Chemical Descriptors Library: Reduced Molecule

Reduced Molecule

reduced_molecule

The reduced molecule concept is a molecular graph where its vertices can contain either another molecule, or an atom itself [Brown, et. al. 2004].

This case is a great example to show the power of the CDL. Because of CDL's generic nature, we can create a plain molecule type, having another molecule as the type for the atoms of this new type.
In other words, instead of writing a new class that provides this fuctionality, we just declare a type. For example :

// First define the type of the molecular properties

  typedef boost::property<mol_propsS, molecular_properties<> >  mol_props_t;

  
// Now define the type of the atomic properties


  typedef boost::property<atom_static_propsS, 
    ::morpho::atomic_props::atomic_properties<> const *, 
    boost::property<indexed_mol_propS, index_mol_t> >  atom_props_t;

    
// Note that we are using an indexed_molecule as an additional type for the atoms!
// The tag indexed_mol_propS is defined later...

// Now we just have to declare the molecule :

    
  typedef molecule<double,mol_props_t,atom_props_t>   reduced_mol_t;

That's it. We now can attach an indexed molecule to the atoms of this type.

Where defined

This type, the property selectors and property accessors are defined in :

#include <morpho/cdl/molecule/reduced_molecule.hpp>

Associated Functions

Fragmentize

The principal function associated to this type is the fragmentize() function.
This function accepts a std::vector of SMARTS strings that indicates the fragments to use for subdivide a molecule. A new node in the reduced_molecule is created each time a fragment is found. The connections of this node will preserve the connectivity to other fragments or atoms of the original molecule.
For example, lets consider that we have the molecule of Figure 1, and we want to fragmentize it using C1CCCCC1, C1CCCC1, and CCCC(=O)C. The result reduced_molecule is shown in Figure 2.

**Figure 1:** Starting molecule

**Figure 2:** Reduced molecule

The function first gets all the fragments possible using the SMARTS algorithm, then it calls an user-defined functor to select which of these fragments to use to create the reduced_molecule, and then calls another user-defined functor that encodes functionality on how to use these fragments to add nodes and connetions to the reduced_molecule.

Prototype

  template <class Molecule, class ReducedMolecule, class ReducedMolCreator,
  class FragSelector>
  void fragmentize(const std::vector<std::string>& fragments_smart,
  Molecule& m, ReducedMolecule& reduced_mol, ReducedMolCreator  redmol_creator,
  FragSelector selector);

Arguments

Parameter	Description	Models
`fragments_smart`	The SMARTS that indicates the fragments to use to subdivide the molecule	std::vector<std::string>
`m`	The molecule to fragmentize (or subdivide)	morpho::cdl::molecule<>
`reduced_mol`	The reduced molecule to create. This parameter should be empty.	morpho::cdl::reduced_molecule<>
`redmol_creator`	Functor that accepts a std::vector<std::vector<size_t> > that contains the vertex indices of the fragments, and a reduced_molecule which will be created out of these fragments. Returns void.	Use make_redmol_all_nodes or make_redmol_fused_nodes
`selector`	Functor that selects the group of fragments to use to create the reduced_molecule. operator() accepts std::vector<std::vector<size_t> > which is the container that have all fragments found, and returns the same type with the selected fragments to use.	Use largests_fragments_selector or all_fragments_selector

Complexity

Approximately M applications of Ni times the Ullmann algorithm; where M is the number of SMARTS given in fragments_smart, and N is 1 if there is no recursive SMARTS, and 1 is added every time a recursive SMARTS is present.
It has been published that the Ullmann's algorithm has a worst-case scenario of O(n!n^3) [Kukluk, 2004 ], where n are the total number of vertices between the subgraph and the graph.

Example

int main() {
  using namespace std;
  using namespace morpho;
  nail_juice<>  j;
  get_juice_from_stream(std::cin, j, 0, smiles_formatT());
  // now construct the molecule
  typedef   molecule<>  M;
  M  m(j);
  
  // create the SMARTS to explode the molecule :
  std::vector<std::string>    fragments_smart;
  
  fragments_smart.push_back("C1CCCCC1");
  fragments_smart.push_back("C(=O)O");
  fragments_smart.push_back("CNC");
  fragments_smart.push_back("ONC(=O)C");
  
  // declare the reduced molecule :
  reduced_molecule  reduced_mol;
  // declare the functor to select the fragments :
  make_redmol_fused_nodes<M,reduced_molecule>    redmol_create(m);
  // now call fragmentize :
  fragmentize(fragments_smart,m,reduced_mol,redmol_create,all_fragments_selector());
  
  // Now we have fragmentized molecule 'm' in a reduced_molecule 'reduced_mol'
  // To see its content, we can :
  
  reduced_mol_t::vertex_iterator  vi, vi_end;
  tie(vi,vi_end) = reduced_mol.vertices();
  while(vi!=vi_end) {
    std::cout << "--- New atom ---. Index : " << *vi << std::endl;
    std::cout << write_nail(
      AtomProperty<index_molS,reduced_mol_t::atom_type>::get(reduced_mol.get_atom(*vi))
      ,smiles_formatT()) << std::endl;
    std::cout << "-- Indexed molecule, dissociations :\n";
    const AtomProperty<index_molS,reduced_mol_t::atom_type>::result_type::dissociations_t&
      diss = AtomProperty<index_molS,reduced_mol_t::atom_type>::get(
        reduced_mol.get_atom(*vi)
      ).get_dissociations();
    for(int i=0;i<diss.size();++i) {
      std::cout << "--> dissociation : " << diss[i] << std::endl;
    }
    std::cerr << "--- Adjacent vertices : ---\n";
    reduced_mol_t::adjacency_iterator  ai, ai_end;
    tie(ai,ai_end) = reduced_mol.adjacent_vertices(*vi);
    while(ai!=ai_end) {
      std::cerr << *ai << ",";
      ++ai;
    }
    std::cout << std::endl << "--end adjacency\n";
    ++vi;
  }
  
  
  return 0;


}

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