public void TestAdd3DCoordinatesForSinglyBondedLigands_IAtomContainer()
{
IAtom atom1 = new Atom("C")
{
Point3D = new Vector3(1, 1, 1)
};
IAtom atom2 = new Atom("H");
IAtom atom3 = new Atom("H");
IAtom atom4 = new Atom("H");
IAtom atom5 = new Atom("H");
IBond bond1 = new Bond(atom1, atom2);
IBond bond2 = new Bond(atom1, atom3);
IBond bond3 = new Bond(atom1, atom4);
IBond bond4 = new Bond(atom1, atom5);
IAtomContainer ac = atom1.Builder.NewAtomContainer();
atom1.FormalNeighbourCount = 4;
atom2.FormalNeighbourCount = 1;
atom3.FormalNeighbourCount = 1;
atom4.FormalNeighbourCount = 1;
atom5.FormalNeighbourCount = 1;
ac.Atoms.Add(atom1);
ac.Atoms.Add(atom2);
ac.Atoms.Add(atom3);
ac.Atoms.Add(atom4);
ac.Atoms.Add(atom5);
ac.Bonds.Add(bond1);
ac.Bonds.Add(bond2);
ac.Bonds.Add(bond3);
ac.Bonds.Add(bond4);
new AtomTetrahedralLigandPlacer3D().Add3DCoordinatesForSinglyBondedLigands(ac);
ModelBuilder3DTest.CheckAverageBondLength(ac);
}
public void TestGet3DCoordinatesForLigands_IAtom_IAtomContainer_IAtomContainer_IAtom_int_Double_double()
{
IAtom atom1 = new Atom("C")
{
Point3D = new Vector3(1, 1, 1)
};
IAtom atom2 = new Atom("H");
IAtom atom3 = new Atom("H");
IAtom atom4 = new Atom("H");
IAtom atom5 = new Atom("H");
IBond bond1 = new Bond(atom1, atom2);
IBond bond2 = new Bond(atom1, atom3);
IBond bond3 = new Bond(atom1, atom4);
IBond bond4 = new Bond(atom1, atom5);
IAtomContainer ac = atom1.Builder.NewAtomContainer();
ac.Atoms.Add(atom1);
ac.Atoms.Add(atom2);
ac.Atoms.Add(atom3);
ac.Atoms.Add(atom4);
ac.Atoms.Add(atom5);
atom1.FormalNeighbourCount = 4;
atom2.FormalNeighbourCount = 1;
atom3.FormalNeighbourCount = 1;
atom4.FormalNeighbourCount = 1;
atom5.FormalNeighbourCount = 1;
ac.Bonds.Add(bond1);
ac.Bonds.Add(bond2);
ac.Bonds.Add(bond3);
ac.Bonds.Add(bond4);
IAtomContainer noCoords = AtomTetrahedralLigandPlacer3D.GetUnsetAtomsInAtomContainer(atom1, ac);
IAtomContainer withCoords = AtomTetrahedralLigandPlacer3D.GetPlacedAtomsInAtomContainer(atom1, ac);
var placer = new AtomTetrahedralLigandPlacer3D();
Vector3[] newPoints = placer.Get3DCoordinatesForLigands(atom1, noCoords, withCoords, null, 4, placer.DefaultBondLengthH, -1);
for (int j = 0; j < noCoords.Atoms.Count; j++)
{
if (newPoints[j] == null)
{
Assert.Fail("No coordinates generated for atom " + j);
}
IAtom ligand = noCoords.Atoms[j];
ligand.Point3D = newPoints[j];
}
ModelBuilder3DTest.CheckAverageBondLength(ac);
}
public void TestMapTemplates_IAtomContainer_Double()
{
var ac = TestMoleculeFactory.MakeBicycloRings();
var th3d = TemplateHandler3D.Instance;
var ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mm2");
var ringSetMolecule = ffc.AssignAtomTyps(ac);
var ringSystems = RingPartitioner.PartitionRings(ringSetMolecule);
var largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
var largestRingSetContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
th3d.MapTemplates(largestRingSetContainer, largestRingSetContainer.Atoms.Count);
for (int i = 0; i < ac.Atoms.Count; i++)
{
Assert.IsNotNull(ac.Atoms[i].Point3D);
}
ModelBuilder3DTest.CheckAverageBondLength(ac);
}