#include <iostream>
#include <fstream>
#include <string>

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/parsmart.h>
#include <openbabel/mcdlutil.h>

using namespace std;
using namespace OpenBabel;

int main(int argc, char* argv[]) {
  OBConversion conv;
  conv.SetInAndOutFormats("SMI", "SDF");

  OBMol mol;
  conv.ReadString(&mol, "COc1cc2ncnc(c2cc1OCCCN1CCOCC1)Nc1ccc(c(c1)Cl)F");
  generateDiagram(&mol);
  mol.SetDimension(2);

  OBSmartsPattern smp;
  smp.Init("C1COCCN1");
  smp.Match(mol);
  vector<vector<int> > mlist = smp.GetUMapList();

  mol.BeginModify();
  OBAtom* a = mol.GetAtom(mlist[0][2]);
  a->SetAtomicNum(16);
  mol.EndModify();

  conv.Write(&mol, &cout);
}