SMARTS stereo matching requires additional checks to ensure we don't …

…accidentally attempt to compare a tetrahedral centre to a double-bond (was causing a class cast). The typical case is when this occurs is when bond orders are not matched. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Mar 30, 2015 · b12d2ca · b12d2ca
1 parent 60d85be
commit b12d2ca
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diff --git a/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java b/tool/smarts/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java
@@ -132,6 +132,9 @@ public boolean apply(final int[] mapping) {
     private boolean checkTetrahedral(int u, int[] mapping) {
 
         int v = mapping[u];
+
+        if (targetTypes[v] != null && targetTypes[v] != Type.Tetrahedral)
+            return false;
 
         ITetrahedralChirality queryElement = (ITetrahedralChirality) queryElements[u];
         ITetrahedralChirality targetElement = (ITetrahedralChirality) targetElements[v];
@@ -188,6 +191,11 @@ private boolean checkGeometric(int u1, int u2, int[] mapping) {
         int v1 = mapping[u1];
         int v2 = mapping[u2];
 
+        if (targetTypes[v1] != null && targetTypes[v1] != Type.Geometric)
+            return false;
+        if (targetTypes[v2] != null && targetTypes[v2] != Type.Geometric)
+            return false;
+
         IDoubleBondStereochemistry queryElement = (IDoubleBondStereochemistry) queryElements[u1];
         IBond[] queryBonds = queryElement.getBonds();
 

diff --git a/tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java b/tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java
@@ -1994,4 +1994,14 @@ public void componentGrouping3() throws Exception {
         assertThat(match("([#8]).([#8])", "OCCO"), is(new int[]{0, 0}));
         assertThat(match("([#8]).([#8])", "O.CCO"), is(new int[]{2, 1}));
     }
+
+    /**
+     * Ensure a class cast exception is not thrown when matching stereochemistry. 
+     * @cdk.bug 1358
+     */
+    @Test
+    public void bug1358() throws Exception {
+        assertThat(match("[$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*)]",
+                         "N#CN/C(=N/CCSCC=1N=CNC1C)NC"), is(new int[]{0, 0}));        
+    }
 }