#1478 Dearomatization causes exception in case of Implicit H count q…

…uery feature set to 4 (i.e. more than 2) (#1570)
epam · Jan 17, 2024 · c661f9d · c661f9d
1 parent 49c01cc
commit c661f9d
Show file tree

Hide file tree

Showing 4 changed files with 140 additions and 11 deletions.
diff --git a/api/tests/integration/ref/arom/basic.py.out b/api/tests/integration/ref/arom/basic.py.out
@@ -467,3 +467,5 @@ M  END
 {"root":{"nodes":[{"$ref":"mol0"}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[0.0,0.0,0.0]},{"label":"C","location":[1.0,0.0,0.0]}],"bonds":[{"type":7,"atoms":[0,1]}]}}
 ***** Dearomatize molecule with custom query without label  *****
 [#6](=[$([#7]-[#8]-[#6](-[#1])(-[#1])-[#6](-[#1])(-[#1])-[#6](-[#1])(-[#1])-[#7](-[#6](-[#1])-[#1])-[#6](-[#1])-[#1]),$([#7]-[#8]-[#6](-[#1])(-[#1])-[#6](-[#1])(-[#1])-[#7](-[#6](-[#1])-[#1])-[#6](-[#1])-[#1]),$([#7]-[#7](-[#1])-[#6](=[#7]-[#1])-[#7](-[#1])-[#1]),$([#6](-[#1])-[#7])])(-[#6]1-[#6](-[H])=[#6](-[H])-[#6](-[$([#1]),$([#17])])=[#6](-[H])-[#6]=1-[H])-[#6]1-[#6](-[H])=[#6]-[#6](-[$([#6;X4]),$([#1])])=[#6](-[H])-[#6]=1-[H]
+***** Dearomatize molecule with atom_aromatic_connectivity < 0 should not cause exception  *****
+c1ccccc1
diff --git a/api/tests/integration/tests/arom/basic.py b/api/tests/integration/tests/arom/basic.py
@@ -359,3 +359,12 @@ def printMoleculeWithRGroups(m):
 )
 m.dearomatize()
 print(m.smarts())
+
+print(
+    "***** Dearomatize molecule with atom_aromatic_connectivity < 0 should not cause exception  *****"
+)
+m = indigo.loadMoleculeFromFile(
+    joinPathPy("molecules/issue_1478.ket", __file__)
+)
+m.dearomatize()
+print(m.smiles())
diff --git a/api/tests/integration/tests/arom/molecules/issue_1478.ket b/api/tests/integration/tests/arom/molecules/issue_1478.ket
@@ -0,0 +1,114 @@
+{
+    "root": {
+        "nodes": [
+            {
+                "$ref": "mol0"
+            }
+        ],
+        "connections": [],
+        "templates": []
+    },
+    "mol0": {
+        "type": "molecule",
+        "atoms": [
+            {
+                "label": "C",
+                "location": [
+                    14.059849222125079,
+                    -9.825074473618729,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    15.790150777932888,
+                    -9.824589053476172,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    14.926637935382303,
+                    -9.324966795472761,
+                    0
+                ],
+                "implicitHCount": 4
+            },
+            {
+                "label": "C",
+                "location": [
+                    15.790150777932888,
+                    -10.825532063144866,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    14.059849222125079,
+                    -10.830020053696668,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    14.928820895512578,
+                    -11.325033204531177,
+                    0
+                ]
+            }
+        ],
+        "bonds": [
+            {
+                "type": 4,
+                "atoms": [
+                    2,
+                    0
+                ]
+            },
+            {
+                "type": 4,
+                "atoms": [
+                    0,
+                    4
+                ]
+            },
+            {
+                "type": 4,
+                "atoms": [
+                    4,
+                    5
+                ]
+            },
+            {
+                "type": 4,
+                "atoms": [
+                    5,
+                    3
+                ]
+            },
+            {
+                "type": 4,
+                "atoms": [
+                    3,
+                    1
+                ]
+            },
+            {
+                "type": 4,
+                "atoms": [
+                    1,
+                    2
+                ]
+            }
+        ],
+        "stereoFlagPosition": {
+            "x": 15.790153526462133,
+            "y": 8.324968418632889,
+            "z": 0
+        }
+    }
+}
diff --git a/core/indigo-core/molecule/src/molecule_dearom.cpp b/core/indigo-core/molecule/src/molecule_dearom.cpp
@@ -971,20 +971,24 @@ void DearomatizationsGroups::_detectAromaticGroups(int v_idx, const int* atom_ex
 
     atom_aromatic_connectivity = max_connectivity - non_aromatic_conn;
     if (atom_aromatic_connectivity < 0)
-        throw Error("atom_aromatic_connectivity < 0 on %s having %d drawn bonds, charge %d, and %d radical electrons", Element::toString(label),
-                    non_aromatic_conn, charge, radical);
-
-    _vertexIsAcceptSingleEdge[v_idx] = true;
-    if (atom_aromatic_connectivity > 0)
     {
-        _vertexIsAcceptDoubleEdge[v_idx] = true;
-        // If number of implicit hydrogens are fixed and double bond is possible then
-        // double bond must exist
-        if (impl_h_fixed)
-            _vertexIsAcceptSingleEdge[v_idx] = false;
+        _vertexIsAcceptSingleEdge[v_idx] = false;
+        _vertexIsAcceptDoubleEdge[v_idx] = false;
     }
     else
-        _vertexIsAcceptDoubleEdge[v_idx] = false;
+    {
+        _vertexIsAcceptSingleEdge[v_idx] = true;
+        if (atom_aromatic_connectivity > 0)
+        {
+            _vertexIsAcceptDoubleEdge[v_idx] = true;
+            // If number of implicit hydrogens are fixed and double bond is possible then
+            // double bond must exist
+            if (impl_h_fixed)
+                _vertexIsAcceptSingleEdge[v_idx] = false;
+        }
+        else
+            _vertexIsAcceptDoubleEdge[v_idx] = false;
+    }
 }
 
 bool* DearomatizationsGroups::getAcceptDoubleBonds(void)