#1205 Fix reaction json saver layout calculation (#1216)

Co-authored-by: Aliakasndr Dziarkach <[email protected]>

api/tests/integration/ref/reaction/save_ket_layout_1205.py.out

@@ -0,0 +1 @@
+Test passed

api/tests/integration/tests/reaction/reactions/issue_1205.ket

@@ -0,0 +1 @@
+{"root":{"nodes":[{"$ref":"mol0"},{"$ref":"mol1"},{"$ref":"mol2"},{"$ref":"mol3"},{"type":"arrow","data":{"mode":"open-angle","pos":[{"x":10.515000343322754,"y":-8.324899673461914,"z":0.0},{"x":15.034599304199219,"y":-8.274900436401368,"z":0.0}]}}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[7.7846999168396,-7.824999809265137,0.0]},{"label":"C","location":[9.515000343322754,-7.82450008392334,0.0]},{"label":"C","location":[8.65149974822998,-7.324900150299072,0.0]},{"label":"C","location":[9.515000343322754,-8.825400352478028,0.0]},{"label":"C","location":[7.7846999168396,-8.829899787902832,0.0]},{"label":"C","location":[8.65369987487793,-9.324899673461914,0.0]}],"bonds":[{"type":2,"atoms":[2,0]},{"type":2,"atoms":[3,1]},{"type":1,"atoms":[0,4]},{"type":1,"atoms":[1,2]},{"type":2,"atoms":[4,5]},{"type":1,"atoms":[5,3]}]},"mol1":{"type":"molecule","atoms":[{"label":"C","location":[16.03459930419922,-7.775000095367432,0.0]},{"label":"C","location":[17.76499938964844,-7.774499893188477,0.0]},{"label":"C","location":[16.90139961242676,-7.274899959564209,0.0]},{"label":"C","location":[17.76499938964844,-8.775400161743164,0.0]},{"label":"C","location":[16.03459930419922,-8.779899597167969,0.0]},{"label":"C","location":[16.903600692749025,-9.274900436401368,0.0]}],"bonds":[{"type":2,"atoms":[2,0]},{"type":2,"atoms":[3,1]},{"type":1,"atoms":[0,4]},{"type":1,"atoms":[1,2]},{"type":2,"atoms":[4,5]},{"type":1,"atoms":[5,3]}]},"mol2":{"type":"molecule","atoms":[{"label":"Cl","location":[12.974800109863282,-8.824899673461914,0.0]}],"bonds":[]},"mol3":{"type":"molecule","atoms":[{"label":"N","location":[12.549799919128418,-7.724899768829346,0.0]}],"bonds":[]}}

api/tests/integration/tests/reaction/reactions/issue_1205.rxn

@@ -0,0 +1,55 @@
+$RXN
+
+ -INDIGO- 0808231408
+
+  1  1  2
+$MOL
+
+  -INDIGO-08082314082D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+    7.7847   -7.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.5150   -7.8245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6515   -7.3249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.5150   -8.8254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.7847   -8.8299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6537   -9.3249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  3  1  2  0  0  0  0
+  4  2  2  0  0  0  0
+  1  5  1  0  0  0  0
+  2  3  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  4  1  0  0  0  0
+M  END
+$MOL
+
+  -INDIGO-08082314082D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+   16.0346   -7.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   17.7650   -7.7745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.9014   -7.2749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   17.7650   -8.7754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.0346   -8.7799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.9036   -9.2749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  3  1  2  0  0  0  0
+  4  2  2  0  0  0  0
+  1  5  1  0  0  0  0
+  2  3  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  4  1  0  0  0  0
+M  END
+$MOL
+
+  -INDIGO-08082314082D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+   12.9748   -8.8249    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+$MOL
+
+  -INDIGO-08082314082D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+   12.5498   -7.7249    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+M  END

api/tests/integration/tests/reaction/save_ket_layout_1205.py

@@ -0,0 +1,28 @@
+import difflib
+import os
+import sys
+
+
+def find_diff(a, b):
+    return "\n".join(difflib.unified_diff(a.splitlines(), b.splitlines()))
+
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+from env_indigo import *
+
+indigo = Indigo()
+r1 = indigo.loadReactionFromFile(
+    joinPathPy("reactions/issue_1205.rxn", __file__)
+)
+with open(joinPathPy("reactions/issue_1205.ket", __file__), "r") as file:
+    ket_ref = file.read()
+ket_out = r1.json()
+diff = find_diff(ket_ref, ket_out)
+if diff:
+    print("Difference found:\n", diff)
+else:
+    print("Test passed")

core/indigo-core/common/math/algebra.h

@@ -21,6 +21,7 @@
 
 #include <algorithm>
 #include <cmath>
+#include <limits>
 
 #include "base_c/defs.h"
 #include "base_cpp/exception.h"
@@ -59,6 +60,16 @@ namespace indigo
 
         float x, y;
 
+        static constexpr auto min_coord()
+        {
+            return std::numeric_limits<decltype(x)>::min();
+        }
+
+        static constexpr auto max_coord()
+        {
+            return std::numeric_limits<decltype(x)>::max();
+        }
+
         inline void set(float xx, float yy)
         {
             x = xx;

core/indigo-core/reaction/src/reaction_json_saver.cpp

@@ -36,20 +36,23 @@ IMPL_ERROR(ReactionJsonSaver, "reaction KET saver");
 
 void ReactionJsonSaver::_fixLayout(BaseReaction& rxn)
 {
-    Vec2f rmax, pmin;
+    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 = rxn.reactantBegin(); i != rxn.reactantEnd(); i = rxn.reactantNext(i))
     {
         rxn.getBaseMolecule(i).getBoundingBox(bb);
         rmax.max(bb.rightTop());
     }
 
+    // Calculate leftBottom of product bounding box
     for (int i = rxn.productBegin(); i != rxn.productEnd(); i = rxn.productNext(i))
     {
         rxn.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)
     {
         ReactionLayout rl(rxn, true);