org.openscience.cdk.qsar.descriptors.atomic
Class IsProtonInAromaticSystemDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptorTest")
public class IsProtonInAromaticSystemDescriptor
extends Object
implements IAtomicDescriptor

This descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions. It is needed to use addExplicitHydrogensToSatisfyValency method.

This descriptor uses these parameters:

Name	Default	Description
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:

qsaratomic

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

IsProtonInAromaticSystemDescriptor()
Constructor for the IsProtonInAromaticSystemDescriptor object

Method Summary

DescriptorValue	calculate(IAtom atom, IAtomContainer atomContainer) The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor object
Object[]	getParameters() Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the IsProtonInAromaticSystemDescriptor object
void	setParameters(Object[] params) Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor object

Methods inherited from class java.lang.Object

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

Constructor Detail

IsProtonInAromaticSystemDescriptor

public IsProtonInAromaticSystemDescriptor()

Constructor for the IsProtonInAromaticSystemDescriptor object

Method Detail

getSpecification

@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification()

Gets the specification attribute of the IsProtonInAromaticSystemDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - Possible Exceptions

See Also:

IDescriptor.getParameters()

getParameters

@TestMethod(value="testGetParameters")
public Object[] getParameters()

Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor 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

@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom,
                                                 IAtomContainer atomContainer)

The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds. It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

atom - The IAtom for which the DescriptorValue is requested

atomContainer - AtomContainer

Returns:

true if the proton is bonded to an aromatic atom.

getParameterNames

@TestMethod(value="testGetParameterNames")
public String[] getParameterNames()

Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name)

Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value