core: reaction layout fix (#734)

* current work * renderer fix * clang fix * simple objects test added * docker hub and npm * multi.ket * reaction layout fix * r-groups numbering fix * pr fixes * pr fixes Co-authored-by: Roman Porozhnetov <Roman_Porozhnetov@epam.com>
epam · May 19, 2022 · 260b321 · 260b321
1 parent a8a5c6d
commit 260b321
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Showing 5 changed files with 29 additions and 21 deletions.
diff --git a/.github/workflows/indigo-ci.yaml b/.github/workflows/indigo-ci.yaml
@@ -1216,4 +1216,4 @@ jobs:
           docker push epmlsop/indigo-service:enhanced-latest
       - name: Publish master
         if: github.ref == 'refs/heads/master'
-        run: docker push epmlsop/indigo-service:enhanced-latest
+        run: docker push epmlsop/indigo-service:enhanced-latest
diff --git a/api/c/indigo/src/indigo_layout.cpp b/api/c/indigo/src/indigo_layout.cpp
@@ -98,19 +98,24 @@ CEXPORT int indigoLayout(int object)
         else if (IndigoBaseReaction::is(obj))
         {
             BaseReaction& rxn = obj.getBaseReaction();
-            ReactionLayout rl(rxn, self.smart_layout);
-            rl.max_iterations = self.layout_max_iterations;
-            rl.layout_orientation = (layout_orientation_value)self.layout_orientation;
-            rl.bond_length = 1.6f;
-            rl.horizontal_interval_factor = self.layout_horintervalfactor;
-
-            rl.make();
-            try
-            {
-                rxn.markStereocenterBonds();
-            }
-            catch (Exception e)
+            if (rxn.isMultistep())
+                throw IndigoError("Multistep layout is not implemented yet.");
+            else
             {
+                ReactionLayout rl(rxn, self.smart_layout);
+                rl.max_iterations = self.layout_max_iterations;
+                rl.layout_orientation = (layout_orientation_value)self.layout_orientation;
+                rl.bond_length = 1.6f;
+                rl.horizontal_interval_factor = self.layout_horintervalfactor;
+
+                rl.make();
+                try
+                {
+                    rxn.markStereocenterBonds();
+                }
+                catch (Exception e)
+                {
+                }
             }
         }
         else

diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp
@@ -892,6 +892,10 @@ void MoleculeJsonSaver::saveMolecule(BaseMolecule& bmol, Writer<StringBuffer>& w
     int n_rgroups = mol->rgroups.getRGroupCount();
     for (int i = 1; i <= n_rgroups; ++i)
     {
+        RGroup& rgroup = mol->rgroups.getRGroup(i);
+        if (rgroup.fragments.size() == 0)
+            continue;
+
         buf.clear();
         out.printf("rg%d", i);
         buf.push(0);

diff --git a/core/indigo-core/reaction/reaction_json_saver.h b/core/indigo-core/reaction/reaction_json_saver.h
@@ -40,7 +40,7 @@ namespace indigo
 
         void saveReaction(BaseReaction& rxn);
         void saveSingleReaction(BaseReaction& rxn, BaseMolecule& merged, MoleculeJsonSaver& json_saver);
-        void saveReactionWithMetadata(BaseReaction& rxn, BaseMolecule& merged, MoleculeJsonSaver& json_saver);
+        void saveMultistepReaction(BaseReaction& rxn, BaseMolecule& merged, MoleculeJsonSaver& json_saver);
 
         bool _add_stereo_desc;
         DECL_ERROR;

diff --git a/core/indigo-core/reaction/src/reaction_json_saver.cpp b/core/indigo-core/reaction/src/reaction_json_saver.cpp
@@ -61,9 +61,8 @@ ReactionJsonSaver::~ReactionJsonSaver()
 {
 }
 
-void ReactionJsonSaver::saveReactionWithMetadata(BaseReaction& rxn, BaseMolecule& merged, MoleculeJsonSaver& json_saver)
+void ReactionJsonSaver::saveMultistepReaction(BaseReaction& rxn, BaseMolecule& merged, MoleculeJsonSaver& json_saver)
 {
-
     for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
         merged.mergeWithMolecule(rxn.getBaseMolecule(i), 0, 0);
 
@@ -93,8 +92,8 @@ void ReactionJsonSaver::saveReactionWithMetadata(BaseReaction& rxn, BaseMolecule
             Value pos_array(kArrayType);
             Value pos1(kObjectType);
             Value pos2(kObjectType);
-            pos1.AddMember("x", Value().SetDouble(ar._begin.x), ket.GetAllocator());
-            pos1.AddMember("y", Value().SetDouble(ar._begin.y), ket.GetAllocator());
+            pos1.AddMember("x", Value().SetDouble(ar._end.x), ket.GetAllocator());
+            pos1.AddMember("y", Value().SetDouble(ar._end.y), ket.GetAllocator());
             pos1.AddMember("z", Value().SetDouble(0.0), ket.GetAllocator());
             pos2.AddMember("x", Value().SetDouble(ar._begin.x), ket.GetAllocator());
             pos2.AddMember("y", Value().SetDouble(ar._begin.y), ket.GetAllocator());
@@ -219,7 +218,7 @@ void ReactionJsonSaver::saveSingleReaction(BaseReaction& rxn, BaseMolecule& merg
         plus.AddMember("type", "plus", ket.GetAllocator());
         Value location(kArrayType);
         location.PushBack(Value().SetDouble(plus_offset.x), ket.GetAllocator());
-        location.PushBack(Value().SetDouble(-plus_offset.y), ket.GetAllocator()); // TODO: remove -
+        location.PushBack(Value().SetDouble(plus_offset.y), ket.GetAllocator());
         location.PushBack(Value().SetDouble(0.0), ket.GetAllocator());
         plus.AddMember("location", location, ket.GetAllocator());
         nodes.PushBack(plus, ket.GetAllocator());
@@ -311,9 +310,9 @@ void ReactionJsonSaver::saveReaction(BaseReaction& rxn)
         merged = std::make_unique<Molecule>();
     }
 
-    if (rxn.metaData().size())
+    if (rxn.isMultistep())
     {
-        saveReactionWithMetadata(rxn, *merged, json_saver);
+        saveMultistepReaction(rxn, *merged, json_saver);
     }
     else
     {