public void DecodeCoordinates()
{
Vector2[] points = IdentityTemplateLibrary.DecodeCoordinates("12.5, 5.5, 4, 2");
Assert.AreEqual(2, points.Length);
Assert.AreEqual(12.5, points[0].X, 0.01);
Assert.AreEqual(5.5, points[0].Y, 0.01);
Assert.AreEqual(4, points[1].X, 0.01);
Assert.AreEqual(2, points[1].Y, 0.01);
}
/// <summary>
/// Convert to an identity template library.
/// </summary>
/// <returns>identity template library</returns>
internal IdentityTemplateLibrary ToIdentityTemplateLibrary()
{
var lib = IdentityTemplateLibrary.Empty();
foreach (var mol in templates)
{
lib.Add(AtomContainerManipulator.Anonymise(mol));
}
return(lib);
}
public void EncodeEntry()
{
var smiles = "CO";
Vector2[] points = new Vector2[] { new Vector2(12.5f, 5.5f), new Vector2(4f, 2f) };
string encoded = IdentityTemplateLibrary.EncodeEntry(new KeyValuePair <string, Vector2[]>(smiles, points));
var entry = IdentityTemplateLibrary.DecodeEntry(encoded);
Assert.AreEqual("CO |(12.5,5.5,;4,2,)|", encoded);
}
/// <summary>
/// Add one template library to another.
/// </summary>
/// <param name="library">another template library</param>
/// <returns>this library with the other one added in (allows chaining)</returns>
public IdentityTemplateLibrary Add(IdentityTemplateLibrary library)
{
foreach (var e in library.templateMap)
{
foreach (var v in e.Value)
{
this.templateMap.Add(e.Key, v);
}
}
return(this);
}
public void Store()
{
IdentityTemplateLibrary lib = IdentityTemplateLibrary.Empty();
lib.Add(IdentityTemplateLibrary.DecodeEntry("[C][C][O] 0, 1, 2, 3, 4, 5"));
lib.Add(IdentityTemplateLibrary.DecodeEntry("[C][C] 0, 1, 2, 3"));
using (var baos = new MemoryStream())
{
lib.Store(baos);
Assert.AreEqual(
"[C][C][O] |(0,1,;2,3,;4,5,)|\n[C][C] |(0,1,;2,3,)|\n",
Encoding.UTF8.GetString(baos.ToArray()));
}
}
public void AssignEthanolNoEntry()
{
IAtomContainer container = new AtomContainer();
container.Atoms.Add(new Atom("O"));
container.Atoms.Add(new Atom("C"));
container.Atoms.Add(new Atom("C"));
container.Atoms[0].ImplicitHydrogenCount = 0;
container.Atoms[1].ImplicitHydrogenCount = 0;
container.Atoms[2].ImplicitHydrogenCount = 0;
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
container.AddBond(container.Atoms[1], container.Atoms[2], BondOrder.Single);
Assert.IsFalse(IdentityTemplateLibrary.Empty().AssignLayout(container));
}
/// <summary>
/// Load a template library from an input stream.
/// </summary>
/// <returns>loaded template library</returns>
/// <exception cref="IOException">low level IO error</exception>
public static IdentityTemplateLibrary Load(Stream ins)
{
using (var br = new StreamReader(ins))
{
string line = null;
var library = new IdentityTemplateLibrary();
while ((line = br.ReadLine()) != null)
{
// skip comments
if (line[0] == '#')
{
continue;
}
library.Add(DecodeEntry(line));
}
return(library);
}
}
public void AssignEthanol()
{
IAtomContainer container = new AtomContainer();
container.Atoms.Add(new Atom("O"));
container.Atoms.Add(new Atom("C"));
container.Atoms.Add(new Atom("C"));
container.Atoms[0].ImplicitHydrogenCount = 0;
container.Atoms[1].ImplicitHydrogenCount = 0;
container.Atoms[2].ImplicitHydrogenCount = 0;
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
container.AddBond(container.Atoms[1], container.Atoms[2], BondOrder.Single);
IdentityTemplateLibrary lib = IdentityTemplateLibrary.Empty();
lib.Add(IdentityTemplateLibrary.DecodeEntry("OCC 4, 5, 2, 3, 0, 1"));
Assert.IsTrue(lib.AssignLayout(container));
Assert.AreEqual(4, container.Atoms[0].Point2D.Value.X, 0.01);
Assert.AreEqual(5, container.Atoms[0].Point2D.Value.Y, 0.01);
Assert.AreEqual(2, container.Atoms[1].Point2D.Value.X, 0.01);
Assert.AreEqual(3, container.Atoms[1].Point2D.Value.Y, 0.01);
Assert.AreEqual(0, container.Atoms[2].Point2D.Value.X, 0.01);
Assert.AreEqual(1, container.Atoms[2].Point2D.Value.Y, 0.01);
}