#2309 - Update layout for pathway reaction on canvas (#2439)

api/c/indigo/src/indigo_layout.cpp

@@ -107,7 +107,7 @@ CEXPORT int indigoLayout(int object)
             BaseReaction& rxn = obj.getBaseReaction();
             if (rxn.isPathwayReaction())
             {
-                PathwayLayout pl(static_cast<PathwayReaction&>(rxn));
+                PathwayLayout pl(static_cast<PathwayReaction&>(rxn), self.layout_options);
                 pl.make();
             }
             else

api/c/indigo/src/indigo_reaction.cpp

@@ -455,6 +455,7 @@ CEXPORT int indigoLoadReaction(int source)
         loader.ignore_noncritical_query_features = self.ignore_noncritical_query_features;
         loader.dearomatize_on_load = self.dearomatize_on_load;
         loader.arom_options = self.arom_options;
+        loader.layout_options = self.layout_options;
         auto rxn = loader.loadReaction(false);
         std::unique_ptr<IndigoBaseReaction> rxnptr;
         if (rxn->isPathwayReaction())

api/c/indigo/src/indigo_savers.cpp

@@ -875,10 +875,9 @@ CEXPORT int indigoSaveCdxml(int item, int output)
         if (IndigoBaseReaction::is(obj))
         {
             ReactionCdxmlSaver saver(out);
-            if (obj.type == IndigoObject::REACTION)
+            if (obj.type == IndigoObject::REACTION || obj.type == IndigoObject::PATHWAY_REACTION)
             {
-                Reaction& rxn = obj.getReaction();
-                saver.saveReaction(rxn);
+                saver.saveReaction(obj.getBaseReaction());
             }
             else if (obj.type == IndigoObject::QUERY_REACTION)
             {

api/tests/integration/tests/layout/ref/balance.ket

@@ -107,7 +107,7 @@
             {
                 "label": "C",
                 "location": [
-                    6.40000057220459,
+                    6.400000095367432,
                     0.7999999523162842,
                     0.0
                 ]
@@ -123,7 +123,7 @@
             {
                 "label": "C",
                 "location": [
-                    6.40000057220459,
+                    6.400000095367432,
                     -0.7999999523162842,
                     0.0
                 ]

api/tests/integration/tests/reaction/pathway.py

@@ -41,7 +41,7 @@ def find_diff(a, b):
     # with open(os.path.join(ref_path, filename) + ".ket", "w") as file:
     #     file.write(rxn_txt)
 
-    rxn_ref = open(os.path.join(ref_path, filename) + ".ket", "r").read()
+    rxn_ref = open(getRefFilepath(filename + ".ket"), "r").read()
 
     diff = find_diff(rxn_ref, rxn_txt)
     if not diff:

api/tests/integration/tests/reaction/ref/pathway1.ket

@@ -1 +1 @@
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