org.openscience.cdk.hash

Class HashGeneratorMaker

java.lang.Object

org.openscience.cdk.hash.HashGeneratorMaker

public final class HashGeneratorMaker
extends Object

Fluent API for creating hash generators. The maker is first configured with one or more attributes. Once fully configured the generator is made by invoking atomic(), molecular() or ensemble(). The order of the built-in configuration methods does not matter however when specifying custom encoders with encode(AtomEncoder) the order they are added is the order they will be used. Therefore one can expect different hash codes if there is a change in the order they are specified.
Examples

 // simple
 MoleculeHashGenerator generator = new HashGeneratorMaker().depth(16)
                                                           .elemental()
                                                           .molecular();

 // fast
 MoleculeHashGenerator generator = new HashGeneratorMaker().depth(8)
                                                           .elemental()
                                                           .isotopic()
                                                           .charged()
                                                           .orbital()
                                                           .molecular();
 // comprehensive
 MoleculeHashGenerator generator = new HashGeneratorMaker().depth(32)
                                                           .elemental()
                                                           .isotopic()
                                                           .charged()
                                                           .chiral()
                                                           .perturbed()
                                                           .molecular();
 

Author:

John May

Source code:

master

Belongs to CDK module:

hash

Constructor Summary

Constructors

Constructor and Description
HashGeneratorMaker()

Method Summary

Modifier and Type	Method and Description
AtomHashGenerator	atomic() Given the current configuration create an AtomHashGenerator.
HashGeneratorMaker	charged() Discriminate protonation states.
HashGeneratorMaker	chiral() Generate different hash codes for stereoisomers.
HashGeneratorMaker	depth(int depth) Specify the depth of the hash generator.
HashGeneratorMaker	elemental() Discriminate elements.
HashGeneratorMaker	encode(AtomEncoder encoder) Add a custom encoder to the hash generator which will be built.
EnsembleHashGenerator	ensemble() Given the current configuration create an EnsembleHashGenerator.
HashGeneratorMaker	isotopic() Discriminate isotopes.
MoleculeHashGenerator	molecular() Given the current configuration create an MoleculeHashGenerator.
HashGeneratorMaker	orbital() Discriminate atomic orbitals.
HashGeneratorMaker	perturbed() Discriminate atoms experiencing uniform environments.
HashGeneratorMaker	radical() Discriminate free radicals.
HashGeneratorMaker	suppressHydrogens() Suppress any explicit hydrogens in the encoding of hash values.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HashGeneratorMaker

public HashGeneratorMaker()

Method Detail

depth

public HashGeneratorMaker depth(int depth)

Specify the depth of the hash generator. Larger values discriminate more molecules.

Parameters:

depth - how deep should the generator hash

Returns:

reference for fluent API

Throws:

IllegalArgumentException - if the depth was less then zero

elemental

public HashGeneratorMaker elemental()

Discriminate elements.

Returns:

fluent API reference (self)

See Also:

BasicAtomEncoder.ATOMIC_NUMBER

isotopic

public HashGeneratorMaker isotopic()

Discriminate isotopes.

Returns:

fluent API reference (self)

See Also:

BasicAtomEncoder.MASS_NUMBER

charged

public HashGeneratorMaker charged()

Discriminate protonation states.

Returns:

fluent API reference (self)

See Also:

BasicAtomEncoder.FORMAL_CHARGE

orbital

public HashGeneratorMaker orbital()

Discriminate atomic orbitals.

Returns:

fluent API reference (self)

See Also:

BasicAtomEncoder.ORBITAL_HYBRIDIZATION

radical

public HashGeneratorMaker radical()

Discriminate free radicals.

Returns:

fluent API reference (self)

See Also:

BasicAtomEncoder.FREE_RADICALS

chiral

public HashGeneratorMaker chiral()

Generate different hash codes for stereoisomers. The currently supported geometries are:

• Tetrahedral
• Double Bond
• Cumulative Double Bonds

Returns:

fluent API reference (self)

suppressHydrogens

public HashGeneratorMaker suppressHydrogens()

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.

Returns:

fluent API reference (self)

perturbed

public HashGeneratorMaker perturbed()

Discriminate atoms experiencing uniform environments. This method uses MinimumEquivalentCyclicSet to break symmetry but depending on application one may need a more comprehensive method. Please refer to perturbWith(EquivalentSetFinder) for further configuration details.

Returns:

fluent API reference (self)

See Also:

MinimumEquivalentCyclicSet, perturbWith(EquivalentSetFinder)

encode

public HashGeneratorMaker encode(AtomEncoder encoder)

Add a custom encoder to the hash generator which will be built. Although not enforced, the encoder should be stateless and should not modify any passed inputs.

Parameters:

encoder - an atom encoder

Returns:

fluent API reference (self)

Throws:

NullPointerException - no encoder provided

ensemble

public EnsembleHashGenerator ensemble()

Given the current configuration create an EnsembleHashGenerator.

Returns:

instance of the generator

Throws:

IllegalArgumentException - no depth or encoders were configured

molecular

public MoleculeHashGenerator molecular()

Given the current configuration create an MoleculeHashGenerator.

Returns:

instance of the generator

Throws:

IllegalArgumentException - no depth or encoders were configured

atomic

public AtomHashGenerator atomic()

Given the current configuration create an AtomHashGenerator.

Returns:

instance of the generator

Throws:

IllegalArgumentException - no depth or encoders were configured