Class ALOGPDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class ALOGPDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity [Ghose, A.K. and Crippen, G.M. . Journal of Computational Chemistry. 1986. 7, Ghose, A.K. and Crippen, G.M. . Journal of Chemical Information and Computer Science. 1987. 27]. Note The code assumes that aromaticity has been detected before evaluating this descriptor. The code also expects that the molecule will have hydrogens explicitly set. For SD files, this is usually not a problem since hydrogens are explicit. But for the case of molecules obtained from SMILES, hydrogens must be made explicit.TODO: what should sub return if have missing fragment? Just report sum for other fragments? Or report as -9999 and then do not use descriptor if have this value for any chemicals in cluster?
Returns three valuesParameters for this descriptor: Name Default Description no parameters - ALogP - Ghose-Crippen LogKow
- ALogP2
- amr - molar refractivity
- Author:
- Todd Martin
- See Also:
CDKHydrogenAdder
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Keywords:
- logP, lipophilicity, refractivity
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Constructor Summary
Constructors Constructor Description ALOGPDescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer container)
The AlogP descriptor.String[]
getDescriptorNames()
Returns an array of names for each descriptor value calculated.IDescriptorResult
getDescriptorResultType()
Returns the specific type of the DescriptorResult object.String[]
getParameterNames()
Returns the names of the parameters for this descriptor.Object[]
getParameters()
Returns the current parameter values.Object
getParameterType(String name)
Returns a class matching that of the parameter with the given name.DescriptorSpecification
getSpecification()
Returns aIImplementationSpecification
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 for this descriptor.-
Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor
clone
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise
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Constructor Detail
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ALOGPDescriptor
public ALOGPDescriptor() throws CDKException
- Throws:
CDKException
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Method Detail
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calculate
public DescriptorValue calculate(IAtomContainer container)
The AlogP descriptor. TODO Ideally we should explicit H addition should be cached- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- the molecule to calculate on- Returns:
- the result of the calculation
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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 theDescriptorValue
object. Note that the same result can be achieved by interrogating theDescriptorValue
object; this method allows you to do the same thing, without actually calculating the descriptor.- Specified by:
getDescriptorResultType
in interfaceIMolecularDescriptor
- Returns:
- an object that implements the
IDescriptorResult
interface indicating the actual type of values returned by the descriptor in theDescriptorValue
object
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getSpecification
public DescriptorSpecification getSpecification()
Description copied from interface:IDescriptor
Returns aIImplementationSpecification
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 interfaceIDescriptor
- Returns:
- An object containing the descriptor specification
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getParameterNames
public String[] getParameterNames()
Description copied from interface:IDescriptor
Returns the names of the parameters for this descriptor. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- An array of String containing the names of the parameters that this descriptor can accept.
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getParameterType
public Object getParameterType(String name)
Description copied from interface:IDescriptor
Returns a class matching that of the parameter with the given name. May only return null for when 'name' does not match any parameters returned by the getParameters() method.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- The name of the parameter whose type is requested- Returns:
- An Object of the class corresponding to the parameter with the supplied name
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setParameters
public void setParameters(Object[] params) throws CDKException
Description copied from interface:IDescriptor
Sets the parameters for this descriptor. Must be done before calling calculate as the parameters influence the calculation outcome.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- An array of Object containing the parameters for this descriptor- Throws:
CDKException
- if invalid number of type of parameters are passed to it- See Also:
IDescriptor.getParameters()
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getParameters
public Object[] getParameters()
Description copied from interface:IDescriptor
Returns the current parameter values. If not parameters have been set, it must return the default parameters. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- An array of Object containing the parameter default values
- See Also:
IDescriptor.setParameters(java.lang.Object[])
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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 asALOGPDescriptor
the return array will have a single element- Specified by:
getDescriptorNames
in interfaceIDescriptor
- Returns:
- An array of descriptor names, equal in length to the number of descriptor calculated..
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initialise
public void initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
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