From 4336396b42fa4eb9e549e035580956d81a6ff6f2 Mon Sep 17 00:00:00 2001
From: even1024 <roman.porozhnetov@gmail.com>
Date: Thu, 30 Jan 2025 11:25:16 +0100
Subject: [PATCH] sort fix

---
 .../ref/layout/acs_style_reaction.py.out      |  2 +
 .../tests/layout/ref/acs_issue_2458.ket       | 66 ++++++++++++++-----
 .../src/reaction_multistep_detector.cpp       | 10 +--
 utils/indigo-depict/main.c                    |  2 +-
 4 files changed, 59 insertions(+), 21 deletions(-)

diff --git a/api/tests/integration/ref/layout/acs_style_reaction.py.out b/api/tests/integration/ref/layout/acs_style_reaction.py.out
index 9f08549e40..ae0379efba 100644
--- a/api/tests/integration/ref/layout/acs_style_reaction.py.out
+++ b/api/tests/integration/ref/layout/acs_style_reaction.py.out
@@ -25,3 +25,5 @@ acs_issue_2389.ket:SUCCEED
    Molecule #4: Success
    Molecule #5: Success
    Molecule #6: Success
+   Molecule #7: Success
+   Molecule #8: Success
diff --git a/api/tests/integration/tests/layout/ref/acs_issue_2458.ket b/api/tests/integration/tests/layout/ref/acs_issue_2458.ket
index 71d349214d..79a641a4ea 100644
--- a/api/tests/integration/tests/layout/ref/acs_issue_2458.ket
+++ b/api/tests/integration/tests/layout/ref/acs_issue_2458.ket
@@ -22,6 +22,12 @@
             {
                 "$ref": "mol6"
             },
+            {
+                "$ref": "mol7"
+            },
+            {
+                "$ref": "mol8"
+            },
             {
                 "type": "arrow",
                 "data": {
@@ -33,7 +39,7 @@
                             "z": 0.0
                         },
                         {
-                            "x": 16.708332,
+                            "x": 20.458332,
                             "y": 0.0,
                             "z": 0.0
                         }
@@ -284,9 +290,9 @@
         "type": "molecule",
         "atoms": [
             {
-                "label": "O",
+                "label": "P",
                 "location": [
-                    10.423611,
+                    9.451388,
                     0.902778,
                     0.0
                 ]
@@ -323,12 +329,26 @@
         "bonds": []
     },
     "mol5": {
+        "type": "molecule",
+        "atoms": [
+            {
+                "label": "O",
+                "location": [
+                    16.048611,
+                    0.902778,
+                    0.0
+                ]
+            }
+        ],
+        "bonds": []
+    },
+    "mol6": {
         "type": "molecule",
         "atoms": [
             {
                 "label": "N",
                 "location": [
-                    17.854164,
+                    21.604164,
                     1.309017,
                     0.0
                 ]
@@ -336,7 +356,7 @@
             {
                 "label": "C",
                 "location": [
-                    18.805222,
+                    22.555222,
                     1.0,
                     0.0
                 ]
@@ -344,7 +364,7 @@
             {
                 "label": "C",
                 "location": [
-                    17.26638,
+                    21.01638,
                     0.5,
                     0.0
                 ]
@@ -352,7 +372,7 @@
             {
                 "label": "C",
                 "location": [
-                    18.805222,
+                    22.555222,
                     -0.0,
                     0.0
                 ]
@@ -360,7 +380,7 @@
             {
                 "label": "N",
                 "location": [
-                    19.671247,
+                    23.421247,
                     1.5,
                     0.0
                 ]
@@ -368,7 +388,7 @@
             {
                 "label": "N",
                 "location": [
-                    17.854166,
+                    21.604166,
                     -0.309017,
                     0.0
                 ]
@@ -376,7 +396,7 @@
             {
                 "label": "C",
                 "location": [
-                    19.671247,
+                    23.421247,
                     -0.5,
                     0.0
                 ]
@@ -384,7 +404,7 @@
             {
                 "label": "C",
                 "location": [
-                    20.537273,
+                    24.287273,
                     1.0,
                     0.0
                 ]
@@ -392,7 +412,7 @@
             {
                 "label": "N",
                 "location": [
-                    20.537273,
+                    24.287273,
                     0.0,
                     0.0
                 ]
@@ -400,7 +420,7 @@
             {
                 "label": "O",
                 "location": [
-                    19.671247,
+                    23.421247,
                     -1.5,
                     0.0
                 ]
@@ -408,7 +428,7 @@
             {
                 "label": "N",
                 "location": [
-                    21.403297,
+                    25.153297,
                     1.5,
                     0.0
                 ]
@@ -501,13 +521,27 @@
             }
         ]
     },
-    "mol6": {
+    "mol7": {
         "type": "molecule",
         "atoms": [
             {
                 "label": "P",
                 "location": [
-                    15.076388,
+                    16.951387,
+                    0.902778,
+                    0.0
+                ]
+            }
+        ],
+        "bonds": []
+    },
+    "mol8": {
+        "type": "molecule",
+        "atoms": [
+            {
+                "label": "O",
+                "location": [
+                    19.798611,
                     0.902778,
                     0.0
                 ]
diff --git a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp
index 7e276b1e52..91950f6c21 100644
--- a/core/indigo-core/reaction/src/reaction_multistep_detector.cpp
+++ b/core/indigo-core/reaction/src/reaction_multistep_detector.cpp
@@ -1432,9 +1432,9 @@ void ReactionMultistepDetector::constructSimpleArrowReaction(BaseReaction& rxn)
             switch (comp.component_type)
             {
             case ReactionComponent::MOLECULE: {
-                if (comp.molecule && comp.summ_block_idx != ReactionComponent::NOT_CONNECTED &&
-                    _component_summ_blocks[comp.summ_block_idx].role != BaseReaction::UNDEFINED)
+                if (comp.molecule && comp.summ_block_idx != ReactionComponent::NOT_CONNECTED)
                 {
+                    auto role = _component_summ_blocks[comp.summ_block_idx].role;
                     auto& cmol = *comp.molecule;
                     for (int idx = cmol.vertexBegin(); idx < cmol.vertexEnd(); idx = cmol.vertexNext(idx))
                     {
@@ -1449,10 +1449,12 @@ void ReactionMultistepDetector::constructSimpleArrowReaction(BaseReaction& rxn)
                             rxn.addCatalystCopy(cmol, 0, 0);
                             break;
                         case KProductArea:
-                            rxn.addProductCopy(cmol, 0, 0);
+                            if (role != BaseReaction::UNDEFINED)
+                                rxn.addProductCopy(cmol, 0, 0);
                             break;
                         default:
-                            rxn.addReactantCopy(cmol, 0, 0);
+                            if (role != BaseReaction::UNDEFINED)
+                                rxn.addReactantCopy(cmol, 0, 0);
                             break;
                         }
                         break;
diff --git a/utils/indigo-depict/main.c b/utils/indigo-depict/main.c
index bc0b64e516..1f468387d5 100644
--- a/utils/indigo-depict/main.c
+++ b/utils/indigo-depict/main.c
@@ -1059,7 +1059,7 @@ int main(int argc, char* argv[])
         _prepare(obj, p.aromatization);
         if (p.action == ACTION_LAYOUT)
         {
-            indigoLayout(obj);
+            //indigoLayout(obj);
             if (p.out_ext == OEXT_CML)
                 indigoSaveCmlToFile(obj, p.outfile);
             else if (p.out_ext == OEXT_RXN)