Get Started
API Reference
NumpyDataset
DiskDataset
ImageDataset
CSVLoader
UserCSVLoader
ImageLoader
JsonLoader
SDFLoader
FASTALoader
InMemoryLoader
DFTYamlLoader
SAMLoader
ConvMol
MultiConvMol
WeaveMol
GraphData
DFTSystem
DFTEntry
Dataset
DataLoader
load_bace_classification()
load_bace_regression()
load_bbbc001()
load_bbbc002()
load_bbbc004()
load_bbbp()
load_cell_counting()
load_chembl()
load_chembl25()
load_clearance()
load_clintox()
load_delaney()
load_factors()
load_freesolv()
load_hiv()
load_hopv()
load_hppb()
load_kaggle()
load_kinase()
load_lipo()
load_bandgap()
load_perovskite()
load_mp_formation_energy()
load_mp_metallicity()
load_muv()
load_nci()
load_pcba()
load_pdbbind()
load_ppb()
load_qm7()
load_qm8()
load_qm9()
load_sampl()
load_sider()
load_thermosol()
load_tox21()
load_toxcast()
load_uspto()
load_uv()
load_zinc15()
load_Platinum_Adsorption()
MACCSKeysFingerprint
MATFeaturizer
CircularFingerprint
PubChemFingerprint
Mol2VecFingerprint
RDKitDescriptors
MordredDescriptors
CoulombMatrix
CoulombMatrixEig
AtomicCoordinates
BPSymmetryFunctionInput
SmilesToSeq
SmilesToImage
OneHotFeaturizer
SparseMatrixOneHotFeaturizer
RawFeaturizer
SNAPFeaturizer
RdkitGridFeaturizer
AtomicConvFeaturizer
LCNNFeaturizer
SAMFeaturizer
SmilesTokenizer
BasicSmilesTokenizer
HuggingFaceFeaturizer
GroverAtomVocabTokenizer
GroverBondVocabTokenizer
GroverAtomVocabularyBuilder
GroverAtomVocabularyBuilder.__init__()
GroverAtomVocabularyBuilder.build()
GroverAtomVocabularyBuilder.build_from_csv()
GroverAtomVocabularyBuilder.save()
GroverAtomVocabularyBuilder.load()
GroverAtomVocabularyBuilder.atom_to_vocab()
GroverAtomVocabularyBuilder.encode()
PFMFeaturizer
BertFeaturizer
RobertaFeaturizer
RxnFeaturizer
BindingPocketFeaturizer
UserDefinedFeaturizer
DummyFeaturizer
Featurizer
MolecularFeaturizer
MaterialCompositionFeaturizer
MaterialStructureFeaturizer
ComplexFeaturizer
hf_vocab
RandomSplitter
RandomGroupSplitter
RandomStratifiedSplitter
SingletaskStratifiedSplitter
IndexSplitter
SpecifiedSplitter
TaskSplitter
ScaffoldSplitter
MolecularWeightSplitter
MaxMinSplitter
ButinaSplitter
FingerprintSplitter
Splitter
Splitter.k_fold_split()
Splitter.train_valid_test_split()
Splitter.train_test_split()
Splitter.split()
NormalizationTransformer
MinMaxTransformer
ClippingTransformer
LogTransformer
CDFTransformer
PowerTransformer
BalancingTransformer
DuplicateBalancingTransformer
ImageTransformer
FeaturizationTransformer
CoulombFitTransformer
IRVTransformer
DAGTransformer
RxnSplitTransformer
Transformer
Transformer.__init__()
Transformer.transform()
Transformer.transform_array()
Transformer.transform_on_array()
Transformer.untransform()
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()
SklearnModel
SklearnModel.__init__()
SklearnModel.fit()
SklearnModel.predict_on_batch()
SklearnModel.predict()
SklearnModel.save()
SklearnModel.reload()
GBDTModel
GBDTModel.__init__()
GBDTModel.fit()
GBDTModel.fit_with_eval()
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__()
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__()
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.__init__()
RobustMultitaskClassifier
RobustMultitaskClassifier.__init__()
RobustMultitaskClassifier.default_generator()
RobustMultitaskRegressor
RobustMultitaskRegressor.__init__()
RobustMultitaskRegressor.default_generator()
ProgressiveMultitaskClassifier
ProgressiveMultitaskClassifier.__init__()
ProgressiveMultitaskRegressor
ProgressiveMultitaskRegressor.__init__()
ProgressiveMultitaskRegressor.add_adapter()
ProgressiveMultitaskRegressor.fit()
ProgressiveMultitaskRegressor.fit_task()
WeaveModel
WeaveModel.__init__()
WeaveModel.compute_features_on_batch()
WeaveModel.default_generator()
DTNNModel
DTNNModel.__init__()
DTNNModel.compute_features_on_batch()
DTNNModel.default_generator()
DAGModel
DAGModel.__init__()
DAGModel.default_generator()
GraphConvModel
GraphConvModel.__init__()
GraphConvModel.default_generator()
MPNNModel
MPNNModel.__init__()
MPNNModel.default_generator()
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.__init__()
ScScoreModel.default_generator()
SeqToSeq
SeqToSeq.__init__()
SeqToSeq.fit_sequences()
SeqToSeq.predict_from_sequences()
SeqToSeq.predict_from_embeddings()
SeqToSeq.predict_embeddings()
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
TextCNNModel
TextCNNModel.__init__()
TextCNNModel.build_char_dict()
TextCNNModel.smiles_to_seq_batch()
TextCNNModel.default_generator()
TextCNNModel.smiles_to_seq()
AtomicConvModel
AtomicConvModel.__init__()
AtomicConvModel.default_generator()
AtomicConvModel.save()
AtomicConvModel.reload()
Smiles2Vec
Smiles2Vec.__init__()
Smiles2Vec.default_generator()
ChemCeption
ChemCeption.__init__()
ChemCeption.build_inception_module()
ChemCeption.default_generator()
NormalizingFlowModel
NormalizingFlowModel.__init__()
NormalizingFlowModel.create_nll()
NormalizingFlowModel.save()
NormalizingFlowModel.reload()
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.get_global_step()
TorchModel.load_from_pretrained()
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.__init__()
CNN.default_generator()
MultitaskRegressor
MultitaskRegressor.__init__()
MultitaskRegressor.default_generator()
MultitaskFitTransformRegressor
MultitaskFitTransformRegressor.__init__()
MultitaskFitTransformRegressor.default_generator()
MultitaskFitTransformRegressor.predict_on_generator()
MultitaskClassifier
MultitaskClassifier.__init__()
MultitaskClassifier.default_generator()
CGCNNModel
CGCNNModel.__init__()
GATModel
GATModel.__init__()
GCNModel
GCNModel.__init__()
AttentiveFPModel
AttentiveFPModel.__init__()
PagtnModel
PagtnModel.__init__()
AtomConvModel
AtomConvModel.__init__()
AtomConvModel.default_generator()
InfoGraphModel
InfoGraphModel.__init__()
InfoGraphModel.build_components()
InfoGraphModel.build_model()
InfoGraphModel.loss_func()
InfoGraphModel.restore()
InfoGraphStarModel
InfoGraphStarModel.__init__()
InfoGraphStarModel.build_components()
InfoGraphStarModel.build_model()
InfoGraphStarModel.loss_func()
InfoGraphStarModel.default_generator()
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.__init__()
InfoMax3DModular.build_components()
InfoMax3DModular.build_model()
InfoMax3DModular.loss_func()
LCNNModel
LCNNModel.__init__()
MEGNetModel
MEGNetModel.__init__()
MATModel
MATModel.__init__()
MATModel.pad_array()
MATModel.pad_sequence()
MATModel.default_generator()
NormalizingFlow
DMPNNModel
DMPNNModel.__init__()
DMPNNModel.default_generator()
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()
SeqToSeqModel
SeqToSeqModel.__init__()
SeqToSeqModel.fit_sequences()
SeqToSeqModel.predict_from_sequences()
SeqToSeqModel.predict_embedding()
SeqToSeqModel.predict_from_embedding()
GAN.forward()
GAN.discrim_loss_fn()
GAN.gen_loss_fn()
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.__init__()
WGANModel.create_generator_loss()
WGANModel.create_discriminator_loss()
Weave
Weave.__init__()
Weave.forward()
XCModel
XCModel.__init__()
DCLightningModule
DCLightningModule.__init__()
DCLightningModule.configure_optimizers()
DCLightningModule.training_step()
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.__init__()
PINNModel.default_generator()
HuggingFaceModel
HuggingFaceModel.__init__()
HuggingFaceModel.load_from_pretrained()
HuggingFaceModel.fit_generator()
Chemberta
Chemberta.__init__()
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()
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.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.forward()
DTNNStep.forward()
DTNNGather.forward()
GradientPenaltyLayer
GradientPenaltyLayer.__init__()
GradientPenaltyLayer.forward()
MolGANConvolutionLayer.forward()
MolGANAggregationLayer.forward()
MolGANMultiConvolutionLayer.forward()
MolGANEncoderLayer.forward()
EdgeNetwork.__init__()
EdgeNetwork.forward()
WeaveLayer.forward()
WeaveGather.forward()
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.forward()
FerminetElectronFeature
FerminetElectronFeature.__init__()
FerminetElectronFeature.forward()
FerminetEnvelope
FerminetEnvelope.__init__()
FerminetEnvelope.forward()
MXMNetLocalMessagePassing
MXMNetLocalMessagePassing.__init__()
MXMNetLocalMessagePassing.forward()
MXMNetSphericalBasisLayer
MXMNetSphericalBasisLayer.__init__()
MXMNetSphericalBasisLayer.forward()
GroverMPNEncoder
GroverAttentionHead
GroverMTBlock
GroverTransEncoder
GroverEmbedding
GroverAtomVocabPredictor
GroverBondVocabPredictor
GroverFunctionalGroupPredictor
GroverPretrain
GroverFinetune
ScaledDotProductAttention
SelfAttention
GroverReadout
Linear
Linear.__init__()
BaseNNXC
BaseNNXC.get_edensityxc()
BaseNNXC.getparamnames()
NNLDA
NNLDA.__init__()
NNLDA.get_edensityxc()
NNPBE
NNPBE.__init__()
NNPBE.get_edensityxc()
HybridXC
HybridXC.__init__()
HybridXC.family
HybridXC.get_edensityxc()
XCNNSCF
XCNNSCF.__init__()
XCNNSCF.get_xc()
XCNNSCF.run()
DFTXC
DFTXC.__init__()
DFTXC.forward()
to_one_hot()
from_one_hot()
normalize_weight_shape()
normalize_labels_shape()
normalize_prediction_shape()
handle_classification_mode()
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
Metric.__init__()
Metric.compute_metric()
Metric.compute_singletask_metric()
HyperparamOpt
HyperparamOpt.__init__()
HyperparamOpt.hyperparam_search()
GridHyperparamOpt
GridHyperparamOpt.hyperparam_search()
GaussianProcessHyperparamOpt
GaussianProcessHyperparamOpt.__init__()
GaussianProcessHyperparamOpt.hyperparam_search()
MetaLearner
MetaLearner.compute_model()
MetaLearner.variables
MetaLearner.select_task()
MetaLearner.get_batch()
MetaLearner.parameters()
MAML
MAML.__init__()
MAML.fit()
MAML.restore()
MAML.train_on_current_task()
MAML.predict_on_batch()
MAML.save_checkpoint()
MAML.get_checkpoints()
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()
Policy
Policy.__init__()
Policy.create_model()
A2C
A2C.__init__()
A2C.fit()
A2C.predict()
A2C.select_action()
A2C.restore()
A2CLossDiscrete
A2CLossDiscrete.__init__()
PPO
PPO.__init__()
PPO.fit()
PPO.predict()
PPO.select_action()
PPO.restore()
PPOLoss
PPOLoss.__init__()
BindingPocketFinder
BindingPocketFinder.find_pockets()
ConvexHullPocketFinder
ConvexHullPocketFinder.__init__()
ConvexHullPocketFinder.find_all_pockets()
ConvexHullPocketFinder.find_pockets()
PoseGenerator
PoseGenerator.generate_poses()
VinaPoseGenerator
VinaPoseGenerator.__init__()
VinaPoseGenerator.generate_poses()
GninaPoseGenerator
GninaPoseGenerator.__init__()
GninaPoseGenerator.generate_poses()
Docker
Docker.__init__()
Docker.dock()
pairwise_distances()
cutoff_filter()
vina_nonlinearity()
vina_repulsion()
vina_hydrophobic()
vina_hbond()
vina_gaussian_first()
vina_gaussian_second()
vina_energy_term()
pad_array()
get_data_dir()
download_url()
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()
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()
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()
CoordinateBox
CoordinateBox.__init__()
CoordinateBox.__contains__()
CoordinateBox.center()
CoordinateBox.volume()
CoordinateBox.contains()
intersect_interval()
union()
merge_overlapping_boxes()
get_face_boxes()
Evaluator
Evaluator.__init__()
Evaluator.output_statistics()
Evaluator.output_predictions()
Evaluator.compute_model_performance()
GeneratorEvaluator
GeneratorEvaluator.__init__()
GeneratorEvaluator.compute_model_performance()
relative_difference()
seq_one_hot_encode()
encode_bio_sequence()
hhblits()
hhsearch()
MSA_to_dataset()
unit_vector()
angle_between()
generate_random_unit_vector()
generate_random_rotation_matrix()
is_angle_within_cutoff()
fourier_encode_dist()
aggregate_mean()
aggregate_max()
aggregate_min()
aggregate_std()
aggregate_var()
aggregate_moment()
aggregate_sum()
scale_identity()
scale_amplification()
scale_attenuation()
hash_ecfp()
hash_ecfp_pair()
vectorize()
convert_atom_to_voxel()
convert_atom_pair_to_voxel()
voxelize()
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()
extract_grover_attributes()
write_vina_conf()
write_gnina_conf()
load_docked_ligands()
prepare_inputs()
read_gnina_log()
get_print_threshold()
set_print_threshold()
get_max_print_size()
set_max_print_size()
FakeGraphGenerator
FakeGraphGenerator.__init__()
FakeGraphGenerator.sample()
ElectronSampler
ElectronSampler.__init__()
ElectronSampler.sampled_electrons
ElectronSampler.harmonic_mean()
ElectronSampler.log_prob_gaussian()
ElectronSampler.gauss_initialize_position()
ElectronSampler.electron_update()
ElectronSampler.move()
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()
ValGrad
ValGrad.__init__()
ValGrad.__add__()
ValGrad.__mul__()
CGTOBasis
CGTOBasis.__init__()
CGTOBasis.wfnormalize_()
AtomCGTOBasis
AtomCGTOBasis.__init__()
BaseXC
BaseXC.family
BaseXC.get_edensityxc()
BaseXC.get_vxc()
BaseXC.getparamnames()
BaseXC.__add__()
BaseXC.__mul__()
BaseXC.__rmul__()
AddBaseXC
AddBaseXC.__init__()
AddBaseXC.family
AddBaseXC.get_vxc()
AddBaseXC.get_edensityxc()
AddBaseXC.getparamnames()
MulBaseXC
MulBaseXC.__init__()
MulBaseXC.family
MulBaseXC.get_vxc()
MulBaseXC.get_edensityxc()
MulBaseXC.getparamnames()
BaseGrid
BaseGrid.dtype
BaseGrid.device
BaseGrid.coord_type
BaseGrid.get_dvolume()
BaseGrid.get_rgrid()
BaseGrid.getparamnames()
BaseDF
BaseDF.build()
BaseDF.get_elrep()
BaseDF.j2c
BaseDF.j3c
BaseDF.getparamnames()
BaseHamilton
BaseHamilton.nao
BaseHamilton.kpts
BaseHamilton.df
BaseHamilton.build()
BaseHamilton.setup_grid()
BaseHamilton.get_nuclattr()
BaseHamilton.get_kinnucl()
BaseHamilton.get_overlap()
BaseHamilton.get_elrep()
BaseHamilton.get_exchange()
BaseHamilton.get_vext()
BaseHamilton.get_vxc()
BaseHamilton.ao_orb2dm()
BaseHamilton.aodm2dens()
BaseHamilton.get_e_hcore()
BaseHamilton.get_e_elrep()
BaseHamilton.get_e_exchange()
BaseHamilton.get_e_xc()
BaseHamilton.ao_orb_params2dm()
BaseHamilton.dm2ao_orb_params()
BaseHamilton.getparamnames()
KSCalc
KSCalc.__init__()
KSCalc.energy()
KSCalc.aodmtot()
KSCalc.dens()
KSCalc.force()
hashstr()
BaseQCCalc
BaseQCCalc.get_system()
BaseQCCalc.run()
BaseQCCalc.energy()
BaseQCCalc.aodm()
BaseQCCalc.dm2energy()
BaseQCCalc.getparamnames()
SpinParam.u
SpinParam.d
_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
BaseSystem
BaseSystem.densityfit()
BaseSystem.get_hamiltonian()
BaseSystem.set_cache()
BaseSystem.get_orbweight()
BaseSystem.get_nuclei_energy()
BaseSystem.setup_grid()
BaseSystem.get_grid()
BaseSystem.requires_grid()
BaseSystem.getparamnames()
BaseSystem.make_copy()
BaseSystem.atompos
BaseSystem.atomzs
BaseSystem.atommasses
BaseSystem.spin
BaseSystem.charge
BaseSystem.numel
BaseSystem.efield
RadialGrid
RadialGrid.__init__()
RadialGrid.coord_type
RadialGrid.dtype
RadialGrid.device
RadialGrid.get_dvolume()
RadialGrid.get_rgrid()
RadialGrid.__getitem__()
RadialGrid.getparamnames()
get_xw_integration
SlicedRadialGrid
SlicedRadialGrid.__init__()
BaseGridTransform
BaseGridTransform.x2r()
BaseGridTransform.get_drdx()
DE2Transformation
DE2Transformation.__init__()
DE2Transformation.x2r()
DE2Transformation.get_drdx()
LogM3Transformation
LogM3Transformation.__init__()
LogM3Transformation.x2r()
LogM3Transformation.get_drdx()
TreutlerM4Transformation
TreutlerM4Transformation.__init__()
TreutlerM4Transformation.x2r()
TreutlerM4Transformation.get_drdx()
get_grid_transform
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__()
_check_identical_objs()
get_pure_function()
set_default_option()
get_and_pop_keys()
get_method()
dummy_context_manager()
assert_runtime()
wrap_gmres()
exactsolve()
solve_ABE()
get_batchdims()
setup_precond()
dot()
gmres()
setup_linear_problem()
safedenom()
get_largest_eival()
get_attr
del_attr
unsorted_segment_sum()
segment_sum()
chunkify()
get_memory()
gaussian_integral()
TensorNonTensorSeparator()
tallqr()
to_fortran_order()
get_np_dtype()
batch_coulomb_matrix_features()
batch_elements()
create_input_array()
create_output_array()
su2_generators()
so3_generators()
change_basis_real_to_complex()
wigner_D()
indent()
shape2str()
Development Guide
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