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

java.lang.Object
  org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class HBondAcceptorCountDescriptor
extends java.lang.Object
implements IMolecularDescriptor

This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types. The following groups are counted as hydrogen bond acceptors:

• any oxygen where the formal charge of the oxygen is non-positive (i.e. formal charge <= 0) except
1. an aromatic ether oxygen (i.e. an ether oxygen that is adjacent to at least one aromatic carbon)
2. an oxygen that is adjacent to a nitrogen
• any nitrogen where the formal charge of the nitrogen is non-positive (i.e. formal charge <= 0) except
1. a nitrogen that is adjacent to an oxygen

Returns a single value named nHBAcc.

This descriptor uses these parameters:

Name	Default	Description
checkAromaticity	false	true if the aromaticity has to be checked

This descriptor works properly with AtomContainers whose atoms contain implicit hydrogens or explicit hydrogens.

Author:

ulif

Belongs to the set:

qsar-descriptors

Created on:

2005-22-07

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

revision 11707

Constructor Summary

HBondAcceptorCountDescriptor()
Constructor for the HBondAcceptorCountDescriptor object

Method Summary

DescriptorValue	calculate(IAtomContainer atomContainer) Calculates the number of H bond acceptors.
java.lang.String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
java.lang.String[]	getParameterNames() Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.
java.lang.Object[]	getParameters() Gets the parameters attribute of the HBondAcceptorCountDescriptor object.
java.lang.Object	getParameterType(java.lang.String name) Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the HBondAcceptorCountDescriptor object.
void	setParameters(java.lang.Object[] params) Sets the parameters attribute of the HBondAcceptorCountDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

HBondAcceptorCountDescriptor

public HBondAcceptorCountDescriptor()

Constructor for the HBondAcceptorCountDescriptor object

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the HBondAcceptorCountDescriptor object.

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

public void setParameters(java.lang.Object[] params)
                   throws CDKException

Sets the parameters attribute of the HBondAcceptorCountDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - a boolean true means that aromaticity has to be checked

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

public java.lang.Object[] getParameters()

Gets the parameters attribute of the HBondAcceptorCountDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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

getDescriptorNames

@TestMethod(value="testNamesConsistency")
public java.lang.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(IAtomContainer atomContainer)

Calculates the number of H bond acceptors.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - AtomContainer

Returns:

number of H bond acceptors

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.

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 java.lang.String[] getParameterNames()

Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public java.lang.Object getParameterType(java.lang.String name)

Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value