Filter out automorphisms more efficiently

TUCAN-nest · Dec 21, 2024 · 6e0c24d · 6e0c24d
1 parent 8fd73f8
commit 6e0c24d
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Showing 2 changed files with 5 additions and 9 deletions.
diff --git a/docs/refinement_tree.ipynb b/docs/refinement_tree.ipynb
@@ -172,15 +172,14 @@
    "source": [
     "## Feedback on performance and correctness\n",
     "\n",
-    "Currently (HEAD commit on `main` at December 04) `pytest tests/test_canonicalization.py::test_permutation_invariance` fails for 4 structures (exclusively timeout failures, no invariance failures):\n",
+    "Currently (HEAD commit on `main` at December 21) `pytest tests/test_canonicalization.py::test_permutation_invariance` fails for 3 structures (exclusively timeout failures, no invariance failures):\n",
     "\n",
     "```\n",
-    "============================================================= short test summary info =============================================================\n",
-    "FAILED tests/test_canonicalization.py::test_permutation_invariance[C28_H36_N8_Zn_C_F3_S_O3_2_C4_H8_O_in_Pca21] - Failed: Timeout >10.0s\n",
+    "======================================================== short test summary info ========================================================\n",
     "FAILED tests/test_canonicalization.py::test_permutation_invariance[C240] - Failed: Timeout >10.0s\n",
     "FAILED tests/test_canonicalization.py::test_permutation_invariance[C180] - Failed: Timeout >10.0s\n",
     "FAILED tests/test_canonicalization.py::test_permutation_invariance[C36_H72_Cl4_N14_Zn2_0_5_CH3CN_2_5_Et2O_in_P-1] - Failed: Timeout >10.0s\n",
-    "==================================================== 4 failed, 229 passed in 148.72s (0:02:28) ====================================================\n",
+    "=============================================== 3 failed, 230 passed in 118.62s (0:01:58) ===============================================\n",
     "\n",
     "```\n",
     "\n",

diff --git a/tucan/canonicalization.py b/tucan/canonicalization.py
@@ -75,12 +75,9 @@ def filter_out_automorphisms(ms: list[nx.Graph]) -> list[nx.Graph]:
     labelings = set()
 
     for m in ms:
-        m_relabeled_by_partition = nx.relabel_nodes(
-            m,
-            dict(zip(list(m), nx.get_node_attributes(m, PARTITION).values())),
-        )
+        partitions = list(nx.get_node_attributes(m, PARTITION).values())
         labeling = tuple(
-            sorted([tuple(sorted(edge)) for edge in m_relabeled_by_partition.edges()])
+            sorted([tuple(sorted(partitions[n] for n in edge)) for edge in m.edges()])
         )
 
         if labeling in labelings: