Class SmallRingDescriptor
java.lang.Object
org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
- All Implemented Interfaces:
IDescriptor
,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 -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtomContainer mol) Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.String[]
Returns the names of the descriptors made available by this class.Returns a placeholder with the descriptor size and type.String[]
Get parameters: empty, there are none.Object[]
Get parameters: returns empty array, there are none.getParameterType
(String name) Parameter types: there aren't any.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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Constructor Details
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SmallRingDescriptor
public SmallRingDescriptor()
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Method Details
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initialise
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
Fetch descriptor specification.- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- An object containing the descriptor specification
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setParameters
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:
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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:
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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
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
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
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
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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