Class XLogPDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.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 Details

    • 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
    • ORTHOPAIR

      public static final SmartsPattern ORTHOPAIR
  • Constructor Details

    • XLogPDescriptor

      public XLogPDescriptor()
      Constructor for the XLogPDescriptor object.
  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the XLogPDescriptor object.
      Specified by:
      getSpecification in interface IDescriptor
      Returns:
      The specification value
    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the XLogPDescriptor object.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - The new parameters value
      Throws:
      CDKException - Description of the Exception
      See Also:
    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the XLogPDescriptor object.
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      The parameters value [boolean checkAromaticity, boolean salicylFlag]
      See Also:
    • 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