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 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 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 void TestNewStrand()
{
IChemObjectBuilder builder = RootObject.Builder;
IStrand strand = builder.NewStrand();
Assert.IsNotNull(strand);
}
public override void TestClone()
{
IStrand strand = (IStrand)NewChemObject();
object clone = strand.Clone();
Assert.IsTrue(clone is IStrand);
}
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 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 virtual void TestGetStrandNames()
{
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.Keys, oBioPolymer.GetStrandNames()));
}
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 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 void TestBioPolymer()
{
IBioPolymer oBioPolymer = new BioPolymer();
Assert.IsNotNull(oBioPolymer);
Assert.AreEqual(oBioPolymer.GetMonomerMap().Count(), 0);
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";
IMonomer oMono3 = oBioPolymer.Builder.NewMonomer();
oMono3.MonomerName = "GLYA16";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom3 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom4 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom5 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.Atoms.Add(oAtom1);
oBioPolymer.AddAtom(oAtom2, oStrand1);
oBioPolymer.AddAtom(oAtom3, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom4, oMono2, oStrand2);
oBioPolymer.AddAtom(oAtom5, oMono3, oStrand2);
Assert.IsNotNull(oBioPolymer.Atoms[0]);
Assert.IsNotNull(oBioPolymer.Atoms[1]);
Assert.IsNotNull(oBioPolymer.Atoms[2]);
Assert.IsNotNull(oBioPolymer.Atoms[3]);
Assert.IsNotNull(oBioPolymer.Atoms[4]);
Assert.AreEqual(oAtom1, oBioPolymer.Atoms[0]);
Assert.AreEqual(oAtom2, oBioPolymer.Atoms[1]);
Assert.AreEqual(oAtom3, oBioPolymer.Atoms[2]);
Assert.AreEqual(oAtom4, oBioPolymer.Atoms[3]);
Assert.AreEqual(oAtom5, oBioPolymer.Atoms[4]);
Assert.IsNull(oBioPolymer.GetMonomer("0815", "A"));
Assert.IsNull(oBioPolymer.GetMonomer("0815", "B"));
Assert.IsNull(oBioPolymer.GetMonomer("0815", ""));
Assert.IsNull(oBioPolymer.GetStrand(""));
Assert.IsNotNull(oBioPolymer.GetMonomer("TRP279", "A"));
Assert.AreEqual(oMono1, oBioPolymer.GetMonomer("TRP279", "A"));
Assert.AreEqual(oBioPolymer.GetMonomer("TRP279", "A").Atoms.Count, 1);
Assert.IsNotNull(oBioPolymer.GetMonomer("HOH", "B"));
Assert.AreEqual(oMono2, oBioPolymer.GetMonomer("HOH", "B"));
Assert.AreEqual(oBioPolymer.GetMonomer("HOH", "B").Atoms.Count, 1);
Assert.AreEqual(oBioPolymer.GetStrand("B").Atoms.Count, 2);
Assert.AreEqual(oBioPolymer.GetStrand("B").GetMonomerMap().Count(), 2);
Assert.IsNull(oBioPolymer.GetStrand("C"));
Assert.IsNotNull(oBioPolymer.GetStrand("B"));
}
/// <summary>
/// Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
/// 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>
/// <param name="oStrand"></param>
public void AddAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
{
base.AddAtom(oAtom, oMonomer, oStrand);
if (!sequentialListOfMonomers.Contains(oMonomer.MonomerName))
{
sequentialListOfMonomers.Add(oMonomer.MonomerName);
}
}
public virtual void TestGetStrandName()
{
IStrand oStrand = (IStrand)NewChemObject();
oStrand.StrandName = "A";
Assert.AreEqual("A", oStrand.StrandName);
}
public virtual void TestSetStrandType_String()
{
IStrand oStrand = (IStrand)NewChemObject();
oStrand.StrandType = "DNA";
Assert.AreEqual("DNA", oStrand.StrandType);
}
/// <summary> Adds the atom oAtom to a specified Monomer of a specified Strand.
/// Additionally, it keeps record of the iCode.
///
/// </summary>
/// <param name="oAtom"> The atom to add
/// </param>
/// <param name="oMonomer"> The monomer the atom belongs to
/// </param>
public override void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
{
base.addAtom(oAtom, oMonomer, oStrand);
if (!sequentialListOfMonomers.Contains(oMonomer.MonomerName))
{
sequentialListOfMonomers.Add(oMonomer.MonomerName);
}
}
public override void TestAddAtom_IAtom()
{
IStrand oStrand = (IStrand)NewChemObject();
IAtom oAtom1 = oStrand.Builder.NewAtom("C");
IAtom oAtom2 = oStrand.Builder.NewAtom("C");
oStrand.Atoms.Add(oAtom1);
oStrand.Atoms.Add(oAtom2);
Assert.AreEqual(2, oStrand.Atoms.Count);
}
public override ICDKObject Clone(CDKObjectMap map)
{
var clone = (BioPolymer)base.Clone(map);
clone.strands = new Dictionary <string, IStrand>();
foreach (var strandPair in strands)
{
string name = strandPair.Key;
IStrand original = strandPair.Value;
IStrand cloned = (IStrand)original.Clone(map);
clone.strands.Add(name, cloned);
}
return(clone);
}
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);
}
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 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);
}
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 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);
}
public override void TestRemoveStrand_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.IsTrue(pdbPolymer.GetStrandNames().Contains(oStrand1.StrandName));
Assert.AreEqual(1, pdbPolymer.Atoms.Count);
pdbPolymer.RemoveStrand("A");
Assert.IsFalse(pdbPolymer.GetStrandNames().Contains(oStrand1.StrandName));
Assert.AreEqual(0, pdbPolymer.Atoms.Count);
}
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);
}
/// <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
}
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"));
}
/// <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 virtual void addAtom(IAtom oAtom, IStrand oStrand)
{
int atomCount = base.AtomCount;
// Add atom to AtomContainer
base.addAtom(oAtom);
if (atomCount != base.AtomCount && oStrand != null)
{
// Maybe better to throw nullpointer 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.ContainsValue(oStrand.StrandName))
{
strands[oStrand.StrandName] = oStrand;
}
}
/* notifyChanged() is called by addAtom in
* AtomContainer */
}
/// <summary> Adds the atom oAtom to a specified Monomer of a specified Strand.
/// Additionally, it keeps record of the iCode.
///
/// </summary>
/// <param name="oAtom"> The atom to add
/// </param>
/// <param name="oMonomer"> The monomer the atom belongs to
/// </param>
public override void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
{
base.addAtom(oAtom, oMonomer, oStrand);
if (!sequentialListOfMonomers.Contains(oMonomer.MonomerName))
sequentialListOfMonomers.Add(oMonomer.MonomerName);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="aSessionId">
/// The unique identifier of the session that the tab is in.
/// </param>
/// <param name="aTabKey">
/// An identifier for this tab, unique within its session.
/// </param>
/// <param name="aListener">
/// A listener that will be notified about changes to the state of the
/// event queue. Used to implement the "server health" app.
/// Important: The event-handler will be invoked while some app-state
/// locks are held. To avoid deadlock, it's a good idea to use
/// TabStatusQueue to transfer the events to another thread.
/// </param>
/// <param name="aClock">
/// Provides access to the current UTC time. Production code should
/// likely use ()=>DateTime.UtcNow, testing code will want more direct
/// control over the perceived time.
/// </param>
/// <param name="aTimeoutPolicy">
/// Policy on how long to keep long polls alive and how long to
/// keep a tab alive with no outstanding long poll.
/// </param>
/// <param name="aTimerThread">
/// Timer for scheduling maintenance work, such as checking for
/// expired tabs and long polls.
/// </param>
/// <param name="aAppsStateThread">
/// The soft thread for scheduling all asynchronous work. When we
/// get invoked from the timer thread, we dispatch back to this
/// thread before touching any of our mutable state.
/// </param>
/// <param name="aSession">
/// Something that wants to know when a tab should expire due to
/// inactivity.
/// </param>
/// <param name="aAppRecord">
/// AppRecord associated with the tab.
/// </param>
public ServerTab(
string aSessionId,
string aTabKey,
ITabStatusListener aListener,
Func<DateTime> aClock,
ServerTabTimeoutPolicy aTimeoutPolicy,
ITimerThread aTimerThread,
IStrand aAppsStateThread,
ISession aSession,
AppRecord aAppRecord)
{
SessionId = aSessionId;
iListener = aListener;
iAppsStateThread = aAppsStateThread;
iSession = aSession;
iTimerThread = aTimerThread;
iClock = aClock;
iTimeoutPolicy = aTimeoutPolicy;
TabKey = aTabKey;
AppRecord = aAppRecord;
iEventQueue = new JsonEventQueue(12000);// aEventQueue;
iLastRead = iClock();
iTimerCallback = iTimerThread.RegisterCallback(
()=>iAppsStateThread.ScheduleExclusive(DoMaintenance));
RescheduleMaintenance();
}
/// <summary> Adds the atom to a specified Strand and a specified Monomer.
///
/// </summary>
/// <param name="oAtom">
/// </param>
/// <param name="oMonomer">
/// </param>
/// <param name="oStrand">
/// </param>
public virtual void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
{
int atomCount = base.AtomCount;
// Add atom to AtomContainer
base.addAtom(oAtom);
if (atomCount != base.AtomCount && oStrand != null)
{
oStrand.addAtom(oAtom, oMonomer); // Same problem as above: better to throw nullpointer exception?
if (!strands.ContainsKey(oStrand.StrandName))
{
strands[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
* */
}
/// <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 virtual void addAtom(IAtom oAtom, IStrand oStrand)
{
int atomCount = base.AtomCount;
// Add atom to AtomContainer
base.addAtom(oAtom);
if (atomCount != base.AtomCount && oStrand != null)
{
// Maybe better to throw nullpointer 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.ContainsValue(oStrand.StrandName))
{
strands[oStrand.StrandName] = oStrand;
}
}
/* notifyChanged() is called by addAtom in
AtomContainer */
}