Package org.openscience.cdk.qsar.descriptors.molecular

Class XLogPDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class XLogPDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

    Prediction of logP based on the atom-type method called XLogP. Requires all hydrogens to be explicit.

    For description of the methodology see Ref. [Wang, R., Fu, Y., and Lai, L.. Journal of Chemical Information and Computer Sciences. 1997. 37] and [Wang, R., Gao, Y., and Lai, L.. Perspectives in Drug Discovery and Design. 2000. 19]. Actually one molecular factor is missing (presence of para Hs donor pair).

    Parameters for this descriptor:
    Name Default Description
    checkAromaticity false True is the aromaticity has to be checked
    salicylFlag false True is to use the salicyl acid correction factor

    changed 2005-11-03 by chhoppe
    -Internal hydrogen bonds are implemented
    CDK IDescriptor was validated against xlogp2.1
    As mentioned in the xlogP tutorial don't use charges, always draw bonds. To some extend we can support charges but not in every case.

    CDK follows the program in following points (which is not documented in the paper):
    -Atomtyp 7 is -0.137
    -Atomtype 81 is -0.447
    -pi system does not consider P or S
    -ring system >3
    -aromatic ring systems ≥6
    -N atomtypes: (ring) is always (ring)c
    -F 83 is not 0.375, the program uses 0.512 [2005-11-21]
    -hydrophobic carbon is 1-3 relationship not 1-4 [2005-11-22]
    -Atomtype C 34/35/36 perception corrected [2005-11-22]; before Atomtype perception ring perception is done -> slows run time

    In question:
    -Correction factor for salicylic acid (in paper, but not used by the program)
    -Amid classification is not consequent (in 6 rings (R2)N-C(R)=0 is eg 46 and in !6 membered rings it is amid)
    -sometimes O=C(R)-N(R)-C(R)=O is an amid ... sometimes not
    -Value for internal H bonds is in paper 0.429 but for no454 it is 0.643
    -pi system defintion, the neighbourhood is unclear

    changed 2005-11-21 by chhoppe
    -added new parameter for the salicyl acid correction factor
    -Corrected P and S perception for charges

    Author:
    mfe4, chhoppe
    Dictionary pointer(s):
    xlogP in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:xlogP]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Keywords:
    XLogP, descriptor
    Created on:
    2004-11-03

    • Field Detail

      • C_TERMINAL_AMINO_ACID

        public static final SmartsPattern C_TERMINAL_AMINO_ACID

      • P_AMINO_SULPHONIC_ACID

        public static final SmartsPattern P_AMINO_SULPHONIC_ACID

      • SALICYLIC_ACID_PTRN

        public static final SmartsPattern SALICYLIC_ACID_PTRN

    • Constructor Detail

      • XLogPDescriptor

        public XLogPDescriptor()
        Constructor for the XLogPDescriptor object.

    • Method Detail

      • 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..

      • calculate

        public DescriptorValue calculate​(IAtomContainer atomContainer)
        Calculates the xlogP for an atom container. If checkAromaticity is true, the method check the aromaticity, if false, means that the aromaticity has already been checked. It is necessary to use before the call of this mehtod the addExplicitHydrogensToSatisfyValency method (HydrogenAdder classe).
        Specified by:
        calculate in interface IMolecularDescriptor
        Parameters:
        atomContainer - AtomContainer
        Returns:
        XLogP is a double

      • 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

      • getParameterNames

        public String[] getParameterNames()
        Gets the parameterNames attribute of the XLogPDescriptor object.
        Specified by:
        getParameterNames in interface IDescriptor
        Returns:
        The parameterNames value

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the XLogPDescriptor object.
        Specified by:
        getParameterType in interface IDescriptor
        Parameters:
        name - Description of the Parameter
        Returns:
        The parameterType value

      • initialise

        public void initialise​(IChemObjectBuilder builder)
        Default implementation of initialise allows optional override.
        Specified by:
        initialise in interface IDescriptor
        Parameters:
        builder - chem object build