Class AtomDegreeDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractAtomicDescriptor
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- org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
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- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
public class AtomDegreeDescriptor extends AbstractAtomicDescriptor implements IAtomicDescriptor
This class returns the number of not-Hs substituents of an atom, also defined as "atom degree".Parameters for this descriptor: Name Default Description no parameters - Author:
- mfe4
- Dictionary pointer(s):
- atomDegree in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:atomDegree]
- Source code:
- main
- Belongs to CDK module:
- qsaratomic
- Created on:
- 2004-11-13
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Constructor Summary
Constructors Constructor Description AtomDegreeDescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtom atom, IAtomContainer container)
This method calculates the number of not-H substituents of an atom.String[]
getDescriptorNames()
Returns an array of names for each descriptor value calculated.String[]
getParameterNames()
Gets the parameterNames attribute of the AtomDegreeDescriptor object.Object[]
getParameters()
Gets the parameters attribute of the AtomDegreeDescriptor object.Object
getParameterType(String name)
Gets the parameterType attribute of the AtomDegreeDescriptor 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)
This descriptor does not have any parameter to be set.-
Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor
cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer
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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
This descriptor does not have any parameter to be set.- 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()
Gets the parameters attribute of the AtomDegreeDescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- 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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calculate
public DescriptorValue calculate(IAtom atom, IAtomContainer container)
This method calculates the number of not-H substituents of an atom.- Specified by:
calculate
in interfaceIAtomicDescriptor
- Parameters:
atom
- The IAtom for which the DescriptorValue is requestedcontainer
- TheIAtomContainer
for which this descriptor is to be calculated for- Returns:
- The number of bonds on the shortest path between two atoms
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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the AtomDegreeDescriptor 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 AtomDegreeDescriptor object.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- An Object of class equal to that of the parameter being requested
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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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