public void BuckyballTest()
{
var mol = MoleculeReader.ReadMolfile("NCDK.FaulonSignatures.Data.buckyball.mol");
var mqg = new MoleculeQuotientGraph(mol);
Console.Out.WriteLine(mqg);
Assert.AreEqual(32, mqg.GetVertexCount());
Assert.AreEqual(49, mqg.GetEdgeCount());
Assert.AreEqual(6, mqg.NumberOfLoopEdges());
}
public void TestLargeExample()
{
var filename = "NCDK.FaulonSignatures.Data.large_example.sdf";
foreach (var molecule in MoleculeReader.ReadSDFFile(filename))
{
MoleculeSignature signature = new MoleculeSignature(molecule);
Console.Out.WriteLine(signature.GetGraphSignature());
}
}
public void TestSDF()
{
var filename = "NCDK.FaulonSignatures.Data.test.sdf";
int molNr = 0;
foreach (var molecule in MoleculeReader.ReadSDFFile(filename))
{
Console.Out.WriteLine(++molNr);
MoleculeSignature signature = new MoleculeSignature(molecule);
Console.Out.WriteLine(signature.GetGraphSignature());
//Console.Out.WriteLine(signature.GetVertexSignature(0));
}
}
public void BuckyballWithoutMultipleBonds()
{
var mol = MoleculeReader.ReadMolfile("NCDK.FaulonSignatures.Data.buckyball.mol");
foreach (Molecule.Bond bond in mol.Bonds())
{
bond.order = Molecule.BondOrder.Single;
}
var mqg = new MoleculeQuotientGraph(mol);
Console.Out.WriteLine(mqg);
Assert.AreEqual(1, mqg.GetVertexCount());
Assert.AreEqual(1, mqg.GetEdgeCount());
Assert.AreEqual(1, mqg.NumberOfLoopEdges());
}
public void TestCanonicalLabelling()
{
var filename = "NCDK.FaulonSignatures.Data.multCycle.sdf";
foreach (var molecule in MoleculeReader.ReadSDFFile(filename))
{
MoleculeSignature signature = new MoleculeSignature(molecule);
Console.Out.WriteLine(molecule.GetAtomCount());
Assert.AreEqual(false, signature.IsCanonicallyLabelled());
}
string filenameCanLabel = "NCDK.FaulonSignatures.Data.multCycleCanLabel.sdf";
foreach (var molecule in MoleculeReader.ReadSDFFile(filenameCanLabel))
{
MoleculeSignature signatureCanLabel = new MoleculeSignature(molecule);
Assert.AreEqual(true, signatureCanLabel.IsCanonicallyLabelled());
}
}
/// <summary>
/// Read a list of Molecule from an InputStream, providing SDFile contents
/// </summary>
/// <param name="stream">InputStream to read from</param>
/// <returns>List of Molecules</returns>
public static List <Molecule> ReadSDFfromStream(Stream stream)
{
List <Molecule> molecules = new List <Molecule>();
try
{
using (var reader = new StreamReader(stream))
{
string line;
int i = 0;
var block = new List <string>();
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith("$$$$", StringComparison.Ordinal))
{
Molecule molecule;
try
{
molecule = MoleculeReader.MakeMolecule(block);
molecules.Add(molecule);
}
catch (Exception e)
{
Console.Error.WriteLine("failed for block " + i + " " + e);
Console.Error.WriteLine(e.StackTrace);
}
block.Clear();
i++;
}
else
{
block.Add(line);
}
}
}
}
catch (IOException ioe)
{
Console.Error.WriteLine(ioe.ToString());
}
return(molecules);
}
public void FaulonsBuckySignatures()
{
var mol = MoleculeReader.ReadMolfile("data/buckyball.mol");
try
{
var filename = "data/buckysigs3.txt";
var sigs = ReadSigs2(filename);
var mqg = new MoleculeQuotientGraph(mol, sigs);
Console.Out.WriteLine(mqg);
Assert.AreEqual(32, mqg.GetVertexCount());
Assert.AreEqual(49, mqg.GetEdgeCount());
Assert.AreEqual(6, mqg.NumberOfLoopEdges());
}
catch (Exception e)
{
Console.Out.WriteLine(e);
return;
}
}
public static void Main(string[] args)
{
if (args.Length < 1)
{
Console.Out.WriteLine("Usage : SDFToSignatures <filename>");
}
string filename = args[0];
int molCount = 0;
foreach (var molecule in MoleculeReader.ReadSDFFile(filename))
{
try
{
molCount++;
Console.Out.WriteLine("Current molecule: " + molCount);
MoleculeSignature signature = new MoleculeSignature(molecule);
// get graph signature
Console.Out.WriteLine(signature.GetGraphSignature());
}
catch (Exception) { }
}
}