public static IAtomContainer PineappleSmell()
{
var pineappleSmell = new AtomContainer();
var carbons = new[]
{
pineappleSmell.AddAtom("C"), pineappleSmell.AddAtom("C"),
pineappleSmell.AddAtom("C"), pineappleSmell.AddAtom("C"),
pineappleSmell.AddAtom("C"), pineappleSmell.AddAtom("C"),
pineappleSmell.AddAtom("C"), pineappleSmell.AddAtom("C"),
};
var oxygens = new[]
{
pineappleSmell.AddAtom("O"), pineappleSmell.AddAtom("O")
};
pineappleSmell.AddBond(carbons[0], carbons[1], BondOrder.Single);
pineappleSmell.AddBond(carbons[1], carbons[2], BondOrder.Single);
pineappleSmell.AddBond(carbons[2], carbons[3], BondOrder.Single);
pineappleSmell.AddBond(carbons[3], carbons[4], BondOrder.Single);
pineappleSmell.AddBond(carbons[4], oxygens[0], BondOrder.Double);
pineappleSmell.AddBond(carbons[4], oxygens[1], BondOrder.Single);
pineappleSmell.AddBond(oxygens[1], carbons[5], BondOrder.Single);
pineappleSmell.AddBond(carbons[5], carbons[6], BondOrder.Single);
pineappleSmell.AddBond(carbons[6], carbons[7], BondOrder.Single);
pineappleSmell.SetProperty(NCDK.CDKPropertyName.Title, nameof(pineappleSmell));
return(pineappleSmell);
}
public static IAtomContainer WashingSoda()
{
var co3 = new AtomContainer();
var carbon = co3.AddAtom("C");
co3.AddBond(carbon, co3.AddAtom("O"), BondOrder.Double);
for (var i = 0; i < 2; i++)
{
var oxy = co3.AddAtom("O");
oxy.FormalCharge = -1;
co3.AddBond(carbon, oxy, BondOrder.Single);
}
var washingSoda = new Crystal(co3);
var sodium00 = washingSoda.AddAtom("Na");
sodium00.FormalCharge = 1;
var sodium01 = washingSoda.AddAtom("Na");
sodium01.FormalCharge = 1;
washingSoda.Title = nameof(washingSoda);
return(washingSoda);
}
public static IAtomContainer RootKiller()
{
var mol = new AtomContainer();
var sulfur = mol.AddAtom("S");
for (var i = 0; i < 2; i++)
{
mol.AddBond(sulfur, mol.AddAtom("O"), BondOrder.Double);
}
var oxy00 = mol.AddAtom("O");
oxy00.FormalCharge = -1;
mol.AddBond(sulfur, oxy00, BondOrder.Single);
var oxy01 = mol.AddAtom("O");
oxy01.FormalCharge = -1;
mol.AddBond(sulfur, oxy01, BondOrder.Single);
var rootKiller = new Crystal(mol);
var mg = rootKiller.AddAtom("Cu");
mg.FormalCharge = 2;
rootKiller.Title = nameof(rootKiller);
return(rootKiller);
}
public static IAtomContainer EpsomSalt()
{
var mol = new AtomContainer();
var sulfur = mol.AddAtom("S");
for (var i = 0; i < 2; i++)
{
mol.AddBond(sulfur, mol.AddAtom("O"), BondOrder.Double);
}
var oxy00 = mol.AddAtom("O");
oxy00.FormalCharge = -1;
mol.AddBond(sulfur, oxy00, BondOrder.Single);
var oxy01 = mol.AddAtom("O");
oxy01.FormalCharge = -1;
mol.AddBond(sulfur, oxy01, BondOrder.Single);
var epsomSalt = new Crystal(mol);
var mg = epsomSalt.AddAtom("Mg");
mg.FormalCharge = 2;
epsomSalt.Title = nameof(epsomSalt);
return(epsomSalt);
}
public static IAtomContainer BakingSoda()
{
var co3h = new AtomContainer();
var carbon = co3h.AddAtom("C");
co3h.AddBond(carbon, co3h.AddAtom("O"), BondOrder.Double);
var oxy00 = co3h.AddAtom("O");
co3h.AddBond(carbon, oxy00, BondOrder.Single);
co3h.AddBond(oxy00, co3h.AddAtom("H"), BondOrder.Single);
var oxy01 = co3h.AddAtom("O");
oxy01.FormalCharge = -1;
co3h.AddBond(carbon, oxy01, BondOrder.Single);
var bakingSoda = new Crystal(co3h);
var sodium = bakingSoda.AddAtom("Na");
sodium.FormalCharge = 1;
bakingSoda.Title = nameof(bakingSoda);
return(bakingSoda);
}
public static IAtomContainer Quicklime()
{
var quicklime = new AtomContainer();
quicklime.AddBond(quicklime.AddAtom("O"), quicklime.AddAtom("Ca"), BondOrder.Double);
quicklime.Title = nameof(quicklime);
return(quicklime);
}
public static IAtomContainer MuriaticAcid()
{
var muriaticAcid = new AtomContainer();
muriaticAcid.AddBond(muriaticAcid.AddAtom("Cl"), muriaticAcid.AddAtom("H"), BondOrder.Single);
muriaticAcid.Title = nameof(muriaticAcid);
return(muriaticAcid);
}
public static IAtomContainer Nos()
{
var nos = new AtomContainer();
var nitrogen = nos.AddAtom("N");
nos.AddBond(nitrogen, nos.AddAtom("O"), BondOrder.Single);
nos.AddBond(nitrogen, nos.AddAtom("O"), BondOrder.Single);
nos.Title = nameof(nos);
return(nos);
}
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 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 CitricAcid()
{
var citricAcid = new AtomContainer();
var carbons = Enumerable.Range(0, 6).Select(i => citricAcid.AddAtom("C")).ToList();
var oxygens = Enumerable.Range(0, 7).Select(i => citricAcid.AddAtom("O")).ToList();
citricAcid.AddBond(oxygens[0], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(oxygens[0], carbons[0], BondOrder.Single);
citricAcid.AddBond(oxygens[1], carbons[0], BondOrder.Double);
citricAcid.AddBond(carbons[0], carbons[1], BondOrder.Single);
citricAcid.AddBond(carbons[1], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(carbons[1], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(carbons[1], carbons[2], BondOrder.Single);
citricAcid.AddBond(oxygens[2], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(carbons[2], oxygens[2], BondOrder.Single);
citricAcid.AddBond(carbons[2], carbons[3], BondOrder.Single);
citricAcid.AddBond(oxygens[3], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(carbons[3], oxygens[3], BondOrder.Single);
citricAcid.AddBond(carbons[3], oxygens[4], BondOrder.Double);
citricAcid.AddBond(carbons[2], carbons[4], BondOrder.Single);
citricAcid.AddBond(carbons[4], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(carbons[4], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(carbons[4], carbons[5], BondOrder.Single);
citricAcid.AddBond(oxygens[5], citricAcid.AddAtom("H"), BondOrder.Single);
citricAcid.AddBond(carbons[5], oxygens[5], BondOrder.Single);
citricAcid.AddBond(carbons[5], oxygens[6], BondOrder.Double);
citricAcid.Title = nameof(citricAcid);
return(citricAcid);
}
public static IAtomContainer Hydronium()
{
var hydronium = new AtomContainer();
var oxy = hydronium.AddAtom("O");
for (var i = 0; i < 3; i++)
{
hydronium.AddBond(oxy, hydronium.AddAtom("H"), BondOrder.Single);
}
hydronium.Title = nameof(hydronium);
return(hydronium);
}
/// <remarks>
/// <![CDATA[
/// Ammonium Acetate by neutralizing clear household ammonia with
/// distilled white vinegar and evaporating to dryness
/// Ammonium Chloride by neutralizing clear household ammonia with
/// hardware store muriatic acid and evaporating to dryness
/// ]]>
/// </remarks>
public static IAtomContainer Ammonia()
{
var ammonia = new AtomContainer();
var nitrogen = ammonia.AddAtom("N");
for (var i = 0; i < 3; i++)
{
ammonia.AddBond(nitrogen, ammonia.AddAtom("H"), BondOrder.Single);
}
ammonia.Title = nameof(ammonia);
return(ammonia);
}
public static IAtomContainer Rust()
{
var rust = new AtomContainer();
var oxygen = Enumerable.Range(0, 3).Select(i => rust.AddAtom("O")).ToList();
var iron = Enumerable.Range(0, 2).Select(i => rust.AddAtom("Fe")).ToList();
rust.AddBond(oxygen[0], iron[0], BondOrder.Double);
rust.AddBond(iron[0], oxygen[1], BondOrder.Single);
rust.AddBond(oxygen[1], iron[1], BondOrder.Single);
rust.AddBond(iron[1], oxygen[2], BondOrder.Double);
rust.Title = "rust";
return(rust);
}
public static IAtomContainer Methenium()
{
var methenium = new AtomContainer();
var carbon = methenium.AddAtom("C");
for (var i = 0; i < 3; i++)
{
methenium.AddBond(carbon, methenium.AddAtom("H"), BondOrder.Single);
}
//the electron pair is gone
carbon.FormalCharge = 1;
methenium.Title = nameof(methenium);
return(methenium);
}
/// <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 NitricAcid()
{
var nitricAcid = new AtomContainer();
var nitrogen = nitricAcid.AddAtom("N");
nitrogen.FormalCharge = 1;
nitricAcid.AddBond(nitrogen, nitricAcid.AddAtom("O"), BondOrder.Double);
var oxy = nitricAcid.AddAtom("O");
oxy.FormalCharge = -1;
nitricAcid.AddBond(nitrogen, oxy, BondOrder.Single);
var oh = nitricAcid.AddBond(nitricAcid.AddAtom("O"), nitricAcid.AddAtom("H"), BondOrder.Single);
nitricAcid.AddBond(nitrogen, oh.Begin, BondOrder.Single);
nitricAcid.Title = nameof(nitricAcid);
return(nitricAcid);
}
public static IAtomContainer Lye()
{
var hydroxideAnion = new AtomContainer();
var oxy = hydroxideAnion.AddAtom("O");
oxy.FormalCharge = -1;
hydroxideAnion.AddBond(oxy, hydroxideAnion.AddAtom("H"), BondOrder.Single);
var lye = new Crystal(hydroxideAnion);
var sodium = lye.AddAtom("Na");
sodium.FormalCharge = 1;
lye.Title = nameof(lye);
return(lye);
}
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 static IAtomContainer Acetonitrile()
{
var acetonitrile = new AtomContainer();
var carbon0 = acetonitrile.AddAtom("C");
for (var i = 0; i < 3; i++)
{
acetonitrile.AddBond(carbon0, acetonitrile.AddAtom("H"), BondOrder.Single);
}
var carbon1 = acetonitrile.AddAtom("C");
acetonitrile.AddBond(carbon0, carbon1, BondOrder.Single);
acetonitrile.AddBond(carbon1, acetonitrile.AddAtom("N"), BondOrder.Triple);
acetonitrile.SetProperty(NCDK.CDKPropertyName.Title, nameof(acetonitrile));
return(acetonitrile);
}
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 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 WoodBleach()
{
var woodBleach = new AtomContainer();
var carbons = new IAtom[2];
for (var i = 0; i < 2; i++)
{
carbons[i] = woodBleach.AddAtom("C");
woodBleach.AddBond(carbons[i], woodBleach.AddAtom("O"), BondOrder.Double);
var oxy = woodBleach.AddAtom("O");
woodBleach.AddBond(carbons[i], oxy, BondOrder.Single);
woodBleach.AddBond(oxy, woodBleach.AddAtom("H"), BondOrder.Single);
}
woodBleach.AddBond(carbons[0], carbons[1], BondOrder.Single);
woodBleach.Title = nameof(woodBleach);
return(woodBleach);
}
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 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 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 MethanesulfonicAcid()
{
var methanesulfonicAcid = new AtomContainer();
var sulfur = methanesulfonicAcid.AddAtom("S");
for (var i = 0; i < 2; i++)
{
methanesulfonicAcid.AddBond(sulfur, methanesulfonicAcid.AddAtom("O"), BondOrder.Double);
}
var oxy = methanesulfonicAcid.AddAtom("O");
methanesulfonicAcid.AddBond(sulfur, oxy, BondOrder.Single);
methanesulfonicAcid.AddBond(oxy, methanesulfonicAcid.AddAtom("H"), BondOrder.Single);
var carbon = methanesulfonicAcid.AddAtom("C");
methanesulfonicAcid.AddBond(sulfur, carbon, BondOrder.Single);
for (var i = 0; i < 3; i++)
{
methanesulfonicAcid.AddBond(carbon, methanesulfonicAcid.AddAtom("H"), BondOrder.Single);
}
methanesulfonicAcid.Title = nameof(methanesulfonicAcid);
return(methanesulfonicAcid);
}
public static IAtomContainer Bleach()
{
var hypochlorite = new AtomContainer();
var oxygen = hypochlorite.AddAtom("O");
var chloride = hypochlorite.AddAtom("Cl");
chloride.FormalCharge = -1;
hypochlorite.AddBond(oxygen, chloride, BondOrder.Single);
var bleach = new Crystal(hypochlorite);
var sodium = bleach.AddAtom("Na");
sodium.FormalCharge = 1;
bleach.Title = nameof(bleach);
return(bleach);
}
public static IAtomContainer Methylamine()
{
var methylamine = new AtomContainer();
var carbon = methylamine.AddAtom("C");
var nitrogen = methylamine.AddAtom("N");
for (var i = 0; i < 3; i++)
{
methylamine.AddBond(carbon, methylamine.AddAtom("H"), BondOrder.Single);
}
for (var i = 0; i < 2; i++)
{
methylamine.AddBond(nitrogen, methylamine.AddAtom("H"), BondOrder.Single);
}
methylamine.AddBond(carbon, nitrogen, BondOrder.Single);
methylamine.Title = nameof(methylamine);
return(methylamine);
}
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);
}
