Package org.openscience.cdk.qsar.descriptors.molecular

Class SmallRingDescriptor

java.lang.Object

org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class SmallRingDescriptor
extends Object
implements IMolecularDescriptor

Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically. Returns these values

1. nSmallRings - total number of small rings (of size 3 through 9)
2. nAromRings - total number of small aromatic rings
3. nRingBlocks - total number of distinct ring blocks
4. nAromBlocks - total number of aromatically connected components
5. nRings3 - total number of 3-membered rings
6. nRings4 - total number of 4-membered rings
7. nRings5 - total number of 5-membered rings
8. nRings6 - total number of 6-membered rings
9. nRings7 - total number of 7-membered rings
10. nRings8 - total number of 8-membered rings
11. nRings9 - total number of 9-membered rings

Dictionary pointer(s):

smallrings in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:smallrings]

Source code:

main

Belongs to CDK module:

qsarmolecular

Keywords:

smallrings, descriptor

Constructor Summary

Constructors

Constructor	Description
SmallRingDescriptor()

Method Summary

Modifier and Type	Method	Description
DescriptorValue	calculate(IAtomContainer mol)	Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.
String[]	getDescriptorNames()	Returns the names of the descriptors made available by this class.
IDescriptorResult	getDescriptorResultType()	Returns a placeholder with the descriptor size and type.
String[]	getParameterNames()	Get parameters: empty, there are none.
Object[]	getParameters()	Get parameters: returns empty array, there are none.
Object	getParameterType(String name)	Parameter types: there aren't any.
DescriptorSpecification	getSpecification()	Fetch descriptor specification.
void	initialise(IChemObjectBuilder builder)	Initialise the descriptor with the specified chem object builder.
void	setParameters(Object[] params)	Set parameters: ignored, there are none.

Methods inherited from class java.lang.Object

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

Constructor Detail

SmallRingDescriptor

public SmallRingDescriptor()

Method Detail

initialise

public void initialise(IChemObjectBuilder builder)

Description copied from interface: IDescriptor

Initialise the descriptor with the specified chem object builder. This allows descriptors that required domain objects, such as for SMARTS queries to initialise correctly. If you do not need domain objects then this method does not need to be implemented.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object builder to use with this descriptor

getSpecification

public DescriptorSpecification getSpecification()

Fetch descriptor specification.

Specified by:

getSpecification in interface IDescriptor

Returns:

An object containing the descriptor specification

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Set parameters: ignored, there are none.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - An array of Object containing the parameters for this descriptor

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Get parameters: returns empty array, there are none.

Specified by:

getParameters in interface IDescriptor

Returns:

An array of Object containing the parameter default values

See Also:

IDescriptor.setParameters(java.lang.Object[])

getDescriptorNames

public String[] getDescriptorNames()

Returns the names of the descriptors made available by this class.

Specified by:

getDescriptorNames in interface IDescriptor

Returns:

An array of descriptor names, equal in length to the number of descriptor calculated..

getDescriptorResultType

public IDescriptorResult getDescriptorResultType()

Returns a placeholder with the descriptor size and type.

Specified by:

getDescriptorResultType in interface IMolecularDescriptor

Returns:

an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object

getParameterNames

public String[] getParameterNames()

Get parameters: empty, there are none.

Specified by:

getParameterNames in interface IDescriptor

Returns:

An array of String containing the names of the parameters that this descriptor can accept.

getParameterType

public Object getParameterType(String name)

Parameter types: there aren't any.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - The name of the parameter whose type is requested

Returns:

An Object of the class corresponding to the parameter with the supplied name

calculate

public DescriptorValue calculate(IAtomContainer mol)

Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

mol - the atoms and bonds that make up the molecular object

Returns:

the various ring-based descriptors generated