Set the ring status of query atoms.

johnmay · johnmay · commit 77d84bcb183c · 2020-10-28T21:11:11.000Z
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
@@ -1816,6 +1816,7 @@ public static void create(IAtomContainer dst,
             }
 
             QueryAtom qatom = new QueryAtom(expr);
+            qatom.setIsInRing(atom.isInRing());
 
             // backward compatibility for naughty methods that are expecting
             // these to be set for a query!
@@ -1873,6 +1874,7 @@ else if (optset.contains(IS_IN_CHAIN) && !bond.isInRing())
             QueryBond qbond = new QueryBond((IAtom) mapping.get(bond.getBegin()),
                                             (IAtom) mapping.get(bond.getEnd()),
                                             expr);
+            qbond.setIsInRing(bond.isInRing());
             // backward compatibility for naughty methods that are expecting
             // these to be set for a query!
             if (optset.contains(Expr.Type.ALIPHATIC_ORDER) ||
