public void TestDoubleCharge()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C22H34N2S2", builder);
formula.Charge = 2;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestWithCo()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C43H50CoN4O16", builder);
formula.Charge = 0;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestWithFe()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C40H46FeN6O8S2", builder);
formula.Charge = 2;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
public void TestNominalMass()
{
IRule rule = new NitrogenRule();
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula("C25H53NO7P", builder);
formula.Charge = 1;
Assert.AreEqual(1.0, rule.Validate(formula), 0.0001);
}
static void Main(string[] args)
{
IAtomContainer mol1 = Chem.MolFromSmiles("[C:1]([C:5]1[CH:10]=[CH:9][C:8]([OH:11])=[CH:7][CH:6]=1)([CH3:4])([CH3:3])[CH3:2]");
IMolecularFormula form1 = MolecularFormulaManipulator.GetMolecularFormula(mol1);
Console.WriteLine(MolecularFormulaManipulator.GetString(form1));
IAtomContainer mol2 = Chem.MolFromFile("/Users/john/My Documents/1,3-diisopropenylbenzene.mol");
var form2 = MolecularFormulaManipulator.GetMolecularFormula(mol2);
Console.WriteLine(MolecularFormulaManipulator.GetString(form2));
}
public string MolFormula => GetMolecularFormula(NativeMol); // get mol formula
/// <summary>
/// GetMolecularFormula
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static string GetMolecularFormula(IAtomContainer mol)
{
if (mol == null)
{
return("");
}
IMolecularFormula moleculeFormula = MolecularFormulaManipulator.GetMolecularFormula(mol);
String formula = MolecularFormulaManipulator.GetString(moleculeFormula);
return(formula);
}
private static void filterInorganicsFromIterator(IChemObjectSet <IAtomContainer> rxnIt)
{
for (int i = rxnIt.Count - 1; i >= 0; --i)
{
var sub = rxnIt[i];
var formula = MolecularFormulaManipulator.GetMolecularFormula(sub);
if (!MolecularFormulaManipulator.ContainsElement(formula, ChemicalElement.C))
{
rxnIt.Remove(sub);
}
}
}
public SingleStructureRandomGeneratorTest()
{
Console.Out.WriteLine("Instantiating MoleculeListViewer");
Console.Out.WriteLine("Instantiating SingleStructureRandomGenerator");
ssrg = new SingleStructureRandomGenerator();
Console.Out.WriteLine("Assining unbonded set of atoms");
AtomContainer ac = GetBunchOfUnbondedAtoms();
mf = MolecularFormulaManipulator.GetString(MolecularFormulaManipulator.GetMolecularFormula(ac));
Console.Out.WriteLine("Molecular Formula is: " + mf);
ssrg.SetAtomContainer(ac);
}
public void TestGeneratorSavesState()
{
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mf1 = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6", builder);
IsotopePattern ip1 = isogen.GetIsotopes(mf1);
Assert.AreEqual(1, ip1.Isotopes.Count);
IMolecularFormula mf2 = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6", builder);
IsotopePattern ip2 = isogen.GetIsotopes(mf2);
Assert.AreEqual(1, ip2.Isotopes.Count);
}
public void TestMultipleFormulasForAMass()
{
var mf = MolecularFormulaManipulator.GetMolecularFormula("C6Cl2", builder);
var isogen = new IsotopePatternGenerator(0.1)
.SetMinIntensity(0.01)
.SetMinResolution(0.01)
.SetStoreFormulas(true);
var pattern = isogen.GetIsotopes(mf);
var isotopes = pattern.Isotopes;
Assert.AreEqual(1, isotopes[0].Formulas.Count);
Assert.AreEqual(1, isotopes[1].Formulas.Count);
Assert.AreEqual(2, isotopes[2].Formulas.Count);
Assert.AreEqual(2, isotopes[3].Formulas.Count);
Assert.AreEqual(3, isotopes[4].Formulas.Count);
}
public static void Script8_3()
{
var parser = new SmilesParser();
var hAdder = CDKHydrogenAdder.GetInstance();
var methanol = parser.ParseSmiles("CO");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(methanol);
hAdder.AddImplicitHydrogens(methanol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(methanol);
var dimethoxymethane = parser.ParseSmiles("COC");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(dimethoxymethane);
hAdder.AddImplicitHydrogens(dimethoxymethane);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(dimethoxymethane);
var water = parser.ParseSmiles("O");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(water);
hAdder.AddImplicitHydrogens(water);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(water);
var reaction = new Reaction();
reaction.Reactants.Add(methanol, 2.0D);
reaction.Products.Add(dimethoxymethane);
reaction.Products.Add(water);
Console.WriteLine("Reactants:");
foreach (var reactant in reaction.Reactants)
{
var formula = MolecularFormulaManipulator.GetMolecularFormula(reactant);
Console.WriteLine(MolecularFormulaManipulator.GetString(formula));
}
Console.WriteLine("Products: ");
foreach (var product in reaction.Products)
{
var formula = MolecularFormulaManipulator.GetMolecularFormula(product);
Console.WriteLine(MolecularFormulaManipulator.GetString(formula));
}
}
public void TestGetIsotopesIMolecularFormulaDeprotonate()
{
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mf1 = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6", builder);
MolecularFormulaManipulator.AdjustProtonation(mf1, -1);
IsotopePattern ip1 = isogen.GetIsotopes(mf1);
Assert.AreEqual(1, ip1.Isotopes.Count);
isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mf2 = MolecularFormulaManipulator.GetMolecularFormula("C6H11O6", builder);
IsotopePattern ip2 = isogen.GetIsotopes(mf2);
Assert.AreEqual(1, ip2.Isotopes.Count);
Assert.AreEqual(ip1.Isotopes[0].Mass, ip2.Isotopes[0].Mass, 0.001);
}
/// <summary>
/// Generates a fingerprint of the default size for the given
/// AtomContainer, using path and ring metrics. It contains the
/// informations from <see cref="Fingerprinter.GetBitFingerprint(IAtomContainer)"/> and bits which tell if the structure
/// has 0 rings, 1 or less rings, 2 or less rings ... 10 or less rings and
/// bits which tell if there is a fused ring system with 1,2...8 or more
/// rings in it. The RingSet used is passed via rs parameter. This must be
/// a smallesSetOfSmallestRings. The List must be a list of all ring
/// systems in the molecule.
/// </summary>
/// <param name="atomContainer">The AtomContainer for which a Fingerprint is generated</param>
/// <param name="ringSet">An SSSR RingSet of ac (if not available, use <see cref="GetBitFingerprint(IAtomContainer)"/>, which does the calculation)</param>
/// <param name="rslist">A list of all ring systems in ac</param>
/// <exception cref="CDKException">for example if input can not be cloned.</exception>
/// <returns>a BitArray representing the fingerprint</returns>
public IBitFingerprint GetBitFingerprint(IAtomContainer atomContainer, IRingSet ringSet, IEnumerable <IRingSet> rslist)
{
var container = (IAtomContainer)atomContainer.Clone();
var fingerprint = fingerprinter.GetBitFingerprint(container);
var size = this.Length;
var weight = MolecularFormulaManipulator.GetTotalNaturalAbundance(MolecularFormulaManipulator.GetMolecularFormula(container));
for (int i = 1; i < 11; i++)
{
if (weight > (100 * i))
{
fingerprint.Set(size - 26 + i); // 26 := RESERVED_BITS+1
}
}
if (ringSet == null)
{
ringSet = Cycles.FindSSSR(container).ToRingSet();
rslist = RingPartitioner.PartitionRings(ringSet);
}
for (int i = 0; i < 7; i++)
{
if (ringSet.Count > i)
{
fingerprint.Set(size - 15 + i); // 15 := RESERVED_BITS+1+10 mass bits
}
}
int maximumringsystemsize = 0;
foreach (var rs in rslist)
{
if (rs.Count > maximumringsystemsize)
{
maximumringsystemsize = rs.Count;
}
}
for (int i = 0; i < maximumringsystemsize && i < 9; i++)
{
fingerprint.Set(size - 8 + i - 3);
}
return(fingerprint);
}
public void TestHydrogen()
{
var mol = builder.NewAtomContainer();
var proton = builder.NewAtom("H");
mol.Atoms.Add(proton);
var type = matcher.FindMatchingAtomType(mol, proton);
Assert.IsNotNull(type);
AtomTypeManipulator.Configure(proton, type);
adder.AddImplicitHydrogens(mol);
Assert.AreEqual(1, mol.Atoms.Count);
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula(mol);
Assert.AreEqual(2, MolecularFormulaManipulator.GetElementCount(formula, ChemicalElement.H));
Assert.AreEqual(0, mol.GetConnectedBonds(proton).Count());
Assert.IsNotNull(proton.ImplicitHydrogenCount);
Assert.AreEqual(1, proton.ImplicitHydrogenCount.Value);
}
public void TestGetIsotopesIMolecularFormulaCharged()
{
IsotopePatternGenerator isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mfPositive = MolecularFormulaManipulator.GetMolecularFormula("C6H11O6Na", builder);
mfPositive.Charge = 1;
IsotopePattern ip1 = isogen.GetIsotopes(mfPositive);
Assert.AreEqual(1, ip1.Isotopes.Count);
isogen = new IsotopePatternGenerator(.1);
IMolecularFormula mfNeutral = MolecularFormulaManipulator.GetMolecularFormula("C6H12O6Na", builder);
mfNeutral.Charge = 0;
IsotopePattern ip2 = isogen.GetIsotopes(mfNeutral);
Assert.AreEqual(1, ip2.Isotopes.Count);
Assert.AreNotEqual(ip1.Isotopes[0].Mass, ip2.Isotopes[0].Mass);
}
/// <summary>
/// Calculates the 3 MI's, 3 ration and the R_gyr value.
/// The molecule should have hydrogens.
/// </summary>
/// <returns>An <see cref="Result"/> containing 7 elements in the order described above</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
var factory = CDK.IsotopeFactory;
factory.ConfigureAtoms(container);
if (!GeometryUtil.Has3DCoordinates(container))
{
throw new ThreeDRequiredException("Molecule must have 3D coordinates");
}
var retval = new List <double>(7);
double ccf = 1.000138;
double eps = 1e-5;
var imat = Arrays.CreateJagged <double>(3, 3);
var centerOfMass = GeometryUtil.Get3DCentreOfMass(container).Value;
double xdif;
double ydif;
double zdif;
double xsq;
double ysq;
double zsq;
for (int i = 0; i < container.Atoms.Count; i++)
{
var currentAtom = container.Atoms[i];
var _mass = factory.GetMajorIsotope(currentAtom.Symbol).ExactMass;
var mass = _mass == null?factory.GetNaturalMass(currentAtom.Element) : _mass.Value;
var p = currentAtom.Point3D.Value;
xdif = p.X - centerOfMass.X;
ydif = p.Y - centerOfMass.Y;
zdif = p.Z - centerOfMass.Z;
xsq = xdif * xdif;
ysq = ydif * ydif;
zsq = zdif * zdif;
imat[0][0] += mass * (ysq + zsq);
imat[1][1] += mass * (xsq + zsq);
imat[2][2] += mass * (xsq + ysq);
imat[1][0] += -1 * mass * ydif * xdif;
imat[0][1] = imat[1][0];
imat[2][0] += -1 * mass * xdif * zdif;
imat[0][2] = imat[2][0];
imat[2][1] += -1 * mass * ydif * zdif;
imat[1][2] = imat[2][1];
}
// diagonalize the MI tensor
var tmp = Matrix <double> .Build.DenseOfColumnArrays(imat);
var eigenDecomp = tmp.Evd();
var eval = eigenDecomp.EigenValues.Select(n => n.Real).ToArray();
retval.Add(eval[2]);
retval.Add(eval[1]);
retval.Add(eval[0]);
var etmp = eval[0];
eval[0] = eval[2];
eval[2] = etmp;
if (Math.Abs(eval[1]) > 1e-3)
{
retval.Add(eval[0] / eval[1]);
}
else
{
retval.Add(1000);
}
if (Math.Abs(eval[2]) > 1e-3)
{
retval.Add(eval[0] / eval[2]);
retval.Add(eval[1] / eval[2]);
}
else
{
retval.Add(1000);
retval.Add(1000);
}
// finally get the radius of gyration
var formula = MolecularFormulaManipulator.GetMolecularFormula(container);
var pri = Math.Abs(eval[2]) > eps
? Math.Pow(eval[0] *eval[1] *eval[2], 1.0 / 3.0)
: Math.Sqrt(eval[0] * ccf / MolecularFormulaManipulator.GetTotalExactMass(formula));
retval.Add(Math.Sqrt(Math.PI * 2 * pri * ccf / MolecularFormulaManipulator.GetTotalExactMass(formula)));
return(new Result(retval));
}
[TestCategory("VerySlowTest")] // structgen is slow... a single method here currently takes ~6 seconds
public void TestDoCrossover_IAtomContainer()
{
IChemObjectSet <IAtomContainer> som;
var filename = "NCDK.Data.Smiles.c10h16isomers.smi";
using (var ins = ResourceLoader.GetAsStream(filename))
using (SMILESReader reader = new SMILESReader(ins))
{
som = reader.Read(CDK.Builder.NewAtomContainerSet());
Assert.AreEqual(99, som.Count, "We must have read 99 structures");
}
// Comment out next line to enable time seed random.
RandomNumbersTool.RandomSeed = 0L;
CrossoverMachine cm = new CrossoverMachine();
string correctFormula = "C10H16";
int errorcount = 0;
for (int i = 0; i < som.Count; i++)
{
int[] hydrogencount1 = new int[4];
foreach (var atom in som[i].Atoms)
{
hydrogencount1[atom.ImplicitHydrogenCount.Value]++;
}
for (int k = i + 1; k < som.Count; k++)
{
try
{
var result = cm.DoCrossover(som[i], som[k]);
int[] hydrogencount2 = new int[4];
foreach (var atom in som[k].Atoms)
{
hydrogencount2[atom.ImplicitHydrogenCount.Value]++;
}
Assert.AreEqual(2, result.Count, "Result size must be 2");
for (int l = 0; l < 2; l++)
{
IAtomContainer ac = result[l];
Assert.IsTrue(ConnectivityChecker.IsConnected(ac), "Result must be connected");
Assert.AreEqual(
MolecularFormulaManipulator.GetString(MolecularFormulaManipulator.GetMolecularFormula(ac)),
correctFormula,
"Molecular formula must be the same as" + "of the input");
int[] hydrogencountresult = new int[4];
int hcounttotal = 0;
foreach (var atom in result[l].Atoms)
{
hydrogencountresult[atom.ImplicitHydrogenCount.Value]++;
hcounttotal += atom.ImplicitHydrogenCount.Value;
}
if (hydrogencount1[0] == hydrogencount2[0])
{
Assert.AreEqual(
hydrogencount1[0], hydrogencountresult[0],
"Hydrogen count of the result must" + " be same as of input");
}
if (hydrogencount1[1] == hydrogencount2[1])
{
Assert.AreEqual(
hydrogencount1[1], hydrogencountresult[1],
"Hydrogen count of the result must" + " be same as of input");
}
if (hydrogencount1[2] == hydrogencount2[2])
{
Assert.AreEqual(
hydrogencount1[2], hydrogencountresult[2],
"Hydrogen count of the result must" + " be same as of input");
}
if (hydrogencount1[3] == hydrogencount2[3])
{
Assert.AreEqual(
hydrogencount1[3], hydrogencountresult[3],
"Hydrogen count of the result must" + " be same as of input");
}
Assert.AreEqual(16, hcounttotal);
}
}
catch (CDKException)
{
errorcount++;
}
}
}
Assert.IsTrue(errorcount < 300, "We tolerate up to 300 errors");
}
// Private procedures
private void WriteCrystal(ICrystal crystal)
{
var title = crystal.Title;
if (title != null && title.Trim().Length > 0)
{
Writeln($"TITL {title.Trim()}");
}
else
{
Writeln("TITL Produced with CDK (http://cdk.sf.net/)");
}
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
double alength = a.Length();
double blength = b.Length();
double clength = c.Length();
double alpha = Vectors.RadianToDegree(Vectors.Angle(b, c));
double beta = Vectors.RadianToDegree(Vectors.Angle(a, c));
double gamma = Vectors.RadianToDegree(Vectors.Angle(a, b));
Write("CELL " + 1.54184.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(blength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(clength.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(alpha.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(beta.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Write(gamma.ToString("F4", NumberFormatInfo.InvariantInfo) + " ");
Writeln("ZERR " + ((double)crystal.Z).ToString("F5", NumberFormatInfo.InvariantInfo)
+ " 0.01000 0.01000 0.01000 0.0100 0.0100 0.0100");
string spaceGroup = crystal.SpaceGroup;
if (string.Equals("P1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
}
else if (string.Equals("P 2_1 2_1 2_1", spaceGroup, StringComparison.Ordinal))
{
Writeln("LATT -1");
Writeln("SYMM 1/2+X , 1/2-Y , -Z");
Writeln("SYMM -X , 1/2+Y , 1/2-Z");
Writeln("SYMM 1/2-X , -Y , 1/2+Z");
}
string elemNames = "";
string elemCounts = "";
IMolecularFormula formula = MolecularFormulaManipulator.GetMolecularFormula(crystal);
var asortedElements = MolecularFormulaManipulator.Elements(formula).ToReadOnlyList();
foreach (var element in asortedElements)
{
string symbol = element.Symbol;
elemNames += symbol + " ".Substring(symbol.Length);
string countS = MolecularFormulaManipulator.GetElementCount(formula, element).ToString(NumberFormatInfo.InvariantInfo);
elemCounts += countS + " ".Substring(countS.Length);
}
Writeln("SFAC " + elemNames);
Writeln("UNIT " + elemCounts);
/* write atoms */
for (int i = 0; i < crystal.Atoms.Count; i++)
{
IAtom atom = crystal.Atoms[i];
Vector3 cartCoord = atom.Point3D.Value;
Vector3 fracCoord = CrystalGeometryTools.CartesianToFractional(a, b, c, cartCoord);
string symbol = atom.Symbol;
string output = symbol + (i + 1);
Write(output);
for (int j = 1; j < 5 - output.Length; j++)
{
Write(" ");
}
Write(" ");
string elemID = null;
for (int elemidx = 0; elemidx < asortedElements.Count; elemidx++)
{
var elem = asortedElements[elemidx];
if (elem.Symbol.Equals(symbol, StringComparison.Ordinal))
{
elemID = (elemidx + 1).ToString(NumberFormatInfo.InvariantInfo);
break;
}
}
Write(elemID);
Write(" ".Substring(elemID.Length));
Write(fracCoord.X.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Write(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " ");
Writeln(fracCoord.Y.ToString("F5", NumberFormatInfo.InvariantInfo) + " 11.00000 0.05000");
}
Writeln("END");
}