enhance graph descriptors

pyproject.toml

@@ -4,12 +4,14 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synutility"
-version = "0.0.13"
+version = "0.0.14"
 authors = [
     {name="Tieu Long Phan", email="[email protected]"}
 ]
 description = "Utility for reaction modeling using graph grammar"
 readme = "README.md"
+long-description = {file = "CHANGELOG.md"}
+long-description-content-type = "text/markdown"
 requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -32,4 +34,4 @@ all = ["drfp==0.3.6", "xgboost>=2.1.1", "fgutils>=0.1.3", "rxn-chem-utils==1.5.0
 homepage = "https://github.com/TieuLongPhan/SynUtils"
 source = "https://github.com/TieuLongPhan/SynUtils"
 issues = "https://github.com/TieuLongPhan/SynUtils/issues"
-documentation = "https://tieulongphan.github.io/SynUtils/"
+documentation = "https://tieulongphan.github.io/SynUtils/"

synutility/SynAAM/its_construction.py

@@ -1,6 +1,6 @@
 import networkx as nx
 from typing import Tuple, Dict, Any
-from copy import deepcopy
+from copy import deepcopy, copy
 
 
 class ITSConstruction:
@@ -136,7 +136,7 @@ def add_edges_to_ITS(
         Returns:
         - nx.Graph: The updated graph with added edges.
         """
-        new_ITS = deepcopy(ITS)
+        new_ITS = ITS.copy()
 
         # Add edges from G and H
         for graph_from, graph_to, reverse in [(G, H, False), (H, G, True)]:

synutility/SynGraph/Descriptor/graph_descriptors.py

@@ -115,18 +115,30 @@ def check_graph_type(G: nx.Graph) -> str:
             return "Complex Cyclic"
 
     @staticmethod
-    def get_cycle_member_rings(G: nx.Graph) -> List[int]:
+    def get_cycle_member_rings(G: nx.Graph, type="minimal") -> List[int]:
         """
-        Finds all cycles in the graph and returns a list of their sizes.
+        Identifies all cycles in the given graph using cycle bases to ensure no overlap
+        and returns a list of the sizes of these cycles (member rings),
+        sorted in ascending order.
 
         Parameters:
-        - G (nx.Graph): The graph to analyze.
+        - G (nx.Graph): The NetworkX graph to be analyzed.
 
         Returns:
-        - List[int]: Sorted list of cycle sizes.
+        - List[int]: A sorted list of cycle sizes (member rings) found in the graph.
         """
-        GraphDescriptor._validate_graph_input(G)
-        return sorted(len(cycle) for cycle in nx.minimum_cycle_basis(G))
+        if not isinstance(G, nx.Graph):
+            raise TypeError("Input must be a networkx Graph object.")
+
+        if type == "minimal":
+            cycles = nx.minimum_cycle_basis(G)
+        else:
+            cycles = nx.cycle_basis(G)
+        member_rings = [len(cycle) for cycle in cycles]
+
+        member_rings.sort()
+
+        return member_rings
 
     @staticmethod
     def get_element_count(graph: nx.Graph) -> Dict[str, int]: