RosettaCommons · rclune · Apr 22, 2026 · Jun 4, 2026 · Jul 10, 2026
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,13 @@
+.git
+.gitignore
+**/__pycache__
+**/*.pyc
+*.egg-info
+.eggs
+.pytest_cache
+.ruff_cache
+.mypy_cache
+.venv
+venv
+docs/_build
+tests/
diff --git a/.gitignore b/.gitignore
@@ -171,3 +171,6 @@ tinker/
 **/.claude
 CLAUDE.md
 .github/workflows/claude*.yml
+
+# Local docker files
+Dockerfile
diff --git a/docs/conf.py b/docs/conf.py
@@ -44,8 +44,11 @@
     "sphinx.ext.viewcode",  # Add source code links
     "sphinx.ext.napoleon",  # Google/NumPy style docstrings
     "sphinx_gallery.gen_gallery",  # Generates auto_examples/ from examples/
+    "myst_parser", # Support for Markdown files
+    "sphinx_design", # For better layout and design components
 ]
 
+
 templates_path = ["_templates"]
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/GALLERY_HEADER.rst", "ml/preprocessing.rst"]
 

diff --git a/docs/docs_requirements.txt b/docs/docs_requirements.txt
@@ -5,4 +5,6 @@ sphinx-autodoc-typehints>=1.20.0,<2
 nbsphinx>=0.8.9,<1
 sphinx-gallery>=0.8.1,<1
 ghp-import>=2.0.0,<3
-pandoc>=2.0.0,<3
+pandoc>=2.0.0,<3
+myst-parser>=5.0.0
+sphinx_design?=>0.7.0
diff --git a/docs/examples/annotate_and_save_structures.py b/docs/examples/annotate_and_save_structures.py
@@ -220,6 +220,6 @@ def fix_boolean_annotation(atom_array: struc.AtomArray, annotation_name: str) ->
 
 ########################################################################
 # Related Examples
-# ---------------
+# ----------------
 #
 # - :doc:`pocket_conditioning_transform` - Create custom transforms for ligand pocket identification and ML feature generation
diff --git a/docs/examples/dataset_exploration.py b/docs/examples/dataset_exploration.py
@@ -239,7 +239,7 @@ def simple_loading_fn(raw_data: Any) -> dict:
 
 ########################################################################
 # Related Examples
-# ---------------
+# ----------------
 #
 # - :doc:`load_and_visualize_structures` - Learn how to load and explore protein structures
 # - :doc:`pocket_conditioning_transform` - Create custom transforms for ligand pocket identification and ML feature generation

diff --git a/docs/examples/load_and_visualize_structures.py b/docs/examples/load_and_visualize_structures.py
@@ -170,7 +170,7 @@
 
 ########################################################################
 # Related Examples
-# ---------------
+# ----------------
 #
 # - :doc:`annotate_and_save_structures` - Learn how to add custom annotations to structures and save them for later use
 # - :doc:`pocket_conditioning_transform` - Create custom transforms for ligand pocket identification and ML feature generation
diff --git a/docs/examples/pocket_conditioning_transform.py b/docs/examples/pocket_conditioning_transform.py
@@ -29,7 +29,7 @@
 # Conventions
 # -----------
 # **A.** Store information in ``AtomArray`` annotations, not in the state dictionary.
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #
 # This ensures robustness when atoms are added/removed downstream.
 #
@@ -39,7 +39,7 @@
 # - ❌ Store ``pocket_atom_indices`` in dictionary (which creates significant dependencies with operations that delete or re-order atoms)
 #
 # **B.** Within ``forward()``, call a stand-alone function with the same name as the transform class.
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #
 # We thus maintain an object-oriented and a functional API, making our core logic re-usable and testable outside of the ``Transform`` framework.
 #