Index

A

accuracy_score() (in module torch_molecule.utils.generic.metrics) add_fingerprint_feature() (in module torch_molecule.utils.graph.graph_from_smiles) aggregate() (GCNConv_BF method) (GCNConv_GRIN method) (GINConv_BF method) (GINConv_GRIN method) atom_feature_vector_to_dict() (in module torch_molecule.utils.graph.features) atom_to_feature_vector() (in module torch_molecule.utils.graph.features) AtomEncoder (class in torch_molecule.nn.gnn) AttentionWithNodeMask (class in torch_molecule.nn.attention) AttrMaskMolecularEncoder (class in torch_molecule.encoder.attrmask.modeling_attrmask)

autofit() (BaseMolecularPredictor method) (BFGNNMolecularPredictor method) (DIRMolecularPredictor method) (GNNMolecularPredictor method) (GREAMolecularPredictor method) (GRINMolecularPredictor method) (IRMMolecularPredictor method) (LSTMMolecularPredictor method) (RPGNNMolecularPredictor method) (SGIRMolecularPredictor method) (SMILESTransformerMolecularPredictor method) (SSRMolecularPredictor method)

B

BaseModel (class in torch_molecule.base.base) BaseMolecularEncoder (class in torch_molecule.base.encoder) BaseMolecularGenerator (class in torch_molecule.base.generator) BaseMolecularPredictor (class in torch_molecule.base.predictor)

BFGNNMolecularPredictor (class in torch_molecule.predictor.bfgnn.modeling_bfgnn) bond_feature_vector_to_dict() (in module torch_molecule.utils.graph.features) bond_to_feature_vector() (in module torch_molecule.utils.graph.features) BondEncoder (class in torch_molecule.nn.gnn) build_molecule_with_partial_charges() (in module torch_molecule.utils.graph.graph_to_smiles)

C

CATEGORICAL (ParameterType attribute) CategoricalEmbedder (class in torch_molecule.nn.embedder) check_valency() (in module torch_molecule.utils.graph.graph_to_smiles) check_valid() (in module torch_molecule.utils.graph.graph_to_smiles)

ClusterContinuousEmbedder (class in torch_molecule.nn.embedder) connect_fragments() (in module torch_molecule.utils.graph.graph_to_smiles) ContextPredMolecularEncoder (class in torch_molecule.encoder.contextpred.modeling_contextpred) correct_mol() (in module torch_molecule.utils.graph.graph_to_smiles) create_model_card() (in module torch_molecule.utils.hf)

D

data (SMILESDataset attribute) dataset_info() (in module torch_molecule.datasets) DeFoGMolecularGenerator (class in torch_molecule.generator.defog.modeling_defog)

DemoDiffMolecularGenerator (class in torch_molecule.generator.demodiff.modeling_demodiff) DigressMolecularGenerator (class in torch_molecule.generator.digress.modeling_digress) DIRMolecularPredictor (class in torch_molecule.predictor.dir.modeling_dir)

E

EdgePredMolecularEncoder (class in torch_molecule.encoder.edgepred.modeling_edgepred) encode() (AttrMaskMolecularEncoder method) (BaseMolecularEncoder method) (ContextPredMolecularEncoder method) (EdgePredMolecularEncoder method) (GraphMAEMolecularEncoder method) (HFPretrainedMolecularEncoder method) (InfoGraphMolecularEncoder method) (MoamaMolecularEncoder method) (SANDMolecularEncoder method) (SupervisedMolecularEncoder method)

F

fast_attn (AttentionWithNodeMask attribute) fit() (AttrMaskMolecularEncoder method) (BaseMolecularEncoder method) (BaseMolecularGenerator method) (BaseMolecularPredictor method) (BFGNNMolecularPredictor method) (ContextPredMolecularEncoder method) (DeFoGMolecularGenerator method) (DemoDiffMolecularGenerator method) (DigressMolecularGenerator method) (DIRMolecularPredictor method) (EdgePredMolecularEncoder method) (GDSSMolecularGenerator method) (GenMolMolecularGenerator method) (GNNMolecularPredictor method) (GraphDITMolecularGenerator method) (GraphGAMolecularGenerator method) (GraphMAEMolecularEncoder method) (GREAMolecularPredictor method) (GRINMolecularPredictor method) (HFPretrainedMolecularEncoder method) (HFPretrainedMolecularGenerator method) (InfoGraphMolecularEncoder method) (IRMMolecularPredictor method) (JTVAEMolecularGenerator method) (LSTMMolecularGenerator method) (LSTMMolecularPredictor method) (MoamaMolecularEncoder method) (MolGPTMolecularGenerator method) (Oracle method) (RPGNNMolecularPredictor method) (SANDMolecularEncoder method) (SGIRMolecularPredictor method) (SMILESTransformerMolecularPredictor method) (SSRMolecularPredictor method) (SupervisedMolecularEncoder method)

FLOAT (ParameterType attribute) forward() (AtomEncoder method) (AttentionWithNodeMask method) (BondEncoder method) (CategoricalEmbedder method) (ClusterContinuousEmbedder method) (GCNConv method) (GCNConv_BF method) (GCNConv_GRIN method) (GINConv method) (GINConv_BF method) (GINConv_GRIN method) (GNN_node method) (GNN_node_Virtualnode method) (MLP method) (TimestepEmbedder method)

G

GCNConv (class in torch_molecule.nn.gnn) GCNConv_BF (class in torch_molecule.nn.gnn) GCNConv_GRIN (class in torch_molecule.nn.gnn) GDSSMolecularGenerator (class in torch_molecule.generator.gdss.modeling_gdss) generate() (BaseMolecularGenerator method) (DeFoGMolecularGenerator method) (DemoDiffMolecularGenerator method) (DigressMolecularGenerator method) (GDSSMolecularGenerator method) (GenMolMolecularGenerator method) (GraphDITMolecularGenerator method) (GraphGAMolecularGenerator method) (HFPretrainedMolecularGenerator method) (JTVAEMolecularGenerator method) (LSTMMolecularGenerator method) (MolGPTMolecularGenerator method) GenMolMolecularGenerator (class in torch_molecule.generator.genmol.modeling_genmol) get_atom_feature_dims() (in module torch_molecule.utils.graph.features) get_augmented_property() (in module torch_molecule.utils.graph.graph_from_smiles)

get_bond_feature_dims() (in module torch_molecule.utils.graph.features) get_existing_repo_data() (in module torch_molecule.utils.hf) get_mol() (in module torch_molecule.utils.graph.graph_to_smiles) get_params() (BaseModel method) getmaccsfingerprint() (in module torch_molecule.utils.graph.features) getmorganfingerprint() (in module torch_molecule.utils.graph.features) GINConv (class in torch_molecule.nn.gnn) GINConv_BF (class in torch_molecule.nn.gnn) GINConv_GRIN (class in torch_molecule.nn.gnn) GNN_node (class in torch_molecule.nn.gnn) GNN_node_Virtualnode (class in torch_molecule.nn.gnn) GNNMolecularPredictor (class in torch_molecule.predictor.gnn.modeling_gnn) graph_from_smiles() (in module torch_molecule.utils.graph.graph_from_smiles) graph_to_smiles() (in module torch_molecule.utils.graph.graph_to_smiles) GraphDITMolecularGenerator (class in torch_molecule.generator.graph_dit.modeling_graph_dit) GraphGAMolecularGenerator (class in torch_molecule.generator.graph_ga.modeling_graph_ga) GraphMAEMolecularEncoder (class in torch_molecule.encoder.graphmae.modeling_graphmae) GREAMolecularPredictor (class in torch_molecule.predictor.grea.modeling_grea) GRINMolecularPredictor (class in torch_molecule.predictor.grin.modeling_grin) groups (SMILESDataset attribute)

H

HFPretrainedMolecularEncoder (class in torch_molecule.encoder.pretrained.modeling_pretrained)

HFPretrainedMolecularGenerator (class in torch_molecule.generator.pretrained.modeling_pretrained) HuggingFaceCheckpointManager (class in torch_molecule.utils.checkpoint)

I

info (SMILESDataset attribute) InfoGraphMolecularEncoder (class in torch_molecule.encoder.infograph.modeling_infograph) init_weights() (in module torch_molecule.utils.generic.weights)

INTEGER (ParameterType attribute) IRMMolecularPredictor (class in torch_molecule.predictor.irm.modeling_irm) is_fitted_ (BaseModel attribute)

J

JTVAEMolecularGenerator (class in torch_molecule.generator.jtvae.modeling_jtvae)

L

list_datasets() (in module torch_molecule.datasets) load() (BaseModel method) (HFPretrainedMolecularEncoder method) load_admet() (in module torch_molecule.datasets) load_broad6k() (in module torch_molecule.datasets) load_chembl2k() (in module torch_molecule.datasets) load_dataset() (in module torch_molecule.datasets) load_from_hf() (BaseModel method) (HFPretrainedMolecularEncoder method) load_from_local() (BaseModel method) (HFPretrainedMolecularGenerator method) (SANDMolecularEncoder method)

load_from_pretrained() (GenMolMolecularGenerator method) (SANDMolecularEncoder method) load_gasperm() (in module torch_molecule.datasets) load_model_from_hf() (HuggingFaceCheckpointManager static method) load_model_from_local() (LocalCheckpointManager static method) load_qm9() (in module torch_molecule.datasets) load_toxcast() (in module torch_molecule.datasets) load_zinc250k() (in module torch_molecule.datasets) LocalCheckpointManager (class in torch_molecule.utils.checkpoint) LOG_FLOAT (ParameterType attribute) LSTMMolecularGenerator (class in torch_molecule.generator.lstm.modeling_lstm) LSTMMolecularPredictor (class in torch_molecule.predictor.lstm.modeling_lstm)

M

mean_absolute_error() (in module torch_molecule.utils.generic.metrics) mean_squared_error() (in module torch_molecule.utils.generic.metrics) merge_task_configs() (in module torch_molecule.utils.hf) message() (GCNConv method) (GCNConv_BF method) (GCNConv_GRIN method) (GINConv method) (GINConv_BF method) (GINConv_GRIN method) MLP (class in torch_molecule.nn.mlp) MoamaMolecularEncoder (class in torch_molecule.encoder.moama.modeling_moama) model (BaseModel attribute) model_class (BaseModel attribute) module torch_molecule.generator.graph_ga.oracle torch_molecule.nn.attention torch_molecule.nn.embedder torch_molecule.nn.gnn torch_molecule.nn.mlp torch_molecule.utils.checker torch_molecule.utils.checkpoint torch_molecule.utils.format torch_molecule.utils.generic.metrics torch_molecule.utils.generic.pseudo_tasks torch_molecule.utils.generic.weights torch_molecule.utils.graph.features torch_molecule.utils.graph.graph_from_smiles torch_molecule.utils.graph.graph_to_smiles torch_molecule.utils.hf torch_molecule.utils.search

mol2smiles() (in module torch_molecule.utils.graph.graph_to_smiles) MolecularInputChecker (class in torch_molecule.utils.checker) MolGPTMolecularGenerator (class in torch_molecule.generator.molgpt.modeling_molgpt)

O

Oracle (class in torch_molecule.generator.graph_ga.oracle)

P

param_type (ParameterSpec attribute) ParameterSpec (class in torch_molecule.utils.search) ParameterType (class in torch_molecule.utils.search) parse_list_params() (in module torch_molecule.utils.search) predict() (BaseMolecularPredictor method) (BFGNNMolecularPredictor method) (DIRMolecularPredictor method) (GNNMolecularPredictor method) (GREAMolecularPredictor method) (GRINMolecularPredictor method) (IRMMolecularPredictor method) (LSTMMolecularPredictor method) (RPGNNMolecularPredictor method) (SGIRMolecularPredictor method) (SMILESTransformerMolecularPredictor method) (SSRMolecularPredictor method)

push_to_huggingface() (HuggingFaceCheckpointManager static method)

R

r2_score() (in module torch_molecule.utils.generic.metrics) roc_auc_score() (in module torch_molecule.utils.generic.metrics)

root_mean_squared_error() (in module torch_molecule.utils.generic.metrics) RPGNNMolecularPredictor (class in torch_molecule.predictor.rpgnn.modeling_rpgnn)

S

safe_index() (in module torch_molecule.utils.graph.features) SANDMolecularEncoder (class in torch_molecule.encoder.sand.modeling_sand) sanitize_config() (in module torch_molecule.utils.format) save() (BaseModel method) save_model_to_local() (LocalCheckpointManager static method) save_to_hf() (BaseModel method) save_to_local() (BaseModel method) (HFPretrainedMolecularGenerator method) (SANDMolecularEncoder method) select_atom_with_available_valency() (in module torch_molecule.utils.graph.graph_to_smiles)

select_atoms_with_available_valency() (in module torch_molecule.utils.graph.graph_to_smiles) serialize_config() (in module torch_molecule.utils.format) set_params() (BaseModel method) SGIRMolecularPredictor (class in torch_molecule.predictor.sgir.modeling_sgir) sigmoid() (in module torch_molecule.utils.generic.metrics) SMILESDataset (class in torch_molecule.datasets.constant) SMILESTransformerMolecularPredictor (class in torch_molecule.predictor.smiles_transformer.modeling_transformer) SSRMolecularPredictor (class in torch_molecule.predictor.ssr.modeling_ssr) subsample() (SMILESDataset method) suggest_parameter() (in module torch_molecule.utils.search) SupervisedMolecularEncoder (class in torch_molecule.encoder.supervised.modeling_supervised)

T

target (SMILESDataset attribute) target_names (SMILESDataset attribute) timestep_embedding() (TimestepEmbedder static method) TimestepEmbedder (class in torch_molecule.nn.embedder) torch_molecule.generator.graph_ga.oracle module torch_molecule.nn.attention module torch_molecule.nn.embedder module torch_molecule.nn.gnn module torch_molecule.nn.mlp module torch_molecule.utils.checker module torch_molecule.utils.checkpoint module torch_molecule.utils.format module

torch_molecule.utils.generic.metrics module torch_molecule.utils.generic.pseudo_tasks module torch_molecule.utils.generic.weights module torch_molecule.utils.graph.features module torch_molecule.utils.graph.graph_from_smiles module torch_molecule.utils.graph.graph_to_smiles module torch_molecule.utils.hf module torch_molecule.utils.search module train_test_split() (SMILESDataset method) try_to_connect_fragments() (in module torch_molecule.utils.graph.graph_to_smiles)

U

update() (GCNConv method) (GINConv method)

V

validate_inputs() (MolecularInputChecker static method)

validate_smiles() (MolecularInputChecker static method) value_range (ParameterSpec attribute)