/// <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 AtomSignatureTest()
{
atomContainer = builder.NewAtomContainer();
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.AddBond(atomContainer.Atoms[0], atomContainer.Atoms[1], BondOrder.Double);
atomSignature = new AtomSignature(0, atomContainer);
}
public void CuneaneCubaneHeightTest()
{
IAtomContainer cuneane = AbstractSignatureTest.MakeCuneane();
IAtomContainer cubane = AbstractSignatureTest.MakeCubane();
int height = 1;
AtomSignature cuneaneSignature = new AtomSignature(0, height, cuneane);
AtomSignature cubaneSignature = new AtomSignature(0, height, cubane);
string cuneaneSigString = cuneaneSignature.ToCanonicalString();
string cubaneSigString = cubaneSignature.ToCanonicalString();
Assert.AreEqual(cuneaneSigString, cubaneSigString);
}
public void ConvertEdgeLabelToColorTest()
{
IAtomContainer ac = MakeBenzene(); // doesn't really matter
AtomSignature atomSignature = new AtomSignature(0, ac);
int aromaticColor = atomSignature.ConvertEdgeLabelToColor("p");
Assert.IsTrue(aromaticColor > 0);
int singleColor = atomSignature.ConvertEdgeLabelToColor("");
int doubleColor = atomSignature.ConvertEdgeLabelToColor("=");
int tripleColor = atomSignature.ConvertEdgeLabelToColor("#");
Assert.IsTrue(singleColor < doubleColor);
Assert.IsTrue(doubleColor < tripleColor);
}
/// <inheritdoc/>
public override string SignatureStringForVertex(int vertexIndex)
{
AtomSignature atomSignature;
int height = base.Height;
if (height == -1)
{
atomSignature = new AtomSignature(vertexIndex, this.molecule);
}
else
{
atomSignature = new AtomSignature(vertexIndex, height, this.molecule);
}
return(atomSignature.ToCanonicalString());
}
public void AllEqualAtHeightTest(IAtomContainer molecule, int height)
{
IDictionary <string, int> sigfreq = new Dictionary <string, int>();
for (int i = 0; i < molecule.Atoms.Count; i++)
{
AtomSignature atomSignature = new AtomSignature(i, height, molecule);
string canonicalSignature = atomSignature.ToCanonicalString();
if (sigfreq.ContainsKey(canonicalSignature))
{
sigfreq[canonicalSignature] = sigfreq[canonicalSignature] + 1;
}
else
{
sigfreq[canonicalSignature] = 1;
}
}
Assert.AreEqual(1, sigfreq.Keys.Count);
}
public void GetAromaticEdgeLabelTest()
{
IAtomContainer benzeneRing = builder.NewAtomContainer();
for (int i = 0; i < 6; i++)
{
benzeneRing.Atoms.Add(builder.NewAtom("C"));
}
for (int i = 0; i < 6; i++)
{
IAtom a = benzeneRing.Atoms[i];
IAtom b = benzeneRing.Atoms[(i + 1) % 6];
IBond bond = builder.NewBond(a, b);
benzeneRing.Bonds.Add(bond);
bond.IsAromatic = true;
}
AtomSignature signature = new AtomSignature(0, benzeneRing);
for (int i = 0; i < 6; i++)
{
Assert.AreEqual("p", signature.GetEdgeLabel(i, (i + 1) % 6), "Failed for " + i);
}
}
/// <inheritdoc/>
public override string SignatureStringForVertex(int vertexIndex, int height)
{
AtomSignature atomSignature = new AtomSignature(vertexIndex, height, this.molecule);
return(atomSignature.ToCanonicalString());
}
