toxtree.plugins.ames.descriptors

Class DescriptorStructurePresence<T>

java.lang.Object

toxtree.plugins.ames.descriptors.DescriptorStructurePresence<T>

All Implemented Interfaces:

org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor

Direct Known Subclasses:

DescriptorBridgedBiphenyl, DescriptorHasNO2Group, DescriptorIsAniline

public abstract class DescriptorStructurePresence<T>
extends Object
implements org.openscience.cdk.qsar.IMolecularDescriptor

Field Summary

Fields

Modifier and Type	Field and Description
protected ambit2.smarts.query.ISmartsPattern<T>	fragment
protected static Logger	logger
protected String[]	paramNames
protected String	resultName

Constructor Summary

Constructors

Constructor and Description
DescriptorStructurePresence()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer container)
protected abstract ambit2.smarts.query.ISmartsPattern<T>	createSmartsPattern()
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType()
String[]	getParameterNames()
Object[]	getParameters()
Object	getParameterType(String name)
String[]	getParamNames()
String	getResultName()
String	getSMARTS()
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
void	setParameters(Object[] params)
void	setParamNames(String[] paramNames)
void	setResultName(String resultName)
void	setSMARTS(String smarts)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

logger

protected static transient Logger logger

paramNames

protected String[] paramNames

fragment

protected ambit2.smarts.query.ISmartsPattern<T> fragment

resultName

protected String resultName

Constructor Detail

DescriptorStructurePresence

public DescriptorStructurePresence()

Method Detail

getSMARTS

public String getSMARTS()

createSmartsPattern

protected abstract ambit2.smarts.query.ISmartsPattern<T> createSmartsPattern()

setSMARTS

public void setSMARTS(String smarts)
               throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainer container)

Specified by:

calculate in interface org.openscience.cdk.qsar.IMolecularDescriptor

getDescriptorResultType

public org.openscience.cdk.qsar.result.IDescriptorResult getDescriptorResultType()

Specified by:

getDescriptorResultType in interface org.openscience.cdk.qsar.IMolecularDescriptor

getParameterNames

public String[] getParameterNames()

Specified by:

getParameterNames in interface org.openscience.cdk.qsar.IDescriptor

getParameterType

public Object getParameterType(String name)

Specified by:

getParameterType in interface org.openscience.cdk.qsar.IDescriptor

getParameters

public Object[] getParameters()

Specified by:

getParameters in interface org.openscience.cdk.qsar.IDescriptor

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

setParameters

public void setParameters(Object[] params)
                   throws org.openscience.cdk.exception.CDKException

Specified by:

setParameters in interface org.openscience.cdk.qsar.IDescriptor

Throws:

org.openscience.cdk.exception.CDKException

getParamNames

public String[] getParamNames()

setParamNames

public void setParamNames(String[] paramNames)

setResultName

public void setResultName(String resultName)

getResultName

public String getResultName()

toString

public String toString()

Overrides:

toString in class Object

getDescriptorNames

public String[] getDescriptorNames()

Specified by:

getDescriptorNames in interface org.openscience.cdk.qsar.IDescriptor

initialise

public void initialise(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Specified by:

initialise in interface org.openscience.cdk.qsar.IDescriptor