public void TestToString()
{
IAtomContainer triazole = TestMoleculeFactory.Make123Triazole();
ShortestPathWalker walker = new ShortestPathWalker(triazole);
Assert.AreEqual(
"C->C1N->C1N1N->C1N2N->C2C->C2C1N->N->N1C->N1C2C->N1N->N1N1C->N1N2N->N2N->N2N1C->N2N1N",
walker.ToString());
}
public void TestPaths()
{
var triazole = TestMoleculeFactory.Make123Triazole();
var walker = new ShortestPathWalker(triazole);
var expected = new SortedSet <string>(new[] { "C", "N2N1N", "N", "N1N1C", "N1C2C", "C1N", "N2N1C",
"C1N2N", "C1N1N", "N1C", "C2C1N", "C2C", "N2N", "N1N2N", "N1N" });
var actual = walker.GetPaths();
Assert.IsTrue(Compares.AreDeepEqual(expected, actual));
}
/// <summary>
/// Get all paths of lengths 0 to the specified length.
///
/// This method will find all paths upto length N starting from each atom in the molecule and return the unique set
/// of such paths.
/// </summary>
/// <param name="container">The molecule to search</param>
/// <returns>A map of path strings, keyed on themselves</returns>
private static int[] FindPaths(IAtomContainer container)
{
var walker = new ShortestPathWalker(container);
// convert paths to hashes
var paths = new List <int>();
int patternIndex = 0;
foreach (var s in walker.GetPaths())
{
var toHashCode = Strings.GetJavaHashCode(s);
paths.Insert(patternIndex, toHashCode);
patternIndex++;
}
// Add ring information
IRingSet sssr = Cycles.FindEssential(container).ToRingSet();
RingSetManipulator.Sort(sssr);
foreach (var ring in sssr)
{
var toHashCode = Strings.GetJavaHashCode(ring.Atoms.Count.ToString(NumberFormatInfo.InvariantInfo));
paths.Insert(patternIndex, toHashCode);
patternIndex++;
}
// Check for the charges
var l = new List <string>();
foreach (var atom in container.Atoms)
{
var charge = atom.FormalCharge ?? 0;
if (charge != 0)
{
l.Add(atom.Symbol + charge.ToString(NumberFormatInfo.InvariantInfo));
}
}
{
l.Sort();
var toHashCode = Lists.GetHashCode(l);
paths.Insert(patternIndex, toHashCode);
patternIndex++;
}
l = new List <string>();
// atom stereo parity
foreach (var atom in container.Atoms)
{
var st = atom.StereoParity;
if (st != StereoAtomParities.Undefined)
{
l.Add(atom.Symbol + st.ToString(NumberFormatInfo.InvariantInfo));
}
}
{
l.Sort();
var toHashCode = Lists.GetHashCode(l);
paths.Insert(patternIndex, toHashCode);
patternIndex++;
}
if (container.SingleElectrons.Count > 0)
{
var radicalInformation = new StringBuilder();
radicalInformation.Append("RAD: ").Append(container.SingleElectrons.Count);
paths.Insert(patternIndex, Strings.GetJavaHashCode(radicalInformation.ToString()));
patternIndex++;
}
if (container.LonePairs.Count > 0)
{
var lpInformation = new StringBuilder();
lpInformation.Append("LP: ").Append(container.LonePairs.Count);
paths.Insert(patternIndex, Strings.GetJavaHashCode(lpInformation.ToString()));
patternIndex++;
}
return(paths.ToArray());
}