public void ProlineNamedCorrectly()
{
var aminoAcidReference = AminoAcidLibrary.Proline(1);
PdbAminoAcidAtomNamer.AssignNames(aminoAcidReference);
var moleculeStructure = aminoAcidReference.Molecule.MoleculeStructure;
var nitrogen = moleculeStructure.GetVertexFromId(aminoAcidReference.FirstAtomId).Object;
Assume.That(nitrogen.Element, Is.EqualTo(ElementName.Nitrogen));
Assert.That(nitrogen.AminoAcidAtomName, Is.EqualTo("N"));
var carbonEnd = moleculeStructure.GetVertexFromId(aminoAcidReference.LastAtomId).Object;
Assume.That(carbonEnd.Element, Is.EqualTo(ElementName.Carbon));
Assert.That(carbonEnd.AminoAcidAtomName, Is.EqualTo("C"));
var remainingNonHydrogenAtoms = moleculeStructure.Vertices
.Select(v => v.Object)
.Where(atom => atom.Element != ElementName.Hydrogen)
.Except(new[] { nitrogen, carbonEnd })
.ToList();
Assert.That(remainingNonHydrogenAtoms.Count, Is.EqualTo(5));
var oxygen = remainingNonHydrogenAtoms.Single(atom => atom.Element == ElementName.Oxygen);
Assert.That(oxygen.AminoAcidAtomName, Is.EqualTo("O"));
var sideChainCarbons = remainingNonHydrogenAtoms.Where(atom => atom.Element == ElementName.Carbon).ToList();
Assert.That(sideChainCarbons.Count, Is.EqualTo(4));
Assert.That(sideChainCarbons.Select(atom => atom.AminoAcidAtomName), Is.EquivalentTo(new[] { "CA", "CB", "CG", "CD" }));
}
public void TestMasses()
{
var newlibrary1 = new AminoAcidLibrary();
//Dictionary<string, Compound> dictionaryIn1 = newlibrary1.LoadLibrary();
//foreach (KeyValuePair<string, Compound> matterObject in dictionaryIn1)
//{
// totalMass += matterObject.Value.MassMonoIsotopic;
// textM = matterObject.Value.MassMonoIsotopic.ToString() + "," + matterObject.Value.Symbol.ToString() + "," + matterObject.Value.Name.ToString() + Environment.NewLine;
// //Console.Write(textM);
//}
//Assert.AreEqual(totalMass, 2475.1616262881598);
var newlibrary2 = new CrossRingLibrary();
//Dictionary<string, Compound> dictionaryIn2 = newlibrary2.LoadLibrary();
//foreach (KeyValuePair<string, Compound> matterObject in dictionaryIn2)
//{
// totalMass += matterObject.Value.MassMonoIsotopic;
// textM = matterObject.Value.MassMonoIsotopic.ToString() + "," + matterObject.Value.Symbol.ToString() + "," + matterObject.Value.Name.ToString() + Environment.NewLine;
// //Console.Write(textM);
//}
//Assert.AreEqual(totalMass, 1432.3950300356437);
var newlibrary3 = new ElementLibrary();
//Dictionary<string, Element> dictionaryIn3 = newlibrary3.LoadLibrary();
//foreach (KeyValuePair<string, Element> matterObject in dictionaryIn3)
//{
// totalMass += matterObject.Value.MassMonoIsotopic;
// textM = matterObject.Value.MassMonoIsotopic.ToString() + "," + matterObject.Value.Symbol.ToString() + "," + matterObject.Value.Name.ToString() + Environment.NewLine;
// //Console.Write(textM);
//}
//Assert.AreEqual(totalMass, 12899.589616552506);
var newlibrary4 = new MiscellaneousMatterLibrary();
//Dictionary<string, Compound> dictionaryIn4 = newlibrary4.LoadLibrary();
//foreach (KeyValuePair<string, Compound> matterObject in dictionaryIn4)
//{
// totalMass += matterObject.Value.MassMonoIsotopic;
// textM = matterObject.Value.MassMonoIsotopic.ToString() + "," + matterObject.Value.Symbol.ToString() + "," + matterObject.Value.Name.ToString() + Environment.NewLine;
// //Console.Write(textM);
//}
//Assert.AreEqual(totalMass, 295.99644294548898);
var newlibrary5 = new MonosaccharideLibrary();
//Dictionary<string, Compound> dictionaryIn5 = newlibrary5.LoadLibrary();
//foreach (KeyValuePair<string, Compound> matterObject in dictionaryIn5)
//{
// totalMass += matterObject.Value.MassMonoIsotopic;
// textM = matterObject.Value.MassMonoIsotopic.ToString() + "," + matterObject.Value.Symbol.ToString() + "," + matterObject.Value.Name.ToString() + Environment.NewLine;
// //Console.Write(textM);
//}
//Assert.AreEqual(totalMass, 1687.5704282280092);
var newlibrary6 = new SubAtomicParticleLibrary();
//Dictionary<string, SubAtomicParticle> dictionaryIn6 = newlibrary6.LoadLibrary();
//foreach (KeyValuePair<string, SubAtomicParticle> matterObject in dictionaryIn6)
//{
// totalMass += matterObject.Value.MassMonoIsotopic;
// textM = matterObject.Value.MassMonoIsotopic.ToString() + "," + matterObject.Value.Symbol.ToString() + "," + matterObject.Value.Name.ToString() + Environment.NewLine;
// //Console.Write(textM);
//}
//Assert.AreEqual(totalMass, 2.0164899626494304);
}
