Class RDFProtonDescriptor_GHR
java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
This class calculates GHR proton descriptors used in neural networks for H1 NMR
shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74]. It only applies to (explicit) hydrogen atoms,
requires aromaticity to be perceived (possibly done via a parameter), and
needs 3D coordinates for all atoms.
Name | Default | Description |
checkAromaticity | false | True is the aromaticity has to be checked |
- Author:
- Federico
- This class is affected by these bug(s):
- 1632419
- Dictionary pointer(s):
- rdfProtonCalculatedValues in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:rdfProtonCalculatedValues]
- Source code:
- main
- Belongs to CDK module:
- qsaratomic
- Created on:
- 2006-12-11
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtom atom, IAtomContainer varAtomContainerSet) Calculates the descriptor value for the given IAtom.calculate
(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset) String[]
Returns an array of names for each descriptor value calculated.String[]
Gets the parameterNames attribute of the RDFProtonDescriptor objectObject[]
Gets the parameters attribute of the RDFProtonDescriptor objectgetParameterType
(String name) Gets the parameterType attribute of the RDFProtonDescriptor objectGets the specification attribute of the RDFProtonDescriptor_GHR objectvoid
initialise
(IChemObjectBuilder builder) Default implementation of initialise allows optional override.void
setParameters
(Object[] params) Sets the parameters attribute of the RDFProtonDescriptor objectMethods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor
cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer
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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RDFProtonDescriptor_GHR
public RDFProtonDescriptor_GHR()Constructor for the RDFProtonDescriptor object
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Method Details
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getSpecification
Gets the specification attribute of the RDFProtonDescriptor_GHR object- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
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setParameters
Sets the parameters attribute of the RDFProtonDescriptor object- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- Parameters are the proton position and a boolean (true if you need to detect aromaticity)- Throws:
CDKException
- Possible Exceptions- See Also:
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getParameters
Gets the parameters attribute of the RDFProtonDescriptor object- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- See Also:
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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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calculate
Description copied from interface:IAtomicDescriptor
Calculates the descriptor value for the given IAtom.- Specified by:
calculate
in interfaceIAtomicDescriptor
- Parameters:
atom
- AnIAtom
for which this descriptor should be calculatedvarAtomContainerSet
- TODO- Returns:
- An object of
DescriptorValue
that contain the calculated value as well as specification details
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calculate
public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset) -
getParameterNames
Gets the parameterNames attribute of the RDFProtonDescriptor object- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
Gets the parameterType attribute of the RDFProtonDescriptor object- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
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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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