public void TestNewStrand()
{
IChemObjectBuilder builder = RootObject.Builder;
IStrand strand = builder.NewStrand();
Assert.IsNotNull(strand);
}
/// <summary>
/// Creates a BioPolymer from a sequence of amino acid as identified by a
/// the sequence of their one letter codes. It uses the given <see cref="IChemObjectBuilder"/>
/// to create a data model.
/// </summary>
/// <example>
/// For example:
/// <code>
/// IBioPolymer protein = ProteinBuilderTool.CreateProtein("GAGA", Silent.ChemObjectBuilder.Instance);
/// </code>
/// </example>
/// <seealso cref="CreateProtein(string)"/>
public static IBioPolymer CreateProtein(string sequence, IChemObjectBuilder builder)
{
var templates = AminoAcids.MapBySingleCharCode;
var protein = builder.NewBioPolymer();
var strand = builder.NewStrand();
IAminoAcid previousAA = null;
for (int i = 0; i < sequence.Length; i++)
{
string aminoAcidCode = "" + sequence[i];
Debug.WriteLine($"Adding AA: {aminoAcidCode}");
if (string.Equals(aminoAcidCode, " ", StringComparison.Ordinal))
{
// fine, just skip spaces
}
else
{
IAminoAcid aminoAcid = templates[aminoAcidCode];
if (aminoAcid == null)
{
throw new CDKException("Cannot build sequence! Unknown amino acid: " + aminoAcidCode);
}
aminoAcid = (IAminoAcid)aminoAcid.Clone();
aminoAcid.MonomerName = aminoAcidCode + i;
Debug.WriteLine($"protein: {protein}");
Debug.WriteLine($"strand: {strand}");
AddAminoAcidAtCTerminus(protein, aminoAcid, strand, previousAA);
previousAA = aminoAcid;
}
}
// add the last oxygen of the protein
var oxygen = builder.NewAtom("O");
// ... to amino acid
previousAA.Atoms.Add(oxygen);
var bond = builder.NewBond(oxygen, previousAA.CTerminus, BondOrder.Single);
previousAA.Bonds.Add(bond);
// ... and to protein
protein.AddAtom(oxygen, previousAA, strand);
protein.Bonds.Add(bond);
return(protein);
}