/// <summary>
/// Create a perturbed hash generator using the provided seed generator to
/// initialise atom invariants and using the provided stereo factory.
/// </summary>
/// <param name="seeds"></param>
/// <param name="simple">generator to encode the initial values of atoms</param>
/// <param name="pseudorandom">pseudorandom number generator used to randomise hash distribution</param>
/// <param name="factory">a stereo encoder factory</param>
/// <param name="finder">equivalent set finder for driving the systematic perturbation</param>
/// <param name="suppression">suppression of atoms (these atoms are 'ignored' in the hash generation)</param>
/// <exception cref="ArgumentException">depth was less then 0</exception>
/// <exception cref="ArgumentNullException"> seed generator or pseudo random was null</exception>
/// <seealso cref="SeedGenerator"/>
public PerturbedAtomHashGenerator(SeedGenerator seeds, AbstractAtomHashGenerator simple, Pseudorandom pseudorandom,
IStereoEncoderFactory factory, EquivalentSetFinder finder, AtomSuppression suppression)
: base(pseudorandom)
{
this.finder = finder;
this.factory = factory;
this.simple = simple ?? throw new ArgumentNullException(nameof(simple), "no simple generator provided");
this.seeds = seeds ?? throw new ArgumentNullException(nameof(seeds), "no seed generator provided");
this.suppression = suppression ?? throw new ArgumentNullException(nameof(suppression), "no suppression provided, use AtomSuppression.None()");
}
/// <summary>
/// Create a basic hash generator using the provided seed generator to
/// initialise atom invariants and using the provided stereo factory.
/// </summary>
/// <param name="seedGenerator">generator to seed the initial values of atoms</param>
/// <param name="pseudorandom">pseudorandom number generator used to randomise hash distribution</param>
/// <param name="factory">a stereo encoder factory</param>
/// <param name="suppression">defines which atoms are suppressed - that is masked from the hash</param>
/// <param name="depth">depth of the hashing function, larger values take longer</param>
/// <exception cref="ArgumentException">depth was less then 0</exception>
/// <exception cref="ArgumentNullException"> seed generator or pseudo random was null</exception>
/// <seealso cref="SeedGenerator"/>
public SuppressedAtomHashGenerator(
IAtomHashGenerator seedGenerator, Pseudorandom pseudorandom,
IStereoEncoderFactory factory, AtomSuppression suppression, int depth)
: base(pseudorandom)
{
if (depth < 0)
{
throw new ArgumentOutOfRangeException(nameof(depth), "depth cannot be less then 0");
}
this.seedGenerator = seedGenerator ?? throw new ArgumentNullException(nameof(seedGenerator), "seed generator cannot be null");
this.factory = factory;
this.suppression = suppression;
this.depth = depth;
}
/// <summary>
/// Suppress any explicit hydrogens in the encoding of hash values. The
/// generation of hashes acts as though the hydrogens are not present and as
/// such preserves stereo-encoding.
/// </summary>
/// <returns>fluent API reference (self)</returns>
public HashGeneratorMaker SuppressHydrogens()
{
this.suppression = AtomSuppression.AnyHydrogens;
return(this);
}
/// <summary>
/// Create a new seed generator using the provided <see cref="IAtomEncoder"/> and
/// pseudorandom number generator.
/// </summary>
/// <param name="encoder">a method for encoding atom invariant properties</param>
/// <param name="pseudorandom">number generator to randomise initial invariants</param>
/// <param name="suppression">indicates which vertices should be suppressed</param>
/// <exception cref="ArgumentNullException">encoder or pseudorandom number generator was null</exception>
public SeedGenerator(IAtomEncoder encoder, Pseudorandom pseudorandom, AtomSuppression suppression)
: base(pseudorandom)
{
this.encoder = encoder ?? throw new ArgumentNullException(nameof(encoder), "encoder cannot be null");
this.suppression = suppression ?? throw new ArgumentNullException(nameof(suppression), "suppression cannot be null, use AtomSuppression.Unsuppressed()");
}
/// <summary>
/// Create a new seed generator using the provided <see cref="IAtomEncoder"/>.
/// </summary>
/// <param name="encoder">a method for encoding atom invariant properties</param>
/// <param name="suppression"></param>
/// <exception cref="ArgumentNullException">encoder was null</exception>
/// <seealso cref="ConjugatedAtomEncoder"/>
public SeedGenerator(IAtomEncoder encoder, AtomSuppression suppression)
: this(encoder, new Xorshift(), suppression)
{
}
/// <summary>
/// Create a basic hash generator using the provided seed generator to
/// initialise atom invariants and no stereo configuration.
/// </summary>
/// <param name="seedGenerator">generator to seed the initial values of atoms</param>
/// <param name="pseudorandom">pseudorandom number generator used to randomise hash distribution</param>
/// <param name="suppression">defines which atoms are suppressed (i.e. masked) from the hash code</param>
/// <param name="depth">depth of the hashing function, larger values take longer</param>
/// <exception cref="ArgumentException">depth was less then 0</exception>
/// <exception cref="ArgumentNullException">seed generator or pseudo random was null</exception>
/// <seealso cref="SeedGenerator"/>
public SuppressedAtomHashGenerator(IAtomHashGenerator seedGenerator, Pseudorandom pseudorandom,
AtomSuppression suppression, int depth)
: this(seedGenerator, pseudorandom, StereoEncoderFactory.Empty, suppression, depth)
{
}