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

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

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

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

This descriptor uses no parameters.

This descriptor works properly with AtomContainers whose atoms contain either implicit or explicit hydrogen atoms. It does not work with atoms that contain neither implicit nor explicit hydrogens. Returns a single value named nHBDon.

This descriptor uses these parameters:

Name Default Description
no parameters

Author:
ulif
Belongs to the set:
qsar-descriptors
Created on:
2005-22-07
Belongs to CDK module:
qsarmolecular
Dictionary pointer(s):
hBondDonors in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:hBondDonors]
Source code:
HEAD

Constructor Summary
HBondDonorCountDescriptor()
          Constructor for the HBondDonorCountDescriptor object
 
Method Summary
 DescriptorValue calculate(IAtomContainer atomContainer)
          Calculates the number of H bond donors.
 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 of the HBondDonorCountDescriptor.
 Object[] getParameters()
          Gets the parameters of the HBondDonorCountDescriptor instance.
 Object getParameterType(String name)
          Gets the parameterType of the HBondDonorCountDescriptor.
 DescriptorSpecification getSpecification()
          Gets the specification attribute of the HBondDonorCountDescriptor object
 void setParameters(Object[] params)
          Sets the parameter of this HBondDonorCountDescriptor instance.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

HBondDonorCountDescriptor

public HBondDonorCountDescriptor()
Constructor for the HBondDonorCountDescriptor object

Method Detail

getSpecification

@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification()
Gets the specification attribute of the HBondDonorCountDescriptor 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 parameter of this HBondDonorCountDescriptor instance.

Specified by:
setParameters in interface IDescriptor
Parameters:
params - this descriptor does not have any parameters
Throws:
CDKException - Description of the Exception
See Also:
IDescriptor.getParameters()

getParameters

@TestMethod(value="testGetParameters")
public Object[] getParameters()
Gets the parameters of the HBondDonorCountDescriptor instance.

Specified by:
getParameters in interface IDescriptor
Returns:
null as this descriptor does not have any parameters
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)
Calculates the number of H bond donors.

Specified by:
calculate in interface IMolecularDescriptor
Parameters:
atomContainer - AtomContainer
Returns:
number of H bond donors

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 of the HBondDonorCountDescriptor.

Specified by:
getParameterNames in interface IDescriptor
Returns:
null as this descriptor does not have any parameters

getParameterType

@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name)
Gets the parameterType of the HBondDonorCountDescriptor.

Specified by:
getParameterType in interface IDescriptor
Parameters:
name - Description of the Parameter
Returns:
null as this descriptor does not have any parameters