Index

A

accuracy_score() (in module torch_molecule.utils.generic.metrics) add_fingerprint_feature() (in module torch_molecule.utils.graph.graph_from_smiles) 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() (torch_molecule.base.predictor.BaseMolecularPredictor method) (torch_molecule.predictor.dir.modeling_dir.DIRMolecularPredictor method) (torch_molecule.predictor.gnn.modeling_gnn.GNNMolecularPredictor method) (torch_molecule.predictor.grea.modeling_grea.GREAMolecularPredictor method) (torch_molecule.predictor.irm.modeling_irm.IRMMolecularPredictor method) (torch_molecule.predictor.lstm.modeling_lstm.LSTMMolecularPredictor method) (torch_molecule.predictor.rpgnn.modeling_rpgnn.RPGNNMolecularPredictor method) (torch_molecule.predictor.sgir.modeling_sgir.SGIRMolecularPredictor method) (torch_molecule.predictor.smiles_transformer.modeling_transformer.SMILESTransformerMolecularPredictor method) (torch_molecule.predictor.ssr.modeling_ssr.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)

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 (torch_molecule.utils.search.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

DEFAULT_METRICS (torch_molecule.base.predictor.BaseMolecularPredictor attribute) device (torch_molecule.base.base.BaseModel attribute)

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() (torch_molecule.base.encoder.BaseMolecularEncoder method) (torch_molecule.encoder.attrmask.modeling_attrmask.AttrMaskMolecularEncoder method) (torch_molecule.encoder.contextpred.modeling_contextpred.ContextPredMolecularEncoder method) (torch_molecule.encoder.edgepred.modeling_edgepred.EdgePredMolecularEncoder method) (torch_molecule.encoder.graphmae.modeling_graphmae.GraphMAEMolecularEncoder method) (torch_molecule.encoder.infograph.modeling_infograph.InfoGraphMolecularEncoder method) (torch_molecule.encoder.moama.modeling_moama.MoamaMolecularEncoder method) (torch_molecule.encoder.pretrained.modeling_pretrained.HFPretrainedMolecularEncoder method) (torch_molecule.encoder.supervised.modeling_supervised.SupervisedMolecularEncoder method)

F

fast_attn (torch_molecule.nn.attention.AttentionWithNodeMask attribute) fit() (torch_molecule.base.encoder.BaseMolecularEncoder method) (torch_molecule.base.generator.BaseMolecularGenerator method) (torch_molecule.base.predictor.BaseMolecularPredictor method) (torch_molecule.encoder.attrmask.modeling_attrmask.AttrMaskMolecularEncoder method) (torch_molecule.encoder.contextpred.modeling_contextpred.ContextPredMolecularEncoder method) (torch_molecule.encoder.edgepred.modeling_edgepred.EdgePredMolecularEncoder method) (torch_molecule.encoder.graphmae.modeling_graphmae.GraphMAEMolecularEncoder method) (torch_molecule.encoder.infograph.modeling_infograph.InfoGraphMolecularEncoder method) (torch_molecule.encoder.moama.modeling_moama.MoamaMolecularEncoder method) (torch_molecule.encoder.pretrained.modeling_pretrained.HFPretrainedMolecularEncoder method) (torch_molecule.encoder.supervised.modeling_supervised.SupervisedMolecularEncoder method) (torch_molecule.generator.digress.modeling_digress.DigressMolecularGenerator method) (torch_molecule.generator.gdss.modeling_gdss.GDSSMolecularGenerator method) (torch_molecule.generator.graph_dit.modeling_graph_dit.GraphDITMolecularGenerator method) (torch_molecule.generator.graph_ga.modeling_graph_ga.GraphGAMolecularGenerator method) (torch_molecule.generator.graph_ga.oracle.Oracle method) (torch_molecule.generator.molgpt.modeling_molgpt.MolGPTMolecularGenerator method) (torch_molecule.predictor.dir.modeling_dir.DIRMolecularPredictor method) (torch_molecule.predictor.gnn.modeling_gnn.GNNMolecularPredictor method) (torch_molecule.predictor.grea.modeling_grea.GREAMolecularPredictor method) (torch_molecule.predictor.irm.modeling_irm.IRMMolecularPredictor method) (torch_molecule.predictor.lstm.modeling_lstm.LSTMMolecularPredictor method) (torch_molecule.predictor.rpgnn.modeling_rpgnn.RPGNNMolecularPredictor method) (torch_molecule.predictor.sgir.modeling_sgir.SGIRMolecularPredictor method) (torch_molecule.predictor.smiles_transformer.modeling_transformer.SMILESTransformerMolecularPredictor method) (torch_molecule.predictor.ssr.modeling_ssr.SSRMolecularPredictor method)

FLOAT (torch_molecule.utils.search.ParameterType attribute) forward() (torch_molecule.nn.attention.AttentionWithNodeMask method) (torch_molecule.nn.embedder.CategoricalEmbedder method) (torch_molecule.nn.embedder.ClusterContinuousEmbedder method) (torch_molecule.nn.embedder.TimestepEmbedder method) (torch_molecule.nn.gnn.AtomEncoder method) (torch_molecule.nn.gnn.BondEncoder method) (torch_molecule.nn.gnn.GCNConv method) (torch_molecule.nn.gnn.GINConv method) (torch_molecule.nn.gnn.GNN_node method) (torch_molecule.nn.gnn.GNN_node_Virtualnode method) (torch_molecule.nn.mlp.MLP method)

G

GCNConv (class in torch_molecule.nn.gnn) GDSSMolecularGenerator (class in torch_molecule.generator.gdss.modeling_gdss) generate() (torch_molecule.base.generator.BaseMolecularGenerator method) (torch_molecule.generator.digress.modeling_digress.DigressMolecularGenerator method) (torch_molecule.generator.gdss.modeling_gdss.GDSSMolecularGenerator method) (torch_molecule.generator.graph_dit.modeling_graph_dit.GraphDITMolecularGenerator method) (torch_molecule.generator.graph_ga.modeling_graph_ga.GraphGAMolecularGenerator method) (torch_molecule.generator.molgpt.modeling_molgpt.MolGPTMolecularGenerator method) 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() (torch_molecule.base.base.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) 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)

H

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

HuggingFaceCheckpointManager (class in torch_molecule.utils.checkpoint)

I

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

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

L

load() (torch_molecule.base.base.BaseModel method) (torch_molecule.encoder.pretrained.modeling_pretrained.HFPretrainedMolecularEncoder method) load_from_hf() (torch_molecule.base.base.BaseModel method) (torch_molecule.encoder.pretrained.modeling_pretrained.HFPretrainedMolecularEncoder method) load_from_local() (torch_molecule.base.base.BaseModel method)

load_model_from_hf() (torch_molecule.utils.checkpoint.HuggingFaceCheckpointManager static method) load_model_from_local() (torch_molecule.utils.checkpoint.LocalCheckpointManager static method) LocalCheckpointManager (class in torch_molecule.utils.checkpoint) LOG_FLOAT (torch_molecule.utils.search.ParameterType attribute) 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() (torch_molecule.nn.gnn.GCNConv method) (torch_molecule.nn.gnn.GINConv method) MLP (class in torch_molecule.nn.mlp) MoamaMolecularEncoder (class in torch_molecule.encoder.moama.modeling_moama) model (torch_molecule.base.base.BaseModel attribute) model_class (torch_molecule.base.base.BaseModel attribute) model_name (torch_molecule.base.base.BaseModel attribute) (torch_molecule.base.encoder.BaseMolecularEncoder attribute) (torch_molecule.base.generator.BaseMolecularGenerator attribute) (torch_molecule.base.predictor.BaseMolecularPredictor 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)

N

num_task (torch_molecule.base.predictor.BaseMolecularPredictor attribute)

O

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

P

param_type (torch_molecule.utils.search.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() (torch_molecule.base.predictor.BaseMolecularPredictor method) (torch_molecule.predictor.dir.modeling_dir.DIRMolecularPredictor method) (torch_molecule.predictor.gnn.modeling_gnn.GNNMolecularPredictor method) (torch_molecule.predictor.grea.modeling_grea.GREAMolecularPredictor method) (torch_molecule.predictor.irm.modeling_irm.IRMMolecularPredictor method) (torch_molecule.predictor.lstm.modeling_lstm.LSTMMolecularPredictor method) (torch_molecule.predictor.rpgnn.modeling_rpgnn.RPGNNMolecularPredictor method) (torch_molecule.predictor.sgir.modeling_sgir.SGIRMolecularPredictor method) (torch_molecule.predictor.smiles_transformer.modeling_transformer.SMILESTransformerMolecularPredictor method) (torch_molecule.predictor.ssr.modeling_ssr.SSRMolecularPredictor method)

push_to_huggingface() (torch_molecule.utils.checkpoint.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) sanitize_config() (in module torch_molecule.utils.format) save() (torch_molecule.base.base.BaseModel method) save_model_to_local() (torch_molecule.utils.checkpoint.LocalCheckpointManager static method) save_to_hf() (torch_molecule.base.base.BaseModel method) save_to_local() (torch_molecule.base.base.BaseModel 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() (torch_molecule.base.base.BaseModel method) SGIRMolecularPredictor (class in torch_molecule.predictor.sgir.modeling_sgir) sigmoid() (in module torch_molecule.utils.generic.metrics) SMILESTransformerMolecularPredictor (class in torch_molecule.predictor.smiles_transformer.modeling_transformer) SSRMolecularPredictor (class in torch_molecule.predictor.ssr.modeling_ssr) suggest_parameter() (in module torch_molecule.utils.search) SupervisedMolecularEncoder (class in torch_molecule.encoder.supervised.modeling_supervised)

T

task_type (torch_molecule.base.predictor.BaseMolecularPredictor attribute) timestep_embedding() (torch_molecule.nn.embedder.TimestepEmbedder static method) TimestepEmbedder (class in torch_molecule.nn.embedder) token_drop() (torch_molecule.nn.embedder.CategoricalEmbedder method) 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 try_to_connect_fragments() (in module torch_molecule.utils.graph.graph_to_smiles)

U

update() (torch_molecule.nn.gnn.GCNConv method) (torch_molecule.nn.gnn.GINConv method)

V

validate_inputs() (torch_molecule.utils.checker.MolecularInputChecker static method)

validate_smiles() (torch_molecule.utils.checker.MolecularInputChecker static method) value_range (torch_molecule.utils.search.ParameterSpec attribute)