/// <summary>
/// Add a ChargeGroup to the MDMolecule if not already present.
/// </summary>
/// <param name="chargeGroup"><see cref="ChargeGroup"/> to add</param>
public void AddChargeGroup(ChargeGroup chargeGroup)
{
if (chargeGroups == null)
{
chargeGroups = new List <ChargeGroup>();
}
//Check if exists
if (chargeGroups.Contains(chargeGroup))
{
Console.Out.WriteLine("Charge group: " + chargeGroup.GetNumber() + " already present in molecule: " + Id);
return;
}
chargeGroups.Add(chargeGroup);
}
public void TestMDMolecule()
{
MDMolecule mol = new MDMolecule();
mol.Atoms.Add(builder.NewAtom("C")); // 0
mol.Atoms.Add(builder.NewAtom("C")); // 1
mol.Atoms.Add(builder.NewAtom("C")); // 2
mol.Atoms.Add(builder.NewAtom("C")); // 3
mol.Atoms.Add(builder.NewAtom("C")); // 4
mol.Atoms.Add(builder.NewAtom("C")); // 5
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single); // 1
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Double); // 2
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single); // 3
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Double); // 4
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single); // 5
mol.AddBond(mol.Atoms[5], mol.Atoms[0], BondOrder.Double); // 6
//Create 2 residues
var ac = builder.NewAtomContainer();
ac.Atoms.Add(mol.Atoms[0]);
ac.Atoms.Add(mol.Atoms[1]);
ac.Atoms.Add(mol.Atoms[2]);
Residue res1 = new Residue(ac, 0, mol);
res1.Name = "myResidue1";
mol.AddResidue(res1);
var ac2 = builder.NewAtomContainer();
ac2.Atoms.Add(mol.Atoms[3]);
ac2.Atoms.Add(mol.Atoms[4]);
ac2.Atoms.Add(mol.Atoms[5]);
Residue res2 = new Residue(ac2, 1, mol);
res2.Name = "myResidue2";
mol.AddResidue(res2);
//Test residue creation
Assert.AreEqual(res1.GetParentMolecule(), mol);
Assert.AreEqual(res2.GetParentMolecule(), mol);
Assert.AreEqual(res1.Atoms.Count, 3);
Assert.AreEqual(res2.Atoms.Count, 3);
Assert.AreEqual(res1.Name, "myResidue1");
Assert.AreEqual(res2.Name, "myResidue2");
Assert.IsNotNull(mol.GetResidues());
Assert.AreEqual(mol.GetResidues().Count, 2);
Assert.AreEqual(mol.GetResidues()[0], res1);
Assert.AreEqual(mol.GetResidues()[1], res2);
//Create 2 chargegroups
var ac3 = builder.NewAtomContainer();
ac3.Atoms.Add(mol.Atoms[0]);
ac3.Atoms.Add(mol.Atoms[1]);
ChargeGroup chg1 = new ChargeGroup(ac3, 0, mol);
mol.AddChargeGroup(chg1);
var ac4 = builder.NewAtomContainer();
ac4.Atoms.Add(mol.Atoms[2]);
ac4.Atoms.Add(mol.Atoms[3]);
ac4.Atoms.Add(mol.Atoms[4]);
ac4.Atoms.Add(mol.Atoms[5]);
ChargeGroup chg2 = new ChargeGroup(ac4, 1, mol);
mol.AddChargeGroup(chg2);
//Test chargegroup creation
Assert.AreEqual(chg1.GetParentMolecule(), mol);
Assert.AreEqual(chg2.GetParentMolecule(), mol);
Assert.AreEqual(chg1.Atoms.Count, 2);
Assert.AreEqual(chg2.Atoms.Count, 4);
Assert.IsNotNull(mol.GetChargeGroups());
Assert.AreEqual(mol.GetChargeGroups().Count, 2);
Assert.AreEqual(mol.GetChargeGroups()[0], chg1);
Assert.AreEqual(mol.GetChargeGroups()[1], chg2);
}
/// <summary>
/// Create a benzene molecule with 2 residues and 2 charge groups
/// </summary>
/// <returns></returns>
public MDMolecule MakeMDBenzene()
{
MDMolecule mol = new MDMolecule();
mol.Atoms.Add(builder.NewAtom("C")); // 0
mol.Atoms.Add(builder.NewAtom("C")); // 1
mol.Atoms.Add(builder.NewAtom("C")); // 2
mol.Atoms.Add(builder.NewAtom("C")); // 3
mol.Atoms.Add(builder.NewAtom("C")); // 4
mol.Atoms.Add(builder.NewAtom("C")); // 5
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single); // 1
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Double); // 2
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single); // 3
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Double); // 4
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single); // 5
mol.AddBond(mol.Atoms[5], mol.Atoms[0], BondOrder.Double); // 6
//Create 2 residues
var ac = builder.NewAtomContainer();
ac.Atoms.Add(mol.Atoms[0]);
ac.Atoms.Add(mol.Atoms[1]);
ac.Atoms.Add(mol.Atoms[2]);
Residue res1 = new Residue(ac, 0, mol);
res1.Name = "myResidue1";
mol.AddResidue(res1);
var ac2 = builder.NewAtomContainer();
ac2.Atoms.Add(mol.Atoms[3]);
ac2.Atoms.Add(mol.Atoms[4]);
ac2.Atoms.Add(mol.Atoms[5]);
Residue res2 = new Residue(ac2, 1, mol);
res2.Name = "myResidue2";
mol.AddResidue(res2);
//Create 2 chargegroups
var ac3 = builder.NewAtomContainer();
ac3.Atoms.Add(mol.Atoms[0]);
ac3.Atoms.Add(mol.Atoms[1]);
ChargeGroup chg1 = new ChargeGroup(ac3, 2, mol);
chg1.SetSwitchingAtom(mol.Atoms[1]);
mol.AddChargeGroup(chg1);
var ac4 = builder.NewAtomContainer();
ac4.Atoms.Add(mol.Atoms[2]);
ac4.Atoms.Add(mol.Atoms[3]);
ac4.Atoms.Add(mol.Atoms[4]);
ac4.Atoms.Add(mol.Atoms[5]);
ChargeGroup chg2 = new ChargeGroup(ac4, 3, mol);
chg2.SetSwitchingAtom(mol.Atoms[4]);
mol.AddChargeGroup(chg2);
return(mol);
}