org.openscience.cdk.qsar.descriptors.atompair
Class PiContactDetectionDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

All Implemented Interfaces:

IAtomPairDescriptor, IDescriptor

public class PiContactDetectionDescriptor
extends Object
implements IAtomPairDescriptor

This class checks if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighboors of the atoms).

This descriptor uses these parameters:

Name	Default	Description
firstAtom	0	The position of the first atom
secondAtom	0	The position of the second atom
checkAromaticity	false	True is the aromaticity has to be checked

Author:

mfe4

Belongs to the set:

qsar-descriptors

Created on:

2004-11-03

Belongs to CDK module:

qsar

Dictionary pointer(s):

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

Source code:

HEAD

Constructor Summary

PiContactDetectionDescriptor()
Constructor for the PiContactDetectionDescriptor object.

Method Summary

DescriptorValue	calculate(IAtom first, IAtom second, IAtomContainer atomContainer) The method returns if two atoms have pi-contact.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the PiContactDetectionDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the PiContactDetectionDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the PiContactDetectionDescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the PiContactDetectionDescriptor object.
void	setParameters(Object[] params) Sets the parameters attribute of the PiContactDetectionDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

PiContactDetectionDescriptor

public PiContactDetectionDescriptor()

Constructor for the PiContactDetectionDescriptor object.

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the PiContactDetectionDescriptor object.

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the PiContactDetectionDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - Parameters contains a boolean (true if is needed a checkAromaticity)

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the PiContactDetectionDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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

getDescriptorNames

@TestMethod(value="testNamesConsistency")
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 decsriptor (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(IAtom first,
                                 IAtom second,
                                 IAtomContainer atomContainer)

The method returns if two atoms have pi-contact.

Specified by:

calculate in interface IAtomPairDescriptor

Parameters:

atomContainer - AtomContainer

first - The first IAtom of the pair for which this descriptor should be calculated

second - The second IAtom of the pair for which this descriptor should be calculated

Returns:

true if the atoms have pi-contact

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the PiContactDetectionDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the PiContactDetectionDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value