org.openscience.cdk.qsar.descriptors.molecular

Class FractionalPSADescriptor

java.lang.Object

org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class FractionalPSADescriptor
extends Object
implements IMolecularDescriptor

Polar surface area expressed as a ratio to molecular size. Calculates tpsaEfficiency, which is to TPSADescriptor / molecular weight, in units of square Angstroms per Dalton. Other related descriptors may also be useful to add, e.g. ratio of polar to hydrophobic surface area.

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Keywords:

volume, descriptor

Constructor Summary

Constructors

Constructor and Description
FractionalPSADescriptor()

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer mol) Calculates the topological polar surface area and expresses it as a ratio to molecule size.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
String[]	getParameterNames() Returns the names of the parameters for this descriptor.
Object[]	getParameters() Returns the current parameter values.
Object	getParameterType(String name) Returns a class matching that of the parameter with the given name.
DescriptorSpecification	getSpecification() Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
void	initialise(IChemObjectBuilder builder) Initialise the descriptor with the specified chem object builder.
void	setParameters(Object[] params) Sets the parameters for this descriptor.

Methods inherited from class java.lang.Object

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

Constructor Detail

FractionalPSADescriptor

public FractionalPSADescriptor()

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()

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class. These fields are used in the map:

• Specification-Reference: refers to an entry in a unique dictionary
• Implementation-Title: anything
• Implementation-Identifier: a unique identifier for this version of this class
• Implementation-Vendor: CDK, JOELib, or anything else

Specified by:

getSpecification in interface IDescriptor

Returns:

An object containing the descriptor specification

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters for this descriptor. Must be done before calling calculate as the parameters influence the calculation outcome.

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()

Returns the current parameter values. If not parameters have been set, it must return the default parameters. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

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()

Description copied from interface: IDescriptor

Returns an array of names for each descriptor value calculated. Many descriptors return multiple values. In general it is useful for the descriptor to indicate the names for each value. In many cases, these names can be as simple as X1, X2, ..., XN where X is a prefix and 1, 2, ..., N are the indices. On the other hand it is also possible to return other arbitrary names, which should be documented in the Javadocs for the descriptor (e.g., the CPSA descriptor). Note that by default if a descriptor returns a single value (such as ALOGPDescriptor the return array will have a single element

Specified by:

getDescriptorNames in interface IDescriptor

Returns:

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

calculate

public DescriptorValue calculate(IAtomContainer mol)

Calculates the topological polar surface area and expresses it as a ratio to molecule size.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

mol - The IAtomContainer whose volume is to be calculated

Returns:

descriptor(s) retaining to polar surface area

getDescriptorResultType

public IDescriptorResult getDescriptorResultType()

Returns the specific type of the DescriptorResult object. The return value from this method really indicates what type of result will be obtained from the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.

Additionally, the length indicated by the result type must match the actual length of a descriptor calculated with the current parameters. Typically, the length of array result types vary with the values of the parameters. See IDescriptor for more details.

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()

Returns the names of the parameters for this descriptor. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

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)

Returns a class matching that of the parameter with the given name. May only return null for when 'name' does not match any parameters returned by the getParameters() method.

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