@@ -24,8 +24,8 @@ bool atomCompat(const ATOM_SPTR &a1, const ATOM_SPTR &a2,
   // " " << a2->getIdx() << std::endl;
   bool res;
   if (useQueryQueryMatches && a1->hasQuery() && a2->hasQuery()) {
-    res = static_cast<QueryAtom *>(a1.get())
-              ->QueryMatch(static_cast<QueryAtom *>(a2.get()));
+    res = static_cast<QueryAtom *>(a1.get())->QueryMatch(
+        static_cast<QueryAtom *>(a2.get()));
   } else {
     res = a1->Match(a2);
   }
// $Id$
//
//  Copyright (C) 2003-2010 Greg Landrum and Rational Discovery LLC
//
//   @@ 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 "SubstructUtils.h"
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <boost/dynamic_bitset.hpp>

namespace RDKit {

bool atomCompat(const ATOM_SPTR &a1, const ATOM_SPTR &a2,
                bool useQueryQueryMatches) {
  PRECONDITION(a1, "bad atom");
  PRECONDITION(a2, "bad atom");
  // std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 <<
  // " " << a2->getIdx() << std::endl;
  bool res;
  if (useQueryQueryMatches && a1->hasQuery() && a2->hasQuery()) {
    res = static_cast<QueryAtom *>(a1.get())
              ->QueryMatch(static_cast<QueryAtom *>(a2.get()));
  } else {
    res = a1->Match(a2);
  }
  return res;
}

bool chiralAtomCompat(const ATOM_SPTR &a1, const ATOM_SPTR &a2) {
  PRECONDITION(a1, "bad atom");
  PRECONDITION(a2, "bad atom");
  // std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 <<
  // " " << a2->getIdx() << std::endl;
  bool res = a1->Match(a2);
  if (res) {
    std::string s1, s2;
    bool hascode1 = a1->getPropIfPresent(common_properties::_CIPCode, s1);
    bool hascode2 = a2->getPropIfPresent(common_properties::_CIPCode, s2);
    if (hascode1 || hascode2) {
      res = hascode1 && hascode2 && s1 == s2;
    }
  }
  return res;
}

bool bondCompat(const BOND_SPTR &b1, const BOND_SPTR &b2,
                bool useQueryQueryMatches) {
  PRECONDITION(b1, "bad bond");
  PRECONDITION(b2, "bad bond");
  bool res;
  if (useQueryQueryMatches && b1->hasQuery() && b2->hasQuery()) {
    res = static_cast<QueryBond *>(b1.get())
              ->QueryMatch(static_cast<QueryBond *>(b2.get()));
  } else {
    res = b1->Match(b2);
  }
  // std::cout << "\t\tbondCompat: "<< b1->getIdx() << "-" << b2->getIdx() << ":
  // " << res << std::endl;
  return res;
}

void removeDuplicates(std::vector<MatchVectType> &v, unsigned int nAtoms) {
  //
  //  This works by tracking the indices of the atoms in each match vector.
  //  This can lead to unexpected behavior when looking at rings and queries
  //  that don't specify bond orders.  For example querying this molecule:
  //    C1CCC=1
  //  with the pattern constructed from SMARTS C~C~C~C will return a
  //  single match, despite the fact that there are 4 different paths
  //  when valence is considered.  The defense of this behavior is
  //  that the 4 paths are equivalent in the semantics of the query.
  //  Also, OELib returns the same results
  //
  std::vector<boost::dynamic_bitset<> > seen;
  std::vector<MatchVectType> res;
  for (std::vector<MatchVectType>::const_iterator i = v.begin(); i != v.end();
       ++i) {
    boost::dynamic_bitset<> val(nAtoms);
    for (MatchVectType::const_iterator ci = i->begin(); ci != i->end(); ++ci) {
      val.set(ci->second);
    }
    if (std::find(seen.begin(), seen.end(), val) == seen.end()) {
      // it's something new
      res.push_back(*i);
      seen.push_back(val);
    }
  }
  v = res;
}
}

Is this an unrelated bug fix?