public virtual void Or()
{
ICycleFinder cf = Cycles.Or(Cycles.AllSimpleFinder, Cycles.GetAllFinder(3));
IAtomContainer fullerene = GetFullerene();
CheckSize(cf.Find(fullerene, fullerene.Atoms.Count), 120);
}
/// <summary>
/// Internal method to wrap cycle computations which <i>should</i> be
/// tractable. That is they currently won't throw the exception - if the
/// method does throw an exception an internal error is triggered as a sanity
/// check.
/// </summary>
/// <param name="finder">the cycle finding method</param>
/// <param name="container">the molecule to find the cycles of</param>
/// <param name="length">maximum size or cycle to find</param>
/// <returns>the cycles of the molecule</returns>
private static Cycles _invoke(ICycleFinder finder, IAtomContainer container, int length)
{
try
{
return(finder.Find(container, length));
}
catch (IntractableException e)
{
throw new IntractableException($"Cycle computation should not be intractable: {e.Message}");
}
}
/// <summary>
/// ApplyAromaticity
///
/// Mimics the CDKHuckelAromaticityDetector
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.cdk(), Cycles.cdkAromaticSet());
///
/// Mimics the DoubleBondAcceptingAromaticityDetector
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.cdkAllowingExocyclic(), Cycles.cdkAromaticSet());
///
/// A good model for writing SMILES
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.all());
///
/// A good model for writing MDL/Mol2
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.piBonds(), Cycles.all());
///
/// </summary>
/// <param name="mol"></param>
/// <param name="electronDonation"></param>
/// <param name="cycleFinder"></param>
/// <returns></returns>
public static bool ApplyAromaticity(
IAtomContainer mol,
ElectronDonation electronDonation,
ICycleFinder cycleFinder)
{
Aromaticity aromaticity = new Aromaticity(electronDonation, cycleFinder);
try
{
bool isAromatic = aromaticity.Apply(mol);
return(isAromatic);
}
catch (Exception e)
{
string msg = e.Message; // cycle computation was intractable
return(false);
}
}
/// <summary>
/// Filter any cycles produced by the <paramref name="primary"/> cycle finder and
/// only allow those without a chord.
/// </summary>
/// <param name="primary">the primary cycle finder</param>
internal Unchorded(ICycleFinder primary)
{
this.primary = primary;
}
/// <summary>
/// Create a fallback for two cycle finders.
/// </summary>
/// <param name="primary">the primary cycle finder</param>
/// <param name="auxiliary">the auxiliary cycle finder</param>
internal Fallback(ICycleFinder primary, ICycleFinder auxiliary)
{
this.primary = primary;
this.auxiliary = auxiliary;
}
/// <summary>
/// Internal method to wrap cycle computations which <i>should</i> be
/// tractable. That is they currently won't throw the exception - if the
/// method does throw an exception an internal error is triggered as a sanity
/// check.
/// </summary>
/// <param name="finder">the cycle finding method</param>
/// <param name="container">the molecule to find the cycles of</param>
/// <returns>the cycles of the molecule</returns>
private static Cycles _invoke(ICycleFinder finder, IAtomContainer container)
{
return(_invoke(finder, container, container.Atoms.Count));
}
/// <summary>
/// Derive a new cycle finder that only provides cycles without a chord.
/// </summary>
/// <param name="original">find the initial cycles before filtering</param>
/// <returns>cycles or the original without chords</returns>
public static ICycleFinder GetUnchorded(ICycleFinder original)
{
return(new Unchorded(original));
}
/// <summary>
/// Use an auxiliary cycle finder if the primary method was intractable.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Graphs.Cycles_Example.cs+Or6"]/*' />
/// It is possible to nest multiple levels.
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Graphs.Cycles_Example.cs+OrARE"]/*' />
/// </example>
/// <param name="primary">primary cycle finding method</param>
/// <param name="auxiliary">auxiliary cycle finding method if the primary failed</param>
/// <returns>a new cycle finder</returns>
public static ICycleFinder Or(ICycleFinder primary, ICycleFinder auxiliary)
{
return(new Fallback(primary, auxiliary));
}
/// <summary>
/// Create an aromaticity model using the specified electron donation
/// <paramref name="model"/> which is tested on the <paramref name="cycles"/>. The <paramref name="model"/> defines
/// how many π-electrons each atom may contribute to an aromatic system. The
/// <paramref name="cycles"/> defines the <see cref="ICycleFinder"/> which is used to find
/// cycles in a molecule. The total electron donation from each atom in each
/// cycle is counted and checked. If the electron contribution is equal to
/// "4n + 2" for a "n >= 0" then the cycle is considered
/// aromatic.
/// </summary>
/// <remarks>
/// Changing the electron contribution model or which cycles
/// are tested affects which atoms/bonds are found to be aromatic. There are
/// several <see cref="ElectronDonation"/> models and <see cref="Cycles"/>
/// available. A good choice for the cycles
/// is to use <see cref="Cycles.AllSimpleFinder()"/> falling back to
/// <see cref="Cycles.RelevantFinder"/> on failure. Finding all cycles is very
/// fast but may produce an exponential number of cycles. It is therefore not
/// feasible for complex fused systems and an exception is thrown.
/// In such cases the aromaticity can either be skipped or a simpler
/// polynomial cycle set <see cref="Cycles.RelevantFinder"/> used.
/// </remarks>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Aromaticities.Aromaticity_Example.cs+ctor"]/*' />
/// </example>
/// <param name="model"></param>
/// <param name="cycles"></param>
/// <seealso cref="ElectronDonation"/>
/// <seealso cref="Cycles"/>
public Aromaticity(ElectronDonation model, ICycleFinder cycles)
{
this.model = model ?? throw new ArgumentNullException(nameof(model));
this.cycles = cycles ?? throw new ArgumentNullException(nameof(cycles));
}
public void Main()
{
{
IChemObjectSet <IAtomContainer> containers = null;
#region AllSimpleFinder
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// handle error - note it is common that finding all simple cycles in chemical graphs is intractable
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region MCB
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - MCB should never be intractable
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region Relevant
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - there may be an exponential number of cycles but this is not currently checked
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region Essential
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - essential cycles do not check tractability
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region TripletShort
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - triple short cycles do not check tractability
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region VertexShort
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - vertex short cycles do not check tractability
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region EdgeShort
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - edge short cycles do not check tractability
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region CDKAromaticSetFinder
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - edge short cycles do not check tractability
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region AllOrVertexShortFinder
ICycleFinder cf = Cycles.AllSimpleFinder;
foreach (var container in containers)
{
try
{
Cycles cycles = cf.Find(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// ignore error - edge short cycles do not check tractability
}
}
#endregion
}
{
#region Or6
// all cycles or all cycles size <= 6
ICycleFinder cf = Cycles.Or(Cycles.AllSimpleFinder, Cycles.GetAllFinder(6));
#endregion
}
{
#region OrARE
// all cycles or relevant or essential
ICycleFinder cf = Cycles.Or(Cycles.AllSimpleFinder, Cycles.Or(Cycles.RelevantFinder, Cycles.EssentialFinder));
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
#region FindAll
foreach (var container in containers)
{
try
{
Cycles cycles = Cycles.FindAll(container);
IRingSet rings = cycles.ToRingSet();
}
catch (IntractableException)
{
// handle error - note it is common that finding all simple cycles in chemical graphs is intractable
}
}
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
IAtomContainer container = null;
#region FindMCB
Cycles cycles = Cycles.FindMCB(container);
IRingSet rings = cycles.ToRingSet();
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
IAtomContainer container = null;
#region FindSSSR
Cycles cycles = Cycles.FindSSSR(container);
IRingSet rings = cycles.ToRingSet();
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
IAtomContainer container = null;
#region FindRelevant
Cycles cycles = Cycles.FindRelevant(container);
IRingSet rings = cycles.ToRingSet();
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
IAtomContainer container = null;
#region FindEssential
Cycles cycles = Cycles.FindEssential(container);
IRingSet rings = cycles.ToRingSet();
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
IAtomContainer container = null;
#region FindTripletShort
Cycles cycles = Cycles.FindTripletShort(container);
IRingSet rings = cycles.ToRingSet();
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
IAtomContainer container = null;
#region FindVertexShort
Cycles cycles = Cycles.FindVertexShort(container);
IRingSet rings = cycles.ToRingSet();
#endregion
}
{
IChemObjectSet <IAtomContainer> containers = null;
IAtomContainer container = null;
#region FindEdgeShort
Cycles cycles = Cycles.FindEdgeShort(container);
IRingSet rings = cycles.ToRingSet();
#endregion
}
}
public static void Main(string[] args)
{
{
var molecules = new Silent.AtomContainerSet();
#region
ElectronDonation model = ElectronDonation.DaylightModel;
ICycleFinder cycles = Cycles.Or(Cycles.AllSimpleFinder, Cycles.GetAllFinder(6));
Aromaticity aromaticity = new Aromaticity(model, cycles);
// apply our configured model to each molecule
foreach (IAtomContainer molecule in molecules)
{
aromaticity.Apply(molecule);
}
#endregion
}
{
#region ctor
// mimics the CDKHuckelAromaticityDetector
Aromaticity aromaticity_cdk = new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder);
// mimics the DoubleBondAcceptingAromaticityDetector
Aromaticity aromaticity_exo = new Aromaticity(ElectronDonation.CDKAllowingExocyclicModel, Cycles.CDKAromaticSetFinder);
// a good model for writing SMILES
Aromaticity aromaticity_smi = new Aromaticity(ElectronDonation.DaylightModel, Cycles.AllSimpleFinder);
// a good model for writing MDL/Mol2
Aromaticity aromaticity_mdl = new Aromaticity(ElectronDonation.PiBondsModel, Cycles.AllSimpleFinder);
#endregion
}
{
#region FindBonds
Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllSimpleFinder);
IAtomContainer container = TestMoleculeFactory.MakeAnthracene();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
try
{
var bonds = aromaticity.FindBonds(container);
int nAromaticBonds = bonds.Count();
}
catch (CDKException)
{
// cycle computation was intractable
}
#endregion
}
{
#region Apply
Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllSimpleFinder);
IAtomContainer container = TestMoleculeFactory.MakeAnthracene();
try
{
if (aromaticity.Apply(container))
{
//
}
}
catch (CDKException)
{
// cycle computation was intractable
}
#endregion
}
{
#region CDKLegacy_CDKAromaticSetFinder
new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder);
#endregion
}
{
#region CDKLegacy_AllFinder_RelevantFinder
new Aromaticity(ElectronDonation.CDKModel, Cycles.Or(Cycles.AllSimpleFinder, Cycles.RelevantFinder));
#endregion
}
}
