyzymd.compare.config.ContactsPlotSettings attribute) (polyzymd.compare.config.DistancesPlotSettings attribute) (polyzymd.compare.config.PlotSettings attribute) (polyzymd.compare.config.PlotTheme attribute) (polyzymd.compare.config.RMSFPlotSettings attribute) (polyzymd.compare.config.SSPlotSettings attribute) (polyzymd.compare.config.TriadPlotSettings attribute) (polyzymd.compare.core.base.ANOVASummary attribute) (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4] (polyzymd.compare.core.base.BaseConditionSummary attribute) (polyzymd.compare.core.base.PairwiseComparison attribute) (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute) (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute) (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute) (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute) (polyzymd.compare.results.exposure.ExposureComparisonResult attribute) (polyzymd.compare.results.exposure.ExposureConditionSummary attribute) (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute) (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute) (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute) (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute) (polyzymd.compare.results.polymer_affinity.PolymerTypeScore attribute) (polyzymd.compare.settings.BindingFreeEnergyAnalysisSettings attribute) (polyzymd.compare.settings.BindingFreeEnergyComparisonSettings attribute) (polyzymd.compare.settings.BindingPreferenceFieldsMixin attribute) (polyzymd.compare.settings.CatalyticTriadAnalysisSettings attribute) (polyzymd.compare.settings.CatalyticTriadComparisonSettings attribute) (polyzymd.compare.settings.ContactsAnalysisSettings attribute) (polyzymd.compare.settings.ContactsComparisonSettings attribute) (polyzymd.compare.settings.DistancePairSettings attribute) (polyzymd.compare.settings.DistancesAnalysisSettings attribute) (polyzymd.compare.settings.DistancesComparisonSettings attribute) (polyzymd.compare.settings.ExposureAnalysisSettings attribute) (polyzymd.compare.settings.ExposureComparisonSettings attribute) (polyzymd.compare.settings.PolymerAffinityScoreComparisonSettings attribute) (polyzymd.compare.settings.PolymerAffinityScoreSettings attribute) (polyzymd.compare.settings.RMSFAnalysisSettings attribute) (polyzymd.compare.settings.RMSFComparisonSettings attribute) (polyzymd.compare.settings.SecondaryStructureAnalysisSettings attribute) (polyzymd.compare.settings.SecondaryStructureComparisonSettings attribute) (polyzymd.compare.settings.TriadPairSettings attribute) (polyzymd.config.schema.AtomSelectionConfig attribute) (polyzymd.config.schema.BoxConfig attribute) (polyzymd.config.schema.CoSolventSpec attribute) (polyzymd.config.schema.EnzymeConfig attribute) (polyzymd.config.schema.EquilibrationStageConfig attribute) (polyzymd.config.schema.ForceFieldConfig attribute) (polyzymd.config.schema.IonConfig attribute) (polyzymd.config.schema.MonomerSpec attribute) (polyzymd.config.schema.OutputConfig attribute) (polyzymd.config.schema.PolymerConfig attribute) (polyzymd.config.schema.PolymerPackingConfig attribute) (polyzymd.config.schema.PositionRestraintConfig attribute) (polyzymd.config.schema.PrimarySolventConfig attribute) (polyzymd.config.schema.ReactionConfig attribute) (polyzymd.config.schema.RestraintConfig attribute) (polyzymd.config.schema.SimulationConfig attribute) (polyzymd.config.schema.SimulationPhaseConfig attribute) (polyzymd.config.schema.SimulationPhasesConfig attribute) (polyzymd.config.schema.SolventConfig attribute) (polyzymd.config.schema.SubstrateConfig attribute) (polyzymd.config.schema.ThermodynamicsConfig attribute)

module polyzymd.builders.enzyme polyzymd.builders.polymer polyzymd.builders.solvent polyzymd.builders.substrate polyzymd.builders.system_builder polyzymd.compare.binding_free_energy_formatters polyzymd.compare.cli polyzymd.compare.comparators.binding_free_energy polyzymd.compare.comparators.contacts polyzymd.compare.comparators.distances polyzymd.compare.comparators.exposure polyzymd.compare.comparators.polymer_affinity polyzymd.compare.comparators.rmsf polyzymd.compare.comparators.triad polyzymd.compare.config polyzymd.compare.core.base polyzymd.compare.core.registry polyzymd.compare.plotters.binding_free_energy polyzymd.compare.plotters.exposure polyzymd.compare.plotters.polymer_affinity polyzymd.compare.polymer_affinity_formatters polyzymd.compare.results.binding_free_energy polyzymd.compare.results.exposure polyzymd.compare.results.polymer_affinity polyzymd.compare.settings polyzymd.compare.statistics polyzymd.config.loader polyzymd.config.schema polyzymd.core.parameters polyzymd.core.restraints polyzymd.simulation.continuation polyzymd.simulation.runner polyzymd.workflow.daisy_chain polyzymd.workflow.slurm molecule (polyzymd.builders.solvent.CoSolvent attribute), [1] (polyzymd.builders.substrate.SubstrateBuilder property) monomers (polyzymd.config.schema.PolymerConfig attribute), [1] MonomerSpec (class in polyzymd.config.schema) MONTE_CARLO (polyzymd.config.schema.BarostatType attribute) MONTE_CARLO_ANISOTROPIC (polyzymd.config.schema.BarostatType attribute) movebadrandom (polyzymd.config.schema.PolymerPackingConfig attribute), [1]

N

n_contacts (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] n_exposed_in_group (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] n_pairs (polyzymd.compare.settings.CatalyticTriadAnalysisSettings property) n_replicates (polyzymd.compare.core.base.BaseConditionSummary attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.exposure.ExposureConditionSummary attribute) (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] n_sphere_points (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] na (polyzymd.builders.solvent.SolvationCounts attribute), [1] nacl_concentration (polyzymd.builders.solvent.SolventComposition attribute), [1] (polyzymd.config.schema.IonConfig attribute), [1] NAGL (polyzymd.config.schema.ChargeMethod attribute) name (polyzymd.builders.solvent.CoSolvent attribute), [1] (polyzymd.compare.config.ComparisonConfig attribute), [1] (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute) (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] (polyzymd.compare.settings.CatalyticTriadAnalysisSettings attribute), [1] (polyzymd.config.schema.CoSolventSpec attribute), [1] (polyzymd.config.schema.EnzymeConfig attribute), [1] (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.MonomerSpec attribute), [1] (polyzymd.config.schema.RestraintConfig attribute), [1] (polyzymd.config.schema.SimulationConfig attribute), [1] (polyzymd.config.schema.SubstrateConfig attribute), [1] (polyzymd.core.parameters.SimulationPhase attribute), [1] (polyzymd.core.restraints.RestraintDefinition attribute), [1]

naming_template (polyzymd.config.schema.OutputConfig attribute), [1] neutralize (polyzymd.builders.solvent.SolventComposition attribute), [1] (polyzymd.config.schema.IonConfig attribute), [1] nodes (polyzymd.workflow.slurm.SlurmConfig attribute), [1] NOSE_HOOVER (polyzymd.config.schema.ThermostatType attribute) NPT (polyzymd.config.schema.Ensemble attribute) ntasks (polyzymd.workflow.slurm.SlurmConfig attribute), [1] num_samples (polyzymd.core.parameters.IntegratorParameters attribute), [1] NVE (polyzymd.config.schema.Ensemble attribute) NVT (polyzymd.config.schema.Ensemble attribute)

O

one_way_anova() (in module polyzymd.compare.statistics) OPC (polyzymd.config.schema.WaterModel attribute) output (polyzymd.config.schema.SimulationConfig attribute), [1]

output_dir (polyzymd.compare.config.PlotSettings attribute), [1] output_file (polyzymd.workflow.slurm.JobContext attribute), [1] output_script_dir (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] OutputConfig (class in polyzymd.config.schema)

P

p_value (polyzymd.compare.core.base.ANOVASummary attribute), [1] (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] (polyzymd.compare.statistics.ANOVAResult attribute), [1] (polyzymd.compare.statistics.TTestResult attribute), [1] pack_polymers() (polyzymd.builders.system_builder.SystemBuilder method) packing (polyzymd.config.schema.PolymerConfig attribute), [1] padding (polyzymd.config.schema.BoxConfig attribute), [1] (polyzymd.config.schema.PolymerPackingConfig attribute), [1] pairs (polyzymd.compare.settings.CatalyticTriadAnalysisSettings attribute), [1] (polyzymd.compare.settings.DistancesAnalysisSettings attribute), [1] pairwise_comparisons (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] PairwiseComparison (class in polyzymd.compare.core.base) parameters (polyzymd.core.parameters.SimulationPhase attribute), [1] parse_analysis_settings() (polyzymd.compare.config.ComparisonConfig class method) parse_comparison_settings() (polyzymd.compare.config.ComparisonConfig class method) parse_replicate_range() (in module polyzymd.workflow.slurm) partition (polyzymd.workflow.slurm.SlurmConfig attribute), [1] partition_name (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] pdb_path (polyzymd.builders.enzyme.EnzymeBuilder property) (polyzymd.config.schema.EnzymeConfig attribute), [1] percent_change (polyzymd.compare.core.base.PairwiseComparison attribute), [1] percent_change() (in module polyzymd.compare.statistics) plot() (polyzymd.compare.plotters.binding_free_energy.BFEBarPlotter method) (polyzymd.compare.plotters.binding_free_energy.BFEHeatmapPlotter method) (polyzymd.compare.plotters.exposure.ExposureChaperoneFractionPlotter method) (polyzymd.compare.plotters.exposure.ExposureEnrichmentHeatmapPlotter method) (polyzymd.compare.plotters.polymer_affinity.AffinityGroupBarPlotter method) (polyzymd.compare.plotters.polymer_affinity.AffinityStackedBarPlotter method) plot_settings (polyzymd.compare.config.ComparisonConfig attribute), [1] plot_type() (polyzymd.compare.plotters.binding_free_energy.BFEBarPlotter class method) (polyzymd.compare.plotters.binding_free_energy.BFEHeatmapPlotter class method) (polyzymd.compare.plotters.exposure.ExposureChaperoneFractionPlotter class method) (polyzymd.compare.plotters.exposure.ExposureEnrichmentHeatmapPlotter class method) (polyzymd.compare.plotters.polymer_affinity.AffinityGroupBarPlotter class method) (polyzymd.compare.plotters.polymer_affinity.AffinityStackedBarPlotter class method) PlotSettings (class in polyzymd.compare.config) PlotTheme (class in polyzymd.compare.config) polymer_resnames (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] polymer_selection (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1] (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] polymer_type (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerTypeScore attribute), [1] polymer_type_scores (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] polymer_type_selections (polyzymd.compare.settings.BindingPreferenceFieldsMixin attribute), [1] polymer_types (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1] PolymerAffinityScoreComparator (class in polyzymd.compare.comparators.polymer_affinity) PolymerAffinityScoreComparisonSettings (class in polyzymd.compare.settings) PolymerAffinityScoreResult (class in polyzymd.compare.results.polymer_affinity) PolymerAffinityScoreSettings (class in polyzymd.compare.settings) PolymerBuilder (class in polyzymd.builders.polymer) PolymerConfig (class in polyzymd.config.schema) PolymerGenerationMode (class in polyzymd.config.schema) polymerization (polyzymd.config.schema.ReactionConfig attribute), [1] PolymerPackingConfig (class in polyzymd.config.schema) polymers (polyzymd.config.schema.SimulationConfig attribute), [1] PolymerTypeScore (class in polyzymd.compare.results.polymer_affinity) polyzymd.builders.enzyme module polyzymd.builders.polymer module polyzymd.builders.solvent module polyzymd.builders.substrate module polyzymd.builders.system_builder module polyzymd.compare.binding_free_energy_formatters module polyzymd.compare.cli module polyzymd.compare.comparators.binding_free_energy module polyzymd.compare.comparators.contacts module polyzymd.compare.comparators.distances module

polyzymd.compare.comparators.exposure module polyzymd.compare.comparators.polymer_affinity module polyzymd.compare.comparators.rmsf module polyzymd.compare.comparators.triad module polyzymd.compare.config module polyzymd.compare.core.base module polyzymd.compare.core.registry module polyzymd.compare.plotters.binding_free_energy module polyzymd.compare.plotters.exposure module polyzymd.compare.plotters.polymer_affinity module polyzymd.compare.polymer_affinity_formatters module polyzymd.compare.results.binding_free_energy module polyzymd.compare.results.exposure module polyzymd.compare.results.polymer_affinity module polyzymd.compare.settings module polyzymd.compare.statistics module polyzymd.config.loader module polyzymd.config.schema module polyzymd.core.parameters module polyzymd.core.restraints module polyzymd.simulation.continuation module polyzymd.simulation.runner module polyzymd.workflow.daisy_chain module polyzymd.workflow.slurm module polyzymd_version (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] position_restraints (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] PositionRestraintConfig (class in polyzymd.config.schema) presentation() (polyzymd.compare.config.PlotTheme class method) pressure (polyzymd.config.schema.ThermodynamicsConfig attribute), [1] (polyzymd.core.parameters.BarostatParameters attribute), [1] primary (polyzymd.config.schema.SolventConfig attribute), [1] primary_metric_sem (polyzymd.compare.core.base.BaseConditionSummary property) (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary property) (polyzymd.compare.results.exposure.ExposureConditionSummary property) (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary property) primary_metric_value (polyzymd.compare.core.base.BaseConditionSummary property) (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary property) (polyzymd.compare.results.exposure.ExposureConditionSummary property) (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary property) PrimarySolventConfig (class in polyzymd.config.schema) probabilities (polyzymd.builders.polymer.PolymerBuilder property) probability (polyzymd.config.schema.MonomerSpec attribute), [1] probe_radius_nm (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] production (polyzymd.config.schema.SimulationPhasesConfig attribute), [1] projects_dir (polyzymd.workflow.slurm.JobContext attribute), [1] projects_directory (polyzymd.config.schema.OutputConfig attribute), [1] protein (polyzymd.config.schema.ForceFieldConfig attribute), [1] protein_chain (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] protein_group (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] protein_groups (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] (polyzymd.compare.settings.BindingPreferenceFieldsMixin attribute), [1] protein_partitions (polyzymd.compare.settings.BindingPreferenceFieldsMixin attribute), [1] protein_selection (polyzymd.compare.settings.ContactsAnalysisSettings attribute), [1] (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] publication() (polyzymd.compare.config.PlotTheme class method)

Q

qos (polyzymd.workflow.slurm.SlurmConfig attribute), [1] quantity_from_dict() (in module polyzymd.core.parameters) (in module polyzymd.simulation.continuation)

quantity_to_dict() (in module polyzymd.core.parameters)

R

random_seed (polyzymd.config.schema.PolymerConfig attribute), [1] ranking (polyzymd.compare.core.base.BaseComparisonResult attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9] (polyzymd.compare.results.exposure.ExposureComparisonResult attribute) ranking_by_transient_fraction (polyzymd.compare.results.exposure.ExposureComparisonResult attribute), [1] ReactionConfig (class in polyzymd.config.schema) reactions (polyzymd.config.schema.PolymerConfig attribute), [1] reference_file (polyzymd.compare.settings.RMSFAnalysisSettings attribute), [1] reference_frame (polyzymd.compare.settings.RMSFAnalysisSettings attribute), [1] reference_line_color (polyzymd.compare.config.PlotTheme attribute) reference_line_style (polyzymd.compare.config.PlotTheme attribute) reference_line_width (polyzymd.compare.config.PlotTheme attribute) reference_mode (polyzymd.compare.settings.RMSFAnalysisSettings attribute), [1] register() (polyzymd.compare.core.registry.ComparatorRegistry class method) replicate (polyzymd.workflow.daisy_chain.SubmissionResult attribute), [1] replicate_num (polyzymd.workflow.slurm.JobContext attribute), [1] replicate_values (polyzymd.compare.core.base.BaseConditionSummary attribute), [1] (polyzymd.compare.results.exposure.ExposureConditionSummary attribute) replicates (polyzymd.compare.config.ConditionConfig attribute), [1] (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] report_checkpoint (polyzymd.core.parameters.ReporterParameters attribute), [1] report_state (polyzymd.core.parameters.ReporterParameters attribute), [1] report_state_data (polyzymd.core.parameters.ReporterParameters attribute), [1] report_trajectory (polyzymd.core.parameters.ReporterParameters attribute), [1] reporter_params (polyzymd.core.parameters.SimulationParameters attribute), [1] ReporterParameters (class in polyzymd.core.parameters)

reporting_interval (polyzymd.core.parameters.IntegratorParameters property) residue_name (polyzymd.builders.solvent.CoSolvent attribute), [1] (polyzymd.config.schema.CoSolventSpec attribute), [1] (polyzymd.config.schema.MonomerSpec attribute), [1] (polyzymd.config.schema.SubstrateConfig attribute), [1] resolve() (polyzymd.core.restraints.AtomSelection method) resolve_default_paths() (polyzymd.config.schema.ReactionConfig class method) resolve_output_dir() (polyzymd.compare.config.PlotSettings class method) resolve_path() (polyzymd.compare.config.ConditionConfig class method) restraint_type (polyzymd.core.restraints.RestraintDefinition attribute), [1] RestraintConfig (class in polyzymd.config.schema) RestraintDefinition (class in polyzymd.core.restraints) RestraintFactory (class in polyzymd.core.restraints) restraints (polyzymd.config.schema.SimulationConfig attribute), [1] RestraintType (class in polyzymd.config.schema) (class in polyzymd.core.restraints) RHOMBIC_DODECAHEDRON (polyzymd.config.schema.BoxShape attribute) RMSFAnalysisSettings (class in polyzymd.compare.settings) RMSFComparator (class in polyzymd.compare.comparators.rmsf) RMSFComparisonSettings (class in polyzymd.compare.settings) RMSFPlotSettings (class in polyzymd.compare.config) run_equilibration() (polyzymd.simulation.runner.SimulationRunner method) run_equilibration_stage() (polyzymd.simulation.runner.SimulationRunner method) run_production() (polyzymd.simulation.runner.SimulationRunner method) run_segment() (polyzymd.simulation.continuation.ContinuationManager method) run_staged_equilibration() (polyzymd.simulation.runner.SimulationRunner method)

S

salt_concentration (polyzymd.config.schema.ThermodynamicsConfig attribute) samples (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] save() (polyzymd.compare.core.base.BaseComparisonResult method), [1], [2], [3], [4] (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult method) (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult method) save_checkpoint (polyzymd.config.schema.OutputConfig attribute), [1] save_config() (in module polyzymd.config.loader) save_history() (polyzymd.simulation.runner.SimulationRunner method) save_script() (polyzymd.workflow.slurm.SlurmScriptGenerator method) save_state_data (polyzymd.config.schema.OutputConfig attribute), [1] save_topology() (polyzymd.builders.system_builder.SystemBuilder method) score_a (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] score_b (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] scratch_dir (polyzymd.workflow.slurm.JobContext attribute), [1] scratch_directory (polyzymd.config.schema.OutputConfig attribute), [1] script_path (polyzymd.workflow.daisy_chain.SubmissionResult attribute), [1] sdf_directory (polyzymd.config.schema.PolymerConfig attribute), [1] sdf_path (polyzymd.builders.substrate.SubstrateBuilder property) (polyzymd.config.schema.SubstrateConfig attribute), [1] SecondaryStructureAnalysisSettings (class in polyzymd.compare.settings) SecondaryStructureComparisonSettings (class in polyzymd.compare.settings) segment_index (polyzymd.simulation.continuation.ContinuationManager property) (polyzymd.workflow.daisy_chain.SubmissionResult attribute), [1] (polyzymd.workflow.slurm.JobContext attribute), [1] selection (polyzymd.compare.settings.RMSFAnalysisSettings attribute), [1] (polyzymd.config.schema.AtomSelectionConfig attribute), [1] (polyzymd.core.restraints.AtomSelection attribute), [1] selection_a (polyzymd.compare.settings.DistancePairSettings attribute), [1] (polyzymd.compare.settings.TriadPairSettings attribute), [1] selection_b (polyzymd.compare.settings.DistancePairSettings attribute), [1] (polyzymd.compare.settings.TriadPairSettings attribute), [1] sem_chaperone_fraction (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] sem_transient_fraction (polyzymd.compare.results.exposure.ExposureConditionSummary attribute), [1] sequence_counts (polyzymd.builders.polymer.PolymerBuilder property) shape (polyzymd.config.schema.BoxConfig attribute), [1] show_cf_by_aa_class_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_cf_by_partition_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_contact_fraction_profile_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_enrichment_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_error (polyzymd.compare.config.RMSFPlotSettings attribute), [1] show_error_bars (polyzymd.compare.config.AffinityPlotSettings attribute), [1] (polyzymd.compare.config.BFEPlotSettings attribute), [1] show_residence_time_profile_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_rt_by_aa_class_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_rt_by_partition_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_system_coverage_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_threshold (polyzymd.compare.config.DistancesPlotSettings attribute), [1] show_user_partition_error (polyzymd.compare.config.ContactsPlotSettings attribute), [1] show_watermark (polyzymd.compare.config.PlotTheme attribute)

significant (polyzymd.compare.core.base.ANOVASummary attribute), [1] (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.statistics.ANOVAResult property) (polyzymd.compare.statistics.TTestResult property) sim_config (polyzymd.workflow.daisy_chain.DaisyChainSubmitter property) simulation (polyzymd.simulation.continuation.ContinuationManager property) (polyzymd.simulation.runner.SimulationRunner property) simulation_phases (polyzymd.config.schema.SimulationConfig attribute), [1] SimulationConfig (class in polyzymd.config.schema) SimulationParameters (class in polyzymd.core.parameters) SimulationPhase (class in polyzymd.core.parameters) SimulationPhaseConfig (class in polyzymd.config.schema) SimulationPhasesConfig (class in polyzymd.config.schema) SimulationRunner (class in polyzymd.simulation.runner) slurm_config (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] slurm_logs_subdir (polyzymd.config.schema.OutputConfig attribute), [1] SlurmConfig (class in polyzymd.workflow.slurm) SlurmScriptGenerator (class in polyzymd.workflow.slurm) small_fontsize (polyzymd.compare.config.PlotTheme attribute) small_molecule (polyzymd.config.schema.ForceFieldConfig attribute), [1] smiles (polyzymd.builders.solvent.CoSolvent attribute), [1] (polyzymd.config.schema.CoSolventSpec attribute), [1] (polyzymd.config.schema.MonomerSpec attribute), [1] solvate() (polyzymd.builders.solvent.SolventBuilder method) (polyzymd.builders.system_builder.SystemBuilder method) solvate_from_config() (polyzymd.builders.solvent.SolventBuilder method) solvated_topology (polyzymd.builders.solvent.SolventBuilder property) (polyzymd.builders.system_builder.SystemBuilder property) solvation_counts (polyzymd.builders.solvent.SolventBuilder property) SolvationCounts (class in polyzymd.builders.solvent) solvent (polyzymd.config.schema.SimulationConfig attribute), [1] SolventBuilder (class in polyzymd.builders.solvent) SolventComposition (class in polyzymd.builders.solvent) SolventConfig (class in polyzymd.config.schema) source_path (polyzymd.compare.config.ComparisonConfig attribute) SPCE (polyzymd.config.schema.WaterModel attribute) SSPlotSettings (class in polyzymd.compare.config) state_data (polyzymd.core.parameters.ReporterParameters attribute), [1] style (polyzymd.compare.config.PlotSettings attribute), [1] SubmissionResult (class in polyzymd.workflow.daisy_chain) submit_all() (polyzymd.workflow.daisy_chain.DaisyChainSubmitter method) submit_daisy_chain() (in module polyzymd.workflow.daisy_chain) submit_replicate() (polyzymd.workflow.daisy_chain.DaisyChainSubmitter method) substrate (polyzymd.config.schema.SimulationConfig attribute), [1] SubstrateBuilder (class in polyzymd.builders.substrate) SubstrateConfig (class in polyzymd.config.schema) suptitle_fontsize (polyzymd.compare.config.PlotTheme attribute) surface_exposure_threshold (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] (polyzymd.compare.settings.BindingPreferenceFieldsMixin attribute), [1] SystemBuilder (class in polyzymd.builders.system_builder)

T

t_statistic (polyzymd.compare.core.base.PairwiseComparison attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] (polyzymd.compare.statistics.TTestResult attribute), [1] target_density (polyzymd.config.schema.BoxConfig attribute), [1] temperature (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.ThermodynamicsConfig attribute), [1] (polyzymd.core.parameters.BarostatParameters attribute), [1] (polyzymd.core.parameters.ThermostatParameters attribute), [1] temperature_a_K (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] temperature_b_K (polyzymd.compare.results.binding_free_energy.FreeEnergyPairwiseEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScorePairwiseEntry attribute), [1] temperature_end (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] temperature_groups (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerAffinityScoreResult attribute), [1] temperature_increment (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] temperature_interval (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] temperature_K (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.AffinityScoreEntry attribute), [1] temperature_start (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] termination (polyzymd.config.schema.ReactionConfig attribute), [1] theme (polyzymd.compare.config.PlotSettings attribute), [1] thermo_params (polyzymd.core.parameters.SimulationParameters attribute), [1] thermodynamics (polyzymd.config.schema.SimulationConfig attribute), [1] ThermodynamicsConfig (class in polyzymd.config.schema) ThermoParameters (class in polyzymd.core.parameters) thermostat (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] (polyzymd.core.parameters.ThermostatParameters attribute), [1] thermostat_params (polyzymd.core.parameters.ThermoParameters attribute), [1] thermostat_timescale (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] ThermostatParameters (class in polyzymd.core.parameters) ThermostatType (class in polyzymd.config.schema) threshold (polyzymd.compare.settings.CatalyticTriadAnalysisSettings attribute), [1] (polyzymd.compare.settings.DistancePairSettings attribute), [1] (polyzymd.compare.settings.DistancesAnalysisSettings attribute), [1] threshold_line_color (polyzymd.compare.config.TriadPlotSettings attribute), [1] tick_fontsize (polyzymd.compare.config.PlotTheme attribute) time_limit (polyzymd.workflow.slurm.SlurmConfig attribute), [1] time_step (polyzymd.config.schema.EquilibrationStageConfig attribute), [1] (polyzymd.config.schema.SimulationPhaseConfig attribute), [1] (polyzymd.core.parameters.IntegratorParameters attribute), [1] timescale (polyzymd.core.parameters.ThermostatParameters attribute), [1] tiny_fontsize (polyzymd.compare.config.PlotTheme attribute) TIP3P (polyzymd.config.schema.WaterModel attribute) TIP4P (polyzymd.config.schema.WaterModel attribute) TIP4PEW (polyzymd.config.schema.WaterModel attribute) title_fontsize (polyzymd.compare.config.PlotTheme attribute) title_fontweight (polyzymd.compare.config.PlotTheme attribute) to_analysis_yaml_dict() (polyzymd.compare.config.AnalysisSettingsContainer method) (polyzymd.compare.settings.BindingFreeEnergyAnalysisSettings method) (polyzymd.compare.settings.CatalyticTriadAnalysisSettings method) (polyzymd.compare.settings.ContactsAnalysisSettings method) (polyzymd.compare.settings.DistancePairSettings method) (polyzymd.compare.settings.DistancesAnalysisSettings method) (polyzymd.compare.settings.ExposureAnalysisSettings method) (polyzymd.compare.settings.PolymerAffinityScoreSettings method) (polyzymd.compare.settings.RMSFAnalysisSettings method) (polyzymd.compare.settings.SecondaryStructureAnalysisSettings method) (polyzymd.compare.settings.TriadPairSettings method)

to_dict() (polyzymd.compare.statistics.ANOVAResult method) (polyzymd.compare.statistics.EffectSize method) (polyzymd.compare.statistics.TTestResult method) (polyzymd.core.parameters.BarostatParameters method) (polyzymd.core.parameters.IntegratorParameters method) (polyzymd.core.parameters.ReporterParameters method) (polyzymd.core.parameters.SimulationParameters method) (polyzymd.core.parameters.SimulationPhase method) (polyzymd.core.parameters.ThermoParameters method) (polyzymd.core.parameters.ThermostatParameters method) to_json() (polyzymd.core.parameters.SimulationParameters method) to_signac_statepoint() (polyzymd.config.schema.SimulationConfig method) to_yaml() (polyzymd.compare.config.ComparisonConfig method) (polyzymd.config.schema.SimulationConfig method) tolerance (polyzymd.config.schema.BoxConfig attribute), [1] (polyzymd.config.schema.PolymerPackingConfig attribute), [1] top_residues (polyzymd.compare.settings.ContactsComparisonSettings attribute), [1] topology (polyzymd.builders.enzyme.EnzymeBuilder property) total_equilibration_duration (polyzymd.config.schema.SimulationPhasesConfig property) total_equilibration_samples (polyzymd.config.schema.SimulationPhasesConfig property) total_n_contacts (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerTypeScore attribute), [1] total_production_time_ns (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] total_samples (polyzymd.workflow.daisy_chain.DaisyChainConfig attribute), [1] total_score (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerTypeScore attribute), [1] total_score_per_replicate (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerTypeScore attribute), [1] total_score_uncertainty (polyzymd.compare.results.polymer_affinity.AffinityScoreConditionSummary attribute), [1] (polyzymd.compare.results.polymer_affinity.PolymerTypeScore attribute), [1] total_solvent_molecules (polyzymd.builders.solvent.SolvationCounts property) total_steps (polyzymd.core.parameters.IntegratorParameters property) total_time (polyzymd.core.parameters.IntegratorParameters attribute), [1] traj_ext (polyzymd.core.parameters.ReporterParameters attribute), [1] trajectory_format (polyzymd.config.schema.OutputConfig attribute), [1] transient_lower (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] transient_upper (polyzymd.compare.settings.ExposureAnalysisSettings attribute), [1] TriadComparator (class in polyzymd.compare.comparators.triad) TriadPairSettings (class in polyzymd.compare.settings) TriadPlotSettings (class in polyzymd.compare.config) TRUNCATED_OCTAHEDRON (polyzymd.config.schema.BoxShape attribute) TTestResult (class in polyzymd.compare.statistics) type (polyzymd.config.schema.PrimarySolventConfig attribute), [1] (polyzymd.config.schema.RestraintConfig attribute), [1] type_prefix (polyzymd.config.schema.PolymerConfig attribute), [1]

U

units (polyzymd.compare.results.binding_free_energy.BindingFreeEnergyResult attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyConditionSummary attribute), [1] (polyzymd.compare.results.binding_free_energy.FreeEnergyEntry attribute), [1] (polyzymd.compare.settings.BindingFreeEnergyAnalysisSettings attribute), [1]

update_frequency (polyzymd.core.parameters.BarostatParameters attribute), [1] UPPER_WALL (polyzymd.config.schema.RestraintType attribute) (polyzymd.core.restraints.RestraintType attribute) use_kde (polyzymd.compare.config.DistancesPlotSettings attribute), [1] use_pbc (polyzymd.compare.settings.DistancesAnalysisSettings attribute), [1]

V

validate() (polyzymd.builders.enzyme.EnzymeBuilder method) (polyzymd.builders.polymer.PolymerBuilder method) (polyzymd.builders.solvent.SolventBuilder method) (polyzymd.builders.substrate.SubstrateBuilder method) validate_alignment_frame_required() (polyzymd.compare.settings.DistancesAnalysisSettings method) validate_alignment_mode() (polyzymd.compare.settings.DistancesAnalysisSettings class method) validate_and_populate() (polyzymd.config.schema.CoSolventSpec method) validate_comparison_coverage() (polyzymd.compare.config.ComparisonConfig method) validate_config() (polyzymd.compare.config.ComparisonConfig method) validate_enrichment_normalization() (polyzymd.compare.settings.ContactsAnalysisSettings class method) validate_ensemble_barostat() (polyzymd.config.schema.SimulationPhaseConfig method) validate_equilibration_mode() (polyzymd.config.schema.SimulationPhasesConfig method) validate_fdr_alpha() (polyzymd.compare.settings.ContactsComparisonSettings class method) validate_generation_mode_requirements() (polyzymd.config.schema.PolymerConfig method) validate_group_name() (polyzymd.config.schema.PositionRestraintConfig class method)

validate_grouping() (polyzymd.compare.settings.ContactsAnalysisSettings class method) validate_npt_barostat() (polyzymd.config.schema.EquilibrationStageConfig method) validate_pairs() (polyzymd.compare.settings.CatalyticTriadAnalysisSettings class method) (polyzymd.compare.settings.DistancesAnalysisSettings class method) validate_pdb_path() (polyzymd.config.schema.EnzymeConfig class method) validate_probabilities_sum_to_one() (polyzymd.config.schema.PolymerConfig method) validate_protein_partitions() (polyzymd.compare.settings.ContactsAnalysisSettings method) validate_reference_mode() (polyzymd.compare.settings.RMSFAnalysisSettings class method) validate_reference_params() (polyzymd.compare.settings.RMSFAnalysisSettings method) validate_replicate_range() (in module polyzymd.workflow.slurm) validate_sdf_path() (polyzymd.config.schema.SubstrateConfig class method) validate_temperature_mode() (polyzymd.config.schema.EquilibrationStageConfig method) validate_units() (polyzymd.compare.settings.BindingFreeEnergyAnalysisSettings class method) validate_volume_fractions() (polyzymd.config.schema.SolventConfig method) volume_fraction (polyzymd.builders.solvent.CoSolvent attribute), [1] (polyzymd.config.schema.CoSolventSpec attribute), [1]

W

warn_deprecated_segments() (polyzymd.config.schema.SimulationPhasesConfig class method) water (polyzymd.builders.solvent.SolvationCounts attribute), [1] (polyzymd.config.schema.ForceFieldConfig attribute) water_model (polyzymd.builders.solvent.SolventComposition attribute), [1]

water_volume_fraction (polyzymd.builders.solvent.SolventComposition property) WaterModel (class in polyzymd.config.schema) working_dir (polyzymd.simulation.continuation.ContinuationManager property) (polyzymd.simulation.runner.SimulationRunner property) (polyzymd.workflow.slurm.JobContext property)