public void TestNewPDBAtom_IElement()
{
IChemObjectBuilder builder = RootObject.Builder;
IPDBAtom atom = builder.NewPDBAtom(ChemicalElement.R);
Assert.IsNotNull(atom);
}
public void TestGetMonomerNamesInSequentialOrder()
{
PDBPolymer pdbPolymer = new PDBPolymer();
Assert.AreEqual(0, pdbPolymer.GetMonomerNames().Count());
IStrand oStrand1 = pdbPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = pdbPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = pdbPolymer.Builder.NewMonomer();
oMono2.MonomerName = "CYS280";
IPDBAtom oPDBAtom2 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom3 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.AddAtom(oPDBAtom2, oMono1, oStrand1);
pdbPolymer.AddAtom(oPDBAtom3, oMono2, oStrand1);
Assert.IsNotNull(pdbPolymer.Atoms[0]);
Assert.IsNotNull(pdbPolymer.Atoms[1]);
Assert.AreEqual(oPDBAtom2, pdbPolymer.Atoms[0]);
Assert.AreEqual(oPDBAtom3, pdbPolymer.Atoms[1]);
var monomers = pdbPolymer.GetMonomerNamesInSequentialOrder().GetEnumerator();
monomers.MoveNext();
Assert.AreEqual("TRP279", monomers.Current);
monomers.MoveNext();
Assert.AreEqual("CYS280", monomers.Current);
}
public override void TestGetMonomerCount()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
Assert.AreEqual(0, pdbPolymer.GetMonomerMap().Count());
IStrand oStrand1 = pdbPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IStrand oStrand2 = pdbPolymer.Builder.NewStrand();
oStrand2.StrandName = "B";
IMonomer oMono1 = pdbPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = pdbPolymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IPDBAtom oPDBAtom1 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom2 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom3 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.Add(oPDBAtom1);
pdbPolymer.AddAtom(oPDBAtom2, oMono1, oStrand1);
pdbPolymer.AddAtom(oPDBAtom3, oMono2, oStrand2);
Assert.IsNotNull(pdbPolymer.Atoms[0]);
Assert.IsNotNull(pdbPolymer.Atoms[1]);
Assert.IsNotNull(pdbPolymer.Atoms[2]);
Assert.AreEqual(oPDBAtom1, pdbPolymer.Atoms[0]);
Assert.AreEqual(oPDBAtom2, pdbPolymer.Atoms[1]);
Assert.AreEqual(oPDBAtom3, pdbPolymer.Atoms[2]);
Assert.AreEqual(2, pdbPolymer.GetMonomerMap().Count());
}
public override void TestGetStrands()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
IStrand oStrand1 = pdbPolymer.Builder.NewStrand();
IStrand oStrand2 = pdbPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
oStrand2.StrandName = "B";
IMonomer oMono1 = pdbPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = pdbPolymer.Builder.NewMonomer();
oMono2.MonomerName = "GLY123";
IPDBAtom oPDBAtom1 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom2 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.AddAtom(oPDBAtom1, oMono1, oStrand1);
pdbPolymer.AddAtom(oPDBAtom2, oMono2, oStrand2);
IDictionary <string, IStrand> strands = new Dictionary <string, IStrand>
{
{ "A", oStrand1 },
{ "B", oStrand2 }
};
Assert.IsTrue(Compares.AreDeepEqual(strands, pdbPolymer.GetStrandMap()));
}
public void TestNewPDBAtom_String_Point3d()
{
IChemObjectBuilder builder = RootObject.Builder;
IPDBAtom atom = builder.NewPDBAtom("C", new Vector3(1, 2, 3));
Assert.IsNotNull(atom);
}
public override void TestDefaultChargeValue()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
Assert.AreEqual(0.00, atom.Charge.Value, 0.00000001);
}
public void TestNewPDBAtom_String()
{
IChemObjectBuilder builder = RootObject.Builder;
IPDBAtom atom = builder.NewPDBAtom("O");
Assert.IsNotNull(atom);
}
public override void TestGetMonomer_String_String()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
IStrand oStrand1 = pdbPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IStrand oStrand2 = pdbPolymer.Builder.NewStrand();
oStrand2.StrandName = "B";
IMonomer oMono1 = pdbPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = pdbPolymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IPDBAtom oPDBAtom1 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom2 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom3 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.AddAtom(oPDBAtom1, oMono1, oStrand1);
pdbPolymer.AddAtom(oPDBAtom2, oMono1, oStrand1);
pdbPolymer.AddAtom(oPDBAtom3, oMono2, oStrand2);
Assert.AreEqual(oMono1, pdbPolymer.GetMonomer("TRP279", "A"));
Assert.AreEqual(oMono2, pdbPolymer.GetMonomer("HOH", "B"));
}
public void TestPDBPolymer()
{
IPDBPolymer pdbPolymer = new PDBPolymer();
Assert.IsNotNull(pdbPolymer);
Assert.AreEqual(pdbPolymer.GetMonomerMap().Count(), 0);
IStrand oStrand1 = pdbPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IStrand oStrand2 = pdbPolymer.Builder.NewStrand();
oStrand2.StrandName = "B";
IMonomer oMono1 = pdbPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = pdbPolymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IMonomer oMono3 = pdbPolymer.Builder.NewMonomer();
oMono3.MonomerName = "GLYA16";
IPDBAtom oPDBAtom1 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom2 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom3 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom4 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom5 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.Atoms.Add(oPDBAtom1);
pdbPolymer.AddAtom(oPDBAtom2, oStrand1);
pdbPolymer.AddAtom(oPDBAtom3, oMono1, oStrand1);
pdbPolymer.AddAtom(oPDBAtom4, oMono2, oStrand2);
pdbPolymer.AddAtom(oPDBAtom5, oMono3, oStrand2);
Assert.IsNotNull(pdbPolymer.Atoms[0]);
Assert.IsNotNull(pdbPolymer.Atoms[1]);
Assert.IsNotNull(pdbPolymer.Atoms[2]);
Assert.IsNotNull(pdbPolymer.Atoms[3]);
Assert.IsNotNull(pdbPolymer.Atoms[4]);
Assert.AreEqual(oPDBAtom1, pdbPolymer.Atoms[0]);
Assert.AreEqual(oPDBAtom2, pdbPolymer.Atoms[1]);
Assert.AreEqual(oPDBAtom3, pdbPolymer.Atoms[2]);
Assert.AreEqual(oPDBAtom4, pdbPolymer.Atoms[3]);
Assert.AreEqual(oPDBAtom5, pdbPolymer.Atoms[4]);
Assert.IsNull(pdbPolymer.GetMonomer("0815", "A"));
Assert.IsNull(pdbPolymer.GetMonomer("0815", "B"));
Assert.IsNull(pdbPolymer.GetMonomer("0815", ""));
Assert.IsNull(pdbPolymer.GetStrand(""));
Assert.IsNotNull(pdbPolymer.GetMonomer("TRP279", "A"));
Assert.AreEqual(oMono1, pdbPolymer.GetMonomer("TRP279", "A"));
Assert.AreEqual(pdbPolymer.GetMonomer("TRP279", "A").Atoms.Count, 1);
Assert.IsNotNull(pdbPolymer.GetMonomer("HOH", "B"));
Assert.AreEqual(oMono2, pdbPolymer.GetMonomer("HOH", "B"));
Assert.AreEqual(pdbPolymer.GetMonomer("HOH", "B").Atoms.Count, 1);
Assert.AreEqual(pdbPolymer.GetStrand("B").Atoms.Count, 2);
Assert.AreEqual(pdbPolymer.GetStrand("B").GetMonomerMap().Count(), 2);
Assert.IsNull(pdbPolymer.GetStrand("C"));
Assert.IsNotNull(pdbPolymer.GetStrand("B"));
}
/// <summary>
/// Adds the atom oAtom to a specified Monomer. Additionally, it keeps
/// record of the iCode.
/// </summary>
/// <param name="oAtom">The IPDBAtom to add</param>
/// <param name="oMonomer">The monomer the atom belongs to</param>
public void AddAtom(IPDBAtom oAtom, IMonomer oMonomer)
{
base.AddAtom(oAtom, oMonomer);
if (!sequentialListOfMonomers.Contains(oMonomer.MonomerName))
{
sequentialListOfMonomers.Add(oMonomer.MonomerName);
}
}
public virtual void TestGetTempFactor()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.TempFactor = 0.0;
Assert.AreEqual(atom.TempFactor.Value, 0.0, 001);
}
public virtual void TestGetOccupancy()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.Occupancy = 1.0;
Assert.AreEqual(atom.Occupancy.Value, 1.0, 0.01);
}
public virtual void TestGetOxt()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.Oxt = true;
Assert.IsTrue(atom.Oxt);
}
public virtual void TestGetAltLoc()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.AltLoc = "123";
Assert.AreEqual("123", atom.AltLoc);
}
public virtual void TestGetSerial()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.Serial = 123;
Assert.AreEqual(123, atom.Serial.Value);
}
public virtual void TestGetResName()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.ResName = "PHE";
Assert.AreEqual("PHE", atom.ResName);
}
public virtual void TestGetChainID()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.ChainID = "123";
Assert.AreEqual("123", atom.ChainID);
}
public virtual void TestGetName()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.Name = "123";
Assert.AreEqual("123", atom.Name);
}
public virtual void TestGetRecord()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.Record = "ATOM 1635 N PHE 105 -3.504 9.019 -14.276 1.00 0.00 N";
Assert.AreEqual("ATOM 1635 N PHE 105 -3.504 9.019 -14.276 1.00 0.00 N", atom.Record);
}
public virtual void TestGetHetAtom()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.HetAtom = true;
Assert.IsTrue(atom.HetAtom.Value);
}
public virtual void TestGetResSeq()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.ResSeq = "123";
Assert.AreEqual("123", atom.ResSeq);
}
public override void TestClone()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
object clone = atom.Clone();
Assert.IsTrue(clone is IAtom);
}
public override void TestClonePoint3d()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
atom.Point3D = new Vector3(2, 3, 4);
IAtom clone = (IAtom)atom.Clone();
Assert.AreEqual(clone.Point3D.Value.X, 2.0, 0.001);
}
public override void TestSetPoint3dPoint3d()
{
Vector3 point3d = new Vector3(1, 2, 3);
IPDBAtom a = (IPDBAtom)NewChemObject();
a.Symbol = "C";
a.Point3D = point3d;
Assert.AreEqual(point3d, a.Point3D);
}
public override void TestGetPoint3d()
{
Vector3 point3d = new Vector3(1, 2, 3);
IPDBAtom a = (IPDBAtom)NewChemObject();
a.Point3D = point3d;
Assert.IsNotNull(a.Point3D);
AssertAreEqual(point3d, a.Point3D.Value, 0.001);
}
public virtual void TestAddAtom_IPDBAtom()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
IPDBAtom oPDBAtom1 = pdbPolymer.Builder.NewPDBAtom("C");
IPDBAtom oPDBAtom2 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.Add(oPDBAtom1);
pdbPolymer.Add(oPDBAtom2);
Assert.AreEqual(2, pdbPolymer.Atoms.Count);
}
public override void TestSetFractionalPoint3dPoint3d()
{
IPDBAtom a = (IPDBAtom)NewChemObject();
a.Symbol = "C";
a.FractionalPoint3D = new Vector3(0.5, 0.5, 0.5);
Vector3 fract = a.FractionalPoint3D.Value;
Assert.IsNotNull(fract);
Assert.AreEqual(0.5, fract.X, 0.001);
Assert.AreEqual(0.5, fract.Y, 0.001);
Assert.AreEqual(0.5, fract.Z, 0.001);
}
public override void TestToString()
{
IPDBAtom atom = (IPDBAtom)NewChemObject();
atom.Symbol = "C";
string description = atom.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
public override void TestGetStrand_String()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
IStrand oStrand1 = pdbPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = pdbPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IPDBAtom oPDBAtom1 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.AddAtom(oPDBAtom1, oMono1, oStrand1);
Assert.AreEqual(oStrand1, pdbPolymer.GetStrand("A"));
}
public virtual void TestAddAtom_IPDBAtom_IMonomer()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
IPDBMonomer oMono1 = pdbPolymer.Builder.NewPDBMonomer();
oMono1.MonomerName = "TRP279";
IStrand oStrand1 = pdbPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IPDBAtom oPDBAtom1 = pdbPolymer.Builder.NewPDBAtom("C");
pdbPolymer.AddAtom(oPDBAtom1, oMono1, oStrand1);
Assert.AreEqual(1, pdbPolymer.GetMonomer("TRP279", "A").Atoms.Count);
}
