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 virtual void TestGetStrands()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
IStrand oStrand2 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
oStrand2.StrandName = "B";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oBioPolymer.Builder.NewMonomer();
oMono2.MonomerName = "GLY123";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom2, oMono2, oStrand2);
IDictionary <string, IStrand> strands = new Dictionary <string, IStrand>
{
{ "A", oStrand1 },
{ "B", oStrand2 }
};
Assert.IsTrue(Compares.AreDeepEqual(strands, oBioPolymer.GetStrandMap()));
}
public virtual void TestGetMonomer_String_String()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
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.AddAtom(oAtom1, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom2, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom3, oMono2, oStrand2);
Assert.AreEqual(oMono1, oBioPolymer.GetMonomer("TRP279", "A"));
Assert.AreEqual(oMono2, oBioPolymer.GetMonomer("HOH", "B"));
}
public virtual void TestAddAtom_IAtom_IMonomer_IStrand()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom2, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom1, null, oStrand1);
Assert.AreEqual(2, oBioPolymer.GetMonomer("TRP279", "A").Atoms.Count);
Assert.AreEqual(0, oBioPolymer.GetMonomer("", "A").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);
}
public virtual void TestGetStrand_String()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
Assert.AreEqual(oStrand1, oBioPolymer.GetStrand("A"));
}
public virtual void TestRemoveStrand_String()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
Assert.IsTrue(oBioPolymer.GetStrandNames().Contains(oStrand1.StrandName));
Assert.AreEqual(1, oBioPolymer.Atoms.Count);
oBioPolymer.RemoveStrand("A");
Assert.IsFalse(oBioPolymer.GetStrandNames().Contains(oStrand1.StrandName));
Assert.AreEqual(0, oBioPolymer.Atoms.Count);
}