org.openscience.cdk.graph

Class AtomContainerPermutor

java.lang.Object

org.openscience.cdk.graph.Permutor

org.openscience.cdk.graph.AtomContainerPermutor

All Implemented Interfaces:

Iterator<IAtomContainer>

Direct Known Subclasses:

AtomContainerAtomPermutor, AtomContainerBondPermutor

public abstract class AtomContainerPermutor
extends Permutor
implements Iterator<IAtomContainer>

The base class for permutors of atom containers, with a single abstract method containerFromPermutation that should be implemented in concrete derived classes.

Author:

maclean

Source code:

master

Belongs to CDK module:

standard

Keywords:

permutation

Created on:

2009-09-09

Field Summary

Fields

Modifier and Type	Field and Description
protected IAtomContainer	atomContainer The atom container that is permuted at each step.

Constructor Summary

Constructors

Constructor and Description
AtomContainerPermutor(int size, IAtomContainer atomContainer) Start the permutor off with an initial atom container, and the size of the permutation.

Method Summary

Modifier and Type	Method and Description
abstract IAtomContainer	containerFromPermutation(int[] permutation) Convert a permutation (expressed as a list of numbers) into a permuted atom container.
IAtomContainer	next()
IAtomContainer	randomNext() Get a new container, but randomly skip forwards in the list of possible permutations to generate it.
void	remove()

Methods inherited from class org.openscience.cdk.graph.Permutor

calculateMaxRank, getCurrentPermutation, getNextPermutation, getRandomNextPermutation, getRank, hasNext, setPermutation, setRank

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining, hasNext

Field Detail

atomContainer

protected IAtomContainer atomContainer

The atom container that is permuted at each step.

Constructor Detail

AtomContainerPermutor

public AtomContainerPermutor(int size,
                             IAtomContainer atomContainer)

Start the permutor off with an initial atom container, and the size of the permutation.

Parameters:

atomContainer -

Method Detail

containerFromPermutation

public abstract IAtomContainer containerFromPermutation(int[] permutation)

Convert a permutation (expressed as a list of numbers) into a permuted atom container. This will differ depending on the desired effect of the permutation (atoms or bonds, for example).

Returns:

the atom container corresponding to this permutation

randomNext

public IAtomContainer randomNext()

Get a new container, but randomly skip forwards in the list of possible permutations to generate it.

Returns:

a random next permuted atom container

next

public IAtomContainer next()

Specified by:

next in interface Iterator<IAtomContainer>

remove

public void remove()

Specified by:

remove in interface Iterator<IAtomContainer>