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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class CPSADescriptor
extends java.lang.Object
implements IMolecularDescriptor

Calculates 29 Charged Partial Surface Area (CPSA) descriptors.

The CPSA's were developed by Stanton et al. ([Stanton, D.T. and Jurs, P.C. , Development and Use of Charged Partial Surface Area Structural Descriptors in Computer Assissted Quantitative Structure Property Relationship Studies, Analytical Chemistry, 1990, 62:2323-2329]) and are related to the Polar Surface Area descriptors. The original implementation was in the ADAPT software package and the the definitions of the individual descriptors are presented in the following table. This class returns a DoubleArrayResult containing the 29 descriptors in the order described in the table.

A Summary of the 29 CPSA Descriptors

IDescriptor	Meaning
PPSA-1	partial positive surface area -- sum of surface area on positive parts of molecule
PPSA-2	partial positive surface area * total positive charge on the molecule
PPSA-3	charge weighted partial positive surface area
PNSA-1	partial negative surface area -- sum of surface area on negative parts of molecule
PNSA-2	partial negative surface area * total negative charge on the molecule
PNSA-3	charge weighted partial negative surface area
DPSA-1	difference of PPSA-1 and PNSA-1
DPSA-2	difference of FPSA-2 and PNSA-2
DPSA-3	difference of PPSA-3 and PNSA-3
FPSA-1	PPSA-1 / total molecular surface area
FFSA-2	PPSA-2 / total molecular surface area
FPSA-3	PPSA-3 / total molecular surface area
FNSA-1	PNSA-1 / total molecular surface area
FNSA-2	PNSA-2 / total molecular surface area
FNSA-3	PNSA-3 / total molecular surface area
WPSA-1	PPSA-1 * total molecular surface area / 1000
WPSA-2	PPSA-2 * total molecular surface area /1000
WPSA-3	PPSA-3 * total molecular surface area / 1000
WNSA-1	PNSA-1 * total molecular surface area /1000
WNSA-2	PNSA-2 * total molecular surface area / 1000
WNSA-3	PNSA-3 * total molecular surface area / 1000
RPCG	relative positive charge -- most positive charge / total positive charge
RNCG	relative negative charge -- most negative charge / total negative charge
RPCS	relative positive charge surface area -- most positive surface area * RPCG
RNCS	relative negative charge surface area -- most negative surface area * RNCG
THSA	sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2
TPSA	sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2
RHSA	THSA / total molecular surface area
RPSA	TPSA / total molecular surface area

NOTE: The values calculated by this implementation will differ from those calculated by the original ADAPT implementation of the CPSA descriptors. This is because the original implementation used an analytical surface area algorithm and used partial charges obtained from MOPAC using the AM1 Hamiltonian. This implementation uses a numerical algorithm to obtain surface areas (see NumericalSurface) and obtains partial charges using the Gasteiger-Marsilli algorithm (see GasteigerMarsiliPartialCharges).

However, a comparison of the values calculated by the two implementations indicates that they are qualitatively the same.

This descriptor uses these parameters:

Name	Default	Description
		no parameters

Author:

Rajarshi Guha

Belongs to the set:

qsar-descriptors

Created on:

2005-05-16

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

revision 11707

Constructor Summary

CPSADescriptor()

Method Summary

DescriptorValue	calculate(IAtomContainer atomContainer) Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
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 CPSADescriptor object.
java.lang.Object[]	getParameters() Gets the parameters attribute of the CPSADescriptor object.
java.lang.Object	getParameterType(java.lang.String name) Gets the parameterType attribute of the CPSADescriptor object.
DescriptorSpecification	getSpecification() Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(java.lang.Object[] params) Sets the parameters attribute of the CPSADescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

CPSADescriptor

public CPSADescriptor()

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Description copied from interface: IDescriptor

Returns a Map which specifies which descriptor is implemented by this class. These fields are used in the map:

• Specification-Reference: refers to an entry in a unique dictionary
• Implementation-Title: anything
• Implementation-Identifier: a unique identifier for this version of this class
• Implementation-Vendor: CDK, JOELib, or anything else

Specified by:

getSpecification in interface IDescriptor

Returns:

An object containing the descriptor specification

setParameters

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

Sets the parameters attribute of the CPSADescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - Description of the Exception

See Also:

getParameters()

getParameters

public java.lang.Object[] getParameters()

Gets the parameters attribute of the CPSADescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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..

getParameterNames

public java.lang.String[] getParameterNames()

Gets the parameterNames attribute of the CPSADescriptor 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 CPSADescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value

calculate

public DescriptorValue calculate(IAtomContainer atomContainer)

Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - Parameter is the atom container.

Returns:

An ArrayList containing 29 elements in the order described above

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