Be strict when placing partial rings, check bond count in addition to…

… atom count.
cdk · Oct 7, 2018 · 9a74c3d · 9a74c3d
1 parent 617b36d
commit 9a74c3d
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java
@@ -116,13 +116,14 @@ public RingPlacer() {
      */
     public void placeRing(IRing ring, IAtomContainer sharedAtoms, Point2d sharedAtomsCenter, Vector2d ringCenterVector,
                           double bondLength) {
-        int sharedAtomCount = sharedAtoms.getAtomCount();
-        logger.debug("placeRing -> sharedAtomCount: " + sharedAtomCount);
-        if (sharedAtomCount > 2) {
+        int numSharedAtoms = sharedAtoms.getAtomCount();
+        int numSharedBonds = sharedAtoms.getBondCount();
+        logger.debug("placeRing -> sharedAtomCount: " + numSharedAtoms);
+        if (numSharedAtoms > 2 && numSharedBonds > 1) {
             placeBridgedRing(ring, sharedAtoms, sharedAtomsCenter, ringCenterVector, bondLength);
-        } else if (sharedAtomCount == 2) {
+        } else if (numSharedAtoms == 2 && numSharedBonds == 1) {
             placeFusedRing(ring, sharedAtoms, ringCenterVector, bondLength);
-        } else if (sharedAtomCount == 1) {
+        } else if (numSharedAtoms == 1 && numSharedBonds == 0) {
             placeSpiroRing(ring, sharedAtoms, sharedAtomsCenter, ringCenterVector, bondLength);
         }
     }
@@ -533,7 +534,7 @@ public void placeFusedRing(IRing ring,
     }
 
     /**
-     * Completes the layout of a partiallyed laid out ring.
+     * Completes the layout of a partially laid out ring.
      *
      * @param rset ring set
      * @param ring the ring to complete

diff --git a/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java b/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
@@ -1288,4 +1288,16 @@ public void alignReactionBondBrokenAndMade() throws CDKException {
         for (IAtom atom : ReactionManipulator.toMolecule(reaction).atoms())
             assertNotNull(atom.getPoint2d());
     }
+
+    @Test
+    public void alignReactionBondBrokenAndMade2() throws CDKException {
+        String smiles = "[CH2:2]1[CH2:3][CH:4]2[CH2:5][CH2:6][CH:1]1[O:7]2.[IH:8]>>[OH:7][C@H:1]1[CH2:6][CH2:5][C@H:4]([I:8])[CH2:3][CH2:2]1";
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IReaction reaction =  smipar.parseReactionSmiles(smiles);
+        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+        sdg.setAlignMappedReaction(true);
+        sdg.generateCoordinates(reaction);
+        for (IAtom atom : ReactionManipulator.toMolecule(reaction).atoms())
+            assertNotNull(atom.getPoint2d());
+    }
 }