void Main()
{
IAtomContainer m = TestMoleculeFactory.MakeBenzene();
// converter is thread-safe and can be used by multiple threads
CDKToBeam c2g = new CDKToBeam();
Beam.Graph g = c2g.ToBeamGraph(m);
// get the SMILES notation from the Beam graph
string smi = g.ToSmiles();
}
public void QuadrupleBond()
{
var mock_u = new Mock <IAtom>(); var u = mock_u.Object;
var mock_v = new Mock <IAtom>(); var v = mock_v.Object;
var b = new Bond(u, v, BondOrder.Quadruple);
var o = new Dictionary <IAtom, int>()
{
[u] = 0,
[v] = 1,
};
var c2g = new CDKToBeam();
Assert.AreEqual(Beam.Bond.Quadruple.CreateEdge(0, 1), c2g.ToBeamEdge(b, o));
}
public void AromaticBond()
{
var mock_u = new Mock <IAtom>(); var u = mock_u.Object;
var mock_v = new Mock <IAtom>(); var v = mock_v.Object;
var b = new Bond(u, v)
{
IsAromatic = true
};
var o = new Dictionary <IAtom, int>()
{
[u] = 0,
[v] = 1,
};
mock_u.SetupGet(n => n.IsAromatic).Returns(true);
mock_v.SetupGet(n => n.IsAromatic).Returns(true);
var c2g = new CDKToBeam();
Assert.AreEqual(Beam.Bond.Aromatic.CreateEdge(0, 1), c2g.ToBeamEdge(b, o));
}
/// <summary>
/// Creates a SMILES string of the flavour specified as a parameter
/// and write the output order to the provided array.
/// </summary>
/// <remarks>
/// The output order allows one to arrange auxiliary atom data in the
/// order that a SMILES string will be read. A simple example is seen below
/// where 2D coordinates are stored with a SMILES string. This method
/// forms the basis of CXSMILES.
/// </remarks>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Smiles.SmilesGenerator_Example.cs+Create_IAtomContainer_int_int"]/*' />
/// </example>
/// <param name="molecule">the molecule to write</param>
/// <param name="order">array to store the output order of atoms</param>
/// <returns>the SMILES string</returns>
/// <exception cref="CDKException">a valid SMILES could not be created</exception>
public static string Create(IAtomContainer molecule, SmiFlavors flavour, int[] order)
{
try
{
if (order.Length != molecule.Atoms.Count)
{
throw new ArgumentException("the array for storing output order should be the same length as the number of atoms");
}
var g = CDKToBeam.ToBeamGraph(molecule, flavour);
// apply the canonical labelling
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.Canonical))
{
// determine the output order
var labels = Labels(flavour, molecule);
g = g.Permute(labels);
if ((flavour & SmiFlavors.AtomAtomMapRenumber) == SmiFlavors.AtomAtomMapRenumber)
{
g = Functions.RenumberAtomMaps(g);
}
if (!SmiFlavorTool.IsSet(flavour, SmiFlavors.UseAromaticSymbols))
{
g = g.Resonate();
}
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.StereoCisTrans))
{
// FIXME: required to ensure canonical double bond labelling
g.Sort(new Graph.VisitHighOrderFirst());
// canonical double-bond stereo, output be C/C=C/C or C\C=C\C
// and we need to normalise to one
g = Functions.NormaliseDirectionalLabels(g);
// visit double bonds first, prefer C1=CC=C1 to C=1C=CC1
// visit hydrogens first
g.Sort(new Graph.VisitHighOrderFirst()).Sort(new Graph.VisitHydrogenFirst());
}
var smiles = g.ToSmiles(order);
// the SMILES has been generated on a reordered molecule, transform
// the ordering
var canorder = new int[order.Length];
for (int i = 0; i < labels.Length; i++)
{
canorder[i] = order[labels[i]];
}
System.Array.Copy(canorder, 0, order, 0, order.Length);
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.CxSmilesWithCoords))
{
smiles += CxSmilesGenerator.Generate(GetCxSmilesState(flavour, molecule), flavour, null, order);
}
return(smiles);
}
else
{
string smiles = g.ToSmiles(order);
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.CxSmilesWithCoords))
{
smiles += CxSmilesGenerator.Generate(GetCxSmilesState(flavour, molecule), flavour, null, order);
}
return(smiles);
}
}
catch (IOException e)
{
throw new CDKException(e.Message);
}
}
