org.openscience.cdk.structgen

Class RandomGenerator

java.lang.Object

org.openscience.cdk.structgen.RandomGenerator

public class RandomGenerator
extends Object

RandomGenerator is a generator of constitutional isomers. It needs to be provided with a starting constitution and it makes random moves in constitutional space from there. This generator was first suggested by J.-L. Faulon [Faulon, J. L., Stochastic generator of chemical structure .2. Using simulated annealing to search the space of constitutional isomers, Journal of Chemical Information and Computer Sciences, 1996, 36:731-740].

Unlike the VicinitySampler, this methods does not sample the full Faulon vicinity.

See Also:

VicinitySampler

Source code:

master

Belongs to CDK module:

structgen

Keywords:

structure generator

Constructor Summary

Constructors

Constructor and Description
RandomGenerator(IAtomContainer molecule) Constructs a RandomGenerator with a given starting structure.

Method Summary

Methods

Modifier and Type	Method and Description
void	acceptStructure() Tell the RandomGenerator to accept the last structure that had been proposed.
IAtomContainer	getMolecule() Returns the molecule which reflects the current state of this stochastic structure generator.
void	mutate(IAtomContainer ac) Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".
IAtomContainer	proposeStructure() Proposes a structure which can be accepted or rejected by an external entity.
void	setMolecule(IAtomContainer molecule) Assigns a starting structure to this generator.

Methods inherited from class java.lang.Object

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

Constructor Detail

RandomGenerator

public RandomGenerator(IAtomContainer molecule)

Constructs a RandomGenerator with a given starting structure.

Parameters:

molecule - The starting structure

Method Detail

proposeStructure

public IAtomContainer proposeStructure()

Proposes a structure which can be accepted or rejected by an external entity. If rejected, the structure is not used as a starting point for the next random move in structure space.

Returns:

A proposed molecule

acceptStructure

public void acceptStructure()

Tell the RandomGenerator to accept the last structure that had been proposed.

mutate

public void mutate(IAtomContainer ac)

Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".

setMolecule

public void setMolecule(IAtomContainer molecule)

Assigns a starting structure to this generator.

Parameters:

molecule - a starting structure for this generator

getMolecule

public IAtomContainer getMolecule()

Returns the molecule which reflects the current state of this stochastic structure generator.

Returns:

The molecule