Index _ | A | B | C | D | E | F | G | H | I | K | 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.inference_speed.inference_speed.InferenceSpeedBenchmark method) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark method) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark method) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark 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.inference_speed.inference_speed.InferenceSpeedBenchmark method) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark method) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark method) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark method) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark method) ASESimulationEngineWithCalculator (class in mlipaudit.utils.simulation) average_density (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityStructureResult attribute) (mlipaudit.benchmarks.water_density.water_density.WaterDensityResult attribute) average_equilibrated_density() (in module mlipaudit.utils.molecular_liquids) average_forward_time (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedStructureResult attribute) average_step_time (mlipaudit.benchmarks.inference_speed.inference_speed.MDBackendResult attribute) avg_density_deviation (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityResult 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.inference_speed.inference_speed.InferenceSpeedBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark 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_densities() (in module mlipaudit.utils.molecular_liquids) 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 data_dir (mlipaudit.benchmark.Benchmark property) data_name (mlipaudit.benchmark.Benchmark attribute) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityBenchmark attribute) (mlipaudit.benchmarks.water_density.water_density.WaterDensityBenchmark attribute) dataset (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) densities (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityStructureResult attribute) (mlipaudit.benchmarks.water_density.water_density.WaterDensityResult attribute) density_deviation (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityStructureResult attribute) (mlipaudit.benchmarks.water_density.water_density.WaterDensityResult attribute) description (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) (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) drift_slope_ev_per_ps (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) E energy_drift_ev (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) energy_drift_ratio (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) 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.inference_speed.inference_speed.InferenceSpeedStructureResult 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.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationResult attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult 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.solvent_density.solvent_density.SolventDensityResult attribute) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityStructureResult 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_density.water_density.WaterDensityModelOutput attribute) (mlipaudit.benchmarks.water_density.water_density.WaterDensityResult 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) forward_times (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedModelOutput attribute) (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedStructureResult attribute) 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) get_solvent_system_names() (in module mlipaudit.utils.molecular_liquids) graph_cutoff_angstrom (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedResult attribute) 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) I InferenceSpeedBenchmark (class in mlipaudit.benchmarks.inference_speed.inference_speed) InferenceSpeedModelOutput (class in mlipaudit.benchmarks.inference_speed.inference_speed) InferenceSpeedResult (class in mlipaudit.benchmarks.inference_speed.inference_speed) InferenceSpeedStructureResult (class in mlipaudit.benchmarks.inference_speed.inference_speed) intercept_ev (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) K kinetic_energies_ev (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationModelOutput attribute) kinetic_energy_std_ev (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult 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) md (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedStructureResult attribute) md_step_times (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedModelOutput attribute) MDBackendResult (class in mlipaudit.benchmarks.inference_speed.inference_speed) 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.inference_speed.inference_speed module mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions module mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band module mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation 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.solvent_density.solvent_density module mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution module mlipaudit.benchmarks.stability.stability module mlipaudit.benchmarks.tautomers.tautomers module mlipaudit.benchmarks.water_density.water_density 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.molecular_liquids 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.inference_speed.inference_speed.InferenceSpeedBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark 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.inference_speed.inference_speed mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation mlipaudit.benchmarks.reactivity.reactivity mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability mlipaudit.benchmarks.ring_planarity.ring_planarity mlipaudit.benchmarks.sampling.sampling mlipaudit.benchmarks.solvent_density.solvent_density mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution mlipaudit.benchmarks.stability.stability mlipaudit.benchmarks.tautomers.tautomers mlipaudit.benchmarks.water_density.water_density mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution mlipaudit.io mlipaudit.run_mode mlipaudit.scoring mlipaudit.ui.page_wrapper mlipaudit.utils.inference mlipaudit.utils.molecular_liquids 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) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationModelOutput attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationResult 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.inference_speed.inference_speed.InferenceSpeedBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark 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.inference_speed.inference_speed.InferenceSpeedStructureResult attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationModelOutput attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) num_bad_rmsds (mlipaudit.benchmarks.reference_geometry_stability.reference_geometry_stability.ReferenceGeometryStabilityDatasetResult attribute) num_episodes (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedStructureResult 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.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) num_steps (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedStructureResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityStructureResult attribute) NVEEnergyConservationBenchmark (class in mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation) NVEEnergyConservationModelOutput (class in mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation) NVEEnergyConservationResult (class in mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation) NVEStructureResult (class in mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation) 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) potential_energies_ev (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationModelOutput 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_density (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityStructureResult attribute) (mlipaudit.benchmarks.water_density.water_density.WaterDensityResult 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.inference_speed.inference_speed.InferenceSpeedBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark 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.inference_speed.inference_speed.InferenceSpeedBenchmark attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark attribute) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark 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) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityBenchmark attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark attribute) (mlipaudit.benchmarks.water_density.water_density.WaterDensityBenchmark attribute) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark 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.inference_speed.inference_speed.InferenceSpeedBenchmark method) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsBenchmark method) (mlipaudit.benchmarks.nudged_elastic_band.nudged_elastic_band.NudgedElasticBandBenchmark method) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.solvent_density.solvent_density.SolventDensityBenchmark 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_density.water_density.WaterDensityBenchmark method) (mlipaudit.benchmarks.water_radial_distribution.water_radial_distribution.WaterRadialDistributionBenchmark method) run_simulation() (in module mlipaudit.utils.simulation) run_solvent_npt_simulations() (in module mlipaudit.utils.molecular_liquids) run_water_npt_simulation() (in module mlipaudit.utils.molecular_liquids) 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) 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.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationResult attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult 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_density.solvent_density.SolventDensityResult attribute) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityStructureResult 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_density.water_density.WaterDensityResult 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_density.water_density.WaterDensityModelOutput 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.solvent_density.solvent_density.SolventDensityModelOutput 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.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationBenchmark 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.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 (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) skipped_structures (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsModelOutput attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationModelOutput attribute) SolventDensityBenchmark (class in mlipaudit.benchmarks.solvent_density.solvent_density) SolventDensityModelOutput (class in mlipaudit.benchmarks.solvent_density.solvent_density) SolventDensityResult (class in mlipaudit.benchmarks.solvent_density.solvent_density) SolventDensityStructureResult (class in mlipaudit.benchmarks.solvent_density.solvent_density) 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) step_time_samples (mlipaudit.benchmarks.inference_speed.inference_speed.MDBackendResult 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.inference_speed.inference_speed.InferenceSpeedStructureResult attribute) (mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions.NoncovalentInteractionsSystemResult attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingSystemResult attribute) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityStructureResult 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.inference_speed.inference_speed.InferenceSpeedModelOutput attribute) (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedResult attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationModelOutput attribute) (mlipaudit.benchmarks.sampling.sampling.SamplingModelOutput attribute) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityModelOutput attribute) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityResult 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.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationResult attribute) (mlipaudit.benchmarks.stability.stability.StabilityResult attribute) structures (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedResult attribute) (mlipaudit.benchmarks.solvent_density.solvent_density.SolventDensityResult attribute) (mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionResult attribute) system_class (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult 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) times_ps (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEEnergyConservationModelOutput attribute) (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) timestep_fs (mlipaudit.benchmarks.inference_speed.inference_speed.InferenceSpeedStructureResult attribute) tm_score_trajectory (mlipaudit.benchmarks.folding_stability.folding_stability.FoldingStabilityMoleculeResult attribute) total_drift_ev (mlipaudit.benchmarks.nve_energy_conservation.nve_energy_conservation.NVEStructureResult attribute) U UIPageWrapper (class in mlipaudit.ui.page_wrapper) W WaterDensityBenchmark (class in mlipaudit.benchmarks.water_density.water_density) WaterDensityModelOutput (class in mlipaudit.benchmarks.water_density.water_density) WaterDensityResult (class in mlipaudit.benchmarks.water_density.water_density) 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)