Class SmallRingDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class SmallRingDescriptor extends Object implements IMolecularDescriptor
Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically. Returns these values- nSmallRings - total number of small rings (of size 3 through 9)
- nAromRings - total number of small aromatic rings
- nRingBlocks - total number of distinct ring blocks
- nAromBlocks - total number of aromatically connected components
- nRings3 - total number of 3-membered rings
- nRings4 - total number of 4-membered rings
- nRings5 - total number of 5-membered rings
- nRings6 - total number of 6-membered rings
- nRings7 - total number of 7-membered rings
- nRings8 - total number of 8-membered rings
- nRings9 - total number of 9-membered rings
- Dictionary pointer(s):
- smallrings in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:smallrings]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Keywords:
- smallrings, descriptor
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Constructor Summary
Constructors Constructor Description SmallRingDescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer mol)
Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.String[]
getDescriptorNames()
Returns the names of the descriptors made available by this class.IDescriptorResult
getDescriptorResultType()
Returns a placeholder with the descriptor size and type.String[]
getParameterNames()
Get parameters: empty, there are none.Object[]
getParameters()
Get parameters: returns empty array, there are none.Object
getParameterType(String name)
Parameter types: there aren't any.DescriptorSpecification
getSpecification()
Fetch descriptor specification.void
initialise(IChemObjectBuilder builder)
Initialise the descriptor with the specified chem object builder.void
setParameters(Object[] params)
Set parameters: ignored, there are none.
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Method Detail
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initialise
public void initialise(IChemObjectBuilder builder)
Description copied from interface:IDescriptor
Initialise the descriptor with the specified chem object builder. This allows descriptors that required domain objects, such as for SMARTS queries to initialise correctly. If you do not need domain objects then this method does not need to be implemented.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object builder to use with this descriptor
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getSpecification
public DescriptorSpecification getSpecification()
Fetch descriptor specification.- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- An object containing the descriptor specification
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setParameters
public void setParameters(Object[] params) throws CDKException
Set parameters: ignored, there are none.- 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()
Get parameters: returns empty array, there are none.- 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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getDescriptorNames
public String[] getDescriptorNames()
Returns the names of the descriptors made available by this class.- Specified by:
getDescriptorNames
in interfaceIDescriptor
- Returns:
- An array of descriptor names, equal in length to the number of descriptor calculated..
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getDescriptorResultType
public IDescriptorResult getDescriptorResultType()
Returns a placeholder with the descriptor size and type.- 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()
Get parameters: empty, there are none.- 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)
Parameter types: there aren't any.- 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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calculate
public DescriptorValue calculate(IAtomContainer mol)
Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
mol
- the atoms and bonds that make up the molecular object- Returns:
- the various ring-based descriptors generated
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