YaoYinYing · YaoYinYing · Aug 11, 2025
diff --git a/docs/api.rst b/docs/api.rst
@@ -0,0 +1,8 @@
+RosettaPy API Reference
+========================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Packages
+
+   api/rosettapy
diff --git a/docs/api/rosettapy.analyser.rst b/docs/api/rosettapy.analyser.rst
@@ -0,0 +1,28 @@
+RosettaPy.analyser
+===================
+
+.. automodule:: RosettaPy.analyser
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Modules
+-------
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   RosettaPy.analyser.ddg
+   RosettaPy.analyser.reu
+
+Key Classes
+-----------
+
+.. autoclass:: RosettaPy.analyser.RosettaEnergyUnitAnalyser
+   :members:
+   :show-inheritance:
+
+.. autoclass:: RosettaPy.analyser.RosettaCartesianddGAnalyser
+   :members:
+   :show-inheritance:
diff --git a/docs/api/rosettapy.app.rst b/docs/api/rosettapy.app.rst
@@ -0,0 +1,22 @@
+RosettaPy.app
+==============
+
+.. automodule:: RosettaPy.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Modules
+-------
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   RosettaPy.app.cart_ddg
+   RosettaPy.app.fastrelax
+   RosettaPy.app.mutate_relax
+   RosettaPy.app.pross
+   RosettaPy.app.rosettaligand
+   RosettaPy.app.utils.CA_constraints
+   RosettaPy.app.utils.smiles2param
diff --git a/docs/api/rosettapy.common.rst b/docs/api/rosettapy.common.rst
@@ -0,0 +1,35 @@
+RosettaPy.common
+=================
+
+.. automodule:: RosettaPy.common
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Modules
+-------
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   RosettaPy.common.mutation
+
+Key Classes
+-----------
+
+.. autoclass:: RosettaPy.common.mutation.Mutation
+   :members:
+   :show-inheritance:
+
+.. autoclass:: RosettaPy.common.mutation.Chain
+   :members:
+   :show-inheritance:
+
+.. autoclass:: RosettaPy.common.mutation.RosettaPyProteinSequence
+   :members:
+   :show-inheritance:
+
+.. autoclass:: RosettaPy.common.mutation.Mutant
+   :members:
+   :show-inheritance:
diff --git a/docs/api/rosettapy.node.rst b/docs/api/rosettapy.node.rst
@@ -0,0 +1,35 @@
+RosettaPy.node
+===============
+
+.. automodule:: RosettaPy.node
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Modules
+-------
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   RosettaPy.node.dockerized
+   RosettaPy.node.mpi
+   RosettaPy.node.native
+   RosettaPy.node.utils
+   RosettaPy.node.wsl
+
+Key Classes
+-----------
+
+.. autoclass:: RosettaPy.node.MpiNode
+   :members:
+
+.. autoclass:: RosettaPy.node.Native
+   :members:
+
+.. autoclass:: RosettaPy.node.WslWrapper
+   :members:
+
+.. autoclass:: RosettaPy.node.dockerized.RosettaContainer
+   :members:
diff --git a/docs/api/rosettapy.rosetta.rst b/docs/api/rosettapy.rosetta.rst
@@ -0,0 +1,16 @@
+RosettaPy.rosetta
+==================
+
+.. automodule:: RosettaPy.rosetta
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Key Classes
+-----------
+
+.. autoclass:: RosettaPy.rosetta.Rosetta
+   :members:
+
+.. autoclass:: RosettaPy.rosetta.RosettaScriptsVariableGroup
+   :members:
diff --git a/docs/api/rosettapy.rosetta_finder.rst b/docs/api/rosettapy.rosetta_finder.rst
@@ -0,0 +1,16 @@
+RosettaPy.rosetta_finder
+=========================
+
+.. automodule:: RosettaPy.rosetta_finder
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Key Classes
+-----------
+
+.. autoclass:: RosettaPy.rosetta_finder.RosettaBinary
+   :members:
+
+.. autoclass:: RosettaPy.rosetta_finder.RosettaFinder
+   :members:
diff --git a/docs/api/rosettapy.rst b/docs/api/rosettapy.rst
@@ -0,0 +1,21 @@
+RosettaPy Package
+=================
+
+.. automodule:: RosettaPy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 1
+
+   rosettapy.analyser
+   rosettapy.app
+   rosettapy.common
+   rosettapy.node
+   rosettapy.utils
+   rosettapy.rosetta
+   rosettapy.rosetta_finder
diff --git a/docs/api/rosettapy.utils.rst b/docs/api/rosettapy.utils.rst
@@ -0,0 +1,34 @@
+RosettaPy.utils
+================
+
+.. automodule:: RosettaPy.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Modules
+-------
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   RosettaPy.utils.escape
+   RosettaPy.utils.repository
+   RosettaPy.utils.task
+   RosettaPy.utils.tools
+
+Key Items
+---------
+
+.. autofunction:: RosettaPy.utils.render
+
+.. autofunction:: RosettaPy.utils.print_diff
+
+.. autofunction:: RosettaPy.utils.zip_render
+
+.. autoclass:: RosettaPy.utils.RosettaCmdTask
+   :members:
+
+.. autoclass:: RosettaPy.utils.RosettaScriptsVariableGroup
+   :members:
diff --git a/docs/conf.py b/docs/conf.py
@@ -33,12 +33,42 @@
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinx.ext.doctest",
     "sphinx.ext.intersphinx",
     "sphinx.ext.ifconfig",
     "sphinx.ext.viewcode",  # Add links to highlighted source code
     "sphinx.ext.napoleon",  # to render Google format docstrings
     "sphinx.ext.githubpages",
+    "sphinx_copybutton",
+]
+
+# Autosummary settings
+autosummary_generate = True
+
+# Autodoc defaults
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "show-inheritance": True,
+    "inherited-members": True,
+}
+
+# Display type hints in the description
+autodoc_typehints = "description"
+
+# Mock heavy/optional third-party deps during doc build
+autodoc_mock_imports = [
+    "Bio",
+    "pandas",
+    "numpy",
+    "matplotlib",
+    "docker",
+    "git",
+    "rdkit",
+    "joblib",
+    "joblib_progress",
+    "tree",
 ]
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/docs/getting-started.rst b/docs/getting-started.rst
@@ -0,0 +1,52 @@
+Getting Started
+===============
+
+Installation
+------------
+
+.. code-block:: bash
+
+   pip install RosettaPy -U
+
+Prerequisites
+-------------
+
+- Rosetta must be compiled and installed with a valid license.
+- Ensure the `rosetta_scripts` binary is available locally or in a supported container.
+
+Minimal Example
+---------------
+
+.. code-block:: python
+
+   import os
+   from RosettaPy import Rosetta, RosettaScriptsVariableGroup
+   from RosettaPy.node import node_picker
+
+   rosetta = Rosetta(
+       bin="rosetta_scripts",
+       flags=["/path/to/flags.txt"],
+       opts=["-in:file:s", "/path/to/input.pdb", "-parser:protocol", "/path/to/protocol.xml"],
+       output_dir="./outputs",
+       job_id="demo",
+       run_node=node_picker("native"),
+       verbose=False,
+   )
+
+   # Optional: supply RosettaScripts variables
+   rsv = RosettaScriptsVariableGroup.from_dict({
+       "TASKOPERATIONS": ["OperateOnCertainResidues"],
+   })
+
+   rosetta.opts.append(rsv)
+   tasks = rosetta.run(nstruct=2)
+
+   # Each task contains the composed command; running returns execution results
+   for t in tasks:
+       print(t.cmd)
+
+Where to go next
+----------------
+
+- See the guides for specific workflows like PROSS, FastRelax, RosettaLigand, Supercharge, MutateRelax, and Cartesian ddG.
+- Explore the full API reference for classes and functions.
diff --git a/docs/guides.rst b/docs/guides.rst
@@ -0,0 +1,14 @@
+Guides
+======
+
+This section provides end-to-end examples for common tasks.
+
+.. toctree::
+   :maxdepth: 1
+
+   guides/pross
+   guides/fastrelax
+   guides/rosettaligand
+   guides/supercharge
+   guides/mutate_relax
+   guides/cart_ddg
diff --git a/docs/guides/cart_ddg.rst b/docs/guides/cart_ddg.rst
@@ -0,0 +1,23 @@
+Cartesian ddG Workflow
+======================
+
+Example
+-------
+
+.. code-block:: python
+
+   from RosettaPy.app.cart_ddg import CartesianddG
+   from RosettaPy.common.mutation import Mutant, Mutation, RosettaPyProteinSequence, Chain
+   from RosettaPy.node import node_picker
+
+   wt = RosettaPyProteinSequence(chains=[Chain(chain_id="A", sequence="IRGWEEGVAQM")])
+   mutant = Mutant(mutations=[Mutation(chain_id="A", position=10, wt_res="Q", mut_res="V")], wt_protein_sequence=wt)
+
+   app = CartesianddG(
+       pdb="/path/to/wt.pdb",
+       mutant=mutant,
+       output_dir="./outputs",
+       node=node_picker("native"),
+   )
+   ddg = app.run(nstruct=25)
+   print(ddg)
diff --git a/docs/guides/fastrelax.rst b/docs/guides/fastrelax.rst
@@ -0,0 +1,18 @@
+FastRelax Workflow
+==================
+
+Example
+-------
+
+.. code-block:: python
+
+   from RosettaPy.app.fastrelax import FastRelax
+   from RosettaPy.node import node_picker
+
+   fr = FastRelax(
+       pdb="/path/to/input.pdb",
+       output_dir="./outputs",
+       node=node_picker("native"),
+   )
+   scores = fr.run(nstruct=10)
+   print(scores.describe())