void Main()
{
#region
IAtomContainer container = TestMoleculeFactory.MakeAlphaPinene();
HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
hydrogenPlacer.PlaceHydrogens2D(container, 1.5);
#endregion
}
public void TestNoConnections()
{
var hydrogenPlacer = new HydrogenPlacer();
var container = builder.NewAtomContainer();
var atom = builder.NewAtom("C", new Vector2(0, 0));
container.Atoms.Add(atom);
hydrogenPlacer.PlaceHydrogens2D(container, atom, 1.5);
}
public void UnPlacedNonHydrogen()
{
var hydrogenPlacer = new HydrogenPlacer();
// c2 is unplaced
var c1 = builder.NewAtom("C", Vector2.Zero);
var c2 = builder.NewAtom("C");
var m = builder.NewAtomContainer();
m.Atoms.Add(c1);
m.Atoms.Add(c2);
m.Bonds.Add(builder.NewBond(c1, c2));
hydrogenPlacer.PlaceHydrogens2D(m, 1.5);
}
public void TestH2()
{
var hydrogenPlacer = new HydrogenPlacer();
// h1 has no coordinates
var h1 = builder.NewAtom("H");
var h2 = builder.NewAtom("H", Vector2.Zero);
var m = builder.NewAtomContainer();
m.Atoms.Add(h1);
m.Atoms.Add(h2);
m.Bonds.Add(builder.NewBond(h1, h2));
hydrogenPlacer.PlaceHydrogens2D(m, 1.5);
Assert.IsNotNull(h1.Point2D);
}
public void TestBug933572()
{
var ac = builder.NewAtomContainer();
ac.Atoms.Add(builder.NewAtom("H"));
ac.Atoms[0].Point2D = Vector2.Zero;
AddExplicitHydrogens(ac);
var hPlacer = new HydrogenPlacer();
hPlacer.PlaceHydrogens2D(ac, 36);
for (int i = 0; i < ac.Atoms.Count; i++)
{
Assert.IsNotNull(ac.Atoms[i].Point2D);
}
}
/// <summary>
/// This one tests adding hydrogens to all atoms of a molecule and doing the
/// layout for them. It is intended for visually checking the work of
/// HydrogenPlacer, not to be run as a JUnit test. Thus the name without
/// "test".
/// </summary>
public void VisualFullMolecule2DEvaluation()
{
var hydrogenPlacer = new HydrogenPlacer();
var filename = "NCDK.Data.MDL.reserpine.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins, ChemObjectReaderMode.Strict);
var chemFile = reader.Read(builder.NewChemFile());
var seq = chemFile[0];
var model = seq[0];
var mol = model.MoleculeSet[0];
var bondLength = GeometryUtil.GetBondLengthAverage(mol);
Debug.WriteLine("Read Reserpine");
Debug.WriteLine("Starting addition of H's");
AddExplicitHydrogens(mol);
Debug.WriteLine("ended addition of H's");
hydrogenPlacer.PlaceHydrogens2D(mol, bondLength);
}
public void TestPlaceHydrogens2D()
{
var hydrogenPlacer = new HydrogenPlacer();
var dichloromethane = builder.NewAtomContainer();
var carbon = builder.NewAtom("C");
var carbonPos = new Vector2(0.0, 0.0);
carbon.Point2D = carbonPos;
var h1 = builder.NewAtom("H");
var h2 = builder.NewAtom("H");
var cl1 = builder.NewAtom("Cl");
var cl1Pos = new Vector2(0.0, -1.0);
cl1.Point2D = cl1Pos;
var cl2 = builder.NewAtom("Cl");
var cl2Pos = new Vector2(-1.0, 0.0);
cl2.Point2D = cl2Pos;
dichloromethane.Atoms.Add(carbon);
dichloromethane.Atoms.Add(h1);
dichloromethane.Atoms.Add(h2);
dichloromethane.Atoms.Add(cl1);
dichloromethane.Atoms.Add(cl2);
dichloromethane.Bonds.Add(builder.NewBond(carbon, h1));
dichloromethane.Bonds.Add(builder.NewBond(carbon, h2));
dichloromethane.Bonds.Add(builder.NewBond(carbon, cl1));
dichloromethane.Bonds.Add(builder.NewBond(carbon, cl2));
Assert.IsNull(h1.Point2D);
Assert.IsNull(h2.Point2D);
// generate new coords
hydrogenPlacer.PlaceHydrogens2D(dichloromethane, carbon);
// check that previously set coordinates are kept
Assert.IsTrue(Vector2.Distance(carbonPos, carbon.Point2D.Value) < 0.01);
Assert.IsTrue(Vector2.Distance(cl1Pos, cl1.Point2D.Value) < 0.01);
Assert.IsTrue(Vector2.Distance(cl2Pos, cl2.Point2D.Value) < 0.01);
Assert.IsNotNull(h1.Point2D);
Assert.IsNotNull(h2.Point2D);
}
public void TestNullContainer()
{
var hydrogenPlacer = new HydrogenPlacer();
hydrogenPlacer.PlaceHydrogens2D(null, builder.NewAtom(), 1.5);
}
public void TestAtomWithoutCoordinates()
{
var hydrogenPlacer = new HydrogenPlacer();
hydrogenPlacer.PlaceHydrogens2D(builder.NewAtomContainer(), builder.NewAtom(), 1.5);
}