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

java.lang.Object
  extended by 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