public static IAtomContainer Acetone()
{
var acetone = new AtomContainer();
var carbon0 = acetone.AddAtom("C");
for (var i = 0; i < 3; i++)
{
acetone.AddBond(carbon0, acetone.AddAtom("H"), BondOrder.Single);
}
var carbon1 = acetone.AddAtom("C");
acetone.AddBond(carbon0, carbon1, BondOrder.Single);
acetone.AddBond(carbon1, acetone.AddAtom("O"), BondOrder.Double);
var carbon2 = acetone.AddAtom("C");
for (var i = 0; i < 3; i++)
{
acetone.AddBond(carbon2, acetone.AddAtom("H"), BondOrder.Single);
}
acetone.AddBond(carbon1, carbon2, BondOrder.Single);
acetone.SetProperty(NCDK.CDKPropertyName.Title, nameof(acetone));
return(acetone);
}
public static IAtomContainer Propane()
{
var propane = new AtomContainer();
var carbon = new[]
{
propane.AddAtom("C"),
propane.AddAtom("C"),
propane.AddAtom("C")
};
propane.AddBond(carbon[0], carbon[1], BondOrder.Single);
propane.AddBond(carbon[1], carbon[2], BondOrder.Single);
for (var j = 0; j < 3; j++)
{
propane.AddBond(carbon[0], propane.AddAtom("H"), BondOrder.Single);
}
for (var j = 0; j < 2; j++)
{
propane.AddBond(carbon[1], propane.AddAtom("H"), BondOrder.Single);
}
for (var j = 0; j < 3; j++)
{
propane.AddBond(carbon[2], propane.AddAtom("H"), BondOrder.Single);
}
propane.SetProperty(NCDK.CDKPropertyName.Title, nameof(propane));
return(propane);
}
public static IAtomContainer RubbingAlcohol()
{
var rubbingAlcohol = new AtomContainer();
var carbonTop = rubbingAlcohol.AddAtom("C");
for (var i = 0; i < 3; i++)
{
rubbingAlcohol.AddBond(carbonTop, rubbingAlcohol.AddAtom("H"), BondOrder.Single);
}
var carbonBottom = rubbingAlcohol.AddAtom("C");
for (var i = 0; i < 3; i++)
{
rubbingAlcohol.AddBond(carbonBottom, rubbingAlcohol.AddAtom("H"), BondOrder.Single);
}
var carbonCenter = rubbingAlcohol.AddAtom("C");
rubbingAlcohol.AddBond(carbonCenter, carbonTop, BondOrder.Single);
rubbingAlcohol.AddBond(carbonCenter, carbonBottom, BondOrder.Single);
rubbingAlcohol.AddBond(carbonCenter, rubbingAlcohol.AddAtom("H"), BondOrder.Single);
var oxy = rubbingAlcohol.AddAtom("O");
rubbingAlcohol.AddBond(carbonCenter, oxy, BondOrder.Single);
rubbingAlcohol.AddBond(oxy, rubbingAlcohol.AddAtom("H"), BondOrder.Single);
rubbingAlcohol.SetProperty(NCDK.CDKPropertyName.Title, nameof(rubbingAlcohol));
return(rubbingAlcohol);
}
public static IAtomContainer Vinegar()
{
var vinegar = new AtomContainer();
var carbon0 = vinegar.AddAtom("C");
for (var i = 0; i < 3; i++)
{
vinegar.AddBond(carbon0, vinegar.AddAtom("H"), BondOrder.Single);
}
var carbon1 = vinegar.AddAtom("C");
vinegar.AddBond(carbon0, carbon1, BondOrder.Single);
vinegar.AddBond(carbon1, vinegar.AddAtom("O"), BondOrder.Double);
var oxy = vinegar.AddAtom("O");
vinegar.AddBond(carbon1, oxy, BondOrder.Single);
vinegar.AddBond(oxy, vinegar.AddAtom("H"), BondOrder.Single);
vinegar.SetProperty(NCDK.CDKPropertyName.Title, nameof(vinegar));
return(vinegar);
}
public static IAtomContainer Ethanol()
{
var ethanol = new AtomContainer();
var carbon00 = ethanol.AddAtom("C");
for (var i = 0; i < 3; i++)
{
ethanol.AddBond(carbon00, ethanol.AddAtom("H"), BondOrder.Single);
}
var carbon01 = ethanol.AddAtom("C");
ethanol.AddBond(carbon00, carbon01, BondOrder.Single);
for (var i = 0; i < 2; i++)
{
ethanol.AddBond(carbon01, ethanol.AddAtom("H"), BondOrder.Single);
}
var oxy = ethanol.AddAtom("O");
ethanol.AddBond(carbon01, oxy, BondOrder.Single);
ethanol.AddBond(oxy, ethanol.AddAtom("H"), BondOrder.Single);
ethanol.SetProperty(NCDK.CDKPropertyName.Title, nameof(ethanol));
return(ethanol);
}
public static IAtomContainer AppleSmell()
{
var appleSmell = new AtomContainer();
var carbons = new[]
{
appleSmell.AddAtom("C"), appleSmell.AddAtom("C"),
appleSmell.AddAtom("C"), appleSmell.AddAtom("C"),
appleSmell.AddAtom("C"), appleSmell.AddAtom("C"),
};
var oxygens = new[]
{
appleSmell.AddAtom("O"), appleSmell.AddAtom("O")
};
appleSmell.AddBond(carbons[0], carbons[1], BondOrder.Single);
appleSmell.AddBond(carbons[1], carbons[2], BondOrder.Single);
appleSmell.AddBond(carbons[2], carbons[3], BondOrder.Single);
appleSmell.AddBond(carbons[3], oxygens[0], BondOrder.Double);
appleSmell.AddBond(carbons[3], oxygens[1], BondOrder.Single);
appleSmell.AddBond(oxygens[1], carbons[4], BondOrder.Single);
appleSmell.AddBond(carbons[4], carbons[5], BondOrder.Single);
appleSmell.SetProperty(NCDK.CDKPropertyName.Title, nameof(appleSmell));
return(appleSmell);
}
public static IAtomContainer Ethylene()
{
var ethylene = new AtomContainer();
var carbon = new[]
{
new Atom(ChemicalElement.C),
new Atom(ChemicalElement.C),
};
for (var i = 0; i < carbon.Length; i++)
{
ethylene.Atoms.Add(carbon[i]);
for (var j = 0; j < 2; j++)
{
var hij = new Atom(ChemicalElement.H);
ethylene.Atoms.Add(hij);
ethylene.Bonds.Add(new Bond(carbon[i], hij, BondOrder.Single));
}
}
ethylene.Bonds.Add(new Bond(carbon[0], carbon[1], BondOrder.Double));
ethylene.SetProperty(NCDK.CDKPropertyName.Title, nameof(ethylene));
return(ethylene);
}
public static IAtomContainer Glycine()
{
var glycine = new AtomContainer();
var nitrogen = glycine.AddAtom("N");
for (var i = 0; i < 2; i++)
{
glycine.AddBond(nitrogen, glycine.AddAtom("H"), BondOrder.Single);
}
var carbon0 = glycine.AddAtom("C");
glycine.AddBond(nitrogen, carbon0, BondOrder.Single);
for (var i = 0; i < 2; i++)
{
glycine.AddBond(carbon0, glycine.AddAtom("H"), BondOrder.Single);
}
var carbon1 = glycine.AddAtom("C");
glycine.AddBond(carbon0, carbon1, BondOrder.Single);
glycine.AddBond(carbon1, glycine.AddAtom("O"), BondOrder.Double);
var oxy = glycine.AddAtom("O");
glycine.AddBond(carbon1, oxy, BondOrder.Single);
glycine.AddBond(oxy, glycine.AddAtom("H"), BondOrder.Single);
glycine.SetProperty(NCDK.CDKPropertyName.Title, nameof(glycine));
return(glycine);
}
public static AtomContainer GetProgrammaticButanone()
{
var mol = new AtomContainer();
var c00 = new Atom(ChemicalElement.C);
mol.Atoms.Add(c00);
for (var i = 0; i < 3; i++)
{
var h = new Atom(ChemicalElement.H);
var bond = new Bond(c00, h, BondOrder.Single);
mol.Bonds.Add(bond);
mol.Atoms.Add(h);
}
var c01 = new Atom(ChemicalElement.C);
mol.Atoms.Add(c01);
for (var i = 0; i < 2; i++)
{
var h = new Atom(ChemicalElement.H);
var bond = new Bond(c01, h, BondOrder.Single);
mol.Bonds.Add(bond);
mol.Atoms.Add(h);
}
mol.Bonds.Add(new Bond(c00, c01, BondOrder.Single));
var c02 = new Atom(ChemicalElement.C);
mol.Atoms.Add(c02);
var o00 = new Atom(ChemicalElement.O);
mol.Atoms.Add(o00);
mol.Bonds.Add(new Bond(c02, o00, BondOrder.Double));
mol.Bonds.Add(new Bond(c01, c02, BondOrder.Single));
var c03 = new Atom(ChemicalElement.C);
mol.Atoms.Add(c03);
for (var i = 0; i < 3; i++)
{
var h = new Atom(ChemicalElement.H);
var bond = new Bond(c03, h, BondOrder.Single);
mol.Bonds.Add(bond);
mol.Atoms.Add(h);
}
mol.Bonds.Add(new Bond(c02, c03, BondOrder.Single));
mol.SetProperty(NCDK.CDKPropertyName.Title, "butanone");
return(mol);
}
public void TestInChI()
{
var mol = new AtomContainer();
string inchi = "InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)";
mol.SetProperty(CDKPropertyName.InChI, inchi);
IAtomContainer roundTrippedMol = CMLRoundTripTool.RoundTripMolecule(convertor, mol);
Assert.IsNotNull(roundTrippedMol);
Assert.AreEqual(inchi, roundTrippedMol.GetProperty <string>(CDKPropertyName.InChI));
}
/// <summary>
/// see https://pubchem.ncbi.nlm.nih.gov/compound/6389
/// </summary>
public static IAtomContainer Trichlorofluoromethane()
{
var trichlorofluoromethane = new AtomContainer();
var carbon = trichlorofluoromethane.AddAtom("C");
for (var i = 0; i < 3; i++)
{
trichlorofluoromethane.AddBond(carbon, trichlorofluoromethane.AddAtom("Cl"), BondOrder.Single);
}
trichlorofluoromethane.AddBond(carbon, trichlorofluoromethane.AddAtom("F"), BondOrder.Single);
trichlorofluoromethane.SetProperty(NCDK.CDKPropertyName.Title, nameof(trichlorofluoromethane));
return(trichlorofluoromethane);
}
public static IAtomContainer DiethylEther()
{
var diethylEther = new AtomContainer();
var carbon0 = diethylEther.AddAtom("C");
for (var i = 0; i < 3; i++)
{
diethylEther.AddBond(carbon0, diethylEther.AddAtom("H"), BondOrder.Single);
}
var carbon1 = diethylEther.AddAtom("C");
diethylEther.AddBond(carbon0, carbon1, BondOrder.Single);
for (var i = 0; i < 2; i++)
{
diethylEther.AddBond(carbon1, diethylEther.AddAtom("H"), BondOrder.Single);
}
var oxy = diethylEther.AddAtom("O");
diethylEther.AddBond(carbon1, oxy, BondOrder.Single);
var carbon2 = diethylEther.AddAtom("C");
diethylEther.AddBond(oxy, carbon2, BondOrder.Single);
for (var i = 0; i < 2; i++)
{
diethylEther.AddBond(carbon2, diethylEther.AddAtom("H"), BondOrder.Single);
}
var carbon3 = diethylEther.AddAtom("C");
for (var i = 0; i < 3; i++)
{
diethylEther.AddBond(carbon3, diethylEther.AddAtom("H"), BondOrder.Single);
}
diethylEther.AddBond(carbon2, carbon3, BondOrder.Single);
diethylEther.SetProperty(NCDK.CDKPropertyName.Title, nameof(diethylEther));
return(diethylEther);
}
public static IAtomContainer Water()
{
var water = new AtomContainer();
var oxy = water.AddAtom("O");
oxy.Charge = -0.5;
var h1 = water.AddAtom("H");
h1.Charge = 0.25;
var h2 = water.AddAtom("H");
h2.Charge = 0.25;
water.AddBond(oxy, h1, BondOrder.Single);
water.AddBond(oxy, h2, BondOrder.Single);
water.SetProperty(NCDK.CDKPropertyName.Title, nameof(water));
return(water);
}
public static IAtomContainer Refrigerant()
{
var refrigerant = new AtomContainer();
var carbon = refrigerant.AddAtom("C");
for (var i = 0; i < 2; i++)
{
refrigerant.AddBond(carbon, refrigerant.AddAtom("Cl"), BondOrder.Single);
}
for (var i = 0; i < 2; i++)
{
refrigerant.AddBond(carbon, refrigerant.AddAtom("F"), BondOrder.Single);
}
refrigerant.SetProperty(NCDK.CDKPropertyName.Title, nameof(refrigerant));
return(refrigerant);
}
public void TestWrite_IAtomContainer_MultIAtomContainer()
{
StringWriter writer = new StringWriter();
SDFWriter sdfWriter = new SDFWriter(writer);
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty("foo", "bar");
sdfWriter.Write(molecule);
molecule = new AtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty("toys", "r-us");
sdfWriter.Write(molecule);
sdfWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("foo") != -1);
Assert.IsTrue(writer.ToString().IndexOf("bar") != -1);
Assert.IsTrue(writer.ToString().IndexOf("toys") != -1);
Assert.IsTrue(writer.ToString().IndexOf("r-us") != -1);
Assert.IsTrue(writer.ToString().IndexOf("$$$$") != -1);
}
public static IAtomContainer Antifreeze()
{
var antifreeze = new AtomContainer();
var oxy0 = antifreeze.AddAtom("O");
antifreeze.AddBond(antifreeze.AddAtom("H"), oxy0, BondOrder.Single);
var carbon0 = antifreeze.AddAtom("C");
antifreeze.AddBond(oxy0, carbon0, BondOrder.Single);
for (var i = 0; i < 2; i++)
{
antifreeze.AddBond(carbon0, antifreeze.AddAtom("H"), BondOrder.Single);
}
var carbon1 = antifreeze.AddAtom("C");
antifreeze.AddBond(carbon0, carbon1, BondOrder.Single);
for (var i = 0; i < 2; i++)
{
antifreeze.AddBond(carbon1, antifreeze.AddAtom("H"), BondOrder.Single);
}
var oxy1 = antifreeze.AddAtom("O");
antifreeze.AddBond(carbon1, oxy1, BondOrder.Single);
antifreeze.AddBond(oxy1, antifreeze.AddAtom("H"), BondOrder.Single);
antifreeze.SetProperty(NCDK.CDKPropertyName.Title, nameof(antifreeze));
return(antifreeze);
}
public static IAtomContainer DDT()
{
var ddt = new AtomContainer();
var benzeneLeft = Benzene();
benzeneLeft.AddBond(benzeneLeft.Atoms[0], benzeneLeft.AddAtom("Cl"), BondOrder.Single);
var benzeneRight = Benzene();
benzeneRight.AddBond(benzeneRight.Atoms[0], benzeneRight.AddAtom("Cl"), BondOrder.Single);
var carbon00 = ddt.AddAtom("C");
benzeneLeft.Atoms.Add(carbon00);
benzeneLeft.AddBond(benzeneLeft.Atoms[3], carbon00, BondOrder.Single);
benzeneRight.Atoms.Add(carbon00);
benzeneRight.AddBond(benzeneRight.Atoms[3], carbon00, BondOrder.Single);
ddt.AddAtomContainer(benzeneLeft);
ddt.AddAtomContainer(benzeneRight);
var carbon01 = ddt.AddAtom("C");
ddt.AddBond(carbon00, carbon01, BondOrder.Single);
for (var i = 0; i < 3; i++)
{
ddt.AddBond(carbon01, ddt.AddAtom("Cl"), BondOrder.Single);
}
ddt.SetProperty(NCDK.CDKPropertyName.Title, "DDT");
return(ddt);
}