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

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

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

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

The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE). This descriptor has no parameters. The result of this descriptor is a vector of 5 values, corresponding to a maximum of four protons for any given atom. If an atom has fewer than four protons, the remaining values are set to Double.NaN. Also note that the values for the neighbors are not returned in a particular order (though the order is fixed for multiple runs for the same atom).

Author:

mfe4

Belongs to the set:

qsar-descriptors

Created on:

2004-11-03

Belongs to CDK module:

qsaratomic

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

ProtonTotalPartialChargeDescriptor()
Constructor for the ProtonTotalPartialChargeDescriptor object

Method Summary

DescriptorValue	calculate(IAtom atom, IAtomContainer ac) The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor object
Object[]	getParameters() Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the ProtonTotalPartialChargeDescriptor object
void	setParameters(Object[] params) This descriptor does not have any parameter to be set.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProtonTotalPartialChargeDescriptor

public ProtonTotalPartialChargeDescriptor()

Constructor for the ProtonTotalPartialChargeDescriptor object

Method Detail

getSpecification

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

Gets the specification attribute of the ProtonTotalPartialChargeDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

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

This descriptor does not have any parameter to be set.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - An array of Object containing the parameters for this descriptor

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

IDescriptor.getParameters()

getParameters

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

Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor object

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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 ac)

The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili 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

ac - AtomContainer

Returns:

an array of doubles with partial charges of [heavy, proton_1 ... proton_n]

getParameterNames

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

Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor 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 ProtonTotalPartialChargeDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

An Object of class equal to that of the parameter being requested