update docs

.gitignore

@@ -1,3 +1,4 @@
 .idea
 .venv
-tests/test-results/
+tests/test-results/
+docs/_build/

.readthedocs.yaml

@@ -0,0 +1,28 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - pdf
+  - epub
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt

README.md

@@ -1,7 +1,7 @@
 # ChemGED
 
-ChemGED is a Python package for enabling the appoximate graph edit distance (GED) computation between 
-chemicals. Normally, GED is a NP-hard problem, but ChemGED uses heuristics to approximate the GED in 
+ChemGED is a Python package for enabling the appoximate graph edit distance (GED) computation between
+chemicals. Normally, GED is a NP-hard problem, but ChemGED uses heuristics to approximate the GED in
 a reasonable time.
 
 ## Installation
@@ -12,8 +12,8 @@ pip install chemged
 ```
 
 ## Usage
-To use ChemGED, you just create an ``ApproximateChemicalGED`` object, and then call the 
-``compute_ged`` method with two chemical structures. They can be SMILES *or* 
+To use ChemGED, you just create an ``ApproximateChemicalGED`` object, and then call the
+``compute_ged`` method with two chemical structures. They can be SMILES *or*
 [RDKit](https://www.rdkit.org/docs/index.html) Mol objects.
 
 ```python
@@ -33,25 +33,36 @@ approx_ged = ged_calc.compute_ged(MolFromSmiles(chemical1), MolFromSmiles(chemic
 ChemGED also implements ``pdist`` and ``cdist`` functions to compute pairwise distances between
 sets of chemicals. These will return as Numpy arrays.
 
-> [!NOTE]  
+> [!NOTE]
 > ``pdist`` will return the vector-form distance vector, while ``cdist`` will return a
 > square-form distance matrix. ``scipy.spatial.distance.squareform`` can be used to convert
 > the vector-form distance vector to a square-form distance matrix.
 
 ```python
+from chemged import pdist, cdist
 
+# Create a list of chemicals
+chemicals = ["CCO", "CCN", "CC", "C"]
+
+# Compute pairwise distances
+distances_vector = pdist(chemicals)
+print(distances_vector)  # Vector form
+
+# Compute all-vs-all distances
+distances_matrix = cdist(chemicals, chemicals)
+print(distances_matrix)  # Square form
 ```
 
+## Documentation
+For more detailed documentation, please visit [ReadTheDocs](https://chemged.readthedocs.io/).
 
 ## Implementation
-
-The approach used here uses bipartite graph matching[[1]](#1), and most of its implementation in python 
+The approach used here uses bipartite graph matching[[1]](#1), and most of its implementation in python
 is based off scripts from https://github.com/priba/aproximated_ged/tree/master.
 ChemGED uses [RDKit](https://www.rdkit.org/docs/index.html) to handle chemicals inside python.
 
-
 ## References
-<a id="1">[1]</a> 
-Riesen, Kaspar, and Horst Bunke. 
-"Approximate graph edit distance computation by means of bipartite graph matching." 
-Image and Vision computing 27.7 (2009): 950-959
+<a id="1">[1]</a>
+Riesen, Kaspar, and Horst Bunke.
+"Approximate graph edit distance computation by means of bipartite graph matching."
+Image and Vision computing 27.7 (2009): 950-959

docs/api.rst

@@ -0,0 +1,45 @@
+=============
+API Reference
+=============
+
+This page provides detailed documentation for all the classes and functions in the ChemGED package.
+
+ApproximateChemicalGED
+----------------------
+
+.. autoclass:: src.chemged.ApproximateChemicalGED
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ChemicalGEDCostMatrix
+---------------------
+
+.. autoclass:: src.chemged.ChemicalGEDCostMatrix
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+UniformElementCostMatrix
+------------------------
+
+.. autoclass:: src.chemged.UniformElementCostMatrix
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Chemical Utilities
+==================
+
+.. automodule:: src.chemged.chem_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Plotting Utilities
+==================
+
+.. automodule:: src.chemged.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/chemical_graph_attributes.rst

@@ -0,0 +1,26 @@
+.. _chem-graph-attributes:
+
+=========================
+Chemical Graph Attributes
+=========================
+
+ChemGED uses the NetworkX library to represent chemical graphs. Each node in the graph represents an atom,
+and each edge represents a bond between atoms. The attributes of these nodes and edges are crucial for
+calculating the graph edit distance (GED) accurately.
+
+By default, the ``mol_to_nx`` function in ChemGED will convert a chemical into a NetworkX graph with the following
+atom attributes stored in the node:
+
+- **atomic_number**: The atomic number of the atom (e.g., 6 for Carbon, 8 for Oxygen).
+- **degree**: The degree of the atom in the graph (number of bonds).
+- **formal_charge**: The formal charge of the atom.
+- **hybridization**: The hybridization state of the atom (e.g., 'sp3', 'sp2').
+- **is_aromatic**: A boolean indicating if the atom is part of an aromatic ring.
+- **is_in_ring**: A boolean indicating if the atom is part of a ring structure.
+- **hydrogen**: The number of hydrogen atoms attached to the atom.
+
+Chemical bond attributes are stored in the graph. The edge attributes include:
+- **bond_type**: The type of bond (e.g., 'single', 'double', 'triple', 'aromatic').
+
+While these are the current attributes stored in the graph, you can extend or modify these attributes as
+needed for your specific use case.

docs/conf.py

@@ -0,0 +1,63 @@
+"""Configuration file for the Sphinx documentation builder."""
+
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import sys
+
+
+sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath("../src"))
+
+from chemged import __version__ as version
+
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+source_suffix = ".rst"
+master_doc = "index"
+
+project = "ChemGED"
+copyright = "2025, James Wellnitz"
+author = "James Wellnitz"
+release = version  # Added for ReadTheDocs compatibility
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+
+# -- Extension configuration -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#configuration
+
+autodoc_member_order = "bysource"
+autodoc_typehints = "description"
+
+# -- Intersphinx configuration -----------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#configuration
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "networkx": ("https://networkx.org/documentation/stable/", None),
+}
+
+issues_uri = "https://github.com/molecularmodelinglab/ChemGED/{issue}"
+issues_pr_uri = "https://github.com/molecularmodelinglab/ChemGED/pull/{pr}"