Class LongestAliphaticChainDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class LongestAliphaticChainDescriptor extends AbstractMolecularDescriptor
Counts the number of atoms in the longest aliphatic chain.Parameters for this descriptor: Name Default Description checkRingSystem false True is the CDKConstant.ISINRING has to be set Returns a single value named nAtomLAC
- Author:
- chhoppe from EUROSCREEN, John Mayfield
- Dictionary pointer(s):
- largestAliphaticChain in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:largestAliphaticChain]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Created on:
- 2006-1-03
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Field Summary
Fields Modifier and Type Field Description static String
CHECK_RING_SYSTEM
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Constructor Summary
Constructors Constructor Description LongestAliphaticChainDescriptor()
Constructor for the LongestAliphaticChainDescriptor object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer mol)
Calculate the count of atoms of the longest aliphatic chain 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 LongestAliphaticChainDescriptor object.Object[]
getParameters()
Gets the parameters attribute of the LongestAliphaticChainDescriptor object.Object
getParameterType(String name)
Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.DescriptorSpecification
getSpecification()
Returns aMap
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 LongestAliphaticChainDescriptor 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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Field Detail
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CHECK_RING_SYSTEM
public static final String CHECK_RING_SYSTEM
- See Also:
- Constant Field Values
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Method Detail
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getSpecification
public DescriptorSpecification getSpecification()
Returns aMap
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
- 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 LongestAliphaticChainDescriptor object.This descriptor takes one parameter, which should be Boolean to indicate whether aromaticity has been checked (TRUE) or not (FALSE).
- Parameters:
params
- The new parameters value- Throws:
CDKException
- if more than one parameter or a non-Boolean parameter is specified- See Also:
getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the LongestAliphaticChainDescriptor object.- 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- Returns:
- An array of descriptor names, equal in length to the number of descriptor calculated..
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calculate
public DescriptorValue calculate(IAtomContainer mol)
Calculate the count of atoms of the longest aliphatic chain in the suppliedIAtomContainer
.The method require one parameter: if checkRingSyste is true the CDKConstant.ISINRING will be set
- Parameters:
mol
- TheIAtomContainer
for which this descriptor is to be calculated- Returns:
- the number of atoms in the longest aliphatic chain of this AtomContainer
- See Also:
setParameters(java.lang.Object[])
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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 the
DescriptorValue
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.- 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 LongestAliphaticChainDescriptor object.- Returns:
- The parameterNames value
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getParameterType
public Object getParameterType(String name)
Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.- 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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