public void Impossible_octatetraene()
{
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(0, 1)
.ConnectWithDoubleBond(1, 2)
.Add(2, 3)
.ConnectWithDoubleBond(3, 4)
.Add(4, 5)
.ConnectWithDoubleBond(5, 6)
.Add(6, 7)
.ConnectWithDoubleBond(7, 0)
.Geometric(1, 2).Together(0, 3)
.Geometric(3, 4).Opposite(2, 5)
.Geometric(5, 6).Together(4, 7)
.Geometric(7, 0).Together(6, 1)
.Build();
Assert.AreEqual(g.ToSmiles(), "C=1/C=C\\C=C/C=C\\C1");
}
public void CorrectCyclicDb()
{
// C\C=C/C1=C(CCC1)\C=C/C
// 0 1 2 3 4 567 8 9 0
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(0, 1)
.ConnectWithDoubleBond(1, 2)
.Add(2, 3)
.ConnectWithDoubleBond(3, 4)
.Add(4, 5)
.Add(5, 6)
.Add(6, 7)
.Add(7, 3)
.Add(4, 8)
.ConnectWithDoubleBond(8, 9)
.Add(9, 10)
.Geometric(1, 2).Opposite(0, 3)
.Geometric(8, 9).Opposite(4, 10)
.Geometric(3, 4).Opposite(2, 8)
.Build();
}
public void ResolveConflict3()
{
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(0, 1)
.ConnectWithDoubleBond(1, 2)
.Add(2, 3)
.ConnectWithDoubleBond(3, 4)
.Add(4, 5)
.Add(3, 6)
.ConnectWithDoubleBond(6, 7)
.Add(7, 8)
.Geometric(1, 2).Configure(0, 3, Opposite)
.Geometric(7, 6).Configure(8, 3, Opposite)
.Geometric(3, 4).Configure(2, 5, Opposite)
.Build();
}
public void Conjugated_resolve_conflict2()
{
// we assign the first, third then second - the second one cause
// a conflict and we must flip one of the others
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(0, 1)
.ConnectWithDoubleBond(1, 2)
.Add(2, 3)
.ConnectWithDoubleBond(3, 4)
.Add(4, 5)
.ConnectWithDoubleBond(5, 6)
.Add(6, 7)
.Geometric(1, 2).Opposite(0, 3)
.Geometric(5, 6).Together(4, 7)
.Geometric(3, 4).Together(2, 5)
.Build();
Assert.AreEqual(g.ToSmiles(), "F/C=C/C=C\\C=C/F");
}
public void E_1_2_difluroethene()
{
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(0, 1)
.ConnectWithDoubleBond(1, 2)
.Add(2, 3)
.Geometric(1, 2).Opposite(0, 3)
.Build();
Assert.AreEqual(g.ToSmiles(), "F/C=C/F");
}
public void BuildExtendedTetrahedral()
{
GraphBuilder gb = GraphBuilder.Create(4);
gb = gb.Add(Element.Carbon, 3)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 3)
.ConnectWithSingleBond(0, 1)
.ConnectWithDoubleBond(1, 2)
.ConnectWithDoubleBond(2, 3)
.ConnectWithSingleBond(3, 4)
.CreateExtendedTetrahedral(2).LookingFrom(1)
.Neighbors(2, 3, 4)
.Winding(Configuration.AL1)
.Build();
}
public void Suppress_benzene()
{
GraphBuilder gb = GraphBuilder.Create(5);
Assert.AreEqual("C=1C=CC=CC1",
gb.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(0, 1)
.Add(1, 2, Bond.Double)
.Add(2, 3)
.Add(3, 4, Bond.Double)
.Add(4, 5)
.Add(5, 0, Bond.Double).Build().ToSmiles());
}
public void ExtendedCisTrans()
{
GraphBuilder gb = GraphBuilder.Create(6)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.ConnectWithSingleBond(0, 1)
.ConnectWithDoubleBond(1, 2)
.ConnectWithDoubleBond(2, 3)
.ConnectWithDoubleBond(3, 4)
.ConnectWithSingleBond(4, 5)
.CreateExtendedGeometric(1, 4)
.Configure(0, 5, Configuration.ConfigurationDoubleBond.Together);
Assert.AreEqual("C/C=C=C=C\\C", gb.Build().ToSmiles());
}
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]");
}
public void Conjugated_consider_existing()
{
// the second configuration considers the existing configuration
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(0, 1)
.ConnectWithDoubleBond(1, 2)
.Add(2, 3)
.ConnectWithDoubleBond(3, 4)
.Add(4, 5)
.Geometric(1, 2).Together(0, 3)
.Geometric(3, 4).Together(2, 5)
.Build();
Assert.AreEqual(g.ToSmiles(), "F/C=C\\C=C/F");
}
public void OutputOrder()
{
Graph g = GraphBuilder.Create(5)
.Add(Element.Carbon, 3)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 2)
.Add(Element.Carbon, 3)
.Add(Element.Carbon, 2)
.Add(Element.Carbon, 3)
.Add(0, 1)
.Add(1, 2)
.Add(1, 3)
.Add(2, 4)
.Add(4, 5)
.Build();
g.Sort(new Graph.CanOrderFirst());
int[] visited = new int[g.Order];
Assert.AreEqual(g.ToSmiles(visited), "CC(CCC)C");
Assert.IsTrue(Compares.AreEqual(new int[] { 0, 1, 2, 5, 3, 4 }, visited));
}
public void Conjugated_resolve_conflict()
{
// assigning the second one first means we have to consider this
// on the first one
GraphBuilder gb = GraphBuilder.Create(5);
Graph g = gb.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Carbon)
.Add(AtomImpl.AliphaticSubset.Fluorine)
.Add(0, 1)
.ConnectWithDoubleBond(1, 2)
.Add(2, 3)
.ConnectWithDoubleBond(3, 4)
.Add(4, 5)
.Geometric(3, 4).Together(2, 5)
.Geometric(1, 2).Together(0, 3)
.Build();
Assert.AreEqual(g.ToSmiles(), "F\\C=C/C=C\\F");
}
public void BuildCHEMBL1204342()
{
GraphBuilder gb = GraphBuilder.Create(50);
gb.Add(Element.Carbon, 3)
.Add(Element.Carbon, 3)
.Add(Element.Carbon, 3)
.Add(Element.Carbon, 3)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 1)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Carbon, 0)
.Add(Element.Nitrogen, 1)
.Add(Element.Nitrogen, 1)
.Add(Element.Nitrogen, 1)
.Add(Element.Nitrogen, 1)
.Add(Element.Nitrogen, 0)
.Add(Element.Nitrogen, 0)
.Add(Element.Nitrogen, 0)
.Add(Element.Nitrogen, 0)
.Add(Element.Oxygen, 0)
.Add(Element.Chlorine, 1)
.Add(0, 20, Bond.Implicit)
.Add(1, 20, Bond.Implicit)
.Add(2, 21, Bond.Implicit)
.Add(3, 21, Bond.Implicit)
.Add(4, 8, Bond.Double)
.Add(4, 22, Bond.Implicit)
.Add(5, 9, Bond.Double)
.Add(5, 22, Bond.Implicit)
.Add(6, 10, Bond.Double)
.Add(6, 23, Bond.Implicit)
.Add(7, 11, Bond.Double)
.Add(7, 23, Bond.Implicit)
.Add(8, 24, Bond.Implicit)
.Add(9, 24, Bond.Implicit)
.Add(10, 25, Bond.Implicit)
.Add(11, 25, Bond.Implicit)
.Add(12, 14, Bond.Double)
.Add(12, 26, Bond.Implicit)
.Add(13, 15, Bond.Double)
.Add(13, 27, Bond.Implicit)
.Add(14, 28, Bond.Implicit)
.Add(15, 29, Bond.Implicit)
.Add(16, 17, Bond.Double)
.Add(16, 32, Bond.Implicit)
.Add(17, 33, Bond.Implicit)
.Add(18, 26, Bond.Double)
.Add(18, 30, Bond.Implicit)
.Add(19, 27, Bond.Double)
.Add(19, 31, Bond.Implicit)
.Add(20, 40, Bond.Implicit)
.Add(21, 41, Bond.Implicit)
.Add(22, 32, Bond.Double)
.Add(23, 33, Bond.Double)
.Add(24, 36, Bond.Double)
.Add(25, 37, Bond.Double)
.Add(26, 34, Bond.Implicit)
.Add(27, 35, Bond.Implicit)
.Add(28, 30, Bond.Implicit)
.Add(28, 42, Bond.Double)
.Add(29, 31, Bond.Implicit)
.Add(29, 43, Bond.Double)
.Add(30, 44, Bond.Double)
.Add(31, 45, Bond.Double)
.Add(32, 46, Bond.Implicit)
.Add(33, 46, Bond.Implicit)
.Add(34, 38, Bond.Double)
.Add(34, 40, Bond.Implicit)
.Add(35, 39, Bond.Double)
.Add(35, 41, Bond.Implicit)
.Add(36, 42, Bond.Implicit)
.Add(36, 44, Bond.Implicit)
.Add(37, 43, Bond.Implicit)
.Add(37, 45, Bond.Implicit);
gb.Geometric(23, 33).Together(6, 17)
.Geometric(25, 37).Together(10, 43)
.Geometric(24, 36).Together(8, 42)
.Geometric(22, 32).Opposite(4, 16);
Assert.AreEqual("CC(C)NC(C=1C=CC=2C(C1)=N\\C(=C3\\C=CC(/C=C3)=C\\4C=C/C(=C/5C=C/C(C=C5)=C/6\\N=C7C=CC(=CC7=N6)C(=N)NC(C)C)/O4)\\N2)=N.Cl", gb.Build().ToSmiles());
}
