public void UnlabelledHydrogens()
{
IAtomContainer container = CDK.SmilesParser
.ParseSmiles("[H]C([H])([H])[H]");
Assert.IsTrue(Compares.AreEqual(new long[] { 2, 1, 3, 4, 5 }, InChINumbersTools.GetUSmilesNumbers(container)));
}
public void Bug1370()
{
IAtomContainer container = CDK.SmilesParser
.ParseSmiles("O=[Bi]Cl");
Assert.IsTrue(Compares.AreEqual(new long[] { 3, 1, 2 }, InChINumbersTools.GetUSmilesNumbers(container)));
}
public void ParseMultipleDisconnected()
{
// O.N1C=NC=C1.O.O=O
Assert.IsTrue(Compares.AreEqual(
new long[] { 8, 4, 3, 5, 2, 1, 9, 6, 7 },
InChINumbersTools.ParseUSmilesNumbers(
"AuxInfo=1/1/N:5,6,3,4,2;8,9;1;7/E:(1,2)(4,5);(1,2);;/F:6,5,3,2,4;3m/E:;m;;/rA:9ONCNCCOOO/rB:;s2;d3;s4;s2d5;;;d8;/rC:;;;;;;;;;",
Mock(9))));
}
public void ParseDisconnected()
{
// O.N1C=NC=C1
Assert.IsTrue(Compares.AreEqual(
new long[] { 6, 4, 3, 5, 2, 1 },
InChINumbersTools.ParseUSmilesNumbers(
"AuxInfo=1/1/N:5,6,3,4,2;1/E:(1,2)(4,5);/F:6,5,3,2,4;m/rA:6ONCNCC/rB:;s2;d3;s4;s2d5;/rC:;;;;;;",
Mock(6))));
}
public void ParseRecMet()
{
// C(=O)O[Pt](N)(N)Cl
Assert.IsTrue(Compares.AreEqual(
new long[] { 7, 6, 1, 5, 3, 4, 2 },
InChINumbersTools.ParseUSmilesNumbers(
"AuxInfo=1/1/N:3,2,4;7;5;6;1/E:(2,3);;;;/F:5m/E:m;;;;/CRV:;;2*1-1;/rA:7PtOCONNCl/rB:s1;s2;d3;s1;s1;s1;/rC:;;;;;;;/R:/0/N:3,7,5,6,4,2,1/E:(3,4)",
Mock(7))));
}
public void ParseFixedH()
{
// N1C=NC=C1
Assert.IsTrue(Compares.AreEqual(
new long[] { 4, 3, 5, 2, 1 },
InChINumbersTools.ParseUSmilesNumbers(
"AuxInfo=1/1/N:4,5,2,3,1/E:(1,2)(4,5)/F:5,4,2,1,3/rA:5NCNCC/rB:s1;d2;s3;s1d4;/rC:;;;;;",
Mock(5))));
}
public void FixedH()
{
var parser = CDK.SmilesParser;
var atomContainer = parser.ParseSmiles("N1C=NC2=CC=CC=C12");
string auxInfo = InChINumbersTools.AuxInfo(atomContainer, InChIOption.FixedH);
string expected = "AuxInfo=1/1/" + "N:6,7,5,8,2,4,9,3,1/" + "E:(1,2)(3,4)(6,7)(8,9)/" + "F:7,6,8,5,2,9,4,1,3/"
+ "rA:9NCNCCCCCC/" + "rB:s1;d2;s3;d4;s5;d6;s7;s1s4d8;/" + "rC:;;;;;;;;;";
Assert.AreEqual(expected, auxInfo);
}
public void TestSimpleNumbering()
{
IAtomContainer container = new AtomContainer();
container.Atoms.Add(new Atom("O"));
container.Atoms.Add(new Atom("C"));
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
long[] numbers = InChINumbersTools.GetNumbers(container);
Assert.AreEqual(2, numbers.Length);
Assert.AreEqual(2, numbers[0]);
Assert.AreEqual(1, numbers[1]);
}
public void TestGlycine_uSmiles()
{
var parser = CDK.SmilesParser;
var atomContainer = parser.ParseSmiles("C(C(=O)O)N");
long[] numbers = InChINumbersTools.GetNumbers(atomContainer);
Assert.AreEqual(5, numbers.Length);
Assert.AreEqual(1, numbers[0]);
Assert.AreEqual(2, numbers[1]);
Assert.AreEqual(4, numbers[2]);
Assert.AreEqual(5, numbers[3]);
Assert.AreEqual(3, numbers[4]);
}
public void TestHydrogens()
{
IAtomContainer container = new AtomContainer();
container.Atoms.Add(new Atom("H"));
container.Atoms.Add(new Atom("C"));
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
container.Atoms.Add(new Atom("H"));
container.AddBond(container.Atoms[1], container.Atoms[2], BondOrder.Single);
container.Atoms.Add(new Atom("H"));
container.AddBond(container.Atoms[1], container.Atoms[3], BondOrder.Single);
container.Atoms.Add(new Atom("H"));
container.AddBond(container.Atoms[1], container.Atoms[4], BondOrder.Single);
long[] numbers = InChINumbersTools.GetNumbers(container);
Assert.AreEqual(5, numbers.Length);
Assert.AreEqual(0, numbers[0]);
Assert.AreEqual(1, numbers[1]);
Assert.AreEqual(0, numbers[2]);
Assert.AreEqual(0, numbers[3]);
Assert.AreEqual(0, numbers[4]);
}
public void Protons()
{
IAtomContainer container = CDK.SmilesParser
.ParseSmiles("[H+].[H+].F[Si-2](F)(F)(F)(F)F");
Assert.IsTrue(Compares.AreDeepEqual(new long[] { 8, 9, 1, 7, 2, 3, 4, 5, 6 }, InChINumbersTools.GetUSmilesNumbers(container)));
}
public void FavorCarbonyl()
{
IAtomContainer container = CDK.SmilesParser.ParseSmiles("P([O-])=O");
Assert.IsTrue(Compares.AreEqual(new long[] { 3, 2, 1 }, InChINumbersTools.GetUSmilesNumbers(container)));
}
public void ParseStandard()
{
Assert.IsTrue(Compares.AreEqual(
new long[] { 3, 2, 1 },
InChINumbersTools.ParseUSmilesNumbers("AuxInfo=1/0/N:3,2,1/rA:3OCC/rB:s1;s2;/rC:;;;", Mock(3))));
}