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 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 virtual void TestGetMonomerNames()
{
IPolymer oPolymer = (IPolymer)NewChemObject();
Assert.AreEqual(0, oPolymer.GetMonomerNames().Count());
IMonomer oMono1 = oPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oPolymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom1 = oPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oPolymer.Builder.NewAtom("C");
IAtom oAtom3 = oPolymer.Builder.NewAtom("C");
oPolymer.Atoms.Add(oAtom1);
oPolymer.AddAtom(oAtom2, oMono1);
oPolymer.AddAtom(oAtom3, oMono2);
IDictionary <string, IMonomer> monomers = new Dictionary <string, IMonomer>
{
//IMonomer oMon = Builder.NewMonomer();
{ "TRP279", oMono1 },
{ "HOH", oMono2 }
};
Assert.AreEqual(2, oPolymer.GetMonomerNames().Count());
Assert.IsTrue(oPolymer.GetMonomerNames().Contains(oMono1.MonomerName));
Assert.IsTrue(oPolymer.GetMonomerNames().Contains(oMono2.MonomerName));
Assert.IsTrue(Compares.AreDeepEqual(monomers.Keys, oPolymer.GetMonomerNames()));
}
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 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 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 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 TestNewMonomer()
{
IChemObjectBuilder builder = RootObject.Builder;
IMonomer monomer = builder.NewMonomer();
Assert.IsNotNull(monomer);
}
public virtual void TestAddAtom_IAtom_IMonomer()
{
IPolymer oPolymer = (IPolymer)NewChemObject();
IMonomer oMono1 = oPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = null;
IAtom oAtom1 = oPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oPolymer.Builder.NewAtom("C");
IAtom oAtom3 = oPolymer.Builder.NewAtom("C");
oPolymer.Atoms.Add(oAtom1);
oPolymer.AddAtom(oAtom2, oMono1);
oPolymer.AddAtom(oAtom3, oMono2);
Assert.IsNotNull(oPolymer.Atoms[0]);
Assert.IsNotNull(oPolymer.Atoms[1]);
Assert.IsNotNull(oPolymer.Atoms[2]);
Assert.AreEqual(oAtom1, oPolymer.Atoms[0]);
Assert.AreEqual(oAtom2, oPolymer.Atoms[1]);
Assert.AreEqual(oAtom3, oPolymer.Atoms[2]);
Assert.AreEqual(3, oPolymer.Atoms.Count);
Assert.AreEqual(1, oPolymer.GetMonomer("TRP279").Atoms.Count);
Assert.AreEqual(1, oPolymer.GetMonomerMap().Count());
Assert.IsNotNull(oPolymer.GetMonomer("TRP279"));
Assert.AreEqual(oMono1, oPolymer.GetMonomer("TRP279"));
}
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()));
}
private CMLMolecule CDKPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer, bool setIDs)
{
var cmlMolecule = new CMLMolecule
{
Convention = "PDB",
DictRef = "pdb:model"
};
var mapS = pdbPolymer.GetStrandMap();
foreach (var key in mapS.Keys)
{
var strand = mapS[key];
var monomerNames = new List <string>(strand.GetMonomerNames());
monomerNames.Sort();
foreach (var name in monomerNames)
{
IMonomer monomer = strand.GetMonomer(name);
CMLMolecule clmono = CDKMonomerToCMLMolecule(monomer, true);
cmlMolecule.Add(clmono);
}
}
return(cmlMolecule);
}
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 TestSetMonomerType_String()
{
IMonomer oMonomer = (IMonomer)NewChemObject();
oMonomer.MonomerType = "TRP";
Assert.AreEqual("TRP", oMonomer.MonomerType);
}
public virtual void TestSetMonomerName_String()
{
IMonomer m = (IMonomer)NewChemObject();
m.MonomerName = "TRP279";
Assert.AreEqual("TRP279", m.MonomerName);
}
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 TestToString()
{
IPolymer polymer = (IPolymer)NewChemObject();
IMonomer oMono1 = polymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = polymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom2 = polymer.Builder.NewAtom("C");
IAtom oAtom3 = polymer.Builder.NewAtom("C");
polymer.AddAtom(oAtom2, oMono1);
polymer.AddAtom(oAtom3, oMono2);
IDictionary <string, IMonomer> monomers = new Dictionary <string, IMonomer>
{
{ "TRP279", oMono1 },
{ "HOH", oMono2 }
};
string description = polymer.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
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"));
}
public override void TestClone()
{
IMonomer oMonomer = (IMonomer)NewChemObject();
object clone = oMonomer.Clone();
Assert.IsTrue(clone is IMonomer);
Assert.AreNotSame(oMonomer, clone);
}
/// <summary> Adds the atom oAtom to a specified Monomer. 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)
{
base.addAtom(oAtom, oMonomer);
if (!sequentialListOfMonomers.Contains(oMonomer.MonomerName))
{
sequentialListOfMonomers.Add(oMonomer.MonomerName);
}
}
/// <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);
}
}
private Group TranslateCDKMonomer(IMonomer iMonomer)
{
// find type
Type cdkType = iMonomer.GetType();
if (cdkType is AminoAcid)
{
AminoAcid amino = (AminoAcid)iMonomer;
//AminoMonomer monomer = new AminoMonomer();
}
return(null);
}
public override void TestToString()
{
IMonomer oMonomer = (IMonomer)NewChemObject();
oMonomer.MonomerType = "TRP";
string description = oMonomer.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
public override ICDKObject Clone(CDKObjectMap map)
{
var clone = (Strand)base.Clone(map);
clone.monomers = new Dictionary <string, IMonomer>();
foreach (var pair in monomers)
{
string monomerName = pair.Key;
IMonomer monomer = pair.Value;
var clonedMonomer = (IMonomer)monomer.Clone(map);
clone.monomers.Add(monomerName, clonedMonomer);
}
return(clone);
}
public void TestStrand()
{
IStrand oStrand = new Strand();
Assert.IsNotNull(oStrand);
Assert.AreEqual(oStrand.GetMonomerMap().Count(), 0);
IMonomer oMono1 = oStrand.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oStrand.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IMonomer oMono3 = oStrand.Builder.NewMonomer();
oMono3.MonomerName = "GLYA16";
IAtom oAtom1 = oStrand.Builder.NewAtom("C");
IAtom oAtom2 = oStrand.Builder.NewAtom("C");
IAtom oAtom3 = oStrand.Builder.NewAtom("C");
IAtom oAtom4 = oStrand.Builder.NewAtom("C");
IAtom oAtom5 = oStrand.Builder.NewAtom("C");
oStrand.AddAtom(oAtom1);
oStrand.AddAtom(oAtom2);
oStrand.AddAtom(oAtom3, oMono1);
oStrand.AddAtom(oAtom4, oMono2);
oStrand.AddAtom(oAtom5, oMono3);
Assert.IsNotNull(oStrand.Atoms[0]);
Assert.IsNotNull(oStrand.Atoms[1]);
Assert.IsNotNull(oStrand.Atoms[2]);
Assert.IsNotNull(oStrand.Atoms[3]);
Assert.IsNotNull(oStrand.Atoms[4]);
Assert.AreEqual(oAtom1, oStrand.Atoms[0]);
Assert.AreEqual(oAtom2, oStrand.Atoms[1]);
Assert.AreEqual(oAtom3, oStrand.Atoms[2]);
Assert.AreEqual(oAtom4, oStrand.Atoms[3]);
Assert.AreEqual(oAtom5, oStrand.Atoms[4]);
Assert.IsNull(oStrand.GetMonomer("0815"));
Assert.IsNotNull(oStrand.GetMonomer(""));
Assert.IsNotNull(oStrand.GetMonomer("TRP279"));
Assert.AreEqual(oMono1, oStrand.GetMonomer("TRP279"));
Assert.AreEqual(oStrand.GetMonomer("TRP279").Atoms.Count, 1);
Assert.IsNotNull(oStrand.GetMonomer("HOH"));
Assert.AreEqual(oMono2, oStrand.GetMonomer("HOH"));
Assert.AreEqual(oStrand.GetMonomer("HOH").Atoms.Count, 1);
Assert.AreEqual(oStrand.GetMonomer("").Atoms.Count, 2);
Assert.AreEqual(oStrand.Atoms.Count, 5);
Assert.AreEqual(oStrand.GetMonomerMap().Count(), 3);
}
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 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 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"));
}
/// <summary>
/// Adds the atom oAtom to a specified Monomer.
/// </summary>
/// <param name="oAtom">The atom to add</param>
/// <param name="oMonomer">The monomer the atom belongs to</param>
public void AddAtom(IAtom oAtom, IMonomer oMonomer)
{
if (!Contains(oAtom))
{
base.Atoms.Add(oAtom); // this calls notify
if (oMonomer != null)
{ // Not sure what's better here...throw nullpointer exception?
oMonomer.Atoms.Add(oAtom);
if (!monomers.ContainsKey(oMonomer.MonomerName))
{
monomers.Add(oMonomer.MonomerName, oMonomer);
}
}
}
}
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 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);
}
/// <summary> Adds the atom oAtom to a specified Monomer. 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)
{
base.addAtom(oAtom, oMonomer);
if (!sequentialListOfMonomers.Contains(oMonomer.MonomerName))
sequentialListOfMonomers.Add(oMonomer.MonomerName);
}
/// <summary> Adds the atom oAtom to a specified Monomer.
///
/// </summary>
/// <param name="oAtom"> The atom to add
/// </param>
/// <param name="oMonomer"> The monomer the atom belongs to
/// </param>
public virtual void addAtom(IAtom oAtom, IMonomer oMonomer)
{
if (!contains(oAtom))
{
base.addAtom(oAtom);
if (oMonomer != null)
{
// Not sure what's better here...throw nullpointer exception?
oMonomer.addAtom(oAtom);
if (!monomers.ContainsKey(oMonomer.MonomerName))
{
monomers[oMonomer.MonomerName] = oMonomer;
}
}
}
/* notifyChanged() is called by addAtom in
AtomContainer */
}
/// <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
* */
}
