org.openscience.cdk.fragment

Class MurckoFragmenter

java.lang.Object

org.openscience.cdk.fragment.MurckoFragmenter

All Implemented Interfaces:

IFragmenter

public class MurckoFragmenter
extends Object
implements IFragmenter

An implementation of the Murcko fragmenation method (Bemis, G.W. and Murcko, M.A. . Journal of Medicinal Chemistry. 1996. 39). As an implementation of IFragmenter this class will return the Murcko frameworks (i.e., ring systems + linkers) along with the ring systems ia getFragments. The class also provides methods to extract the ring systems and frameworks separately. For all these methods, the user can retrieve the substructures as canonical SMILES strings or as IAtomContainer objects. Note that in contrast to the original paper which implies that a single molecule has a single framework, this class returns multiple frameworks consisting of all combinations of ring systems and linkers. The "true" Murcko framework is simply the largest framework.

Author:

Rajarshi Guha

See Also:

ExhaustiveFragmenter

Source code:

master

Belongs to CDK module:

fragment

Keywords:

fragment, framework

Constructor Summary

Constructors

Constructor and Description
MurckoFragmenter() Instantiate Murcko fragmenter.
MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize) Instantiate Murcko fragmenter.
MurckoFragmenter(boolean singleFrameworkOnly, int minimumFragmentSize, MoleculeHashGenerator generator) Instantiate Murcko fragmenter.

Method Summary

Modifier and Type	Method and Description
void	generateFragments(IAtomContainer atomContainer) Perform the fragmentation procedure.
String[]	getFragments() This returns the frameworks and ring systems from a Murcko fragmentation.
IAtomContainer[]	getFragmentsAsContainers() Get all frameworks and ring systems as IAtomContainer objects.
String[]	getFrameworks() Get frameworks as SMILES strings.
IAtomContainer[]	getFrameworksAsContainers() Get frameworks as IAtomContainer as objects.
String[]	getRingSystems() Get the ring system fragments as SMILES strings.
IAtomContainer[]	getRingSystemsAsContainers() Get rings systems as IAtomContainer objects.
static IAtomContainer	scaffold(IAtomContainer mol) Computes the Murcko Scaffold for the provided molecule in linear time.
void	setComputeRingFragments(boolean val) Sets whether to calculate ring fragments (true by default).

Methods inherited from class java.lang.Object

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

Constructor Detail

MurckoFragmenter

public MurckoFragmenter()

Instantiate Murcko fragmenter. Considers fragments with 5 or more atoms and generates multiple frameworks if available.

MurckoFragmenter

public MurckoFragmenter(boolean singleFrameworkOnly,
                        int minimumFragmentSize)

Instantiate Murcko fragmenter.

Parameters:

singleFrameworkOnly - if true, only the true Murcko framework is generated.

minimumFragmentSize - the smallest size of fragment to consider

MurckoFragmenter

public MurckoFragmenter(boolean singleFrameworkOnly,
                        int minimumFragmentSize,
                        MoleculeHashGenerator generator)

Instantiate Murcko fragmenter.

Parameters:

singleFrameworkOnly - if true, only the true Murcko framework is generated.

minimumFragmentSize - the smallest size of fragment to consider

generator - An instance of a MoleculeHashGenerator to be used to check for duplicate fragments

Method Detail

setComputeRingFragments

public void setComputeRingFragments(boolean val)

Sets whether to calculate ring fragments (true by default).

Parameters:

val - true/false

generateFragments

public void generateFragments(IAtomContainer atomContainer)
                       throws CDKException

Perform the fragmentation procedure.

Specified by:

generateFragments in interface IFragmenter

Parameters:

atomContainer - The input molecule

Throws:

CDKException

scaffold

public static IAtomContainer scaffold(IAtomContainer mol)

Computes the Murcko Scaffold for the provided molecule in linear time. Note the return value contains the same atoms/bonds as in the input and an additional clone and valence adjustments may be required.

Parameters:

mol - the molecule

Returns:

the atoms and bonds in the scaffold

getFragments

public String[] getFragments()

This returns the frameworks and ring systems from a Murcko fragmentation. To get frameworks, ring systems and side chains seperately, use the respective functions

Specified by:

getFragments in interface IFragmenter

Returns:

a String[] of the fragments.

See Also:

getRingSystems(), getRingSystemsAsContainers(), getFrameworks(), getFrameworksAsContainers()

getFragmentsAsContainers

public IAtomContainer[] getFragmentsAsContainers()

Get all frameworks and ring systems as IAtomContainer objects.

Specified by:

getFragmentsAsContainers in interface IFragmenter

Returns:

An array of structures representing frameworks and ring systems

getRingSystems

public String[] getRingSystems()

Get the ring system fragments as SMILES strings.

Returns:

a String[] of the fragments.

getRingSystemsAsContainers

public IAtomContainer[] getRingSystemsAsContainers()

Get rings systems as IAtomContainer objects.

Returns:

an array of ring systems.

getFrameworks

public String[] getFrameworks()

Get frameworks as SMILES strings.

Returns:

an array of SMILES strings

getFrameworksAsContainers

public IAtomContainer[] getFrameworksAsContainers()

Get frameworks as IAtomContainer as objects.

Returns:

an array of frameworks.