Backport fix from PR #432

corelib/src/libs/SireMol/molid.cpp

@@ -266,6 +266,8 @@ QList<MolNum> MolIdx::map(const Molecules &molecules) const
             molnums.append(it.key());
             break;
         }
+
+        --i;
     }
 
     BOOST_ASSERT(not molnums.isEmpty());

corelib/src/libs/SireSearch/idengine.cpp

@@ -31,8 +31,8 @@
 #include "SireBase/booleanproperty.h"
 #include "SireBase/parallel.h"
 
-#include "SireMol/atomelements.h"
 #include "SireMol/atomcoords.h"
+#include "SireMol/atomelements.h"
 #include "SireMol/core.h"
 #include "SireMol/iswater.h"
 
@@ -1155,9 +1155,63 @@ SelectResult IDIndexEngine::searchMolIdx(const SelectResult &mols, const SelectR
 {
     QList<Molecule> matches;
 
-    int idx = 0;
     int count = context.listCount();
 
+    if (_is_single_value(this->vals))
+    {
+        // For a single index value, apply Python-style negative-index mapping
+        // and do a strict bounds check. Out-of-bounds returns no match,
+        // consistent with residx/atomidx behaviour.
+        // We read the raw start value from RangeValue directly, bypassing the
+        // _to_single_value helper which maps against INT_MAX and corrupts
+        // negative indices.
+        auto rv = boost::get<RangeValue>(this->vals[0]);
+
+        if (not rv.start)
+            return SelectResult(matches);
+
+        int v = *rv.start;
+
+        if (v < 0)
+            v = count + v;
+
+        if (v < 0 or v >= count)
+            return SelectResult(matches);
+
+        int idx = 0;
+
+        for (const auto &mol : context)
+        {
+            if (idx == v)
+            {
+                if (&mols == &context)
+                {
+                    matches.append(mol->molecule());
+                }
+                else
+                {
+                    const auto molnum = mol->data().number();
+
+                    for (const auto &m : mols)
+                    {
+                        if (m->data().number() == molnum)
+                        {
+                            matches.append(m->molecule());
+                            break;
+                        }
+                    }
+                }
+                break;
+            }
+
+            idx += 1;
+        }
+
+        return SelectResult(matches);
+    }
+
+    int idx = 0;
+
     for (const auto &mol : context)
     {
         if (this->match(idx, count))

doc/source/changelog.rst

@@ -40,6 +40,10 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 
 * Map the end-state ``element`` property when performing hydrogen mass repartitioning on perturbable molecules.
 
+* Fixed out-of-bounds ``molidx`` searches silently returning the last molecule instead of
+  raising a ``KeyError``. Out-of-bounds positive and negative single-index values now
+  behave consistently with ``residx`` and ``atomidx``.
+
 `2025.4.0 <https://github.com/openbiosim/sire/compare/2025.3.0...2025.4.0>`__ - February 2026
 ---------------------------------------------------------------------------------------------