public void TestRemoveMolecule()
{
Debug.WriteLine("***TestRemoveMolecule***");
bool itIsInThere = false;
TemplateHandler th = new TemplateHandler();
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
sdg.Molecule = mol;
sdg.GenerateCoordinates();
mol = sdg.Molecule;
var smiles = "C1=C(C)C2CC(C1)C2(C)(C)";
var smilesMol = sp.ParseSmiles(smiles);
itIsInThere = th.MapTemplates(smilesMol);
Debug.WriteLine($"Alpha-Pinene found by templateMapper: {itIsInThere}");
Assert.IsFalse(itIsInThere);
th.AddMolecule(mol);
Debug.WriteLine("now adding template for alpha-Pinen and trying again.");
itIsInThere = th.MapTemplates(smilesMol);
Debug.WriteLine($"Alpha-Pinene found by templateMapper: {itIsInThere}");
Assert.IsTrue(itIsInThere);
Debug.WriteLine("now removing template for alpha-Pinen again and trying again.");
th.RemoveMolecule(mol);
itIsInThere = th.MapTemplates(smilesMol);
Debug.WriteLine($"Alpha-Pinene found by templateMapper: {itIsInThere}");
Assert.IsFalse(itIsInThere);
}
/// <summary>
/// Singleton template instance, mainly useful for aligning molecules.
/// </summary>
/// <remarks>
/// If the template does not have coordinates an error is thrown.
/// For safety we clone the molecule.
/// </remarks>
/// <param name="template">the molecule</param>
/// <returns>new template handler</returns>
public static TemplateHandler CreateSingleton(IAtomContainer template)
{
var handler = new TemplateHandler();
var copy = (IAtomContainer)template.Clone();
handler.AddMolecule(copy);
return(handler);
}
public void TestDetection()
{
TemplateHandler th = new TemplateHandler();
var smiles = "CC12C3(C6CC6)C4(C)C1C5(C(CC)C)C(C(CC)C)2C(C)3C45CC(C)C";
var mol = sp.ParseSmiles(smiles);
Assert.IsTrue(th.MapTemplates(mol));
}
public void TestOtherBondOrder()
{
bool itIsInThere = false;
TemplateHandler th = new TemplateHandler();
IAtomContainer mol = TestMoleculeFactory.MakeSteran();
itIsInThere = th.MapTemplates(mol);
Assert.IsTrue(itIsInThere);
mol.Bonds[0].Order = BondOrder.Double;
itIsInThere = th.MapTemplates(mol);
Assert.IsTrue(itIsInThere);
}
public void TestOtherElements()
{
bool itIsInThere = false;
TemplateHandler th = new TemplateHandler();
IAtomContainer mol = TestMoleculeFactory.MakeSteran();
itIsInThere = th.MapTemplates(mol);
Assert.IsTrue(itIsInThere);
mol.Atoms[0].Symbol = "N";
itIsInThere = th.MapTemplates(mol);
Assert.IsTrue(itIsInThere);
}
public void Convert()
{
var templateHandler = new TemplateHandler();
using (var bout = new MemoryStream())
{
templateHandler.ToIdentityTemplateLibrary().Store(bout);
Assert.AreEqual(
"C1C2CC3CC1CC(C2)C3 |(-1.07,-1.59,;.38,-1.21,;1.82,-1.59,;1.07,-.29,;-.38,-.67,;-1.82,-.29,;-1.82,1.21,;-.37,1.59,;.38,.29,;1.07,1.21,)|\n"
+ "C12C3C4C1C5C2C3C45 |(.62,-.99,;-.88,-1.12,;-1.23,.43,;.26,.57,;.88,1.12,;1.23,-.43,;-.26,-.57,;-.62,.98,)|\n"
+ "C1C2CC3C4CC5CC(C14)C(C2)C3C5 |(-1.82,2.15,;-.37,2.53,;1.07,2.15,;1.07,.65,;-.38,.27,;-.38,-1.23,;.37,-2.53,;-1.07,-2.15,;-1.07,-.65,;-1.82,.65,;.38,-.27,;.38,1.23,;1.82,-.65,;1.82,-2.15,)|\n"
+ "C1CCC2C(C1)CCC3C4CCCC4CCC23 |(-6.51,.72,;-6.51,-.78,;-5.22,-1.53,;-3.92,-.78,;-3.92,.72,;-5.22,1.47,;-2.62,1.47,;-1.32,.72,;-1.32,-.78,;-.02,-1.53,;1.41,-1.07,;2.29,-2.28,;1.41,-3.49,;-.02,-3.03,;-1.32,-3.78,;-2.62,-3.03,;-2.62,-1.53,)|\n"
+ "C1CCCCCCCCCCCCC1 |(-.04,1.51,;1.26,.76,;1.26,-.74,;2.56,-1.49,;2.56,-2.99,;1.29,-3.72,;1.31,-5.29,;-.09,-5.89,;-1.34,-5.24,;-1.34,-3.74,;-2.63,-2.99,;-2.63,-1.49,;-1.34,-.74,;-1.34,.76,)|\n",
System.Text.Encoding.UTF8.GetString(bout.ToArray()));
}
}
/// <summary>
/// Loads a molecule with two adamantanes and one cubane
/// substructure and tests whether all are found.
/// </summary>
public void GetMappedSubstructures_IAtomContainer()
{
// Set up molecule reader
var filename = "NCDK.Data.MDL.diadamantane-cubane.mol";
var ins = ResourceLoader.GetAsStream(filename);
var molReader = new MDLReader(ins, ChemObjectReaderMode.Strict);
// Read molecule
var molecule = molReader.Read(builder.NewAtomContainer());
// Map templates
var th = new TemplateHandler();
var mappedStructures = th.GetMappedSubstructures(molecule);
// Do the Assert.assertion
Assert.AreEqual(3, mappedStructures.Count, "3 mapped templates");
}
public void TestInit()
{
TemplateHandler th = new TemplateHandler();
Assert.AreEqual(5, th.TemplateCount);
}