Index

_

__init__() (bioverse.benchmark.Benchmark method) (bioverse.metrics.topk_recovery.TopkRecoveryMetric method) (bioverse.transforms.is_surface_residue.IsSurfaceResidue method)

A

Adapter (class in bioverse.adapter) AlphaFoldAdapter (class in bioverse.adapters.alpha_fold) AlphaFoldExclusionAdapter (class in bioverse.adapters.alpha_fold_exclusion) AlphaFoldInvBenchAdapter (class in bioverse.adapters.alpha_fold_inv_bench)

AresAdapter (class in bioverse.adapters.ares) Assets (class in bioverse.data) AuprcMetric (class in bioverse.metrics.auprc) AurocMetric (class in bioverse.metrics.auroc)

B

BackboneBondAngles (class in bioverse.transforms.backbone_bond_angles) BackboneEdgeRbf (class in bioverse.transforms.backbone_edge_rbf) BackboneNodeRbf (class in bioverse.transforms.backbone_node_rbf) BalancedBinaryAccuracyMetric (class in bioverse.metrics.balanced_binary_accuracy) BalancedMultiClassAccuracyMetric (class in bioverse.metrics.balanced_multi_class_accuracy) Batch (class in bioverse.data) BatchProxy (class in bioverse.data) Benchmark (class in bioverse.benchmark) BinaryAccuracyMetric (class in bioverse.metrics.binary_accuracy) bioverse.adapter module bioverse.benchmark module bioverse.data module bioverse.dataset module

bioverse.metric module bioverse.processor module bioverse.sampler module bioverse.task module bioverse.transform module bioverse.utilities.config module bioverse.utilities.io module BlosumScoreMetric (class in bioverse.metrics.blosum_score)

C

CifProcessor (class in bioverse.processors.cif) CoefficientOfDeterminationMetric (class in bioverse.metrics.coefficient_of_determination) Compose (class in bioverse.transform) ComposedDataset (class in bioverse.dataset)

compute() (bioverse.metrics.topk_recovery.TopkRecoveryMetric method) CoreAndSurfaceDistance (class in bioverse.transforms.core_and_surface_distance) CreateFeatureFromOthers (class in bioverse.transforms.create_feature_from_others) Curvature (class in bioverse.transforms.curvature)

D

Dataset (class in bioverse.dataset) DeduplicateAtoms (class in bioverse.transforms.deduplicate_atoms) Dihedrals (class in bioverse.transforms.dihedrals) download() (bioverse.adapter.Adapter method) (bioverse.adapters.alpha_fold.AlphaFoldAdapter class method) (bioverse.adapters.alpha_fold_exclusion.AlphaFoldExclusionAdapter class method) (bioverse.adapters.alpha_fold_inv_bench.AlphaFoldInvBenchAdapter class method) (bioverse.adapters.ares.AresAdapter class method) (bioverse.adapters.protein_gym.ProteinGymAdapter class method) (bioverse.adapters.protein_inv_bench.ProteinInvBenchAdapter class method) (bioverse.adapters.proteinshake.ProteinShakeAdapter class method) (bioverse.adapters.quantum_machines.QuantumMachinesAdapter class method) (bioverse.adapters.revised_molecular_dynamics.RevisedMolecularDynamicsAdapter class method) (bioverse.adapters.weng_docking.WengDockingAdapter class method)

E

EdgeLocalDirections (class in bioverse.transforms.edge_local_directions) EdgePosEmb (class in bioverse.transforms.edge_pos_emb)

EdgeVectors (class in bioverse.transforms.edge_vectors) EnrichmentFactorMetric (class in bioverse.metrics.enrichment_factor)

F

F1ScoreMetric (class in bioverse.metrics.f1_score) FilterResiduesByValue (class in bioverse.transforms.filter_residues_by_value)

FilterSequenceLength (class in bioverse.transforms.filter_sequence_length) FmaxMetric (class in bioverse.metrics.fmax) FrameSampler (class in bioverse.samplers.frame)

I

Identity (class in bioverse.transforms.identity) index() (bioverse.sampler.Sampler method) (bioverse.samplers.frame.FrameSampler method) (bioverse.samplers.interface_pair.InterfacePairSampler method) (bioverse.samplers.molecule.MoleculeSampler method) (bioverse.samplers.mutation.MutationSampler method) (bioverse.samplers.pairwise.PairwiseSampler method) (bioverse.samplers.residue.ResidueSampler method)

InterfacePairSampler (class in bioverse.samplers.interface_pair) InverseFoldingTask (class in bioverse.tasks.inverse_folding) IsSurfaceResidue (class in bioverse.transforms.is_surface_residue) IteratorWithLength (class in bioverse.utilities.io)

K

KnnGraph (class in bioverse.transforms.knn_graph)

L

LinearResidueGraph (class in bioverse.transforms.linear_residue_graph)

LocalReferenceFrames (class in bioverse.transforms.local_reference_frames) LRUCache (class in bioverse.utilities.io)

M

MacroPrecisionMetric (class in bioverse.metrics.macro_precision) MacroRecallMetric (class in bioverse.metrics.macro_recall) MaskedResiduePredictionTask (class in bioverse.tasks.masked_residue_prediction) MeanAbsoluteErrorMetric (class in bioverse.metrics.mean_absolute_error) MeanActiveRankMetric (class in bioverse.metrics.mean_active_rank) MeanAngularErrorMetric (class in bioverse.metrics.mean_angular_error) MeanSquaredErrorMetric (class in bioverse.metrics.mean_squared_error) Metric (class in bioverse.metric) module bioverse.adapter bioverse.benchmark bioverse.data bioverse.dataset bioverse.metric bioverse.processor bioverse.sampler bioverse.task bioverse.transform bioverse.utilities.config bioverse.utilities.io

MoleculeSampler (class in bioverse.samplers.molecule) MultiClassAccuracyMetric (class in bioverse.metrics.multi_class_accuracy) MultiLabelAccuracyMetric (class in bioverse.metrics.multi_label_accuracy) MultiMetric (class in bioverse.metric) MutationEffectPredictionTask (class in bioverse.tasks.mutation_effect_prediction) MutationSampler (class in bioverse.samplers.mutation)

N

NormalizeVector (class in bioverse.transforms.normalize_vector)

O

OneHotAtomFeatures (class in bioverse.transforms.one_hot_atom_features)

OneHotResidueFeatures (class in bioverse.transforms.one_hot_residue_features) Orientations (class in bioverse.transforms.orientations)

P

package() (bioverse.dataset.Dataset method) PairwisePropertyPredictionTask (class in bioverse.tasks.pairwise_property_prediction) PairwiseSampler (class in bioverse.samplers.pairwise) PdbProcessor (class in bioverse.processors.pdb) PearsonsRMetric (class in bioverse.metrics.pearsons_r) PerplexityMetric (class in bioverse.metrics.perplexity)

PrecisionMetric (class in bioverse.metrics.precision) Processor (class in bioverse.processor) PropertyPredictionTask (class in bioverse.tasks.property_prediction) ProteinGymAdapter (class in bioverse.adapters.protein_gym) ProteinInvBenchAdapter (class in bioverse.adapters.protein_inv_bench) ProteinShakeAdapter (class in bioverse.adapters.proteinshake)

Q

QuantumMachinesAdapter (class in bioverse.adapters.quantum_machines)

R

Rbf (class in bioverse.transforms.rbf) RecallMetric (class in bioverse.metrics.recall) RecoveryMetric (class in bioverse.metrics.recovery) RelativeEdgeFramePositions (class in bioverse.transforms.relative_edge_frame_positions) ResidueBackboneAtoms (class in bioverse.transforms.residue_backbone_atoms) ResidueFrames (class in bioverse.transforms.residue_frames)

ResidueLocalDirections (class in bioverse.transforms.residue_local_directions) ResiduePositions (class in bioverse.transforms.residue_positions) ResiduePseudoCb (class in bioverse.transforms.residue_pseudo_cb) ResidueSampler (class in bioverse.samplers.residue) Result (class in bioverse.metric) RevisedMolecularDynamicsAdapter (class in bioverse.adapters.revised_molecular_dynamics)

S

Sampler (class in bioverse.sampler) SceneSplit (class in bioverse.transforms.scene_split) Sidechains (class in bioverse.transforms.sidechains)

SpearmansRhoMetric (class in bioverse.metrics.spearmans_rho) Split (class in bioverse.data) Standardize (class in bioverse.transforms.standardize) StandardizePairwise (class in bioverse.transforms.standardize_pairwise)

T

Task (class in bioverse.task) TokenizeAtoms (class in bioverse.transforms.tokenize_atoms) TokenizeProperty (class in bioverse.transforms.tokenize_property)

TokenizeResidues (class in bioverse.transforms.tokenize_residues) TopKAccuracyMetric (class in bioverse.metrics.top_k_accuracy) TopkRecoveryMetric (class in bioverse.metrics.topk_recovery) Transform (class in bioverse.transform)

V

VirtualScreenTask (class in bioverse.tasks.virtual_screen)

W

WengDockingAdapter (class in bioverse.adapters.weng_docking)

X

XyzProcessor (class in bioverse.processors.xyz)