In verbose output, check that the query molecule exists before using it. (#9040)

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>

Code/GraphMol/FMCS/CMakeLists.txt

@@ -10,6 +10,7 @@ rdkit_headers(FMCS.h
 
 rdkit_test(testFMCS testFMCS_Unit.cpp LINK_LIBRARIES
 FMCS )
+rdkit_catch_test(testFMCSCatch testFMCS_catch_tests.cpp LINK_LIBRARIES FMCS)
 
 if(RDK_BUILD_PYTHON_WRAPPERS)
 add_subdirectory(Wrap)

Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp

@@ -417,18 +417,21 @@ void MaximumCommonSubgraph::makeInitialSeeds() {
         if (!QueryMoleculeSingleMatchedAtom) {
           QueryMoleculeSingleMatchedAtom = candQueryMoleculeSingleMatchedAtom;
         } else {
-          QueryMoleculeSingleMatchedAtom = (std::max)(
-              candQueryMoleculeSingleMatchedAtom,
-              QueryMoleculeSingleMatchedAtom, [](const Atom *a, const Atom *b) {
-                if (a->getDegree() != b->getDegree()) {
-                  return (a->getDegree() < b->getDegree());
-                } else if (a->getFormalCharge() != b->getFormalCharge()) {
-                  return (a->getFormalCharge() < b->getFormalCharge());
-                } else if (a->getAtomicNum() != b->getAtomicNum()) {
-                  return (a->getAtomicNum() < b->getAtomicNum());
-                }
-                return (a->getIdx() < b->getIdx());
-              });
+          QueryMoleculeSingleMatchedAtom =
+              (std::max)(candQueryMoleculeSingleMatchedAtom,
+                         QueryMoleculeSingleMatchedAtom,
+                         [](const Atom *a, const Atom *b) {
+                           if (a->getDegree() != b->getDegree()) {
+                             return (a->getDegree() < b->getDegree());
+                           } else if (a->getFormalCharge() !=
+                                      b->getFormalCharge()) {
+                             return (a->getFormalCharge() <
+                                     b->getFormalCharge());
+                           } else if (a->getAtomicNum() != b->getAtomicNum()) {
+                             return (a->getAtomicNum() < b->getAtomicNum());
+                           }
+                           return (a->getIdx() < b->getIdx());
+                         });
         }
       }
     }
@@ -1049,7 +1052,10 @@ MCSResult MaximumCommonSubgraph::find(const std::vector<ROMOL_SPTR> &src_mols) {
       unsigned int itarget = &tag - &Targets.front();
       MatchVectType match;
 
-      bool target_matched = SubstructMatch(*tag.Molecule, *res.QueryMol, match);
+      bool target_matched =
+          res.QueryMol && SubstructMatch(*tag.Molecule, *res.QueryMol, match)
+              ? true
+              : false;
       if (!target_matched) {
         std::cout << "Target " << itarget + 1
                   << (target_matched ? " matched " : " MISMATCHED ")
@@ -1246,7 +1252,9 @@ bool MaximumCommonSubgraph::match(Seed &seed) {
   for (const auto &tag : Targets) {
     unsigned int itarget = &tag - &Targets.front();
 #ifdef VERBOSE_STATISTICS_ON
-    { ++VerboseStatistics.MatchCall; }
+    {
+      ++VerboseStatistics.MatchCall;
+    }
 #endif
     bool target_matched = false;
     if (!seed.MatchResult.empty() && !seed.MatchResult.at(itarget).empty()) {
@@ -1297,7 +1305,9 @@ bool MaximumCommonSubgraph::matchIncrementalFast(Seed &seed,
                                                  unsigned int itarget) {
 // use and update results of previous match stored in the seed
 #ifdef VERBOSE_STATISTICS_ON
-  { ++VerboseStatistics.FastMatchCall; }
+  {
+    ++VerboseStatistics.FastMatchCall;
+  }
 #endif
   const auto &target = Targets.at(itarget);
   auto &match = seed.MatchResult.at(itarget);

Code/GraphMol/FMCS/testFMCS_catch_tests.cpp

@@ -0,0 +1,38 @@
+//
+// Copyright (C) David Cosgrove and other RDKit contributors 2026.
+//
+//   @@ All Rights Reserved @@
+//  This file is part of the RDKit.
+//  The contents are covered by the terms of the BSD license
+//  which is included in the file license.txt, found at the root
+//  of the RDKit source tree.
+
+#include <GraphMol/SmilesParse/SmilesParse.h>
+
+#include "FMCS.h"
+
+#include <catch2/catch_all.hpp>
+
+using namespace RDKit;
+
+TEST_CASE("Github9034") {
+  std::vector<ROMOL_SPTR> mols;
+  const char *smi[] = {
+      "C1CCCCC1",
+      "C1CCCC1",
+  };
+
+  for (auto &i : smi) {
+    mols.emplace_back(v2::SmilesParse::MolFromSmiles(i));
+  }
+  MCSParameters p;
+  p.Verbose = true;
+  p.StoreAll = true;
+  auto res = findMCS(mols, &p);
+  // The bug was a crash caused by p.Verbose = true.  So the real test
+  // is whether this completes correctly, but check a few things.
+  CHECK(res.DegenerateSmartsQueryMolDict.size() == 4);
+  for (const auto &r : res.DegenerateSmartsQueryMolDict) {
+    CHECK(r.second->getNumAtoms() == 5);
+  }
+}