public override void TestGetMonomerCount()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
Assert.AreEqual(0, oBioPolymer.GetMonomerMap().Count());
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IStrand oStrand2 = oBioPolymer.Builder.NewStrand();
oStrand2.StrandName = "B";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oBioPolymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom3 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.Atoms.Add(oAtom1);
oBioPolymer.AddAtom(oAtom2, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom3, oMono2, oStrand2);
Assert.IsNotNull(oBioPolymer.Atoms[0]);
Assert.IsNotNull(oBioPolymer.Atoms[1]);
Assert.IsNotNull(oBioPolymer.Atoms[2]);
Assert.AreEqual(oAtom1, oBioPolymer.Atoms[0]);
Assert.AreEqual(oAtom2, oBioPolymer.Atoms[1]);
Assert.AreEqual(oAtom3, oBioPolymer.Atoms[2]);
Assert.AreEqual(2, oBioPolymer.GetMonomerMap().Count());
}
public void TestCreateProtein()
{
IBioPolymer protein = ProteinBuilderTool.CreateProtein("GAGA", CDK.Builder);
Assert.IsNotNull(protein);
Assert.AreEqual(4, protein.GetMonomerMap().Count());
Assert.AreEqual(1, protein.GetStrandMap().Count());
Assert.AreEqual(18 + 1, protein.Atoms.Count);
// 1=terminal oxygen
Assert.AreEqual(14 + 3 + 1, protein.Bonds.Count);
// 3 = extra back bone bonds, 1=bond to terminal oxygen
}
/// <summary>
/// Builds a protein by connecting a new amino acid at the C-terminus of the
/// given strand. The acidic oxygen of the added amino acid is removed so that
/// additional amino acids can be added savely. But this also means that you
/// might want to add an oxygen at the end of the protein building!
/// </summary>
/// <param name="protein">protein to which the strand belongs</param>
/// <param name="aaToAdd">amino acid to add to the strand of the protein</param>
/// <param name="strand">strand to which the protein is added</param>
/// <param name="aaToAddTo"></param>
public static IBioPolymer AddAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo)
{
// then add the amino acid
AddAminoAcid(protein, aaToAdd, strand);
// Now think about the protein back bone connection
if (protein.GetMonomerMap().Any() && (aaToAddTo != null))
{
// make the connection between that aminoAcid's N-terminus and the
// protein's C-terminus
protein.Bonds.Add(aaToAdd.Builder.NewBond(aaToAddTo.CTerminus,
aaToAdd.NTerminus, BondOrder.Single));
} // else : no current C-terminus, so nothing special to do
return(protein);
}
