Index

A

AdamW (class in pahelix.networks.optimizer) apply_bert_mask() (in module pahelix.utils.language_model_tools)

apply_optimize() (pahelix.networks.optimizer.AdamW method) atom_numeric_feat() (in module pahelix.utils.compound_tools)

C

check_smiles_validity() (in module pahelix.utils.compound_tools) collate_fn() (pahelix.featurizers.featurizer.Featurizer method) (pahelix.featurizers.pretrain_gnn_featurizer.PreGNNAttrMaskFeaturizer method) (pahelix.featurizers.pretrain_gnn_featurizer.PreGNNContextPredFeaturizer method) (pahelix.featurizers.pretrain_gnn_featurizer.PreGNNSupervisedFeaturizer method)

CompoundConstants (class in pahelix.utils.compound_tools) convert_token_to_id() (pahelix.utils.protein_tools.ProteinTokenizer method) convert_tokens_to_ids() (pahelix.utils.protein_tools.ProteinTokenizer method) create_standardized_mol_id() (in module pahelix.utils.compound_tools)

F

Featurizer (class in pahelix.featurizers.featurizer) forward() (pahelix.model_zoo.pretrain_gnns_model.PreGNNAttrmaskModel method) (pahelix.model_zoo.pretrain_gnns_model.PreGNNContextpredModel method) (pahelix.model_zoo.pretrain_gnns_model.PreGNNSupervisedModel method) (pahelix.model_zoo.pretrain_gnns_model.PretrainGNNModel method) (pahelix.model_zoo.protein_sequence_model.ProteinSequenceModel method)

G

gat_layer() (in module pahelix.networks.gnn_block) gcn_layer() (in module pahelix.networks.gnn_block) gen_features() (pahelix.featurizers.featurizer.Featurizer method) (pahelix.featurizers.pretrain_gnn_featurizer.PreGNNAttrMaskFeaturizer method) (pahelix.featurizers.pretrain_gnn_featurizer.PreGNNContextPredFeaturizer method) (pahelix.featurizers.pretrain_gnn_featurizer.PreGNNSupervisedFeaturizer method) gen_token_ids() (pahelix.utils.protein_tools.ProteinTokenizer method) generate_scaffold() (in module pahelix.utils.splitters) get_chembl_filtered_task_num() (in module pahelix.datasets.chembl_filtered_dataset) get_default_bace_task_names() (in module pahelix.datasets.bace_dataset) get_default_bbbp_task_names() (in module pahelix.datasets.bbbp_dataset) get_default_clintox_task_names() (in module pahelix.datasets.clintox_dataset) get_default_esol_task_names() (in module pahelix.datasets.esol_dataset)

get_default_freesolv_task_names() (in module pahelix.datasets.freesolv_dataset) get_default_hiv_task_names() (in module pahelix.datasets.hiv_dataset) get_default_lipophilicity_task_names() (in module pahelix.datasets.lipophilicity_dataset) get_default_muv_task_names() (in module pahelix.datasets.muv_dataset) get_default_sider_task_names() (in module pahelix.datasets.sider_dataset) get_default_tox21_task_names() (in module pahelix.datasets.tox21_dataset) get_default_toxcast_task_names() (in module pahelix.datasets.toxcast_dataset) get_distributed_optimizer() (in module pahelix.utils.paddle_utils) get_gasteiger_partial_charges() (in module pahelix.utils.compound_tools) get_largest_mol() (in module pahelix.utils.compound_tools) get_part_files() (in module pahelix.utils.data_utils) gin_layer() (in module pahelix.networks.gnn_block) graph_data_obj_to_nx_simple() (in module pahelix.featurizers.pretrain_gnn_featurizer)

I

IndexSplitter (class in pahelix.utils.splitters)

InMemoryDataset (class in pahelix.datasets.inmemory_dataset) iter_batch() (pahelix.datasets.inmemory_dataset.InMemoryDataset method)

L

load_bace_dataset() (in module pahelix.datasets.bace_dataset) load_bbbp_dataset() (in module pahelix.datasets.bbbp_dataset) load_chembl_filtered_dataset() (in module pahelix.datasets.chembl_filtered_dataset) load_clintox_dataset() (in module pahelix.datasets.clintox_dataset) load_esol_dataset() (in module pahelix.datasets.esol_dataset) load_freesolv_dataset() (in module pahelix.datasets.freesolv_dataset) load_hiv_dataset() (in module pahelix.datasets.hiv_dataset) load_lipophilicity_dataset() (in module pahelix.datasets.lipophilicity_dataset) load_mutag_dataset() (in module pahelix.datasets.mutag_dataset)

load_muv_dataset() (in module pahelix.datasets.muv_dataset) load_npz_to_data_list() (in module pahelix.utils.data_utils) load_partial_params() (in module pahelix.utils.paddle_utils) load_ptc_mr_dataset() (in module pahelix.datasets.ptc_mr_dataset) load_sider_dataset() (in module pahelix.datasets.sider_dataset) load_tox21_dataset() (in module pahelix.datasets.tox21_dataset) load_toxcast_dataset() (in module pahelix.datasets.toxcast_dataset) load_zinc_dataset() (in module pahelix.datasets.zinc_dataset) lstm_encoder() (in module pahelix.networks.lstm_block)

M

max_recv() (in module pahelix.networks.gnn_block) mean_recv() (in module pahelix.networks.gnn_block) module pahelix.datasets.bace_dataset pahelix.datasets.bbbp_dataset pahelix.datasets.chembl_filtered_dataset pahelix.datasets.clintox_dataset pahelix.datasets.esol_dataset pahelix.datasets.freesolv_dataset pahelix.datasets.hiv_dataset pahelix.datasets.inmemory_dataset pahelix.datasets.lipophilicity_dataset pahelix.datasets.mutag_dataset pahelix.datasets.muv_dataset pahelix.datasets.ptc_mr_dataset pahelix.datasets.sider_dataset pahelix.datasets.tox21_dataset pahelix.datasets.toxcast_dataset pahelix.datasets.zinc_dataset pahelix.featurizers.featurizer pahelix.featurizers.pretrain_gnn_featurizer pahelix.model_zoo.pretrain_gnns_model pahelix.networks.gnn_block pahelix.networks.lstm_block pahelix.networks.resnet_block pahelix.networks.transformer_block pahelix.utils.compound_tools pahelix.utils.data_utils pahelix.utils.language_model_tools pahelix.utils.paddle_utils pahelix.utils.protein_tools pahelix.utils.splitters

mol_to_graph_data() (in module pahelix.utils.compound_tools) multi_head_attention() (in module pahelix.networks.transformer_block)

N

nx_to_graph_data_obj_simple() (in module pahelix.featurizers.pretrain_gnn_featurizer)

P

pahelix.datasets.bace_dataset module pahelix.datasets.bbbp_dataset module pahelix.datasets.chembl_filtered_dataset module pahelix.datasets.clintox_dataset module pahelix.datasets.esol_dataset module pahelix.datasets.freesolv_dataset module pahelix.datasets.hiv_dataset module pahelix.datasets.inmemory_dataset module pahelix.datasets.lipophilicity_dataset module pahelix.datasets.mutag_dataset module pahelix.datasets.muv_dataset module pahelix.datasets.ptc_mr_dataset module pahelix.datasets.sider_dataset module pahelix.datasets.tox21_dataset module pahelix.datasets.toxcast_dataset module pahelix.datasets.zinc_dataset module pahelix.featurizers.featurizer module

pahelix.featurizers.pretrain_gnn_featurizer module pahelix.model_zoo.pretrain_gnns_model module pahelix.networks.gnn_block module pahelix.networks.lstm_block module pahelix.networks.resnet_block module pahelix.networks.transformer_block module pahelix.utils.compound_tools module pahelix.utils.data_utils module pahelix.utils.language_model_tools module pahelix.utils.paddle_utils module pahelix.utils.protein_tools module pahelix.utils.splitters module positionwise_feed_forward() (in module pahelix.networks.transformer_block) pre_post_process_layer() (in module pahelix.networks.pre_post_process) PreGNNAttrMaskFeaturizer (class in pahelix.featurizers.pretrain_gnn_featurizer) PreGNNAttrmaskModel (class in pahelix.model_zoo.pretrain_gnns_model) PreGNNContextPredFeaturizer (class in pahelix.featurizers.pretrain_gnn_featurizer) PreGNNContextpredModel (class in pahelix.model_zoo.pretrain_gnns_model) PreGNNSupervisedFeaturizer (class in pahelix.featurizers.pretrain_gnn_featurizer) PreGNNSupervisedModel (class in pahelix.model_zoo.pretrain_gnns_model) PretrainGNNModel (class in pahelix.model_zoo.pretrain_gnns_model) ProteinSequenceModel (class in pahelix.model_zoo.protein_sequence_model) ProteinTokenizer (class in pahelix.utils.protein_tools)

R

random() (in module pahelix.networks.gnn_block) RandomScaffoldSplitter (class in pahelix.utils.splitters)

RandomSplitter (class in pahelix.utils.splitters) reset_idxes() (in module pahelix.featurizers.pretrain_gnn_featurizer) resnet_encoder() (in module pahelix.networks.resnet_block)

S

save_data() (pahelix.datasets.inmemory_dataset.InMemoryDataset method) save_data_list_to_npz() (in module pahelix.utils.data_utils) ScaffoldSplitter (class in pahelix.utils.splitters) smiles_to_graph_data() (in module pahelix.utils.compound_tools) split() (pahelix.utils.splitters.IndexSplitter method) (pahelix.utils.splitters.RandomScaffoldSplitter method) (pahelix.utils.splitters.RandomSplitter method) (pahelix.utils.splitters.ScaffoldSplitter method)

split_rdkit_mol_obj() (in module pahelix.utils.compound_tools) sum_recv() (in module pahelix.networks.gnn_block)

T

tokenize() (pahelix.utils.protein_tools.ProteinTokenizer method) transform_contextpred() (in module pahelix.featurizers.pretrain_gnn_featurizer)

transformer_encoder() (in module pahelix.networks.transformer_block) transformer_encoder_layer() (in module pahelix.networks.transformer_block)