Fixes #265

cdk · Aug 22, 2017 · 9f5ec19 · 9f5ec19
1 parent 5851070
commit 9f5ec19
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diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -387,6 +387,11 @@ private void label(final ITetrahedralChirality element) {
                 p *= indexParity(i); // implicit H, adjust parity
             } else {
                 bonds[n] = container.getBond(focus, atoms[i]);
+                if (bonds[n] == null)
+                    throw new IllegalArgumentException("Inconsistent stereo,"
+                                                       + " tetrahedral centre"
+                                                       + " contained atom not"
+                                                       + " stored in molecule");
                 atoms[n] = atoms[i];
                 n++;
             }

diff --git a/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java b/tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
@@ -668,6 +668,17 @@ public void atropisomerWedgeBonds() throws CDKException {
 
     }
 
+    @Test(expected = IllegalArgumentException.class)
+    public void inconsistentStereoState() throws CDKException {
+        final String smi = "O[C@]([H])(C)CCC";
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles(smi);
+        mol.removeBond(1);
+        mol.removeAtomOnly(2); // unsafe-removes
+        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+        sdg.generateCoordinates(mol);
+    }
+
     static IAtom atom(String symbol, int hCount, double x, double y) {
         IAtom a = new Atom(symbol);
         a.setImplicitHydrogenCount(hCount);