Index

A

Activation (class in pahelix.networks.basic_block) AdamW (class in pahelix.networks.optimizer) apply_bert_mask() (in module pahelix.utils.language_model_tools) apply_optimize() (pahelix.networks.optimizer.AdamW method) atom_to_feat_vector() (pahelix.utils.compound_tools.CompoundKit static method)

AtomEmbedding (class in pahelix.networks.compound_encoder) AtomFloatEmbedding (class in pahelix.networks.compound_encoder) AttrmaskCollateFn (class in pahelix.featurizers.pretrain_gnn_featurizer) AttrmaskModel (class in pahelix.model_zoo.pretrain_gnns_model) AttrmaskTransformFn (class in pahelix.featurizers.pretrain_gnn_featurizer)

B

BondAngleFloatRBF (class in pahelix.networks.compound_encoder)

BondEmbedding (class in pahelix.networks.compound_encoder) BondFloatRBF (class in pahelix.networks.compound_encoder)

C

cal_loss() (pahelix.model_zoo.protein_sequence_model.ProteinCriterion method) check_partial_charge() (pahelix.utils.compound_tools.CompoundKit static method) check_smiles_validity() (in module pahelix.utils.compound_tools) ClassificationTaskModel (class in pahelix.model_zoo.protein_sequence_model) collate_fn() (pahelix.featurizers.het_gnn_featurizer.DDiFeaturizer method)

Compound3DKit (class in pahelix.utils.compound_tools) CompoundKit (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)

D

data_list (pahelix.datasets.inmemory_dataset.InMemoryDataset attribute)

DDiFeaturizer (class in pahelix.featurizers.het_gnn_featurizer)

F

forward() (pahelix.model_zoo.pretrain_gnns_model.AttrmaskModel method) (pahelix.model_zoo.pretrain_gnns_model.PretrainGNNModel method) (pahelix.model_zoo.pretrain_gnns_model.SupervisedModel method) (pahelix.model_zoo.protein_sequence_model.ClassificationTaskModel method) (pahelix.model_zoo.protein_sequence_model.LstmEncoderModel method) (pahelix.model_zoo.protein_sequence_model.PretrainTaskModel method) (pahelix.model_zoo.protein_sequence_model.ProteinEncoderModel method) (pahelix.model_zoo.protein_sequence_model.ProteinModel method) (pahelix.model_zoo.protein_sequence_model.RegressionTaskModel method) (pahelix.model_zoo.protein_sequence_model.ResnetEncoderModel method) (pahelix.model_zoo.protein_sequence_model.SeqClassificationTaskModel method) (pahelix.model_zoo.protein_sequence_model.TransformerEncoderModel method) (pahelix.model_zoo.seq_vae_model.VAE method) (pahelix.networks.basic_block.Activation method) (pahelix.networks.basic_block.MLP method) (pahelix.networks.compound_encoder.AtomEmbedding method) (pahelix.networks.compound_encoder.AtomFloatEmbedding method) (pahelix.networks.compound_encoder.BondAngleFloatRBF method) (pahelix.networks.compound_encoder.BondEmbedding method) (pahelix.networks.compound_encoder.BondFloatRBF method) (pahelix.networks.gnn_block.GIN method) (pahelix.networks.gnn_block.GraphNorm method) (pahelix.networks.gnn_block.MeanPool method) (pahelix.networks.involution_block.Involution2D method)

forward_decoder() (pahelix.model_zoo.seq_vae_model.VAE method) forward_encoder() (pahelix.model_zoo.seq_vae_model.VAE method)

G

gen_token_ids() (pahelix.utils.protein_tools.ProteinTokenizer method) generate_scaffold() (in module pahelix.utils.splitters) get_2d_atom_poses() (pahelix.utils.compound_tools.Compound3DKit static method) get_atom_feature_dims() (in module pahelix.utils.compound_tools) get_atom_feature_id() (pahelix.utils.compound_tools.CompoundKit static method) get_atom_feature_size() (pahelix.utils.compound_tools.CompoundKit static method) get_atom_names() (pahelix.utils.compound_tools.CompoundKit static method) get_atom_poses() (pahelix.utils.compound_tools.Compound3DKit static method) get_atom_value() (pahelix.utils.compound_tools.CompoundKit static method) get_bond_feature_dims() (in module pahelix.utils.compound_tools) get_bond_feature_id() (pahelix.utils.compound_tools.CompoundKit static method) get_bond_feature_size() (pahelix.utils.compound_tools.CompoundKit static method) get_bond_lengths() (pahelix.utils.compound_tools.Compound3DKit static method) get_bond_value() (pahelix.utils.compound_tools.CompoundKit static method) get_chembl_filtered_task_num() (in module pahelix.datasets.chembl_filtered_dataset) get_data_loader() (pahelix.datasets.inmemory_dataset.InMemoryDataset method) get_daylight_functional_group_counts() (pahelix.utils.compound_tools.CompoundKit static method) 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_ddi_task_names() (in module pahelix.datasets.ddi_dataset) get_default_dti_task_names() (in module pahelix.datasets.dti_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_ppi_task_names() (in module pahelix.datasets.ppi_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_esol_stat() (in module pahelix.datasets.esol_dataset) get_freesolv_stat() (in module pahelix.datasets.freesolv_dataset) get_gasteiger_partial_charges() (in module pahelix.utils.compound_tools) get_largest_mol() (in module pahelix.utils.compound_tools) get_lipophilicity_stat() (in module pahelix.datasets.lipophilicity_dataset) get_maccs_fingerprint() (pahelix.utils.compound_tools.CompoundKit static method) get_MMFF_atom_poses() (pahelix.utils.compound_tools.Compound3DKit static method) get_morgan2048_fingerprint() (pahelix.utils.compound_tools.CompoundKit static method) get_morgan_fingerprint() (pahelix.utils.compound_tools.CompoundKit static method) get_part_files() (in module pahelix.utils.data_utils) get_ring_size() (pahelix.utils.compound_tools.CompoundKit static method) get_superedge_angles() (pahelix.utils.compound_tools.Compound3DKit static method) GIN (class in pahelix.networks.gnn_block) graph_dim (pahelix.model_zoo.pretrain_gnns_model.PretrainGNNModel property) GraphNorm (class in pahelix.networks.gnn_block)

I

IndexSplitter (class in pahelix.utils.splitters) init_weights() (pahelix.model_zoo.protein_sequence_model.ResnetEncoderModel method) (pahelix.model_zoo.protein_sequence_model.TransformerEncoderModel method)

InMemoryDataset (class in pahelix.datasets.inmemory_dataset) Involution2D (class in pahelix.networks.involution_block)

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_davis_dataset() (in module pahelix.datasets.davis_dataset) load_ddi_dataset() (in module pahelix.datasets.ddi_dataset) load_dti_dataset() (in module pahelix.datasets.dti_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_json_config() (in module pahelix.utils.basic_utils)

load_kiba_dataset() (in module pahelix.datasets.kiba_dataset) load_lipophilicity_dataset() (in module pahelix.datasets.lipophilicity_dataset) load_muv_dataset() (in module pahelix.datasets.muv_dataset) load_npz_to_data_list() (in module pahelix.utils.data_utils) load_ppi_dataset() (in module pahelix.datasets.ppi_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) LstmEncoderModel (class in pahelix.model_zoo.protein_sequence_model)

M

MeanPool (class in pahelix.networks.gnn_block) MLP (class in pahelix.networks.basic_block) module pahelix.datasets.bace_dataset pahelix.datasets.bbbp_dataset pahelix.datasets.chembl_filtered_dataset pahelix.datasets.clintox_dataset pahelix.datasets.davis_dataset pahelix.datasets.ddi_dataset pahelix.datasets.dti_dataset pahelix.datasets.esol_dataset pahelix.datasets.freesolv_dataset pahelix.datasets.hiv_dataset pahelix.datasets.inmemory_dataset pahelix.datasets.kiba_dataset pahelix.datasets.lipophilicity_dataset pahelix.datasets.muv_dataset pahelix.datasets.ppi_dataset pahelix.datasets.sider_dataset pahelix.datasets.tox21_dataset pahelix.datasets.toxcast_dataset pahelix.datasets.zinc_dataset pahelix.featurizers.het_gnn_featurizer pahelix.featurizers.pretrain_gnn_featurizer pahelix.model_zoo.pretrain_gnns_model pahelix.model_zoo.protein_sequence_model pahelix.networks.basic_block pahelix.networks.compound_encoder pahelix.networks.gnn_block pahelix.networks.lstm_block pahelix.networks.resnet_block pahelix.networks.transformer_block pahelix.utils.basic_utils pahelix.utils.compound_tools pahelix.utils.data_utils pahelix.utils.language_model_tools pahelix.utils.splitters

mol_to_geognn_graph_data() (in module pahelix.utils.compound_tools) mol_to_geognn_graph_data_MMFF3d() (in module pahelix.utils.compound_tools) mol_to_geognn_graph_data_raw3d() (in module pahelix.utils.compound_tools) mol_to_graph_data() (in module pahelix.utils.compound_tools) mp_pool_map() (in module pahelix.utils.basic_utils) multi_head_attention() (in module pahelix.networks.transformer_block)

N

new_mol_to_graph_data() (in module pahelix.utils.compound_tools) new_smiles_to_graph_data() (in module pahelix.utils.compound_tools)

node_dim (pahelix.model_zoo.pretrain_gnns_model.PretrainGNNModel property) num_nodes_stat() (in module pahelix.featurizers.het_gnn_featurizer) nx_graph_build() (in module pahelix.featurizers.het_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.davis_dataset module pahelix.datasets.ddi_dataset module pahelix.datasets.dti_dataset module pahelix.datasets.esol_dataset module pahelix.datasets.freesolv_dataset module pahelix.datasets.hiv_dataset module pahelix.datasets.inmemory_dataset module pahelix.datasets.kiba_dataset module pahelix.datasets.lipophilicity_dataset module pahelix.datasets.muv_dataset module pahelix.datasets.ppi_dataset module pahelix.datasets.sider_dataset module pahelix.datasets.tox21_dataset module pahelix.datasets.toxcast_dataset module pahelix.datasets.zinc_dataset module

pahelix.featurizers.het_gnn_featurizer module pahelix.featurizers.pretrain_gnn_featurizer module pahelix.model_zoo.pretrain_gnns_model module pahelix.model_zoo.protein_sequence_model module pahelix.networks.basic_block module pahelix.networks.compound_encoder module pahelix.networks.gnn_block module pahelix.networks.lstm_block module pahelix.networks.resnet_block module pahelix.networks.transformer_block module pahelix.utils.basic_utils module pahelix.utils.compound_tools module pahelix.utils.data_utils module pahelix.utils.language_model_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) PretrainGNNModel (class in pahelix.model_zoo.pretrain_gnns_model) PretrainTaskModel (class in pahelix.model_zoo.protein_sequence_model) ProteinCriterion (class in pahelix.model_zoo.protein_sequence_model) ProteinEncoderModel (class in pahelix.model_zoo.protein_sequence_model) ProteinModel (class in pahelix.model_zoo.protein_sequence_model) ProteinTokenizer (class in pahelix.utils.protein_tools)

R

RandomScaffoldSplitter (class in pahelix.utils.splitters) RandomSplitter (class in pahelix.utils.splitters) rdchem_enum_to_list() (in module pahelix.utils.compound_tools)

RegressionTaskModel (class in pahelix.model_zoo.protein_sequence_model) resnet_encoder() (in module pahelix.networks.resnet_block) ResnetEncoderModel (class in pahelix.model_zoo.protein_sequence_model)

S

safe_index() (in module pahelix.utils.compound_tools) sample() (pahelix.model_zoo.seq_vae_model.VAE method) sample_z_prior() (pahelix.model_zoo.seq_vae_model.VAE method) 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) SeqClassificationTaskModel (class in pahelix.model_zoo.protein_sequence_model)

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) SupervisedCollateFn (class in pahelix.featurizers.pretrain_gnn_featurizer) SupervisedModel (class in pahelix.model_zoo.pretrain_gnns_model) SupervisedTransformFn (class in pahelix.featurizers.pretrain_gnn_featurizer)

T

tensor2string() (pahelix.model_zoo.seq_vae_model.VAE method) tokenize() (pahelix.utils.protein_tools.ProteinTokenizer method) transform() (pahelix.datasets.inmemory_dataset.InMemoryDataset method)

transformer_encoder() (in module pahelix.networks.transformer_block) transformer_encoder_layer() (in module pahelix.networks.transformer_block) TransformerEncoderModel (class in pahelix.model_zoo.protein_sequence_model)

V

VAE (class in pahelix.model_zoo.seq_vae_model)