public void TestAlign()
{
{
IAtomContainer ac;
var filename = "NCDK.Data.HIN.gravindex.hin";
var ins = ResourceLoader.GetAsStream(filename);
ISimpleChemObjectReader reader = new HINReader(ins);
ChemFile content = (ChemFile)reader.Read((ChemObject) new ChemFile());
var cList = ChemFileManipulator.GetAllAtomContainers(content);
ac = cList.First();
KabschAlignment ka = new KabschAlignment(ac, ac);
Assert.IsNotNull(ka);
ka.Align();
double rmsd = ka.RMSD;
Assert.IsTrue(1e-8 > rmsd);
Assert.IsNotNull(ka.RotationMatrix);
}
{
double[][] p1 = new[] { new[] { 16.754, 20.462, 45.049 }, new[] { 19.609, 18.145, 46.011 }, new[] { 17.101, 17.256, 48.707 },
new[] { 13.963, 18.314, 46.820 }, new[] { 14.151, 15.343, 44.482 }, new[] { 14.959, 12.459, 46.880 }, new[] { 11.987, 13.842, 48.862 },
new[] { 9.586, 12.770, 46.123 }, new[] { 11.006, 9.245, 46.116 }, new[] { 10.755, 9.090, 49.885 } };
double[][] p2 = new[] { new[] { 70.246, 317.510, 188.263 }, new[] { 73.457, 317.369, 190.340 }, new[] { 71.257, 318.976, 193.018 },
new[] { 68.053, 317.543, 191.651 }, new[] { 68.786, 313.954, 192.637 }, new[] { 70.248, 314.486, 196.151 },
new[] { 67.115, 316.584, 196.561 }, new[] { 64.806, 313.610, 196.423 }, new[] { 66.804, 311.735, 199.035 },
new[] { 66.863, 314.832, 201.113 } };
Atom[] a1 = new Atom[10];
Atom[] a2 = new Atom[10];
for (int i = 0; i < 10; i++)
{
a1[i] = new Atom("C");
Vector3 newCoord = new Vector3
{
X = p1[i][0],
Y = p1[i][1],
Z = p1[i][2]
};
a1[i].Point3D = newCoord;
a2[i] = new Atom("C");
newCoord = new Vector3
{
X = p2[i][0],
Y = p2[i][1],
Z = p2[i][2]
};
a2[i].Point3D = newCoord;
}
var ka = new KabschAlignment(a1, a2);
ka.Align();
var rmsd = ka.RMSD;
Assert.AreEqual(0.13479726, rmsd, 0.00000001);
}
}
public static void Main()
{
{
#region
var ac1 = new AtomContainer(); // molecule 1
var ac2 = new AtomContainer(); // molecule 2
try
{
KabschAlignment sa = new KabschAlignment(ac1.Atoms, ac2.Atoms);
sa.Align();
Console.Out.WriteLine(sa.RMSD);
}
catch (CDKException) { }
#endregion
}
{
#region substructure
AtomContainer ac1 = new AtomContainer(); // whole molecules
AtomContainer ac2 = new AtomContainer(); //
IAtom[] a1 = ac1.Atoms.ToArray(); // some subsets of atoms from the two molecules
IAtom[] a2 = ac2.Atoms.ToArray(); //
try
{
var sa = new KabschAlignment(a1, a2);
sa.Align();
var cm1 = sa.CenterOfMass;
foreach (var a in ac1.Atoms)
{
a.Point3D = a.Point3D.Value - cm1;
}
sa.RotateAtomContainer(ac2);
// display the two AtomContainer's
}
catch (CDKException) { }
#endregion
}
}