Class KappaShapeIndicesDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class KappaShapeIndicesDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs;
a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH :
"they are intended to capture different aspects of molecular shape. Note that hydrogens are ignored.
In the following description, n denotes the number of atoms in the hydrogen suppressed graph,
m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2
and let p3 denote the number of paths of length 3".
Returns three values in the order
- Kier1 - First kappa shape index
- Kier2 - Second kappa shape index
- Kier3 - Third kappa (κ) shape index
This descriptor does not have any parameters.
- Author:
- mfe4
- Dictionary pointer(s):
- kierValues in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:kierValues]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Keywords:
- Kappe shape index, descriptor
- Created on:
- 2004-11-03
-
Constructor Summary
ConstructorsConstructorDescriptionConstructor for the KappaShapeIndicesDescriptor object -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtomContainer container) calculates the kier shape indices for an atom containerString[]
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 KappaShapeIndicesDescriptor objectObject[]
Gets the parameters attribute of the KappaShapeIndicesDescriptor objectgetParameterType
(String name) Gets the parameterType attribute of the KappaShapeIndicesDescriptor objectGets the specification attribute of the KappaShapeIndicesDescriptor objectvoid
initialise
(IChemObjectBuilder builder) Default implementation of initialise allows optional override.void
setParameters
(Object[] params) Sets the parameters attribute of the KappaShapeIndicesDescriptor objectMethods 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
-
Constructor Details
-
KappaShapeIndicesDescriptor
public KappaShapeIndicesDescriptor()Constructor for the KappaShapeIndicesDescriptor object
-
-
Method Details
-
getSpecification
Gets the specification attribute of the KappaShapeIndicesDescriptor object- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
-
setParameters
Sets the parameters attribute of the KappaShapeIndicesDescriptor 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 KappaShapeIndicesDescriptor 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..
-
calculate
calculates the kier shape indices for an atom container- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- AtomContainer- Returns:
- kier1, kier2 and kier3 are returned as arrayList of doubles
-
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
-
getParameterNames
Gets the parameterNames attribute of the KappaShapeIndicesDescriptor object- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
-
getParameterType
Gets the parameterType attribute of the KappaShapeIndicesDescriptor object- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
-
initialise
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
-