public virtual void TestGetMonomers()
{
IStrand oStrand = (IStrand)NewChemObject();
IMonomer oMono1 = oStrand.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oStrand.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom2 = oStrand.Builder.NewAtom("C");
IAtom oAtom3 = oStrand.Builder.NewAtom("C");
oStrand.AddAtom(oAtom2, oMono1);
oStrand.AddAtom(oAtom3, oMono2);
IDictionary <string, IMonomer> monomers = new Dictionary <string, IMonomer>();
IMonomer oMon = oStrand.Builder.NewMonomer();
oMon.MonomerName = "";
oMon.MonomerType = "Unknown";
monomers.Add("", oMon);
monomers.Add("TRP279", oMono1);
monomers.Add("HOH", oMono2);
Assert.IsTrue(Compares.AreDeepEqual(monomers.Keys, oStrand.GetMonomerNames()));
}
public override void TestToString()
{
IStrand oStrand = (IStrand)NewChemObject();
IMonomer oMono1 = oStrand.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oStrand.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom2 = oStrand.Builder.NewAtom("C");
IAtom oAtom3 = oStrand.Builder.NewAtom("C");
oStrand.AddAtom(oAtom2, oMono1);
oStrand.AddAtom(oAtom3, oMono2);
IDictionary <string, IMonomer> monomers = new Dictionary <string, IMonomer>();
IMonomer oMon = oStrand.Builder.NewMonomer();
oMon.MonomerName = "";
oMon.MonomerType = "Unknown";
monomers.Add("", oMon);
monomers.Add("TRP279", oMono1);
monomers.Add("HOH", oMono2);
string description = oStrand.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
public void AddAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
{
int atomCount = Atoms.Count;
// Add atom to AtomContainer
base.Atoms.Add(oAtom);
if (atomCount != base.Atoms.Count // OK, super did not yet contain the atom
// Add atom to Strand (also adds the atom to the monomer).
&& oStrand != null)
{
oStrand.AddAtom(oAtom, oMonomer); // Same problem as above: better to throw nullpointer exception?
if (!strands.ContainsKey(oStrand.StrandName))
{
strands.Add(oStrand.StrandName, oStrand);
}
}
// The reasoning above is: All Monomers have to belong to a Strand and
// all atoms belonging to strands have to belong to a Monomer => ?
// oMonomer != null and oStrand != null, oAtom is added to BioPolymer
// and to oMonomer in oStrand ? oMonomer == null and oStrand != null,
// oAtom is added to BioPolymer and default Monomer in oStrand ?
// oMonomer != null and oStrand == null, oAtom is added to BioPolymer,
// but not to a Monomer or Strand (especially good to maybe throw
// exception in this case) ? oMonomer == null and oStrand == null, oAtom
// is added to BioPolymer, but not to a Monomer or Strand
}
public virtual void TestAddAtom_IAtom_IMonomer()
{
IStrand oStrand = (IStrand)NewChemObject();
IMonomer oMono1 = oStrand.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oStrand.Builder.NewAtom("C");
IAtom oAtom2 = oStrand.Builder.NewAtom("C");
IAtom oAtom3 = oStrand.Builder.NewAtom("C");
oStrand.AddAtom(oAtom1);
oStrand.AddAtom(oAtom2);
oStrand.AddAtom(oAtom3, oMono1);
Assert.AreEqual(2, oStrand.GetMonomer("").Atoms.Count);
Assert.AreEqual(1, oStrand.GetMonomer("TRP279").Atoms.Count);
}
public virtual void TestGetMonomerCount()
{
IStrand oStrand = (IStrand)NewChemObject();
IMonomer oMono1 = oStrand.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oStrand.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom2 = oStrand.Builder.NewAtom("C");
IAtom oAtom3 = oStrand.Builder.NewAtom("C");
oStrand.AddAtom(oAtom2, oMono1);
oStrand.AddAtom(oAtom3, oMono2);
Assert.AreEqual(2, oStrand.GetMonomerMap().Count());
}
public virtual void TestGetMonomer_String()
{
IStrand oStrand = (IStrand)NewChemObject();
IMonomer oMono1 = oStrand.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oStrand.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom2 = oStrand.Builder.NewAtom("C");
IAtom oAtom3 = oStrand.Builder.NewAtom("C");
oStrand.AddAtom(oAtom2, oMono1);
oStrand.AddAtom(oAtom3, oMono2);
Assert.AreEqual(oMono1, oStrand.GetMonomer("TRP279"));
Assert.AreEqual(oMono2, oStrand.GetMonomer("HOH"));
Assert.IsNull(oStrand.GetMonomer("TEST"));
}
public virtual void TestRemoveMonomer_String()
{
IStrand oStrand = (IStrand)NewChemObject();
IMonomer oMono1 = oStrand.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oStrand.Builder.NewAtom("C");
oStrand.AddAtom(oAtom1, oMono1);
Assert.IsTrue(oStrand.GetMonomerNames().Contains(oMono1.MonomerName));
Assert.AreEqual(1, oStrand.Atoms.Count);
oStrand.RemoveMonomer("TRP279");
Assert.IsFalse(oStrand.GetMonomerNames().Contains(oMono1.MonomerName));
Assert.AreEqual(0, oStrand.Atoms.Count);
}
/// <summary>
/// Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence
/// the atom will be added to a Monomer of type Unknown in the specified Strand.
/// </summary>
/// <param name="oAtom">The atom to add</param>
/// <param name="oStrand">The strand the atom belongs to</param>
public void AddAtom(IAtom oAtom, IStrand oStrand)
{
int atomCount = base.Atoms.Count;
// Add atom to AtomContainer
base.Atoms.Add(oAtom);
if (atomCount != base.Atoms.Count && oStrand != null)
{ // Maybe better to throw null pointer exception here, so user realises that
// Strand == null and Atom only gets added to this BioPolymer, but not to a Strand.
oStrand.AddAtom(oAtom);
if (!strands.ContainsKey(oStrand.StrandName))
{
strands.Add(oStrand.StrandName, oStrand);
}
}
// NotifyChanged() is called by AddAtom in AtomContainer
}