Backmerge: #2318 - The reaction with retrosynthetic arrow is displaye…

…d not correct after clicking on Aromatize (#2394)
epam · Sep 17, 2024 · 2772c0c · 2772c0c
1 parent 04356f1
commit 2772c0c
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Showing 12 changed files with 117 additions and 78 deletions.
diff --git a/api/c/indigo/src/indigo.cpp b/api/c/indigo/src/indigo.cpp
@@ -211,12 +211,14 @@ void Indigo::initReactionJsonSaver(ReactionJsonSaver& saver)
 {
     saver.add_stereo_desc = json_saving_add_stereo_desc;
     saver.pretty_json = json_saving_pretty;
+    saver.use_native_precision = json_use_native_precision;
 }
 
 void Indigo::initReactionJsonSaver(PathwayReactionJsonSaver& saver)
 {
     saver.add_stereo_desc = json_saving_add_stereo_desc;
     saver.pretty_json = json_saving_pretty;
+    saver.use_native_precision = json_use_native_precision;
 }
 
 void Indigo::initRxnfileSaver(RxnfileSaver& saver)

diff --git a/api/tests/integration/ref/formats/ket_retrosynthetic_arrow.py.out b/api/tests/integration/ref/formats/ket_retrosynthetic_arrow.py.out
@@ -74,4 +74,6 @@ ket_simple_arrow_retro_arrow_sum_of_products.smi:SUCCEED
 output format: SMARTS
 ket_simple_arrow_retro_arrow_sum_of_products.smarts:SUCCEED
 output format: CML
-ket_simple_arrow_retro_arrow_sum_of_products.cml:SUCCEED
+ket_simple_arrow_retro_arrow_sum_of_products.cml:SUCCEED
+issue 2318
+ket_simple_arrow_retro_arrow_sum_of_products.cml:SUCCEED
diff --git a/api/tests/integration/tests/basic/ref/issue_1576.ket b/api/tests/integration/tests/basic/ref/issue_1576.ket
@@ -118,9 +118,9 @@
             }
         ],
         "stereoFlagPosition": {
-            "x": 3.0,
-            "y": 1.0,
-            "z": 0.0
+            "x": 3.000000,
+            "y": 1.000000,
+            "z": 0.000000
         }
     }
 }
diff --git a/api/tests/integration/tests/formats/ket_retrosynthetic_arrow.py b/api/tests/integration/tests/formats/ket_retrosynthetic_arrow.py
@@ -93,3 +93,18 @@ def getCML(reaction):
         else:
             print(filename + ":FAILED")
             print(diff)
+
+print("issue 2318")
+indigo.setOption("json-use-native-precision", "1")
+fname = os.path.join(root_rea, "ket_retro_arrow.ket")
+rxn = indigo.loadReactionFromFile(fname)
+# with open(fname, "w") as file:
+#     file.write(rxn.json())
+with open(fname, "r") as file:
+    ref_json = file.read()
+diff = find_diff(ref_json, rxn.json())
+if not diff:
+    print(filename + ":SUCCEED")
+else:
+    print(filename + ":FAILED")
+    print(diff)
diff --git a/api/tests/integration/tests/formats/reactions/ket_retro_arrow.ket b/api/tests/integration/tests/formats/reactions/ket_retro_arrow.ket
@@ -13,55 +13,53 @@
                     "mode": "retrosynthetic",
                     "pos": [
                         {
-                            "x": 17.023752881253245,
+                            "x": 17.023752,
                             "y": -8.175,
-                            "z": 0
+                            "z": 0.0
                         },
                         {
-                            "x": 18.750181019051478,
+                            "x": 18.750181,
                             "y": -8.175,
-                            "z": 0
+                            "z": 0.0
                         }
                     ]
                 }
             }
-        ],
-        "connections": [],
-        "templates": []
+        ]
     },
     "mol0": {
         "type": "molecule",
         "atoms": [
             {
                 "label": "C",
                 "location": [
-                    15.246467820890256,
-                    -9.074998653426483,
-                    0
+                    15.246468,
+                    -9.074999,
+                    0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    15.246467820890256,
-                    -8.075000455066647,
-                    0
+                    15.246468,
+                    -8.075001,
+                    0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    14.38044431997395,
-                    -7.5750013465735195,
-                    0
+                    14.380445,
+                    -7.575001,
+                    0.0
                 ]
             },
             {
                 "label": "N",
                 "location": [
-                    16.11249117279522,
-                    -7.5750013465735195,
-                    0
+                    16.112492,
+                    -7.575001,
+                    0.0
                 ]
             }
         ],
@@ -95,25 +93,25 @@
             {
                 "label": "O",
                 "location": [
-                    19.987496757286365,
-                    -8.075000455066647,
-                    0
+                    19.987497,
+                    -8.075001,
+                    0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    20.853495224297802,
-                    -8.574999544933355,
-                    0
+                    20.853495,
+                    -8.575,
+                    0.0
                 ]
             },
             {
                 "label": "O",
                 "location": [
-                    21.71955568002605,
-                    -8.075000455066647,
-                    0
+                    21.719555,
+                    -8.075001,
+                    0.0
                 ]
             }
         ],

diff --git a/core/indigo-core/layout/src/reaction_layout.cpp b/core/indigo-core/layout/src/reaction_layout.cpp
@@ -42,21 +42,38 @@ void ReactionLayout::fixLayout()
 
     Vec2f rmax{Vec2f::min_coord(), Vec2f::min_coord()}, pmin{Vec2f::max_coord(), Vec2f::max_coord()};
     Rect2f bb;
-    // Calculate rightTop of reactant bounding box
-
-    for (int i = _r.reactantBegin(); i != _r.reactantEnd(); i = _r.reactantNext(i))
+    if (_r.isRetrosyntetic())
     {
-        _r.getBaseMolecule(i).getBoundingBox(bb);
-        rmax.max(bb.rightTop());
-    }
+        // Calculate rightTop of product bounding box
+        for (int i = _r.productBegin(); i != _r.productEnd(); i = _r.productNext(i))
+        {
+            _r.getBaseMolecule(i).getBoundingBox(bb);
+            rmax.max(bb.rightTop());
+        }
 
-    // Calculate leftBottom of product bounding box
-    for (int i = _r.productBegin(); i != _r.productEnd(); i = _r.productNext(i))
-    {
-        _r.getBaseMolecule(i).getBoundingBox(bb);
-        pmin.min(bb.leftBottom());
+        // Calculate leftBottom of reactant bounding box
+        for (int i = _r.reactantBegin(); i != _r.reactantEnd(); i = _r.reactantNext(i))
+        {
+            _r.getBaseMolecule(i).getBoundingBox(bb);
+            pmin.min(bb.leftBottom());
+        }
     }
+    else
+    {
+        // Calculate rightTop of reactant bounding box
+        for (int i = _r.reactantBegin(); i != _r.reactantEnd(); i = _r.reactantNext(i))
+        {
+            _r.getBaseMolecule(i).getBoundingBox(bb);
+            rmax.max(bb.rightTop());
+        }
 
+        // Calculate leftBottom of product bounding box
+        for (int i = _r.productBegin(); i != _r.productEnd(); i = _r.productNext(i))
+        {
+            _r.getBaseMolecule(i).getBoundingBox(bb);
+            pmin.min(bb.leftBottom());
+        }
+    }
     // if left side of product bb at left of right side of reactant bb - fix layout
     if (rmax.x > pmin.x)
     {

diff --git a/core/indigo-core/molecule/molecule_json_saver.h b/core/indigo-core/molecule/molecule_json_saver.h
@@ -50,7 +50,7 @@ namespace indigo
         void saveMolecule(BaseMolecule& bmol);
         void saveMolecule(BaseMolecule& bmol, JsonWriter& writer);
 
-        static void saveMetaData(JsonWriter& writer, MetaDataStorage& meta);
+        void saveMetaData(JsonWriter& writer, MetaDataStorage& meta);
         static std::string monomerId(const TGroup& tg);
         static std::string monomerKETClass(const std::string& class_name);
         static std::string monomerHELMClass(const std::string& class_name);