/// <summary>
/// Calculates the topological polar surface area and expresses it as a ratio to molecule size.
/// </summary>
/// <returns>Descriptor(s) retaining to polar surface area</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
// type & assign implicit hydrogens
var matcher = CDK.AtomTypeMatcher;
foreach (var atom in container.Atoms)
{
var type = matcher.FindMatchingAtomType(container, atom);
AtomTypeManipulator.Configure(atom, type);
}
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(container);
double polar = 0;
double weight = 0;
// polar surface area: chain it off the TPSADescriptor
var tpsa = new TPSADescriptor();
var value = tpsa.Calculate(container);
polar = value.Value;
// molecular weight
foreach (var atom in container.Atoms)
{
weight += CDK.IsotopeFactory.GetMajorIsotope(atom.Symbol).ExactMass.Value;
weight += (atom.ImplicitHydrogenCount ?? 0) * 1.00782504;
}
return(new Result(weight == 0 ? 0 : polar / weight));
}
public StabilizationPlusChargeDescriptor(IAtomContainer container)
{
this.clonedContainer = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(this.clonedContainer);
this.container = container;
}
/// <summary>
/// This method calculate the ATS Autocorrelation descriptor.
/// </summary>
public Result Calculate(IAtomContainer container, int count = DefaultSize)
{
container = (IAtomContainer)container.Clone();
container = AtomContainerManipulator.RemoveHydrogens(container);
var w = ListConvertion(container);
var natom = container.Atoms.Count;
var distancematrix = TopologicalMatrix.GetMatrix(container);
var masSum = new double[count];
for (int k = 0; k < count; k++)
{
for (int i = 0; i < natom; i++)
{
for (int j = 0; j < natom; j++)
{
if (distancematrix[i][j] == k)
{
masSum[k] += w[i] * w[j];
}
else
{
masSum[k] += 0;
}
}
}
if (k > 0)
{
masSum[k] = masSum[k] / 2;
}
}
return(new Result(masSum));
}
/// <summary>
/// Calculates the FMF descriptor value for the given <see cref="IAtomContainer"/>.
/// </summary>
/// <returns>An object of <see cref="Result"/> that contains the
/// calculated FMF descriptor value as well as specification details</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
var fragmenter = new MurckoFragmenter(true, 3);
fragmenter.GenerateFragments(container);
var framework = fragmenter.GetFrameworksAsContainers().ToReadOnlyList();
var ringSystems = fragmenter.GetRingSystemsAsContainers().ToReadOnlyList();
{
double result;
if (framework.Count == 1)
{
result = framework[0].Atoms.Count / (double)container.Atoms.Count;
}
else if (framework.Count == 0 && ringSystems.Count == 1)
{
result = ringSystems[0].Atoms.Count / (double)container.Atoms.Count;
}
else
{
result = 0;
}
return(new Result(result));
}
}
/// <summary>
/// Calculate the complexity in the supplied <see cref="IAtomContainer"/>.
/// </summary>
/// <returns>the complexity</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
int a = 0;
double h = 0;
foreach (var atom in container.Atoms)
{
switch (atom.AtomicNumber)
{
default:
h++;
goto case AtomicNumbers.C;
case AtomicNumbers.C:
a++;
goto case AtomicNumbers.H;
case AtomicNumbers.H:
break;
}
}
var b = container.Bonds.Count + AtomContainerManipulator.GetImplicitHydrogenCount(container);
var c = Math.Abs(b * b - a * a + a) + (h / 100);
return(new Result(c));
}
/// <param name="maxIterations">Number of maximum iterations</param>
/// <param name="checkLonePairElectron">Checking lone pair electrons. Default <see langword="true"/></param>
/// <param name="maxResonanceStructures">Number of maximum resonance structures to be searched</param>
public PartialPiChargeDescriptor(IAtomContainer container,
int maxIterations = int.MaxValue,
bool checkLonePairElectron = true,
int maxResonanceStructures = int.MaxValue)
{
clonedContainer = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(clonedContainer);
var pepe = new GasteigerPEPEPartialCharges();
if (checkLonePairElectron)
{
CDK.LonePairElectronChecker.Saturate(clonedContainer);
}
if (maxIterations != int.MaxValue)
{
pepe.MaxGasteigerIterations = maxIterations;
}
if (maxResonanceStructures != int.MaxValue)
{
pepe.MaxResonanceStructures = maxResonanceStructures;
}
foreach (var catom in clonedContainer.Atoms)
{
catom.Charge = 0;
}
pepe.AssignGasteigerPiPartialCharges(clonedContainer, true);
this.container = container;
}
/// <summary>
/// Calculate sp3/sp2 hybridization ratio in the supplied <see cref="IAtomContainer"/>.
/// </summary>
/// <returns>The ratio of sp3 to sp2 carbons</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
int nsp2 = 0;
int nsp3 = 0;
foreach (var atom in container.Atoms)
{
if (!atom.AtomicNumber.Equals(AtomicNumbers.C))
{
continue;
}
switch (atom.Hybridization)
{
case Hybridization.SP2:
nsp2++;
break;
case Hybridization.SP3:
nsp3++;
break;
}
}
double ratio = nsp3 / (double)(nsp2 + nsp3);
return(new Result(ratio));
}
/// <summary>
/// Returns deep copy of the molecule
/// </summary>
/// <param name="container"></param>
/// <returns>deep copy of the mol</returns>
public static IAtomContainer MakeDeepCopy(IAtomContainer container)
{
var newAtomContainer = (IAtomContainer)container.Clone();
newAtomContainer.NotifyChanged();
return(newAtomContainer);
}
public override void TestClone()
{
IAtomContainer molecule = (IAtomContainer)NewChemObject();
object clone = molecule.Clone();
Assert.IsTrue(clone is IAtomContainer);
Assert.AreNotSame(molecule, clone);
}
/// <summary>
/// Singleton template instance, mainly useful for aligning molecules.
/// </summary>
/// <remarks>
/// If the template does not have coordinates an error is thrown.
/// For safety we clone the molecule.
/// </remarks>
/// <param name="template">the molecule</param>
/// <returns>new template handler</returns>
public static TemplateHandler CreateSingleton(IAtomContainer template)
{
var handler = new TemplateHandler();
var copy = (IAtomContainer)template.Clone();
handler.AddMolecule(copy);
return(handler);
}
private bool ShowIt(IAtomContainer molecule, string name)
{
StructureDiagramGenerator sdg = new StructureDiagramGenerator {
Molecule = (IAtomContainer)molecule.Clone()
};
sdg.GenerateCoordinates(new Vector2(0, 1));
return(true);
}
public Result Calculate(IAtomContainer container,
Func <IAtomContainer, double> calcLogP = null,
Func <IAtomContainer, int> calcHBondAcceptorCount = null,
Func <IAtomContainer, int> calcHBondDonorCount = null,
Func <IAtomContainer, double> calcWeight = null,
Func <IAtomContainer, int> calcRotatableBondsCount = null)
{
// do aromaticity detection
if (checkAromaticity)
{
container = (IAtomContainer)container.Clone(); // don't mod original
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
Aromaticity.CDKLegacy.Apply(container);
}
calcLogP = calcLogP ?? (mol => new XLogPDescriptor().Calculate(mol, correctSalicylFactor: true).Value);
calcHBondAcceptorCount = calcHBondAcceptorCount ?? (mol => new HBondAcceptorCountDescriptor().Calculate(mol).Value);
calcHBondDonorCount = calcHBondDonorCount ?? (mol => new HBondDonorCountDescriptor().Calculate(mol).Value);
calcWeight = calcWeight ?? (mol => new WeightDescriptor().Calculate(mol).Value);
calcRotatableBondsCount = calcRotatableBondsCount ?? (mol => new RotatableBondsCountDescriptor().Calculate(mol, includeTerminals: false, excludeAmides: true).Value);
int lipinskifailures = 0;
var xlogPvalue = calcLogP(container);
var acceptors = calcHBondAcceptorCount(container);
var donors = calcHBondDonorCount(container);
var mwvalue = calcWeight(container);
// exclude (heavy atom) terminal bonds
// exclude amide C-N bonds because of their high rotational barrier
// see Veber, D.F. et al., 2002, 45(12), pp.2615–23.
var rotatablebonds = calcRotatableBondsCount(container);
if (xlogPvalue > 5.0)
{
lipinskifailures += 1;
}
if (acceptors > 10)
{
lipinskifailures += 1;
}
if (donors > 5)
{
lipinskifailures += 1;
}
if (mwvalue > 500.0)
{
lipinskifailures += 1;
}
if (rotatablebonds > 10.0)
{
lipinskifailures += 1;
}
return(new Result(lipinskifailures));
}
public IPAtomicHOSEDescriptor(IAtomContainer container)
{
this.container = container;
container = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
CDK.LonePairElectronChecker.Saturate(container);
this.clonedContainer = container;
}
public static IAtomContainer CreateAnyAtomAtomContainer(IAtomContainer atomContainer)
{
var query = (IAtomContainer)atomContainer.Clone();
for (int i = 0; i < query.Atoms.Count; i++)
{
query.Atoms[i].Symbol = "C";
}
return(query);
}
/// <summary>
/// Given a structure in the correct configuration (explicit H and aromatised) it will return the logP as a Double
/// or if it is out of domain (encounters an unknown atomtype) it will return <see cref="Double.NaN"/>.
/// </summary>
/// <param name="container">the structure to calculate which have explicit H and be aromatised.</param>
/// <returns>The calculated logP</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
var hAdder = CDK.HydrogenAdder;
hAdder.AddImplicitHydrogens(container);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(container);
Aromaticity.CDKLegacy.Apply(container);
return(new JPlogPCalculator(container, coeffs).Calculate());
}
public ProtonTotalPartialChargeDescriptor(IAtomContainer container)
{
clonedContainer = (IAtomContainer)container.Clone();
var peoe = new GasteigerMarsiliPartialCharges {
MaxGasteigerIterations = 6
};
peoe.AssignGasteigerMarsiliSigmaPartialCharges(this.clonedContainer, true);
this.container = container;
}
public IsProtonInAromaticSystemDescriptor(IAtomContainer container, bool checkAromaticity = false)
{
clonedAtomContainer = (IAtomContainer)container.Clone();
if (checkAromaticity)
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(clonedAtomContainer);
Aromaticity.CDKLegacy.Apply(clonedAtomContainer);
}
this.container = container;
}
/// <param name="maxIterations">Number of maximum iterations</param>
public SigmaElectronegativityDescriptor(IAtomContainer container, int maxIterations = int.MaxValue)
{
this.clonedContainer = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(this.clonedContainer);
electronegativity = new Electronegativity();
if (maxIterations != int.MaxValue)
{
electronegativity.MaxIterations = maxIterations;
}
this.container = container;
}
/// <summary>
/// Calculates the descriptor value using the <see cref="VABCVolume"/> class.
/// </summary>
/// <returns>A double containing the volume</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone(); // don't mod original
try
{
return(new Result(VABCVolume.Calculate(container)));
}
catch (CDKException e)
{
return(new Result(e));
}
}
/// <param name="maxIterations">Number of maximum iterations</param>
public PartialSigmaChargeDescriptor(IAtomContainer container, int maxIterations = int.MaxValue)
{
clonedContainer = (IAtomContainer)container.Clone();
var peoe = new GasteigerMarsiliPartialCharges();
if (maxIterations != int.MaxValue)
{
peoe.MaxGasteigerIterations = maxIterations;
}
peoe.AssignGasteigerMarsiliSigmaPartialCharges(clonedContainer, true);
this.container = container;
}
public PiContactDetectionDescriptor(IAtomContainer container, bool checkAromaticity = false)
{
clonedContainer = (IAtomContainer)container.Clone();
mol = clonedContainer.Builder.NewAtomContainer(clonedContainer);
if (checkAromaticity)
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
}
acSet = ConjugatedPiSystemsDetector.Detect(mol);
this.container = container;
}
/// <summary>
/// Calculate the count of aromatic atoms in the supplied <see cref="IAtomContainer"/>.
/// </summary>
/// <remarks>
/// The method take a boolean checkAromaticity: if the boolean is <see langword="true"/>, it means that
/// aromaticity has to be checked.
/// </remarks>
/// <returns>the number of aromatic bonds</returns>
public Result Calculate(IAtomContainer container)
{
if (checkAromaticity)
{
container = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
Aromaticity.CDKLegacy.Apply(container);
}
var count = container.Bonds.Count(bond => bond.IsAromatic);
return(new Result(count));
}
/// <summary>
/// Returns IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which
/// is atom Hydrogen then its not removed.
/// </summary>
/// <param name="atomContainer"></param>
/// <returns>IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which is atom Hydrogen then its not removed.</returns>
public static IAtomContainer RemoveHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
{
var map = new CDKObjectMap(); // maps original object to clones.
if (atomContainer.Bonds.Count > 0)
{
var mol = (IAtomContainer)atomContainer.Clone(map);
List <IAtom> remove = new List <IAtom>(); // lists removed Hs.
foreach (var atom in atomContainer.Atoms)
{
if (atom.AtomicNumber.Equals(AtomicNumbers.H))
{
remove.Add(atom);
}
}
foreach (var a in remove)
{
mol.RemoveAtomAndConnectedElectronContainers(map.Get(a));
}
foreach (var atom in mol.Atoms.Where(n => !n.ImplicitHydrogenCount.HasValue))
{
atom.ImplicitHydrogenCount = 0;
}
// Recompute hydrogen counts of neighbours of removed Hydrogens.
mol = RecomputeHydrogens(mol, atomContainer, remove, map);
return(mol);
}
else
{
var mol = (IAtomContainer)atomContainer.Clone(map);
if (string.Equals(atomContainer.Atoms[0].Symbol, "H", StringComparison.OrdinalIgnoreCase))
{
Console.Error.WriteLine("WARNING: single hydrogen atom removal not supported!");
}
return(mol);
}
}
/// <summary>
/// This method calculate the ATS Autocorrelation descriptor.
/// </summary>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
var hAdder = CDK.HydrogenAdder;
hAdder.AddImplicitHydrogens(container);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(container);
Aromaticity.CDKLegacy.Apply(container);
// get the distance matrix for pol calcs as well as for later on
var distancematrix = PathTools.ComputeFloydAPSP(AdjacencyMatrix.GetMatrix(container));
var w = Listpolarizability(container, distancematrix);
var natom = container.Atoms.Count;
var polarizabilitySum = new double[5];
for (int k = 0; k < 5; k++)
{
for (int i = 0; i < natom; i++)
{
if (container.Atoms[i].AtomicNumber.Equals(AtomicNumbers.H))
{
continue;
}
for (int j = 0; j < natom; j++)
{
if (container.Atoms[j].AtomicNumber.Equals(AtomicNumbers.H))
{
continue;
}
if (distancematrix[i][j] == k)
{
polarizabilitySum[k] += w[i] * w[j];
}
else
{
polarizabilitySum[k] += 0.0;
}
}
}
if (k > 0)
{
polarizabilitySum[k] = polarizabilitySum[k] / 2;
}
}
return(new Result(polarizabilitySum));
}
/// <summary>
/// Returns IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which
/// is atom Hydrogen then its not removed.
/// </summary>
/// <param name="atomContainer"></param>
/// <returns>IAtomContainer without Hydrogen. If an AtomContainer has atom single atom which is atom Hydrogen then its not removed.</returns>
public static IAtomContainer ConvertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
{
IAtomContainer mol = (IAtomContainer)atomContainer.Clone();
ConvertImplicitToExplicitHydrogens(mol);
if (mol.Atoms.Count > 1)
{
mol = RemoveHydrogens(mol);
}
else if (string.Equals(mol.Atoms.First().Symbol, "H", StringComparison.OrdinalIgnoreCase))
{
Console.Error.WriteLine("WARNING: single hydrogen atom removal not supported!");
}
return(mol);
}
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone(); // don't mod original
// do aromaticity detection
if (checkAromaticity)
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
Aromaticity.CDKLegacy.Apply(container);
}
var count = tools.Select(n => n.MatchAll(container).Count()).Sum();
return(new Result(count));
}
/// <summary>
/// Determine the number of amino acids groups the supplied <see cref="IAtomContainer"/>.
/// </summary>
/// <returns>the number of aromatic atoms of this AtomContainer</returns>
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
var results = new List <int>(substructureSet.Count);
var universalIsomorphismTester = new UniversalIsomorphismTester();
foreach (var substructure in substructureSet)
{
var maps = universalIsomorphismTester.GetSubgraphMaps(container, substructure);
results.Add(maps.Count());
}
return(new Result(results));
}
public void TestClone()
{
IAtomContainer molecule = TestMoleculeFactory.MakeAlphaPinene();
IAtomContainer clonedMol = (IAtomContainer)molecule.Clone();
Assert.IsTrue(molecule.Atoms.Count == clonedMol.Atoms.Count);
for (int f = 0; f < molecule.Atoms.Count; f++)
{
for (int g = 0; g < clonedMol.Atoms.Count; g++)
{
Assert.IsNotNull(molecule.Atoms[f]);
Assert.IsNotNull(clonedMol.Atoms[g]);
Assert.IsTrue(molecule.Atoms[f] != clonedMol.Atoms[g]);
}
}
}
public void TestFingerPrint()
{
IFingerprinter printer = new GraphOnlyFingerprinter();
IAtomContainer mol1 = CreateMolecule(molecule_test_2);
IAtomContainer mol2 = CreateMolecule(ethanolamine);
Assert.IsTrue(new UniversalIsomorphismTester().IsSubgraph(mol1, mol2), "SubGraph does NOT match");
BitArray bs1 = printer.GetBitFingerprint((IAtomContainer)mol1.Clone()).AsBitSet();
BitArray bs2 = printer.GetBitFingerprint((IAtomContainer)mol2.Clone()).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs1, bs2), "Subset (with fingerprint) does NOT match");
// Match OK
Debug.WriteLine("Subset (with fingerprint) does match");
}
public Result Calculate(IAtomContainer container)
{
container = (IAtomContainer)container.Clone();
int nSpiro = 0;
Cycles.MarkRingAtomsAndBonds(container);
foreach (var atom in container.Atoms)
{
if (GetSpiroDegree(container, atom) != 0)
{
nSpiro++;
}
}
return(new Result(nSpiro));
}
/// <summary> Returns a ringset containing all rings in the given AtomContainer
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be searched for rings
/// </param>
/// <returns> A RingSet with all rings in the AtomContainer
/// </returns>
/// <exception cref="CDKException"> An exception thrown if something goes wrong or if the timeout limit is reached
/// </exception>
public virtual IRingSet findAllRings(IAtomContainer atomContainer)
{
startTime = (System.DateTime.Now.Ticks - 621355968000000000) / 10000;
SpanningTree spanningTree;
try
{
spanningTree = new SpanningTree((IAtomContainer)atomContainer.Clone());
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
throw new CDKException("Could not clone IAtomContainer!", e);
}
spanningTree.identifyBonds();
if (spanningTree.BondsCyclicCount < 37)
{
findAllRings(atomContainer, false);
}
return findAllRings(atomContainer, true);
}
private static void getLargestAtomContainer(IAtomContainer firstAC, IAtomContainer secondAC)
{
if (firstAC.AtomCount < secondAC.AtomCount)
{
IAtomContainer tmp;
try
{
tmp = (IAtomContainer)firstAC.Clone();
firstAC = (IAtomContainer)secondAC.Clone();
secondAC = (IAtomContainer)tmp.Clone();
}
//UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
catch (System.Exception e)
{
// TODO Auto-generated catch block
SupportClass.WriteStackTrace(e, Console.Error);
}
}
}