synkit 0.0.7__tar.gz → 0.0.9__tar.gz

{synkit-0.0.7 → synkit-0.0.9}/.gitignore

@@ -19,4 +19,5 @@ Data/Benchmark/*
 # *.png
 *.json.gz
 run.sh
-docs/*
+docs/*
+run_rdcanon.py

synkit-0.0.9/.readthedocs.yml

@@ -0,0 +1,24 @@
+# Read the Docs configuration file
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+# 1) Tell RTD this is v2 of the schema
+version: 2
+
+# 2) Pick your build image and interpreter
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# 3) Install your package + any doc-only extras
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements: 
+        - docs
+
+# 4) Point Sphinx at your conf.py and choose HTML
+sphinx:
+  configuration: doc/conf.py
+  builder: html

{synkit-0.0.7 → synkit-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synkit
-Version: 0.0.7
+Version: 0.0.9
 Summary: Utility for reaction modeling using graph grammar
 Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
 Project-URL: source, https://github.com/TieuLongPhan/SynKit
@@ -22,6 +22,10 @@ Requires-Dist: seaborn>=0.13.2
 Provides-Extra: all
 Requires-Dist: numpy>=2.2.0; extra == 'all'
 Requires-Dist: torch>=2.2.0; extra == 'all'
+Provides-Extra: docs
+Requires-Dist: sphinx-rtd-theme; extra == 'docs'
+Requires-Dist: sphinx>=6.0; extra == 'docs'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'docs'
 Description-Content-Type: text/markdown
 
 # SynKit

{synkit-0.0.7 → synkit-0.0.9}/Test/Chem/Reaction/test_canon_rsmi.py

@@ -7,7 +7,11 @@ from synkit.IO.chem_converter import rsmi_to_graph
 class TestCanonRSMI(unittest.TestCase):
     def setUp(self):
         # Use generic backend for deterministic behavior
-        self.canon = CanonRSMI(backend="wl", wl_iterations=5)
+        self.canon = CanonRSMI(
+            backend="wl",
+            wl_iterations=5,
+            node_attrs=["element", "aromatic", "charge", "hcount", "neighbors"],
+        )
         # Example reaction SMILES with atom-map labels
         self.input_rsmi = "[CH3:3][CH2:5][OH:10]>>[CH2:3]=[CH2:5].[OH2:10]"
         # After expand_aam and canonicalisation, since backend is generic,

{synkit-0.0.7 → synkit-0.0.9}/Test/Graph/ITS/test_its_construction.py

@@ -21,21 +21,21 @@ class TestITSConstruction(unittest.TestCase):
         self.H.add_edge(1, 2, order=1)  # Different order
 
     def test_ITSGraph(self):
-        ITS = ITSConstruction.ITSGraph(self.G, self.H)
+        ITS = ITSConstruction().ITSGraph(self.G, self.H)
         self.assertTrue(isinstance(ITS, nx.Graph))
         self.assertEqual(len(ITS.nodes()), 2)
         self.assertEqual(len(ITS.edges()), 1)
         self.assertEqual(ITS[1][2]["order"], (2, 1))
 
     def test_get_node_attributes_with_defaults(self):
-        attributes = ITSConstruction.get_node_attributes_with_defaults(self.G, 1)
+        attributes = ITSConstruction().get_node_attributes_with_defaults(self.G, 1)
         self.assertEqual(attributes, ("C", False, 2, 0, ["", ""]))
 
     def test_add_edges_to_ITS(self):
         ITS = nx.Graph()
         ITS.add_node(1, element="C", aromatic=False, hcount=3, charge=0)
         ITS.add_node(2, element="C", aromatic=False, hcount=3, charge=0)
-        new_ITS = ITSConstruction.add_edges_to_ITS(ITS, self.G, self.H)
+        new_ITS = ITSConstruction().add_edges_to_ITS(ITS, self.G, self.H)
         self.assertTrue(isinstance(new_ITS, nx.Graph))
         self.assertEqual(len(new_ITS.edges()), 1)
         self.assertEqual(new_ITS[1][2]["order"], (2, 1))
@@ -43,7 +43,7 @@ class TestITSConstruction(unittest.TestCase):
     def test_add_standard_order_attribute(self):
         graph = nx.Graph()
         graph.add_edge(1, 2, order=(1, 2))
-        updated_graph = ITSConstruction.add_standard_order_attribute(graph)
+        updated_graph = ITSConstruction().add_standard_order_attribute(graph)
         self.assertEqual(updated_graph[1][2]["standard_order"], -1)
 
 

{synkit-0.0.7 → synkit-0.0.9}/Test/Graph/ITS/test_its_expand.py

@@ -12,6 +12,7 @@ class TestPartialExpand(unittest.TestCase):
             "[CH3:1][CH2:2][CH2:3][Cl:4].[NH2:5][H:6]"
             + ">>[CH3:1][CH2:2][CH2:3][NH2:5].[Cl:4][H:6]"
         )
+        print(output_rsmi)
         self.assertTrue(AAMValidator.smiles_check(output_rsmi, expected_rsmi, "ITS"))
 
 

{synkit-0.0.7 → synkit-0.0.9}/Test/IO/test_chemical_converter.py

@@ -86,7 +86,10 @@ class TestChemicalConversions(unittest.TestCase):
     def test_smiles_to_graph_valid(self):
         # Test converting a valid SMILES to a graph
         result = smiles_to_graph(
-            "[CH3:1][CH2:2][OH:3]", False, True, True, use_index_as_atom_map=True
+            "[CH3:1][CH2:2][OH:3]",
+            False,
+            True,
+            True,
         )
         self.assertIsInstance(result, nx.Graph)
         self.assertEqual(result.number_of_nodes(), 3)
@@ -94,7 +97,10 @@ class TestChemicalConversions(unittest.TestCase):
     def test_smiles_to_graph_invalid(self):
         # Test converting an invalid SMILES string to a graph
         result = smiles_to_graph(
-            "invalid_smiles", True, False, False, use_index_as_atom_map=True
+            "invalid_smiles",
+            True,
+            False,
+            False,
         )
         self.assertIsNone(result)
 

{synkit-0.0.7 → synkit-0.0.9}/Test/Rule/Modify/test_molecule_rule.py

@@ -1,6 +1,6 @@
 import unittest
 from synkit.Rule.Modify.molecule_rule import MoleculeRule
-from synkit.Graph.Matcher import GraphMatcherEngine
+from synkit.Graph.Matcher.graph_matcher import GraphMatcherEngine
 import importlib
 
 MOD_AVAILABLE = importlib.util.find_spec("mod") is not None

{synkit-0.0.7 → synkit-0.0.9}/Test/Rule/Modify/test_rule_utils.py

@@ -7,7 +7,8 @@ from synkit.Rule.Modify.rule_utils import (
     strip_context,
     _increment_gml_ids,
 )
-from synkit.Graph.Matcher import GraphMatcherEngine, SubgraphMatch
+from synkit.Graph.Matcher.graph_matcher import GraphMatcherEngine
+from synkit.Graph.Matcher.subgraph_matcher import SubgraphMatch
 import importlib
 
 MOD_AVAILABLE = importlib.util.find_spec("mod") is not None

synkit-0.0.9/build-doc.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+set -e
+
+echo "Checking and installing documentation dependencies..."
+
+# Function to check and install a Python package if missing
+install_if_missing() {
+    PACKAGE=$1
+    python -c "import $PACKAGE" 2>/dev/null || {
+        echo "Installing $PACKAGE..."
+        pip install "$PACKAGE"
+    }
+}
+
+# Check and install main Sphinx packages
+install_if_missing sphinx
+install_if_missing sphinx_rtd_theme
+
+# sphinxcontrib-bibtex can have a dash in its import, so:
+pip show sphinxcontrib-bibtex >/dev/null 2>&1 || {
+    echo "Installing sphinxcontrib-bibtex..."
+    pip install sphinxcontrib-bibtex
+}
+
+echo "Building Sphinx documentation..."
+
+# Build the docs (adjust source/build dirs as needed)
+python3 -m sphinx -b html ./doc ./docs
+
+echo "Documentation built in ./docs"

{synkit-0.0.7 → synkit-0.0.9}/doc/api.rst

@@ -2,15 +2,6 @@
 API
 ====
 
-IO Module
-=========
-The `IO` module provides tools for handling input and output operations related to the chemical converter. It allows seamless interaction with various chemical data formats.
-
-.. automodule:: synkit.IO.chem_converter
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 Chem Module
 ===========
 The `Chem` module provides tools for handling input and output operations related to the chemical converter. It allows seamless interaction with various chemical data formats.
@@ -198,3 +189,47 @@ The ``synkit.Vis`` package offers a suite of **visualization utilities** for bot
    :members:
    :undoc-members:
    :show-inheritance:
+
+IO Module
+=========
+The `IO` module provides tools for handling input and output operations related to the chemical converter. It allows seamless interaction with various chemical data formats.
+
+Chemical Conversion
+-------------------
+.. automodule:: synkit.IO.chem_converter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: synkit.IO.mol_to_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: synkit.IO.graph_to_mol
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: synkit.IO.nx_to_gml
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: synkit.IO.gml_to_nx
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+IO Functions
+------------
+
+.. automodule:: synkit.IO.data_io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: synkit.IO.data_io
+   :members:
+   :undoc-members:
+   :show-inheritance:

{synkit-0.0.7 → synkit-0.0.9}/doc/conf.py

@@ -1,31 +1,34 @@
-# 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
 
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+sys.path.insert(0, os.path.abspath(".."))
 
+# -- Project information -----------------------------------------------------
 project = "synkit"
-copyright = "2025, Tieu-Long Phan"
 author = "Tieu-Long Phan"
+release = "0.0.8"
+version = release
 
 # -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.githubpages",
     "sphinxcontrib.bibtex",
+    # "sphinx.ext.napoleon",  # un-comment if using Google/NumPy docstrings
 ]
+
 bibtex_bibfiles = ["refs.bib"]
 templates_path = ["_templates"]
 exclude_patterns = []
 autosectionlabel_prefix_document = True
 
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "show-inheritance": True,
+}
 
+# -- Options for HTML output -------------------------------------------------
 html_theme = "sphinx_rtd_theme"
 html_static_path = ["_static"]

{synkit-0.0.7 → synkit-0.0.9}/doc/index.rst

@@ -1,5 +1,6 @@
 Welcome to synkit documentation!
 ================================
+This is documentation for synkit version |version| (release |release|).
 
 .. toctree::
    :caption: Contents

{synkit-0.0.7 → synkit-0.0.9}/doc/io.rst

@@ -102,31 +102,31 @@ Set ``core=True`` to include only the **reaction center**, and ``useSmile=True``
    :linenos:
 
    from synkit.IO import (
-       rsmi_to_its,
-       smart_to_gml,
-       its_to_gml,
-       save_text_as_gml,
-       load_gml_as_text,
+      rsmi_to_its,
+      smart_to_gml,
+      its_to_gml,
+      save_text_as_gml,
+      load_gml_as_text,
    )
 
    # Define the aldol reaction template
    reaction = (
-       '[CH3:1][CH:2]=[O:3].'
-       '[CH:4]([H:7])([H:8])[CH:5]=[O:6]'
-       '>>'
-       '[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].'
-       '[O:3]([H:7])([H:8])'
+      '[CH3:1][CH:2]=[O:3].'
+      '[CH:4]([H:7])([H:8])[CH:5]=[O:6]'
+      '>>'
+      '[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].'
+      '[O:3]([H:7])([H:8])'
    )
 
    # Option 1: Direct SMARTS → GML
-   gml_rule_1 = smart_to_gml(reaction, core=True, useSmile=False)
+   gml_rule_1 = smart_to_gml(reaction, core=True, useSmiles=False)
 
    # Option 2: SMILES → ITS → GML
    its_graph = rsmi_to_its(reaction, core=True)
    gml_rule_2 = its_to_gml(its_graph, core=True)
 
    # Save to disk
-   save_text_as_gml("aldol_rule.gml", gml_rule_2)
+   save_text_as_gml(gml_text=gml_rule_2, file_path="aldol_rule.gml")
 
    # Load back into text
    loaded_rule = load_gml_as_text("aldol_rule.gml")

synkit-0.0.9/doc/requirements.txt

@@ -0,0 +1,3 @@
+sphinx
+sphinx-rtd-theme
+sphinxcontrib-bibtex

{synkit-0.0.7 → synkit-0.0.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "0.0.7"
+version = "0.0.9"
 authors = [
     {name="Tieu Long Phan", email="tieu@bioinf.uni-leipzig.de"}
 ]
@@ -30,7 +30,11 @@ dependencies = [
 
 [project.optional-dependencies]
 all = ["numpy>=2.2.0", "torch>=2.2.0"]
-
+docs = [
+  "sphinx>=6.0",
+  "sphinx-rtd-theme",
+  "sphinxcontrib-bibtex",
+]
 [project.urls]
 homepage = "https://github.com/TieuLongPhan/SynKit"
 source = "https://github.com/TieuLongPhan/SynKit"

{synkit-0.0.7 → synkit-0.0.9}/synkit/Chem/Reaction/aam_validator.py

@@ -85,10 +85,10 @@ class AAMValidator:
         its_graphs, rc_graphs = [], []
         try:
             for rsmi in (mapped_smile, ground_truth):
-                G, H = rsmi_to_graph(
-                    rsmi=rsmi, sanitize=True, drop_non_aam=True, light_weight=True
+                G, H = rsmi_to_graph(rsmi=rsmi, sanitize=True, drop_non_aam=True)
+                its = ITSConstruction().ITSGraph(
+                    G, H, ignore_aromaticity=ignore_aromaticity
                 )
-                its = ITSConstruction.ITSGraph(G, H, ignore_aromaticity)
                 its_graphs.append(its)
                 rc_graphs.append(get_rc(its))
 

synkit-0.0.9/synkit/Graph/Canon/__init__.py

@@ -0,0 +1,3 @@
+from .canon_graph import GraphCanonicaliser, CanonicalGraph
+
+__all__ = ["GraphCanonicaliser", "CanonicalGraph"]

{synkit-0.0.7/synkit/Graph → synkit-0.0.9/synkit/Graph/Canon}/canon_graph.py

@@ -63,6 +63,7 @@ from networkx.algorithms.graph_hashing import (
     weisfeiler_lehman_subgraph_hashes as _wl_hashes,
 )
 from .canon_algs import canon_morgan
+from .nauty import NautyCanonicalizer
 
 __all__: list[str] = ["CanonicalGraph", "GraphCanonicaliser", "CanonicalRule"]
 
@@ -145,14 +146,14 @@ class GraphCanonicaliser:
     def __init__(
         self,
         *,
-        backend: Literal["generic", "wl", "morgan"] = "generic",
+        backend: Literal["generic", "wl", "morgan", "nauty"] = "generic",
         wl_iterations: int = 3,
         morgan_radius: int = 3,
         node_attrs: List[str] = ["element", "aromatic", "charge", "hcount"],
         node_sort_key: T_NodeSortKey = _default_node_key,
         edge_sort_key: T_EdgeSortKey = _default_edge_key,
     ) -> None:
-        if backend not in {"generic", "wl", "morgan"}:
+        if backend not in {"generic", "wl", "morgan", "nauty"}:
             raise ValueError("backend must be 'generic' or 'wl' or 'morgan' ")
         self.backend: Literal["generic", "wl", "morgan"] = backend
         self._wl_k: int = wl_iterations
@@ -161,6 +162,8 @@ class GraphCanonicaliser:
         self._edge_key: T_EdgeSortKey = edge_sort_key
         self._wl_node_attrs: Tuple[str, ...] = tuple(node_attrs)
         self._mg_node_attrs: List[str] = node_attrs
+        if self.backend == "nauty":
+            self.nauty = NautyCanonicalizer(node_attrs=node_attrs, edge_attrs=["order"])
 
     # ------------------------------------------------------------------ #
     # High‑level helpers                                                 #
@@ -220,6 +223,8 @@ class GraphCanonicaliser:
             return self._canon_generic(g)
         elif self.backend == "wl":
             return self._canon_wl(g)
+        elif self.backend == "nauty":
+            return self._canon_nauty(g)
         else:
             return canon_morgan(
                 g, morgan_radius=self._mg_k, node_attributes=self._mg_node_attrs
@@ -228,6 +233,9 @@ class GraphCanonicaliser:
         #     self._canon_generic(g) if self.backend == "generic" else self._canon_wl(g)
         # )
 
+    def _canon_nauty(self, g: nx.Graph) -> nx.Graph:
+        return self.nauty.canonical_form(g)
+
     def _canon_generic(self, g: nx.Graph) -> nx.Graph:
         """Pure attribute‑sort strategy – O(|V| log |V| + |E| log |E|)."""
         nodes_sorted = sorted(g.nodes(data=True), key=lambda x: self._node_key(*x))
@@ -274,6 +282,7 @@ class GraphCanonicaliser:
         wl_hash = _wl_hashes(
             g2,
             node_attr=node_attr,
+            edge_attr="order",
             iterations=self._wl_k,
         )