Package org.openscience.cdk.qsar
Class AbstractAtomicDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractAtomicDescriptor
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- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
- Direct Known Subclasses:
AtomDegreeDescriptor
,AtomHybridizationDescriptor
,AtomHybridizationVSEPRDescriptor
,AtomValenceDescriptor
,BondsToAtomDescriptor
,CovalentRadiusDescriptor
,DistanceToAtomDescriptor
,EffectiveAtomPolarizabilityDescriptor
,InductiveAtomicHardnessDescriptor
,InductiveAtomicSoftnessDescriptor
,IPAtomicHOSEDescriptor
,IPAtomicLearningDescriptor
,IsProtonInAromaticSystemDescriptor
,IsProtonInConjugatedPiSystemDescriptor
,PartialPiChargeDescriptor
,PartialSigmaChargeDescriptor
,PartialTChargeMMFF94Descriptor
,PartialTChargePEOEDescriptor
,PeriodicTablePositionDescriptor
,PiElectronegativityDescriptor
,ProtonAffinityHOSEDescriptor
,ProtonTotalPartialChargeDescriptor
,RDFProtonDescriptor_G3R
,RDFProtonDescriptor_GDR
,RDFProtonDescriptor_GHR
,RDFProtonDescriptor_GHR_topol
,RDFProtonDescriptor_GSR
,SigmaElectronegativityDescriptor
,StabilizationPlusChargeDescriptor
,VdWRadiusDescriptor
public abstract class AbstractAtomicDescriptor extends Object implements IAtomicDescriptor
Abstract atomic descriptor class with helper functions for descriptors that require the whole molecule to calculate the descriptor values, which in turn need to be cached for all atoms, so that they can be retrieved one by one.- Source code:
- main
- Belongs to CDK module:
- qsar
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Constructor Summary
Constructors Constructor Description AbstractAtomicDescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
cacheDescriptorValue(IAtom atom, IAtomContainer container, IDescriptorResult value)
Caches a DescriptorValue for a given IAtom.IDescriptorResult
getCachedDescriptorValue(IAtom atom)
Returns the cached DescriptorValue for the given IAtom.void
initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.boolean
isCachedAtomContainer(IAtomContainer container)
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.qsar.IAtomicDescriptor
calculate
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Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
getDescriptorNames, getParameterNames, getParameters, getParameterType, getSpecification, initialise, setParameters
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Method Detail
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isCachedAtomContainer
public boolean isCachedAtomContainer(IAtomContainer container)
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.- Parameters:
container
-- Returns:
- false, if the cache is for a different IAtomContainer
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getCachedDescriptorValue
public IDescriptorResult getCachedDescriptorValue(IAtom atom)
Returns the cached DescriptorValue for the given IAtom.- Parameters:
atom
- the IAtom for which the DescriptorValue is requested- Returns:
- null, if no DescriptorValue was cached for the given IAtom
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cacheDescriptorValue
public void cacheDescriptorValue(IAtom atom, IAtomContainer container, IDescriptorResult value)
Caches a DescriptorValue for a given IAtom. This method may only be called after setNewContainer() is called.- Parameters:
atom
- IAtom to cache the value forvalue
- DescriptorValue for the given IAtom
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initialise
public void initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
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