/// <summary>
/// <p>Converts a reaction to an 'inlined' reaction stored as a molecule. All
/// reactants, agents, products are added to the molecule as disconnected
/// components with atoms flagged as to their role <see cref="ReactionRole"/> and
/// component group.</p>
/// <p>
/// The inlined reaction, stored in a molecule can be converted back to an explicit
/// reaction with <see cref="ToReaction"/>. Data stored on the individual components (e.g.
/// titles is lost in the conversion).
/// </p>
/// </summary>
/// <param name="rxn">reaction to convert</param>
/// <returns>inlined reaction stored in a molecule</returns>
/// <seealso cref="ToReaction"/>
public static IAtomContainer ToMolecule(IReaction rxn)
{
if (rxn == null)
{
throw new ArgumentNullException(nameof(rxn), "Null reaction provided");
}
IChemObjectBuilder bldr = rxn.Builder;
IAtomContainer mol = bldr.NewAtomContainer();
mol.SetProperties(rxn.GetProperties());
mol.Id = rxn.Id;
int grpId = 0;
foreach (IAtomContainer comp in rxn.Reactants)
{
AssignRoleAndGrp(comp, ReactionRole.Reactant, ++grpId);
mol.Add(comp);
}
foreach (IAtomContainer comp in rxn.Agents)
{
AssignRoleAndGrp(comp, ReactionRole.Agent, ++grpId);
mol.Add(comp);
}
foreach (IAtomContainer comp in rxn.Products)
{
AssignRoleAndGrp(comp, ReactionRole.Product, ++grpId);
mol.Add(comp);
}
return(mol);
}