org.openscience.cdk.qsar.descriptors.atomic
Class PartialTChargeMMFF94Descriptor

java.lang.Object
  org.openscience.cdk.qsar.AbstractAtomicDescriptor
      org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94DescriptorTest")
public class PartialTChargeMMFF94Descriptor
extends AbstractAtomicDescriptor

The calculation of total partial charges of an heavy atom is based on MMFF94 model.

This descriptor uses these parameters:

Name	Default	Description
		no parameters

Author:

Miguel Rojas

See Also:

MMFF94PartialCharges

Belongs to the set:

qsar-descriptors

Created on:

2006-04-11

Belongs to CDK module:

builder3d

This class is affected by these bug(s):

1628461

Dictionary pointer(s):

partialTChargeMMFF94 in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:partialTChargeMMFF94]

Source code:

cdk-1.4.x

Constructor Summary

PartialTChargeMMFF94Descriptor()
Constructor for the PartialTChargeMMFF94Descriptor object

Method Summary

DescriptorValue	calculate(IAtom atom, IAtomContainer ac) The method returns partial charges assigned to an heavy atom through MMFF94 method.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor object
Object[]	getParameters() Gets the parameters attribute of the PartialTChargeMMFF94Descriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the PartialTChargeMMFF94Descriptor object
void	setParameters(Object[] params) This descriptor does not have any parameter to be set.

Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor

cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer

Methods inherited from class java.lang.Object

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

Constructor Detail

PartialTChargeMMFF94Descriptor

public PartialTChargeMMFF94Descriptor()

Constructor for the PartialTChargeMMFF94Descriptor object

Method Detail

getSpecification

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

Gets the specification attribute of the PartialTChargeMMFF94Descriptor object

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.

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 PartialTChargeMMFF94Descriptor object

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

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 through MMFF94 method. It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

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 PartialTChargeMMFF94Descriptor object

Returns:

The parameterNames value

getParameterType

@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name)

Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor object

Parameters:

name - Description of the Parameter

Returns:

The parameterType value