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());
}
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 void TestNewPDBPolymer()
{
IChemObjectBuilder builder = RootObject.Builder;
IPDBPolymer polymer = builder.NewPDBPolymer();
Assert.IsNotNull(polymer);
}
public override void TestClone()
{
IPDBPolymer polymer = (IPDBPolymer)NewChemObject();
object clone = polymer.Clone();
Assert.IsTrue(clone is IBioPolymer);
}
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 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 TestAddStructure_IPDBStructure()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
IPDBStructure structure = pdbPolymer.Builder.NewPDBStructure();
pdbPolymer.Add(structure);
Assert.AreEqual(1, pdbPolymer.GetStructures().Count());
}
public override void TestToString()
{
IPDBPolymer pdbPolymer = (IPDBPolymer)NewChemObject();
string description = pdbPolymer.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
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 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 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 CMLMolecule CDKPDBPolymerToCMLMolecule(IPDBPolymer pdbPolymer)
{
return(CDKPDBPolymerToCMLMolecule(pdbPolymer, true));
}