Index _ | A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | V _ __init__() (rnaglib.algorithms.Hasher method) (rnaglib.algorithms.SimFunctionNode method) (rnaglib.dataset.RNADataset method) (rnaglib.dataset_transforms.CDHitComputer method) (rnaglib.dataset_transforms.ClusterSplitter method) (rnaglib.dataset_transforms.Collater method) (rnaglib.dataset_transforms.DefaultBasePairLoader method) (rnaglib.dataset_transforms.DistanceComputer method) (rnaglib.dataset_transforms.DSTransform method) (rnaglib.dataset_transforms.EdgeLoaderGenerator method) (rnaglib.dataset_transforms.NameSplitter method) (rnaglib.dataset_transforms.RandomSplitter method) (rnaglib.dataset_transforms.RedundancyRemover method) (rnaglib.dataset_transforms.Splitter method) (rnaglib.dataset_transforms.StructureDistanceComputer method) (rnaglib.tasks.BenchmarkBindingSite method) (rnaglib.tasks.BindingSite method) (rnaglib.tasks.ChemicalModification method) (rnaglib.tasks.ClassificationTask method) (rnaglib.tasks.gRNAde method) (rnaglib.tasks.InverseFolding method) (rnaglib.tasks.LigandIdentification method) (rnaglib.tasks.ProteinBindingSite method) (rnaglib.tasks.ResidueClassificationTask method) (rnaglib.tasks.RNAClassificationTask method) (rnaglib.tasks.RNAGo method) (rnaglib.tasks.Task method) (rnaglib.tasks.VirtualScreening method) (rnaglib.transforms.AnnotationTransform method) (rnaglib.transforms.AnnotatorFromDict method) (rnaglib.transforms.BindingSiteAnnotator method) (rnaglib.transforms.ChainFilter method) (rnaglib.transforms.ChainNameTransform method) (rnaglib.transforms.ChainSplitTransform method) (rnaglib.transforms.CifMetadata method) (rnaglib.transforms.ConnectedComponentPartition method) (rnaglib.transforms.DummyAnnotator method) (rnaglib.transforms.FeaturesComputer method) (rnaglib.transforms.FilterTransform method) (rnaglib.transforms.GraphRepresentation method) (rnaglib.transforms.NameFilter method) (rnaglib.transforms.PartitionFromDict method) (rnaglib.transforms.PartitionTransform method) (rnaglib.transforms.PDBIDNameTransform method) (rnaglib.transforms.PointCloudRepresentation method) (rnaglib.transforms.RBPTransform method) (rnaglib.transforms.Representation method) (rnaglib.transforms.ResidueAttributeFilter method) (rnaglib.transforms.ResidueNameFilter method) (rnaglib.transforms.ResolutionFilter method) (rnaglib.transforms.RfamTransform method) (rnaglib.transforms.RibosomalFilter method) (rnaglib.transforms.RingRepresentation method) (rnaglib.transforms.RNAAttributeFilter method) (rnaglib.transforms.RNAFMTransform method) (rnaglib.transforms.SecondaryStructureTransform method) (rnaglib.transforms.SequenceRepresentation method) (rnaglib.transforms.SizeFilter method) (rnaglib.transforms.SmallMoleculeBindingTransform method) (rnaglib.transforms.Transform method) (rnaglib.transforms.VoxelRepresentation method) A annotate_all() (in module rnaglib.prepare_data) AnnotationTransform (class in rnaglib.transforms) AnnotatorFromDict (class in rnaglib.transforms) B BasePairPredictor (class in rnaglib.learning.models) BenchmarkBindingSite (class in rnaglib.tasks) bfs() (in module rnaglib.algorithms) BindingSite (class in rnaglib.tasks) BindingSiteAnnotator (class in rnaglib.transforms) build_graph_from_cif() (in module rnaglib.prepare_data) build_iso() (in module rnaglib.config.build_iso_mat) build_model() (rnaglib.learning.models.Classifier method) (rnaglib.learning.models.Embedder method) C cdhit_wrapper() (in module rnaglib.utils) CDHitComputer (class in rnaglib.dataset_transforms) ChainFilter (class in rnaglib.transforms) ChainNameTransform (class in rnaglib.transforms) ChainSplitTransform (class in rnaglib.transforms) ChemicalModification (class in rnaglib.tasks) chop_all() (in module rnaglib.prepare_data) cif_remove_residues() (in module rnaglib.utils) CifMetadata (class in rnaglib.transforms) circular_layout() (in module rnaglib.drawing.rna_layout) ClassificationTask (class in rnaglib.tasks) Classifier (class in rnaglib.learning.models) ClusterSplitter (class in rnaglib.dataset_transforms) Collater (class in rnaglib.dataset_transforms) ConnectedComponentPartition (class in rnaglib.transforms) current_device (rnaglib.learning.models.Classifier property) (rnaglib.learning.models.Embedder property) D DefaultBasePairLoader (class in rnaglib.dataset_transforms) DistanceComputer (class in rnaglib.dataset_transforms) DotPredictor (class in rnaglib.learning.models) download_graphs() (in module rnaglib.utils) DSTransform (class in rnaglib.dataset_transforms) DummyAnnotator (class in rnaglib.transforms) dump_json() (in module rnaglib.utils) E EdgeLoaderGenerator (class in rnaglib.dataset_transforms) Embedder (class in rnaglib.learning.models) extract_graphlet() (in module rnaglib.algorithms) F FeaturesComputer (class in rnaglib.transforms) FilterTransform (class in rnaglib.transforms) forward() (rnaglib.learning.models.BasePairPredictor method) (rnaglib.learning.models.Classifier method) (rnaglib.learning.models.DotPredictor method) (rnaglib.learning.models.Embedder method) fr3d_to_graph() (in module rnaglib.prepare_data) G ged() (in module rnaglib.algorithms) get_loader() (in module rnaglib.dataset_transforms) get_undirected_iso() (in module rnaglib.config.build_iso_mat) GraphRepresentation (class in rnaglib.transforms) gRNAde (class in rnaglib.tasks) H Hasher (class in rnaglib.algorithms) I InverseFolding (class in rnaglib.tasks) L LigandIdentification (class in rnaglib.tasks) load_graph() (in module rnaglib.utils) load_json() (in module rnaglib.utils) locarna_wrapper() (in module rnaglib.utils) M make_label() (in module rnaglib.drawing.rna_draw) module rnaglib.algorithms rnaglib.config.build_iso_mat rnaglib.dataset rnaglib.dataset_transforms rnaglib.drawing.rna_draw rnaglib.drawing.rna_layout rnaglib.learning.learn rnaglib.learning.models rnaglib.prepare_data rnaglib.tasks rnaglib.transforms rnaglib.utils N NameFilter (class in rnaglib.transforms) NameSplitter (class in rnaglib.dataset_transforms) P PartitionFromDict (class in rnaglib.transforms) PartitionTransform (class in rnaglib.transforms) PDBIDNameTransform (class in rnaglib.transforms) PointCloudRepresentation (class in rnaglib.transforms) pretrain_unsupervised() (in module rnaglib.learning.learn) process_axis() (in module rnaglib.drawing.rna_draw) ProteinBindingSite (class in rnaglib.tasks) R RandomSplitter (class in rnaglib.dataset_transforms) RBPTransform (class in rnaglib.transforms) RedundancyRemover (class in rnaglib.dataset_transforms) Representation (class in rnaglib.transforms) rescale_layout() (in module rnaglib.drawing.rna_layout) ResidueAttributeFilter (class in rnaglib.transforms) ResidueClassificationTask (class in rnaglib.tasks) ResidueNameFilter (class in rnaglib.transforms) ResolutionFilter (class in rnaglib.transforms) RfamTransform (class in rnaglib.transforms) RibosomalFilter (class in rnaglib.transforms) RingRepresentation (class in rnaglib.transforms) rna_align_wrapper() (in module rnaglib.utils) rna_draw() (in module rnaglib.drawing.rna_draw) rna_draw_grid() (in module rnaglib.drawing.rna_draw) rna_draw_pair() (in module rnaglib.drawing.rna_draw) rna_from_pdbid() (in module rnaglib.dataset) RNAAttributeFilter (class in rnaglib.transforms) RNAClassificationTask (class in rnaglib.tasks) RNADataset (class in rnaglib.dataset) RNAFMTransform (class in rnaglib.transforms) rnaglib.algorithms module rnaglib.config.build_iso_mat module rnaglib.dataset module rnaglib.dataset_transforms module rnaglib.drawing.rna_draw module rnaglib.drawing.rna_layout module rnaglib.learning.learn module rnaglib.learning.models module rnaglib.prepare_data module rnaglib.tasks module rnaglib.transforms module rnaglib.utils module RNAGo (class in rnaglib.tasks) S SecondaryStructureTransform (class in rnaglib.transforms) SequenceRepresentation (class in rnaglib.transforms) SimFunctionNode (class in rnaglib.algorithms) SizeFilter (class in rnaglib.transforms) SmallMoleculeBindingTransform (class in rnaglib.transforms) Splitter (class in rnaglib.dataset_transforms) StructureDistanceComputer (class in rnaglib.dataset_transforms) T Task (class in rnaglib.tasks) train_linkpred() (in module rnaglib.learning.learn) train_supervised() (in module rnaglib.learning.learn) Transform (class in rnaglib.transforms) V VirtualScreening (class in rnaglib.tasks) VoxelRepresentation (class in rnaglib.transforms)