deepchem
2.4.0
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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
Development Guide
Licensing and Commercial Uses
Contibuting to DeepChem as a Scientist
Scientist FAQ
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What if I want to release data? Can DeepChem help?
Is MoleculeNet just about molecules?
Does MoleculeNet allow for releasing data under different licenses?
Coding Conventions
Code Formatting
Linting
Docstrings
Unit Tests
Testing Machine Learning Models
Type Annotations
Infrastructures
GitHub
Conda Forge
Docker Hub
PyPI
Amazon Web Services
S3
Route 53
Certificate Manager
Cloudfront
GoDaddy
Digital Ocean
API Reference
Data
Datasets
NumpyDataset
DiskDataset
ImageDataset
Data Loaders
CSVLoader
UserCSVLoader
ImageLoader
JsonLoader
SDFLoader
FASTALoader
InMemoryLoader
Data Classes
Graph Data
Base Classes (for develop)
Dataset
DataLoader
MoleculeNet
Contributing a new dataset to MoleculeNet
BACE Dataset
BBBC Datasets
BBBP Datasets
Cell Counting Datasets
Chembl Datasets
Chembl25 Datasets
Clearance Datasets
Clintox Datasets
Delaney Datasets
Factors Datasets
HIV Datasets
HOPV Datasets
HPPB Datasets
KAGGLE Datasets
Kinase Datasets
Lipo Datasets
Materials Datasets
MUV Datasets
NCI Datasets
PCBA Datasets
PDBBIND Datasets
PPB Datasets
QM7 Datasets
QM8 Datasets
QM9 Datasets
SAMPL Datasets
SIDER Datasets
Thermosol Datasets
Tox21 Datasets
Toxcast Datasets
USPTO Datasets
UV Datasets
ZINC15 Datasets
Featurizers
Featurizer
MolecularFeaturizer
ConvMolFeaturizer
WeaveFeaturizer
MACCSKeysFingerprint
CircularFingerprint
PubChemFingerprint
Mol2VecFingerprint
RDKitDescriptors
MordredDescriptors
CoulombMatrix
CoulombMatrixEig
AtomCoordinates
SmilesToSeq
SmilesToImage
OneHotFeaturizer
ComplexFeaturizer
RdkitGridFeaturizer
AtomConvFeaturizer
MaterialStructureFeaturizer
SineCoulombMatrix
CGCNNFeaturizer
MaterialCompositionFeaturizer
ElementPropertyFingerprint
ElemNetFeaturizer
BindingPocketFeaturizer
UserDefinedFeaturizer
BPSymmetryFunctionInput
RawFeaturizer
Tokenizers
SmilesTokenizer
BasicSmilesTokenizer
Splitters
General Splitters
RandomSplitter
RandomGroupSplitter
RandomStratifiedSplitter
SingletaskStratifiedSplitter
IndexSplitter
SpecifiedSplitter
TaskSplitter
Molecule Splitters
ScaffoldSplitter
MolecularWeightSplitter
MaxMinSplitter
ButinaSplitter
FingerprintSplitter
Base Splitter (for develop)
Transformers
General Transformers
NormalizationTransformer
MinMaxTransformer
ClippingTransformer
LogTransformer
CDFTransformer
PowerTransformer
BalancingTransformer
DuplicateBalancingTransformer
ImageTransformer
FeaturizationTransformer
Specified Usecase Transformers
CoulombFitTransformer
IRVTransformer
DAGTransformer
ANITransformer
Base Transformer (for develop)
Model Classes
Model Cheatsheet
Model
Scikit-Learn Models
SklearnModel
Gradient Boosting Models
GBDTModel
Deep Learning Infrastructure
Losses
Optimizers
Keras Models
KerasModel
MultitaskRegressor
MultitaskFitTransformRegressor
MultitaskClassifier
TensorflowMultitaskIRVClassifier
RobustMultitaskClassifier
RobustMultitaskRegressor
ProgressiveMultitaskClassifier
ProgressiveMultitaskRegressor
WeaveModel
DTNNModel
DAGModel
GraphConvModel
MPNNModel
ScScoreModel
SeqToSeq
GAN
WGAN
CNN
TextCNNModel
AtomicConvModel
Smiles2Vec
ChemCeption
NormalizingFlowModel
PyTorch Models
TorchModel
CGCNNModel
GATModel
GCNModel
AttentiveFPModel
MPNNModel
Layers
Metrics
Metric Utilities
Metric Shape Handling
Metric Functions
Metric Class
Hyperparameter Tuning
Hyperparameter Optimization API
Grid Hyperparameter Optimization
Gaussian Process Hyperparameter Optimization
Metalearning
MetaLearner
MAML
Reinforcement Learning
Environments
Policies
A2C
PPO
Docking
Binding Pocket Discovery
Pose Generation
Docking
Pose Scoring
Utilities
Data Utilities
Array Utilities
Data Directory
URL Handling
File Handling
Molecular Utilities
Molecular Fragment Utilities
Coordinate Box Utilities
Evaluation Utils
Genomic Utilities
Geometry Utilities
Hash Function Utilities
Voxel Utils
Graph Convolution Utilities
Debug Utilities
Docking Utilities
Print Threshold
deepchem
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Index
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C
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E
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_
__call__() (A2CLossDiscrete method)
(ConformerGenerator method)
(Featurizer method)
(PPOLoss method)
__contains__() (CoordinateBox method)
__init__() (A2C method)
(A2CLossDiscrete method)
(AdaGrad method)
(Adam method)
(ANIFeat method)
(ANITransformer method)
(AtomicConvModel method)
(AtomicConvolution method)
(AtomicCoordinates method)
(AtomShim method)
(AttentiveFPModel method)
(AttnLSTMEmbedding method)
(BalancingTransformer method)
(BasicSmilesTokenizer method)
(BPSymmetryFunctionInput method)
(ButinaSplitter method)
(CDFTransformer method)
(CGCNNFeaturizer method)
(CGCNNModel method)
(ChemCeption method)
(CircularFingerprint method)
(ClippingTransformer method)
(CNN method)
(CombineMeanStd method)
(ConformerGenerator method)
(ConvexHullPocketFinder method)
(ConvMol method)
(ConvMolFeaturizer method)
(CoordinateBox method)
(CoulombFitTransformer method)
(CoulombMatrix method)
(CoulombMatrixEig method)
(CSVLoader method)
(DAGGather method)
(DAGLayer method)
(DAGModel method)
(DAGTransformer method)
(DataLoader method)
(Dataset method)
(DiskDataset method)
(Docker method)
(DTNNEmbedding method)
(DTNNGather method)
(DTNNModel method)
(DTNNStep method)
(DuplicateBalancingTransformer method)
(ElementPropertyFingerprint method)
(Environment method)
(Evaluator method)
(ExponentialDecay method)
(FASTALoader method)
(FeaturizationTransformer method)
(FingerprintSplitter method)
(GAN method)
(GATModel method)
(GBDTModel method)
(GCNModel method)
(GeneratorEvaluator method)
(GradientDescent method)
(GraphCNN method)
(GraphConv method)
(GraphConvModel method)
(GraphData method)
(GraphGather method)
(GraphPool method)
(GymEnvironment method)
(Highway method)
(HyperparamOpt method)
(ImageDataset method)
(ImageLoader method)
(ImageTransformer method)
(InMemoryLoader method)
(InteratomicL2Distances method)
(IRVTransformer method)
(IterRefLSTMEmbedding method)
(JsonLoader method)
(KerasModel method)
(LinearCosineDecay method)
(LogTransformer method)
(LSTMStep method)
(MACCSKeysFingerprint method)
(MAML method)
(MessagePassing method)
(Metric method)
(MinMaxTransformer method)
(Model method)
(Mol2VecFingerprint method)
(MolecularFragment method)
(MoleculeLoadException method)
(MordredDescriptors method)
(MPNNModel method)
,
[1]
(MultiConvMol method)
(MultitaskClassifier method)
(MultitaskFitTransformRegressor method)
(MultitaskRegressor method)
(NeighborList method)
(NeighborListComplexAtomicCoordinates method)
(NormalizationTransformer method)
(NormalizingFlowModel method)
(NumpyDataset method)
(OneHotFeaturizer method)
(Optimizer method)
(Policy method)
(PolynomialDecay method)
(PowerTransformer method)
(PPO method)
(PPOLoss method)
(ProgressiveMultitaskClassifier method)
(ProgressiveMultitaskRegressor method)
(PubChemFingerprint method)
(RandomGroupSplitter method)
(RawFeaturizer method)
(RDKitDescriptors method)
(RdkitGridFeaturizer method)
(RMSProp method)
(RobustMultitaskClassifier method)
(RobustMultitaskRegressor method)
(ScScoreModel method)
(SDFLoader method)
(SeqToSeq method)
(SetGather method)
(SineCoulombMatrix method)
(SingletaskStratifiedSplitter method)
(SklearnModel method)
(Smiles2Vec method)
(SmilesToImage method)
(SmilesTokenizer method)
(SmilesToSeq method)
(SpecifiedSplitter method)
(TaskSplitter method)
(TensorflowMultitaskIRVClassifier method)
(TextCNNModel method)
(TorchModel method)
(Transformer method)
(UserCSVLoader method)
(UserDefinedFeaturizer method)
(VinaPoseGenerator method)
(WeaveFeaturizer method)
(WeaveGather method)
(WeaveLayer method)
(WeaveModel method)
(WeaveMol method)
(WeightedLinearCombo method)
(WGAN method)
__len__() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
__module__ (GraphConvConstants attribute)
(MultiConvMol attribute)
(WeaveMol attribute)
A
A2C (class in deepchem.rl.a2c)
A2CLossDiscrete (class in deepchem.rl.a2c)
accuracy_score() (in module deepchem.metrics)
action_shape() (Environment property)
AdaGrad (class in deepchem.models.optimizers)
Adam (class in deepchem.models.optimizers)
add_adapter() (ProgressiveMultitaskRegressor method)
add_hydrogens_to_mol() (in module deepchem.utils.rdkit_utils)
add_padding_tokens() (SmilesTokenizer method)
add_shard() (DiskDataset method)
add_special_tokens_ids_sequence_pair() (SmilesTokenizer method)
add_special_tokens_ids_single_sequence() (SmilesTokenizer method)
add_special_tokens_single_sequence() (SmilesTokenizer method)
agglomerate_mols() (ConvMol static method)
AlphaShareLayer (class in deepchem.models.layers)
angle_between() (in module deepchem.utils.geometry_utils)
angular_symmetry() (ANIFeat method)
(ANITransformer method)
ANIFeat (class in deepchem.models.layers)
ANITransformer (class in deepchem.trans)
atom_features() (in module deepchem.feat.graph_features)
atom_to_id() (in module deepchem.feat.graph_features)
AtomicConvModel (class in deepchem.models)
AtomicConvolution (class in deepchem.models.layers)
AtomicCoordinates (class in deepchem.feat)
AtomShim (class in deepchem.utils.fragment_utils)
AttentiveFPModel (class in deepchem.models)
AttnLSTMEmbedding (class in deepchem.models.layers)
auc() (in module deepchem.metrics)
B
balanced_accuracy_score() (in module deepchem.metrics)
BalancingTransformer (class in deepchem.trans)
BasicSmilesTokenizer (class in deepchem.feat)
bedroc_score() (in module deepchem.metrics)
BetaShare (class in deepchem.models.layers)
BinaryCrossEntropy (class in deepchem.models.losses)
BindingPocketFeaturizer (class in deepchem.feat)
BindingPocketFinder (class in deepchem.dock.binding_pocket)
bond_fdim_base (GraphConvConstants attribute)
bond_features() (in module deepchem.feat.graph_features)
BPSymmetryFunctionInput (class in deepchem.feat)
build() (AlphaShareLayer method)
(ANITransformer method)
(AtomicConvolution method)
(AttnLSTMEmbedding method)
(BetaShare method)
(DAGGather method)
(DAGLayer method)
(DTNNEmbedding method)
(DTNNGather method)
(DTNNStep method)
(EdgeNetwork method)
(GatedRecurrentUnit method)
(GraphCNN method)
(GraphConv method)
(GraphEmbedPoolLayer method)
(Highway method)
(IterRefLSTMEmbedding method)
(LSTMStep method)
(MessagePassing method)
(SetGather method)
(VinaFreeEnergy method)
(WeaveGather method)
(WeaveLayer method)
(WeightedLinearCombo method)
build_char_dict() (TextCNNModel static method)
build_inception_module() (ChemCeption method)
ButinaSplitter (class in deepchem.splits)
C
call() (AlphaShareLayer method)
(ANIFeat method)
(AtomicConvolution method)
(AttnLSTMEmbedding method)
(BetaShare method)
(CombineMeanStd method)
(DAGGather method)
(DAGLayer method)
(DTNNEmbedding method)
(DTNNGather method)
(DTNNStep method)
(EdgeNetwork method)
(GatedRecurrentUnit method)
(GraphCNN method)
(GraphConv method)
(GraphEmbedPoolLayer method)
(GraphGather method)
(GraphPool method)
(Highway method)
(InteratomicL2Distances method)
(IterRefLSTMEmbedding method)
(LSTMStep method)
(MessagePassing method)
(NeighborList method)
(SetGather method)
(SluiceLoss method)
(Stack method)
(SwitchedDropout method)
(VinaFreeEnergy method)
(WeaveGather method)
(WeaveLayer method)
(WeightedLinearCombo method)
CategoricalCrossEntropy (class in deepchem.models.losses)
CDFTransformer (class in deepchem.trans)
center() (CoordinateBox method)
CGCNNFeaturizer (class in deepchem.feat)
CGCNNModel (class in deepchem.models)
ChemCeption (class in deepchem.models)
CircularFingerprint (class in deepchem.feat)
ClippingTransformer (class in deepchem.trans)
CNN (class in deepchem.models)
CombineMeanStd (class in deepchem.models.layers)
complete_shuffle() (DiskDataset method)
ComplexFeaturizer (class in deepchem.feat)
compute_charges() (in module deepchem.utils.rdkit_utils)
compute_features_on_batch() (DTNNModel method)
(WeaveModel method)
compute_metric() (Metric method)
compute_model() (MetaLearner method)
compute_model_performance() (Evaluator method)
(GeneratorEvaluator method)
compute_nbr_list() (NeighborList method)
compute_saliency() (KerasModel method)
(TorchModel method)
compute_singletask_metric() (Metric method)
concordance_index() (in module deepchem.metrics)
ConformerGenerator (class in deepchem.utils.conformers)
construct_hydrogen_bonding_info() (in module deepchem.utils.molecule_feature_utils)
contains() (CoordinateBox method)
convert_atom_pair_to_voxel() (in module deepchem.utils.voxel_utils)
convert_atom_to_voxel() (in module deepchem.utils.voxel_utils)
convert_tokens_to_string() (SmilesTokenizer method)
ConvexHullPocketFinder (class in deepchem.dock.binding_pocket)
ConvMol (class in deepchem.feat.mol_graphs)
ConvMolFeaturizer (class in deepchem.feat)
CoordinateBox (class in deepchem.utils.coordinate_box_utils)
copy() (DiskDataset method)
cosine_dist() (in module deepchem.models.layers)
coulomb_matrix() (CoulombMatrix method)
CoulombFitTransformer (class in deepchem.trans)
CoulombMatrix (class in deepchem.feat)
CoulombMatrixEig (class in deepchem.feat)
create_dataset() (CSVLoader method)
(DataLoader method)
(DiskDataset static method)
(FASTALoader method)
(ImageLoader method)
(InMemoryLoader method)
(JsonLoader method)
(SDFLoader method)
(UserCSVLoader method)
create_discriminator() (GAN method)
create_discriminator_loss() (GAN method)
(WGAN method)
create_generator() (GAN method)
create_generator_loss() (GAN method)
(WGAN method)
create_model() (Policy method)
create_nll() (NormalizingFlowModel method)
CSVLoader (class in deepchem.data)
cutoff_filter() (in module deepchem.dock.pose_scoring)
D
DAGGather (class in deepchem.models.layers)
DAGLayer (class in deepchem.models.layers)
DAGModel (class in deepchem.models)
DAGTransformer (class in deepchem.trans)
data_dir (DiskDataset attribute)
DataLoader (class in deepchem.data)
Dataset (class in deepchem.data)
default_generator() (AtomicConvModel method)
(ChemCeption method)
(CNN method)
(DAGModel method)
(DTNNModel method)
(GraphConvModel method)
(KerasModel method)
(MPNNModel method)
(MultitaskClassifier method)
(MultitaskFitTransformRegressor method)
(MultitaskRegressor method)
(RobustMultitaskClassifier method)
(RobustMultitaskRegressor method)
(ScScoreModel method)
(Smiles2Vec method)
(TextCNNModel method)
(TorchModel method)
(WeaveModel method)
descriptors (MordredDescriptors attribute)
(RDKitDescriptors attribute)
DiskDataset (class in deepchem.data)
distance_cutoff() (ANIFeat method)
(ANITransformer method)
distance_matrix() (ANIFeat method)
(ANITransformer method)
(AtomicConvolution method)
distance_tensor() (AtomicConvolution method)
dock() (Docker method)
Docker (class in deepchem.dock.docking)
download_url() (in module deepchem.utils.data_utils)
DTNNEmbedding (class in deepchem.models.layers)
DTNNGather (class in deepchem.models.layers)
DTNNModel (class in deepchem.models)
DTNNStep (class in deepchem.models.layers)
DuplicateBalancingTransformer (class in deepchem.trans)
E
edge_features (GraphData attribute)
edge_index (GraphData attribute)
EdgeNetwork (class in deepchem.models.layers)
ElementPropertyFingerprint (class in deepchem.feat)
ElemNetFeaturizer (class in deepchem.feat)
embed_molecule() (ConformerGenerator method)
encode_bio_sequence() (in module deepchem.utils.genomics_utils)
Environment (class in deepchem.rl)
evaluate() (Model method)
evaluate_generator() (KerasModel method)
(TorchModel method)
Evaluator (class in deepchem.utils.evaluate)
expand() (CoulombFitTransformer method)
ExponentialDecay (class in deepchem.models.optimizers)
F
f1_score() (in module deepchem.metrics)
FASTALoader (class in deepchem.data)
features_to_id() (in module deepchem.feat.graph_features)
FeaturizationTransformer (class in deepchem.trans)
featurize() (BindingPocketFeaturizer method)
(ComplexFeaturizer method)
(DataLoader method)
(Featurizer method)
(MaterialCompositionFeaturizer method)
(MaterialStructureFeaturizer method)
(MolecularFeaturizer method)
Featurizer (class in deepchem.feat)
find_all_pockets() (ConvexHullPocketFinder method)
find_distance() (in module deepchem.feat.graph_features)
find_pockets() (BindingPocketFinder method)
(ConvexHullPocketFinder method)
FingerprintSplitter (class in deepchem.splits)
fit() (A2C method)
(GBDTModel method)
(KerasModel method)
(MAML method)
(Model method)
(PPO method)
(ProgressiveMultitaskRegressor method)
(SklearnModel method)
(TorchModel method)
fit_gan() (GAN method)
fit_generator() (KerasModel method)
(TorchModel method)
fit_on_batch() (KerasModel method)
(Model method)
(TorchModel method)
fit_sequences() (SeqToSeq method)
fit_task() (ProgressiveMultitaskRegressor method)
fit_with_eval() (GBDTModel method)
from_dataframe() (Dataset static method)
(DiskDataset static method)
(ImageDataset static method)
(NumpyDataset static method)
from_DiskDataset() (NumpyDataset static method)
from_json() (NumpyDataset static method)
from_numpy() (DiskDataset static method)
from_one_hot() (in module deepchem.metrics)
G
GAN (class in deepchem.models)
GatedRecurrentUnit (class in deepchem.models.layers)
GATModel (class in deepchem.models)
gaussian_distance_matrix() (AtomicConvolution method)
gaussian_first() (VinaFreeEnergy method)
gaussian_histogram() (WeaveGather method)
gaussian_second() (VinaFreeEnergy method)
GaussianProcessHyperparamOpt (class in deepchem.hyper)
GBDTModel (class in deepchem.models)
GCNModel (class in deepchem.models)
generate_conformers() (ConformerGenerator method)
generate_poses() (PoseGenerator method)
(VinaPoseGenerator method)
generate_random_rotation_matrix() (in module deepchem.utils.geometry_utils)
generate_random_unit_vector() (in module deepchem.utils.geometry_utils)
generate_scaffolds() (ScaffoldSplitter method)
GeneratorEvaluator (class in deepchem.utils.evaluate)
get_adjacency_list() (ConvMol method)
get_atom_chirality_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_atom_features() (ConvMol method)
(MultiConvMol method)
(WeaveMol method)
get_atom_formal_charge() (in module deepchem.utils.molecule_feature_utils)
get_atom_hybridization_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_atom_hydrogen_bonding_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_atom_is_in_aromatic_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_atom_partial_charge() (in module deepchem.utils.molecule_feature_utils)
get_atom_total_degree_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_atom_total_num_Hs_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_atom_type_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_atoms_in_nbrs() (NeighborList method)
get_atoms_with_deg() (ConvMol method)
get_batch() (MetaLearner method)
get_bond_graph_distance_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_bond_is_conjugated_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_bond_is_in_same_ring_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_bond_stereo_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_bond_type_one_hot() (in module deepchem.utils.molecule_feature_utils)
get_cells() (NeighborList method)
get_cells_for_atoms() (NeighborList method)
get_checkpoints() (KerasModel method)
(TorchModel method)
get_closest_atoms() (NeighborList method)
get_conditional_input_shapes() (GAN method)
get_config() (AlphaShareLayer method)
(ANIFeat method)
(AtomicConvolution method)
(AttnLSTMEmbedding method)
(BetaShare method)
(CombineMeanStd method)
(DAGGather method)
(DAGLayer method)
(DTNNEmbedding method)
(DTNNGather method)
(DTNNStep method)
(EdgeNetwork method)
(GatedRecurrentUnit method)
(GraphCNN method)
(GraphConv method)
(GraphEmbedPoolLayer method)
(GraphGather method)
(GraphPool method)
(Highway method)
(InteratomicL2Distances method)
(IterRefLSTMEmbedding method)
(LSTMStep method)
(MessagePassing method)
(NeighborList method)
(SetGather method)
(SluiceLoss method)
(Stack method)
(SwitchedDropout method)
(VinaFreeEnergy method)
(WeaveGather method)
(WeaveLayer method)
(WeightedLinearCombo method)
get_conformer_energies() (ConformerGenerator method)
get_conformer_rmsd() (ConformerGenerator static method)
get_contact_atom_indices() (in module deepchem.utils.fragment_utils)
get_data_dir() (in module deepchem.utils.data_utils)
get_data_input_shapes() (GAN method)
get_data_shape() (DiskDataset method)
get_deg_adjacency_lists() (ConvMol method)
(MultiConvMol method)
get_deg_slice() (ConvMol method)
get_face_boxes() (in module deepchem.utils.coordinate_box_utils)
get_feature_list() (in module deepchem.feat.graph_features)
get_global_step() (KerasModel method)
(TorchModel method)
get_interatomic_distances() (CoulombMatrix static method)
get_intervals() (in module deepchem.feat.graph_features)
get_label_means() (DiskDataset method)
get_label_stds() (DiskDataset method)
get_max_print_size() (in module deepchem.utils.debug_utils)
get_model_filename() (Model static method)
get_molecule_force_field() (ConformerGenerator method)
get_motif_scores() (in module deepchem.metrics.genomic_metrics)
get_neighbor_cells() (NeighborList method)
get_noise_batch() (GAN method)
get_noise_input_shape() (GAN method)
get_null_mol() (ConvMol static method)
get_num_atoms() (MultiConvMol method)
(WeaveMol method)
get_num_atoms_with_deg() (ConvMol method)
get_num_features() (WeaveMol method)
get_num_molecules() (MultiConvMol method)
get_num_tasks() (Model method)
get_number_shards() (DiskDataset method)
get_pair_edges() (WeaveMol method)
get_pair_features() (WeaveMol method)
get_params_filename() (Model static method)
get_print_threshold() (in module deepchem.utils.debug_utils)
get_pssm_scores() (in module deepchem.metrics.genomic_metrics)
get_shape() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
get_shard() (DiskDataset method)
get_shard_ids() (DiskDataset method)
get_shard_size() (DiskDataset method)
get_shard_w() (DiskDataset method)
get_shard_y() (DiskDataset method)
get_statistics() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
get_task_names() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
get_task_type() (Model method)
get_vector() (ElemNetFeaturizer method)
get_xyz_from_mol() (in module deepchem.utils.rdkit_utils)
GetAtomicNum() (AtomShim method)
GetAtoms() (MolecularFragment method)
GetCoords() (AtomShim method)
(MolecularFragment method)
GetNumAtoms() (MolecularFragment method)
GetPartialCharge() (AtomShim method)
GradientDescent (class in deepchem.models.optimizers)
GraphCNN (class in deepchem.models.layers)
GraphConv (class in deepchem.models.layers)
GraphConvConstants (class in deepchem.feat.graph_features)
GraphConvModel (class in deepchem.models)
GraphData (class in deepchem.feat.graph_data)
GraphEmbedPoolLayer (class in deepchem.models.layers)
GraphGather (class in deepchem.models.layers)
GraphPool (class in deepchem.models.layers)
GridHyperparamOpt (class in deepchem.hyper)
GymEnvironment (class in deepchem.rl)
H
handle_classification_mode() (in module deepchem.metrics)
hash_ecfp() (in module deepchem.utils.hash_utils)
hash_ecfp_pair() (in module deepchem.utils.hash_utils)
Highway (class in deepchem.models.layers)
HingeLoss (class in deepchem.models.losses)
hydrogen_bond() (VinaFreeEnergy method)
hydrophobic() (VinaFreeEnergy method)
hyperparam_search() (GaussianProcessHyperparamOpt method)
(GridHyperparamOpt method)
(HyperparamOpt method)
HyperparamOpt (class in deepchem.hyper)
I
id_to_features() (in module deepchem.feat.graph_features)
ids() (Dataset property)
(DiskDataset property)
(ImageDataset property)
(NumpyDataset property)
ImageDataset (class in deepchem.data)
ImageLoader (class in deepchem.data)
ImageTransformer (class in deepchem.trans)
in_silico_mutagenesis() (in module deepchem.metrics.genomic_metrics)
IndexSplitter (class in deepchem.splits)
InMemoryLoader (class in deepchem.data)
InteratomicL2Distances (class in deepchem.models.layers)
intersect_interval() (in module deepchem.utils.coordinate_box_utils)
intervals (GraphConvConstants attribute)
IRVTransformer (class in deepchem.trans)
is_angle_within_cutoff() (in module deepchem.utils.geometry_utils)
iterbatches() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
IterRefLSTMEmbedding (class in deepchem.models.layers)
itersamples() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
itershards() (DiskDataset method)
J
jaccard_index() (in module deepchem.metrics)
jaccard_score() (in module deepchem.metrics)
JsonLoader (class in deepchem.data)
K
k_fold_split() (ButinaSplitter method)
(FingerprintSplitter method)
(IndexSplitter method)
(MaxMinSplitter method)
(MolecularWeightSplitter method)
(RandomGroupSplitter method)
(RandomSplitter method)
(RandomStratifiedSplitter method)
(ScaffoldSplitter method)
(SingletaskStratifiedSplitter method)
(SpecifiedSplitter method)
(Splitter method)
(TaskSplitter method)
kappa_score() (in module deepchem.metrics)
KerasModel (class in deepchem.models)
L
L1Loss (class in deepchem.models.losses)
L2Loss (class in deepchem.models.losses)
LearningRateSchedule (class in deepchem.models.optimizers)
legacy_metadata (DiskDataset attribute)
LinearCosineDecay (class in deepchem.models.optimizers)
load_bace_classification() (in module deepchem.molnet)
load_bace_regression() (in module deepchem.molnet)
load_bandgap() (in module deepchem.molnet)
load_bbbc001() (in module deepchem.molnet)
load_bbbc002() (in module deepchem.molnet)
load_bbbp() (in module deepchem.molnet)
load_cell_counting() (in module deepchem.molnet)
load_chembl() (in module deepchem.molnet)
load_chembl25() (in module deepchem.molnet)
load_clearance() (in module deepchem.molnet)
load_clintox() (in module deepchem.molnet)
load_csv_files() (in module deepchem.utils.data_utils)
load_data() (in module deepchem.utils.data_utils)
load_dataset_from_disk() (in module deepchem.utils.data_utils)
load_delaney() (in module deepchem.molnet)
load_docked_ligands() (in module deepchem.utils.vina_utils)
load_factors() (in module deepchem.molnet)
load_from_disk() (in module deepchem.utils.data_utils)
load_from_pretrained() (KerasModel method)
(TorchModel method)
load_hiv() (in module deepchem.molnet)
load_hopv() (in module deepchem.molnet)
load_hppb() (in module deepchem.molnet)
load_json_files() (in module deepchem.utils.data_utils)
load_kaggle() (in module deepchem.molnet)
load_kinase() (in module deepchem.molnet)
load_lipo() (in module deepchem.molnet)
load_metadata() (DiskDataset method)
load_molecule() (in module deepchem.utils.rdkit_utils)
load_mp_formation_energy() (in module deepchem.molnet)
load_mp_metallicity() (in module deepchem.molnet)
load_muv() (in module deepchem.molnet)
load_nci() (in module deepchem.molnet)
load_pcba() (in module deepchem.molnet)
load_pdbbind() (in module deepchem.molnet)
load_perovskite() (in module deepchem.molnet)
load_pickle_files() (in module deepchem.utils.data_utils)
load_ppb() (in module deepchem.molnet)
load_qm7() (in module deepchem.molnet)
load_qm8() (in module deepchem.molnet)
load_qm9() (in module deepchem.molnet)
load_sampl() (in module deepchem.molnet)
load_sdf_files() (in module deepchem.utils.data_utils)
load_sider() (in module deepchem.molnet)
load_thermosol() (in module deepchem.molnet)
load_tox21() (in module deepchem.molnet)
load_toxcast() (in module deepchem.molnet)
load_uspto() (in module deepchem.molnet)
load_uv() (in module deepchem.molnet)
load_zinc15() (in module deepchem.molnet)
LogTransformer (class in deepchem.trans)
Loss (class in deepchem.models.losses)
LSTMStep (class in deepchem.models.layers)
M
MACCSKeysFingerprint (class in deepchem.feat)
mae_score() (in module deepchem.metrics)
make_pytorch_dataset() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
make_tf_dataset() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
MAML (class in deepchem.metalearning)
MaterialCompositionFeaturizer (class in deepchem.feat)
MaterialStructureFeaturizer (class in deepchem.feat)
matrix_mul() (IRVTransformer static method)
matthews_corrcoef() (in module deepchem.metrics)
MaxMinSplitter (class in deepchem.splits)
mean_absolute_error() (in module deepchem.metrics)
mean_squared_error() (in module deepchem.metrics)
memory_cache_size() (DiskDataset property)
merge() (DiskDataset static method)
(NumpyDataset static method)
merge_molecular_fragments() (in module deepchem.utils.fragment_utils)
merge_overlapping_boxes() (in module deepchem.utils.coordinate_box_utils)
MessagePassing (class in deepchem.models.layers)
metadata_df (DiskDataset attribute)
MetaLearner (class in deepchem.metalearning)
Metric (class in deepchem.metrics)
minimize_conformers() (ConformerGenerator method)
MinMaxTransformer (class in deepchem.trans)
Model (class in deepchem.models)
Mol2VecFingerprint (class in deepchem.feat)
MolecularFeaturizer (class in deepchem.feat)
MolecularFragment (class in deepchem.utils.fragment_utils)
MolecularWeightSplitter (class in deepchem.splits)
MoleculeLoadException (class in deepchem.utils.rdkit_utils)
MordredDescriptors (class in deepchem.feat)
move() (DiskDataset method)
MPNNModel (class in deepchem.models)
(class in deepchem.models.torch_models)
MultiConvMol (class in deepchem.feat.mol_graphs)
MultitaskClassifier (class in deepchem.models)
MultitaskFitTransformRegressor (class in deepchem.models)
MultitaskRegressor (class in deepchem.models)
N
n_actions() (Environment property)
NeighborList (class in deepchem.models.layers)
NeighborListComplexAtomicCoordinates (class in deepchem.feat)
node_features (GraphData attribute)
node_pos_features (GraphData attribute)
nonlinearity() (VinaFreeEnergy method)
NormalizationTransformer (class in deepchem.trans)
normalize() (CoulombFitTransformer method)
normalize_labels_shape() (in module deepchem.metrics)
normalize_prediction_shape() (in module deepchem.metrics)
normalize_weight_shape() (in module deepchem.metrics)
NormalizingFlowModel (class in deepchem.models.normalizing_flows)
num_edges (GraphData attribute)
num_edges_features (GraphData attribute)
num_node_features (GraphData attribute)
num_nodes (GraphData attribute)
NumpyDataset (class in deepchem.data)
O
one_hot_encode() (in module deepchem.utils.molecule_feature_utils)
one_of_k_encoding() (in module deepchem.feat.graph_features)
one_of_k_encoding_unk() (in module deepchem.feat.graph_features)
OneHotFeaturizer (class in deepchem.feat)
Optimizer (class in deepchem.models.optimizers)
output_predictions() (Evaluator method)
output_statistics() (Evaluator method)
P
pad_array() (in module deepchem.utils.data_utils)
pad_smile() (OneHotFeaturizer method)
pair_features() (in module deepchem.feat.graph_features)
pairwise_distances() (in module deepchem.dock.pose_scoring)
pearson_r2_score() (in module deepchem.metrics)
pixel_error() (in module deepchem.metrics)
Policy (class in deepchem.rl)
PolynomialDecay (class in deepchem.models.optimizers)
PoseGenerator (class in deepchem.dock.pose_generation)
possible_atom_list (GraphConvConstants attribute)
possible_bond_stereo (GraphConvConstants attribute)
possible_chirality_list (GraphConvConstants attribute)
possible_formal_charge_list (GraphConvConstants attribute)
possible_hybridization_list (GraphConvConstants attribute)
possible_number_radical_e_list (GraphConvConstants attribute)
possible_numH_list (GraphConvConstants attribute)
possible_valence_list (GraphConvConstants attribute)
PowerTransformer (class in deepchem.trans)
PPO (class in deepchem.rl.ppo)
PPOLoss (class in deepchem.rl.ppo)
prc_auc_score() (in module deepchem.metrics)
precision_recall_curve() (in module deepchem.metrics)
precision_score() (in module deepchem.metrics)
predict() (A2C method)
(KerasModel method)
(Model method)
(PPO method)
(SklearnModel method)
(TorchModel method)
predict_embedding() (KerasModel method)
(TorchModel method)
predict_embeddings() (SeqToSeq method)
predict_from_embeddings() (SeqToSeq method)
predict_from_sequences() (SeqToSeq method)
predict_gan_generator() (GAN method)
predict_on_batch() (KerasModel method)
(MAML method)
(Model method)
(SklearnModel method)
(TorchModel method)
predict_on_generator() (KerasModel method)
(MultitaskFitTransformRegressor method)
(TorchModel method)
predict_uncertainty() (KerasModel method)
(TorchModel method)
predict_uncertainty_on_batch() (KerasModel method)
(TorchModel method)
prepare_inputs() (in module deepchem.utils.vina_utils)
ProgressiveMultitaskClassifier (class in deepchem.models)
ProgressiveMultitaskRegressor (class in deepchem.models)
prune_conformers() (ConformerGenerator method)
PubChemFingerprint (class in deepchem.feat)
R
r2_score() (in module deepchem.metrics)
radial_cutoff() (AtomicConvolution method)
radial_symmetry() (ANIFeat method)
(ANITransformer method)
radial_symmetry_function() (AtomicConvolution method)
RandomGroupSplitter (class in deepchem.splits)
randomize_coulomb_matrix() (CoulombMatrix method)
RandomSplitter (class in deepchem.splits)
RandomStratifiedSplitter (class in deepchem.splits)
RawFeaturizer (class in deepchem.feat)
RDKitDescriptors (class in deepchem.feat)
RdkitGridFeaturizer (class in deepchem.feat)
realize() (CoulombFitTransformer method)
(IRVTransformer method)
recall_score() (in module deepchem.metrics)
reduce_molecular_complex_to_contacts() (in module deepchem.utils.fragment_utils)
reference_lists (GraphConvConstants attribute)
relative_difference() (in module deepchem.utils.evaluate)
reload() (Model method)
(NormalizingFlowModel method)
(SklearnModel method)
remove_pad() (SmilesToSeq method)
repulsion() (VinaFreeEnergy method)
reset() (Environment method)
(GymEnvironment method)
reshard() (DiskDataset method)
restore() (A2C method)
(KerasModel method)
(MAML method)
(PPO method)
(TorchModel method)
rms_score() (in module deepchem.metrics)
RMSProp (class in deepchem.models.optimizers)
RobustMultitaskClassifier (class in deepchem.models)
RobustMultitaskRegressor (class in deepchem.models)
roc_auc_score() (in module deepchem.metrics)
S
safe_index() (in module deepchem.feat.graph_features)
save() (Model method)
(NormalizingFlowModel method)
(SklearnModel method)
save_checkpoint() (KerasModel method)
(TorchModel method)
save_dataset_to_disk() (in module deepchem.utils.data_utils)
save_to_disk() (DiskDataset method)
(in module deepchem.utils.data_utils)
save_vocabulary() (SmilesTokenizer method)
ScaffoldSplitter (class in deepchem.splits)
ScScoreModel (class in deepchem.models)
SDFLoader (class in deepchem.data)
select() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
select_action() (A2C method)
(PPO method)
select_task() (MetaLearner method)
seq_one_hot_encode() (in module deepchem.utils.genomics_utils)
SeqToSeq (class in deepchem.models)
set_max_print_size() (in module deepchem.utils.debug_utils)
set_print_threshold() (in module deepchem.utils.debug_utils)
set_shard() (DiskDataset method)
SetGather (class in deepchem.models.layers)
ShannonEntropy (class in deepchem.models.losses)
shuffle_each_shard() (DiskDataset method)
shuffle_shards() (DiskDataset method)
SigmoidCrossEntropy (class in deepchem.models.losses)
SineCoulombMatrix (class in deepchem.feat)
SingletaskStratifiedSplitter (class in deepchem.splits)
SklearnModel (class in deepchem.models)
SluiceLoss (class in deepchem.models.layers)
Smiles2Vec (class in deepchem.models)
smiles_from_seq() (SmilesToSeq method)
smiles_to_seq() (TextCNNModel method)
smiles_to_seq_batch() (TextCNNModel method)
SmilesToImage (class in deepchem.feat)
SmilesTokenizer (class in deepchem.feat)
SmilesToSeq (class in deepchem.feat)
SoftmaxCrossEntropy (class in deepchem.models.losses)
sparse_shuffle() (DiskDataset method)
SparseSoftmaxCrossEntropy (class in deepchem.models.losses)
SpecifiedSplitter (class in deepchem.splits)
split() (ButinaSplitter method)
(FingerprintSplitter method)
(IndexSplitter method)
(MaxMinSplitter method)
(MolecularWeightSplitter method)
(RandomGroupSplitter method)
(RandomSplitter method)
(RandomStratifiedSplitter method)
(ScaffoldSplitter method)
(SingletaskStratifiedSplitter method)
(SpecifiedSplitter method)
(Splitter method)
(TaskSplitter method)
Splitter (class in deepchem.splits)
Stack (class in deepchem.models.layers)
state() (Environment property)
state_dtype() (Environment property)
state_shape() (Environment property)
step() (Environment method)
(GymEnvironment method)
strip_hydrogens() (in module deepchem.utils.fragment_utils)
subset() (DiskDataset method)
sum_neigh() (GraphConv method)
SwitchedDropout (class in deepchem.models.layers)
T
TaskSplitter (class in deepchem.splits)
TensorflowMultitaskIRVClassifier (class in deepchem.models)
terminated() (Environment property)
TextCNNModel (class in deepchem.models)
to_dataframe() (Dataset method)
(DiskDataset method)
(ImageDataset method)
(NumpyDataset method)
to_dgl_graph() (GraphData method)
to_json() (NumpyDataset static method)
to_one_hot() (in module deepchem.metrics)
to_pyg_graph() (GraphData method)
to_seq() (SmilesToSeq method)
tokenize() (BasicSmilesTokenizer method)
TorchModel (class in deepchem.models)
train_on_current_task() (MAML method)
train_test_split() (ButinaSplitter method)
(FingerprintSplitter method)
(IndexSplitter method)
(MaxMinSplitter method)
(MolecularWeightSplitter method)
(RandomGroupSplitter method)
(RandomSplitter method)
(RandomStratifiedSplitter method)
(ScaffoldSplitter method)
(SingletaskStratifiedSplitter method)
(SpecifiedSplitter method)
(Splitter method)
(TaskSplitter method)
train_valid_test_split() (ButinaSplitter method)
(FingerprintSplitter method)
(IndexSplitter method)
(MaxMinSplitter method)
(MolecularWeightSplitter method)
(RandomGroupSplitter method)
(RandomSplitter method)
(RandomStratifiedSplitter method)
(ScaffoldSplitter method)
(SingletaskStratifiedSplitter method)
(SpecifiedSplitter method)
(Splitter method)
(TaskSplitter method)
transform() (ANITransformer method)
(BalancingTransformer method)
(CDFTransformer method)
(ClippingTransformer method)
(CoulombFitTransformer method)
(DAGTransformer method)
(Dataset method)
(DiskDataset method)
(DuplicateBalancingTransformer method)
(FeaturizationTransformer method)
(ImageDataset method)
(ImageTransformer method)
(IRVTransformer method)
(LogTransformer method)
(MinMaxTransformer method)
(NormalizationTransformer method)
(NumpyDataset method)
(PowerTransformer method)
(Transformer method)
transform_array() (ANITransformer method)
(BalancingTransformer method)
(CDFTransformer method)
(ClippingTransformer method)
(CoulombFitTransformer method)
(DAGTransformer method)
(DuplicateBalancingTransformer method)
(FeaturizationTransformer method)
(ImageTransformer method)
(IRVTransformer method)
(LogTransformer method)
(MinMaxTransformer method)
(NormalizationTransformer method)
(PowerTransformer method)
(Transformer method)
transform_on_array() (ANITransformer method)
(BalancingTransformer method)
(CDFTransformer method)
(ClippingTransformer method)
(CoulombFitTransformer method)
(DAGTransformer method)
(DuplicateBalancingTransformer method)
(FeaturizationTransformer method)
(ImageTransformer method)
(IRVTransformer method)
(LogTransformer method)
(MinMaxTransformer method)
(NormalizationTransformer method)
(PowerTransformer method)
(Transformer method)
Transformer (class in deepchem.trans)
U
UG_to_DAG() (DAGTransformer method)
union() (in module deepchem.utils.coordinate_box_utils)
unit_vector() (in module deepchem.utils.geometry_utils)
untargz_file() (in module deepchem.utils.data_utils)
untransform() (ANITransformer method)
(BalancingTransformer method)
(CDFTransformer method)
(ClippingTransformer method)
(CoulombFitTransformer method)
(DAGTransformer method)
(DuplicateBalancingTransformer method)
(FeaturizationTransformer method)
(ImageTransformer method)
(IRVTransformer method)
(LogTransformer method)
(MinMaxTransformer method)
(NormalizationTransformer method)
(OneHotFeaturizer method)
(PowerTransformer method)
(Transformer method)
untransform_grad() (NormalizationTransformer method)
unzip_file() (in module deepchem.utils.data_utils)
UserCSVLoader (class in deepchem.data)
UserDefinedFeaturizer (class in deepchem.feat)
V
VAE_ELBO (class in deepchem.models.losses)
VAE_KLDivergence (class in deepchem.models.losses)
variables() (MetaLearner property)
vectorize() (in module deepchem.utils.hash_utils)
vina_energy_term() (in module deepchem.dock.pose_scoring)
vina_gaussian_first() (in module deepchem.dock.pose_scoring)
vina_gaussian_second() (in module deepchem.dock.pose_scoring)
vina_hbond() (in module deepchem.dock.pose_scoring)
vina_hydrophobic() (in module deepchem.dock.pose_scoring)
vina_nonlinearity() (in module deepchem.dock.pose_scoring)
vina_repulsion() (in module deepchem.dock.pose_scoring)
VinaFreeEnergy (class in deepchem.models.layers)
VinaPoseGenerator (class in deepchem.dock.pose_generation)
vocab_size() (SmilesTokenizer property)
volume() (CoordinateBox method)
voxelize() (in module deepchem.utils.voxel_utils)
W
w() (Dataset property)
(DiskDataset property)
(ImageDataset property)
(NumpyDataset property)
WeaveFeaturizer (class in deepchem.feat)
WeaveGather (class in deepchem.models.layers)
WeaveLayer (class in deepchem.models.layers)
WeaveModel (class in deepchem.models)
WeaveMol (class in deepchem.feat.mol_graphs)
WeightedLinearCombo (class in deepchem.models.layers)
WGAN (class in deepchem.models)
write_data_to_disk() (DiskDataset static method)
write_molecule() (in module deepchem.utils.rdkit_utils)
write_vina_conf() (in module deepchem.utils.vina_utils)
X
X() (Dataset property)
(DiskDataset property)
(ImageDataset property)
(NumpyDataset property)
X_transform() (CoulombFitTransformer method)
(IRVTransformer method)
Y
y() (Dataset property)
(DiskDataset property)
(ImageDataset property)
(NumpyDataset property)
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