public void GetAtomContainerTest()
{
MoleculeFromSignatureBuilder builder = new MoleculeFromSignatureBuilder(CDK.Builder);
builder.MakeGraph();
Assert.IsNotNull(builder.GetAtomContainer());
}
public IAtomContainer Reconstruct(string signature)
{
ColoredTree tree = AbstractVertexSignature.Parse(signature);
MoleculeFromSignatureBuilder builder = new MoleculeFromSignatureBuilder(CDK.Builder);
builder.MakeFromColoredTree(tree);
return(builder.GetAtomContainer());
}
/// <summary>
/// Builder for molecules (rather, for atom containers) from signature
/// strings.
/// </summary>
/// <param name="signatureString">the signature string to use</param>
/// <param name="coBuilder"><see cref="IChemObjectBuilder"/> to build the returned atom container from</param>
/// <returns>an atom container</returns>
public static IAtomContainer FromSignatureString(string signatureString, IChemObjectBuilder coBuilder)
{
ColoredTree tree = AtomSignature.Parse(signatureString);
MoleculeFromSignatureBuilder builder = new MoleculeFromSignatureBuilder(coBuilder);
builder.MakeFromColoredTree(tree);
return(builder.GetAtomContainer());
}
public void MakeVertexTest()
{
MoleculeFromSignatureBuilder builder = new MoleculeFromSignatureBuilder(CDK.Builder);
builder.MakeGraph();
builder.MakeVertex("C");
IAtomContainer product = builder.GetAtomContainer();
Assert.AreEqual(1, product.Atoms.Count);
}
public void MakeEdgeTest_tripleBond()
{
MoleculeFromSignatureBuilder builder = new MoleculeFromSignatureBuilder(CDK.Builder);
builder.MakeGraph();
builder.MakeVertex("C");
builder.MakeVertex("C");
builder.MakeEdge(0, 1, "C", "C", "#");
IAtomContainer product = builder.GetAtomContainer();
Assert.AreEqual(2, product.Atoms.Count);
Assert.AreEqual(1, product.Bonds.Count);
Assert.AreEqual(BondOrder.Triple, product.Bonds[0].Order);
}
public void MakeEdgeTest_aromaticBond()
{
MoleculeFromSignatureBuilder builder = new MoleculeFromSignatureBuilder(CDK.Builder);
builder.MakeGraph();
builder.MakeVertex("C");
builder.MakeVertex("C");
builder.MakeEdge(0, 1, "C", "C", "p");
IAtomContainer product = builder.GetAtomContainer();
Assert.AreEqual(2, product.Atoms.Count);
Assert.AreEqual(1, product.Bonds.Count);
IBond bond = product.Bonds[0];
Assert.AreEqual(BondOrder.Single, bond.Order);
Assert.IsTrue(bond.IsAromatic);
}