Backmerge: #2417 - The layout is incorrect with retrosynthetic arrow

Backmerge to master
epam · Sep 29, 2024 · e183801 · e183801
1 parent d09a7d3
commit e183801
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Showing 7 changed files with 91 additions and 50 deletions.
diff --git a/api/tests/integration/ref/formats/ket_retrosynthetic_arrow.py.out b/api/tests/integration/ref/formats/ket_retrosynthetic_arrow.py.out
@@ -76,4 +76,6 @@ ket_simple_arrow_retro_arrow_sum_of_products.smarts:SUCCEED
 output format: CML
 ket_simple_arrow_retro_arrow_sum_of_products.cml:SUCCEED
 issue 2318
-ket_simple_arrow_retro_arrow_sum_of_products.cml:SUCCEED
+ket_retro_arrow.ket:SUCCEED
+issue 2417
+ket_retro_arrow.ket:SUCCEED
diff --git a/api/tests/integration/tests/formats/ket_retrosynthetic_arrow.py b/api/tests/integration/tests/formats/ket_retrosynthetic_arrow.py
@@ -100,7 +100,8 @@ def getCML(reaction):
 
 print("issue 2318")
 indigo.setOption("json-use-native-precision", "1")
-fname = os.path.join(root_rea, "ket_retro_arrow.ket")
+filename = "ket_retro_arrow.ket"
+fname = os.path.join(root_rea, filename)
 rxn = indigo.loadReactionFromFile(fname)
 # with open(fname, "w") as file:
 #     file.write(rxn.json())
@@ -112,3 +113,13 @@ def getCML(reaction):
 else:
     print(filename + ":FAILED")
     print(diff)
+print("issue 2417")
+rxn.layout()
+# with open(fname, "w") as file:
+#     file.write(rxn.json())
+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
@@ -13,13 +13,13 @@
                     "mode": "retrosynthetic",
                     "pos": [
                         {
-                            "x": 17.023752,
-                            "y": -8.175,
+                            "x": 5.071281,
+                            "y": 0.0,
                             "z": 0.0
                         },
                         {
-                            "x": 18.750181,
-                            "y": -8.175,
+                            "x": 9.271282,
+                            "y": 0.0,
                             "z": 0.0
                         }
                     ]
@@ -33,32 +33,32 @@
             {
                 "label": "C",
                 "location": [
-                    15.246468,
-                    -9.074999,
+                    2.685641,
+                    -1.2,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    15.246468,
-                    -8.075001,
+                    2.685641,
+                    0.4,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    14.380445,
-                    -7.575001,
+                    1.3,
+                    1.2,
                     0.0
                 ]
             },
             {
                 "label": "N",
                 "location": [
-                    16.112492,
-                    -7.575001,
+                    4.071281,
+                    1.2,
                     0.0
                 ]
             }
@@ -93,24 +93,24 @@
             {
                 "label": "O",
                 "location": [
-                    19.987497,
-                    -8.075001,
+                    10.271282,
+                    0.4,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    20.853495,
-                    -8.575,
+                    11.656923,
+                    -0.4,
                     0.0
                 ]
             },
             {
                 "label": "O",
                 "location": [
-                    21.719555,
-                    -8.075001,
+                    13.042563,
+                    0.4,
                     0.0
                 ]
             }

diff --git a/api/tests/integration/tests/formats/ref/ket_retro_arrow.cml b/api/tests/integration/tests/formats/ref/ket_retro_arrow.cml
@@ -4,9 +4,9 @@
 <reactantList>
 <molecule>
     <atomArray>
-        <atom id="a0" elementType="O" x2="19.9875" y2="-8.075"/>
-        <atom id="a1" elementType="C" x2="20.8535" y2="-8.575"/>
-        <atom id="a2" elementType="O" x2="21.7196" y2="-8.075"/>
+        <atom id="a0" elementType="O" x2="10.2713" y2="0.4"/>
+        <atom id="a1" elementType="C" x2="11.6569" y2="-0.4"/>
+        <atom id="a2" elementType="O" x2="13.0426" y2="0.4"/>
     </atomArray>
     <bondArray>
         <bond atomRefs2="a0 a1" order="1"/>
@@ -17,10 +17,10 @@
 <productList>
 <molecule>
     <atomArray>
-        <atom id="a0" elementType="C" x2="15.2465" y2="-9.075"/>
-        <atom id="a1" elementType="C" x2="15.2465" y2="-8.075"/>
-        <atom id="a2" elementType="C" x2="14.3804" y2="-7.575"/>
-        <atom id="a3" elementType="N" x2="16.1125" y2="-7.575"/>
+        <atom id="a0" elementType="C" x2="2.68564" y2="-1.2"/>
+        <atom id="a1" elementType="C" x2="2.68564" y2="0.4"/>
+        <atom id="a2" elementType="C" x2="1.3" y2="1.2"/>
+        <atom id="a3" elementType="N" x2="4.07128" y2="1.2"/>
     </atomArray>
     <bondArray>
         <bond atomRefs2="a0 a1" order="1"/>

diff --git a/api/tests/integration/tests/formats/ref/ket_retro_arrow_2000.rxn b/api/tests/integration/tests/formats/ref/ket_retro_arrow_2000.rxn
@@ -8,9 +8,9 @@ $MOL
   -INDIGO-01000000002D
 
   3  2  0  0  0  0  0  0  0  0999 V2000
-   19.9875   -8.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   20.8535   -8.5750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   21.7196   -8.0750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   10.2713    0.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   11.6569   -0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.0426    0.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
 M  END
@@ -19,10 +19,10 @@ $MOL
   -INDIGO-01000000002D
 
   4  3  0  0  0  0  0  0  0  0999 V2000
-   15.2465   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   15.2465   -8.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   14.3804   -7.5750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   16.1125   -7.5750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6856   -1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6856    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3000    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.0713    1.2000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   2  4  1  0  0  0  0

diff --git a/api/tests/integration/tests/formats/ref/ket_retro_arrow_3000.rxn b/api/tests/integration/tests/formats/ref/ket_retro_arrow_3000.rxn
@@ -7,9 +7,9 @@ M  V30 BEGIN REACTANT
 M  V30 BEGIN CTAB
 M  V30 COUNTS 3 2 0 0 0
 M  V30 BEGIN ATOM
-M  V30 1 O 19.9875 -8.075 0.0 0
-M  V30 2 C 20.8535 -8.575 0.0 0
-M  V30 3 O 21.7196 -8.075 0.0 0
+M  V30 1 O 10.2713 0.4 0.0 0
+M  V30 2 C 11.6569 -0.4 0.0 0
+M  V30 3 O 13.0426 0.4 0.0 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2
@@ -21,10 +21,10 @@ M  V30 BEGIN PRODUCT
 M  V30 BEGIN CTAB
 M  V30 COUNTS 4 3 0 0 0
 M  V30 BEGIN ATOM
-M  V30 1 C 15.2465 -9.075 0.0 0
-M  V30 2 C 15.2465 -8.075 0.0 0
-M  V30 3 C 14.3804 -7.575 0.0 0
-M  V30 4 N 16.1125 -7.575 0.0 0
+M  V30 1 C 2.68564 -1.2 0.0 0
+M  V30 2 C 2.68564 0.4 0.0 0
+M  V30 3 C 1.3 1.2 0.0 0
+M  V30 4 N 4.07128 1.2 0.0 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2

diff --git a/core/indigo-core/layout/src/reaction_layout.cpp b/core/indigo-core/layout/src/reaction_layout.cpp
@@ -117,17 +117,35 @@ void ReactionLayout::_updateMetadata()
     Rect2f react_box, product_box, catalyst_box;
     bool last_single_reactant = false;
     bool first_single_product = false;
+    bool is_retrosyntetic = _r.isRetrosyntetic();
     if (_r.reactantsCount() > 0)
     {
-        processSideBoxes(pluses, react_box, BaseReaction::REACTANT);
-        for (int i = _r.reactantBegin(); i != _r.reactantEnd(); i = _r.reactantNext(i))
-            last_single_reactant = _r.getBaseMolecule(i).vertexCount() == 1;
+        if (is_retrosyntetic)
+        {
+            processSideBoxes(pluses, react_box, BaseReaction::PRODUCT);
+            for (int i = _r.productBegin(); i != _r.productEnd(); i = _r.productNext(i))
+                last_single_reactant = _r.getBaseMolecule(i).vertexCount() == 1;
+        }
+        else
+        {
+            processSideBoxes(pluses, react_box, BaseReaction::REACTANT);
+            for (int i = _r.reactantBegin(); i != _r.reactantEnd(); i = _r.reactantNext(i))
+                last_single_reactant = _r.getBaseMolecule(i).vertexCount() == 1;
+        }
     }
 
     if (_r.productsCount() > 0)
     {
-        processSideBoxes(pluses, product_box, BaseReaction::PRODUCT);
-        first_single_product = _r.getBaseMolecule(_r.productBegin()).vertexCount() == 1;
+        if (is_retrosyntetic)
+        {
+            processSideBoxes(pluses, product_box, BaseReaction::REACTANT);
+            first_single_product = _r.getBaseMolecule(_r.reactantBegin()).vertexCount() == 1;
+        }
+        else
+        {
+            processSideBoxes(pluses, product_box, BaseReaction::PRODUCT);
+            first_single_product = _r.getBaseMolecule(_r.productBegin()).vertexCount() == 1;
+        }
     }
 
     if (_r.catalystCount() > 0)
@@ -139,14 +157,18 @@ void ReactionLayout::_updateMetadata()
     // calculate arrow size and position
     Vec2f arrow_head(0, 0);
     Vec2f arrow_tail(0, 0);
-    if (_r.productsCount() == 0)
+
+    constexpr float shift = 1.0f;
+    int prod_count = is_retrosyntetic ? _r.reactantsCount() : _r.productsCount();
+    int react_count = is_retrosyntetic ? _r.productsCount() : _r.reactantsCount();
+    if (prod_count == 0)
     {
         arrow_tail.x = react_box.right() + reaction_margin_size + atom_label_margin;
         arrow_tail.y = react_box.middleY();
         arrow_head.x = arrow_tail.x + default_arrow_size + atom_label_margin;
         arrow_head.y = arrow_tail.y;
     }
-    else if (_r.reactantsCount() == 0)
+    else if (react_count == 0)
     {
         arrow_head.x = product_box.left() - reaction_margin_size - atom_label_margin;
         arrow_head.y = product_box.middleY();
@@ -273,7 +295,10 @@ void ReactionLayout::make()
         }
     };
 
-    processReactionElements(_r.reactantBegin(), _r.reactantEnd(), &BaseReaction::reactantNext);
+    if (_r.isRetrosyntetic())
+        processReactionElements(_r.productBegin(), _r.productEnd(), &BaseReaction::productNext);
+    else
+        processReactionElements(_r.reactantBegin(), _r.reactantEnd(), &BaseReaction::reactantNext);
 
     if (_r.catalystCount())
     {
@@ -295,7 +320,10 @@ void ReactionLayout::make()
     else
         _pushSpace(line, default_arrow_size + reaction_margin_size * 2);
 
-    processReactionElements(_r.productBegin(), _r.productEnd(), &BaseReaction::productNext);
+    if (_r.isRetrosyntetic())
+        processReactionElements(_r.reactantBegin(), _r.reactantEnd(), &BaseReaction::reactantNext);
+    else
+        processReactionElements(_r.productBegin(), _r.productEnd(), &BaseReaction::productNext);
 
     _ml.bondLength = bond_length;
     _ml.reactionComponentMarginSize = reaction_margin_size;