#1631 - Revert back previous change, resetting _radicals only if it h…

…as no info or it's 0, added integration tests
epam · Feb 18, 2025 · ab367e4 · ab367e4
1 parent 63791e4
commit ab367e4
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Showing 4 changed files with 28 additions and 2 deletions.
diff --git a/api/tests/integration/ref/basic/fold_unfold.py.out b/api/tests/integration/ref/basic/fold_unfold.py.out
@@ -1393,3 +1393,13 @@ testing auto mode for [H][H]
 testing auto mode for [2H]C
 5
 2
+testing [CH3] |^1:0|
+[C]([H])([H])[H] |^1:0|
+testing [CH2] |^3:0|
+[C]([H])[H] |^3:0|
+testing [CH2] |^4:0|
+[C]([H])[H] |^4:0|
+testing [CH]C1=CC=CO1 |^4:0|
+[C]([H])C1OC([H])=C([H])C=1[H] |^4:0|
+testing C1C=CC=C([CH])C=1 |^4:5|
+C1([H])=C([H])C([C][H])=C([H])C([H])=C1[H] |^4:5|
diff --git a/api/tests/integration/tests/basic/fold_unfold.py b/api/tests/integration/tests/basic/fold_unfold.py
@@ -124,6 +124,13 @@ def testFoldUnfoldQueryReaction(smiles):
         print(mol.countAtoms())
 
 
+def testFoldUnfoldWithExplicitRadicals(smiles):
+    print("testing " + smiles)
+    mol = indigo.loadMolecule(smiles)
+    mol.unfoldHydrogens()
+    print(mol.smiles())
+
+
 testFoldUnfoldSDF(
     joinPathPy("../../../../../data/molecules/basic/sugars.sdf", __file__)
 )
@@ -193,3 +200,12 @@ def testFoldUnfoldQueryReaction(smiles):
 testAutoFoldUnfoldSingleReaction("[H]CC>>CC")
 testAutoFoldUnfoldSingleMol("[H][H]")
 testAutoFoldUnfoldSingleMol("[2H]C")
+
+# Monoradical
+testFoldUnfoldWithExplicitRadicals("[CH3] |^1:0|")
+# Diradical (singlet)
+testFoldUnfoldWithExplicitRadicals("[CH2] |^3:0|")
+# Diradical (triplet)
+testFoldUnfoldWithExplicitRadicals("[CH2] |^4:0|")
+testFoldUnfoldWithExplicitRadicals("[CH]C1=CC=CO1 |^4:0|")
+testFoldUnfoldWithExplicitRadicals("C1C=CC=C([CH])C=1 |^4:5|")
diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp
@@ -4887,7 +4887,7 @@ void BaseMolecule::unfoldHydrogens(Array<int>* markers_out, int max_h_cnt, bool
             for (int j = 0; j < h_cnt; j++)
             {
                 int new_h_idx = addAtom(ELEM_H);
-                int new_bond_idx = addBond_Silent(i, new_h_idx, BOND_SINGLE);
+                int new_bond_idx = addBond(i, new_h_idx, BOND_SINGLE);
 
                 if (only_selected) // if only selected atoms - select new H too
                 {

diff --git a/core/indigo-core/molecule/src/molecule.cpp b/core/indigo-core/molecule/src/molecule.cpp
@@ -201,7 +201,7 @@ void Molecule::_validateVertexConnectivity(int idx, bool validate)
             _atoms[idx].explicit_valence = false;
             _valence[idx] = -1;
         }
-        if (_radicals.size() > idx)
+        if (_radicals.size() > idx && _radicals[idx] <= 0)
         {
             _radicals[idx] = -1;
         }