org.openscience.cdk.qsar.descriptors.molecular
Class PetitjeanNumberDescriptor

java.lang.Object
  extended by org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptorTest")
public class PetitjeanNumberDescriptor
extends Object
implements IMolecularDescriptor

According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph. The distance is obtained from the distance matrix as the count of edges between the two vertices. If r(i) is the largest matrix entry in row i of the distance matrix D, then the radius is defined as the smallest of the r(i). The graph diameter D is defined as the largest vertex eccentricity in the graph. (http://www.edusoft-lc.com/molconn/manuals/400/chaptwo.html)

This descriptor uses these parameters:

Name Default Description
no parameters
Returns a single value named PetitjeanNumber.

Author:
mfe4
Belongs to the set:
qsar-descriptors
Keywords:
Petit-Jean, number
Created on:
December 7, 2004, 2004-11-03
Belongs to CDK module:
qsarmolecular
Dictionary pointer(s):
petitjeanNumber in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:petitjeanNumber]
Source code:
HEAD

Constructor Summary
PetitjeanNumberDescriptor()
          Constructor for the PetitjeanNumberDescriptor object
 
Method Summary
 DescriptorValue calculate(IAtomContainer atomContainer)
          Evaluate the descriptor for the molecule.
 String[] getDescriptorNames()
          Returns an array of names for each descriptor value calculated.
 IDescriptorResult getDescriptorResultType()
          Returns the specific type of the DescriptorResult object.
 String[] getParameterNames()
          Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
 Object[] getParameters()
          Gets the parameters attribute of the PetitjeanNumberDescriptor object
 Object getParameterType(String name)
          Gets the parameterType attribute of the PetitjeanNumberDescriptor object
 DescriptorSpecification getSpecification()
          Gets the specification attribute of the PetitjeanNumberDescriptor object
 void setParameters(Object[] params)
          Sets the parameters attribute of the PetitjeanNumberDescriptor object
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PetitjeanNumberDescriptor

public PetitjeanNumberDescriptor()
Constructor for the PetitjeanNumberDescriptor object

Method Detail

getSpecification

@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification()
Gets the specification attribute of the PetitjeanNumberDescriptor 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 PetitjeanNumberDescriptor object

Specified by:
setParameters in interface IDescriptor
Parameters:
params - The new parameters value
Throws:
CDKException - Description of the Exception
See Also:
IDescriptor.getParameters()

getParameters

@TestMethod(value="testGetParameters")
public Object[] getParameters()
Gets the parameters attribute of the PetitjeanNumberDescriptor 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(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.

Specified by:
calculate in interface IMolecularDescriptor
Parameters:
atomContainer - AtomContainer
Returns:
petitjean number

getDescriptorResultType

@TestMethod(value="testGetDescriptorResultType")
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.

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

@TestMethod(value="testGetParameterNames")
public String[] getParameterNames()
Gets the parameterNames attribute of the PetitjeanNumberDescriptor 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 PetitjeanNumberDescriptor object

Specified by:
getParameterType in interface IDescriptor
Parameters:
name - Description of the Parameter
Returns:
The parameterType value