org.openscience.cdk.qsar.descriptors.protein

Class TaeAminoAcidDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class TaeAminoAcidDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

An implementation of the TAE descriptors for amino acids. The TAE descriptors ([Breneman, C.M. and Thompson, T.R. and Rhem, M. and Dung, M. , Electron Density Modeling of Large Systems Using the Transferable Atom Equivalent Method , Computers and Chemistry, 1995, 19:161] [Breneman, C.M. and Rhem, M. , A QSPR Analysis of HPLC Column Capacity Factors for a set of High-Energy Materials Using Electronic Van der Waals Surface Property Descriptors Computed by the Transferable Atom Equivalent Method , Journal of Computational Chemistry, 1997, 18:182-197] [Whitehead, C.E. and Sukumar, N. and Breneman, C.M. and Ryan, M.D. , Transferable Atom Equivalent Multi-Centered Multipole Expansion Method, Journal of Computational Chemistry, 2003, 24:512-529]) are derived from pre-calculated quantum mechanical parameters. This class uses the parameters for amino acids and thus evaluates a set of 147 descriptors for peptide sequences. The class expects that it will be supplied an object which implements the IBioPolymer. Thus ordinary AtomContainer objects will result in an exception. The descriptors are returned in the following order (see here for a detailed description of the individual descriptors):

 Energy Population VOLTAE SurfArea
 SIDel.Rho.N Del.Rho.NMin Del.Rho.NMax Del.Rho.NIA Del.Rho.NA1
 Del.Rho.NA2 Del.Rho.NA3 Del.Rho.NA4 Del.Rho.NA5 Del.Rho.NA6
 Del.Rho.NA7 Del.Rho.NA8 Del.Rho.NA9 Del.Rho.NA10 SIDel.K.N
 Del.K.Min Del.K.Max Del.K.IA Del.K.NA1 Del.K.NA2
 Del.K.NA3 Del.K.NA4 Del.K.NA5 Del.K.NA6 Del.K.NA7
 Del.K.NA8 Del.K.NA9 Del.K.NA10 SIK SIKMin
 SIKMax SIKIA SIKA1 SIKA2 SIKA3
 SIKA4 SIKA5 SIKA6 SIKA7 SIKA8
 SIKA9 SIKA10 SIDel.G.N Del.G.NMin Del.G.NMax
 Del.G.NIA Del.G.NA1 Del.G.NA2 Del.G.NA3 Del.G.NA4
 Del.G.NA5 Del.G.NA6 Del.G.NA7 Del.G.NA8 Del.G.NA9
 Del.G.NA10 SIG SIGMin SIGMax SIGIA
 SIGA1 SIGA2 SIGA3 SIGA4 SIGA5
 SIGA6 SIGA7 SIGA8 SIGA9 SIGA10
 SIEP SIEPMin SIEPMax SIEPIA SIEPA1
 SIEPA2 SIEPA3 SIEPA4 SIEPA5 SIEPA6
 SIEPA7 SIEPA8 SIEPA9 SIEPA10 EP1
 EP2 EP3 EP4 EP5 EP6
 EP7 EP8 EP9 EP10 PIPMin
 PIPMax PIPAvg PIP1 PIP2 PIP3
 PIP4 PIP5 PIP6 PIP7 PIP8
 PIP9 PIP10 PIP11 PIP12 PIP13
 PIP14 PIP15 PIP16 PIP17 PIP18
 PIP19 PIP20 Fuk FukMin FukMax
 Fuk1 Fuk2 Fuk3 Fuk4 Fuk5
 Fuk6 Fuk7 Fuk8 Fuk9 Fuk10
 Lapl LaplMin LaplMax Lapl1 Lapl2
 Lapl3 Lapl4 Lapl5 Lapl6 Lapl7
 Lapl8 Lapl9 Lapl10
 

Parameters for this descriptor:

Name	Default	Description
		no parameters

Author:

Rajarshi Guha

See Also:

IBioPolymer

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarprotein

Created on:

2006-08-23

Constructor Summary

Constructors

Constructor and Description
TaeAminoAcidDescriptor()

Method Summary

Methods

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer container) Calculates the 147 TAE descriptors for amino acids.
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 attribute of the TaeAminOAcidDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the TaeAminoAcidDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the TaeAminoAcidDescriptor object.
DescriptorSpecification	getSpecification() Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters attribute of the TaeAminoAcidDescriptor object.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.qsar.IDescriptor

initialise

Constructor Detail

TaeAminoAcidDescriptor

public TaeAminoAcidDescriptor()

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Description copied from interface: IDescriptor

Returns a IImplementationSpecification 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(Object[] params)
                   throws CDKException

Sets the parameters attribute of the TaeAminoAcidDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the TaeAminoAcidDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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

getDescriptorNames

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 descriptor (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 String[] getParameterNames()

Gets the parameterNames attribute of the TaeAminOAcidDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the TaeAminoAcidDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value

calculate

public DescriptorValue calculate(IAtomContainer container)

Calculates the 147 TAE descriptors for amino acids.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - Parameter is the atom container which should implement IBioPolymer.

Returns:

A DoubleArrayResult value representing the 147 TAE descriptors

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

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build