#1534 Presence of stand alone H2 molecule on the canvas breaks Add e…

…xplicit hydrogens feature (it stops working) Fix code. Update UTs
epam · Jan 22, 2024 · b8d2337 · b8d2337
1 parent 84a1f90
commit b8d2337
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Showing 4 changed files with 58 additions and 5 deletions.
diff --git a/api/wasm/indigo-ketcher/indigo-ketcher.cpp b/api/wasm/indigo-ketcher/indigo-ketcher.cpp
@@ -449,7 +449,7 @@ namespace indigo
                 IndigoObject atom(_checkResult(indigoNext(iatoms.id)));
                 // indigoAtomicNumber can return -1 for non-standard atoms
                 // just skip these atoms
-                if (indigoAtomicNumber(atom.id) == 1) // hydrogen
+                if (indigoAtomicNumber(atom.id) == 1 && indigoDegree(atom.id) > 0) // hydrogen
                 {
                     fold = true;
                     break;

diff --git a/api/wasm/indigo-ketcher/test/test.js b/api/wasm/indigo-ketcher/test/test.js
@@ -558,6 +558,27 @@ M  END
             assert.equal(unfold_smiles, '{"struct":"C([H])([H])([H])C([H])([H])[H]","format":"smiles","original_format":"chemical/x-daylight-smiles"}');
             options.delete();
         });
+
+        test("convert_explicit_hydrogens", "auto_with_single_h", () => {
+            let options = new indigo.MapStringString();
+            options.set("output-content-type", "application/json");
+            const unfold_smiles = indigo.convert_explicit_hydrogens("CC.[HH]", "auto", "smiles", options);
+            assert.equal(unfold_smiles, '{"struct":"C([H])([H])([H])C([H])([H])[H].[H][H]","format":"smiles","original_format":"chemical/x-daylight-smiles"}');
+            const fold_smiles = indigo.convert_explicit_hydrogens("C([H])([H])([H])C([H])([H])[H].[H][H]", "auto", "smiles", options);
+            assert.equal(fold_smiles, '{"struct":"CC.[HH]","format":"smiles","original_format":"chemical/x-daylight-smiles"}');
+            options.delete();
+        });
+
+        test("convert_explicit_hydrogens", "auto_single_h", () => {
+            let options = new indigo.MapStringString();
+            options.set("output-content-type", "application/json");
+            const unfold_smiles = indigo.convert_explicit_hydrogens("[HH]", "auto", "smiles", options);
+            assert.equal(unfold_smiles, '{"struct":"[H][H]","format":"smiles","original_format":"chemical/x-daylight-smiles"}');
+            const fold_smiles = indigo.convert_explicit_hydrogens("[H][H]", "auto", "smiles", options);
+            assert.equal(fold_smiles, '{"struct":"[HH]","format":"smiles","original_format":"chemical/x-daylight-smiles"}');
+            options.delete();
+        });
+
     }
 
     // Dearomatize

diff --git a/utils/indigo-service/backend/service/tests/api/indigo_test.py b/utils/indigo-service/backend/service/tests/api/indigo_test.py
@@ -2979,7 +2979,7 @@ def test_convert_cdxml(self):
 
     def test_convert_explicit_hydrogens_auto(self):
         params = {
-            "struct": "CC",
+            "struct": "CC.[HH]",
             "mode": "auto",
             "output_format": "chemical/x-daylight-smiles",
             "input_format": "chemical/x-daylight-smiles",
@@ -2993,7 +2993,7 @@ def test_convert_explicit_hydrogens_auto(self):
         self.assertEqual(200, result.status_code)
         result_data = json.loads(result.text)
         self.assertEqual(
-            "C([H])([H])([H])C([H])([H])[H]", result_data["struct"]
+            "C([H])([H])([H])C([H])([H])[H].[H][H]", result_data["struct"]
         )
         params = {
             "struct": result_data["struct"],
@@ -3008,7 +3008,7 @@ def test_convert_explicit_hydrogens_auto(self):
         )
         self.assertEqual(200, result.status_code)
         result_data = json.loads(result.text)
-        self.assertEqual("CC", result_data["struct"])
+        self.assertEqual("CC.[HH]", result_data["struct"])
 
     def test_convert_explicit_hydrogens_fold(self):
         params = {
@@ -3046,6 +3046,37 @@ def test_convert_explicit_hydrogens_unfold(self):
             "C([H])([H])([H])C([H])([H])[H]", result_data["struct"]
         )
 
+    def test_convert_explicit_hydrogens_auto_h(self):
+        params = {
+            "struct": "[HH]",
+            "mode": "auto",
+            "output_format": "chemical/x-daylight-smiles",
+            "input_format": "chemical/x-daylight-smiles",
+        }
+        headers, data = self.get_headers(params)
+        result = requests.post(
+            self.url_prefix + "/convert_explicit_hydrogens",
+            headers=headers,
+            data=data,
+        )
+        self.assertEqual(200, result.status_code)
+        result_data = json.loads(result.text)
+        self.assertEqual("[H][H]", result_data["struct"])
+        params = {
+            "struct": result_data["struct"],
+            "output_format": "chemical/x-daylight-smiles",
+            "input_format": "chemical/x-daylight-smiles",
+        }
+        headers, data = self.get_headers(params)
+        result = requests.post(
+            self.url_prefix + "/convert_explicit_hydrogens",
+            headers=headers,
+            data=data,
+        )
+        self.assertEqual(200, result.status_code)
+        result_data = json.loads(result.text)
+        self.assertEqual("[HH]", result_data["struct"])
+
     def test_convert_sequences(self):
         headers, data = self.get_headers(
             {

diff --git a/utils/indigo-service/backend/service/v2/indigo_api.py b/utils/indigo-service/backend/service/v2/indigo_api.py
@@ -985,7 +985,8 @@ def convert_explicit_hydrogens():
         while iatoms.hasNext():
             atom = iatoms.next()
             try:
-                if atom.atomicNumber() == 1:  # Hydrogen
+                if atom.atomicNumber() == 1 and atom.degree() > 0:
+                    # Hydrogen connected to something - fold
                     fold = True
                     break
             except IndigoException: