Index

_

__getitem__() (dgllife.data.AstraZenecaChEMBLSolubility method) (dgllife.data.BACE method) (dgllife.data.BBBP method) (dgllife.data.ClinTox method) (dgllife.data.ESOL method) (dgllife.data.FreeSolv method) (dgllife.data.HIV method) (dgllife.data.Lipophilicity method) (dgllife.data.MoleculeCSVDataset method) (dgllife.data.MUV method) (dgllife.data.PCBA method) (dgllife.data.PDBBind method) (dgllife.data.PubChemBioAssayAromaticity method) (dgllife.data.SIDER method) (dgllife.data.TencentAlchemyDataset method) (dgllife.data.Tox21 method) (dgllife.data.ToxCast method) (dgllife.data.UnlabeledSMILES method) (dgllife.data.USPTOCenter method) (dgllife.data.USPTORank method) (dgllife.data.WLNCenterDataset method) (dgllife.data.WLNRankDataset method) __init__() (dgllife.utils.AttentiveFPAtomFeaturizer method) (dgllife.utils.AttentiveFPBondFeaturizer method) (dgllife.utils.BaseAtomFeaturizer method) (dgllife.utils.BaseBondFeaturizer method) (dgllife.utils.CanonicalAtomFeaturizer method) (dgllife.utils.CanonicalBondFeaturizer method) (dgllife.utils.ConcatFeaturizer method) (dgllife.utils.MolToBigraph method) (dgllife.utils.PAGTNAtomFeaturizer method) (dgllife.utils.PAGTNEdgeFeaturizer method) (dgllife.utils.PretrainAtomFeaturizer method) (dgllife.utils.PretrainBondFeaturizer method) (dgllife.utils.SMILESToBigraph method) (dgllife.utils.ToGraph method)

__len__() (dgllife.data.AstraZenecaChEMBLSolubility method) (dgllife.data.BACE method) (dgllife.data.BBBP method) (dgllife.data.ClinTox method) (dgllife.data.ESOL method) (dgllife.data.FreeSolv method) (dgllife.data.HIV method) (dgllife.data.Lipophilicity method) (dgllife.data.MoleculeCSVDataset method) (dgllife.data.MUV method) (dgllife.data.PCBA method) (dgllife.data.PDBBind method) (dgllife.data.PubChemBioAssayAromaticity method) (dgllife.data.SIDER method) (dgllife.data.TencentAlchemyDataset method) (dgllife.data.Tox21 method) (dgllife.data.ToxCast method) (dgllife.data.UnlabeledSMILES method) (dgllife.data.USPTOCenter method) (dgllife.data.USPTORank method) (dgllife.data.WLNCenterDataset method) (dgllife.data.WLNRankDataset method)

A

ACNN (class in dgllife.model.model_zoo.acnn) ACNN_graph_construction_and_featurization() (in module dgllife.utils) add_edge_or_not() (dgllife.model.model_zoo.dgmg.DGMG method) add_node_and_update() (dgllife.model.model_zoo.dgmg.DGMG method) analyze_mols() (in module dgllife.utils) AstraZenecaChEMBLSolubility (class in dgllife.data) atom_chiral_tag_one_hot() (in module dgllife.utils) atom_chirality_type_one_hot() (in module dgllife.utils) atom_degree() (in module dgllife.utils) atom_degree_one_hot() (in module dgllife.utils) atom_explicit_valence() (in module dgllife.utils) atom_explicit_valence_one_hot() (in module dgllife.utils) atom_formal_charge() (in module dgllife.utils) atom_formal_charge_one_hot() (in module dgllife.utils) atom_hybridization_one_hot() (in module dgllife.utils) atom_implicit_valence() (in module dgllife.utils) atom_implicit_valence_one_hot() (in module dgllife.utils) atom_is_aromatic() (in module dgllife.utils)

atom_is_aromatic_one_hot() (in module dgllife.utils) atom_is_chiral_center() (in module dgllife.utils) atom_is_in_ring() (in module dgllife.utils) atom_is_in_ring_one_hot() (in module dgllife.utils) atom_mass() (in module dgllife.utils) atom_num_radical_electrons() (in module dgllife.utils) atom_num_radical_electrons_one_hot() (in module dgllife.utils) atom_total_degree() (in module dgllife.utils) atom_total_degree_one_hot() (in module dgllife.utils) atom_total_num_H() (in module dgllife.utils) atom_total_num_H_one_hot() (in module dgllife.utils) atom_type_one_hot() (in module dgllife.utils) atomic_number() (in module dgllife.utils) atomic_number_one_hot() (in module dgllife.utils) AttentiveFPAtomFeaturizer (class in dgllife.utils) AttentiveFPBondFeaturizer (class in dgllife.utils) AttentiveFPGNN (class in dgllife.model.gnn.attentivefp) AttentiveFPPredictor (class in dgllife.model.model_zoo.attentivefp_predictor) AttentiveFPReadout (class in dgllife.model.readout.attentivefp_readout)

B

BACE (class in dgllife.data) BaseAtomFeaturizer (class in dgllife.utils) BaseBondFeaturizer (class in dgllife.utils) BBBP (class in dgllife.data) bond_direction_one_hot() (in module dgllife.utils)

bond_is_conjugated() (in module dgllife.utils) bond_is_conjugated_one_hot() (in module dgllife.utils) bond_is_in_ring() (in module dgllife.utils) bond_is_in_ring_one_hot() (in module dgllife.utils) bond_stereo_one_hot() (in module dgllife.utils) bond_type_one_hot() (in module dgllife.utils)

C

CanonicalAtomFeaturizer (class in dgllife.utils) CanonicalBondFeaturizer (class in dgllife.utils) choose_dest_and_update() (dgllife.model.model_zoo.dgmg.DGMG method) ClinTox (class in dgllife.data)

compute_metric() (dgllife.utils.Meter method) ConcatFeaturizer (class in dgllife.utils) ConsecutiveSplitter (class in dgllife.utils) count_step() (dgllife.model.model_zoo.dgmg.DGMG method)

D

dgllife.model.gnn.attentivefp module dgllife.model.gnn.gat module dgllife.model.gnn.gcn module dgllife.model.gnn.gin module dgllife.model.gnn.gnn_ogb module dgllife.model.gnn.graphsage module dgllife.model.gnn.mgcn module dgllife.model.gnn.mpnn module dgllife.model.gnn.nf module dgllife.model.gnn.pagtn module dgllife.model.gnn.schnet module dgllife.model.gnn.weave module dgllife.model.gnn.wln module dgllife.model.model_zoo.acnn module dgllife.model.model_zoo.attentivefp_predictor module dgllife.model.model_zoo.dgmg module dgllife.model.model_zoo.gat_predictor module dgllife.model.model_zoo.gatv2_predictor module dgllife.model.model_zoo.gcn_predictor module

dgllife.model.model_zoo.gin_predictor module dgllife.model.model_zoo.gnn_ogb_predictor module dgllife.model.model_zoo.hadamard_link_predictor module dgllife.model.model_zoo.jtvae module dgllife.model.model_zoo.mgcn_predictor module dgllife.model.model_zoo.mlp_predictor module dgllife.model.model_zoo.mpnn_predictor module dgllife.model.model_zoo.nf_predictor module dgllife.model.model_zoo.pagtn_predictor module dgllife.model.model_zoo.potentialnet module dgllife.model.model_zoo.schnet_predictor module dgllife.model.model_zoo.weave_predictor module dgllife.model.model_zoo.wln_reaction_center module dgllife.model.model_zoo.wln_reaction_ranking module dgllife.model.readout.attentivefp_readout module dgllife.model.readout.mlp_readout module dgllife.model.readout.weave_readout module dgllife.model.readout.weighted_sum_and_max module DGMG (class in dgllife.model.model_zoo.dgmg)

E

EarlyStopping (class in dgllife.utils)

ESOL (class in dgllife.data)

F

feat_size() (dgllife.utils.AttentiveFPAtomFeaturizer method) (dgllife.utils.AttentiveFPBondFeaturizer method) (dgllife.utils.BaseAtomFeaturizer method) (dgllife.utils.BaseBondFeaturizer method) (dgllife.utils.CanonicalAtomFeaturizer method) (dgllife.utils.CanonicalBondFeaturizer method) (dgllife.utils.PAGTNAtomFeaturizer method) (dgllife.utils.PAGTNEdgeFeaturizer method) forward() (dgllife.model.gnn.attentivefp.AttentiveFPGNN method) (dgllife.model.gnn.gat.GAT method) (dgllife.model.gnn.gcn.GCN method) (dgllife.model.gnn.gin.GIN method) (dgllife.model.gnn.gnn_ogb.GNNOGB method) (dgllife.model.gnn.graphsage.GraphSAGE method) (dgllife.model.gnn.mgcn.MGCNGNN method) (dgllife.model.gnn.mpnn.MPNNGNN method) (dgllife.model.gnn.nf.NFGNN method) (dgllife.model.gnn.pagtn.PAGTNGNN method) (dgllife.model.gnn.schnet.SchNetGNN method) (dgllife.model.gnn.weave.WeaveGNN method) (dgllife.model.gnn.wln.WLN method) (dgllife.model.model_zoo.acnn.ACNN method) (dgllife.model.model_zoo.attentivefp_predictor.AttentiveFPPredictor method) (dgllife.model.model_zoo.dgmg.DGMG method) (dgllife.model.model_zoo.gat_predictor.GATPredictor method) (dgllife.model.model_zoo.gatv2_predictor.GATv2Predictor method) (dgllife.model.model_zoo.gcn_predictor.GCNPredictor method) (dgllife.model.model_zoo.gin_predictor.GINPredictor method) (dgllife.model.model_zoo.gnn_ogb_predictor.GNNOGBPredictor method) (dgllife.model.model_zoo.hadamard_link_predictor.HadamardLinkPredictor method) (dgllife.model.model_zoo.jtvae.JTNNVAE method) (dgllife.model.model_zoo.mgcn_predictor.MGCNPredictor method) (dgllife.model.model_zoo.mlp_predictor.MLPPredictor method) (dgllife.model.model_zoo.mpnn_predictor.MPNNPredictor method) (dgllife.model.model_zoo.nf_predictor.NFPredictor method) (dgllife.model.model_zoo.pagtn_predictor.PAGTNPredictor method) (dgllife.model.model_zoo.potentialnet.PotentialNet method) (dgllife.model.model_zoo.schnet_predictor.SchNetPredictor method) (dgllife.model.model_zoo.weave_predictor.WeavePredictor method) (dgllife.model.model_zoo.wln_reaction_center.WLNReactionCenter method) (dgllife.model.model_zoo.wln_reaction_ranking.WLNReactionRanking method) (dgllife.model.readout.attentivefp_readout.AttentiveFPReadout method) (dgllife.model.readout.mlp_readout.MLPNodeReadout method) (dgllife.model.readout.weave_readout.WeaveGather method) (dgllife.model.readout.weighted_sum_and_max.WeightedSumAndMax method)

FreeSolv (class in dgllife.data)

G

GAT (class in dgllife.model.gnn.gat) GATPredictor (class in dgllife.model.model_zoo.gat_predictor) GATv2Predictor (class in dgllife.model.model_zoo.gatv2_predictor) gaussian_histogram() (dgllife.model.readout.weave_readout.WeaveGather method) GCN (class in dgllife.model.gnn.gcn) GCNPredictor (class in dgllife.model.model_zoo.gcn_predictor)

get_log_prob() (dgllife.model.model_zoo.dgmg.DGMG method) get_mol_3d_coordinates() (in module dgllife.utils) GIN (class in dgllife.model.gnn.gin) GINPredictor (class in dgllife.model.model_zoo.gin_predictor) GNNOGB (class in dgllife.model.gnn.gnn_ogb) GNNOGBPredictor (class in dgllife.model.model_zoo.gnn_ogb_predictor) GraphSAGE (class in dgllife.model.gnn.graphsage)

H

HadamardLinkPredictor (class in dgllife.model.model_zoo.hadamard_link_predictor)

HIV (class in dgllife.data)

I

ignore_large() (dgllife.data.USPTORank method) (dgllife.data.WLNRankDataset method)

init_weights() (dgllife.model.model_zoo.dgmg.DGMG method)

J

JTNNVAE (class in dgllife.model.model_zoo.jtvae)

K

k_fold_split() (dgllife.utils.ConsecutiveSplitter static method) (dgllife.utils.MolecularWeightSplitter static method) (dgllife.utils.RandomSplitter static method) (dgllife.utils.ScaffoldSplitter static method) (dgllife.utils.SingleTaskStratifiedSplitter static method)

k_nearest_neighbors() (in module dgllife.utils)

L

Lipophilicity (class in dgllife.data) load_molecule() (in module dgllife.utils)

load_pretrained() (in module dgllife.model) load_smiles_from_txt() (in module dgllife.utils)

M

Meter (class in dgllife.utils) MGCNGNN (class in dgllife.model.gnn.mgcn) MGCNPredictor (class in dgllife.model.model_zoo.mgcn_predictor) MLPNodeReadout (class in dgllife.model.readout.mlp_readout) MLPPredictor (class in dgllife.model.model_zoo.mlp_predictor) module dgllife.model.gnn.attentivefp dgllife.model.gnn.gat dgllife.model.gnn.gcn dgllife.model.gnn.gin dgllife.model.gnn.gnn_ogb dgllife.model.gnn.graphsage dgllife.model.gnn.mgcn dgllife.model.gnn.mpnn dgllife.model.gnn.nf dgllife.model.gnn.pagtn dgllife.model.gnn.schnet dgllife.model.gnn.weave dgllife.model.gnn.wln dgllife.model.model_zoo.acnn dgllife.model.model_zoo.attentivefp_predictor dgllife.model.model_zoo.dgmg dgllife.model.model_zoo.gat_predictor dgllife.model.model_zoo.gatv2_predictor dgllife.model.model_zoo.gcn_predictor dgllife.model.model_zoo.gin_predictor dgllife.model.model_zoo.gnn_ogb_predictor dgllife.model.model_zoo.hadamard_link_predictor dgllife.model.model_zoo.jtvae dgllife.model.model_zoo.mgcn_predictor dgllife.model.model_zoo.mlp_predictor dgllife.model.model_zoo.mpnn_predictor dgllife.model.model_zoo.nf_predictor dgllife.model.model_zoo.pagtn_predictor dgllife.model.model_zoo.potentialnet dgllife.model.model_zoo.schnet_predictor dgllife.model.model_zoo.weave_predictor dgllife.model.model_zoo.wln_reaction_center dgllife.model.model_zoo.wln_reaction_ranking dgllife.model.readout.attentivefp_readout dgllife.model.readout.mlp_readout dgllife.model.readout.weave_readout dgllife.model.readout.weighted_sum_and_max

mol_to_bigraph() (in module dgllife.utils) mol_to_complete_graph() (in module dgllife.utils) mol_to_graph() (in module dgllife.utils) mol_to_nearest_neighbor_graph() (in module dgllife.utils) MolecularWeightSplitter (class in dgllife.utils) MoleculeCSVDataset (class in dgllife.data) MolToBigraph (class in dgllife.utils) MPNNGNN (class in dgllife.model.gnn.mpnn) MPNNPredictor (class in dgllife.model.model_zoo.mpnn_predictor) multiprocess_load_molecules() (in module dgllife.utils) MUV (class in dgllife.data)

N

NFGNN (class in dgllife.model.gnn.nf)

NFPredictor (class in dgllife.model.model_zoo.nf_predictor)

O

one_hot_encoding() (in module dgllife.utils)

P

PAGTNAtomFeaturizer (class in dgllife.utils) PAGTNEdgeFeaturizer (class in dgllife.utils) PAGTNGNN (class in dgllife.model.gnn.pagtn) PAGTNPredictor (class in dgllife.model.model_zoo.pagtn_predictor) PCBA (class in dgllife.data) PDBBind (class in dgllife.data)

PN_graph_construction_and_featurization() (in module dgllife.utils) PotentialNet (class in dgllife.model.model_zoo.potentialnet) prepare_log_prob() (dgllife.model.model_zoo.dgmg.DGMG method) PretrainAtomFeaturizer (class in dgllife.utils) PretrainBondFeaturizer (class in dgllife.utils) PubChemBioAssayAromaticity (class in dgllife.data)

R

RandomSplitter (class in dgllife.utils) reset_parameters() (dgllife.model.gnn.attentivefp.AttentiveFPGNN method) (dgllife.model.gnn.gat.GAT method) (dgllife.model.gnn.gcn.GCN method) (dgllife.model.gnn.gin.GIN method) (dgllife.model.gnn.gnn_ogb.GNNOGB method) (dgllife.model.gnn.graphsage.GraphSAGE method) (dgllife.model.gnn.mgcn.MGCNGNN method) (dgllife.model.gnn.mpnn.MPNNGNN method) (dgllife.model.gnn.nf.NFGNN method) (dgllife.model.gnn.pagtn.PAGTNGNN method) (dgllife.model.gnn.schnet.SchNetGNN method) (dgllife.model.gnn.weave.WeaveGNN method) (dgllife.model.gnn.wln.WLN method) (dgllife.model.model_zoo.gnn_ogb_predictor.GNNOGBPredictor method) (dgllife.model.model_zoo.nf_predictor.NFPredictor method)

rollout() (dgllife.model.model_zoo.dgmg.DGMG method)

S

ScaffoldSplitter (class in dgllife.utils) SchNetGNN (class in dgllife.model.gnn.schnet) SchNetPredictor (class in dgllife.model.model_zoo.schnet_predictor) set_mean_and_std() (dgllife.data.TencentAlchemyDataset method) SIDER (class in dgllife.data)

SingleTaskStratifiedSplitter (class in dgllife.utils) smiles_to_bigraph() (in module dgllife.utils) smiles_to_complete_graph() (in module dgllife.utils) smiles_to_nearest_neighbor_graph() (in module dgllife.utils) SMILESToBigraph (class in dgllife.utils) step() (dgllife.utils.EarlyStopping method)

T

task_pos_weights() (dgllife.data.BACE method) (dgllife.data.BBBP method) (dgllife.data.ClinTox method) (dgllife.data.HIV method) (dgllife.data.MoleculeCSVDataset method) (dgllife.data.MUV method) (dgllife.data.PCBA method) (dgllife.data.SIDER method) (dgllife.data.Tox21 method) (dgllife.data.ToxCast method)

teacher_forcing() (dgllife.model.model_zoo.dgmg.DGMG method) TencentAlchemyDataset (class in dgllife.data) ToGraph (class in dgllife.utils) Tox21 (class in dgllife.data) ToxCast (class in dgllife.data) train_val_test_split() (dgllife.utils.ConsecutiveSplitter static method) (dgllife.utils.MolecularWeightSplitter static method) (dgllife.utils.RandomSplitter static method) (dgllife.utils.ScaffoldSplitter static method) (dgllife.utils.SingleTaskStratifiedSplitter static method)

U

UnlabeledSMILES (class in dgllife.data) update() (dgllife.utils.Meter method)

USPTOCenter (class in dgllife.data) USPTORank (class in dgllife.data)

W

WeaveGather (class in dgllife.model.readout.weave_readout) WeaveGNN (class in dgllife.model.gnn.weave) WeavePredictor (class in dgllife.model.model_zoo.weave_predictor) WeightedSumAndMax (class in dgllife.model.readout.weighted_sum_and_max)

WLN (class in dgllife.model.gnn.wln) WLNCenterDataset (class in dgllife.data) WLNRankDataset (class in dgllife.data) WLNReactionCenter (class in dgllife.model.model_zoo.wln_reaction_center) WLNReactionRanking (class in dgllife.model.model_zoo.wln_reaction_ranking)