update doc

Author: KiddoZhu

README.md

@@ -1,6 +1,10 @@
-[![TorchDrug](asset/logo.svg)](https://torchdrug.ai/)
-
-----------------------------
+[![TorchDrug](asset/torchdrug_logo_full.svg)](https://torchdrug.ai/)
+<h1 align="center">
+  with
+  <a href="https://torchprotein.ai/">
+    <img src="asset/torchprotein_logo_tight.svg" alt="TorchProtein" style="height:26px" />
+  </a>
+</h1>
 
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Tbnr1Fog_YjkqU1MOhcVLuxqZ4DC-c8-#forceEdit=true&sandboxMode=true)
 [![Contributions](https://img.shields.io/badge/contributions-welcome-blue)](https://github.com/DeepGraphLearning/torchdrug/blob/master/CONTRIBUTING.md)
@@ -26,7 +30,7 @@ Installation
 ------------
 
 TorchDrug can be installed on either Linux, Windows or macOS. It is compatible with
-Python 3.7/3.8 and PyTorch >= 1.8.0.
+Python 3.7/3.8/3.9 and PyTorch >= 1.8.0.
 
 ### From Conda ###
 

asset/logo.svg renamed to asset/torchdrug_logo_full.svg

@@ -16,6 +16,11 @@ Molecule
 .. autoclass:: Molecule
     :members:
 
+Protein
+^^^^^^^
+.. autoclass:: Protein
+    :members:
+
 PackedGraph
 ^^^^^^^^^^^
 .. autoclass:: PackedGraph
@@ -26,6 +31,11 @@ PackedMolecule
 .. autoclass:: PackedMolecule
     :members:
 
+PackedProtein
+^^^^^^^^^^^^^
+.. autoclass:: PackedProtein
+    :members:
+
 Dictionary
 ^^^^^^^^^^
 .. autoclass:: Dictionary
@@ -45,6 +55,21 @@ MoleculeDataset
 .. autoclass:: MoleculeDataset
     :members:
 
+ProteinDataset
+^^^^^^^^^^^^^^
+.. autoclass:: ProteinDataset
+    :members:
+
+ProteinPairDataset
+^^^^^^^^^^^^^^^^^^
+.. autoclass:: ProteinPairDataset
+    :members:
+
+ProteinLigandDataset
+^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: ProteinLigandDataset
+    :members:
+
 NodeClassificationDataset
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 .. autoclass:: NodeClassificationDataset
@@ -104,6 +129,8 @@ Atom Features
 
 .. autofunction:: atom_synthon_completion
 
+.. autofunction:: atom_residue_symbol
+
 Bond Features
 ^^^^^^^^^^^^^
 .. autofunction:: bond_default
@@ -114,6 +141,12 @@ Bond Features
 
 .. autofunction:: bond_pretrain
 
+Residue Features
+^^^^^^^^^^^^^^^^
+.. autofunction:: residue_default
+
+.. autofunction:: residue_symbol
+
 Molecule Features
 ^^^^^^^^^^^^^^^^^
 .. autofunction:: molecule_default
@@ -154,4 +187,4 @@ abbreviated chemical symbol for atomic number ``i``.
 For a full list of elements, please refer to `the perodic table`_.
 
 .. _the perodic table:
-    https://en.wikipedia.org/wiki/Periodic_table
+    https://en.wikipedia.org/wiki/Periodic_table

asset/torchprotein_logo_tight.svg

@@ -141,6 +141,103 @@ PCQM4M
     :members:
 
 
+Protein Property Prediction Datasets
+------------------------------------
+
+BetaLactamase
+^^^^^^^^^^^^^
+.. autoclass:: BetaLactamase
+    :members:
+
+Fluorescence
+^^^^^^^^^^^^
+.. autoclass:: Fluorescence
+    :members:
+
+Stability
+^^^^^^^^^
+.. autoclass:: Stability
+    :members:
+
+Solubility
+^^^^^^^^^^
+.. autoclass:: Solubility
+    :members:
+
+BinaryLocalization
+^^^^^^^^^^^^^^^^^^
+.. autoclass:: BinaryLocalization
+    :members:
+
+SubcellularLocalization
+^^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: SubcellularLocalization
+    :members:
+
+EnzymeCommission
+^^^^^^^^^^^^^^^^
+.. autoclass:: EnzymeCommission
+    :members:
+
+GeneOntology
+^^^^^^^^^^^^
+.. autoclass:: GeneOntology
+    :members:
+
+AlphaFoldDB
+^^^^^^^^^^^
+.. autoclass:: AlphaFoldDB
+    :members:
+
+Protein Structure Prediction Datasets
+-------------------------------------
+
+Fold
+^^^^
+.. autoclass:: Fold
+    :members:
+
+SecondaryStructure
+^^^^^^^^^^^^^^^^^^
+.. autoclass:: SecondaryStructure
+    :members:
+
+ProteinNet
+^^^^^^^^^^
+.. autoclass:: ProteinNet
+    :members:
+
+Protein-Protein Prediction Datasets
+-----------------------------------
+
+HumanPPI
+^^^^^^^^
+.. autoclass:: HumanPPI
+    :members:
+
+YeastPPI
+^^^^^^^^
+.. autoclass:: YeastPPI
+    :members:
+
+PPIAffinity
+^^^^^^^^^^^
+.. autoclass:: PPIAffinity
+    :members:
+
+Protein Ligand Prediction Datasets
+----------------------------------
+
+BindingDB
+^^^^^^^^^
+.. autoclass:: BindingDB
+    :members:
+
+PDBBind
+^^^^^^^
+.. autoclass:: PDBBind
+    :members:
+
 Retrosynthesis Datasets
 -----------------------
 

doc/source/api/data.rst

@@ -50,6 +50,11 @@ ContinuousFilterConv
 .. autoclass:: ContinuousFilterConv
     :members:
 
+GeometricRelationalGraphConv
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: GeometricRelationalGraphConv
+    :members:
+
 GraphAttentionConv
 ^^^^^^^^^^^^^^^^^^
 .. autoclass:: GraphAttentionConv
@@ -152,6 +157,25 @@ ConditionalFlow
     :members:
 
 
+Sequence Encoder Blocks
+-----------------------
+
+ProteinResNetBlock
+^^^^^^^^^^^^^^^^^^
+.. autoclass:: ProteinResNetBlock
+    :members:
+
+SelfAttentionBlock
+^^^^^^^^^^^^^^^^^^
+.. autoclass:: SelfAttentionBlock
+    :members:
+
+ProteinBERTBlock
+^^^^^^^^^^^^^^^^
+.. autoclass:: ProteinBERTBlock
+    :members:
+
+
 Distribution Layers
 -------------------
 
@@ -165,6 +189,69 @@ IndependentGaussian
     :members:
 
 
+Graph Construction Layers
+-------------------------
+
+These layers belong to `torchdrug.layers.geometry`.
+
+.. currentmodule:: torchdrug.layers.geometry
+
+GraphConstruction
+^^^^^^^^^^^^^^^^^
+.. autoclass:: GraphConstruction
+    :members:
+
+SpatialLineGraph
+^^^^^^^^^^^^^^^^
+.. autoclass:: SpatialLineGraph
+    :members:
+
+BondEdge
+^^^^^^^^
+.. autoclass:: BondEdge
+    :members:
+
+KNNEdge
+^^^^^^^
+.. autoclass:: KNNEdge
+    :members:
+
+SpatialEdge
+^^^^^^^^^^^
+.. autoclass:: SpatialEdge
+    :members:
+
+SequentialEdge
+^^^^^^^^^^^^^^
+.. autoclass:: SequentialEdge
+    :members:
+
+AlphaCarbonNode
+^^^^^^^^^^^^^^^
+.. autoclass:: AlphaCarbonNode
+    :members:
+
+IdentityNode
+^^^^^^^^^^^^
+.. autoclass:: IdentityNode
+    :members:
+
+RandomEdgeMask
+^^^^^^^^^^^^^^
+.. autoclass:: RandomEdgeMask
+    :members:
+
+SubsequenceNode
+^^^^^^^^^^^^^^^
+.. autoclass:: SubsequenceNode
+    :members:
+
+SubspaceNode
+^^^^^^^^^^^^
+.. autoclass:: SubspaceNode
+    :members:
+
+
 Functional Layers
 -----------------
 

doc/source/api/datasets.rst

@@ -3,7 +3,6 @@ torchdrug.metrics
 
 .. currentmodule:: torchdrug.metrics
 
-
 Basic Metrics
 -------------
 
@@ -32,16 +31,36 @@ Accuracy
 
 Matthews Correlation Coefficient
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. autofuction:: matthews_corrcoef
+.. autofunction:: matthews_corrcoef
 
 Pearson Correlation Coefficient
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 .. autofunction:: pearsonr
 
-Spearman Correlation Coefficient
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Spearman's Rank Correlation Coefficient
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 .. autofunction:: spearmanr
 
+Variadic Accuracy
+^^^^^^^^^^^^^^^^^
+.. autofunction:: variadic_accuracy
+
+Variadic Area Under ROC
+^^^^^^^^^^^^^^^^^^^^^^^
+.. autofunction:: variadic_area_under_roc
+
+Variadic Area Under PRC
+^^^^^^^^^^^^^^^^^^^^^^^
+.. autofunction:: variadic_area_under_prc
+
+Variadic Top Precision
+^^^^^^^^^^^^^^^^^^^^^^
+.. autofunction:: variadic_top_precision
+
+F1 Max
+^^^^^^
+.. autofunction:: f1_max
+
 
 Chemical Metrics
 ----------------