public void Create_symbol_defaultToUnknown()
{
IAtom a = AtomBuilder.Create("N/A")
.Build();
Assert.AreEqual(a.Element, Element.Unknown);
}
public void Create_symbol_null()
{
IAtom a = AtomBuilder.Create((string)null)
.Build();
Assert.AreEqual(a.Element, Element.Unknown);
}
public void Aliphatic_carbon_class1()
{
IAtom a = AtomBuilder.Aliphatic(Element.Carbon)
.AtomClass(1)
.Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.AtomClass, 1);
}
public void Aliphatic_charged_carbon_minus2()
{
IAtom a = AtomBuilder.Aliphatic(Element.Carbon)
.Charge(-2)
.Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.Charge, -2);
}
public void Aliphatic_carbon_3_hydrogens()
{
IAtom a = AtomBuilder.Aliphatic(Element.Carbon)
.NumOfHydrogens(3)
.Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.NumOfHydrogens, 3);
}
public void Aliphatic_carbon_14()
{
IAtom a = AtomBuilder.Aliphatic(Element.Carbon)
.Isotope(13)
.Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.Isotope, 13);
}
public void Aliphatic_charged_carbon_plus1()
{
IAtom a = AtomBuilder.Aliphatic(Element.Carbon)
.Cation
.Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.Charge, +1);
}
public void IsAromatic_element_cl()
{
try
{
IAtom a = AtomBuilder.Aromatic(Chlorine).Build();
Assert.Fail();
}
catch (ArgumentException)
{ }
}
public void Create_symbol_non_IsAromatic()
{
try
{
IAtom a = AtomBuilder.Create("cl").Build();
Assert.Fail();
}
catch (ArgumentException)
{ }
}
public void IsAromatic_symbol_null()
{
try
{
IAtom a = AtomBuilder.Aromatic((string)null).Build();
Assert.Fail();
}
catch (ArgumentNullException)
{ }
}
public void IsAromatic_element_c()
{
IAtom a = AtomBuilder.Aromatic(Carbon).Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.Isotope, -1);
Assert.AreEqual(a.Charge, 0);
Assert.AreEqual(a.AtomClass, 0);
Assert.AreEqual(a.IsAromatic(), true);
}
public void IsAromatic_element_null()
{
try
{
IAtom a = AtomBuilder.Aromatic((Element)null).Build();
Assert.Fail();
}
catch (ArgumentNullException)
{ }
}
public void Aliphatic_symbol_c()
{
IAtom a = AtomBuilder.Aliphatic("C").Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.Isotope, -1);
Assert.AreEqual(a.Charge, 0);
Assert.AreEqual(a.AtomClass, 0);
Assert.AreEqual(a.IsAromatic(), false);
}
public void IsAromatic_symbol_cl()
{
try
{
IAtom a = AtomBuilder.Aromatic("Cl").Build();
Assert.Fail();
}
catch (ArgumentException)
{ }
}
public void IsAromatic_symbol_n()
{
IAtom a = AtomBuilder.Aromatic("N")
.Build();
Assert.AreEqual(a.Element, Element.Nitrogen);
Assert.AreEqual(a.Isotope, -1);
Assert.AreEqual(a.Charge, 0);
Assert.AreEqual(a.AtomClass, 0);
Assert.AreEqual(a.IsAromatic(), true);
}
public void Create_symbol_IsAromatic_c()
{
IAtom a = AtomBuilder.Create("c")
.Build();
Assert.AreEqual(a.Element, Element.Carbon);
Assert.AreEqual(a.Isotope, -1);
Assert.AreEqual(a.Charge, 0);
Assert.AreEqual(a.AtomClass, 0);
Assert.AreEqual(a.IsAromatic(), true);
}
public void Aliphatic_element_n()
{
IAtom a = AtomBuilder.Aliphatic(Element.Nitrogen)
.Build();
Assert.AreEqual(a.Element, Element.Nitrogen);
Assert.AreEqual(a.Isotope, -1);
Assert.AreEqual(a.Charge, 0);
Assert.AreEqual(a.AtomClass, 0);
Assert.AreEqual(a.IsAromatic(), false);
}
public void Aliphatic_carbon_negative_hydrogens()
{
try
{
IAtom a = AtomBuilder.Aliphatic(Element.Carbon)
.NumOfHydrogens(-3)
.Build();
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{ }
}
public void Anticlockwise_parity()
{
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomBuilder.Aliphatic("C").Build())
.Add(AtomImpl.AliphaticSubset.Nitrogen)
.Add(AtomImpl.AliphaticSubset.Oxygen)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomBuilder.ExplicitHydrogen())
.Add(0, 1)
.Add(0, 2)
.Add(0, 3)
.Add(0, 4)
.CreateTetrahedral(0).LookingFrom(1)
.Neighbors(2, 3, 4)
.Parity(-1)
.Build()
.Build();
Assert.AreEqual(g.ToSmiles(), "[C@](N)(O)(C)[H]");
}
private static void Traverse(State s, int idx)
{
s.visit[idx] = true;
var mapIdx = s.g.GetAtom(idx).AtomClass;
if (mapIdx != 0)
{
if (s.map[mapIdx] == 0)
{
s.map[mapIdx] = ++s.nMaps;
}
mapIdx = s.map[mapIdx];
s.g.SetAtom(idx, AtomBuilder.FromExisting(s.g.GetAtom(idx)).AtomClass(mapIdx).Build());
}
foreach (var e in s.g.GetEdges(idx))
{
int nbr = e.Other(idx);
if (!s.visit[nbr])
{
Traverse(s, nbr);
}
}
}
public void Aliphatic_carbon_class_negative()
{
IAtom a = AtomBuilder.Aliphatic(Element.Carbon)
.AtomClass(-10)
.Build();
}
public void IsAromatic_Unknown_from_element()
{
Assert.IsNotNull(AtomBuilder.Aromatic(Unknown).Build());
}
/// <summary>
/// Add an aliphatic element with the specified number of carbons.
/// </summary>
/// <param name="e">element</param>
/// <param name="hCount">number of hydrogens</param>
/// <returns>graph builder for adding more atoms/connections</returns>
public GraphBuilder Add(Element e, int hCount)
{
return(Add(AtomBuilder.Aliphatic(e)
.NumOfHydrogens(hCount)
.Build()));
}
public void IsAromatic_Unknown_from_symbol()
{
Assert.IsNotNull(AtomBuilder.Aromatic("*").Build());
Assert.IsNotNull(AtomBuilder.Aromatic("R").Build());
}