Class FMFDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
An implementation of the FMF descriptor characterizing complexity of a molecule.
The descriptor is described in [Yang, Y. et. al.. J. Med. Chem.. 2010. ASAP] and is an approach to
characterizing molecular complexity based on the Murcko framework present
in the molecule. The descriptor is the ratio of heavy atoms in the framework to the
total number of heavy atoms in the molecule. By definition, acyclic molecules
which have no frameworks, will have a value of 0.
Note that the authors consider an isolated ring system to be a framework (even
though there is no linker).
This descriptor returns a single double value, labeled as "FMF"
- Author:
- Rajarshi Guha
- See Also:
- Dictionary pointer(s):
- FMF in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:FMF]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtomContainer container) Calculates the FMF descriptor value for the givenIAtomContainer
.String[]
Returns an array of names for each descriptor value calculated.Returns the specific type of the FMF descriptor value.String[]
Returns the names of the parameters for this descriptor.Object[]
Returns the current parameter values.getParameterType
(String name) Returns a class matching that of the parameter with the given name.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 for this descriptor.Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor
clone
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise
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Constructor Details
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FMFDescriptor
public FMFDescriptor()
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Method Details
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calculate
Calculates the FMF descriptor value for the givenIAtomContainer
.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- AnIAtomContainer
for which this descriptor should be calculated- Returns:
- An object of
DescriptorValue
that contains the calculated FMF descriptor value as well as specification details
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getDescriptorResultType
Returns the specific type of the FMF descriptor value. The FMF descriptor is a single, double value. 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.Additionally, the length indicated by the result type must match the actual length of a descriptor calculated with the current parameters. Typically, the length of array result types vary with the values of the parameters. See
IDescriptor
for more details.- Specified by:
getDescriptorResultType
in interfaceIMolecularDescriptor
- Returns:
- an instance of the
DoubleResultType
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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
- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- An object containing the descriptor specification
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getParameterNames
Returns the names of the parameters for this descriptor. Since this descriptor takes no parameters, null is returned- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- null, since there are no parameters
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getParameterType
Returns a class matching that of the parameter with the given name. Since this descriptor has no parameters, null is always returned- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- The name of the parameter whose type is requested- Returns:
- null, since this descriptor has no parameters
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setParameters
Sets the parameters for this descriptor. This method does nothing, since the descriptor has no parameters- 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
Returns the current parameter values. null is returned since the descriptor has no parameters- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- null, since there are no parameters
- See Also:
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getDescriptorNames
Returns an array of names for each descriptor value calculated. Since this descriptor returns a single value, the array has a single element, viz., "FMF"- Specified by:
getDescriptorNames
in interfaceIDescriptor
- Returns:
- A 1-element string array, with the value "FMF"
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initialise
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
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