update docs

Author: liugangcode

docs/source/api/encoder.rst

@@ -3,10 +3,13 @@ Molecular Encoder Models
 
 This section documents the encoder(representation learning) models in `torch_molecule.encoder`.
 
-.. rubric:: MoAma for Molecular Representation Learning
+.. contents::
+   :local:
+   :depth: 1
 
+.. rubric:: MoAma for Molecular Representation Learning
 .. automodule:: torch_molecule.encoder.moama
-   :members:
+   :members: 
    :undoc-members:
    :show-inheritance:
 

docs/source/api/generator.rst

@@ -3,6 +3,10 @@ Molecular Generation Models
 
 This section documents the generation models in `torch_molecule.generator`.
 
+.. contents::
+   :local:
+   :depth: 1
+   
 .. rubric:: GraphDiT for Un/Multi-conditional Molecular Generation
 
 .. automodule:: torch_molecule.generator.graph_dit

docs/source/api/index.rst

@@ -4,8 +4,9 @@ API Reference
 This section documents the main modules and classes in `torch_molecule`.
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
    :caption: Main Components:
+   :hidden:
 
    predictor
    generator

docs/source/api/predictor.rst

@@ -3,6 +3,10 @@ Molecular Property Prediction Models
 
 This section documents the predictor models in `torch_molecule.predictor`.
 
+.. contents::
+   :local:
+   :depth: 1
+
 .. (Add predictors here as needed. You might write summaries and link submodules.)
 
 .. rubric:: Graph Neural Networks

docs/source/index.rst

@@ -18,8 +18,9 @@ Welcome to the torch-molecule documentation. torch-molecule is an actively devel
    example
 
 .. toctree::
-   :maxdepth: 2
-   :caption: API for main modules:
+   :maxdepth: 3
+   :caption: Main Components:
+   :hidden:
 
    api/predictor
    api/generator