Class WeightedPathDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class WeightedPathDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
Evaluates the weighted path descriptors.
These decsriptors were described by Randic ([Randic, M.
. Journal of Chemical Information and Computer Science. 1984. 24]) and characterize molecular
branching. Five descriptors are calculated, based on the implementation in the ADAPT
software package. Note that the descriptor is based on identifying all paths between pairs of
atoms and so is NP-hard. This means that it can take some time for large, complex molecules.
The class returns a
DoubleArrayResult
containing the five
descriptors in the order described below.
WTPT1 | molecular ID |
WTPT2 | molecular ID / number of atoms |
WTPT3 | sum of path lengths starting from heteroatoms |
WTPT4 | sum of path lengths starting from oxygens |
WTPT5 | sum of path lengths starting from nitrogens |
Name | Default | Description |
no parameters |
- Author:
- Rajarshi Guha
- Dictionary pointer(s):
- weightedPath in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:weightedPath]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Created on:
- 2006-01-15
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtomContainer container) Calculates the weighted path descriptors.String[]
Returns an array of names for each descriptor value calculated.Returns the specific type of the DescriptorResult object.String[]
Gets the parameterNames attribute of the WeightedPathDescriptor object.Object[]
Gets the parameters attribute of the WeightedPathDescriptor object.getParameterType
(String name) Gets the parameterType attribute of the WeightedPathDescriptor object.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 attribute of the WeightedPathDescriptor object.static boolean
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
-
WeightedPathDescriptor
public WeightedPathDescriptor()
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Method Details
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getSpecification
Description copied from interface:IDescriptor
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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setParameters
Sets the parameters attribute of the WeightedPathDescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The new parameters value- Throws:
CDKException
- Description of the Exception- See Also:
-
getParameters
Gets the parameters attribute of the WeightedPathDescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- See Also:
-
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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getParameterNames
Gets the parameterNames attribute of the WeightedPathDescriptor object.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
Gets the parameterType attribute of the WeightedPathDescriptor object.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
-
unique
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calculate
Calculates the weighted path descriptors.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- Parameter is the atom container.- Returns:
- A DoubleArrayResult value representing the weighted path values
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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 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.- 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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initialise
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
-