/// <summary>
/// Atom-atom mapping of the input molecule to the bare container constructed from the InChI connection table.
/// This makes it possible to map the positions of the mobile hydrogens in the InChI back to the input molecule.
/// </summary>
/// <param name="inchiMolGraph">molecule (bare) as defined in InChI</param>
/// <param name="mol">user input molecule</param>
/// <exception cref="CDKException"></exception>
private static void MapInputMoleculeToInChIMolgraph(IAtomContainer inchiMolGraph, IAtomContainer mol)
{
var iter = VentoFoggia.CreateIdenticalFinder(inchiMolGraph,
AtomMatcher.CreateElementMatcher(), BondMatcher.CreateAnyMatcher())
.MatchAll(mol)
.Limit(1)
.ToAtomMaps();
var i = iter.FirstOrDefault();
if (i != null)
{
foreach (var e in i)
{
var src = e.Key;
var dst = e.Value;
var position = src.Id;
dst.Id = position;
Debug.WriteLine($"Mapped InChI {src.Symbol} {src.Id} to {dst.Symbol} {dst.Id}");
}
}
else
{
throw new ArgumentException($"{CANSMI.Create(inchiMolGraph)} {CANSMI.Create(mol)}");
}
}
public IAtomContainer RemoveMolecule(IAtomContainer molecule)
{
for (int i = 0; i < templates.Count; i++)
{
if (VentoFoggia.CreateIdenticalFinder(templates[i], anonAtomMatcher, anonBondMatcher).Matches(molecule))
{
elemPatterns.RemoveAt(i);
anonPatterns.RemoveAt(i);
var ret = templates[i];
templates.RemoveAt(i);
return(ret);
}
}
return(null);
}
/// <summary>
/// Checks if one of the loaded templates is isomorph to the given
/// Molecule. If so, it assigns the coordinates from the template to the
/// respective atoms in the Molecule, and marks the atoms as ISPLACED.
/// </summary>
/// <param name="molecule">The molecule to be check for potential templates</param>
/// <returns>True if there was a possible mapping</returns>
public bool MapTemplateExact(IAtomContainer molecule)
{
foreach (var template in templates)
{
var mappings = VentoFoggia.CreateIdenticalFinder(template, anonAtomMatcher, anonBondMatcher).MatchAll(molecule);
foreach (var atoms in mappings.ToAtomMaps())
{
foreach (var e in atoms)
{
e.Value.Point2D = e.Key.Point2D;
e.Value.IsPlaced = true;
}
if (atoms.Count != 0)
{
return(true);
}
}
}
return(false);
}