Merge pull request #10 from Ramprasad-Group/Fix-Idempotence-for--some…

…-polymers

Fix idempotence issues for some polymers

canonicalize_psmiles/canonicalize.py

@@ -252,6 +252,13 @@ def unify(psmiles: str) -> str:
 
     sm = Chem.MolToCXSmiles(mol)
     mol = Chem.RWMol(Chem.MolFromSmiles(sm))
+    Chem.Kekulize(mol, clearAromaticFlags=True)
+
+    # FIX GH #8 idempotence of some PSMILES
+    Chem.Kekulize(mol, clearAromaticFlags=True)
+    sm = Chem.MolToCXSmiles(mol)
+    mol = Chem.RWMol(Chem.MolFromSmiles(sm))
+
 
     if logging.DEBUG >= logging.root.level:
         nb_display(mol)

tests/test_canonicalization.py

@@ -353,4 +353,17 @@ def test_canonicalize_multiple():
     for s in sm_init:
         canonicalize_smiles.append(canonicalize(s))
     one_smiles = list(set(canonicalize_smiles))
-    assert one_smiles == ["[*]c1sc(-c2sc(-c3sc([*])c4nccnc34)c3c2OCCO3)c2c1OCCO2"]
+    assert one_smiles == ["[*]c1sc(-c2sc(-c3sc([*])c4nccnc34)c3c2OCCO3)c2c1OCCO2"]
+
+def test_idempotence_of_canonicalization():
+    """ Canonicalizing some PSMILES twice switches between two PSMILES string  
+    """
+    sm1= "[*]c1ccc(Oc2ccc(-c3cc(-c4ccccc4)c4cc(Oc5ccc6nc([*])cc(-c7ccccc7)c6c5)ccc4n3)cc2)cc1"
+    sm2 = "[*]c1ccc2nc(-c3ccc(C4(c5ccc(-c6cc(-c7ccccc7)c7cc(C8([*])c9ccccc9-c9ccccc98)ccc7n6)cc5)c5ccccc5-c5ccccc54)cc3)cc(-c3ccccc3)c2c1"
+    sm3 = "[*]Oc1ccc(-c2cnc3ccc(-c4ccc5nc(-c6ccc(Oc7ccc([*])cc7)cc6)cnc5c4)cc3n2)cc1"
+
+    can = canonicalize
+
+    assert can(can(sm1)) == "[*]c1ccc(Oc2ccc(-c3cc(-c4ccccc4)c4cc(Oc5ccc6nc([*])cc(-c7ccccc7)c6c5)ccc4n3)cc2)cc1"
+    assert can(can(sm2)) == "[*]c1ccc(C2(c3ccc(-c4cc(-c5ccccc5)c5cc(C6(c7ccc8nc([*])cc(-c9ccccc9)c8c7)c7ccccc7-c7ccccc76)ccc5n4)cc3)c3ccccc3-c3ccccc32)cc1"
+    assert can(can(sm3)) == "[*]Oc1ccc(-c2cnc3ccc(-c4ccc5nc(-c6ccc(Oc7ccc([*])cc7)cc6)cnc5c4)cc3n2)cc1"