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rnaglib 0.0.1
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rnaglib 0.0.1

Get Started

  • Homepage
  • Installation
  • Quickstart
  • Citing

Tutorials

  • How to train a model
  • How to build your own task
  • Using 2.5D RNA graphs

Data Reference

  • What is an RNA 2.5D graph?
  • RNA Annotation Reference
  • How is the data built?
  • Available Benchmark Tasks

A peek under the hood

  • Overview
  • RNADataset
  • RNA Transforms
  • RNADataset Transforms
  • Task

Package Reference

  • Algorithms
    • rnaglib.algorithms.bfs
    • rnaglib.algorithms.ged
    • rnaglib.algorithms.SimFunctionNode
    • rnaglib.algorithms.Hasher
    • rnaglib.algorithms.extract_graphlet
  • Data preparation
  • Datasets
    • rnaglib.dataset.rna_from_pdbid
    • rnaglib.dataset.RNADataset
  • Dataset transforms
    • rnaglib.dataset_transforms.DSTransform
    • rnaglib.dataset_transforms.Splitter
    • rnaglib.dataset_transforms.DistanceComputer
    • rnaglib.dataset_transforms.RedundancyRemover
    • rnaglib.dataset_transforms.ClusterSplitter
    • rnaglib.dataset_transforms.RandomSplitter
    • rnaglib.dataset_transforms.NameSplitter
    • rnaglib.dataset_transforms.CDHitComputer
    • rnaglib.dataset_transforms.StructureDistanceComputer
    • rnaglib.dataset_transforms.Collater
    • rnaglib.dataset_transforms.get_loader
    • rnaglib.dataset_transforms.EdgeLoaderGenerator
    • rnaglib.dataset_transforms.DefaultBasePairLoader
  • Transforms
    • rnaglib.transforms.Transform
    • rnaglib.transforms.AnnotationTransform
    • rnaglib.transforms.RfamTransform
    • rnaglib.transforms.RNAFMTransform
    • rnaglib.transforms.PDBIDNameTransform
    • rnaglib.transforms.ChainNameTransform
    • rnaglib.transforms.SecondaryStructureTransform
    • rnaglib.transforms.SmallMoleculeBindingTransform
    • rnaglib.transforms.RBPTransform
    • rnaglib.transforms.AnnotatorFromDict
    • rnaglib.transforms.DummyAnnotator
    • rnaglib.transforms.CifMetadata
    • rnaglib.transforms.BindingSiteAnnotator
    • rnaglib.transforms.FilterTransform
    • rnaglib.transforms.SizeFilter
    • rnaglib.transforms.RNAAttributeFilter
    • rnaglib.transforms.ResidueAttributeFilter
    • rnaglib.transforms.ResidueNameFilter
    • rnaglib.transforms.RibosomalFilter
    • rnaglib.transforms.NameFilter
    • rnaglib.transforms.ChainFilter
    • rnaglib.transforms.ResolutionFilter
    • rnaglib.transforms.PartitionTransform
    • rnaglib.transforms.ChainSplitTransform
    • rnaglib.transforms.ConnectedComponentPartition
    • rnaglib.transforms.PartitionFromDict
    • rnaglib.transforms.Representation
    • rnaglib.transforms.SequenceRepresentation
    • rnaglib.transforms.GraphRepresentation
    • rnaglib.transforms.PointCloudRepresentation
    • rnaglib.transforms.VoxelRepresentation
    • rnaglib.transforms.RingRepresentation
    • rnaglib.transforms.FeaturesComputer
  • ML Tasks
    • rnaglib.tasks.Task
    • rnaglib.tasks.ClassificationTask
    • rnaglib.tasks.ResidueClassificationTask
    • rnaglib.tasks.RNAClassificationTask
    • rnaglib.tasks.RNAGo
    • rnaglib.tasks.BindingSite
    • rnaglib.tasks.BenchmarkBindingSite
    • rnaglib.tasks.ChemicalModification
    • rnaglib.tasks.ProteinBindingSite
    • rnaglib.tasks.InverseFolding
    • rnaglib.tasks.gRNAde
    • rnaglib.tasks.LigandIdentification
    • rnaglib.tasks.VirtualScreening
  • Visualization
  • Model Training
  • Utils
    • rnaglib.utils.load_graph
    • rnaglib.utils.download_graphs
    • rnaglib.utils.dump_json
    • rnaglib.utils.load_json
    • rnaglib.utils.cdhit_wrapper
    • rnaglib.utils.rna_align_wrapper
    • rnaglib.utils.locarna_wrapper
    • rnaglib.utils.cif_remove_residues
  • Configurations
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Copyright © 2021, Vincent Mallet et al.
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