Class FractionalCSP3Descriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class FractionalCSP3Descriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
An implementation of the Fractional CSP3 descriptor described in [Lovering, Frank et. al.. J. Med. Chem.. 2009. 52]. This descriptor is characterizing non-flatness of a molecule. This descriptor returns a single double value, labeled as "Fsp3"- Author:
- Kazuya Ujihara
- Dictionary pointer(s):
- Fsp3 in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:Fsp3]
- Belongs to CDK module:
- qsarmolecular
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Constructor Summary
Constructors Constructor Description FractionalCSP3Descriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer mol)
Calculates the Fsp3 descriptor value for the givenIAtomContainer
.String[]
getDescriptorNames()
Returns an array of names for each descriptor value calculated.IDescriptorResult
getDescriptorResultType()
Returns the specific type of the Fsp3 descriptor value.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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Method Detail
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getSpecification
public DescriptorSpecification getSpecification()
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()
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)
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
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()
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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calculate
public DescriptorValue calculate(IAtomContainer mol)
Calculates the Fsp3 descriptor value for the givenIAtomContainer
.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
mol
- AnIAtomContainer
for which this descriptor should be calculated- Returns:
- An object of
DescriptorValue
that contains the calculated Fsp3 descriptor value
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getDescriptorResultType
public IDescriptorResult getDescriptorResultType()
Returns the specific type of the Fsp3 descriptor value. The Fsp3 descriptor is a single, double value.- Specified by:
getDescriptorResultType
in interfaceIMolecularDescriptor
- Returns:
- an instance of the
DoubleResultType
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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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