/// <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.FindIdentical(inchiMolGraph,
AtomMatcher.CreateElementMatcher(), BondMatcher.CreateAnyMatcher())
.MatchAll(mol)
.Limit(1)
.ToAtomMap();
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>
/// Adds a Molecule to the list of templates use by this TemplateHandler.
/// </summary>
/// <param name="molecule">The molecule to be added to the TemplateHandler</param>
public void AddMolecule(IAtomContainer molecule)
{
if (!GeometryUtil.Has2DCoordinates(molecule))
{
throw new ArgumentException("Template did not have 2D coordinates");
}
// we want a consistent scale!
GeometryUtil.ScaleMolecule(molecule, GeometryUtil.GetScaleFactor(molecule, StructureDiagramGenerator.DefaultBondLength));
templates.Add(molecule);
anonPatterns.Add(VentoFoggia.CreateSubstructureFinder(molecule,
anonAtomMatcher,
anonBondMatcher));
elemPatterns.Add(VentoFoggia.CreateSubstructureFinder(molecule,
elemAtomMatcher,
anonBondMatcher));
}
/// <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);
}
void Main()
{
IAtomContainer queryStructure = null;
IChemObjectSet <IAtomContainer> ms = null;
{
#region 1
IAtomContainer query = queryStructure;
Pattern pattern = VentoFoggia.CreateSubstructureFinder(query);
int hits = 0;
foreach (var m in ms)
{
if (pattern.Matches(m))
{
hits++;
}
}
#endregion
}
{
#region 2
IAtomContainer query = queryStructure;
Pattern pattern = VentoFoggia.CreateSubstructureFinder(query);
int hits = 0;
foreach (var m in ms)
{
int[] match = pattern.Match(m);
if (match.Length > 0)
{
hits++;
}
}
#endregion
}
}
public override Pattern Create(IAtomContainer container)
{
return(VentoFoggia.FindSubstructure(container));
}
