Program: 39426
Project: 39426
Buggy source:
private synchronized void setSourceSingleAtomMap(List<Map<IAtom,IAtom>> mappings) throws CDKException {
  int counter=0;
  BondEnergies be=BondEnergies.getInstance();
  for (  IAtom sourceAtom : source.atoms()) {
    for (    IAtom targetAtom : target.atoms()) {
      Map<IAtom,IAtom> mapAtoms=new HashMap<IAtom,IAtom>();
      if (sourceAtom instanceof IQueryAtom) {
        if (((IQueryAtom)sourceAtom).matches(targetAtom)) {
          mapAtoms.put(sourceAtom,targetAtom);
          List<IBond> Bonds=target.getConnectedBondsList(targetAtom);
          double totalOrder=0;
          for (          IBond bond : Bonds) {
            Order bondOrder=bond.getOrder();
            if (bondOrder == null) {
              continue;
            }
            totalOrder+=bondOrder.numeric() + be.getEnergies(bond);
          }
          if (targetAtom.getFormalCharge() != sourceAtom.getFormalCharge()) {
            totalOrder+=0.5;
          }
          connectedBondOrder.put(counter,totalOrder);
          mappings.add(counter++,mapAtoms);
        }
      }
 else       if (sourceAtom.getSymbol().equalsIgnoreCase(targetAtom.getSymbol())) {
        mapAtoms.put(sourceAtom,targetAtom);
        List<IBond> Bonds=target.getConnectedBondsList(targetAtom);
        double totalOrder=0;
        for (        IBond bond : Bonds) {
          Order bondOrder=bond.getOrder();
          if (bondOrder == null) {
            continue;
          }
          totalOrder+=bondOrder.numeric() + be.getEnergies(bond);
        }
        if (targetAtom.getFormalCharge() != sourceAtom.getFormalCharge()) {
          totalOrder+=0.5;
        }
        connectedBondOrder.put(counter,totalOrder);
        mappings.add(counter,mapAtoms);
        counter++;
      }
    }
  }
}

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