#2417 - The layout is incorrect with retrosynthetic arrow (#2437)

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

api/tests/integration/tests/formats/ket_retrosynthetic_arrow.py

@@ -85,6 +85,8 @@ def getCML(reaction):
 
         print("output format: " + format_name)
 
+        # with open(os.path.join(ref_path, filename), "w") as file:
+        #     file.write(parsed_format)
         with open(os.path.join(ref_path, filename), "r") as file:
             format_ref = file.read()
         diff = find_diff(format_ref, parsed_format)
@@ -96,7 +98,8 @@ 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())
@@ -108,3 +111,13 @@ 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)

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
                 ]
             }

api/tests/integration/tests/formats/ref/ket_retro_arrow.b64cdx

@@ -1 +1 @@
-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

api/tests/integration/tests/formats/ref/ket_retro_arrow.cdxml

@@ -18,11 +18,11 @@
     </colortable>
     <page HeightPages="1" WidthPages="1">
         <fragment id="4">
-            <n id="5" p="457.394043 272.249969"/>
-            <n id="6" p="457.394043 242.250031"/>
-            <n id="7" p="431.413330 227.250031"/>
-            <n id="8" Element="7" NumHydrogens="2" p="483.374756 227.250031">
-                <t p="483.374756 227.250031" LabelJustification="Left">
+            <n id="5" p="80.569229 36.000000"/>
+            <n id="6" p="80.569229 -12.000000"/>
+            <n id="7" p="39.000000 -36.000000"/>
+            <n id="8" Element="7" NumHydrogens="2" p="122.138428 -36.000000">
+                <t p="122.138428 -36.000000" LabelJustification="Left">
                     <s font="3" size="10" face="96">NH</s>
                     <s font="3" size="10" face="32">2</s>
                 </t>
@@ -32,22 +32,22 @@
             <b id="18" B="6" E="8"/>
         </fragment>
         <fragment id="9">
-            <n id="10" Element="8" NumHydrogens="1" p="599.624939 242.250031">
-                <t p="599.624939 242.250031" LabelJustification="Left">
+            <n id="10" Element="8" NumHydrogens="1" p="308.138458 -12.000000">
+                <t p="308.138458 -12.000000" LabelJustification="Left">
                     <s font="3" size="10" face="96">OH</s>
                 </t>
             </n>
-            <n id="11" p="625.604858 257.250000"/>
-            <n id="12" Element="8" NumHydrogens="1" p="651.586670 242.250031">
-                <t p="651.586670 242.250031" LabelJustification="Left">
+            <n id="11" p="349.707703 12.000000"/>
+            <n id="12" Element="8" NumHydrogens="1" p="391.276917 -12.000000">
+                <t p="391.276917 -12.000000" LabelJustification="Left">
                     <s font="3" size="10" face="96">OH</s>
                 </t>
             </n>
             <b id="19" B="10" E="11"/>
             <b id="20" B="11" E="12"/>
         </fragment>
-        <arrow id="13" BoundingBox="562.505432 245.250000 510.712555 245.250000" FillType="None" ArrowheadHead="Full" ArrowheadType="Angle" HeadSize="600" ArrowheadCenterSize="600" ArrowheadWidth="150" ArrowShaftSpacing="600" Head3D="562.005432 245.250000 0.000000" Tail3D="511.212555 245.250000 0.000000"/>
-        <graphic id="21" SupersededBy="13" GraphicType="Line" ArrowType="RetroSynthetic" HeadSize="600" BoundingBox="562.005432 245.250000 511.212555 245.250000"/>
+        <arrow id="13" BoundingBox="278.138458 -0.000000 152.138428 -0.000000" FillType="None" ArrowheadHead="Full" ArrowheadType="Angle" HeadSize="600" ArrowheadCenterSize="600" ArrowheadWidth="150" ArrowShaftSpacing="600" Head3D="277.638458 0.000000 0.000000" Tail3D="152.638428 0.000000 0.000000"/>
+        <graphic id="21" SupersededBy="13" GraphicType="Line" ArrowType="RetroSynthetic" HeadSize="600" BoundingBox="277.638458 0.000000 152.638428 0.000000"/>
         <scheme>
             <step ReactionStepReactants="4" ReactionStepProducts="9" ReactionStepArrows="21"/>
         </scheme>

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"/>

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

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

core/indigo-core/layout/src/reaction_layout.cpp

@@ -103,17 +103,35 @@ 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)
@@ -126,14 +144,16 @@ void ReactionLayout::_updateMetadata()
     Vec2f arrow_tail(0, 0);
 
     constexpr float shift = 1.0f;
-    if (_r.productsCount() == 0)
+    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() + shift;
         arrow_tail.y = react_box.middleY();
         arrow_head.x = arrow_tail.x + shift;
         arrow_head.y = arrow_tail.y;
     }
-    else if (_r.reactantsCount() == 0)
+    else if (react_count == 0)
     {
         arrow_head.x = product_box.left() - shift;
         arrow_head.y = product_box.middleY();
@@ -216,13 +236,19 @@ void ReactionLayout::make()
 
     // layout molecules in a row with the intervals specified
     Metalayout::LayoutLine& line = _ml.newLine();
-    for (int i = _r.reactantBegin(); i < _r.reactantEnd(); i = _r.reactantNext(i))
-    {
-        bool single_atom = _getMol(i).vertexCount() == 1;
-        if (i != _r.reactantBegin())
-            _pushSpace(line, plus_interval_factor);
-        _pushMol(line, i);
-    }
+    auto processReactionElements = [this, &line](int begin, int end, std::function<int(BaseReaction&, int)> next) {
+        for (int i = begin; i < end; i = next(_r, i))
+        {
+            if (i != begin)
+                _pushSpace(line, plus_interval_factor);
+            _pushMol(line, i);
+        }
+    };
+
+    if (_r.isRetrosyntetic())
+        processReactionElements(_r.productBegin(), _r.productEnd(), &BaseReaction::productNext);
+    else
+        processReactionElements(_r.reactantBegin(), _r.reactantEnd(), &BaseReaction::reactantNext);
 
     if (_r.catalystCount())
     {
@@ -241,13 +267,10 @@ void ReactionLayout::make()
 
     _pushSpace(line, bond_length);
 
-    for (int i = _r.productBegin(); i < _r.productEnd(); i = _r.productNext(i))
-    {
-        bool single_atom = _getMol(i).vertexCount() == 1;
-        if (i != _r.productBegin())
-            _pushSpace(line, plus_interval_factor);
-        _pushMol(line, i);
-    }
+    if (_r.isRetrosyntetic())
+        processReactionElements(_r.reactantBegin(), _r.reactantEnd(), &BaseReaction::reactantNext);
+    else
+        processReactionElements(_r.productBegin(), _r.productEnd(), &BaseReaction::productNext);
 
     _ml.bondLength = bond_length;
     _ml.horizontalIntervalFactor = horizontal_interval_factor;