public void TestMixedNamespaces()
{
var ins = ResourceLoader.GetAsStream(this.GetType(), "US06358966-20020319-C00001-enr.cml");
var reader = new CMLReader(ins);
try
{
IChemFile cfile = reader.Read(ChemObjectBuilder.Instance.NewChemFile());
Assert.AreEqual(34, ChemFileManipulator.GetAtomCount(cfile));
Assert.AreEqual(39, ChemFileManipulator.GetBondCount(cfile));
}
finally
{
reader.Close();
}
}
public void TestObjectCountsChemFile(IChemFile chemFile, int chemSequenceCount, int chemModelCount,
int moleculeCount, int atomCount, int strandCount, int monomerCount, int structureCount)
{
var container = GetFirstAtomContainer(chemFile, chemSequenceCount, chemModelCount, moleculeCount);
Assert.IsTrue(container is IBioPolymer);
var polymer = (IBioPolymer)container;
// chemical validation
Assert.AreEqual(atomCount, ChemFileManipulator.GetAtomCount(chemFile));
Assert.AreEqual(strandCount, polymer.GetStrandMap().Count);
Assert.AreEqual(monomerCount, polymer.GetMonomerMap().Count());
Assert.IsTrue(polymer is IPDBPolymer);
var pdb = (IPDBPolymer)polymer;
// PDB validation
Assert.AreEqual(structureCount, pdb.GetStructures().Count());
}
void AssertAtomCount(int expectedAtomCount, IChemObject chemObject)
{
if (expectedAtomCount != -1)
{
if (chemObject is IChemFile)
{
Assert.AreEqual(expectedAtomCount, ChemFileManipulator.GetAtomCount((IChemFile)chemObject));
}
else if (chemObject is IChemModel)
{
Assert.AreEqual(expectedAtomCount, ChemModelManipulator.GetAtomCount((IChemModel)chemObject));
}
else if (chemObject is IAtomContainer)
{
Assert.AreEqual(expectedAtomCount, ((IAtomContainer)chemObject).Atoms.Count);
}
else if (chemObject is IReaction)
{
Assert.AreEqual(expectedAtomCount, ReactionManipulator.GetAtomCount((IReaction)chemObject));
}
}
}
public void Test114D()
{
var filename = "NCDK.Data.PDB.114D.pdb";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new PDBReader(ins);
Assert.IsNotNull(reader);
var chemFile = (IChemFile)reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(1, model.MoleculeSet.Count());
var container = model.MoleculeSet[0];
Assert.IsTrue(container is IBioPolymer);
var polymer = (IBioPolymer)container;
Assert.IsTrue(polymer.GetStrand("A") is IPDBStrand, "Strand A is not a PDBStrand");
var strandA = (IPDBStrand)polymer.GetStrand("A");
var lst = strandA.GetMonomerNamesInSequentialOrder().GetEnumerator();
lst.MoveNext();
var monomer1 = lst.Current;
var mono1 = strandA.GetMonomer(monomer1);
Assert.IsNotNull(mono1);
Assert.IsNotNull(mono1.MonomerName);
Assert.IsTrue(mono1 is IPDBMonomer, "Monomer is not a PDBMonomer");
var pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual(pdbMonomer.ResSeq, "1");
lst.MoveNext();
var monomer2 = lst.Current;
var mono2 = strandA.GetMonomer(monomer2);
Assert.IsTrue(mono2 is IPDBMonomer, "Monomer is not a PDBMonomer");
var pdbMonomer2 = (IPDBMonomer)mono2;
Assert.AreEqual(pdbMonomer2.ResSeq, "2");
// chemical validation
Assert.AreEqual(552, ChemFileManipulator.GetAtomCount(chemFile));
Assert.AreEqual(2, polymer.GetStrandMap().Count());
Assert.AreEqual(24, polymer.GetMonomerMap().Count());
Assert.IsTrue(polymer.GetStrandNames().Contains("A"));
Assert.IsTrue(polymer.GetStrandNames().Contains("B"));
Assert.IsFalse(polymer.GetStrandNames().Contains("C"));
Assert.AreEqual(24, polymer.GetMonomerMap().Count());
Assert.IsTrue(polymer is IPDBPolymer);
var pdb = (IPDBPolymer)polymer;
// PDB validation
Assert.AreEqual(0, pdb.GetStructures().Count());
}
