Package org.openscience.cdk.qsar

Class AbstractAtomicDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

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

Constructor Summary

Constructors

Constructor	Description
AbstractAtomicDescriptor()

Method Summary

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

Methods inherited from interface org.openscience.cdk.qsar.IAtomicDescriptor

calculate

Methods inherited from interface org.openscience.cdk.qsar.IDescriptor

getDescriptorNames, getParameterNames, getParameters, getParameterType, getSpecification, initialise, setParameters

Constructor Detail

AbstractAtomicDescriptor

public AbstractAtomicDescriptor()

Method Detail

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

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

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 for

value - DescriptorValue for the given IAtom

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build