30.1 Normalization Reactions

The OEUniMolecularRxn class is designed to apply a set of transformations defined by a reaction to exactly one reactant molecule. All possible transformations are applied to the initial set of atoms and bonds of an input molecule. For example, a reaction that affects a particular type of functional group will be automatically be applied twice a to bi-functional molecule. The number of transformations applied by the OEUniMolecularRxn class is limited in order to prevent infinite loops. Consider a hypothetical reaction that methylates a methyl group. If a methyl group added in a reaction were allowed to react again, the methyl groups of a molecule would be methylated ad infinitum. The first protection against infinite loops provided by OEUniMolecularRxn is that only original atoms and bonds of the input molecule are allowed to react. Atoms and bonds created by a reaction are excluded from involvement in further reactions. A more subtle source of potential infinite loops are reactions where products atoms still match the reactant pattern after they have been involved in a chemical transformation. The OEUniMolecularRxn class allows a set of atom that match a reactant pattern to react only a single time.

The following code demonstrates the use of the OEUniMolecularRxn class. The OEUniMolecularRxn in this case is initialized using a SMIRKS pattern. The example reaction protonates and charges an amine nitrogen. When the OEUniMolecularRxn class is applied to 1,2-ethanediamine both nitrogens are charged and protonated to yield 1,2-ethanediaminium. The example reaction was intentionally written to demonstrate the protection mechanisms in place to prevent underspecified reactions from causing infinite loops. The product 1,2-ethanediaminium still matches the reactant pattern, however, subsequent reactions terminate when no unreacted atoms are identified.

#include "oechem.h"
#include <iostream>

using namespace OEChem;
using namespace std;

int main()
{
  OEUniMolecularRxn umr("[N:1]>>[Nh3+:1]");

  OEGraphMol mol;
  OEParseSmiles(mol,"NCCN");
  umr(mol);

  std::string smi;
  OECreateSmiString(smi,mol);

  cout << "smiles = " << smi << endl;

  return 0;
}

				OEChem - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1