Fix potential problem with stereo-matching - the end points of the ta…

…rget double bond must be in the same stereo element. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jan 19, 2014 · 0d66616 · 0d66616
1 parent 1a2dc9f
commit 0d66616
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 0 deletions.
diff --git a/src/main/org/openscience/cdk/isomorphism/SmartsStereoMatch.java b/src/main/org/openscience/cdk/isomorphism/SmartsStereoMatch.java
@@ -212,6 +212,12 @@ private boolean checkGeometric(int u1, int u2, int[] mapping) {
 
         IDoubleBondStereochemistry targetElement = (IDoubleBondStereochemistry) targetElements[v1];
 
+        // although the atoms were mapped and 'v1' and 'v2' are bond in double-bond
+        // elements they are not in the same element 
+        if (targetElement.getStereoBond().getAtom(0) != target.getAtom(v1)
+                || targetElement.getStereoBond().getAtom(1) != target.getAtom(v2))
+            return false;
+
         // bond is undirected so we need to ensure v1 is the first atom in the bond
         // we also need to to swap the substituents later
         boolean swap = false;

diff --git a/src/main/org/openscience/cdk/isomorphism/StereoMatch.java b/src/main/org/openscience/cdk/isomorphism/StereoMatch.java
@@ -202,6 +202,12 @@ private boolean checkGeometric(int u1, int u2, int[] mapping) {
         IDoubleBondStereochemistry queryElement = (IDoubleBondStereochemistry) queryElements[u1];
         IDoubleBondStereochemistry targetElement = (IDoubleBondStereochemistry) targetElements[v1];
 
+        // although the atoms were mapped and 'v1' and 'v2' are bond in double-bond
+        // elements they are not in the same element 
+        if (targetElement.getStereoBond().getAtom(0) != target.getAtom(v1)
+                || targetElement.getStereoBond().getAtom(1) != target.getAtom(v2))
+            return false;
+
         // bond is undirected so we need to ensure v1 is the first atom in the bond
         // we also need to to swap the substituents later
         boolean swap = false;