API reference

Base classes and utilities

• Benchmark
  • Benchmark
  • BenchmarkResult
  • ModelOutput
• I/O of model outputs and benchmark results
  • write_benchmark_result_to_disk
  • load_benchmark_result_from_disk
  • load_benchmark_results_from_disk
  • write_scores_to_disk
  • load_score_from_disk
  • load_scores_from_disk
  • write_model_output_to_disk
  • load_model_output_from_disk
• Run Mode
  • RunMode
• Scoring
  • compute_metric_score
  • compute_benchmark_score
• Trajectory Helpers
  • create_mdtraj_trajectory_from_simulation_state
  • create_ase_trajectory_from_simulation_state
  • create_mdtraj_trajectory_from_positions
• Inference and simulation helpers
  • run_inference
  • get_simulation_engine
  • run_simulation
  • ASESimulationEngineWithCalculator
• Molecular Liquids Helpers
  • compute_densities
  • average_equilibrated_density
  • run_water_npt_simulation
  • run_solvent_npt_simulations
  • get_solvent_system_names
• UI page wrapper
  • UIPageWrapper

Benchmark implementations

• Conformer Selection
  • ConformerSelectionBenchmark
  • ConformerSelectionResult
  • ConformerSelectionMoleculeResult
  • ConformerSelectionModelOutput
  • ConformerSelectionMoleculeModelOutput
• Dihedral Scan
  • DihedralScanBenchmark
  • DihedralScanResult
  • DihedralScanFragmentResult
  • DihedralScanModelOutput
  • FragmentModelOutput
• Noncovalent Interactions
  • NoncovalentInteractionsBenchmark
  • NoncovalentInteractionsResult
  • NoncovalentInteractionsSystemResult
  • NoncovalentInteractionsModelOutput
  • NoncovalentInteractionsSystemModelOutput
• Tautomers
  • TautomersBenchmark
  • TautomersResult
  • TautomersMoleculeResult
  • TautomersModelOutput
• Ring planarity
  • RingPlanarityBenchmark
  • RingPlanarityResult
  • RingPlanarityMoleculeResult
  • RingPlanarityModelOutput
• Reference Geometry Stability
  • ReferenceGeometryStabilityBenchmark
  • ReferenceGeometryStabilityResult
  • ReferenceGeometryStabilityDatasetResult
  • ReferenceGeometryStabilityModelOutput
  • MoleculeModelOutput
• Bond length distribution
  • BondLengthDistributionBenchmark
  • BondLengthDistributionResult
  • BondLengthDistributionMoleculeResult
  • BondLengthDistributionModelOutput
  • MoleculeModelOutput
• Reactivity
  • ReactivityBenchmark
  • ReactivityResult
  • ReactivityModelOutput
• Nudged Elastic Band
  • NudgedElasticBandBenchmark
  • NEBResult
  • NEBModelOutput
• Water Radial Distribution
  • WaterRadialDistributionBenchmark
  • WaterRadialDistributionResult
  • WaterRadialDistributionModelOutput
• Solvent radial distribution
  • SolventRadialDistributionBenchmark
  • SolventRadialDistributionResult
  • SolventRadialDistributionStructureResult
  • SolventRadialDistributionModelOutput
• Water Density
  • WaterDensityBenchmark
  • WaterDensityResult
  • WaterDensityModelOutput
• Solvent Density
  • SolventDensityBenchmark
  • SolventDensityResult
  • SolventDensityStructureResult
  • SolventDensityModelOutput
• Folding Stability
  • FoldingStabilityBenchmark
  • FoldingStabilityResult
  • FoldingStabilityMoleculeResult
  • FoldingStabilityModelOutput
• Sampling
  • SamplingBenchmark
  • SamplingResult
  • SamplingSystemResult
  • SamplingModelOutput
  • ResidueTypeBackbone
  • ResidueTypeSidechain
• Stability
  • StabilityBenchmark
  • StabilityResult
  • StabilityStructureResult
  • StabilityModelOutput
• NVE energy conservation
  • NVEEnergyConservationBenchmark
  • NVEEnergyConservationResult
  • NVEStructureResult
  • NVEEnergyConservationModelOutput
• Inference Speed
  • InferenceSpeedBenchmark
  • InferenceSpeedResult
  • InferenceSpeedStructureResult
  • MDBackendResult
  • InferenceSpeedModelOutput