update api doc

Author: SuperXiang

docs/api_doc/datasets.rst

@@ -106,8 +106,8 @@ pdbbind_dataset
 ===============
 
 .. automodule:: pahelix.datasets.pdbbind_dataset
-   :members: load_pdbbind_dataset
-   :inherited-members:
+
+.. autofunction:: pahelix.datasets.pdbbind_dataset.load_pdbbind_dataset
 
 ppi_dataset
 ===========

docs/api_doc/featurizers.rst

@@ -4,18 +4,38 @@ pahelix.featurizers
 
 .. contents:: Table of Contents
 
-featurizer
-==========
+het_gnn_featurizer
+==================
 
 .. automodule:: pahelix.featurizers.het_gnn_featurizer
-   :members: DDiFeaturizer, num_nodes_stat, nx_graph_build
+
+.. autoclass:: pahelix.featurizers.het_gnn_featurizer.DDiFeaturizer
+   :members:
    :inherited-members:
 
+.. autofunction:: pahelix.featurizers.het_gnn_featurizer.num_nodes_stat
+
+.. autofunction:: pahelix.featurizers.het_gnn_featurizer.nx_graph_build
+
 pretrain_gnn_featurizer
 =======================
 
 .. automodule:: pahelix.featurizers.pretrain_gnn_featurizer
-   :members: AttrmaskTransformFn, AttrmaskCollateFn, SupervisedTransformFn, SupervisedCollateFn
+
+.. autoclass:: pahelix.featurizers.pretrain_gnn_featurizer.AttrmaskTransformFn
+   :members:
+   :inherited-members:
+
+.. autoclass:: pahelix.featurizers.pretrain_gnn_featurizer.AttrmaskCollateFn
+   :members:
+   :inherited-members:
+
+.. autoclass:: pahelix.featurizers.pretrain_gnn_featurizer.SupervisedTransformFn
+   :members:
+   :inherited-members:
+
+.. autoclass:: pahelix.featurizers.pretrain_gnn_featurizer.SupervisedCollateFn
+   :members:
    :inherited-members:
 
 Helpful Link

docs/api_doc/model_zoo.rst

@@ -14,23 +14,22 @@ pretrain_gnns_model
 protein_sequence_model
 ======================
 
-.. autoclass:: pahelix.model_zoo.protein_sequence_model
+.. automodule:: pahelix.model_zoo.protein_sequence_model
    :members: LstmEncoderModel, ResnetEncoderModel, TransformerEncoderModel, PretrainTaskModel, SeqClassificationTaskModel, ClassificationTaskModel, RegressionTaskModel, ProteinEncoderModel, ProteinModel, ProteinCriterion
    :inherited-members:
 
 sd_vae_model
 ============
 
-.. autoclass:: pahelix.model_zoo.sd_vae_model
+.. automodule:: pahelix.model_zoo.sd_vae_model
    :members: StateDecoder, PerpCalculator, MyPerpLoss, CNNEncoder, MolVAE
    :inherited-members:
 
 seq_vae_model
 ============
 
-.. autoclass:: pahelix.model_zoo.seq_vae_model
-   :members: VAE
-   :inherited-members:
+.. autoclass:: pahelix.model_zoo.seq_vae_model.VAE
+   :members:
 
 Helpful Link
 ============

docs/api_doc/networks.rst

@@ -8,8 +8,12 @@ basic_block
 ===========
 
 .. automodule:: pahelix.networks.basic_block
-   :members: Activation, MLP
-   :inherited-members:
+
+.. autoclass:: pahelix.networks.compound_encoder.Activation
+   :members:
+
+.. autoclass:: pahelix.networks.compound_encoder.MLP
+   :members:
 
 compound_encoder
 ================
@@ -28,9 +32,8 @@ gnn_block
 involution_block
 ================
 
-.. automodule:: pahelix.networks.involution_block
-   :members: Involution2D
-   :inherited-members:
+.. autoclass:: pahelix.networks.involution_block.Involution2D
+   :members:
 
 lstm_block
 ==========
@@ -42,9 +45,8 @@ lstm_block
 optimizer
 =========
 
-.. automodule:: pahelix.networks.optimizer
-   :members: AdamW
-   :inherited-members:
+.. autoclass:: pahelix.networks.optimizer.AdamW
+   :members:
 
 pre_post_process
 ================

docs/api_doc/utils.rst

@@ -15,7 +15,7 @@ compound_tools
 ==============
 
 .. automodule:: pahelix.utils.compound_tools
-   :members: get_gasteiger_partial_charges, create_standardized_mol_id, check_smiles_validity, split_rdkit_mol_obj, get_largest_mol, rdchem_enum_to_list, CompoundKit, Compound3DKit, mol_to_graph_data, mol_to_md_graph_data, mol_to_polar_graph_data
+   :members: get_gasteiger_partial_charges, create_standardized_mol_id, check_smiles_validity, split_rdkit_mol_obj, get_largest_mol, rdchem_enum_to_list, CompoundKit, Compound3DKit, mol_to_graph_data, mol_to_md_graph_data, mol_to_polar_graph_data, mol_to_superedge_graph_data
    :inherited-members:
 
 data_utils