diff --git a/docs/source/API.rst b/docs/source/API.rst
index 771f432..ad34c50 100644
--- a/docs/source/API.rst
+++ b/docs/source/API.rst
@@ -5,6 +5,12 @@ This section provides documentation for the `fava.py` module.
 
 .. automodule:: fava
    :members:
-   :exclude-members: argument_parser, custom_formatwarning, main
    :undoc-members:
    :show-inheritance:
+   :exclude-members: argument_parser, custom_formatwarning, main, load_data, create_protein_pairs
+
+   # List the members in the order you want them to appear
+   :members:
+       VAE
+       cook
+       pairs_after_cutoff