org.openscience.cdk.fragment

Class ExhaustiveFragmenter

java.lang.Object

org.openscience.cdk.fragment.ExhaustiveFragmenter

All Implemented Interfaces:

IFragmenter

@TestClass(value="org.openscience.cdk.fragment.ExhaustiveFragmenterTest")
public class ExhaustiveFragmenter
extends Object
implements IFragmenter

Generate fragments exhaustively.

This fragmentation scheme simply breaks single non-ring bonds. By default fragments smaller than 6 atoms in size are not considered, but this can be changed by the user. Side chains are retained.

Author:

Rajarshi Guha

Keywords:

fragment

Constructor Summary

Constructors

Constructor and Description
ExhaustiveFragmenter() Instantiate fragmenter with default minimum fragment size.
ExhaustiveFragmenter(int minFragSize) Instantiate fragmenter with user specified minimum fragment size.

Method Summary

Methods

Modifier and Type	Method and Description
void	generateFragments(IAtomContainer atomContainer) Generate fragments for the input molecule.
String[]	getFragments() Get the fragments generated as SMILES strings.
IAtomContainer[]	getFragmentsAsContainers() Get the fragments generated as IAtomContainer objects..
void	setMinimumFragmentSize(int minFragSize) Set the minimum fragment size.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExhaustiveFragmenter

@TestMethod(value="testEF1,testEF2,testEF3")
public ExhaustiveFragmenter()

Instantiate fragmenter with default minimum fragment size.

ExhaustiveFragmenter

@TestMethod(value="testEF1,testEF2,testEF3")
public ExhaustiveFragmenter(int minFragSize)

Instantiate fragmenter with user specified minimum fragment size.

Parameters:

minFragSize - the minimum fragment size desired

Method Detail

setMinimumFragmentSize

@TestMethod(value="testMinSize")
public void setMinimumFragmentSize(int minFragSize)

Set the minimum fragment size.

Parameters:

minFragSize - the smallest size fragment that will be returned

generateFragments

@TestMethod(value="testEF1,testEF2,testEF3,testEF4,testEF5,testEF6,testEF7")
public void generateFragments(IAtomContainer atomContainer)
                       throws CDKException

Generate fragments for the input molecule.

Specified by:

generateFragments in interface IFragmenter

Parameters:

atomContainer - The input molecule.

Throws:

CDKException - if ring detection fails

getFragments

@TestMethod(value="testEF1,testEF2,testEF3,testEF4,testEF5,testEF6,testEF7")
public String[] getFragments()

Get the fragments generated as SMILES strings.

Specified by:

getFragments in interface IFragmenter

Returns:

a String[] of the fragments.

getFragmentsAsContainers

@TestMethod(value="testEF5,testEF6,testEF7")
public IAtomContainer[] getFragmentsAsContainers()

Get the fragments generated as IAtomContainer objects..

Specified by:

getFragmentsAsContainers in interface IFragmenter

Returns:

a IAtomContainer[] of the fragments.