Match the semantic of the bond expressions. Unless someone asks for IS_IN_CHAIN don't add it in, hexane (acyclic) is a subsgraph of cyclohexane (cyclic).

johnmay · johnmay · commit 39549c0d5760 · 2020-10-28T19:52:17.000Z
diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
@@ -1776,9 +1776,10 @@ public static QueryAtomContainer create(IAtomContainer mol, Expr.Type... opts) {
             if (optset.contains(TOTAL_DEGREE))
                 expr.and(new Expr(DEGREE,
                                   atom.getBondCount() + atom.getImplicitHydrogenCount()));
-            if (optset.contains(IS_IN_RING) ||
-                optset.contains(IS_IN_CHAIN))
-                expr.and(new Expr(atom.isInRing() ? IS_IN_RING : IS_IN_CHAIN));
+            if (optset.contains(IS_IN_RING) && atom.isInRing())
+                expr.and(new Expr(IS_IN_RING));
+            if (optset.contains(IS_IN_CHAIN) && !atom.isInRing())
+              expr.and(new Expr(IS_IN_CHAIN));
             if (optset.contains(IMPL_H_COUNT))
                 expr.and(new Expr(IMPL_H_COUNT));
             if (optset.contains(RING_BOND_COUNT)) {
