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296 lines
6.6 KiB
ReStructuredText
296 lines
6.6 KiB
ReStructuredText
.. _apidata:
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dgl.data
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=========
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.. currentmodule:: dgl.data
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Utils
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-----
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.. autosummary::
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:toctree: ../../generated/
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utils.get_download_dir
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utils.download
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utils.check_sha1
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utils.extract_archive
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utils.split_dataset
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utils.save_graphs
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utils.load_graphs
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utils.load_labels
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.. autoclass:: dgl.data.utils.Subset
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:members: __getitem__, __len__
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Dataset Classes
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---------------
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Stanford sentiment treebank dataset
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```````````````````````````````````
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For more information about the dataset, see `Sentiment Analysis <https://nlp.stanford.edu/sentiment/index.html>`__.
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.. autoclass:: SST
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:members: __getitem__, __len__
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Karate Club dataset
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```````````````````````````````````
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.. autoclass:: KarateClub
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:members: __getitem__, __len__
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Citation Network dataset
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```````````````````````````````````
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.. autoclass:: CitationGraphDataset
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:members: __getitem__, __len__
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Cora Citation Network dataset
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```````````````````````````````````
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.. autoclass:: CoraDataset
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:members: __getitem__, __len__
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CoraFull dataset
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```````````````````````````````````
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.. autoclass:: CoraFull
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:members: __getitem__, __len__
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Amazon Co-Purchase dataset
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```````````````````````````````````
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.. autoclass:: AmazonCoBuy
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:members: __getitem__, __len__
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Coauthor dataset
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```````````````````````````````````
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.. autoclass:: Coauthor
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:members: __getitem__, __len__
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BitcoinOTC dataset
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```````````````````````````````````
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.. autoclass:: BitcoinOTC
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:members: __getitem__, __len__
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ICEWS18 dataset
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```````````````````````````````````
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.. autoclass:: ICEWS18
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:members: __getitem__, __len__
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QM7b dataset
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```````````````````````````````````
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.. autoclass:: QM7b
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:members: __getitem__, __len__
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GDELT dataset
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```````````````````````````````````
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.. autoclass:: GDELT
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:members: __getitem__, __len__
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Mini graph classification dataset
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`````````````````````````````````
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.. autoclass:: MiniGCDataset
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:members: __getitem__, __len__, num_classes
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Graph kernel dataset
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````````````````````
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For more information about the dataset, see `Benchmark Data Sets for Graph Kernels <https://ls11-www.cs.tu-dortmund.de/staff/morris/graphkerneldatasets>`__.
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.. autoclass:: TUDataset
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:members: __getitem__, __len__
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Graph isomorphism network dataset
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```````````````````````````````````
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A compact subset of graph kernel dataset
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.. autoclass:: GINDataset
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:members: __getitem__, __len__
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Protein-Protein Interaction dataset
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```````````````````````````````````
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.. autoclass:: PPIDataset
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:members: __getitem__, __len__
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Molecular Graphs
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----------------
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To work on molecular graphs, make sure you have installed `RDKit 2018.09.3 <https://www.rdkit.org/docs/Install.html>`__.
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Data Loading and Processing Utils
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`````````````````````````````````
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We adapt several utilities for processing molecules from
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`DeepChem <https://github.com/deepchem/deepchem/blob/master/deepchem>`__.
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.. autosummary::
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:toctree: ../../generated/
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chem.add_hydrogens_to_mol
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chem.get_mol_3D_coordinates
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chem.load_molecule
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chem.multiprocess_load_molecules
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Featurization Utils for Single Molecule
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```````````````````````````````````````
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For the use of graph neural networks, we need to featurize nodes (atoms) and edges (bonds).
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General utils:
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.. autosummary::
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:toctree: ../../generated/
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chem.one_hot_encoding
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chem.ConcatFeaturizer
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chem.ConcatFeaturizer.__call__
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Utils for atom featurization:
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.. autosummary::
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:toctree: ../../generated/
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chem.atom_type_one_hot
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chem.atomic_number_one_hot
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chem.atomic_number
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chem.atom_degree_one_hot
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chem.atom_degree
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chem.atom_total_degree_one_hot
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chem.atom_total_degree
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chem.atom_implicit_valence_one_hot
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chem.atom_implicit_valence
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chem.atom_hybridization_one_hot
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chem.atom_total_num_H_one_hot
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chem.atom_total_num_H
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chem.atom_formal_charge_one_hot
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chem.atom_formal_charge
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chem.atom_num_radical_electrons_one_hot
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chem.atom_num_radical_electrons
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chem.atom_is_aromatic_one_hot
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chem.atom_is_aromatic
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chem.atom_chiral_tag_one_hot
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chem.atom_mass
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chem.BaseAtomFeaturizer
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chem.BaseAtomFeaturizer.feat_size
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chem.BaseAtomFeaturizer.__call__
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chem.CanonicalAtomFeaturizer
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Utils for bond featurization:
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.. autosummary::
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:toctree: ../../generated/
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chem.bond_type_one_hot
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chem.bond_is_conjugated_one_hot
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chem.bond_is_conjugated
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chem.bond_is_in_ring_one_hot
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chem.bond_is_in_ring
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chem.bond_stereo_one_hot
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chem.BaseBondFeaturizer
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chem.BaseBondFeaturizer.feat_size
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chem.BaseBondFeaturizer.__call__
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chem.CanonicalBondFeaturizer
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Graph Construction for Single Molecule
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``````````````````````````````````````
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Several methods for constructing DGLGraphs from SMILES/RDKit molecule objects are listed below:
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.. autosummary::
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:toctree: ../../generated/
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chem.mol_to_graph
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chem.smiles_to_bigraph
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chem.mol_to_bigraph
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chem.smiles_to_complete_graph
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chem.mol_to_complete_graph
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chem.k_nearest_neighbors
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Graph Construction and Featurization for Ligand-Protein Complex
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```````````````````````````````````````````````````````````````
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Constructing DGLHeteroGraphs and featurize for them.
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.. autosummary::
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:toctree: ../../generated/
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chem.ACNN_graph_construction_and_featurization
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Dataset Classes
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```````````````
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If your dataset is stored in a ``.csv`` file, you may find it helpful to use
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.. autoclass:: dgl.data.chem.MoleculeCSVDataset
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:members: __getitem__, __len__
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Currently four datasets are supported:
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* Tox21
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* TencentAlchemyDataset
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* PubChemBioAssayAromaticity
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* PDBBind
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.. autoclass:: dgl.data.chem.Tox21
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:members: __getitem__, __len__, task_pos_weights
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.. autoclass:: dgl.data.chem.TencentAlchemyDataset
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:members: __getitem__, __len__, set_mean_and_std
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.. autoclass:: dgl.data.chem.PubChemBioAssayAromaticity
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:members: __getitem__, __len__
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.. autoclass:: dgl.data.chem.PDBBind
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:members: __getitem__, __len__
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Dataset Splitting
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`````````````````
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We provide support for some common data splitting methods:
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* consecutive split
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* random split
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* molecular weight split
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* Bemis-Murcko scaffold split
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* single-task-stratified split
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.. autoclass:: dgl.data.chem.ConsecutiveSplitter
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:members: train_val_test_split, k_fold_split
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.. autoclass:: dgl.data.chem.RandomSplitter
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:members: train_val_test_split, k_fold_split
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.. autoclass:: dgl.data.chem.MolecularWeightSplitter
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:members: train_val_test_split, k_fold_split
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.. autoclass:: dgl.data.chem.ScaffoldSplitter
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:members: train_val_test_split, k_fold_split
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.. autoclass:: dgl.data.chem.SingleTaskStratifiedSplitter
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:members: train_val_test_split, k_fold_split
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