public override void TestToString()
{
IAminoAcid m = (IAminoAcid)NewChemObject();
IAtom nTerminus = m.Builder.NewAtom("N");
m.AddNTerminus(nTerminus);
string description = m.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
m = (IAminoAcid)NewChemObject();
IAtom cTerminus = m.Builder.NewAtom("C");
m.AddCTerminus(cTerminus);
description = m.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
public void TestNewAminoAcid()
{
IChemObjectBuilder builder = RootObject.Builder;
IAminoAcid aa = builder.NewAminoAcid();
Assert.IsNotNull(aa);
}
/// <summary>
/// Removes the singly bonded oxygen from the acid group of the AminoAcid.
/// </summary>
/// <param name="acid">AminoAcid from which to remove the oxygen</param>
/// <exception cref="CDKException">when the C-terminus is not defined for the given AminoAcid</exception>
public static void RemoveAcidicOxygen(IAminoAcid acid)
{
if (acid.CTerminus == null)
{
throw new CDKException("Cannot remove oxygen: C-terminus is not defined!");
}
var atomsToRemove = new List <IAtom>();
// ok, look for the oxygen which is singly bonded
foreach (var bond in acid.GetConnectedBonds(acid.CTerminus))
{
if (bond.Order == BondOrder.Single)
{
for (int j = 0; j < bond.Atoms.Count; j++)
{
if (bond.Atoms[j].AtomicNumber.Equals(AtomicNumbers.O))
{
// yes, we found a singly bonded oxygen!
atomsToRemove.Add(bond.Atoms[j]);
}
}
}
}
foreach (var atom in atomsToRemove)
{
acid.RemoveAtom(atom);
}
}
/// <summary> Removes the singly bonded oxygen from the acid group of the AminoAcid.
///
/// </summary>
/// <param name="acid">AminoAcid from which to remove the oxygen
/// </param>
/// <throws> CDKException when the C-terminus is not defined for the given AminoAcid </throws>
public static void removeAcidicOxygen(IAminoAcid acid)
{
if (acid.getCTerminus() == null)
{
throw new CDKException("Cannot remove oxygen: C-terminus is not defined!");
}
IBond[] bonds = acid.getConnectedBonds(acid.getCTerminus());
// ok, look for the oxygen which is singly bonded
for (int i = 0; i < bonds.Length; i++)
{
if (bonds[i].Order == CDKConstants.BONDORDER_SINGLE)
{
IAtom[] atoms = bonds[i].getAtoms();
for (int j = 0; j < atoms.Length; j++)
{
if (atoms[j].Symbol.Equals("O"))
{
// yes, we found a singly bonded oxygen!
acid.removeAtomAndConnectedElectronContainers(atoms[j]);
}
}
}
}
}
/// <summary> Adds the singly bonded oxygen from the acid group of the AminoAcid.
///
/// </summary>
/// <param name="acid"> AminoAcid to which to add the oxygen
/// </param>
/// <throws> CDKException when the C-terminus is not defined for the given AminoAcid </throws>
public static void addAcidicOxygen(IAminoAcid acid)
{
if (acid.getCTerminus() == null)
throw new CDKException("Cannot add oxygen: C-terminus is not defined!");
acid.addBond(acid.Builder.newBond(acid.getCTerminus(), acid.Builder.newAtom("O"), CDKConstants.BONDORDER_SINGLE));
}
public virtual void TestAddNTerminus_IAtom()
{
IAminoAcid m = (IAminoAcid)NewChemObject();
IAtom nTerminus = m.Builder.NewAtom("N");
m.AddNTerminus(nTerminus);
Assert.AreEqual(nTerminus, m.NTerminus);
}
/// <summary> Adds the singly bonded oxygen from the acid group of the AminoAcid.
///
/// </summary>
/// <param name="acid"> AminoAcid to which to add the oxygen
/// </param>
/// <throws> CDKException when the C-terminus is not defined for the given AminoAcid </throws>
public static void addAcidicOxygen(IAminoAcid acid)
{
if (acid.getCTerminus() == null)
{
throw new CDKException("Cannot add oxygen: C-terminus is not defined!");
}
acid.addBond(acid.Builder.newBond(acid.getCTerminus(), acid.Builder.newAtom("O"), CDKConstants.BONDORDER_SINGLE));
}
public void TestRemoveAcidicOxygen_IAminoAcid()
{
IAminoAcid glycine = builder.NewAminoAcid();
glycine.Add(CDK.SmilesParser.ParseSmiles("C(C(=O)O)N"));
Assert.AreEqual(5, glycine.Atoms.Count);
glycine.AddCTerminus(glycine.Atoms[1]);
AminoAcidManipulator.RemoveAcidicOxygen(glycine);
Assert.AreEqual(4, glycine.Atoms.Count);
}
public void TestAddAcidicOxygen_IAminoAcid()
{
// FIXME: I think this is the proper test, but it currently fails
IAminoAcid glycine = builder.NewAminoAcid();
glycine.Add(CDK.SmilesParser.ParseSmiles("C(C=O)N"));
Assert.AreEqual(4, glycine.Atoms.Count);
glycine.AddCTerminus(glycine.Atoms[1]);
AminoAcidManipulator.AddAcidicOxygen(glycine);
Assert.AreEqual(5, glycine.Atoms.Count);
}
private static IBioPolymer AddAminoAcid(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand)
{
foreach (var atom in aaToAdd.Atoms)
{
protein.AddAtom(atom, aaToAdd, strand);
}
foreach (var bond in aaToAdd.Bonds)
{
protein.Bonds.Add(bond);
}
return(protein);
}
/// <summary>
/// Adds the singly bonded oxygen from the acid group of the AminoAcid.
/// </summary>
/// <param name="acid">AminoAcid to which to add the oxygen</param>
/// <exception cref="CDKException">when the C-terminus is not defined for the given AminoAcid</exception>
public static void AddAcidicOxygen(IAminoAcid acid)
{
if (acid.CTerminus == null)
{
throw new CDKException("Cannot add oxygen: C-terminus is not defined!");
}
IAtom acidicOxygen = acid.Builder.NewAtom("O");
acid.Atoms.Add(acidicOxygen);
acid.Bonds.Add(acid.Builder.NewBond(acid.CTerminus, acidicOxygen, BondOrder.Single));
}
/// <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);
}
/// <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);
}
public static Protein ToProtein(ISequence <INucleobase> nucleobaseChain)
{
Debug.Assert(nucleobaseChain.Count % 3 == 0);
var protein = new Protein();
IEnumerator <INucleobase> enumerator = nucleobaseChain.GetEnumerator();
while (enumerator.MoveNext())
{
INucleobase nb1 = enumerator.Current;
enumerator.MoveNext();
INucleobase nb2 = enumerator.Current;
enumerator.MoveNext();
INucleobase nb3 = enumerator.Current;
IAminoAcid aa = ToAminoAcid(nb1, nb2, nb3);
protein.Add(aa);
}
return(protein);
}
public RepeatedAcid(IAminoAcid aminoAcid, string times)
{
this.aminoAcid = aminoAcid;
if (times.StartsWith("(") && times.EndsWith(")"))
{
string withoutBrackets = times.Substring(1, times.Length - 2);
if (withoutBrackets.Contains(",")) //"(1,2)
{
var numbers = withoutBrackets.Split(',');
from = int.Parse(numbers[0]);
to = int.Parse(numbers[1]);
}
else // "(1)"
{
to = from = int.Parse(withoutBrackets);
}
}
else //""
{
from = to = 1;
}
}
/// <summary> Removes the singly bonded oxygen from the acid group of the AminoAcid.
///
/// </summary>
/// <param name="acid">AminoAcid from which to remove the oxygen
/// </param>
/// <throws> CDKException when the C-terminus is not defined for the given AminoAcid </throws>
public static void removeAcidicOxygen(IAminoAcid acid)
{
if (acid.getCTerminus() == null)
throw new CDKException("Cannot remove oxygen: C-terminus is not defined!");
IBond[] bonds = acid.getConnectedBonds(acid.getCTerminus());
// ok, look for the oxygen which is singly bonded
for (int i = 0; i < bonds.Length; i++)
{
if (bonds[i].Order == CDKConstants.BONDORDER_SINGLE)
{
IAtom[] atoms = bonds[i].getAtoms();
for (int j = 0; j < atoms.Length; j++)
{
if (atoms[j].Symbol.Equals("O"))
{
// yes, we found a singly bonded oxygen!
acid.removeAtomAndConnectedElectronContainers(atoms[j]);
}
}
}
}
}
public override void TestClone()
{
IAminoAcid aa = (IAminoAcid)NewChemObject();
object clone = aa.Clone();
Assert.IsTrue(clone is IAminoAcid);
Assert.AreNotSame(aa, clone);
aa = (IAminoAcid)NewChemObject();
IAtom nTerminus = aa.Builder.NewAtom("N");
aa.AddNTerminus(nTerminus);
clone = aa.Clone();
Assert.IsTrue(clone is IAminoAcid);
Assert.AreNotSame(aa, clone);
aa = (IAminoAcid)NewChemObject();
IAtom cTerminus = aa.Builder.NewAtom("C");
aa.AddCTerminus(cTerminus);
clone = aa.Clone();
Assert.IsTrue(clone is IAminoAcid);
Assert.AreNotSame(aa, clone);
}
public virtual void TestGetNTerminus()
{
IAminoAcid m = (IAminoAcid)NewChemObject();
Assert.IsNull(m.NTerminus);
}
public void AddVariableModification(IMass modificaiton, IAminoAcid aminoAcid)
{
}
public void AddVariableModification(IMass modificaiton, IAminoAcid aminoAcid)
{
}
