/// <summary>
/// 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.
/// </summary>
/// <remarks>
/// The inlined reaction, stored in a molecule can be converted back to an explicit
/// reaction with <see cref="ToReaction(IAtomContainer)"/>. Data stored on the individual components (e.g.
/// titles is lost in the conversion).
/// </remarks>
/// <param name="rxn">reaction to convert</param>
/// <returns>inlined reaction stored in a molecule</returns>
/// <seealso cref="ToReaction(IAtomContainer)"/>
public static IAtomContainer ToMolecule(IReaction rxn)
{
if (rxn == null)
{
throw new ArgumentNullException(nameof(rxn), "Null reaction provided");
}
var bldr = rxn.Builder;
var mol = bldr.NewAtomContainer();
mol.SetProperties(rxn.GetProperties());
mol.Id = rxn.Id;
int grpId = 0;
foreach (IAtomContainer comp in rxn.Reactants)
{
AssignRoleAndGroup(comp, ReactionRole.Reactant, ++grpId);
mol.Add(comp);
}
foreach (IAtomContainer comp in rxn.Agents)
{
AssignRoleAndGroup(comp, ReactionRole.Agent, ++grpId);
mol.Add(comp);
}
foreach (IAtomContainer comp in rxn.Products)
{
AssignRoleAndGroup(comp, ReactionRole.Product, ++grpId);
mol.Add(comp);
}
return(mol);
}
private CMLReaction CDKReactionToCMLReaction(IReaction reaction, bool setIDs)
{
var cmlReaction = new CMLReaction();
if (useCMLIDs && setIDs)
{
IDCreator.CreateIDs(reaction);
}
if (!string.IsNullOrEmpty(reaction.Id))
{
cmlReaction.Id = reaction.Id;
}
var props = reaction.GetProperties();
foreach (var key in props.Keys)
{
var value = props[key];
if (value is string)
{
if (!string.Equals(key.ToString(), CDKPropertyName.Title, StringComparison.Ordinal))
{
var scalar = new CMLScalar();
this.CheckPrefix(scalar);
scalar.DictRef = "cdk:reactionProperty";
scalar.Title = key.ToString();
scalar.SetValue(value.ToString());
cmlReaction.Add(scalar);
}
}
}
// reactants
var cmlReactants = new CMLReactantList();
foreach (var reactant in reaction.Reactants)
{
var cmlReactant = new CMLReactant();
cmlReactant.Add(CDKAtomContainerToCMLMolecule(reactant));
cmlReactants.Add(cmlReactant);
}
// products
var cmlProducts = new CMLProductList();
foreach (var product in reaction.Products)
{
var cmlProduct = new CMLProduct();
cmlProduct.Add(CDKAtomContainerToCMLMolecule(product));
cmlProducts.Add(cmlProduct);
}
// substance
var cmlSubstances = new CMLSubstanceList();
foreach (var agent in reaction.Agents)
{
var cmlSubstance = new CMLSubstance();
cmlSubstance.Add(CDKAtomContainerToCMLMolecule(agent));
cmlSubstances.Add(cmlSubstance);
}
if (reaction.Id != null)
{
cmlReaction.Id = reaction.Id;
}
cmlReaction.Add(cmlReactants);
cmlReaction.Add(cmlProducts);
cmlReaction.Add(cmlSubstances);
return(cmlReaction);
}
