Program: 39428
Project: 39428
Buggy source:
private synchronized void setTargetSingleAtomMap(List<Map<IAtom,IAtom>> mappings) throws CDKException {
  int counter=0;
  BondEnergies be=BondEnergies.getInstance();
  for (  IAtom targetAtom : target.atoms()) {
    for (    IAtom sourceAtoms : source.atoms()) {
      Map<IAtom,IAtom> mapAtoms=new HashMap<IAtom,IAtom>();
      if (targetAtom instanceof IQueryAtom) {
        if (((IQueryAtom)targetAtom).matches(sourceAtoms)) {
          if (targetAtom.getSymbol().equalsIgnoreCase(sourceAtoms.getSymbol())) {
            mapAtoms.put(sourceAtoms,targetAtom);
            List<IBond> Bonds=source.getConnectedBondsList(sourceAtoms);
            double totalOrder=0;
            for (            IBond bond : Bonds) {
              Order bondOrder=bond.getOrder();
              if (bondOrder == null) {
                continue;
              }
              totalOrder+=bondOrder.numeric() + be.getEnergies(bond);
            }
            if (sourceAtoms.getFormalCharge() != targetAtom.getFormalCharge()) {
              totalOrder+=0.5;
            }
            connectedBondOrder.put(counter,totalOrder);
            mappings.add(counter,mapAtoms);
            counter++;
          }
        }
      }
 else       if (targetAtom.getSymbol().equalsIgnoreCase(sourceAtoms.getSymbol())) {
        mapAtoms.put(sourceAtoms,targetAtom);
        List<IBond> Bonds=source.getConnectedBondsList(sourceAtoms);
        double totalOrder=0;
        for (        IBond bond : Bonds) {
          Order bondOrder=bond.getOrder();
          if (bondOrder == null) {
            continue;
          }
          totalOrder+=bondOrder.numeric() + be.getEnergies(bond);
        }
        if (sourceAtoms.getFormalCharge() != targetAtom.getFormalCharge()) {
          totalOrder+=0.5;
        }
        connectedBondOrder.put(counter,totalOrder);
        mappings.add(counter,mapAtoms);
        counter++;
      }
    }
  }
}

Fixed version (ground truth):
private synchronized void setTargetSingleAtomMap(List<Map<IAtom,IAtom>> mappings) throws CDKException {
  int counter=0;
  BondEnergies be=BondEnergies.getInstance();
  for (  IAtom targetAtom : target.atoms()) {
    for (    IAtom sourceAtoms : source.atoms()) {
      Map<IAtom,IAtom> mapAtoms=new HashMap<>();
      if (targetAtom instanceof IQueryAtom) {
        if (((IQueryAtom)targetAtom).matches(sourceAtoms)) {
          if (targetAtom.getSymbol().equalsIgnoreCase(sourceAtoms.getSymbol())) {
            mapAtoms.put(sourceAtoms,targetAtom);
            List<IBond> Bonds=source.getConnectedBondsList(sourceAtoms);
            double totalOrder=0;
            for (            IBond bond : Bonds) {
              Order bondOrder=bond.getOrder();
              if (bondOrder == null) {
                continue;
              }
              totalOrder+=bondOrder.numeric() + be.getEnergies(bond);
            }
            if (!Objects.equals(sourceAtoms.getFormalCharge(),targetAtom.getFormalCharge())) {
              totalOrder+=0.5;
            }
            connectedBondOrder.put(counter,totalOrder);
            mappings.add(counter,mapAtoms);
            counter++;
          }
        }
      }
 else       if (targetAtom.getSymbol().equalsIgnoreCase(sourceAtoms.getSymbol())) {
        mapAtoms.put(sourceAtoms,targetAtom);
        List<IBond> Bonds=source.getConnectedBondsList(sourceAtoms);
        double totalOrder=0;
        for (        IBond bond : Bonds) {
          Order bondOrder=bond.getOrder();
          if (bondOrder == null) {
            continue;
          }
          totalOrder+=bondOrder.numeric() + be.getEnergies(bond);
        }
        if (!Objects.equals(sourceAtoms.getFormalCharge(),targetAtom.getFormalCharge())) {
          totalOrder+=0.5;
        }
        connectedBondOrder.put(counter,totalOrder);
        mappings.add(counter,mapAtoms);
        counter++;
      }
    }
  }
}