separation.cpp

#include <iostream>
#include <string>
#include <sstream>

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/builder.h>

using namespace std;
using namespace OpenBabel;

int main(int argc, char** argv){
  string smiles = "c1ccc2c(c1)ccc(c2c3c4ccccc4ccc3C(=O)O)C(=O)O";
  stringstream ss(smiles);
  OBConversion conv(&ss, &std::cout);
  conv.SetInAndOutFormats("smi", "smi");

  OBMol mol;
  conv.Read(&mol);

  // Get fragments using CopySubstructure
  // Copy all atoms
  OBBitVec atomsToCopy;
  FOR_ATOMS_OF_MOL(atom, mol) {
    atomsToCopy.SetBitOn(atom->GetIdx());
  }

  // Exclude rotatable bonds
  OBBitVec bondsToExclude;
  FOR_BONDS_OF_MOL(bond, mol) {
    if (bond->IsRotor()) {
      bondsToExclude.SetBitOn(bond->GetIdx());
    }
  }

  // Generate fragments by copy
  OBMol mol_copy;
  mol.CopySubstructure(mol_copy, &atomsToCopy, &bondsToExclude);

  // Separate each disconnected fragments as different molecules
  vector<OBMol> fragments = mol_copy.Separate(); 
  cout << "Original separation" << endl;
  for(vector<OBMol>::iterator i=fragments.begin(); i!=fragments.end(); i++) {
    cout << conv.WriteString(&*i, true) << endl;
  }

  OBMol mol2 = mol;
  FOR_BONDS_OF_MOL(bond, mol2) {
    if (bond->IsRotor()) {
      mol2.DeleteBond(&*bond);
    }
  }

  cout << "New separation" << endl;
  fragments = mol2.Separate(); 
  for(vector<OBMol>::iterator i=fragments.begin(); i!=fragments.end(); i++) {
    cout << conv.WriteString(&*i, true) << endl;
  }
}