epam#2741 Image missing stereochemistry information when using abbrev…

…iations (epam#2742)
mestrelab-chemoinformatics · Feb 4, 2025 · 121b7d2 · 121b7d2
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diff --git a/api/tests/integration/ref/rendering/render_reactions.py.out b/api/tests/integration/ref/rendering/render_reactions.py.out
@@ -15,3 +15,5 @@ issue 2512 two short equilibrium half arrows
 issue_2512.png rendering status: OK
 issue 2513 elliptical-arc-arrow render error
 issue_2513.png rendering status: OK
+issue 2741 missing stereochemistry
+missing_stereochemistry_2741.png rendering status: OK
diff --git a/api/tests/integration/tests/rendering/reactions/missing_stereochemistry_2741.cdxml b/api/tests/integration/tests/rendering/reactions/missing_stereochemistry_2741.cdxml
@@ -0,0 +1,356 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE CDXML SYSTEM "https://static.chemistry.revvitycloud.com/cdxml/CDXML.dtd" >
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diff --git a/api/tests/integration/tests/rendering/ref/linux/missing_stereochemistry_2741.png b/api/tests/integration/tests/rendering/ref/linux/missing_stereochemistry_2741.png
diff --git a/api/tests/integration/tests/rendering/ref/mac/missing_stereochemistry_2741.png b/api/tests/integration/tests/rendering/ref/mac/missing_stereochemistry_2741.png
diff --git a/api/tests/integration/tests/rendering/ref/win/missing_stereochemistry_2741.png b/api/tests/integration/tests/rendering/ref/win/missing_stereochemistry_2741.png
diff --git a/api/tests/integration/tests/rendering/render_reactions.py b/api/tests/integration/tests/rendering/render_reactions.py
@@ -117,6 +117,16 @@ def renderRxnfile(filename, outfile):
 renderer.renderToFile(rxn, joinPathPy("out/" + png_fname, __file__))
 print(checkImageSimilarity(png_fname))
 
+print("issue 2741 missing stereochemistry")
+indigo.resetOptions()
+indigo.setOption("render-output-format", "png")
+fname = "missing_stereochemistry_2741"
+png_fname = fname + ".png"
+cdxml_fname = joinPathPy("reactions/%s.cdxml" % fname, __file__)
+rxn = indigo.loadReactionFromFile(cdxml_fname)
+renderer.renderToFile(rxn, joinPathPy("out/" + png_fname, __file__))
+print(checkImageSimilarity(png_fname))
+
 if isIronPython():
     renderer.Dispose()
     indigo.Dispose()
diff --git a/core/render2d/src/render_internal.cpp b/core/render2d/src/render_internal.cpp
@@ -874,8 +874,9 @@ void MoleculeRenderInternal::_prepareSGroups(bool collapseAtLeastOneSuperatom)
                                     else
                                     {
                                         Molecule& amol = mol.asMolecule();
-                                        bondID = amol.addBond(superAtomID, neighboringAtomID, amol.getBondOrder(neighboringBondID));
+                                        bondID = amol.addBond(neighboringAtomID, superAtomID, amol.getBondOrder(neighboringBondID));
                                         amol.setEdgeTopology(bondID, amol.getBondTopology(neighboringBondID));
+                                        amol.setBondDirection(bondID, mol.getBondDirection(neighboringBondID));
                                     }
                                     if (_bondMappingInv.find(bondID) != _bondMappingInv.end())
                                         _bondMappingInv.erase(bondID);