Class WHIMDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class WHIMDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
Holistic descriptors described by Todeschini et al [Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null]. The descriptors are based on a number of atom weightings. There are 6 different possible weightings:- unit weights
- atomic masses
- van der Waals volumes
- Mulliken atomic electronegativites
- atomic polarizabilities
- E-state values described by Kier & Hall
For each weighting scheme we can obtain
- 11 directional WHIM descriptors (λ1 .. 3, ν1 .. 2, γ1 .. 3, η1 .. 3)
- 6 non-directional WHIM descriptors (T, A, V, K, G, D)
Though [Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null] mentions that for planar molecules only 8 directional WHIM descriptors are required the current code will return all 11. The descriptor returns 17 values for a given weighting scheme, named as follows:
- Wlambda1
- Wlambda2
- wlambda3
- Wnu1
- Wnu2
- Wgamma1
- Wgamma2
- Wgamma3
- Weta1
- Weta2
- Weta3
- WT
- WA
- WV
- WK
- WG
- WD
- unity
- mass
- volume
- eneg
- polar
Parameters for this descriptor: Name Default Description type unity Type of weighting as described above - Author:
- Rajarshi Guha
- Dictionary pointer(s):
- WHIM in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:WHIM]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Keywords:
- WHIM, descriptor
- Created on:
- 2004-12-1
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Constructor Summary
Constructors Constructor Description WHIMDescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for.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 WHIMDescriptor object.Object[]
getParameters()
Gets the parameters attribute of the WHIMDescriptor object.Object
getParameterType(String name)
Gets the parameterType attribute of the WHIMDescriptor object.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 attribute of the WHIMDescriptor object.-
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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Method Detail
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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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setParameters
public void setParameters(Object[] params) throws CDKException
Sets the parameters attribute of the WHIMDescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The new parameter values. The Object array should have a single element which should be a String. The possible values of this String are: unity, mass, volume, eneg, polar- Throws:
CDKException
- if the parameters are of the wrong type- See Also:
getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the WHIMDescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- Two element array of Integer representing number of highest and lowest eigenvalues to return respectively
- See Also:
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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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the WHIMDescriptor object.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
public Object getParameterType(String name)
Gets the parameterType attribute of the WHIMDescriptor object.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
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calculate
public DescriptorValue calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for. the specified weighting scheme- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- Parameter is the atom container.- Returns:
- An ArrayList containing the descriptors in the order described above.
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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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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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