#include "oechem.h"

#include <iostream>

using namespace std;
using namespace OEChem;
using namespace OESystem;

int main()
{
  OEGraphMol m1,m2;

  OEParseSmiles(m1, "c1cc(O)c(O)cc1CCN");
  OEParseSmiles(m2, "c1c(O)c(O)c(Cl)cc1CCCBr");

  OEMCSSearch mcss(m1,OEExprOpts::DefaultAtoms,OEExprOpts::DefaultBonds);

  unsigned int count;
  OEIter<OEMatchBase> match;
  for (count=1,match = mcss.Match(m2);match;++match,count++)
  {
    OEIter<OEMatchPair<OEAtomBase> > apr;

    cout << "Match " << count << ':' << endl;
    cout << "pattern atoms: ";
    for (apr = match->GetAtoms();apr;++apr)
      cout << apr->pattern->GetIdx() << ' ';
    cout << endl;

    cout << "target atoms:  ";
    for (apr = match->GetAtoms();apr;++apr)
      cout << apr->target->GetIdx() << ' ';
    cout << endl;

    OEGraphMol m3;
    OESubsetMol(m3,match,true);
    string smi;
    OECreateSmiString(smi,m3);
    cout << "match smiles = " << smi << endl;
  }

  return 0;
}