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  • Installation
    • Stable version
    • Nightly build version
    • Google Colab
    • Docker
    • Jupyter Notebook
    • From source with conda
    • From source lightweight guide
  • Requirements
    • Hard requirements
    • Soft requirements
  • Tutorials
    • Data Handling
    • Feature Engineering
    • Data Splitting
    • Model Training and Evaluating
    • More Tutorials
  • Examples
    • Delaney (ESOL)
      • MultitaskRegressor
      • GraphConvModel
    • ChEMBL
      • MultitaskRegressor
      • GraphConvModel
  • Known Issues & Limitations
    • Broken features
    • Experimental features
  • Docker Tutorial
    • Using deepchem with docker:
    • Hands-on tutorial
  • Documentation Tutorial
    • Building the Documentation
    • Testing

API Reference

  • Data
    • Datasets
      • NumpyDataset
        • NumpyDataset
      • DiskDataset
        • DiskDataset
      • ImageDataset
        • ImageDataset
    • Data Loaders
      • CSVLoader
        • CSVLoader
      • UserCSVLoader
        • UserCSVLoader
      • ImageLoader
        • ImageLoader
      • JsonLoader
        • JsonLoader
      • SDFLoader
        • SDFLoader
      • FASTALoader
        • FASTALoader
      • FASTQLoader
        • FASTQLoader
      • InMemoryLoader
        • InMemoryLoader
      • Density Functional Theory YAML Loader
        • DFTYamlLoader
      • SAM Loader
        • SAMLoader
      • BAM Loader
        • BAMLoader
      • CRAM Loader
        • CRAMLoader
    • Data Classes
      • Graph Data
        • ConvMol
        • MultiConvMol
        • WeaveMol
        • GraphData
      • Weighted Directed Graph Data
        • WeightedDirectedGraphData
      • Density Functional Theory Data
        • DFTSystem
        • DFTEntry
    • Base Classes (for develop)
      • Dataset
        • Dataset
      • DataLoader
        • DataLoader
  • MoleculeNet
    • MoleculeNet Cheatsheet
    • Contributing a new dataset to MoleculeNet
    • Example Usage
    • BACE Dataset
      • load_bace_classification()
      • load_bace_regression()
    • BBBC Datasets
      • load_bbbc001()
      • load_bbbc002()
      • load_bbbc003()
      • load_bbbc004()
      • load_bbbc005()
    • BBBP Datasets
      • load_bbbp()
    • Cell Counting Datasets
      • load_cell_counting()
    • Chembl Datasets
      • load_chembl()
    • Chembl25 Datasets
      • load_chembl25()
    • Clearance Datasets
      • load_clearance()
    • Clintox Datasets
      • load_clintox()
    • Delaney Datasets
      • load_delaney()
    • Factors Datasets
      • load_factors()
    • Freesolv Dataset
      • load_freesolv()
    • HIV Datasets
      • load_hiv()
    • HOPV Datasets
      • load_hopv()
    • HPPB Datasets
      • load_hppb()
    • KAGGLE Datasets
      • load_kaggle()
    • Kinase Datasets
      • load_kinase()
    • Lipo Datasets
      • load_lipo()
    • Materials Datasets
      • load_bandgap()
      • load_perovskite()
      • load_mp_formation_energy()
      • load_mp_metallicity()
    • MUV Datasets
      • load_muv()
    • NCI Datasets
      • load_nci()
    • PCBA Datasets
      • load_pcba()
    • PDBBIND Datasets
      • load_pdbbind()
    • PPB Datasets
      • load_ppb()
    • QM7 Datasets
      • load_qm7()
    • QM8 Datasets
      • load_qm8()
    • QM9 Datasets
      • load_qm9()
    • SAMPL Datasets
      • load_sampl()
    • SIDER Datasets
      • load_sider()
    • Thermosol Datasets
      • load_thermosol()
    • Tox21 Datasets
      • load_tox21()
    • Toxcast Datasets
      • load_toxcast()
    • USPTO Datasets
      • load_uspto()
    • UV Datasets
      • load_uv()
    • ZINC15 Datasets
      • load_zinc15()
    • Platinum Adsorption Dataset
      • load_Platinum_Adsorption()
  • Featurizers
    • Molecule Featurizers
      • Graph Convolution Featurizers
        • ConvMolFeaturizer
        • WeaveFeaturizer
        • MolGanFeaturizer
        • MolGraphConvFeaturizer
        • EquivariantGraphFeaturizer
        • PagtnMolGraphFeaturizer
        • DMPNNFeaturizer
        • GroverFeaturizer
        • RDKitConformerFeaturizer
        • MXMNetFeaturizer
        • Utilities
      • MACCSKeysFingerprint
        • MACCSKeysFingerprint
      • MATFeaturizer
        • MATFeaturizer
      • CircularFingerprint
        • CircularFingerprint
      • PubChemFingerprint
        • PubChemFingerprint
      • Mol2VecFingerprint
        • Mol2VecFingerprint
      • RDKitDescriptors
        • RDKitDescriptors
      • MordredDescriptors
        • MordredDescriptors
      • CoulombMatrix
        • CoulombMatrix
      • CoulombMatrixEig
        • CoulombMatrixEig
      • AtomCoordinates
        • AtomicCoordinates
      • BPSymmetryFunctionInput
        • BPSymmetryFunctionInput
      • SmilesToSeq
        • SmilesToSeq
      • SmilesToImage
        • SmilesToImage
      • OneHotFeaturizer
        • OneHotFeaturizer
      • SparseMatrixOneHotFeaturizer
        • SparseMatrixOneHotFeaturizer
      • RawFeaturizer
        • RawFeaturizer
      • SNAPFeaturizer
        • SNAPFeaturizer
    • Molecular Complex Featurizers
      • RdkitGridFeaturizer
        • RdkitGridFeaturizer
      • AtomicConvFeaturizer
        • AtomicConvFeaturizer
    • Inorganic Crystal Featurizers
      • MaterialCompositionFeaturizer
        • ElementPropertyFingerprint
        • ElemNetFeaturizer
      • MaterialStructureFeaturizer
        • SineCoulombMatrix
        • CGCNNFeaturizer
      • LCNNFeaturizer
        • LCNNFeaturizer
    • Biological Sequence Featurizers
      • SAMFeaturizer
        • SAMFeaturizer
      • BAMFeaturizer
        • BAMFeaturizer
      • CRAMFeaturizer
        • CRAMFeaturizer
      • FASTAFeaturizer
        • FASTAFeaturizer
    • DeepVariant Featurizers
      • RealignerFeaturizer
        • RealignerFeaturizer
      • PileupFeaturizer
        • PileupFeaturizer
    • Molecule Tokenizers
      • SmilesTokenizer
        • SmilesTokenizer
      • BasicSmilesTokenizer
        • BasicSmilesTokenizer
      • HuggingFaceFeaturizer
        • HuggingFaceFeaturizer
      • GroverAtomVocabTokenizer
        • GroverAtomVocabTokenizer
      • GroverBondVocabTokenizer
        • GroverBondVocabTokenizer
    • Vocabulary Builders
      • GroverAtomVocabularyBuilder
        • GroverAtomVocabularyBuilder.__init__()
        • GroverAtomVocabularyBuilder.build()
        • GroverAtomVocabularyBuilder.build_from_csv()
        • GroverAtomVocabularyBuilder.save()
        • GroverAtomVocabularyBuilder.load()
        • GroverAtomVocabularyBuilder.atom_to_vocab()
        • GroverAtomVocabularyBuilder.encode()
      • GroverAtomVocabularyBuilder
        • GroverAtomVocabularyBuilder.__init__()
        • GroverAtomVocabularyBuilder.build()
        • GroverAtomVocabularyBuilder.build_from_csv()
        • GroverAtomVocabularyBuilder.save()
        • GroverAtomVocabularyBuilder.load()
        • GroverAtomVocabularyBuilder.atom_to_vocab()
        • GroverAtomVocabularyBuilder.encode()
    • Sequence Featurizers
      • PFMFeaturizer
        • PFMFeaturizer
    • Other Featurizers
      • BertFeaturizer
        • BertFeaturizer
      • RobertaFeaturizer
        • RobertaFeaturizer
      • RxnFeaturizer
        • RxnFeaturizer
      • BindingPocketFeaturizer
        • BindingPocketFeaturizer
      • UserDefinedFeaturizer
        • UserDefinedFeaturizer
      • DummyFeaturizer
        • DummyFeaturizer
    • Base Featurizers (for developers)
      • Featurizer
        • Featurizer
      • MolecularFeaturizer
        • MolecularFeaturizer
      • MaterialCompositionFeaturizer
        • MaterialCompositionFeaturizer
      • MaterialStructureFeaturizer
        • MaterialStructureFeaturizer
      • ComplexFeaturizer
        • ComplexFeaturizer
      • PolymerFeaturizer
        • PolymerFeaturizer
      • VocabularyBuilder
        • VocabularyBuilder
      • HuggingFaceVocabularyBuilder
        • hf_vocab
  • Splitters
    • General Splitters
      • RandomSplitter
        • RandomSplitter
      • RandomGroupSplitter
        • RandomGroupSplitter
      • RandomStratifiedSplitter
        • RandomStratifiedSplitter
      • SingletaskStratifiedSplitter
        • SingletaskStratifiedSplitter
      • IndexSplitter
        • IndexSplitter
      • SpecifiedSplitter
        • SpecifiedSplitter
      • TaskSplitter
        • TaskSplitter
    • Molecule Splitters
      • ScaffoldSplitter
        • ScaffoldSplitter
      • MolecularWeightSplitter
        • MolecularWeightSplitter
      • MaxMinSplitter
        • MaxMinSplitter
      • ButinaSplitter
        • ButinaSplitter
      • FingerprintSplitter
        • FingerprintSplitter
    • Base Splitter (for develop)
      • Splitter
        • Splitter.k_fold_split()
        • Splitter.train_valid_test_split()
        • Splitter.train_test_split()
        • Splitter.split()
  • Transformers
    • General Transformers
      • NormalizationTransformer
        • NormalizationTransformer
      • MinMaxTransformer
        • MinMaxTransformer
      • ClippingTransformer
        • ClippingTransformer
      • LogTransformer
        • LogTransformer
      • CDFTransformer
        • CDFTransformer
      • PowerTransformer
        • PowerTransformer
      • BalancingTransformer
        • BalancingTransformer
      • DuplicateBalancingTransformer
        • DuplicateBalancingTransformer
      • ImageTransformer
        • ImageTransformer
      • FeaturizationTransformer
        • FeaturizationTransformer
    • Specified Usecase Transformers
      • CoulombFitTransformer
        • CoulombFitTransformer
      • IRVTransformer
        • IRVTransformer
      • DAGTransformer
        • DAGTransformer
      • RxnSplitTransformer
        • RxnSplitTransformer
    • Base Transformer (for develop)
      • Transformer
        • Transformer.__init__()
        • Transformer.transform()
        • Transformer.transform_array()
        • Transformer.transform_on_array()
        • Transformer.untransform()
  • Model Classes
    • Model Cheatsheet
    • Model
      • Model
        • Model.__init__()
        • Model.fit_on_batch()
        • Model.predict_on_batch()
        • Model.reload()
        • Model.get_model_filename()
        • Model.get_params_filename()
        • Model.save()
        • Model.fit()
        • Model.predict()
        • Model.evaluate()
        • Model.get_task_type()
        • Model.get_num_tasks()
  • Scikit-Learn Models
    • SklearnModel
      • SklearnModel
        • SklearnModel.__init__()
        • SklearnModel.fit()
        • SklearnModel.predict_on_batch()
        • SklearnModel.predict()
        • SklearnModel.save()
        • SklearnModel.reload()
  • Gradient Boosting Models
    • GBDTModel
      • GBDTModel
        • GBDTModel.__init__()
        • GBDTModel.fit()
        • GBDTModel.fit_with_eval()
  • Deep Learning Infrastructure
    • Losses
      • Loss
      • L1Loss
      • HuberLoss
      • L2Loss
      • HingeLoss
      • SquaredHingeLoss
      • PoissonLoss
      • BinaryCrossEntropy
      • CategoricalCrossEntropy
      • SigmoidCrossEntropy
      • SoftmaxCrossEntropy
      • SparseSoftmaxCrossEntropy
      • VAE_ELBO
      • VAE_KLDivergence
      • ShannonEntropy
      • GlobalMutualInformationLoss
      • LocalMutualInformationLoss
      • GroverPretrainLoss
      • EdgePredictionLoss
      • GraphNodeMaskingLoss
      • GraphEdgeMaskingLoss
      • DeepGraphInfomaxLoss
      • GraphContextPredLoss
      • DensityProfileLoss
      • NTXentMultiplePositives
        • NTXentMultiplePositives.__init__()
    • Optimizers
      • Optimizer
        • Optimizer.__init__()
      • LearningRateSchedule
      • AdaGrad
        • AdaGrad.__init__()
      • Adam
        • Adam.__init__()
      • AdamW
        • AdamW.__init__()
      • SparseAdam
        • SparseAdam.__init__()
      • RMSProp
        • RMSProp.__init__()
      • GradientDescent
        • GradientDescent.__init__()
      • ExponentialDecay
        • ExponentialDecay.__init__()
      • PolynomialDecay
        • PolynomialDecay.__init__()
      • LinearCosineDecay
        • LinearCosineDecay.__init__()
      • LambdaLRWithWarmup
        • LambdaLRWithWarmup.__init__()
  • Keras Models
    • KerasModel
      • KerasModel
        • KerasModel.__init__()
        • KerasModel.fit()
        • KerasModel.fit_generator()
        • KerasModel.fit_on_batch()
        • KerasModel.predict_on_generator()
        • KerasModel.predict_on_batch()
        • KerasModel.predict_uncertainty_on_batch()
        • KerasModel.predict()
        • KerasModel.predict_embedding()
        • KerasModel.predict_uncertainty()
        • KerasModel.evaluate_generator()
        • KerasModel.compute_saliency()
        • KerasModel.default_generator()
        • KerasModel.save_checkpoint()
        • KerasModel.get_checkpoints()
        • KerasModel.restore()
        • KerasModel.get_global_step()
        • KerasModel.load_from_pretrained()
    • TensorflowMultitaskIRVClassifier
      • TensorflowMultitaskIRVClassifier
        • TensorflowMultitaskIRVClassifier.__init__()
    • RobustMultitaskClassifier
      • RobustMultitaskClassifier
        • RobustMultitaskClassifier.__init__()
        • RobustMultitaskClassifier.default_generator()
    • RobustMultitaskRegressor
      • RobustMultitaskRegressor
        • RobustMultitaskRegressor.__init__()
        • RobustMultitaskRegressor.default_generator()
    • ProgressiveMultitaskClassifier
      • ProgressiveMultitaskClassifier
        • ProgressiveMultitaskClassifier.__init__()
    • ProgressiveMultitaskRegressor
      • ProgressiveMultitaskRegressor
        • ProgressiveMultitaskRegressor.__init__()
        • ProgressiveMultitaskRegressor.add_adapter()
        • ProgressiveMultitaskRegressor.fit()
        • ProgressiveMultitaskRegressor.fit_task()
    • WeaveModel
      • WeaveModel
        • WeaveModel.__init__()
        • WeaveModel.compute_features_on_batch()
        • WeaveModel.default_generator()
    • DTNNModel
      • DTNNModel
        • DTNNModel.__init__()
        • DTNNModel.default_generator()
    • DAGModel
      • DAGModel
        • DAGModel.__init__()
        • DAGModel.default_generator()
    • GraphConvModel
      • GraphConvModel
        • GraphConvModel.__init__()
        • GraphConvModel.default_generator()
    • MPNNModel
      • MPNNModel
        • MPNNModel.__init__()
        • MPNNModel.default_generator()
    • BasicMolGANModel
      • BasicMolGANModel
        • BasicMolGANModel.__init__()
        • BasicMolGANModel.get_noise_input_shape()
        • BasicMolGANModel.get_data_input_shapes()
        • BasicMolGANModel.create_generator()
        • BasicMolGANModel.create_discriminator()
        • BasicMolGANModel.predict_gan_generator()
    • ScScoreModel
      • ScScoreModel
        • ScScoreModel.__init__()
        • ScScoreModel.default_generator()
    • SeqToSeq
      • SeqToSeq
        • SeqToSeq.__init__()
        • SeqToSeq.fit_sequences()
        • SeqToSeq.predict_from_sequences()
        • SeqToSeq.predict_from_embeddings()
        • SeqToSeq.predict_embeddings()
    • GAN
      • GAN
        • GAN.__init__()
        • GAN.get_noise_input_shape()
        • GAN.get_data_input_shapes()
        • GAN.get_conditional_input_shapes()
        • GAN.get_noise_batch()
        • GAN.create_generator()
        • GAN.create_discriminator()
        • GAN.create_generator_loss()
        • GAN.create_discriminator_loss()
        • GAN.fit_gan()
        • GAN.predict_gan_generator()
      • WGAN
        • WGAN
    • TextCNNModel
      • TextCNNModel
        • TextCNNModel.__init__()
        • TextCNNModel.build_char_dict()
        • TextCNNModel.smiles_to_seq_batch()
        • TextCNNModel.default_generator()
        • TextCNNModel.smiles_to_seq()
    • AtomicConvModel
      • AtomicConvModel
    • Smiles2Vec
      • Smiles2Vec
        • Smiles2Vec.__init__()
        • Smiles2Vec.default_generator()
    • ChemCeption
      • ChemCeption
        • ChemCeption.__init__()
        • ChemCeption.build_inception_module()
        • ChemCeption.default_generator()
    • NormalizingFlowModel
      • NormalizingFlowModel
        • NormalizingFlowModel.__init__()
        • NormalizingFlowModel.create_nll()
        • NormalizingFlowModel.save()
        • NormalizingFlowModel.reload()
  • PyTorch Models
    • TorchModel
      • TorchModel
        • TorchModel.__init__()
        • TorchModel.fit()
        • TorchModel.fit_generator()
        • TorchModel.fit_on_batch()
        • TorchModel.predict_on_generator()
        • TorchModel.predict_on_batch()
        • TorchModel.predict_uncertainty_on_batch()
        • TorchModel.predict()
        • TorchModel.predict_embedding()
        • TorchModel.predict_uncertainty()
        • TorchModel.evaluate_generator()
        • TorchModel.compute_saliency()
        • TorchModel.default_generator()
        • TorchModel.save_checkpoint()
        • TorchModel.get_checkpoints()
        • TorchModel.restore()
        • TorchModel.compile()
        • TorchModel.get_global_step()
        • TorchModel.load_from_pretrained()
    • ModularTorchModel
      • ModularTorchModel
        • ModularTorchModel.__init__()
        • ModularTorchModel.build_model()
        • ModularTorchModel.build_components()
        • ModularTorchModel.loss_func()
        • ModularTorchModel.freeze_components()
        • ModularTorchModel.unfreeze_components()
        • ModularTorchModel.fit_generator()
        • ModularTorchModel.load_from_pretrained()
        • ModularTorchModel.save_checkpoint()
        • ModularTorchModel.restore()
    • CNN
      • CNN
        • CNN.__init__()
        • CNN.default_generator()
    • MultitaskRegressor
      • MultitaskRegressor
        • MultitaskRegressor.__init__()
        • MultitaskRegressor.default_generator()
    • MultitaskFitTransformRegressor
      • MultitaskFitTransformRegressor
        • MultitaskFitTransformRegressor.__init__()
        • MultitaskFitTransformRegressor.default_generator()
        • MultitaskFitTransformRegressor.predict_on_generator()
    • MultitaskClassifier
      • MultitaskClassifier
        • MultitaskClassifier.__init__()
        • MultitaskClassifier.default_generator()
    • CGCNNModel
      • CGCNNModel
        • CGCNNModel.__init__()
    • GATModel
      • GATModel
        • GATModel.__init__()
    • GCNModel
      • GCNModel
        • GCNModel.__init__()
    • AttentiveFPModel
      • AttentiveFPModel
        • AttentiveFPModel.__init__()
    • PagtnModel
      • PagtnModel
        • PagtnModel.__init__()
    • AtomConvModel
      • AtomConvModel
        • AtomConvModel.__init__()
        • AtomConvModel.default_generator()
    • MPNNModel
      • MPNNModel
        • MPNNModel.__init__()
    • InfoGraphModel
      • InfoGraphModel
        • InfoGraphModel.__init__()
        • InfoGraphModel.build_components()
        • InfoGraphModel.build_model()
        • InfoGraphModel.loss_func()
        • InfoGraphModel.restore()
    • InfoGraphStarModel
      • InfoGraphStarModel
        • InfoGraphStarModel.__init__()
        • InfoGraphStarModel.build_components()
        • InfoGraphStarModel.build_model()
        • InfoGraphStarModel.loss_func()
        • InfoGraphStarModel.default_generator()
    • GNNModular
      • GNNModular
        • GNNModular.__init__()
        • GNNModular.build_components()
        • GNNModular.build_gnn()
        • GNNModular.build_model()
        • GNNModular.loss_func()
        • GNNModular.masked_node_loss_loader()
        • GNNModular.masked_edge_loss_loader()
        • GNNModular.infomax_loss_loader()
        • GNNModular.context_pred_loss_loader()
        • GNNModular.default_generator()
    • InfoMax3DModular
      • InfoMax3DModular
        • InfoMax3DModular.__init__()
        • InfoMax3DModular.build_components()
        • InfoMax3DModular.build_model()
        • InfoMax3DModular.loss_func()
    • LCNNModel
      • LCNNModel
        • LCNNModel.__init__()
    • MEGNetModel
      • MEGNetModel
        • MEGNetModel.__init__()
    • MATModel
      • MATModel
        • MATModel.__init__()
        • MATModel.pad_array()
        • MATModel.pad_sequence()
        • MATModel.default_generator()
    • NormalizingFlowModel
      • NormalizingFlowModel
        • NormalizingFlowModel.__init__()
        • NormalizingFlowModel.fit()
    • DMPNNModel
      • DMPNNModel
        • DMPNNModel.__init__()
        • DMPNNModel.default_generator()
    • GroverModel
      • GroverModel
        • GroverModel.__init__()
        • GroverModel.build_components()
        • GroverModel.build_model()
        • GroverModel.get_loss_func()
        • GroverModel.loss_func()
        • GroverModel.atom_vocab_random_mask()
        • GroverModel.bond_vocab_random_mask()
        • GroverModel.restore()
    • DTNNModel
      • DTNNModel
        • DTNNModel.__init__()
        • DTNNModel.default_generator()
    • SeqToSeqModel
      • SeqToSeqModel
        • SeqToSeqModel.__init__()
        • SeqToSeqModel.fit_sequences()
        • SeqToSeqModel.predict_from_sequences()
        • SeqToSeqModel.predict_embedding()
        • SeqToSeqModel.predict_from_embedding()
    • GAN
      • GAN
        • GAN.__init__()
        • GAN.forward()
        • GAN.get_noise_batch()
        • GAN.create_generator_loss()
        • GAN.create_discriminator_loss()
        • GAN.discrim_loss_fn()
        • GAN.gen_loss_fn()
    • GANModel
      • GANModel
        • GANModel.__init__()
        • GANModel.get_noise_input_shape()
        • GANModel.get_data_input_shapes()
        • GANModel.get_conditional_input_shapes()
        • GANModel.create_generator()
        • GANModel.create_discriminator()
        • GANModel.fit_gan()
        • GANModel.predict_gan_generator()
    • WGANModel
      • WGANModel
        • WGANModel.__init__()
        • WGANModel.create_generator_loss()
        • WGANModel.create_discriminator_loss()
    • BasicMolGANModel
      • BasicMolGANModel
        • BasicMolGANModel.__init__()
        • BasicMolGANModel.get_noise_input_shape()
        • BasicMolGANModel.get_data_input_shapes()
        • BasicMolGANModel.create_generator()
        • BasicMolGANModel.create_discriminator()
        • BasicMolGANModel.predict_gan_generator()
    • Weave
      • Weave
        • Weave.__init__()
        • Weave.forward()
    • WeaveModel
      • WeaveModel
        • WeaveModel.__init__()
        • WeaveModel.compute_features_on_batch()
        • WeaveModel.default_generator()
    • ProgressiveMultitaskClassifier
      • ProgressiveMultitaskClassifier
        • ProgressiveMultitaskClassifier.__init__()
    • ProgressiveMultitaskRegressor
      • ProgressiveMultitaskRegressor
        • ProgressiveMultitaskRegressor.__init__()
    • RobustMultitaskClassifier
      • RobustMultitaskClassifier
        • RobustMultitaskClassifier.__init__()
        • RobustMultitaskClassifier.default_generator()
    • RobustMultitaskRegressor
      • RobustMultitaskRegressor
        • RobustMultitaskRegressor.__init__()
    • Density Functional Theory Model - XCModel
      • XCModel
        • XCModel.__init__()
    • TextCNNModel
      • TextCNNModel
        • TextCNNModel.__init__()
        • TextCNNModel.default_generator()
        • TextCNNModel.build_char_dict()
        • TextCNNModel.smiles_to_seq()
        • TextCNNModel.convert_bytes_to_char()
        • TextCNNModel.smiles_to_seq_batch()
    • PINNModel
      • PINNModel
        • PINNModel.__init__()
        • PINNModel.predict()
    • UNetModel
      • UNetModel
        • UNetModel.__init__()
    • _GraphConvTorchModel
      • _GraphConvTorchModel
        • _GraphConvTorchModel.__init__()
        • _GraphConvTorchModel.forward()
    • GraphConvModel
      • GraphConvModel
        • GraphConvModel.__init__()
        • GraphConvModel.default_generator()
    • Smiles2Vec
      • Smiles2Vec
        • Smiles2Vec.__init__()
        • Smiles2Vec.forward()
    • Smiles2VecModel
      • Smiles2VecModel
        • Smiles2VecModel.__init__()
    • MXMNet
      • MXMNet
        • MXMNet.__init__()
        • MXMNet.init()
        • MXMNet.indices()
        • MXMNet.forward()
    • LSTMGenerator
      • LSTMGenerator
        • LSTMGenerator.__init__()
        • LSTMGenerator.default_generator()
        • LSTMGenerator.fit()
        • LSTMGenerator.fit_generator()
        • LSTMGenerator.restore()
        • LSTMGenerator.load_from_pretrained()
        • LSTMGenerator.sample()
    • InceptionV3Model
      • InceptionV3Model
        • InceptionV3Model.__init__()
        • InceptionV3Model.adjust_learning_rate()
        • InceptionV3Model.fit()
        • InceptionV3Model.save()
        • InceptionV3Model.reload()
    • MobileNetV2Model
      • MobileNetV2Model
        • MobileNetV2Model.__init__()
        • MobileNetV2Model.save()
        • MobileNetV2Model.reload()
    • MultitaskIRVClassifier
      • MultitaskIRVClassifier
        • MultitaskIRVClassifier.__init__()
    • HNN
      • HNN
        • HNN.__init__()
        • HNN.forward()
        • HNN.hamiltonian()
        • HNN.symplectic_gradient()
    • HNNModel
      • HNNModel
        • HNNModel.__init__()
        • HNNModel.predict_hamiltonian()
        • HNNModel.symplectic_gradient()
    • FNO
      • FNO
        • FNO.__init__()
        • FNO.forward()
    • FNOModel
      • FNOModel
        • FNOModel.__init__()
    • LNN
      • LNN
        • LNN.__init__()
        • LNN.forward()
        • LNN.calculate_dynamics()
        • LNN.lagrangian()
    • LNNModel
      • LNNModel
        • LNNModel.__init__()
        • LNNModel.predict_lagrangian()
        • LNNModel.calculate_dynamics()
        • LNNModel.save()
        • LNNModel.reload()
    • SE3TransformerModel
      • SE3TransformerModel
        • SE3TransformerModel.__init__()
        • SE3TransformerModel.save()
        • SE3TransformerModel.reload()
    • TFNModel
      • TFNModel
        • TFNModel.__init__()
        • TFNModel.save()
        • TFNModel.reload()
    • ChemCeptionLayer
      • ChemCeptionLayer
        • ChemCeptionLayer.__init__()
        • ChemCeptionLayer.forward()
    • ChemCeption
      • ChemCeption
        • ChemCeption.__init__()
        • ChemCeption.build_components()
        • ChemCeption.build_inception_module()
        • ChemCeption.build_model()
        • ChemCeption.loss_func()
        • ChemCeption.default_generator()
  • PyTorch Lightning Models
    • DCLightningModule
      • DCLightningModule
        • DCLightningModule.__init__()
        • DCLightningModule.configure_optimizers()
        • DCLightningModule.training_step()
        • DCLightningModule.predict_step()
        • DCLightningModule.on_save_checkpoint()
        • DCLightningModule.on_load_checkpoint()
    • LightningTorchModel
      • LightningTorchModel
        • LightningTorchModel.__init__()
        • LightningTorchModel.fit()
        • LightningTorchModel.predict()
        • LightningTorchModel.save_checkpoint()
        • LightningTorchModel.restore()
  • Jax Models
    • JaxModel
      • JaxModel
        • JaxModel.__init__()
        • JaxModel.fit()
        • JaxModel.predict_on_generator()
        • JaxModel.predict_on_batch()
        • JaxModel.predict()
        • JaxModel.get_global_step()
        • JaxModel.evaluate_generator()
        • JaxModel.default_generator()
    • PinnModel
      • PINNModel
        • PINNModel.__init__()
        • PINNModel.default_generator()
  • Hugging Face Models
    • HuggingFaceModel
      • HuggingFaceModel.__init__()
      • HuggingFaceModel.load_from_pretrained()
      • HuggingFaceModel.fit_generator()
      • HuggingFaceModel.fill_mask()
    • Chemberta
      • Chemberta.__init__()
    • MoLFormer
      • MoLFormer
        • MoLFormer.__init__()
    • ProtBERT
      • ProtBERT
        • ProtBERT.__init__()
        • ProtBERT.get_last_hidden_state()
    • DeepAbLLM
      • DeepAbLLM
        • DeepAbLLM.task
        • DeepAbLLM.model_path
        • DeepAbLLM.n_tasks
        • DeepAbLLM.is_esm_variant
        • DeepAbLLM.__init__()
        • DeepAbLLM._mask_seq_pos()
        • DeepAbLLM.redesign_residue()
        • DeepAbLLM._optimize_residue_pos()
        • DeepAbLLM.redesign_sequence()
        • DeepAbLLM.__init__()
        • DeepAbLLM.redesign_residue()
        • DeepAbLLM.redesign_sequence()
    • OneFormer
      • OneFormer
        • OneFormer.__init__()
        • OneFormer.fit_generator()
  • Trainer
    • DistributedTrainer
  • Layers
    • Layers Cheatsheet
    • Keras Layers
      • InteratomicL2Distances
        • InteratomicL2Distances.__init__()
        • InteratomicL2Distances.get_config()
        • InteratomicL2Distances.call()
      • GraphConv
        • GraphConv.__init__()
        • GraphConv.build()
        • GraphConv.get_config()
        • GraphConv.call()
        • GraphConv.sum_neigh()
      • GraphPool
        • GraphPool.__init__()
        • GraphPool.get_config()
        • GraphPool.call()
      • GraphGather
        • GraphGather.__init__()
        • GraphGather.get_config()
        • GraphGather.call()
      • MolGANConvolutionLayer
        • MolGANConvolutionLayer.__init__()
        • MolGANConvolutionLayer.call()
        • MolGANConvolutionLayer.get_config()
      • MolGANAggregationLayer
        • MolGANAggregationLayer.__init__()
        • MolGANAggregationLayer.call()
        • MolGANAggregationLayer.get_config()
      • MolGANMultiConvolutionLayer
        • MolGANMultiConvolutionLayer.__init__()
        • MolGANMultiConvolutionLayer.call()
        • MolGANMultiConvolutionLayer.get_config()
      • MolGANEncoderLayer
        • MolGANEncoderLayer.__init__()
        • MolGANEncoderLayer.call()
        • MolGANEncoderLayer.get_config()
      • LSTMStep
        • LSTMStep.__init__()
        • LSTMStep.get_config()
        • LSTMStep.build()
        • LSTMStep.call()
      • AttnLSTMEmbedding
        • AttnLSTMEmbedding.__init__()
        • AttnLSTMEmbedding.get_config()
        • AttnLSTMEmbedding.build()
        • AttnLSTMEmbedding.call()
      • IterRefLSTMEmbedding
        • IterRefLSTMEmbedding.__init__()
        • IterRefLSTMEmbedding.get_config()
        • IterRefLSTMEmbedding.build()
        • IterRefLSTMEmbedding.call()
      • SwitchedDropout
        • SwitchedDropout.get_config()
        • SwitchedDropout.call()
      • WeightedLinearCombo
        • WeightedLinearCombo.__init__()
        • WeightedLinearCombo.get_config()
        • WeightedLinearCombo.build()
        • WeightedLinearCombo.call()
      • CombineMeanStd
        • CombineMeanStd.__init__()
        • CombineMeanStd.get_config()
        • CombineMeanStd.call()
      • Stack
        • Stack.get_config()
        • Stack.call()
      • VinaFreeEnergy
        • VinaFreeEnergy.get_config()
        • VinaFreeEnergy.build()
        • VinaFreeEnergy.nonlinearity()
        • VinaFreeEnergy.repulsion()
        • VinaFreeEnergy.hydrophobic()
        • VinaFreeEnergy.hydrogen_bond()
        • VinaFreeEnergy.gaussian_first()
        • VinaFreeEnergy.gaussian_second()
        • VinaFreeEnergy.call()
      • NeighborList
        • NeighborList.__init__()
        • NeighborList.get_config()
        • NeighborList.call()
        • NeighborList.compute_nbr_list()
        • NeighborList.get_atoms_in_nbrs()
        • NeighborList.get_closest_atoms()
        • NeighborList.get_cells_for_atoms()
        • NeighborList.get_neighbor_cells()
        • NeighborList.get_cells()
      • AtomicConvolution
        • AtomicConvolution.__init__()
        • AtomicConvolution.get_config()
        • AtomicConvolution.build()
        • AtomicConvolution.call()
        • AtomicConvolution.radial_symmetry_function()
        • AtomicConvolution.radial_cutoff()
        • AtomicConvolution.gaussian_distance_matrix()
        • AtomicConvolution.distance_tensor()
        • AtomicConvolution.distance_matrix()
      • AlphaShareLayer
        • AlphaShareLayer.get_config()
        • AlphaShareLayer.build()
        • AlphaShareLayer.call()
      • SluiceLoss
        • SluiceLoss.get_config()
        • SluiceLoss.call()
      • BetaShare
        • BetaShare.get_config()
        • BetaShare.build()
        • BetaShare.call()
      • ANIFeat
        • ANIFeat.__init__()
        • ANIFeat.get_config()
        • ANIFeat.call()
        • ANIFeat.distance_matrix()
        • ANIFeat.distance_cutoff()
        • ANIFeat.radial_symmetry()
        • ANIFeat.angular_symmetry()
      • GraphEmbedPoolLayer
        • GraphEmbedPoolLayer.get_config()
        • GraphEmbedPoolLayer.build()
        • GraphEmbedPoolLayer.call()
      • GraphCNN
        • GraphCNN.__init__()
        • GraphCNN.get_config()
        • GraphCNN.build()
        • GraphCNN.call()
      • Highway
        • Highway.__init__()
        • Highway.get_config()
        • Highway.build()
        • Highway.call()
      • WeaveLayer
        • WeaveLayer.__init__()
        • WeaveLayer.get_config()
        • WeaveLayer.build()
        • WeaveLayer.call()
      • WeaveGather
        • WeaveGather.__init__()
        • WeaveGather.get_config()
        • WeaveGather.build()
        • WeaveGather.call()
        • WeaveGather.gaussian_histogram()
      • DTNNEmbedding
        • DTNNEmbedding.__init__()
        • DTNNEmbedding.get_config()
        • DTNNEmbedding.build()
        • DTNNEmbedding.call()
      • DTNNStep
        • DTNNStep.__init__()
        • DTNNStep.get_config()
        • DTNNStep.build()
        • DTNNStep.call()
      • DTNNGather
        • DTNNGather.__init__()
        • DTNNGather.get_config()
        • DTNNGather.build()
        • DTNNGather.call()
      • DAGLayer
        • DAGLayer.__init__()
        • DAGLayer.get_config()
        • DAGLayer.build()
        • DAGLayer.call()
      • DAGGather
        • DAGGather.__init__()
        • DAGGather.get_config()
        • DAGGather.build()
        • DAGGather.call()
      • MessagePassing
        • MessagePassing.__init__()
        • MessagePassing.get_config()
        • MessagePassing.build()
        • MessagePassing.call()
      • EdgeNetwork
        • EdgeNetwork.get_config()
        • EdgeNetwork.build()
        • EdgeNetwork.call()
      • GatedRecurrentUnit
        • GatedRecurrentUnit.get_config()
        • GatedRecurrentUnit.build()
        • GatedRecurrentUnit.call()
      • SetGather
        • SetGather.__init__()
        • SetGather.get_config()
        • SetGather.build()
        • SetGather.call()
    • Torch Layers
      • AtomicConv
        • AtomicConv.__init__()
        • AtomicConv.forward()
      • MultilayerPerceptron
        • MultilayerPerceptron.__init__()
        • MultilayerPerceptron.build_layers()
        • MultilayerPerceptron.forward()
      • CNNModule
        • CNNModule.__init__()
        • CNNModule.forward()
      • ScaleNorm
        • ScaleNorm.__init__()
        • ScaleNorm.forward()
      • MATEncoderLayer
        • MATEncoderLayer.__init__()
        • MATEncoderLayer.forward()
      • MultiHeadedMATAttention
        • MultiHeadedMATAttention.__init__()
        • MultiHeadedMATAttention.forward()
      • SublayerConnection
        • SublayerConnection.__init__()
        • SublayerConnection.forward()
      • PositionwiseFeedForward
        • PositionwiseFeedForward.__init__()
        • PositionwiseFeedForward.forward()
      • MATEmbedding
        • MATEmbedding.__init__()
        • MATEmbedding.forward()
      • MATGenerator
        • MATGenerator.__init__()
        • MATGenerator.forward()
      • cosine_dist()
      • GraphNetwork
        • GraphNetwork.__init__()
        • GraphNetwork.forward()
      • Affine
        • Affine.__init__()
        • Affine.forward()
        • Affine.inverse()
      • RealNVPLayer
        • RealNVPLayer.__init__()
        • RealNVPLayer.forward()
        • RealNVPLayer.inverse()
      • DMPNNEncoderLayer
        • DMPNNEncoderLayer.__init__()
        • DMPNNEncoderLayer.forward()
      • InfoGraphEncoder
        • InfoGraphEncoder.__init__()
        • InfoGraphEncoder.forward()
      • GINEncoder
        • GINEncoder.__init__()
        • GINEncoder.forward()
      • SetGather
        • SetGather.__init__()
        • SetGather.forward()
      • GNN
        • GNN.__init__()
        • GNN.forward()
      • GNNHead
        • GNNHead.__init__()
        • GNNHead.forward()
      • LocalGlobalDiscriminator
        • LocalGlobalDiscriminator.__init__()
        • LocalGlobalDiscriminator.forward()
      • AtomEncoder
        • AtomEncoder.__init__()
        • AtomEncoder.reset_parameters()
        • AtomEncoder.forward()
      • BondEncoder
        • BondEncoder.__init__()
        • BondEncoder.forward()
      • PNALayer
        • PNALayer.__init__()
        • PNALayer.forward()
        • PNALayer.message_func()
        • PNALayer.reduce_func()
        • PNALayer.pretrans_edges()
      • PNAGNN
        • PNAGNN.__init__()
        • PNAGNN.forward()
      • PNA
        • PNA.__init__()
        • PNA.forward()
      • Net3DLayer
        • Net3DLayer.__init__()
        • Net3DLayer.forward()
        • Net3DLayer.message_function()
        • Net3DLayer.update_function()
      • Net3D
        • Net3D.__init__()
        • Net3D.forward()
        • Net3D.output_node_func()
        • Net3D.input_edge_func()
      • DTNNEmbedding
        • DTNNEmbedding.__init__()
        • DTNNEmbedding.forward()
      • DTNNStep
        • DTNNStep.__init__()
        • DTNNStep.forward()
      • DTNNGather
        • DTNNGather.__init__()
        • DTNNGather.forward()
      • GradientPenaltyLayer
        • GradientPenaltyLayer.__init__()
        • GradientPenaltyLayer.forward()
      • MolGANConvolutionLayer
        • MolGANConvolutionLayer.__init__()
        • MolGANConvolutionLayer.forward()
      • MolGANAggregationLayer
        • MolGANAggregationLayer.__init__()
        • MolGANAggregationLayer.forward()
      • MolGANMultiConvolutionLayer
        • MolGANMultiConvolutionLayer.__init__()
        • MolGANMultiConvolutionLayer.forward()
      • MolGANEncoderLayer
        • MolGANEncoderLayer.__init__()
        • MolGANEncoderLayer.forward()
      • EdgeNetwork
        • EdgeNetwork.__init__()
        • EdgeNetwork.forward()
      • WeaveLayer
        • WeaveLayer.__init__()
        • WeaveLayer.forward()
      • WeaveGather
        • WeaveGather.__init__()
        • WeaveGather.forward()
        • WeaveGather.gaussian_histogram()
      • MXMNetGlobalMessagePassing
        • MXMNetGlobalMessagePassing.__init__()
        • MXMNetGlobalMessagePassing.forward()
        • MXMNetGlobalMessagePassing.message()
      • MXMNetBesselBasisLayer
        • MXMNetBesselBasisLayer.__init__()
        • MXMNetBesselBasisLayer.reset_parameters()
        • MXMNetBesselBasisLayer.forward()
      • DTNN
        • DTNN.__init__()
        • DTNN.forward()
      • VariationalRandomizer
        • VariationalRandomizer.__init__()
        • VariationalRandomizer.forward()
        • VariationalRandomizer.add_loss()
      • EncoderRNN
        • EncoderRNN.__init__()
        • EncoderRNN.forward()
      • DecoderRNN
        • DecoderRNN.__init__()
        • DecoderRNN.forward()
      • SeqToSeq
        • SeqToSeq.__init__()
        • SeqToSeq.forward()
      • FerminetElectronFeature
        • FerminetElectronFeature.__init__()
        • FerminetElectronFeature.forward()
      • FerminetEnvelope
        • FerminetEnvelope.__init__()
        • FerminetEnvelope.forward()
      • MXMNetLocalMessagePassing
        • MXMNetLocalMessagePassing.__init__()
        • MXMNetLocalMessagePassing.forward()
      • MXMNetSphericalBasisLayer
        • MXMNetSphericalBasisLayer.__init__()
        • MXMNetSphericalBasisLayer.forward()
      • HighwayLayer
        • HighwayLayer.__init__()
        • HighwayLayer.forward()
      • GraphConv
        • GraphConv.__init__()
        • GraphConv.forward()
        • GraphConv.sum_neigh()
      • GraphPool
        • GraphPool.__init__()
        • GraphPool.get_config()
        • GraphPool.forward()
      • GraphGather
        • GraphGather.__init__()
        • GraphGather.get_config()
        • GraphGather.forward()
      • ClampExp
        • ClampExp.__init__()
        • ClampExp.forward()
      • ConstScaleLayer
        • ConstScaleLayer.__init__()
        • ConstScaleLayer.forward()
      • cosine_dist()
      • DAGLayer
        • DAGLayer.__init__()
        • DAGLayer.get_config()
        • DAGLayer.forward()
      • DAGGather
        • DAGGather.__init__()
        • DAGGather.get_config()
        • DAGGather.forward()
      • SpectralConv
        • SpectralConv.__init__()
        • SpectralConv.forward()
      • Stem
        • Stem.__init__()
        • Stem.forward()
      • InceptionResnetA
        • InceptionResnetA.__init__()
        • InceptionResnetA.forward()
      • InceptionResnetB
        • InceptionResnetB.__init__()
        • InceptionResnetB.forward()
      • FNOBlock
        • FNOBlock.__init__()
        • FNOBlock.forward()
      • InceptionResnetC
        • InceptionResnetC.__init__()
        • InceptionResnetC.forward()
      • ReductionA
        • ReductionA.__init__()
        • ReductionA.forward()
      • ReductionB
        • ReductionB.__init__()
        • ReductionB.forward()
      • Flow Layers
        • Flow
        • Affine
        • MaskedAffineFlow
        • ActNorm
        • ClampExp
        • ConstScaleLayer
        • MLPFlow
        • NormalizingFlow
      • Grover Layers
        • GroverMPNEncoder
        • GroverAttentionHead
        • GroverMTBlock
        • GroverTransEncoder
        • GroverEmbedding
        • GroverEmbedding
        • GroverAtomVocabPredictor
        • GroverBondVocabPredictor
        • GroverFunctionalGroupPredictor
        • GroverPretrain
        • GroverFinetune
      • Attention Layers
        • ScaledDotProductAttention
        • SelfAttention
        • SphericalHarmonics
        • SE3Attention
        • Fiber
        • SE3LayerNorm
        • SE3RadialFunc
        • SE3PairwiseConv
        • SE3Sum
        • SE3Cat
        • SE3AvgPooling
        • SE3MultiHeadAttention
        • SE3AttentiveSelfInteraction
        • SE3SelfInteraction
        • SE3GraphConv
        • SE3GraphNorm
        • SE3PartialEdgeConv
        • SE3ResidualAttention
      • Readout Layers
        • GroverReadout
    • Jax Layers
      • Linear
        • Linear.__init__()
    • Density Functional Theory Layers
      • DFTXC
        • DFTXC.__init__()
        • DFTXC.forward()
    • InceptionV3 Layers
    • MobileNetV2 Layers
      • InvertedResidual
        • InvertedResidual.__init__()
        • InvertedResidual.forward()
    • ChemCeption Layers
      • Stem
        • Stem.__init__()
        • Stem.forward()
      • InceptionResnetA
        • InceptionResnetA.__init__()
        • InceptionResnetA.forward()
      • InceptionResnetB
        • InceptionResnetB.__init__()
        • InceptionResnetB.forward()
      • InceptionResnetB
        • InceptionResnetB.__init__()
        • InceptionResnetB.forward()
      • ReductionA
        • ReductionA.__init__()
        • ReductionA.forward()
      • ReductionB
        • ReductionB.__init__()
        • ReductionB.forward()
  • Metrics
    • Metric Utilities
      • to_one_hot()
      • from_one_hot()
    • Metric Shape Handling
      • normalize_weight_shape()
      • normalize_labels_shape()
      • normalize_prediction_shape()
      • handle_classification_mode()
    • Metric Functions
      • matthews_corrcoef()
      • recall_score()
      • r2_score()
      • mean_squared_error()
      • mean_absolute_error()
      • precision_score()
      • precision_recall_curve()
      • auc()
      • jaccard_score()
      • f1_score()
      • roc_auc_score()
      • accuracy_score()
      • balanced_accuracy_score()
      • top_k_accuracy_score()
      • pearson_r2_score()
      • jaccard_index()
      • pixel_error()
      • prc_auc_score()
      • rms_score()
      • mae_score()
      • kappa_score()
      • bedroc_score()
      • concordance_index()
      • get_motif_scores()
      • get_pssm_scores()
      • in_silico_mutagenesis()
    • Metric Class
      • Metric
        • Metric.__init__()
        • Metric.compute_metric()
        • Metric.compute_singletask_metric()
  • Hyperparameter Tuning
    • Hyperparameter Optimization API
      • HyperparamOpt
        • HyperparamOpt.__init__()
        • HyperparamOpt.hyperparam_search()
    • Grid Hyperparameter Optimization
      • GridHyperparamOpt
        • GridHyperparamOpt.hyperparam_search()
    • Gaussian Process Hyperparameter Optimization
      • GaussianProcessHyperparamOpt
        • GaussianProcessHyperparamOpt.__init__()
        • GaussianProcessHyperparamOpt.hyperparam_search()
  • Metalearning
    • MetaLearner
      • MetaLearner
        • MetaLearner.compute_model()
        • MetaLearner.variables
        • MetaLearner.select_task()
        • MetaLearner.get_batch()
        • MetaLearner.parameters()
  • Tensorflow implementation
    • MAML
      • MAML
        • MAML.__init__()
        • MAML.fit()
        • MAML.restore()
        • MAML.train_on_current_task()
        • MAML.predict_on_batch()
  • Torch implementation
    • MAML
      • MAML
        • MAML.__init__()
        • MAML.fit()
        • MAML.restore()
        • MAML.train_on_current_task()
        • MAML.predict_on_batch()
        • MAML.save_checkpoint()
        • MAML.get_checkpoints()
  • Reinforcement Learning
    • Environments
      • Environment
        • Environment.__init__()
        • Environment.state
        • Environment.terminated
        • Environment.state_shape
        • Environment.state_dtype
        • Environment.n_actions
        • Environment.action_shape
        • Environment.reset()
        • Environment.step()
      • GymEnvironment
        • GymEnvironment.__init__()
        • GymEnvironment.reset()
        • GymEnvironment.step()
    • Policies
      • Policy
        • Policy.__init__()
        • Policy.create_model()
    • Tensorflow implementation
    • A2C
      • A2C
        • A2C.__init__()
        • A2C.fit()
        • A2C.predict()
        • A2C.select_action()
        • A2C.restore()
      • A2CLossDiscrete
        • A2CLossDiscrete.__init__()
    • PPO
      • PPO
        • PPO.__init__()
        • PPO.fit()
        • PPO.predict()
        • PPO.select_action()
        • PPO.restore()
      • PPOLoss
        • PPOLoss.__init__()
    • Torch implementation
      • A2CLossDiscrete
        • A2CLossDiscrete.__init__()
      • A2CLossContinuous
        • A2CLossContinuous.__init__()
    • A2C
      • A2C
        • A2C.__init__()
        • A2C.fit()
        • A2C.predict()
        • A2C.select_action()
        • A2C.restore()
        • A2C.save_checkpoint()
        • A2C.get_checkpoints()
    • PPO
      • PPO
        • PPO.__init__()
        • PPO.fit()
        • PPO.predict()
        • PPO.select_action()
        • PPO.restore()
        • PPO.save_checkpoint()
        • PPO.get_checkpoints()
      • PPOLoss
        • PPOLoss.__init__()
  • Docking
    • Binding Pocket Discovery
      • BindingPocketFinder
        • BindingPocketFinder.find_pockets()
      • ConvexHullPocketFinder
        • ConvexHullPocketFinder.__init__()
        • ConvexHullPocketFinder.find_all_pockets()
        • ConvexHullPocketFinder.find_pockets()
    • Pose Generation
      • PoseGenerator
        • PoseGenerator.generate_poses()
      • VinaPoseGenerator
        • VinaPoseGenerator.__init__()
        • VinaPoseGenerator.generate_poses()
      • GninaPoseGenerator
        • GninaPoseGenerator.__init__()
        • GninaPoseGenerator.generate_poses()
    • Docking
      • Docker
        • Docker.__init__()
        • Docker.dock()
    • Pose Scoring
      • pairwise_distances()
      • cutoff_filter()
      • vina_nonlinearity()
      • vina_repulsion()
      • vina_hydrophobic()
      • vina_hbond()
      • vina_gaussian_first()
      • vina_gaussian_second()
      • vina_energy_term()
  • Utilities
    • Data Utilities
      • Array Utilities
        • pad_array()
      • Data Directory
        • get_data_dir()
      • URL Handling
        • download_url()
      • File Handling
        • untargz_file()
        • unzip_file()
        • load_data()
        • load_sdf_files()
        • load_csv_files()
        • load_json_files()
        • load_pickle_files()
        • load_from_disk()
        • save_to_disk()
        • load_dataset_from_disk()
        • save_dataset_to_disk()
    • Molecular Utilities
      • ConformerGenerator
        • ConformerGenerator.__init__()
        • ConformerGenerator.generate_conformers()
        • ConformerGenerator.embed_molecule()
        • ConformerGenerator.get_molecule_force_field()
        • ConformerGenerator.minimize_conformers()
        • ConformerGenerator.get_conformer_energies()
        • ConformerGenerator.prune_conformers()
        • ConformerGenerator.get_conformer_rmsd()
      • MoleculeLoadException
        • MoleculeLoadException.__init__()
      • get_xyz_from_mol()
      • add_hydrogens_to_mol()
      • compute_charges()
      • load_molecule()
      • write_molecule()
    • Molecular Fragment Utilities
      • MolecularFragment
        • MolecularFragment.__init__()
        • MolecularFragment.GetAtoms()
        • MolecularFragment.GetNumAtoms()
        • MolecularFragment.GetCoords()
      • AtomShim
        • AtomShim.__init__()
        • AtomShim.GetAtomicNum()
        • AtomShim.GetPartialCharge()
        • AtomShim.GetCoords()
      • strip_hydrogens()
      • merge_molecular_fragments()
      • get_contact_atom_indices()
      • reduce_molecular_complex_to_contacts()
    • Coordinate Box Utilities
      • CoordinateBox
        • CoordinateBox.__init__()
        • CoordinateBox.__contains__()
        • CoordinateBox.center()
        • CoordinateBox.volume()
        • CoordinateBox.contains()
      • intersect_interval()
      • union()
      • merge_overlapping_boxes()
      • get_face_boxes()
    • Evaluation Utils
      • Evaluator
        • Evaluator.__init__()
        • Evaluator.output_statistics()
        • Evaluator.output_predictions()
        • Evaluator.compute_model_performance()
      • GeneratorEvaluator
        • GeneratorEvaluator.__init__()
        • GeneratorEvaluator.compute_model_performance()
      • relative_difference()
    • Genomic Utilities
      • seq_one_hot_encode()
      • encode_bio_sequence()
      • hhblits()
      • hhsearch()
      • MSA_to_dataset()
    • Geometry Utilities
      • unit_vector()
      • angle_between()
      • generate_random_unit_vector()
      • generate_random_rotation_matrix()
      • is_angle_within_cutoff()
    • Graph Utilities
      • fourier_encode_dist()
      • aggregate_mean()
      • aggregate_max()
      • aggregate_min()
      • aggregate_std()
      • aggregate_var()
      • aggregate_moment()
      • aggregate_sum()
      • scale_identity()
      • scale_amplification()
      • scale_attenuation()
    • Hash Function Utilities
      • hash_ecfp()
      • hash_ecfp_pair()
      • vectorize()
    • Voxel Utils
      • convert_atom_to_voxel()
      • convert_atom_pair_to_voxel()
      • voxelize()
    • Graph Convolution Utilities
      • one_hot_encode()
      • get_atom_type_one_hot()
      • construct_hydrogen_bonding_info()
      • get_atom_hydrogen_bonding_one_hot()
      • get_atom_is_in_aromatic_one_hot()
      • get_atom_hybridization_one_hot()
      • get_atom_total_num_Hs_one_hot()
      • get_atom_chirality_one_hot()
      • get_atom_formal_charge()
      • get_atom_partial_charge()
      • get_atom_total_degree_one_hot()
      • get_bond_type_one_hot()
      • get_bond_is_in_same_ring_one_hot()
      • get_bond_is_conjugated_one_hot()
      • get_bond_stereo_one_hot()
      • get_bond_graph_distance_one_hot()
    • Grover Utilities
      • extract_grover_attributes()
    • Debug Utilities
    • Docking Utilities
      • write_vina_conf()
      • write_gnina_conf()
      • load_docked_ligands()
      • prepare_inputs()
      • read_gnina_log()
      • Print Threshold
        • get_print_threshold()
        • set_print_threshold()
        • get_max_print_size()
        • set_max_print_size()
    • Fake Data Generator
      • FakeGraphGenerator
        • FakeGraphGenerator.__init__()
        • FakeGraphGenerator.sample()
    • Electron Sampler
      • ElectronSampler
        • ElectronSampler.__init__()
        • ElectronSampler.sampled_electrons
        • ElectronSampler.harmonic_mean()
        • ElectronSampler.log_prob_gaussian()
        • ElectronSampler.gauss_initialize_position()
        • ElectronSampler.electron_update()
        • ElectronSampler.move()
    • Density Functional Theory Utilities
      • Lattice
        • Lattice.__init__()
        • Lattice.lattice_vectors()
        • Lattice.recip_vectors()
        • Lattice.volume()
        • Lattice.params
        • Lattice.get_lattice_ls()
        • Lattice.get_gvgrids()
        • Lattice.estimate_ewald_eta()
      • SpinParam
        • SpinParam.__init__()
        • SpinParam.sum()
        • SpinParam.reduce()
        • SpinParam.apply_fcn()
      • ValGrad
        • ValGrad.__init__()
        • ValGrad.__add__()
        • ValGrad.__mul__()
      • CGTOBasis
        • CGTOBasis.__init__()
        • CGTOBasis.wfnormalize_()
      • AtomCGTOBasis
        • AtomCGTOBasis.__init__()
      • MulBaseXC
        • MulBaseXC.__init__()
        • MulBaseXC.family
        • MulBaseXC.get_vxc()
        • MulBaseXC.get_edensityxc()
        • MulBaseXC.getparamnames()
      • CalcLDALibXCPol
        • CalcLDALibXCPol.forward()
        • CalcLDALibXCPol.backward()
      • CalcLDALibXCUnpol
        • CalcLDALibXCUnpol.forward()
        • CalcLDALibXCUnpol.backward()
      • CalcGGALibXCUnpol
        • CalcGGALibXCUnpol.forward()
        • CalcGGALibXCUnpol.backward()
      • CalcGGALibXCPol
        • CalcGGALibXCPol.forward()
        • CalcGGALibXCPol.backward()
      • CalcMGGALibXCUnpol
        • CalcMGGALibXCUnpol.forward()
        • CalcMGGALibXCUnpol.backward()
      • CalcMGGALibXCPol
        • CalcMGGALibXCPol.forward()
        • CalcMGGALibXCPol.backward()
      • loadbasis()
      • _read_float()
      • _get_basis_file()
      • _normalize_basisname()
      • _download_basis()
      • _expand_angmoms()
      • BaseDF
        • BaseDF.build()
        • BaseDF.get_elrep()
        • BaseDF.j2c
        • BaseDF.j3c
        • BaseDF.getparamnames()
      • _Config
        • _Config.THRESHOLD_MEMORY
        • _Config.CHUNK_MEMORY
        • _Config.VERBOSE
        • _Config.Usage
        • _Config.__init__()
      • BaseOrbParams
        • BaseOrbParams.params2orb()
        • BaseOrbParams.orb2params()
      • QROrbParams
        • QROrbParams.params2orb()
        • QROrbParams.orb2params()
      • MatExpOrbParams
        • MatExpOrbParams.params2orb()
        • MatExpOrbParams.orb2params()
      • parse_moldesc
      • EditableModule
        • EditableModule.getparams()
        • EditableModule.setparams()
        • EditableModule.cached_getparamnames()
        • EditableModule.getparamnames()
        • EditableModule.getuniqueparams()
        • EditableModule.setuniqueparams()
        • EditableModule.assertparams()
      • normalize_bcast_dims()
      • get_bcasted_dims()
      • match_dim()
      • LinearOperator
        • LinearOperator.__new__()
        • LinearOperator.m()
        • LinearOperator.__init__()
        • LinearOperator.getlinopparams()
        • LinearOperator.uselinopparams()
        • LinearOperator.mv()
        • LinearOperator.mm()
        • LinearOperator.rmv()
        • LinearOperator.rmm()
        • LinearOperator.fullmatrix()
        • LinearOperator.scipy_linalg_op()
        • LinearOperator.getparamnames()
        • LinearOperator.H
        • LinearOperator.matmul()
        • LinearOperator.__add__()
        • LinearOperator.__sub__()
        • LinearOperator.dtype
        • LinearOperator.device
        • LinearOperator.shape
        • LinearOperator.is_hermitian
        • LinearOperator.is_mv_implemented
        • LinearOperator.is_mm_implemented
        • LinearOperator.is_rmv_implemented
        • LinearOperator.is_rmm_implemented
        • LinearOperator.is_fullmatrix_implemented
        • LinearOperator.is_getparamnames_implemented
      • AddLinearOperator
        • AddLinearOperator.__init__()
      • MulLinearOperator
        • MulLinearOperator.__init__()
      • AdjointLinearOperator
        • AdjointLinearOperator.__init__()
        • AdjointLinearOperator.H
      • MatmulLinearOperator
        • MatmulLinearOperator.__init__()
      • MatrixLinearOperator
        • MatrixLinearOperator.__init__()
      • PureFunction
        • PureFunction.__init__()
        • PureFunction.objparams()
        • PureFunction.set_objparams()
        • PureFunction.restore_objparams()
        • PureFunction.useobjparams()
        • PureFunction.disable_state_change()
      • FunctionPureFunction
      • EditableModulePureFunction
        • EditableModulePureFunction.__init__()
      • TorchNNPureFunction
        • TorchNNPureFunction.__init__()
      • PureFunction
        • PureFunction.__init__()
        • PureFunction.objparams()
        • PureFunction.set_objparams()
        • PureFunction.restore_objparams()
        • PureFunction.useobjparams()
        • PureFunction.disable_state_change()
      • _check_identical_objs()
      • get_pure_function()
      • set_default_option()
      • get_and_pop_keys()
      • get_method()
      • dummy_context_manager()
      • assert_runtime()
      • _set_initial_v()
      • _take_eigpairs()
      • exacteig()
      • degen_symeig()
      • davidson()
      • lsymeig()
      • usymeig()
      • symeig()
      • symeig_torchfcn
        • symeig_torchfcn.forward()
        • symeig_torchfcn.backward()
      • _check_degen()
      • ortho()
      • jac()
      • _Jac
        • _Jac.__init__()
      • _setup_idxs()
      • connect_graph()
      • wrap_gmres()
      • exactsolve()
      • solve_ABE()
      • get_batchdims()
      • setup_precond()
      • dot()
      • gmres()
      • setup_linear_problem()
      • safedenom()
      • get_largest_eival()
      • solve()
      • broyden1_solve()
      • _rootfinder_solve()
      • cg()
      • bicgstab()
      • solve_torchfcn
        • solve_torchfcn.forward()
        • solve_torchfcn.backward()
      • anderson_acc()
      • gd()
      • adam()
      • TerminationCondition()
      • _nonlin_solver()
      • broyden1()
      • broyden2()
      • linearmixing()
      • _safe_norm()
      • _nonline_line_search()
      • _scalar_search_armijo()
      • TerminationCondition()
      • Jacobian
        • Jacobian.setup()
        • Jacobian.solve()
        • Jacobian.update()
      • BroydenFirst
        • BroydenFirst.__init__()
        • BroydenFirst.setup()
        • BroydenFirst.solve()
        • BroydenFirst.update()
      • BroydenSecond
      • LinearMixing
        • LinearMixing.__init__()
        • LinearMixing.setup()
        • LinearMixing.solve()
        • LinearMixing.update()
      • LowRankMatrix
        • LowRankMatrix.__init__()
        • LowRankMatrix.mv()
        • LowRankMatrix.rmv()
        • LowRankMatrix.append()
        • LowRankMatrix.reduce()
      • FullRankMatrix
        • FullRankMatrix.__init__()
        • FullRankMatrix.mv()
        • FullRankMatrix.rmv()
        • FullRankMatrix.append()
        • FullRankMatrix.reduce()
      • rootfinder()
      • equilibrium()
      • minimize()
      • _RootFinder
        • _RootFinder.forward()
        • _RootFinder.backward()
      • _get_rootfinder_default_method()
      • _get_equilibrium_default_method()
      • _get_minimizer_default_method()
      • _Tableau
        • _Tableau.c
        • _Tableau.b
        • _Tableau.a
        • _Tableau.c
        • _Tableau.b
        • _Tableau.a
        • _Tableau.__getnewargs__()
        • _Tableau.__new__()
      • explicit_rk()
      • rk38_ivp()
      • fwd_euler_ivp()
      • rk4_ivp()
      • mid_point_ivp()
    • Attribute Utilities
      • get_attr
      • set_attr
      • del_attr
    • Polymer Weighted Directed Graph Data Utilities
      • handle_hydrogen()
      • make_polymer_mol()
      • parse_polymer_rules()
      • tag_atoms_in_repeating_unit()
      • onek_encoding_unk()
      • remove_wildcard_atoms()
      • Polymer Weighted Directed Graph String Validator
        • PolyWDGStringValidator
    • Polymer Conversion Utilities
      • PSMILES2WDGConverter
        • PSMILES2WDGConverter.__init__()
        • PSMILES2WDGConverter.index_wildcards()
        • PSMILES2WDGConverter.add_indicies_to_smiles_from_meta()
        • PSMILES2WDGConverter.make_wdgraph_string_from_meta()
        • PSMILES2WDGConverter.convert_smiles_to_SMARTS()
        • PSMILES2WDGConverter.convert_smiles_to_MOD_SMARTS()
        • PSMILES2WDGConverter.compose_from_meta()
        • PSMILES2WDGConverter.convert()
      • WDG2PSMILESConverter
        • WDG2PSMILESConverter.__init__()
        • WDG2PSMILESConverter.get_wildcard_bond_indecies()
        • WDG2PSMILESConverter.convert_smiles_part()
        • WDG2PSMILESConverter.replace_SMARTS()
        • WDG2PSMILESConverter.replace_mod_SMARTS()
        • WDG2PSMILESConverter.convert()
    • Pytorch Utilities
      • unsorted_segment_sum()
      • segment_sum()
      • chunkify()
      • get_memory()
      • gaussian_integral()
      • TensorNonTensorSeparator()
      • tallqr()
      • to_fortran_order()
      • get_np_dtype()
      • unsorted_segment_max()
      • unweighted_coul_ft()
      • get_complex_dtype()
    • Batch Utilities
      • batch_coulomb_matrix_features()
      • batch_elements()
      • create_input_array()
      • create_output_array()
    • Periodic Table Utilities
      • get_atomz()
    • Equivariance Utilities
      • su2_generators()
      • so3_generators()
      • change_basis_real_to_complex()
      • wigner_D()
      • semifactorial()
      • pochhammer()
      • lpmv()
      • SphericalHarmonics()
      • get_element()
      • get()
      • get_matrix_kernel()
      • basis_transformation_Q_J()
      • get_spherical_from_cartesian()
      • kron()
      • precompute_sh()
      • get_basis()
      • get_r()
      • get_equivariant_basis_and_r()
      • fiber2head()
      • LieGroup
        • LieGroup.rep_dim
        • LieGroup.lie_dim
        • LieGroup.q_dim
        • LieGroup.__init__()
        • LieGroup.exp()
        • LieGroup.log()
        • LieGroup.lifted_elems()
        • LieGroup.inv()
        • LieGroup.distance()
        • LieGroup.lift()
        • LieGroup.expand_like()
        • LieGroup.elems2pairs()
      • T
        • T.__init__()
        • T.exp()
        • T.log()
        • T.lifted_elems()
        • T.elems2pairs()
      • sinc()
      • sincc()
      • cosc()
      • coscc()
      • sinc_inv()
      • cross_matrix()
      • uncross_matrix()
      • SO3
        • SO3.lie_dim
        • SO3.rep_dim
        • SO3.q_dim
        • SO3.__init__()
        • SO3.exp()
        • SO3.log()
        • SO3.sample()
        • SO3.lifted_elems()
      • SE3
        • SE3.lie_dim
        • SE3.rep_dim
        • SE3.q_dim
        • SE3.__init__()
        • SE3.exp()
        • SE3.log()
        • SE3.lifted_elems()
        • SE3.distance()
    • Miscellaneous Utilities
      • indent()
      • shape2str()
      • memoize_method()
      • UnimplementedError
      • GetSetParamsError
      • ConvergenceWarning
      • MathWarning
      • Uniquifier
        • Uniquifier.__init__()
        • Uniquifier.get_unique_objs()
        • Uniquifier.map_unique_objs()
    • SafeOperations Utilities
      • safepow()
      • safenorm()
      • occnumber()
      • get_floor_and_ceil()
      • safe_cdist()
    • Lightning Utilities
      • collate_dataset_fn()
    • Caching Utils
      • FileSystemMutex()
      • cached_dirpklgz()

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