Class HybridizationRatioDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class HybridizationRatioDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
IMolecularDescriptor
that reports the fraction of sp3 carbons to sp2 carbons. Note that it only considers carbon atoms and rather than use a simple ratio it reports the value of Nsp3/ (Nsp3 + Nsp2). The original form of the descriptor (i.e., simple ratio) has been used to characterize molecular complexity, especially in the are of natural products , which usually have a high value of the sp3 to sp2 ratio.- Author:
- Rajarshi Guha
- Dictionary pointer(s):
- hybratio in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:hybratio]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
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Constructor Summary
Constructors Constructor Description HybridizationRatioDescriptor()
Constructor for the HybridizationRatioDescriptor object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the suppliedIAtomContainer
.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 HybridizationRatioDescriptor object.Object[]
getParameters()
Gets the parameters attribute of the HybridizationRatioDescriptor object.Object
getParameterType(String name)
Gets the parameterType attribute of the HybridizationRatioDescriptor object.DescriptorSpecification
getSpecification()
Returns aDescriptorSpecification
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 HybridizationRatioDescriptor 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()
Returns aDescriptorSpecification
which specifies which descriptor is implemented by this class. 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 HybridizationRatioDescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The new parameters value- Throws:
CDKException
- if more than 1 parameter is specified or if the parameter is not of type String- See Also:
getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the HybridizationRatioDescriptor object. This descriptor takes no parameters- 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(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the suppliedIAtomContainer
.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- The AtomContainer for which this descriptor is to be calculated.- Returns:
- The ratio of sp3 to sp2 carbons
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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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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the HybridizationRatioDescriptor object. This descriptor takes no parameters- 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 HybridizationRatioDescriptor object. This descriptor takes no parameters- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- the parameter name- Returns:
- An Object whose class is that of the parameter 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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