Index _ | A | B | C | D | E | F | G | H | L | M | N | O | P | R | S | T | U | W _ __init__() (mlipaudit.benchmark.Benchmark method) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark method) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark method) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark method) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark method) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark method) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark method) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark method) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark method) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark method) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark method) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark method) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark method) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark method) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark method) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark method) A abs_deviation (mlipaudit.benchmarks.tautomers.tautomers.TautomersMoleculeResult attribute) analyze() (mlipaudit.benchmark.Benchmark method) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark method) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark method) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark method) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark method) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark method) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark method) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark method) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark method) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark method) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark method) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark method) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark method) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark method) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark method) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark method) ASESimulationEngineWithCalculator (class in mlipaudit.utils.simulation) average_episode_time (mlipaudit.benchmarks.scaling.scaling.ScalingStructureResult attribute) average_episode_times (mlipaudit.benchmarks.scaling.scaling.ScalingModelOutput attribute) average_step_time (mlipaudit.benchmarks.scaling.scaling.ScalingStructureResult attribute) avg_deviation (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionMoleculeResult attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionResult attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityMoleculeResult attribute) avg_mae (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) avg_match (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) avg_peak_deviation (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionResult attribute) avg_pearson_p (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) avg_pearson_r (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) avg_rmsd (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityDatasetResult attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityResult attribute) avg_rmse (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) avg_tm_score (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) B barrier_height_error (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) Benchmark (class in mlipaudit.benchmark) BenchmarkResult (class in mlipaudit.benchmark) BondLengthDistributionBenchmark (class in mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution) BondLengthDistributionModelOutput (class in mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution) BondLengthDistributionMoleculeResult (class in mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution) BondLengthDistributionResult (class in mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution) C category (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark attribute) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark attribute) chi1 (mlipaudit.benchmarks.sampling.sampling.ResidueTypeSidechain attribute) chi2 (mlipaudit.benchmarks.sampling.sampling.ResidueTypeSidechain attribute) chi3 (mlipaudit.benchmarks.sampling.sampling.ResidueTypeSidechain attribute) chi4 (mlipaudit.benchmarks.sampling.sampling.ResidueTypeSidechain attribute) chi5 (mlipaudit.benchmarks.sampling.sampling.ResidueTypeSidechain attribute) compute_benchmark_score() (in module mlipaudit.scoring) compute_metric_score() (in module mlipaudit.scoring) ConformerSelectionBenchmark (class in mlipaudit.benchmarks.conformer_selection.conformer_selection) ConformerSelectionModelOutput (class in mlipaudit.benchmarks.conformer_selection.conformer_selection) ConformerSelectionMoleculeModelOutput (class in mlipaudit.benchmarks.conformer_selection.conformer_selection) ConformerSelectionMoleculeResult (class in mlipaudit.benchmarks.conformer_selection.conformer_selection) ConformerSelectionResult (class in mlipaudit.benchmarks.conformer_selection.conformer_selection) convergence_rate (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NEBResult attribute) create_ase_trajectory_from_simulation_state() (in module mlipaudit.utils.trajectory_helpers) create_mdtraj_trajectory_from_positions() (in module mlipaudit.utils.trajectory_helpers) create_mdtraj_trajectory_from_simulation_state() (in module mlipaudit.utils.trajectory_helpers) D dataset (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) description (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) DEV (mlipaudit.run_mode.RunMode attribute) deviation (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) deviation_trajectory (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionMoleculeResult attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityMoleculeResult attribute) DihedralScanBenchmark (class in mlipaudit.benchmarks.dihedral_scan.dihedral_scan) DihedralScanFragmentResult (class in mlipaudit.benchmarks.dihedral_scan.dihedral_scan) DihedralScanModelOutput (class in mlipaudit.benchmarks.dihedral_scan.dihedral_scan) DihedralScanResult (class in mlipaudit.benchmarks.dihedral_scan.dihedral_scan) distance_profile (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) drift_frame (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) E energy_predictions (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.FragmentModelOutput attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityModelOutput attribute) energy_profile (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemModelOutput attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) exploded_frame (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) exploded_systems (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) F failed (mlipaudit.benchmark.BenchmarkResult attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionMoleculeResult attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionResult attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.MoleculeModelOutput attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeModelOutput attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.FragmentModelOutput attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NEBResult attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.MoleculeModelOutput attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityDatasetResult attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityResult attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityMoleculeResult attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingStructureResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersMoleculeResult attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionModelOutput attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) failed_reactions (mlipaudit.benchmarks.reactivity.reactivity.ReactivityModelOutput attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) failed_structures (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsModelOutput attribute) FAST (mlipaudit.run_mode.RunMode attribute) first_solvent_peak (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) FoldingStabilityBenchmark (class in mlipaudit.benchmarks.folding_stability.folding_stability) FoldingStabilityModelOutput (class in mlipaudit.benchmarks.folding_stability.folding_stability) FoldingStabilityMoleculeResult (class in mlipaudit.benchmarks.folding_stability.folding_stability) FoldingStabilityResult (class in mlipaudit.benchmarks.folding_stability.folding_stability) fragment_name (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.FragmentModelOutput attribute) FragmentModelOutput (class in mlipaudit.benchmarks.dihedral_scan.dihedral_scan) fragments (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanModelOutput attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) G get_benchmark_class() (mlipaudit.ui.page_wrapper.UIPageWrapper class method) get_page_func() (mlipaudit.ui.page_wrapper.UIPageWrapper class method) get_simulation_engine() (in module mlipaudit.utils.simulation) group (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) H hellinger_distance_backbone_dihedrals (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) hellinger_distance_backbone_total (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) hellinger_distance_sidechain_dihedrals (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) hellinger_distance_sidechain_total (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) L load_benchmark_result_from_disk() (in module mlipaudit.io) load_benchmark_results_from_disk() (in module mlipaudit.io) load_model_output_from_disk() (in module mlipaudit.io) load_score_from_disk() (in module mlipaudit.io) load_scores_from_disk() (in module mlipaudit.io) M mae (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) mae_activation_energy (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) mae_barrier_height (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) mae_deviation (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityResult attribute) mae_enthalpy_of_reaction (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) mae_interaction_energy_all (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) mae_interaction_energy_datasets (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) mae_interaction_energy_subsets (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) match_secondary_structure (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) max_abs_deviation_radius_of_gyration (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) max_tm_score (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) min_rmsd (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) mlip_interaction_energy (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) mlipaudit.benchmark module mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution module mlipaudit.benchmarks.conformer_selection.conformer_selection module mlipaudit.benchmarks.dihedral_scan.dihedral_scan module mlipaudit.benchmarks.folding_stability.folding_stability module mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions module mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band module mlipaudit.benchmarks.reactivity.reactivity module mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability module mlipaudit.benchmarks.ring_planarity.ring_planarity module mlipaudit.benchmarks.sampling.sampling module mlipaudit.benchmarks.scaling.scaling module mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution module mlipaudit.benchmarks.stability.stability module mlipaudit.benchmarks.tautomers.tautomers module mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution module mlipaudit.io module mlipaudit.run_mode module mlipaudit.scoring module mlipaudit.ui.page_wrapper module mlipaudit.utils.inference module mlipaudit.utils.simulation module mlipaudit.utils.trajectory_helpers module model_output_class (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark attribute) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark attribute) ModelOutput (class in mlipaudit.benchmark) module mlipaudit.benchmark mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution mlipaudit.benchmarks.conformer_selection.conformer_selection mlipaudit.benchmarks.dihedral_scan.dihedral_scan mlipaudit.benchmarks.folding_stability.folding_stability mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band mlipaudit.benchmarks.reactivity.reactivity mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability mlipaudit.benchmarks.ring_planarity.ring_planarity mlipaudit.benchmarks.sampling.sampling mlipaudit.benchmarks.scaling.scaling mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution mlipaudit.benchmarks.stability.stability mlipaudit.benchmarks.tautomers.tautomers mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution mlipaudit.io mlipaudit.run_mode mlipaudit.scoring mlipaudit.ui.page_wrapper mlipaudit.utils.inference mlipaudit.utils.simulation mlipaudit.utils.trajectory_helpers src.mlipaudit molecule_name (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionMoleculeResult attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.MoleculeModelOutput attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeModelOutput attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.MoleculeModelOutput attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityMoleculeResult attribute) MoleculeModelOutput (class in mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution) (class in mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability) molecules (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionModelOutput attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionResult attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionModelOutput attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionResult attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityModelOutput attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityResult attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersResult attribute) N n_skipped_unallowed_elements (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsModelOutput attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) name (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark attribute) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark attribute) NEBModelOutput (class in mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band) NEBResult (class in mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band) NoncovalentInteractionsBenchmark (class in mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions) NoncovalentInteractionsModelOutput (class in mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions) NoncovalentInteractionsResult (class in mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions) NoncovalentInteractionsSystemModelOutput (class in mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions) NoncovalentInteractionsSystemResult (class in mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions) NudgedElasticBandBenchmark (class in mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band) num_atoms (mlipaudit.benchmarks.scaling.scaling.ScalingStructureResult attribute) num_bad_rmsds (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityDatasetResult attribute) num_episodes (mlipaudit.benchmarks.scaling.scaling.ScalingStructureResult attribute) num_exploded (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityDatasetResult attribute) num_failed (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionModelOutput attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionModelOutput attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanModelOutput attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityModelOutput attribute) num_frames (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) num_steps (mlipaudit.benchmarks.scaling.scaling.ScalingStructureResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) O openff_charged (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityModelOutput attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityResult attribute) openff_neutral (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityModelOutput attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityResult attribute) outliers_ratio_backbone_dihedrals (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) outliers_ratio_backbone_total (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) outliers_ratio_sidechain_dihedrals (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) outliers_ratio_sidechain_total (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) P peak_deviation (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) pearson_p (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) pearson_r (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) phi (mlipaudit.benchmarks.sampling.sampling.ResidueTypeBackbone attribute) predicted_energy_diff (mlipaudit.benchmarks.tautomers.tautomers.TautomersMoleculeResult attribute) predicted_energy_profile (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeModelOutput attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) predictions (mlipaudit.benchmarks.tautomers.tautomers.TautomersModelOutput attribute) psi (mlipaudit.benchmarks.sampling.sampling.ResidueTypeBackbone attribute) R radii (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) radius_of_gyration_deviation (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) radius_of_gyration_fluctuation (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) range_of_interest (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) rdf (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) reaction_ids (mlipaudit.benchmarks.reactivity.reactivity.ReactivityModelOutput attribute) reaction_results (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NEBResult attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) ReactivityBenchmark (class in mlipaudit.benchmarks.reactivity.reactivity) ReactivityModelOutput (class in mlipaudit.benchmarks.reactivity.reactivity) ReactivityResult (class in mlipaudit.benchmarks.reactivity.reactivity) ref_energy_diff (mlipaudit.benchmarks.tautomers.tautomers.TautomersMoleculeResult attribute) reference_energy_profile (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) reference_interaction_energy (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) ReferenceGeometryStabilityBenchmark (class in mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability) ReferenceGeometryStabilityDatasetResult (class in mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability) ReferenceGeometryStabilityModelOutput (class in mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability) ReferenceGeometryStabilityResult (class in mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability) required_elements (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark attribute) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark attribute) ResidueTypeBackbone (class in mlipaudit.benchmarks.sampling.sampling) ResidueTypeSidechain (class in mlipaudit.benchmarks.sampling.sampling) result_class (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark attribute) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark attribute) reusable_output_id (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark attribute) RingPlanarityBenchmark (class in mlipaudit.benchmarks.ring_planarity.ring_planarity) RingPlanarityModelOutput (class in mlipaudit.benchmarks.ring_planarity.ring_planarity) RingPlanarityMoleculeResult (class in mlipaudit.benchmarks.ring_planarity.ring_planarity) RingPlanarityResult (class in mlipaudit.benchmarks.ring_planarity.ring_planarity) rmsd_backbone_dihedrals (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) rmsd_backbone_total (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) rmsd_sidechain_dihedrals (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) rmsd_sidechain_total (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) rmsd_trajectory (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) rmsd_values (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityDatasetResult attribute) rmse (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanFragmentResult attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) rmse_activation_energy (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) rmse_enthalpy_of_reaction (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) rmse_interaction_energy_all (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) rmse_interaction_energy_datasets (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) rmse_interaction_energy_subsets (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) run_inference() (in module mlipaudit.utils.inference) run_model() (mlipaudit.benchmark.Benchmark method) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark method) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark method) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark method) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark method) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark method) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark method) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark method) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark method) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark method) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark method) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark method) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark method) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark method) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark method) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark method) run_simulation() (in module mlipaudit.utils.simulation) RunMode (class in mlipaudit.run_mode) S SamplingBenchmark (class in mlipaudit.benchmarks.sampling.sampling) SamplingModelOutput (class in mlipaudit.benchmarks.sampling.sampling) SamplingResult (class in mlipaudit.benchmarks.sampling.sampling) SamplingSystemResult (class in mlipaudit.benchmarks.sampling.sampling) ScalingBenchmark (class in mlipaudit.benchmarks.scaling.scaling) ScalingModelOutput (class in mlipaudit.benchmarks.scaling.scaling) ScalingResult (class in mlipaudit.benchmarks.scaling.scaling) ScalingStructureResult (class in mlipaudit.benchmarks.scaling.scaling) score (mlipaudit.benchmark.BenchmarkResult attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionResult attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanResult attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityResult attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NEBResult attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityResult attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityResult attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersResult attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionResult attribute) simulation_state (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.MoleculeModelOutput attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.MoleculeModelOutput attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionModelOutput attribute) simulation_states (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityModelOutput attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NEBModelOutput attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingModelOutput attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingModelOutput attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionModelOutput attribute) (mlipaudit.benchmarks.stability.stability.StabilityModelOutput attribute) skip_if_elements_missing (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution.BondLengthDistributionBenchmark attribute) (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionBenchmark attribute) (mlipaudit.benchmarks.dihedral_scan.dihedral_scan.DihedralScanBenchmark attribute) (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.reactivity.reactivity.ReactivityBenchmark attribute) (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityBenchmark attribute) (mlipaudit.benchmarks.ring_planarity.ring_planarity.RingPlanarityBenchmark attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingBenchmark attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingBenchmark attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark attribute) (mlipaudit.benchmarks.stability.stability.StabilityBenchmark attribute) (mlipaudit.benchmarks.tautomers.tautomers.TautomersBenchmark attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark attribute) skipped_structures (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsModelOutput attribute) SolventRadialDistributionBenchmark (class in mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution) SolventRadialDistributionModelOutput (class in mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution) SolventRadialDistributionResult (class in mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution) SolventRadialDistributionStructureResult (class in mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution) spearman_correlation (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) spearman_p_value (mlipaudit.benchmarks.conformer_selection.conformer_selection.ConformerSelectionMoleculeResult attribute) src.mlipaudit module StabilityBenchmark (class in mlipaudit.benchmarks.stability.stability) StabilityModelOutput (class in mlipaudit.benchmarks.stability.stability) StabilityResult (class in mlipaudit.benchmarks.stability.stability) StabilityStructureResult (class in mlipaudit.benchmarks.stability.stability) STANDARD (mlipaudit.run_mode.RunMode attribute) structure_id (mlipaudit.benchmarks.tautomers.tautomers.TautomersMoleculeResult attribute) structure_ids (mlipaudit.benchmarks.tautomers.tautomers.TautomersModelOutput attribute) structure_name (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingStructureResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) structure_names (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityModelOutput attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingModelOutput attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingModelOutput attribute) (mlipaudit.benchmarks.scaling.scaling.ScalingResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionModelOutput attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityModelOutput attribute) structure_results (mlipaudit.benchmarks.stability.stability.StabilityResult attribute) structures (mlipaudit.benchmarks.scaling.scaling.ScalingResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionResult attribute) system_id (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemModelOutput attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) systems (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsModelOutput attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingResult attribute) T TautomersBenchmark (class in mlipaudit.benchmarks.tautomers.tautomers) TautomersModelOutput (class in mlipaudit.benchmarks.tautomers.tautomers) TautomersMoleculeResult (class in mlipaudit.benchmarks.tautomers.tautomers) TautomersResult (class in mlipaudit.benchmarks.tautomers.tautomers) tm_score_trajectory (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) U UIPageWrapper (class in mlipaudit.ui.page_wrapper) W WaterRadialDistributionBenchmark (class in mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution) WaterRadialDistributionModelOutput (class in mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution) WaterRadialDistributionResult (class in mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution) write_benchmark_result_to_disk() (in module mlipaudit.io) write_model_output_to_disk() (in module mlipaudit.io) write_scores_to_disk() (in module mlipaudit.io)