Added Structure.adjacency_dict property

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
     rev: v1.4.0
     hooks:
       - id: detect-secrets
-        stages: [pre-commit]
+        stages: [commit]
         exclude: '.*\.(lock|ipynb)$'
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
@@ -36,7 +36,7 @@ repos:
     hooks:
       - id: tests
         name: tests
-        stages: [pre-push]
+        stages: [push]
         language: system
         entry: uv run pytest
         types: [python]

pyproject.toml

@@ -70,7 +70,7 @@ dev = [
     "matplotlib>=3.0.0",
     "py3Dmol>=2.2.1",
     "pint>=0.24.4",
-    "qcinf>=0.2.1",
+    "qcinf[all]>=0.2.1",
 ]
 
 docs = [

src/qcio/models/structure.py

@@ -1,5 +1,5 @@
 import warnings
-from collections import Counter
+from collections import Counter, defaultdict
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, ClassVar
 
@@ -279,6 +279,15 @@ def adjacency_matrix(self) -> np.ndarray:
             adj[j, i] = order
         return adj
 
+    @property
+    def adjacency_dict(self) -> dict[int, list[int]]:
+        """Return adjacency dictionary where each key maps to a list of bonded atom indices."""
+        adjacency = defaultdict(list)
+        for i, j, _ in self.connectivity:
+            adjacency[i].append(j)
+            adjacency[j].append(i)
+        return adjacency
+
     @classmethod
     def from_xyz(
         cls,

tests/test_structure.py

@@ -64,6 +64,16 @@ def test_to_from_file_json(test_data_dir, tmp_path):
     assert caffeine_copy.charge == caffeine.charge
 
 
+def test_adjacency_matrix(water):
+    expected = np.array([[0, 1, 1], [1, 0, 0], [1, 0, 0]])
+    assert np.array_equal(expected, water.adjacency_matrix)
+
+
+def test_adjacency_dict(water):
+    expected = {0: [1, 2], 1: [0], 2: [0]}
+    assert expected == water.adjacency_dict
+
+
 def test_structure_model_dump_connectivity(water):
     # Test that connectivity is a list of lists of floats
     # Must cast all to the same type as toml cannot handle mixed types