Package org.openscience.cdk.qsar.descriptors.protein

Class 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. et. al.. Computers and Chemistry. 1995. 19] [Breneman, C.M. and Rhem, M. . Journal of Computational Chemistry. 1997. 18] [Whitehead, C.E. et. al.. Journal of Computational Chemistry. 2003. 24]) 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:
    main
    Belongs to CDK module:
    qsarprotein
    Created on:
    2006-08-23

    • 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

      • 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